Senior Exercise Contract

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.

The senior exercise for molecular biology students can be fulfilled by an Experimental Senior Thesis, MB194A,B  or a Senior Library Thesis-Grant Proposal, MOBI191A,B. The same type of general deadlines and guidelines apply to both and culminate in the writing of a comprehensive Research Report (written thesis) or Grant Proposal, respectively, and an oral presentation at the molecular biology symposium.    

The senior exercise 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, being able to distinguish between an important question and a trivial one, to justify your choice of question to others and convey why your topic of interest is important and exciting to study. You will also identify and use the appropriate tools for the particular field of molecular biology you are investigating, learn about advantages, limitations and how they permit you to test your hypotheses.

Of critical importance for students undertaking an Experimental Senior Thesis 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 as part of an independent research project in a professor's laboratory may be continued as a MOBI 194 Research Project.

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 focus on the single most relevant research paper in the area of your research project. In terms of how to format your talk you should make clear from the beginning the nature and significance of your thesis project and how it relates to the chosen paper.  You may then cover a main experiment from the research article of your choice making sure to analyze it critically and in depth explaining in detail the procedure or approach used (could be more than one experiment you choose to present, depends if you can fit all you want to say in the minutes, 8 to 10, you are given for your presentation). You then finalize your talk relating back to your project and transitioning into any progress you have made. Remember to take into consideration the guidelines and tips given to you on how to give a successful oral presentation. All students are expected to participate and provide feedback.

The second talk will take place in the spring semester. This is where you will introduce your thesis project. What is the major question you are addressing? Why is it important to address this and how are you planning on addressing it? 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. Present the experimental approaches you plan on using and include results that you have up to date. 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 spring semester in the Senior Molecular Biology Symposium.

The Research Project Report (written Senior Thesis)

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 and it is due at the end of the first semester (see deadlines section).
  • 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, 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.
    • Information Literacy Rubric: Take in consideration the information literacy rubric (See document Information Literacy Rubric in Sakai site) to assess the literature you cite. By using this rubric it will help you assess how well you are addressing all three aspects of information literacy, attribution, evaluation of sources and communication of evidence.

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 and complete report 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.

Senior Library thesis - Grant proposal:

The Grant Proposal you write will describe a series of experiments that would normally take two to three years to perform.   Accordingly, the research will comprise a series of experiments, rather than a single experiment.  The proposal should contain the following sections:

  • 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 propose to do. 
  • Introduction - A comprehensive introduction in which you clearly state why the problem you have chosen is scientifically interesting and worthy of study.  You should include an in depth review of relevant literature on 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. Specific Aims provides an overview of your entire project: what is the problem, the question you want to address, Why is it important to study? What is your hypothesis and how will your hypothesis be addressed? The introduction is due at the end of the first semester (see deadlines section).
  • Proposed Research - A detailed discussion of the experiments you will conduct to accomplish your Specific Aims (Two to three well designed experiments is usually enough). What experiments will you perform, and what observations do you expect to make?  What control experiments will you conduct?  What difficulties do you anticipate with your experimental design, and how will you overcome these difficulties?  What corroborative experiments might you undertake?  You must describe in detail the expected or possible results of your proposed experiments and discuss why they support (or refute) your hypothesis.  If the results do not support your hypothesis, what additional experiments would you undertake to provide that support. You must include an explicit description of the materials and methods used in each of the experiments you propose.  This need not be as detailed as the Materials and Methods section of most published papers.  Rather, you should clearly describe what you will be doing, what is the theoretical basis for major experimental procedures, what specifically is required to undertake each procedure, and how you will obtain, or make yourself whatever specialized reagents, probes, antibodies, etc., that are required.
  • Summary - A concluding paragraph in which you restate the problem, summarize the possible results of your experiments, state their significance and raise future lines of experimentation.
  • Literature Cited - A list of all papers cited in the 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.
    • Information Literacy Rubric: Take in consideration the information literacy rubric (See document Information Literacy Rubric in Sakai site) to assess the literature you cite. By using this rubric it will help you assess how well you are addressing all three aspects of information literacy, attribution, evaluation of sources and communication of evidence.

Generally, the total length of the Library thesis – Grant Proposal, exclusive of figures, bibliography and title page, should not be less than 15 pages. There is no maximum page limit, although clarity and conciseness will be taken into consideration when evaluating the thesis. The student and thesis advisor should also meet to agree upon the appropriate format/organization of the final thesis manuscript. A common format consists of Times New Roman, 12-point font, double-spaced, 1-inch left hand margin.

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 your oral presentations 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.