The University of the West Indies
St. Augustine Campus
COURSE/PROGRAMME APPROVAL PROCESS CHECKLIST
Course/Programme Title:
Department:
Minor in Biology
Life Sciences
Faculty:
APPROVAL/REVIEW RECEIVED
APPROVAL PROCESS
Yes
Stakeholders/
External Review:
Faculty Curriculum
Review Committee/
Other
Intra-Campus Review
Library
AQAC Meeting Date:
No
COMMENTS RECEIVED
Science and Technology
ACTION TAKEN
Date Approved/
Review Received
x
x
No additional library resources required
CETL
x
Courses associated with the proposed
revision to the Minor in Biology were
approved by the Centre for Excellence in
Teaching and Learning during the 105-2016
Academic Year. And as such, the proposed
revision to the Minor in Biology has been
reviewed and approved.
Cross-Campus Reviews:
x
25/02/2016
Cave Hill
The proposal is straightforward and welljustified in your document. You have our
full support.
None necessary
SECRETARIAT
VERIFICATION
DATE
- The proposal was circulated among staff.
Mona
x
24/02/2016
- Overall, there were no major
queries/concerns. It is a coherent
programme of study and training in the
biological sciences.
None necessary
- The programme provides exposure to the
fundamental principles of biology, including
studies of the structure, organization, and
diversity of life.
- It was noted that the layout of the credits
on page 2 could be more clearly explained,
as initially it seems that the total advanced
credits for the minor is 24.
Open Campus
Boards/Committees:
Faculty Board
AQAC
x
NB: Items listed in no particular order
Verified By:
Faculty/Department:
Approved By:
Academic Board
Date:
Office of the Campus Registrar,
St. Augustine,
November 20, 2013
Secretariat:
CF&GPC
BUS
UF&GPC
BANNER SAS
ACTT
The University of the West Indies
Faculty of Science and Technology – St. Augustine Campus
Department of Life Sciences (DLS)
Proposal for Revision of the Minor in Biology
January 2016
1
Introduction: Present requirements and philosophy of the DLS Biology Minor.
The present structure of the Minor in Biology is based on a philosophy that offers non-biology
majors an understanding of the organism at each organizational level (sub-organismal, organismal
and whole systems/environment interactions). This is reflected in the course selection for the minor
which includes courses that examine the biodiversity of plants and animals, biochemistry, genetics,
evolutionary biology and functional design in biology.
The current course requirements for the DLS Biology Minor are stated below:
Level I courses:
BIOL1262 (Living Organisms I)
BIOL1263 (Living Organisms II)
BIOL1362 (Biochemistry I)
BIOL1364 (Genetics I)
Additionally, students must complete 15 advanced level credits (5 courses) inclusive of the two
3-credit core courses listed below:
Level II- III CORE courses:
BIOL2262 (Evolutionary Biology)
BIOL3164 (Function and Design in Biology)
Students must ALSO select three (3) additional courses (9 credits) taken from the following list
of optional courses:
Level II- III OPTIONAL courses:
BIOL2165 (Genetics II)
BIOL2360 (Biochemistry II)
BIOL3770 (Plant Pathogens)
BIOL2464 (Fundamentals of Ecology)
BIOL2764 (Physiology of Plants)
BIOL2867 (Physiology of Animals)
2
The pre-requisites for the core course BIOL3164 includes BIOL3773, which is not an optional
course in the minor, in addition to BIOL2764 AND BIOL2867. Therefore to complete the minor
in Biology, the student must complete at least 18 advanced credits as follows:
-
BIOL2262 - Evolutionary Biology
BIOL2764 – Physiology of Plants
BIOL2867 – Physiology of Animals
BIOL3164 - Function and Design in Biology
One Elective from BIOL2165 - Genetics II, BIOL2360 - Biochemistry II, BIOL3770Plant Pathogens, BIOL2464 - Fundamentals of Ecology
BIOL3773 – Plant Anatomy (not part of the minor)
This current structure requires students to complete more than the normal 15 credits required for
the biology minor. Additionally, the structure does not offer any choice or flexibility to students
choosing the Biology Minor.
In contrast to majors, minors are generally designed to give students a breadth of knowledge on a
topic outside of their major degree. Therefore while the Major focuses on mastering a particular
field, the Minor should be about exploration of a new topic.
Proposed Structure of the new DLS Biology Minor.
The Biosciences Subject Benchmark Statement document section 5.2.1(i), page 13, stresses that
“a common element to all biosciences degree programs is the need to facilitate interdisciplinary
and multidisciplinary approaches in advancing knowledge and understanding of the processes
and mechanisms of life”. This idea can be supported and encouraged by allowing a scope in our
Biology Minors that attracts students from other science/ non-science disciplines to explore
content in biology. The student should thus be offered some flexibility in choosing what they are
interested to explore and should be allowed a course selection that supports their major from an
interdisciplinary perspective.
Biology programs in a few top-ranking universities in the USA, Canada and Australia were
reviewed. These higher education institutions, namely Stanford University, The University of
Toronto, MIT, Rutgers, Boston University and the Australian National University, collectively
highlighted six core areas common in a typical Biology Minor (Appendix 1) as defined by their
respective offerings. These areas include Cell & Molecular Biology*, Genetics, Biodiversity,
Evolution/Ecology and Biochemistry. Of these core areas, Genetics, Biodiversity and
Biochemistry are presently addressed at Level I of the Biology Minor. To cover the remaining core
areas as suggested by the composition of the typical Biology Minor, students should be required
to complete an Evolutionary biology course and a Cell Biology course.
*The Molecular Biology in this context examines structure and form of biological molecules,
topics that are covered in DLS offerings of Biochemistry I and Genetics I.
3
The proposed requirements for the DLS Biology Minor as per the justification stated above are as
follows:
Level I CORE courses:
BIOL1262 (Living Organisms I)
BIOL1263 (Living Organisms II)
BIOL1362 (Biochemistry I)
BIOL1364 (Genetics I)
Additionally, students must complete 15 advanced level credits (5 courses) inclusive of the two
3-credit core courses listed below:
Level II CORE courses:
BIOL2061 (Cell and Developmental Biology)
BIOL2262 (Evolutionary Biology)
Students must ALSO select three (3) additional Level II-III Biology courses (total of 9 credits)
from the list below. Students may choose freely from the list of Level II Biology courses. However,
students wishing to pursue any Level III Biology courses must first seek departmental advising on
prerequisites, course availability, timetabling and other academic guidance.
List of Level II Biology courses
BIOL 2163- Biostatistics
BIOL 2164- Principles of Molecular Biology
BIOL 2165- Genetics II
BIOL 2265- Fundamentals of Microbiology
BIOL 2360- Biochemistry IIA
BIOL 2464- Fundamentals of Ecology
BIOL 2764- Physiology of Plants
BIOL 2867- Physiology of Animals
4
List of Level III Biology courses
BIOL 3063- Marine Ecology and Oceanography
BIOL 3162- Principles of Microbial Biotechnology
BIOL 3164- Function & Design in Biology
BIOL 3263- Introduction to Bioinformatics
BIOL 3363- Medical Biotechnology
BIOL 3366- Plant Biotechnology and Genetic Engineering
BIOL 3409- Caribbean Coral Reefs
BIOL 3462- The Ecology of Freshwaters
BIOL 3465- Tropical Forest Ecology and Use
BIOL 3466- Coastal Ecosystems & Resource Management
BIOL 3468- Biodiversity and Conservation
BIOL 3768- Plant Diversity & Systematics
BIOL 3769- Plant Genetic Improvement
BIOL 3770- Plant Pathogens
BIOL 3771- Environmental Plant Physiology
BIOL 3772- Plant Development
BIOL 3773- Plant Anatomy
BIOL 3866- Parasite Biology
BIOL 3867- Biology of Animal Behaviour
BIOL 3868- The Ecology of Humans
BIOL 3870- Insect Biology
BIOL 3960- Environmental Microbiology
BIOL 3961- Principles of Medical Microbiology
BIOL 3970- Aquaculture
BIOL 3971- Fisheries Management
BIOL 3XXX - Caribbean Island Ecology and Biogeography
See Appendix II for course descriptions. Note that assessments and grading schemes for several
course outlines have since been amended to the new UWI grading scheme.
Please note all courses were approved by CELT in Semester II 2012/2013.
5
Resources Needed:
The courses that comprise the newly proposed Minor in Biology are all pre-existing courses that
were revised in the recent DLS departmental-wide change from 4-credit to 3 credit course
weightings. As such, no new resources are needed to facilitate the implementation of this new
proposed structure. There are no new courses for this proposed Biology Minor.
Summary: The proposed structure of the new Biology Minor in the DLS resolves previous issues
related to credit loadings but maintains adherence to the philosophical underpinnings by providing
students with an understanding of biology at the sub-organismal, organismal and whole systems
levels. The modifications proposed in the structure of the new minor, not only benchmarks our
minor to international standards, but also allows non-biology major students to explore, with some
measure of flexibility, courses with greater relevance to their major degree program.
6
Appendix I: Examination of Biology Minor offerings at a few Top-Ranked International
Universities
University Name
Summary of Requirements for minor
Details of Requirements for minor
The University
Students interested in biology
BIO 120H1 – Adaptation and Biodiversity
of Toronto
must take 2 Level I courses + ANY 2
and BIO 130H1 – Molecular and Cell Biology.
from the list of core courses
EEB BIO220H1; Genomes to Ecosystems
CSB BIO230H1 – Genes to Organisms;
38 Programs
EEB BIO251H1; Form, function and plant dev.
in Life Sci.
CSB BIO270H1; BIO271H1 (Animal Phys I and II);
Rank: Top 16
CSB BIO260H1 (Concepts in Genetics)
Stanford
6 courses including two courses
2 courses from the Bio Core
University
from the Bio Core Lecture series
(BIO 41, 42, 43, BIOHOPK 43) must be taken,
BIO 41: Genetics, Biochemistry, and Mol Biology
BIO 42: Cell Biology and Animal Physiology
BIO 43: Plant Biology, Evolution, and Ecology
Rank : Top 5
MIT
BIOHOPK 43: Plant Biology, Evolution, and Ecology
Core: organic chemistry, genetics and
List of 22 courses - range of biology sub-disciplines
general biochemistry
Total of 60 units for the Biology minor
Each course = 12 units
Rank : Top 5
also select any 2 from the list
Australian
This biology minor= 24 units
Evolution, Ecology and Genetics
National
Any two core courses (6 credits each)
Molecular and Cell Biology
University
Plus minimum two 6-credit courses
Human Biology
Rank: 19th
from ANY 2000-3000 level BIOL courses
Diversity of Life
Boston
Five 4-credit courses. (3 Bio courses)
Cell and Molecular Biology
University
The 2 core courses in biology
Neurobiology and behavior
cover the topics:
Ecology and Evolution
Rank: 37th
cell and molecular biology
neurobiology and behavior, and
ecology and evolution.
Core areas identified include Cell & Molecular Biology, Evolution, Ecology, Genetics,
Biodiversity, Biochemistry.
7
APPENDIX II- DESCRIPTION OF CORE AND ELECTIVE COURSES IN BIOLOGY MINOR
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND AGRICULTURE
DEPARTMENT OF LIFE SCIENCES
Course Description
Title: BIOL 1262 Living Organisms 1
Credits: 3
Level: Undergraduate –Year 1
Semester: 1
Offering Department: Department of Life Sciences, Faculty of Science and Agriculture, The
University of the West Indies, St. Augustine
Course coverage: Origin and evolution of living organisms, prokaryotes, autotrophic protists, non
vascular and vascular plants.
Pre-requisites:
CAPE Biology (Units I and II) or OR Preliminary Biology I and II (BIOL0061 and BIOL0062) OR
equivalent.
Significance/ Rationale:
Prokaryotic organisms have been present on earth for almost four billion years. These early bacteria
evolved diverse physical and metabolic characteristics that contributed to creating conditions
necessary for the emergence and sustenance of higher forms of life. Photosynthetic bacteria gave rise
to algae, from which plants evolved. As primary producers, plants form the most important foundation
for the maintenance of heterotrophic organisms on earth. Plant evolution entailed a number of
strategies to escape the aquatic environment and survive the new challenges imposed by the need for
support, acquisition of nutrients, and reproduction on land. Some of the first plants were more
successful than others, notably the ferns and conifers. Higher plants remain rooted to one spot
throughout their lives, yet with the simple structural elements of root, stem, leaf, they have evolved
into some 235,000 species, ranging enormously in size, occupying many diverse and challenging
habitats, with plants of some species surviving for thousands of years. The greatest success came with
the evolution of the flower, and flowering plants account for all but about 33,000 species of land
plants.
1
Enrolment Capacity: 400 students (maximum)
Purpose of Course
This course is designed primarily for 1st year students registered for the Biology degree option in the
Department of Life Sciences. The course provides an introduction to the theories on the origin of life
on earth and the diversity of autotrophic protists and plants. The characteristics, range of structure,
reproduction, life cycles and habitats of selected protists and plants are covered. Laboratory exercises
will provide an opportunity for ‘hands on’ experience with representative members of various groups’
in particular local species.
Letter to Student
Welcome to this Level 1 Introductory course on Living Organisms. The aim of this handout is to
provide you with an outline of the course content as well as related information with respect to course
objectives and methods of assessment. This 3 credit course will be taught through a series of lectures
(18 hours), practicals (12 two-hour sessions) and tutorials (6 hours). Attendance at all sessions will
be absolutely necessary if you hope to do well in the course.
Instructor Information
BIOL1262 will be managed by a course coordinator and would be taught be a team of experienced
biology lecturers, supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office
hours for the coordinator and lecturers are posted on the faculty bulletin boards and are available from
the Department of Life Sciences’ general office. Team members can also be contacted via e-mail.
Dr. Judy Rouse-Miller (Course Coordinator)
Natural Sciences Building (Old Wing)
Ext. 83089
[email protected]
XXXXXX (TA)
Content
BIOL1262 covers the following content:
Evolutionary Concepts
Archaebacteria & Eubacteria
Autotrophic protists; classification, characteristics, identification
Phylogeny and classification of plants
Physical features, challenges and adaptations of plants in aquatic and terrestrial environments;
The plant life cycle – alternation of generation
Bryophytes
2
Seedless vascular plants
Seed plants – Gymnosperms
Seed plants – Angiosperms (form and function)
Photosynthetic systems
Reproductive systems
Ecology of plants
Goal
The goal of BIOL1262 is to provide students with a foundation on the concepts of origin of the
prokaryotes and the evolution and diversity of photosynthetic organisms, as a prerequisite for
advanced biology courses in the Department of Life Sciences.
General Objectives
1. Introduce students to the major groups of prokaryotes, autotrophic protists and plants, their
evolutionary associations, and adaptive radiation
2. Develop skills appropriate to the study of plants and prokaryotes in the laboratory
Learning Objectives
Upon successful completion of this course, students should be able to:
1. Outline the main theories on the origin of life on earth
2. Describe the characteristic features of selected prokaryotes
3. Compare the biology of autotrophic protists and plants.
4. Classify and identify common plants that occur in the Caribbean using the Linnaean system
5. Arrange taxonomic and non – taxonomic terms of formal and informal classification
schemes to show the relationship between the terms.
6. Explain the functional consequences of different types of body and tissue organization in
plants
7. Outline general trends in plant evolution
8. Identify the sequence of events/processes and the structures of the generalised plant life
cycle
9. Outline the life cycle of the major plant groups (Bryophytes, Pteridophytes, Gymnosperms
and Angiosperms)
10. Outline the main associations between the major taxonomic groups of plants
11. Describe the adaptive radiation of the major groups of plants
12. Construct a dichotomous key based on observable morphological characteristics which
could be used to key out a group of plants from terrestrial and aquatic environments
13. Describe the challenges to existence faced by the early aquatic colonizers of land
14. Solve simple problems in plant science
15. Demonstrate laboratory skills appropriate to the study and interpretation of living and
preserved botanical specimens
3
Mode of Delivery:
Lectures -18 hours:
Didactic; interactive
Tutorials -6 hours:
Interactive; mind maps; problem-solving
Laboratory classes- 24 hours
(12 two- hour sessions):
Interactive practical tasks; problem-solving
Assessment:
Final Examination: 50% (One 2-hour Comprehensive paper)
Course Work: 50%
- Writing across the curriculum; critical thinking exercises
- Laboratory reports (10 x 2% )
- One in-course test
- Tutorial Attendance and participation
5%
20%
20%
5%
ASSIGNMENTS:
Coursework in BIOL1262 will be assessed in the following ways:
1. Writing across the curriculum- critical thinking exercises-5%.
These activities are designed to encourage students to become active learners by engaging
knowledge to further develop understanding. The exercises would help students understand content
and express ideas. A total of five (5) simple exercises out of eight (8) worth a total of 5 marks (1
mark per exercise) would be given during lectures or tutorials (no more than one per week) without
advanced notice. Each exercise would take between 5 – 10 minutes to complete and would
comprise of varying activities including:
Focused free-writing: Students are asked to write briefly on their knowledge of a topic; identifying
misconceptions from previous knowledge and new information learnt.
Glossary: Students are asked to prepare a glossary 5 terms which they met for the first time in the
previous lecture.
Complete the life cycle: Students are asked to complete the life cycle diagram given to demonstrate
their knowledge of the sequence of events and structures which occur in the plant life cycle
Construction of dichotomous key: Students are asked to construct a dichotomous key to which can
be used to key out (identify) a group of specimens.
Concept map: Students are asked to prepare a concept map which shows the relationship between
kingdom, division, major plant group terms, and common names used throughout the lecture.
4
Group presentation- The tutorial class would be divided into groups and each group would be
required to design the sporophyte generation of a plant, which based on its morphological features
would be placed into one of the plant divisions studied – the presentation should include a diagram
which is 1-5x the actual size of the plant.
Reflective statement: students should write a reflective statement on one of the labs completed:
students should identify problems encountered, techniques mastered or improved, what was done
well and why and what was learnt and what is unclear.
2. In-course Test-20%
One in-course test would be given worth 20%. The test would be given in week 12 of the semester
and would comprise of MCQs and structured questions.
3. Laboratory reports-20%
Students would be required to submit 12 lab reports/completed worksheets for practical exercises.
Each report/completed worksheet would be worth 2 marks.
4. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned at the
end of the semester. Participation would include more than just showing up at tutorial – some
evidence of an active role in the tutorial discussion would be required to obtain the full 5% for
participation. At the beginning of the semester, the students in each tutorial would engage in
developing the exact assessment criteria for this assignment, and the student-developed criteria will
be used to determine each student’s participation grade.
Cheating, including plagiarism, would not be tolerated. Incidents of cheating would be dealt with
according to UWI’s rules and regulations including:
-
Examination Regulations for First Degrees, Associate Degrees, Diplomas and
Certificates. Section (B) Cheating. Regulations 96–102;
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf.
-
University Regulations on Plagiarism (First Degrees, Diplomas and Certificates).
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
5
EVALUATION: BIOL1262 will be evaluated in two ways – (a) through the offices of the Class
Representative and the Life Sciences Student-Staff Liaison Committee, and (b) an end of semester
course evaluation survey. The class will elect four class representatives (one per lab stream), whose
role is to act as a mediator between the Life Sciences academic staff and the students in the class.
The representatives will attend Liaison Committee meetings (held at least twice per semester),
where they will present feedback on the course to the Department for action. The UWI performs a
course evaluation survey at the end of every semester, and this information will also be used for
overall assessment of the course and guide possible actions for improvement in subsequent
semesters.
TEACHING STRATEGIES: A combination of teaching strategies will be adopted in BIOL1262.
The primary teaching strategy will be based on the face to face classroom lectures and discussions.
Videos of lecture presentations would be made available to students prior to the lecture session via
podcast media. Students are advised to view these videos before the lecture so that more emphasis
can be placed on discussions and answering questions, thereby facilitating deep learning. This would
also afford the time to have assessment exercises on “writing across the curriculum”. MyeLearning
will be utilized throughout the course as a means to provide access to course materials such as
Powerpoint presentation files, animations, weblinks, lessons and quizzes. This medium would also
be used as a portal for student-lecturer communications and the dissemination of coursework
feedback.
A total of six tutorial sessions would be given for the semester. These would be small group
sessions which would be conducted by instructors or tutors, who would normally by senior
postgraduate students in Life Sciences. Students must attend tutorial sessions. Tutorials sheets will
be assigned prior to each session via myeLearning, and students are expected to attempt the
solutions before coming to tutorial. The goal of the tutorial session is to give students a more
hands-on experience with the course material and easier access to course instructors. Students will
be expected to ask and answer questions on material that is unclear, propose solutions to questions
on the tutorial sheet and to generally participate fully in the tutorial activities. Tutors will not merely
be going through the answers to the tutorial questions in these sessions.
Practical sessions would include demonstrations and problem solving exercises to develop practical
skills and enhance understanding of content covered in the theory section. These exercises would
include analysis of specimens, experiments and use of identification keys to assign organisms into
different levels of taxa
In order to pass the course, you must gain an overall passing mark of 40%. Any student who
misses more than 25% of practical classes or tutorial sessions without a medical or other valid
excuse can be debarred from writing the final exam.
6
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
Texts
Essential Texts
1. Peter Raven, Ray Evert, and Susan Eichhorn 2005. Plant Biology 7th Edition, WH Freeman
Publishers.
2. Bidlack, James and Shelley Jansky. (2010) Stern's Introductory Plant Biology, 12th Ed.
McGraw-Hill Science/Engineering/Math
Recommended reading:
Hickey, M. and King, C.2000. The Cambridge Illustrated Glossary of Botanical Terms
Kingsley R. Stern, Shelley Jansky, James Bidlack (2007) Introductory Plant Biology, 11th Ed.
McGraw-Hill Companies.
7
James D. Mauseth (2008) Botany: An Introduction to Plant Biology, 4th Ed. Jones & Bartlett
Publishers.
Ennos and R and E. Sheffield 2000. Plant Life, Blackwell Science, USA.
Joanne Willey, Linda Sherwood and Chris Woolverton (2007) Prescott, Harley and Klein’s
Microbiology (7th edition), McGraw-Hill
Handouts
1. Classification handout
2. Dichotomous keys
3. Alternation of generation life cycle
4. Guidelines for making Biological Drawings
5. Guidelines for preparing the lab report
6. Technical terms
Online resources
1.
2.
3.
4.
UCMP Glossary Life History http://www.ucmp.berkeley.edu/glossary/gloss6lifehist.html
UCMP Glossary http://www.ucmp.berkeley.edu/glossary/gloss8botany.html
Classification: http://www.botany.hawaii.edu/faculty/wong/BOT135/Lect04_c.htm
The National Herbarium http://sta.uwi.edu/herbarium/
Readings
1.
2.
3.
4.
5.
6.
7.
8.
9.
Botany, An Introduction to Plant Biology by James Mauseth 2nd ed.
Chapter 1 Introduction to Plants and Botany pp 1-13
Chapter 4 Growth and Division of the Cell pp 84-85
Chapter 18 Classification and Systematics pp 492-494, 507-509
Chapter 21 Algae pp 575 -578, 591-593
Chapter 22 Non- vascular plants pp 611-614
Chapter 23Vascular plants without seed pp 636-639
Chapter 24 Seed Plants I: Gymnosperms pp 672-675
Chapter 25 Seed Plants II: Angiosperms pp 703-70
8
Course Calendar
LECTURE TOPICS (by week)
Week Practical
General Biology
1
2
Lecture/Tutorial
Laboratory Techniques
Lecture 1. Introduction; The scientific inquiry process. Evolution
explains unity and diversity of life ; Levels of organization in biology:
Structure and function are correlated in all levels of organization in biology
Lecture 2. Origin of Life –Theories
Isolation and
observation of
prokaryotes
Lecture 3. Diversity of contemporary life on earth: the origin of prokaryotes,
evolution of the eukaryotic cell, the genesis of multicellular life, and the
adaptive radiations of plants and animals
Tutorial 1 Glossary: Students are asked to prepare a glossary 5 terms
which they met for the first time in the previous lecture.
3
Prokaryotes
4
Autotrophic protists
Chlorophyta,
Phaeophyta
and
Rhodophyta
Lecture 4: Structure and function of prokaryotic cells, Diversity of
prokaryotes
Lecture 5 Dichotomous keys
Lecture 6. Plant - like Protists – Algae - Chlorophyta, Phaeophyta and
Rhodophyta – characteristics adaptation to habitat
Tutorial 2.Construction of dichotomous key: Students are asked to construct
a dichotomous key to which can be used to key out (identify) a group of
specimens.
5
Non-vascular plants,
Bryophytes-liverworts,
Lecture 7.Characteristics of Plants
Classification (Hierarchal classification)
Concept map: Students are asked to prepare a concept map which shows
the relationship between kingdom, division, major plant group terms, and
common names used throughout the lecture.
Lecture 8. Alternation of generation Life cycle – reproduction and
variability
6
Non-vascular plants,
Bryophytes-mosses
Lecture 9. Characteristics of Bryophytes – adaptations to environment –
life cycle, reproductive strategy
Tutorial 3 Complete the life cycle: Students are asked to complete the life
cycle diagram given to demonstrate their knowledge of the sequence of
events and structures which occur in the plant life cycle
7
Vascular non seed
plants - Pteridophytes:
lycopods, ferns
Lecture 10. Physical characteristics of the aquatic and terrestrial
environments, requirements for plant survival, challenges to existence faced
by the early aquatic colonisers of land
The dichotomous key
and identification of
plants
Lecture 11. Characteristics of the Microphyllophyta, adaptations to
environment, life cycle, reproductive strategy, ecology
9
Focused free-writing: Students are asked to write briefly on their
knowledge of a topic; identifying misconceptions from previous
knowledge and new information learnt.
8
Vascular non seed
plants - Pteridophytes:
ferns
The dichotomous key
and identification of
plants
9
Vascular seed plants –
Gymnosperms – cycads
and pines
Lecture 12. Characteristics of the Pteridophyta, adaptations to
environment, life cycle, reproductive strategy, ecology
Tutorial 4. Complete the life cycle: Students are asked to complete the life
cycle diagram given to demonstrate their knowledge of the sequence of
events and structures which occur in the plant life cycle
Lecture 13. Gymnosperms characteristic features –morphological
characteristics, adaptations, life cycle, reproductive strategy , ecology
Lecture 14. Gymnosperms characteristic features–life cycle, reproductive
strategy, ecology
10
11
12
13
Angiosperms –, seed
germination, flower
structure, monocot and
dicot characteristics
Angiosperm families:
Virtual Herbarium,
Campus field exercise:
Identification of plants
Review- Lab based
Identification
of
unknown to level of
division in the urban
habitat
Lecture 15. Angiosperms - characteristic features, organ: flowers, stem, leaf,
root – structure and function –photosynthesis
Tutorial 5. Reflective statement: students should write a reflective
statement on one of the labs completed: students should identify problems
encountered, techniques mastered or improved, what was done well and
why and what was learnt and what is unclear.
Lecture 16. Angiosperms life cycle, reproduction
Lecture 17 Evolution of the seed habit, Angiosperm seed structure
Lecture 18. Concept of the ideal land plant, ecology
Tutorial 6. Group presentation- The tutorial class would be divided into
groups and each group would be required to design the sporophyte
generation of a plant, which based on its morphological features would be
placed into one of the plant divisions studied – the presentation should
include a diagram which is 1-5x the actual size of the plant.
Review
10
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND AGRICULTURE
DEPARTMENT OF LIFE SCIENCES
Course Description
Title: BIOL1263- Living Organisms II
Credits: 3
Level: Undergraduate –Year 1
Semester: 1
Offering Department: Department of Life Sciences, Faculty of Science and Agriculture, The
University of the West Indies, St. Augustine
Course coverage: Diversity of animals: Protozoa, Porifera; Cnidaria, Platyhelminthes, Nematoda,
Annelida, Arthropoda, Mollusca, Echinodermata, Chordata; Major fungal & fungal-like organisms
including Chytridiomycetes, Zygomycetes, Ascomycetes, Basidiomycetes, Oomycetes,
Hyphochytriomycota, Plasmodiophorids & Labyrinthulids
Pre-requisites:
CAPE Biology (Units I and II) or OR Preliminary Biology I and II (BIOL0061 and BIOL0062) OR
equivalent.
Significance/ Rationale:
Animals are very diverse with more than 1.5 million species described. These represent vast levels of
genetic and ecological diversity. When a person thinks of an animal they probably think of a
vertebrate, one having a backbone. However, vertebrates account for only about 50,000 species; the
rest are invertebrates, animals without backbones. Regardless, all animals share certain
characteristics: they are multicellular, heterotrophic, require oxygen for aerobic respiration,
reproduce-either sexually or asexually, go through a period of embryonic development, and can move
during at least part of their life.
Fungi are also a very large, diverse group of eukaryotic organisms with ~90,000 species described
out of an estimated 1.5 million species that are thought to exist on earth. These organisms have critical
roles in maintaining the environment for sustaining higher forms of life and are utilized in many
processes related to medicine, agriculture and industries. However, some species are also causative
agents for important human, animal and plant diseases.
11
Enrolment Capacity: 400 students (maximum)
Purpose of Course
The purpose of this course is to introduce students to this amazing diversity of animal and fungal life
through lectures which highlight evolutionary innovations, unique characteristics, as well as features
shared by other groups. Laboratory exercises will provide an opportunity for ‘hands on’ experience
with representative members of various groups’ in particular local species. Tutorials are small group
sessions for students to discuss key topics and related issues.
Letter to Student
Welcome to this Level 1 Introductory course on Living Organisms. The aim of this handout is to
provide you with an outline of the course content as well as related information with respect to course
objectives and methods of assessment. This 3 credit course will be taught through a series of lectures
(18 hours), practicals (8 three-hour sessions) and tutorials (6 hours). Attendance at all sessions will
be absolutely necessary if you hope to do well in the course.
Instructor Information
BIOL1263 will be managed by a course coordinator and would be taught be a team of experienced
biology lecturers, supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office
hours for the coordinator and lecturers are posted on the faculty bulletin boards and are available from
the Department of Life Sciences’ general office. Team members can also be contacted via e-mail.
Prof. Dave Chadee (Course Coordinator)
Natural Sciences Building (New Wing)
Ext. 83740
[email protected]
Dr. Adesh Ramsubhag (lecturer)
Rm. 220 Natural sciences Building (Old wing)
Ext. 83086
[email protected]
XXXXXX (TA)
Content
BIOL1263 covers the following content:
A survey of the phylogeny and characteristics of major invertebrate and vertebrate animal groups.
Special topics include
12
1.
2.
3.
4.
5.
6.
7.
theories of the origin of unicellularity and multicellularity
cell and tissue levels of organization
origins and functional significance of body cavities
early embryonic development
metamerism and tagmosis (tagmatization)
colonization of land by arthropods and vertebrates
evolutionary trends in vertebrates
A survey of the phylogeny and characteristics of major groups of fungi:
1.
2.
3.
4.
5.
6.
Introduction to Mycology and importance of fungi to humans and the environment.
Chytridiomycota
Zygomycetes: Mucorales, Endogonales and Entomophthorales) & Trichomycetes
Ascomycetes (and Deuteromycetes)
Basidiomycetes
Fungal-like organisms: Hyphochytriomycota, Plasmodiophorids & Labyrinthulids
Oomycetes
Goal
The goal of BIOL1263 is to provide students with a foundation in introductory diversity of animals
and fungi, as a prerequisite for advanced biology courses in the Department of Life Sciences.
General Objectives
1. Introduce students to the major groups of:
a. animals, their evolutionary associations, and adaptive radiation; and
b. fungi as decomposers, symbionts, and pathogens
2. Develop practical skills appropriate to the study of animals and fungi in the laboratory
Learning Objectives
Upon successful completion of this course, students should be able to:
1. Describe the characteristic features of major groups of animals and fungi;
2. Classify common animals and fungi using the Linnaean system;
3. Explain the functional consequences of different types of body organization of
animals; this includes such factors as level of complexity (single-cell, tissue, organsystem), type of symmetry, whether the body is wormlike, and whether the body is
substantially modified (e.g. for a parasitic way of life);
4. Categorize the major groups of animals based on neo-Darwinian evolutionary
principles
5. Explain the adaptive radiation of the major groups of animals and fungi
6. Solve simple problems in zoology
7. Compare the roles of fungi as primary decomposers, symbionts, and pathogens
13
8. Demonstrate laboratory skills appropriate to the study and interpretation of living and
preserved specimens of animals and fungi
Mode of Delivery:
Lectures -18 hours:
Didactic; interactive
Tutorials -6 hours:
Interactive; mind maps; problem-solving
Laboratory classes- 24 hours (8
three-hour sessions):
Interactive practical tasks; problem-solving
Assessment:
Final Examination: 50% (One 2-hour Comprehensive paper )
Course Work: 50%
- Writing across the curriculum exercises:
- Laboratory reports (10 x 2% ):
- One in-course test;
- Tutorial Attendance and participation:
5%
20%
20%
5%
ASSIGNMENTS:
Coursework in BIOL1263 will be assessed in the following ways:
5. Writing across curriculum exercises-5%.
These activities are designed to encourage students to become active learners by engaging
knowledge to further develop understanding. The exercises would help students
understanding content and expressing ideas. A total of five simple exercises worth a total of
5 marks (1 mark per exercise) would be given during lectures or tutorials (no more than one
per week). Each exercise would take between 5 – 10 minutes to complete and would comprise
of varying activities including:
a. Focused free-writing- Students may be asked to briefly write on their understanding or
perspective on a subject/topic covered or on how the subject/topic may be connected to other
situations.
b. Entry slips- Short responses to questions posed at the beginning of class;
c. Answering questions. One or few questions would be given which students must
answer and submit for grading.
d. Short summary. Students are asked to summarize main points of a reading assignment
in a short paragraph.
e. Group presentation- The tutorial class would be divided into groups and each group
would be required to make a short presentation on a document provided.
14
6. In-course Test-20%
One in-course test would be given worth 20%. The test would be given in week 12 of the
semester and would comprise MCQs and structured questions.
7. Laboratory reports-20%
Students would be required to submit 8 laboratory reports/completed worksheets for practical
exercises. Each report/completed worksheet would be worth 2 marks.
8. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned
at the end of the semester. Participation would include more than just showing up at tutorial
– some evidence of an active role in the tutorial discussion would be required to obtain the
full 5% for participation. At the beginning of the semester, the students in each tutorial would
engage in developing the exact assessment criteria for this assignment, and the studentdeveloped criteria will be used to determine each student’s participation grade.
Cheating, including plagiarism, would not be tolerated. Incidents of cheating would be dealt with
according to UWI’s rules and regulations including:
-
Examination Regulations for First Degrees, Associate Degrees, Diplomas and
Certificates. Section (B) Cheating. Regulations 96–102;
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf.
-
University Regulations on Plagiarism (First Degrees, Diplomas and Certificates).
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
EVALUATION: BIOL1263 will be evaluated in two ways – (a) through the offices of the Class
Representative and the Life Sciences Student-Staff Liaison Committee, and (b) an end of semester
course evaluation survey. The class will elect four class representatives (one per lab stream), whose
role is to act as a mediator between the Life Sciences academic staff and the students in the class.
The representatives will attend Liaison Committee meetings (held at least twice per semester), where
they will present feedback on the course to the Department for action. The UWI performs a course
evaluation survey at the end of every semester, and this information will also be used for overall
assessment of the course and guide possible actions for improvement in subsequent semesters.
15
TEACHING STRATEGIES: A combination of teaching strategies will be adopted in BIOL1263.
The primary teaching strategy will be based on the face to face classroom lectures and discussions.
Videos of lecture presentations would be made available to students prior to the lecture session via
podcast media. Students are advised to view these videos before the lecture so that more emphasis
can be placed on discussions and answering questions, thereby facilitating deep learning. This would
also afford the time to have assessment exercises on “writing across the curriculum”. MyeLearning
will be utilized throughout the course as a means to provide access to course materials such as
Powerpoint presentation files, animations, weblinks, lessons and quizzes. This medium would also
be used as a portal for student-lecturer communications and the dissemination of coursework
feedback.
A total of six tutorial sessions would be give for the semester. These would be small group sessions
which would be conducted by instructors or tutors, who would normally by senior postgraduate
students in Life Sciences. Students must attend tutorial sessions. Tutorials sheets will be assigned
prior to each session via myeLearning, and students are expected to attempt the solutions before
coming to tutorial. The goal of the tutorial session is to give students a more hands-on experience
with the course material and easier access to course instructors. Students will be expected to ask and
answer questions on material that is unclear, propose solutions to questions on the tutorial sheet and
to generally participate fully in the tutorial activities. Tutors will not merely be going through the
answers to the tutorial questions in these sessions.
Practical sessions would include demonstrations and problem solving exercises to develop practical
skills and enhance understanding of content covered in the theory section. These exercises would
include dissection and analysis of specimens, experiments and use of identification keys to assign
organisms into different levels of taxa.
In order to pass the course, you must gain a passing mark of 40% from both the coursework
and the final theory exam. Any student who misses more than 25% of practical classes or
tutorial sessions without a medical or other valid excuse can be debarred from writing the final
exam.
Recommended Text
Hickman CP, Roberts LS, Keen SL, Larson A, and Eisenhower DJ (2007). Animal Diversity. Fourth
edition. McGraw Hill Higher Education
Useful reading
Introductory Mycology by Alexopolus, Mims and Blackwell, 4th Edition, 1996, Wiley
Useful websites
16
www.mhhe.com/hickmanad4e (animals):
http://tolweb.org/fungi (fungi)
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
Course Calendar
LECTURE TOPICS (by week)
Week Practical
Lecture/Tutorial
1
Lecture 1:
Complexity, diversity and classification of
animals; Origin of eukaryotes; Protozoa;
Origin of the Metazoa
Lecture 2:
Porifera; Cnidaria
2
Tutorial 1
17
Lecture 3:
Platyhelminthes; Bilateral symmetry;
Triploblastic condition;
Writing across the curriculum exercise
3
4
5
Dinoflagellates e.g.
Trypanosomaslides
Sarcodines e.g
Amoeba
Ciliates e.g
Paramecium
Apicomplexans e.g
Plasmodium
Lecture 4:
Nematoda; Early embryonic development
Body cavities;
Lecture 5:
Annelida: Body organization and phylogenetic;
Placement; Life habits and diversity;
Metamerism and tagmosis (tagmatization);
Tutorial 2
Lecture 6:
Writing across the curriculum exercise
Porifera- Diversity
of Poriferanssponges
CnidariaLecture 7:
Examination of live
material- Hydra
Obelia, Jellyfishes,
sea
anemones and
Corals
Arthropoda: Exoskeleton, adaptations to life
and land Arthropoda: Metamorphosis and
diversity
Lecture 8:
Mollusca: Body plan, diversity; Echinodermata
Chordata: Origin and phylogeny;
Invertebrate chordates
PlatyhelminthesDiversity of
Flatworms
18
TurbellariansBipalium
MonogeneansGyrodactylus
TrematodesFasciola
Cestodes-Taenia
Demonstration of
preserved
specimens
6
NematodesDiversity of
nematodes
Examination of
Preserved
Specimens e.g.
slides
Tutorial 3
Lecture 9:
Chordata: Fishes Diversity
Writing across the curriculum exercise
Annelids –
earthworms
7
InsectsCockroaches,
Beetles, stink bugs,
wasps, honey bees
and flies
Lecture 10:
Chordata: Amphibians Diversity
Lecture 11:
Chordata: Reptiles diversity and adaptation to
land
PomaceaPernaShrimp
Tarantula-
19
Star fish, sea
urchin, Sea
cucumber.
8
Molluscan Diversity
Polyplacophora
(Chitons)
Gastropodssnails and slugs
Tutorial 4
Lecture 12:
Chordata: Birds; evolution and adaptation of
flight; Chordata:
Writing across the curriculum exercise
Pelecypodabivalves- clams,
oysters and mussels
Cephalopodsoctopus and squids
Arthropod Diversity
Crustaceafiddle crab,
woodlice, barnacles
Arachnida-scorpions,
spiders, ticks and
mites
Myriapodacentipedes,
millipedes
9
Bufo marinus:
Tadpoles- Hyla
Freshwater fish
Anolis
Birds
10
Mammals
Zygomycetes
11
Ascomycetes
Basidiomycetes
Oomycetes
12
Lecture 13:
Mammals
Lecture 14:
Classification and diversity of fungi;
importance of fungi to humans and the
environment.
Tutorial 5
Lecture 15:
Chytridiomycota; Zygomycetes
Lecture 16:
Writing across the curriculum exercise
Ascomycetes (and Deuteromycetes)
Lecture 17:
Basidiomycetes
Lecture 18:
Fungal-like organisms
In course Test
Tutorial 6
20
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND AGRICULTURE
DEPARTMENT OF LIFE SCIENCES
Course Description
Title: BIOL1362- Biochemistry I
(This course replaces the Biochemistry component of BIOL1061 Cell Biology & Genetics)
Credits: 3 (23 hours of Lectures, 8 hours of Tutorials and 12 hours of Practicals)
Level: Undergraduate -Year I
Semester: II
Offering Department: Department of Life Sciences, Faculty of Science and Agriculture, The
University of the West Indies, St. Augustine.
Course coverage: Functions of organelles, endosymbiotic theory, limits on cell size; structurefunction relationships of the major classes of biomolecules; introductory enzymology; glycolysis and
the metabolism of macronutrients.
Pre-requisites:
CAPE Biology (or equivalent). A solid background in chemistry is assumed and a pass in CHEM
1061 or CHEM 1062 is strongly recommended.
Significance/Rationale:
Biochemistry is a fundamental sub-discipline of Biology but also incorporates organic, inorganic and
physical chemistry. Molecular biology has revolutionized every aspect of the study of Biology and a
grasp of current and future trends in Biology, including Ecology, requires an appreciation of life at
the molecular level. This begins with the study of basic concepts in Biochemistry.
Enrolment capacity: 400 students (maximum)
21
Purpose of the Course
This course provides an introductory treatment of concepts in Biochemistry. In many regards,
students will be learning a vast new language as well as new insight into the molecular logic of life
– how the structure/form of molecules is related to their diverse functions. At the end of the course,
students are expected to have a basic understanding of the biochemical nature of life.
Letter to the Student
This course aims to render you literate in the discipline of Biochemistry – to lay the foundation for
further study in biochemistry, genetics, microbiology, molecular biology, natural products and
several other disciplines. You will build the vocabulary and gain a basic understanding of the
biochemical concepts necessary to follow fast-paced developments in biology. The most cursory
glance at any top-ranked journal in any of the Biological sciences will reveal the extent to which
Biochemistry and Molecular Biology continue to revolutionize our thinking. Moreover, Biochemistry
and Molecular Biology serve as unifying disciplines, impacting on fields as diverse as medicine,
forensics, pharmaceutics, cosmetics, ecology, agriculture, biotechnology and anthropology to name
a few. A career in science, whether as a researcher, science administrator, educator or in science
popularization, requires that you be literate in this discipline.
It is a demanding discipline that requires you to keep up with pace at which you will be introduced
to the fundamentals and to practise its vocabulary and application to problems and questions of life
as introduced in your tutorial exercises.
Course Content and Objectives (Note: h* denotes lecture hour)
TOPIC 1 - Cell Organelles (3h)
Cell Theory and the Theory of endosymbiosis. Structure and function of cellular organelles:
Endoplasmic reticulum, Golgi apparatus, Chloroplast, Lysosomes, Peroxisomes, Glyoxysomes,
Mitochondria, Nucleus, cytoskeleton The proteasome.
At the end of this section students should be able to:


Describe the theory of endosymbiosis
Explain how the structure of organelles in eukaryotic cells is related to their function
22
TOPIC 2 - Chemistry of Carbohydrates (3h)
General formula. Monosaccharides – aldoses and ketoses, trioses, tetroses, pentoses, hexoses
and heptoses. Representation of monosaccharide structures – Fischer and Haworth projection
formulae, ring formation, furanose and pyranose forms. Stereoisomerism – chirality and optical
activity, enantiomers, epimers, anomers, D and L designations. Glycosidic bond formation,
common disaccharides and polysaccharides – sucrose, maltose, lactose, starch, glycogen, cellulose,
chitin, hyaluronate and chondroitin sulphates. Glycoproteins – fish antifreeze protein,
ribonuclease B and human IgG.
At the end of this section, students should be able to:











Identify ketoses and aldoses and explain the tests used to distinguish between them.
Draw Fischer and Haworth projection formulae for named tetrose, pentose and hexose sugars.
Define: stereoisomers, diastereoisomers, enantiomers, epimers, anomers and give named
examples.
Distinguish between D & L sugars.
Identify chiral carbons and calculate the number of stereoisomers a molecule can have.
Distinguish between hemiacetals, hemiketals, acetals and ketals and the significance to
reducing and non-reducing sugars.
Describe the oxidation and dehydration reactions of monosaccharides.
Write reactions for glycoside formation, including ring formation.
Identify and draw glycosidic bonds and identify the structures of common disaccharides.
Relate polysaccharide structure to function
Design a flow chart to elucidate the nature of unknown carbohydrates in the laboratory.
TOPIC 3 - Chemistry of Lipids (2h)
Definition of lipid. Fatty acids – nomenclature and physical properties, oxidation, reduction and
ester formation. Triacylglycerols and waxes – structure and function. Structure and function of
complex lipids: phosphoglycerides, sphingolipids, and glycolipids – membrane structure.
Arachidonic acid and eicosanoid formation, cholesterol and derivatives.
At the end of this section, students should be able to:






Define the terms: lipid, amphiphilic (amphipathic) and differentiate between hydrolysable and
non-hydrolysable lipids and between simple and complex lipids.
State the roles of different kinds of lipids.
Use different nomenclature to represent fatty acids.
Relate structures of lipids to their physical properties and reactions.
Relate structures of lipids to their functions.
Identify the different classes of lipids from their chemical formulae
23
TOPIC 4 - Amino acid & Protein Chemistry (3h)
Classification of the 20 common amino acids based on charge, polarity, aromaticity and affinity for
water. Ionization of amino acids, pK values, the Henderson-Hasselbalch Equation, determination
of pI values, Introduction to acid-base behavior. The peptide bond and protein structure. 1o, 2 o, 3
o and 4 o structure. Simple and conjugated proteins. Classification of proteins based on structure
and function.
At the end of this section, students should be able to:











State the different classes into which amino acids may be grouped and give named examples
of amino acids belonging to each class.
Describe the acid-base behaviour and ionization of amino acids and define the term
ampholyte.
Calculate the pI of any amino acid given its pK values.
Draw and interpret titration curves and utilize the Henderson-Hasselbalch Equation to predict
the ratios of ionized species at given pH values.
Describe the formation and characteristics of peptide bonds.
Describe how pH and ionic strength affect protein solubility.
Define what is meant by protein primary structure and outline the possible outcomes of
altering amino acids within a protein.
Explain what is meant by sequence homology and how it might be used to elucidate functions
of proteins
Describe protein secondary structures and the impacts of proline and glycine on secondary
structure.
Define tertiary and quaternary structures and briefly describe the importance of disulphide
bridges.
Describe the phenomenon of protein denaturation and renaturation.
TOPIC 5 - Nucleotides and Nucleic Acids (2h)
Composition – nitrogenous base, phosphate group and pentose sugar. Nucleosides and
nucleotides –cellular functions. Pyrimidine and purine bases. Polarity of nucleic acids – 5 3 .
DNA double helical structure: A-, B-, and Z-DNA, major and minor grooves, interaction with
tra s riptio fa tors, ase pairi g a d ase sta ki g. Chargaff s o ser atio s. “ize a d
organization of DNA. Some RNA structures. Central role of ATP in bioenergetics. Substrate-level
phosphorylation.
At the end of this section, students should be able to:

Distinguish between nucleosides & nucleotides, between purines & pyrimidines and between
RNA and DNA.
24









Outline the functions of nucleotides as: building blocks of nucleic acids, sources of energy used
to drive unfavourable reactions and components of coenzymes
Describe the nature of the phosphodiester bridge and how it gives polarity to polynucleotides
and the labile nature of this bond in RNA relative to DNA
Describe the factors which facilitate specific base pairing and state the observations on DNA
composition made by Erwin Chargaff.
Describe the features of the Watson-Crick model of DNA (B-DNA) including the factors which
contribute to the stability of the double helix.
Describe how B-DNA differs from A- and Z-DNA.
Describe the factors which contribute to the flexibility of the DNA molecule
Describe the spontaneous reactions which can take place in DNA: deamination, depurination
and reactions between adjacent thymine bases
Describe the hyperchromic effect and the effect of high salt concentration on the melting
temperature of double-stranded DNA.
Describe the factors which promote the hydrolysis of ATP
TOPIC 6 - Enzymes (4h)
The nature of enzymes. Specificity of enzyme action – the active site. Activation energy and
transition states. Initial velocity and substrate concentration. The Michaelis-Menten Equation.
Determination of Vmax and KM values - the Lineweaver-Burk plot, the Eadie Hofstee plot. Enzyme
inhibition- reversible inhibition: competitive, uncompetitive and non-competitive inhibition,
allosteric inhibition, substrate inhibition. Quantitation of enzyme activity – international units, S.I.
units and specific activity.
At the end of this section, students should be able to:










Define the terms: apoenzyme, holoenzyme, coenzyme, prosthetic groups, isoenzyme,
metalloenzyme, metal-activated enzyme, active site, transition state, activation energy.
Briefly describe different hypotheses proposed to explain enzyme specificity and catalysis.
List the mechanisms which are used to regulate enzyme activity
Briefly describe the six broad groups into which enzymes are classified and give named
examples from each class
Distinguish between absolute and group specificity and describe the properties of enzyme
active sites
Use the Michaelis-Menten and Lineweaver-Burk equations to determine kinetic parameters for
enzymes and relate them to the equation of a hyperbolic curve and a straight line respectively
List the assumptions inherent in the derivation of the Michaelis-Menten equation
Distinguish between different kinds of reversible enzyme inhibitors based on the mode of
binding as well as on the effect of the inhibitor on enzyme kM and Vmax values.
Describe how and why pH and temperature affect enzyme activity
Use enzyme units to define enzyme activity.
25
TOPIC 7 - Glycolysis (3h)
Anaerobic breakdown of hexose sugars to trioses. The pathway and its regulation through
allosteric and hormonal control of phosphofructokinase, hexokinase and pyruvate kinase. Net
energy yield from glycolysis. Entry of fructose and galactose into glycolysis. End product of
glycolysis – pyruvate, lactate or ethanol?
At the end of this section, students should be able to:








List the types of cells/tissues which must rely on glycolysis to provide energy and explain the
reasons for this dependence
State the other purposes served by this pathway
List the names of enzymes catalyzing each reaction
List the substrates and products of each reaction
Describe the sub-cellular location of the pathway and how the cofactors are regenerated
State the sites where ATP is generated
Describe how the pathway is regulated
Describe what happens in the pathway under aerobic and anaerobic conditions: what products
are formed and what cofactors are limiting
TOPIC 8 - Overview of Metabolism (2h)
Catabolism of amino acids, lipids and carbohydrates leads to generation of Acetyl CoA. Common
fate of acetyl CoA – The tricarboxylic acid cycle and the electron transport chain. Synthetic paths
from the TCA.
At the end of this section, students should be able to:
 Show how acetyl-CoA is central to the catabolism of the macronutrients protein,
carbohydrates and lipids.
 Describe how the tricarboxylic acid cycle generates reducing power
 Describe how the electron transport chain utilizes reducing power to generate an
electrochemical gradient that is in turn used to generate chemical power in the form of ATP
Assignments
Tutorial sheets on each topic to be prepared in written format
Preparation of Laboratory Reports
26
In-Course Assessment
Laboratory reports
20%
In-course tests
20%
Total
40%
Evaluation
Course work
40%
2-hr. final Theory-
60%
MCQ s, stru tured a d essa
Teaching Strategies
These include lectures and other supporting materials on myelearning, as well as small group
tutorial sessions. In course tests are cumulative to encourage students to keep abreast of the
material as presented and also to retain work done early in the semester. Case-studies will be
employed where appropriate to encourage problem-solving and critical thinking skills.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
27
Essential Text -Any one of:
1. Lehninger Principles of Biochemistry by David L. Nelson, Michale M. Cox and Albert
Lehninger. 6th Edition.
2. Biochemistry by Jeremy M. Berg, John L. Tymoczko and Lubert Stryer, 7th Edition.
3. Principles of Biochemistry by H. Robert Horton 4th Edition (ISBN 0131453068).
BIOL 1362 COURSE CALENDER
WEEK
1
LECTURES
1
Cell Organelles
2
Cell Organelles
PRACTICALS
Tutorial
2
3
Cell Organelles
4
Carbohydrate chemistry
1. Virtual Lab – Cell Organelles
TUTORIAL
3
5
Carbohydrate chemistry
6
Carbohydrate chemistry
Review of Exercise 1
TUTORIAL
4
7
Lipid chemistry
8
Lipid chemistry
2. Carbohydrates & Lipids
TUTORIAL
5
9
Amino Acids & Proteins
Review of Exercise 2
In-Course Examination # 1
28
TUTORIAL
6
10
Amino Acids & Proteins
11
Amino Acids & Proteins
3. Preparation and assay of phenolase
and peroxidise from sweet and Irish
potato
TUTORIAL
7
12
Nucleic acids
13
Nucleic acids
Review of Exercise 3
TUTORIAL
8
14
Enzymes
4. Demonstration of Dehydrogenase
enzyme activity
15
Enzymes
TUTORIAL
9
16
Enzymes
17
Enzymes
TUTORIAL
10
18
Glycolysis
Review of Exercise 4
19
In-Course Examination #2
TUTORIAL
11
20
Glycolysis
21
Glycolysis
TUTORIAL
12
22
Overview of metabolism
23
Overview of metabolism
TUTORIAL
29
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND AGRICULTURE
DEPARTMENTOF LIFE SCIENCES
Course Outline
Course Title: Introductory Genetics
Course Code: BIOL 1364
Credits: 3
Level: ONE
Semester: TWO
Pre-requisites & Assumed Knowledge:
CAPE Biology OR BIOL 0061: Preliminary Biology I and BIOL 0062 Preliminary Biology II
Students are expected to have a prior basic knowledge and understanding of the following:




Chromosomes
Mitosis & Meiosis
Prokaryotes & Eukaryotes
DNA structure & replication
Course Descritpion
This course aims to present an introduction to the basic principles of Genetics and will equip
students with the necessary foundation for advanced level courses in Biology & Biochemistry at the
Department of Life Sciences, University of the West Indies. The course content has only been
slightly modified from what has been previously taught in the Genetics component of “BIOL 1061
– Cell Biology & Genetics”. The previously taught BIOL 1061 delivered all course content in just
six weeks which is too intensive of an approach. This course is being implemented to maintain the
current requirements for the Biology major while offering students more flexibility and time to
assimilate concepts being presented.
Major topics to be covered include: The Nuclear Genome, The Cell Cycle & Mendelian Genetics,
Extensions of Mendelian Genetics, including the molecular basis of heredity, Linkage analysis &
Gene Mapping, Sex Linkage & Sex Determination, The Extrachromosomal Genome and
Extrachromosomal Inheritance.
Students will have the opportunity to work on problem sheets to calculate genotypic and phenotypic
ratios and to access simulations of mitosis and meiosis as well as drosophila transmission Genetics
on-line Feed- back sessions will take place after each In- course Test.
30
The course consists of 23 (50-min) lectures 3 hrs of In-Course Tests, supplemented with 6 tutorial
sessions. In addition students will have the opportunity to gain experience in the laboratory through
implementation of 5 three-hour practical sessions.
Lectures and Tutorials, Review and feedback sessions:
Practicals:
31.5 credit hours
7.5 credit hours (3 x 5 = 15 hours/2)
Course Assessment
ASSESSMENT
In-course Examination #1
In-course Examination #2
Laboratory/Practical Exercises (3)
Tutorial Question Sheets
Final Examination
Total
WEIGHTING
10%
15%
15%
10%
50%
100%
Course Calendar
Practical sessions held in alternate weeks
Week Lecture subjects
Tutorials and
Labs.
1
(3h)
Lect1: Course Overview & Introduction to Genetics
2
(5h)
Lect.#3: Introduction to the Human Genome and the Cell Cycle Lab. #1- Basic
Microscopy &
Visualization of
Lect.#4: Mitosis & Meiosis
Chromosomes
(3h)
3
(3h)
Lect.#5: Mendelian Patterns of Inheritance
4
(5h)
Lect. #7&8: Intra-allelic Interactions
Tutorial #1
Lect. #2: Chromosome Structure & Morphology
Tutorial #2
Lect.#6: Predicting Inheritance & Goodness-of-Fit Testing
In-course Test
#1
Lab.#2Chromosome
staining (3h)
31
Week Lecture subjects
Tutorials and
Labs.
Tutorial #3
Feedback on InCourse Test#1
5
(3h)
Lect. # 9&10: Inter-allelic Interactions
6
(5h)
Lect. #11: Environmental Effects on Mendelian Inheritance
7
(3h)
Lect. # 12: Multiple Allelism
Lab.#3Drosophila
Transmission
Genetics (3h)
Lect.#13 :Polygenic Traits & Quantitative Inheritance
Tutorial #4
Lect. #14 :Introduction to Linkage & Linkage Relationships
8
(5h)
Lect. #15: Linkage Mapping
Lect. # 16: Linkage Analysis in Ascomycetes 1
In-Course Test
#2
Lab.#4- ChiSquare Problem
Solving
9
(3h)
Lect. # 17 :Linkage Analysis in Ascomycetes 2
Tutorial #5
Lect.# 18: Sex Determination Systems in Animals
Feedback on InCourse Test#2
10
(5h)
Lect. # 19: Sex Determination Systems in Plants
In-Course Test
#3
Lect. # 20 : Sex Linkage & Inheritance of Sex-linked Traits
Lab#5- Linkage
Analysis
Problem Sheets
11
(3h)
Lect. # 21: Pedigree Analysis
Tutorial#6
Lect. # 22: Extrachromosomal Inheritance 1
Feedback on InCourse Test#3
12
(3h)
Lect. # 23 :Extrachromosomal Inheritance 2
None
13
None
Lect. # 24 Revision Lecture (1h)
32
Lecture Outline & Learning Outcomes
Lecture 1: An Introduction to Genetics
 A definition of genetics
 Branches of genetics
 DNA is the genetic material
By the end of this lecture students should be able to:
Describe what the study of genetics entails and give an outline of the various branches of
study in the subject field.
Explain why the genetic material can either be DNA or RNA
Describe the crucial experiments that proved nucleic acids as the genetic material of living
organisms
Lectures 2, 3 & 4: Chromosomes & Heredity







Chromosome structure & morphology
Chromosome staining & banding nomenclature
The human genome
Features of homologous chromosomes
Defining key terms
The cell cycle
Mitosis & Meiosis
By the end of these lecture students should be able to:
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
Distinguish between DNA and chromosomes and explain the chromosome theory of
inheritance.
Describe the basic morphology of chromosomes and define and illustrate metacentric, submetacentric, acrocentric & telocentric chromosomes.
Describe G-banding as a chromosomal staining technique that produces specific banding
patterns.
Use the established nomenclature for the identification of specific chromosomal regions and
sub-regions.
Describe the human genome as comprising 22 pairs of autosomes and a pair of sex
chromosomes.
Explain the term ploidy using humans as examples of diploids
Describe the features of homologous chromosomes.
Define the following key terms: gene, allele, locus, Central Dogma, dominant, recessive,
homozygous, heterozygous, genotype, phenotype, variation & mutation.
33
ix.
x.
xi.
xii.
Outline the different phases of the eukaryotic cell cycle (G0, G1, S, G2 & M phases) and
describe what is taking place in each of these phases.
Describe in detail and illustrate the processes of mitotic and meiotic cell division and
compare these two processes, commenting on the significance of each.
Distinguish between random chromosome assortment & crossing over as the basis of
recombination.
Explain how variation is generated and clearly distinguish between the processes of
recombination & mutation.
Lectures 5 & 6: Mendelian Genetics







Mendel’s Laws & The Law of Product Probability
Monohybrid Inheritance
Dihybrid inheritance
Trihybrid Inheritance
Test-crosses
Predicting Inheritance
Goodness-of-fit Testing (Chi-Square Test)
By the end of these lectures students should be able to:
i.
ii.
iii.
iv.
v.
vi.
vii.
Compare the behavior of chromosomes in meiosis with that of ‘Mendel’s particles’.
State Mendel’s laws: (The law of segregation and the law of independent assortment).
Predict the outcome of monohybrid, dihybrid and trihybrid crosses using Mendel’s laws, the
law of product probability and by application of the Punnet Square.
Show how the inheritance of complex characteristics (monogenic, digenic, oligogenic &
polygenic traits) can be resolved by using the law of product probability and the branch
method.
Explain the purpose of the test-cross and apply it to determine unknown parental genotypes.
Test predicted outcomes of crosses and expected Mendelian phenotypic ratios against
empirical values by employing the chi-square test.
Predict the inheritance of characteristics by building hypothetical models and testing them.
Lecture 7&8: Extensions of Mendelian Inheritance – Intra-allelic Interactions
 Modifications of expected Mendelian phenotypic ratios by interaction between alleles of the
same gene controlling a single trait:
a. Complete dominance
b. Incomplete dominance
c. Co-dominance
d. Over dominance
e. No dominance
34
f. Lethal allelic relationships
By the end of these lectures students should be able to:
i.
ii.
iii.
Explain the non-conformance of empirical phenotypic ratios with expected Mendelian ratios
and list the modifying factors that may cause them to vary significantly.
Demonstrate that intra-allelic interactions stem from the relationship between alleles of the
same gene.
Outline and explain the various intra-allelic relationships and the underlying biochemical
basis for each of these interactions, clearly showing in each case how they modify expected
Mendelian phenotypic ratios.
Lecture 9 & 10: Extensions of Mendelian Inheritance – Inter-allelic Interactions
 Modifications of expected Mendelian phenotypic ratios by interaction between alleles of
different genes controlling a single trait:
a. Recessive epistasis
b. Duplicate recessive epistasis
c. Dominant epistasis
d. Duplicate dominant epistasis
e. Dominant/Recessive interaction
f. Duplicate interaction
By the end of this lecture students should be able to:
i.
ii.
iii.
Recognize that inter-allelic interactions stem from the relationship between alleles of
different genes.
Describe the different classes of epistasis (complementary, inhibitory and duplicate) and the
types of epistases within each of the classes.
Outline and explain the various inter-allelic relationships and the underlying biochemical/
molecular basis for each of these interactions, clearly showing in each case how they modify
expected Mendelian phenotypic ratios.
Lecture 11& 12: Extensions of Mendelian Inheritance
 Environmental Effects
 Multiple Allelism
By the end of this lecture students should be able to:
i.
Explain how both external and internal environmental effects can alter gene expression
patterns and by extension modify phenotypes/ phenotypic ratios.
35
ii.
iii.
iv.
v.
vi.
vii.
Provide examples of modifying environmental effects and explain how they operate.
Define and distinguish between ‘gene penetrance’ and ‘expressivity’ and explain their use as
measures of the extent to which a gene manifests itself under varying environmental
conditions giving specific examples for each.
Explain the concept of multiple alleles at a single gene locus and its effect on phenotypic
variation within a population.
Describe specific examples of multiple allelism, highlighting the dominance relationships
between members of the multiple allelic series.
Explain that although genes may have multiple alleles, the alleles obey the same rule of
transmission.
Describe how multiple allelism can lead to greater genetic variability in populations.
Lecture 13: Polygenic Traits & Quantitative Inheritance
 Polygenic Traits and Polygenic Inheritance
 Concept Heritability and Heritability Estimates
By the end of this lecture students should be able to:
i.
ii.
iii.
iv.
v.
Explain what is meant by the term polygenic traits and cite relevant examples of such traits.
Distinguish between quantitative (oligogenic) and qualitative (polygenic) traits and
between oligogenic inheritance and polygenic inheritance
Explain the reasons why polygenic traits show a normal distribution
Explain the differences between studying the inheritance of oligogenic vs polygenic traits.
Define and distinguish between the terms ‘heritability in the broad sense’ and ‘heritability
in the narrow sense’ and explain the significance of these measures to breeders.
Lectures 14 & 15: Linkage analysis & Mapping
 Definition of Linkage & Linkage Relationships
 Two-point linkage mapping
 Three-point linkage mapping
By the end of these lectures students should be able to:
i.
ii.
iii.
Distinguish between synteny and linkage
Distinguish clearly between a genetic map vs physical map; and the advantages and
disadvantages of each.
Explain the consequences of linked genes. Distinguish between types of linkage, complete,
incomplete and no linkage and explain the effect each has on the phenotypic ratios obtained
in the F2 and testcross generations
36
iv.
v.
vi.
vii.
viii.
ix.
x.
xi.
xii.
xiii.
xiv.
Explain the relationship between chiasma frequency and recombination frequency and type
of linkage.
Calculate recombination frequencies based on F2 or test-cross data
Calculate the test cross ratio when the F2 ratio is given or vice versa
Use the proper notation for representing linked genes and determine whether the linked
genes are in coupling phase or repulsion phase.
Predict outcomes when considering linked genes in both cis (coupling) configuration and
trans (repulsion) configuration.
Express recombination frequencies as percentages and use them to determine map distances
between genes in map units (m.u.) or centi-Morgans (cM).
Calculate and determine map distances between genes based on recombination frequencies
obtained from either F2 data or test-cross data.
Clearly indicate the advantages of three-point linkage analysis as compared to two-point
linkage analysis.
To conduct linkage analysis, using test cross data obtained by test crossing a triple
heterozygote
Apply the two-point (2 gene markers) and three-point system (3 gene markers) of mapping
genes.
Describe the use of genetic maps in breeding.
Lecture 16 & 17: Linkage Analysis in Ascomycetes
 Overview of Fungal Reproductive Cycle in Ascomycetes
 Ordered Tetrad Analysis
 Unordered Tetrad Analysis
By the end of this lecture students should be able to:
i.
ii.
iii.
iv.
v.
vi.
vii.
Describe the sexual reproductive cycle in Ascomycetes.
Perform linkage analysis on the meiotic products contained within asci (sacs).
Distinguish clearly between ordered tetrad analysis vs unordered tetrad analysis.
Illustrate the difference between first and second division segregation types.
Carry out linkage analysis and calculate map distances between genes based on ordered
tetrad analysis.
Illustrate the formation of parental ditypes, non-parental ditypes and tetratypes in fungi with
unordered tetrads.
Carry out linkage analysis and calculate map distances between genes based on unordered
tetrad analysis.
Lectures 18, 19 & 20 Sex Determination and Sex Linkage
 Sex Determination Systems
37
 Sex chromosome based inheritance
By the end of these lectures students should be able to:
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
ix.
x.
Define the term sex chromosome vs autosomal chromosomes
Describe the sex determining mechanisms in the animal kingdom – sex chromosome
mediated methods viz: XY-XX; XO-XX; ZW-ZZ; Z0-ZZ; Chromosome Balance Theory of
Sex Determination; haplo-diploidy; haplo-diploidy and complementary genes; genic control
of sex.
Explain the following mechanisms of sex determination using appropriate examples to
illustrate:
a. Mammalian XY-XX system
b. Protenor XX-XO system
c. Birds ZW-ZZ system
d. ZO-ZZ system
e. Sex Balance Theory (genic balance)
f. Yeast (MATa – MATα mating types)
g. Environmental sex determination
Distinguish between the terms homogametic and heterogametic sex
Describe Morgan’s experiments involving the transmission of sex-linked traits in Drosophila
melanogaster.
Describe the sex determining mechanisms in various plants.
Distinguish clearly between Monoecy and Dioecy.
Distinguish clearly between autosomal vs sex linked vs holandric gene inheritance
Describe and illustrate the criss-cross mode of inheritance as it relates to sex-linked traits.
Illustrate and compare the differences observed in the outcomes for reciprocal crosses
involving sex-linked traits.
Lecture 21: Analysis of Sex-Linked Traits in Humans




X-linked Recessive Inheritance
X-linked Dominant Inheritance
Y-linked Inheritance
Pedigree Analysis
By the end of this lecture students should be able to:
i.
ii.
iii.
iv.
Explain the mechanisms by which X-linked and Y-linked traits are inherited.
Distinguish between the inheritance patterns observed for X-linked recessive, X-linked
dominant, Y-linked, autosomal recessive and autosomal dominant traits.
Define and state the purpose of pedigree charts.
Analyze and interpret the structure of pedigree charts and the associated symbols with an
aim of determining the mode of transmission of a particular trait.
38
Lectures 22 & 23: Extrachromosomal Inheritance




Chloroplast & Mitochondrial Genomes
Features of Cytoplasmic Inheritance
Nuclear-Cytoplasmic Interaction
Maternal Effects
By the end of this lecture students should be able to:
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
Relate the genomes of prokaryotes to organellar genomes
Describe the structure and organization of organellar genomes (chloroplasts &
mitochondria).
Distinguish between nuclear genomes and extra-chromosomal genomes
Distinguish between nuclear and extra-chromosomal inheritance using appropriate examples
to illustrate.
Explain nuclear-cytoplasmic gene interaction using a named example.
Define the term maternal effect and clearly explain the underlying mechanism of inheritance
involved using appropriate examples.
Distinguish between maternal effect and extra-chromosomal inheritance.
Distinguish between diminishing and non-diminishing maternal effects.
Lecture 24: Review Session
Practical Exercises
1. Introduction to Basic Microscopy: Visualization of different stages of mitosis and meiosis
By the end of this laboratory exercise students should be able to:
- Know the parts of the microscope and thereby employ proper usage
- Identify the different stages of mitosis and meiosis from pre-prepared slides
- Draw accurate diagrams of chromosomes and their arrangement at the different stages of
mitosis and meiosis
- Calculate magnification values for drawings
2. Chromosome Staining
By the end of this laboratory exercise students should be able to:
- Employ the Feulgen staining technique to prepare fresh slides for the visualization
of chromosomes in different plant tissues
- Identify sources of error and employ precautions to ensure good squash preparations are
obtained
39
- Identify the different stages of mitosis and meiosis from the newly prepared slides
- Calculate the mitotic index and estimate the time spent in various stages of the cell cycle
3. Drosophila Transmission Genetics (Virtual Laboratory Exercise)
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
Recommended Texts
1. Brooker, Robert J. Genetics: Analysis & Principles 3rd Edition McGraw Hill Higher
Education 2008. ISBN: 9780071287647
2. Snustad, D. Peter & Simmons, Michael J. Principles of Genetics 5th Edition John Wiley &
Sons Inc. 2009. ISBN: 9780470388259
40
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE CODE: BIOL 2061
COURSE TITLE: Cell & Developmental Biology
CREDITS: 3
LEVEL: II
SEMESTER: I
PRE-REQUISITE(S): BIOL1263 Living Organisms II or BIOL1261 Diversity of Organisms or
(BIOL1065 Diversity of Plants and Animals and AGRI1012 Microbiology) and either BIOL1362
Biochemistry I and BIOL1364 Genetics I or BIOL1061 Cell Biology and Genetics
COURSE DESCRIPTION
The course begins with a review of the structure and function of cellular membranes and organelles
and the role of the cytoskeleton in cell shape and motility. The fundamental processes operating
during embryonic development and cellular differentiation of plants and animals will then be
examined. The principles of development will be considered at the organismal, cellular and molecular
levels for a complete understanding of developmental processes. Students will be introduced to
important experiments that have led to an understanding of the basic principles of development. The
application of stem cells in research and associated ethical considerations will form the basis of class
discussions and debates.
COURSE RATIONALE
Cell and Developmental Biology is a core course for the Biology program in the Department of Life
Sciences. It serves to build upon the student’s basic knowledge of cell biology, and to introduce
students to the fundamental concepts of developmental processes in several model organisms.
Overall, this course is an essential component of the core biology degree as it examines the underling
processes in a variety of model systems applicable to all major fields of biology.
41
INSTRUCTOR INFORMATION
Name of course coordinator:
Dr. Georgette Briggs
Office address and phone:
Biochemistry Office, Floor 2, Old wing,
Natural Sciences Building
Email address:
[email protected]
Office hours:
Fridays 1:00-2:00 pm
Preferred method of contact:
Email
Communication policy: Students should use their UWI email account for communication and can
expect a response within 48 hours.
COURSE GOALS:
On completion of this course, students should have:




