Topic Selection (Experimental and Grant proposal theses)

Senior Exercise Contract

By the end of their junior year, students submit to Dr. Negritto a signed contract, a one-page abstract, and a list of 3 references that they have read. There must be a clear hypothesis to be tested in the senior thesis project.
Deadline: Contracts and topic selection must be turned in at the latest by the first week of the fall semester of Senior year.

First Semester Fall 2019

Thursday, September 5. Class meeting

Discuss class requirements, deadlines, and other important business. Location: SC 103, 11 a.m., with Prof. Negritto

Thursday, September 12. Workshop 1: How to Make an Oral Presentation

An introduction to talking about your science. We will also go over the program’s Information Literacy Rubric so that students can begin working on the literature review portion of their theses. 
Location: SC 104, 11 a.m., with Prof. Negritto.

Thursday, September 19. Workshop 2: Searching the Literature and Citation Management

Location:  11 a.m., Keck 3 at the Claremont Colleges Library, Honnold/Mudd Library, 3rd floor, Mudd side of the library, with Katie Kohn, Ph.D., STEM librarian.

Thursday, September 26. Workshop 3: How to Write a Grant Proposal

Mandatory for Library-Grant proposal thesis students.  All students are welcome and encouraged to attend. Thinking of applying to an NSF graduate fellowship?  This could be useful!

Location: SC 104, 11 a.m., with Prof. Negritto.

Friday, October 4. Annotated Bibliography

(Experimental and Grant proposal theses)
Submit an annotated bibliography of at least 10 references on your senior thesis topic.
Deadline: 5 p.m., to your drop box on the Sakai Molecular Biology Senior Thesis master site.                                         

Thursdays, October 3, 10, and 17. First Oral Presentation (schedule to be determined in class)

(Experimental and Grant proposal theses)

In this first presentation, you will talk about the single most relevant research paper in the area of your research project. Begin with a brief description of your thesis and describe how the paper you selected relates to it. Then cover a main experiment from the article, making sure to describe what the experiment addresses, the procedure and/or approach used, and finally, analyze the data critically and in-depth.  You may present more than one experiment, but plan your time carefully so you don't exceed the time limit. End by relating the experiment(s) you presented back to your thesis research project.
Time Limit: 8 to 10 minutes (plan carefully, practice extensively!)
Location: Frary Dining Hall, PDR North

Friday October 18. Mid-Semester Evaluation

(Experimental theses only)

By October 18 you must meet with your thesis advisor to receive feedback on your thesis progress (see Evaluation Form in syllabus). If you are not meeting the requirements for the molecular biology thesis, you have until the end of the semester to remedy the concerns outlined in the evaluation.

Experimental: If you decide to withdraw from MOBI194A (by October 18) you will receive no credit (NC) for the Fall semester. You must sign up for a Senior Library Thesis-Grant Proposal in Molecular Biology, MOBI191, in the Spring semester (0.5 credit).

Thursdays, October 24 and 31. Workshop 4: Writing Workshop (Introduction, Figures/Figure Legends)

Tips on Scientific writing, and guidelines for writing your senior thesis.
Location: SC 104, 11 a.m., with Prof. Negritto.

Thursdays, November 21 and December 5. Peer Review on thesis draft

Students will do a peer review on a classmate’s thesis introduction draft document. Prior to this class meeting, students should read the guidelines on peer evaluations (word file on Sakai: Writing Peer Evaluation Guidelines). Bring a hard copy of a draft of your Introduction (printed double-spaced).
Location: SC 104, 11 a.m., with Prof. Negritto.

Monday, December 9. Research Progress Report I

Experimental: Full Introduction / Outline of remaining sections
Grant proposal: Full Introduction / Specific Aims

Experimental: You need to submit an introduction of your senior thesis. This introduction should consist of a careful analysis of the state of knowledge in your area of research (by now, you have done an exhaustive literature search on your topic of interest). The introduction should state clearly why the problem you have chosen is scientifically interesting and worthy of study and consist of a review of the relevant literature. You should clearly describe the question you are investigating and place it in context of previous research that has been done in the field.

Include the results you have obtained up to date in an outline format (bullet points with one or two sentences at the most). Present analyzed data either as a figure with figure legends (figure legends should be detailed, and formatted per the guidelines discussed in the molecular biology lab class) or tables with appropriate footnotes. The other sections of the report (materials and methods, results you are working on, and discussion) are also to be written in an outline format.

