Genetics and Developmental Biology Area of Concentration

Area Description

• Overview
• Major Advisor and the Advisory (Thesis) Committee
• Plan of Study
• Laboratory Rotations/Independent Studies
• GDB Journal Club
• GDB Research-in-Progress Meetings
• GDB Seminar Series and Department Retreat
• Summary of the Plan of Study
• Preliminary (General) Exam
• "Thesis Prospectus": Dissertation Proposal to the Graduate School
• Oral Defense/Final Exam and the Dissertation
• Summary of Major Events in attaining the Ph.D.
  
• Expectations for Faculty Membership
  

Overview

The Genetics and Developmental Biology area of concentration (GDB AoC) provides qualified students with fundamental interdisciplinary training in modern molecular genetics and developmental biology, emphasizing cellular and molecular aspects as well as tissue interactions. Areas of research include the mapping and cloning of human genes responsible for disease, RNA processing (including RNA editing, alternative splicing, antisense regulation, and RNA interference), the molecular mechanisms of aging, signal transduction pathways, microbial pathogenesis, developmental neurobiology, cell differentiation, musculoskeletal development, morphogenesis and pattern formation, reproductive biology and endocrinology. Faculty members are from several basic science and clinical departments and study a wide range of organisms including yeast, parasites, worms, fruit flies, birds, mice, and humans. Students are encouraged to obtain in-depth training in molecular genetics and developmental biology. The GDB AoC prepares students to compete for job opportunities in traditional medical and dental school departments as well as a productive research career in either academia or industry.

Note: Any questions not answered by this web page should be directed to the GDB AoC Director or pursued via the UConn Health Center Graduate School Registrar's Office or the Associate Dean of the Graduate School.

Selection of the GDB AoC: Major Advisor and the Advisory (Thesis) Committee

Upon entering the Biomedical Sciences (BMS) Ph.D. program, a student will be assigned an advisory committee to assist in the selection of suitable courses and rotation laboratories. At the end of the first year of study, students will formally select a Major Advisor who will be responsible for both the course work and research components of the student's doctoral career. If the major advisor is or becomes an active member of the Genetics and Developmental Biology area of concentration (GDB AoC), the student may choose to enter GDB AoC. The major advisor will work with the student to formulate an advisory committee. This committee will comprise the major advisor plus at least two other faculty members of the GDB AoC, including at least one faculty member on the GDB AoC executive committee. Together with the major advisor, the committee will monitor the student's progress, help organize a Plan of Study (i.e., select courses to be taken) and serve in a general advisory capacity. The committee, with the major advisor, will administer the preliminary (general) examination. After completion of the preliminary examination, the advisory committee will serve as a Ph.D. thesis advisory committee, meeting with the student twice each year: once as part of the GDB Research-in-Progress series, and once approximately half a year later. This committee may be expanded to up to five members. Additional advisors may be members of another UConn Health Center area of concentration, or even of another program within the UConn graduate faculty. In some cases, an external associate advisor – from the faculty of another university, for example – may be added to the committee if s/he is considered to be expert in the area of the student's dissertation research. In such a case, the student's major advisor must write a letter to the Graduate School requesting such status for the external advisor, including the individual's curriculum vitae.

Plan of Study

With the guidance of the major advisor and the advisory committee, the student will develop an individualized schedule of courses toward the degree. This must be submitted as a formal Plan of Study and approved by the Graduate School before the end of the second year of graduate study. The plan consists of a list and sequence of courses that the student needs to complete as part of his/her Ph.D. program. The full transcript of Ph.D. course work will consist of 44 credit hours beyond the B.S. degree, or 24 credit hours beyond the MS degree. The student's plan of study should include courses offered at the Health Center [PDF] (see also a searchable Blackboard course catalog) or other UConn campuses, preferably from the graduate catalog, but not excluding undergraduate courses in topics that are crucial to the overall Plan of Study or research aims of the student. Detailed information regarding the Ph.D. Plan of Study is outlined in the UConn Health Center Graduate School Handbook and the UConn Graduate Catalog. In general, the student will take formal course work during only the first two years. However, each student is required to register for the Genetics and Developmental Biology Journal Club every semester, with a final-semester exemption for a student writing his/her dissertation. An example plan for the first year is outlined below:

To remain eligible for continued assistantship support, second year students must complete at least 8 credits of regularly-graded courses per year. An example plan of study for the second year is presented below.