An understanding of the fundamental processes operating during key developmental
processes
An appreciation of the role of developmental processes in disease
The ability to critically analyze scientific experiments and their findings
Gained skills in presenting and defending a logical, scientifically supported argument.
CONTENT
Developmental biology overall, seeks to understand the complexity that underlies the different cell
types and organs, the emergence of form and patterns, and the communication between cells to
achieve these processes. Almost every disease is linked to a developmental failure. As such, a portion
of this course focuses on models that examine the links between basic developmental errors and
disease.
LECTURE OUTLINE AND LEARNING OUTCOMES
Students completing this course should be able to:
Lecture 1: Structure & Function of Biological Membranes


Explain the general properties of biological membranes.
Describe the molecular components of biological membranes.
42








Explain the role of various phospholipids in membrane structure.
Describe the properties of the phospholipid bilayer.
Explain how proteins are associated with membranes and outline some of their key functions.
Describe the basis of membrane fluidity and its importance.
Describe the nature of membrane asymmetry and its functional significance.
Describe the role of membrane carbohydrates.
Describe the electrical property of membranes and explain its significance.
Describe mechanisms of transport across membranes using specific examples of channels and
carriers.
Lecture 2: Mitochondria & Chloroplasts





Describe and illustrate the basic structural features of mitochondria.
Give an overview of mitochondrial function.
Describe and illustrate the basic structural features of chloroplasts.
Give an overview of chloroplast function.
Discuss the evolutionary origin/development of mitochondria & chloroplasts.
Lecture 3: The Nucleus







Describe the basic structure of the nucleus and its components.
Describe the structure of the membranes comprising the nuclear envelope and explain its relationship
to the endoplasmic reticulum.
Discuss the evolution of the nucleus.
Describe the composition of the nuclear matrix.
Describe the structure, composition and function of the nucleoli.
Describe the structure and function of nuclear pore complexes.
Explain the mechanism of transport across nuclear membranes.
Lecture 4: The Endoplasmic Reticulum & Golgi Apparatus





Describe the structure of the Smooth and Rough ER.
Compare and contrast the major functions of the Smooth and Rough ER.
Describe the structure of the Golgi apparatus.
Explain the major functions of the Golgi apparatus.
Describe the processing of membrane proteins from the ER to their destination via the Golgi
apparatus.
Lectures 5 & 6: Secretion & Exocytosis and Endocytosis



Define exocytosis as the terminal stage of secretion leading to the release of newly synthesized
proteins from the cell
Describe the different types of proteins and cells typically involved in secretion
Explain the movement of proteins through the secretory pathway with particular emphasis on the
role of the ER and the Golgi membranes in protein sorting & glycosylation
43







Describe the internal signal sequences in newly synthesized proteins responsible for their
translocation and determining their ultimate destination
Outline the glycosylatic reactions essential for passage through the secretory pathway
Explain the process of vesicle formation and describe the role of various coat proteins involved
Describe the motor protein mediated movement of vesicles along microtubules
Define endocytosis as the transport of extracellular material into the cell.
Describe the different mechanisms of endocytosis (phagocytosis, pinocytosis & receptor-mediated
endocytosis) and their functions and roles in different cell types.
Explain the role of clathrin in the invagination process of receptor-mediated endocytosis.
Lecture 8: Endosomes, Lysosomes & Peroxisomes






Describe the processing of early endosomes including the sorting of their components and recycling
to the cell surface.
Explain the role of lysosomes in the processing of endosomes.
Describe the structure, function and origin of the peroxisome.
Describe the oxidative reactions of the peroxisome.
Explain the role of signal sequences and the mechanism of import of proteins into the peroxisome.
Highlight the importance of peroxisomal function and its involvement in Zellweger syndrome.
Lectures 9 & 10: The Cytoskeleton & Organelle Movement







Define the cytoskeleton.
Describe the subunit composition and assembly characteristics of each of its constituent elements
and their roles.
Explain the role of the cytoskeleton in normal cellular function including its association with key
regulatory binding proteins.
Identify and explain the role of key cytoskeletal structures and proteins responsible for enabling and
regulating organelle and chromosome movement in the cell.
Explain the role of dynein and kinesin in the mechanism of organelle movement along microtubules.
Explain the critical role of motor proteins and cytoskeletal protein turnover in sorting replicated
chromatids to daughter cells in mitosis.
Describe examples of human diseases associated with cytoskeletal protein dysfunction.
Lecture 11: Cell Motility






Identify actin rich structures within the cell that are important for cell motility.
Describe the organization of actin into specialized structures associated with cell motility and cell
shape.
Explain the role of cytoskeletal proteins and actin microfilament turnover in cell motility
Describe the structure of cilia and flagella.
Explain how organized assemblies of actin filaments and motor proteins work in combination to
drive cell movements.
Describe the basic structure, function and dysfunction of the axoneme.
44
Lecture 12: The Extracellular Matrix




Identify the major components of the Extracellular Matrix (ECM) and describe their molecular
structure, roles and distribution in specific tissues
Describe the structure of integrins and their interaction with specific components of the ECM.
Describe specific examples of clinically important conditions involving ECM-integrin interactions
emphasizing how integrin dysfunction may be related to disease conditions
Relate actin-based cell motility to ECM/integrin complexes.
Lecture 13: Cellular Junctions & Cell Adhesion




Identify and illustrate the appearance of the major types of cell junctions.
Describe the molecular structure of the major types of cell junctions.
Explain the distribution of cell junctions in relation to their functions in multicellular organisms.
Highlight the importance of cell junctions and describe specific diseases in humans involving cell
junction abnormalities.
Lectures 14, 15 & 16: Cell Communication






Describe the signals (chemicals & signaling molecules) involved in controlling cell function
Define the terms ligand and receptor
Describe the main cell surface receptor superfamilies (ligand-gated ion channels, G-protein coupled
receptors, enzyme-linked cell surface receptors) and intracellular recptors
Explain in outline the mechanisms of signal transduction including the generation of 2nd messengers
(cyclic AMP, cyclic GMP and the phosphoinositide pathway)
Explain the action of various signaling molecules on intracellular recptors in relation to the changes
induced
Identify and explain the intracellular mechanisms of the five major families of signal proteins
primarily involved in the induction of animal development (Receptor tyrosine kinases, TGFβ
superfamily, Wnt, Hedgehog, Delta-Notch)
Lectures 17 & 18: Polarity & Development






Explain the role of regulatory DNA in defining specific programs of development.
Explain the role of morphogens and their interplay with extracellular inhibitors in defining cellular
development.
Explain the role of maternal effect genes in the organization of asymmetric egg division.
Explain the specific cell-cell interactions involved in patterning and the role of developmental
signals in cell differentiation (Wnt, Delta-Notch signalling).
Explain the role of heterochronic genes in controlling the timing of development.
Explain the role of apoptosis in developmental programs
45
Lecture 19: Stem Cells & Ethics


Define the term potency (unipotency, oligopotency, multipotency, pluripotency, totipotency,
terminally differentiated) as it relates to stem cells, cellular development and specialization.
Discuss some of the ethical concerns associated with stem cell research & experimentation.
Lectures 20 & 21: Embryogenesis



Describe the stages of fertilization with particular emphasis on the molecular changes occurring in
the formation of the zygote.
Describe the morphological and molecular changes occurring in the transition phases of development
from zygote through morula to blastocyst, the inner cell mass and trophoblast.
Explain the fates and roles of the cells of each of the three germ layers: ectoderm, endoderm and
mesoderm in the formation of specific tissues (myotome, sclerotome, nervous tissue & respiratory
system).
Lectures 22 - 27: Models of Development
 Caenorhabdatis elegans: Model of Development
 Drosophila melanogaster: Model of Body Plan Patterning
 Arabidopsis thaliana: Model of Development
Lectures 28 & 29: Organogenesis & Appendage Patterning



Identify the regulatory genes involved in defining cells fated to appendage development
Explain the role of Wingless, Hedgehog, Dpp & Notch signaling in the patterning the wing disc
Highlight some of the mechanisms involved in patterning vertebrate (Gallus gallus model) limbs
Lecture 30: Problems of Development

Highlight relevant case studies relating to problems in development
COURSE ASSESSMENT
In-course test 1:
10 %
In-course test 2:
10 %
Written Paper:
10 %
Ethics Debate (on-line)
10 %
On-line Discussion Forums
10 %
Final examination (2 hours)
50 %
46
EVALUATION
The elected Class Representative and/or Deputy will attend meetings with the course teacher(s)
organized at every 4th week, and present feedback from the students attending that course or stream.
This feedback is normally provided both orally and in written form for transmission to the lecturer.
Apart from that the representatives will be attending the Liaison Committee meeting, and give their
feedbacks to the committee.
Students may comment on any aspect of the course or facilities. Students will be encouraged to submit
their feedback (oral/written) during tutorials directly to the course teacher and appropriate actions
will be taken by the teacher then and there.
Results of in-course tests, and feedback of online discussion forums will be presented to the class.
This will help students to check their progress constantly and also helps the instructor to identify the
weak areas and thereby could alert and advise students individually to alter their approach of study
and completing the work.
The final reflective feedback and comments about the entire course and teaching will be collected on
the last day of the course. This will be saved for analysis and utilized as a base for improvement for
the next offering in the following year.
COURSE DELIVERY & TEACHING STRATEGIES
The course will be delivered via 28 one-hour lectures and supplemented with 3 tutorial sessions In
addition students will have the opportunity to gain skills in oral communication, argument
formation and execution (debating) and collaborative group research and presentation. The course
would be delivered via lectures and tutorials. Online forum discussions & debates, written reports,
and virtual labs, would also be used to encourage student participation and collaborative learning.
COURSE CALENDAR
WEEK
1
Lecture/Tutorial
Lecture 1: Course introduction and review of structure & function
of Biological Membranes
Lecture 2: Mitochondria & Chloroplasts
Lecture 3: The Nucleus
2
Lecture 4: The Endoplasmic Reticulum & Golgi Apparatus
Lecture 5 : Secretion & Exocytosis
Lecture 6: Secretion & Exocytosis
47
Activity
3
Tutorial
Lecture 8: Endosomes, Lysosomes & Peroxisomes
Topics given
for written
assignment
Lectures 9 : The Cytoskeleton & Organelle Movement
4
Lectures 10: The Cytoskeleton & Organelle Movement
Lecture 11: Cell Motility
Online
discussion
forum
Lecture 12: The Extracellular Matrix
5
Tutorial
Lecture 13: Cellular Junctions & Cell Adhesion
In course
exam
In-course #1 (Weeks 1-4)
6
Lecture 14: Cell Communication
Online
discussion
forum
Lecture 15: Cell Communication
Lecture 16: Cell Communication
7
Lecture 17: Polarity & Development
Lecture 18: Polarity & Development
Written paper
due
Lecture 19: Stem Cells & Ethics
8
Tutorial
Lectures 20: Embryogenesis
Lecture 21: Embryogenesis
9
In-course #2 (Weeks 5-8)
In course
exam
Lecture 23: Models of Development
Lecture 23: Models of Development
10
Lecture 24: Models of Development
Online
discussion
forum
Lecture 25: Models of Development
Lecture 26: Models of Development
48
Lecture 27: Models of Development
11
Lecture 28: Organogenesis & Appendage Patterning
Online ethics
debate
Online Ethics Debate
Lecture 29: Organogenesis & Appendage Patterning
12
Lecture 30: Problems of Development Lecture
Course Review Tutorial
13
Course Review Tutorial
Recommended Texts


Developmental Biology, Scott F. Gilbert, 9th Edition; Sinauer Associates, Inc. 2010
Molecular Biology of the Cell, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin
Raff, Keith Roberts, and Peter Walter. 4th Edition; 2002
Other Texts

Patterns & Experiments in Developmental Biology, Johnson & Volpe 3rd Edition;
McGraw-Hill companies, Inc. 2001. ISBN 0-07-237965-0

Embryology: An Introduction to Developmental Biology Stanley Shostak 1991.
Harper/Collins, New York ISBN 0-06-046126-8

Principles of Development Lewis Wolpert, Rosa Beddington, Thomas Jessell, Peter
Lawrence, Elliot Meyerowitz, Jim Smith. 2nd Edition, 2002. Oxford University Press ISBN
0-19-924939-3

Cells, Embryos And Evolution฀John Gerhart and Marc Kirschner฀ 1997฀Blackwell
Science฀ISBN 0-86542-574-4
ADDITIONAL INFORMATION
Student Attendance
Attendance in the in-course exams and participation in the online discussions and ethics debate are
mandatory. Any student who misses any of the mandatory activities, is advised to consult immediately
49
in person or by email with the course instructor regarding their make-up options. Absence must be
accompanied by a written excuse or medical submitted to the Main office, Life Sciences within 7
days of the missed session. Any student who was inexcusably absent or who does not write an incourse exam or a quiz will receive 0% for that exercise.
How to study for this course
Students are encouraged to work together in small cohesive groups as much as possible to go through
the course content. As we go through the various topics, students should attempt to answer all the
sample questions placed on myelearning and discuss the answers amongst themselves. All
comments, questions and concerns provided on a particular topic will be addressed during the
discussion segments of laboratories and during class time. To support the material presented in class,
several texts have been recommended. These texts would also be supplemented by various scientific
journal articles available to you via the myelearning platform. Use the responses and comments for
your quizzes and in-course examinations as a guide to answering the questions properly. There are
several past paper questions in the library and students are encouraged to practice these questions.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
50
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE OUTLINE
COURSE CODE & TITLE: BIOL 2262 - EVOLUTIONARY BIOLOGY
NO. OF CREDITS: 3
LEVEL II
SEMESTER I
PREREQUISITES: BIOL 1364 AND any two of the following: BIOL1262, BIOL1263, or
BIOL1362
COURSE DESCRIPTION
Concepts of evolutionary biology are the basis of understanding all of modern biology. Following a
short historical introduction, about one-quarter of the course is devoted to population genetics and
evolutionary mechanisms at the population level. This leads to treatment of the nature of species,
the history of life and past evolutionary patterns, special forms of evolution and phylogenetic
analysis. The basic teaching/learning approaches include lectures, tutorials and practical exercises
in the lab and field. Assessment is designed to encourage students to work continuously with the
course materials, explore and critically analyse research in this dynamic field.
COURSE RATIONALE
This course is designed to provide the foundation of modern evolutionary biology that must be at
the heart of all biological education. It is a core course for all students in the B.Sc. General majoring
in Biology or in the B.Sc. (Special Option) Biology with Specialisations.
INSTRUCTOR INFORMATION
Name of course coordinator:
To be assigned
Office address and phone:
Email address:
Office hours:
Preferred method of contact:
Communication policy: Students should use their UWI email account for communication and can
expect a response within 48 hours.
LETTER TO THE STUDENT
Dear student,
Welcome to BIOL 2262 Evolutionary Biology. This is a core course in the Biology degree which
serves to provide a basic foundation for students to understand the mechanisms of change in living
51
organisms or biological evolution. It attempts to answer some of the simplest questions e.g. How
did life originate? Why are there so many species on Earth?
You will be exposed to modern evolutionary biology which is based on new methodologies in
genetics and molecular biology, rigorous application of the scientific method, and observational and
experimental evidence from a variety of field and lab situations.
You will be expected to refer to a broad range of topics in biology from the molecular to the
geological scales e.g. molecular biology, population genetics, anatomy, physiology, behaviour and
ecology.
In addition, we expect you to think like a practicing scientist in one of the broadest and most
complex fields in biology i.e. to apply the principles of the scientific method, to evaluate your own
ideas and critique those of others, think analytically and solve problems.
On completion of this course you will be able to apply evolutionary concepts to all aspects of
biology and see how evolution shapes even the future of our own species.
Please read the Course Outline carefully and keep the Course Schedule close to hand as it contains
all the activities and assessments during the semester. In particular take note of the policies on
plagiarism and attendance requirements.
We are here to ensure your success in this course and at UWI generally and encourage you to come
to us with any academic or other challenges you may face that could affect your attendance and
performance.
We look forward to meeting each of you and engaging in productive stimulating discussions over
the coming semester.
Course Coordinator
CONTENT:
BIOL2262 includes the following topics: the development of ideas in evolutionary biology;
processes leading to change within populations i.e. microevolution (including modifications of the
Hardy-Weinberg equilibrium, natural selection, random genetic drift, molecular evolution); large
scale processes at the geological time scale i.e. macroevolution; key events in the evolution of
organisms over time and the evidence for such change such as the fossil record; special forms of
selection such as coevolution, sexual and kin selection; the species concept and speciation
mechanisms; and basic concepts in systematics i.e. classification and analysis of relationships
among species.
GOALS/AIMS
The course aims to
 provide a solid grounding in modern evolutionary biology concepts with reference to
examples and evidence derived from a variety of field and laboratory studies
 encourage students to apply principles of modern evolutionary biology in their experiences
of the natural world
52
LEARNING OUTCOMES
At the end of this course, students will be able to:
Topic: The development of ideas in evolutionary biology
1. Outline the history of evolutionary ideas and define basic concepts in modern evolutionary
biology.
2. Define and explain what genetic diversity is, discuss its origins, measurements and
importance to the evolutionary process.
3. Outline the main stages in the evolution of the human species and discuss the importance of
evolution in understanding human populations, health and disease.
Topic: Processes leading to change within populations i.e. microevolution
4. Use the Hardy-Weinberg Principle to infer population stability/instability and use derived
Hardy-Weinberg Equations to calculate and predict allelic and genotypic frequencies of
genetic disorders and other traits in populations.
5. Use modifications of the Hardy-Weinberg equations to understand, explain and predict
phenomena as it applies to Multiple Alleles, Sex Linked Traits and Non-random Mating
(Hardy-Weinberg Extensions).
6. Calculate the extent of inbreeding in pedigrees and populations and derive inferences from
their results.
7. Identify and discuss the forces that violate Hardy-Weinberg equilibrium (evolutionary
forces) and result in evolution.
8. Explain how Natural Selection and Random Genetic Drift (the strong evolutionary forces)
modify allelic and genotypic frequencies over time to result in population divergence and
speciation (microevolution).
9. Identify and discuss the causes of and the differences between natural selection and random
genetic drift.
10. Discuss how the high levels of molecular diversity in nature may be explained by the
Neutral Theory of Molecular Evolution.
11. Define what a Molecular Clock is and explain why they can be used to estimate rates of
divergence between species.
12. Prove how knowledge of the Neutral Theory of Evolution assists in validation of the
existence of Molecular Clocks.
13. Describe how genes control development and discuss the role of development in micro- and
macroevolution.
Topic: Large scale processes at the geological time scale i.e. macroevolution
14. Explain how fossils are formed and dated and discuss how they contribute to our
understanding of past life.
15. Briefly describe major events in the planet’s geological history and how they influenced
fossil formation and the fossil record.
16. Outline major divisions of geological time and look at major patterns of fossil record; stasis,
punctuation and Cope’s Law
53
Topic: Special forms of selection
17. Distinguish between asexual and sexual reproduction and discuss the advantages and
disadvantages of each.
18. Explain the concept of genomic conflict and give examples where genomic conflict may
occur.
19. Analyze how natural selection interacts with tradeoffs to design life histories and sex
allocation for reproductive success in terms of age and size of organisms on maturation,
number of offspring, factors influencing life expectancy, how offspring gender influences
parental care.
20. Define “sexual selection” and its two main forms and explain why each acts mainly on
males.
21. Outline the logic of the theory of kin selection and explain how it harmonizes altruism with
the theory of evolution by natural selection.
22. Define “co-evolution” and discuss some of its major manifestations.
23. Define “mimicry” and its two main forms and discuss how batesian-mimetic complexes may
evolve.
Topic: The species concept; speciation mechanisms; basic concepts in systematics
24. Define “species” according to the biological species concept and discuss the problems
associated with this concept.
25. Outline and distinguish among the scenarios for speciation (allopatry, sympatry, parapatry)
showing the importance and mechanisms of reproductive isolation.
26. Discuss the advantages of using phylogenetic characters over phenetic characters in the
construction of cladograms and the importance of synapomorphies in the construction of
phylogenetic trees.
27. Recognize and interpret phylogenetic relationships when presented with a phylogenic tree.
28. Define and explain the terms “monophyly”, “paraphyly” and “polyphyly” as they relate to
phylogenetic trees.
29. Outline the differences between homology and homoplasy and explain how homoplasy can
occur and lead to polyphyly.
30. Use comparative genetics, embryology and anatomy (biology) to illustrate evolutionary
similarities among various groups of organisms.
31. Outline how comparative biology provides strong evidence for the phenomenon of evolution
Topic: General skills
32. Apply principles of the scientific method, evaluate and critique the work of others, think
analytically and solve problems; write scientific reports.
54
COURSE ASSESSMENT
Students must obtain 50% or more in the sum of marks for all course components below to
pass this course (refer to new UWI Grading Scheme below).
% Final Description / Assignments
Component
Grade
(see Course Calendar for submission details)
2-hour written exam with multiple choice, short paragraph and
Final exam
50%
essay questions
Coursework
50%
Broken down as follows:
10%
 Tutorials, WACE
 Performance in tutorial and informal writing exercises and
activities
5%
 Critical Readings
 Journal Article Critical Review Report
15%
 Incourse tests
 2 tests (each 7.5%) including multiple choice, short
answers, short paragraphs or essay
20%
 Practicals
 Performance and reporting of 4 practical exercises
Please note guidelines and policies for attendance and plagiarism under ‘Additional
Information’ and below.
ASSIGNMENTS
A variety of strategies will be utilized to assess the following Learning Outcomes:
Assessment:
Learning Outcomes covered:
LO 1-32
 Tutorials, Writing Across the Curriculum (WACE) (10%):
Continuous evaluation of participation and performance and
contributions throughout the semester
 Journal Article Critical Review Report (5%): Written critique LO 32
of a journal paper
LO 1-32
 Incourse tests (15%): 2 tests (each 7.5%) each 50 minutes
duration including multiple choice, short answers, short
paragraphs or essay
LO 2-5; 6-8; 13-14; 18-22;
 Practicals (20%): Practical performance and reporting of 4
32
practical exercises during the semester
See Course Calendar for Lab and Assignment due dates.
EVALUATION
 Feedback on the course will be obtained informally from students on an ongoing basis by
regular interactions and meetings among students, demonstrators, instructors, teaching
assistants and the Course Coordinator in practicals and tutorials.
 Formal feedback will be via election of Class Representatives who sit on the Departmental
Student-Staff Liaison Committee meetings held twice during the semester. Class reps will
channel both concerns and commendations to the meeting as guided by the Department’s
Standard Operating Procedures.
55


Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation
questionnaire administered anonymously and confidentially at the end of the semester.
All feedback will be considered on an ongoing basis and corrective action or adjustments
made or discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES
The course comprises 24 1-hour lectures, 3 1-hour tutorials and 4 5-hour practical sessions.
Tutorials are taken up with collective problem solving with minimal lecture-style talking by the
instructor. However, lectures always have a certain tutorial aspect, and the instructor can be
expected to pose questions to members of the class in every lecture hour.
Lecture and practical content are integrated and there will be continuous reference from one to the
other. Students are expected to read and use the resources provided to expand topics summarized in
lecture.
RESOURCES
There are extensive resources available on this topic in the university library and on the internet. In
the Main Library relevant textbooks on evolutionary biology mostly have call numbers around
QH366 and some are placed on reserve. Selected web-based resources and websites will be posted
on myelearning. Students are expected to obtain and read the required textbook which fully covers
all the topics in the course. Supporting resources based on the main textbook (videos, self-tests and
activities) are also linked from myeLearning.
Practical exercises in the field and lab will make use of standard equipment and materials. In
addition, we will have access to the department’s significant library of natural-history movies on
DVD.
READINGS
Category A text (available for purchase in UWI Bookshop, student resources available online):
 Stearns, S. & R. Hoekstra. 2005. Evolution. Oxford University Press.
Category B texts (available in UWI Main Library):
 Allendorf, F.W., G.H Luikart, and S.N. Aitken. 2012. Conservation and the Genetics of
Populations. Wiley-Blackwell, 2 ed.
 Avers, C.J. 1989. Pattern & Process in Evolution. Oxford: Oxford Univ. Press.
 Others as assigned and/or made available on MyeLearning.
Websites:
 University of California, Berkeley. "Understanding Evolution”
http://evolution.berkeley.edu/evolibrary/home.php
 Stearns, S. & R. Hoekstra. 2005. Evolution. Oxford University Press
http://global.oup.com/uk/orc/biosciences/evolution/stearns2e/01student/selftest/
 Stephen C. Stearns. Videolectures.net http://videolectures.net/stephen_c_stearns/
56
COURSE CALENDAR
Note that Saturday is regarded as a school day at UWI, and class exercises are sometimes scheduled
for the weekend. See last page for detailed Course Calendar.
ADDITIONAL INFORMATION:
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment, student conduct, essential skills, and support at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Attendance: Students are reminded that they must attend and report satisfactorily on a
minimum of 75% of the practical sessions and tutorials. Failure to do so may result in
debarment from the final examination.
 Medicals, excuses: Any student who misses a class, test or assignment is advised to consult
immediately in person or by email with the TA or Course Coordinator regarding reasons for
their absence and make-up options. Absence must be explained in writing within 7 days of the
missed session by either a written/emailed excuse sent to the TA or Course Coordinator, and/or
a medical certificate submitted to the Health Service Unit and copied to the Departmental
Secretary, Life Sciences and the Course Coordinator.
 Makeups: As a general principle, medicals or other excuses may only excuse a student’s
presence at an assigned time. Students must still complete the assigned work (make-up lab
report or make-up test) in order to obtain the marks for that item of coursework. The student is
responsible for liaising with the Course Coordinator or Teaching Assistant to ensure the
assigned make-up is completed. Normally only ONE make-up session will be held. Any
student who was inexcusably absent from a practical or test or does not submit a practical
report (initial or make-up) will receive 0% for that exercise. Note that a field trip cannot be
repeated for a make-up so you should make every effort to attend field trips.
 Late submission: A penalty at 10% of mark per day late will be applied unless formal approval
for late submission is given by the TA or Course Coordinator using the guidelines above for
medicals, excuses.
 Assignment submission: You will be informed whether reports should be in HARD or SOFT
copy format. HARD COPY reports should be submitted in the practical session or afterwards into
a labelled deposit box for your bench/demonstrator in the outer Zoology office and the student
list must be signed. Submissions anywhere else will not be assessed. These will be returned at a
time arranged by the TA or demonstrator. We are not responsible for reports left uncollected or
submitted inexcusably late. SOFT COPY reports should be submitted as instructed through the
relevant assignment link on the BIOL2262 myelearning page.
 Plagiarism: Students are hereby informed that plagiarism is forbidden and all unsupervised
coursework items must be accompanied by a completed Plagiarism Declaration form in order to
be assessed. Specific items may require submission through Turnitin on myeLearning. Refer to
57



‘University Regulations on Plagiarism’ available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
Safety in the lab and field: Medical Data and Emergency Contact forms must be completed in
the first lab session when safety briefings will be given. Standard laboratory protocols for conduct
and dress code are in effect once you are present in a Life Sciences laboratory (Undergraduate
Student Handbook section 8). Dress code includes mandatory lab coats, adequate clothing to
protect the body, and closed shoes. NO sandals, slippers or open-toed shoes will be allowed in the
lab or field. Marks will be deducted for non-adherence to these protocols.
Field work: Details are given in section 8 of the Undergraduate Student Handbook
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf . Field trips are specified on the
attached Course Calendar so you can be adequately prepared. You will not be allowed on the field
trip if a Medical Data form has not been submitted.
Accessibility: If you have a disability and have not disclosed the nature of your disability and
the support you need, you are invited to contact the Academic Support/Disabilities Liaison Unit
(ASDLU) of The University of the West Indies (UWI), St. Augustine Campus. Phone: 662-2002
extension 83866, 83921, 83923 and 84254; Fax: 662-2002 extension 83922; Email:
[email protected] ; http://sta.uwi.edu/asdlu/forms.asp
HOW TO STUDY FOR THIS COURSE
 Attend: You should attend all lectures, tutorials and practicals since satisfactory attendance
(>75%) is required by the UWI regulations. Students who attend regularly perform better than
those who do not. You should attend to obtain the full value of the lecturer’s presence. Lecturers
routinely synthesise and summarise large amounts of information, prioritise, evaluate, discuss
and explain this information. They provide the conceptual framework of the course which you
must then fill in with details and examples through independent study.
 Prepare: You should prepare before classes so you can clarify any difficult points with the
lecturer or engage in meaningful discussion of any controversial topics. This will enhance and
deepen your understanding as well as contribute to course assessment in tutorials and practicals.
This is your opportunity for continuous assessment to monitor your progress and to accumulate
coursework marks incrementally.
 Review: You should review learning outcomes for each topic or activity and make sure you
understand and can actually achieve those outcomes. If you can’t, please clarify with the
lecturer. You must make thorough use of the resources provided (textbooks, myeLearning) from
the first week. You should check into myeLearning frequently to review updated materials,
assignments, notices and activities.
 Study: In addition to timetabled contact time, you are expected to devote additional hours of
independent study: reviewing class materials and notes, reading/viewing/using resource
materials, completing assignments and preparing for assessments. You are strongly encouraged
to make your own notes from lectures, textbooks and other source materials throughout the
semester to improve your skills of comprehension, organisation, planning and writing. Working
in study groups is strongly supported for those who learn best this way as it shares workloads,
58

builds camaraderie and social skills. However, please don’t rote-learn prepared essays and
always double check the accuracy of your colleagues’ work.
Connect: You are encouraged to interact regularly with staff, even outside of the assigned class
times to ensure prompt, satisfactory solution of any problems and to monitor progress.
GRADING SYSTEM:
The NEW UWI grading scheme effective 2014/15 is given below. See
http://www.uwi.edu/gradingpolicy/ for details.
GRADE
A+
A
AB+
B
BC+
C
F1
F2
F3
QUALITY
POINT
4.30
4.00
3.70
3.30
3.00
2.70
2.30
2.00
1.70
1.30
0
% RANGE
Grade Definition
90-100
80-89
75-79
70-74
65-69
60-64
55-59
50-54
45-49
40-44
0-39
Exceptional
Outstanding
Excellent
Very good
Good
Satisfactory
Fair
Acceptable
Unsatisfactory
Weak
Poor
NA/JS/MAK: 01 October 2015
59
BIOL2262 COURSE CALENDAR:
WEEK
1
2
3
4
5
6
7
8
9
LECTURES, TESTS
1. Course Introduction.
2. History of ideas in evolutionary
biology
3. Basic concepts in evolutionary
biology
4. Populations, genes, alleles &
genetic variation
5. Hardy-Weinberg equilibrium & its
applications
6. Hardy-Weinberg Extensions
7. Violations of Hardy-Weinberg
equilibrium:
The Weak Evolutionary Forces
8. Violations of Hardy-Weinberg
equilibrium:
The Strong Evolutionary Forces
9. The Strong Evolutionary Forces:
Selection
10. The Strong Evolutionary Forces:
Selection
11. Development in evolution
12. In-course Test 1 [7.5%]
13. Key events in evolution
14. The fossil record and life’s history
15. Evolution of sex; Genomic conflict
16. Life history evolution
17. Sexual selection; Kin selection
18. Co-evolution & Mimicry
10
19. Species concept & speciation
20. Molecular Evolution and cladistics
11
21. Phylogeny & systematics
22. Comparative Biology
12
23. Human evolution & evolutionary
medicine
24. In-course Test 2 [7.5%]
13
25. Review of Exams/Feedback
26. Course Review
NA/JS/MAK: 01 October 2015
PRACTICALS, TUTORIALS ,
ASSIGNMENTS
 Briefing on ‘Journal Article Critical
Review Report’
 WACE 1 [2%]
 Practical 1: Introduction to HardyWeinberg Equilibrium [5%]
 Tutorial 1 [2%]
 Practical 2: Violations of HardyWeinberg Equilibrium: Small populations
and its consequences [5%]
 Tutorial 2 [2%]
 Practical 3: Fossils Field Trip/Lab [5%]
 Submit ‘Journal Article Critical Review
Report’ [5%]
 Practical 4: Videos on Evolution [5%]
 Tutorial 3 [2%]
 WACE 2 [2%]
60
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND AGRICULTURE
DEPARTMENT OF LIFE SCIENCES
Course Description
COURSE CODE: BIOL2163
COURSE TITLE: Biostatistics
NO. OF CREDITS: 3 (23 hours of formal lectures, 6 hours of Tutorials and 20 hours of Practical work solving
problems by hand or using statistical software).
LEVEL: Undergraduate, Level II
PRE-REQUISITES: MATH 1115 or MATH 1125 or AGRI 1003 or Unit I or II CAPE Pure Mathematics or
Unit I or II CAPE Applied Maths or Cambridge GCE A’level Mathematics or A/O’ Level Add Maths or
equivalent and 9 Credits of Level 1 Life Sciences courses chosen from the following BIOL1262 Living Organisms
I, BIOL1263 Living Organisms II, BIOL1364 Genetics I, BIOL1362 Biochemistry I, BIOL1261 Diversity of
Organisms and BIOL1061 Cell Biology and Genetics
COURSE DESCRIPTION: This course introduces statistical concepts and analytical methods that can be
applied to data in the biological, life sciences and environmental sciences. It will teach the basic concepts of
experimental design, quantitative analysis of data, and statistical inferences. This course emphasises applications
and will help students to statistically evaluate data from biological experiments. Assessment is designed to make
students work continuously with the course materials, exploring and critically analysing research and real world
data. Assessment will be continuous through assigned problem sheets allowing continuous feedback and guidance
on problem solving techniques.
COURSE RATIONALE: This Semester I, Level 2 course is part of the core of the Biology degree as well as
the Biology and Biochemistry Majors in the Department of Life Sciences. It is also forms part of the core of the
B.Sc. Environmental Science and Sustainable Technology. It is designed for students doing their first statistics
course, including those with limited mathematical backgrounds. Students should have at least completed an
introductory maths course including algebra. It equips students with basic experimental and data management
skills needed for most areas of the biological sciences. The student will be introduced to the basics of scientific
enquiry, from formulating hypotheses, designing experiments (particularly field experiments), performing
appropriate statistical tests to test hypotheses and stating the outcome of the statistical test in a clear concise
manner that is comprehensible to a reader who does not have specialist knowledge of the subject matter.
61
INSTRUCTOR INFORMATION:
Name of instructor(s): Dr Isaac Dialsingh
Office address and phone: Dept. of Mathematics & Statistics, Second Floor, New Wing, Natural Sciences
Building
Email address: [email protected]
Office hours: Thursday 1-3 pm
LETTER TO THE STUDENT:
Welcome to Biostatistics. In this course you will be introduced to a range of fundamental statistical techniques
which equip you with the basics of scientific enquiry. This will include formulating hypotheses, designing
experiments (particularly field experiments), performing appropriate statistical tests to test hypotheses and stating
the outcome of the statistical test in a clear concise manner that is comprehensible to a reader who does not have
specialist knowledge of the subject matter. The course will be taught in blended mode comprising both face-toface and online delivery. You are expected to engage with the materials provided online, in face-to-face lectures
and tutorials as well as explore and interact with these to develop the essential skills of critical thinking (clarity,
accuracy, relevance, logic, breadth, depth, precision, significance, completeness and fairness). Activities will be
diverse and you are strongly encouraged to ask questions, offer new ideas, solve problems and think innovatively
to maximise the value of your learning experience. Biostatistics lectures and practical sessions are scheduled
during the first semester of year 2 and are sequenced to cover the basic statistical needs of the other advanced
courses in the programme. Students will be assigned to one of the practical streams during the practical session
in week 1. The Course Manual containing background information and objectives for the course and lecture notes
for the Biostatistics section is available online in myeLearning. You should print a copy and bring this for use in
the Biostatistics. You should also read the essential texts (listed below). Additional material and notes for lectures,
tutorials and practical exercisess will be supplied via myeLearning. Tutorials will be held bi-weekly. Students
will be assigned by the Instructor to a tutorial group during the practical session of week 1. The online teaching
tool myeLearning will be used extensively during this course for:
(i)
communication between staff and students
(ii)
official posting of important notices
(iii)
providing of course details, lecture objectives, practical guides, data for practical exercises, tutorial
briefings; this year it is the only source of the full course manual.
You are expected to become proficient in the use of myeLearning and check in on a regular basis (at least once
per week, well before your practical class).
CONTENT:
The following Topics will be covered:
Introduction to Biostatistics
 Course Overview
 Types of Data
 Experimental Design
Describing, Exploring and Comparing Data
 Frequency distributions
 Visualizing Data
 Measures of Central Tendency
 Measures of Variation
Probability Theory and Distributions
 The Addition Rule
 The Multiplication Rule
62




Conditional Probability
The Standard Normal Distribution
The Binomial Probability Distribution
The Poisson Probability Distribution
Estimates and Sample sizes with One Sample
 Estimating a Population Proportion
 Estimating a Population Mean
 Estimating a Population Variance
Hypothesis Testing with One Sample
 Basics of Hypothesis Testing
 Testing a claim about a Proportion
 Testing a claim about a Mean, Standard Deviation or Variance
Inferences from Two Samples
 Inferences about Two Proportions
 Inferences about Two Means
Correlation and Regression
 Correlation
 Regression
Multinomial Experiments and Goodness of Fit
 Goodness of Fit
Analysis of Variance
 One-Way ANOVA
 Two-Way ANOVA
Nonparametric Statistics
 Sign Test
 Wilcoxon Test
 Kruskal-Wallis Test
 Rank Correlation
GOALS/AIMS:
This course aims to:
 Review the range of routine statistical tests and provide the student with a basic theoretical
understanding.
 Develop confidence in the students in deciding which statistical test to use in a particular situation.
 Develop competence in the student in carrying out the statistical test accurately by hand first before
using statistical software
LEARNING OUTCOMES*
Upon completion of the course, students will be able to:
63
 interpret statistical data
 Express the results of statistical evaluation in a clear and concise manner, comprehensible to a reader
who does not have specialist knowledge of the subject matter.
 Recognize and give examples of different types of data arising in life sciences disciplines
 Interpret differences in data distributions via visual displays
 Calculate standard normal scores and resulting probabilities
 Calculate and interpret confidence intervals for population means and proportions
 Interpret and explain a p-value
 Perform a two-sample t-test and interpret the results; calculate a 95% confidence interval for the
difference in population means
 Select an appropriate test for comparing two populations on a continuous measure, when the two sample
t-test is not appropriate
 interpret results from Analysis of Variance (ANOVA), a technique used to compare means amongst
more than two independent populations
 Choose an appropriate method for comparing proportions between two groups; construct a 95%
confidence interval for the difference in population proportions
 interpret relative risks and odds ratios when comparing two populations
 Use the MINITAB or other statistical software to
o Perform two sample comparisons of means and create confidence intervals for the population
mean differences
o Compare proportions amongst two independent populations
o Interpret output from statistical software packages related to the various estimation and
hypothesis testing procedures covered in the course procedures.
COURSE ASSESSMENT
Assessment will be based on a student’s final mark from the coursework components below.
% Final
Description
Component
Grade
2-hour written exam with statistical exercises. NonFinal exam
50%
programmable calculators will be required.
2 tests (each 5%) based on short answer or multiple choice
In-course tests
10%
questions
Tutorials, online
Oral face-to-face contribution in interactive discussions.
10%
activities
Online quizzes.
Statistics research
4-5 page data analysis written report targeted at a
10%
report
statistically naive reader.
Practical
Performance and reporting of problem sheets in 5 practical
20%
Exercises
exercises
ASSIGNMENTS
 2 coursework tests (5% each): 50 minutes duration including short answer or multiple choice questions
 Tutorials, online activities (10%): Continuous evaluation of participation and performance and contributions
throughout the semester (discussions, wiki/ glossary, blogs).
 Reading/ research project (10%): On one occasion during the last month of the course, the instructor will
designate a data analysis problem requiring a 3-5 page written report from the students. The report should be
64
written for a statistically naive reader. Practicals (20%): Practical performance and written lab report at 5
practical exercises during the semester.
1. Biostatistics 1: visualizing data
2. Biostatistics 2: analysis of frequency data
3. Biostatistics 3: regression & correlation
4. Biostatistics 4: analysis of two groups
5. Biostatistics 5: analysis of Rank data
EVALUATION
 Feedback on the course will be obtained informally from students on an ongoing basis by regular
interactions and meetings among students, demonstrators, teaching assistants and the Course Coordinator in
practicals and tutorials.
 Formal feedback will be via election of Class Representatives who sit on the Departmental Student-Staff
Liaison Committee meetings held twice during the semester. Class reps will channel both concerns and
commendations to the meeting as guided by the Department’s Standard Operating Procedures.
 Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an ongoing basis and corrective action or adjustments made or discussed
with students promptly or incorporated the following year.
TEACHING STRATEGIES
Contact hours (38 credit hours):
Lectures: 23 h
Tutorials: 6 h
Practicals: 10 h (5x4 h = 20 h)




Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of available
information, update current issues and events, and prioritise content relevant to course assessment.
Practicals: Fortnightly practical sessions will provide hands on experience for students to gain skills required
for solving basic statistical problems by hand using a calculator as necessary. Once basic competency is
mastered students so that students understand what they are doing, they will be introduced to more automated
methods using statistical software. Participation and performance in the practicals will be assessed as well as
reports based on the practical activities.
Tutorials: Tutorials will cover course topics in a highly interactive format using a variety of collaborative
active learning techniques. In addition to clarifying details of course content, specific transferrable skills will
be addressed e.g. performing calculations, report writing and summarisation for the statistical naive reader,
critiquing online and face-to-face.
myelearning: The online teaching tool, myeLearning, will be used extensively during this course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
 self-test quizzes, questionnaires, surveys
 interactive activities such as discussions, wikis, glossaries, blogs
RESOURCES
Most resources are available myeLearning including
65



Lecture presentations including learning objectives, summaries, recommended readings and links to
papers, articles and websites with interactive resources and videos for those who prefer to learn using
these modalities
‘General Resources’ provides direct links to general websites, articles and publications relevant to the
whole course
Tutorials may have specific supporting resources particularly on skills development
READINGS
Essential and Recommended texts are in the Reserve Section, UWI Main Library or via links in the course
outline and myelearning.
Essential Texts
1. Barnard, C., Gilbert, F. & McGregor, P. 2007. Asking Questions in Biology: a Guide to Hypothesistesting, Experimental Design and Presentation in Practical Work and Research Projects. 3rd edition.
Harlow: Pearson Education.
2. Department of Life Sciences. 2013/14. BIOLxxxx Biostatistics. Course Manual. This will only be
available online in myelearning, and students should print their own copies.
Recommended Texts
Any of the texts below should be used for supplementing the text books, following up on lectures, and for
research for practical reports.
1. Triola M.M. and Triola MF. 2006. Biostatistics for the Biological and Health Sciences 2006. Pearson/
Addison Wesley, Boston. (QH323.5.T75 2006)
2. Rosner B. 2010. Fundamentals of Biostatistics, 7th ed. Duxbury Press, Boston (QH323.5.R822)
3. Zar, J.H. 1984. Biostatistical Analysis. 2nd ed. Prentice-Hall, N.J.
COURSE CALENDAR
WEEK
1.
2.
3.
4.
5.
6.
7.
8.
LECTURES
27. Course Overview
28. Experimental Design
29. Descriptive Statistics
30. Descriptive Statistics
31. Introduction to Probability
32. Probability distributions
33. Estimating a population proportion
34. Estimating a population mean and
variance
35. Basics of hypothesis testing
36. Testing claims about Proportions and
Means
37. Inferences about Two Proportions
38. Inferences about Two Means
39. Correlation
40. Regression
41. Multinomial Experiments
42. Goodness of Fit
PRACTICALS
TUTORIALS
Practical 1:
Assignments
Tutorial 1
Practical 2:
Tutorial 2
Deadline online activity 1
Practical 3:
Tutorial 3
Test 1
Practical 4:
Tutorial 4
Deadline online activity 2
66
9.
10.
11.
12.
43. One-Way ANOVA
44. Two-Way ANOVA
45. Non-Parametric Statistics: The Sign
Test
46. Non-Parametric Statistics: The
Wilcoxon Test
47. Non-Parametric Statistics: The
Kruskal-Wallis Test
48. Non-Parametric Statistics: Rank
Correlation
49. Course Review
Practical 5:
Tutorial 5
Tutorial 6
Submit final research
report
Test 2
13.
ADDITIONAL INFORMATION
HOW TO STUDY FOR THIS COURSE
Students should attend all lectures, tutorials, and practicals. The lectures are designed to cover the most important
points in each subject area, in the opinion of the lecturer, and are condensed from a much greater volume of
material. Students who do not attend lectures miss the benefit of this work by the lecturer, and have to review the
textbooks themselves. Although less satisfactory than attending lectures, independent study has been made easier
by detailed learning objectives cross-referenced to sections of the textbook. Practical instructions are provided on
myelearning well before the start of the class, and should be read before attending the class to make full benefit
of the class time. Tutorials are designed to help students with aspects that have proved difficult in the past, rather
than providing new material.
GRADING SYSTEM Students will be graded fairly on work that they have done themselves. Incidents of
cheating (this includes plagiarism) will be dealt with according to the UWI regulations1. The Grade Point Average
(GPA) system now in use in the UWI is generally used to determine your class of honours when you graduate.
Since BIOL 2xxx is a Level II course, your GPA in this course is used to determine your class of honours. Your
ability to receive GATE funding in the next academic year is riding on your GPA – should you have a GPA of
less than 1.0 at the end of the academic year, GATE will be discontinued, and you will have to pay your own
tuition. You will only be able to reapply for GATE after you raise your GPA to 1.0 or greater.
To calculate your GPA, find the Quality Points that correspond to the grade in each course. Multiply the number
of quality points by the credit weighting for the course, add up all these numbers, then divide by the number of
credits. See below for an example.
Let’s say you have taken the following courses:
Course
Credits Grade Quality Points
CHEM 1XX0
3
B+
3.3
CHEM 1XX1
3
A
4.0
MATH 1115
3
B
3.0
1
Examination Regulations for First Degrees, Associate Degrees, Diplomas and Certificates. Section (B) Cheating. Regulations 96–
102; http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf.
University Regulations on Plagiarism (First Degrees, Diplomas and Certificates).
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
67
Then your GPA calculation would look like this:
Course
Calculation
CHEM
Credits x Quality Pts. =
3 x 3.3 =
1XX0
CHEM
Credits x Quality Pts. =
3 x 4.0 =
1XX1
MATH
Credits x Quality Pts. =
3 x 3.0 =
1115
Total C x QP = 9.9 + 12.0 + 9.0 =
Total # of credits =
3+3+3=
GPA =
30.9 / 9 =
Total
9.9
12.0
9.0
30.9
9
3.43
The performance criteria that is expected of you to obtain each grade is outlined in the following table. This
information should give you some idea of the level at which you should be working, to achieve the grades you
wish to get. And should your grade not quite match up to your own expectations, take another look at the table,
and see where you may have gone astray.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
68
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE CODE: BIOL2164
COURSE TITLE: Principles of Molecular Biology
NO. OF CREDITS: 3
LEVEL: II
SEMESTER: II
PRE-REQUISITE(S): Either BIOL1362 Biochemistry I and BIOL1364 Genetics I or BIOL1061 Cell Biology
and Genetics
ANTI-REQUISITE(S): BIOL3061 Molecular Biology
COURSE DESCRIPTION
This course provides an introduction to recombinant DNA technology, R-DNA cloning, and applications of RDNA technology. It examines the importance of restriction endonucleases in gene cloning, methods of
construction of vectors and their applications in developing gene libraries. The methods of screening and
enrichment of libraries are also examined. The principles of the Polymerase Chain Reaction (PCR) and its
applications including paternity testing and fingerprinting, are also discussed. The principles of sequencing and
the expansion of next-generation sequencing techniques are examined. Approaches to locating genes, including
map-based gene isolation, and methods of regulating gene expression, including RNAi, co-suppression, and overexpression are discussed using detailed examples. All techniques are further examined under general and holistic
approaches to studying the genome, through forward and reverse genetics approaches, functional genomics,
transcriptomics, proteomics and metabolomics. In this course, the theoretical prinicples discussed during the
lectures are reinforced by practical activites that aid in student learning anf understanding. As this is a practical –
based course, activities in the lab, such as quizzes, lab reports and discussions are all assessed.
COURSE RATIONALE
This course is a techniques-based course that seeks to provide students with the requisite knowledge that is the
basis of many of the applied experimental techniques in biology and biotechnology. The student, upon completion
of this course, should have a comprehensive understanding and practical expertise in basic molecular biology
techniques including DNA extraction, Restriction Enzyme digestion, Hybridization techniques and PCR. This
foundation is important for the understanding of more advanced techniques and their application in many biologyrelated fields. This course is a core course in the Biology degree and directly services the Biotechnology option
listed in the program.
69
INSTRUCTOR INFORMATION
Name of course coordinator:
Dr. Georgette Briggs
Office address and phone:
Biochemistry Office, Floor 2, Old wing,
Natural Sciences Building
Email address:
[email protected]
Office hours:
Mondays and Fridays 2:00-3:00 pm
Preferred method of contact:
Email
Communication policy: Students should use their UWI email account for communication and can expect a
response within 48 hours (Monday to Saturday).
COURSE GOALS:
On completion of this course, students should have:
 An appreciation of the role of R-DNA technology in the advancement of scientific research
 An understanding of the theory that underlies the basic molecular biology techniques
 An appreciation of the applications of molecular biology techniques in addressing real-life situations
 Developed laboratory skills in the molecular biology techniques covered
 The ability to interpret the outcomes of experimental scenarios
 Acquired the knowledge to aid in evaluating the applicability of molecular biology techniques to
specific experimental aims
 Acquired specific analytical skills with respect to problems in molecular biology
CONTENT
The Principles of Molecular Biology focuses on the techniques that underlie many of the experiments used many
biology disciplines. The course begins with a review of each of the biological molecules (DNA, RNA and
proteins) in relation to the Central Dogma, and how they can be detected in the lab. This is followed by an
understanding of the application of these detection techniques to real-world situations and further, how DNA can
be amplified via PCR. The second module addresses the manipulation of the molecules in the form of R-DNA
technology. The importance of hybridization methods and PCR in gene cloning and principles of gene and
genome sequencing. The third module addresses the use of methods to control and regulate gene expression,
allowing the examination of various processes at the cell and organismal levels.
The general topics include:
- Principles of Recombinant DNA technology and gene cloning
- Hybridization, PCR and its applications
- Vectors and gene cloning strategies
- Construction of genomic libraries
- Gene identification and mapping
- Control and regulation of gene expression
- Forward and Reverse genetics
- Transcriptomics, proteomics and metabolomics
- Bioinformatics methods and tools
70
LEARNING OUTCOMES
Students completing this course should be able to:
 Explain the applicability of R-DNA technology to biological research and discovery
 Explain, illustrate and interpret the experimental steps of the molecular biological techniques covered
 Demonstrate efficient lab skills in the experimental techniques covered
 Apply molecular biological techniques to the elucidation of real-life scenarios
 Make critical evaluations of the applicability of molecular biological techniques to experimental aims
 Communicate ideas and critically evaluate hypothetical scenarios
COURSE ASSESSMENT
As stated in the DLS hanbook, students must pass (40%) the practical component of the course to be allowed to
sit the final exam. As previously indicated, this is a techniques-based course and therefore 22% of the course
marks is assigned to content knowledge and practical skill in this area. The three in-course tests, examines content
knowledge in the three modules of the course.
In-course test 1:
In-course test 2:
In-course test 3:
Practical reports/quizzes
Practical (lab etiquette/participation)
Final examination (2 hours)
7%
7%
7%
27%
2%
50 %
EVALUATION
The elected Class Representative and/or Deputy will attend meetings with the course teacher(s) organized at every
4th week, and present feedback from the students attending that course or stream. This feedback is normally
provided both orally and in written form for transmission to the lecturer. Apart from that the representatives will
be attending the Liaison Committee meeting, and give their feedbacks to the committee.
Students may comment on any aspect of the course or facilities. Students will be encouraged to submit
their feedback (oral/written) during tutorials directly to the course teacher and appropriate actions will be taken
by the teacher then and there.
Results of in-course tests, quiz and other course assignments will be analyzed and presented in the class.
This will help students to check their progress constantly and also helps the instructor to identify the weak areas
and thereby could alert and advise students individually to alter their approach of study and completing the work.
The final reflective feedback and comments about the entire course and teaching will be collected on the
last day of the course. This will be saved for analysis and utilized as a base for improvement for the next offering
in the following year.
TEACHING STRATEGIES
The instruction for this course would comprise of 2 lectures per week (50 mins each), and one practical (3 hr)
practical session every 2 weeks. Additionally, instructional videos, tutorials and practical labs (wet and virtual
labs) would be utilized to support the teaching. This course is also my e-learning supported, and many other
resources are readily available for the students. In this course, the practical component is essential in reinforcing
the content taught in the lectures. Students in the practical sessions, work in groups of 4 during these hands-on
71
sessions, for which experimental planning (pre-labs) and small group discussions are required. This format
therefore addresses a range of learning styles, as outlined in the DLS undergraduate handbook.
RESOURCES
Recommended reading:
Primrose, S.B. and Twyman, R.M. 2006. Principles of Gene Manipulation and Genomics
7th Edn. Blackwell Publishing Ltd.
Lodish, H., Berk, A., et al. 2007. Molecular Cell Biology, 6th edn. Freeman.
Weaver, R.F. 2006. Molecular Biology, 4th edn. McGraw Hill Higher Education.
Glick, B.R., Pasternak, J.J. 2010. Molecular Biotechnology: Principles and Applications of Recombinant
DNA. ASM Press
Other resources:
The course instructor will upload in “my e-learning”, periodically (at the beginning and during the course),
important research articles, review papers, book chapters and other related study materials. Students are expected
to read them as these were considered and included as portions of the syllabus and covered during examinations.
COURSE CALENDAR
Week
Lecture Topic
Wk1 Course Introduction and Overview/Central Dogma
Wk1
Wk2
Wk2
Wk3
Restriction Endonucleases
Principles of detection via hybridization
Principles of detection via hybridization
Amplyfying DNA for detection PCR
Wk3
Wk4
Wk4
Wk5
Amplyfying DNA for detection PCR
Principles of sequencing
CLASS TUTORIAL
IN COURSE I: wks 1 to 4
Wk5
Wk6
Wk6
Wk7
Introduction to R-DNA technology
Vectors and cloning strategies
Vectors and cloning strategies
Genomic Libraries: Construction and screening
Wk7
Genomic Libraries: enrichment
Lab Schedule
Lab Safety Talk, Lab
tour, lab apparatuses
and equipment
Lab#1:DNA extraction
and RE digest
Lab#2: Cloning and
transformation
Lab#3: Virtual labs
(Southern, Northern,
Western & PCRs)
setting-up transfer
72
Hybridize a prepared
membrane
Wk8
Wk8
Wk9
Locating genes: shot gunning, map-based gene isolation
CLASS TUTORIAL
IN COURSE II: wks 5 to 7
Lab#4 Washes and
detection
Wk9 Control of gene expression: silencing, anitsense and RNAi Setting-up a PCR (mock
sample)
Wk10 Control of gene expression: silencing, anitsense and RNAi
Wk10 Forward/Reverse Genetics
Wk11 Transcriptomics, proteomics and metabolomics
Lab #5: Gene
databases
Wk11 Transcriptomics, proteomics and metabolomics
Wk12 CLASS TUTORIAL / course review
Wk12 CLASS TUTORIAL/course review
ADDITIONAL INFORMATION
Attendance
Attendance in the in-course exams and the quizzes is mandatory. Any student who misses an in-course exam or
a quiz is advised to consult immediately in person or by email with the course instructor regarding their make-up
options. Absence must be accompanied by a written excuse or medical submitted to the Main office, Life Sciences
within 7 days of the missed session. Any student who was inexcusably absent or who does not write an in-course
exam or a quiz will receive 0% for that exercise.
How to study for this course
Students are encouraged to work together in small cohesive groups as much as possible to go through the course
content. As we go through the various topics, students should attempt to answer all the sample questions placed
on my e-learning and discuss the answers amongst themselves. All comments, questions and concerns provided
on a particular topic will be addressed during the discussion segments of laboratories and during class time. Your
Departmental course textbook on my e-learning contains all the topics to be taught and the textbook content is
aligned similarly as the lectures; please read the textbook. Use the responses and comments for your quizzes and
in-course examinations as a guide to answering the questions properly. There are several past paper questions in
the library and students are encouraged to practice these questions.
73
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
74
THE UNIVERSITY OF THE WEST INDIES
ST AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
Course title: Genetics II
Course Code: BIOL2165
Credits: 3
Level: TWO
Semester: ONE
Pre-requisites: BIOL1364 Genetics I or BIOL1061 Cell Biology and Genetics and 6 credits from among the
following courses: BIOL1262 Living Organisms I, BIOL1263 Living Organisms II, BIOL1362 Biochemistry I
or BIOL1261 Diversity of Organisms.
Anti-requisite: BIOL2162 Advanced Genetics.
Course Description: Genetics II is a core course for the Biology programme in the Department of Life Sciences.
The major topics of the course are cytogenetics (including epigenetics and developmental genetics), prokaryotic/
viral genetics, and molecular genetics (including genomics). Cytogenetics explores chromosomal macromutations
(chromosomal deletions, duplications, inversions and translocations) and their associated cytogenetic effects on
plants and animals. Epigenetics and developmental genetics is a new area of study that explains the environmental
influence on chromatin dynamics, DNA methylation, development and ultimately on inheritance. An introductory
treatment of developmental genetics is also given to understand master control genes (homeotic genes) that
regulate a cascade of genes that control development. Prokaryotic/ viral genetics provides insights into
prokaryotic/ viral reproduction, recombination; genetic complementation, mapping; and genetic regulation.
Molecular genetics provides the fundamental basis for the understanding of Molecular Biology and as such deals
with DNA replication, transcription, translation and controls. Genomics provides an insight into where genetics
is evolving (including an introduction to applications).
Assumed Knowledge: Students should be skilled in the basic principles of genetics including the nuclear
genome; the cell cycle; Mendelian genetics and extensions; and gene mapping. In addition, students should have
mastered the basic concepts of Biochemistry including the structure and function of biomolecules.
Course organization
The course is divided into three sections: cytogenetics (40%), prokaryotic/ viral genetics (20%), and molecular
genetics (40%).
75
Cytogenetics will be taught in the first 5 weeks in the following order:
Chromosomal macromutations (their detection-both cytological and genetic, and the significance of each type of
macromutation (benefits, associated conditions and diseases, evolutionary significance) – deletions, duplications
(including multigene families and homeotic genes), inversions, translocations, autopolyploids, allopolyploids,
aneuploids; epigenetics; and homeobox genes.
Prokaryotic genetics will be taught in weeks 6 and 7 in the following order:
Importance of prokaryotic genetics, comparison of prokaryotic and eukaryotic genomes, recombination in
prokaryotes (transformation, transduction and conjugation), conjugation mapping, recombination and
complementation tests (their uses and limitations), and transposition; viral genetics- bacteriophage genetics
(mating, recombination, genetic mapping).
Molecular genetics focusses mainly on the eukaryotic genome and will be taught from week-8 to week-12
in the following order:
DNA replication, transcription, translation, their associated processes, end products and their regulation; the
genetic code; and genomics (including the evolution of today’s concept of a gene and a gene locus).
Purpose of the course
Genetics II (BIOL 2XXX) aims to build on the foundation of basic principles in Genetics through the delivery of
advanced topics spanning three major topics: Cytogenetics, Prokaryotic Genetics and Molecular Genetics. This
course will serve as a core requirement for the fulfillment of the Biology major in the Department of Life Sciences,
University of the West Indies. Furthermore, this course serves as the feeder course to Microbiology, Microbial
Biotechnology, Molecular Biology, Plant Biotechnology, Animal Biotechnology, and Crop Improvement as well
as several M. Phil. and Ph.D. programmes offered in these aforementioned areas in the Department of Life
Sciences. Careers which demand an advanced knowledge of Genetics include Plant Breeders, Conservation
Geneticists, Biotechnologists and Genetic Engineers as well as teachers of Biology at the secondary and tertiary
school levels.
Lecturer information
Dr. Winston Elibox, Room 312, 3rd Floor Natural Science Building, Tel: 6622002 Ext. 83108; E-mail:
[email protected]
Office hours: Monday – Friday: 12:00 p.m. – 4:00 p.m.
Communication Policy: I prefer communication via e-mail using your UWI email account.
Letter to the students
Dear Students,
I wish you a warm welcome to BIOL2XXX- Genetics II. I am excited that you have decided to pursue this course
which will build on the concepts that you have learned in Genetics I (BIOL1364) and specifically provide you
with a sound knowledge in advanced topics in genetics such as chromosomal macromutations; epigenetics and
developmental genetics, prokaryotic/ viral genetics and molecular genetics. Chromosomal aberrations such as
76
deletions, duplications, inversions and translocations can have profound effects on plants and animals including
several genetic diseases of humans. All the multiple gene families that are responsible for things like immunity,
expression of haemoglobin, and body architecture are a result of duplications. Furthermore most of our important
cash crops are derived by duplication of identical or non-identical genomes (polyploids). We can use translocation
heterozygotes to control insect pests. This course will further show you that although twins have the same genetic
make-up, because of their life history, they are epigenetically different. The area of developmental genetics will
show you how a simple egg can become an adult of its species based on pre-programmed processes encoded by
master control genes (homeotic genes). You will see why prokaryotes are able to recombine and form new strains
that can pose potential threats to us and our food sources. Finally, you will gain sound knowledge on how DNA
is maintained from generation to generation, how it is replicated, how and when it is transcribed and how the
transcribed mRNA is eventually translated to form the polypeptides/ proteins that carry out the functions of a
body.
The course is very modern and gives a brief introduction to all the modern tools of genetics that are currently
being used in the fields of biotechnology, molecular biology, crop improvement, conservation and medicine.
Hence this course serves as a foundation course for many of your advanced courses as well as many of your future
M. Phil. and Ph.D. programmes. The course is myelearning supported and several resources including the course
handbook and other suggested readings can be accessed at your convenience. Several thought provoking questions
will be posted in the discussion forum of myelearning as we go through the course content and you are
encouraged to participate. Please check your timetables and pay particular attention to lecture times, quizzes,
incourse examinations and tutorials. I wish you a fruitful semester and I look forward to working with all of you.
Sincerely,
Dr. Winston Elibox
Lecturer
Course Content
Topic 1: Cytogenetics





Regulation of gene expression at the chromosomal level
Specialized forms of chromosomes
Chromosomal mutations, changes in chromosome structure: The origins, inheritance, evolutionary
significance and diagnosis of chromosomal deletions, duplications (including multiple gene families),
inversions and translocations
Chromosomal mutations, changes in chromosome number: The origins, inheritance, evolutionary
significance and diagnosis of euploidy (autopolyploid and allopolyploid), and aneuploidy
Epigenetics (heritable changes in gene function without a change in DNA sequence in chromosomes):
DNA methylation results in different phenotypes in genetically identical organisms; types of epigenetic
imprinting; role of epigenetic markers in the remodeling of chromatin; inheritance of epigenetic imprints;
role of epigenetics in establishing and maintaining cell identity; epigenetic switching
77

Homeobox genes (master control genes): Importance of homeobox genes in developmental processes in
multicellular organisms; identifying homeobox genes; phylogenetic distribution of homeotic genes;
regulation of homeotic gene complexes
Topic 2: Prokaryotic/ viral genetics





Prokaryotic genome structure and organization
Genetic recombination in prokaryotes: conjugation, transduction and transformation
Mechanism of each type of genetic recombination
Creating genetic maps for bacterial chromosomes using conjugation
Transposition (Transposons – mobile segments that cannot exist independent of a replicon): structure of
the three types of transposons- insertion sequence elements, composite and non-composite; mechanism
of transposition; significance of transposons in multiple drug resistance in bacteria

Gene fine structure analysis: recombination and complementation testing in bacteria; recombination and
complementation spot test in bacteriophages; Benzer’s deletion mapping technique in bacteriophages
Topic 3: Molecular genetics








Molecular organization of the eukaryotic genome
Genomics- evolution of the modern concept of a gene
DNA replication in viruses, prokaryotes and eukaryotes
DNA transcription in prokaryotes and eukaryotes
Post transcriptional modifications and mRNA processing
Regulation of gene expression in prokaryotes (negative, positive and attenuation)
Regulation of gene expression in viruses (bacteriophages )
Regulation of genes in eukaryotes (facultative and condensed chromatin, position effects, methylation),
transcriptional control, post-transcriptional control, translational control and post-translational control.

