Genetics and Gene Techniques
7,5 hp. (5MO112)
Course leader:
Tracy Nissan (TN) [email protected]
Additional lecturers:
Vicky Shingler (VSh)
Gemma Atkinson (GAt)
Monica Holmberg (MHo)
Johannes Hanson (JHa)
Jan Larsson (JLa)
Christer Larsson (CLa)
Anders Byström (ABy)
Department of Molecular Biology
Department of Molecular Biology
Department of Medical Biosciences
Umeå Plant Science Centre (Department of Plant Physiology)
Department of Molecular Biology
Department of Molecular Biology
Department of Molecular Biology
Laboratory assistants:
Ala Javadi: [email protected]
Tony Karlsborn: [email protected]
Course administrator:
Eva-Christine Lundström, [email protected]
Lecture rooms:
785 28 69
Minor groove (MG, floor 0), Minor Groove, floor 0, Building 6L,
Forsörjningsvägen, Sjukhusområdet
Thymine/Uracil (T/U, floor 1), Dept. Molecular Biology, Building 6K
Laboratory:
Yellow lab (A109 course laboratories), Building 6A (unless otherwise
stated)
EXAMS
15 Febraury: 09.00-13.00, Östra paviljongen (ÖP)
(roomnumbertobeannounced2to3daysbeforetheexam)
Re-Exam: 24 April: 16.00-20.00, ÖP
(roomnumbertobeannounced2to3daysbeforetheexam)
Course Literature:
1. Hartwell et al. "Genetics, from genes to genomes",
(International 4th or 5th edition) McGraw – Hill. ISBN 00711021590 partially supports this course
This book is recommended for both this course (5MO112) and the course that immediately
follows (5MO113).
Note: Online electronic 4th editions of this book can be downloaded for free at:
https://www.youtube.com/watch?v=8rKo5C4QCHY
Also check out the animations on:
http://highered.mcgraw-hill.com/sites/007352526x/student_view0/
Note: an international version of the 5th Edition is available for 678 kr from Bokus:
http://www.bokus.com/bok/9781259095542/genetics-from-genes-to-genomes-intl-ed/
No text book is ever perfect for a given course and some subject matters are either poorly
covered or covered in a fragmentary way. Hence, additionally recommend reading:
For molecular biology (methods):
Molecular Biology of the Cell, Fifth Edition (2007). Alberts, Johnson, Lewis, Raff,
Roberts, Walter; Garland Science
or Download the free book Genetics and Molecular Biology at
http://gene.bio.jhu.edu/bm2whole.pdf
For bacterial genetics (free on-line text books) and/or:
Fundamental Bacterial Genetics (2004). Trun and Trempy; Blackwell
2. Additional important information is provided in lectures
(including laboratory introductions) and lecture handouts.
3. Other useful information is provided by on-line resources (see next sheet)
Course components:
Lectures, laboratory exercises, and problem solving classes.
Mandatory components:
Laboratory classes and associated reports. Attendance at lectures and problem solving classes is,
of course, highly recommended.
Absence from mandatory exercises due to illness should immediately be reported to the course
administrator.
Course literature and useful resources:
Reading advice for “Genetics and genetic techniques, 5MO112”:
Know that genetics is a constantly developing field. Emphasis for this course is therefore on up-to-date
information given out in lectures (hand-outs), and supplementary information given during laboratory
exercises and problem solving classes. Textbooks are good, but cannot substitute for lectures and other
exercises.
1. Genetics - From Genes to Genomes, International 4th or 5th edition. Hartwell L.H., Hood L., Goldberg
M.L., Reynolds A.E., Silver L.M. Mc-Graw-Hill.
Most relevant Chapters (see next page for associated lectures)
Chapters 1:
Genetics: the study of biological information
Chapters 2:
Mendel’s principles of heredity
Chapters 3:
Extensions to Mendel’s laws
Chapters 4:
The chromosome theory of inheritance
Chapters 5:
Linkage, recombination and the mapping of genes on chromosomes
Chapters 6:
DNA structure, replication, and recombination
Chapters 7:
Anatomy and function of a gene: dissection through mutation
Chapters 8:
Gene Expression: the flow of information from DNA to RNA to protein
Chapters 9:
Digital analysis of DNA
2. Additional important information is provided in lectures including laboratory introductions
3. Other useful information is provided by on-line resources
Text books: e.g.
Robert Schleif: Genetics and Molecular Biology at
http://gene.bio.jhu.edu/bm2whole.pdf
Todar’s Online textbook of Bacteriology at
http://www.textbookofbacteriology.net/index.html
(search for e.g. “genetics)
Simply Google e.g. “free on-line textbook bacterial genetics” for other options
Genetic glossaries: e.g.
http://www.genetics.edu.au/Publications-and-Resources/glossary-1
http://ghr.nlm.nih.gov/glossary
http://anthro.palomar.edu/mendel/glossary.htm
Simply Google e.g. “genetics glossary” for other options
Videos: e.g.
