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MICa 8002

Structure, Function, and Genetics of Bacteria and Viruses

Fall Semester 2018

T-Th 2:30-4:25 pm


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

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


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 bacteriology module taught by Dr. Dunny. 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. In the second half of the course, Dr. Rice will teach a six-week module on virology. 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: Dunny (+ Rice on Sept. 7)

Course intro; Horizontal gene transfer

Group discussion & 1 Student presentation: A. Villarreal  
Week 2: Dunny Lectures on DNA repair, recombination, mutagenesis and transposition

Group discussion of two papers

 Hand out term paper assignment
Week 3: Dunny Student presentations of two recombination/repair papers- Paper 1 - A Amani; Paper 2- R Lee Student presentations of two transposition papers-Paper 1- Class: Paper 2- F. Sjaastad
Week 4: Dunny Sensing and regulation of transcription and translation Two Student presentations- Paper 1- D. Leprich; Paper 2- M Brisse
Week 5:
Dunny Development and decision making Two Student presentations- Paper 1 - K Jackson; Paper 2- class discussion
Term paper "plan"
Week 6:
Dunny Sociomicrobiology: communication, cooperation and cheating Two Student presentations:
Paper 1- J Blankenhorn; Paper 2- M Smith
Take-home midterm given out
Week 7:
Rice Fundamentals of virology, virus entry
Take-home midterm due
Week 8:
Dunny & Rice Scientific writing and in-class work on term papers

Week 9:
Rice RNA virus replication Student presentations
Week 10: Rice DNA virus replication, retrovirus replication Student presentations

Term paper first draft due
Week 11: Rice Virus assembly and release Student presentations:
Week 12: Rice & Dunny Non-coding RNAs in bacteria and viruses (part 1) THANKSGIVING (no class)  
Week 13: Rice Host defenses against viruses Student presentations
Week 14: Rice Viral persistence and latency Student presentations
Term paper due
Week 15: Dunny & Rice Non-coding RNAs in bacteria and viruses (part 2) Group discussion of two papers dealing with non-coding RNAs 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
"Question + Next experiment" assignments
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.

PRESENTATIONS: Presenter intructions.

* Set up an appointment with the instructor one to a few days prior to the presentation to discuss plans for the presentation and to hash out any confusing scientific 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).

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 the graphic art 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). Below are the guidelines for how to organize your presentation.

1. Introduction (~5 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 two most important figures (15-20 min).

* Present only the two most important figures. However, you are responsible for summarizing other findings in the paper so the class can follow the logical flow of the paper. Be prepared to answer questions from the audience on all aspects of the paper.

* 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. Class will present other important figures.
 The instructor will call on members of the class to present other important figures or to discuss scientific points including techniques and conclusions.

4. Summary and discussion (10 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?

PRESENTATIONS: Instructions for every one else.

Each week, all students will be asked to complete a short writing assignment called the "Question + Next Experiment" assignment, to be based on one of the papers from the literature that is assigned for that week. Submit this via the Moodle site using the supplied link. The assignment has an a) and b) part:

a) Write a question about the paper. In 1-2 sentence, summarize one aspect of the paper that you did not understand fully (e.g., it could relate to techniques, conclusions, interpretations). Be prepared to ask your question during or after the paper presentation. The presenter will provide an answer if possible, and then we can discuss as a group.

b) Propose a "next experiment". 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 for the next experiment paragraph 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; if you submit your answer late, your score will be lowered, but it is still better to submit late than not at all.  Note that although we will read at least 2 papers a week, you just need to do the "Question/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 "term-paper" writing assignment (1200-1800 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.