*Electives may be taken from any of the UConn course offerings. The following is a list of some of the recommended elective courses:

• MEDS 5322 - Developmental Biology, 2 credits
• MEDS 5369 - Advanced Genetics and Mol. Bio., 3 credits
• MEDS 5418 - Stem Cells and Regenerative Biology, 3 credits
• MEDS 5376 - Developmental Neurobiology, 3 credits
• MEDS 5325 - Practical Apps. of Sequence Analysis, 2 credits
• MEDS 5351 - Biochemistry II, 3 credits
• MEDS 5329 - Core Immunology, 2 credits
• MEDS 5467 - Biostatistics, 3 credits

The major focus of the third and later years of graduate study will be on the completion of the thesis.

Laboratory Rotations/Independent Studies

Students are encouraged to set up their lab rotations as soon as possible. Students will perform rotations in at least three different laboratories during the first year. Ideally, the first rotation will occur during the first summer. During each rotation, the student will spend one full-time semester or summer in a hands-on laboratory learning experience. The rotation project will be presented in a talk by the student at the end of the semester. These rotations are designed to allow the student to get a detailed exposure to the research interests of different laboratories before selecting a major advisor under whom the student will do his/her dissertation research.

GDB Journal Club

The GDB AoC prides itself on a student-centered format for the weekly Journal Club, with active participation by all members of the group. The GDB JC meets Mondays at 12 noon during the academic year. Each student who is a member of the AoC or is rotating during the first spring semester will be scheduled for one journal club presentation. The following guidelines have been in effect for the past several years. A Blackboard site for the current year's GDB JC course is maintained, as well as a calendar page.

Guidelines on good journal club meetings, and grading:

Attendance will be graded on an individual basis and will count for 1/3 of each student's grade. Excuses related to scientific meetings, exams, or illness will be allowed. Excuses related to daily personal life or experimental schedules will not. If you have got a special case let the course faculty know ahead of time.

Participation and Presentation will be graded on a class-wide/team basis. The presenter is not assigned an individual grade for his/her performance. Again, the goal is to encourage universal participation and interest in a discussion of the chosen paper and topic. We need to make good use of the full hour. The same cumulative letter grade for these aspects of the meeting is awarded to all students attending, and the score comprises 2/3 of each person's individual grade (the other third depending on punctuality and attendance).

Selecting a paper outside your expertise will enhance both your learning experience and the amount and depth of discussion at the meeting. Please select from outside your area of current research. The presenter may actually clarify his/her own understanding by querying or learning from the audience, and all in the group will benefit from good Q/A stimulated by a joint exploration of a novel topic. Keep in mind, also, that flawed papers are good fodder for critique and constructive discussion by our students. Finding a perfectly crafted paper will not necessarily generate a good discussion. Finding a paper that addresses an important topic and then contrasting its strengths, weaknesses – while proposing possible solutions to the problems in the work – is often the best recipe for an A+ grade on the meeting. The faculty will have ideas for suggested papers if you have trouble finding one in your own reading, but we strongly encourage you to explore independently in making your selection.

A crucial job for the presenter is to ensure high-quality visuals during the discussion. If a paper's PDF file contains reduced or compressed images that do not project well, be certain to acquire the high-resolution figures from the website of the journal. Please also invest at least 5-10 minutes of your presentation to background material that frames the significance of the questions being addressed in the chosen paper. Do not forget that the opening of your presentation is a great time to elicit questions or comments from the audience, sounding out the amount of background knowledge that your peers have of the chosen topic. Budget your time – perhaps focusing on only a subset of the data in a long paper – and manage the conversation (if necessary) so that discussion of the results and conclusions of the paper will be completed by 1 p.m. There is no extra credit for overly long meetings.

