Dr. Annkatrin Rose

Independent Study, Capstone and Honors Research
(BIO 2500/3500/5500/4501/4518/4519)

These courses allow students to conduct an independent research project and receive credit for it on their transcript or program of study. All of these require permission of the instructor and a special course form to be filled out for registration.

BIO 2500, BIO 3500, and BIO5500 are Independent Studies at the undergraduate sophomore and junior level, or graduate level, respectively, and can be taken for 1-4 credit hours per term, with no more than 6 hours counting toward a Bio major or graduate program of studies and no more than 3 hours counting toward a Bio minor. The area of your checksheet that they would count under would be determined in discussion with the department chair. The course catalog does not contain a description for Independent Study, as the requirements and grading for each study may differ and are outlined in a prospectus drawn up by the student and instructor. Each project is unique in consideration of the student's level of experience and the credit hours received.

BIO 4501 is Independent Research as a "Capstone Experience in designing and conducting an independent research project. Students will report the results of their study in the form of a paper appropriate for publication in a scientific journal and will present a public seminar on their research." (Undergraduate Bulletin)

Prerequisites for Capstone Research are senior standing and completion of a junior writing course. This course counts for three credit hours.

BIO 4518 is Honors Research for the "initiation of a research project in the laboratory, field, or classroom under the supervision of a biology faculty member. At least one semester prior to the start of the research project, the student must formally confer with a thesis advisor and must also submit and have approved a formal research proposal." (Undergraduate Bulletin)

Prerequisites for Honors Research is admission to the Biology Honors Program. This course counts for three credit hours and is followed by BIO4519 - Honors Thesis.

BIO 4519 is the Honors Thesis following an Honors Research project and counts for another three credit hours. As part of this course, "an oral report on the project will be presented in a public seminar. A written thesis will be approved by a committee comprised, at minimum, of the thesis advisor and another faculty member." (Undergraduate Bulletin)

Prerequisite for this course is the completion of BIO4518 - Honors Research - and the student must receive a grade of B or higher in both to graduate with Biology Honors. The Honors Thesis counts as a Capstone Experience.

Procedures:

Students interested in independent research should make an appointment to discuss their interests and the possible research opportunities in my lab. Depending on the number of ongoing projects, funding, availability of lab space, and teaching schedules, it may be difficult to fit another project in. According to policy, instructors should not conduct more than two different Independent Study courses per term. So plan early and be flexible!

Since the research in my lab revolves around plant molecular biology, I highly recommend that students interested in conducting an independent research project familiarize themselves with this subject area and acquire some experience in lab techniques such as pipetting, centrifugation, PCR and gel electrophoresis. I strongly encourage volunteering your help for at least one semester before embarking on your own project to collect some hands-on experience, get a feel whether the type of bench work we do suits you, and demonstrate your willingness and capability to "learn the ropes."

If things are working out, the next step would be to fill out the Independent Study form and draw up a prospectus outlining the goals and objectives of the proposed research project. These are turned in for approval by the department chair. In most cases, the second page of the Independent Study form is sufficient, but in some cases such as Honors or Graduate research, the prospectus may be more involved.

Expectations:

The university expects that you spend two to three hours of study time outside of class for every hour of class time. This means if you sign up for an independent study for 3 credit hours, you should plan on spending on average 9-12 hours per week in the lab or on reading and writing assignments related to the project. If you sign up for 1 hour of credit, you should plan on spending 3-4 hours per week. Your final report should accordingly reflect the time and effort you put into researching the topic and conducting your experiments in the lab.

Your grade will be based on your performance on items as outlined in the Independent Study form and/or undergraduate bulletin. Typical requirements may include:

• writing and submitting a grant proposal to the Office of Student Research to help with funding lab supplies needed for the project
• keeping an up-to-date and complete notebook record of all your work in the lab
• attending weekly lab meetings to report on your progress and troubleshoot problems you've encountered
• reading papers and protocols related to your project and be able to summarize and explain them
• reporting your efforts and results at the end of the study, e.g. in a talk or poster presentation or in the form of a written report consisting of introduction, methods, results, discussion, and references
• writing an abstract that concisely summarizes your entire project
• writing detailed protocols for any new lab procedures you have developed over the course of your project

Example Projects

Analysis of Plant Mutants: My lab is studying the function of chloroplast proteins by examining the phenotypes of mutant plants lacking these proteins (called knock-out mutants). Many of the Independent Research projects in my lab concentrate on some aspect of analyzing these plants. This involves phenotype analysis and genotyping of plants by DNA extraction and PCR to determine homozygous wildtype, heterozygous, and homozygous mutant individuals. Phenotypic studies may include microscopy, photosynthesis measurements, and molecular analysis of plants.

Protein Studies: We are also looking at the proteins themselves to examine their localization in the plant and involvement in membrane structure, protein complexes, and photosynthesis. Examples for projects done by undergraduates in the past include the expression of a plant protein in E. coli and affinity purification to generate an antiserum for further experiments, and analysis of protein expression in plant tissue via Western blotting and immunofluorescence microscopy using this antiserum. Another project is using the yeast two-hybrid system to determine the protein-protein interaction domain and gene activation domain through the use of deletion constructs of a protein of interest.

Expression Studies: Another aspect we are studying is the transcription of the genes that code for our proteins of interest. For some of our genes of interest, we are examining data from microarray analyses using online databases and bioinformatics tools. However, not all our genes are included in these datasets. Experimental projects use real time PCR and promoter-reporter studies to determine in which plant tissues these genes are expressed.