Department of
Biochemistry and Molecular Medicine

BMS 705 Syllabus

BMS 705 - Cellular Structure and Metabolism

Course Coordinator: Dr. Mike Schaller
Instructors: Michael Gunther, Michael Schaller, Steven Frisch, Gregory Dick, Visvannathan Ramamurthy Classroom: Room 4007, HSN (Monday through Friday, 9:00 – 10:00 a.m.)

We strongly encourage students to talk to lecturers about any aspect of the material covered in a lecture, review questions, extra reading, etc.

Textbook

Molecular Cell Biology, 7th Edition, W.H. Freeman and Company, New York, 2012. This textbook is available in the bookstore.

Journal Club

Students will be divided into 2-3 groups for each journal club session. Each journal club session will focus on one paper chosen by the professor lecturing at that time. Students are required to hand in at the beginning of each journal club session a review of the paper in your own words. Plagiarism of any portion of the review will result in a grade of zero for that journal club and possible disciplinary action. In addition, you should be prepared to actively participate in the discussion of the paper. Additional information for preparing for journal club will be provided later.

All students will be expected to attend all journal club sessions, and any unexcused absence will result in a grade of zero for that journal club session. An excused absence requires the PRIOR approval of the course coordinator (Dr. Schaller), and it requires the prior submission of the review.

Your grade for journal club will be based on the cumulative average of your summaries/critiques of the papers and the quality of your active participation during journal club.

Exams

There will be four exams, each of 2.5 hours duration. Questions will include multiple choice, short answer, and longer essays.

Review

There will be a review of material every Monday in Room 4007 from 9-10AM. Students are encouraged to ask questions and discuss material with the lecturers at any time. Faculty will provide review questions/homework to help you practice for the exams. Some of the review questions/homework will be graded (but will not affect your course score) to provide feedback to you regarding the quality of answers that is expected.

Grading

The final grade will be based on the following proportioning of grades:
Exams - 80%
Journal Clubs - 20%

Journal Club for BMS 705 Students

Purpose of Journal Club

The Journal Club is designed to give you experience in critically reading and discussing research papers covering a broad range of topics.

Organization

You will be divided into 2-3 groups for each journal club session. Each journal club session will focus on one paper chosen by the professor lecturing at that time. Faculty facilitators will be rotated among the different discussion groups in different journal club sessions.

You will be expected to attend all journal club sessions, and any unexcused absence will result in a grade of zero for that session. An excused absence requires PRIOR approval by the course coordinator (Dr. Schaller), and it still requires the prior submission of the summary you will write for each journal club.

Criteria for evaluation and grading

Initially, the faculty member will facilitate the discussion of the papers, but you will be expected to play an increasingly active, primary role as the semester progresses.

You must hand in at the beginning of each journal club session a typed summary of 300 words or less that: (1) summarizes the purpose of the paper and the conclusions reached; and (2) make a legitimate attempt to critique the paper, providing, in your own words, an evaluation of how well the conclusions of the paper are supported by the data. (This should be about one page in length, single spaced).

Remember, the summary and critique must be in your own words! Plagiarism of the summary or critique will result in a grade of zero for that journal club. We realize that critiquing the paper in detail is a challenging task, especially given your lack of familiarity with the field of research, but we do ask (and expect) that you will make a legitimate effort to critique the paper and participate in discussing the paper.

In addition to the written narrative, you should be prepared to describe or discuss the following:

  • the purpose of each experiment
  • the methods used for each experiment
  • the data in each figure or table
  • were appropriate control experiments performed?
  • the conclusions drawn from the data-how well are they supported by the data?
  • how the paper has added to our knowledge
  • at least one experiment that would continue the work

How to Read Journal Articles

Learning to read journal articles, like any skill, requires practice. Do not be discouraged if you feel you are lost. This is a common reaction for new graduate students. Please note that to truly read a paper in sufficient depth to discuss the results can easily take 3 hours or more and usually requires reading the paper at least twice. With experience this time can decrease but sometimes in a new subject area you will still need a long time to fully grasp a paper. Often, you need to come back to a paper after first reading about background materials. Plan on taking separate notes on the paper. This will aid you in answering questions such as, "What is the purpose of this paper?" or "Why were the experiments in Figure 2 done?"

Try to apply the following approach to aid you in a more thorough consideration of the important points of the paper:

  1. Read the introduction several times if necessary. This really tells you what the authors were thinking. It will probably be necessary to look up some background material and some of the terminology. Do this first or you will not understand anything else in the paper.
  2. Survey the Methods to see what experimental systems are being employed and the kinds of assays that are being used. You should look up unfamiliar methods in your required texts to discover what types of information the methods can provide. Do not be afraid to consult the faculty about specific techniques.
  3. As you read the results, focus on each figure/table and answer the following questions:
    1. What is being tested in this experiment?
    2. How is this experiment being done?
    3. What results do I see and how does this compare to what the authors report?
    4. Critique the experiment. Identify what the controls are. Were sufficient controls done to corroborate the results?
    5. Are the conclusions appropriate for the type of experiments done?
    Remember that points d and e are the hardest and will only come with practice and experience in the laboratory; however, no manuscript is perfect and it is important to understand the limitations of the authors’ conclusions. This will require that you write down information. It will also take a great deal of time. Be sure to plan this time into your weekly schedule.
  4. The discussion will be the most variable portion of the paper. Sometimes you will read this and have a good understanding of the authors’ ideas about their results and how they compare to the literature. Other times this section will be impenetrable ramblings. If you feel the latter is the case remember this is poor writing and not your fault. In general, if you have done step 3 well - reading the discussion should go quite easily. Regardless of whether the authors outline a clear set of conclusions for you or if you have to think them up on your own, you should come to the discussion of the paper with a list of 2 to 4 conclusions of the work (this is a general range that will apply to most papers). Remember you should also know which experiments support these conclusions.
  5. The ideal will be if they have a model that you can use to enhance your understanding. Consider drawing one of your own to test if you understand the paper. On your own, you must consider how this paper extends your knowledge and if the conclusions are appropriate for the results. Bring your ideas on these points to our discussions.