Remember, the attending faculty member will be looking for everyone to participate from the audience. If all members of the group have not offered at least some question or comment during discussion by the middle of the semester, the participation grade (no matter how good the discussion among other participants) for the entire class will start to drop. It is not hard to keep the team participation grade high, as long as each member of the group is conscious of his/her need to contribute regularly to the discussion.

GDB Research-in-Progress Meetings

Students in the GDB AoC are required to attend and present in the weekly Research-in Progress meetings, held each Tuesday at 12 noon during the academic year (see schedule). Presentations can be viewed live or as recordings via MediaSite online. Each student who is a member of the AoC will be scheduled for one RIP seminar presentation per academic year. The student's major advisor and advisory (thesis) committee will be scheduled to attend the talk, and a private meeting of the student and her/his committee will follow the presentation. This will count as one of the student's two mandatory thesis committee meetings per year. The second biannual committee meeting will be scheduled for the summer, and will not be associated with the RIP seminar series.

GDB Seminar Series and Department Retreat

The GDB Department conducts an invited seminar series, meeting every second Thursday at 12 noon during the academic year (see schedule). Each student who is a member of the GDB AoC is required to attend the seminars. Following each Thursday talk, a group of students will host the speaker for lunch, with time for informal discussions. Any student who recommends the invitation of a speaker in the series will also be welcomed at dinner with the speaker and other hosting faculty.

Each winter, the GDB Department holds an off-site retreat, with an agenda including a "state of the department" overview presentation by the department chair, one seminar by a faculty member of the department, one seminar by a departmental student, and one seminar by a faculty member from the Storrs campus. Each year, a poster session has includes presentations by students in GDB and other departments whose advisors are members of the GDB AoC. All active members of the GDB AoC faculty are invited to attend the event. Attendance and presentation of a poster or talk is mandatory for every student in the AoC (second year and later students).

Summary of the Plan of Study

As outlined above, there are three ways to earn the 44 credits required for a Ph.D.: Traditional courses, journal clubs and lab rotations/independent studies/graduate research. Traditional courses (i.e., not including journal club, lab rotation/research) should make up 15 credit hours of the 44 total. GDB journal club will typically comprise at least 8 credit hours. Fifteen credit hours must be of GRAD 6950, Dissertation Research. Additional credit hours can be taken as lab rotations/independent study.

Preliminary (General) Exam

The preliminary examination is a qualifying examination given to all students in the Genetics and Developmental Biology Area of Concentration of the UConn Health Center Biomedical Sciences Ph.D. Program. Passing this exam formally admits the student to doctoral candidacy. Each GDB AoC student must complete the preliminary examination by the end of the second academic year in order to retain continued support of tuition and stipend. Students should plan according to this requirement in scheduling the prelim exam. Two GDB-specific prerequisite courses, or GDB-director-approved equivalents, must be completed before taking the prelim exam. MEDS 5327 (Logic of Modern Biology) is required along with any one of the following: MEDS 5322 (Developmental Biology), MEDS 5369 (Advanced Genetics and Mol. Bio.), MEDS 5418 (Stem Cells and Regenerative Biology). The intent of the prelim exam is to test the student's ability to formulate an original research proposal and to construct and defend a sound hypothesis-driven experimental approach to accomplish the proposal's specific aims.