The nature of the genetic code, degeneracy of the genetic code

DNA translation: structure and function of the ribosomes, role of tRNA, steps in DNA translation

Post translational modifications
Course Goals
At the end of this course, students should have:

Acquired knowledge of chromosomal macromutations; their importance, detection; associated disorders
and evolutionary significance; and possible applications in medicine and agriculture.
 Acquired knowledge in epigenetics and developmental genetics; their importance in differentiation,
dedifferentiation, development and maintenance of cell types in various tissues and organs.
 Acquired knowledge of prokaryotic/ viral genetics, the importance of studying their genetics; and their
use in the production of high density genetic maps.
 Acquired knowledge of the various steps that result in a gene in the DNA of a chromosome being
replicated, transcribed and translated into a polypeptide (protein) and the degeneracy of the genetic code;
genomics and the evolution of the concept of a gene and locus and the methods of gene regulation.
General objectives
The course aims at providing students with the knowledge, comprehension and application of advanced genetic
principles in the areas of cytogenetics, prokaryotic/ viral genetics and molecular genetics through lectures,
78
discussions, assignments and tutorials. More specifically, the course will deal with the organization, structure,
function and regulation of the genetic material of prokaryotes and eukaryotes at the molecular and gross levels.
An introduction to the concept of the gene and methodologies that have led to the advancement of knowledge on
gene control will also be presented. To assess learning, three incourse exams during weeks 5, 8 and 12; three
quizzes (weeks 2, 6 and 10) based on three assignments; and one worksheet will be given and graded. The course
is myelearning supported and your manual contains specific course objectives as well as lecture and assignment
outlines and more. Students’ answers to the course questions posted on myelearning will also be used to assess
learning.
Learning outcomes:
At the end of this course, students will be able to:
Topic 1: Cytogenetics
Introduction to Chromosomes & Chromatin
i.
ii.
iii.
iv.
v.
vi.
vii.
viii.
ix.
Define cytogenetics, state the chromosome theory of inheritance and explain how it led to the evolution
of cytogenetics.
Describe chromosome structure at the macro and ultra-levels and define the unineme model.
Describe the procedure by which karyotyping is performed and state its importance in determining basic
chromosome number, size, shape, chromosomal macromutations, ploidy levels.
Differentiate between heterochromatin and euchromatin in a chromosome.
Define and distinguish between the different types of heterochromatin: facultative, constitutive &
condensed.
Describe the staining methods used to visualize the forms of chromatin making up chromosomes (Feulgen
staining, G-banding, FISH, Q-banding, R-banding).
Discuss the role of chromatin in regulating gene expression at the chromosomal level with a clear
definition of the phenomenon of position effects.
Define and describe polytene chromosomes & lampbrush chromosomes as two examples of specialized
forms of chromosomes.
Explain the significance of polytene and lampbrush chromosomes and their role in tissue specific
amplification of gene expression.
Changes in chromosomal structure
Chromosomal Macromutations: Deletions
i.
ii.
Define deletions.
Describe and distinguish between the different types of chromosomal deletions with the aid of appropriate
diagrams.
iii. Describe the cytological and genetic methods used to detect chromosomal deletions.
iv.
Explain the consequences of deletions and describe the inheritance of deletions using specific examples.
v.
Explain the evolutionary significance of chromosomal deletions.
Chromosomal Macromutations: Duplications
i.
Define duplications.
79
ii.
Describe and distinguish between the different types of chromosomal duplications with the aid of
appropriate diagrams.
iii. Describe the cytological and genetic methods used to detect chromosomal duplications.
iv.
Explain the consequences of duplications and describe the inheritance of duplications using specific
examples.
v.
Explain the evolutionary significance of chromosomal duplications using specific examples.
vi.
Define multigene family (a form of chromosomal duplication) and briefly describe specific examples of
these (immune system super-family, collagen gene family, cytochrome P450 gene family).
vii.
Describe how multigene families arise and evolve to generate functional diversity, environmental
flexibility & developmental flexibility using the immune system super family as an example.
viii. Define the term, pseudogene, as it relates to gene families and explain how they arise.
Chromosomal Macromutations: Inversions
i.
ii.
Define inversions.
Describe and distinguish between paracentric and pericentric inversions with the aid of appropriate
diagrams.
iii. Describe the cytological and genetic methods used to detect chromosomal inversions.
iv.
Explain and illustrate the meiotic consequences of crossovers within inversion loops for pericentric and
paracentric inversion heterozygotes.
v.
Describe and explain the phenotypic effects associated with chromosomal inversions using specific
examples.
vi.
Define the term apparent crossover suppression as it relates to chromosomal inversions and explain how
it differs from actual crossover suppression associated with other chromosomal macromutations such as
deletions.
vii.
Explain the evolutionary significance of chromosomal inversions using specific examples.
Chromosomal Macromutations: Translocations
i.
ii.
iii.
iv.
Define translocations.
Describe and illustrate the different types of chromosomal translocations.
Describe the cytological and genetic indicators used to detect chromosomal translocations.
Describe and distinguish between alternate, adjacent-1 & adjacent-2 segregation patterns observed in
meiosis for translocation heterozygotes.
v.
Explain and illustrate the meiotic consequences of translocations in heterozygotes.
vi.
Describe and explain the phenotypic effects associated with chromosomal translocations using specific
examples (Robertsonian translocation; Down syndrome, familial Down syndrome).
vii.
Explain the application of translocation heterozygotes in pest control.
viii. Explain the evolutionary significance of chromosomal translocations using specific examples.
Changes in chromosome number
Polyploidy
i.
ii.
iii.
Define and distinguish between the basic chromosome number (x), the haploid number (n) and the total
chromosome number.
Define the term polyploidy.
Define and distinguish between the two main forms of ploidy: euploidy & aneuploidy.
80
iv.
v.
vi.
vii.
viii.
ix.
Define and distinguish between autopolyploidy and allopolyploidy as forms of euploidy.
Explain how non-disjunction in mitosis and meiosis can lead to the formation of autopolyploids.
Explain how autopolyploidy can be induced artificially.
Describe the inheritance of autopolyploidy and explain the sterility observed in triploids.
Describe the polyploidy series in Musa spp. (autopolyploids).
Explain and illustrate how interspecific hybridization followed by duplication and diplodization can lead
to the formation of fertile allopolyploids.
x. Discuss the role of allopolyploidy in evolution using specific examples.
xi. Define and distinguish between the two forms of aneuploidy: hypoploidy & hyperploidy
Heritable changes in cellular expression that occur without a change in the DNA sequence
Epigenetics & Chromatin Dynamics
i.
ii.
Define the terms epigenetics and imprinting.
Describe the process of DNA methylation and explain its epigenetic effect on chromatin remodeling and
gene expression.
iii. Identify methylation, phosphorylation & acetylation as epigenetic markers and describe the mechanism
by which these epigenetic patterns are established on histone proteins in the remodeling of chromatin.
iv.
Explain how epigenetic imprints are inherited.
v.
Explain the role of epigenetics in establishing and maintaining cell identity.
vi.
Define the term epigenetic switching and differentiate between this process in plants and animals.
vii.
Explain the significance of epigenetics in the development of cancer in humans.
Master control genes that regulate a cascade of other genes and control development in multicellular
organisms
Homeotic genes- master control genes
i.
ii.
iii.
iv.
v.
vi.
vii.
Define homeotic genes as being gene families that share a common DNA sequence element (homeobox)
in multicellular organisms
Explain the function of homeotic genes- master control genes (switch genes) that specify developmental
patterns (regulation) by turning different processes of cellular differentiation on or off.
Discuss how homeotic genes begin regulation from the very early stages of embryogenesis.
Discuss the mechanism of function of homeotic genes in Drosophila melanogaster.
Discuss the origin and phylogenetic distribution of homeotic genes.
Describe how homeotic genes are identified.
Discuss how mutations in homeotic gene families such as the Hox gene can affect rib and limb
development in humans.
Topic 2: Prokaryotic/ viral genetics
Genetic Recombination in Bacteria - Conjugation
i.
Describe the main distinguishing features between eukaryotic and prokaryotic genomes with particular
regard to structure, organization, inheritance/transmission & recombination.
81
ii.
Define the term conjugation as it relates to bacterial recombination and state the requirements for
successful genetic transfer via bacterial conjugation.
iii. Describe the U-tube experiment that provided evidence for conjugation as a mechanism of gene transfer
between bacterial cells, eventually leading to genetic recombination.
iv.
Describe the functions of the F-factor and its role in bacterial conjugation.
v.
Define and distinguish between donor (F+-strain) and recipient cells (F--strain).
vi.
Define the terms plasmid and episome and explain how they are different from each other.
vii.
Compare and contrast bacterial conjugation involving F+, Hfr & Lfr strains giving detailed descriptions
of the mechanism of transfer from donor to recipient.
viii. Define the term F’-factor and explain how it is formed.
ix. Define the term F-mediated sexduction and explain how it leads to the formation of merozygotes.
x. Differentiate between F+, Hfr, Lfr & F’ strains with respect to the nature of the F-factor, the ability to
convert recipients to donors, fate of transferred DNA, recombination frequency & probability of
recombination for any given bacterial gene.
xi. Describe the three conjugation mapping methods- interrupted mating, gradient of transfer and
recombination mapping- used in constructing genetic maps of the bacterial chromosome.
xii. Critically assess the three mapping techniques in relation to each other highlighting any advantages or
disadvantages that might be associated.
xiii. Perform problem-based solving in case studies involving conjugation mapping.
Genetic Recombination in Bacteria – Transduction (mediated through a bacteriophage)
i.
ii.
Define the term bacteriophage and distinguish between virulent and temperate phages.
Compare and contrast the lytic and lysogenic infection cycles of λ-phage with the aid of appropriate
diagrams.
iii. Define and distinguish between the terms prophage & lysogen.
iv.
Describe in detail the production of generalized & specialized transducing particles.
v.
Compare and contrast generalized and specialized modes of transduction especially with respect to the
type of phage life cycle employed, range of transducing capability, efficiency of transduction, probability
of transduction for a given gene & fate of transferred DNA.
vi.
Distinguish between Hft-lysate and Lft-lysate.
Genetic Recombination in Bacteria - Transformation
i.
ii.
Define the term transformation as it relates to genetic recombination in bacteria.
Explain in detail the mechanism of bacterial transformation, highlighting the steps and the essential
requirements for the process to occur.
iii. Describe Griffith’s experiment which demonstrated genetic recombination via transformation in
Pneumococci bacteria.
iv.
Define the term competency and describe how competency can be artificially induced in bacteria.
v.
Discuss the factors that affect transformation efficiency.
Transposition in prokaryotes (ability of genes to change position in the bacterial chromosome)
i.
Define the term transposition as the mobilization of genetic elements from one location in the genome to
another.
82
ii.
Describe and illustrate the structure of the three types of transposons: insertion sequence elements,
composite and non-composite transposons and distinguish between them.
iii. Explain the function of transposase enzyme in the mobilization of insertion sequence elements.
iv.
Describe the mechanism of transposition of insertion sequence elements and explain how target site
sequences become duplicated.
v.
Discuss the role and significance of transposons in multiple drug resistance.
Gene Fine Structure Analysis in prokaryotes
i.
ii.
iii.
iv.
v.
vi.
Define complementation and distinguish it from recombination.
Explain the difference the between recombination testing and complementation testing especially with
respect to their uses.
Describe in detail how recombination testing and complementation (cis-trans) testing are carried out.
Discuss the merits and limitations of complementation tests.
Construct complementation maps based on cis-trans test data.
Define and distinguish between the terms cistron, muton & recon.
Gene Fine Structure Analysis in viruses
i.
ii.
Describe the inheritance of plaque morphology in bacteriophages.
Describe the complementation spot test to determine whether mutations are in the same or different
cistrons.
iii. Describe the role of complementation and recombination in the mapping of the rII-locus in bacteriophage
T4.
iv.
Describe Benzer’s deletion mapping technique and discuss its significance in gene fine structure analysis.
Topic 3: Molecular genetics
Molecular genetics- molecular organization of the eukaryotic genome
i.
ii.
Outline the experiments that clearly showed that DNA is the genetic material.
Discuss the components that make up the non-repetitive, moderately repetitive and highly repetitive
sequences of the genome and the role of each of the three types of sequences.
iii. Define the terms intron and exon and discuss the functions of each.
iv.
Critically discuss the evolutionary origin of introns: (introns first, introns early, introns late).
v.
Discuss the theories on the evolution of genes in light of the understanding of the variation of gene
structure in organisms.
Genomics
i.
ii.
iii.
iv.
v.
Define the term genomics and discuss the importance of genomic analysis.
Describe and differentiate between functional and comparative genomics.
Demonstrate knowledge of gene estimates for the human genome and discuss why previous estimates
have been continually lowered.
Discuss the organization and complexity of the human genome.
Describe and discuss the functions and origins of non-genic sequences in the human genome: (STR’s,
LINES, SINES, microsatellites, minisatellites & VNTR’s).
83
vi.
Outline the evolution of concept of a gene and gene locus from the Mendelian concept to the modern
concept using genomics.
vii.
Describe the role of STR’s and microsatellites in DNA fingerprinting.
Genotypic function of DNA - DNA structure and models of replication
i.
Describe the structure of DNA including its double helical nature consisting of complementary antiparallel
strands (opposite polarity) and its major components.
ii.
Define nucleotides as the building blocks of DNA molecules and state the constituents of a nucleotide
monomer unit.
iii. Differentiate between the terms nucleotide and nucleoside.
iv.
Describe in detail the Messelson & Stahl experiment which demonstrated the semi-conservative model of
DNA replication.
v.
Describe and explain the experimental evidence to support a bi-directional mode of DNA replication.
vi.
Describe and distinguish between theta-mode (moving fork) and sigma-mode (rolling circle) replication.
vii.
Identify the enzymes involved in DNA replication as DNA polymerases and state the necessary
requirements for successful DNA replication.
viii. Explain what is meant by semi-discontinuous replication of DNA and describe the evidence that revealed
this characteristic feature of DNA replication.
ix. Define the terms leading strand, lagging strand & Okazaki fragment as they relate to semi-discontinuous
DNA replication.
x. Explain what is meant by the growing point paradox of DNA replication and how it has been resolved.
xi. Define the term replisome as a multi-enzyme complex responsible for the replication of DNA.
xii. Illustrate the structure of a typical prokaryotic replisome by means of a clearly labeled diagram and
describe the functions of the constituent enzymes.
xiii. Differentiate between the replication apparatus of prokaryotes and eukaryotes.
xiv. Describe in detail the steps involved in DNA replication (initiation, elongation & termination) and how
they are facilitated by the replisome.
xv. Compare and contrast prokaryotic and eukaryotic DNA replication with particular emphasis on
differences relating to the linear nature of eukaryotic chromosomes and the circularity nature of
prokaryotic DNA molecules.
Phenotypic Function of DNA - Transcription
i.
ii.
iii.
iv.
v.
vi.
vii.
Define the term transcription as it relates to the Central dogma of biology.
Identify the enzyme involved in DNA transcription as RNA polymerase and describe its characteristic
features including the essential requirements for its function.
Explain in detail the steps involved in the process of transcription (initiation, elongation & termination).
Compare and contrast the process of transcription in prokaryotes and eukaryotes.
Draw and annotate the typical structure of prokaryotic and eukaryotic genes identifying the major
differences between the two.
Explain the consequences of the eukaryotic split-gene structure on the production of mature mRNA and
the need to remove introns from heterogeneous mRNA by splicing.
Describe and illustrate the steps involved in intron-splicing pathways that lead to the production of mature
mRNA in eukaryotes.
84
viii.
Describe the post-transcriptional modifications involved in the production of mature eukaryotic mRNA
that affect mRNA stability: 3’-polyadenylation & 5’-capping.
Regulation of Prokaryotic Gene Expression – lac Operon (negative control with superimposed positive
control)
i.
ii.
iii.
Explain the importance of systems to regulate the expression of genes.
Define the term operon and explain the advantage of gene expression using an operon system.
Explain what is meant by a negative control system and a positive control system and be able to
differentiate between the two.
iv.
Distinguish between the two types of negative control systems: inducible & repressible and give examples
of such systems.
v.
Describe and illustrate the structure of the lac operon.
vi.
List and explain the functions of the structural genes of the lac operon along with the regulatory sequences
involved in controlling expression of the genes.
vii.
Explain the differences between cis-acting and trans-acting control elements.
viii. Explain in detail how the negative and positive control systems of the lac operon function to regulate
expression of the structural genes.
Regulation of Prokaryotic Gene Expression – trp operon (negative control with superimposed attenuation)
i.
ii.
Describe and illustrate the structure of the trp operon.
Identify and explain the functions of the structural genes of the trp operon along with the regulatory
sequences involved in controlling expression of the genes.
iii. Explain in detail how the negative control system of the trp operon functions to regulate expression of the
structural genes.
iv.
Define the term attenuation and explain in detail how it is employed in the regulation of the trp operon.
v.
Explain the alternative TRAP mechanism of control of the trp operon in B. subtilis.
Temporal control of genes in bacteriophages
i.
Describe and discuss how altering the specificity of RNA polymerase by modification of the sigma factor
in the host by the SPO1 phage can result in transcription of the phage genes in a temporal manner.
ii.
Describe and discuss how anti-termination regulates the transcription of genes of the lambda phage in a
temporal manner.
Regulation of genes in eukaryotes: facultative and condensed chromatin, position effects, methylation
i.
Discuss how RNA polymerase cannot bind to chromatin in tightly coiled heterochromatic regions in
eukaryotic genomes resulting in non-transcription of genes in that region.
ii.
Discuss how facultative heterochromatin is regulated to provide environmental flexibility.
iii. Discuss how transcription of genes in the euchromatin can be affected by their proximity to the
heterochromatic regions.
iv.
Discuss how methylation of genes prevents their transcription and this methylation can be heritable
(epigenetics).
Phenotypic Function of DNA - Translation
i.
Define the term translation as it relates to the Central dogma of biology.
85
ii.
Describe the basic structure of prokaryotic and eukaryotic ribosomes and outline their role in the process
of translation.
iii. Describe the function of tRNA molecules in the process of translation.
iv.
Define the terms codon & anti-codon.
v.
Define the Shine-Dalgarno consensus sequence and explain its importance in the initiation of translation
of prokaryotic mRNA.
vi.
Explain in detail the steps involved in the process of translation (initiation, elongation & termination).
vii.
Discuss how post translation modifications such as clipping, targeting proteins to organelles, protein
folding, glycosylation and phosphorylation are important for functionality of the translated protein.
The genetic code
i.
ii.
iii.
Describe the nature of the genetic code and explain what is meant by the following features: triplet code,
non-overlapping code, commaless/gapless code, degenerate code & universal code.
Describe the experiments that provided evidence to demonstrate the triplet nature of the genetic code.
Explain how Crick’s Wobble hypothesis and iso-accepting species of tRNA enable the cell system to cope
with the degeneracy of the genetic code.
Assignments/ quizzes/ worksheet
a.
Multigene families
By the end of this exercise students should be able to:
i.
ii.
iii.
iv.
v.
vi.
Define multigene families
Outline different types of multigene families
Define multigene superfamily with examples
Explain the origin of multigene families
Describe how members of multigene families tend to retain more structural similarity than would be
expected over evolutionary time
Describe the evolutionary significance of multigene families.
b.
Epigenetics
By the end of this exercise students should be able to:
i.
ii.
iii.
Explain why identical twins become epigenetically different as they age, based on their life histories
Explain the role of epigenetic changes in the induction of cancers in humans
Show how a human’s diet epigenetic imprint can be inherited in his/ her progenies.
c.
Bacterial transformation
By the end of this exercise students should be able to:
i.
ii.
iii.
iv.
Describe the process of introducing a GFP-plasmid into Xanthomonas axonopodis pv. dieffenbachiae
using electroporation
Relate the process to the normal process of bacterial transformation.
Explain the role of the GFP fluorescence as a selectable marker
Outline the advantages of GFP fluorescence over selection on specific growth media supplemented with
antibiotics
86
v.
State the factors which influence transformation efficiency.
d.
Worksheet on conjugation mapping in bacteria
By the end of this worksheet students should be able to:
i.
ii.
Calculate genetic distances between bacterial genes
Construct genetic maps of bacterial chromosomes based on case studies using the methods of interrupted
mating, gradient of transfer and recombination mapping.
Course assessment
 In-course
Incourse examinations will include multiple choice questions, structural and short answer type questions. These
exams will assess knowledge, comprehension, application and analysis of course content.
The quizzes for the assignments will allow students the opportunity to read, comprehend, interpret, analyze and
summarize reports written in the scientific manner and as well reinforce and extend what is learned during class
time.
The worksheet on conjugation will allow students to calculate genetic distances and construct genetic maps based
on the three methods (interrupted mating, gradient of transfer and recombination mapping). (See the course
calendar for the assessment schedule).
Assessment
In-course Examination #1
In-course Examination #2
In-course Examination #3
Class quiz #1
Class quiz #2
Class quiz #3
Worksheet
Final Examination
Total
Weighting
10%
10%
10%
5%
5%
5%
5%
50%
100%
The final examination comprises multiple choice questions, short answer questions with four to five parts,
structured questions and essay type questions. These questions are meant to test students’ ability to recall,
comprehend, apply and analyze course content in a critical and logical manner. Students are required to answer
ALL questions.
 Overall assessment
Incourse
50%
Final Theory Exam (2 hours)
50%
87
Evaluation
Two student representatives will be elected from the class. Student feedback will be obtained officially from the
staff-student liaison meetings held twice per semester. However, students are encouraged to give their feedback
on the course via myelearning at any time. Comments will be assessed critically by the instructor, course
coordinator and first examiner and weaknesses will be addressed to improve on the course in the future.
Teaching Strategies
The course consists of 33 lectures, THREE assignments (for quizzes), ONE worksheet and THREE tutorials. The
course is myelearning supported and your manual contains specific course objectives as well as lecture outlines,
past exam papers and model answers.
Recommended Texts
3. Brooker, Robert J. Genetics: Analysis & Principles 3rd Edition McGraw Hill Higher Education 2008. ISBN:
9780071287647
4. Snustad, D. Peter & Simmons, Michael J. Principles of Genetics 5th Edition John Wiley & Sons Inc. 2009.
ISBN: 9780470388259
5. Genetics: A Conceptual Approach (Benjamin A. Pierce)
6. Principles of Genetics 7th Edition (Robert H. Tamarin)
7. Genes VIII (Benjamin Lewin)
8. Molecular Cell Biology (Lodish et al.)
9. Molecular Biology of The Cell (Alberts et al.)
Course Calendar
Course Delivery: Topics covered
Week
Lecture Subjects
1
Course Overview
Introduction to Cytogenetics: Chromosome primary & secondary structure
chromosome ultra-structure- Chromatin/ Distribute paper on Evolution of
Cytogenetics Multigene Families **
Chromosomal Macromutations: Deletions
2
Chromosomal Macromutations: Duplications-1
Chromosomal Macromutations: Duplications-2/ Quiz #1- Evolution of
multigene families**
Chromosomal Macromutations: Inversions
3
Chromosomal Macromutations: Translocations-1
Chromosomal Macromutations: Translocations-2
Ploidy: Autopolyploidy
4
Ploidy: Allopolyploidy; Aneuploidy
Epigenetics & Chromatin Dynamics-1/ Distribute paper on Epigenetics**
88
Epigenetics & Chromatin Dynamics-2
5
Homeobox genes
In-course Examination #1
Genetic Transfer in Bacteria: Conjugation
6
Prokaryotic
genetics
Conjugation Mapping
Genetic transfer in bacteria: transduction and transformation/ Quiz #2:
Epigenetics**
Prokaryotic genetics: transposition
7
Gene Fine Structure Analysis in Bacteria: Recombination Testing &
Complementation Testing/ Distribute worksheet on conjugation mapping**
Gene Fine Structure Analysis - bacteriophages: Deletion Mapping
In-course Examination # 2
8
Molecular genetics- organization of the eukaryotic genome
Molecular
genetics
Molecular genetics- organization of the eukaryotic genome continues/
Distribute paper on bacterial transformation**
Genomics/ Collect worksheet on conjugation mapping**
9
DNA Structure & Models of Replication
DNA Structure & models of replication continues
DNA Structure & models of replication continues
10
Phenotypic function of DNA: Transcription (Prokaryotes)
Phenotypic function of DNA: Post-transcriptional Processing of Eukaryotic
mRNA/ Quiz #3: Bacterial transformation**
Regulation of Prokaryotic Gene Expression: negative control- lac Operon
11
Regulation of Prokaryotic Gene Expression: negative control with
superimposed attenuation- trp Operon; positive control
Temporal control of genes in bacteriophages
Control in eukaryotes- facultative and condensed heterochromatin, position
effects, methylation
12
Translation and post translational regulation
In-course Examination #3
Tutorial
13
Tutorial
Tutorial
Additional information
89
Attendance
Attendance in the incourse exams and the quizzes is mandatory. Any student who misses an incourse exam or a
quiz is advised to consult immediately in person or by email with the course instructor regarding their make-up
options. Absence must be accompanied by a written excuse or medical submitted to the Main office, Life Sciences
within 7 days of the missed session. Any student who was inexcusably absent or who does not write an incourse
exam, a quiz or the worksheet will receive 0% for that exercise.
How to study for this course
You are encouraged to work together in small cohesive groups as much as possible to go through the course
content. As we go through the various topics, students should attempt to answer all the sample questions placed
on myelearning and discuss the answers amongst themselves. All comments, questions and concerns provided
on a particular topic will be addressed during class time, via myelearning or FaceBook (account to be created).
Your departmental course textbook on myelearning contains all the topics to be taught and the textbook content
is aligned similarly as the lectures; please read the textbook. Use the responses and comments for your incourse
examinations, quizzes and worksheet as a guide to answering the questions properly. There are several pass paper
questions in the library and you are encouraged to attempt these questions.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
90
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
Course code: BIOL 2265
Course Title: Fundamentals of Microbiology
Number of Credits: 3
Level: Undergraduate –Year II
Semester: 2
Pre-requisites: Either BIOL1262 Living Organisms I and BIOL1263 Living Organisms II or BIOL1261
Diversity of Organisms or (BIOL1065 Diversity of Plants and Animals and AGRI1012 Microbiology) and either
BIOL1362 Biochemistry I and BIOL1364 Genetics I or BIOL1061 Cell Biology and Genetics.
Anti-requisites: BIOL2263 General Microbiology
Course description
An overview of the biology, taxonomy and phylogeny of the bacteria, fungi and viruses. Bacterial genetic
recombination, growth, nutrition as well as carbon and energy metabolism. Principles of classical and molecularbased methods used in identification and enumeration of microorganisms.
Significance/rationale
Microbiology is one of the core sub-disciplines of biology. Microorganisms have been on earth for billions of
years and have influenced the physical and chemical conditions necessary for the evolution of higher forms of
life. They represent by an unimaginably long distance the largest biological diversity on earth and their activity
is essential to the survival of humans on earth. Although some microbes are responsible for human, animal and
plant diseases they contribute positively to human welfare as they play critical roles in food & agriculture,
industry, medicine and the environment. This course covers an overview of the biology, taxonomy and phylogeny
of the archaebacteria, eubacteria, fungi and viruses. Bacterial genetic recombination, growth, nutrition as well as
carbon and energy metabolism will be covered. Additional topics include traditional and molecular based methods
used in analytical and diagnostic microbiology.
Purpose of Course:
The course provides fundamental training in theoretical and practical microbiology as part of the major in biology
in the Department of Life Sciences, UWI, St. Augustine. The course will also be useful to students who may have
an interest in other disciplines which have microbiological applications such as environmental biology and
ecology, remediation technology, microbial natural product chemistry, biotechnology, biochemistry, medicine.
This course will also serve as the prerequisite for the more specialized Level III courses in microbiology and
related disciplines including microbial biotechnology and the courses in the minor programme in microbiology.
Instructor Information
BIOLXXXX will be managed by a course coordinator and would be taught be a team of experienced lecturers,
supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office hours for the coordinator
91
and lecturers are posted on the faculty bulletin boards and are available from the Department of Life Sciences’
general office. Team members can also be contacted via e-mail.
Name: Adesh Ramsubhag (Co-ordinator)
E-mail: [email protected]
Office location: Rm. 220, Natural Sciences Building, Old Wing
Office hours: Check Notice Boards
Phone: 662-2002 Ext. 83086
Name: XXXX (Teaching assistant)
E-mail:
Office location:
Office hours:
Phone: 662-2002 Ext.
Letter to students
Welcome to BIOL-XXXX- Fundamentals of Microbiology. This course covers the fundamental biology of major
groups of microorganisms including bacteria, fungi and viruses. Significant attention is also placed on covering
the basic methods used in microbiology. The course is taught through a series of 18 lectures, 12 tutorials and 12
hours of labs. The course is quite extensive and students must make a sincere effort to do well. It is important to
attend lectures in order to benefit from more in depth analysis and details that cannot be gained from downloading
and reading the PowerPoint and video presentations of the lectures. Please make use of supplementary information
provided to strengthen foundation and enhance understanding of material covered.
Content:
BIOLXXXX covers the following content:
Microbial diversity
Microbial growth and nutrition
Bacterial genetic recombination
Fungi
Viruses
Carbon and energy metabolism of chemotrophs
Bacterial photosynthesis
Control of microorganisms
Enumeration of microorganisms
Biochemical and molecular identification of microorganisms
Immunology and serology
Microbial ecology
Course goal:
The goal of the course is to provide student with general knowledge on the biology of microorganisms and develop
basic practical skills used in their study.
General Objectives:
Students completing the course will have:
1. A fundamental understanding of the diversity, taxonomy, physiology and genetics of bacteria, fungi and
viruses;
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2. Basic practical skills used in microbiology
3. An understanding of the means to controlling microorganisms
Learning objectives:
Upon completing this course, students will be able to
- describe the general features of microbial diversity and structure and function of prokaryotic and
eukaryotic cells;
- review of diversity and importance of microorganism to humans and environment;
- differentiate and identify major taxonomic groups of fungi and fungal-like organisms based on
morphology, nutrition, reproduction and ecology;
- describe the general structural, genetic and reproductive characteristics of viruses
- describe the general characteristics and life cycles of named bacteriophages and animal viruses;
- describe the general characteristics of the HIV virus ;
- explain how the virus affects humans in causing AIDS as well as how the disease is managed;
- explain the different ways by which genetic changes can take place in bacteria;
- explain the function of different types of culture media;
- explain carbon and energy metabolic processes of microbes;
- compare and contrast carbon and energy metabolism between chemoheterotrophs and chemoautotrophs;
- compare and contrast chemotrophic and phototrophic respiration;
- explain how intrinsic and extrinsic factors affect microbial growth and activity;
- describe the mechanisms used by microorganisms to survive harsh/extreme conditions;
- describe the typical bacterial growth curve and explain the processes influencing and/or taking place at
each phase;
- explain how growth process can be controlled under continuous culture conditions;
- explain how microbial cultures can be isolates and purified;
- describe the different way to control microorganisms;
- explain the effect of different control factors on microbial cells;
- explain how the effectiveness of disinfectants can be assessed;
- explain the principles of classifying and naming microorganisms using conventional and current
taxonomic tools;
- explain the differences between Eubacteria and Archaebacteria;
- compare and contrast the different methods use in enumerating microorganisms;
- describe and explain the interactions of among microorganisms and between microorganisms and other
forms of life;
Mode of Delivery:
Lectures -18 hours:
Didactic; interactive
Tutorials -12 hours:
Interactive; mind maps; problem-solving
Laboratory classes- 12 hours
(4 three- hour sessions):
Interactive practical tasks; problem-solving
ASSIGNMENTS:
Coursework for BIOLXXX will be assigned as follows:
9. Writing across curriculum exercises-5%.
93
These activities are designed to encourage students to become active learners by engaging knowledge to
further develop understanding. The exercises would help students understanding content and expressing
ideas. A total of five simple exercises worth a total of 5 marks (1 mark per exercise) would be given during
lectures or tutorials (no more than one per week). Each exercise would take between 5 – 10 minutes to
complete and would comprise of varying activities including:
a. Focused free-writing- Students may be asked to briefly write on their understanding or perspective on a
subject/topic covered or on how the subject/topic may be connected to other situations.
b. Entry slips- Short responses to questions posed at the beginning of class;
c. Answering questions. One or few questions would be given which students must answer and
submit for grading.
d. Short summary. Students are asked to summarize main points of a reading assignment in a short
paragraph.
e. Group presentation- The tutorial class would be divided into groups and each group would be
required to make a short presentation on a document provided.
f. Complete the life cycle: Students are asked to complete the life cycle diagram given to demonstrate
their knowledge of the sequence of events and structures which occur in the microbial organism’s
life cycle.
g. Construction of dichotomous key: Students are asked to construct a dichotomous key to which can
be used to key out (identify) a group of specimens.
h. Reflective statement: students should write a reflective statement on one of the labs completed:
students should identify problems encountered, techniques mastered or improved, what was done
well and why and what was learnt and what is unclear.
10. In-course Test-20%
One written in-course test would be given worth 10% per test in week 7. Two online tests will also be
given in weeks 4 and 11 work 5% each. The tests would comprise of MCQs and structured questions.
11. Laboratory reports-20%
Students are required to submit two full lab reports worth 4% each in addition to four completed
worksheets worth 2 mark each. Two lab quizzes would also be given during the 2nd and 4th practical
sessions. Each lab quiz would worth 2 marks each.
12. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned at the end
of the semester. Participation shall include more than just showing up at tutorial – some evidence of an
active role in the tutorial discussion would be required to obtain the full 5% for participation. At the
beginning of the semester, the students in each tutorial would engage in developing the exact assessment
criteria for this assignment, and the student-developed criteria will be used to determine each student’s
participation grade.
Cheating, including plagiarism, would not be tolerated. Incidents of cheating would be dealt with according to
UWI’s rules and regulations including:
-
Examination Regulations for First Degrees, Associate Degrees, Diplomas and Certificates. Section (B) Cheating.
Regulations 96–102; http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf.
-
University
Regulations
on
Plagiarism
(First
Degrees,
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
Diplomas
and
Certificates).
94
Assessment:
Course Work: 50%
- Writing across the curriculum; critical thinking exercises
- Incourse test
o One written tests
o Two online tests - (2 X 5%)
- Practical exercises
o Laboratory reports
(2 full reports X 4% and 4 worksheets X 2% )
o Laboratory quizzes (2 X 2%)
- Tutorial Attendance and participation
Final Semester Examination:
- One 2-hour comprehensive written paper comprising of
o 35 MCQs worth 35% of paper
o 5 short answer questions worth 35% of paper
o 1 essay-type question worth 30% of paper
o All questions in this paper shall be compulsory
5%
10%
10%
16%
4%
5%
50%
EVALUATION: BIOLXXXX will be evaluated in two ways – (a) through the offices of the Class
Representative and the Life Sciences Student-Staff Liaison Committee, and (b) an end of semester course
evaluation survey. The class will elect four class representatives (one per lab stream), whose role is to act as a
mediator between the Life Sciences academic staff and the students in the class. The representatives will attend
Liaison Committee meetings (held at least twice per semester), where they will present feedback on the course
to the Department for action. The UWI performs a course evaluation survey at the end of every semester, and
this information will also be used for overall assessment of the course and guide possible actions for
improvement in subsequent semesters.
TEACHING STRATEGIES: A combination of teaching strategies will be adopted in BIOLXXXX.
The primary teaching strategy will be based on the face to face classroom lectures and discussions. Videos of
lecture presentations would be made available to students prior to the lecture session via podcast media. Students
are advised to view these videos before the lecture so that more emphasis can be placed on discussions and
answering questions, thereby facilitating deep learning. This would also afford the time to have assessment
exercises on “writing across the curriculum”. MyeLearning will be utilized throughout the course as a means to
provide access to course materials such as Powerpoint presentation files, animations, weblinks, lessons and
quizzes. This medium would also be used as a portal for student-lecturer communications and the dissemination
of coursework feedback.
A total of 12 tutorial sessions would be given for the semester. These would be small group sessions which
would be conducted by instructors or tutors, who would normally by senior postgraduate students in Life
Sciences. Students must attend tutorial sessions. Tutorials sheets will be assigned prior to each session via
myeLearning, and students are expected to attempt the solutions before coming to tutorial. The goal of the
tutorial session is to give students a more hands-on experience with the course material and easier access to
course instructors. Students will be expected to ask and answer questions on material that is unclear, propose
solutions to questions on the tutorial sheet and to generally participate fully in the tutorial activities. Tutors will
not merely be going through the answers to the tutorial questions in these sessions.
95
Practical sessions would include demonstrations and problem solving exercises to develop practical skills and
enhance understanding of content covered in the theory section. These exercises would include analysis of
specimens, experiments and use of identification keys to assign organisms into different levels of taxa.
In order to pass the course, you must gain an overall passing mark of 40%. Any student who misses more
than 25% of practical classes or tutorial sessions without a medical or other valid excuse can be debarred
from writing the final exam.
RESOURCES:
Text books:
- Willey, J.M., Sherwood, LM., and Woolverton, C.J. (2010) Prescott’s Microbiology (8th Edition),
McGraw-Hill, New York
-
Benson, H.J (2002), Microbiological Applications (Eight Edition), McGraw-Hill, New York
Suggested additional readings:
- Madigan, M and Martinko, J (2005), Brock Biology of Microbiology (Eleventh Edition), Prentice
Hall, New Jersey
Teaching materials:
- Electronic copies of presentations as well as supplementary handouts will be made available to
students;
-
Internet links to web-based resources will be provided to students
Lab coat:
- Each student should have suitable Lab coat to use for practical exercises. Students not having lab coats
will not be permitted in the lab.
COURSE CALENDAR/SCHEDULE:
Introduction and review
Microbial growth and nutrition
Fungi
Viruses
Carbon and energy metabolism of chemotrophs
Bacterial photosynthesis
Control of microorganisms
Bacterial genetic recombination
Enumeration of microorganisms
Biochemical and molecular identification of microorganisms
Immunology and serology
Microbial ecology
96
Course calendar:
Week
1
Practical exercise
Lecture/Tutorial
Lecture 1: Introduction; microbial diversity and importance to humans
and the environment
Lecture 2: Microbial growth and nutrition
Tutorial 1:
2
Lecture 3: Fungi and fungal-like organisms
Tutorial 2:
3
Review of basic aseptic and microbiological methods
Isolation of bacteria and partial establishment of
Koch’s Postulates
Lecture 4: Fungi and fungal-like organisms
Lecture 5: Viruses
Tutorial 3:
Staining and microscopic examination of bacteria
Morphological diversity of bacteria
4
Lecture 6: Viruses
Tutorial 4:
Online test- MCQs (5%)
5
Lab quiz based on previous session
Lecture 7: Bacterial genetic recombination
Isolation and Enumeration of fungi
Lecture 8: Bacterial genetic recombination
Observation and morphological identification of
Fungi
Tutorial 5:
Observation of viral infected plants
6
Lecture 9: Carbon and energy metabolism
Tutorial 6:
7
Lab quiz based on previous sessions
Lecture 10: Carbon and energy metabolism
Enumeration of Identification of bacteria based on
biochemical tests
Tutorial 7:
8
Written incourse test (in lecture slot) – MCQs, structured questions
(10%)
Lecture 11: Bacterial photosynthesis
Tutorial 8:
9
Molecular identification of bacteria, fungi and
viruses
Lecture 12: Control of microorganisms
Lecture 13: Biochemical
microorganisms
and
molecular
identification
of
Tutorial 9:
97
10
Lecture 14: Biochemical
microorganisms
and
molecular
identification
of
Lecture 15: Immunology and serology 2
Tutorial 10:
11
Lecture 16: Immunology and serology 2
Lecture 17: Microbial ecology
Tutorial 11:
Online test- MCQs (5%)
12
Lecture 18: Microbiology ecology
Tutorial 12:
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
98
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTNE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
Course code: BIOL 2360
Course Title: Biochemistry IIA
Credits: 3
Level: 2
Semester: 1
Pre-requisites:
Either BIOL1362 Biochemistry I or BIOL 1061 Cell Biology and Genetics and either CHEM 1062 Basic
Chemistry for Life Sciences or CAPE Chemistry or CHEM0060/1 Preliminary Chemistry I & II and either
BIOL1262 Living Organisms I or BIOL1263 Living Organisms II or BIOL1261 Diversity of Organisms.
Anti-requisites:
BIOL2361 Biomolecules & Energy Metabolism; BIOL2365 Comparative Biochemistry
Course Description
Biochemistry is a fundamental sub-discipline of Biology. This course starts off by exploring the question – Why
is life thermodynamically possible? We will also examine how we digest and metabolize sugars, fats and proteins.
Subsequently, we will discuss the roles of the main hormones involved in the fed and fasting states and finally
we will look at two common metabolic disorders in the Caribbean, diabetes and obesity.
Course Rationale:
BIOL 2XXX is a core course for the Biology Major in the Department of Life Sciences. This course builds on
the topics covered in the year 1 Biochemistry course, BIOL 1362. It covers key biochemical concepts required
for understanding modern Biology. Materials covered in this course will be an asset for students who wish to
further their studies in fields of medicine or nutrition or wish to pursue careers in teaching or the pharmaceutical
industry.
Instructor’s information:
Mr. Jason Matthew
Email: [email protected]
Facebook: BiochemJM
Blog: http://biochemjm.wordpress.com/
YouTube: Biochem JM; http://www.youtube.com/user/BiochemJM/featured
Website: https://sites.google.com/site/biochemjm/
Phone: 662-2002 ext 82080
Office: Old Nat Sci Wing, 2nd Floor; Rm 318
Letter to the students:
Dear Biochemians,
Congratulations on passing your first year courses. We look forward to guiding you on the rest of your journey
here at the UWI. We shall implement a learner-centric approach to this course. There are screencast versions of
all the BIOL 2365 lectures so that you can follow and learn at your own pace. This, however, is not a one-way
service. You too will be required to create 15-minute YouTube videos of topics from the syllabus. You will have
99
access to a database of student videos from previous years so that you can get a sense of what is required from
your videos. I am hoping that you get a better understanding of the topics by seeing it explained by your peers.
You will be networking and collaborating with students from the other UWI campuses as well as globally via my
BiochemJM Blog and Facebook services. Together, we shall challenge the traditional roles in the classroom and
have students present and teach the course. The classroom will be filled with interaction and discussion. It is my
sincerest wish that you learn from this course by challenging yourself to think outside the box. Remember, the
riskiest thing you can do in life is not to take chances. The safest thing you can do is be remarkable. Imagine,
create and innovate.
See you in class,
Biochem JM
Content:
Topics to be covered in this course include:
 Bioenergetics
 Membranes
 Enzyme action
 Carbohydrate metabolism
 Lipid metabolism
 Nitrogen metabolism
 Integration of metabolism
Goals / Aims:
At the end of this course, students will be able to:
 Describe the major metabolic pathways involving carbohydrates, lipids and nitrogen containing
compounds, highlighting certain key enzymatic reactions for their regulatory importance
 Apply what they have learnt in the metabolism section of the course to some everyday metabolic
disorders such as diabetes and obesity
 Explain the mechanism of enzyme action and how their activities in the cell are controlled
 Explain the thermodynamics of high- energy compounds and redox chemistry.
 Apply critical thinking and creativity to explain selected biochemical concepts
 Demonstrate effective communication skills in the areas of interviewing and presenting
 Demonstrate project management skills and actively use podcasts as a medium for positive student
expression.
 Brainstorm and design themes and content for your podcast
 Complete pre-production and production of your podcast and create a high-quality video podcast
Learning Outcomes:
Topic 1: Orientation (1h)
At the end of this section, students should be able to:
 Appreciate the rationale for this course
 State what is expected from them in this course – attendance of tutorials, labs etc
 State how they will be assessed throughout this course
 Navigate and access the Facebook, Blog, YouTube , Website and myelearning services for this course
 Basic manipulation of video editing software – MS MovieMaker, iMovie, and FinalCut Pro
 Create a podcast using CamStudio
 Start preparing their group video project
(This will be supplemented with instructional YouTube videos specifically created for this orientation session)
Topic 2: Bioenergetics (1h)
Gibbs free energy, enthalpy, entropy, equilibrium constant, mass action ratio, ATP, thioesters
100
At the end of this section, students should be able to:
 Draw energy profile diagrams
 Explain what makes a process spontaneous
 Distinguish between ΔG and ΔGo’
 Explain how the change in free energy depends on reactant concentrations
 Discuss how a thermodynamically unfavorable reaction can occur invivo
 Explain the structural basis for the high group transfer potential of ATP
 Explain how phosphorylated compounds, thioesters and reduced cofactors transfer free energy
 Explain why cells control metabolic reactions with large free energy changes
Active learning topics: The role of phosphocreatine in muscle, comparison of ATP generation in sprinters vs.
distance runners or migratory birds vs. birds that rarely fly
Topic 3: Membranes (3h)
Fluid mosaic model, the thermodynamics of membrane transport, membrane potential, action potential, porins,
gated channels, membrane fusion, acetylcholine, SNAREs
At the end of this section, students should be able to:
 Describe the fluid mosaic model of membrane structure
 State the factors which limit membrane protein mobility
 Explain why glycoproteins and glycolipids face the cell exterior
 State what is a membrane potential
 Calculate the membrane potential when ion concentrations are known
 Describe the role of the cell membrane in maintaining membrane potential
 Describe how an action potential is generated and propagated
 Determine when transmembrane movement of a substance is thermodynamically favorable
 Compare active and passive transport
 Compare Na,K-ATPase to other transport systems in terms of mechanism and energy requirement
 Summarize the role of ATP in P-type ATPases and ABC transporters
 Compare secondary active transporters to other transporters in terms of mechanism and energy
requirements
 Describe the sequence of events at the nerve muscle synapse
 Describe how the structure of the SNARE complex is related to its function
 Explain why changes in bilayer curvature are required for exocytosis
Active learning topics: Olestra, spicy Indian dishes and whole-milk yogurt, aquaporins, succinylcholine (muscle
relaxant), lidocaine (anesthetic), digitalis, botulinum toxin
Topic 4: Enzyme Action (1h)
Substrate channeling. Control of enzyme activity.
At the end of this section, students should be able to:
 Using the PDH complex describe
 the mechanism and benefits of substrate channeling
 regulation of enzyme activity
Topic 5: Carbohydrate metabolism (4h)
Glycolysis (recap), gluconeogenesis, glycogen metabolism, pentose phosphate pathway, Cori cycle
101
At the end of this section, students should be able to:
 Recall from BIOL 1362 course (pre-req) the role of glycolysis, its enzyme reactions and how it is
regulated
 Describe the reactions of gluconeogenesis
 Describe how glucogenic precursors can give rise to glucose
 Compare and contrast the glycolysis/gluconeogenesis pathways
 Describe the Cori cycle
 Describe glycogen metabolism (synthesis and degradation pathways).
 Illustrate both the oxidative and non-oxidative branches of the pentose phosphate pathway and explain
the importance of this pathway to cells with respect to providing unusual monosaccharides, biosynthetic
reducing equivalents and intermediates for both synthesis of nitrogenous bases and glycolytic
intermediates
Active learning topics: Glycogen storage diseases, hemolytic anemia, alcoholism and hypoglycaemia,
Topic 6: Lipid metabolism (5h)
Digestion, mobilization and transport of fats. De novo biosynthesis of fatty acids – fatty acid synthase enzyme
complex. Role of acetyl CoA carboxylase. Oxidation of fatty acids. Ketogenesis.
At the end of this section, students should be able to:
 Describe the role of bile and pancreatic lipase in digestion of dietary lipids
 Describe the role of lipoprotein lipase
 Describe the fate of glycerol in the body
 State the different plasma lipoproteins and describe how they are different
 Explain the roles of lipoproteins and apolipoproteins
 Describe the committed step of fatty acid synthesis by showing that acetyl CoA carboxylase is a
bifunctional enzyme
 Describe the reactions of the De Novo synthesis of fatty acids
 Discuss how fatty acids can be synthesized in the liver from carbohydrates
 Describe the role of hormone sensitive lipase
 Describe the carnitine shuttle mechanism
 Describe the reactions in fatty acid  oxidation
 Compare the oxidation of saturated, unsaturated and odd-chain fatty acids
 Compare fatty acid synthesis with  oxidation
 State the conditions for ketogenesis
 Give examples of ketone bodies
 Describe the reactions involved in ketogenesis
Active learning topics: MCAD deficiency and  oxidation, -oxidation is a chemical source of water for desert
animals, brown adipose tissue, white adipose tissue lacking glycerol kinase, LDL and cardiovascular disease,
Orlistat, ketonuria
Topic 7: Nitrogen Metabolism (3h)
Nitrogen fixation, protein degradation (endogenous, dietary), transamination, oxidative deamination, urea cycle,
102
nucleotide metabolism.
At the end of this section, students should be able to:
 Describe the structure of the nitrogenase complex and state how its structure is suited for the reaction it
catalyzes
 State the reaction of glutamine synthetase.
 State what is an essential amino acid
 Describe the mechanisms for degrading endogenous proteins
 State the enzymes and organs involved in digesting dietary proteins
 Describe transamination reactions using ALT and AST enzymes
 State the reactions of glutamate dehydrogenase
 Explain how transamination, oxidative deamination and reductive amination are involved in amino acid
metabolism
 Describe how ammonia is transported to the liver
 Describe the reactions of the urea cycle
 State signs and symptoms of urea cycle enzyme deficiency diseases.
 Outline the roles of nucleotides in the cell
 State which amino acids are required for purine and pyrimidine de novo synthesis
 State the regulated step for purine and pyrimidine de novo synthesis
 Compare CPSI to CPSII
Active learning topics: Urea cycle enzyme diseases, gout, phosphocreatine, NOS
Topic 8: Integration of Metabolism (5h)
Well fed and fasting states, roles of insulin and glucagon.
At the end of this section, students should be able to:
 Classify insulin and glucagon as peptide hormones
 Describe the mechanism of action for insulin and glucagon
 Describe the metabolic effects of insulin and glucagon including the organs where these effects are
taking place.
 Explain how glycolysis and gluconeogenesis are reciprocally regulated
 Explain how glycogenesis and glycogenolysis are reciprocally regulated
 Explain how fatty acid synthesis and fatty acid breakdown are regulated
 Discuss how malonyl CoA affects lipid and carbohydrate metabolism
Active learning topics: Diabetes, obesity, metabolic syndrome.
Course Assessment
Overview
Coursework
Final exam
50%
50%
Coursework assessment (50%):
Biochemians Got Talent (BGT; 15%): Students are asked to create 15-minute videos on any topic off the BIOL
2365 course syllabus. (More details about this project are given in Appendix I; pg 12)
103
Case Studies (10%): a problem-based approach involving ‘real life’ situations will be used for selected topics of
the syllabus to encourage problem-solving and critical thinking skills.
Bring Your Notes End of Semester exam (10%): A 1 hour written exam covering all topics from weeks 1 - 11.
Students will be given a note card from the instructor in week 8 of the semester. Students will be allowed to
write whatever notes they want on the note card, which they are allowed to bring into the exam in week 12.
Class participation and continuous assessment (5%): Students will be assessed continuously throughout the
semester using a variety of strategies:
1. answering 10 minute quizzes on Moodle or in the classroom. These quizzes will be based on the basic
concepts of the course.
2. contributing to the BiochemJM blog
Practical (10%):
Carbohydrate metabolism
At the end of this practical, students should be able to:
 Understand specific enzyme catalyzed reactions in carbohydrate metabolism
 Interpret kinetic data for enzymes – rates of reaction and inhibition
 Use various techniques including micropipetting and spectrophotography
 Write up a biochemical lab report
Final exam (50%):
2-hour written examination at the end of the semester consisting of three sections:
 Section A 25 MCQ (25%)
 Section B True and False, matching, fill in the blanks (25%)
 Section C Essay type questions (50%)
ALL questions on paper are compulsory.
Evaluation:
 Feedback on the course will be obtained informally from students on an ongoing basis by regular interactions
and meetings among students, demonstrators and teaching assistants.
 Formal feedback will be via election of Class Representatives who sit on the Departmental Student-Staff
Liaison Committee meetings held twice during the semester. Class reps will channel both concerns and
commendations to the meeting as guided by the Department’s Standard Operating Procedures.
 Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an ongoing basis and corrective action or adjustments made or discussed
with students promptly or incorporated the following year.
Teaching Strategies:
 Face to face time in the classroom
 Highly interactive
 Students will be making presentations (mostly on the active learning topics outlined for each
topic) in class
 Question and answer game show type of sessions
 This course is Moodle supported.
 Links to podcasts and useful websites will be posted
 Links to open source PDF journal articles will be posted
104
 Students will have access to course outline, lecture schedule and assignments (instructions and
questions)
 Means by which students will be quizzed online
 Students will access their coursework marks
 Official form of communication between instructor and students
The BiochemJM YouTube channel
 Screencast versions of all the BIOL 2365 lectures have been posted on this channel. Students can
learn at their own pace and it frees up the actual face to face time for more interactive activities
in the classroom
 Student created videos. Students create 15 minute videos on any topic of the syllabus and post
them up on the BiochemJM channel. This will enable peer review learning with students in the
course as well as students regionally and globally
The Biochem JM Facebook page and the BiochemJM Blog
 Students have an avenue to reflect about the course with their peers
 Exchange of ideas between fellow students as well as international students
 Mentorship from past students who did the course
 Real time communication with the instructor
 Discussion forum


Resources:
Text Books (Library resources) and Lab. Requisitions (Department’s resources) are available.
Department of Life Sciences & Main Library Computer labs to access online services.
Readings:
Main Text
C.W. Pratt and K. Cornely: Essential Biochemistry 2nd Edition. Wiley & Sons 2011
Secondary texts
J.M. Berg, J.L. Tymoczko and L. Stryer: Biochemistry 7th Edition. W.H. Freeman and Co.
P.C. Champe, R. A. Harvey and D. R. Ferrier: Lippincott’s Illustrated Reviews 3rd edition. Lippincott Williams
& Wilkins
D. L. Nelson and M. M. Cox: Principles of Biochemistry 5th Edition. W.H. Freeman and Co.
Course Calender (subject to review)
Week
Lecture subjects
1
Orientation [1]
Bioenergetics [1]
2
Membranes [2]
3
Membranes [1]
Enzyme action [1]
4
Carb Metab [2]
5
Carb Metab [2]
Tutorials / Assignments / Labs
Tutorial#1
Tutorial #2
105
6
Lipid Metab [2]
Lab: Carbohydrate metabolism
7
Lipid Metab [2]
Case Study #1; Tutorial #3
8
Lipid Metab [1]
Nitrogen Metab [1]
Tutorial #4
9
Nitrogen Metab [2]
Case Study #2
10
Integration of Metab [2]
Tutorial #5
11
Integration of Metab [2]
Tutorial #6
Video Project is due
12
Integration of Metab [1]
End of Semester Exam [1]
13
Review
[ ] = number of hours
Additional information:
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
 As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned time.
Students must still complete the assigned work (make-up lab report or make-up test) in order to obtain the
marks for that item of coursework. The student is responsible for liaising with the Course Coordinator or
Teaching Assistants to ensure the assigned make-up is completed.
 Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available
from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals.
 Prior preparation is strongly advised to able to fully participate in activities and obtain the full value of the
sessions.
 Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myelearning on a frequent regular
basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned
tutorial times to ensure prompt, satisfactory solution of any problems and to monitor progress.
106
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
Appendix I:
BGT instruction manual
The University of the West Indies
The Faculty of Science and Technology
Life Sciences Department
BIOL 2365: Comparative Biochemistry
Biochemians Got Talent (10%)
Imagine, Create, Innovate
Lecturer in charge of project:
107
Mr. Jason Matthew
Email: [email protected]
Facebook: BiochemJM
Blog: http://biochemjm.wordpress.com/
YouTube: Biochem JM; http://www.youtube.com/user/BiochemJM/featured
Phone: 662-2002 ext 82080
Desired outcomes:
After completing this project you should be able to:

Apply critical thinking and creativity to explain selected biochemical concepts

Demonstrate effective communication skills in the areas of interviewing and presenting

Demonstrate project management skills and actively use podcasts as a medium for positive student
expression.

Brainstorm and design themes and content for your podcast

Complete pre-production and production of your podcast and create a high-quality video podcast.
Navigation:
Topic
Page
Your mission
3
Groups
3
Available resources
4
Suggested programs to use
4
Acceptable video file format
4
Important dates
5
Final submission
6
Late submission
6
Project outline rubric
7
Final submission rubric
8
Assessment overview
9
Copyright Guidelines
9
108
Your Mission:
Students are required to make a 15-minute video covering topic(s) or concept(s) taught in this BIOL 2365 course.
The methodologies used in this project should only be limited by your imagination, creativity, innovation and
sadly by financial resources.
Here are some possibilities:

Songs

Plays/skits

Interviews

Tutorials

Debates
Group:
Students are to work in groups of 5. Students will decide the members of their group. Please see the lecturer if
you are having difficulty in this process. Each group is required to elect a project leader. The project leader is
required to meet with the lecturer to discuss progress of the project as well as handle any administrative matters
on behalf of the group.
Important questions to ask yourselves
What is the purpose of the podcast?
Who is our desired audience?
What topics/themes should be covered during the recording?
Who will work on each portion of the podcast?
Delinquency
All members of the group are required to participate equally in this project. Students are encouraged to report any
form of delinquency from their peers to their lecturer. All information will be kept strictly confidential. The
lecturer will interview the delinquent student in question and, if found guilty, adequate deductions to the student’s
mark will be made.
Available resources:

A camcorder is available for use. Your group will be held responsible for any damage to the camcorder
and compensation will be sought via your caution money.
109

Projector

Please consult with the lecturer as soon as possible if you require any additional resources. All attempts
will be made to source them for you.
Suggested programs to explore:

Powerpoint

Keynote

Camtasia

Final Cut Pro

iMovie

Blender

YouTube Xtranormal Movie Maker
http://www.youtube.com/create_detail/Xtranormal

YouTube GoAnimate:
http://www.youtube.com/create_detail/GoAnimate
Acceptable video file formats:

.AVI

.WMV

.MOV
Please keep file size under 2GBs.
Please consult with lecturer if you want to use another file format.
Important dates:

Date: Project leaders are to submit a Microsoft (MS) Word doc. containing the following information via
a Turnitin link on myelearning
o Working title of project (can be refined throughout the project)
o Names and ID nos. of project leader and other members of the group
o Contact information of project leader (cell, email)

Date: At least 2 members of the group are to meet with the lecturer to discuss their project.
o This should be a 15 min meeting.
o You are required to discuss with the lecturer
 Your plans for this project
 Resources you will be using / require
Date: Project leaders are to submit a Group project outline (MS Word doc) containing the following
information via a Turnitin link on myelearning:

110
o Names and ID nos. of project leader and other members of the group
o Working title of project
o Synopsis
 Objectives
 Biochemical themes / topics covered (list them)
 Description of what you plan to do
o Resources
o Contribution of each member
This exercise will be marked. Please see assessment section for details

Date: Project leaders of each group are to update lecturer on progress of their project. This can be done
via email, FB, Skype

Date: Project leaders of each group are to update lecturer on progress of their project. This can be done
via email, FB, Skype

Date: Submit project to the Biochem Office Rm 217. Please sign the submission sheet provided.
Submission:
All files are to be submitted electronically on a CD or DVD. In addition to the video file you are required to
submit a MS Word doc (or equivalent) indicating the following:

Names and ID nos. of project leader and other members of the group

Title of project

Abstract (<250 words)

Contribution of each member
Please submit CD / DVD in a sealed envelope and submit to the Biochem Office Rm 217; Mon 12 th November
2012; 8am – 3:30pm. Please ask the secretary to stamp the date on your envelope before submitting and sign the
submission sheet provided.
One submission per group.
Late Submission:
0.25% of the 10% will be deducted for each day late.
Assessment:
Project outlines and final submissions will be marked as a group, that is all members of a group will be given the
same mark. However students found guilty of delinquency will be individually penalized.
111
Project Outline:
ASSESSMENT CRITERIA
EXCELLENT
GOOD
WEAK
All components
Formatting
are present
[5 mks]
Date
Page number
[5]
Headings and subheadings
 Names and ID#:
 Working title of project:
 Synopsis
Objectives
Biochemical themes / topics
Procedure
 Resources
 Contribution of each
member
1-2 components
are absent
All or most
components
missing
[3 - 4]
[0-2]
All information
is given
concisely
All information
given but could
have been
summarized
more
Some
information
missing
Content [10 mks]
Biochemical
themes and
topics come
from the BIOL
2365 syllabus
Objectives and
procedures give
a clear direction
for the project.
Biochemical
themes and
topics come
from the BIOL
2365 syllabus
Some objectives
and details of
the procedure
are vague
Biochemical
themes and
topics are not
related to the
BIOL 2365
syllabus
Objectives and
details of
procedure are
vague
[0-2]
[7-10]
Final submission:
ASSESSMENT
EXCELLENT
CRITERIA
Well articulated,
Delivery
animated, lively
[5 mks]
presentation, kept
interest, well paced
[3-6]
GOOD
WEAK
Well articulated,
rarely losing
interest, few slips or
pauses
Poorly articulated
with numerous slips
or pauses
112
Abstract
[10 mks]
[5]
[3 – 4.5]
[1 – 2.5]
Highlights the major
points covered
Highlights some of
the points covered
Highlights few
points covered
Concisely describes the
content and scope of the
video
Partially describes
the content and
scope of the video
Does not describe
the content and
scope of the video
Adds no new
information, but simply
summarizes the
information in the video
Crucial keywords
that describe the
video are missing
Crucial keywords
that describe the
paper are missing
Exceeds the word
limit
Exceeds the word
limit
[8 -10]
[5-7]
[0-4]
No errors in the
information given
Few errors in the
information given
Many errors in the
information given
Excellent understanding
of the biochemical
concepts discussed
Good understanding
of the biochemical
concepts discussed
Poor understanding
of the biochemical
concepts discussed
No errors in spelling /
pronunciation of
common biochemical
terms
Few errors in
spelling /
pronunciation of
common
biochemical terms
Many errors in
spelling /
pronunciation of
common
biochemical terms
Ensures all the crucial
keywords that describe
the video appear in
either the title or the
abstract.
Meets the word limit.
Content
[15 mks]
[11 – 15]
Creativity
[10mks]
[5-10]
[0-5]
Excellent use of
technology
Good use of
technology
Poor use of
technology
Presented content in a
very creative manner
Presented content in
a fairly creative
manner
[5 – 7]
Little or no
creativity shown
[8 – 10]
[0– 4]
113
Length of video 15 mins
[5mks]
[5]
Outline as well as video
Time
was submitted on time.
management
for duration of
Met with lecturer on
project
stipulated times.
[5 mks]
[5]
16 - 20 mins
> 5mins over or <13
mins
[2.5 – 4.5]
[1 – 2]
Either outline or
video was not
submitted on time
Missed most
deadlines
Did not meet
lecturer on some of
the stipulated times
[2 – 4]
[0 – 1]
Assessment overview:
Project outline: 15 mks
Final submission: 50 mks
Total: 65 mks
This is worth 10% of your final mark.
Copyright guidelines:
These are some general guidelines to adhere to
 up to three minutes or 10 percent, whichever is less, of a single copyrighted motion media work.
 up to 10 percent or 1,000 words, whichever is less, of a single copyrighted work of text.
 an entire poem of less than 250 words or up to 250 words of a longer poem but no more than three poems
by one poet or five poems by different poets from a single anthology.
 up to 30 seconds or 10 percent, whichever is less, of music and lyrics from a single musical work.
 up to five photographs or illustrations by one person and no more than 15 images or 10 percent, whichever
is less, of the photographs or illustrations from a single published work.
 up to 2,500 fields or cell entries or 10 percent, whichever is less, from a numerical database or data table.
YouTube:
Please note that these videos will be posted on the BiochemJM channel for the general public to view and learn
from. Please inform the lecturer if your group has any concerns about this.
Please inform your lecturer of any concerns or queries you may have about this project.
“The riskiest thing you can do in life is not to take chances. The safest thing you can do is be remarkable. Imagine,
create, innovate.... Biochem JM”
114
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE CODE:
BIOL2464
COURSE TITLE:
Fundamentals of Ecology
NO. OF CREDITS:
3
LEVEL:
Undergraduate – Level 2
PREREQUISITES:
(BIOL1262 Living Organisms I AND 6 credits from (BIOL 1263 Living Organisms II
OR BIOL 1362 Biochemistry I OR BIOL 1364 Genetics I)) OR (ESST 1XX1 Biology
for Environmental Sciences AND 6 credits from (ESST 1XX0 Physics for Environmental
Sciences OR ESST 1XX2 Chemistry for Environmental Sciences OR ESST 1XX6
Human Impact on the Environment)).
ANTI-REQUISITE: This course cannot be credited together with BIOL1462 General Ecology and Biometry
ENROLMENT:
Maximum 300 students
COURSE DESCRIPTION:
This course provides an introduction to ecology, the science of organisms and the environment, and gives the
necessary background for advanced courses in ecology. The student will be introduced to the different levels of
ecological organization and the types of studies associated with each. They will be introduced to the major factors
that influence the distribution and abundance of organisms and appreciate the factors that influence the structure
of ecological communities. The functioning of ecosystems in terms of the movement of energy and nutrients will
also be covered. Apart from a general introduction to ecological fieldwork the students will be introduced to
practical skills that will allow them to assess spatial distribution patterns of organisms and estimate their
population sizes and population parameters. The students will investigate community structure and function using
a variety of methods many of which involve fieldwork on campus. The course is organised into lectures and
tutorials covering general and specific concepts in ecology. In tutorials students are expected to prepare,
participate and perform in an active way in order to engage with the content. Assessment will be based on course
tests, practical reports, and a final theory exam.
COURSE RATIONALE:
This course is one of the core level 2 courses for the major in Biology and the Biology degree, and for the
Environmental Science degree. At the end of the course, students are expected to have an understanding of the
fundamentals of ecology which is suitable for the biologist going on to specialize in other areas, or as the basis
for further study for students specializing in ecology, environmental biology, or environmental science.
INSTRUCTOR INFORMATION:
Name of instructor:
Dr A. Hailey (coordinator), Dr M. Oatham
Office address and phone:
Room 226, Zoology Section, New Wing, Natural Sciences Building. Phone ext
82206
[email protected]
Email address:
115
Office hours:
Monday, Wednesday, Thursday, 11-12 a.m., other times by appointment
Preferred methods of contact: Email or myelearning Academic Forum
Communication policy:
Matters concerning the individual student should be raised by email, from the
student’s UWI email account. Matters of interest to the class should be raised as
Academic Forum postings on myelearning. In either case students can expect a
response within 48 hours. DO NOT use myelearning messaging, which is only
supported via email and after some delay.
CONTENT:










Ecology and its domain
Geographic range habitat and niche, abiotic and biotic environment
Ecological role of abiotic factors (climatic and edaphic) on plant and animal populations. Population
performance along physical gradients
Population structure and demography; population change over time, growth models, dispersal, life
tables and resource allocation patterns
Species interactions: competition, predation, herbivory, commensalism, amensalism, and mutualism
Communities; community classification, concepts and attributes
Island communities
Primary and secondary ecological succession
Nutrient cycling and energy flow
Primary and secondary production, trophic levels and ecological efficiency
GOALS/AIMS:
This course aims to
 Introduce students to the major subject and growth areas of ecology
 Relate ecology to other aspects of biology, especially evolution, physiology, and biodiversity
 Give students an introduction to the scientific method, particularly the testing of hypotheses using
quantitative data
LEARNING OUTCOMES:
At the end of the course, the student should be able to:
 Describe the levels of ecological organization and the types of studies associated with each level of
organization
 Evaluate the major factors which affect the distribution and abundance of organisms
 Describe the factors which influence the structure of ecological communities
 Describe the functioning of ecosystems via movement of energy and nutrients
Practical skills should include the ability to
 Assess spatial distribution patterns
 Estimate population sizes and population parameters
 Investigate community structure and function using a variety of methods, including field work
ASSIGNMENTS:
Practicals
6. Qualitative sampling of grassland plants
7. Population analysis of animals
8. Interactions between organisms: predation and competition
9. Quantitative sampling of grassland insects
116
10. Aripo Savanna plant communities
Theory tests
Six short theory tests, taken during tutorials and practicals. The tests will involve multiple choice, short answer,
and notes formats.
COURSE ASSESSMENT:
Coursework practical:
Coursework theory:
Final examination:
25%, based on the best 4 of the 5 practical marks from the written reports and marks
for participation. Due 7 days after the class.
25%, from the best 5 of the 6 marks from the theory tests.
50%. The examination is of 2 hours duration. It is based on essay questions, with
two (2) questions to be completed, one from each section, from a choice of six (6).
EVALUATION:
 Feedback on the course will be obtained informally from students on an ongoing basis by regular interactions
and meetings among students, demonstrators, teaching assistants and the course lecturers in practicals and
tutorials.
 Formal feedback will be via election of Class Representatives who sit on the Departmental Student-Staff
Liaison Committee meetings held twice during the semester. Class reps will channel both concerns and
commendations to the meeting as guided by the Department’s Standard Operating Procedures.
 Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an ongoing basis and corrective action or adjustments made or discussed
with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Contact hours:
36 hours
Lectures:
18 hours
Tutorials:
6 hours
Practicals:
12 hours (5 x 5 hours less 10 minutes = 24 hours)
Lectures and tutorials are given to the whole class, and practicals are usually delivered to the students in three (3)
streams. The course outline, objectives, and practical schedules are available on myelearning, together with the
opportunity for feedback through the Academic Forum. Lecture materials are reduced to promote understanding
of principles rather than transmission of facts, in particular with diagrams simplified to the essentials. Practicals
build from initial qualitative observations on campus, through pre-set quantitative exercises and hypothesis testing
using quantitative data, to a field exercise in an undisturbed habitat. Practical schedules are available before the
class to maximise usefulness of the class time.
RESOURCES:
Essential Text
1. Mackenzie, A., Ball, A. S. & Virdee, S. R. 2001. Instant Notes in Ecology. 2nd ed. London: Taylor &
Francis.
Recommended Texts
These texts should be used for supplementing the course text book, following up on lectures, and for research for
practical reports.
1. Begon, M., Townsend, C. R. & Harper, J. L. 2005. Ecology: Individuals, Populations and Communities. 4th
ed. Oxford: Blackwell.
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2. Beeby, A. & Brennan, A. 2004. First Ecology. 2nd ed. Oxford University Press.
3. Brower, J., Zar, J. & von Ende, C. 1998. Field and Laboratory Methods for General Ecology. 4th ed. Boston:
McGraw Hill.
4. Smith, T.M. & Smith, R.L. 2009. Elements of Ecology. 7th edition. San Francisco: Benjamin Cummings.
COURSE CALENDAR:
Week
1
2
3
4
5
6
Lectures and Tutorials












Course Overview
(Tutorial)
Evolution and the niche
Individual ecology
Population: distribution
Population: numbers and
distribution
Population: demography
Population regulation
Tutorial
Interactions between species
Tutorial
Life history strategies
Applied ecology: harvesting and
species conservation
Community: definitions and
descriptions
Community: diversity and stability
Community change: succession
Island community dynamics
Practicals
Assignments
due
1. Qualitative sampling of
grassland plants
Practical 1
2. Population analysis of
animals
3. Interactions between
organisms
Test 1
Practical 2
Test 2
Test 3
7

8



9

10



Ecosystem processes and
components
Tutorial
Ecosystem: producers
Ecosystem: consumers
11


Ecosystem: nutrient cycling
Tutorial
Practical 5
Test 5
12

Test 6
13


Applied ecology: biodiversity
conservation
Tutorial
Course Review
Practical 3
4. Quantitative sampling of
grassland insects
Practical 4
Test 4
5. Aripo Savanna plant
communities
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ADDITIONAL INFORMATION:




Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet:
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf.
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials. Failure
to do so will result in debarment from the final examination.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
Students should attend all lectures, tutorials, and practicals. The lectures are designed to cover the most important
points in each subject area, in the opinion of the lecturer, and are condensed from a much greater volume of
material. Students who do not attend lectures miss the benefit of this work by the lecturer, and have to review the
textbooks themselves. Although less satisfactory than attending lectures, independent study has been made easier
by detailed learning objectives cross-referenced to sections of the textbook. Practical instructions are provided on
myelearning well before the start of the class, and should be read before attending the class to make full benefit
of the class time. Tutorials are designed to help students with aspects that have proved difficult in the past, rather
than providing new material.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
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THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DESCRIPTION
COURSE CODE:
BIOL 2764
COURSE TITLE:
SEMESTER:
Physiology of Plants
2
LEVEL:
2
NO OF CREDITS:
3
PRE-REQUISITES: BIOL1262 - Living Organisms I or BIOL1261 Diversity of Organisms or (BIOL1065
Diversity of Plants and Animals and AGRI1012 Microbiology) and either BIOL1364 Genetics I and BIOL 1362
Biochemistry I or BIOL1061 Cell Biology and Genetics
ANTI-REQUISITE: BIOL2761 Plant Physiology
The first part of the course provides the essential concepts of plant physiology with comprehensive coverage of
water relations, mineral uptake, and photosynthesis. The second part of the course explores how these resources
are translated into plant growth and provides an introduction to how plants respond to environmental signals at
the whole plant level.
PURPOSE OF THE COURSE/COURSE RATIONALE
The course provides an understanding of how plants gain the resources need for growth and survival. This information is
essential to understanding the functioning of ecosystems and the application of plant biology. Within the Life Sciences
department it will be a core module for the Biology Degree/Biology major.
INSTRUCTOR’S INFORMATION
Name of course coordinator:
Aidan D. Farrell
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Office address and phone:
220, Zoology Office, Natural Sciences Building, New Wing Natural Sciences
Building
Email address:
Office hours:
[email protected]
9:00 - 5:00 daily (email for appointment)
Preferred method of contact:
Email
Communication policy:
Students should use their UWI email account for communication and can expect
a response within 48 hours
CONTENT
Plant Physiology focuses on how plants gain the resources needed for growth. There is detailed coverage of the key
mechanisms at the whole plant level. The course begins with a detailed description of how plants acquire water, carbon and
nutrients. This is followed by an examination of how these resources are utilised for growth. The remainder of the course
looks in detail at examples of how plants use extrinsic signals to respond to their environment. Topics are divided as follows:









Plant anatomy review
Plant water relations
Photosynthesis & translocation
Membranes and mineral uptake
Cell expansion & plant growth
Phytochrome
Plant growth regulators
Nastic and Tropic movements
Control of flowering
GOALS/AIMS
This course aims to:




Review the essential concepts in whole plant physiology
Provide students with the knowledge needed to analyses and evaluate physiological process at the whole plant level
Enable students to describe the role of these physiological processes in ecosystems
Enable students to develop skills in problem solving and interpretation through ‘first-hand’ experience of how
physiological mechanisms are discovered
LEARNING OUTCOMES
At the end of this course students should be able to:





