BIO3120 Microbiology in Genomics Era
Instructor: Martin Wu ([email protected])
Office hour: Tuesday 1:30-2:30PM
TA: Eric Swanson ([email protected])
Office hours: Wednesday 10-11AM, Thursday 4-5PM
Why should you care about microbes?
Microbes are everywhere and microbes rule! Do you know that microbes are responsible for
producing the oxygen in one out of every five breaths we take? Do you know that microbes make
delicious foods we depend on and enjoy: cheese, yogurt, beer, bread, kimchi? How are microbes
living in our guts linked to obesity? How could one pathogen wipe out half of the entire European
population once in history? If you are interested in learning how microbes impact humans and our
planet, you are in the right place. In this course, we will explore how microbes rule the world and how
genomics has revolutionized the way we study them.
What will you learn in this course?
By the end of the course, you will be able to apply the knowledge you learn to real life situations. For
example, when you read a headline in a newspaper about E. coli O157 outbreak, you will be able to
explain to your friends how E. coli causes bloody diarrhea. You will be able to understand why we are
losing the battle of antibiotic resistance against pathogens, its implications and how we can address
this problem. You can become a detective and know how to investigate the mystery behind the 2001
anthrax bioterrorism attack using cutting-edge genomic technologies. You will be able to propose new
ideas on how we can tame microbes to build a clean and sustainable future. You will acquire a
conceptual and practical framework of microbiology that you can apply to solve these grand
challenges facing human society in the 21st century.
How do you and I know if you’re learning?
In-class exercises (30 points, 10%)
In many classes, I will ask you to answer several questions using Learning Catalytics. These questions
will review the key concepts and ideas you have learned in the classes and your responses will be used
to gauge how well you understand them. You will receive 0.5 point for each question that you answer
and 0.5 point for each question you answer correctly. For logistic reasons, I do not allow students to
make up missed questions. However, there will be more than 30 in-class exercise questions. Once you
have earned 30 points, you will not earn any additional credit. Answers written on paper will not be
accepted, so bring an internet-enabled device to each class. You may not use another student's account
to answer questions for them. Answering questions for another student, whether they are present or
absent, is a violation of the honor code.
Out-of-the-class problems and activities (60 points, 20%)
The homework is designed to hone your skills in in critical thinking, analytic reasoning, and problem
solving. For each homework, you will be asked to either read a scientific paper and answer questions
or solve a real-life problem by applying the key concepts and ideas you learn in the class. The
homework can be multiple-choice or short-answer questions. You will collaborate with your
classmates and work as a team. Each team member is expected to contribute intellectually. The effort
of each team member will be peer evaluated using a score system.
Exams (210 points, 70%)
Three exams will challenge you with multiple-choice questions to assess your understanding of the
foundational knowledge, your critical thinking skills to apply concepts to novel situations and your
ability to integrate ideas to solve problems.
Grading
Your final letter grade will be based on a total of 300 points and will assigned as follows:
Letter Grade
Points
Letter Grade
Points
A+
291-300
C
219-230
A
279-290
C-
210-218
A-
270-278
D+
201-209
B+
261-269
D
189-200
B
249-260
D-
180-188
B-
240-248
F
<180</td>
C+
231-239
The point cutoff for a grade may be lowered if the class median is lower than 240 points. The point
cutoffs will not be raised.
Course materials
Textbook
Microbiology: An Evolving Science (third edition) by Joan L. Slonczewski and John W. Foster. You
can rent the eTextbook from CourseSmart for 6 months for $53.33. Because microbiology is a fast
evolving science, I will also provide newspaper and magazine articles, papers from the current
scientific literature that provide the most recent information on the subject matter. These materials,
together with assigned textbook readings will be posted on the class website. There will be material
covered in class that is not in the reading. Conversely, there will be material covered in the textbook
that is not covered in class. The assigned readings are designed to help you fill in yourself. Only topics
that have been covered in the lectures will be tested.
Learning Catalytics
We will be using Learning Catalytics, a student response system for in-class exercises. To use
Learning Catalytics, you will need to bring an internet enabled device (smart phone, iPad, iPod Touch,
tablet, or laptop) to every class. If you will not have access to an internet enabled device, please let me
know. You can purchase access to Learning Catalytics here ($12 for 6 months or $20 for one year)
Class policy
Please be considerate to your neighbors and the lecturer. Cell phones should be turned off or put on
vibration mode during the lecture. Laptop and mobile device usage during the lecture should be
restricted to class related notetaking and research. Using a device for non-class related activities (IM,
tweet, facebook, online shopping etc) is distracting to the students around and behind you and
therefore is strongly discouraged.
The exams will be closed-book, multiple choice questions. Use of computers, cell phones, books, class
notes will not be allowed during exams. However, you can bring a calculator and you are allowed to
bring one note card (4x6 inch) to the exam with any notes that you may need. Only topics covered in
lectures will be tested. Make up exams can only be given if verifiable documentation about why the
exam was missed is provided and the student inform the instructor before the exam or within one day
after the exam.