Primer design video
https://www.youtube.com/watch?v=c-f1H07D_70
Restriction enzyme mapping 1 and 2 (PSC2
https://www.youtube.com/watch?v=yR_heZ4n4Gc
https://www.youtube.com/watch?v=MeTWD8ECeiQ
Note: these videos are a must see viewing before attending respective lecture and/or problem
solving class (PSC)
ORGANIZATION
COURSE CONTENT
GeneralandBacterialGeneticAnalysis 1.
ThecentraldogmaChapters1andWheredomutationscomefrom?–Spontaneousand
inducedfidelitymistakesChapter7
2.
ThekeytoolsofthegeneticistPartsofChapter8andMutations,selectionsandscreens
Chapters6.1-6.4,7.1-7.3
3.
DNAcloningandgeneticanalysisinbacteriaIChapters9.1-9.2(andvideos)
(restrictionenzymes,cloning,genomicandcDNAlibraries)
4.
GenetransferandgeneticanalysisinbacteriaIIPartsofchapters14and15¤
(conjugation,transformation,andtransductioninnatureandasgenetictools)
5.
6.
7.
8.
9.
MGT*:PCRfromcloningtoforensics¤-seeindex(andvideos)
MGT*:DetectingDNA,RNAandproteins¤-seeindex
MGT*:DNAsequencingandDNA-proteininteractions¤-seeindex
MGT*:GeneandoperonfusionsPartsofchapters14and15
MGT*Introductiontobioinformaticmethodsforsequenceanalysis
MGT*:HomologousrecombinationandallelicreplacementinbacteriaChapter6.5andparts
ofChapter14
MGT*:MolecularGeneticTechniquescommontogeneticdissectionsinallorganisms
GeneticAnalysisindiploidOrganisms
10.
11.
12.
14-15.
MendelianGeneticsandtheprinciplesofinheritanceChapter2&partsofchapter3
Linkage,recombinationandgenemappingPartsofchapters3and4
Locatingdiseaseassociatedalleles¤
GeneticanalysisinyeastIandII–asamodelgeneticorganismChapter5.5-5.6
16.
Plantbiotechnologyandtransgenicplants¤
18.
Arabidopsisasamodelgeneticorganism¤
Note:L17isadiscussiononBioethicalconsiderations
Overview of other course components – labs and PSCs:
Laboratory exercises
Lab. 1: Transfer of genetic material between bacteria via conjugation
Lab. 2: PCR and DNA cloning – introducing desired mutations
Lab. 3: Allelic replacement of a gene in E. coli
Lab. 4: Yeast cell types and mating
Lab. 5: Yeast complementation analysis
Problem solving classes (PSCs) to reinforce key concepts and to stimulate critical thinking.
Note: YouTube videos are a must see viewing before attending the respective PSC.
PSC 1: Codons, reading frames and mutations
PSC 2: Restriction enzymes, cloning and complementation
PSC 3: Primer design
PSC 4: Northern, Southern and Western
PSC 5: Gene fusions and reporters
PSC 6: Blast interpretations (in conjunction with Lab. 2, assistants)
PSC 7: Genetic problems - Yeast genetics (assistants in conjunction with Labs 4 & 5)
Learning Goals (FSR’s) for this course:
-
Be able to describe how genetic material is inherited, mapped, analyzed and identified
in bacteria and eukaryotes.
-
Be able to describe how genetic material can mutate and the effects of these mutations.
-
Be able to describe how the external environment can affect the genetic material
-
Be able to describe how the genetic material can be utilized in bio-techniques
-
Be able to demonstrate practical skill in execution, interpretation and statistical
processing of data from genetic and gene technology experiments
DATES, LECTURES and TEACHERS
January 16th, 2017 to February 15th, 2017.
