BMB 500

Senior Seminar

Spring 2009

 

Purposes of the course/Course Format/Individual Project/Grading/Deadlines/
Topics for Project/Research Tools/Schedule

 

 


Guest Speakers:

Feb. 26: Jaclyn W. McAlees (Centre BIO alumna), Graduate Student, Integrated Biomedical Science Graduate Program, The Ohio State University

March 16 : Angie Purvis, Ph.D. (Centre BMB alumna), Postdoctoral Fellow, Department of Medicine, Washington University, St. Louis

April 14: Warren Lockette, M.D., Adjunct Associate Professor of Molecular & Integrative Physiology, University of Michigan.

 

 

Purposes of the Course:
  • To provide the student with an in-depth exposure to primary scientific literature and to scientists actively engaged in research.
  • To develop the student's ability to critically analyze scientific research papers.
  • To allow the student to hone his/her oral presentation skills, both in groups and individually.
  • To provide the opportunity for independent library research of the scientific literature on a specialized topic.
  • To refine the student's ability to think and write critically.

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Course Format

Class meetings:

This course is not your typical course. There are no lectures or labs. We are covering material that has not been covered by any previous class. We are all expected to contribute to the education of each other.

How does this work?

The term has been divided into 3 "cycles." Each cycle consists of approximately 2 weeks and revolves around a set of 3 research papers (1 review and 2 primary research papers). In addition, the end of the term is devoted to individual student presentations. For each cycle, student groups will present three papers in a "journal-club" format. Class meetings 1-3 of the cycle will be used to critically examine each of the three papers (review paper in meeting 1, and research papers in meetings 2 and 3). Students will present one paper per meeting in the form of a group presentation using PowerPoint. Three cycles, each with 3 papers, means a total of 9 group presentations during the term. Each student will present a total of 3 group presentations. Presentations will be videotaped, and each student presenter must review the videotape prior to his/her individual evaluation meeting with the professors.

Division of Responsibility Among the Team of Presenters:

A group of 3-4 students will present each paper, and everyone in the class is responsible for critically reading each paper. One student out of the presenting group will be designated as a moderator. It is the moderator's responsibility to decide who will present specific parts of the paper and to provide overall organization to the presentation. All students involved in the presentation should have an "equivalent" amount of material to cover. We strongly recommend that this division NOT simply be along the lines of Introduction, Materials and Methods, Results and Discussion. Instead, the moderator should give a brief background on the area of research to be covered (what's the BIG PICTURE?), a summary of questions being raised by the paper, and a preview of the experimental design of the work, drawing attention to what is strategic in that design. The actual experiments themselves should then be divided up with each student, addressing the immediate sub-question of his/her group of experiments.

The moderator in opening and closing remarks is expected to place the paper in context: What's the big picture? What's the significance of the research? Is it relevant to material covered in previous papers?

The respective section presenter is responsible for presenting an entire subsection of the work - including purpose, methods and results - that are associated with that subsection. Each section presentation should begin by briefly RE-stating the immediate objectives of that section, although if another member of the group has just done that this can be eliminated. Next, the presenter should introduce the techniques and/or design elements which are strategic to that portion of the work before getting into the details of the experiments. For unfamiliar techniques, the presenter is expected to summarize the underlying theoretical principles and the main procedural steps that are involved. The key is to point out why THAT particular technique was used to address the specific question. Do not list every "fact" in the methods section (e.g. don't tell us the buffer pH, unless it was critical to the experiment). The inability to carry out such an overview usually indicates that the presenter does not grasp the key elements of the procedure. During the course of the presentation, questions will arise about the methods and/or terms used in the work. Such questions are strongly encouraged. The student presenters should make every effort to anticipate such questions and find answers prior to the presentation.

Finally, the presenter should present the results in as clear and graphic a way as possible (graphs, tables, diagrams, etc.). Figures from the paper should be scanned or otherwise imported into PowerPoint. Go to http://web.centre.edu/training/handouts.htm (scroll down to Microsoft Powerpoint) for tips on effective Powerpoint presentations. In many instances, the presenter can improve the original illustrations by magnification, the use of color, simplification, and labeling, etc. The objective is: how could this illustration be improved to get its point across quickly and accurately to a less-than-expert audience?

Please refer to Chapter 10, pages 215-226 in Writing Papers in the Biological Sciences, 4 th edition by Victoria E. McMillan for guidelines on preparing your presentations.