Homework will be assigned and submitted online using Collab. Since I will provide immediate
feedback after the due date, late or missed homework assignments will receive 0 points.
The points you earn for each activity will be posted on Collab in the GradeBook section. If you
believe a question on your exam/homework was incorrectly graded, you must contact the TA within
one week of the day the exam/homework point was posted – no considerations will be made after this
one-week window.
In the past, some students have asked for special exception to policies for this course. For example,
students have asked for extra assignments or work to improve a student’s grade. No exemption or
opportunity will be given to a student unless it can be made available to the entire class.
Recording of lectures/presentations is allowed for personal use only. Students may not post such
recordings on any internet site.
Twitter
Microbes are so relevant to our daily life. I will tweet news and videos that I think are cool. You can
follow @microbesrule1.
FAQ
Topics & Schedule
Module 1 Microbial Cell
Class 1. (01/13) The three laws of microbiology
Reading: none
Slides
Class 2. (01/15) Why are microbes small?
(Cell structure and function I)
Reading: Chapter 3 pages 79-91; Extending the upper limit temperature for life
Slides
Class 3. (01/20) What are microbes made of?
(Cell structure and function II)
Reading: Chapter 2 pages 55-57; Chapter 3 pages 91-99, 112-116
Optional: Intelligent Design Dover Trial (youtube).
Optional: Chemotaxis animation
Slides
Class 4. (01/22) How do we culture microbes?
(Microbial culture)
Reading: Chapter 4 pages 119-123, 127-139, 145-152
Class 5. (01/27) How does a bacterial cell grow?
(Microbial growth)
Reading: Chapter 3 pages 104-107; Chapter 4 pages 139-143
Class 6. (01/29) Why are microbes everywhere?
(Environmental influences on microbial growth)
Reading: Chapter 5 pages 157-175
Module 2 Microbial Metabolic Diversity
Class 7. (02/03) How do microbes live without oxygen?
(Fermentation)
Reading: Chapter 13 pages 491-508, 516-527
Class 8. (02/05) Exam I
Class 9. (02/10) How do microbes breathe?
(Respiration I)
Reading: Chapter 14 pages 539-571
Class 10. (02/12) How do microbes breathe?
(Respiration II)
Reading: Chapter 14 pages 539-571
Class 11. (02/17) Can microbes be “green”?
(Phototrophy I)
Reading: Chapter 14 pages 571-582
Class 12. (02/19) Class canceled
Class 13. (02/24) Can microbes be “green”?
(Phototrophy II)
Reading: Chapter 14 pages 571-582
Class 14. (02/26) How do microbes eat a buffet?
(Catabolism)
Reading: Chapter 13 pages 510-516, 527-532, ##
Class 15. (03/03) How do microbes build from scratch?
(Autotrophy)
Reading: Chapter 15 pages 585-601
Module 3 Genes and Genomes
Class 16. (03/05) How do microbes decode DNA?
(From genes to proteins I)
Reading: Chapter 8 pages 275-301
Spring break
Class 17. (03/17) How do microbes decode DNA?
(From genes to proteins II)
Reading: Chapter 8 pages 301-311
Class 18. (03/19) Exam II
Class 19 (03/24) How do microbes “think”?
(Gene regulation I)
Reading: Chapter 10 pages 365-375
Class 20. (03/26) How do microbes “think”?
(Gene regulation II)
Reading: Chapter 10 pages 382-388, 397-400
Class 21. (03/31) How to decode a bacterium?
(Genome and genome sequencing)
Reading: Chapter 7 pages 237-244, 258-260, 267-270
Class 22. (04/02) Can we predict a bacterial cell?
(Genome annotation)
Reading: Chapter 8 pages 312-318
Class 23. (04/07) How do microbes evolve?
(Microbial evolution)
Reading: Chapter 9 pages 321-337, 358-361
Module 4 Microbes and Human
Class 24. (04/09) Who are there and what are they doing?
(Microbial diversity & Ecology)
Reading: Chapter 17 pages 681-691, 696-702; Chapter 21 pages 841-849
Class 25. (04/14) Microbes R us?
(Human microbiota)
Reading: Chapter 23 pages 925-935
Class 26 (04/16) What makes a bug a pathogen?
(Pathogenesis)
Reading: Chapter 25 pages 1010-1033. 1036-37
Class 27. (04/21) What are the five microbial diseases you should know?
(Microbial diseases I)
Reading: Chapter 25 pages 1045-46, Chapter 26 pages 1051-56, 1066-72, 1079-81, 1096-98.
Class 28. (04/23) What are the five microbial diseases you should know?
(Microbial diseases II)
Reading: Chapter 1 pages 21-22, Chapter 26 pages 1083-87
Class 29. (04/28) Exam III