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MICa 8002

Fall Semester 2016

Structure, Function, and Genetics of Bacteria and Viruses

T-Th 2:30-4:25 pm, 2-143 Wallin Medical Biosciences Building (WMBB)

Dr. Stephen Rice (Virology section):
Dept. of Microbiology and Immunology
Office: 1-115 Microbiology Research Facility (MRF)
Ph: 612-626-4183

Dr. Gary Dunny (Bacteriology section):
Dept. of Microbiology and Immunology
Office: 4-117 Microbiology Research Facility (MRF)
Phone: 612-625-9930

Course description:
This is a rigorous and comprehensive course in the molecular microbiology of bacteria and viruses, designed for graduate students who have completed undergraduate-level courses in microbiology, biochemistry, and genetics. The course will include didactic lectures by the instructors on the current state of knowledge in prokaryotic microbiology and animal virology. The course will also focus on teaching students how to read, critique and present papers from the primary scientific literature. Learning activities will include student presentation of research papers, in-class discussions, and a term paper. Grades will be assessed based on oral presentations, writing assignments, take-home exams, and class participation. The course is open to all MICaB graduate students, as well as to graduate students from other programs, pending approval by the instructors

Schedule overview:
The class will commence with a six-week virology module taught by Dr. Rice. This will be followed by a one-week "transition" module taught by both instructors that will focus on the term paper assignment. We will discuss scientific writing and have and in-class discussion and peer review of student term paper topics. Starting with week 8, Dr. Dunny will teach a six-week module on bacteriology. Interspersed in the last module will be two jointly-taught sessions that will focus on a topic that spans both bacteriology and virology. This year's topic is non-coding RNA in bacterial and viral life-cycles

Week Instructor Tuesday session Thursday session Assignments
Week 1: Sept. 6,8 Rice (+ Dunny on Sept. 8) Course intro; fundamentals of virology Virus entry  
Week 2: Sept. 13,15 Rice RNA viruses: gene expression and genome replication Student presentation:
Week 3: Sept.20, 22 Rice DNA viruses: gene expression and genome replication Student presentations:
Term paper assignment given
Week 4: Sept. 27,29 Rice Virus assembly and release Student presentations:
Week 5:
Oct.4, 6
Rice Host defenses against viruses Student presentations:
Term paper "plan" due Oct. 4
Week 6:
Oct. 11,13
Rice Persistent viral infections; Viruses and cancer Student presentations:
Week 7:
Oct. 18,20
Dunny & Rice Transition Week – scientific writing and in class work on student term papers Student presentations:
Take-home exam given out
Week 8:
Oct.25, 27
Dunny Horizontal gene transfer Student presentations:

Take home exam due
Week 9:
Nov. 1,3
Dunny Recombination and transposition Student presentations:
Term paper first draft due Nov 4
Week 10: Nov. 8,10 Dunny Regulation of transcription initiation and elongation Student presentations:

Week 11: Nov. 15,17 Dunny Sensing and adaptation Student presentations:
Week 12: Nov. 22 Dunny & Rice Non-coding RNAs in bacteria and viruses (part 1) THANKSGIVING (no class)  
Week 13: Nov. 29, Dec 1 Dunny Development and decision making Student presentations:
Week 14: Dec.6,8 Dunny Sociomicrobiology: Communication, cooperation and cheating Student presentations:
Term paper due, Dec. 8
Week 15: Dec. 13 Dunny & Rice Non-coding RNAs in bacteria and viruses (part 2)   Take home exam given out


Assigned Reading:
There is no required text for the course, but there are two recommended texts: “Molecular Genetics of Bacteria” 4th Ed.(Abbreviated MGBIV in reading assignments) by Larry Snyder  et al (ASM Press, 2013; ISBN 978-1-55581-627)- if you have access to the 3rd edition of this text (Abbreviated MGBIII) you may also use this for background reading,  and Principles of Virology, 4th Ed, vols. 1 and 2 (abbreviated PV in reading assignments), by S. Flint, V. Racaniello, G. Rall and A. Skalka, (ASM Press, 2015; ISBN 9781555819330). These texts are particularly recommended for students who plan to continue on in the fields of bacteriology or virology. 

In addition, numerous papers from the scientific literature will be assigned during the course. These will be posted on the course Moodle site and will accessible as pdf files.

Moodle site: Course materials and communications will be organized through the course Moodle site.