The members of the class who are not presenting are expected to participate in the discussion. Especially at the end of the presentation, the class as a whole is expected to engage in a critical discussion of the work presented, noting where there are alternative interpretations and/or additional studies that need to be performed.

Peer Evaluations : After each group (and individual) presentation, non-presenting students will complete peer evaluation forms, which allow classmates to provide input on both style and substance of the presentation. Thoughtful completion of these evaluations will be considered part of the participation grade for non-presenters.

Visits By Outside Speakers

By the end of the third meeting of each cycle, we should be well-versed in the topic and prepared for a seminar to be given by a researcher in that field. The seminars will be at 4:00 p.m. After the seminar, we will take our guest speaker to Chowan for dinner. All students are required to attend the seminar and dinner (3 total). Mark your calendars and plan ahead.

Individual Project

A major portion of your seminar grade is based on an individual project. You are to choose a current topic in biochemistry, molecular or cellular biology, and prepare a paper and oral presentation on this topic. You may choose a topic from the attached list or come up with one of your own after preliminary literature research. All topics must be approved; one student per topic. You may not choose a topic that you worked on in BMB 210. Once your topic is approved, you should do further literature research to refine what you want to cover. This will result in a sentence outline keyed to a bibliography (not an annotated bibliography) . Use the most current information available on your topic. This project is not a complete literature review, but should focus on a very specific question or series of studies. The outline should provide a brief introduction to the topic (supported by appropriate secondary and tertiary references) and specific details about the experiments done in the 2 or 3 key (and recent) primary research papers that will be the focus of your paper and presentation. Please refer to Hacker's Rules for Writers for proper outline format. You then will write an 8-10 page paper . You are encouraged to include figures (e.g. schematics, graphs, and images) in your paper as well as in your talk. The figures are not to be included in the page count of your paper (i.e. 8-10 pages of text).

You must turn in one hard copy and email an electronic copy of your paper to your instructor by 2:00 p.m. on the due date. You must also submit an electronic copy to turnitin.com by the due date (detailed instructions with log-in and password will be provided later).

You may not use direct quotes--every part of your paper should be IN YOUR OWN WORDS. Each paper will be checked for plagiarism (see the Student Handbook).

Please refer to Writing Papers in the Biological Sciences, 4 th edition by Victoria E. McMillan, particularly chapters 1, 5, 6, 7, and 8, for guidelines on preparing your paper and presentation.

Paper Overview:

  • 8-10 pages (not including figures or the Literature Cited section)
  • Include figures (e.g. background schematics & data from papers -- graphs, photos, etc.)
  • Minimum of 12 recent references - a mix of primary (at least 5), secondary and tertiary
  • No quotes! Every part of your paper should be IN YOUR OWN WORDS!
  • Turn in hard and electronic copies and submit to turnitin.com.
  • You must turn in your original graded papers with the revised version

  Prior to your seminar, you will receive comments and a grade on your first paper submission. You then will revise the paper based on our comments and prepare your seminar based on your paper. Your seminar should be 30-35 minutes in length. Two students will be scheduled to give their seminars during each class meeting. Seminar dates will be determined on a first-come, first-served basis. Your revised final paper will be subject to the same checks described above. Turn in your original, graded papers with the revised version.

Deadlines ( all assignments are due at the beginning of the class period)

  • Individual topic selection: 2/9
  • Outline/Bibliography: 3/18
  • Paper - 1st submission: 4/15 (hard and electronic copies and submit to turnitin.com)
  • Paper - 2nd submission: 5/11 (hard and electronic copies and submit to turnitin.com)
  • Individual seminars: 4/22-5/6

Grading

Evaluation during the term:

Each student will schedule an individual meeting with your professor during the week following each presentation to receive feedback and grade. The tape of the presentation MUST be viewed before the meeting.

A. Paper presentations : 40% of BMB 500 grade

  • Apparent preparation for presentation: 50% of presentation grade.
  • Effectiveness of presentation itself (includes effectiveness as moderator): 50% of presentation grade.

 

B. Individual Project : 45% of BMB 500 grade.

  • Outline/Bibliography: 15% of project grade.
  • Paper: 60% of project grade

•  1st submission: 30%

•  2nd submission: 30%

•  Seminar: 25% of project grade.