Describe how plants acquire the resources needed for growth
Differentiate between different mechanisms for resource acquisition
Recognise the general system of signal perception, transduction and response in plants
Describe and contrast specific examples plants responding to extrinsic signals
Interpret experimental evidence relating to plant physiology
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COURSE ASSESSMENT
Students are required to achieve a grade of 40% overall, irrespective of their performance in individual components.
Component
%
Final
Grade
Description
Final exam
50%
2-hour written exam with 20 multiple choice questions, and a choice of 2
out of 4 essay questions
In-course test 1
15%
Resource acquisition: multiple choice and short structured questions
In-course test 2
15%
Growth and responses to environment: multiple choice and short
structured questions
Practicals
20%
Performance and reporting of practical exercises
TEACHING STRATEGIES
Contact hours (36 credit hours):
Lectures: 18 h
Tutorials: 6 h
Practicals: 12 hours (4 x 6 hours = 24 hours)




Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of available information, and
prioritise content relevant to course assessment.
Practicals: Fortnightly practicals will provide hands on experience for students to gain skills required for conducting
well designed laboratory sampling and experiments; to problem solve and trouble shoot in real-life situations; and to
become familiar with performing and interpreting physiological experiments. Performance in the practicals will be
assessed as well as reports based on the practical activities.
Tutorials: Tutorials will cover course topics in a highly interactive format using a variety of collaborative active
learning techniques.
Myelearning: MyeLearning, will be used extensively during this course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
RESOURCES
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Many resources are available via MyeLearning including:



Lecture presentations (including learning objectives)
‘General Resources’- direct links to videos, web-tools and publications relevant to the course
Discussion forums
Essential texts:
Plant Physiology. Taiz and Zeiger. 2010 (Sinauer Associates) (In Reserve Section, UWI, St Augustine, Main Library)
Texts for further reading:
Introduction to Plant Physiology. Hopkins & Huner. 2008 (John Wiley & Sons)
Plant Physiology. Salisbury and Ross. 1992 (Wadsworth)
Lehninger Principles of Biochemistry. Nelson & Cox. 2008 (Freeman)
Biochemistry & Molecular Biology of Plants. 2002. Buchanan et al. (Wiley)
Web links:
http://5e.plantphys.net/
http://plantphys.info/plant_physiology/schedule.shtml
http://plantsinaction.science.uq.edu.au/edition1/?q=content/contents-page
Practical equipment:
All equipment will be provided by the Dept. Life Sciences, except the Infrared Gas Analyser which will be demonstrated
by the Dept. of Food Production



Glasshouse space for growing and treating plants.
Psychrometer, Porometer, Pressure chamber, Infrared Gas Analyser, Variable light rigs, Darkroom, light filters.
Light microscopes, Micro balances, Drying ovens, Microwave ovens, Cork-borers, Razor blades, glassware, etc.
123
COURSE CALENDAR
Week Lecture
1
Introduction
Plant Anatomy Review
2
Water Relations
Water Relations
3
SPAC
Stomata & Transpiration
4
Translocation & Partitioning
Photosynthesis: light reactions
5
Photosynthesis: carbon reactions
Photosynthesis: whole plant
6
Tutorial
In course test I
7
Phytochrome
Plant Growth Regulators
8
Cell expansion and Plant growth
Cell expansion and Plant growth
9
Membranes / Ion uptake
Mineral Nutrition
10
Nastic & Tropic Movements
Lab/Tutorial
Deadlines
Water Relations
Water Relations
Practical report
Gas Exchange
Gas Exchange
Practical report
In course test I
Germination, Nutrition
& Hormones (Part A)
Practical report
Germination, Nutrition
& Hormones (Part B)
Practical report
Control of flowering
11
12
Tutorial
In course test II
In course test II
Tutorial
Tutorial
124
ADDITIONAL INFORMATION





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials. Failure to do
so will result in debarment from the final examination.
As a ge eral pri iple, edi als or other e uses a o l e use a stude t s prese e at a assig ed ti e. “tude ts
must still complete the assigned work (make-up lab report or make-up test) in order to obtain the marks for that
item of coursework. The student is responsible for liaising with the Course Coordinator or Teaching Assistants to
ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
su issio through Tur iti o
eLear i g. ‘efer to U i ersit ‘egulatio s o Plagiaris a aila le fro
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:



Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able to fully
participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised to become familiar with
them and start utilising them from the first week. Regular updates on course progress and materials are also highly
recommended and you should check into you r UWI email and myelearning on a frequent regular basis to review
materials, assignments and activities.
Students are encouraged to interact regularly with staff on their projects, even outside of the assigned tutorial times to
ensure prompt, satisfactory solution of any problems and to monitor progress.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
125
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND AGRICULTURE
DEPARTMENT OF LIFE SCIENCES
TITLE:
BIOL2867 Physiology of Animals
CREDITS:
3
LEVEL:
Undergraduate-Year II
SEMESTER: II
PRE-REQUISITES:
BIOL1263 Living Organisms II and BIOL1362 Biochemistry I and either BIOL1364 Genetics I or ESST 1001
Biology for Environmental Sciences
ANTI-REQUISITES:
BIOL2862 Animal Physiology
OFFERING DEPARTMENT:
Department of Life Sciences, Faculty of Science and Agriculture, The University of the West Indies, St.
Augustine.
COURSE COVERAGE:
Physiology of Animals is the study of how animals’ function. It is a broad-based course which provides an
introduction to molecular and cellular physiology and the principal physiological systems in animals, and how
these systems function to maintain homeostasis in various environments. It covers fundamental concepts in
osmoregulation and excretion, neurophysiology, muscle physiology, respiration, thermo-physiology, circulation
and gas transport, endocrinology, and cardiovascular physiology. We also look at some of the major stressors on
physiological processes and show how animals have been able to deal them. Typical stressors that are covered
include osmotic pressures, water limitation, hypoxia, altitude, depth, temperature extremes and exercise. While
126
animal physiology examines systems and processes common to all animal species, this course will focus on
vertebrates, with a special emphasis on mammalian systems.
SIGNIFICANCE/RATIONALE:
The physiology of animals is a study of how animal function and respond to changes in their environment. This
course allows us to understand the basic physiological functioning of animals and how these allow animals to
deal with stressors in their environments. Knowledge of certain aspects of the natural history, morphology,
behaviour, and environment of an animal is necessary to fully appreciate the importance of its physiology.
ENROLMENT CAPACITY: 200 students (maximum)
PURPOSE OF THE COURSE
This course provides a basic understanding of the physiological functioning of animals. This discipline is
principally concerned with how animals are physiologically adapted to the environment in which they live.
INSTRUCTOR’S INFORMATION
Dr Azad Mohammed (Coordinator)
Room 222, Natural Sciences Building, UWI- Life Sciences
Phone: 868-662-2002 Extn. 82046; Fax: 868-663-5241
Email: [email protected]
Preferred contact – By Email
Professor John Agard
Room 220, Natural Sciences Building, UWI- Life Sciences
Phone: 868-662-2002 Extn. 83095; Fax: 868-663-5241
Email: [email protected]
Preferred contact – By Email
Office-Contact hours (Coordinator)
Day
Monday
Tuesday
Wednesday
Thursday
Friday
Time
8-10AM
8-10AM
8-10AM
8-10AM
8-10AM
LETTER TO THE STUDENT
Dear Students,
I would like to extent a very warm welcome to you as we get prepared for the start of BIOL xxxx - Physiology
of Animal. I am Dr Azad Mohammed, your Course Coordinator. Part of this course is also being taught by
127
Professor John Agard. This course is fully supported through myelearning, which we update regularly. Please feel
free to contact me (course teacher)/TA/demonstrator for any academic help and assistance. Please know that we
are here to support your learning and success as a student in FSA.
This course is designed to provide you with an understanding of the basic principles of comparative physiology
and their ecological and evolutionary significance. Another goal of the course is to teach students how to critically
investigate physiological problems experimentally in relation to an animal’s environment and the strategies used
to solve these problems.
A few points to note:
The Course Schedule (dates/activities) is available on the course page and should be downloaded for your
reference and continued guidance, as soon as you have access.
Please take the time to read the policy on plagiarism.
Once again, I would like to take this opportunity to welcome you and look forward to some healthy interactions
over the course of the next semester.
Your Course Coordinator
Dr Azad Mohammed.
‘there are no strangers in this world, only friends you haven’t yet met’
CONTENT
The course covers several major physiological systems in the body. It explores the structure and function of
animals and allows students to gain some knowledge on the diversity, as well as similarities in the physiology of
animal - at the microscopic as well as macroscopic level.
Respiratory Physiology
The initial part of the course looks at respiratory systems and explains how these have become modifies in
different groups of organisms allowing them to live in specific environments. The respiratory systems of airbreathing vertebrates, the gill system of fish, the insect tracheal system, and the unidirectional gas exchange
system of birds
It also looks at the principles of gas exchange and shows how the respiratory gasses are transported to and away
from tissues via the circulatory system. It also looks at the adaptations of these systems under extreme conditions.
Osmoregulation
One of the main challenges that organisms face is maintenance of internal homeostatic conditions. this sections
looks specifically at the process of regulating water potential in order to keep fluid and electrolyte balance within
a cell or organism relative to the surrounding. It is the way by which an organism maintains
suitable concentration of solutes and amount of water in the body fluids.
Thermal Physiology
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Thermo regulation is another mechanism used to homeostatic conditions of tissues. This topic will look
specifically at temperature regulations and the strategies most organism use to deal with changing ambient
environmental conditions.
Neurophysiology
Sensory and neuro physiology covers the broad range of topic specifically looking at how stimuli are integrated,
transmitted and interpreted by the body. We examine the structure of the neuron and how it is able to achieve its
function.
Nueromuscular physiology
Neuromuscular Physiology can be studied at the most simple levels by using the classical models of nerve
signaling to muscles through acetylcholine receptors. This topic shall investigate the structure and function of the
neuromuscular junction and the sequence of events that occur following stimulation of the muscle to the eventual
contraction.
Digestion
Digestive physiology is concerned with the tissues that contribute to the physical and chemical breakdown of
food. It would focus on the chemical processes that break food into forms that can be transported and metabolized
into other molecules.
COURSE GOALS:
The main goal of the course is to familiarize students with the principles of physiology and its ecological and
evolutionary significance. Another goal of the course is to teach students how to critically investigate
physiological problems experimentally in relation to an animal’s environment and the strategies used to solve
these problems.
COURSE OBJECTIVES:
At the end of the course, the student should be able to have a good understanding of the following:


The structure and functions of the major physiological systems found in vertebrate and invertebrate
organisms and how these systems integrate in the whole animal.
a. The respiratory systems (ventilation, diffusion and perfusion of blood) of air-breathing vertebrates,
the gill system of teleost fish, the insect tracheal system, and the unidirectional gas exchange
system of birds.
b. The function of the nervous system including synaptic transmission and sensory perception in
vertebrates and invertebrates
c. The skeletal muscle system and the physiology of muscle contraction in response to stimulation.
The basic principles of physiological regulation and homeostasis,
a. How organism are able to maintain normal homeostatic function under extreme temperature
changes, and mechanisms for adaptation.
b. Osmotic regulation and ionic balance
AIMS/GOALS
At the end of the course you should
• have a thorough knowledge and understanding of many aspects of animal physiology based on
129
attendance at lectures and reference to the recommended textbook
• be able to perform and write-up experiments in animal physiology having done the practicals and
obtained feedback from marked work
• be able to assess your knowledge of animal physiology in preparation for the exams.
LEARNING OUTCOMES
At the end of this course students will be able to:






record and interpret physiological phenomena in appropriate units.
analyze and interpret laboratory data using graphical and statistical tools.
investigate physiological phenomena using appropriate lab methods.
search the library and internet to obtain literature pertinent to a chosen physiological topic.
actively seek and assimilate information from texts, assigned articles and reference texts.
work collaboratively with one or more lab partners.
Dispositional outcomes:


Students will understand the relevance and importance of physiology in the Major of their degree.
Students will not hesitate to ask questions or seek help from the instructors when material is difficult or
confusing.
Mode of Delivery:
Lectures -24 hours:
Didactic; interactive
Tutorials - 6 hours:
Interactive; mind maps; problem-solving
Laboratory classes- 20 hours (4
Interactive practical tasks; problem-solving
five-hour sessions):
COURSE ASSESSMENT
Assessment would be based on a combination of in-course assessment (50%) and final examination (50%).
In-course assessments consist of both theory and practical components, and together make up the 50% of the final
marks. A student missing an in-course examination because of an illness or legitimate emergency will be allowed
to do a makeup examination the date of which will be advertised and shall be within 7 days of the first test. In
such a circumstance, the student should make every reasonable attempt to contact the instructors as soon as
possible. While make-up exams will cover the same content area as a missed exam, the exam format and specific
questions may be different. There shall be no makeup labs, students missing a practical exercise must submit a
valid medical within 7 days of the practical. Failure to do so will mean that a grade of zero will be given for that
practical. Those who submit a valid medical will be given a final practical mark that is an average of all their
marks. Any student missing more than 25% of practical classes or tutorial sessions without a medical or other
valid excuse can be debarred from writing the final exam.
Final exam: Duration 2 hrs; Essay and short answer questions. The final paper may include a compulsory section.
The contribution of each component to the final grades is as follows:
130
EVALUATION
Course Work: 50%
-
Writing across the curriculum exercises:
Laboratory reports (10 x 2% ):
In-course test 1:
In-course test 2:
Tutorial Attendance and participation:
Final examination (2 hours)
5%
20%
10%
10%
5%
50 %
Coursework in BIOL2XXX will be assessed in the following ways:
1. Writing across curriculum exercises-5%.
These activities are designed to encourage students to become active learners by engaging knowledge to
further develop understanding. The exercises would help students understanding content and expressing
ideas. A total of five simple exercises worth a total of 5 marks (1 mark per exercise) would be given during
lectures or tutorials (no more than one per week). Each exercise would take between 5 – 10 minutes to
complete and would comprise of varying activities including:
a. Focused free-writing: Students may be asked to briefly write on their understanding or perspective
on a subject/topic covered or on how the subject/topic may be connected to other situations.
b. Entry slips-: Short responses to questions posed at the beginning of class;
c. Answering questions: One or few questions would be given which students must answer and
submit for grading.
d. Short summary: Students are asked to summarize main points of a reading assignment in a short
paragraph.
e. Group presentation: The tutorial class would be divided into groups and each group would be
required to make a short presentation on a document provided.
2. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned at the end of
the semester. Participation would include more than just showing up at tutorial – some evidence of an
active role in the tutorial discussion would be required to obtain the full 5% for participation. At the
beginning of the semester, the students in each tutorial would engage in developing the exact assessment
criteria for this assignment, and the student-developed criteria will be used to determine each student’s
participation grade.
3. In-course Test-20%
Two in-course tests would be given worth 20%. The test would be given in weeks 6 and 12 of the semester
and would comprise MCQs and short answer questions.
4. Practicals (20%):
Practicals will contribute 20% to the final grade. There will be 4 practical sessions for the duration of the
course. The final mark for each practical will consist of the final report (70%) and a performance mark
(30%). Late lab submission would be penalized by a 15% deduction of the final grade for each day late.
5. Final examination (60%)
131
The final paper would consist of a 2hr examination which includes a compulsory section. It would have a
mixture of short answer and essay type questions.
COURSE ASSESSMENT
EVALUATION
BIOLxxxx will be evaluated in two ways – (a) through the Class Representative and the Life Sciences StudentStaff Liaison Committee, and (b) an end of semester course evaluation survey.




Feedback will be obtained informally from students on an ongoing basis by regular interactions and meetings
among students, demonstrators, teaching assistants and the Course Coordinator in practicals and tutorials.
Formal feedback will be via Class Representatives who sit on the Departmental Student-Staff Liaison
Committee meetings held twice during the semester. Class reps will report concerns and commendations to
the meeting as guided by the Department’s Standard Operating Procedures.
Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
All feedback will be considered on an ongoing basis and corrective action or adjustments made or discussed
with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Course objectives will be achieved through the aid of the following learning activities:
1.
2.
3.
4.
Assigned readings
Class lecture and videos
Web page resources
Practical exercises
The material presented in all modes of instruction will be sufficient in content to allow students to have a good
understanding of the topics. Lectures will help to direct the students to some of the more important details of each
topic. Assigned readings will serve to supplement lectures. These include lectures notes, web based materials and
original research papers on topics covered. We would also request that students post links to interesting articles
for discussion in the forums in the course page.
RESOURCES
Text books:
Principles of Animal Physiology 2nd Edition
Christopher D. Moyes and Patricia M. Schulte.
OTHER RESOURCES:
Discussion topics will be placed online for class comments.
READINGS
132
Instructors will periodically upload in my-elearning important research articles, review papers, book chapters and
other related study materials.
Students are expected to consult prescribed text books for relevant chapters for complete details and for
preparation for examinations
Students are expected to download those files or visit the suggested websites or read relevant book
chapters/journal articles before they come for the following class. These were considered and included as portions
of the syllabus and covered fully during examinations.
BIOL 2862 COURSE SCHEDULE
WEEK LECTURES
1
1.
2.
2
3.
4.
3
4
Regulation of heartbeat (Azad Mohammed)
6.
Regulation of heartbeat (Azad Mohammed)
7.
Cardiovascular responses to diving in
mammals and birds (Azad Mohammed)
Cardiovascular responses to high altitude
(Azad Mohammed)
Tutorial (Azad Mohammed)
9.
5
Properties of air and water as respiratory
media. Comparative respiration and gas
exchange efficiency of integuments, gills,
mammalian lungs and bird lungs (John
Agard)
Comparative respiration and gas exchange
efficiency (cont’d) (John Agard)
Respiratory pigments and the factors that 1 The effects of oxygen and carbon
modify their activity (Azad Mohammed)
dioxide
concentration
on
respiration in insects.
Gas transport and acid-base balance of the
Objective: To understand what is the
blood. (Azad Mohammed)
primary stimulus for respiration.
5.
8.
PRACTICALS
10.
Q10 and thermal increment. Ectothermy; the
zone of tolerance, adaptations to cold and
heat (John Agard)
11.
Endothermy, the thermo neutral zone,
responses to heat and cold. Heterothermy:
torpor and hibernation. (John Agard)
12.
Tutorial (John Agard)
2
The effect of temperature on the
heart rate of an ectotherm.
Objective: to understand how
temperature
affects
Q10
in
ectotherms
133
6
13.
14.
15.
7
8
Coursework exam 1 (Azad Mohammed)
3 Cardiovascular and respiratory
physiology of humans
Excretory systems (Azad Mohammed)
Objective: Give students an idea of
how cardiovascular physiology
Water and osmotic regulation. Ionic changes to meet the demands of
regulation (Azad Mohammed)
environmental conditions.
16.
Digestion
We would investigate the tissues that
contribute to the physical and chemical
breakdown of food. Focus would also be on
the chemical processes that break food into
forms that can be transported and
metabolized into other molecules (Azad
Mohammed)
17.
Digestion
We would investigate the tissues that
contribute to the physical and chemical
breakdown of food. Focus would also be on
the chemical processes that break food into
forms that can be transported and
metabolized into other molecules (Azad
Mohammed)
18.
Tutorial (Azad Mohammed)
19.
The ultra structure of muscles (Azad 4. The Physiology of skeletal
Mohammed)
muscles.
Objectives:
The regulation of muscle contractions (Azad
- Name and describe the phases of a
Mohammed)
muscle twitch
- Explain why the “all or none” law
is reflected in the activity of a single
muscle cell, but not in an intact
skeletal muscle.
- Understand that the graded
response of skeletal muscles is a
function of the number of muscle
fibers stimulated and the frequency
of the stimulus.
- Define
and
explain
the
physiological
basis
of
the
following;
 Subminimal, minimal, maximal and
supramaximal stimuli
 Latent period
 Wave summation
 Tetanus
 Muscle fatigue
20.
134
Explain the effect of load on skeletal
muscle
9
10
11
12
21.
The mechanics of muscle contraction (Azad
Mohammed)
22.
The propagation and transmission of action
potentials (John Agard)
23.
Tutorial (John Agard)
24.
The synapse; excitation and inhibition (John
Agard)
25.
The synapse; neuronal integration (John Presentation of labs (5%)
Agard)
26.
Tutorial (John Agard)
27.
The organization of sensory systems (John
Agard)
28.
Transmission and sorting
information (John Agard)
29.
Tutorial (Azad Mohammed)
30.
Coursework exam II (Azad Mohammed)
of
sensory
-
ADDITIONAL INFORMATION
Students must attend 75% of their practicals. Failure to do so may result in the student being debarred from the
final examination. (Examination regulations Section II part 19
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf).
In order to pass the course, you must gain a overall mark of 40% from both the coursework and the final
theory exam. Any student who misses more than 25% of practical classes or tutorial sessions without a
medical or other valid excuse can be debarred from writing the final exam.
If you do have a disability and have not disclosed the nature of your disability and the support you need, you are
invited to contact the Academic Support/Disabilities Liaison Unit (ASDLU) of The University of the West Indies
(UWI), St. Augustine Campus.
Phone: 662-2002 extension 83866, 83921, 83923 and 84254
Fax: 662-2002 extension 83922
Email: [email protected]
http://sta.uwi.edu/asdlu/forms.asp
Additional information posted in the Department of Life Science hand book may be consulted for additional
details regarding,
Role of Lectures, Tutorials and Practical’s,
Attendance,
Online Teaching Resources,
135
General safety guidelines in Lab and
General Safety Practices
Accident and incident reporting forms.
Academic Dishonesty:
Academic dishonesty, which includes plagiarism and cheating, is an extremely serious academic offense and
carries penalties varying from failure in an assignment to possible suspension from the University.
http://sta.uwi.edu/fsa/lifesciences/accountability.pdf (Department of Life Sciences Handbook)
HOW TO STUDY FOR THIS COURSE




The lectures will be delivered using power point presentation and slides/videos depicting real-time
scenarios and thoroughly discussed.
These will be posted on myelearning) the day after the lecture.
Students should read all the relevant materials given.
They should also attempt past paper questions which we can review.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade
Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
April 2012
136
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DESCRIPTION
COURSE CODE:
BIOL3063
COURSE TITLE:
SEMESTER:
Marine Ecology and Oceanography
2
LEVEL:
2
NO OF CREDITS:
3
Pre-requisites: Either BIOL1262 Living Organisms I and BIOL1263 Living Organisms II or BIOL1261
Diversity of Organisms or (BIOL1065 Diversity of Plants and Animals AND AGRI1012 Microbiology) and
either BIOL2XXX Fundamentals of Ecology OR BIOL1462 General Ecology and Biometry
Anti-requisites: BIOL2063 Marine Ecology
COURSE DESCRIPTION:
This course is an introduction to marine ecology and related aspects of oceanography and marine biology. It
emphasizes ecological processes and adaptations that act to structure marine associations and permit their
persistence through time. Lectures provide an overview of characteristics, biodiversity and ecology of these
marine ecosystems. They will also highlight concepts, ideas and hypotheses of how marine ecosystems function.
These principles are examined on a global oceanographic scale.
The course will also explore the structure and function of marine communities and ecosystems; threats to marine
ecosystems and include management strategies to provide sustainable benefits both to the ecosystems and human
wellbeing.
Students are expected to have a basic foundation in ecology and biodiversity. In addition to providing a foundation
of theoretical knowledge, this course will emphasise practical skills and expose students to field and laboratory
approaches for studying freshwater systems. It is an interactive ‘hands-on’ course where students are expected to
prepare, participate and perform in an active way to engage with the content in a variety of ways. Assessment is
designed to encourage students to work continuously with the course materials, explore and critically analyse
research in this rapidly developing field.
PURPOSE OF THE COURSE/RATIONALE:
This is a core course for the Ecology & Environmental Biology minor in the Department of Life Sciences and is
an essential area in environmental sciences, environmental biology and environmental management. It also
broadens the scope of studies in biology, plant biology and zoology.
137
Marine ecosystems systems are diverse environments that support unique communities of organisms and provide
invaluable ecosystem services for human survival and well-being. At the same time they are heavily impacted by
humans since they integrate all activities on land, in the water and even the atmosphere. An appreciation of these
systems is necessary for their effective management.
INSTRUCTOR INFORMATION:
Name of course co-ordinator: Dr. Judith Gobin
Office address and phone: Room 222, Natural Sciences Building, UWI- Life Sciences,
868-662-2002 Extn. 82046; Fax: 868-663-5241.
Email: [email protected] , Preferred contact – By Email
Office hours: Mondays 12.00 to 2.00, Wednesdays 12.00 to 2.00
LETTER TO STUDENTS:
Dear Students,
I would like to extend a very warm welcome to you as we get prepared for the start of BIOL 3XXX – Marine
Ecology & Oceanography. I am Dr Judith Gobin, your Course Coordinator. Part of this course is also being
taught by Professor John Agard. This course is fully supported through myelearning, which we update regularly.
Please feel free to contact me (course teacher), your TA or demonstrator for any academic help and assistance.
Please know that we are here to support your learning and success as a student in FSA.
This course is designed to provide you with an understanding of the main marine ecosystems and their ecological
significance. Another goal of the course is to teach students how to critically investigate the marine environment
in terms of communities of organisms and water quality.
A few points to note:



The Course Schedule (dates/activities) is available on the course page and should be downloaded for your
reference and continued guidance, as soon as you have access.
The major Field trip is on-board a Research Vessel and this trip is mandatory. Students do not necessarily
have to be good swimmers (although this would be great!) since we have strict regulations with respect to
our safety at sea.
Please take the time to read the UWI’s policy on plagiarism.
Once again, I would like to take this opportunity to welcome you and look forward to some healthy interactions
over the course of the next semester. So, let’s get your feet wet!
Your Course Coordinator
Dr Judith Gobin.
138
CONTENT:
Topics will include:
Introduction to the Marine Environment and the different marine ecosystems.
Properties of seawater, some basic oceanography and some basic ecological principles.
Phytoplankton communities, shallow-water subtidal benthic associations, intertidal ecology, estuaries and salt
marshes, tropical communities (coral reefs and mangroves), oceanic nekton and the deep sea environment.
Lectures also cover the different adaptations by organisms for living in the different environments. Relevant
examples are introduced from both tropical (including local to Trinidad and Tobago and the Caribbean) and
temperate systems
COURSE GOALS:
This course aims to:




Provide students with an introduction to marine ecology and related aspects of oceanography and marine
biology.
Introduce students to ecological processes and adaptations that act to structure marine associations and
permit their persistence through time.
Provide lectures and information which highlight concepts, ideas and hypotheses of how marine ecosystems
function.
Include a survey of local marine habitats and organisms and examine principles on a global oceanographic
scale.
GENERAL OBJECTIVES:
The general objectives of the course are to:






Provide course materials, activities and assessment using both face-to-face and online modalities
Facilitate opportunities for students to engage with general concepts and specific examples to develop a
comprehensive understanding of the nature of marine ecosystems and their biodiversity
Allow students to observe, analyze and recognize the marine ecological communities of a local marine
habitat in Trinidad and Tobago;
Allow students to carry out ecological surveys including evaluations to determine environmental impacts
on marine communities.
Guide students in critically analysing and exploring questions in marine ecology and oceanography.
Facilitate discussion on the management of marine ecosystems and their impacts on human well being.
139
LEARNING OUTCOMES:
Upon successful completion of this course, the student will be able to:
1. Describe the ocean environment in terms of geology, geography, chemistry and water movement;
2. Identify the major taxonomic groups living in the ocean;
3. Critically evaluate the main hypotheses explaining how marine ecosystems function;
4. Describe the major ecosystems of the ocean in terms of physical and biological characteristics;
5. Analyze the marine environment and marine species' adaptations to the most important environmental
parameters;
6. Observe, analyze and identify the marine ecological communities of Trinidad and Tobago;
7. Carry out ecological surveys to determine environmental impacts on marine communities.
COURSE ASSESSMENT:
Assessment will be based on a student’s final mark from the coursework components below.
Component
Final exam
In-course tests
% Final Grade
50%
20%
Tutorials, online
activities
Practicals
10%
20%
Description
2-hour written exam to answer 2 essay questions
2 tests (each 10%). The 1st- a Research Essay and
the 2nd a multiple choice, true/false, short response
question paper.
Performance in interactive discussions and
activities face-to-face and online
Performance and reporting of 5 practical exercises
ASSIGNMENTS:
Students will also have two in-course tests, each covering specific areas of the course. These are designed to
determine if the students can correctly recall all that was covered in the previous weeks of the course. The 1 st
is an 1 Essay question and the 2nd is a multiple-choice question exam. (together total 20%)
140
Students will have to submit a written report for each of four practical exercises. These are designed to relate
to all of the major topics that are covered in the lectures. The practical assessment will consist of four (5hr)
Laboratory exercises plus 2 Journals associated with the Labs. Together these account for 20% of the final grade.
Practical write-ups are handed in at the end of each lab. (6.00pm)
Journals are handed in 1 week after the Field trip. (4.00pm)
EVALUATION:
At the onset- students are asked to pop in to see the Course Co-ordinator or to make an appointment- to
address any problems they may be having.
Both Dr. Gobin and Prof. Agard have an open-door policy (once they are on-campus and available).
Chosen Class Representatives will attend meetings with the staff/student Liaison Committee, and give their
feedbacks/comments on the course to the committee.
Class Reps. are advised to address issues to me directly as soon as possible since there are only 2 meetings of
this Committee per semester. This means issues may get delayed in being addressed.
The UWI/IDU course evaluation forms at the end of the semester will be used to address and improve on the
specific comments/feedback as best as possibly.
TEACHING Strategies:
Credits: 3 computed as follows:
Lectures: 23 h
Tutorials: 6 h
Total = 2.4 cr
Practicals: = 20h (0.8)
Course objectives will be achieved through the aid of the following learning activities:
1.
Class lecture and videos
5.
6.
7.
8.
Assigned readings
Web page resources including published scientific papers
Field exercises
Practical exercises (laboratory)
141
The material presented in all modes of instruction will be sufficient in content to allow students to have a good
understanding of the topics.
Class lectures will help to focus the student to some of the more important details of each topic.
Field e er ises ill e pose stude ts to the
sampling in the marine environment.
ari e e iro
e t a d allo
the
ha ds-o
e perie e at
Writing up the Field journal- gives students the opportunity to observe, note and process
Field and sampling information before returning to the laboratory.
Laboratory exercises will allow students to calculate, evaluate and synthesise the information and details
gathered in the field.
Assigned readings will complement lectures. These include additional lectures notes, web based materials and
original research papers on topics covered during lectures and practicals.
RESOURCES:
myeLearning: The online teaching tool, myeLearning, will be used extensively during this course for
communication among students and staff (email, discussions), official posting of important notices (coursework
assessment notices, instructions, and in-course results), provision of course details, lecture notes, practical guides,
tutorial briefings and provision of recommended resource materials and links to resources on specific websites.
Tutorials may have specific supporting resources particularly on skills development.
Essential and Recommended texts are in the Reserve Section, UWI Main Library or via links in the course outline
and myeLearning
Text books:
Marine Biology. James W. Nybakken. 5th/6th Editions.
OTHER RESOURCES:
myeLearning (through my.uwi.edu) will be the main online resource.
Discussion topics will be placed online for class comments.
There is also a Facebook page- UWI Marine Ecology.
142
COURSE CALENDAR:
WEEK
LECTURES
1
Introduction to the # 1 Introduction to
Course
Field
samplingmethodology,
Bathymetry
and
instruments
&
topography of the
Physical and Chemical
ocean floor: major
Properties
of
subdivisions of the
Seawater.
world ocean
2
Sea floor spreading, Tutorial 1
plate tectonics and
continental drift
3
Atmospheric
# 2 Sea/coastal area
Circulation Oceanic
trip
Circulation
4
Primary Production
The Classic Model of
the Ocean Ecosystem:
zooplankton grazing,
PRACTICALS
Assignments
DVD/Blue
PlanetPlankton & Tutorial 2
A changing Model of
the Ocean Ecosystem:
microorganisms,
nanoplankton,
bacteria and the
marine
planktonic
food web
5
Soft bottom Benthic #
3
Sorting &
ecology: Macrofauna Identification
and
analysis of plankton
Meiofauna
and benthic fauna
from
sea
trip
Sea/coastal area trip.
Report write-up
143
WEEK
LECTURES
PRACTICALS
6
Rocky Shores
DVD/Blue
Planet- Test 1
Coastal seas
&
Tutorial 3
Sandy Shores
7
Esutaries
Mudflats
Marshes
and
Assignments
# 4 East Coast rocky
shore and/or sandy
Salt
shore (beach profiles),
or mud-flat. Field tripincludes journal writeup.
8
Mangrove
Swamps DVD/Blue
Planetand wetlands
Seagrasses & Tutorial
4
Seagrass beds
9
Coral Reef- Physiology # 5 East Coast rocky
of coral growth and shore and/or sandy
nutrition.
shore (beach profiles),
benthic
faunaLaboratory write-up.
Coral Reef Ecology
10
Deep-Sea Biology
Oceanic Nekton
11
12
DVD/Blue
PlanetCoral Reefs & Tutorial
5
Marine ecosystems & Tutorial 6
Management
–
Pollution
and
Degradation
Marine ecosystems,
Biodiversity
and
Human well being
.
Test 2
13
144
ADDITIONAL INFORMATION:
Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at- http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf
and to the General Information and General Regulations in the Faculty Booklet available fromhttp://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials. Failure to
do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned time.
Students must still complete the assigned work (make-up lab report or make-up test) in order to obtain the marks
for that item of coursework. The student is responsible for liaising with the Course Coordinator or Teaching
Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able to fully
participate in activities and obtain the full value of the sessions. Thorough use should be made of the resources
provided and students are strongly advised to become familiar with them and start utilising them from the first
week. Students are encouraged to interact regularly with staff even outside of the assigned tutorial times to ensure
prompt, satisfactory solution of any problems.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
145
40-44
F2
Weak
1.3
0-39
F3
Poor
0
J.F.GOBIN 05 MARCH 2013
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
Course code: BIOL 3162
Course Title: Principles of Microbial Biotechnology
Number of Credits: 3
.
Level: Undergraduate –Year III
Pre-requisites:
Biology Stream
BIOL2265- Fundamentals of Microbiology
BIOL 2164- Principles of Molecular Biology
BIOL3369- Laboratory Skills in Biotechnology
Biochemistry stream
BIOC2262 Gene Expression
BIOC3162- Experimental Biochemistry and Molecular Biology
Anti-requisite: BIOL3262 Microbial Biotechnology
Semester: 2
Offering Department:
Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St.
Augustine
Course description
This course focuses on the applications of microorganisms in a range of processes that are beneficial for humans
and the environment. The topics covered include isolation, screening, genetic manipulation and culturing of
microorganisms for selected biotechnological applications related to industries, health, agriculture and the
environment. The course is organized into face-to-face lectures, tutorials and practical exercises. General and
specific concepts would be covered in lectures while tutorials would be interactive, with students expected to
prepare and fully participate in discussions and other class activities. Students will be continuously assessed via
in-course tests, activities during lectures and tutorials, and attendance and participation in tutorials. Students’
practical exercises will be assessed and there is also a final end-of-semester theory examination.
146
Purpose of course/rationale
The course is a core requirement for the specialization in Biotechnology in the Department of Life Sciences, UWI,
St. Augustine. It will be highly beneficial to students with core interests in microbiology and biotechnology. It is
designed to introduce students to fundamental theoretical principles and develop key practical skills in microbial
biotechnology. Microbial biotechnology is currently one of the most important sub-disciplines of biotechnology,
having contributed significantly to medicine, agriculture, the environment and industries in terms of a host of new
drugs, chemicals and processes. The prospects for microbial biotechnology are even brighter with the
development of new metagenomic approaches of exploiting the potential of unculturable microorganisms, which
represent the overwhelming majority of microbes in the environment.
Instructor Information
BIOL 3XXX will be managed by a course coordinator and would be taught by a team of experienced lecturers,
supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office hours for the coordinator and
lecturers are posted on the faculty bulletin boards and are available from the Department of Life Sciences’ general
office. Team members can also be contacted via e-mail.
Name: Dr Adesh Ramsubhag (Co-ordinator)
E-mail: [email protected]
Office location: Rm. 220, Natural Sciences Building, Old Wing
Office hours: Check Notice Boards
Phone: 662-2002 Ext. 83086
Name: XXXX (Teaching assistant)
E-mail:
Office location:
Office hours:
Phone: 662-2002 Ext.
Letter to students
Welcome to BIOL 3XXX- Principles of Microbial Biotechnology. This course provides an exciting opportunity
to be introduced into the exciting field of modern biotechnology. It would provide a platform for developing a
fundamental understanding of theoretical concepts and practical skills in exploring and applying the enormous
diversity of microbes for applications beneficial to humans and the environment. A major emphasis would be to
develop critical thinking skills. Interactive participation in lectures, tutorials and practical sessions is essential.
Please feel free to ask questions or offer alternative perspectives. You would also need to focus on personal
attributes of team work and inter-personal skills required for group work, in addition to organizational skill and
time management. I wish you the most interesting and intellectually stimulating experience in this course.
Content:
BIOL3XXX covers the following content:
Overview of Microbial biotechnology: history, scope and future prospects
Microbial bioprospecting: isolating and screening microorganisms for various applications
Metagenomic approach for harnessing biotechnological potential of microorganisms
Principles of fermentation
Microbial production of proteins
147
Microbial production of primary metabolites: organic acids and amino acids
Microbial production of secondary metabolites: antibiotics
Recombinant and synthetic vaccines
Microbial biofertilizers
Biological control of pests and diseases
Microbial production of polysaccharides and polyesters
Ethanol production
Bioremediation
Improvement of microorganisms
Course goal:
The goal of the course is to expose students to general theoretical concepts and develop fundamental practical
skills in microbial biotechnology.
General Objectives:
Students completing the course will have:
4. A critical review of biotechnological processes employing microbial cells or genes applied to medicine,
the environment, agriculture and industries.
5. Fundamental practical skills in isolating, screening and applying microorganisms in biotechnology
processes.
Learning objectives:
Upon completing this course, students will be able to
- Devise culture based strategies for isolating and screening microorganisms for a range of biotechnological
applications;
- Review the metagenomic strategies for harnessing microbial genes for beneficial applications;
- Compare and contrast culture based and metagenomic strategies for biotechnological exploitation of
microorganisms;
- Explain the culturing techniques used for obtaining microbial cells and metabolic products;
- Explain the fundamental principles of microbial production of biological compounds, including the choice
of organisms, culturing processes, metabolic pathways and means of improving productivity:
o proteins
o organic acids and amino acids
o antibiotics
o recombinant and synthetic vaccines
o ethanol production
o polysaccharides and polyesters
- Formulate strategies for developing microbial biofertilizers and biopesticides;
- Explain the principles of land farming, composting, biosparging and bioventing methods of
bioremediation;
- Compare and contrast in-situ and ex-situ bioremediation strategies;
- Propose bioremediation strategies for in-situ and ex-situ treatment of petroleum contaminated soils;
- Explain how microbes can be improved by conventional and genetic engineering techniques.
Mode of Delivery:
Lectures -18 hours:
Tutorials -12 hours:
Practical project-
Didactic; interactive
Interactive; mind maps; problem-solving
Group project comprising of an equivalent to 12 hr/student
148
ASSIGNMENTS:
Coursework for BIOL 3XXX will be assigned as follows:
6. Writing across curriculum exercises-5%.
These activities are designed to encourage students to become active learners by engaging knowledge to
further develop understanding. The exercises would help students understanding content and expressing
ideas. A total of five simple exercises worth a total of 5 marks (1 mark per exercise) would be given during
lectures or tutorials (no more than one per week). Each exercise would take between 5 – 10 minutes to
complete and would comprise of varying activities including:
a. Focused free-writing- Students may be asked to briefly write on their understanding or perspective on a
subject/topic covered or on how the subject/topic may be connected to other situations.
b. Entry slips- Short responses to questions posed at the beginning of class;
c. Answering questions. One or few questions would be given which students must answer and
submit for grading.
d. Short summary. Students are asked to summarize main points of a reading assignment in a short
paragraph.
e. Group presentation- The tutorial class would be divided into groups and each group would be
required to make a short presentation on a document provided.
7. In-course Test-20%
One written in-course test would be given worth 10% per test in week 7. Two online tests will also be
given in weeks 4 and 11 worth 5% each. The tests would comprise of MCQs and structured questions.
8. Practical reports-20%
Students are required to conduct group projects aimed at isolating, screening, identifying and demonstrate
potential usefulness of microorganism from the environment. The project is worth 20% as follows:
proposal- 2%; literature review- 2%, poster presentation – 3%, oral presentation- 3%, final report – 6%,
continuous assessment – 4%.
9. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned at the end of
the semester. Participation shall include more than just showing up at tutorial – some evidence of an
active role in the tutorial discussion would be required to obtain the full 5% for participation. At the
beginning of the semester, the students in each tutorial would engage in developing the exact assessment
criteria for this assignment, and the student-developed criteria will be used to determine each student’s
participation grade.
Cheating, including plagiarism, would not be tolerated. Incidents of cheating would be dealt with according to
UWI’s rules and regulations including:
-
Examination Regulations for First Degrees, Associate Degrees, Diplomas and Certificates. Section
(B)
Cheating.
Regulations
96–102;
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf.
-
University Regulations on Plagiarism (First Degrees, Diplomas
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
and
Certificates).
Assessment:
149
Course Work: 50%
- Writing across the curriculum; critical thinking exercises
- Incourse test
o One written test
o Two online tests - (2 X 5%)
- Group Project
- Tutorial Attendance and participation
Final Semester Examination: 50%
- One 2-hour comprehensive written paper comprising of
o 5 short answer questions worth 6% each
o 2 essay-type question worth 35% each
- All questions in this paper shall be compulsory
TOTAL
5%
10%
10%
20%
5%
30%
70%
100%
EVALUATION: BIOL3XXX will be evaluated in two ways – (a) through the offices of the Class Representative
and the Life Sciences Student-Staff Liaison Committee, and (b) an end of semester course evaluation survey. The
class will elect four class representatives (one per lab stream), whose role is to act as a mediator between the Life
Sciences academic staff and the students in the class. The representatives will attend Liaison Committee meetings
(held at least twice per semester), where they will present feedback on the course to the Department for action.
The UWI performs a course evaluation survey at the end of every semester, and this information will also be used
for overall assessment of the course and guide possible actions for improvement in subsequent semesters.
TEACHING STRATEGIES: A combination of teaching strategies will be adopted in BIOL3XXX.
The primary teaching strategy will be based on the face to face classroom lectures and discussions. Videos of
lecture presentations would be made available to students prior to the lecture session via podcast media. Students
are advised to view these videos before the lecture so that more emphasis can be placed on discussions and
answering questions, thereby facilitating deep learning. This would also afford the time to have assessment
exercises on “writing across the curriculum”. MyeLearning will be utilized throughout the course as a means to
provide access to course materials such as Powerpoint presentation files, animations, weblinks, lessons and
quizzes. This medium would also be used as a portal for student-lecturer communications and the dissemination
of coursework feedback.
A total of 12 tutorial sessions would be given for the semester. These would be small group sessions which would
be conducted by instructors or tutors, who would normally by senior postgraduate students in Life Sciences.
Students must attend tutorial sessions. Tutorials sheets will be assigned prior to each session via myeLearning,
and students are expected to attempt the solutions before coming to tutorial. The goal of the tutorial session is to
give students a more hands-on experience with the course material and easier access to course instructors.
Students will be expected to ask and answer questions on material that is unclear, propose solutions to questions
on the tutorial sheet and to generally participate fully in the tutorial activities. Tutors will not merely be going
through the answers to the tutorial questions in these sessions.
The practical component of the course would comprise of a project to isolate, screen, identify and demonstrate
potential usefulness of microorganism from the environment. Each group would be assigned to a demonstrator
who would provide laboratory guidance in the completion of the project.
150
In order to pass the course, you must gain an overall passing mark of 40%. Any student who misses more
than 25% of practical or tutorial sessions without a medical or other valid excuse can be debarred from
writing the final exam.
RESOURCES:
Text books:
Alexander N. Glazer and Hiroshi Nikaido, Microbial Biotechnology: Fundamentals of Applied Microbiology,
Cambridge University Press; 2nd edition, October 1, 2007, ISBN-10: 0521842107
Suggested additional readings:
- Lee Yuan Kun (Ed.), Microbial Biotechnology: Principles And Applications, World Scientific Pub Co
Inc; 2 nd edition (August 24, 2006), ISBN-10: 9812566775
-
Internet links to web-based resources will be provided to students
Lab coat:
- Each student should have suitable Lab coat to use for practical exercises. Students not having lab coats
will not be permitted in the lab.
COURSE CALENDAR/SCHEDULE:
Course calendar:
Week
Lecture/Tutorial
1
Lecture 1: Introduction; Course overview; class rules, lecturer and
student expectations, safety; introduction of project;
Lecture 2: Overview of Microbial biotechnology: history, scope and
future prospects
Tutorial 1: Introduction and overview
2
Lecture 3: Microbial bioprospecting using culture-based strategies
Tutorial 2: Microbial bioprospecting
3
Lecture 4: Metagenomic approach for harnessing biotechnological
potential of microorganisms
Lecture 5: Principles of fermentation
Tutorial 3: Metagenomics
4
Lecture 6: Microbial production of proteins
Tutorial 4: Fermentation and microbial production of proteins
151
Week
Lecture/Tutorial
Online test- MCQs (5%)
5
Lecture 7: Microbial production of primary metabolites: organic acids
and amino acids
Lecture 8: Microbial production of secondary metabolites: antibiotics
Tutorial 5: Organic acids and amino acids
6
Lecture 9: Recombinant and synthetic vaccines
Tutorial 6: Production of antibiotics and vaccines
7
Lecture 10: Microbial biofertilizers
Tutorial 7: Biofertilizers
8
Written incourse test (in lecture slot) – MCQs, structured questions
(10%)
Lecture 11: Microbial biofertilizers
Tutorial 8: Biofertilizers
9
Lecture 12: Biological control of pests and diseases
Lecture 13: Biological control of pests and diseases
Tutorial 9: Biological control
10
Lecture 14: Microbial production of polysaccharides and polyesters
Lecture 15: Ethanol production
Tutorial 10:Polysaccharides, polyesters and ethanol
11
Lecture 16: Bioremediation
Lecture 17: Bioremediation
Tutorial 11: Bioremediation
Online test- MCQs (5%)
152
Week
12
Lecture/Tutorial
Lecture 18: Improvement of microorganisms
Tutorial 12: Bioremediation
Project guidelines
Week
Activity
Comments
1
Decide on project
As guided by lecturer and TA
2
Write and submit preliminary project
- No marks allocated.
proposal- Must be written after consultation with
- Title:
demonstrator and lecturer
- Introduction-some
relevant
background information and
justification
(problem,
- Must be approved by lecturer before lab
knowledge/technology
gap;
work can commence.
relevance of research area in
solving problem, bridging gap in
knowledge/technology)
- Goal and objectives:
- Proposed approach (broad
perspective of methodology
without going into fine details)
3
Start laboratory work under guidance of Preliminary proposal much be approved before
demonstrator
starting
4
Final proposal due;
Proposal worth 2 marks (to be marked by
- Title:
lecturer)
- Introduction-some
relevant
background information and
justification
(problem,
knowledge/technology
gap;
relevance of research area in
solving problem, bridging gap in
knowledge/technology)
- Goal and objectives:
- Proposed
methodology
–
include all details)
- Anticipated results
- Expected outcomes (to science,
humans etc)
- Literature cited
Continue laboratory work
153
5
Continue laboratory work
6
Literature review due
Literature review worth 2 marks (To be marked
by lecturer)
Continue Laboratory work
See:
http://www.ais.up.ac.za/med/tnm800/tnmwritingliteraturereviewlie.ht
m
http://www.sdc.uwo.ca/writing/gradhandouts/Academic%20Tasks%20
-%20Literature%20Reviews%20-%20Presentation.pdf
7-10
Continue laboratory work
Poster worth 3 marks (To be marked by a panel
including lecturer, TA, other lecturers)
Prepare poster presentation
Work on final report
11
Oral presentation of research
Oral presentation worth 3 marks (To be marked
by a panel including lecturer, TA, other
Make adjustments to final report if lecturers)
necessary
12
Submit final report
Final report worth 6 marks (To be marked by
lecturer)
Continuous assessment
4 marks (to be marked by demonstrators and TA
based on observations and interviews with
group
members
and
laboratory
technicians/assistants).
Contributions
to
different phases would be separately assessed:
- Conceptual framework and research
proposal
- Literature review
- Isolations
- Screening/evaluation of isolates
- Identification
- Storage of isolates
- Preparation of poster
- Final report
The criteria for allocation of marks would
include:
- Participation
- Punctuality
- Laboratory etiquette
- Quality of work
154
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
155
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTNE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE CODE:
COURSE TITLE:
SEMESTER:
LEVEL:
NO OF CREDITS:
BIOL 3164
Function and Design in Biology
II
II
3
PRE-REQUISITES:
Either BIOL1262 Living Organisms 1 or BIOL1261 Diversity of Organisms or (BIOL1065 Diversity of Plants
and Animals and AGRI1012 Microbiology); and either BIOL 2XXX Physiology of Plants or BIOL2761 Plant
Physiology and either BIOL2XXX Physiology of Animals or BIOL2862 Animal Physiology; AND BIOL3XXX
Plant Anatomy
ANTI-REQUISITE(S): BIOL3264 Functional Design in Biology
COURSE DESCRIPTION
This course offers a fresh approach to the study of the structure and function of living things. It does not follow
the traditional approach based on phylogeny, processes, or organ systems, but looks at how organisms are
designed to best make use of the physical characteristics of the environment in which they live. The course goes
further than presentation of didactic lectures. For example, students are asked to critique the commonly held belief
that cells are the building blocks of living things, and instead consider that cells are incomplete subunits of the
organism, so that morphology is not related to anatomy. In the same vein, the concept of Bernoulli’s Principle is
shown to be inadequate to explain flight. Analogies are used wherever possible to explain concepts, such as
comparing the anatomy of stems and bones to beams and girders, using the Forth Rail Bridge as an engineered
analogue of stems. Lectures, tutorials, and practicals are designed to encourage thinking about concepts rather
than remembering details.
PURPOSE OF THE COURSE/COURSE RATIONALE
The course provides an understanding of how organisms are constructed to optimize their various functions.
Within the Life Sciences Department it will be an optional elective course.
This 3 credit version of the course includes a reduction in theoretical background and elimination of derivation
of equations in order to make the course approachable to students with a wider background.
INSTRUCTOR INFORMATION
Instructor:
Dr. Gregor Barclay
156
Office phone:
E-mail:
Office location:
Office hours:
(868) 662-2002 x83112
[email protected]
324, Natural Sciences Building, Old Wing
8:30 - 4:30 daily
Instructor:
E-mail:
Office phone:
Office location:
Office hours:
Dr. Ayub Khan
[email protected]
(868) 662-2002 x83087
224, Old Wing, Natural Sciences Building
8:30 - 4:30 daily
CONTENT
The course begins with the rationale for Functional Design in Organisms and the historical background of
biomechanics, leading into a class discussion of the similarly named but otherwise unrelated Intelligent Design.
Course content includes both fundamental considerations of functional implications of organismal size, shape and
geometry, composition, structure and strength, and mechanics of feeding and mobility.








Scaling in biology
Stress and strain in biology
Biomechanics of cell walls, tissues and organs
Locomotion on land
Viscoelasticity of biological materials
Flow in tubes
Flight
Swimming dynamics
GOALS/AIMS
The aim of this course is to enable students to understand how organisms overcome constraints imposed by the
laws of physics and the properties of matter and capitalize on opportunities in ways that allow them to prosper.
GENERAL OBJECTIVES
The lectures and practical schedule are designed so that at the end of this course students should be able to:
 Differentiate between support systems
 Explain the mechanics of locomotion in the water and air, and on land.
 Contrast life dominated by viscous forces versus inertial forces
 Describe methods of locomotion and drag reduction
 Interpret experimental biomechanical evidence.
LEARNING OUTCOMES
157
At the end of this course students will be able to:
1. Critique the cell theory versus the organismal concept of plant and animal construction.
2. Relate the surface area to volume of organisms in the context of size, shape, and geometry.
3. Evaluate the structural characteristics of various biological materials.
4. Compare the arrangement of support structures in organisms with beams, trusses, & columns.
5. Apply the physics of support to derive safety factors in support systems and tune design to the mechanical
characteristics of the environment.
6. Categorize support systems: Tensile, strutted; nearly rigid surfaces, hollow cylinders and shells;
pressurized systems, and muscular hydrostats.
7. Describe the mechanics of motility: Muscle and bone as levers; muscular hydrostats.
8. Evaluate the relationships between viscosity and flow displayed by shear stress, modulus, strain, and rate;
laminar/turbulent flow, Reynolds numbers, streamlining, flow in biological pipes
9. Evaluate the influence of pressure on flow: Bernoulli’s Principle in nature- pressure and drag; skin
friction; drag coefficient and flexibility; lift & circulation, dynamics of flight & swimming.
COURSE ASSESSMENT
Students are required to achieve a minimum grade of 40% overall, irrespective of their performance in
individual components.
In-course test 1:
In-course test 2:
Five tutorial exercises
Five practical reports
Final examination (2 hours)
10 %
10 %
10%
20 %
50 %
TEACHING STRATEGIES
Lectures, practicals, and tutorials are designed accommodate a range of learning styles, as outlined in Ch. 7 of the
DLS undergraduate handbook. The course combines lectures/tutorials with interactive practical sessions that
allow students to become familiar with performing and interpreting biomechanical experiments. Tutorials follow
the practical sessions with students in small groups each with a dedicated demonstrator.
158
RESOURCES
Essential Text
S. Vogel, Comparative Biomechanics: Life's Physical World (2003), Princeton University Press
Recommended texts
Alexander, R. M (1999) Energy for Animal Life, Oxford University Press.
Ennos, R. 2012. Solid Biomechanics. Princeton: Princeton University Press.
Niklas, K.J. 1992. Plant Biomechanics. An Engineering Approach to Plant Form and Function.University of
Chicago Press.
Vogel, S. 1994. Life in Moving Fluids. Princeton University Press.
Practical equipment:
Stop watches, meter rulers, egg crushing apparatus, glassware, balances, spring scales, graph paper, etc. All
equipment will be provided by the Department of Life Sciences.
COURSE CALENDAR
Week Lecture
1
Course Introduction and Overview of course
requirements
Basic Anatomy/Morphology
Lab/Tutorial
GFB
GFB
2
Surface area/Volume: Size shape & geometry in biology GFB
Scaling of size and function
AK
3
Stress and strain in biology
Shape, stress and architecture
AK
AK
4
Shape, stress and design of biological structures
Plant cell wall biomechanics
AK
GFB
5
Cell wall and plant construction
Evolution of trees
GFB
GFB
6
Review
In course test 1
GFB
GFB
7
Locomotion on land, ballistic movement
Froude s u er a d gait
AK
AK
Plant allometry
Morphological design
and strength
Froude s u
gait analysis
er a d
159
Week Lecture
8
Viscoelastic behaviour of biological materials I
Viscoelastic behaviour of biological materials II
AK
AK
9
Flow in tubes
Bird flight
GFB
GFB
10
Drag reduction
Swimming dynamics
AK
AK
11
Review
In course test 2
AK
AK
12
Course Review
Course Review
GFB
AK
Lab/Tutorial
Tutorial on video
on Physics of Plants
Laminar and
turbulent flow
ADDITIONAL INFORMATION
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
 As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned time.
Students must still complete the assigned work (make-up lab report or make-up test) in order to obtain the
marks for that item of coursework. The student is responsible for liaising with the Course Coordinator or
Teaching Assistants to ensure the assigned make-up is completed.
 Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available
from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able to
fully participate in activities and obtain the full value of the sessions.
 Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should check into your UWI email and myeLearning on a
frequent regular basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned
tutorial times to ensure prompt, satisfactory solution of any problems and to monitor progress.
160
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
161
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE: BIOL3263
COURSE TITLE: INTRODUCTION TO BIOINFORMATICS
NO. OF CREDITS: 3
LEVEL: III, Sem. 1
PREREQUISITE(S): BIOL2164 Principles of Molecular Biology
COURSE DESCRIPTION:
This course introduces students to bioinformatics tools and methods. It provides the conceptual background for
using bioinformatics tools and application methods and offers skills and training on computational molecular
biology and related fields. It gives an understanding about major advances in the analysis of genomes, sequences
and their structures and also critically discusses the strength and limitations of the methods. The lecture
component of this course provides the necessary conceptual backing and the practical component provides
assignments for utilizing bioinformatics tools. Problem-based learning methods would be employed to teach the
utility of bioinformatics tools. Teaching approaches include lectures, tutorials and lab sessions. Topics include
(but not limited to) bioinformatics databases, sequence and structure alignment, protein structure prediction,
protein folding, protein-protein interaction, simulation, and molecular dynamics.
COURSE RATIONALE
The global availability of genome sequence information for human, animal, plant and micro-organism systems
has led to the development of new technologies dependent on bioinformatics. Scientists require the combined
skills of molecular biology and computer science to exploit these data for the various applications. For those who
wish to perform research in life sciences, it is essential to be aware of the databases and software programs. There
is a current necessity to develop combined skills at the undergraduate level itself so that students have been well
exposed to this emerging field. Basic knowledge on bioinformatics is essential for Biology students especially
concentrating on biotechnology branch. Fundamental learning and training in this field would provide
opportunities for undertaking advanced study or training in bioinformatics and computational biology wherein
career opportunities are fast emerging at the present and future times.
INSTRUCTOR INFORMATION
162
BIOL3XXX will be managed by a course coordinator and would be taught be a team of experienced lecturers,
supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office hours for the coordinator and
lecturers are posted on the faculty bulletin boards and are available from the Department of Life Sciences’ general
office. Team members can also be contacted via e-mail.
Name of instructor(s):
Office address and phone:
Email address:
Office hours:
XXXXXX
XXXXXX
XXXXXX
XXXXXX
LETTER TO THE STUDENT
Welcome to BIOL3XXX- Introduction to Bioinformatics. This course covers the basic bioinformatic concepts
and methods widely used currently for bioinformatic analyses and research. Bioinformatic methods are
increasingly used over multiple fields in molecular biology and biotechnology covering plants, microbe and by
extension to applications of biotechnology including medicine, environment, industry and agriculture. The course
is taught through a series of 24 lectures/tutorials and 6 lab (wet and virtual) sessions. The course is quite extensive
and students must make a sincere effort to do well by fullest participation and involvement. It is important to
attend lectures. Please make use of supplementary information provided to strengthen foundation and enhance
understanding of material covered.
SPECIAL REQUIREMENTS:
Students should have basic mathematical skills which they would have acquired from the basic mathematics
courses underwent in Year 1 or elsewhere.
This course extensively uses computers and software. Therefore students are encouraged to own a computer
system (laptop) and have in their possession throughout the course period. The required software is downloadable
through privileged access and user sign up to all bonafide students registered for the course.
CONTENT
This course is designed to introduce the most important and basic concepts, methods, and tools used in
Bioinformatics. Topics include (but not limited to) bioinformatics databases, sequence and structure alignment,
protein structure prediction, protein folding, protein-protein interaction, simulation models, and molecular
dynamics. Emphasis will be put on the understanding and utilization of these concepts and algorithms. The
objective of this course is to introduce students in to field of bioinformatics and make them familiar with the use
of basic bioinformatics tools.
GOALS/AIMS
This course aims to:
 Build a range of competencies in transferrable skills as applied to experimental bioinformatics and
computational biotechnology.
 Expose students to the general techniques used for conducting research in Bioinformatics.
 Incorporate specialist practical skills and provides adequate pre-required hands on knowledge and exposure
on bioinformatics techniques essential for undertaking higher studies/research/profession in bioinformatics
and biotechnology.
163
LEARNING OUTCOMES
At the end of the course students should be able to:
 Apply the major transferrable skills relevant to using tools in bioinformatics.
 Analyze the applicability of bioinformatics techniques in Biotechnology and Molecular biology.
 Explain, illustrate and interpret the principle, mechanism and experimental steps of various bioinformatics
tools and analytical procedures.
 Review specific bioinformatics methodologies and tools used in research in selected problems in
biotechnology.
 Demonstrate hands on lab skills in the analytical techniques covered.
 Apply bioinformatics techniques to the elucidation of real-life scenarios.
 Evaluate the applicability of bioinformatics techniques to experimental aims.
 Critique, analyze and discuss the relevant case studies/journal articles/projects and reports for relevance
and applicability of methodology.
COURSE ASSESSMENT
50% Course work
50% Final examination
Course assessment components
In-course tests (2x10%)
Assignements/Online activities (3x5%)
Tutorial participation & lab quizzes/lab project
Final examination
% split up details
20%
15%
15%
50%
EVALUATION
 The elected Class Representative and/or Deputy will attend meetings with the course teacher(s) organized at
every 4th week, and present feedback from the students attending that course or stream. This feedback is
normally provided both orally and in written form for transmission to the lecturer. Apart from that the
representatives will be attending the Liaison Committee meeting, and give their feedbacks to the committee.
 Students may comment on any aspect of the course or facilities. Students will be encouraged to submit their
feedback (oral/written) during tutorials directly to the course teacher and appropriate actions will be taken by
the teacher then and there.
 Results of in-course tests, quiz and other course assignments will be analyzed and presented in the class. This
will help students to check their progress constantly and also helps the instructor to identify the weak areas and
thereby could alert and advise students individually to alter their approach of study and completing the work.
 The final reflective feedback and comments about the entire course and teaching will be collected on the last
day of the course. This will be saved for analysis and utilized as a base for improvement for the next offering
in the following year.
TEACHING STRATEGIES
Credits: 3 computed as follows:
Lectures and Tutorials:
24 h (2 cr)
164
Practical work:
24 h (1 cr)
The instruction for this course would comprise of 2 lectures per week and one practical session per alternate week.
Additionally, instructional videos, tutorials and virtual labs would be utilized to support the teaching. Formal
lectures and tutorials will provide introduction to specific topics and allow for discussion in an interactive setting.
Case studies, journal papers and data analyses will be carried out in small group settings. Course materials and
readings will be available online in advance so that discussion and critiquing can take place within the assigned
class time. This course is also mye-learning supported, and many other resources are readily available for the
students. Students in the practical sessions, work in groups of 4 during these hands-on sessions, for which
experimental planning (pre-labs) and small group discussions are required.
RESOURCES
Recommended reading:
Mount, D. 2004. Bioinformatics: Sequence and Genome Analysis, II edn, Cold Spring Harbor Laboratory Press.
Xiong, J. 2006. Essential Bioinformatics Cambridge University Press.
Peyzner, P., Shamir, R. 2011. Bioinformatics for Biologists Cambridge University Press.
Pevsner, J. 2009. Bioinformatics and Functional Genomics (2nd edition, Wiley-Blackwell.
COURSE CALENDAR
Week
Lecture + Tutorial
Wk1
Introduction to Bioinformatics
Wk1
Importance and uses of bioinformatics
Wk2
Information networks and uses
Wk2
Nucleic Acid sequence Databases I
Wk3
Nucleic Acid sequence Databases II
Wk3
Tutorial
Wk4
Wk4
Wk5
Protein sequence databases I
Protein sequence databases II
Metagenomics
Wk5
Wk6
Wk6
Sequence Alignment tools I
Sequence Alignment tools II
Protein structure analyses I
Wk7
Wk7
Wk8
Wk8
Wk9
Wk9
Wk10
Wk10
Wk11
Tutorial
Protein structure analyses II
RNA secondary structure
Primer design
Genome Projects
Phylogenetic trees
Tutorial
Gene regulatory modules
Micro RNA regulatory modules
Lab
DNA databases and
sequence analysis
Multiple Sequence
Alignment
In-course test; Sequence
assembly
Motifs and Patterns
Gene structures, genotyping
Incourse test;
165
Genome variations, primer
design
Wk11
Wk12
Wk12
Wk13
Wk13
Genome
variations,
Simple
Polymorphisms
Systematic Literature Search
Microarray data analysis
Review Tutorial
Review Tutorial
Nucleotide
ADDITIONAL INFORMATION:
Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf




Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/fsa/documents/UGFacultyBooklet.pdf.
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to
obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may
require submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ at
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:




Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able
to fully participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myelearning on a frequent regular
basis to review materials, assignments and activities.
Students are encouraged to interact regularly with staff, even outside of the assigned tutorial times to
ensure prompt, satisfactory solution of any problems and to monitor progress.
Good group management is essential and requires good communication and interpersonal skills.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
166
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE: BIOL3363
COURSE TITLE: MEDICAL BIOTECHNOLOGY
NO. OF CREDITS: 3
LEVEL: III, Sem. 1
PRE-REQUISITE(S): Principles of Molecular Biology
COURSE DESCRIPTION
Biotechnology as a field has very high relevance and application to human and animal medicine. With the advent
of research we are at a stage to unravel the molecular mechanisms of several diseases and disorders. These studies
have opened up a new era for the management of several problems facing human health and longevity.
Biotechnology innovation is in a large part driven by the requirement for improvements in medical diagnosis and
therapy for a range of diseases including autoimmune diseases, diseases of inflammation and cancer. This course
gives students a detailed insight into the principles and techniques of biotechnology applied to human medicine.
Topics include (but not limited to) biopharmaceuticals, stem cell technologies, tissue engineering and regenerative
medicine, proteomics, antibody technologies, nanomedicine and molecular diagnostics. The teaching and learning
methods include lectures/tutorials, and field trips to medical facilities (within Trinidad).
COURSE RATIONALE
This course focuses on some of the main areas in which biotechnology has generated medical products and areas
of current research which promise to deliver “future cures”. The global availability of genome sequence
167
information for humans and various pathogenic organisms and information on molecular mechanisms have placed
us in a right situation to develop and formulate precise treatments and diagnostic procedures for various diseases
and disorders. For those who wish to perform research in health sciences, it is essential to be aware of the
scientific developments taking place in this seminal field. There is a current necessity to develop good
understanding of this field at the undergraduate level itself so that students have been well exposed to this
emerging field. Biology students and those focusing on Biotechnology should be aware of advancements taking
place in medical biotechnology. Fundamental learning and training on this field would provide opportunities for
undertaking advanced study or research in medical biotechnology wherein career opportunities are emerging.
INSTRUCTOR INFORMATION
BIOL3XXX will be managed by a course coordinator and would be taught be a team of experienced lecturers,
supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office hours for the coordinator and
lecturers are posted on the faculty bulletin boards and are available from the Department of Life Sciences’ general
office. Team members can also be contacted via e-mail.
Name of instructor(s):
Office address and phone:
Email address:
Office hours:
XXXXXX
XXXXXX
XXXXXX
XXXXXX
LETTER TO THE STUDENT
Welcome to BIOL3XXX- Medical Biotechnology. We are living in the era of exciting medical technology which
is dawning on the corridors of biotechnology. Fuelled by a greater understanding of how our bodies work and
technological innovations, we are living longer and more productively than ever before. But still we are struggling
to find cures and remedies for several life threatening diseases and conditions, for which biotechnology should
store the solution. This course investigates these advances; it provides an overview of medical conditions with
their implications and the technologies developed to combat them. Subjects covered include biopharmaceuticals,
stem cell technologies, tissue engineering and regenerative medicine, proteomics, antibody technologies,
nanomedicine and molecular diagnostics. The course is taught through a series of lectures/tutorials, and field
trips. The course is quite extensive and students must make a sincere effort to do well by fullest participation and
involvement. It is important to attend lectures. Please make use of supplementary information provided to
strengthen foundation and enhance understanding of material covered.
CONTENT
This course is designed to introduce the most important applications of biotechnological advancements for human
medicine and therapy. The course includes study of molecular mechanisms underlying important diseases,
applications of biotechnology to the diagnosis and treatment of disease as well as the development of drugs and
therapeutic agents. The topics include by not limited to: molecular mechanisms of diseases, molecular diagnostic
procedures, drug development, novel therapeutic technologies including antibody therapy, stem cell therapy,
somatic gene transfer and gene therapy, novel vaccines, nanomedicines, tissue engineering & regenerative
medicine and novel bio-materials for human medicine. The objective is to help the students to expose to the
frontiers of biotechnological research developments and to reinforce the importance of this field to enable future
advancements.
GOALS/AIMS
168
This course aims to:
 Present students with the background to medical problems and the technologies currently used to address
them through biotechnological means.
 Expose to scientific development and application of these new technologies as well as their limitations.
 Present opportunities for further investigation and tests their innovative thought processes.
 Expose and update students to the constantly evolving biotechnological procedures and techniques and
motivate them to develop interest and for undertaking higher studies/research in medical biotechnology.
LEARNING OUTCOMES
At the end of the course students should be able to:
 Discuss the concepts, principles, key techniques and milestone achievements that have engendered the
rise of Medical Biotechnology as means to find solutions to current health care challenges.
 Analyse, interpret and critically evaluate the emerging technologies.
 Justify the appropriateness of selected technologies in developing novel approaches for human health and
cure.
 Evaluate the ethical components of novel technologies and appreciate their relevance in the spirit of
sustainable human life and health.
 Analyse primary research papers, evaluate complex information and creatively use this information in the
synthesis of their own presentations.
 Extrapolate and apply the learned new technologies for finding solutions for local, regional and global
health problems and real-life scenarios.
 Critique, analyze and discuss the relevant case studies, projects and reports for relevance and applicability
of methodology.
COURSE ASSESSMENT*
50% Course work
50% Final exam
Course assessment components
In-course tests (2x10%)
Assignment & Presentations (10%) and Journal club (10%)
Tutorial participation (3%) & field trip reports (7%)
Final examination
% split up details
20%
20%
10%
50%
EVALUATION
 The elected Class Representative and/or Deputy will attend meetings with the course teacher(s) organized at
every 4th week, and present feedback from the students attending that course or stream. This feedback is
normally provided both orally and in written form for transmission to the lecturer. Apart from that the
representatives will be attending the Liaison Committee meeting, and give their feedbacks to the committee.
 Students may comment on any aspect of the course or facilities. Students will be encouraged to submit their
feedback (oral/written) during tutorials directly to the course teacher and appropriate actions will be taken by
the teacher then and there.
169
 Results of in-course tests, quiz and other course assignments will be analyzed and presented in the class. This
will help students to check their progress constantly and also helps the instructor to identify the weak areas and
thereby could alert and advise students individually to alter their approach of study and completing the work.
 The final reflective feedback and comments about the entire course and teaching will be collected on the last
day of the course. This will be saved for analysis and utilized as a base for improvement for the next offering
in the following year.
TEACHING STRATEGIES*
Credits: 3 computed as follows
Lectures+Tutorials: 26 h (2.2 cr)
Practicals:
20 h (0.8 cr)
The instruction for this course would comprise 2 Lectures with inbuilt tutorials (40 min lecture+10 min tutorial)
per week and 4 practicals involving visits to medical and research facilities. Additionally, instructional videos
would be utilized to support the teaching. Formal lectures and tutorials will provide introduction to specific topics
and allow for discussion in an interactive setting. Case studies/journal papers discussion will be carried out in
small group settings. Course materials and readings will be available online in advance so that discussion and
critiquing can take place within the assigned class time. This course is also myeLearning supported, and many
other resources are readily available for the students.
RESOURCES
Recommended reading:
Nallari, P., Veugopal Rao, V. 2010. Medical Biotechnology, 1/e, Oxford Univ. Press, India.
Pongracz, J., Mary Keen, M. 2008. Medical Biotechnology, Elsevier Health Sciences.
Killeen, A. 2004. Principles of Molecular Pathology, Humana Press.
170
COURSE CALENDAR*
Week
Wk1
Wk1
Wk2
Wk2
Wk3
Wk3
Wk4
Wk4
Wk5
Wk5
Lecture + Tutorial
Lab
Introduction to Biotechnology and Human health
Molecular Mechanisms of Diseases
Molecular Mechanisms of Diseases
Importance of human genomics and proteomics in health
and cure (Journal 1)
Principle of Therapeutics & Drug Action
Molecular Medicine
Molecular Medicine
Biochemical Correlates of Diseases (Journal 2)
Metabolomics and human medicine
Clinical Immunoassays Techniques
Wk6
Molecular diagnostics
Wk6
Wk7
Wk7
Wk8
Wk8
Wk9
Molecular diagnostics
Role of Vaccines in Medicine
Novel vaccines
Recombinant Therapeutic Proteins
Antibody Therapies (Journal 3)
Wound Healing and Biomaterials
Wk9
Biopharmaceutical products (Assignment)
Wk10
Wk10
Drug Discovery Assays (Journal 4)
Nanodrugs
Wk11
Wk11
Stem cell therapies
Gene therapies
Wk12
Therapeutic Drug Monitoring (Journal 5)
Wk12
Personalized medicine and Ethical components of
biotechnology
Review Tutorial
Review Tutorial
Wk13
Wk13
Visit to Mount Hope
diagnostic facility
In-course test
Visit to Cancer hospital
Presentation;
Visit to cell culture
facility
Visit to pharmacology
facility
Visit to Virology lab,
In-course test
171
ADDITIONAL INFORMATION:





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf.
Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/fsa/documents/UGFacultyBooklet.pdf .
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to
obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may
require submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ at
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:





Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able
to fully participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myelearning on a frequent regular
basis to review materials, assignments and activities.
Students are encouraged to interact regularly with staff, even outside of the assigned tutorial times to
ensure prompt, satisfactory solution of any problems and to monitor progress.
Good group management is essential and requires good communication and interpersonal skills.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
172
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE CODE: BIOL3366
COURSE TITLE: PLANT BIOTECHNOLOGY AND GENETIC ENGINEERING
NO. OF CREDITS: 3
LEVEL: III, Sem. 2
PRE-REQUISITE(S): Either BIOL2XXX Principles of Molecular Biology and BIOL3XXX Laboratory Skills
in Biotechnology OR BIOL3XXX Gene Expression and BIOL3XXX Experimental
Biochemistry and Molecular Biology.
ANTI-REQUISITE: BIOL3762 Plant Biotechnology
COURSE DESCRIPTION
This course introduces students to plant transformation technologies and genetic engineering methodologies for
the introduction of beneficial traits into economically important plants. It also introduces students to plant tissue
culture techniques and the impact of this technology on preservation of plant species and plant tissue based
production of proteins and secondary metabolites. Topics include, Tissue culture applications in plant
biotechnology; Advanced study of Gene sources and Gene expression; Promoters, selectable markers and reporter
genes; Plant Transformation systems; Biology of Agrobacterium - mediated transformation; Agrobacterium –
mediated gene transformation – methodology; Direct gene-transfer methods, Particle bombardment; Transgene
Integration; Evaluation of Transgenics; Management of Gene silencing; Genetic engineering of plants for novel
traits; herbicide tolerance, enhancing pest resistance, disease resistance; resistance to plant viruses, enhanced
product qualities; Marker aided selection and gene pyramiding; Biofarming and plant expression systems;
Phytoremediation, Genetic engineering of biofuel crops; Genetically modified crops - ethical, social biosafety
and environmental issues. The teaching and learning methods include lectures/tutorials, group discussion, journal
paper discussion and lab sessions. The teaching and learning methods include lectures/tutorials, and lab sessions.
173
COURSE RATIONALE
This course focuses on advancements in plant biotechnology, which have provided solutions to present day
agricultural problems. In the light of gradual paucity of natural resources and environmental concerns, agricultural
productivity which has attained a plateau could be further improved only through biotechnological approaches.
Otherwise situations may jeopardize global food production and would lead to food shortage in the near future.
The global availability of genome sequence information and gene cloning of important plants have placed us in a
right situation to develop biotechnology/genetic engineering-based solutions to the current problems of crop and
food production. For those who wish to perform research in life sciences, it is essential to be aware of the scientific
developments taking place in this seminal field. There is a current necessity to develop good understanding of
this field at the undergraduate level itself, so that students have been well exposed to this emerging field.
Fundamental learning and training on this field would provide opportunities for undertaking advanced study plant
sciences and biotechnology.
INSTRUCTOR INFORMATION
BIOL3XXX will be managed by a course coordinator and would be taught be a team of experienced lecturers,
supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office hours for the coordinator and
lecturers are posted on the faculty bulletin boards and are available from the Department of Life Sciences’ general
office. Team members can also be contacted via e-mail.
Name of instructor(s):
Office address and phone:
Email address:
Office hours:
Dr. Jayaraj Jayaraman
Rm.220, Nat Sci. Bldg
[email protected]
Consult Life Sciences office
LETTER TO THE STUDENT
Welcome to Plant biotechnology and genetic engineering. The global population is predicted to peak at over 9
billion during the second half of this century. To provide food and dignified living conditions, agricultural
productivity should have to increase 50% by 2030 and 70% by 2050. This task is extremely urgent and
challenging, as it will have to coincide with a transition to more sustainable agricultural practices and as
agricultural land is lost due to climate change and urbanisation. This course will focus on plants in exploring the
fundamental constraints and analyze biotechnological opportunities and solutions for sustainable food production,
as well as the use of plants to supply high-value products. Topics to be covered include, application of plant tissue
culture applications in plant biotechnology and genetic engineering, plant transformation systems; management
of gene silencing; genetic engineering of plants for novel traits; herbicide tolerance, enhancing diseases and pest
resistance, biofarming, enhanced product qualities; Marker aided selection and gene pyramiding; genetically
modified crops - ethical, social biosafety and environmental issues.
The course is taught through a series of 26 lectures and 6 lab (wet and virtual) sessions. The course is quite
extensive and students must make a sincere effort to do well by fullest participation and involvement. It is
important to attend lectures and labs. Please make use of supplementary information provided to strengthen
foundation and enhance understanding of material covered.
CONTENT
174
This course explores the broad area of plant biotechnology and plant genetic engineering, including the scientific
principles underpinning these practices. Topics covered are: Introduction to Plant Biotechnology; Principles of
Plant tissue culture techniques; Tissue culture applications in plant biotechnology and genetic engineering;
Advanced study of Gene sources and Gene expression; Promoters, selectable markers and reporter genes; Plant
Transformation systems; Biology of Agrobacterium - mediated transformation; Agrobacterium – mediated gene
transformation – methodology; Direct gene-transfer methods, Particle bombardment; Transgene Integration;
Evaluation of Transgenics; Management of Gene silencing; Genetic engineering of plants for novel traits;
herbicide tolerance, enhancing pest resistance, disease resistance; resistance to plant viruses, enhanced product
qualities; Marker aided selection and gene pyramiding; Biofarming and plant expression systems;
Phytoremediation, Genetic engineering of biofuel crops; Genetically modified crops - ethical, social biosafety
and environmental issues. The lab sessions covered under BIOL3XXX- Laboratory Skills in Biotechnology will
complement and partially fulfil practical components related to this course.
GOALS/AIMS
This course aims to:
 Present students with the background to the problems faced in agriculture and food production and the
technologies conceived through biotechnological means to address them.
 Expose to the scientific development and application of plant biotechnology and genetic engineering
methods and understand their efficiencies and limitations.
 Expose and update students to the constantly evolving biotechnological procedures and techniques and
motivate them to develop interest and for undertaking higher studies/research in plant biotechnology.
LEARNING OUTCOMES
At the end of the course students should be able to:
 Discuss the concepts, principles, key techniques and milestone achievements that have engendered the
rise of plant biotechnology as solution to current food crisis and uncertainties in agricultural production.
 Analyse, interpret and critically evaluate the emerging technologies.
 Justify the importance of novel biotechnological approaches for improving food production in the near
future.
 Appraise the environmental sustainability of genetically modified crops.
 Evaluate the biosafety of genetically modified crops.
 Explore fullest clarification for the commonest disbeliefs revolving around genetically modified crops.
 Analyse primary research papers, evaluate developed technologies and creatively use this information in
the synthesis of their own presentations.
 Extrapolate and apply the learned new technologies for finding solutions for local, regional and global
agricultural problems and real-life scenarios.
 Critique, analyze and discuss the relevant case studies, projects and jornal papers for relevance and
applicability of methodology.
COURSE ASSESSMENT
50% Course work
50% Final exam
Course assessment components
% split up details
175
In-course tests (2x10%)
20%
Assignments/Presentations
(9%)
and 20%
Journal club (8%) and Tutorial participation
(3%)
Lab Quizzes (2x3=6%) & Lab observation 10%
reports (4%)
Final examination
50%
EVALUATION
 The elected Class Representative and/or Deputy will attend meetings with the course teacher(s) organized at
every 4th week, and present feedback from the students attending that course or stream. This feedback is
normally provided both orally and in written form for transmission to the lecturer. Apart from that the
representatives will be attending the Liaison Committee meeting, and give their feedbacks to the committee.
 Students may comment on any aspect of the course or facilities. Students will be encouraged to submit their
feedback (oral/written) during tutorials directly to the course teacher and appropriate actions will be taken by
the teacher then and there.
 Results of in-course tests, quiz and other course assignments will be analyzed and presented in the class. This
will help students to check their progress constantly and also helps the instructor to identify the weak areas and
thereby could alert and advise students individually to alter their approach of study and completing the work.
 The final reflective feedback and comments about the entire course and teaching will be collected on the last
day of the course. This will be saved for analysis and utilized as a base for improvement for the next offering
in the following year.
TEACHING STRATEGIES
Credits: 3 computed as follows:
Lectures+Tutorials: 24 h (2 cr)
Lab sessions: 24 h (1 cr)
The instruction for this course would comprise of 2 Lectures with inbuilt tutorials per week and 5 lab sessions+1
lab presentation. Additionally, instructional would be utilized to support the teaching. Formal lectures and
tutorials will provide introduction to specific topics and allow for discussion in an interactive setting. Case studies,
journal papers and data analyses will be adopted in small group settings. Course materials and readings will be
available online in advance so that discussion and critiquing can take place within the assigned class time. This
course is also myeLearning supported, and many other resources are readily available for the students.
RESOURCES
Recommended reading:
176
Slater, A., Scott, N.W., Fowler, M.R. 2008. Plant Biotechnology: The Genetic Manipulation of Plants, Oxford,
2008.
Oksman-Caldentey, K. Barz, H.B. (Ed). 2002. Plant Biotechnology and Transgenic Plants, CRC Press.
Primrose, S.B., Twyman, R.M., Old, R.W. 2001. Principles of gene manipulation. Wiley-Blackwell.
Dodds, J.H. 2004. Plant Genetic Engineering, Cambridge University Press.
Razdan, M.K. 2003. Introduction To Plant Tissue Culture, 2/E, Oxford & IBH Publishing Company Pvt. Ltd.
Journals:
Plant Biotechnology journal, Journal of Plant Biochemistry and Biotechnology, Transgenic research
Journal articles and reviews - provided by the lecturer
COURSE CALENDAR
Week
Wk1
Wk1
Wk2
Wk2
Wk3
Wk3
Wk4
Wk4
Wk5
Wk5
Wk6
Wk6
Wk7
Wk7
Wk8
Wk8
Wk9
Wk9
Wk10
Wk10
Wk11
Wk11
Wk12
Lecture + Tutorial
Introduction to the course requirements
Introduction to Plant tissue culture
Applications of plant tissue culture in biotechnology
Plant Transformation systems
Promoters, selectable markers and reporter genes
(Journal 1)
Biology of Agrobacterium - mediated transformation
Agrobacterium – mediated gene transformation –
Methodology
Particle bombardment & direct gene-transfer methods
Transgene Integration and Evaluation of Transgenics
(Journal 2)
Management of Gene silencing
Genetic engineering for herbicide tolerance
Genetic engineering for pest resistance
Genetic engineering for disease resistance (Journal 3)
Lab
Agro-transformation
PIG-based transformation
Incourse test,
Protoplast transformation
Genetic engineering for resistance to plant viruses
Genetic engineering for enhanced product qualities
Genetic engineering for tolerance to abiotic stresses
Genetic engineering for improved photosynthetic Transient gene expression
efficiency and novel traits (Journal 4)
assays (Quiz 1)
Biotechnology for biofuels
Metabolic engineering
Biofarming
Plant-made pharmaceuticals (Journal 5)
Transgene - analysis
through PCR (Quiz 2)
Genetically modified crops: ethical, social and
environmental issues
Genetically modified crops: prospects and constraints –
up-to-date (Assignment)
Marker aided selection
177
Week
Wk12
Lecture + Tutorial
Marker aided selection & gene pyramiding
Wk13
Wk13
Review Tutorial
Review Tutorial
Lab
Incourse test &
Presentations
ADDITIONAL INFORMATION:





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/fsa/documents/UGFacultyBooklet.pdf.
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to
obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may
require submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ at
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:




Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able
to fully participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myelearning on a frequent regular
basis to review materials, assignments and activities.
Students are encouraged to interact regularly with staff, even outside of the assigned tutorial times to
ensure prompt, satisfactory solution of any problems and to monitor progress.
Good group management is essential and requires good communication and interpersonal skills.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
178
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION 2015/16
COURSE CODE and TITLE BIOL3409 Caribbean Coral Reefs
NO. OF CREDITS
3
LEVEL*
3
SEMESTER
2
PREREQUISITES
BIOL3063 Marine Ecology and Oceanography
LETTER TO THE STUDENT
Dear students,
Welcome to BIOL3409 Caribbean Coral Reefs. This advanced-level course on the coral reefs of the Caribbean
places emphasis on the major ecological interactions within coral ecosystems, especially those of the Caribbean
region. This course offers a mix of theoretical knowledge and practical skills development, which is valuable for
those aiming for careers in marine biology, conservation, environmental consulting and marine management. The
course will be taught through lecture sessions with the lecturers as well as special invited lecturers for certain
topics. There will be individual and group assignments, the latter of which should help you to develop
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communication and team skills that are important in the world of work. It is in your best interest to ask questions
and ensure that you understand the concepts and techniques covered in this course.
This course will be taught in blended mode comprising face-to-face lectures, tutorials and practical exercises, as
well as online delivery of resource materials and diverse activities. You should engage with the course materials
and participate fully to develop the essential skills of critical thinking (clarity, accuracy, relevance, logic, breadth,
depth, precision, significance, completeness and fairness). Activities will be diverse, and you are strongly
encouraged to ask questions, offer new ideas, problem-solve, and think innovatively to maximise the value of
your learning experience. There will also be individual and group assignments, which should help you to develop
communication and team skills that are important in the world of work.
If sea conditions allow, there will be one field trip to visit a coral reef. The trip will be made if there are lowenough tides to allow safe access to the reef, and fairly clear water. At such times reef is too shallow for swimming
so you will be able to explore it by walking in the shallow channels between the coral heads. You do not need to
know how to swim, but you should be comfortable enough with water to be able to explore the reef using a snorkel
and mask. To do that, you will need to put your face in the water.
Please read the course outline carefully and keep the course schedule close to hand as it contains all the activities
and assessments for the semester. In particular, take note of the policy on plagiarism and attendance requirements.
We are here to ensure your success in this course and at UWI generally, and encourage you to come to us with
any academic or other challenges you may face that could affect your attendance and performance.
We look forward to meeting each of you and engaging in productive stimulating discussions over the coming
semester.
Dawn A. T. Phillip
Course coordinator
INSTRUCTOR INFORMATION
This course will be taught by a team of lecturers, teaching assistants and demonstrators. Further logistical support
will be provided by laboratory and field support staff. Office hours are posted on departmental notice boards and
the main Life Sciences office
A.T. 2nd floor, new wing, Natural Sciences building, ext. 82047 and 82208
[email protected] (preferred method of contact)
Course
coordinator
Lecturer
Dr. Dawn
Phillip
Lecturer
Dr
Stemann
Instructor
Mr Jahson Alemu I
Peter Bacon Postgraduate Laboratory, 2nd floor, Natural Sciences
building,
ext.
33084
[email protected] (preferred method of contact)
Teaching
assistant
Mr Guy Marley
Teaching assistants’ office, 2nd floor, new wing, Natural Sciences
building,
ext.
82204
[email protected] (preferred method of contact)
Thomas [email protected] (preferred method of contact)
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WEEKLY SCHEDULE
Lectures and tutorials
Mondays
noon–012:50 pm C1
(You are required to attend all Wednesdays 8:00–8:50 am
C2
sessions)
Practical classes
Tuesdays2
2:00–06:00 pm
LS3
(Weeks 3, 5, 9 and 11 – attend all
sessions)
COURSE DESCRIPTION
This course develops students’ knowledge and understanding of the biology of reef-building corals, the diversity
and ecology of coral reef communities, the importance of coral reefs, and the contemporary and historical
challenges they face. In addition, students will be introduced to the ecosystem-based approach to reef
management, and to the economic valuation of reefs. Though the course focusses primarily on Caribbean coral
reefs, reference will be made to reefs in other parts of the world.
COURSE RATIONALE
Caribbean coral reefs are the foundation the Caribbean’s tourism and fishing industries, and thus account for a
sixth of the region’s jobs, and a third of its income (or US$15 billion year-1), and 500 000 tonnes of its food.
Caribbean reefs, however, are suffering so terribly from the effects of overexploitation, pollution and climate
change that it is predicted that all the region’s corals may be dead within 40 years. Sustainably managing the
region’s reef resources has proved difficult because most Caribbean nationals are ignorant of the devastation to
their reefs, and most reef conservation efforts are either understaffed or highly dependent on costly imported
personnel. This course aims to increase the number of graduates with applicable knowledge of coral biology,
coral reef geology, ecology and conservation methods, thereby helping to provide the region with the skilled
workforce it needs to achieve the long-term conservation of its reef resources, to conduct vital new research, and
to sustain economically-important, reef-dependent industries, like tourism and fisheries.
COURSE CONTENT
 An introduction to the reef geography of the wider Caribbean and history of reef resource use in the
Caribbean.
 Coral biology, including taxonomy, anatomy and skeletal morphology, endosymbiosis with zooxanthellae,
calcification and growth, nutrition, defensive behaviour, reproduction and recruitment.
 Environmental conditions required for coral reef formation, geological history of Caribbean reef formation
and types of reefs; dynamics of reef structure formation and erosion.
 Reef community structure, zonation and dynamics.
 Major reef-associated organisms with attention to their ecological function. Uses, including reef fisheries,
tourism and recreation, biodiversity and marine products, and ecosystem services.
 Valuation, including total economic value, use values, option values and non-use values.
 The threats and future challenges to Caribbean coral reefs, including natural disturbances and anthropogenic
activities; hurricanes, tsunamis, and earthquakes; coral diseases and diseases of other reef organisms;
overfishing, deterioration of water quality, physical destruction of reefs, climate change, invasive species.
 An introduction to monitoring methods and the ecosystem-based approach to reef management, including
examples of mitigation actions appropriate to different geographic scales.
2
There is tentatively a field trip on Saturday 19th March
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GOALS AND AIMS
This course aims to
 Develop students’ competence in basic methods and approaches for identifying reef species and evaluating
coral reef ecosystems
 Develop students’ awareness that resource users of coral reef ecosystems are complex and include social beings
operating in various socio-cultural and socio-political contexts that must be understood by managers in order
to effectively manage the resource base
 Introduce students to the range of options that have been used to manage coral reefs and reef resources
GENERAL OBJECTIVES
The general objectives of this course are to
 provide course materials, activities and assessments using both face-to-face and online modalities
 facilitate opportunities for students to engage with general concepts and specific examples to develop a
broad understanding of the complex nature of human impacts on their environment
 guide students in crafting questions and critically analysing and exploring answers to these questions using
investigative hands-on approaches
 facilitate discussion on the relationship between humans and their environment and evaluate potential
solutions for ensuring sustainability and wellbeing of human populations
LEARNING OUTCOMES
Upon successful completion of the course, students should be able to:
 Identify some of the most important Caribbean coral species and describe their biology.
 Categorise the major ecological interactions within coral reef communities.
 Evaluate natural and anthropogenic threats to Caribbean coral reefs and select appropriate mitigation
measures.
 Conduct a monitoring exercise to assess reef health and interpret the data generated.
 Construct a reef management plan using the ecosystem-based approach to management.
 Demonstrate basic skills for researching, analysing, synthesising, evaluating and communicating published
and original environmental information;
 Evaluate specific human-environment interactions and identify resulting environmental issues;
 Develop solutions using a variety of tools and strategic approaches; manage group interactions and work
effectively in teams.
Students should also gain practical skills that will allow them to
 Describe a local coral reef ecosystem and the variety of species
 Accurately identify commercially important reef species using species identification keys
 Sample reef systems to collect community and habitat data
COURSE ASSESSMENT
The final mark for this course comprises the following
Theory examination: one 2-hour written examination
Course work
50%
50%
Consisting of:
– Four laboratory and/or field reports (practical)
(10%)
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– One research report (practical)
(30%)
– Short, weekly quizzes and in-class activities (theory)
(10%)
ASSIGNMENTS
In-course assignments comprise
1. Practical reports, collectively worth 10% of the final course mark. The reports will be based on activities
engaged in during four scheduled laboratory sessions as stipulated in the course schedule. Each report will
utilise a different format: scientific drawings, traditional laboratory report, poster, PowerPoint presentation,
video.
2. A single research project report worth 30% of the final course mark. This research project will be based on
observations made, and data collected during the field trip, but analysed in the consecutive practical session.
3. A single literature-based essay worth 10% of the final course mark. The essay will be a reading-based
assignment focussed on original literature and technical reports.
EVALUATION
 Feedback on the course will be obtained informally from students on an on-going basis by regular interactions
and meetings among students, demonstrators, teaching assistants and the course coordinator in lectures,
tutorials and laboratory sessions.
 Formal feedback will be via election of class representatives who sit on the departmental Student-Staff
Liaison Committee meetings held twice during the semester. Class representatives will channel both
o er s a d o
e datio s to the eeti g as guided the depart e t s sta dard operati g pro edures.
 Formal evaluation of the entire course will be accomplished via a UWI course evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an on-going basis and corrective actions or adjustments made or discussed
with students promptly or incorporated the following year.
TEACHING STRATEGIES
This course will be taught through a mixture of lectures, practical exercises and tutorials. There may also be guest
lectures by experts. Lectures and tutorials in the first half of the semester will provide the conceptual and factual
basis for specific topics and allow for discussion in an interactive setting. Case studies and selected topics may
be presented by guest lecturers. Course materials and readings will be available online in advance to allow
students to be better prepared to engage the lecturers in discussion during class time. Laboratory sessions will
provide hands-on training at a coral reef. Lecturers and demonstrators will be present to provide guidance
In addition, the online teaching tool, myeLearning, will be used extensively during this course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
 discussion on selected topics
Face-to-face contact time will be 36 credit hours, comprising:
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Lectures
24
hours
Tutorials
2 hours
Practical
exercises
20
hours
Lectures will provide valuable synthesis and evaluation of the coral
reef biology, values, threats and conservation measures related to
these ecosystems. Lectures will also be used to update current issues
and events, and prioritise content relevant to course assessment. Case
studies and selected topics may be presented by guest lecturers.
Lecture sessions will be interactive, with students encouraged to ask
questions, share knowledge and experiences. Course materials and
readings will be available online in advance to allow students to be
better prepared to engage the lecturers in discussion during class time.
Tutorials will cover course topics in an interactive format using a
variety of collaborative active learning techniques. In addition to
clarifying details of course content, specific transferrable skills may
be addressed, e.g., essay and report writing, critiquing and oral
presentation.
Four 5-hr practical sessions3 will provide hands-on experience for
students to gain skills required for conducting well-designed coral
reef monitoring and research. Some time will also be assigned during
these sessions for demonstrators and lecturers to guide students on
their research projects.
RESOURCES
Most resources are available myeLearning including
Lecture outlines – including learning objectives, summaries, recommended readings, some presentations
Resources – links to papers, articles and websites
Tutorials – guidelines for tutorial activities and specific supporting resources
Practical exercises – guidelines for practical activities and specific supporting resources (texts, articles,
websites)
 Group project – detailed instructions and supporting websites to guide students in navigating the challenges
of working on a group project. These will include information on working in teams, as well as some literature
on the research topic.
Essential and recommended texts are in the Reserve Section, Alma Jordan Library, or are available via links in
the course outline and myeLearning.




Essential texts
Sheppard, CRC, Davy SK, Pilling GM. 2009. The Biology of Coral Reefs. Oxford University Press. ISBN 978-0-19856636-6
Humaan P & DeLoach N (2002) The Reef Set: Reef Fishes, Reef Creatures and Reef Coral. 2nd Edition. New World
Publications, 1250 p. ISBN:1878348337, ISBN-13:978-1878348333.
Supplementary texts
3
Conditions permitting, there may be a weekend field trip, in which case two practical sessions will be combined into that single trip.
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Rohwer F, Youle M, Vosten D (2010) Coral Reefs in the Microbial Seas. Plaid Press ISBN-10: 0982701209, ISBN13: 978-0982701201.
Useful websites
NOAA s Coral Health and Monitoring Program at http://www.coral.noaa.gov: this website, with its many links
is a good entry point into online information on coral reefs.
ADDITIONAL INFORMATION
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf.
 Refer to the general information and general regulations in the Faculty of Science and Technology
Undergraduate
Booklet
available
from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf.
 Attendance: Students are reminded that they must attend and report satisfactorily on a minimum of 75% of
the practical sessions and tutorials. Failure to do so will result in debarment from the final examination
(Extracts from Examination Regulations for First Degrees, Associate Degree, Diplomas and Certificates,
section II (18) available from http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf).
 Medical and other excuses: Any student who misses a class, test or assignment is advised to consult
immediately in person or by email with the teaching assistant or course coordinator regarding reasons for
their absence and recoup options. Absence must be explained in writing within 7 days of the missed session
by either a written/emailed excuse sent to the TA or course coordinator, and/or a medical certificate
submitted to the Health Service Unit and copied to the secretary, main office, Department of Life Sciences.
The depart e t s op should ha e appe ded to it i for atio o courses affected, course coordinator or
TA responsible for those courses, and course events involved.
 Make-up sessions: As a general principle, medical or other e uses a o l e use a stude t s prese e at
an assigned time. Students must still complete the assigned work (make-up lab report or make-up test) in
order to obtain the marks for that item of course work. The student is responsible for liaising with the course
coordinator or teaching assistant to ensure the assigned make-up exercise is completed. Any student who
was inexcusably absent from a practical or test, or who does not submit a practical report (initial or makeup) will receive 0% for that exercise. Note that a field trip cannot be repeated for a make-up opportunity,
so you should make every effort to attend field trips.
 Late submissions: A penalty at 10% of mark per day late will be applied unless formal approval for late
submission is given by the teaching assistant or course coordinator using the guidelines above for medical or
other excuses.
 Assignment submission: Hard copy reports must be submitted into the labelled deposit box for your
bench/demonstrator in the outer Zoology office, and the student list must be signed. Submissions anywhere
else will not be assessed. Reports will be returned at a time arranged by the TA or demonstrator. We are not
responsible for reports left uncollected or submitted inexcusably late. Soft copy reports or other assignments
must be submitted through myeLearning as directed for each assignment.
 Academic dishonesty: Academic dishonesty, which includes plagiarism and cheating, is an extremely serious
academic offense, and carries penalties varying from failure in an assignment to possible suspension from
the university. Students are hereby informed that plagiarism is forbidden, and all unsupervised coursework
185
items must be accompanied by a completed plagiarism declaration form in order to be assessed. Specific
items may require submission through Turnitin on myeLearning. Refer to the University Regulations on
Plagiarism available from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
 Safety in the laboratory and field: Medical data and emergency contact forms must be completed in the first
laboratory session when safety briefings will be given. Standard laboratory protocols for conduct and dress
code are in effect once you are present in a Life Sciences laboratory (Department of Life Sciences Undergraduate
Student Handbook section 8). The dress code includes mandatory laboratory coats, adequate clothing to
protect the body, and closed shoes. NO sandals, slippers or open-toed shoes will be allowed in the laboratory
or in the field. Marks will be deducted for non-adherence to these protocols.
 Field work: Details are given in section 8 of the Department of Life Sciences Undergraduate Student Handbook
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf. Field trips are specified on the attached course
calendar so you can be adequately prepared. You will not be allowed on the field trip if a medical data form has
not been submitted.
 If you have a disability and have not disclosed the nature of your disability and the support you need, you are
invited to contact the Academic Support/Disabilities Liaison Unit (ASDLU) of The University of the West
Indies, St. Augustine Campus. Phone: 662-2002 extension 83866, 83921, 83923 and 84254; Fax: 662-2002
extension 83922; Email: [email protected] ; http://sta.uwi.edu/asdlu/forms.asp.
HOW TO STUDY FOR THIS COURSE
 Firstly, this is not a course where you can rote-learn factual information at the last minute for a test, or
prepare simplistic essays copied off the Internet for assignments. It requires familiarity with a wide range of
topics, informed discussion of broad, complex issues and application of critical thinking skills.
 You should attend all lectures, tutorials and practical sessions since satisfactory attendance (>75%) is
required by the UWI regulations. Attendance records will be taken at all sessions.
 Students who attend regularly perform better than those who do not. You should attend to obtain the full
alue of the le turer s prese e. Le turers routi el s thesise a d su
arise large a ou ts of i for atio ,
and prioritise, evaluate, discuss and explain this information. They provide the conceptual framework of the
course, which you must then fill in with details and examples through independent study.
 You should prepare before classes so you can clarify any difficult points with the lecturer, or engage in
meaningful discussion of any controversial topics. This will enhance and deepen your understanding as well
as contribute to course assessment in tutorials and practical sessions. This is your opportunity for continuous
assessment to monitor your progress and to accumulate coursework marks incrementally.
 You should review learning outcomes for each topic or activity, and make sure you understand and can
actually achieve those outcomes. If you cannot, please clarify with the lecturer. You must make thorough use
of the resources provided (e.g., textbooks, resouces on myeLearning) from the first week. You should check
into myeLearning frequently to review updated materials, assignments, notices and activities.
 In addition to timetabled contact time, you are expected to devote additional hours of independent study:
reviewing class materials and notes, reading/viewing/using resource materials, completing assignments, and
preparing for assessments. You are strongly encouraged to make your own notes from lectures, textbooks
and other source materials throughout the semester to improve your skills of comprehension, organisation,
planning and writing. Working in study groups is strongly supported for those who learn best this way, as it
shares workloads, builds camaraderie and social skills; however, please do not rote-learn prepared essays,
a d al a s dou le he k the a ura of our olleagues ork.
 You are encouraged to interact regularly with staff, even outside of the assigned class times to ensure
prompt, satisfactory resolution of any problems and to monitor progress. Attendance is mandatory for
186
lectures, tutorials and practical sessions. Prior preparation using online course materials is strongly advised
to be able to fully participate in activities, and obtain the full value of the sessions.
 Thorough use should be made of the resources provided, and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myeLearning on a frequent, regular
basis to review materials, assignments and activities. Some online activities will contribute to your final grade
(see course assessment).
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned
laboratory times, to ensure prompt, satisfactory resolution of any problems, and to monitor progress.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
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COURSE CALENDAR
Wk
Date
Lecture topics
Practical dates and topics
1
M18.1
Introduction – location and importance of coral reefs of the
Caribbean
T19.1
Due
dates
DP
2
W20.1
Coral reef geography – definition of coral reef, reef types and
formation
M25.1
Marginal coral reefs and other coral communities
W27.1
Coral reef taxonomy – main reef-building organisms in the
Caribbean
DP
3
M1.2
T2.2
Coral reef taxonomy – other important coral-reef-associated taxa
DP
4
Taxonomy of coral reef
organisms
W3.2
Coral biology 1 – anatomy and reproduction
M8.2
Coral biology 2 – population ecology of corals (Carnival Monday, no
lecture)
W10.2
Geology of Caribbean coral reefs TS
Practical
1 (2.5%)
TS
5
M15.2
T16.2
Coral biology 3 – nutrition, calcification and growth DP
6
W17.2
Coral reef dynamics – reef-building processes, organisms JAI
M22.2
Coral reef dynamics – carbonate budget
W24.2
Coral reef dynamics – environmental controls on reefs (physical
processes and zonation)
JAI
7
M29.2
Coral reef dynamics – ecological relationships on the reef
(competition, aggression, symbioses)
W2.3
Coral reef dynamics – ecological succession
M7.3
Coral reef dynamics – energy and materials; connectivity and reef
resilience
Coral reef health 1
(methods)
Practical
2 (2.5%)
T1.3
JAI
8
Practical
3 (2.5%)
JAI
W9.3
9
M14.3
Importance of coral reefs – tourism, recreation and ecosystem
services
Importance of coral reefs – biodiversity, fisheries and marine
natural products
JAI
T15.3/S19.3
Coral reef health 2 (field)
W16.3
10
M21.3
JAI
W23.3
Valuation of coral reefs – use values and the total economic value;
option values and non-use values
Practical
4 (2.5%)
Threats to coral reefs – natural disturbances
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Threats to coral reefs – anthropogenic impacts (water pollution and
climate change)
11
M28.3
Threats to coral reefs – reef responses (phase shifts, bleaching and
disease) (Easter Monday, no lecture)
JAI
Coral reef health 3 (data)
W30.3
12
T29.3
M4.4
Protecting coral reefs – assessment and monitoring of coral reef
health and function
Protecting coral reefs – mitigation and management (reef
restoration)
Research
report
(30%)
JAI
W6.4
Protecting coral reefs – mitigation and management (Caribbean
reef management programmes, including MPAs)
T12.4
13
T12.4
Tutorials
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
Course code: BIOL3462
Course Title: THE ECOLOGY OF FRESHWATERS
Credits: 3
Level: 3
Semester: 2
Pre-requisites: Either BIOL1262 Living Organisms I and BIOL1263 Living Organisms II or BIOL1261
Diversity of Organisms OR (BIOL1065 Diversity of Plants and Animals and AGRI1012 Microbiology)
AND (BIOL2XXX Fundamentals of Ecology OR BIOL1462 General Ecology and Biometry).
Anti-requisite: BIOL2062 Freshwater Biology
COURSE DESCRIPTION:
This course provides an overview of characteristics, biodiversity and ecology of freshwater systems, e.g.
rivers, lakes, wetlands, and other low salinity inland aquatic environments. The course will cover the
characteristics and variety of freshwater systems; the diversity, biology and ecology of living organisms
found associated with these systems; the structure and function of freshwater communities and
189
ecosystems; threats to freshwater systems and management strategies to provide sustainable benefits for
ecosystems and human wellbeing.
Students are expected to have a basic foundation in ecology and biodiversity. In addition to providing a
foundation of theoretical knowledge, this course will emphasise practical skills and expose students to
field and laboratory approaches for studying freshwater systems. It is an interactive ‘hands-on’ course
where students are expected to prepare, participate and perform in an active way to engage with the
content in a variety of ways. Assessment is designed to encourage students to work continuously with the
course materials, explore and critically analyse research in this rapidly developing field.
PURPOSE OF THE COURSE/RATIONALE:
This is a core course for the Ecology & Environmental Biology specialisation in the Department of Life
Sciences and is an essential area in environmental sciences, environmental biology and environmental
management. It also broadens the scope of studies in biology, plant biology and zoology.
Freshwater systems are diverse environments that support unique communities of organisms and provide
invaluable ecosystem services for human survival and well-being. At the same time they are heavily
impacted by humans since they integrate all activities on land, in the water and even the atmosphere.
Understanding of these systems is necessary for their effective management.
INSTRUCTOR INFORMATION:
Name of course coordinator:
Mary Alkins-Koo
Office address and phone:
Room 218, Zoology offices, Floor 2, New wing, Natural
Sciences Building
Email address:
[email protected]
Office hours:
Mondays 10-11am, Fridays 11-12am
Preferred method of contact:
Email
Communication policy: Students should use their UWI email account for communication and can expect
a response within 48 hours.
LETTER TO THE STUDENT:
Welcome to ‘The Ecology of Freshwaters’. In this course you will be introduced to freshwater systems
which provide essential water resources and food, they moderate the impact of natural disasters and
provide many other ecosystem services essential for human survival and wellbeing. The course will be
taught in blended mode comprising both face-to-face and online delivery. You are expected to engage
with the materials provided online, in face-to-face lectures and tutorials as well as explore and interact
with these to develop the essential skills of critical thinking (clarity, accuracy, relevance, logic, breadth,
depth, precision, significance, completeness and fairness). Activities will be diverse and you are strongly
encouraged to ask questions, offer new ideas, problem solve and think innovatively to maximise the value
of your learning experience.
Please read the Course Outline carefully and keep the Course Schedule close to hand as it contains all the
activities and assessments during the semester. In particular take note of the policy on plagiarism and
attendance requirements.
190
We are here to ensure your success in this course and at UWI generally and encourage you to come to us
with any academic or other challenges you may face that could affect your attendance and performance.
I look forward to meeting each of you and engaging in productive stimulating discussions over the
coming semester.
Dr Mary Alkins-Koo.
Course Coordinator
CONTENT:
Topics will include:
 Origins and distribution of freshwaters
 Physicochemical characteristics of freshwaters
 Freshwater habitats and biodiversity
 Ecology of running waters
 Ecology of standing waters
 Ecology of freshwater wetlands
 Human interactions with freshwater systems
 Investigating freshwater systems
GOALS/AIMS:
This course aims to
 Introduce students to the characteristics and diversity of freshwater systems
 Develop a student’s competence in the methods and approaches for research in freshwater
systems
 Expand a student's knowledge of the diversity and biology of living organisms by reference to
freshwater organisms in particular
 Review the ecology of a range of freshwater systems stressing general concepts that allow for an
understanding of their biodiversity, community structure and function
 Evaluate the range of benefits derived from these systems, how humans interact with them, and
suggest approaches for managing and living sustainably with such ecosystems.
GENERAL OBJECTIVES:
The general objectives of this course are to
 provide course materials, activities and assessment using both face-to-face and online modalities
 facilitate opportunities for students to engage with general concepts and specific examples to
develop a comprehensive understanding of the nature of freshwater systems and their biodiversity
 guide students in critically analysing and exploring questions in freshwater biology and ecology
using investigative hands-on approaches
 facilitate discussion on the relationship between freshwater systems and human wellbeing and
solutions for ensuring sustainable provision of such benefits
LEARNING OUTCOMES:
At the end of this course students should be able to
191









Give examples of the diversity of freshwater systems, compare them and discuss their
distinguishing characteristics
Describe the physicochemical characteristics of a range of standing and running waters and
discuss and evaluate the factors which determine these physicochemical features
Review and evaluate the methods used for measuring basic physicochemical parameters and
sampling the biota in a range of freshwater systems in a variety of contexts
Give examples of the major groups of freshwater flora and fauna and describe their biology
(classification, distinguishing features) and ecology (habitats, adaptations, interactions)
Discuss the factors that determine the distribution and abundance of freshwater biota in standing
and running waters
Discuss the physicochemical and biotic factors that influence the structure and function of
freshwater communities
Review concepts and hypotheses accounting for the structure of ecological communities in
standing and running waters and their functioning in terms of transfer of energy and nutrients
List the values of freshwater systems, describe the range of human uses of these systems, and
discuss human impacts on freshwater environments, communities and ecosystems
Propose general approaches for management of these systems based on a scientific understanding
of these systems.
COURSE ASSESSMENT:
Assessment will be based on a student’s final mark from the coursework components below.
Description
Component
%
Final
Grade
Final exam
Coursework
50%
50%
2-hour written exam with 5 essay questions
Broken down as follows:
2 tests (each 10%) based on multiple choice, true/false, short
response questions or essay
Performance in face-to-face and online discussions and
activities
Performance and reporting of 4 practical exercises
In-course tests
Tutorials, online
activities
Practicals
20%
10%
20%
ASSIGNMENTS:
 2 coursework tests (20%): 2 tests (each 10%) each 50 minutes duration including multiple choice,
true/false, short response questions
 Tutorials, online activities (10%): Continuous evaluation of participation and performance and
contributions throughout the semester (discussions, wiki/ glossary, blogs)
 Practicals (20%): Practical performance and reporting of 4 practical exercises during the semester
EVALUATION:
192




Feedback on the course will be obtained informally from students on an ongoing basis by regular
interactions and meetings among students, demonstrators, teaching assistants and the Course
Coordinator in practicals and tutorials.
Formal feedback will be via election of Class Representatives who sit on the Departmental StudentStaff Liaison Committee meetings held twice during the semester. Class reps will channel both
concerns and commendations to the meeting as guided by the Department’s Standard Operating
Procedures.
Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation
questionnaire administered anonymously and confidentially at the end of the semester.
All feedback will be considered on an ongoing basis and corrective action or adjustments made or
discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Contact hours: 36 h
Lectures: 22 h
Tutorials: 6 h
Practicals: 8 h (4 x4 h = 16h practicals)




Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of available
information, update current issues and events, and prioritise content relevant to course assessment.
Practicals: Fortnightly practicals will provide hands on experience for students to gain skills required
for conducting well designed field and laboratory sampling and experiments in a variety of situations;
to problem solve and trouble shoot in real-life situations; and gain a better appreciation of the
environment and the organisms of freshwater systems. Participation and performance in the practicals
will be assessed as well as reports based on the practical activities.
Tutorials: Tutorials will cover course topics in a highly interactive format using a variety of
collaborative active learning techniques. In addition to clarifying details of course content, specific
transferrable skills will be addressed e.g. essay and report writing, critiquing and oral presentation.
myelearning: The online teaching tool, myeLearning, will be used extensively during this course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course
results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
 self-test quizzes, questionnaires, surveys
 interactive activities such as discussions, wikis, glossaries, blogs
RESOURCES:
Most resources are available myeLearning including
 Lecture presentations including learning objectives, summaries, recommended readings and links
to papers, articles and websites with interactive resources and videos for those who prefer to learn
using these modalities
 ‘General Resources’ provides direct links to general websites, articles and publications relevant to
the whole course
 Tutorials may have specific supporting resources particularly on skills development
193
Essential and Recommended texts are in the Reserve Section, UWI Main Library or via links in the
course outline and myelearning
Readings:
Moss, B. 2010. Ecology of freshwaters: a view for the twenty-first century. Hoboken, NJ: WileyBlackwell. QH541.5.F7 M67 2010
Closs, G., B. Downes, & A. Boulton. 2004. Freshwater Ecology: A scientific introduction. Malden, MA:
Blackwell Pub. QH541.5 F7 C66 2004
Lampert, W. & U. Sommer. 2007. Limnoecology: The ecology of lakes and streams. New York: Oxford
University Press. QH96.57.A1 L3513 2007
Web links:
Water on the Web http://www.waterontheweb.org/
COURSE CALENDAR:
WEEK
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
PRACTICALS
TUTORIALS
LECTURES
50. Course Introduction
51. Origins and distribution of
freshwaters
52. Physicochemical parameters
53. Physicochemical parameters
54. Freshwater habitats and biota
55. Diversity and scale in running
waters
Tutorial 1
Practical 1:
Investigating
freshwaters
56.
57.
58.
59.
Conditions and microdistribution
Longitudinal patterns in rivers
River ecosystems
River Continuum Concept
Tutorial 2
60.
61.
62.
63.
Floodplain Rivers
Flood-Pulse Concept
Diversity of standing waters
Stratification and mixing
Tutorial 3
64.
65.
66.
67.
Lake communities
Lake ecosystems
Tropical lakes
Freshwater wetlands
Tutorial 4
68. Temporary waters
69. River regulation
70. Watershed processes &
management
71. Pollution
72. Freshwater ecosystems and human
well being
Assignments
Practical 2: River
ecology
In-course Test 1
Practical 3: Pond
ecology
Online activity
Practical 4: Data
analysis & report
writing
Tutorial 5
Tutorial 6
In-course Test 2
194
26.
73. Revision/review
ADDITIONAL INFORMATION:
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment,
student conduct, essential skills, and support at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
 As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to
obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
 Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items
must be accompanied by a Coursework Accountability Statement in order to be assessed. Specific
items may require submission through Turnitin on myeLearning. Refer to ‘University Regulations on
Plagiarism’ available from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to
able to fully participate in activities and obtain the full value of the sessions.
 Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress
and materials are also highly recommended and you should be checking into myelearning on a
frequent regular basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned
tutorial times to ensure prompt, satisfactory solution of any problems and to monitor progress.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
195
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
MAK: 18 February 2013
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
Course code: BIOL3465
COURSE TITLE: Tropical Forest Ecology and Use
Credits: 3
Level: 3
Semester: II
Pre-requisites: Either BIOL2XXX Biostatistics and BIOL2XXX Fundamentals of Ecology or BIOL1462
General Ecology and Biometry
Anti-requisite: BIOL3464 -Tropical Forestry Ecology and Management
COURSE DESCRIPTION:
This course is designed to expose students to the tropical forest ecology and how it influences the human
use of tropical forests such as timber production and conservation. The course is organised into background
196
lectures and tutorials covering general and specific concepts in tropical forest ecology and management. In
tutorials students are expected to prepare, participate and perform in an active way in order to engage with
the content. Assessment will be based largely on in course tests and a final theory exam.
PURPOSE OF THE COURSE/RATIONALE:
This is a core course for the Environmental Biology minor in Life Sciences that will provide fundamental
knowledge and concepts in tropical forest ecology that students can apply in most areas they may encounter
in Environmental Biology. At the end of the course the students will be able to understand the issues in
management of tropical forest ecosystems and how they respond to human manipulation.
INSTRUCTOR INFORMATION:
This course will be taught by a team of lecturers, Teaching Assistants and demonstrators. Office hours are
posted on Departmental notice boards and the main Life Sciences office.
Name of course coordinator: Mike Oatham
Office address and phone: Rm 222, Old Wing, Natural Sciences Building (ext 83088)
Email address: [email protected]
Office hours:
Preferred method of contact: Email
Communication policy: Students should use their UWI email account for communication and can expect
a response within 48 hours.
LETTER TO THE STUDENT:
Welcome to ‘Tropical Forest Ecology and Use’. In this course you will be challenged to develop the
fundamental knowledge, skills and attitudes of a practising tropical forest ecologist or forester. This is a
theory course that will require commitment and participation on your part to successfully engage in the
content and to develop the essentials skills of critical thinking (clarity, accuracy, relevance, logic, breadth,
depth, precision, significance, completeness and fairness). You are strongly encouraged to ask questions,
offer new ideas, problem solve and think innovatively to maximise the value of your learning experience.
In addition, teamwork, organisation and time management will be necessary personal attributes to bring to
the course.
CONTENT:
Topics will include
 The characteristics of tropical biomes and tropical forests.
 Nutrients and tropical forests.
 Regulation of biodiversity in tropical forests.
 Succession and regeneration in tropical forests.
 Disturbance in tropical forests.
 History of forestry in the wet tropics.
 Abiotic and biotic problems of tropical forestry.
 Tropical forestry and the goal of sustainable yield.
 Plantation forestry in the wet tropics.
 The social dimension of tropical forestry.
 The future for tropical forest management.
General transferable skills
197

Oral and written communication; manipulation, observation and record-keeping; working with
technology, information and numbers; managing time, people and projects; problem identification
and solving; effective thinking, learning and research; innovation, design and evaluation.
 Evaluating, managing and communicating information in tropical forest ecology
 Reporting ethics including plagiarism
 Managing, analysing and presenting data
GOALS/AIMS:
This course aims to
 build a range of competencies in transferrable skills as applied to Tropical Forest Ecology
 expose students to the general concepts and knowledge used for understanding Tropical Forest
Ecology
 introduce specialist analytical skills needed to manage tropical forests
GENERAL OBJECTIVES:
The general objectives of this course are to
 provide opportunities to develop transferrable skills within a specific context
 provide fundamental preparation and training in general practical and research skills
 introduce specialist practical and research skills and approaches
 inculcate a culture of quality and responsibility in conducting research
 enhance students’ capacity to work effectively in real life situations
LEARNING OUTCOMES:
At the end of this course students should be able to
 Describe the major ecological processes shaping tropical forests.
 Describe the uses of tropical forests, the conflicts and synergies in these uses and will understand
the ecological effects of the different uses and their conflicts.
 Describe how the formulation of forest management regimes can cater to different uses particularly
timber production.
 Describe how local and international economic pressures are bought to bear on forest management
in the tropics.
 Effectively find, evaluate and manage published information from a variety of sources.
 Use spreadsheet, word processing and presentation software to carry out tasks related to critically
assessing and synthesizing reports from the scientific literature.
 Review basic ethical principles for appropriate scientific conduct
 Function effectively in real life situations by integrating knowledge, skills and attitudes with
innovation and problem-solving approaches
COURSE ASSESSMENT:
Assessment will be based on a student’s final mark from the coursework components below.
Component
% Final Grade
In-course tests/ quizzes
Practical Reports
Final Theory Exam
100% broken down as follows:
30%
30%
40%
ASSIGNMENTS:
198
Topic Quizzes (30%) made up of:
10 Topic Quizzes (3% each) each week during the semester from week 2 to week 11
Practical Reports (30%) made up of:
Skills Test (week 2) (5%); 5 Practical Reports (5% each) due in weeks 5, 7, 9, 11 & 13
EVALUATION:
 Feedback will be obtained informally from students on an ongoing basis by regular interactions and
meetings among students, demonstrators, teaching assistants and the Course Coordinator in practicals
and tutorials.
 Formal feedback will be via election of Class Representatives who sit on the Departmental StudentStaff Liaison Committee meetings held twice during the semester. Class reps will channel both
concerns and commendations to the meeting as guided by the Department’s Standard Operating
Procedures.
 Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an ongoing basis and corrective action or adjustments made or
discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Delivery: contact hours (39 credit hours):
Lectures/Tutorials: 24 h (24 credit hours)
Practical work: 30 h (15 credit hours)
 Lectures and tutorials will provide introduction to specific topics and allow for discussion in an
interactive setting
 Practicals will provide hands-on training in general approaches and specific techniques in the form of
laboratory sessions or field trips
RESOURCES:
Lectures and Tutorials
 Lecture room with internet connection and multi-media projector
Practicals
 Transport to field sites for practical work
 Field equipment such as 50m tapes, 1m dress-maker’s tapes, compasses, binoculars and first aid kits
COURSE CALENDAR:
Week Topic
1
Lectures/Tutorials
Global Distribution of 

Tropical Forests
Climate and altitude
Other
Tropical
Ecosystems
199
Practicals
Assignments
Week Topic
Lectures/Tutorials
2
Local Distribution of 

Tropical Forests
Soils
Fire
3
Changes in Tropical 
Forest Distribution

4
Physiognomy
and 
Floristics of Tropical

Forests
5
Competition in Tropical 
Forest Ecosystems
Tropical ecosystems
through time
Global climate change
and tropical forests
Structure of tropical
forest ecosystems
Floristics of tropical
forest ecosystems
Life history strategies
of tropical rainforest
plants
Tropical
Forest
Dynamics
Herbivory
and
Predation
Mutualisms
and
Commensal
Reasons for diversity
in tropical forests
Monodominance in
tropical rainforests. A
Trinidad example
Loss and degradation
of tropical forests
Importance of tropical
forests to human
society
History of tropical
forest management
Basic
silviculture
terms and practices
Replacement
and
clearing systems of
timber production
Natural regeneration
and
restoration
systems of timber
production
Biodiversity
conservation
in
production forests
Sustainable
forest
management in the
Victoria-Mayaro
Forest Reserve

6
Other Biotic Interactions 
in Tropical Forests

7
Biodiversity levels and 
Maintenance

8
Tropical Forests in the 
Anthropocene

9
History of Tropical 
Forest Management

10
Timber
Systems
Production 

11
Timber Production and 
Biodiversity
Conservation

Practicals
Assignments
Field Skills for Practical
Skills
Tropical
Forest Test
Ecology
Topic Quiz 1
200
Topic Quiz 2
Biotic and Abiotic Topic Quiz 3
Characteristics of
Tropical Forest
Topic Quiz 4
Practical Report 1
Structure
of Topic Quiz 5
tropical
forest
ecosystems
Topic Quiz 6
Practical Report 2
Loss of tropical Topic Quiz 7
forests?
Topic Quiz 8
Practical Report 3
Plantation
natural
structure
diversity
and Topic Quiz 9
forest
and
Topic Quiz 10
Practical Report 4
Week Topic
12
Lectures/Tutorials
Other Tropical Forest 
Services

Practicals
Assignments
Carbon Sequestration Carbon
and REDD
sequestration
in
Watershed protection tropical forests
13
Practical Report 5
ADDITIONAL INFORMATION:
 Please refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/fsa/documents/UGFacultyBooklet.pdf .
 Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
 As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to
obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
 Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must
be accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may
require submission through Turnitin on myeLearning.
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals.
 Full use should be made of the resources provided and students are strongly advised to become familiar
with them and start utilising them from the first week.
 Students are encouraged to interact regularly with their lecturer on their projects, even outside of the
assigned tutorial times to ensure satisfactory solution of any problems and to monitor progress.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
201
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
TITLE:
BIOL 3466- Coastal Ecosystems and Resource Management
CREDITS:
3
LEVEL:
Undergraduate -Year III
SEMESTER: II
PRE-REQUISITES: BIOL 3XXX Marine Ecology & Oceanography
ANTI-REQUISITE: BIOL3461 Coastal Ecosystem Management
OFFERING DEPARTMENT:
Department of Life Sciences, Faculty of Science and Agriculture, The University of the West
Indies, St. Augustine.
COURSE COVERAGE:
This course will provide students with an understanding of the characteristics of the major coastal ecosystems
of the Caribbean and adjacent regions. It emphasises the ecological processes that determine resource values
and functions and highlights the reasons for habitat and resource degradation. The course examines the
principles and practices of coastal ecosystem management and reviews the major coastal management
initiatives in the region.
The course also includes field surveys which cover many of the issues covered in the lectures.
202
PURPOSE OF THE COURSE /RATIONALE:
This course will provide students with an understanding of the characteristics of the major coastal ecosystems
of the Caribbean and adjacent regions. It emphasises the ecological processes that determine resource values
and functions and highlights the reasons for habitat and resource degradation. The course examines the
principles and practices of coastal ecosystem management and reviews the major coastal management
initiatives in the region.
The course also includes field surveys which cover many of the issues covered in the lectures.
Students are introduced to ecosystems as resources and some basic management principles are also
introduced. For each ecosystems- the goods, services and attributes are described. Students are
exposed to a number of management tools and applications using relevant Caribbean examples.
INSTRUCTOR’S INFORMATION
Dr. Judith Gobin (Coordinator)
Room 222, Natural Sciences Building, UWI- Life Sciences
Phone: 868-662-2002 Extn. 82046; Fax: 868-663-5241
Email: [email protected]
Preferred contact – By Email
Office-Contact hours (Coordinator)
Day
Monday
Tuesday
Wednesday
Thursday
Friday
Time
10.00 am to 4.00 pm
10.00 am to 4.00 pm
10 .00 am to 4.00 pm
10.00am to 12.00am
LETTER TO THE STUDENT
Dear Students,
I would like to extent a very warm welcome to you as we get prepared for the start of BIOL 3461 –
Coastal Ecosystems Management. I am Dr Judith Gobin, your Course Coordinator. This course is
fully supported through myelearning, which we update regularly. Please feel free to contact me
(course teacher)or your TA/demonstrator for any academic help and assistance. Please know that we
are here to support your learning and success as a student in FSA.
This course is designed to provide you with an understanding of a number of coastal resources and
their significance in terms of their resource values. Another goal of the course is to teach students
203
how to critically assess environmental problems and how to devise appropriate management
strategies.
A few points to note:
The Course Schedule (dates/activities) is available on the course page and should be downloaded for
your reference and continued guidance, as soon as you have access.
Please take the time to read the policy on plagiarism.
Once again, I would like to take this opportunity to welcome you and look forward to some healthy
interactions over the course of the next semester. So, let’s get your feet wet!
Your Course Coordinator
Dr Judith Gobin.
CONTENT
This course introduces students to a number of coastal ecosystems and their associated resources. We begin
with Mangroves, Coral Reefs, the sea and sandy beaches. We then look at impacts of a variety of activities on
the ecosystems and their resources. We also evaluate the best management strategy or option which may be
applied to sustain the resource values.
COURSE GOALS:
This course aims to:




Provide students with an understanding of the characteristics of the major coastal ecosystems of the
Caribbean and adjacent regions.
Re-emphasise the ecological processes that determine resource values and functions and highlights the
reasons for habitat and resource degradation.
Examine the principles and practices of coastal ecosystem management and reviews the major coastal
management initiatives in the region.
Include field surveys which cover many of the issues covered in the lectures. The emphasis throughout the
course will be on Caribbean coastal ecosystems, especially those of Trinidad & Tobago.
COURSE OBJECTIVES:
Upon successful completion of this course, the student will be able to appreciate and understand as well as have
gained practical experience under the following headings:
 Coastal Resources: - this by examination of the natural resources associated with beaches, wetlands,
estuaries, harbours and other shoreline features.

Development Impacts and Pollution Ecology: - this by examination of the kinds of development
impacts and pollution affecting coastal ecosystems, especially organic, oil, pesticide, heavy-metal,
physical and thermal pollution, their sources, effects and remedies.

Coastal zone and Resource Management: - this by Coastal surveys, environmental monitoring,
water quality criteria, zoning, legislation and enforcement.
204

Resource Use, Protection and Conservation: - this by Coastal zone use, protection and conservation.
Their purposes, criteria, development and management.
LEARNING OUTCOMES:
At the end of this course students will be able to:
Skill outcomes:
 Interpret coastal and marine/environmental data from the field.
 Analyze and interpret field data using appropriate coastal zone management tools eg. baseline
surveys, environmental impact assessments, management plans etc..
 Actively seek and assimilate information from texts, assigned articles and reference texts.
Dispositional outcomes:
 Describe he relevance and importance of the need for management of coastal zones and associated
ecosystems .
 Ask questions or seek help from the instructors when material is difficult or confusing.
ASSIGNMENT
Students will have to submit a written report for each of six practical exercises. These are designed to
relate to all of the major topics that are covered in the lectures.
Students will also have two in-course tests, each covering specific areas of the course. These are
designed to determine if the students can correctly recall all that was covered in the previous weeks
of the course. The 1st is an 1 Essay question and the 2nd is a multiple-choice question exam.
COURSE ASSESSMENT
Incourse assessments consist of both theory and practical components, and together make up the 40%
incourse marks. A student missing an incourse examination because of an illness or legitimate
emergency will be allowed to do a makeup examination the date of which will be advertised and shall
be within 7 days of the first test. In such a circumstance, the student should make every reasonable
attempt to contact the instructors as soon as possible. While make-up exams will cover the same
content area as a missed exam, the exam format and specific questions may be different. There shall
be no makeup labs, students missing a practical exercise must submit a valid medical within 7 days
of the practical. Students must attend 75% of their practicals. Failure to do so may result in the student
being debarred from the final examination (Examination regulations Section II part 19
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf).
If you do have a disability and have not disclosed the nature of your disability and the support you
need, you are invited to contact the Academic Support/Disabilities Liaison Unit (ASDLU) of The
University of the West Indies (UWI), St. Augustine Campus.
Phone: 662-2002 extension 83866, 83921, 83923 and 84254
Fax: 662-2002 extension 83922
Email: [email protected]
http://sta.uwi.edu/asdlu/forms.asp
Academic Dishonesty:
205
Academic dishonesty, which includes plagiarism and cheating, is an extremely serious academic
offense and carries penalties varying from failure in an assignment to possible suspension from the
University. http://sta.uwi.edu/fsa/lifesciences/accountability.pdf (Department of Life Sciences
Handbook)
ASSESSMENT
Students would be assessed on both their practical and theoretical knowledge of the topics.
Component
% Final Grade
Description
Final exam
50%
2-hour written exam to
answer 2 essay questions
In-course tests
20%
2 tests (each 10%) . The 1st- a
Research Essay and the 2nd- a
multiple choice, true/false,
short response question paper.
Tutorials, online
10%
Performance in interactive
discussions and activities
face-to-face and online
20%
Performance and reporting of
5 practical exercises
activities
Practicals
ASSIGNMENTS:
Students will also have two in-course tests, each covering specific areas of the course. These are designed to
determine if the students can correctly recall all that was covered in the previous weeks of the course. The 1st
is an 1 Essay question and the 2nd is a multiple-choice question exam. (together total 20%)
Students will have to submit a written report for each of four practical exercises. These are designed to relate
to all of the major topics that are covered in the lectures. The practical assessment will consist of four (5hr)
Laboratory exercises plus 2 Journals associated with the Labs. Together these account for 20% of the final
grade.
Practical write-ups are handed in at the end of each lab. (6.00pm)
Journals are handed in 1 week after the Field trip. (4.00pm)
EVALUATION:
At the onset- students are asked to pop in to see the Course Co-ordinator or to make an appointment- to
address any problems they may be having.
206
Dr. Gobin has an open-door policy (once on-campus and available).
Chosen Class Representatives will attend meetings with the staff/student Liaison Committee, and give their
feedbacks/comments on the course to the committee.
Class Reps. are advised to address issues to me directly as soon as possible since there are only 2 meetings of
this Committee per semester. This means issues may get delayed in being addressed.
The UWI/IDU course evaluation forms at the end of the semester will be used to address and improve on the
specific comments/feedback as best as possibly.
TEACHING STRATEGIES:
Course objectives will be achieved through the aid of the following learning activities:
1.
Assigned readings
9.
Class lecture and videos
10.
Web page resources including published scientific papers
11.
Practical exercises
The material presented in all modes of instruction will be sufficient in content to allow students to have a good
understanding of the topics. Class lectures will help to focus the student to some of the more important details
of each topic. Assigned readings will serve supplement lectures. These include lectures notes, web based
materials and original research papers on topics covered during lectures. We would also request that
students post links to interesting articles for discussion in the forums in the course page.
Contact hours (39 credit hours):
Lectures: 23 h
Tutorials: 6 h
Practicals: 10 h (4 x 5hr = 20h practicals)
RESOURCES
Text books:
Internet resources (as recommended bu the Co-ordinator)
Designated readings: Lectures, powerpoints and an e-text are on my-elearning)
OTHER RESOURCES:
My-elearning (through my.uwi.edu) will be the main online resource.
Discussion topics will be placed online for class comments.
There is also a Facebook page- UWI Coastal Ecosystems.
READINGS
Instructors will periodically upload in my-elearning important research articles, review papers, book
chapters and other related study materials.
Students are expected to consult prescribed text books for relevant chapters for complete details and
for preparation for examinations
Students are expected to download those files or visit the suggested websites or read relevant book
chapters/journal articles before they come for the following class. These were considered and included
as portions of the syllabus and covered fully during examinations.
207
ADDITIONAL INFORMATION
Additional information posted in the Department of Life Science hand book may be consulted for
additional details regarding,
Role of Lectures, Tutorials and Practical’s,
Attendance,
Online Teaching Resources,
General safety guidelines in Lab and
General Safety Practices
Accident and incident reporting forms.
HOW TO STUDY FOR THIS COURSE
Understanding biological science involves understanding many difficult concepts and vocabulary, not just
knowing facts. The student should know that the details to these concepts are important. While the student
will have lecture outlines, they can only succeed in this class by making careful lecture notes and reading
the corresponding material in the textbook before and after the lecture. The student should carefully review
these lecture notes as often as possible. In addition, the students’ study activities should include: reviewing
all of the internet resource materials provided, and making flashcards for some topics. The student should
use these card for self-testing as often as possible.
Students are recommended to establish study groups and study together. The students in these groups may
test each other's knowledge and understanding of the information. They may also take turns teaching each
other. Within these groups, students should attempt past paper questions and can also submit these to the
lecturers for comments.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
208
0-39
F3
Poor
0
BIOL 3XXX Management of Coastal Ecosystems
WEEK
LECTURES
1
Introduction to Coasts
and Caribbean Coastal
Ecosystems
Beach
structure and processes
Beaches,
Strand
Communities
&
Resources
2
Coral
Reefs
and
Resources/ Mangrove
Area Resources
Mangrove-Coral ReefSeagrass interactions
Tutorial
Coastal Development
and Impacts
Impacts of development
on Corals, Mangroves
and Seagrasses.
3
4
5
6
7
8
PRACTICALS
Assignments
Field trip
Location: Port of Spain,
North- west peninsula
and North coast
(JGobin)
Concept & Nature of
Coastal
Pollution.
Causes & Impacts of Oil
Pollution(AM)
Environmental
Field trip
Standards & Toxicity Location: North east
Coast (Saturday)
Testing
Oil Residue Control in
Trinidad Waters
Tutorial
Environmental Impact
Assessments
Legal Provisions for
Coastal Management
Resource Management Laboratory excercises
Options & Practices
Resource Inventories
and Mapping, Data
Collection and Analyses
Tutorial
Management Responses
to Climate Change and
Sea
Level
Rise,
Hurricanes etc.
209
Test 1
9
Management Responses
to over-exploitation
Coastal
Zone Laboratory excercises
management
and
conservation
Tutorial
10
Coastal Protected Areas
and Marine Parks
11
Public Participation and
Coastal Zone
Management
12
13
.
Tutorial
Tutorial
Test 2
JGobin 2013-02-15
210
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE: BIOL 3468
COURSE TITLE: Biodiversity and Conservation
NO. OF CREDITS: 3
LEVEL: 3
PRE-REQUISITE(S): BIOL2XXX Fundamentals of Ecology and either BIOL2XXX Biostatistics
OR ESST2XXX Environmental Statistics OR BIOL1462 General Ecology and Biometry.
ANTI-REQUISITES: BIOL3062 Conservation Biology
COURSE DESCRIPTION: This course introduces students to one of the most important issues facing
biologists and society at large today and in the coming decades: the enormous loss of biological diversity
that accompanies the expansion of human populations. The objectives of this course are to provide students
with an understanding of biodiversity, the threats to it and methods for preventing its loss. The perspective
will be primarily biological, but social and economic aspects will be covered also. Because of the
complexity of the issues involved, the course tries to foster interdisciplinary thinking and problem solving.
This interdisciplinary approach to biodiversity problems is called Conservation Biology. Teaching for he
course will be approached in a “hybrid online” manner with lectures presented online with recorded video
and audio and the lecture contact periods given over to a mix of exercises such as debates, quizzes, roleplaying and question and answer sessions. Practical exercises involving field work, literature review and
synthesis work and computer simulation/exercises will also be applied to gain more practical skills.
COURSE RATIONALE: This is a core course for the Environmental Biology minor in Life Sciences
that will provide fundamental knowledge and concepts in conservation of biodiversity that students can
apply in most areas they may encounter in Environmental Biology. At the end of the course the students
will be able to understand the issues in management of tropical biodiversity and how they respond to human
manipulation.
INSTRUCTOR INFORMATION: This course will be taught by a team of lecturers, Teaching
Assistants and demonstrators. Office hours are posted on Departmental notice boards and the main Life
Sciences office.
Name of instructor(s): Mike Oatham (Coordinator)
Office address and phone: Rm 222, Old Wing, Natural Sciences Building (ext 83088)
211
Email address: [email protected]
Office hours:
Preferred method of contact: Email
Communication policy: Students should use their UWI email account for communication and can expect a
response within 48 hours.
CONTENT
Topics will include:
 Types and distribution of biodiversity;
 Loss of biodiversity and its consequences;
 Endangered species;
 Population viability analysis and monitoring.
 Conservation practices for protected areas, biosphere reserves,
 Restoration ecology;
 Ex situ conservation strategies and population genetic considerations;
 Establishing new populations by translocation and reintroduction;
 Legal and institutional aspects:
 Land tenure systems and species and habitat protection;
 National conservation legislation;
 Conservation authorities and organizations;
 International programmes; international conservation treaties and conventions;
 Conservation education.
General transferable skills
 Oral and written communication; manipulation, observation and record-keeping; working with
technology, information and numbers; managing time, people and projects; problem identification
and solving; effective thinking, learning and research; innovation, design and evaluation.
 Evaluating, managing and communicating information in tropical forest ecology
 Reporting ethics including plagiarism
 Managing, analysing and presenting data
GOALS/AIMS
The goals of this course are to
 describe what biodiversity is and where biodiversity is located globally and locally
 examine the reasons why biodiversity needs to be conserved
 expose students to the currently accepted approaches to conserving biological diversity
 provide opportunities to develop transferrable skills within a specific context
 provide fundamental preparation and training in general practical and research skills
 introduce specialist practical and research skills and approaches
 inculcate a culture of quality and responsibility in conducting research
 enhance students’ capacity to work effectively in real life situations
212
LEARNING OUTCOMES
At the end of this course students should be able to:
 Describe the different levels of biodiversity and its global distribution.
 Describe where Trinidad and Tobago fits into the global biodiversity context.
 Assess how biological diversity is being lost around the world, how we know this is happening and
which species and ecosystems are most vulnerable to extinction.
 Explain how describing the population dynamics of a species is critical to understanding if a species
is in danger of extinction and how this knowledge will allow effective conservation actions to be
developed for the species.
 Explain how in-situ conservation through protected areas is planned and executed.
 Describe what restoration ecology is and what attempts at restoration ecology have been made in
Trinidad and Tobago
 Explain the basic principles of conservation genetics and how they are important to conservation
of biodiversity
 Evaluate the legal and institutional measures put in place in Trinidad and Tobago for the
conservation of biodiversity and the effectiveness of these measures in the current social and
economic context
 Effectively find, evaluate and manage published information from a variety of sources.
 Use spreadsheet, word processing and presentation software to carry out tasks related to critically
assessing and synthesizing reports from the scientific literature.
 Review basic ethical principles for appropriate scientific conduct
 Function effectively in real life situations by integrating knowledge, skills and attitudes with
innovation and problem-solving approaches
ASSIGNMENTS
Topic Quizzes (30%) made up of:
10 Topic Quizzes (3% each) each week during the semester from week 2 to week 11
Practical Reports (30%) made up of:
4 Practical Reports (16%- 4% each) due in weeks 2, 5, 10, & 12
Conservation Video Group Project (14%) made up of:
Concept of Video Project and Seminar (4%)
Final Conservation Video Production (10%)
COURSE ASSESSMENT
Assess e t ill e ased o a stude t s fi al ark from the coursework components below.
Component
% Final Grade
100% broken down as follows:
In-course tests/ quizzes
30%
Practical Reports
16%
Conservation Video Production 14%
213
Final Theory Exam
40%
EVALUATION




Feedback will be obtained informally from students on an ongoing basis by regular interactions and
meetings among students, demonstrators, teaching assistants and the Course Coordinator in practicals
and tutorials.
Formal feedback will be via election of Class Representatives who sit on the Departmental StudentStaff Liaison Committee meetings held twice during the semester. Class reps will channel both
concerns and commendations to the meeting as guided by the Department’s Standard Operating
Procedures.
Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
All feedback will be considered on an ongoing basis and corrective action or adjustments made or
discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES
Delivery: credits: 3 as follows
Lectures/Tutorials: 24 h (2 credits)
Practical work: 24 h (1 credit)
 Lectures and tutorials will provide introduction to specific topics and allow for discussion in an
interactive setting
 Practicals will provide hands-on training in general approaches and specific techniques in the form of
laboratory sessions or field trips
RESOURCES*
Lectures and Tutorials
 Lecture room with internet connection and multi-media projector
 myeLearning page
Practicals
 Transport to field sites for practical work
 Field equipment such as 50m tapes, 1m dress-maker’s tapes, compasses, binoculars and first aid kits
READINGS
Required:
Primack R.B. 2010. Essentials of conservation biology. 5th Ed. Sinauer Associates, Sunderland, MA.
585pp.
Supplementary:
Meffe, G. K., and C. R. Carroll. 1997. Principles of Conservation Biology. 2nd ed. Sinauer Associates,
Sunderland, MA. 673 pp.
214
COURSE CALENDAR*
Topic
Lectures
Practicals
Assignments
Week 1.
Why should we care 
about Conservation of
Biodiversity?

