MICB404
January 26, 2009
Microbiology 404
Microbial Genetics
Spring 2009
Instructor:
Office:
Office hours:
Lab:
Phone:
E-mail:
Required text:
Dr. Frank Rosenzweig
Health Science Bldg 416
MWF 12-1PM; and by appointment.
Health Sciences Bldg 301
243-4834
Frank.Rosenzweig@mso.umt.edu
L. Snyder & W. Champness (2006) Molecular Genetics of Bacteria. ASM
Press, 3rd Ed. Additional reading in electronic format will be placed on Reserve
in the University Library.
Lecture:
Forestry 305 MWF 11:10 – 12:00N
Course Description – Microbial Genetics is a senior/graduate level course. It satisfies a core
requirement for degrees in Microbiology and Cell & Molecular Biology; it also fulfills the
University General Writing Requirement in the major field of study.
The course examines the transmission of heritable traits by microbes, and the methods and
principles used to study inheritance. The role of genetic variation in driving microbial
evolution will be an underlying theme. The major outcomes for the student will be:
•
•
•
Sound understanding of the core principles and paradigms of microbial genetics
Familiarity with research techniques used in that discipline
Development of skills in critical thinking, cogent writing, and scientific
problem-solving
Course assessment will reflect the student’s performance in these areas.
Grading*
Category
Quizzes (3) and Seminars (2)
Mid-term exams
Final exam
Research proposal
No. points
5 * 20 pts
2 * 150 pts
1 * 200 pts
1 * 300 pts
Total
100
300
200
300
900 pts
TENTATIVELY, GRADES WILL BE ASSIGNED ON A STRAIGHT SCALE WHERE,
> 90 %
A
> 810 pts
720 – 809 pts
80 – 89 %
B
630 – 719 pts
70 – 79 %
C
540 – 629 pts
60 – 69 %
D
< 539
< 59%
F
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MICB404
January 26, 2009
Graduate students enrolled in MICB404 are expected to fulfill 2 additional requirements
either to earn a letter grade or a Pass. First, they will summarize and critically evaluate 3-4
papers centered on a topic of relevance to the course and, hopefully, their plans for graduate
research. The topic and associated papers will be chosen in consultation with the instructor at
least one month prior to the presentation. The critical summary will be no less than 3, and no
more 5 pages in length, 1-inch margins, 12-pt Arial font.
Second, they will present a 20-25 PowerPoint lecture to the class on their chosen topic.
On April 27th, students will announce their topics to the class, and each distribute one of the 34 papers, preferably a short review article. The presentation will be in PowerPoint, last no more
than 20 minutes and be delivered on either May 6th or 8th. After the presentation, the grad
student will lead a ~5 minute discussion. All research materials will be turned in to the
instructor.
EXPLANATION OF CATEGORIES
Quizzes (3) and Seminars (2) [100 pts] There will three unannounced quizzes, each worth 20
pts (60 pts total). These will typically be given within one week of a major exam; quizzes
will enable students to test their readiness for exams, and help the professor to assess
students’ grasp of the lectures and readings.
MICB404 students will also receive credit for attending two genetics-related research
seminars. DBS seminars are presented Monday at 4-5PM in Skaggs 117. In addition to the
regular seminar series, there are two ongoing searches (Virology and Genomics), as well as a
Chemistry Dept seminar series that is often heavy on genetics. To earn credit MICB404
students will write a brief evaluation of the seminars they attend using the rubric that will be
distributed first day of class. Write-ups will be worth 20 pts each (40 pts total).
Mid-term Exams [150 pts] There will be two mid-term exams. Typically, each will consist of
60% essay, 25% short answer, 15% multiple choice and True/False. Essay questions will be
designed to test not only your grasp of concepts and the supporting facts, but also their
application in problem-solving. For example, you might be given a set of observations, and
then be asked to hypothesize a mechanism that accounts for these observations as well as a
set of experiments to test your hypothesis. If appropriate, you will be expected to indicate
your mode of statistical inference; you will always be expected to clearly state your null
hypothesis. Short answer questions will consist of defining terms and/or drawing structures.
The nature of multiple choice and T/F questions is self-evident.
Final Exam [200 pts] The Final Exam will be comprehensive. 60% of the Final will consist of
material to which you were exposed prior to April 12. If you fared poorly on either of your
mid-term exams, a good performance on the Final will work strongly in your favor.
Writing project [300 pts] MICB 404 is a senior-/graduate-level course. Given the nature of
the field and the realities of the job market, many MICB 404 students will eventually need
post-graduate training. It is your instructor’s responsibility to help prepare you for this next
stage of your career. That next stage will require you to think critically and write cogently.
Critically reviewing the scientific literature is one of the best ways to hone your skills in
these areas. Good grants(wo)manship is essential to success in academia or industry.
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MICB404
January 26, 2009
The grade you earn on your writing project will have FIVE COMPONENTS, and therefore
five deadlines. Your instructor will give you feedback within 2 class periods after an
assignment has been turned in. Also, MICB404 has engaged the services of the University
Writing Center (102 Social Sciences Bldg. Ph: 243-2266; E-mail: growl@mso.umt.edu ).
Students and instructor will participate in three (optional, evening) Writing Workshops, the
first in early February. Students will be required to consult with UWC tutors, and have each of
the four writing project elements reviewed and signed by UWC staff. Each of these five
elements must be submitted as hard and electronic copy.
A mock National Science Foundation proposal constitutes a major portion of your
grade in MICB404, and is the mechanism by which it satisfies the upper-division University
Writing Requirement. Guidelines for your proposal will be handed out as a separate document.
Below are the due dates, and the points allocated to each required assignment. Late
assignments will not be accepted, unless arrangements have been made with the instructor in
advance of the due date.
(1) [25 pts] February 6th During the 2nd week of class you will schedule and attend a one-onone conference with your instructor to brainstorm about topics for your Proposal.
(2) [25 pts] On February 20th you will turn in a 1-page Summary and Specific Aims. The
Specific Aims should identify the hypotheses you plan to test, and explain the overall
significance of your project.
(3) [50 pts] On March 16th you will turn in a refined 2-page summary plus a detailed 2-3 page
outline that fleshes out your ideas. You will also submit a partial reference list consisting of
at least 5 citations.
(4) [100 pts] On April 13th a complete rough draft is due that meets proposal guidelines
described in the ancillary materials distributed to you the first day of class.
(5) [100 pts] On May 4th your final draft is due.
Writing Workshops – Three 90-minute writing workshops will be held over the course of the
semester. The aim of these sessions is to provide you with guidance in your project.
Workshops are optional, but strongly recommended; unless otherwise specified, they will be
held in HS207 during the early evening (e.g., 6:00 – 7:30PM). Pizza and pop will be on hand,
courtesy of your Professor.
MICB404 satisfies the University General Writing Requirement.
GENERAL NOTES
1. Course prerequisites: BIOL221 (Cell and Molecular Biology) and MICB300
(General Microbiology).
2. Reserve readings will be available in paper and electronic format from the Mansfield
Library (http://eres.lib.umt.edu or use links from within the course Blackboard site, see
below).
3. Other course materials, communication with Professor Rosenzweig and among
students will be made available via Blackboard (https://courseware.umt.edu).
4. Cell phones and similar devices must be turned off during class and, especially,
during examinations.
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MICB404
January 26, 2009
ACADEMIC HONESTY
Appropriate ethical behavior in the classroom is required of every student. Academic
misconduct is subject to an academic penalty by the course instructor and/or a disciplinary
sanction by the University. All written assignments in this class must be completely original.
Definition: Academic Dishonesty “cheating” and “plagiarism”, the theft of ideas and other
forms of intellectual property – published or unpublished.
Definition: Plagiarism is the use of another writer’s words or ideas without acknowledging
the source. Plagiarism also means “passing off a source’s information, ideas, or words as
your own by omitting to cite them, which makes it an act of lying, cheating, and stealing.”
Definition: Cheating is defined as obtaining or attempting to obtain, or aiding another to
obtain credit for work, or any improvement in evaluation of performance, by any
dishonest/deceptive means. All students need to be familiar with the Student Conduct
Code,
which
is
available
for
review
online
at
www.umt.edu/SA/VPSA/index.cfm/page/2585
Accommodations
Your professor is happy to work with students and Disability Services for Students (DSS) to
make accommodations that facilitate students’ class participation and learning. Please see
your instructor at the beginning of the term to plan for these accommodations.
Student Behavior
In general, students are expected to attend each class session. Please complete assigned
readings before class and be prepared to engage in group discussion. Written assignments are
due at the start of class on the assigned day; submit hard and electronic copies. If you cannot
meet the deadline for a particular written assignment, you are responsible for making
alternate arrangements with your instructor and do so before the actual due date. Late
assignments will not be accepted. All written work must conform to guidelines specified in
the
“Style
Sheet”
handed
out
first
day
of
class.
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MICB404
Syllabus
January 26, 2009
MICB404
Microbial Genetics
Spring 2009
DATE
TOPICS
READING
1. Jan 26 (M)
Course mechanics & Introduction
2. Jan 28 (W)
Microbial genomes: Sources of genetic variation?
3. Jan 30 (F)
Nucleic acid structure I: Fidelity & error in DNA replication Ch. 1
4. Feb 2 (M)
Nucleic acid structure II: Fidelity & error in DNA replication Ch. 1 Writing Proj: Conference
5. Feb 4 (W)
Bacterial mutants: How do we talk about microbial genetics? Ch. 3
6. Feb 6 (F)
Mutagenesis: How do we estimate mutation rate?
Ch. 3
7. Feb 9 (M)
Isolating mutants: How do we devise selections, screens,
enrichments for specific categories of mutations?
Ch. 14
8. Feb 11 (W)
Mechanisms of mutagenesis: What do different mutagens do? Ch. 3, Ch. 11 Writing workshop #1
9. Feb 13 (F)
Reversion and suppression: What can we learn by restoring
functions lost by mutation?
10. Feb 16 (M)
President’s Day Holiday
11. Feb 18 (W)
Lateral gene transfer: Overview & evolutionary implications
Skim Intro to Ch. 5, 6, & 9 plus
Assigned reading
12. Feb 20 (F)
Biology of plasmids: I. Classification & structure
Ch. 4 Writing Proj: Specific Aims
13. Feb 23 (M)
Biology of plasmids: II. Control of copy number
Ch. 4
14. Feb 25 (W)
Biology of plasmids: II. Control of segregation
Ch. 4
15. Feb 27 (F)
Conjugation: Mechanisms of plasmid-mediated gene transfer Ch. 5
Ch. 1, p. 474 and W. Arber 2000
Ch. 3
16. March 2 (M) OPEN DATE: Catch-up and review
17. March 4 (W) EXAM 1 [=150 pts]
Writing workshop #2
18. March 6 (F) Transformation: Food and sex in the microbial world
Ch. 6 plus Assigned reading
19. March 9 (M) Phage, lytic growth and restriction-modification systems
Ch. 7 plus Assigned reading
20. March 11 (W) Transduction: Generalized & specialized transduction
Ch. 8
21. March 13 (F) DNA repair: I. Specific pathways
Ch. 11
22. March 16 (M) Homologous recombination
Ch. 10. Writing Proj: Detailed outline
23. March 18 (W) DNA repair: II. RecA-dependent pathways
Ch. 10 & Ch. 14 plus Assigned read
24. March 20 (F) Transposable elements: I. Discovery & classification
Ch. 9
25. March 23 (M) Transposable elements: II. Regulation & utility
Ch. 9 & Ch. 14
n
26. March 25 (W) Transposable elements: III. Med & evol perspectives
Assigned reading
27. March 27 (M) Operon and gene fusions
Ch. 2 & Ch. 11
MARCH 30 – APRIL 3
28. April 6 (M)
SPRING VACATION
Gene expression: I. Mechanics of transcription
Ch. 2 & Ch. 12
29. April 8 (W) Gene expression: II. Regulation of transcription
Ch. 12
30. April 10 (F) Global regulation I. Nutritional stimuli
Ch. 13
31. April 13 (M) Global regulation II. Heat shock, SOS & stringent response
Ch. 13 Writing Proj: Rough Draft Due
32. April 15 (W) EXAM 2 [=150 pts]
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MICB404
January 26, 2009
33. April 17 (F) Epigenesis as a regulatory mechanism is Bacteria
Assigned reading
34. April 20 (M) Comparative Genomics: I. Evolution of genome size
And complexity
Assigned reading
Writing workshop #3
35. April 22 (W) Comparative Genomics: II. Evolution of virulence and
temperance
Text pp. 457-464 plus Assigned reading
36. April 24 (F) Comparative Genomics: III. Mosaicism and phylogeny
Assigned reading
37. April 27 (M) Eukaryotic microbes: I. Analysis of cell cycle in yeast
Assigned reading
38. April 29 (W) Eukaryotic microbes: II. Phenotypic switching in Candida
Assigned reading
39. April 30 (F) Eukaryotic microbes: III. Co-evolution of Plasmodia & their hosts
40. May 4 (M)
Eukaryotic microbes: IV. Antigen switching in Trypanosomes Assigned reading
Writing proj: Final Draft due
41. May 6 (W)
OPEN DATE: Catch-up and review
42. May 8 (F)
GRAD STUDENT PRESENTATIONS & DISCUSSION
MAY 9 – MAY 10
THURSSDAY, MAY 14TH
STUDY DAYS
10:10AM – 12:10PM
6
COMPREHENSIVE FINAL [=200 PTS]