Molecular Biology Senior Exercise
2009-2010 Guidelines

In the Senior year Molecular Biology majors will have the opportunity to demonstrate that they can think independently and creatively about the field and can use the research tools of the discipline. In addition, they will have the opportunity to discuss important information about their theses with other students and faculty.

Experimental Senior thesis:

The senior thesis comprises at least two semesters (MB191a in the Fall and MB191b in the Spring semester of your senior year) of research in a Pomona College laboratory, which culminates in the writing of a comprehensive Research Report and an oral presentation at the molecular biology symposium.

When beginning your thesis work, you must first identify an interesting, unsolved problem in molecular biology and then design a research protocol to address it. In order to complete the requirements for the major, you must:

1) Identify a problem, write an abstract not to exceed one page describing your research project with a list of 3 references and submit a Senior Exercise Contract before the end of your Junior year to Dr.Negritto (see deadlines below).
2) Work in lab during the Fall and Spring semesters of your senior year the equivalent of at least 2 full afternoons per week. 

3) Participate in a total of 3 oral presentations, one in the Fall and two in the Spring, in addition to submitting the written reports specified in the deadlines section below.
4) Submit a written Research Report and present your thesis in the Senior Molecular Biology Symposium at the end of the Spring semester of your senior year.

Deadlines for 2009-2010:

Thursday April 29, 2008. Topic selection for senior thesis: Juniors by the end of MOBI188 must submit to Dr. Negritto a signed contract (Senior Exercise Contract), a one page abstract, and a list of 3 references that you have read. There must be a clear hypothesis to be tested in your senior thesis project.

Friday September 25, 2009. Submit an annotated bibliography of at least 10 references on your senior thesis topic. (see sample)

Friday October 2 and 9, 2009. First oral presentation you introduce your thesis project in the format of a mini grant proposal (15 minute presentation plus 5 minutes for questions) (see link to guidelines for writing a mini grant proposal). You are also expected to attend the talks given by your classmates (at least 6 other talks).

Monday November 30, 2009. Research progress report/outline. You need to submit a progress report on your original investigation. The report should consist of a carefully written and complete introduction including all the references you have obtained to date (make sure by now you have done an exhaustive literature search on your topic of interest). The results you have obtained up to date are also included in this report and explained in detail including figures. The other sections of the report such as materials and methods, results you are working on, and discussion (whatever is feasible at such an early date) are to be written in an outline format.

Friday February 5, 2010. Oral presentation on your progress report and discuss what you need to accomplish next.

Friday March 26, 2010. Submission of thesis to both readers. On or before this date, you must submit 2 copies of your thesis to Dr. Negritto. The thesis will be handed to your readers so that his or her input can be taken into account in the final draft.

Monday April 5, 2010. Return of thesis with comments and suggestions. Each of the two readers will comment extensively; it is up to you to obtain this input from them.

April 22 and 23, 2010. Final thesis presentation in the Senior Molecular Biology Symposium, practice talks are scheduled before hand for each student if wanted.

April 30, 2010. Submission of 3 copies of the final revised version of senior thesis to Dr. Negritto, please also submit by email your thesis as an attached file.

Important: Your final grade in the course will be assessed a penalty of one grade point per day, weekends included, when deadlines for any of these deadlines are missed. All deadlines are at 5PM on the designated day. Senior theses may not be submitted after the last day of classes (Wednesday prior to finals week); if not submitted, a failing grade for senior thesis will result.

The grades for MOBI191a and b are determined by your thesis advisors which take into consideration the time spent in lab, how you work in lab, how your thesis project is advancing, written reports, your final thesis oral presentation and your performance and participation in your other 2 oral presentations.

Identification of the problem for your senior experimental thesis:

You may find that this is the most difficult part of your senior exercise. To help define the problem which you will investigate the following suggestions may be helpful.

a) Identify from your classes those fields which were of interest to you and in which there were unanswered questions or considerable research remaining to be done.

b) Read current issues of journals as Science and Nature. Each issue contains a section called Research News, or News and Views, in which research in "hot" areas of research is reviewed and, often, unanswered problems defined. In addition, such journals as Trends in ...., Current Opinion in ...., Annual Review of ...., contain comprehensive reviews of broad fields, while others, such as Cell, contain shorter, more narrowly focused "minireviews".

c) Think about the laboratory exercises you have completed, particularly in the Molecular Biology Laboratory course, or during a summer research project, or in an upper division, laboratory course. By now, you should have an idea of how scientists work in the lab and what can be realistically accomplished, given time and the appropriate resources. How might you expand your lab experience into a specific project?

d) Review the material presented by faculty in MB188 about the research currently conducted in their laboratories. The faculty are more qualified than anyone else to supervise research in their fields of expertise, and, as importantly, they will have the laboratory resources required for such research.

e) Talk to your professors and other scientists about projects of potential interest. We want to help you as best as we can, and we may be able to assist in identifying topics that are suitable, or too complex, or too trivial. However, be reasonably prepared before you begin these discussions. We will not provide a list of topics for your selection. Most importantly, give yourself plenty of time to undertake the readings and discussions necessary to identify the topic of your proposal. It is not an overstatement to say that the most important parameter limiting the ultimate quality of your Senior Exercise is the selection and definition of the question you pose. The choice of faculty readers and problem go hand-in-hand, and your primary reader will not sign your "contract" unless they are persuaded that your problem is well chosen and thought out and that they have the appropriate background to be an adviser. Approach your prospective advisers well before the deadline for submission of the "contract".