______Week 3_____________________________________________________________________
Monday 16th
09.00-10.00 MG – Roll call and introduction with overview of the course (TN)
10.00-12.00 MG – The central dogma and Where do mutations come from? – Spontaneous
and induced fidelity mistakes (TN)
Break
13.00-15.00 MG – L2 The key tools of the geneticist: Mutations, selections and screens (VSh)
15.15-16.45 T/U – PSC 1: codons, reading frames and mutations (TN)
Tuesday 17th
09.00-11.00
Break
12.00-14.00
14.15-15.45
MG – L3. DNA cloning and genetic analysis in bacteria I (VSh)
MG – L4. Gene transfer and genetic analysis in bacteria II (CLa)
T/U – PSC 2: Restriction enzymes, cloning and complementation (TN)
Wednesday 18th
09.00-10.00 A109 – Lab safari and safety (Assistants)
10.00-11.00 MG – Introduction to Lab 1: Gene transfer in bacteria Day 1 (Assistants)
Break
12.00-14.00 MG – L5. MGT: PCR from cloning to forensics (TN)
14.15-16.00 MG – PSC 3: Primer design (TN)
16.00~17.00 A109 – Lab 1 Day 1 continued
Thursday 19th
09.00-13.45 MG – L6. MGT: Detecting DNA, RNA and proteins (TN)
MG – PSC 4: Northern, Southern and Western (TN)
14.00-15.00 A109 – Lab 1 Day 2 (Assistants)
Friday 20th
09.00-11.00
Break
12.00-14.30
14.30~16.00
16.15~17.00
T/U – L7. MGT: DNA sequencing and DNA-protein interaction techniques (TN)
T/U – L8. Gene and operon fusion (VSh) with PSC5
A109 – Lab 1 Day 3 (Assistants)
T/U – Introduction to Lab 2: PCR - introducing a desired mutation (by Assistants)
In preparation for early start on Monday 23rd
*Use any spare time productively to answer the lab quiz questions and recommended reading
______Week 4_____________________________________________________________________
Monday 23rd January
08.00-14.30 A109 – Lab 2 Day 1 (PCR amplification predictions and round 1 PCR)
15.00~17.00 T/U – L9 Introduction to bioinformatic methods for sequence analysis (GAt)
Tuesday 24th January
08.00-14.30 A109 – Lab 2. Day 2 (PCR purifications, analysis and round 2 PCR overnight)
Break
15.00-17.00 T/U – L10. Molecular Genetic Techniques: Homologous recombination and
allelic replacement in bacteria (CLa)
Wednesday 25th January
09.00-11.00 MG – L11. Mendelian Genetics and the principles of inheritance (JLa)
Break
12.00~17.00 A109 – Lab 2. Day 3 Round 2 PCR analysis and dry lab
Thursday 26th January
09.00-11.00 T/U – L12. Linkage, recombination and gene mapping (JLa)
Break
12.00-14.00 T/U – L13. Locating disease associated alleles (MHo)
14.00~17.00 MG – Lab 2. Day 4 “computer lab” Part B
Friday 27th January
08.30~11.30 A109 – Introduction to Lab 3 Allelic replacement (by Assistants)
A109 – Lab 3 Day 1 (single cell streaking)
Break
12.30-14.00 T/U – L14. Yeast genetics I (ABy)
14.15-15.30 T/U – PSC 7: Yeast genetics problems (by Assistants with ABy)
______Week 5_____________________________________________________________________
Monday 30th January
09.00~12.00 T/U – Lab 2. Day 5 Part C; PSC 6: Blast interpretations (Assistants) (computer lab)
Tuesday 31st January
08.00~12.30 A109 – Lab 3. Day 2 (Assistants; single cell streaking of two colonies)
Uniaden 2017 – no scheduled events in the afternoon
Wednesday 1st February
09.30~11.15 T/U – Lab 2. Part C PSC 6: Blast interpretations (continued if necessary)
11.15~12.00 T/U – Introduction to Labs 4 and 5 (by Assistants)
Break
13.00-16.00 A109 – Lab 3. Day 3 (Assistants: single cell streaking)
A109 – Lab 5. Day 1
Thursday 2nd February
10.00~12.00 A109 – Lab 3. Day 4 (Assistants single cell streaking)
A109 – Lab 5. Day 2
Break
13.00-15.00 T/U – L16. Plant biotechnology and transgenic plants (JHa)
15.00-17.00 T/U – Yeast Genetics II (ABy)
Friday 3rd February
13.30-14.45 T/U – L17. Bioethical considerations (TN)
Break
15.00~17.00 A109 – Lab 3. Day 5 (Assistants; single cell streaking)
A109 – Lab 5. Day 3 (Assistants)
Note: Assistants will monitor plates over the weekend and move them to the cold room until
needed.
Use spare time during labs and non-scheduled periods productively to answer the lab quiz
questions, for recommended reading, and for general study of course material
______Week 6_____________________________________________________________________
Monday 6th February
*08.30~12.00 A109 – Lab 3. Day 6 (colony patching)
A109 – Lab 4. Day 1
A109 – Lab 5. Day 4
*Note that this laboratory session is co-shared with another course
Break
14.00-16.00 T/U – L18. Genetic Model Organisms - Arabidopsis (JHa)
Tuesday 7th February
08.00~14.00 A109 – Lab 3. Day 7 (PCR and re-streaking)
A109 – Lab 4. Day 2 (Assistants)
A109 – Lab 5. Day 5 (Assistants)
Wednesday 8th February
08.00-10.00 A109 – Lab 3. Day 7
(analyze PCR products and correlate with phenotypes)
A109 – Lab 4. Day 3 (Assistants)
A109 – Lab 5. Day 6 (Assistants)
Lab cleaning
Break
10-30-12.30
T/U – Lab round-up and question time (Assistants)
Thursday 9th February
Work with assignments and STUDY
(Recommend preparation for Q and A session on Monday)
Friday 10th February
17.00
Dead-line for completed Laboratory Questionnaires to be submitted
electronically to the assistants using the ‘Urkund’ client email addresses:
Lab 1 and 2 to Ala Javadi
Submit to: [email protected]
Lab 3 to 5 to Tony Karlsborn
Submit to: [email protected]
______Week 7_____________________________________________________________________
Monday13thFebruary
12.00-14.00
“Openoffice”inT/U:QandAsession(TN)
–Thisisyourchancetogethelpwithstudyquestions
–Besuretocomepreparedwithquestionsonaspectsthatyouareuncertainabout
Courseassessment/feedback
Tuesday14thFebruary
Self-Study