Introduction
to Measurement and Representation
Conservation Biology of Diversity: Ground flora of
Conservation
Values Tropical Forest.
and Ethics
Week 2.
What is Biodiversity 
and Why do we have
it?

Biodiversity. What is
Biodiversity?
Biodiversity: Processes.
Why so many Species?
Practical Report 1.
Topic Quiz 1
Week 3.
Extinctions


Biological Conservation Video
Extinctions
Productions. Presentation of
Vulnerability to
Extinction and the Evil Concepts
Trinity
Video Production
Concept Seminars
Topic Quiz 2
Week 4.
Biodiversity Loss:
Landscape scale
processes

Topic Quiz 3
Population Genetics

Species Demography
and Meta-populations
Fragmentation and
Biodiversity
Conservation
Conservation Genetics
Introduction to
worksheets.
Population Genetics
Genetics of Small
Populations
Problems of conserving
small populations
In situ and ex situ
methods
Week 5.


Week 6.
Endangered Species
Conservation


Week 7.
Determining

Conservation Actions

Week 8.
Restoration Ecology


Week 9.
Protected Areas for
Conservation of
Biodiversity


Topic Quiz 4
Practical Report (Cons.
Genetics) 2.
Topic Quiz 5
Biological Conservation Video Topic Quiz 6
Conservation Triage:
Defining conservation Productions. Work on Videos
priorities
Population Viability
Analysis and Species
Recovery Planning
Topic Quiz 7
Restoration Ecology.
Techniques
Restoration Ecology.
Objectives
Protected Areas.
Topic Quiz 8
Designing and
Establishing Protected
Areas
Managing Protected
Areas
215
Topic
Lectures
Week 10. Conservation of
Biodiversity and
Human Society

Week 11. Conservation of
Biodiversity at a
National Level



Week 12. National and Regional 
Conservation of
Biodiversity

Practicals
Assignments
Resource Use by Local
Communities
Economics of
Biological Conservation
Topic Quiz 9
Practical Report 3.
Role of Institutions and Attitudes to Conservation:
Campus Survey
Policymaking in
Conservation
Environmental Law
Topic Quiz 10
Biodiversity of Trinidad
and Tobago and its
Conservation
Caribbean Conservation
Practical Report 4
Week 13.
Biological Conservation
Video Productions
ADDITIONAL INFORMATION





Please refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/fsa/documents/UGFacultyBooklet.pdf .
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to
obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must
be accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may
require submission through Turnitin on myeLearning.
HOW TO STUDY FOR THIS COURSE



Attendance is mandatory for lectures, tutorials and practicals.
Full use should be made of the resources provided and students are strongly advised to become familiar
with them and start utilising them from the first week.
Students are encouraged to interact regularly with their lecturer on their projects, even outside of the
assigned tutorial times to ensure satisfactory solution of any problems and to monitor progress.
216
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
217
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
Course code: BIOL3768
Course Title: Plant Diversity and Systematics
Credits: 3
Level: 3
Semester: 2
Pre-requisites: BIOL1262 Living Organisms 1 or BIOL1261 Diversity of Organisms and either
BIOL2XXX Physiology of Plants or BIOL2761 Plant Physiology
COURSE DESCRIPTION:
This course provides an overview of plant diversity and systematics and explores the origin and
diversity of vascular land plants emphasizing flowering plants in the flora of Trinidad and Tobago.
The course covers taxonomy (identification, nomenclature, and classification), diversity,
morphology and evolution of vascular plant groups, as well as phylogenetics (phenetics, cladistics,
morphology and molecules). Practicals focus on skills and activities necessary for indentifying
vascular plants in Trinidad and Tobago and the tools necessary for the understanding of the study
of systematics. The course would be taught using interactive lectures, tutorials and hands on
practical sessions. Assessment would consist of a final written examination and in course, online
and practical assignments.
PURPOSE OF THE COURSE/RATIONALE:
This is a core course for the Plant Biology option in the Department of Life Sciences and is an
essential area in plant and, environmental biology. It also broadens the scope of studies in
biology.
INSTRUCTOR INFORMATION:
Name of course coordinator:
Judy Rouse-Miller
Office address and phone:
Room 322, Floor 3, Old wing, Natural Sciences Building
Email address:
[email protected]
Office hours:
Mondays 10-11am, Fridays 11 am -12 noon
Preferred method of contact:
Email
Communication policy: Students should use their UWI email account for communication.
218
LETTER TO THE STUDENT
Welcome to this course “Plant Diversity and Systematics” This course lays a foundation,
improving your knowledge and skills for identifying plants; and then progresses to increase the
range of plants you are able to identify. At the end of this course you will be able to look at
plants with greater focus, critically observing the characteristics that differentiate a plant from
others, and placing it into a group (family or genus) which exhibits those characteristics. This is a
valuable skill for students interested in the environment and careers in ecology and the
environment.
CONTENT:
Topics will include:
 Phylogenetics - phenetics, cladistics, morphology and molecules
 Classification, identification, nomenclature, emphasizing flowering plant families
 Diversity, morphology and evolution vascular plant groups:
 Lycophytes
 Pteridophytes
 Gymnosperms
 Early diverging angiosperm families
 Eudicots: Eurosids I evolution and morphology
 Eudicots: Asterids I morphology and evolution
 Petaloid monocots: morphology and evolution.
 Commelinoid monocots I morphology and evolution
 Extant ferns
 Incorporating phylogenies into conservation decisions
 The future of systematics
GOALS/AIMS:
This course aims to:
 Introduce students to the diversity and systematic of vascular plants with emphasis on
flowering plants
 Expand a student's knowledge of the diversity and biology of living organisms by
reference to vascular plants
 Link traditional and modern approaches in plant systematics
GENERAL OBJECTIVES:
The general objectives of this course are to:
 Provide course materials, activities and assessment using both face-to-face and online
activities
219



Facilitate opportunities for students to engage with general concepts and specific
examples to develop a comprehensive understanding of the plant diversity and systematic
Guide students in critically analysing and exploring concepts in plant diversity and
systematics using investigative hands-on approaches
Facilitate discussion on the relationship between plants groups
LEARNING OUTCOMES:
At the end of this course students should be able to:
 Outline the methods used in plant systematics
 Evaluate the contribution of modern methods used in plant systematics
 Discuss key concepts in plant diversity
 Conduct a plant systematic investigation given the necessary tools
 Identify native plants from a range of natural environments using a range of techniques and
resources, including the herbarium.
 Characterise plant species based on morphological characteristics
 Analyse systematic data in particular and scientific data in general
 Outlines the implications of systematic data for other biological disciplines
COURSE ASSESSMENT:
Assessment will be based on a student’s final mark from the coursework components below.
Description
Component
%
Final
Grade
Final exam
50%
In-course tests
10 %
2-hour written exam to answer 2 out of 5 essay questions
1 test based on multiple choice, true/false, short response
questions
Performance in face-to-face and online discussions and activities
Tutorials, online
activities
Plant Collection
Systematics
Project
10%
20%
10%
Collect 20 plants representative of a range of local families:
Systematics Project
ASSIGNMENTS:
 1 coursework test (10%): 50 minutes duration including multiple choice, true/false, short
response questions
 Tutorials, online activities (10%): Continuous evaluation of participation and performance
and contributions throughout the semester (discussions, wiki/ glossary, blogs)
 Plant Collection ( 20%): 25 plants representative of a range of families: pressed, dried and
mounted
220

Systematics Project (10 %): Practical performance and reporting at 5 practical exercises
during the semester
EVALUATION:
 Feedback on the course will be obtained informally from students on an on-going basis by
regular interactions and meetings among students, demonstrators, teaching assistants and the
Course Coordinator in practicals and tutorials.
 Formal feedback will be via election of Class Representatives who sit on the Departmental
Student-Staff Liaison Committee meetings held twice during the semester. Class reps will
channel both concerns and commendations to the meeting as guided by the Department’s
Standard Operating Procedures.
 Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation
questionnaire administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an on-going basis and corrective action or adjustments
made or discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Contact hours :36
Lectures: 22 h
Tutorials: 6 h
Practicals: 8 h (4 x4 h = 16 h practicals)




Lectures: Lectures will provide valuable synthesis and evaluation knowledge of diversity and
systematics.
Practicals: Fortnightly practicals will provide hands on experience for students to gain skills
required for identification local flora. Participation and performance in the practicals will be
assessed as well as reports based on the practical activities.
Tutorials: Tutorials will cover course topics in an interactive format using collaborative
learning techniques.
myeLearning: The online teaching tool, myeLearning, will be used extensively during this
course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and incourse results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
 self-test quizzes, questionnaires, surveys
 interactive activities such as discussions, wikis, glossaries, blogs
221
RESOURCES:
Most resources are available in myeLearning including
 Lecture presentations including learning objectives, summaries, recommended readings
and links to papers, articles and websites with interactive resources and
 ‘General Resources’ provides direct links to general websites, articles and publications
relevant to the whole course
 Tutorials may have specific supporting resources particularly on skills development
 Essential and Recommended texts are in the Reserve Section, UWI Main Library or via
links in the course outline and myeLearning
Essential texts
Simpson, MG. 2006. Plant Systematics. Elsevier Inc, Burlington MA
Harris, JG. and Harris-Woolf, M. Plant Identification Terminology: An Illustrated Glossary, ed.
2, Spring Lake Publishing
Ennos and R and E. Sheffield 2000. Plant Life Blackwell Science, USA.
Recommended text
Carrington, S. 1998. Wild Plants of the Eastern Caribbean. London: MacMillan Education, Ltd.
Comeau, P.L., Comeau, P. L. and Johnson, W. 2003. The palm book of Trinidad and Tobago
including the Lesser Antilles. The International Palm Society.
Quesnel, V. C. and Farrell, T.F. 2000. Native Trees of Trinidad and Tobago. Trinidad: The Trinidad
and Tobago Field Naturalists’ Club.
Woodland, Dennis W. 2009 Contempory Plant Systematics 4th edition Andrews University Press
COURSE CALENDAR:
WEEK
27.
28.
PRACTICALS
TUTORIALS
LECTURES
74. Course Introduction
75. Phylogenetics I: What are
phylogenetic trees? How to
read them.
76. Phylogenetics I: cont’d –
Choosing the best tree for your
needs.
77. Phylogenetics II: Molecular
characters
Practical 1: Computer
exercise -Learning to
use phylogenetic
software I
Finding DNA
sequences in
GenBank, aligning
the sequences, and
making phylogenetic
trees
222
Assignments
Lab report due
WEEK
PRACTICALS
TUTORIALS
Tutorial 1Systematics project
LECTURES
Assignments
29.
78. Phylogenetics III: The power of
modelling
79. Local flora and plant
communities
30.
80. Lycophyte and Pteridophyte
morphology and evolution
81. Gymnosperm morphology and
evolution
Practical 2:
Lycophyte
Pteridophyte and
gymnosperm
morphology and
identification
31.
82. Classification and
Nomenclature.
83. Origin of flowering plants:
moncot/dicot evolution and
morphology
84. Early diverging angiosperm
families
85. Eudicots: Eurosids I evolution
and morphology
Tutorial 2 –
Systematics project
Practical 3: Tools in
identifying
angiosperm plant
families
Lab report due
86. Eudicots: Eurosids II evolution
and morphology
87. Eudicots: Asterids I
morphology and evolution
88. Eudicots: Asterids II
morphology and evolution
89. Eudicots: Asteraceae
morphology and evolution
90. Petaloid monocots: morphology
and evolution.
91. Commelinoid monocots I
morphology and evolution
92. Commelinoid monocots II:
Poales
93. Extant ferns ancient or recent?
94. Incorporating phylogenies into
conservation decisions
95. The future of systematics
96. Review
97. Review
Tutorial 3
Systematics Project
32.
33.
34.
35.
36.
37.
38.
Lab report due
Practical 4: Field Trip
– Plant Collections
Tutorial 4
In Course Test
Tutorial 5
Tutorial 6
223
Submit Plant
Collection
WEEK
39.
PRACTICALS
TUTORIALS
LECTURES
Assignments
98. Review
ADDITIONAL INFORMATION:
 Students should access the Life Sciences Undergraduate Handbook for general guidelines for
teaching, assessment, student conduct, essential skills, and support at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Additionally, general information and regulations pertaining to the degree programme can be
found in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Students are reminded that tutorials and practicals are compulsory. An attendance register
will be kept for these sessions.
 As a general rule, medicals or other excuses may only excuse a student’s presence at an
assigned time. Students must complete the assigned tutorial/practical content. The student is
responsible for liaising with the Course Coordinator or Teaching Assistant to ensure the
assigned make-up is completed.
 Plagiarism is forbidden and all coursework items must be accompanied by a Coursework
Accountability Statement in order to be assessed. Specific items must be submitted through
Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is necessary
to be able to fully participate in activities and obtain the full value of the sessions.
 Use should be made of the resources provided and students should begin this from week.
Myelearning should be checked on a regular and frequent basis.
 Students are expected to interact with Herbarium staff on their plant projects, to ensure
prompt, satisfactory solution of any problems and to monitor progress.
224
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
JRM: 24 January 2013
225
THE UNIVERSITY OF THE WEST INDIES
ST AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
Title:
BIOL3769 – Plant Genetic Improvement
Credits:
3
Level:
Undergraduate Year 3
Semester:
1
Pre-requisites: BIOL2XXX Genetics II OR BIOL2162 Advanced Genetics OR AGCP2001
Principles of Crop Science and Production
Anti-requisite: BIOL3763 Crop Improvement
Offering Department: Department of Life Sciences, Faculty of Science and Technology, the
University of the West Indies, St. Augustine.
Course description: Plant Genetic Improvement is an elective for the Biology programme.
The course deals with methods of plant breeding and the impact of biotechnology on plant
breeding. The course addresses problems peculiar to the Caribbean so that students develop an
appreciation of the problems, and the role of plant breeding in achieving a sustainable agricultural
production system in the region.
Students pursuing this course will acquire knowledge and skills to genetically manipulate
autogamous, allogamous and vegetatively propagated plants using the plant breeding process
towards developing sustainable agricultural production systems.
Enrolment capacity: 50 students
Course organization
The course is divided into 10 major topics that progress naturally from each other. Students are
introduced to the importance of plant breeding in fashioning variability that leads to the
development of new, genetically superior varieties; the plant breeding process; the concept of
evolution and domestication of plant species, man using plant breeding to design plants for his
specific needs and desires; the factors that can and have contributed to genetic erosion (loss of
germplasm) in several crop plants and the measures that can be taken to protect and conserve the
variation present in domesticated plants; evolution of reproductive systems in plants; measures
226
used by plant breeders to augment plant genetic variability; manipulation of plant genetic
variability; breeding methods in self-pollinated plants; breeding methods in cross-pollinated
plants; and breeding methods in vegetatively propagated plants.
Purpose of the course
Plant Genetic Improvement (BIOL XXXX) has served as undergraduate course supporting M. Phil
and PhD programmes in Life Sciences for many years. Students from the programme having
completed graduate level programmes have found fruitful employment in the areas of teaching,
research and agricultural policy in many countries in the Caribbean and worldwide. This course is
earmarked to serve future MSc programmes in plant genetic resource management and utilization.
Most countries in the Caribbean region have identified cultivation of low yielding and unadapted
varieties of crop plants as amongst the most important deterrents to sustainable crop production.
The high cost of production in the region is associated with lack of tolerance to biotic and abiotic
stresses. With climate change looming, Plant Genetic Improvement is looked upon as the most
viable option to create sustainable livelihoods. Much of the work for which the University of the
West Indies and the Department of Life Sciences are known for comes from genetic improvement
work done in a number of field and vegetable plant species (pigeon peas, bodi, blackeye peas,
tomato, pepper), ornamental species (anthurium and orchids) and tree species (cocoa). Numerous
high quality publications on Plant Genetic Improvement have also emanated from the Department
of Life Sciences.
Plant Genetic Improvement methods are being increasingly versatile by moving from phenotypic
selection to molecular marker assisted breeding approaches, to genomics based selection
approaches. Similarly traditional mutation breeding approaches have been replaced by targeted
mutagenesis, to ‘tilling’ approaches. However, traditional breeding approaches still remain an
essential part of stacking ‘transgenes’ and ‘cleaning up the genetic background’ in transgenics.
Students without the basic skills of Plant Genetic Improvement may not be able to function in the
new genomics driven world.
Lecturer information
Dr. Winston Elibox, Room 312, 3rd Floor Natural Science Building, Tel: 6622002 Ext. 83108; Email: [email protected]
Office hours: Monday – Friday: 12:00 p.m. – 4:00 p.m.
Communication Policy: I prefer communication via e-mail using your UWI email account.
Letter to the students
Dear Students,
I wish you a warm welcome to Plant Genetic Improvement (BIOL3XXX). I am excited that you
have decided to pursue this course which will provide you with the knowledge and skills of plant
genetic improvement and the traditional and cutting edge tools used in this modern field. This is
the primary advanced level course that generates most of the graduate research in the Department
227
of Life Sciences in the areas of Plant Breeding and Biotechnology. Furthermore, it’s the only
course of its kind offered by the University; hence, you are part of the very prestigious group of
students and future scholars. The course is myelearning supported and several resources including
the course handbook and other suggested readings can be accessed at your convenience. Several
thought provoking questions will be posted in the discussion forum of myelearning as we go
through the course content and you are encouraged to participate. Please check your timetables
and pay particular attention to lecture times, tutorials, assignment submission deadlines and incourse assessments. I wish you a fruitful semester and I look forward to working with all of you.
Sincerely,
Dr. Winston Elibox
Lecturer
Content
Topic 1: Importance of plant breeding in plant improvement
 Role of plant genetic improvement in sustainable agriculture
 Breeding objectives to improve yield, adaptability and quality
Topic 2: Plant breeding process
 Important elements of the plant breeding process
 Factors that determine the course of the plant breeding process to enhance
economically important traits
Topic 3: Evolution and domestication of plant species
 Changes that occurred with domestication of wild plants (crops)
 Factors that eventually led to differentiation in a crop species and in what form such
variability presently exist
 Evolutionary history of some important crop plants
 Importance of centers of diversity of crop plants
Topic 4: Genetic erosion and methods of conservation
 Factors that lead to genetic erosion
 The Green Revolution and its role in genetic erosion
 Effects of genetic erosion: inbreeding depression, bottleneck effect, loss of land
races
 Curbing genetic erosion- crop germplasm conservation- in situ vs. genebanks
Topic 5: Evolution of reproductive systems in plants
 Reproductive systems in plants- Vegetative vs. Sexual reproduction
 Self-pollinators vs. Cross-pollinators
 Apomixis and its use in Plant Breeding
 Male sterility and its use in Plant Breeding
 Incompatibility systems in plants
228
Topic 6: Creating genetic variability in crop plants
 Mutations
 Somaclonal variations (mutations in tissue culture)
 Hybridization: intraspecific, interspecific
 Polyploidy/ Chromosome manipulation methods
 Genetic Engineering
Topic 7: Manipulation of genetic variability
 Selection: Natural selection vs. Artificial selection
 Principles of Selection, factors affecting genetic advance, heritability estimates,
heritability and response to selection
 Molecular markers: Marker assisted selection; Advantages of marker assisted
selection
Topic 8: Breeding methods in self-pollinated crop plants
 Pedigree method
 Isolines, multilines and composites
 Bulk method
 Single seed descent
 Back cross method
 Double haploid breeding
Topic 9: Breeding methods in cross-pollinated crop plants
 Mass selection
 Ear-to-row selection
 Progeny selection and line breeding
 Recurrent selection methods
 Hybrid breeding- single cross and double cross varieties
 Synthetic varieties
Topic 10: Breeding methods in vegetatively propagated crops
 Clonal breeding- macropropagation vs. micropropagation
Goals
At the end of this course students should have:

Acquired skills to genetically manipulate autogamous, allogamous and vegetatively
propagated crop plants using the plant breeding process

Understood the importance of the process in a sustainable agricultural production system
General Objectives
The course aims at providing students with the knowledge and skills required for Plant Genetic
Improvement through lectures, discussions, a field trip and tutorials. The course is broken up into
229
10 topics in a sequential (logical) order and class topics are reinforced and extended during
assignments, the field trip and class discussions. To assess learning, three incourse exams (weeks
4, 8 and 12) and three assignments (week 2, 5, 9) will be given and graded. For the assignments,
students will be split into smaller groups and given two weeks to prepare the reports for each
assignment. However, each student must submit an individual report for each exercise.
Furthermore, students will get to see an actual case of plant genetic improvement in practice
through a field exercise (week 11), and should be able to formulate breeding strategies to
genetically improve any crop of interest. Students must submit a report on the field trip for grading.
The course is myelearning supported and your manual contains specific course objectives as well
as lecture outlines and more. Students’ answers to the course questions posted on myelearning
will also be used to assess learning.
Learning Outcomes:
At the end of this course a student should be able to:
Topic 1- Importance of plant breeding

Describe the role of plant genetic improvement in attaining a sustainable agricultural production
system that will meet the increasing demand for food, clothing and other industrial products
derived from crop plants in the 21st century.

Discuss the role of plant genetic improvement in the management of pests and diseases;
specifically


outline breeding objectives that would lead to increases in productivity and profitability,
adaptability and quality.

explain 'ideotype breeding'.
Discuss the statement 'Good seed can substitute for inputs in crop management'.
Topic 2 - The plant breeding process

Define the important elements in the plant breeding process.

Discuss the factors that determine genetic variability of a crop plant species and how genetic
variability can be further enhanced in crop genetic improvement programmes.

Discuss the factors that determine the course of plant breeding such as breeding system,
heritability of trait, type of crop plant- tree/annual/ornamental, end variety desired and economic
considerations.
Topic 3 - Crop domestication and crop evolution

Define the term domestication.

Discuss the major changes that took place as a result of domestication.
230

Explain what factors led to differentiation in a crop plant species and in what form such variability
presently exist.
Topic 4 - Genetic erosion and methods of conservation

Define the term 'genetic erosion' and describe the processes that have contributed to it.

Discuss methods that can be used to minimize genetic erosion and justify the need for these
methods in conservation programmes.

Discuss the concept of center of diversity (Vavilov vs. Harlan) and its importance to a crop
species.

Discuss the roles of a gene bank and the major players in the conservation process.

Differentiate between primary, secondary and tertiary germplasm and their importance in
conservation efforts.

Discuss the evolutionary history of some important food crop species- the grasses (corn, wheat,
rye, barley, sugar cane), banana.
Topic 5 - Evolution of reproductive systems in crop plants
 Asexual reproduction (vegetation) vs. sexual reproduction.

Show that the objectives in breeding for any crop species, method of breeding and the types of
varieties produced depend on the 'breeding system of that particular species.

Sexual reproduction



Distinguish between autogamous, allogamous and vegetatively propagated crops.
Describe the mechanisms in crops that enforce/ promote autogamy and those that enforce/promote
allogamy.
Distinguish between sterility and incompatibility systems.





Self-incompatibility
Define self-incompatibility.
Classify the various types of self- incompatibility.
Give a comparative account on the types of self-incompatibility.
Describe methods of overcoming the self –incompatibility systems.





Male sterility
Define male sterility.
Explain the various types of male sterility.
Describe the use of male sterility systems in hybrid seed production.
describe how the various male-sterile lines are maintained.


Apomixis
Define apomixis.
231




Describe the types of apomixis producing diploids and those producing haploids and among those
producing haploids the types leading to maternal, paternal or mixed haploids.
Describe how the apomictic processes in some important crop plants can be manipulated in
breeding.
Manipulating breeding systems for man’s benefit
Describe how plant-breeding systems can be manipulated to the advantage of the breeder based
on genetic understanding of breeding systems.
Topic 6- Creating genetic variability
 Outline methods used to generate variability in breeding programmes.
 Mutation breeding





Explain the role of mutations in the evolution of crops, since domestication, with examples;
should be able to discuss the various schools of thoughts for and against mutation breeding as
a source of variability in breeding programmes.
Discuss methods that are used in the induction of mutations - physical vs. chemicals;
haplophase vs. diplophase; seeds vs. whole plants or vegetative parts etc.
Discuss the advantages and disadvantages of mutation breeding programmes in plant genetic
improvement.
discuss the role mutation breeding programmes have played in plant genetic improvement in
the past
Discuss the use of mutation breeding in forward genetics, targeted mutagenesis and tilling.

Somaclonal variations in plant breeding

Define somaclonal variation and list factors that predispose somaclonal variation.

Describe the cellular mechanisms (both genetic and epigenetic) that result in somaclonal
variation.

Discuss the role that somaclonal variants have played in the past in selected crop plants.

Polyploidy in plant breeding

Describe the role of ploidy in the evolution of crop plants.

Discuss the factors that have led to the success of autopolyploids and allopolyploids.

Explain the difficulties that arise when breeding higher ploidies.

Discuss the role autopolyploids have played in plant genetic improvement in the past.


Hybridization: intraspecific hybridization vs. interspecific hybridization
Intraspecific hybridization in plant breeding

Discuss the factors that contribute to variation in the F2 generation.

Show the influence of parental choice and mating designs on variability.
232


Show that plant breeding is a numbers game as the probability of finding a progeny plant
with superior economic traits increases with greater numbers of diverse crosses.
Interspecific hybridization in plant breeding
 Describe the barriers to interspecific hybridization.
 Differentiate between different crossability barriers: prezygotic vs. postzygotic; hybrid
sterility vs. genetic instability.
 Discuss the various methods used in plant genetic improvement to exploit interspecific
hybrids with examples viz. vegetative propagation of F1 hybrids; allopolyploids;
introgression; chromosome manipulation.
 Describe chromosome manipulation methods used in plant breeding
 demonstrate diagrammatically how chromosome addition lines and
substitution lines are produced.



Genetic engineering in plant breeding
Discuss the importance of genetic engineering as a method of plant genetic improvement
Describe the impact genetic engineering has had on plant genetic improvement.
Topic 7- Manipulation of genetic variability

Principles of selection

Define selection; define the role of selection as an evolutionary force.

Distinguish between stabilizing selection, directional selection and disruptive selection.

Explain natural selection vs. artificial selection .
 Describe the response of various traits to selection.
 Explain the factors that determine response to selection (genetic gain).

Describe the factors that affect selection intensity (cost, no. of characters; variability for future
selection).
 Describe how a genetically variable population is created in the start of a breeding programme
and how variability is maintained throughout the breeding programme to ensure continuous
response to selection.
 Define heritability and be able to list problems encountered with phenotypic selection when
heritability is low.
 Distinguish between heritability in the broad sense and narrow sense.
 Describe the methods used in the determination of heritability estimates and be able to work
problems in the estimation of it.
 Explain how breeders deal with characteristics with low heritability.
 outline the following: reduce environmental influences; proper experimental designs; grid
mass selection; late generation selection; progeny testing; indirect selection and marker
assisted selection.
 discuss the rationale for late generation selection.
233

describe various methods of indirect selection methods used - selection of component
traits; selection of an ideotype; marker assisted selection.

Methods of selection

Distinguish between tandem selection methods and simultaneous selection methods.

Discuss the merits and demerits of independent culling and index selection.

Self-pollinated crop plants (autogamous crops)



pedigree selection

bulk selection
Cross-pollinated crop plants (allogamous crops)

Define mass selection.

Discuss the advantages and disadvantages of mass selection.

Define progeny selection.

Discuss the advantages and disadvantages of progeny selection.

Define ear-to-row selection in corn.

Discuss the advantages and disadvantages of ear-to-row selection.

Define single plant / line selection.

Discuss the advantages and disadvantages of single plant/ line selection.

Define recurrent selection.

Discuss the advantages and disadvantages of recurrent selection.
Marker assisted selection for characteristics with low heritability

Discuss the reasons for poor responses to selection for characteristics with low heritability,
genetic linkage.

Explain the rationale for marker assisted selection.

Describe the use of morphological, biochemical and molecular markers that are linked to
other important traits with low heritability.

Describe how RFLP markers are generated.

Explain the role of RFLP markers in plant genetic improvement.

Explain the merits and demerits of using RAPD markers as opposed to RFLP markers.
Topic 8 - Breeding methods in autogamous crop plants

Outline the objectives in breeding self-pollinated crop plants.

Pedigree breeding leads to pureline varieties

outline the objectives of pedigree breeding.

describe the steps in pedigree breeding.
234

discuss the advantages and disadvantages of pedigree breeding.

Bulk population breeding method

outline the objectives of bulk breeding.

describe the steps in bulk breeding.

discuss the advantages and disadvantages of bulk breeding.

Single seed descent breeding method

outline the objectives of single seed descent breeding method.

describe the single seed descent method.

discuss the advantages and disadvantages of the single seed descent method.

Haploid breeding

outline the objectives of haploid breeding.

describe methods for creating haploids.

discuss the advantages and disadvantages of haploid breeding.

Double haploid breeding:

describe methods for creating double haploids.

discuss the advantages and disadvantages of double haploid breeding.

Backcross breeding

outline the objectives of backcross breeding.

describe the backcross breeding method.

discuss the advantages and disadvantages of backcross breeding.

distinguish between purelines, isolines, multilines, composite varieties, bulk varieties.
Topic 9 - Objectives of breeding in cross pollinated (allogamous) crop plants

Breeding methods in allogamous crop plants


Population improvement method of breeding

outline the objectives of population improvement method of breeding.

discuss the steps involved in the population improvement method of breeding.

discuss that the population improvement method of breeding leads to the production of
open-pollinated varieties (OPVs).
Hybrid breeding in allogamous crop plants

outline the objectives of hybrid breeding in allogamous crop plants.

describe the steps involved in hybrid breeding.

discuss the advantages and disadvantages of hybrid breeding in allogamous crop plants.

discuss the factors that lead to hybrid vigor and how this is exploited in hybrid breeding.
235


describe how inbred lines, single crosses and double crosses are created and outline the
reasons for creating each type of hybrid.
Breeding of synthetic varieties

define synthetic varieties.

outline the objectives of breeding synthetic varieties.

describe the steps involved in creating synthetic varieties.

discuss the advantages and disadvantages of synthetic varieties.

Discuss the advantages and disadvantages of hybrid varieties vs. open pollinated varieties
(OPVs).

Distinguish between population improvement methods and population enhancement
methods.
Topic 10 - Breeding methods in vegetatively propagated crop plants

Clonal breeding

describe clonal breeding and its advantages and disadvantages.

describe the use of macropropagation and micropropagation techniques in clonal breeding.
Assignments/ field trips

Students to research the Green revolution (1940s to late 1970s) and the present day gene
revolution (5%).

differentiate between the green revolution which revolutionized crop genetic improvement and
gene revolution.

outline the successes and failures of the green revolution and gene revolution.

explain why the green revolution was so wide spread and why the gene revolution has not made
significant impact in developing and underdeveloped countries.
 Group exercise - Evolution and domestication of selected crop plant species (5%).
Students will be placed into groups of five and asked to research the evolution and
domestication of one crop species per group. Each group will make a 15 minute power point
presentation to the class.
At the end of this exercise, students will be able to:

present information about the crop as it pertains to the uses of the crop, its evolution, center
of origin and diversity, time since domestication, the movement of the crop around the
world, the changes that have been brought about by domestication, the different varieties
present in cultivation today.

show that the greater the length of time that a crop has been domesticated, the greater its
diversity, adaptability and uses by man.
236


Field trip to the International Cocoa Genebank Trinidad (5%).
Students will be given a guided tour of the International Cocoa Genebank at Centeno, Trinidad to
see how a genebank is managed.
 At the end of the field trip, students should be able to list the problems associated with cocoa
germplasm conservation (lack of adequate skilled labour, financial constraints, lack of adequate
equipment, problems with mislabeling of clones, managing diseases in the collection, problems
with providing planting material to stake holders upon request, duplications in the gene bank); list
the opportunities for having the international genebank (all the genetic variability in cocoa is
available for use; genetic fingerprinting to determine unique clones and eliminate duplications;
population enhancement methods; possibility of obtaining funding for research projects;
hybridization efforts create exciting new variability, new textures and flavours).

Worksheet: calculation of heritability in the broad and narrow sense and their use in
breeding; realized heritability vs. heritability estimates (5%).
At the end of this worksheet, students will be able to:

Calculate heritability estimates from data obtained from different experimental
designs.

Use different statistical methods to calculate heritability estimates.

Calculate true heritability- realized heritability.

Show the importance of obtaining heritability estimates in breeding programmes in
order to determine how much improvement can be made per breeding cycle.
Course assessment
 In-course
Incourse examinations will include multiple choice questions, structural and short answer type
questions. These exams will assess knowledge, comprehension and application of course content.
The assignments and field trip will allow students the opportunity to write reports using the
scientific method and as well reinforce and extend what is learned during class time as well as
allow students to analyze real life situations in Plant Genetic Improvement. (See the course
calendar for the assessment schedule).
Incourse exam-1
Incourse exam-2
Incourse exam-3
Field trip/ worksheet/ assignment reports
10%
10%
10%
20%
237
Total incourse marks
50%
The final examination comprises multiple choice questions, short answer questions with four to
five parts, structured questions and essay type questions. The final examination will also test
students’ ability to recall, comprehend, apply and analyze course content in a critical and logical
manner. Students are required to answer ALL questions.
 Overall assessment
Incourse
Final Theory Exam (2 hours)
50%
50%
Evaluation
Two student representatives will be elected from the class. Students’ feedback will be obtained
officially from the staff-student liaison meetings held twice per semester. However, students are
encouraged to give their feedback on the course via myelearning at any time. Comments will be
assessed critically by the instructor, course coordinator and first examiner and weaknesses will be
addressed to improve on the course in the future.
Teaching Strategies
The course consists of 32 lectures, ONE field trip, THREE assignments and THREE tutorials. The
course is myelearning supported and your manual contains specific course objectives as well as
lecture and lab outlines, past exam papers and model answers.
Resources
Text
Category A
Simmonds, N.W. 1979. Principles of Crop Improvement. Longman Inc, NY, USA.
Simmonds, N, W., and Smartt, J. 1999. Principles of Crop Improvement, 2nd Ed. Blackwell
Science, Oxford, UK.
Category B
Allard, R.W. 1999. Principles of Plant Breeding 2nd ed. John Wiley and Sons, NY, USA.
Chrispeels, M. J., and Sadava, D. E. 2003. Plant, Genes and Crop Biotechnology. Jones &
Barlett Learning, MA, USA.
238
Category C
Poleman, J.M. 1979. Breeding field crops. AVI Publishing Company, Connecticut, U.S.A.
Fehr, W.R. 1990. Principles of cultivar development Vol1 &Vol11. Macmillan Publishing
Company, NY, USA.
Stalker, H.T. and Murphy, J.P. 1992. Plant Breeding in the 1990s. CAB International, Wallingford,
UK.
Readings
 http://kkvinod.webs.com/share/cms.pdf
 http://theagricos.com/plant-breeding/self-incompatibility/sporophytic-selfincompatibility-ssi/
 Self-incompatibility Deborah Charlesworth
 F1000 Biology Reports 2010, 2:68 (doi:10.3410/B2-68)
http://f1000.com/reports/b/2/68/pdf
Course Calendar
Week Topic
1
Introduction- overview
Objectives of plant genetic improvement
Plant breeding process/ Structure and importance of genetic diversity
2
Evolution and domestication of crop plant species
Genetic erosion and conservation of genetic resources
Green revolution and its effects on crop plant diversity/ green evolution
assignment given
3
Breeding Systems in Plants/ review of flower structure
Mechanisms for enforcing breeding systems
Self-incompatibility/ self-sterility
4
Male sterility
Apomixis
INCOURSE EXAMINATION-1
Manipulating breeding systems for man’s benefit/ collect assignment on
5
green revolution
Mutation breeding-1 (conventional methods)
Mutation breeding-2 (targeted mutagenesis/ tilling)/ Students are grouped
and given assignment on the evolution and domestication of selected crop
plant species
6
Exploitation of somaclonal variations
239
7
8
9
10
11
12
13
Induction and exploitation of polyploids
Exploitation of intraspecific hybridization
Crossability barriers to interspecific hybridization
Exploitation of interspecific hybridization/ Collect assignment on evolution
and domestication of selected crop plant species
Bioengineering (genetic engineering) – GMO’s
INCOURSE EXAMINATION-2
Principles of selection / Students are asked to read up on the functions of
the International Cocoa Genebank in Trinidad.
Types of selection/ Marker assisted selection
Heritability and response to selection-1
Heritability and response to selection-2
Autogamous crop plants- Pedigree method of breeding/ Students are
provided with worksheet on calculating heritability estimates for various
traits
Autogamous crop plants- bulk population method of breeding
Autogamous crop plants- single seed descent method of breeding
Autogamous crop plants- haploid method of breeding/ Collection of
assignment on calculating heritability estimates
Autogamous crop plants- backcross method of breeding
Allogamous crop plants- Population improvement and enhancement methods
Field trip to International Cocoa Genebank/ discussions
Allogamous crop plants- Hybrid breeding/ synthetic varieties/ Collection of
report pertaining to the fieldtrip to the International Cocoa Genebank
Clonal breeding in vegetative crop plants/
INCOURSE EXAMINATION -3
Tutorial
Tutorial
Tutorial
Additional information
Attendance
Students should attend all sessions in the course. Attendance for the field trip is mandatory. Any
student who misses the field trip or an incourse exam is advised to consult immediately in person
or by email with the course instructor regarding their make-up options. Absence must be
accompanied by a written excuse or medical submitted to the Main office, Life Sciences within 7
days of the missed session. Any student who was inexcusably absent from the field trip or incourse
exam, or who does not submit an assignment report will receive 0% for that exercise.
240
How to study for this course
Students are encouraged to work together in small cohesive groups as much as possible to go
through the course content. As we go through the various topics, students should attempt to answer
all the sample questions placed on myelearning and discuss the answers amongst themselves. All
comments, questions and concerns provided on a particular topic will be addressed during class
time. Your course textbook on myelearning contains all the topics to be taught and its content is
aligned similarly as the lectures; please read the textbook. Each new topic covered has its basis in
previous topics. Link the parts of the course to see the big picture. Use the feedback for your reports
and incourse examinations as a guide to answering questions and writing reports properly. There
are several pass paper questions in the library and students are encouraged to attempt these
questions. Finally, students are encouraged to design sample breeding programmes for various
types of crops with different floral biology and for different uses.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
241
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
TITLE: BIOL3770- PLANT PATHOGENS
CREDITS: 3
LEVEL: Undergraduate-Year III
SEMESTER: I
PRE-REQUISITES: BIOL2XXX Fundamentals of Microbiology
ANTI-REQUISITE: BIOL3767 Biology of Plant Pathogens
COURSE DESCRIPTION:
This course introduces the learner to the field of plant pathology and provides basic information
on the biology and epidemiology and disease cycle of important plant pathogens affecting plants
of this region. This course provides comprehensive knowledge about plant pathogens and their
interactions with the host. Topics include: Biology of plant pathogens; Classification of plant
pathogens; their cellular organization, structure; Examples of pathogens; Pathogen-life cycles,
disease cycle; Symptomology; epidemiology, spread, survival; Host-pathogen interactions,
mechanism of infection, physiological and biochemical processes of infection; Host resistance and
defense mechanisms; Principles of disease management; Molecular-based pathogen detection and
disease diagnosis. This course will be taught through lectures/tutorials, lab sessions, field trips.
Students are expected to complete a group project.
COURSE RATIONALE:
Plant pathology has grown into an important field of plant science and biology. Damage and yield
loss of crops by plant diseases may result in hunger and starvation, especially in developing and
underdeveloped countries. The estimated annual global loss ranges betweens of 30 to 50 percent
for major crops. In some years, losses are much greater, producing catastrophic results for those
who depend on the crop for food. Major disease outbreaks among food crops have led to famines
and mass migrations throughout history. With the projected increase in population in the coming
decades it becomes increasingly challenging to improve the yields beyond thresholds and one the
constraints is management of plant diseases. Hence imparting knowledge about plant pathogens
and diseases is important particularly to students majoring biology or agriculture.
Knowledge about microorganisms is a must and an important component of any basic or applied
life sciences program. This course is precisely compatible with the present and future missions of
the University. UWI plays a major role in promoting and conducting basic and applied research
towards improving the agricultural productivity of the Caribbean region towards self-sufficiency
before the end of first quarter of this century. It would be made possible only by imparting
knowledge and by training students on understanding the basic issues related to crop protection,
242
disease diagnosis and pathogen identification. In this context this course introduces the learner to
the field of plant pathology and provides opportunities for further learning and for research. This
course serves as a necessary component of microbiology concentration for students majoring B.Sc.
Biology.
INSTRUCTOR’S INFORMATION
Dr. Jayaraj Jayaraman
Room 221, Natural Sciences Building, UWI- Life Sciences
Phone: 868-662-2002 Extn. 3092; Fax: 868-663-5241
http://sta.uwi.edu/fsa/lifesciences/jjayaraman.asp
Email: Jayaraj [email protected]
Preferred contact – By Email
LETTER TO THE STUDENT
Welcome to the course, “Plant Pathogens”.
This course which provides an opportunity to learn more about the basics of biology of plant
pathogenic organisms and their interactions with the host plants in detail.
This course comprises both theory (2 hours/week) and practical sessions (6). The practical classes
impart skills on isolation and inoculation of plant pathogenic microbes and molecular-based
detection of pathogens in diseased plants and produce. Prior knowledge on microbes, as listed in
the pre-requisites is essential for better understanding of the contents of this course. Students will
be able to access the course material and work on the exercises through online through
myelearning. Course materials are located and constantly updated in myeLearning.
CONTENT
The course covers,
 Biology of plant pathogens including, plant pathogens-types, their cellular organization,
life cycle, propagation, primary and secondary spread and survival.
 Plant-microbe interaction including, pathogenic and non-pathogenic plant interactions,
 Mechanism of pathogenesis of plant pathogens.
 Symptomology, physiology of parasitism, plant defense mechanisms, Pathogen
variability.
 Host-resistance, sources and inheritance of resistance, R-genes, resistance mechanisms,
genetics and genomics of resistance.
 Relevance of knowledge on pathogens for developing integrated disease management
methods.
 identification of plant diseases, isolation and identification of plant pathogens, inoculation
methods and principles of molecular- based detection techniques.
GOALS/AIMS
The goals and aims of this course are to,

Offer required knowledge on the nature and life cycle of plant pathogenic microorganisms.
243



Impart practical skills on identification of pathogens, diagnosis of disease symptoms,
isolation of pathogens by pure culture methods, inoculation techniques and introduction
to molecular-based diagnosis.
Provide necessary knowledge and information on the phenomenon of pathogen infection
and their physiological and biochemical mechanisms, host-pathogen interactions, host
responses, host resistance mechanisms including R and avr genes.
Teach the principles and develop competence for identification of plant pathogens and
disease diagnostic techniques.
Enhance the understanding of current scientific research advancements in plant pathology.

.
LEARNING OUTCOMES
At the end of this course students will be able to,




Investigate and identify a plant disease based on classical and molecular approaches.
Ascertain the causal agents (biotic and abiotic).
Distinguish the symptoms and causal pathogens.
Summarize the principles involved in molecular-based detection techniques and
demonstrate their utility in some practical situations.
 Illustrate the disease cycles of pathogens, mode of spread and survival.
 Discuss the mechanisms of infection, physiology of infected plants and host-pathogen
interaction, virulence and pathogenicity.
 Analyze and summarize the mechanisms of resistance and justify the implications of
resistance as a means of disease management.
 Illustrate the principles of disease management strategies and relate with the knowledge
on plant pathogens.
COURSE ASSESSMENT
50% Course work
50% Final examination
Course assessment components
% split up details
Incourse tests (2x9%)
18%
Assignment (4%) &/Online activities (6%)
10%
Group Project
15%
Lab quiz (2x2%) and lab observation report (3%)
7%
Final examination
50%
244
EVALUATION
 The elected Class Representative and/or Deputy will attend meetings with the course
teacher(s) organized at every 4th week, and present feedback from the students attending that
course or stream. This feedback is normally provided both orally and in written form for
transmission to the lecturer. Apart from that the representatives will be attending the Liaison
Committee meeting, and give their feedbacks to the committee.
 Students may comment on any aspect of the course or facilities. Students will be encouraged
to submit their feedback (oral/written) during tutorials directly to the course teacher and
appropriate actions will be taken by the teacher then and there.
 Results of in-course tests, quiz and other course assignments will be analyzed and presented
in the class. This will help students to check their progress constantly and also helps the
instructor to identify the weak areas and thereby could alert and advise students individually
to alter their approach of study and completing the work.
 The final reflective feedback and comments about the entire course and teaching will be
collected on the last day of the course. This will be saved for analysis and utilized as a base
for improvement for the next offering in the following year.
TEACHING STRATEGIES*
Contact hours:
36 h
Lectures &Tutorials: 24 h
Practical work:
12 h
The instruction for this course would comprise of 2 Lectures with inbuilt tutorials (40 min
lecture+10min tutorial) per week and 6 lab sessions. Additionally, instructional videos, tutorials
and practical labs would be utilized to support the teaching. Formal lectures and tutorials will
provide introduction to specific topics and allow for discussion in an interactive setting. Case
studies, journal papers and data will be considered in small group and class settings. Course
materials and readings will be available online in advance so that discussion and critiquing can
take place within the assigned class time. This course is also my e-learning supported, and many
other resources are readily available for the students.
There will be a group project which is one of the components that fulfills the 15% of the
marks. The project will be decided by the course teacher and it will be executed by the students in
groups. The course teacher will supervise and help students in accomplishing the project. The
project normally involves preparation of disease specimens, status report, pathogen isolation and
preparation of cultures and microscopic slides of pathogens. The practical project may be carried
out during the lab hours.
RESOURCES
Recommended reading:
Agrios, G.N. 2005. Principles of plant pathology, Academic Press; 5 edition.
Nicholas, R., Windham, M.K., Windham, A., 2004. Plant pathology: Concepts and laboratory
exercises, CRC Press.
Mehrotra, R.S., Aggarwal, A. 2003. Plant pathology, Tata McGraw Hill.
Narayanasamy, P. 2001, Plant Pathogen-Detection & Disease Diagnosis II edn., CRC Press
245
Narayanasamy, P. 2008, Molecular Biology in Plant Pathogenesis and Disease Management: Vol. 1&2,
Disease development, Springer.
Rangaswami, G., Mahadevan, A. 2006. Diseases of Crop Plants in India, Prentise-Hall of India.
Sharma, P.D. 2004. Plant Pathology, I edition, Rastogi Publications, India.
Journals:
Phytopathology (American Phytopathological Society)
Plant Pathology (Wiley-Blackwell)
Canadian Journal of Plant Pathology (Taylor & Francis)
Annual Review of Phytopathology (Annual Reviews, Inc.)
Other resources:
The ourse tea her ill upload i my e-lear i g , periodi all at the egi i g a d duri g the ourse ,
important research articles, review papers, book chapters and other related study materials. Students
are expected to read them as these were considered and included as portions of the syllabus and
covered during examinations.
Course Calendar
Week
Lecture &Tutorial
Lab
Wk1
Classification of plant pathogens and plant
diseases
Symptomology
Wk1
Field Trip (within Trinidad)
Viral pathogens (classification, life cycle, spread)
Wk2
Viral pathogens (replication, movement)
Wk2
Wk3
Viral pathogens – examples (Activity-1)
MLO s a d ‘LOs a d X le -borne bacteria
246
Isolation of plant pathogens, Quiz1
Wk3
MLO s a d ‘LOs and Xylem-borne bacteria examples
Wk4
Bacterial pathogens (classification., life cycle,
spread)
Wk4
Ba terial pathoge s, e a ples…
Incourse I
Wk5
Fungal pathogens (classifn., life cycle, spread)
Wk5
Fu gal pathoge s, e a ples… A ti it -2)
Wk6
Fu gal pathoge s, e a ples…
Wk6
Nematodes as vectors, nematode-pathogen
complexes
Identification of Plant pathogens
Inoculation of plant pathogens, Quiz
2
Wk7
Phanerogamic parasites
Wk7
Disease cycles (Activity-3)
Wk8
Survival of plant pathogens
Wk8
Spread of pathogens
Wk9
Factors affecting infection
Wk9
Mechanism of infection (Activity-4)
Wk10
Epidemiology
Wk10
Host responses and resistance mechanisms
Wk 11
Genetic resistance
Molecular Plant Diagnosis
Visit to Electron Microscope facility
at Mount Hope, In-course 2
247
Wk11
Induced resistance
Presentation and submission of
Project report & Lab Obs. Report
Wk12
Plant disease diagnosis
Wk12
Principles of Plant disease management
Wk13
Review Tutorial
Wk13
Review Tutorial
ADDITIONAL INFORMATION:



Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment, student conduct, essential skills, and support, General safety guidelines in Lab
and
General
Safety
Practices
at
http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf . Students are reminded that
they must attend a minimum of 75% of the practical sessions and tutorials. Failure to do
so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at
an assigned time. Students must still complete the assigned work (make-up lab report or
make-up test) in order to obtain the marks for that item of coursework. The student is
responsible for liaising with the Course Coordinator or Teaching Assistants to ensure the
assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework
items must be accompanied by a Coursework Accountability Statement in order to be
assessed. Specific items may require submission through Turnitin on myeLearning. Refer
to
‘University
Regulations
on
Plagiarism’
at
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:



Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly
advised to able to fully participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised
to become familiar with them and start utilising them from the first week. Regular updates
on course progress and materials are also highly recommended and you should be checking
into myelearning on a frequent regular basis to review materials, assignments and
activities.
Students are encouraged to interact regularly with staff, even outside of the assigned
tutorial times to ensure prompt, satisfactory solution of any problems and to monitor
progress.
248


Good group management is essential and requires good communication and interpersonal
skills.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as
follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE:
COURSE TITLE:
SEMESTER:
LEVEL:
NO OF CREDITS:
PRE-REQUISITES:
BIOL 3771
Environmental Plant Physiology
2
3
3
BIOL2XXX Physiology of Plants or BIOL2761 Plant Physiology
ANTI-REQUISITE: BIOL3766 Plant Ecophysiology
COURSE DESCRIPTION
The course consists of two parts with an in-course exam following each part. The first part
introduces the essential concepts of Environmental Plant Physiology and looks in detail at three
249
important abiotic factors: light, water and temperature. Each topic is covered by lectures and
supported by online materials and by recommended reading. The Practicals complement the
lecture topics and provide an opportunity to assess the students’ comprehension of each topic,
while at the same time providing the students with valuable practical skills in the life sciences.
The second part examines the application of these concepts through a series of case studies looking
at different habitats and applied scenarios. In addition to case studies developed by the instructor,
students work in structured groups to develop and present their own case studies that explore the
role of plant research in meeting the challenge of global climate change. Assessment will be based
on a group presentation, practical reports, two in course exams and a final theory exam.
PURPOSE OF THE COURSE/COURSE RATIONALE
The course is designed to build on the concepts gained in the prerequisite course and illustrate how
basic science can be applied in research and development activities. Environmental Plant
Physiology complements other courses offered in the life science department, focusing on the
abiotic factors that influence plant growth and survival. This course will equip students with the
knowledge of how plants can be used to conserve land, restore ecosystem services, and provide
sustainable food and energy. Within the Life Sciences department it will be a core module for the
minor in Plant Biology and an elective for minors in Biotechnology, and Ecology &environmental
Biology, as well as for the Biology major.
INSTRUCTOR’S INFORMATION
Name of course coordinator:
Office address and phone:
Email address:
Office hours:
Preferred method of contact:
Communication policy:
Aidan D. Farrell
220, Zoology Office, Natural Sciences Building, New
Wing Natural Sciences Building
[email protected]
9:00 - 5:00 daily (email for appointment)
Email
Students should use their UWI email account for
communication and can expect a response within 48 hours
COURSE CONTENT
Environmental Plant Physiology focuses on the interaction between plants and their environment,
exploring the diverse ways in which plants adapt to and manipulate their surroundings.
Environmental Plant Physiology provides a framework for many applications of plant science in
the management of natural and manmade ecosystems. The course begins with an overview of
microclimate, community interactions and of the many factors that limit plant growth and survival.
Subsequent lectures focus on three key abiotic factors and the way plants have adapted to them.
The course includes a case study component (see below: Case Studies and Applications) that
illustrates the importance of current research in supporting a range of sustainable ecosystems, from
rainforest stands to cultivated fields. In addition to case studies developed by the instructor,
students will have the opportunity to develop their own case studies that explore the role of plant
research in meeting the challenge of global climate change.
Essential Concepts in Environmental Plant Physiology
 Microclimate and community interactions
250






Water as an environmental factor
Water stress (drought)
Light as an environmental factor
Light stress (shade and excess)
Temperature as an environmental factor
Temperature stress (chilling and heat)
Case Studies and Applications
 Habitat case study (mangrove)
 Habitat case study (agricultural)
 Environmental Plant Physiology in action (habitat restoration)
 Environmental Plant Physiology in action (crop production)
 The challenge of climate change
GOALS/AIMS
This course aims to:
 Review the essential concepts in Environmental Plant Physiology
 Provide students with the knowledge needed to understand the role of physiological
research in managing and restoring ecosystems
 Enable students to develop practical skills in assessing the performance of plants in various
natural and manmade ecosystems
 Train students to research and present scientific arguments on relevant topical issues
GENERAL OBJECTIVES




To provide explanations of the key concepts in Environmental Plant Physiology
To demonstrate a range of methods used in Environmental Plant Physiology
To describe the application of plant research in the assessment and management of
different ecosystems
To utilise group work and case studies to facilitate the students in applying their
understanding to different systems
LEARNING OUTCOMES
The lecture and practical schedule is designed so that at the end of this course students should be
able to:



Evaluate the suitability of particular environments for a given plant or habitat type
Appraise the performance of living plants in terms of:
Water uptake and utilisation
Primary productivity and gas exchange
Stress tolerance and response
Formulate, research and present scientific arguments on topical issues, such as:
Ecosystem services
Habitat restoration
Sustainable agriculture
251
ASSIGNMENT
Five practical reports will serve to train the students in designing and reporting on experiments.
They will also help to assess the extent to which material presented in the lectures is retained by
the student.
The course includes a case study component (Case Studies and Applications) that illustrates the
importance of current research in supporting a range of sustainable ecosystems. In addition to case
studies developed by the instructor, students will work in structured groups to develop their own
case studies that explore the role of plant research in meeting the challenge of global climate
change. The group presentations form a core part of the teaching strategy. They will allow the
students to interact and to assess their own knowledge relative to that of their colleagues. As well
as assessing their knowledge of Environmental Plant Physiology, this assignment will be used to
evaluate the student’s ability to understand and communicate scientific arguments.
COURSE ASSESSMENT
Students are required to achieve a grade of 40% overall, irrespective of their performance in
individual components.
Component
%
Final
Grade
Final exam
50%
In-course test 1
10%
In-course test 2
10%
Practicals
10%
Case study
20%
Description
2-hour written exam with 20 multiple choice questions, and a
choice of 2 out of 4 essay questions
Essential Concepts in Environmental Plant Physiology: multiple
choice and short structured questions
Case Studies and Applications: multiple choice and short
structured questions
Performance and reporting of practical exercises
Students work in groups to prepare a presentation and handout
on current topics in Environmental Plant Physiology
TEACHING STRATEGIES
Credits: 3 made up as follows:
Lectures:
17 h
Tutorials:
7h
Total = 24 contact hours (2 credits)
Practicals:
24 practical hours (1 credit) (5 x 5 hours less 10 minutes = 24 hours)


Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of
available information, update current issues, and prioritise content relevant to course
assessment.
Practicals: Fortnightly practicals will provide hands on experience for students to gain skills
required for conducting well designed laboratory sampling and experiments; to problem
solve and trouble shoot in real-life situations; and to become familiar the design and
252



implementation of ecophysiological experiments. Participation and performance in the
practicals will be assessed as well as reports based on the practical activities.
Tutorials: Tutorials will cover course topics in a highly interactive format using a variety of
collaborative active learning techniques.
Case study: The case study component is designed to be fully interactive with students
researching and presenting their own case studies to the class. In each case the material
provided in class will be complemented by notes and further reading provided through the
myeLearning system. Students will also be encouraged to use the myeLearning forum in
carrying out group work.
myeLearning: myeLearning, will be used extensively during this course for:
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and incourse results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
Resources
Many resources are available myeLearning including :
 Lecture presentations (including learning objectives)
 ‘General Resources’- direct links to videos, web-tools and publications relevant to the
course
 Discussion forums
Essential texts:
Plant Ecology. 2005. Schulze, et al. Springer [QK901 .S38 2002] (In the Reserve Section, UWI,
St Augustine, Main Library)
Physiological Ecology of Tropical Plants, Luttge U. 2008. (Springer) [QK936 .L88 2008]
(available as ebook from UWI Library)
Texts from prerequisites:
Plant Physiology. Taiz and Zeiger. 2010 (Sinauer Associates)
Ecology: Instant Notes 2nd ed. Mckenzi etal. 2001 (Taylor & Francis)
Texts for further reading:
Environmental Physiology of Plants, A. Fitter and R. Hay. 2002. (Academic Press) [QK717 .F54
2002]
Plants in Action, Atwell etal. 2010. http://sci-wikibook.bacs.uq.edu.au/edition1/
Physiological Plant Ecology. Larcher. 2003 (Springer)
Plant Physiological Ecology. Lambers et al. 2008. (Springer)(available as ebook from UWI
Library)
The Physiology of Crop Yield. Hay and Porter .2006. (Blackwell Publishing)
Practical equipment:
Thermocouple, Quantum sensor, Psychrometer, Data loggers
Infrared Gas Analyser, Chlorophyll florescence
Psychrometer, Porometer, Pressure chamber
253
Conductivity meter, Micro balance, Drying ovens, Microwave ovens
All equipment will be provide from the Dept. Life Sciences, except the Infrared Gas Analyser
which will be demonstrated by the Dept. of Food Production.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
254
COURSE CALENDAR
Week Lecture
1
Practical
Deadlines
Introduction
Stress physiology
The light environment
2
The light environment
Light stress
Practical report
3
The thermal environment
Temperature stress
Heat stress
4
Water in the environment
Water deficit
5
Tutorial: Introduction to the case study
Practical report
Tutorial: review
Water stress
6
In-course Test I
Ecophysiology in action (ecosystem services)
7
Habitat case study: mangroves
Habitat case study: restoration ecology
8
Habitat case study: class presentation
Habitat case study: class presentation
9
Habitat case study: class presentation
Habitat case study: class presentation
10
Climate change (impacts)
Climate change (ecosystem response)
11
Tutorial
In-course Test II
In-course Test I
Practical report
Climate & microclimate
Casestudy handouts
Practical report
Diagnosing stress
Practical report
12
In-course Test II
Tutorial (streamed groups)
Tutorial (streamed groups)
255
ADDITIONAL INFORMATION





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment, student conduct, essential skills, and support at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
Students are reminded that they must attend a minimum of 75% of the practical sessions and
tutorials. Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an
assigned time. Students must still complete the assigned work (make-up lab report or make-up test)
in order to obtain the marks for that item of coursework. The student is responsible for liaising with
the Course Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items
must be accompanied by a Coursework Accountability Statement in order to be assessed. Specific
items may require submission through Turnitin on myeLearning. Refer to ‘University Regulations
on Plagiarism’ available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised
to able to fully participate in activities and obtain the full value of the sessions.
 Thorough use should be made of the resources provided and students are strongly advised to
become familiar with them and start utilising them from the first week. Regular updates on course
progress and materials are also highly recommended and you should check into your UWI email
and myeLearning on a frequent regular basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on their projects, even outside of the
assigned tutorial times to ensure prompt, satisfactory solution of any problems and to monitor
progress.
ADF: 28 FEB 2013
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE: BIOL3772
COURSE TITLE: Plant Development
NO. OF CREDITS: 3
LEVEL: 3
SEMESTER: 2
256
PREREQUISITE(S): BIOL 2XXX Cell and Developmental Biology and either BIOL 2XXX
Physiology of Plants or BIOL2761 Plant Physiology
COURSE CAPACITY ENROLLMENT: 48 students (maximum)
COURSE DESCRIPTION
This course provides an advanced level focus on the molecular genetic, biochemical and physiological
bases of plant development. Concepts of signal perception and transduction are initially reviewed.
Students will be introduced to important experiments that have led to understanding many basic
principles of plant development. Of particular importance is the use of mutation genetics as a tool to
study development. Students in dissecting these experiments would be required to perform planned
experiments and present their results and analysis in a group presentation format.
COURSE RATIONALE
BIOL3xxx is included in the Plant Biology option of the Biology degree. This course builds upon
aspects of plant developmental biology and plant physiology taught in Year II of the programme. The
student, upon completion of this course, should have a comprehensive understanding of the role of
phytohormones in development, and the various developmental processes underlying the nature of
some of the major plant organs.
INSTRUCTOR INFORMATION
Name of course coordinator:
Dr. Georgette Briggs
Office address and phone:
Biochemistry Office, Floor 2, Old wing,
Natural Sciences Building
Email address:
[email protected]
Office hours:
Wednesdays 2:00-4:00 pm
Preferred method of contact:
Email
Communication policy: Students should use their UWI email account for communication and can
expect a response within 48 hours.
CONTENT
The hormonal control of plant development is first examined by discussing in significant detail the
biosynthesis, signalling and developmental effects on growth of each of the major plant hormones (ABA,
GA, Brassinosteroids, Ethylene and Auxin). The second portion of the course, seeks to examine in detail
the genetic control of development of all the major plant organs, including the seed, shoot, root and
flower.
GOALS/AIMS:
On completion of this course, students should have:
 An understanding of the hormonal pathways and interactions that underlie fundamental
processes operating during plant development
 An appreciation of the role of developmental processes in plant disease
 An understanding of the theory that underlies the genetic basis of plant developmental pathways
257
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



