UMEÅ UNIVERSITET
Department of Molecular Biology
Victoria Shingler
Schema 2016
5MO018
Genexpression 7,5 hp
Gene expression technology
COURSE SCHEDULE 5MO019
DEPARTMENT OF MOLECULAR BIOLOGY
_______________
Course dates:
February 18th to March 21st
Exam:
Re Exam:
March 21st; Time: 09.00-13.00, Place: Östra Paviljongen
May 23rd; Time: 16.00-20.00, Place: Östra Paviljongen
Localities:
Lecture room:
Laboratory:
?????? (Building 6K) unless otherwise stated
Green Lab. (Building 6L)
Course Literature: See next page
Course administrator
Course leader:
Course Assistants:
Other Course lecturers:
Matthew Francis (MF)
Martin Gullberg (MG)
Vasili Hauryliuk (VH)
Jörgen Johansson (JJ)
Per Stenberg (PS)
Eva-Christine Lundström, tel. 785 2869
eva-christine.lundstrom@molbiol.umu.se
Victoria Shingler, tel. 785 2534
victoria.shingler@molbiol.umu.se
Lisa Wirebrand: lisa.wirebrand@molbiol.umu.se
Steffi Jimmy: Steffi.jimmy@umu.se
Department of Molecular Biology
Department of Molecular Biology
Department of Molecular Biology
Department of Molecular Biology
Department of Molecular Biology
Course components:
Lectures, laboratory exercises, discussion groups and problem
solving classes.
Mandatory components: Laboratory classes and the associated report, problem solving
classes / discussion groups and scientific articles assignments
are mandatory. Note that laboratory reports and preparation of
written working material for discussion groups have strict
deadlines. Attendance at lectures is, of course, highly
recommended.
Absence from mandatory exercises due to illness should immediately be reported to the
course administrator.
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Course Literature 5MO019:
1] Genetics - From Genes to Genomes, 4th or 5th edition. Hartwell L.H., Hood L., Goldberg M.L.,
Reynolds A.E., Silver L.M. Mc-Graw-Hill.
Note: 4th Editions free download at: https://www.youtube.com/watch?v=8rKo5C4QCHY
This book is recommended for the course 5MO018 and 5MO019:
Check out animations on: http://highered.mcgraw-hill.com/sites/007352526x/student_view0/
Most relevant Chapters for 5MO019
Chapters 8: Gene Expression: the flow of information from DNA to RNA to
protein
Chapters 10: Genomes and proteomes¨
Chapters 15: Gene regulation in prokaryotes
Chapters 16: Gene regulation in eukaryotes
2] Additional important information is provided in lectures (including laboratory
Introductions), together with lecture handouts, reviews and the original articles
for discussion groups.
3] Other useful information is provided by on-line resources [see 5MO018],
2
Overview of lectures, labs, discussion groups and PSCs 5MO019
Lectures:
1. Bacterial transcriptional regulation I (VS)
2. Bacterial transcriptional regulation II (VS)
3. External stimuli and gene regulation: Two-component systems (VS)
4. Signal sensing, regulatory logic, and synthetic regulatory devices (VS)
5. Transcriptional termination and attenuation (JJ)
6. Bacterial translation and control of protein synthesis (TN)
7. Regulation of mRNA stability and function (JJ)
8. Bacterial protein export systems (MF)
9. Global regulation and the “omics” (VS)
10. Protein expression systems: bacterial (VH)
11. Eukaryotic transcriptional regulation (VS)
12. The eukaryotic ribosome and regulation of protein synthesis (VH)
13. How to study eukaryotic cells (MG)
14. Protein expression systems: eukaryotic (MG)
15. Transcriptomics and RNA sequencing (PS)
Laboratory exercises
Gene regulation labs
Lab. 1 Reporter gene technology in gene regulation
Lab. 2 Western analysis
Protein expression labs
Lab. 3 Protein purification via an affinity tag
Lab.4 Dry Lab: Protein expression data interpretation lab
Discussion groups and problem solving classes (PSCs)
Discussion groups and problem solving classes are designed to reinforce key concepts and to
stimulate critical thinking that requires assimilation and interpretation of basic information
given in the lectures.