Grant proposal: A comprehensive introduction that clearly states 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 (by now you should have done an exhaustive literature search on your topic of interest).  Finally, you should clearly and succinctly define a couple of Specific Aims you are thinking of proposing. 

Deadline: Submit two hard copies to Prof. Negritto by 5 p.m., and deposit an electronic version to your drop box on the Sakai Molecular Biology Senior Thesis master site.

Your Fall semester grade takes into consideration your progress report, your presentation, the feedback you provided to other students, your information literacy skills, and your work in lab. A passing grade is required in order to register for experimental senior thesis (2nd half), MOBI194B, in the Spring semester. If a passing grade is not accomplished you must sign up for a Library thesis in Molecular Biology, MOBI191, in the Spring semester.

Second Semester Spring 2020

Fridays February 7, 4 and 21.  Oral Presentation

(Experimental and Grant proposal theses)
This is the first opportunity you have to introduce your thesis project. What is the major question you are addressing? Why is it important to address it 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 and what experimental approaches you plan on using to address this question. Remember to take into consideration the guidelines and tips given to you on how to give a successful oral presentation. Your presentation will be 8–10 minutes, plus 5 minutes for questions. Everyone is expected to attend the talks given by their classmates, to provide feedback, and to ask questions.

Friday, February 21. Research Progress Report II

Experimental: Add Materials and Methods section to the Research Progress Report I and revise Introduction, Figures and Figure Legends with comments received.

Grant proposal: Define Specific Aims and, in outline format, propose experiments to address Specific Aims.
In outline format, identify the experiments and appropriate controls you will propose to do that address the specific Aims. Clearly outline what are the possible results and how these will refute or confirm your hypothesis.

Deadline: Deposit an electronic version to your drop box on the Sakai Molecular Biology Senior Thesis master site by 5 p.m.

Friday, March 6. Grant proposals

Grant proposal: Work on defining in detail the experimental approach you will be taking to address your specific aims. 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, and what specifically is required to undertake each procedure. Additionally you need to clearly describe how you will obtain or make whatever specialized reagents, probes, antibodies, etc., that are required for the procedures you propose.

Deadline: Two hard copies submitted to Prof. Negritto by 5 p.m.; deposit an electronic version to your drop box on the Sakai Molecular Biology Senior Thesis master site.

Friday March 27.  Submission of Thesis

(Experimental and Grant proposal theses)
Deadline: On or before this date submit two hard copies of a complete Thesis, Experimental or Grant Proposal, to Prof. Negritto by Noon and deposit an electronic version to your drop box on the Sakai Molecular Biology Senior Thesis master site.

Guidelines for what should be included in your thesis can be found in the Senior Exercise syllabus. The thesis will be handed to your readers so that their input can be taken into account in the final draft. Note that this first version must be a finished piece of work, not a "rough draft." A graded copy with the comments and suggestions of your advisers will be returned to you no later than ten days after submission (April 6).  You are highly encouraged to incorporate the suggestions you have been receiving up to date from your advisers into the final version. The grade received on the first version will be taken into consideration when determining your final grade.

Monday, April 6.

(Experimental and Grant proposal theses)
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.

Thursday, April 23 and Friday, April 24.  Final Thesis Presentation (an extra presentation date may be added)

(Experimental and Grant proposal theses)
Final oral presentation of your Thesis work in the Senior Molecular Biology Symposium.

Monday, May 4: Final Thesis due

(Experimental and Grant proposal theses)
Deadline: Submit to Dr. Negritto by NOON

  • 3 hard copies of the final, revised version of your Research Report (senior thesis). Binding is optional but strongly encouraged; the molecular biology program will cover the cost of binding, not printing, your thesis at Pomona Duplicating services.
  • Fill out an exit survey; having a current Curriculum vitae on hand will help you be able to answer questions more quickly. A sample exit survey is available for you to look at in the Resources folder of the Sakai Molecular Biology Senior Thesis master site. The exit survey will be taken online thru Qualtrics. At the end of your senior year you will receive a link to the survey.
  • Electronic version of your final Oral Presentation and Research Report (Senior Thesis) or Grant Proposal uploaded onto your drop box on the Sakai Molecular Biology Senior Thesis master site.