Download Microbial Genetics (Kroening)

BIO 375/575 Microbial Genetics
Lecture M & W – 3:30-5:00 P.M. Fall 2006
Text: Snyder, L. and Champness, W. 2003. Molecular Genetics of Bacteria, American
Society for Microbiology, Washington, D. C.. Second Edition. ISBN 1-55581-204-X
Instructor: Dubear Kroening
Phone: 424-1102 (dept.)
email: [email protected]
Office: HS 39
Office hours: M & W 3-3:30 & 5-6 and by appointment
Recommended & Other Useful References:
1. McMillan, V. E. 2001. Writing Papers in the Biological Sciences, Bedford/St. Martin’s.
2. Bushman, F. 2002. Lateral Gene Transfer, Cold Spring Harbor Laboratory Press.
3. Kaper, J. B. and Hacker, J. 1999. Pathogenicity Islands and Other Mobile Virulence
Elements, ASM Press, Washington, D.C.
4. Ptashne, M. 2002. Genes and Signals, Cold Spring Harbor Laboratory Press.
5. Miller, J.R. 1992. A Short Course in Bacterial Genetics: Lab Manual, Cold Spring Harbor
Laboratory Press.
Some genetics and other resources on the INTERNET:
1. Class Web-site, http://www.uwosh.edu/d2l.
2. American Society for Microbiology (ASM) home page: http://www.asmusa.org
3. BioWeb http://bioweb.uwlax.edu/index.htm. (A nice collection of data and tools for genetics
and biology.)
4. DOE Joint Genomics Institute (JGI), Microbial Genome Projects:
http://www.jgi.doe.gov/JGI_microbial/html/index.html
5. ExPASy Molecular Biology Server: http://www.expasy.ch/. (A very useful site for molecular
biology, genomics, and proteomics included predicted peptide mass fingerprints.)
6. VIRTUAL GENOME CENTER: http://alces.med.umn.edu/VGC.html.
7. THE NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION:
http://www.ncbi.nlm.nih.gov/. (This site includes the GenBank and other DNA, protein, and
genomic databases and extremely useful search programs such as “BLAST.” Includes the
MEDLINE literature database such as “Pubmed.”)
8. TIGR (The Institute for Genomic Research): http://www.tigr.org.
9. Kazusa Genome Research Institute: http://www.kazusa.or.jp. (Includes the database for the
genome sequence of the cyanobacterium Synechocystis PCC 6803.)
10. E. coli Genetics Stock Center: http://cgsc.biology.yale.edu/. (a useful site for gene names,
maps, etc.)
11. E. coli Genome Center: http://www.genome.wisc.edu
12. New England Biolabs, Restriction Enzyme Database (NEB-REB): http://rebase.neb.com.
13. The RCSB Protein DATA Bank: http://www.rcsb.org/pdb/.
14. Frontdoor to PROTEIN EXPLORER: http://molvis.sdsc.edu/protexpl/frntdoor.htm (Site for
online use of the PROTEIN EXPLORER program for protein structure viewing &
manipulation).
15. WEBCUTTER (a nice site for on-line restriction site analysis):
http://www.firstmarket.com/cutter/cut2.html
16. NET PRIMER (a site that allows downloaded or on-line design of PCR primers. They also
carry “Plasmid Premier” a program for plasmid design):
http://www.premierbiosoft.com/netprimer.html
17. New England Biolabs, Restriction Enzyme Database (NEB-REB): http://rebase.neb.com.
18. Promega Corporation (Madison, WI): http://www.promega.com/
19. UW-O (Polk) Library: http://www.uwosh.edu/departments/llr/home.html (Polk Library
provides access to a variety of useful literature databases such as Medline and Web of Science
and carries on-line, full-text subscriptions to several relevant journals including Science, the
Nature Journals, and the American Chemical Society (ACS) Journals. Follow on-screen
instructions. Contact the Polk Reference Desk or me for help.)
Course Objectives: Understanding microbial genes, genomes, and gene regulation is
central to understanding the biology of microorganisms. Since the long-ago discoveries
that microorganisms have genes, the structure of DNA, and the role of DNA in heredity
(1940’s and 50’s), microbes have been used extensively to explore the structure, function,
regulation, and evolution of genes. In addition, microbial genetics is essential for
molecular biological studies and manipulation of eukaryotic and prokaryotic organisms
and for practical applications (biotechnology) in diverse areas of life sciences.
Microbiology and microbial genetics are now in the exciting era of “genomic”
and “post-genomic” analysis. Complete genome sequences (genetic blueprints) are now
being solved at astonishing rates and these hold remarkable potential for expanding our
understanding of biology. In this course, we will discuss the structure, function,
expression, and evolution of microbial genes and methods used for their study and
manipulation. Topics include microbial genomes and their evolution; gene discovery,
identification, and mapping; mutation; DNA repair; gene transfer among organisms;
plasmids; transposable elements; genetic recombination; and gene regulation. Our
discussion will include molecular genetic techniques such as gene cloning, hybridization,
microarrays, "proteomics," gene expression, site-directed mutagenesis, and the use of
gene fusions as “reporters” and probes.