Discussion group 1: Paradigms of bacterial transcriptional regulation (VS)
(Dead-line for written material: Feb 25th)
Discussion group 2: Transcriptional reporter genes and biosensors (VS)
(Dead-line for written material: March 3th)
Discussion group 3: Genetic switches in gene regulation (VS)
(Dead-line for written material March 8th)
PSC1: data interpretation - Genetic data and gene regulation (VS)
PSC2: data interpretation - Bacterial regulatory circuitry (VS)
PSC3: data interpretation - Signalling circuitry (VS)
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Overview of laboratory component of the course
Laboratory practical
Gene regulation labs
Lab. 1 Reporter gene technology in gene regulation
Lab. 2 Western analysis
Protein expression labs
Lab. 3 Protein purification via an affinity tag
Lab. 4 Dry Lab: Protein expression data interpretation lab
Introduction to the dry lab.
The aim of the dry lab series incorporated into the practical part of this course is to introduce
you (the student) to concepts and ways of thinking that are usually taught through a practical course in
which you get your hands "wet".
The ability to manipulate and regulate genes and to express proteins is the corner stone of
molecular biology techniques. There are few aspects of modern biology that have not been affected by
the advent of molecular biology in some way, including areas that might not be expected to have a
"molecular" component. In addition to being important in basic research, molecular biology has had
far reaching effects in medical, pharmaceutical, and agricultural industries, in forensics, and in many
other areas of applied science and technology. However, given the time-frame of the course, it is not
possible for us to introduce you practically to all of the molecular biology techniques used in analysis
of gene regulation and expression, or even to undertake all steps in a given analysis. Dry labs are
designed using authentic data to complement your “wet labs”, so that you can reach the more mentally
stimulating part of any practical - the interpretation of genuine experimental results.
Lab. 1: Reporter gene
technology in gene
regulation
Day 1 Thursday Feb 18h (patching and putting up o/n cultures)
Day 2 Friday Feb 19th (growing up strains o/d, developing, data
plotting, and interpretation)
Lab. 2:
Western analysis
Day 1 Monday Feb 22rd (prepare extracts, run gel o/n)
Day 2 Tuesday Feb 23th (electro-blotting, to 1O Ab o/n)
Day 3 Wednesday Feb 24th (washing, 2O Ab, developing)
Day 4 Thursday Feb 25th (buffer day)
Lab. 3:
Protein purification via an
affinity tag
Staggered as below:
March 1st Introduction and preparation for Groups 1 to 4
March 2nd purifications (Grp1-4); and preparation for Groups 5-10
March 3rd purifications (Grp5-10)
&
Dry Lab 4:
Protein expression data
interpretation lab
To be done during incubation/waiting times during Lab 3.
March 7th Open office Lab 4 (assistants LW and SJ) for anyone
who did not manage it then or needs extra help.
Lab round-up: Thursday March 10th
Dead-line for dry Lab 4 papers: Monday March 10th
Dead-line for Lab 1-3 report: Thursday March 15h
4
Week 8 (working week 1 Feb 18th-19th )
Thursday Feb. 18th
09.00-09.30 Roll-Call & Introduction to the course (VS) –
09.30-12.30 L1. Bacterial transcriptional regulation I (VS) –
12.30-13.00 Introductions to the laboratory course &
Discussion group 1 literature assignment (VS) 14.00Lab safety - covered in 5MO018 applies for 5MO019-reminder (Lab)
Introduction to Lab. 1 with introduction to keeping lab notes (LW&SJ)
15.30Lab. 1: Reporter gene technology in gene regulation
Lab. 1: day 1 (plate patching, start overnight cultures)
Thereafter Private study
Friday Feb. 19th
09.00-10.00 Lab. 1: day 2: Start overday cultures and time staggered development and data
cruching) (assistants LW&SJ)
10.00-13.00 L2. Bacterial transcriptional regulation II (VS) 14.00Lab 1 day 2 continued (time staggered development/computer lab)
(Students: be sure to check your answers to the specific questions and plots
of the data with the course assistants before you leave. It is important that
you have this clear for Labs 2-4)
~17.00
(may be earlier, but the bacteria decide….)