Oral presentations

During the fall and spring semester you will participate in a series of seminar presentations.
The first talk, to take place in the fall semester, will consist of introducing the topic of your experimental thesis, your hypothesis and what you want to accomplish.You should present the nature and significance of the problem you are addressing and give extensive background information on what is already known in this area of research (here is where you make use of your bibliographic search), and go over the most important methods used.

The second talk will take place in the Spring semester and consists of reporting your progress in accomplishing your goals, what you have accomplished in the lab and what needs to be done next. All students are expected to contribute to each seminar discussion and also provide written critiques of each talk. A summary of these critiques will then be provided to each speaker so that he or she will become aware of his/her strong points and also know what they need to improve on.

The third talk consists of your final thesis presentation that will take place at the end of the semester in the Senior Molecular Biology Symposium, practice talks are scheduled before hand for each student.

The Research Project

The Research Project will enable you to demonstrate that you have mastered several important scientific skills. These include becoming familiar with a particular field, understanding clearly what is known and what is not known, being able to distinguish between an important question and a trivial one, to justify your choice of question to others and convince them that it is exciting and important. You will also identify and use the tools used in a particular field, learn about their advantages and their limitations and how they permit you to test your hypotheses in the laboratory. Of critical importance is the selection of a project that can be done, given the constraints of time and available resources. Accordingly, projects that were begun as part of the Molecular Biology Laboratory, or during a summer research project, or in an upper division laboratory course, or were begun as part of an independent research project in a professor's laboratory may be continued as a MoBio 191 Research Project. The final Research Report should be written in the general format of a paper submitted to a professional, scientific journal for publication with the modifications described below, so that it is acceptable as a comprehensive thesis.

The written report should include:

Title - A concise statement clearly defining your project.

Abstract - A paragraph outlining the problem you are going to study and summarizing the research activity you have undertaken.

Introduction - A comprehensive introduction in which you clearly state why the problem you have chosen is scientifically interesting and worthy of study. You should summarize the research performed in the field, citing specific experimental studies, and define unanswered questions. Finally, you should clearly and succinctly define the Specific Aims of your research. Be sure that you clearly describe the question you are investigating and place it in context of previous research that has been done in the field, which you describe.The introduction may be limited to 4-5 pages and not be an all inclusive introduction to the entire field in which you are working.

Materials and Methods - A description of the techniques and procedures that you carried out. This should be in sufficient detail so that another scientist, wishing to do so, could repeat your experiments.

Results - This section will be different from the Results section of a published paper. In a thesis you want to describe the process of how you went about your investigations. Describe experiments that did not give the predicted results, as well as those that did. Describe how each step of your work lead to the next. Your thesis should be a resource for someone wishing to continue your work, so that he/she is aware of what "worked" and what did not. Be sure to describe the results of all of your experiments, including the controls, that you have conducted to accomplish your Specific Aims. Data should be clearly and concisely presented in an appropriate form (tables, graphs, photographs of gels or blots, micrographs, etc.) and the results explicitly stated in words. Note that you should not undertake a detailed discussion of the significance of your data in this section.

Discussion - An analysis of the significance of your results. Did you support or refute your original hypothesis, and, if so, describe how and why. Describe problems you may have encountered in your study and what you did, or would do
in the future, to overcome them. Discuss how your results fit in with previously published work in the field. If your results are at odds with those of another laboratory, how would you reconcile this discrepancy. Finally, based on your
results, suggest novel hypotheses and future lines of experimentation that should be undertaken.

Literature Cited - A list of all papers cited in the research proposal. In general, these should be primary, original research reports and not review articles or book chapters. You should only cite those papers that you have critically read yourself, and not papers that are cited in other papers, unless they are acknowledged as such.

You will submit a written copy of the Research Report four weeks before the final version is due. This first version is meant to be a finished piece of work of the work completed to date and not a "rough draft." You should plan to have completed virtually all of your laboratory work in time for submission of the first version of the Research Report. A graded copy with the comments and suggestions of your advisers will be returned to you no later than ten days after submission. You are highly encouraged to incorporate the suggestions of your advisers into the final version submitted. The final, revised Research Report, which will include any additional experimentation you have completed, will be due at the end of the next to last week of classes. The grade received on the first version will be taken into consideration when determining your final grade.

Generally, the total length of the Research Report, exclusive of figures, bibliography and title page, should not be less than 20 pages. There is no maximum page limit, although clarity and conciseness will be taken into
consideration when evaluating the thesis.

General Guidelines
If you have any questions, or are confused about any aspect of your Senior Exercise, please feel free, and do not hesitate, to consult with your advisers. We are here to be used as a resource as much as you desire. Although periodic meetings with your advisers are not required, they are very much encouraged and can help with all aspects of your Senior Exercise, from selection of your topic, to presentation of your seminar and design of your research proposal or project. Copies of previous Molecular Biology Senior Theses are available in the office of Tina Negritto and may be checked out.

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This page was last updated on September 24, 2009.