In addition to regular lectures, we will have discussion sessions in which we
discuss research and review articles related to microbial genetics. Our goals are: 1) to
learn how to read and evaluate scientific articles, 2) to learn how to use genetic methods
to attack biological problems, and 3) and to learn about exciting, current topics in
microbial genetics.
Grading: Your grade will be determined by the percentage of points that you earn on the
assignments (Journal Article Reports, Research Paper, Technique Exercises) as well as
on the exams.
Journal Article Reports: To encourage exploration of current topics, I am requesting
that each student find, read, and write a brief report (no more than 1 page) on a current
journal article related to microbial genetics. You will need approximately one article
every two weeks with the exception of exam weeks. Due dates will be announced. In
your reports you should state the objective of the study reported in the article, the
methods used, and the main conclusions of the work. Some of these articles may be
used subsequently for class discussion.
Literature Discussion/Analysis: Usually one or two papers per week (from Nature,
Science, Journal of Bacteriology, Molecular Microbiology, or other sources) will be
assigned for class discussion. One or more hours per week will be devoted to these
discussions. These discussions will parallel the lecture material. Students are expected to
read assigned papers and should be prepared to give a 5 minute summary of articles in
class. Also be prepared to discuss and/or ask questions about these articles in class.
Grades can be improved by active participation in class discussion.
Grading Policy: 90-100% =A, 80-90% =B, 70-80% = C, 60-70% = D, less than 60%=F.
Grades of AB, BC, and CD will be used, at the discretion of the instructor, for borderline
scores. If the class scores on a particular exam are uniformly low, grades may be
adjusted accordingly. Exams will consist of definition, problem, and discussion
questions. Undergraduates will be graded separately if graduate students consistently
perform better on exams and assignments.
Late Work: Late work will receive no more than 50% of full credit unless a special
arrangement has been made in advance.
Attendance Policy: Students are individually responsible for obtaining class materials,
completing exercises, and meeting course requirements. Students are expected to attend
the literature discussion/analysis sessions. Advanced notification of absences is
expected.
CHEATING POLICY: We operate under the principle of "academic integrity" expected
at this university. UW System guidelines state: "Students are responsible for the honest
completion and representation of their work, for the appropriate citation of sources and
for respect of others' academic endeavors." (s. UWS 14.01, Wis. Adm. Code). Cheating
or obstruction of the efforts of others will not be tolerated in any form. Students caught
cheating will be receive an F grade and may be subject to other disciplinary action.
Class Schedule
The schedule outlined below is tentative and is subject to change. Text readings are
from Molecular Genetics of Bacteria.
Week #
Topics
Readings
1 (9/6)
Introduction
Introduction
2 (9/11)
(9/13)
Chromosomes – Structure and Replication
Chromosomes – cont.
Ch. 1
Ch. 1 – cont.
3 (9/18)
(9/20)
Gene Expression - RNA
Gene Expression – cont.
Ch. 2
Ch. 2 – cont.
4 (9/25)
(9/27)
Mutations
Genetic Analysis
Ch. 3
Ch. 3 – cont.
5 (10/2)
(10/4)
Exam 1 (chapters 1 - 3), Plasmids
Plasmids – cont.
Ch. 4
Ch. 4 – cont.
6 (10/9)
(10/11)
Conjugation
Conjugation – cont.
Ch. 5
Ch. 5 – cont.
7 (10/16)
(10/18)
Transformation
Lytic Bacteriophage
Ch. 6
Ch. 7
8 (10/23)
(10/25)
Lytic Bacteriophage – cont.
Lysogeny
Ch. 7 – cont.
Ch. 8
9 (10/30)
(11/1)
Lysogeny – cont.
Exam 2 (chapters 4 - 8), Transposition
Ch. 8 – cont.
Ch. 9
10 (11/6)
(11/8)
Transposition – cont.
Recombination
Ch. 9 – cont.
Ch. 10
11 (11/13)
(11/15)
Recombination – cont.
DNA Repair (Research paper due)
Ch. 10 – cont.
Ch. 11
12 (11/20)
(11/22)
Mutagenesis
Exam 3 (chapters 9-11), Gene Expression
Ch. 11 – cont.
Ch. 12
13 (11/27)
(11/29)
Gene Expression
Global Regulatory Mechanisms
Ch. 12 – cont.
Ch. 13
14 (12/4)
(12/6)
Global Regulatory Mechanisms
Global Regulatory Mechanisms
Ch. 13 – cont.
Ch. 13 – cont.
15 (12/11)
(12/13)
Genetic Analysis
Genetic Analysis – cont.
Ch. 14
Ch. 14 – cont.