Week 9 (working week 2 Feb 22rd -26th )
Monday Feb 22rd
09.00-11.30 L3. External stimuli and gene regulation: Two-component systems (VS) 12.30-13.30 Introduction to Lab 2: (assistants LW&SJ) – Thymine
Lab 2: Western analysis day 1 (LW&SJ)
(preparation of extract, running gel over-night)
Thereafter Private study for e.g. Discussion group 1 literature assignment
Tuesday Feb. 23th
09.00-10.00 Lab 2: day 2 (assistants LW&SJ) (electroblotting)
10.00-12.00 L4. Signal sensing, regulatory logic, and synthetic regulatory devices (VS)
13.00Lab 2: day 2 (assistants LW&SJ) (electroblotting to drying, staining filter,
blocking, washing, 1O antibody overnight)
Thereafter Private study for e.g. Discussion group 1 literature assignment
Wednesday Feb 24th
09.00Lab 2: day 3 (assistants LW&SJ) washing, 2O Ab and developing
Thereafter Private study for e.g. Discussion group 1 literature assignment
Thursday Feb 25th
09.00-11.00 L5. Transcriptional termination, attenuation (JJ)
12.00Lab 2: buffer day
Thereafter Private study for e.g. Discussion group 1 literature assignment
17.00
Dead-line for Discussion group 1 written material
Friday Feb 26th
09.00-11.00 Discussion group 1 (VS) and Discussion group 2 assignment (VS)
12.00-14.00 L6. Bacterial translation and control of protein synthesis (VH)
14.00
Private study for e.g. Discussion group 2 literature assignment
5
Week 10 (working week 3 Feb 29th to March 4th )
Monday Feb 29th
0.9.00- 11.00 L7. Regulation of mRNA stability and function (JJ)
12.00- 14.00 L8. Bacterial protein export systems (MF)
Thereafter Private study for e.g. Discussion group 2 literature assignment
Tuesday March 1st
09.00-11.00 L9. Global regulation and the “omics” (VS)
12.00-14.00 L10. Protein expression systems: bacterial (VH)
14.00
Introduction to Labs 3 and 4 (LW & SJ)
Lab 3: Protein purification via an affinity tag
Lab 4: Dry Lab: Protein expression data interpretation lab
Lab 3/4: (Preparation of extracts and binding o/n Groups 1-4)
(Private study Groups 5-9)
Wednesday March 2nd
08.30-all day Lab 3/4: Groups 1-4 (purification and running gel, staining, de-staining and
documentation - OBS! Protein (on ice) to be taken immediately over to Uwe
for the next course. (Grps 5-9; Private study)
13.00
Groups 5-9 (preparation of extracts and binding o/n)
Thursday March 3rd
08.30--all day Lab 3/4: Groups 5-9 (purification and running gel, staining, de-staining and
documentation - OBS! Protein (on ice) to be taken immediately over to Uwe
for the next course.
(Grps 1-4; Private study for e.g. Discussion group 2)
17.00
Dead-line for Discussion group 2 written material
Friday March 4th
11.00-14.00 Discussion group 2 (VS) and Discussion group 3 assignment (VS)
14.00Private study for Discussion group 3 literature assignment
6
Week 11 (working week 4 March 7th to March 11th )
Monday March 7th
09.00-11.00 L11. Eukaryotic transcriptional regulation (VS)
12.00-14.00 Open office Lab 4 (assistants LW & SJ)
for anyone who did not manage it during Lab.3 incubations and
waiting times, or needs some extra help.
14.00Private study
Tuesday March 8th
Private study
17.00
Dead-line for Discussion group 3 written material
Wednesday March 9th
09.00-11.00 L12. The eukaryotic ribosome and regulation of protein synthesis (VH)
12.00-13.45 Discussion group 3 (VS)
Thursday March 10th
09.00-11.00 L13. How to study eukaryotic cells (MG)
13.00-14.30 Lab round up (VS or assistants)
15.00-16.00 How to write your Lab report (LW & SJ)
17.00
Dead-line for Lab 4 reports to assistants
Friday March 11th
09.00-11.00 L14. Protein expression systems: eukaryotic (MG)
Private study e.g. Lab report etc
Week 12 (working week 5 March 14th -18th )
Monday March 14th
09.00-11.00 L15. Transcriptomics and RNA sequencing (PS)
Private study e.g. Lab reports and Exam
Tuesday March 15th
All day
Private study e.g. Lab reports and Exam
17.00
Dead-line for Lab reports (to assistants LW & SJ)
Wednesday March 16th
All day
Private study e.g. Exam
Thursday March 17th
All day
Private study e.g. Exam
Friday March 18th
09.00-12.00 Open Office Q and A session (VS and others)
Thereafter, private study
Week 13 (working week 6 March 21rd)
Monday March 21st
EXAM: 09.00-13.00, Place: Östra Paviljongen
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