Micro 402-Microbial Genetics

Micro 402 Microbial Genetics
Fall 2004
Instructor: Dr. Greg Phillips, VMRI Building #6
Phone: 4-1525
e-mail: gregory@iastate.edu
Homepage (with links to course material): http://www.vetmed.iastate.edu/faculty_staff/users/phillips/default.asp
Link to course calendar
Office hours: Mon., Wed., Fri. 8:10-8:50 AM in 224A Science I or by appointment.
Text: Molecular Genetics of Bacteria, 2^nd edition, 2003. L. Snyder and W. Champness, ASM Press, Washington, DC. (ISBN 1-55581-204X)

Course description: This course covers topics essential to understand the genetics and molecular biology of microorganisms, including gene transfer, mutagenesis, replication, DNA repair and recombination, gene expression and regulation, recombinant DNA technology, and genomics. These concepts will be taught using both a traditional lecture format, as well as by review of original research literature. This approach will allow examination in greater depth the design, methodology, and interpretation of experiments of both historical and contemporary relevance to microbial genetics. The goal of this course is not only to develop your comprehension of bacterial genetics, but also to develop your ability to read and critically assess research publications and to understand and appreciate the use of genetics as a tool for answering biological questions. As a general approach to this course, when learning the material continue to ask "how do we know that?" Grading will include three hourly exams, a comprehensive final exam, and assessment of your participation in the review of six research papers. For the latter, you will be responsible for preparing for the discussion periods by carefully reviewing the assigned manuscript to understand the objectives, experimental approach, use of controls, results, conclusions, and potential future direction for the research. To receive credit you must participate in the paper discussion by answering, or even asking insightful questions and submit at the end of the class period a short (no more than one page) summary of the assigned paper. The summary should answer the following questions:

What is the main purpose of the research described in the paper?
What experimental approaches were used?
What conclusions were reached by the described research?

Your participation in the discussions is essential for a successful course!

Course Grading

Exam or Assignment	% of final grade
Exam 1	20
Exam 2	20
Exam 3	20
Final Exam	28
Paper discussion and participation	12

Why is discussion required for this course--why can't we just sit and take notes? While the format for this course may be challenging for some of you at first, it offers several advantages that will help you in your scientific careers at all levels, including:

Increased communication ability. By explaining conceptually challenging concepts you will become a more effective communicator, an ability necessary for your career as successful scientist and teacher.
Learning collaboratively. Hearing interpretations and descriptions of the research from different points of view will either reinforce, or prompt reevaluation of your interpretations.
Creating knowledge together. New insights will emerge from our discussions that result only from group interaction.
Review and reinforcement of understanding. You should be able to connect your contributions to those of others to gain greater insight and understanding.
Improved mental agility by learning how to "think on your feet."
Respecting differences of interpretation. It is important to develop respect for those who may present ideas and interpretation that differ from your own.

Class schedule:

Class Period	Topic, Objectives and Text readings
Aug 23	Introduction to course and course Objectives Review of the structure and replication of the genetic material.
	Objectives: To review the basic structural features of DNA and RNA
	Text readings: Ch. 1:1-17. As a review you should be familiar with the concepts in the Introduction to the text and Ch. 1:46-57.
Aug 25	Mechanisms of DNA replication-the DNA replication machinery
	Objectives: To review the biochemistry of DNA replication of the bacterial chromosome and plasmids, including initiation and termination, and correction of replication errors
	Text readings: Ch. 1:,17-32
Aug 27	The bacterial chromosome
	Objectives: To understand how the structure of the bacterial chromosome contributes to its function as carrier of genetic information
	Ch. 1:32-46
Aug 30	Gene expression
	Objectives: To review the basics of gene expression, including transcription and translation
	Text readings: Ch 2:61-89
Sep 1	Protein folding and membrane protein localization
	Objectives: to understand how posttranslational events can alter the structure and localization of proteins
	Text readings: Ch. 2:89-97
Sep 3	Paper #1
Sep 8	Genetic tools for the study of gene expression; function of antibiotics
	Objectives: to conceptualize how genetics can be used to study gene expression; identify strategies for expression of useful gene products; to summarize the targets of antibiotics
	Text readings: Ch 2:97-105
Sep 10	Mutations and mutagenesis
	Objectives: To review pertinent terminology; to review experiments used to determination the nature of how mutations arise; calculation of mutation rate
	Text readings: 3:113-126
Sep 13	Types of mutations, suppressor mutations
	Objectives: to review the molecular and genetic basis for mutagenesis and suppressor mutations
	Text readings: Ch 3:126-139
Sep 15	Isolation and characterization of mutants
	To review experimental approaches for isolation, mapping and analysis of mutants and mutations
	Text readings: Ch 3: 139-153
Sep 17	Paper #2
Sep 20	Plasmid biology-replication and copy number control
	Objectives: to review the structure and function of extrachromosomal elements
	Text readings: Ch 4:157-172
Sep 22	Plasmid biology-partitioning, incompatibility and cloning vectors
	Objectives: to review the structure and function of extrachromosomal elements
	Text readings: Ch 4:172-184
Sep 24	Exam #1
Sep 27	Genetic exchange between microorganisms-conjugation
	Objectives: to review the discovery of conjugation and to explain its molecular basis
	Text readings: Ch. 5:187-201
Sep 29	Conjugation, continued
	Text readings: Ch. 5:201-214
Oct 1	Genetic exchange between microorganisms-transformation
	Objectives: to understand the genetic basis for natural and artificial competence
	Text readings: Ch 6:217-228
Oct 4	Lytic bacteriophages
	Objectives: to review the growth and replication of lytic bacteriophage
	Text readings: Ch 7:231-252
Oct 6	Genetic analysis of bacteriophages
	Objectives: to review the contribution of lytic bacteriophages to our understanding of gene structure and function
	Text readings: Ch 7:252-267
Oct 8	Paper #3
Oct 11	Genetic exchange between microorganisms-generalized transduction
	Objectives: to understand the genetic and molecular basis for generalized transduction
	Text readings: Ch 7:267-272
Oct 13	Bacteriophage l
	Objectives: to understand the biology of the lytic and lysogenic growth of l
	Text readings: Ch 8:275-282; Ch. 8282-290
Oct 15	Bacteriophage l, continued
Oct 18	Other lysogenic bacteriophage, and genetic analysis of l development
	Objectives: to compare and contrast l with other bacteriophage, including those involved in bacterial pathogenesis; to review experiments leading to our understanding of the biology of l.
	Text readings: Ch. 8:291-300
Oct 20	Transposition-transposable elements
	Objectives: to understand the genetic and molecular basis for the activity of transposable elements and site-specific recombination
	Text readings: Ch 9:303-314
Oct 22	Exam #2
Oct 25	Transposable elements-mechanisms of transpositon and mutagenesis
	Text readings: Ch 9:314-333
Oct 27	Site-specific recombination
	Objectives: to compare and contrast transposition systems with site-specific recombination
	Text readings: Ch 8:333-338
Oct 29	Paper #4
Nov 1	Homologous recombination
	Objectives: to review the genetic and molecular basis for homologous recombination
	Text readings: Ch 10:343-366
Nov 3	Mutagenesis and DNA repair
	Objectives: to review the molecular basis of mutagenesis and its repair
	Text readings: Ch 11:369-379
Nov 5	Mutagenesis and DNA repair, continued
	Text readings: Ch 11:379-389
Nov 8	Mutagenesis and DNA repair-SOS repair
	Text readings: Ch 11:389-400
Nov 10	Regulation of gene expression
	Objectives: to review the fundamental concepts of regulation of bacterial gene expression by negative regulation
	Text readings: Ch 12:403-418
Nov 12	Paper #5
Nov 15	Regulation of gene expression, continued
	Objectives: to review the fundamental concepts of regulation of bacterial gene expression by positive regulation
	Text readings: Ch 12:418-426
Nov 17	Regulation of gene expression-attenuation
	Objectives: to understand mechanisms of regulation by transcriptional attenuation
	Text readings: Ch 12:426-432
Nov 19	Exam #3
Nov 22-26	Thanksgiving break, no classes
Nov 29	Global regulation of gene expression-catabolite repression
	Objectives: to understand the genetics and molecular biology of global gene regulation by examination of specific examples
	Text readings: Ch 13:435-442
Dec 1	Global regulation of gene expression-nitrogen assimilation
	Text readings: Ch 13:442-455
	Global regulation of gene expression-porin synthesis and virulence factors
	Text readings: Ch 13:454-464
Dec 3	Global regulation of gene expression-heat shock
	Text readings: Ch 13:464-467
Dec 6	Gene regulation and expression-ribosomal proteins, and stringent response
	Text Text readings: Ch. 13:467-474
Dec 8	Genomic-scale analysis of bacteria
	Objectives: to understand how genomic-scale approaches are being used for genetic analysis of bacteria
	Text readings: Ch 1:54 (Box 1.4); Ch 13:464
Dec 10	Paper #6
Monday Dec 13	Final exam 7:30-9:30 a.m.

Paper #2

Exam #1

Paper #3

Exam #2

Paper #5

Exam #3

Paper #6