The Proposal

The topic of the prelim exam proposal should be based on the student's thesis research project. The exam should be typed in 12 point Helvetica, Arial, or similar font, with one inch margins and double-spaced. The total length of the proposal (including figures and references) should not exceed 30 pages (double-spaced) and should resemble a professional grant proposal:

• Specific Aims (2 pages): State the specific purposes of the research proposal and the hypothesis to be tested. State concisely the goals of the proposed research and summarize the expected outcome(s), including the impact that the results of the proposed research will exert on the research field(s) involved. List succinctly the specific objectives of the research proposed, e.g., to test a stated hypothesis, create a novel design, solve a specific problem, challenge an existing paradigm or clinical practice, address a critical barrier to progress in the field, or develop new technology.
• Research Strategy (up to 28 pages): Organize the Research Strategy in the specified order and using the instructions provided below. Start each section with the appropriate section heading: Significance, Innovation, Approach.
• (a) Significance: Explain the importance of the problem or critical barrier to progress in the field that the proposed project addresses. Explain how the proposed project will improve scientific knowledge, technical capability, and/or clinical practice in one or more broad fields. Describe how the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field will be changed if the proposed aims are achieved.
• (b) Innovation: Explain how the application challenges and seeks to shift current research or clinical practice paradigms. Describe any novel theoretical concepts, approaches or methodologies, instrumentation or interventions to be developed or used, and any advantage over existing methodologies, instrumentation, or interventions. Explain any refinements, improvements, or new applications of theoretical concepts, approaches or methodologies, instrumentation, or interventions.
• (c) Approach: Describe the overall strategy, methodology, and analyses to be used to accomplish the specific aims of the project. Include how the data will be collected, analyzed, and interpreted as well as any resource sharing plans as appropriate. Discuss potential problems, alternative strategies, and benchmarks for success anticipated to achieve the aims. If the project is in the early stages of development, describe any strategy to establish feasibility, and address the management of any high risk aspects of the proposed work. Point out any procedures, situations, or materials that may be hazardous to personnel and precautions to be exercised.
• References: Each citation must include the names of all authors, name of the book or journal, title of article, volume number, page numbers, and year of publication.

Timetable for submission of the Prelim exam Proposal:

• Step 1: Meeting with an advisory committee consisting of three Genetics and Developmental Biology faculty (i.e, the student's advisory committee) to approve a 2 page outline (double-spaced) of the specific aims of the proposal and answer any questions about procedures associated with the exam. To assure uniformity of the prelim exam, at least one member of the student's prelim exam committee must be the director, associate, or assistant director of the graduate program or a designee. The student will be given 4 weeks from the date of this meeting to complete the written portion of the exam.
• Step II: The student will submit a revised copy of the specific aims of the proposal to the program director and each committee member.
• Step III: Not less than 4 weeks after the first meeting, and at least 1 week before the date of the oral exam, the student will submit a copy of the written proposal to each faculty member present at the first meeting, and to two additional faculty members who have agreed to serve on the student's examination committee.
• Step IV: Oral examination. Students should plan on the examination lasting approximately 2 hours.

Exam Procedure

Prior to the day of the exam: As indicated in the timetable for preparation of the preliminary exam proposal, each student will provide each member of his/her committee with a copy of the proposal at least one week prior to the meeting.

On the day of the exam: The program director, assistant or associate director, or designate, will serve as the chair of each examining committee. Examinations will be scheduled to allow a maximum of 2 hours for each exam. When the committee has gathered and the members have been introduced to the student, the chair should ask the student to leave the room briefly. The topics to be discussed in the student's absence are:

• The student's overall record. Any deficiencies that might need special attention in the oral questioning should be identified.
• The quality of the written proposal. If the quality is so poor as to be unacceptable, the student can be given a "fail" at this point.
• If the proposal is generally acceptable; any specific deficiencies revealed in the written proposal should be identified and pursued in the oral questioning.
• The "ground rules" for the examination should be agreed upon. The student has the opportunity to give a 15-minute presentation. The committee members should decide in advance if they plan to let the student do the presentation uninterrupted or if they plan to interrupt the presentation with questions as they come up. Either format is acceptable, but the student needs to know which will be followed. When the "interrupt" mode is chosen, the discussion might proceed in a direction that does not allow the student to actually complete his/her prepared talk. The student should be assured ahead of time that this might happen and that he/she should not be concerned about getting back to the prepared talk.