C. Participation as a non-presenter in paper discussions: 10% of BMB 500 grade

Your participation is essential. Your willingness to ask and answer questions in class, thoughtful completion of peer evaluation forms, attitude toward the class and assignments, ability to meet deadlines, and your overall effort are all part of this. This is not guaranteed - you have to earn it.

D. Final Exam: 5% of BMB 500 grade. This is a standardized test written by Centre BMB professors over all of the material you have had in all upper-level BMB courses.

 

•  10% penalty for each day past deadline on written assignments. Nothing will be accepted if it is more than one week late (you will get a zero for that grade).

•  You must complete all assignments in order to pass this class.

•  Unexcused absences will reduce your grade.

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Possible Individual Project Topics:

Examples of Individual Project Topics (these are big areas - you will need to focus your topic on specific genes, proteins, organelles, etc.):

  • Protein-DNA/RNA interactions (this includes replication, transcription, translation and splicing complexes)
    - structural relationships
    - functional relationships
  • Prokaryotic DNA replication: interactions with the cell membrane
  • Organelle and membrane biogenesis
  • "Knock-Out" genes: site-specific gene inactivation
  • Receptor-ligand interactions
    - phage display for studying ligand binding
    - molecular modeling of protein/ligand complexes
    - crystallography of receptor and receptor/ligand complexes
  • Remodelling of the extracellular matrix as a developmental mechanism
  • Function of the nuclear matrix
  • Changes in nucleosome assembly/organization during DNA replication, transcription
  • Macromolecular assemblies (multi-subunit protein complexes, ribosomes, viruses, etc.)
  • Molecular mechanisms of steroid receptor/DNA interactions
  • Tyrosine kinases/phosphatases - roles in cell signaling pathways
  • Growth factors (cytokines)
  • Ca++ signaling pathways
  • Protein trafficking
  • Intercellular communication
  • Structure/function relationships in proteins/enzymes (choose specific one)
  • Bioactive lipids
  • Nutrient metabolism
  • Amyloids: structure and function
  • Immediate-early genes (fos/jun)
  • Oncogenes: normal cellular function vs. cancer inducing function
  • Programmed cell death (apoptosis)
  • Translation: the specific role of translation factors
  • RNAi
  • ... or a topic of your choice with the approval of the instructors.

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Research/Search Tools:

  • Literature Searches/Electronic Databases: (access from Library or campus network)
  • MEDLINE: searchable database of all biomedical literature, including basic science journals covering biochemistry, and cell and molecular biology. Access MEDLINE directly at the following site, which is Public Access MEDLINE ("PubMed"): http://www.ncbi.nlm.nih.gov/PubMed/
  • Interlibrary Loan: Individual articles in journals not carried by our library can be obtained for free through an interlibrary loan. Loans may take up to several weeks to arrive, so DO NOT WAIT until the last minute to request it!

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2009 Schedule

2/4 W: Introduction

2/9 M: Individual project topic due; no class

2/11: No class

2/16: Dr. McAlees paper #1 (review)

2/18: Dr. McAlees paper #2

2/23: Dr. McAlees paper #3

2/25: No class

2/26: Dr. McAlees Seminar and dinner, 4:00 p.m. Y202

3/2: No class

3/4: Dr. Purvis paper #1 (review)

3/9: Dr. Purvis paper #2

3/11: Dr. Purvis paper #3

3/16: No class; Dr. Purvis Seminar and dinner, 4:00 p.m. Y202

3/18: Outline/Bibliography due; no class

3/23-25: Spring Break

3/30: No class

4/1: Dr. Lockett paper #1 (review)

4/6: Dr. Lockett paper #2

4/8: Dr. Lockett paper #3

4/13: No class

4/14: No class; Dr. Lockett Seminar and dinner, 4:00 p.m. Y202

4/15: No class; first paper submission due

4/20: No class

4/22:
Student Presentations Section B: 1st: Ted Wright

4/27:
Student Presentations Section B: 1st: Rhi Ledgerwood 2nd: Kate Smiley

4/29:
Student Presentations Section B: 1st: Becky Lindhorst 2nd: Nick LeFevre

5/4:
Student Presentations Section B: 1st: Elijah Mullins 2nd: Chris Fleming

5/6:
Student Presentations Section B:: 1st: Ryan Smith 2nd: Ana Santin

5/11: 2nd paper submission due

5/15: Final Exam, 1:30

 

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last updated on 03/13/2009