Developed laboratory skills in working with the model plant Arabidopsis thaliana
The ability to interpret the outcomes of experimental scenarios
Acquired the knowledge and ability to aid in critically evaluating scientific experiments and
their findings
Acquired specific analytical skills with respect to problems in plant development
Gained skills in presenting and defending a logical, scientifically supported argument
LEARNING OUTCOMES
Students completing this course should be able to:
- Relate the importance of the study of plant development to the fields of plant anatomy and plant
physiology.
- Explain the discovery, biosynthesis, forms, conjugates, bioassays, physicochemical measurement
and effects of applied phytohormones on plants of commercial significance
- Explain the processes and genetic interactions involved in the development of the seed coat, the
seed, the flower, the root and the shoot of the plant.
- Dissect the role of hormonal cross-talk and the effect it can have on devlopmental responses
- Critically evaluate scientific research papers, assessing the relevance and importance of the
scientific findings
COURSE ASSESSMENT
In-course test :
Group research project
- Group seminar presentation (10%)
- Written report (15%)
Written analysis of a scientific article
Participation in online forums/Seminars
Final examination (2 hours)
10%
25%
5%
10%
50 %
Group research project (25%): Students work in groups of four and are assigned a research topic (Week
2), regarding one aspect of plant development. Students must design an experiment, perform that
experiment and record data. The experiment must utilize one of the provided developmental mutants in
Arabidopsis thaliana. A few key references are provided by the lecturer. These topics are discussed
over the three sessions of student group meetings, where experimental design and
analysis/interpretation of relevant research papers are the main focus.
Written report (15%): The written report should reflect the experimental design, methodology, results
and interpretation of results, of the experiments performed by the group. The complete report is due in
Week 9.
Seminar presentation (10%): The seminar presesntation would be 15-20 minutes duration, and would
be presented to the class. These presentations would begin in Week 10 and should be completed in
Week 12. Each group will also produce a one page summary of their topic for fellow students. These
should be brought to the presentation session and will contribute to the presentation assessment.
258
Participation in online forums/Seminars (10%): Marks are awarded for student participation during
seminar presentations. Students participation in schedulded online discussion forums are also awarded
here.
Written analysis of a scientific article (5%): This assignment is due in Week 12 and is a 1000 word
analysis of an approved scientific research article that addresses one of the key plant development
themes discussed in the lectures.
EVALUATION
The elected Class Representative and/or Deputy will attend meetings with the course teacher(s)
organized at every 4th week, and present feedback from the students attending that course or stream.
This feedback is normally provided both orally and in written form for transmission to the lecturer.
Apart from that the representatives will be attending the Liaison Committee meeting, and give their
feedbacks to the committee.
Students may comment on any aspect of the course or facilities. Students will be encouraged to submit
their feedback (oral/written) during tutorials directly to the course teacher and appropriate actions will
be taken by the teacher then and there.
Results of in-course tests, and other course assignments will be analyzed and presented in the class.
This will help students to check their progress constantly and also helps the instructor to identify the
weak areas and thereby could alert and advise students individually to alter their approach of study and
completing the work.
The final reflective feedback and comments about the entire course and teaching will be collected on
the last day of the course. This will be saved for analysis and utilized as a base for improvement for the
next offering in the following year.
COURSE DELIVERY & TEACHING STRATEGIES
The instruction for this course would comprise 2 lectures per week (50 mins each), and one tutorial
session. In total, 24 one-hour lectures will be delivered, supplemented with 4 tutorial sessions, and 3
student group meetings. The student group meetings facilitate project discussion and journal
discussions. The lecturer would be present at these sessions to guide the meetings. Theses are in-class
oppurtunities for the lecturer to observe and guide the student group interaction and interpretation of
the scientific research papers. Students would use these sessions to have confusing concepts clarified
and to also submit up-to-date planning on experimental design for the project. Online forum
discussions, seminar presentations and written reports would also be used to encourage student
participation and collaborative learning. In addition students will have the opportunity to gain skills in
oral communication, and collaborative group research and presentation. This format therefore
addresses a range of learning styles, as outlined in the DLS undergraduate handbook. This course is
also my e-learning supported, and many other resources are readily available for the students.
RESOURCES
Required reading:
259
Plant Physiology Taiz, L & Zeigler, E (2002) (3rd edition)
Biochemistry and Molecular Biology of Plants Buchanan, B, Gruissem, W, and Jones, R .
Mechanisms in Plant Development Leyser, O., & Day, S. (2009).. Chichester: John Wiley & Sons.
Molecular genetics of plant development Howell, S. H. (2000).. Cambridge [u.a.: Cambridge Univ. Press.
Developmental biology of flowering plants Raghavan, V. (2000).. New York, NY [u.a.: Springer.
Recommended reading:
Seed Coat Development and Dormancy, in Annual Plant Reviews Volume 27: Seed
Development, Dormancy and Germination Debeaujon, I., Lepiniec, L., Pourcel, L. and Routaboul,
J.-M. (2007) (eds K. J. Bradford and H. Nonogaki), Blackwell Publishing Ltd, Oxford, UK.
doi: 10.1002/9780470988848.ch2
Lateral Root Formation, in Annual Plant Reviews Volume 37: Root Development Malamy, J. E.
(2009) (ed T. Beeckman), Wiley-Blackwell, Oxford, UK..ch4
Arabidopsis Root Development Luijten, M. and Heidstra, R. (2009), in Annual Plant Reviews
Volume 37: Root Development (ed T. Beeckman), Wiley-Blackwell, Oxford, UK.ch1
Further Reading:
Key review papers and research papers would be used in discussion of the relevant topics. An example
of the phytohormone Auxin reading list is included:
1. Bauly, JM et al. (2000) Overexpression of auxin-binding protein enhances the sensitivity of
guard cells to auxin. Plant Physiol. 124: 1229-1238.
2. Chen, J-G, Shimomura, S, Sitbon, F, Sandberg, G & Jones, AM (2001) The role of auxinbinding protein 1 in the expansion of tobacco leaf cells. Plant J. 28: 607-617.
3. Chen, J-G, Ullah,H, Young, JC, Sussman, MR & Jones, AM (2001)ABP1 is required for
organized cell elongation and division in Arabidopsis embryogenesis Genes Dev. 15: 902-911.
4. Dharmasiri, N & Estelle, M (2004) Auxin signaling and regulated protein degradation" TIBS 9:
302-308.
5. Ellis, B.E., Miles, G.P. (2001) "One for all?" Science 292: 2022-2023.
6. Galweiler, L, et al. (1998) Regulation of polar auxin transport by AtPIN1 in Arabidopsis
vascular tissue. Science 282 2226-2230.
7. Hagen, G, Guilfoyle (2002) Auxin-responsive gene expression: genes, promoters and
regulatory factors. Pl. Mol. Biol. 49: 373-385.
8. Hager, A., Debus, G., Edel, H.G., Stransky, H. & Serrano, R. (1991) Auxin induces exocytosis
and the rapid synthesis of a high-turnover pool of plasma-membrane H+ ATPase. Planta 185
527-537.
9. Hertel, R (1995) Auxin binding protein 1 is a red herring. J Exp. Bot. 46: 461-462.
10. Jones, AL et al. (1998) Auxin-dependant cell expansion mediated by overexpressed auxinbinding protein 1. Science 282: 1114-1117.
11. Kepsinski, S, Leyser, O (2003) An axis of auxin. Nature 426: 132-135.
12. Kutschera, U. & Schopfer, P. (1985) Evidence against the acid-growth theory of auxin action
Planta 163 483-493.
13. Leyser, O (2001) Auxin signalling: the beginning, the middle and the end. Curr. Opinion
in Plant Biology 4: 382-386.
14. Napier, RM, David, KM, Perrot-Rechenmann, C (2002) A short history of auxin binding
proteins. Pl. Mol. Biol. 49: 339-348.
260
15. Schindler, T., Bergfield, R., Hohl, M. & Schopfer, P. (1994) Inhibition of Golgi-apparatus
function by brefeldin A in maize coleoptiles and its consequences on auxin-mediated growth,
cell-wall extensibility and secretion of cell wall proteins. Planta 192 404-413.
16. Steinmann, T et al. (1999) Coordinated polar localization of auxin efflux carrier PIN1 by
GNOM ARF GER. Science 286: 316-318.
17. Trewavas, A.J. & Cleland, R.E. (1983). AIs plant development regulated by changes in the
concentration of growth substances or by changes in the sensitivity to growth substances?@
TIBS, 354-357.
18. Woo, E-J, Marshall, J, Bauly, J, Chen, JG, Venis, M, Napier, RM, Pickersgill, RW (2002)
"Crystal structure of auxin-binding protein 1 in complex with auxin." EMBO Journal
21: 2877-2885.
COURSE CALENDAR
WEEK
1
2
3
4
5
6
LECTURE
Lecture 1: Course introduction and Overview of plant
development
Lecture 2: Review of Signal Perception and
Transduction Pathways. The classical hormone
concept. Review of plant embryogenesis
Lecture 3-4: Auxins – discovery, biosynthesis, natural
vs synthetic auxins, conjugates, bioassays and
physicochemical measurement, effects of applied
auxins and commercial uses.
Lecture 5-6: Gibberellins – discovery, biosynthesis,
range of compounds, conjugates, bioassays and
physicochemical measurement, effects of applied
gibberellins. Commercial uses of gibberellins,
gibberellin biosynthetic inhibitors and genetic
engineering of gibberellin biosyntheis.
Lecture 7-8: Cytokinins – discovery, biosynthesis,
range of compounds, bioassays and physicochemical
measurement. Effects of applied cytokinins and
commercial uses.
Lecture 9-10: Ethylene – discovery, biosynthesis,
physicochemical measurement, effects of applied
ethylene. Commercial uses of ethylene, ethylene
biosynthetic inhibitors and genetic engineering of
ethylene biosyntheis.
Lecture 11-12: Asbscisic acid - discovery,
biosynthesis, bioassay, physicochemical measurement,
effects of applied abscisic acid.
ACTIVITY
Student group and topic
assignments determined
TUTORIAL
STUDENT GROUP
MEETING
TUTORIAL
Online discussion forum
STUDENT GROUP
MEETING
TUTORIAL
Online Exam
261
WEEK
7
8
9
10
11
12
LECTURE
Lecture 13-14: Brassinosteroids- discovery,
biosynthesis, bioassay, physicochemical measurement.
Effects and uses of applied brassinosteroids.
Lecture 15-16: Seed coat development, seed
development & dormancy
Lecture 17-18: The molecular analysis of Flower
Development (the ABC model)
Lecture 19-20: Roots – The initiation, growth and
differentiation of roots
Lecture 21-22: Shoots – stem, leaf & bud
development
Lecture 23-24: Cross-talk: Combinatoral and
Conflicting effects of hormones on specific
developmental processes. (e.g. Auxin and Ethylene;
Auxin and Brassinosteriods)
Abnormal plant growth (deregulation of hormonal
processes).
ACTIVITY
STUDENT GROUP
MEETING
TUTORIAL
Online discussion forum
SUBMISSION OF
WRITTEN REPORT
GROUP
PRESENTATIONS (X3)
GROUP
PRESENTATIONS (X3)
GROUP
PRESENTATIONS (X3)
Written Analysis of
Scientific Paper due.
ADDITIONAL INFORMATION
Student Attendance
Attendance in the in-course exams and participation in the online discussions. Any student who misses
any of the mandatory activities, is advised to consult immediately in person or by email with the course
instructor regarding their make-up options. Absence must be accompanied by a written excuse or medical
submitted to the Main office, Life Sciences within 7 days of the missed session. Any student who was
inexcusably absent or who does not write an in-course exam or a quiz will receive 0% for that exercise.
Students are strongly advised to atten the student group meetings and to participte in the seminars since
these are marked activities.
HOW TO STUDY FOR THIS COURSE
Students are encouraged to work together in small cohesive groups as much as possible to go through
the course content. As we go through the various topics, students should attend the tutorials which are
on a weekly basis, and should ensure that they prepare by reading the relevant journals assigned per
project group. All comments, questions and concerns provided on a particular topic will be addressed
during the discussion segments tutorials, and during student group meetings. To support the material
presented in class, several texts have been recommended. These texts, would also be supplemented by
various scientific journal articles available to you via the myeLearning platform. Use the responses and
comments from the online forum discussions, to clarify misconceptions on any topic, and to aid in your
understanding of the topics.
262
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
GB: 24 Jan 2013
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE:
COURSE TITLE:
SEMESTER:
LEVEL:
NO OF CREDITS:
BIOL 3773
Plant Anatomy
1
3
3
PRE-REQUISITES:
Either BIOL1262 Living Organisms 1 or BIOL1261 Diversity of Organisms or
(BIOL1065 Diversity of Plants and Animals and AGRI1012 Microbiology); and
either BIOL 2XXX Physiology of Plants or BIOL2761 Plant Physiology
Course Description
263
The course integrates developmental and functional aspects to explain the internal structure and external form of
seed plants. The cells, tissues and organs, as well as their modifications, of representative plants are described.
The roles of meristematic activity in primary and secondary growth and in determinate and indeterminate growth
patterns are explained. Practical exercises are integrated with lectures as much as possible and emphasis is
placed on hands-on specimen preparation and on effective use of the light microscope. The course will be
assessed by means of in course theory and practical tests, practical reports, and a final theory exam.
Purpose of the Course/Course Rationale
Knowledge of plant anatomy is fundamental to the study of botany and of plant science in general, and the
subject is no longer covered in other courses offered by the Department of Life Sciences
Instructor’s Information
Instructor:
E-mail:
Office location:
Office hours:
Dr. G. F. Barclay
[email protected]
Rm 324, Old Wing, Natural Sciences Building
9:00 - 5:00 daily (email for appointment)
Course Content
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
1.
2.
3.
4.
5.
Topics
Meristems and growth patterns: primary and secondary growth
Plant architecture and phyllotaxy.
Transport tissues: phloem and xylem.
Protective tissue layers: epidermis, exodermis, endodermis, and periderm.
Support tissues: parenchyma, collenchyma, sclerenchyma, and xylem.
Leaves. Functional design and modifications of structure.
Root and stem structure and modifications. Organs of perennation.
Wood anatomy.
Grasses. Cane and corn plant structure.
Flowers and their modifications.
Pollination mechanisms.
Fruit types, seed modification, and dispersal.
Practical Exercises
Cell types
Anatomy of herbaceous stems and roots
Leaves
Woody stems and anomalous secondary growth
Flowers and fruit
Goals/Aims
The aim of this course is to give students a working knowledge of the structure of seed plants.
Learning Outcomes
At the end of this course students ought to be able to:
1. Compare the anatomy of eudicot and monocot plants and the concepts of primary and secondary growth.
264
2. Distinguish between the different types of phyllotaxy and stem branching
3. Relate the anatomical and morphological features of leaves and their modifications to their functional
characteristics.
4. Differentiate the external morphological root zones, root modifications, organs of perennation, pericycle,
endodermis, casparian band.
5. Compare secondary growth in storage organs with typical secondary growth.
6. Correlate differences in floral structure with fruit structure, and pollination and seed dispersal strategies
7. Classify the organs, tissues, cell layers, and cell types observed in the practical sessions.
8. Create large well labeled illustrations of plant specimens and classify their tissues based on features observed.
Course Assessment
Component
%
Final
Grade
Final exam
50%
In-course test 1
15%
In-course test 2
15%
Practical reports
10%
Practical Quiz
10%
Description
2-hour written exam with 20 multiple choice questions, and a
choice of 2 out of 4 essay questions
10% theory and 5% based on Practicals
10% theory and 5% based on Practicals
Performance and reporting of practical exercises
Quizzes based on identification of plant tissues during practical
Teaching Strategies
Credits: 3
Lectures: 24 lectures
Tutorials: 5 x 1 hour tutorials
Practicals: (5x 3 hr practicals)
Lectures: Lectures, which incorporate some video presentations, will provide valuable synthesis and evaluation
of the growing body of available information, update current issues, and prioritize content relevant to course
assessment.
 Practicals: Fortnightly practicals will provide hands on experience for students to gain skills required for
conducting well designed laboratory sampling and experiments; to problem solve and trouble shoot in reallife situations; and to become familiar with Plant Anatomy.
 Tutorials: Tutorials will cover course topics in a highly interactive format using a variety of collaborative
active learning techniques.
 myeLearning: myeLearning, will be used extensively during this course for:
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course results)
265


provision of course details, lecture notes, practical guides, tutorial briefings
provision of recommended resource materials and links to resources on specific websites
Resources
Many resources are available including:
 Lecture presentations (including learning objectives)
 ‘General Resources’- direct links to videos, web-tools and publications relevant to the course
 Discussion forums
Essential texts:
Esau, K. 1977. Anatomy of Seed Plants. 2nd ed. New Jersey and London: John Wiley & Sons, Inc.
Class Text:
G. F. Barclay. Plants Alive!
Online course resource:
http://sta.uwi.edu/fst/lifesciences/bl11f/
Texts for further reading:
Evert, R.F. 2006. Esau's Plant Anatomy. Meristems, Cells, and Tissues of the Plant Body: their Structure,
Function, and Development. 3rd ed. New Jersey and London: John Wiley & Sons, Inc.
Dickison WC. 2000. Integrative Plant Anatomy. New York: Academic Press.
Bell, A.D., 2008. Plant Form: An Illustrated Guide to Flowering Plant Morphology. Portland and London:
Timber Press
Beck C B (2010) An Introduction to Plant Structure and Development: Plant Anatomy for the Twenty-First
Century. 2nd ed. Cambridge: Cambridge University Press
Mauseth J D (1988) Plant Anatomy. Menlo Park, CA: Benjamin/Cummings
Peterson, R. L. Peterson, C. A. Melville L. H. 2008. Teaching Plant Anatomy Through Creative Laboratory
Exercises. Ottawa, Ontario: NRC Press
COURSE CALENDAR
Week
1
Lecture
Course Introduction
Structure of a typical plant
Lab
Tutorial
2
Vascular tissues
Support tissues
Cell types
Tutorial 1
3
Protective tissues
Root and stem structure
4
Plant Architecture
Phyllotaxy
5
Leaves 1
Leaves 2
6
Review
Deadlines
Practical report
Stems and roots
Tutorial 2
Practical quiz
Practical report
Leaves
Tutorial 3
266
Theory and practical test 1
In-course test 1
7
Modifications of roots, stems, and leaves 1
Modifications of roots, stems, and leaves 2
Practical report
8
Secondary growth
Trees and wood anatomy
9
Grasses
Crop plant anatomy and morphology
10
Flowers and pollination
Fruit structure and seed dispersal
11
Review
Theory and practical test 2
12
Review
Review
Secondary growth
Tutorial 4
Practical quiz
Practical report
Flowers and fruit
Tutorial 5
Practical report
In-course test 2
ADDITIONAL INFORMATION:
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
 As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned time.
Students must still complete the assigned work (make-up lab report or make-up test) in order to obtain the
marks for that item of coursework. The student is responsible for liaising with the Course Coordinator or
Teaching Assistants to ensure the assigned make-up is completed.
 Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available
from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to able to
fully participate in activities and obtain the full value of the sessions.
 Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start using them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myelearning on a frequent regular
basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned tutorial
times to ensure prompt, satisfactory solution of any problems and to monitor progress.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
267
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
GFB: 20 Jan 2013 rev 28 Feb 2013
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE CODE: BIOL 3866
COURSE TITLE: Parasite Biology
NO. OF CREDITS: 3
LEVEL: III
PREREQUISITES:
BIOL1263 Living Organisms II or BIOL1261 Diversity of Organisms or (BIOL1065 Diversity of
Plants and Animals and AGRI1012 Microbiology) and either BIOL 2XXX Physiology of Animals or
BIOL2862 Animal Physiology
ANTI-REQUISITE: BIOL2864 - Parasitism
268
COURSE DESCRIPTION
The course Parasite Biology is divided as follows:
 The study of individual parasites: It is only through the study of a parasite’s biology and functions
that steps can be taken to fight it.
 The study of host-parasite relationships: Disciplines which investigate how the host and parasite(s)
interact include Physiology, Biochemistry, Cell Biology, and Pharmacology.
 Immunology: This deals with the immunological response that is triggered in the host and the ways
in which the parasite attempts to evade it. Disciplines include Cellular and Molecular Immunology.
 Chemotherapy: This area investigates the effect of drugs on both the parasite and the host, as well
effective treatments to ensure the death of the parasite and the recuperation of the host. Disciplines
include Organic Chemistry, Pharmacology, Biochemistry and Medicine.
 Epidemiology: This field looks at the spread of parasitic diseases through study of the host, parasite
and vectors. Disciplines include Tropical Hygiene, Entomology and Geographical distribution.
This course will be taught using a mixture of lectures, seminars and projects, team oral presentations,
individual essays, reading materials and seminar-style classes, laboratory session to reinforce lectures
and for hands on experience identifying, understanding form and function, and evolutionary processes.
Course assessment will be based on a student seminar and an essay on current topics in parasitism
together with lab exercises on form and function, and evolutionary processes. A final examination will
be used to ensure student learning objectives are achieved.
COURSE RATIONALE
Parasitism is a very successful way of life. All of the major groups of animals have parasitic members
and 50% of all known animal species are parasitic at some stage of their life cycle. One of the fascinations
of parasites is the complexity of their life cycles, involving one, two, three or even four consecutive hosts
and alternating between vertebrate hosts and invertebrate hosts and between terrestrial and aquatic
environments. Therefore parasitic adaptations are responses to features in the parasite environment and
this environment is the body of another organism, the host.In addition, approximately 15 million people
still die each year from infectious diseases; most living in developing countries. Six diseases are
considered most detrimental to human health by the World Health Organization, of which five are caused
by parasites and are vector-borne. Consequently, control of parasites should be integrated with the life
cycle of the parasite, the host and the environment.
INSTRUCTOR INFORMATION
Prof. Dave D. Chadee
Natural Sciences Bldg New Wing Room 216, phone 662-2002 ext 83740
[email protected]
Office hours: Monday and Tuesday from 9.00-1200 Noon
LETTER TO THE STUDENT
Dear Student,
269
Welcome to BIOL 3…. The journey from the first day of class to your final day will be filled
with awe and wonder of how such small organisms have adapted and survived for millennia. In addition,
we will study of the relationship between two specific types of organisms, i.e. the parasite and the host.
We will explore the evolutionary aspects of all these interactions between organisms, that is, when there
is an exchange of food and shelter. I will therefore guide you through this process and the understanding
of parasitism as a way of life.
Sincerely,
Dave D. Chadee
Professor of Environmental Biology
CONTENT: (1) Fundamental concepts of Parasitology: morphology, lifecycle, transmission, pathology
and control of selected protest, helminth and arthropod parasites of humans and domesticated animals:
laboratory diagnostic techniques, parasite ecology and evolution, parasite immunology; epidemiology of
ectoparasite infections in the Caribbean region. These concepts will be taught through lectures on the
following topics: Introduction to Protozoan parasites including Malaria, African and American
Trypanosomiasis and Leishmaniasis; Parasites of the Intestines including Nematodes, Cestodes and
Trematodes; Life Cycles of Parasites; Host Specificity, Parasite Immunity, Parasite Diagnosis and
Control; Adaptation/ Evolution of Parasitism, Ectoparasites; Environmental Parasitology; Evidence
Based Parasitology. Practical classes take place in both laboratory and field. Reading in Parasitism and
the development of evolutionary adaptation hypotheses, a laboratory manual will be used to facilitate the
learning process.
(2) Laboratory-based exercises will include identification/diagnosis of a range of parasite infections of
humans and domesticated animals
GOALS/AIMS
The course aims to provide a solid grounding in both theory and practice of parasite biology. The goals
of the Lectures and laboratory sessions are to:
1. study individual parasites, their life cycles, characteristic features as they relate to function
2. study host-parasite relationships and the role physiology, biochemistry, cell biology and
pharmacology plays in establishing these relationships
3. study the immune response that is triggered in the host and the way in which these parasites
attempt to evade it
4. investigate the effects of chemotherapy on both parasites and host
5. determine the susceptible stages of these parasites for developing control/intervention strategies
6. examine the spread of parasitic diseases through the study of host-parasite-vector relationships
7. examine the evolutionary processes which have lead to the success of parasites and parasitism as
a way of life
8. review parasites found in the Caribbean and Latin American region.
270
LEARNING OUTCOMES
At the end of this course, students will be able to:
33. Characterize the global diversity of parasites and discuss putative reasons for their diversity.
34. Define and describe parasitism, mutualism, symbiosis and endosymbiosis to convey a basic
understanding of these topics.
35. Describe, analyze and discuss the main features of parasite-host relationships.
36. Analyze and access the reasons for parasites success and survival.
37. Outline, analyze and evaluate the different parasites life cycle strategies.
38. Characterize the major ectoparasites found in the Caribbean region and compare them with
respect to gross structure and way of life.
39. Characterize, analyze and access the immunological response that is triggered in response to
parasites, the use of diagnostic methods and development of control strategies.
ASSIGNMENTS
The theory coursework, accounting for 10% of total marks, will be a Seminar and an Essay on current
topics of parasitism and will be allotted in mid February. Essay submission by each student will be at the
end of the semester.
COURSE ASSESSMENT
Practical coursework
Lab book ... 25%
Theory coursework
One in-course test ... 5%
Assigned Seminar/essay account ... 10%
Final theory exam ... 60%
EVALUATION
The Department of Life Sciences takes the quality control of its courses very seriously. Students who
have comments on one or another aspect of a course are encouraged to communicate these to the
instructors. More formal feedback is sought through the Staff-Student Liaison Committee, which meets
twice per semester. This departmental committee comprises elected student representatives from each
course in the given semester. In addition, the university conducts a confidential written evaluation of
most courses and their instructors toward the end of each semester.
TEACHING STRATEGIES
Teaching methods
Lectures, Projects using the Team Approach, Team Oral presentations, Individual Essays, Reading
materials and Seminar Style Class, Laboratory session to reinforce lectures and for hands on experience
identifying, understanding form and function, and evolutionary processes.
A combination of teaching strategies will be use including
271





Case studies
Interactive Lectures
Seminars
Projects
Group Discussions
Learning Strategies
 Interviews
 Internet
 Library literature search
 myeLearning,
The course comprises 18 one-hour lectures, six one-hour tutorials and eight three-hour practical sessions.
Tutorials are about collective problem solving with minimal lectures-review by the instructor. However,
lectures always have a certain tutorial aspect, so that the instructor will often pose questions to members
of the class and will expect answers. Where a given topic arises both in a practical exercise and in lecture,
every effort is made to provide answers.
Students are expected to read widely especially the materials available in the university library, on the
internet and on myeLearning, as an extension of the lecture notes.
RESOURCES
Suitable reading matter can be found in the university library, on the internet and on myeLearning. The
library has several relevant textbooks of general Parasitology and a good set of books on the taxonomy,
ecology and behaviour of parasites.
Practical exercises in the lab will utilize a wide range of standard equipment and materials. The course
manual and laboratory manual are placed on MyElearning
READINGS
1. Prescribed: Roberts LS and Janovy J (2009). Gerald D. Schmidt and Larry S. Roberts’ Foundations
of Parasitology. 8th Edition. McGraw-Hill Science/Engineering/Math. ISBN-10: 0073028274
2. Highly recommended :Marquardt WC, Demaree RS and Grieve RB (2000). Parasitology and vector
biology 2nd Edition. Academic Press. ISBN 0124732755, 9780124732759 3.
3. Online resources http://www.med.sc.edu:85/book/parasit-sta.htm
272
COURSE CALENDAR
Week
Practical
1
2
3
4
Lectures/tutorial
Assignments
Introduction to the course, Course
Lab report due
overview and course requirements
The nature of parasites and their
success
Tutorial: Estimating the global
species richness of parasites
Morphology of the Introduction to Protozoan parasites Lab report due
different groups of
including Malaria, African and
parasites
American Trypanosomiasis and
Leishmaniasis
Parasites of the Intestines including
Nematodes, Cestodes and
Trematodes
Tutorial: The impact of these
parasites on health and wellbeing
Geographical
Life Cycles of Parasites
Lab report due
distribution
parasites and
host
5
of
their
Host Specificity
Tutorial: Parasite Adaptation to
Hosts
the Parasite Immunity
Lab report due
6
Investigate
different
stages of
the life cycle of
parasites
7
Parasite Diagnosis and Control;
Tutorial: What is evidence based
Parasitology
Determine the various Ectoparasites - Ticks and Mites
8
In-course test
Lab report due
mechanisms
of
infections and special
features
9
10
Ectoparasites-Fleas and Tungiasis
Tutorial: Ectoparasitic insects
and Environmental Parasitology
the
Compare
contrast
different
morphological
features and their
adaptation
to
different
environments
Lab report due
273
11
12
13
Evolutionary survey of major
parasite orders
Tutorial: Developing control
strategies
Investigate
the Seminar/Lecture - Selected Topic
Assigned
various diagnostic
account
methods available
for identification
of parasites
Review of the lectures, clarifying
course issues and reviewing
holistically the course content.
Seminar/essay
ADDITIONAL INFORMATION
Attendance is not recorded at lectures and tutorials, but missing them is not a good idea. Attendance at
practical exercises is mandatory, and the student should report any excusable absence promptly (in
advance, if this is feasible).
HOW TO STUDY FOR THIS COURSE
Lectures provide a necessary focus for studying, but they do not by any means provide the entirety of
what should be learned. Rather, the student should take lecture material as a point of departure in
extensive outside reading. This supplemental material deepens one’s understanding of principles treated
rather summarily in lecture and provides illustrations of these principles.
It is a good idea to bring your copy of the course manual not only to lab but to lecture as a matter of
course. It includes summaries of all lectures and a number of illustrations and appendices to which
reference will be made in lecture.
ADDITIONAL INFORMATION





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet:
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf.
Attendance is compulsory and an attendance register will be kept for these sessions. Failure to attend
may result in a 10% deduction of marks from the assessment assignments.
Monitoring time spent on the project. Students are advised to arrange exact dates with their
supervisors and to keep a record of key discussion points and decisions. Time spent on the project
activities should be recorded.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items
must be accompanied by a Coursework Accountability Statement in order to be assessed. Specific
items may require submission through Turnitin on myeLearning. Refer to ‘University Regulations
on
Plagiarism’
available
from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
274
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
COURSE CODE:
BIOL3867
COURSE TITLE:
Animal Behaviour
NO. OF CREDITS:
3
LEVEL:
Undergraduate – Level 3
PRE-REQUISITES: BIOL1263 Living Organisms II or BIOL1261 Diversity of Organisms or
(BIOL1065 Diversity of Plants and Animals and AGRI1012 Microbiology) and
either BIOL 2XXX Physiology of Animals or BIOL2862 Animal Physiology
275
ANTI-REQUISITE: BIOL3861 Animal Behaviour
ENROLMENT:
Maximum 70 students
COURSE DESCRIPTION:
This terminal course examines the several complementary approaches (ontogeny, phylogeny, function,
and causation) that have been used in the study of animal behaviour and the major ideas that have been
developed, many of which have spread to other areas of biology. This course builds on previous offerings
of the Department in ecology and zoology, to complete the study of animal biology for students taking
the Zoology option at level III. An introduction is given to social behaviour, which is expanded on in
other level III courses in the zoology option, on humans and insects. A solid background in the structure
and function of the nervous, sensory, and endocrine systems in vertebrates and invertebrates is required
to understand the mechanisms of animal behaviour. In addition, students should have a basic
understanding of animal ecology, for example from the introductory course BIOL1462 General Ecology
and Biometry or BIOL2xxx Fundamentals of Ecology, particularly in evolution, energetics, and
population ecology. The course is organised into lectures and tutorials covering general and specific
concepts in animal behaviour. In tutorials students are expected to prepare, participate and perform in an
active way in order to engage with the content. Assessment will be based on a research essay, practical
reports, and a final theory exam.
COURSE RATIONALE:
This is a core course for the Zoology option in the Department of Life Sciences and is an essential area
in the study of animal biology. Animals are the most complex objects in the known universe, and
behaviour is their major emergent feature. At the end of the course, students are expected to have an
understanding of the principles sufficient to pursue research in animal behaviour or associated subjects
such as biodiversity, conservation, or animal welfare.
INSTRUCTOR INFORMATION:
Name of instructor:
Dr A. Hailey
Office address and phone:
Room 226, Zoology Section, New Wing, Natural Sciences Building.
Phone ext 82206
[email protected]
Email address:
Office hours:
Monday, Wednesday, Thursday, 11-12 a.m., other times by appointment
Preferred methods of contact: Email or myelearning Academic Forum
Communication policy:
Matters concerning the individual student should be raised by email, from
the student’s UWI email account. Matters of interest to the class should be
raised as Academic Forum postings on myelearning. In either case students
can expect a response within 48 hours. DO NOT use myelearning
messaging, which is only supported via email and after some delay.
CONTENT:
General aspects of animal behaviour
 Approaches to animal behaviour
 History of the study of animal behaviour
276


Methods of studying animal behaviour
Evolution of behaviour
Physiological behaviour
 Perception
 Processing
 Organization of behaviour
Ecological behaviour
 Feeding
 Defence
 Territory and social behaviour
Learning and ontogeny
 Instinct and learning
 Types of learning
 Learning and the development of behaviour
Communication
 Communication and signals
 Evolution of signals
 Complex communication - language
Reproductive behaviour
 Reproductive strategies
 Mating systems
 Parental care
GOALS/AIMS:
This course aims to
 Introduce students to the major subject and growth areas of animal behaviour
 Relate animal behaviour to other aspects of animal biology, especially ecology, physiology, and
diversity
 Give students a sound grasp of the scientific method, sufficient to begin to develop and test
hypotheses in animal behaviour
LEARNING OUTCOMES:
Lectures are grouped into six major subject areas of animal behaviour, at the end of which the student
should be able to
1. Plan and carry out a study of animal behaviour, as stand-alone work or as part of a broader
biological enquiry (General)
2. Describe how physiological mechanisms produce behaviour in the individual (Physiological
behaviour)
3. Use the principles of animal behaviour to investigate the function of animals in their environment,
including an introduction to social behaviour (Ecological behaviour)
277
4. Evaluate the complementary approaches of instinct and different types of learning to the
acquisition of behaviour by the individual (Learning and ontogeny)
5. Describe the principles of communication between individuals of the same and different species
(Communication)
6. Evaluate behavioural strategies as components of reproduction and associated activities of
animals (Reproduction)
ASSIGNMENTS:
Practicals
11. Readings in animal behaviour, and formulation of hypotheses (video/library)
12. Chemoreception, vision and orientation (laboratory)
13. Foraging behaviour in ants (outdoor, UWI)
14. Describing behaviour: Captive land vertebrates (zoo)
15. Social facilitation in chicks (laboratory)
Research Essay
A species behaviour account for the Online Guide to the Animals of Trinidad and Tobago (OGATT)
(http://sta.uwi.edu/fst/lifesciences/ogatt.asp). Submitted through myelearning, with a limit of 3%
similarity as determined by Turnitin (excluding references). Students may submit drafts to Turnitin from
week 3 up to the deadline (end of week 11) and view their Turnitin reports to correct any similarity in
excess of this value. The final version remaining at the submission deadline will be marked.
COURSE ASSESSMENT:
Coursework practical:
Coursework theory:
Final examination:
25%, based on the best 4 of the 5 practical marks from the written reports
and marks for participation. Due 7 days after the class
25%, from the research essay. Instructions given in weeks 2 and 3, final
essay due at the end of week 11 through Turnitin on myelearning.
50%. The examination is of 2 hours duration. It is based on essay
questions, with any two (2) questions to be completed from a choice of
five (5).
EVALUATION:
 Feedback on the course will be obtained informally from students on an ongoing basis by regular
interactions and meetings among students, demonstrators, teaching assistants and the Course
Coordinator in practicals and tutorials.
 Formal feedback will be via election of Class Representatives who sit on the Departmental StudentStaff Liaison Committee meetings held twice during the semester. Class reps will channel both
concerns and commendations to the meeting as guided by the Department’s Standard Operating
Procedures.
 Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation
questionnaire administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an ongoing basis and corrective action or adjustments made or
discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Credits:
3
Lectures:
18 hours
Tutorials:
6 hours
Practicals:
24 hours
278
Lectures and tutorials are given to the whole class, and practicals are usually delivered to the students in
two (2) streams. The course outline, objectives, readings, practical schedules, and instructions for the
research essay are available on myelearning, together with the opportunity for feedback through the
Academic Forum. Lecture materials are reduced to promote understanding of principles rather than
transmission of facts, in particular with diagrams simplified to the essentials. Practicals build in sequence
from initial observation and hypothesis formulation, laboratory experiments in physiological behaviour,
through observational studies in a zoo setting and in the field, to the design of group experiments to test
original hypotheses on campus. Practical schedules are available before the class to maximise usefulness
of the class time.
RESOURCES:
Texts:
Alcock, J. (2005). Animal Behavior: An Evolutionary Approach. 8th edition (6th-9th editions are useful).
Sunderland, MA: Sinauer.
Manning, A. & Dawkins, M.S. (2012). An Introduction to Animal Behaviour. 6th edition. Cambridge:
Cambridge University Press. [Available in the campus bookshop]
Ryan, M .J. & Wilczynski, W. (2011). An Introduction to Animal Behaviour: an Integrative Approach.
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. [Available in the campus
bookshop]
Search engine:
http://scholar.google.com/ is given as the preferred source of references for the research essay, as it
accesses academic papers rather than web sites.
READINGS:
Notice to the student: These readings have been selected as background material for the course. Each
corresponds to a numbered lecture, and should be read before the relevant lecture for greatest usefulness.
Where possible, primary sources (i.e. research papers) have been given, to show the type of material that
you should be using as references in your own work (lab reports, and particularly the research essay).
You should also use the same format for referencing (without giving notes). The notes also show which
readings are used by one of the recommended texts, so you can compare the form in which information
reaches the textbooks with the original sources: Alcock (A) or Manning & Dawkins (MD).
1. Tinbergen, N. (1963). On aims and methods of ethology. Z. Tierpsychol. 20: 410-433.
The classic paper on approaches to animal behaviour. A, MD
2. Lehner, P. N. (1987). Design and execution of animal behavior research: an overview. J. Anim.
Sci. 65: 1213-1219.
A short summary review, focusing on domesticated animals, of a subject on which the author
(Lehner, 1979, in literature cited) and others (Martin and Bateson, 1986) have written books.
3. Maynard Smith, J. & Price, G. R. (1973). The logic of animal conflict. Nature 246: 15-18.
A short but difficult theoretical paper, the first use of game theory in animal behavior. MD
4. McComb, K., Reby, D., Baker, L., Moss, C. & Sayialel, S. (2003). Long-distance communication
of acoustic cues to social identity in African elephants. Anim. Behav. 65: 317-329.
A recent paper on perception that relies on good experimental design rather than on advanced
techniques or statistics.
279
5. Ewert, J.-P. (1980). Neurobiological basis for the recognition and localization of environmental
signals: how does a toad brain recognize prey and enemy? Chapter 4 in Neuroethology. Berlin:
Springer-Verlag.
The primary literature on neural processing in behaviour is specialized, so a secondary source is
used: part of a chapter in Ewert’s monograph, describing his own work on toads. MD
6. Page, T. L., Caldarola, P. C. & Pittendrigh, C. S. (1977). Mutual entrainment of bilaterally
distributed circadian pacemakers. Proc. Natl. Acad. Sci. USA 74: 1277-1281.
A fairly accessible paper on the effects of optic lobe lesions on the circadian rhythm of a
cockroach.
7. Cristol, D. A. & Switzer, P. V. (1999). Avian prey-dropping behavior. II. American crows and
walnuts. Behav. Ecol. 10: 220-226.
Testing the predictions of an optimal foraging model. A
8. Burger, J. & Gochfeld, M. (2001). Smooth-billed ani (Crotophaga ani) predation on butterflies
in Mato Grosso, Brazil: risk decreases with increased group size. Behav. Ecol. Sociobiol. 49: 482492.
Group-living may also function as a defence against predation. A
9. Wilkinson, G. S. (1984). Reciprocal food sharing in the vampire bat. Nature 308: 181-184.
The classic study of reciprocal altruism. A, MD
10. Jacobs, L. F., Gaulin, S. J., Sherry, D. F. & Hoffman, G. E. (1990). Evolution of spatial cognition:
sex-specific patterns of spatial behavior predict hippocampal size. Proc. Natl. Acad. Sci. USA 87:
6349-6352.
Sexual differences in (spatial) learning ability in small mammals are associated with differences
in brain anatomy; the size of the hippocampus. A
11. Povinelli, D. J. & Dunphy-Lelii, S. (2001). Do chimpanzees seek explanations? Preliminary
comparative investigations. Can. J. Exp. Psychol. 55: 187-195.
A paper from comparative psychology directly comparing chimpanzees and children.
Chimpanzees show insight learning, but do not go the further step of theorizing, which is
restricted to man.
12. Marler, P. & Tamura, M. (1964). Culturally transmitted patterns of vocal behavior in sparrows.
Science 146: 1483-1486.
Song development in birds as a specialized form of learning. Note the small sample sizes and
lack of statistics in this old but classic paper. A, MD
13. Andersson, M. (1982). Female choice selects for extreme tail length in a widowbird. Nature 299:
818-820.
Experiments on the function of long tails as signals in male birds. A, MD
14. Briskie, J. V., Martin, P. R. & Martin, T. E. (1999). Nest predation and the evolution of nestling
begging calls. Proc. R. Soc. Lond. B 266: 2153-2159.
Nestling begging calls are related to the risk of predation among 24 species of forest birds. A
15. Seyfarth, R. M., Cheney, D. L. & Marler, P. (1980). Monkey responses to three different alarm
calls: evidence of predator classification and semantic communication. Science 210: 801-803.
Vervet monkey alarm calls as a form of language. MD
16. Clutton-Brock, T. H. & Vincent, A. C. J. (1991). Sexual selection and the potential reproductive
rates of males and females. Nature 351: 58-60.
Competition among females for males in species with sex role reversal. A
17. Westcott, D. & Smith, J. N. M. (1997). Lek size variation and its consequences in the ochrebellied flycatcher, Mionectes oleaginous. Behav. Ecol. 8: 396-403.
Both hotshot and hot-spot models of lek formation may operate simultaneously. A
18. Emlen, S. T., Demong, N. J. & Emlen, D. J. (1989). Experimental induction of infanticide in
female wattled jacanas. Auk 106: 1-7.
280
Female infanticide in a bird with sex role reversal. MD
COURSE CALENDAR:
Week
1
Lectures and Tutorials


2


3


4







5
6
7
8



9


10


11





12
13
Introduction to course
(Tutorial)
Approaches to animal
behaviour
Methods of studying
animal behaviour
History of the study of
animal behaviour
(Tutorial)
Evolution of behaviour
Discussion of research
essay (Tutorial)
Perception
Processing
Organization of behaviour
Tutorial
Feeding
Defence
Territory and social
behaviour
Instinct and learning
Types of learning
Learning and the
development of behaviour
Tutorial
Communication and
signals
Evolution of signals
Complex communication language
Reproductive strategies
Mating systems
Parental care
Tutorial
Course review
Practicals
Assignments
due
Readings in animal
behaviour
Practical 1
Chemoreception
Practical 2
Foraging behaviour
Practical 3
Captive land
vertebrates
Practical 4
Social facilitation
Research Essay
Practical 5
281
ADDITIONAL INFORMATION:





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet:
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf.
Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order
to obtain the marks for that item of coursework. The student is responsible for liaising with the Course
Coordinator or Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items
must be accompanied by a Coursework Accountability Statement in order to be assessed. Specific
items may require submission through Turnitin on myeLearning. Refer to ‘University Regulations
on
Plagiarism’
available
from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:



Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly advised to
able to fully participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress
and materials are also highly recommended and you should be checking into myelearning on a
frequent regular basis to review materials, assignments and activities.
Students are advised to read more than one of the many texts in animal behaviour available in the
Alma Jordan Library and the campus bookshop. The approaches of authors to the subject vary widely,
from the mechanistic (Ryan and Wilczynski is the latest of several) to the ecological (e.g. Alcock)
and the zoological/ethological (e.g. Manning and Dawkins). Students will learn best by comparing
these approaches and learning the important ideas in animal behaviour by reinforcement, while seeing
a range of examples and viewpoints, rather than cramming from a single source.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
282
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
AH 28 February 2013
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
Course code: BIOL3868
Course Title: THE ECOLOGY OF HUMANS
Credits: 3
Level: 3
Semester: 1
Pre-requisites: Either BIOL 1263 Living Organisms II or BIOL1261 Diversity of Organisms or (BIOL1065
Diversity of Plants and Animals and AGRI1012 Microbiology) and either BIOL 2XXX Fundamentals of
Ecology or BIOL1462 General Ecology and Biometry.
Anti-requisite: BIOL2461 Humans & the Environment
COURSE DESCRIPTION:
This course focuses on one of the most important animals on Earth today, Homo sapiens, considering the species
from a broad biological and ecological perspective. The course introduces the evolution and origin of modern
humans, the extent of their uniqueness in comparison with other animals and Primates, and the characteristics
that contribute to their unprecedented success and dominance of their environment. We also explore selected
283
aspects of human biology and ecology including genetic and cultural diversity and adaptation; technological and
lifestyle changes and their relationship with health and disease patterns; human populations, resources and
wellbeing; resource depletion, environmental degradation and global climate change. In conclusion we discuss
the future of the human animal.
Students are expected to have a basic foundation in ecology and biodiversity. In addition to providing a
foundation of theoretical knowledge, this course take a ‘hands-on’ approach where students are expected to
prepare, participate and perform in an active way in order to engage with the content in a variety of ways.
Assessment is designed to encourage students to work continuously with the course materials, explore and
critically analyse research in this complex and rapidly developing field.
Students are expected to have a basic foundation in animal biology.
PURPOSE OF THE COURSE/RATIONALE:
This is a core course for the Zoology specialisation in the Department of Life Sciences and is essential
background for environmental sciences, environmental biology and environmental management. It also broadens
the scope of studies in biology, plant biology and zoology. The course is an elective in the Department of Life
Sciences and augments the Biology major and Ecology & Environmental Biology specialisation.
Human actions threaten the very ability of the planet to support themselves and other organisms. It allows
students to look critically at the past and present circumstances of the species to which they belong and craft
solutions to face the future.
INSTRUCTOR INFORMATION:
Name of course coordinator:
Mary Alkins-Koo
Office address and phone:
Room 218, Zoology offices, Floor 2, New wing, Natural Sciences
Building
Email address:
[email protected]
Office hours:
Mondays 10-11am, Fridays 11-12am
Preferred method of contact:
Email
Communication policy: Students should use their UWI email account for communication and can expect a
response within 48 hours.
LETTER TO THE STUDENT:
Welcome to ‘The Ecology of Humans’.
In this course you will be introduced to the species to which you belong. You will investigate it using a broad
biological and ecological perspective to better understand our role on Earth as a dominant species, our
relationships with our environment and other species, and scenarios for the future.
The course will be taught in blended mode comprising both face-to-face and online delivery. You are expected
to engage with the materials provided online, in face-to-face lectures and tutorials as well as explore and interact
with these to develop the essential skills of critical thinking (clarity, accuracy, relevance, logic, breadth, depth,
precision, significance, completeness and fairness). Activities will be diverse and you are strongly encouraged to
ask questions, offer new ideas, problem solve and think innovatively to maximise the value of your learning
experience.
Please read the Course Outline carefully and keep the Course Schedule close to hand as it contains all the
activities and assessments during the semester. In particular take note of the policy on plagiarism and attendance
requirements.
We are here to ensure your success in this course and at UWI generally and encourage you to come to us with
any academic or other challenges you may face that could affect your attendance and performance.
284
I look forward to meeting each of you and engaging in productive stimulating discussions over the coming
semester.
Dr Mary Alkins-Koo.
Course Coordinator
CONTENT:
Topics to be covered in this course include:
 What makes us human?
 The human Primate
 The evolution and origin of modern humans
 Anatomy and bipedalism
 Culture, technology and lifestyles
 Genetic and cultural diversity and adaptation
 The brain, language and intelligence
 Sex, reproduction and life history
 Social behaviour and organisation
 Human populations
 Human well-being and inequity
 Human health and disease
 Resources for the future
 Environmental degradation
 Global climate change
 The future of the human animal
GOALS/AIMS:
This course aims to



Study the human animal from a broad biological and ecological perspective
Evaluate the features that contribute to our unprecedented success and dominance as a species
Explore the major issues facing the species for future survival and consider potential broad approaches
to deal with some of these issues

GENERAL OBJECTIVES
The general objectives of this course are to:




engage students in a critical analysis of current knowledge and understanding of the evolution, biology
and ecology of the modern human species
facilitate discussions on biological and other features of modern humans that have given rise to their
success and dominance
explore the many dimensions of the complex issues facing humans with particular reference to health
and disease, availability of resources, environmental degradation and global climate change
lead students in the creative process of crafting solutions for the major issues facing humans in the future
LEARNING OUTCOMES:
At the end of this course, students should be able to

Evaluate the proposed unique characteristics of the human animal and assess the biological classification
of the human species
285

Give a chronological account of the proposed biological evolution of modern humans from anthropoid
ancestors and the associated stages of cultural and technological development
 Define biological success and dominance and analyse how selected characteristics have contributed to
human success and dominance, e.g. anatomy, diversity, adaptability, the brain, language, intelligence,
reproductive patterns, life history, social behaviour, social organisation, culture, technology and
lifestyles.
 Describe the historical trends in human population growth and regional variation in demographic
parameters, assess the influential factors contributing to such trends and outline projections and
consequences for the future.
 Define the components of human well-being and discuss the status and consequences of inequity within
populations and among nations.
 Assess the impacts of human populations, technology and lifestyles on ecosystems, food, water and
material resources, and the effects of such impacts on human well-being including global climate
change.
 Discuss and evaluate the proposed scenarios for the future of human populations, resources and the
environment.
 Demonstrate skills in analysis, synthesis, evaluation of complex information; good oral and written
communication; craft creative solutions using a variety of tools and strategic approaches; manage group
interactions and work effectively in teams.
COURSE ASSESSMENT:
Assessment will be based on a student’s final mark from the components below.
Component
Final exam
Coursework
% Final
Grade
50%
50%
In-course tests
20%
Tutorials, online activities
15%
Practicals
15%
Description
2-hour written exam with essay questions
Broken down as follows:
2 tests (each 10%) based on multiple choice, true/false, short
response questions or essay
Performance in face-to-face and online discussions and
activities
Performance and reporting of 3 practical exercises
ASSIGNMENTS:

In-course tests (20%): 2 tests (each 10%) each 50 minutes duration including multiple choice, true/false,
short response questions
 Tutorials, online activities (15%): Participation, performance and contributions in face to face tutorials and
online discussions/activities
 Practicals (15%): Practical performance and reporting of 3 practical exercises.
Please note guidelines and policies for attendance and plagiarism under ‘Additional Information’ and below.
EVALUATION:
 Feedback on the course will be obtained informally from students on an ongoing basis by regular
interactions and meetings among students, demonstrators, teaching assistants and the Course Coordinator in
practicals and tutorials.
286



Formal feedback will be via election of Class Representatives who sit on the Departmental Student-Staff
Liaison Committee meetings held twice during the semester. Class reps will channel both concerns and
commendations to the meeting as guided by the Department’s Standard Operating Procedures.
Formal evaluation of the entire course will be accomplished via a UWI Course Evaluation questionnaire
administered anonymously and confidentially at the end of the semester.
All feedback will be considered on an ongoing basis and corrective action or adjustments made or discussed
with students promptly or incorporated the following year.
TEACHING STRATEGIES:
Contact hours 36 hours:
Lectures: 24 h
Tutorials: 6 h
Practicals: 6 h (3x4 h = 12h practicals)

Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of available
information, update current issues and events, and prioritise content relevant to course assessment. Lectures
will generally be ‘flipped’ i.e. students are expected to use online resources to read and prepare in advance
of the lecture so that the session can focus on questions, clarification, expansion and discussion.
 Practicals: Practicals will provide detailed exposure to selected topics and experiences and involve
interactive activities and discussion to analyse, synthesise and evaluate complex issues and concepts.
Participation and performance in the practicals will be assessed as well as reports based on the practical
activities.
 Tutorials: Tutorials will cover course topics in a highly interactive format using a variety of collaborative
active learning techniques. In addition to clarifying details of course content, specific transferrable skills will
be addressed e.g. essay and report writing, critiquing and oral presentation.
 myelearning: The online teaching tool, myeLearning, will be used extensively during this course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials and links to resources on specific websites
 self-test quizzes, questionnaires, surveys
 interactive activities such as discussions, wikis, glossaries, blogs
RESOURCES:
Most resources are available myeLearning including


Lecture presentations - include learning objectives, summaries, recommended readings
Resources - links to papers, articles and websites with interactive resources and videos for those who
prefer to learn using these modalities
 Tutorials - guidelines for tutorial activities and specific supporting resources
 Practicals - guidelines for practical activities and specific supporting resources
Essential and Recommended texts are in the Reserve Section, UWI Main Library or via links in the course
outline and myelearning
Readings:


Diamond, J. 1992. The Third Chimpanzee. Harper.
Jones, S., R. Martin & D. Pilbeam. 1992. The Cambridge Encyclopaedia of Human Evolution.
Cambridge UP.
287
 Kormondy, E.J. & D.E. Brown. 1998. Fundamentals of Human Ecology. Prentice-Hall.
Web links:



Smithsonian Institution, National Museum of Natural History, Human Origins Programme.
http://humanorigins.si.edu/
Human Biology. Wayne State University Press. http://www.bioone.org/loi/hbio
UNEP. 2012. Global Environment Outlook 5 (GEO-5). UNEP. http://www.unep.org/geo/geo5.asp
COURSE CALENDAR:
WEEK
40.
41.
42.
43.
44.
45.
46.
47.
48.
49.
50.
51.
52.
LECTURES
99. Course Introduction
100.
What makes us human?
101.
The human Primate
102.
The evolution and origin of
modern humans
103.
The evolution and origin of
modern humans
104.
Anatomy and bipedalism
105.
Culture, technology and lifestyles
106.
Culture, technology and lifestyles
107.
Genetic and cultural diversity and
adaptation
108.
The brain, language and
intelligence
109.
Sex, reproduction and life history
110.
Social behaviour and organisation
111.
Human populations
112.
Human populations
113.
Human well-being and inequity
114.
Human health and disease
115.
Human health and disease
116.
Resources for the future
117.
Resources for the future
118.
Environmental degradation
119.
Environmental degradation
120.
Global climate change
121.
Global climate change
122.
The future of the human animal
Course review
PRACTICALS
TUTORIALS
Assignments
Tutorial 1
Practical 1: Primate
behaviour (Zoo)
Tutorial 2
Practical 2: Human
biological evolution
Online activity 1
Tutorial 3
In-course Test 1
Practical 3: Lifestyles and
health
Tutorial 4
Tutorial 5
Tutorial 6
Online activity 2
In-course Test 2
ADDITIONAL INFORMATION:
 Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching, assessment, student
conduct, essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
288



Students are reminded that they must attend a minimum of 75% of the practical sessions and tutorials.
Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an assigned time.
Students must still complete the assigned work (make-up lab report or make-up test) in order to obtain the
marks for that item of coursework. The student is responsible for liaising with the Course Coordinator or
Teaching Assistants to ensure the assigned make-up is completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items must be
accompanied by a Coursework Accountability Statement in order to be assessed. Specific items may require
submission through Turnitin on myeLearning. Refer to ‘University Regulations on Plagiarism’ available
from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures, tutorials and practicals.
 Prior preparation is strongly advised to able to fully participate in activities and obtain the full value of the
sessions.
 Thorough use should be made of the resources provided and students are strongly advised to become
familiar with them and start utilising them from the first week. Regular updates on course progress and
materials are also highly recommended and you should be checking into myelearning on a frequent regular
basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned tutorial
times to ensure prompt, satisfactory solution of any problems and to monitor progress.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
289
MAK: 18 February 2013
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION
COURSE CODE: BIOL3870
COURSE TITLE: Insect Biology
NO. OF CREDITS: 3
LEVEL III
PRE-REQUISITE: BIOL 2867 Physiology of Animals or BIOL2862 Animal Physiology
ANTI-REQUISITE: BIOL2866 Entomology
COURSE DESCRIPTION
The first half of the course treats the unity of insects, i.e. those features that are common to all or
many orders. The second half is an evolutionary survey of the insects, with some attention to arachnids,
treating major orders and some families or superfamilies. In addition, one lecture is devoted to a more
in-depth treatment of a selected group of insects or arachnids or a particular theme in arthropod biology.
The basic teaching/learning approach is a traditional one of practical exercises followed by
lectures and reading. Assessment is by means of reports on practical exercises, tests and an individualized
species account.
COURSE RATIONALE
Insects are an extremely speciose and abundant group of organisms on land and in fresh water,
accounting for about half of all known species of organisms. As such, they have enormous ecological
impact, apart from the economic and medical importance of some groups. For a biologist with special
attention to the whole-organism and population levels or organization, then, knowledge of the biology
and diversity of insects is a key part of being educated.
INSTRUCTOR INFORMATION
Christopher K. Starr
290
Natural Sciences Bldg new wing Rm 225, phone ext 3096 or 303-9919
[email protected]
Office hours: Most days from about 07:30 to about 18:30
LETTER TO THE STUDENT
Dear Scholar,
It is my distinct pleasure to welcome you to BIOL 3xxx – Insect Biology. I will not pretend to
regard this subject with cool detachment, as it has been my unshakeable conviction for almost 60 years
that these creatures are, quite simply, the most interesting feature of the known universe. Insects are
ubiquitous and strikingly abundant in land and freshwater environments throughout the inhabitable
world, where they have enormous ecological impact. It is my business to aid you in learning who they
are, what they are like, and their major roles in ecosystems. By doing well in this course, you will arm
yourself with an understanding of a critically important part of the biota.
Sincerely,
Christopher K. Starr
Professor of Entomology
CONTENT: As outlined in the course calendar
GOALS/AIMS
The course aims to provide a solid grounding in both the unity and diversity of the class Insecta,
with some attention to the class Arachnida. Students who do well will have a good understanding of
how insects are built and what distinguishes them from other animals. In addition, they will be familiar
with major orders of insects and their ways of life.
LEARNING OUTCOMES
At the end of this course, students will be able to:
1. Characterize the global diversity of insects and discuss putative reasons for this diversity.
2. Outline the structure and nature of the insect cuticle and its importance in the success of insects.
3. Take a generalized adult insect apart and put it back together again.
4. Define and describe “metamerism” and “tagmosis” to any literate person in such a way as to
convey a satisfying basic understanding.
5. Describe the main features of major organ systems in insects and their functioning, with
emphasis on how these differ from our own organs.
6. Describe the basic structure of wings and how flight works.
7. Explain the concept of the “sensory world” and explain cogently how this differs between
ourselves and a generalized adult diurnal insect.
8. Describe the three major forms of metamorphosis.
9. Hold forth on the developmental, ecological and evolutionary significance of the pupa.
10. Name a dozen orders of insects and outline the distinguishing physical and ecological features
of each.
291
11. Name three groups of ectoparastic insects and compare them with respect to gross structure and
way of life.
12. Name three orders of arachnids and outline the distinguishing physical and ecological features
of each..
ASSIGNMENT
The theory coursework, accounting for 10% of total marks, will be a species account in the style
of those in D.H. Janzen’s (1983) Costa Rican Natural History. Species will be individually assigned to
students by lot early in the semester, with the finished species account due four weeks later.
COURSE ASSESSMENT
Practical coursework
Lab book ... 15%
Two in-course lab tests ... 20%
Theory coursework
Assigned species account ... 15%
Final theory exam ... 50%
EVALUATION
The Department of Life Sciences takes the quality control of its courses very seriously. Students
who have comments on one or another aspect of a course are encouraged to communicate these to the
instructors. More formal feedback is sought through the Staff-Student Liaison Committee, which meets
twice per semester. This departmental committee comprises elected student representatives from each
course in the given semester. In addition, the university conducts a confidential written evaluation of
most courses and their instructors toward the end of each semester.
TEACHING STRATEGIES
The course comprises 18 lectures one-hour lectures, six one-hour tutorials and eight three-hour
practical sessions. Tutorials are about collective problem solving with minimal lecture-style talking by
the instructor. However, lectures always have a certain tutorial aspect, so that the instructor will often
pose questions to members of the class and will expect answers. Students who prefer to sit passively in
class without active involvement should not register for this course.
Where a given topic arises both in a practical exercise and in lecture, every effort is made to treat
it in lab first. That is, it is much preferred in lecture to draw attention to prior practical observations and
try to make sense of them than to say what the student can expect to observe later in the lab or field.
Students are expected to read widely in materials available in the university library, on the internet
and on MyeLearning, as an extension of topics summarized in lecture.
RESOURCES
There is no dearth of suitable reading matter in the university library, on the internet and on
MyeLearning. The library has several relevant textbooks of general entomology (QL461) and a good set
of books on the ecology and behaviour of insects (mostly around QL495), as well as on particular groups
(in the QL500- and QL600-ranges). In some cases, these are placed on reserve.
292
Practical exercises in the field and lab will make use of standard equipment and materials. In
addition, we will have access to the department’s significant library of natural-history movies on DVD.
The course manual is the 2006 edition of the in-house Neotropical Entomology: Study Guide for
BIOL 2866.
READINGS
Ambrose, D.P. 2004. The Insects: Structure, Function and Biodiversity. Ludhiana: Kalyani 821
pp.[Sections 1 and 3 good for weeks 2-6, but disregard for later weeks.]
Chapman, R.F. 1998. The Insects: Structure and Function. Cambridge: Cambridge Univ. Press
770 pp.[Very good for weeks 2-6, although treatment of many topics more detailed than you want.]
Davies, R.G. 1988. Outlines of Entomology. London: Chapman &Hall 408 pp. [Good on all
topics.]
Elzinga, R.J. 2004.Fundamentals of Entomology. 6th ed. Upper Saddle River, New Jersey:
Pearson-Prentice Hall 512 pp. [Good for all topics. Illustrations especially good.Earlier editions also
useful.]
Gillott, C. 2005. Entomology. 3rd ed. Dordrecht: Springer 831 pp.[Very good for first half of
course, okay for second half.Some earlier editions on shelf.]
Ross, H.H., C.A. Ross & J.R.P. Ross 1991.A Textbook of Entomology. 4th ed. Malabar, Florida:
Krieger 666 pp. [Good for second half of course, but disregard for first-half topics. Earlier editions on
shelf.]
See also non-circulating encyclopedias of entomology on shelf at QL462.3.
COURSE CALENDAR
Note that Saturday is regarded as a school day at UWI, with class exercises sometimes scheduled
for that day. Students with scruples against Saturday schoolwork should not register for this course.
Week
1
2
3
Practical
Morphology of a
generalized adult
insect
Field trip to
secondary
lowland forest
4
5
Metamorphosis
and larval growth
rates
Lecture/tutorial
Introduction to the scope and limits of
entomology
The nature of insects and their success
Tutorial: Estimating the global species
richness of insects
Structure and functions of the cuticle
Metamerism, segmentation and tagmosis
Assignment
Lab report due
Internal morphology and physiology
Circulation and respiration
Tutorial: The limits of growth
Internal morphology and physiology
Feeding, excretion and reproduction
Flight
Internal morphology and physiology
Central nervous system and perception
Tutorial: Sensory world of the honey bee
Lab report due
293
Week
6
Practical
Evolutionary
survey:
Primitively
wingless orders,
Odonata,
orthopteroid
orders
7
8
9
10
11
12
Evolutionary
survey:
hemipteroid
orders
Evolutionary
survey:
Coleoptera
Evolutionary
survey:
Lepidoptera,
Diptera,
Siphonaptera
Evolutionary
survey:
Hymenoptera,
Arachnids
Lecture/tutorial
Growth and allometry
Metamorphosis and the nature of the
pupa
Assignment
Lab exam
Collembola and Odonata
Tutorial: Reading the cladogram of insect
orders
Orthopteroid orders
Lab report due
In-depth lecture: Our dear friend the
termite (Isoptera)
Hemiptera
Tutorial: Ectoparasitic insects
Assigned species
account due
Coleoptera
Lepidoptera (moths and butterflies)
Lab report due
Diptera
Tutorial: Shifting balances in
metamorphosis
Hymenoptera
Arachnida
Lab exam
ADDITIONAL INFORMATION
Attendance is not recorded at lectures and tutorials, but missing them is not a good idea.
Attendance at practical exercises is mandatory, and the student should report any excusable absence
promptly (in advance, if this is feasible).
HOW TO STUDY FOR THIS COURSE
It is a regrettable necessity that students must work in isolation during final exams and other tests.
At all other times, collaborative work is warmly encouraged. There is much to be gained from discussion
of topics and problems among classmates.
294
Lectures provide a necessary focus for studying, but they do not by any means provide the entirety
of what should be learned. Rather, the student should take lecture material as a point of departure in
extensive outside reading. This supplemental material deepens one’s understanding of principles treated
rather summarily in lecture and provides illustrations of these principles.
It is a good idea to bring your copy of the course manual not only to lab but to lecture as a matter
of course. It includes summaries of all lectures and a number of illustrations and appendices to which
reference will be made in lecture.
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
Proposal for introducing new course in the Department of Life Sciences
Course code: BIOL 3960
Course Title: Environmental Microbiology
295
Number of Credits: 3
.
Level: Undergraduate –Year III
Pre-requisites:
BIOL 2265 – Fundamentals of Microbiology (at least B-)
BIOL 2164 - Principles of Molecular Biology
BIOL 2165 - Genetics II
BIOL 2360 - Biochemistry IIA
Semester: 1
Offering Department:
Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St.
Augustine
Enrolment capacity: 45
Course description
This course explores the diversity and function of microorganisms in the environment. Emphasis is
placed on metabolic processes employed by microbes to transform organic and inorganic substances as
part of bio-geochemical cycles. The role of microorganisms in pollution of water, soil and air is
considered in addition to microbial processes used in environmental remediation and conservation.
Conventional and molecular-based tools used for detecting, characterizing and monitoring microbes in
the environment are also covered. The teaching and learning methods include lectures/tutorials,
discussion sessions and labs. Assessment would be via coursework (50% comprising incourse tests,
graded practical reports, class participation) and final semester exam (50%).
Purpose of course/rationale
BIOL3960 forms part of the proposed microbiology specialization in the biology degree in the
Department of Life Sciences and it would serve as an elective in the ESST programme in the Faculty of
Science and Technology, UWI, St. Augustine. It will be highly beneficial to students with specific
interest in environmental microbiology and environmental science. The course is designed to introduce
students to fundamental theoretical principles and develop key practical skills in environmental
microbiology. Environmental microbiology is an important sub-discipline of microbiology and is critical
to environmental management and sustainability. It also contributes significantly to environmental health
and microbial biotechnology.
Instructor Information
BIOL 3960 will be managed by a course coordinator and will be taught by a team of experienced
lecturers, supported by a Teaching Assistant/Instructor and laboratory demonstrators. Office hours for
the coordinator and lecturers are posted on the faculty bulletin boards and are available from the
Department of Life Sciences’ general office. Team members can also be contacted via e-mail.
Name: Adesh Ramsubhag (Co-ordinator)
296
E-mail:
Office location:
Office hours:
Phone:
Name:
E-mail:
Office location:
Office hours:
Phone:
Letter to students
Welcome to BIOL 3960- Environmental Microbiology. This course provides an exciting opportunity to
be introduced into the exciting field of environmental microbiology. It would provide a platform for
developing a fundamental understanding of theoretical concepts and practical skills in exploring
microbes in the environment and applying them in management of the environment. A major emphasis
would be to develop critical thinking skills. Interactive participation in lectures, tutorials and practical
sessions is essential. Please feel free to ask questions or offer alternative perspectives. You would also
need to focus on personal attributes of team work and inter-personal skills required for group work, in
addition to organizational skill and time management. I wish you the most interesting and intellectually
stimulating experience in this course.
Content:
BIOL3960 covers the following content:
1. Overview of diversity and distribution of microorganisms in aquatic and terrestrial
environments.
a. Surface
b. Shallow subsurface
c. Deep sub-surface
2. Carbon and energy metabolism of environmental microorganisms in aerobic and anaerobic
environments.
a. Chemoheterotrophy
b. Chemoautotrophy
c. Photoheterotrophy
d. Photoautotrophy
3.
4.
5.
6.
7.
8.
Role of microbial metabolism on bio-geochemical cycles
Survival mechanisms of microbes in extreme environments
Microbial communication and interactions with higher organisms
Pollution microbiology- water, soil and air.
Traditional and new microbial indicators of pollution
Detecting, enumerating and monitoring microorganisms in the environment
a. Culture based methods
b. Direct microscopic counts
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c. Physiological and immunological methods
d. Conventional nucleic acid and PCR based methods
e. “OMICS” based approaches
9. Water, air and soil bioremediation
10. Microbial processes in water and wastewater treatment systems
Course goal:
The goal of the course is to expose students to general theoretical concepts and develop fundamental
practical skills in environmental microbiology.
General Objectives:
Students completing the course will have:
1. A critical review of microbiological processes in the environment;
2. Fundamental practical skills in detecting, enumerating and monitoring environmental
microorganisms.
Learning objectives:
Upon completing this course, students will be able to:
- Summarize the diversity and distribution of major groups of microorganisms in the
environments;
- Explain the carbon and energy metabolic processes of environmental microorganisms;
- Explain the role of microbial metabolism on bio-geochemical cycles;
- Compare the survival mechanisms of microorganisms surviving in extreme environments;
- Explain microbial communication and interactions strategies;
- Assess the role of microorganisms in pollution of water, soil and air;
- Critique the traditional and new microbial indicator-based methods of assessing faecal
pollution;
- Evaluate the various ways of detecting, enumerating and monitoring microorganisms in the
environment
a. Culture based methods;
b. Direct microscopic counts;
c. Physiological and immunological methods;
d. Conventional nucleic acid and PCR based methods;
e. “OMICS” based approaches;
- Devise bioremediation strategies for contaminated water, air and soil;
- Explain the microbial processes in water and wastewater treatment systems.
Mode of Delivery:
Lectures -18 hours:
Tutorials -12 hours:
Practical exercises:
Didactic; interactive
Interactive; mind maps; problem-solving
Five 3-hr sessions
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ASSIGNMENTS:
Coursework for BIOL 3960 will be assigned as follows:
1. In-course Test-20%
Two in-course tests worth 10% each in week 5 and 10.
2. Practical reports-20%
Students are required to complete five laboratory reports based on practical exercises worth 4%
each.
3. Journal paper discussion and reports - 5%
Students will be given one journal article on relevant environmental microbiology research to
study. The paper will be discussed in class and students will be required to submit summary
reports on each paper.
4. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned at
the end of the semester. Participation shall include more than just showing up at tutorial – some
evidence of an active role in the tutorial discussion would be required to obtain the full 5% for
participation. At the beginning of the semester, the students in each tutorial would engage in
developing the exact assessment criteria for this assignment, and the student-developed criteria
will be used to determine each student’s participation grade.
Cheating, including plagiarism, would not be tolerated. Incidents of cheating would be dealt with
according to UWI’s rules and regulations including:
-
Examination Regulations for First Degrees, Associate Degrees, Diplomas and Certificates.
Section
(B)
Cheating.
Regulations
96–102;
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf.
-
University Regulations on Plagiarism (First Degrees, Diplomas and Certificates).
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf.
Assessment:
Course Work: 50%
- Incourse tests (Two written tests X 10%)
- Lab reports
- Journal paper discussion and reports
- Tutorial Attendance and participation
20%
20%
5%
5%
Final Semester Examination: 50%
- One 2-hour comprehensive written paper comprising of
o 4 short answer questions worth 10% each
40%
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TOTAL
o 2 essay-type question worth 30% each
All questions in this paper shall be compulsory
60%
100%
EVALUATION: BIOL3960 will be evaluated in two ways – (a) through the offices of the Class
Representative and the Life Sciences Student-Staff Liaison Committee, and (b) an end of semester course
evaluation survey. The class will elect four class representatives (one per lab stream), whose role is to
act as a mediator between the Life Sciences academic staff and the students in the class. The
representatives will attend Liaison Committee meetings (held at least twice per semester), where they
will present feedback on the course to the Department for action. The UWI performs a course evaluation
survey at the end of every semester, and this information will also be used for overall assessment of the
course and guide possible actions for improvement in subsequent semesters.
TEACHING STRATEGIES: A combination of teaching strategies will be adopted in BIOL3960.
The primary teaching strategy will be based on the face to face classroom lectures and discussions.
Videos of lecture presentations would be made available to students prior to the lecture session via
podcast media. Students are advised to view these videos before the lecture so that more emphasis can
be placed on discussions and answering questions, thereby facilitating deep learning. This would also
afford the time to have assessment exercises on “writing across the curriculum”. MyeLearning will be
utilized throughout the course as a means to provide access to course materials such as Powerpoint
presentation files, animations, weblinks, lessons and quizzes. This medium would also be used as a portal
for student-lecturer communications and the dissemination of coursework feedback.
A total of 12 tutorial sessions would be given for the semester. These would be small group sessions
which would be conducted by instructors or tutors, who would normally by senior postgraduate students
in Life Sciences. Students must attend tutorial sessions. Tutorials sheets will be assigned prior to each
session via myeLearning, and students are expected to attempt the solutions before coming to tutorial.
The goal of the tutorial session is to give students a more hands-on experience with the course material
and easier access to course instructors. Students will be expected to ask and answer questions on material
that is unclear, propose solutions to questions on the tutorial sheet and to generally participate fully in
the tutorial activities. Tutors will not merely be going through the answers to the tutorial questions in
these sessions.
The practical component of the course would comprise of 5 laboratory exercises that include laboratory
management systems, general & specific methodologies applied to environmental microbiology, and
applications to water, soil and air. The exercises would be based on conventional microbiological
techniques and molecular methods such as singleplex and multiplex conventional PCR and qPCR;
metagenomics applications for investigating microbial communities; and molecular-based biosensors.
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In order to pass the course, you must gain an overall passing mark of 50%. Any student who
misses more than 25% of practical or tutorial sessions without a medical or other valid excuse can
be debarred from writing the final exam.
RESOURCES:
Text books:
Essential:
Ian L. Pepper, Charles P. Gerba, Terry J. Gentry (Eds) Environmental Microbiology, Third
Edition Hardcover, 2014, Academic Press, San Diego, USA
Recommended:
Eugene L. Madsen, Environmental Microbiology: From Genomes to Biogeochemistry, 2015,
Wiley-Blackwell, USA
Ian L. Pepper (Author), Charles P. Gerba (Author), Jeffrey W. Brendecke, Environmental
Microbiology, Second Edition: A Laboratory Manual, 2004, Academic Press, San Diego,
USA
Lab coat:
- Each student should have suitable Lab coat to use for practical exercises. Students not having
lab coats will not be permitted in the lab.
Standard microbiology laboratory, equipment, reagents and kits
Microbiology technician and demonstrators
Course calendar:
Week
Lecture/Tutorial/lab
1
Introduction to course
Diversity and distribution of microorganisms in aquatic and terrestrial
environments
2
Tutorial
Microorganisms in the environment:
- Surface
- Shallow subsurface
- Deep sub-surface
Photoheterotrophy vs photoautotrophy
3
Tutorial
Chemoheterotrophy vs chemoautotrophy
Microorganisms and bio-geochemical cycles
Tutorial
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Week
Lecture/Tutorial/lab
Lab: Microbiology Lab, Management of systems (Data management,
Lab safety, Certification, Quality control and standards)
4
Microorganisms and bio-geochemical cycles
Survival mechanisms of microbes in extreme environments
Tutorial
5
Microbial communication and interactions with higher organisms
Tutorial
Lab: General environmental microbiology laboratory methods
Advanced quantitative plating methods; Isolation and quantitation of
phages;
Incourse test- 5% (online)
6
Pollution microbiology- water, soil and air.
Tutorial
7
Pollution microbiology- water, soil and air.
Traditional and new microbial indicators of pollution
Tutorial
Lab: Water microbiology
8
Detecting, enumerating and monitoring microorganisms in the
environment
Tutorial
9
10
11
Journal report due
Detecting, enumerating and monitoring microorganisms in the
environment
Tutorial
Lab: Soil Microbiology
Water, air and soil bioremediation
Tutorial
Incourse test 2 (10%)
Water, air and soil bioremediation
302
Week
Lecture/Tutorial/lab
Tutorial
Lab: Air microbiology
Microbial processes in water and wastewater treatment systems
Tutorial
12
31
Review
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
303
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DESCRIPTION
Course Code: BIOL3961
Course Title: PRINCIPLES OF MEDICAL MICROBIOLOGY
No. of credits: 3
Level: III, Sem I
Prerequisites:
BIOL2265-Fundamentals of Microbiology (minimum grade B-)
BIOL 2164 - Principles of Molecular Biology
BIOL 2165 - Genetics II
BIOL 2360 - Biochemistry IIA
Enrollment Capacity: 45 maximum:
Course Description: BIOL3XXX- Principles Medical Microbiology gives students a detailed insight
into the principles and techniques of microbiology applied to human medicine. It covers medically
important bacteria, viruses, fungi and parasites. Emphasis is placed on classification, detection and
diagnosis of microbial pathogens and parasites in addition to their mechanisms and clinical
manifestation. Students would also gain an understanding of epidemiological factors that contribute to
human infectious disease and be introduced to the uses and challenges of antimicrobial and anti-parasitic
agents for managing microbial diseases. The teaching and learning methods include lectures/tutorials and
laboratory sessions. Assessment would be via coursework (50% comprising incourse tests, graded
practical reports, class participation) and final semester exam (50%).
Course Rationale
BIOLXXXX forms part of the proposed microbiology specialization in the biology degree in the
Department of Life Sciences. It will be highly beneficial to students with specific interest in medical
microbiology. The course is designed to introduce students to fundamental theoretical principles and
develop key practical skills in medical microbiology. There is a current necessity for skill development
in this field at the undergraduate level which will provide students with opportunities for employment in
medical laboratories. The curse will also enable students to prepare for higher studies in Microbiology,
Epidemiology, Biotechnology and Biochemistry.
Instructor Information
BIOL XXXX will be managed by a course coordinator and would be taught be a team of
experienced lecturers, supported by a Teaching Assistant/Instructor and laboratory
304
demonstrators. Office hours for the coordinator and lecturers are posted on the faculty bulletin boards
and are available from the Department of Life Sciences’ general office. Team members can also be
contacted via e-mail.
Name of instructor(s):
Office address and phone:
Email address:
Office hours:
XXXXXX
XXXXXX
XXXXXX
XXXXXX
Letter to Students
Welcome to BIOL XXXX- Principles of Medical Microbiology. This course provides the basic
knowledge about microbial pathogens and parasites as well as information and skills for applications to
human health and disease management. The course is taught through a series of lectures/tutorials, and
laboratory sessions. It is quite extensive and students must make a sincere effort to do well by full
participation and involvement in course activities. It is important to attend lectures. Please make use of
supplementary information provided to strengthen foundation and enhance understanding of material
covered.
Content
An introduction to medical microbiology including general properties, nomenclature, classification and
pathogenicity of bacteria, fungi, viruses and parasites. Systematic study of medically important bacteria,
fungi and parasites. An overview of medically important viruses. Principles of Clinical Bacteriology,
Public Health Bacteriology, Mycobacteriology, Hospital Acquired Infections; Microbial toxins and
enzymes in disease; Innate and adaptive immunity and microbial infections; Laboratory diagnosis of
bacterial, viral and fungal diseases and parasitic infestations. Antimicrobial agents and antibiotic
resistance. Principles of epidemiology of human infectious diseases.
Goals/Aims
This course aims to:

present students with the background on human disease problems caused by microbial pathogens
and parasites.

introduce students to scientific developments and information on human microbial pathogens and
parasites, and their management.

expose and update students to the constantly evolving procedures and techniques of medical
microbiology
Learning Outcomes
At the end of this course students will be able to:
 summarize the characteristic features including morphology, physiology, genetics, modes of
transmission and diseases of medically important bacteria, fungi, viruses and parasites;
305







explain the mechanisms of pathogenesis of microbial pathogens;
explain the role of toxins and enzymes in infectious disease;
discuss host responses and related epidemiology to pathogenic infections and parasitic
infestations;
distinguish the different antimicrobials and antiparasitic agents and explain the development and
spread of resistance to these agents;
compare and contrast the different approaches for diagnosing infectious diseases and parasites;
apply microscopic, biochemical, serological and molecular based tools to diagnose common
infectious diseases and parasites;
demonstrate skills in critical thinking, laboratory experimentation, teamwork and
communication;
Assignments:
Coursework for BIOL 3XXX will be assigned as follows:
1. In-course Test-20%
Two in-course tests worth 10% each in weeks 6 and 11.
2. Practical reports-20%
Students are required to complete five laboratory reports based on practical exercises worth 4%
each.
3. Journal paper discussion and reports - 5%
Students will be given one journal article on relevant medical microbiology research to study.
The paper will be discussed in class and students will be required to submit summary reports on
each paper.
4. Class participation- 5%
Student participation in tutorial sessions will be monitored by the tutor and a grade assigned at
the end of the semester. Participation shall include more than just showing up at tutorial – some
evidence of an active role in the tutorial discussion would be required to obtain the full 5% for
participation. At the beginning of the semester, the students in each tutorial would engage in
developing the exact assessment criteria for this assignment, and the student-developed criteria
will be used to determine each student’s participation grade.
Course Assessment
Coursework: 50%
- Two incourse tests (2 X 10%)
- Lab reports
- Journal paper discussion and reports
Attendance and participation
20%
20%
5%
Tutorial
5%
Final exam – 50%
Evaluation
306
 The elected Class Representative and/or Deputy will attend meetings with the course teacher(s)
organized at every 4th week, and present feedback from the students attending that course or stream.
This feedback is normally provided both orally and in written form for transmission to the lecturer.
Apart from that the representatives will be attending the Liaison Committee meeting, and give their
feedbacks to the committee.
 Students may comment on any aspect of the course or facilities. Students will be encouraged to submit
their feedback (oral/written) during tutorials directly to the course teacher and appropriate actions will
be taken by the teacher then and there.
 Results of in-course tests, quiz and other course assignments will be analyzed and presented in the
class. This will help students to check their progress constantly and also helps the instructor to identify
the weak areas and thereby could alert and advise students individually to alter their approach of study
and completing the work.
 The final reflective feedback and comments about the entire course and teaching will be collected on
the last day of the course. This will be saved for analysis and utilized as a base for improvement for
the next offering in the following year.
Teaching Strategies
Contact hours (36 hours):
Lectures+Tutorials:
26 h
Practicals:
20 h
Students are expected to learn through both directed and self-directed study. Formal instruction for this
course would comprise of 2 Lectures with inbuilt tutorials per week and 5 practicals involving laboratory
exercises. Additionally, instructional videos, would be utilized to support the teaching. Formal lectures
and tutorials will provide introduction to specific topics and allow for discussion in an interactive setting.
Case studies/journal papers discussion will be carried out in small group settings. Course materials and
readings will be available online in advance so that discussion and critiquing can take place within the
assigned class time. This course is fully mye-learning supported, and many other resources would be
readily available for the students.
Resources
Recommended reading:
- Medical Microbiology, 7th Ed. (2012) Murray, Rosenthal, and Pfaller, Elsevier-Mosby,
ISBN: 978-0-323-08692-9
-
Medical Microbiology, 4th Ed. (2004) Ryan and Ray (Eds.), McGraw-Hill, ISBN: 0-83858529-9.
307
-
Medical Microbiology, A Guide to Microbial Infections: Pathogenesis, Immunity, Laboratory
Diagnosis, and Control, 17th Ed. (2007) Greenwood, Slack, and Peutherer (Eds.), Churchill
Livingstone; ISBN: 978-0443102097
-
Medical Microbiology, Anjali Aggarwal (2010) International Scientific Publishing Co., New
Delhi, India. ISBN: 81-8293-034-0.
Lab coat:
Each student should have suitable Lab coat to use for practical exercises.
Students not having lab coats will not be permitted in the lab.
Standard microbiology laboratory, equipment, reagents and kits
Microbiology technician and demonstrators
COURSE CALENDAR
Week
Wk1
Introduction
Lecture + Tutorial
Lab
Bacterial infection, pathogenesis and host responses
Wk2
Gram positive bacteria
Wk3
Gram negative bacteria- Enterobacteriaceae
Culturing and biochemical
identification of bacteria
pathogens
Antibiotic sensitivity testing
Wk4
Actinobacteria-Mycobacterium and Corynebacterium
Spirochetes, Rickettsiae, Chlamydia
Wk5
Mycoplasmas
Nosocomial infections
Wk6
Molecular and serological
identification of bacterial
pathogens
Public health microbiology
Incourse test
Wk7
Principles of epidemiology of infectious human Laboratory diagnosis of
diseases
viral diseases
Antimicrobial chemotherapy, drug resistance
Wk8
Overview of important human viral agents
308
Wk9
Mycology- Yeasts and Moulds
Laboratory diagnosis of
fungal diseases
Journal report due
Wk10
Mycology- Yeasts and Moulds
Wk11
Parasitology- Protozoa and Helminths
Identification of parasites
Incourse test
Wk12
Parasitology- Protozoa and Helminths
Wk13
Review
Additional information:





Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment,
student
conduct,
essential
skills,
and
support
at
http://sta.uwi.edu/fsa/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/fsa/documents/UGFacultyBooklet.pdf .
Students are reminded that they must attend a minimum of 75% of the practical sessions and
tutorials. Failure to do so will result in debarment from the final examination.
As a general principle, medicals or other excuses may only excuse a student’s presence at an
assigned time. Students must still complete the assigned work (make-up lab report or make-up
test) in order to obtain the marks for that item of coursework. The student is responsible for
liaising with the Course Coordinator or Teaching Assistants to ensure the assigned make-up is
completed.
Students are hereby informed that plagiarism is forbidden and all unsupervised coursework items
must be accompanied by a Coursework Accountability Statement in order to be assessed. Specific
items may require submission through Turnitin on myeLearning. Refer to ‘University
Regulations
on
Plagiarism’
available
from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
How to study for this course:




Attendance is mandatory for lectures, tutorials and practicals. Prior preparation is strongly
advised to able to fully participate in activities and obtain the full value of the sessions.
Thorough use should be made of the resources provided and students are strongly advised to
become familiar with them and start utilising them from the first week. Regular updates on course
progress and materials are also highly recommended and you should be checking into
myelearning on a frequent regular basis to review materials, assignments and activities.
Students are encouraged to interact regularly with staff, even outside of the assigned tutorial times
to ensure prompt, satisfactory solution of any problems and to monitor progress.
Good group management is essential and requires good communication and interpersonal skills.
309
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
THE UNIVERSITY OF THE WEST INDIES
ST AUGUSTINE CAMPUS
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION 2015/16
TITLE: Aquaculture
COURSE CODE: BIOL3970
LEVEL: 3
SEMESTER: 1
CREDITS: 3
PRE-REQUISITES: BIOL1262 (Living Organisms 1) and BIOL1263 (Living Organisms 2) and
BIOL2464 (Fundamentals of Ecology)
310
COURSE DESCRIPTION
In Aquaculture you will be exposed to basic knowledge in the related fields of culturing fish in both the
marine and brackish-water environments. You will learn about the various techniques and the exciting
field of aquaculture – which is currently the fastest growing food-production system in the world. The
course covers major trends in aquaculture practices, human and environmental influences on
productivity and sustainability and traditional and modern strategies for managing aquaculture.
Emphasis will be placed on tropical culture species.
Students are expected to have a basic foundation in biology. In addition to providing a foundation of
theoretical knowledge, this course will emphasise practical skills and expose students to field and
laboratory approaches for studying aquaculture systems. It is an interactive ‘hands-on’ course where
students are expected to prepare, participate and perform in an active way to engage with the content in
a variety of ways. Assessment is designed to encourage students to work continuously with the course
materials, explore and critically analyse research in this rapidly developing field.
COURSE RATIONALE
This is a core course for the Marine Biology specialisation, for the BSc. Biology degree in the
Department of Life Sciences, and is an essential area in environmental sciences, environmental biology
and environmental management. It also broadens the scope of studies in biology, plant biology and
zoology. Aquaculture is a critical discipline in today’s world, given the importance of the fish and the
seafood industry as a source of animal protein in the human diet. It is also the basis of a multi-billion
dollar industry.
311
INSTRUCTOR INFORMATION
This course will be taught by two lecturers assisted by a teaching assistant and a few demonstrators.
Further logistical support will be provided by laboratory and field support staff. Office hours are posted
on departmental notice boards and the main Life Sciences office.
First examiner and
course co-ordinator
Dr Dawn A. T.
Phillip
Second examiner and
lecturer
Prof. Indar W.
Ramnarine
Principal lecturer
Ms Rhea KingJulien
Rm 223, Department of Life Sciences
662-2002, ext. 82208
[email protected] (preferred method
of contact)
Dean’s Office, 2nd floor, Chemistry
662-2002, ext. 84484
[email protected] (preferred
method of contact)
[email protected] (preferred method
of contact)
LETTER TO THE STUDENT
Welcome to this level 3 course in aquaculture. This course forms part of the Specialisation in Marine
Biology. The aim of this handout is to provide you with an outline of the course as well as related
information with respect to course objectives and methods of assessment. Having completed BIOL1262
(Living Organisms 1) and BIOL1263 (Living Organisms 2) which are pre-requisite for this course, you
should now be familiar with the diversity and biology of aquatic reptiles, crustaceans, echinoderms,
molluscs and fishes. In this course (BIOL3970), students will be exposed to the broad and exciting field
of aquaculture. In the first five weeks of lectures the general principles of aquaculture will be covered.
This is followed by the biology and culture of several important species of tropical fishes, crustaceans,
molluscs, plants and reptiles. An extensive reading list and important web sites are provided, and
candidates are expected to READ around the topics covered in lectures.
CONTENT
Topics will include: a review of the history, status and future of global aquaculture;
physical and chemical properties of water; water budgets and the general principles of aquaculture:
choice of site, choice of species; choice of system. Lectures will also cover the different system designs
for aquaculture, as well as the ornamental fish trade. Applications to local production in Trinidad and
Tobago and the Caribbean will be discussed. Finally, the environmental aspects and impacts of
aquaculture will be described.
GOALS/AIMS
This course aims to
 Use aquaculture resources as the focus to expand students’ knowledge of the range of aquatic
animals that may be used as culture species.
 Develop students’ competence in basic methods and approaches for aquaculture farm and hatchery
designs.
 Develop students’ awareness through lectures and practical sessions on how to develop and
effectively manage an aquaculture farm or project.
 Introduce the range of aquaculture options highlighting their advantages and disadvantages.
COURSE OBJECTIVES
The general objectives of the course are to:
 provide course materials, activities and assessments using both face-to-face and online modalities
312





facilitate opportunities for students to engage with general concepts and specific examples to
develop a comprehensive understanding of aquaculture
allow students to observe, analyse and recognise a variety of aquaculture methods and practices
allow students to analyse and evaluate the environmental impacts of aquaculture practices
guide students in critically analysing and exploring questions in aquaculture
facilitate discussions on the management of aquaculture in Trinidad and Tobago
LEARNING OUTCOMES
Upon successful completion of this course, the student will be able to:
1.
describe the history and status of aquaculture, including the culture species and countries
2.
identify the important water quality parameters and water budget for aquaculture production
3.
explain the various criteria that are used in choosing a site for aquaculture, and the characteristics
of extensive, semi-intensive, intensive and hyper-intensive aquaculture systems, and differentiate
between static and re-circulating systems
4. explain the factors used in determining site selection and hatchery design, spawning and incubation
techniques, water quality management and general hatchery management techniques and record
keeping
5.
describe the methods applied in pond design and construction, including irrigation and drainage
structures; the pond-conditioning process; lime and fertiliser application rates; and pest and water
quality management
6.
analyse the importance of proteins, lipids, carbohydrates, vitamins and minerals in fish nutrition,
and determine the nutrient requirements of fishes, fish feed formulation and manufacture
7.
describe the major infectious and non-infectious diseases of fishes, including the important
parasites that infect fishes and the subsequent losses that are incurred
8.
explain polyculture systems, including their advantages and disadvantages
9.
design and explain the operations of aquaponic systems, including their advantages and
disadvantages
10. differentiate local areas (in Trinidad and Tobago) and their suitability for aquaculture
11. explain and evaluate the environmental impacts of aquaculture; both positive and negative
12. accurately identify species using species identification keys
13. sample aquaculture farms to collect biological data, particularly length, weight, sex and stage of
maturity
14. progress to advanced studies in aquaculture or related professions.
313
TEACHING METHODOLOGY
ASSIGNMENTS
 Laboratory exercises in weeks 4, 6, 8 and 10 (10%): assessment of practical skills, student
performance during laboratory sessions, and written practical reports
 In-course theory quiz (10%): a single quiz is scheduled for week 6
 Group project due in week 11 (30%): individual contribution to the project report (5%); individual
participation during discussion sessions (5%); final project report (20%)
 Final theory examination (50%)
COURSE ASSESSMENT
The final mark for this course comprises the following
 Theory examination: one 2-hour written examination (50%)
 In-course theory exam (10%)
 In-course practical exercises and group project (40%)
An in-course theory exercise worth 10% is due as in the course schedule. It may include a variety of
types of questions: multiple choice, true/false statements and short paragraph questions. Any material
covered in lectures, tutorials or practical sessions may be tested.
Absence from any scheduled assessment must be accompanied by either a medical submitted to the
Health Service Unit and copied to the main Life Sciences office, or a written excuse or explanation
submitted to Dr Dawn A. T. Phillip or the TA within 7 days of the test. Students must complete a
make-up exercise otherwise they will receive 0% for their in-course theory.
Students are reminded that they are required to attend at least 75% of the lectures, practical exercises
and tutorials. Failure to do so will result in the candidate being debarred from the final examinations.
Any absences must be supported by a written excuse or medical certificate and submitted within 7
days of the missed session. In order to pass this course, students must gain a composite mark of at least
50%. Any make-up coursework assessment may be in the form of an oral examination or essay.
EVALUATION
 Feedback on the course will be obtained informally from students on an on-going basis by regular
interactions and meetings among students, demonstrators, teaching assistants and the course
coordinator in lectures, tutorials and laboratory sessions.
 Formal feedback will be via elected class representatives who sit on the departmental Student-Staff
Liaison Committee meetings held twice during the semester. Class representatives will channel
both concerns and commendations to the meeting, as guided by the department’s standard operating
procedures.
 Formal evaluation of the entire course will be accomplished via a UWI course evaluation
questionnaire administered anonymously and confidentially at the end of the semester.
 All feedback will be considered on an on-going basis, and corrective actions or adjustments made
or discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES
Contact time will be 36 credit hours, comprising
 Lectures:
24 credit hours
 Tutorials:
4 credit hours
314
 Practical exercises:
8 credit hours
This course will be taught through a mixture of lectures, practical exercises and tutorials. There will
also be guest lectures (on listed topics) by experts from the government and private sector. Lectures
and tutorials will provide the conceptual and factual basis for specific topics and allow for discussions
in an interactive setting. Course materials and readings will be available online in advance to allow
students to be better prepared to engage the lecturers in discussion during class time.
RESOURCES
READING LIST
Topic 1
Avault (1996) Fundamentals of Aquaculture
Chapter 1. Getting started
Chapter 2. Aquatic food production and people
FAO (2010) The State of World Fisheries and Aquaculture (www.fao.org)
Part 1: World review of fisheries and aquaculture
Topic 2
Stickney (1976) Principles of warmwater aquaculture
Chapter 2. Water systems
Avault (1996) Fundamentals of Aquaculture
Chapter 6. Water requirements
Boyd (1988) Water quality management for pond fish culture
Chapter 2. Water quality.
Chapter 10. Hydrology of ponds.
Topic 3
Avault (1996) Fundamentals of Aquaculture
Chapter 3. Which species to culture
Chapter 5. Site selection and culture systems.
Stickney (1976) Principles of warmwater aquaculture
Chapter 1. Introduction
Topic 4
Piper et al. (1989) Fish Hatchery Management
Avault (1996) Fundamentals of Aquaculture
Chapter 13. Seed production and stock improvement.
Stickney (1976)
Chapter 6. Reproduction, selective breeding and genetics.
Topic 5
Stickney (1976)
Chapter 2. Water systems.
Bardach et al. (1972) Aquaculture
Appendix: Pond siting and construction
Avault (1996)
Chapter 5. Site selection and culture systems
Boyd (1988)
Chapter 2. Water quality
Chapter 3. Fertilisation
Chapter 4. Liming
Chapter 5. Dynamics of dissolved oxygen
315
Avault (1996)
Chapter 7. Water management
Chapter 8. Fertilisation, liming and pond muds
Stickney (1976)
Chapter 3. Non-conservative aspects of water quality
Chapter 4. Conservative parameters of water quality
Topic 6
Lovell (1989) Nutrition and feeding of fishes.
Avault (1996)
Chapter 9. Feeding and nutrition
Stickney (1976)
Chapter 5. Feeds, nutrition and growth.
Topic 7
Kabata (1985) Parasites and diseases of fish cultures in the tropics.
Noga (1996) Fish disease: Diagnosis and treatment.
Stickney (1976)
Chapter 7. Disease and parasitism
Avault (1996)
Chapter 10. Maintaining health of a culture species.
Topic 8
Bardach xi. (1972)
Chapter 18. Culture of tilapias.
Muir et al. (1982) Recent advances in Aquaculture
Chapter 5. Intensive farming of tilapia
Beveridge et al. (2000) Tilapias: Biology and exploitation.
Costa-Pierce and Rakocy (2000) Tilapia farming in the Americas, vols 1 & 2
Rakocy and Ramnarine (1995) Tilapia farming methods
Ramnarine and Ramnarine (1999) Recent developments in tilapia culture with applications for
the Caribbean
Bardach et al. (1972)
Chapter 32. Shrimp culture.
Nash (1991) Production of aquatic animals
Chapter 2. Marine Penaeid Shrimp
McVey (1983) Handbook of Mariculture
Section II
Nash (1991) Production of aquatic animals
Chapter 3. Freshwater prawns
New (1988) Freshwater prawn culture: a review
Lum Kong and Ramnarine (1988) Biology of the river conch.
Nash (1991)
Chapter 7. Oyster culture.
Chapter 8. Production of mussels.
Bardach (1972)
Chapter 36. Oyster culture.
Ramnarine (1989) Cascadu farming – A manual for the culture of Hoplosternum littorale
Ramnarine (1990) The biology of the cascadu, Hoplosternum littorale
Ramnarine (1994) Larval development and growth of the cascadu Hoplosternum littorale
Ramnarine (1994) A field trial of the semi-intensive culture of the cascadu Hoplosternum littorale
Ramnarine (1995) Induction of nest building and spawning in the cascadu
316
Ramnarine (2001) Hatching trials with eggs of Hoplosternum littorale
Topic 9
Bardach (1972)
Chapter 3. Chinese carp culture.
Little and Muir (1987) Integrated warm water aquaculture
Topic 10
Rakocy (1997) Integrating tilapia culture with vegetable hydroponics in recirculating systems.
Topic 11 The potential for an aquaculture industry in Trinidad and Tobago:
Kenny (1981) Availability of water and land resources.
Bruce (1981) Local species with potential for aquaculture in T&T
Ramnarine (1996) A brief history of aquaculture in Trinidad and Tobago and the prospects for
the development of an aquaculture industry
Ramnarine and Ramnarine (1999) Aquaculture prospects in Trinidad and Tobago.
317
COURSE SCHEDULE
Week
Lectures
Date
Tuesdays, 10 am–noon, TLC TR5
1.
1Sep
2
8Sep
1. Review of the history, status and future of global
aquaculture
2. Trends in global aquaculture production
NO TEACHING
3
3. Physical and chemical properties of water; water
15Sep
budgets
4. General principles of aquaculture: site, species,
systems
4
5. Hatchery design.
22Sep 6. Hatchery operation and management
7. Farm design and pond construction
5
8. Pond and water quality management
29Sep 9. Fish nutrition
6
10. Fish-feed technology and fish energetics.
6Oct 11. Major fish diseases, control methods and vaccines
7
12. Tutorial
13Oct 13. Biology and culture of shrimp
14. Biology and culture of lobsters.
8
15. Biology and culture of prawns
20Oct 16. Biology and culture of oysters and mussels
9
27Oct
10
3Nov
Practical sessions (Fridays
1–6pm, LS 1 &2) and
assessment due dates
17. Biology and culture of snappers and groupers
18. Polyculture and integrated aquaculture
19. Principles of aquaponics.
20. Aquaponics systems
21. Biology and culture of turtles
11
22. Biology and culture of crocodilians
10Nov 23. The ornamental fish trade
12
24. Aquaculture prospects in Trinidad and Tobago.
17Nov 25. Environmental aspects of aquaculturure
13
26. Tutorial
24Nov 27. Tutorial
28. Tutorial
Practical
Practical
In-course quiz
Practical
Practical
Group project due
ADDITIONAL INFORMATION
Refer to the Department of Life Sciences’ Undergraduate Handbook for general guidelines for
teaching, assessment, student conduct, essential skills, and support at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 Refer to the general information and general regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 Attendance: Students are reminded that they must attend and report satisfactorily on a minimum of
75% of the practical sessions and tutorials. Failure to do so will result in debarment from the final
318








examination (examination regulations, section II (18)
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf).
Medicals, excuses: Any student who misses a class, test or assignment is advised to consult
immediately in person or by email with the TA or course coordinator regarding reasons for their
absence and make-up options. Absence must be explained in writing within 7 days of the missed
session by either a written/emailed excuse sent to the TA or course coordinator, and/or a medical
certificate submitted to the Health Service Unit and copied to the Departmental Secretary, Life
Sciences.
Makeups: As a general principle, medicals or other excuses may only excuse a student’s presence
at an assigned time. Students must still complete the assigned work (make-up lab report or make-up
test) in order to obtain the marks for that item of coursework. The student is responsible for liaising
with the course coordinator or teaching assistant to ensure the assigned make-up is completed. Any
student who was inexcusably absent from a practical or test or does not submit a practical
report (initial or make-up) will receive 0% for that exercise. Note that a field trip cannot be
repeated for a make-up so you should make every effort to attend field trips.
Late submission: A penalty at 10% of mark per day late will be applied unless formal approval for
late submission is given by the TA or course coordinator using the guidelines above for medicals,
excuses.
Assignment submission: Hard copy reports must be submitted into the labelled deposit box for
your bench/demonstrator in the outer Zoology Office and the student list must be signed.
Submissions anywhere else will not be assessed. Reports will be returned at a time arranged by the
TA or demonstrator. We are not responsible for reports left uncollected or submitted inexcusably
late. Soft copy reports or other assignments must be submitted through myeLearning as directed for
each assignment.
Academic Dishonesty: Academic dishonesty, which includes plagiarism and cheating, is an
extremely serious academic offense and carries penalties varying from failure in an assignment to
possible suspension from the university. Students are hereby informed that plagiarism is forbidden
and all unsupervised coursework items must be accompanied by a completed plagiarism declaration
form in order to be assessed. Specific items may require submission through Turnitin on
myeLearning. Refer to the ‘University Regulations on Plagiarism’ available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
Safety in the lab and field: Medical data and emergency contact forms must be completed in the
first lab session when safety briefings will be given. Standard laboratory protocols for conduct and
dress code are in effect once you are present in a Department of Life Sciences laboratory
(Undergraduate Student Handbook, section 8). Dress code includes mandatory lab coats, adequate
clothing to protect the body, and closed shoes. NO sandals, slippers or open-toed shoes will be
allowed in the lab or field. Marks will be deducted for non-adherence to these protocols.
Field work: Details are given in section 8 of the Undergraduate Student Handbook
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf . Field trips are specified on the attached
course calendar so you can be adequately prepared. You will not be allowed on the field trip if a
medical data form has not been submitted.
If you have a disability and have not disclosed the nature of your disability and the support you
need, you are invited to contact the Academic Support/Disabilities Liaison Unit (ASDLU) of The
University of the West Indies (UWI), St. Augustine Campus. Phone: 662-2002 extension 83866,
83921, 83923 and 84254; Fax: 662-2002 extension 83922; Email: [email protected] ;
http://sta.uwi.edu/asdlu/forms.asp
319
HOW TO STUDY FOR THIS COURSE
 Attendance is mandatory for lectures, tutorials and practical sessions. Prior preparation is strongly
advised to enable you to fully participate in activities, and obtain the full value of the sessions.
 Thorough use should be made of the resources provided, and students are strongly advised to
become familiar with them and start utilising them from the first week. Regular updates on course
progress and materials are also highly recommended, and you should be checking into myeLearning
on a frequent and regular basis to review materials, assignments and activities.
 Students are encouraged to interact regularly with staff on lecture materials and their assignments,
even outside of the assigned lecture, tutorial and laboratory times, to ensure prompt, satisfactory
solution of any problems and to monitor progress.
 Good group management is essential and requires good communication and interpersonal skills.
GRADING SYSTEM
The UWI grading scheme is as follows:
http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf).
Grade
Quality point
% range
Grade definition
A+
4.30
90–100
Exceptional
A
4.00
80–89
Outstanding
A–
3.70
75–79
Excellent
B+
3.30
70–74
Very good
B
3.00
65–69
Good
B–
2.70
60–64
Satisfactory
C+
2.30
55–59
Fair
C
2.00
50–54
Acceptable
F1
1.70
45–49
Unsatisfactory
F2
1.30
40–44
Weak
F3
0.00
00–39
Poor
320
THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE DOCUMENTATION 2015/16
COURSE CODE and TITLE
NO. OF CREDITS
LEVEL
PREREQUISITES
SEMESTER
BIOL3971 Fisheries Management
3
3
BIOL3063 Marine Ecology and Oceanography
2
WELCOME LETTER TO STUDENTS
Dear student,
Welcome to BIOL3971 Fisheries Management.
In this advanced-level course on the sustainable management of fishery resources, emphasis will be placed on the special
issues related to the management of tropical commercial fisheries, especially those of the Caribbean region. This course is
intended for those students who are interested in careers in the fields of fisheries biology and management. It offers a mix of
theoretical knowledge and practical skills development, which are also valuable for those aiming for careers in marine
biology, conservation, environmental consulting and management You will be introduced to several fisheries management
models, and, as such, you are therefore expected to be able to do basic calculus and simple arithmetic, algebra and
numerical analysis. Students must be comfortable working with relatively simple mathematical and statistical models.
This course will be taught in blended mode comprising face-to-face lectures, tutorials and practical exercises, as well as
online delivery of resource materials and diverse activities. You should engage with the course materials and participate
fully to develop the essential skills of critical thinking (clarity, accuracy, relevance, logic, breadth, depth, precision,
significance, completeness and fairness). Activities will be diverse, and you are strongly encouraged to ask questions, offer
new ideas, problem-solve, and think innovatively to maximise the value of your learning experience. There will also be
individual and group assignments, which should help you to develop communication and team skills that are important in
the world of work.
Please read the course outline carefully and keep the course schedule close to hand as it contains all the activities and
assessments for the semester. In particular, take note of the policy on plagiarism and attendance requirements.
We are here to ensure your success in this course and at UWI generally, and encourage you to come to us with any
academic or other challenges you may face that could affect your attendance and performance.
We look forward to meeting each of you and engaging in productive, stimulating discussions over the coming semester.
Dawn A. T. Phillip
Course coordinator
INSTRUCTOR INFORMATION
This course will be taught by a team of lecturers, teaching assistants and demonstrators. Further logistical support will be
provided by administrative, laboratory and field support staff. Office hours are posted on departmental notice boards and the
main Life Sciences office
Course coordinator
Lecturer
Dr Dawn A.T. Phillip
Lecturer
Prof. Indar W. Ramnarine
Teaching assistant
Zaheer Hosein
2nd floor, new wing, Natural Sciences building
662-2002, ext. 82047 and 82208
[email protected] (preferred method of
contact)
Dean’s Office, 2nd floor, Chemistry
662-2002, ext. 84484
[email protected] (preferred method
of contact)
Teaching Assistant’s office, 2nd floor, new wing,
Natural Sciences building, ext. 82204
[email protected] (preferred method of
321
contact)
WEEKLY SCHEDULE
Lectures and tutorials
(You are required to attend all sessions)
Practical classes
(Weeks 3, 5, 7 and 9 – attend all sessions)
Tuesdays
Wednesdays
Mondays
10:00–10:50 pm
10:00–10:50 am
2:00–06:00 pm
C2
114
212A
COURSE DESCRIPTION
In BIOL3971 Fisheries Management, you will be introduced to concepts in the related fields of fisheries biology, stock
assessment and fisheries management. The course covers major trends in global and regional fisheries and fishing patterns;
human and environmental influences on productivity and sustainability; traditional fish stock assessment models; and
traditional, modern and emerging strategies for managing fisheries. Emphasis will be placed on tropical fisheries, which are
among the most difficult fisheries to manage.
COURSE RATIONALE
This course forms part of the specialisation in marine biology. Having completed BIOL3063 Marine Ecology and
Oceanography, which is a pre-requisite for this course, you should now be familiar with basic oceanography, oceanic and
atmospheric circulation, primary and secondary productivity, plankton cycles and distribution, all of which are key concepts
in understanding the ecology of fisheries resources.
Fisheries biology and management are critical disciplines in today’s world, given the importance of the fishing industry as a
source of animal protein in the human diet; the basis of a multimillion-dollar industry; and the threatened status of many of
the major species on which we depend.
COURSE CONTENT
Topics will include
 Diversity of fishery resources exploited by marine fisheries world wide and in the region
 The Law of the Sea and its implications for management of fishery resources
 Types of fishing gears and techniques used in commercial fisheries
 Fishers and fishery socioeconomics
 Issues and challenges facing commercial fish stocks, including direct and indirect effects of destructive fishing practices,
and other anthropogenic factors such as climate change and habitat alteration
 Key topics in fisheries biology, such as fish reproduction; recruitment of juveniles to the fishery; diet and feeding; age
and growth; fishing and natural mortality; stock structure; and other special topics
 Aims and objectives of fisheries management
 Fisheries management strategies and approaches, including traditional fishery management targets and indices, and more
recent approaches such as participatory and ecosystem-based management
 Fisheries models as standard tools used by fishery managers, and the data requirements for fisheries management
GOALS/AIMS
This course aims to
 Using fishery resources as the focus, expand students’ knowledge of the range of aquatic animals exploited by humans
for their use, and the consequences of over-exploitation of these biological resources
 Develop students’ competence in basic methods and approaches for fisheries stock assessment
 Develop students’ awareness that resource users are complex, social beings operating in various socio-cultural and
socio-political contexts that must be understood by fisheries managers in order to effectively manage the exploitation of
the resource base
 Introduce students to the range of options that have been used, and are being developed, to manage fishery resources
GENERAL OBJECTIVES
The general objectives of this course are to
 provide course materials, activities and assessments using both face-to-face and online modalities
 facilitate opportunities for students to engage with general concepts and specific examples to develop a broad
understanding of the complex nature of human impacts on fishery resources
 guide students in crafting questions and critically analysing and exploring answers to these questions using
investigative, hands-on approaches
322

facilitate discussion on the relationships between the impacts of humans on fishery resources, including impacts on the
marine ecosystems that support these organisms, and evaluate potential solutions for ensuring sustainability of these
exploited resources
LEARNING OUTCOMES
By the end of this course students should be able to:
 List a number of species that form the basis of fisheries at the global, regional and local scales, and discuss the trends
and status of the fishery for specific named ones
 Outline the history and present status of global fisheries, and predict plausible future trends in these
 Discuss some of the factors that influence the productivity and sustainability of global, regional and local fisheries
 Describe the main factors that affect the dynamics of fish populations, and those that influence recruitment
 Discuss various fisheries management strategies and their limitations
 Describe some of the more important relationships between fish stocks, humans and the environment
 Explain why tropical fisheries are considered complex, and suggest options for their effective management
 Demonstrate basic skills for researching, analysing, synthesising, evaluating and communicating published and original
fisheries information; evaluate specific human-environment interactions relevant to fisheries, and identify resulting
sustainability issues; develop solutions using a variety of strategic management approaches; manage group interactions,
and work effectively in teams.
Students should also gain practical skills that will allow them to
 Describe a fishery based on either the target species, or fishing methods, or landing site/home port used by fishers
 Accurately identify commercially-important fishery species using species identification keys
 Sample fishery landings to collect fisheries data, particularly length, weight, sex and stage of maturity
 Dissect fin fish to collect stomach contents, otoliths and gonads, and process these for determination of diet, age, sex and
gonad maturity
 Use fisheries data and models to determine reproductive cycles, mortality, growth, stock structure and various other
fishery indices
COURSE ASSESSMENT
The final mark for this course comprises the following
 Theory examination: one 2-hour written examination (50%)
 In-course theory examination (10%)
 In-course practical exercises (10%) and group project (30%)
ASSIGNMENTS
In-course assignments comprise
4. A theory examination worth 10% is due as in the course schedule. It may include a variety of types of multiple-choice
questions, true/false statements and short-paragraph questions. Any material covered in lectures, tutorials or practical
sessions may be tested.
5. Practical reports, collectively worth 10% of the final course mark. The reports will be based on activities engaged in
during four scheduled laboratory sessions as stipulated in the course schedule.
6. A single group project worth 30% of the final course mark [individual contribution to the project report (5%); individual
participation during discussion sessions (5%); final project report (20%)]. The project will be a reading research project
based on original literature and technical reports, and may incorporate results from the practical exercises
EVALUATION
 Feedback on the course will be obtained informally from students on an on-going basis by regular interactions and
meetings among students, demonstrators, teaching assistants and the course coordinator in lectures, tutorials and
laboratory sessions.
 Formal feedback will be via election of class representatives who sit on the departmental Student-Staff Liaison
Committee meetings held twice during the semester. Class representatives will channel both concerns and
commendations to the meeting, as guided by the department’s standard operating procedures.
 Formal evaluation of the entire course will be accomplished via a UWI course evaluation questionnaire administered
anonymously and confidentially at the end of the semester.
 All feedback will be considered on an on-going basis and corrective actions or adjustments made or discussed with
students promptly, or incorporated the following year.
TEACHING STRATEGIES
323
This course will be taught through a mixture of lectures, practical exercises and tutorials. There may also be guest lectures
by experts from the government and private sector.
In addition, the online teaching tool, myeLearning, will be used extensively during this course for
 communication among students and staff (email, discussions)
 official posting of important notices (coursework assessment notices, instructions, and in-course results)
 provision of course details, lecture notes, practical guides, tutorial briefings
 provision of recommended resource materials, and links to resources on specific web sites
Face-to-face contact time will be 36 credit hours, comprising:
Lectures
24 hours
Lectures will provide valuable synthesis and evaluation of available information
on fisheries biology, stock assessment and management, update current issues and
management approaches, prioritise content relevant to course assessment. Case
studies and selected topics may be presented by guest lecturers. Lecture sessions
will be interactive, with students encouraged to ask questions, share knowledge
and experiences. Course materials and readings will be available online in
advance to allow students to be better prepared to engage the lecturers in
discussion during class time
Tutorials
4 hours
Tutorials will cover course topics in an interactive format using a variety of
collaborative active learning techniques. In addition to clarifying details of course
content, specific transferrable skills may be addressed, e.g., essay and report
writing, critiquing and oral presentation
Practical exercises
16 hours
Four 4-hr practical sessions will provide hands-on experience for students to gain
skills required for conducting well-designed fisheries research. Some time will
also be assigned for conducting discussions and brainstorming sessions for group
projects, under the supervision of their demonstrators and lecturers.
RESOURCES
Most resources are available myeLearning, including
 Lecture outlines – including learning objectives, summaries, recommended readings, some presentations
 Resources – links to papers, articles and websites
 Tutorials – guidelines for tutorial activities, and specific supporting resources
 Practical exercises – guidelines for practical activities, and specific supporting resources (texts, articles, websites)
 Group project – detailed instructions and supporting websites to guide students in navigating the challenges of working
on a group project. These will include information on working in teams, as well as some literature on the research topic.
Essential and recommended texts are in the Reserve Section, Alma Jordan Library, or are available via links in the course
outline and myeLearning.
Essential readings
Text books
Berkes, F.; Mahon, R.; McConney, P.; Pollnac, R.; Pomeroy, R. 2001. Managing Small-Scale Fisheries: Alternative
Directions and Methods. International Development Research Centre, Ottawa, Canada. [SH329.S53 M36 2001]
Food and Agriculture Organisation (FAO) (ed.). 1997. The Law and the Sea: Essays in Memory of Jean Carroz. FAO,
Rome.
King, M. 2010. Fisheries Biology, Assessment and Management, 2nd edition. Blackwell Publishing, Oxford.
Gabriel, O.; Lange, K.; Dahm, E.; Wendt, T.; von Brandt, A. (eds). 2005. Fish Catching Methods of the World, 4th edn.
Blackwell Publishers, Ames, Iowa. [SH344.B69 2005]
Technical reports and conference papers
Ramnarine, I.W. 1998. Towards sustainable fisheries in Trinidad & Tobago. Agriculture in the Caribbean: Issues and
Challenges, Vol. III, pp. 142–148. Continuing Education Programme in Agricultural Technology (CEPAT), 19–21 Aug
1998, The University of the West Indies, St. Augustine, Faculty of Agriculture and Natural Sciences.
Caribbean Regional Fisheries Mechanism (CRFM). 2009. Report of 5th Annual Scientific Meeting – Kingstown, St. Vincent
& the Grenadines, 9–18 June 2009 – National Reports. CRFM Fishery Report 2009. Volume 1, Supplement 1. CRFM
Secretariat, Belize.
CRFM 2011. Report of the 7th Annual Scientific Meeting, Kingstown, St Vincent and the Grenadines, 16–24th June 2011 –
National Reports. CRFM Fishery Report 2011, Volume 1, Supplement 1, CRFM Secretariat, Belize. [For latest reports
see CRFM website http://www.caricom-fisheries.com/Default.aspx]
324
Additional readings
Books
Ellis, R. 2004. The Empty Ocean. Island Press, Washington DC. [QL121.E5794 2003]
Food and Agriculture Organisation (FAO). 2007. The State of World Fisheries and Aquaculture, 2006. FAO, Rome.
Haddon, M. 2010. Modelling and Quantitative Methods in Fisheries, 2nd edn. CRC Press, Boca Raton. [SH331.5.M48 H34]
Jennings, S., Kaiser, M., & Reynolds, J. 2001. Marine Fisheries Ecology. [SH328.J46 2001]
Pitcher, T.; Hart, P.J.B. 1982. Fisheries Ecology. Kluwer Academic Publishers, Dordrecht, Netherlands. [SH328.P57 1983]
Pitcher, T.J; Hart, P.; Pauly, D. (eds). 1998. Reinventing Fisheries Management. Fish and Fisheries Series, Vol. 23. Kluwer
Academic Publishers, Dordrecht, Netherlands. [SH328.R45 1998]
Journal articles
Pauly, D. and Christensen (1995) Primary production required to sustain global fisheries. Letters to Nature, 374, 255–257.
Pauly, D. Chirstensen, V.; Froese, R.; Palomares, M.L.D. (2000) Fishing down aquatic food webs. American Scientist, 88,
46–51.
Pauly, D.; Christensen, V.; Guénette, S.; Pitcher, T.J.; Sumaila, U.R.; Walters, C.J.; Watson, R.; Zeller, D. (2002) Towards
sustainability in world fisheries. Nature, 418, 689–695.
Watson, R. and Pauly, D. (2001) Systematic distortions in world fisheries catch trends. Letters to Nature, 414, 534–536.
Magazine and newspaper articles
Law, R. (1991) Fishing in evolutionary waters: the way we exploit a fishery influences the way a population of fish evolves.
Can we manage this evolution? New Scientist, 1758.
Lemonick, M.D.; Aunapu, G.; Dorfman, A.; McDowell, J. (1997) Under attack. Time Magazine.
Nash, J.M. (1997) The fish crisis. Time Magazine.
ADDITIONAL INFORMATION
 Refer to the Life Sciences’ Undergraduate Handbook for general guidelines for teaching, assessment, student conduct,
essential skills, and support at http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf.
 Refer to the general information and general regulations in the Faculty of Science and Technology’ Undergraduate
Booklet available from http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf.
 Attendance: Students are reminded that they must attend and report satisfactorily on a minimum of 75% of the practical
sessions, lectures and tutorials. Failure to do so will result in debarment from the final examination (Extracts from
Examination Regulations for First Degrees, Associate Degree, Diplomas and Certificates, section II (18) available
from http://sta.uwi.edu/resources/documents/Exam_and_GPA_regulations.pdf).
 Medical and other excuses: Any student who misses a practical or lecture class, test or assignment is advised to consult
immediately in person or by email with the teaching assistant or course coordinator regarding reasons for their absence
and recoup options. Absence must be explained in writing within 7 days of the missed session by either a
written/emailed excuse sent to the TA or course coordinator, and/or a medical certificate submitted to the Health
Service Unit and copied to the secretary, main office, Department of Life Sciences. The department’s copy should
have appended to it information on courses affected, course coordinator or TA responsible for those courses, and course
events involved.
 Make-up sessions: As a general principle, medical or other reasons may only excuse a student’s presence at an assigned
time. Students must still complete the assigned work (make-up lab report or make-up test) in order to obtain the marks
for that item of course work. The student is responsible for liaising with the course coordinator or teaching assistant to
ensure the assigned make-up exercise is completed. Any student who was inexcusably absent from a practical or
test, or who does not submit a practical report (initial or make-up) will receive 0% for that exercise. Note that a
field trip cannot be repeated for a make-up opportunity, so you should make every effort to attend field trips.
 Late submissions: A penalty at 10% of mark per day late will be applied unless formal approval for late submission is
given by the teaching assistant or course coordinator using the guidelines above for medical or other excuses.
 Assignment submission: Hard copy reports must be submitted into the labelled deposit box for your
bench/demonstrator in the outer Zoology office, and the student list must be signed. Submissions anywhere else will
not be assessed. Reports will be returned at a time arranged by the TA or demonstrator. We are not responsible for
reports left uncollected or submitted inexcusably late. Soft copy reports or other assignments must be submitted
through myeLearning as directed for each assignment.
 Academic dishonesty: Academic dishonesty, which includes plagiarism and cheating, is an extremely serious academic
offense, and carries penalties varying from failure in an assignment to possible suspension from the university. Students
are hereby informed that plagiarism is forbidden, and all unsupervised coursework items must be accompanied by a
completed plagiarism declaration form in order to be assessed. Specific items may require submission through Turnitin
325



on myeLearning. Refer to the University Regulations on Plagiarism available from
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
Safety in the laboratory and field: Medical data and emergency contact forms must be completed in the first laboratory
session when safety briefings will be given. Standard laboratory protocols for conduct and dress code are in effect once
you are present in a Life Sciences laboratory (Department of Life Sciences Undergraduate Student Handbook section 8).
The dress code includes mandatory laboratory coats, adequate clothing to protect the body, and closed shoes. NO sandals,
slippers or open-toed shoes will be allowed in the laboratory or in the field. Marks will be deducted for non-adherence to
these protocols.
Field work: Details are given in section 8 of the Department of Life Sciences Undergraduate Student Handbook
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf. Field trips are specified on the attached course calendar so
you can be adequately prepared. You will not be allowed on the field trip if a medical data form has not been submitted.
If you have a disability and have not disclosed the nature of your disability and the support you need, you are invited to
contact the Academic Support/Disabilities Liaison Unit (ASDLU) of The University of the West Indies, St. Augustine
Campus. Phone: 662-2002 extension 83866, 83921, 83923 and 84254; Fax: 662-2002 extension 83922;
Email: [email protected] ; http://sta.uwi.edu/asdlu/forms.asp.
HOW TO STUDY FOR THIS COURSE
 Firstly, this is not a course where you can rote-learn factual information at the last minute for a test, or prepare
simplistic essays copied off the Internet for assignments. It requires familiarity with a wide range of topics, informed
discussion of broad, complex issues and application of critical thinking skills.
 You should attend all lectures, tutorials and practical sessions since satisfactory attendance (>75%) is required by the
UWI regulations. Attendance records will be taken at all sessions.
 Students who attend regularly perform better than those who do not. You should attend to obtain the full value of the
lecturer’s presence. Lecturers routinely synthesise and summarise large amounts of information, and prioritise,
evaluate, discuss and explain this information. They provide the conceptual framework of the course, which you must
then fill in with details and examples through independent study.
 You should prepare before classes so you can clarify any difficult points with the lecturer, or engage in meaningful
discussion of any controversial topics. This will enhance and deepen your understanding as well as contribute to course
assessment in tutorials and practical sessions. This is your opportunity for continuous assessment to monitor your
progress and to accumulate coursework marks incrementally.
 You should review learning outcomes for each topic or activity, and make sure you understand and can actually achieve
those outcomes. If you cannot, please clarify with the lecturer. You must make thorough use of the resources provided
(e.g., textbooks, resouces on myeLearning) from the first week. You should check into myeLearning frequently to
review updated materials, assignments, notices and activities.
 In addition to timetabled contact time, you are expected to devote additional hours of independent study: reviewing
class materials and notes, reading/viewing/using resource materials, completing assignments, and preparing for
assessments. You are strongly encouraged to make your own notes from lectures, textbooks and other source materials
throughout the semester to improve your skills of comprehension, organisation, planning and writing. Working in study
groups is strongly supported for those who learn best this way, as it shares workloads, builds camaraderie and social
skills; however, please do not rote-learn prepared essays, and always double check the accuracy of your colleagues’
work.
 You are encouraged to interact regularly with staff, even outside of the assigned class times to ensure prompt,
satisfactory resolution of any problems and to monitor progress. Attendance is mandatory for lectures, tutorials and
practical sessions. Prior preparation using online course materials is strongly advised to be able to fully participate in
activities, and obtain the full value of the sessions.
 Thorough use should be made of the resources provided, and students are strongly advised to become familiar with
them and start utilising them from the first week. Regular updates on course progress and materials are also highly
recommended and you should be checking into myeLearning on a frequent, regular basis to review materials,
assignments and activities. Some online activities will contribute to your final grade (see course assessment).
 Students are encouraged to interact regularly with staff on their projects, even outside of the assigned laboratory times,
to ensure prompt, satisfactory resolution of any problems, and to monitor progress.
326
Grading scheme: Grading Scheme used in the Faculty of Science & Technology is as follows:
Mark
Grade
Grade Descriptor
Quality Points
90-100
A+
Exceptional
4.3
80-89
A
Outstanding
4.0
75-79
A-
Excellent
3.7
70-74
B+
Very Good
3.3
65-69
B
Good
3.0
60-64
B-
Satisfactory
2.7
55-59
C+
Fair
2.3
50-54
C
Acceptable
2.0
45-49
F1
Unsatisfactory
1.7
40-44
F2
Weak
1.3
0-39
F3
Poor
0
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COURSE CALENDAR
W
k
1
Dat
e
T19
Lecture topics
1.
Introduction to this course (DATP)
2.
Diversity of fishery resources (DATP)
3.
Fishing gear and commercial fishing methods (IR)
4.
World fisheries, history, status and future (IR)
5.
Law of the Sea – implications for fisheries (DATP)
6.
Destructive fishing methods – e.g., incidental catches and
ghost fishing (ZH)
Consequences for stocks – e.g., overfishing, fishing down
the food chain (no lecture)
Other anthropogenic effects – e.g., climate change, habitat
destruction (DATP)
Practical exercises
Assignments
.
1
W2
0
.
1
2
T26
.
1
W2
7
.
1
3
T2.
2
4
W3
.2
T9.
7.
2
W1
8.
0
.
2
5
6
T16
.2
W1
7.2
T23
9.
10. Fisheries biology – food and feeding energetics (DATP)
W2
4
.
2
T1.
3
8
Practical report due
(2.5%)
M15.2
Diet and feeding
11. Fisheries biology – reproduction and recruitment (DATP)
.
2
7
Effects of fishing on the ecosystem (DATP)
M1.2
Fish identification, bycatch statistics
W2
.3
T8.
In-course theory
quiz (10%)
12. Fisheries biology – age and growth (RK)
13. Fisheries biology – mortality, abundance and stock
structure (DATP)
14. Fisheries biology – critical habitats, e.g., spawning and
nursery grounds (GM)
15. Aims of fisheries management (IR)
M14.3
Reproduction and
mortality
Practical report due
(2.5%)
3
W9
16. Data requirements for fisheries management (IR)
.
3
9
T15
.
3
W1
17. Fishery models – surplus-yield models (IR)
M28.3
Age and growth
18. Fishery models – dynamic-pool models (IR)
6
.
3
1
0
T22
19. Fisheries management strategies and approaches (IR)
.
3
W2
3
20. Special issues related to tropical fisheries management
(IR)
Practical report due
(2.5%)
.
3
1
1
T29
21. Fishers and fisheries socioeconomics (DATP)
W3
22. Community-based fisheries management case study
(DATP)
0
.
3
1
2
Group project due
(30%)
.
3
T5.
23. Caribbean fisheries management project (DATP)
4
W6
Practical report due
(2.5%)
24. Fisheries management – future directions4 (DATP)
.
4
1
3
M4
DATP
GM
IR
RK
ZH
Tutorials, including exam
preparations
.
4
DAWN A T PHILLIP
GUY MARLEY
INDAR RAMNARINE (PROF)
ROSEMARIE KISHORE
ZAHEER HOSEIN
The University of the West Indies, St. Augustine
Faculty of Science & Technology
Department of Life Sciences
COURSE CODE & TITLE: BIOL XXXX CARIBBEAN ISLAND ECOLOGY AND
BIOGEOGRAPHY
NO. OF CREDITS: 3
LEVEL: 3
SEMESTER: 1
PREREQUISITES: EITHER (BIOL 2464 Fundamentals of Ecology AND BIOL 2163
Biostatistics) OR BIOL1462 General Ecology and Biometry
4
For example FISHE (http://fishe.edf.org/); new and upcoming alternative fishing techniques, such as electrotrawling (Soetaert et
al. 2013 and errata)
329
Lectures (27 credit hours); Labs/Field trips (10 Credit hours- 0.5 credit hours per contact hour).
Total Credit Hours: 37
This course has been reviewed by the Board of Faculty of Science and Technology.
COURSE DESCRIPTION: This advanced course treats the islands of the Caribbean within a global
perspective. Its subject is the special nature of island environments and their biotas, and its aim is an
understanding of the distributions and ecological relationships of island plants and animals through
an analysis of their origins, evolutionary past, population ecology and community composition. The
course is expected to integrate much of the knowledge that advanced undergraduates have amassed.
Teaching for the course will be approached in a blended/hybrid replacement classroom manner
with asynchronous lectures presented online with recorded video and audio and select, classroom
sessions. Practical exercises involving field work, literature review and synthesis work and
exercises will also be applied to gain more practical skills. Assessment will be based on
coursework (50%) and a final theory exam (50%). Course work will be in the form of written
reports of practical exercises and literature assignments.
COURSE RATIONALE: This is an elective course for the BSc (Biology Major) students and in
the future, for the Ecology and Environmental Biology Specialization in the BSc (Biology with
Specialisations) in Life Sciences that will provide fundamental knowledge and concepts of
Caribbean biodiversity that students can apply in most areas they may encounter in Environmental
Biology. At the end of the course the students will be able to discuss the complex origins,
characteristics and values of Caribbean biodiversity; the nature of threats due to human activities
including global climate change; and evaluate realistic responses to conserve Caribbean island
biodiversity and how it responds to human manipulation.
INSTRUCTOR INFORMATION: This course will be taught by a team of lecturers, Teaching
Assistants and demonstrators. Office hours are posted on Departmental notice boards and the main
Life Sciences office.
Name of instructor(s): Mike Oatham (Coordinator); Linton Arneaud (Teaching Assistant)
Office address and phone: Rm 222, Old Wing, Natural Sciences Building (ext 83088)
Email address: [email protected]
Office hours: Monday 9am-11am; Tues 10am-12pm
Preferred method of contact: Email
330
Communication policy: Students should use their UWI email account for communication and can
expect a response within 48 hours.
LETTER TO THE STUDENT: Welcome to ‘Caribbean Island Ecology and Biogeography’.
In this course you will be challenged to develop the fundamental knowledge, skills and attitudes
of a practising Caribbean ecologist. This is a course with theory and practical components that will
require commitment and participation on your part to successfully engage in the content and to
develop the essentials skills of critical thinking (clarity, accuracy, relevance, logic, breadth, depth,
precision, significance, completeness and fairness). You are strongly encouraged to ask questions,
offer new ideas, problem solve and think innovatively to maximise the value of your learning
experience. In addition, teamwork, organisation and time management will be necessary personal
attributes to bring to the course.
CONTENT
Topics will include:
1. General features of islands. History of island formation, the distinction between continental and
oceanic islands.
2. Climate and seasonality in the Caribbean including extreme events such as hurricanes.
3. Development and composition of island biotic communities. Modes of colonisation, speciation
and adaptive radiation, extinction. Species-area relationships.
4. Case histories of selected islands and archipelagos.
5. Island-like situations on continents. Consequences of ecosystem fragmentation.
6. Human impacts on island ecosystems plus management and adaptation to the effects of global
climate change.
GOALS/AIMS
The goals of this course are to



Describe the characteristics of Caribbean biodiversity and distribution of biodiversity in the
Caribbean
Examine the reasons why biodiversity occurs with these characteristics at these levels in
different parts of the Caribbean
Expose students to the currently accepted approaches to investigating island ecology
331





Provide opportunities to develop transferrable skills within a specific context
Provide fundamental preparation and training in general practical and research skills
Introduce specialist practical and research skills and approaches
Inculcate a culture of quality and responsibility in conducting research
E ha e stude ts apa it to ork effe ti el i real life situatio s
LEARNING OUTCOMES
At the end of this course students should be able to
1. Describe the different levels and characteristics of biodiversity in the Caribbean.
2. Describe the mechanisms for biodiversity patterns in the Caribbean and discuss the reason
for them with specific references to Trinidad and Tobago.
3. Describe the biogeographical processes at work in the Caribbean.
4. Explain how characteristics of species and taxa and their dispersal mechanisms influence their
patterns of distribution in the Caribbean.
5. Describe the physical characteristics of Caribbean islands and discuss how they influence the
species and taxa distribution.
6. Describe the human impacts on island ecosystems and discuss how these are likely to
influence Caribbean island biodiversity into the future.
7. Effectively find, evaluate and manage published information from a variety of sources
including books, journal articles and web resources.
8. Use spreadsheet, word processing and presentation software to carry out tasks related to
critically assessing and synthesizing reports from the scientific literature.
9. Review basic ethical principles for appropriate scientific conduct, for example citing
references and writing to avoid plagiarism
10. Function effectively in real life situations by integrating knowledge, skills and attitudes with
innovation and problem-solving approaches
11. Demonstrate effective oral and written communication
12. Demonstrate effective observation and record-keeping skills
13. Demonstrate effective skills in managing time, people and projects
14. Demonstrate skills in evaluating, managing and communicating information in ecology
332
COURSE ASSESSMENT
Assessment will be based on a student’s final mark from the coursework components below.
Component
% Final Grade
Learning Outcomes
Addressed
100% broken down as
follows:
20%. Paper
3, 4, 5, 6, 7, 8, 9, 11, 13, 14
10% Poster
3, 4, 5, 6, 7, 8, 9, 11, 13, 14
5%. Affinity Patterns
Among Caribbean Islands
1, 2, 3, 4, 7, 10,11, 14
5% Long Distance Dispersal
of Propagules
1, 2, 3, 4, 7, 8, 9, 10, 11, 12,
13, 14
5% Video Lab for Island
Biogeography
1, 2, 3, 4, 7, 8, 9, 10, 11, 12,
13, 14
5% Cloud Forests or Sky
Islands
1, 2, 3, 4, 6, 7, 8, 9, 10, 11,
12, 13, 14
50%
1, 2, 3, 4, 5, 6, 11, 14
Theory coursework
Practical coursework
Final Theory Exam
ASSIGNMENTS
Theory coursework
Theory coursework (30%) will be a paper on an individualized topic (e.g. a particular island or a taxon
with special relevance to islands) and a poster presentation. Topics will be assigned early in the
course, with further guidance from lectures. Each student will submit a written paper by week 6 and
do the poster presentation of his/her topic during week 8. The written paper will be worth 20% of the
theory coursework and the poster presentation 10%. The contrasting methods of communicating the
information will allow the students to understand the value in different contexts.
Practical coursework
333
4 Practical Reports (5% each for a total of 20%). Writing up reports of practical exercises is of
paramount importance. You must hand in your report or question sheet in the time specified or
you will lose 10% of your mark for the assignment per day the report is late (this includes
weekends). If the student is absent from a practical due to a medical condition they must still
submit a report on the same date as all other students unless specifically excused by the
course coordinator. It is the responsibility of the student to obtain any data set required to write
up the report.
EVALUATION:




Feedback on the course will be obtained informally from students on an ongoing basis by
regular interactions and meetings among students, demonstrators, instructors, teaching
assistants and the Course Coordinator in practicals and tutorials.
Formal feedback will be via election of Class Representatives who sit on the
Departmental Student-Staff Liaison Committee meetings held twice during the semester.
Class reps will channel both concerns and commendations to the meeting as guided by
the Department’s Standard Operating Procedures.
Formal evaluation of the entire course will be accomplished via a UWI Course
Evaluation questionnaire administered anonymously and confidentially at the end of the
semester.
All feedback will be considered on an ongoing basis and corrective action or adjustments
made or discussed with students promptly or incorporated the following year.
TEACHING STRATEGIES
The course will be taught in a blended/hybrid replacement classroom manner as a series of face to
face tutorials reinforcing the concepts introduced in recorded lectures posted on myelearning.
Prompt questions will be provided for each online lecture to give the student and lecturer an idea
of how the student is progressing through the course. The face to face tutorials will take the form
of: group completion of a model exam question on the topic; a MCQ or fill in the blank session on
the topic; role playing assignment on the topic or an informal question and answer session.
Coursework theory assignments are designed to make the students search the literature for relevant
information and report it in a structured way.
READINGS
The following Readings will be required in the first instance and more recent and other relevant
readings will be added and will replace other readings in future years.
334






Lomolino, M.V., Riddle,B.R., and Brown, J.H. 2005. Biogeography. 3rd Ed. Sinauer Associates,
Sunderland
Carlquist, S. 1974. Island Biology. New York: Columbia Univ. Press 660 pp.
Cooper, St.G.C. & P.R. Bacon 1981. The Natural Resources of Trinidad and Tobago. London:
Edward Arnold 222 pp.
Gillespie, R.G. & D.A. Clague (eds.) 2009. Encyclopedia of Islands. Berkeley: Univ. California Press
1074 pp.
Whittaker, R.J. 1998. Island Biogeography. Oxford: Oxford Univ. Press 285 pp.
Williamson, M. 1981. Island Populations. Oxford: Oxford Univ. Press 286 pp.
COURSE CALENDAR
Week
Topic
Lectures
1
Islands. What and 
Where are They? 
Introduction
Overview of main islands and
archipelagos
2
The Physical

Setting of
Caribbean Islands


Processes in island formation;
Geological history of the
Caribbean
Caribbean climate and seasons
Tutorial: Assignment of
coursework topics
3
Island

Environments and
Ecosystems

4
Getting to Remote 
Islands and
Biogeographic

Processes on

Continental
Islands
5
The Fate of Island 
Species

Island environments: Land,
freshwater, coastal
Remote or Oceanic Islands.
Physical realities and biotic
distinctiveness
Over-water dispersal: Challenges
and vagaries
Vicariance and relaxation
Tutorial: Species Area
Relationship and the MacArthurWilson Dynamic Equilibrium
Theory
The fate of island species.
Speciation
The fate of island species.
Extinction
Tutorial: Adaptive Radiation

Practicals
Affinity patterns among
Caribbean islands (Lab
Exercise). Due after the lab
Long-distance dispersal of
propagules (field trip.
Manzanilla Beach) Due one
week after the Field Trip
335
Week
Topic
Lectures
6
Selected Islands
Outside of the
Caribbean


Video Lab for Island
Selected islands outside the
Biogeography (Question sheet
Caribbean: Madagascar,
completed in the Lab) Due after
Galápagos Islands
the lab
Selected islands outside the
Caribbean: New Guinea, Hawaiian
Islands
Social insects
Habitat "islands" in continental
settings
7
Island Taxa
Groups


8
Poster
Presentations

Poster Presentations
9
Island Taxa
Groups


Sedentary coastal faunas
Land snails
10
Island Taxa
Groups

Land vertebrates: Amphibians and
reptiles
Land vertebrates: Birds and
mammals
Freshwater faunas
Vascular plants



11
Island Taxa
Groups
12
Humans on Islands 

13
Course Review
Practicals
Cloud Forests or Sky Islands
(Half-day field trip, Arima
Valley). Due one week after the
Field Trip.
Human impacts
Future of island ecosystems
HOW TO STUDY FOR THIS COURSE

Attendance is mandatory for lectures, tutorials and practicals. Full use should be made of
the resources provided and students are strongly advised to become familiar with them and
start utilising them from the first week.
336

Students are encouraged to interact regularly with their lecturer on their projects, even
outside of the assigned tutorial times to ensure satisfactory solution of any problems and to
monitor progress.
ADDITIONAL INFORMATION:







Refer to the Life Sciences Undergraduate Handbook for general guidelines for teaching,
assessment, student conduct, essential skills, and support at
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
Refer to the General Information and General Regulations in the Faculty Booklet available
from http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf
.
Attendance: Students are reminded that they must attend and report satisfactorily on a
minimum of 75% of the practical sessions and tutorials. Failure to do so will result in
debarment from the final examination.
Medicals, excuses: Any student who misses a class, test or assignment is advised to consult
immediately in person or by email with the TA or Course Coordinator regarding reasons for
their absence and make-up options. Absence must be explained in writing within 7 days of
the missed session by either a written/emailed excuse sent to the TA or Course
Coordinator, and/or a medical certificate submitted to the Health Service Unit and copied
to the Departmental Secretary, Life Sciences and the Course Coordinator.
Makeups: As a ge eral pri iple, edi als or other e uses a o l e use a stude t s
presence at an assigned time. Students must still complete the assigned work (make-up lab
report or make-up test) in order to obtain the marks for that item of coursework. The
student is responsible for liaising with the Course Coordinator or Teaching Assistant to
ensure the assigned make-up is completed. Normally only ONE make-up session will be
held. Any student who was inexcusably absent from a practical or test or does not submit
a practical report (initial or make-up) will receive 0% for that exercise. Note that a field
trip cannot be repeated for a make-up so you should make every effort to attend field trips.
Late submission: A penalty at 10% of mark per day late will be applied unless formal
approval for late submission is given by the TA or Course Coordinator using the guidelines
above for medicals, excuses.
Assignment submission: You will be informed whether reports should be in HARD or SOFT
copy format. HARD COPY reports should be submitted in the practical session or afterwards
into a labelled deposit box for your bench/demonstrator in the outer Zoology office and the
student list must be signed. Submissions anywhere else will not be assessed. These will be
returned at a time arranged by the TA or demonstrator. We are not responsible for reports
337




left uncollected or submitted inexcusably late. SOFT COPY reports should be submitted as
instructed through the relevant assignment link on the BIOLXXXX myelearning page.
Plagiarism: Students are hereby informed that plagiarism is forbidden and all unsupervised
coursework items must be accompanied by a completed Plagiarism Declaration form in
order to be assessed. Specific items may require submission through Turnitin on
eLear i g. ‘efer to U i ersit ‘egulatio s o Plagiaris a aila le fro
http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
Safety in the lab and field: Medical Data and Emergency Contact forms must be completed in
the first lab session when safety briefings will be given. Standard laboratory protocols for
conduct and dress code are in effect once you are present in a Life Sciences laboratory
(Undergraduate Student Handbook section 8). Dress code includes mandatory lab coats,
adequate clothing to protect the body, and closed shoes. NO sandals, slippers or open-toed
shoes will be allowed in the lab or field. Marks will be deducted for non-adherence to these
protocols.
Field work: Details are given in section 8 of the Undergraduate Student Handbook
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf . Field trips are specified on
the attached Course Calendar so you can be adequately prepared. You will not be allowed on
the field trip if a Medical Data form has not been submitted.
Accessibility: If you have a disability and have not disclosed the nature of your disability and
the support you need, you are invited to contact the Academic Support/Disabilities Liaison
Unit (ASDLU) of The University of the West Indies (UWI), St. Augustine Campus. Phone: 6622002 extension 83866, 83921, 83923 and 84254; Fax: 662-2002 extension 83922; Email:
[email protected] ; http://sta.uwi.edu/asdlu/forms.asp
338
GRADING SYSTEM:
The NEW UWI grading scheme effective 2014/15 is given below. See
http://www.uwi.edu/gradingpolicy/ for details.
GRADE
QUALITY
POINT
% RANGE
Grade Definition
A+
4.30
90-100
Exceptional
A
4.00
80-89
Outstanding
A-
3.70
75-79
Excellent
B+
3.30
70-74
Very good
B
3.00
65-69
Good
B-
2.70
60-64
Satisfactory
C+
2.30
55-59
Fair
C
2.00
50-54
Acceptable
F1
1.70
45-49
Unsatisfactory
F2
1.30
40-44
Weak
F3
0
0-39
Poor
339
THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE, TRINIDAD AND TOBAGO, WEST INDIES
THE CENTRE FOR EXCELLENCE IN TEACHING AND LEARNING
OFFICE OF THE CAMPUS PRINCIPAL
Telephone: (868) 662-2002 Ext. 82214, 82611 or 224-3736 Fax: (868) 662-0558
e-mail: [email protected]
MEMORANDUM
TO:
Dr. G. Briggs
Life Sciences-Biology
FROM:
Dr Margo Burns
Director, CETL
DATE:
16/04/2016
SUBJECT:
Revision to Minor in Biology
This letter confirms that the courses associated with the proposed revision to the Minor in
Biology were approved by the Centre for Excellence in Teaching and Learning during the 1052016 Academic Year. And as such, the proposed revision to the Minor in Biology has been
reviewed and approved.
As agreed upon, all courses associated with the Minor in Biology will have the revised GPA
structured inserted into the course outlines for the Academic Year 2016-2017.
Congratulations on completing the revision to the Minor in Biology.
Kind regards,
Margo P. Burns, EdD., MPH, MSc(A), RRT(A)
Cc: Secretary, Secretariat, Office of the Campus Registrar
MPB/
Comments from Mona (24 February 2016):
- the proposal was circulated among staff.
- overall, there were no major queries/concerns. It is a coherent programme of study and training
in the biological sciences.
- the programme provides exposure to the fundamental principles of biology, including studies of
the structure, organization, and diversity of life.
- it was noted that the layout of the credits on page 2 could be more clearly explained, as initially
it seems that the total advanced credits for the minor is 24.
Comments from Cave Hill (25 February 2016)
- the proposal is straightforward and well-justified in your document. You have our full support.