Grading:  Course grades will be given based on a potential total of 300 points; we will use a straight scale, rather than a curve to determine grades. Each instructor will be responsible for awarding 150 points, as follows:

Presentation of assigned research paper
"Next experiment" writing assignments (weekly)
Term paper
Take-home exam
Class participation

Presentation of a research paper:

Each week we will discuss papers from the research literature relevant to the topics presented in lectures. One student will be assigned to present one of the papers, following the general format described below. All students are expected to carefully read the assigned papers and to contribute to the class discussion.

Format for student presentations:

Plan for a presentation of ~40-45 minutes. Powerpoint presentation are suggested, but not required. Regarding Powerpoint, keep in mind that you will not be assessed on aesthetic quality of your Powerpoint presentation, but rather on your understanding and presentation of the science (i.e., don't spend undue time formatting your powerpoint). Here are some suggestions for how to organize your presentation.

1. Give a short introduction (5-10 min)

* Introduce yourself (the first time you speak), including your graduate program, and research interests.
* Summarize the major question or hypothesis that the paper addresses. Provide necessary background information, keeping in mind that most of your audience will not be expert in the research area covered.

2. Present the results (15-25 min)

* Go over the most important experiments (given your time constraints). There is no need to go over every experiment (you can briefly summarize experiments you don't have time to cover).
* For each experiment that you do present, use following strategy:

  • Lead in with the question or hypothesis being addressed.
  • Describe the experimental approach in sufficient detail that the class can understand it. This may require explaining the techniques, if they are not standard.
  • Present the results, and explain how the authors interpreted those results.
  • Finish with a statement of the authors conclusion(s). Give your opinion of whether you think their conclusions are valid and explain why or why not.

3. Summarize the the paper and lead the class in discussion (15-20 min).
* Present the major conclusions of the authors.
* Give your overall opinion of the work and its importance to the field
* Engage the class in discussion. Possible talking points:

  • Are there important criticisms of the data, logic or conclusions?
  • Did the authors answer the question/hypothesis they set out to address?
  • Was this work important, or an example of a "minimal publishable unit"?
  • What are the implications of this work in terms of basic biology, human health, or otherwise?
  • Where does the work go from here? What would be a good "follow-up" experiment?

Additional points:

* Keep in mind that you are not an advocate for the authors, nor are you their sworn enemy. Rather, you are an objective third party who is evaluating the science. In the end, you are entitled to have an opinion about the paper, be it positive, negative, or mixed.
* When you are assigned to present a paper, you need to become the expert! This will likely require that you do a considerable amount of background reading (e.g., prior papers by the authors, or research into the experimental technology).
* Students are strongly encouraged to set up an appointment with the instructor one or two days prior to the presentation to discuss the paper.

"Next experiment" assignment:

Each week, all students will be asked to complete a short writing assignment called the "next experiment". The assignment is to propose one experiment based on the assigned paper. The experiment should address a non-trivial question or hypothesis that arises from the work described in the paper. You should state this question or hypothesis in your answer. As well, you should thoroughly explain the experiment in terms of the technology involved and indicate how the results will be interpreted to answer the question or test the hypothesis. The experiment should be readily doable using available technology and should only involve reagents that either already exist or could be realistically obtained in a short time-frame. Please write in scientific prose style, using proper English. Maximum length is 250 words. A single paragraph is usually a sufficient answer. Remember, you are to propose only one experiment, not a five-year grant application, so keep the answer focused! Finally, be prepared to discuss your answer in class.

Submit your answer via the Moodle site by 9 AM the morning of the class at which the paper is to be discussed. Note that although we will read at least 2 papers a week, you just need to do the "next experiment assignment" for just one of the papers. Further instruction will be provided in class for how the students will know which paper to write on.

"Term" paper:

We will assign one longer writing assignment (1500-2000 words). Students will have several weeks to complete a first draft. Feedback will be provided via peer and instructor review. The final paper will be due the last week of class. More details will be provided in class.

Take-home finals:

Each instructor will give out a take-home final on the last day of their module. The exam will encompass the entirety of the material in the module. Students may use any reference material to answer the questions, but cannot consult with any other individual. Students will be given 4-5 days to complete the test.

 Class participation:

This is a graduate class, and as such, students are expected to take an active role in the class discussions! If you are not used to speaking up in class, it is time to start. We hope to promote a comfortable but intellectually stimulating environment where we can all learn from each other.