Term Paper Workshop Uni Due Moodle

Fall Semester 2017

Structure, Function, and Genetics of Bacteria and Viruses

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


Dr. Gary Dunny (Bacteriology section):
Dept. of Microbiology and Immunology
Office: 4-117 Microbiology Research Facility (MRF)
Phone: 612-625-9930
e-mail: dunny001@umn.edu

Dr. Stephen Rice (Virology section):
Dept. of Microbiology and Immunology
Office: 1-115 Microbiology Research Facility (MRF)
Ph: 612-626-4183
e-mail: ricex019@umn.edu


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".

WeekInstructorTuesday sessionThursday sessionAssignments
Week 1: Sept. 5,7Dunny (+ Rice on Sept. 7)

Course intro; Horizontal gene transfer

Group discussion & 1 Student presentation: A. Villarreal 
Week 2: Sept. 12, 14DunnyLectures on DNA repair, recombination, mutagenesis and transposition

Group discussion of two papers

 Hand out term paper assignment
Week 3: Sept. 19,21DunnyStudent presentations of two recombination/repair papers- Paper 1 - A Amani; Paper 2- R LeeStudent presentations of two transposition papers-Paper 1- Class: Paper 2- F. Sjaastad
Week 4: Sept. 26,28 DunnySensing and regulation of transcription and translationTwo Student presentations- Paper 1- D. Leprich; Paper 2- M Brisse
Week 5:
DunnyDevelopment and decision makingTwo Student presentations- Paper 1 - K Jackson; Paper 2- class discussion
Term paper "plan" due Oct. 3
Week 6:
Oct. 10,12
DunnySociomicrobiology: communication, cooperation and cheatingTwo Student presentations:
Paper 1- J Blankenhorn; Paper 2- M Smith
Take-home midterm given out Oct. 12
Week 7:
Oct. 17,19
RiceFundamentals of virology, virus entry
Take-home midterm due Oct. 17
Week 8:
Oct. 24,26
Dunny & RiceScientific writing and in-class work on term papers

Week 9:
Oct 31, Nov 2
RiceRNA virus replicationStudent presentations
Week 10: Nov. 7,9RiceDNA virus replication, retrovirus replicationStudent presentations

Term paper first draft due Nov. 8
Week 11: Nov. 14,16RiceVirus assembly and releaseStudent presentations:
Week 12: Nov. 21Rice & DunnyNon-coding RNAs in bacteria and viruses (part 1)THANKSGIVING (no class) 
Week 13: Nov. 28, 30RiceHost defenses against virusesStudent presentations
Week 14: Dec.5, 7RiceViral persistence and latencyStudent presentations
Term paper due, Dec. 6
Week 15: Dec. 12Dunny & RiceNon-coding RNAs in bacteria and viruses (part 2)Group discussion of two papers dealing with non-coding RNAsTake 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.


For years, Dr. Eric Bauer of the biology department has had students peer-review term papers and lab reports, and struggled to find an effective way to send papers back and forth. What he didn’t know was a solution was right in front of him. With the help of Moodle’s workshop tool, Dr. Bauer has made the process easier and more effective for himself and his students.

Streamlining the review process

Before discovering the workshop tool, Dr. Bauer primarily used email. However, he found the constant coming-and-going of emailing disorganized and unproductive. Through the Moodle tool, the process has been simplified.

“It seemed like a way to streamline writing assignments,” Dr. Bauer said. “I had students email me writing assignments years leading up to [the change to Moodle workshop], and it was such a pain get [student feedback] out of the attachments and manage them. It was harder to tell who had what submitted where and when.”

The tool starts working just as any submission would on Moodle. By the due date, students upload their document for submission by copy and pasting the essay into the text box or attaching their document from their computer. Then, Moodle randomly selects which essays will go to which person and lets the students know that the peer-review process can begin.

The stages of the Moodle worksop tool

“Once the activity deadline arrives, the students are automatically notified which papers they’re responsible for grading,” Dr. Bauer said. “Also, when they go back to Moodle, they’ll have three papers with the names stripped off.”

The students grade by the criteria Dr. Bauer sets, which he can change with any given assignment. Once their grades and comments put into Moodle, students will submit and Dr. Bauer will receive a notification.

“When they’re done scoring, they submit and grades are dumped into Moodle system,” Dr. Bauer said. “I can then read the paper and submit my grades. I tally all the different scores and give each student one final score.”

Limitations of Moodle workshop

While Dr. Bauer appreciates how Moodle’s workshop tool has simplified the peer review process, he acknowledges that the tool could simplify its set-up process.

“The workflow in setting it up and then working through each phase is really cumbersome and non-intuitive,” Dr. Bauer said. “I’ve tried teaching it to two members of my department and in the end, the only way they could set up a workshop in a timely fashion was for them to copy one of my already-existing workshops and just tweak it.”

Dr. Bauer also wishes he could change the grading from actual numbers to simple complete/incomplete, which he tends to favor more. Aside from that, Dr. Bauer’s recommendation would want more anonymity of the grading system.

“It would be nice if the system was ‘double-blind,’” Dr. Bauer said.  “The students already can’t see who assessed them, but it would be even better if they also couldn’t see who they were assessing. On that topic, it would be nice if my assessments were marked as coming from me.  The instructor’s assessments should be made obvious to the students.”

Feedback from students is more valuable

Dr. Bauer has been doing peer-review, both with and without Moodle workshop, for years, and yet he is still surprised at how his students tend to grade their peers.

“[Their grading] is not what I thought it would be,” Dr. Bauer said. “Students are far more critical, and they grade harder than I do. Part of this grading is the written feedback. I don’t mandate that they write comments, but they do and the comments are blunt.”

Despite the harsh critiques, Dr. Bauer thinks the peer-review process is worthwhile, especially because lab reports and term papers have to be written a certain way. He believes that the student feedback teaches students how to write correctly and challenges them to improve their writing skills.

“I think students pay attention to what other students think of them more than what their professor thinks of them,” Dr. Bauer said. For one fellow student to say you have very good work hits home a little bit more. For struggling students, reading through work from other students lets them see how they need to do the assignment well.”

Advice for others

After working with Moodle workshop, Dr. Bauer has learned a trick or two about the tool. He would suggest leaving plenty of time to program the tool to your specific needs.

Also, Dr. Bauer advises using the tool for the simplest assignments with clearly set guidelines.

“The workshop is best used for short assignments—one page or less—or sections of larger assignments,” Dr. Bauer said. “Also, be aware of how much work you are asking the students to do during the assessment process.  Keep the number of criteria under seven or eight.  Very clearly spell out in the criteria what is worthy of each score. In other words, you have to have a clear rubric that the peer reviewers have access to.”

How do you manage peer reviews in your courses? What are your experiences with Moodle’s workshop tool? Let us know in the comments below.

Contact TLT@elon.edu to schedule a consultation to learn more about Moodle’s workshop tool.


Image via Flikr user AJC ajcann.wordpress.com/CC BY-SA 2.0

Casey Brown

Casey Brown is the Writing Intern for Technology with Elon University's Teaching and Learning Technologies Department.

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