The student will then be invited to return to the room. The chair should explain the ground rules to the student, explain the role of the program director/assistant director, committee chair (or designate), and ask the student to begin the presentation. If questioning is slow in getting started, the committee chair should lead off, preferably with a question that the student should be able to answer comfortably. The chair should then turn over the questioning to one of the other examiners. One role of the program director or assistant director is to ensure that the exam is administered fairly and that all exams are administered in a uniform fashion.

Exam questions should be designed to probe the student's depth of knowledge on the chosen subject of the proposal, both theoretical and technical. In addition, exam questions should determine the student's general knowledge of Genetics and Developmental Biology especially as it relates to lecture and seminar courses taken, and rotations completed. When the chair feels that the student has been examined sufficiently, he/she will ask the student to leave the room while the committee discusses the performance. Each student's performance should be evaluated in four areas: 1) quality of the written proposal, 2) quality of the oral presentation, 3) defense of the proposal, and 4) general knowledge. The student will then be asked to re-enter the room and told the outcome of the exam. The result of the exam is then reported to the Graduate School on a form that must be signed by all members of the examining committee.

Possible outcomes

Pass: This is the outcome expected for most students. It can represent a range from absolutely stellar performance to a good, generally solid one.

Conditional Pass: This is used when a particular aspect of the exam showed clear deficiencies or when the overall performance was marginal. The committee must suggest to the Program Director what the student should be required to do to clear the deficiency (such as rewrite the proposal, take a particular course, etc.) If the student is expected to consult with the committee members individually, this should be stated, and a time frame for completing the examination should be established. It is important for the committee chair to put this in writing during the meeting so that there is no ambiguity about what is being asked of the student. When the committee communicates the outcome of the exam to the student, advisors should discuss the conditions of a conditional pass with the student. A passing grade on the preliminary exam will not be communicated to the Graduate School until the conditions set forth have been satisfactorily fulfilled. A failure to do so will delay advancement to Ph.D. candidacy.

Failure: This is the outcome when the written proposal is completely unacceptable or performance on multiple aspects of the exam is unacceptable. A student who fails will automatically get a chance to rewrite the proposal and/or defend it at another oral examination. The amount of time available for completion of the repeat exam must be specified at this time. A student who fails the exam twice must leave the program.

"Thesis Prospectus": Dissertation Proposal to the Graduate School

A prospectus of the student's proposed research project must be completed within 12 months of passing the preliminary exam. This prospectus must be filed on specific forms obtained at the Graduate School Registrar's Office.

Oral Defense/Final Exam and the Dissertation

Formats for the dissertation and the public defense of the thesis are governed by rules of the Graduate School and summarized on a Graduation Checklist. Many GDB AoC students choose to schedule a final private defense meeting of the advisory committee and additional readers, where the content and significance of the thesis are reviewed in detail before the official public thesis defense. Tentative approval of the written dissertation may be granted at this time by the committee. This tentative approval must be granted by the committee prior to scheduling the public defense. The public defense must be announced through the Graduate School at least 2 weeks ahead of time. This final examination entails a formal seminar presented by the student to an audience that must include at least 5 faculty and must include all members of the advisory committee. The student will field and answer questions, and a final (private) vote by all the faculty in attendance will be conducted to accept or reject the dissertation. The report on the Final Examination is then signed by faculty and submitted to the Graduate School.

Summary of Major Events in attaining the Ph.D.

Expectations for Faculty Membership in the GDB Area of Concentration

Faculty who are formally affiliated with the GDB area of concentration will have their membership in the AoC reviewed every 5 years by the AoC executive committee. In order to be retained as an affiliated faculty member in the GDB AoC, one must contribute substantially to the strength of the scientific and educational environment of the AoC in some of the following ways: