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Cell Biology Graduate Program

Program Description

The Cell Biology Area of Concentration (CB AoC) at the University of Connecticut Health Center offers training leading to a Ph.D. in Biomedical Sciences. Faculty members in the CB AoC are engaged in cutting edge research in a wide range of topics related to the molecular and cellular basis of biology and disease, and are from multiple departments and research centers, including but not limited to the Department of Cell Biology, Center for Vascular Biology, Calhoun Cardiology Center, and Department of Molecular Medicine. First year students will take core courses and participate in Cell Biology Journal Club. An equally important activity in the first year is Laboratory Rotations, which offer students opportunities to acquaint themselves with research activities in different laboratories, and identify a Major Thesis Advisor. In the second year, while students continue to take some advanced elective courses, the main emphasis shifts towards research and preparation for general examination. Individual students should form Advisory Committees, and complete general examination before the end of their second year. From third year on, students will continue to participate in Cell Biology Journal Club and focus on their thesis research with the aim of completing their thesis before the end of the 5th year. Through rigorous course and research training, the CB AoC prepares students for successful careers in academic research, biotech industry, and education.


Guide for Graduate Students


Major Advisor and Thesis Advisory Committee

Upon enrollment, each student will meet with the First Year Graduate Advisory Committee of the Graduate School, which will assess the student’s background and preparation, and advise the student on course selection and laboratory rotations. Each student will be assigned a temporary major advisor, who will play a major role on behalf of the Committee in monitoring the student’s progress and serving in a general advisory capacity. Students are expected to choose a major advisor before the end of the first year. The major advisor must be a member of the CB AoC. Upon selection of a thesis laboratory, the Change of Major Advisor Form must be completed.

A student must form an Advisory Committee by December 31 of the second year. The Advisory Committee consists of three members, one of whom is the major advisor. The major advisor and at least one additional committee member must be from CB AoC.  The Chair of the Committee should be a senior faculty member from CB AoC, and cannot be the major advisor. Two Examiners should be recruited as well. All committee members and examiners must be approved by the program director, with approval based on the proposed member’s area of expertise.

The function of the Advisory Committee include: (1) helping to monitor the student’s progress (2) advising the student on developing a Plan of Study (3) administering the general (preliminary) examination and (4) serving in a general advisory capacity. After the student has successfully completed the general examination, the Advisory Committee will serve as the Ph.D. thesis Advisory Committee. The committee should meet with the student at least once a year. All committee members and examiners must be present at the meeting.

Plan of Study
The Plan of Study is specifically formulated for each student and consists of a list of all courses that must be completed as a part of their Ph.D. Program. The Plan should be organized with the help of the major advisor after the student has taken 18 credits of course work. The Plan must be first approved by the Advisory Committee and examiners as well as the AoC director prior to being submitted to Graduate School for approval.  The Plan of Study must be approved prior to taking the General Examination. For requirements for total credits, content course credits, and doctoral dissertation research (GRAD 6950), see http://grad.uchc.edu/current/milestones/index.html. With few exceptions, students will have completed formal courses by the end of their second Fall semester.


Course Requirements

A student must earn a total of at least 45 credits of graduate work to be awarded a Ph.D. degree, including 30 credits of content courses (i.e., courses without GRAD designation) and 15 credits of doctoral thesis dissertation (GRAD 6950). As per requirement by the Graduate School, students must take at least 6 credits of classroom courses each semester of first year (except for the summer), and 6 credits of classroom courses in the second year. Typically, students should have completed all of these 18 formal course credits by the end of the second Fall semester so that a Plan of Study can be submitted and approved in time for General Examination before the end of the second year. Exceptions may be made for those with Master’s degree by credit transfer from some of the previous graduate courses that they have taken at other institutions.  

Required Courses

  • MEDS 6448 Foundations of Biomedical Science I (3 credits)
  • MEDS 6449 Foundations of Biomedical Science II (3 credits)

  • MEDS 5310 Responsible Conduct in Research (1 credit)
  • MEDS 6496 Laboratory Rotations (3 semesters, 1 credit each).
  • MEDS 6497 Cell Biology Journal Club (all semesters, 1 credit each)
  • GRAD 6950 Doctoral Dissertation Research (3 credits per semester, minimum 15 credits

Recommended Electives*

The following is a list of courses most often taken by Cell Biology students.  However with the approval of their Advisory Committee, students can select from any graduate level course offered by the Graduate School.

  • MEDS 5329 Immunobiology I (2 credits, Fall)
  • MEDS 5309 Molecular Basis of Disease (2 credits, Fall)
  • MEDS 5382 Practical Microscopy and Modeling for Cell Biologists (2 credits, Spring)
  • MEDS 5369 Advanced Genetics & Molecular Biology (3 credits, Spring)
  • MEDS 5418 Stem Cell and Regenerative Biology (3 credits, Fall)
  • MEDS 6455 Introduction to Systems Biology (3 credits, Fall)
  • MEDS 6413 Introduction to Cancer Biology (2 credits, Spring)
  • MEDS 5322 Introduction to Developmental Biology (2 credit, Spring)

* The exact credits and time of offering may be subject to change. Students should consult course catalogues in the Graduate School Website under Current Students – Academics – UConn Health Course Offerings.

Typical Course Schedule
Below is a typical course schedule that most CB AoC students tend to follow. Required courses are indicated by asterisks. Recommended courses are also included, but students may omit or replace some of the recommended courses. In any case, students are required to obtain approval by the Advisory Committee before deciding on any specific course schedule.

First Year

Fall
Spring
Summer
MEDS 6448
Foundations of Biomedical Science I*
MEDS 6449
Foundations of Biomedical Science II*


MEDS 6496
Lab Rotation*
MEDS 5329
Immunobiology I (Aug-Oct)
Alternate: MEDS 5309, Molecular Basis of Disease

MEDS 5310
Responsible Conduct in Research*
 
MEDS 6497-F42
Cell Biology Journal Club*
MEDS 5382
Practical Microscopy and Modeling for Cell Biologist
Alternate: MEDS 5369-F40, Advanced Genetics & Molecular Biology

 
MEDS 6496
Lab Rotation*
MEDS 6497-F42
Cell Biology Journal Club*
 
  MEDS 6496
Lab Rotation*
 

 

Second Year

Fall
Spring
Summer
MEDS 6455
Introduction to Systems Biology

MEDS 6497-F42
Cell Biology Journal Club

MEDS 6950
Doctoral Research
MEDS 5418
Stem Cell and Regenerative Biology

MEDS 6950
Doctoral Research
 
MEDS 6497-F42
Cell Biology Journal Club*

   
MEDS 6950
Doctoral Research*

   
If not taken in Fall of 1st year:
MEDS 5309
Molecular Basis of Disease
   


Laboratory Rotations
Each Laboratory Rotation is for one semester and is scheduled under the course heading of MEDS 6496. Besides gaining hand-on experience in research, Laboratory Rotations provide students opportunities to identify laboratories for thesis research. Decision of carrying out thesis research in a particular lab is reached by mutual agreement based on multiple factors, such as the interests of the student and the laboratory, funding, and faculty member’s opinion on student’s research capacity. Sometimes, the laboratories may need time to prepare research materials or other arrangements in anticipation of the arrival of a rotation student. Thus, it is advisable that students contact laboratories in advance to arrange for a rotation. Students are also encouraged to enroll early and carry out the first rotation in the summer before their first Fall semester.

Cell Biology Journal Club
Cell Biology Journal Club provides a forum for students to critically evaluate literature, propose hypothesis, and gain experience in presentation and discussion. All students are required to register for the Cell Biology Journal Club for the tenure of their Ph.D. training, except for the one semester when the student is writing and defending thesis. For this exception from Journal Club, the Advisory Committee is required to make this request to the program director in writing indicating that the student has essentially completed all necessary experiments and is actively engaged in thesis writing.

Research Presentation
Once a year, each CB AoC student must present their research progress at a Research Progress Seminar series which is open to all students, postdoctoral fellows, research staff, and faculty members. All CB graduate students are required to attend the presentations. Substantially prior to presentation, the student should invite the Advisory Committee and Examiners so that they can plan ahead of time and attend the presentation.


Overview of General Examination

The general examination assesses a student’s qualification and potential to conduct independent research that is required for a Ph.D. degree.  The exam is administered to individual students by his/her Advisory Committee and Examiners.  The general exam is designed to assess the student’s ability to formulate a hypothesis, design experiments and interpret data.  It may also cover various aspects of basic knowledge regarding theoretical and technical aspects related to the student’s research area. The exam consists of two parts: (1) a written exam in the form of a NIH RO1-style grant proposal based on the intended Ph.D. thesis research and (2) an oral defense of the grant proposal, once the written proposal is approved by the Advisory Committee and Examiners.  Passing this exam formally admits the student to doctoral candidacy. CB AoC students must complete the general examination by August 20 of the second academic year.

Schedule for General Examination

1. Several months before of the end of the second academic year, the student should hold a meeting with the Advisory Committee and the Examiners to discuss specific aims of an R01 style grant proposal which is based on his/her proposed thesis project. The student should write a one page document on the specific aims, which should be submitted to the Advisory Committee and the Examiners at least three days before a Committee Meeting. At the meeting, committee members and examiners will evaluate the content of the Specific Aims and informally examine the student’s readiness for writing a formal proposal. If not approved, the student will be asked to revise the specific aims based on the critiques provided by the Advisory Committee. Once approved, the student will have 4 weeks to write a formal NIH R01 style grant proposal.
 
2. By four weeks after the approval of the Specific Aims page, a copy of the Grant Proposal must be submitted to each of the committee members and examiners, who will be given 2 weeks to review the proposal. The student will have the responsibility to make all the arrangements for the oral exam.

3. Oral Exam. This will be a private exam attended by the student, the Advisory Committee, the Examiners, and one member of the CB AoC Executive Committee. The role of the CB AoC Executive Committee member is to ensure that the examination procedure is consistent with CB AoC and graduate school policies. However, the AoC executive committee member does not participate in other aspects of the exam and does not vote. After all participants have arrived, the Committee chair will ask the student to leave the room for a few minutes, during which time the Advisory Committee and Examiners will evaluate the quality of the written proposal and general qualification (such as completion of required course credits) of the student, identifying any major deficiencies which may be further addressed during the exam. If the proposal and overall qualification are deemed acceptable, the student will be asked back into the room, and oral exam will proceed. If the proposal and/or general qualification is unacceptable, the student will be given a defined amount of time to revise the proposal, or take any other necessary actions such as taking an additional course. 

During the Oral Exam, the student will present his/her grant proposal. The presentation may be interrupted by questions from the Advisory Committee members and the Examiners. The questions may concern the rationale, experimental design and expected results of the proposed experiments. Questions may also concern any other aspect in the general area of the proposed project. The Oral Exam should not take longer than 2 hours. The student may not be able to finish the presentation depending on the frequency of interruption, but this should not affect the evaluation of the student’s performance. 

After the presentation and question session, the student will be asked to leave the room and the committee will engage in a closed-door discussion. In the discussion the Advisory Committee members and the Examiners will review the student’s overall qualifications, identify any major deficiencies revealed in the oral exam and determine if the student has made sufficient academic progress.  Passing the exam requires unanimous votes from all Advisory Committee members and the Examiners. 

Once the Advisory Committee and the Examiners have reached a conclusion, the student will be asked back to the room and informed of the decision. The result of the exam will be documented in the Report on the General Examination for the Doctoral Degree, which must be signed by all members of the Advisory Committee and the Examiners. The signed form must be submitted to the Graduate School, with one copy submitted to the AoC Director for records.  Additionally, please inform the director of the CB AoC the results of your examination.

Possible outcomes
Pass: Students who have seriously engaged in various activities in the first two years and have made serious efforts to prepare for the exam are expected to pass.  Passing the preliminary exam allows the student to formally be a candidate for a Ph.D. in Biomedical Science and to continue working on research that will lead to a Ph.D. degree.

Conditional Pass: If the overall performance is marginal or a major deficiency is identified such as in the quality of proposal writing or certain areas of background knowledge, the Advisory Committee and the Examiners may agree to give the student a conditional pass. The Committee Chair should inform the student both verbally and in writing the specific issues that need to be addressed to achieve a full pass status. Deadlines to accomplish these tasks should be explicitly stated. Ways of addressing major deficiencies may include but are not limited to significant revision of the proposal, taking a course, and/or re-take the oral exam if necessary. The specific requirements should be documented in writing in an explicit and unambiguous manner. The student may be given a pass if the specified tasks are accomplished before the deadline. However, failure to do so may lead to an eventual fail grade.

Failure: A failing grade can result from an unacceptable proposal or poor performance in multiple aspects of the presentation and oral exam.  A student who fails may be given a second chance to rewrite the proposal and/or another oral examination. The Committee should specify the deadline for the next proposal submission and/or oral exam. A student who fails the exam twice must be dismissed from program.


How to Write an RO1 Grant Porposal for the General Examination

The proposal should be NIH R01 grant style, including Specific Aims (1 page), Research Strategies (12 pages), and a list of References (unlimited page numbers). Completion of the administrative forms is optional.

Specific Aims:
This section should include a central hypothesis, rationales behind the hypothesis, significance and novelty of the project, and brief outlines of experimental approaches. In other words, the Specific Aims page should inform the reviewers (the advisory committee and the examiners in this case) of the overall research project. While there is no strict rule on the number of Specific Aims, a typical R01 grant usually has two or three Specific Aims.

Research Strategies:
This is main body of the grant, and should include several sections: Significance, Innovation, and Approach.

(a) Significance: This section should highlight why the proposed studies will advance scientific knowledge and/or clinical application in a major way. This section is also an appropriate place to include background information, which illustrates the current state of the knowledge and areas that need to be improved through additional research.

(b) Innovation: Explain why the proposed research may lead to paradigm shifting concepts, novel technologies, and/or innovative clinical applications, rather than incremental progresses or minor improvement of current state of knowledge.

 (c) Approach: This section may be divided into two subsections, including Preliminary Studies and Experimental Designs and Methods. Alternatively, Preliminary Data may be imbedded into the Experimental Designs and Methods sections where appropriate.

(c1) Preliminary Studies:
Preliminary Data should be organized in such a way that they help further elaborate the significance and novelty of the project, and provide the background that lead to the experiments to be described in the subsequent subsection;

(c2) Experimental Designs and Methods:
Experimental Designs and Methods should be described separately for each Specific Aim, including a short paragraph at the start of each Specific Aim outlining the rationale why the experiments to be described will address the proposed hypothesis and achieve objectives stated in Specific Aims. Following the rationale paragraph, an overall description of the experiment(s) should be presented in such a way that reviewers can quickly grasp the main idea of the work. Then more detailed descriptions should follow, including specific designs, experimental procedures, data collection, expected results, plans of data interpretation, pitfalls, and potential remedies. In addressing pitfalls, keep in mind the big picture of the study, rather than focusing on minor technical issues. One example of a potential pitfall is what if data indicate that your hypothesis is incorrect?
 
Milestones:
At the end of the Research Strategy section, include a description of anticipated time lines for the accomplishment of various experiments. A table or scheme with time indicated in years will be helpful. Although most students are expected to complete their thesis in three years from the time of passing the general examination, present the grant as a five year plan for the sake of being consistent with a typical NIH R01 style.
References: Each citation must start with the names of authors, title of article, name of journal (or name or a book and editors), year of publication, volume number, and page numbers. Other styles commonly used in major journals such as Cell, Blood, etc are also acceptable.


Candidacy and Thesis Prospectus

Upon passing the General Examination, the student becomes a candidate for the degree of Doctor of Philosophy and is expected to devote full-time to the completion of their dissertation. Within 12 months of passing the General Examination, the student must complete a Dissertation Prospectus form downloadable from the Graduate School website.  The Dissertation Prospectus must be submitted and approved by the Candidate’s Advisory Committee and then filed with the UConn Health Registrar’s Office. It is a requirement of the University of Connecticut graduate school that this be submitted to the graduate school office on the Storrs Campus at least 6 months prior to the expected degree completion date.  It is essential to inform the director of the CB AoC when this form has been filed.

Thesis
When the Advisory Committee reaches a consensus that the student has achieved sufficient research accomplishment, it will authorize the final preparation of the thesis. The thesis must be formatted in accordance to rules of the Graduate School as summarized in the Graduation Checklist. Research-related contents may be written in the manuscript format suitable for publication, but with expanded sections of Introduction and Discussion. The introduction consists of a scholarly and critical review of the current status of the field, rationale for the hypothesis, ending with one or two sentences summarizing major conclusions. Material and Methods section should be sufficiently detailed and accurate to allow replication of the work by any trained researchers or future graduate students. The Discussion section should not simply re-state the results. This section should emphasize on the relationship of the current work to the existing literature, discussing the significance of the findings, and limitations of the data, as well as future directions.  The Thesis must be approved by the Advisory Committee and the Examiners before scheduling the Closed (Private) Oral Examination of the thesis.

Closed Thesis Oral Examination (Private Defense)
At least two weeks prior to a Closed Thesis Oral Examination, the completed thesis is submitted to all members of the Advisory Committee and the Examiners. Closed Oral Examination must occur at least two weeks before the Public Defense due to the time needed to schedule the Public Defense following the closed oral examination. All members of the Advisory Committee, Examiners, and one member of the CB AoC executive committee must be present at the closed oral examination. The role of the CB AoC Executive Committee member is to ensure that the examination procedure is consistent with CB AoC and graduate school policies. However, the AoC executive committee member does not participate in other aspects of the exam and does not vote.

The closed oral exam will be conducted in the following manner:

1.   After all participants have arrived, the student will be asked to leave the room for a few minutes.  The chair of the committee will preside over the closed oral exam.  The chair cannot be the student’s major advisor and must be an Associate Professor or Professor in the CB AoC.  The Committee and the Examiners will briefly review the quality of the thesis. 

2.   If the Committee and the Examiners agree that the thesis is of sufficient qualify for presentation, the student will be invited back into the room to present the thesis. The presentation may be interrupted with questions. The chair of the committee should monitor the process so that the presentation and question session is complete in about 2 hours. To successfully pass the exam, students should demonstrate the ability to 1) present the data in a logical fashion, 2) analyze the data in critical manner, 3) take a broad view of the problem, 4) thoroughly understand technical aspects of his/her research. Following roughly 2 hours of presentation and questions/responses, the student will be asked to leave the room, and the Committee and the Examiners will evaluate the student’s performance in his/her absence.

3.  The student will be evaluated based on the quality of the oral presentation, responses to questions, and general knowledge and ability to logically analyze problems. The student passes the Private Defense only if the all of the Committee members and examiners approve the thesis and Oral Exam. If any Thesis Advisory Committee member or Examiner fails to approve the thesis and/or Closed Oral Examination, the Advisory Committee and the Examiners will decide on an appropriate course of action without the student being present.

 4.   Once a decision has been made, the student will be admitted back into the room, and informed of the decision. If the student passes the exam, a Dissertation Tentative Approval Page will be signed by all Committee Members and Examiners. If the student does not pass the Private Defense, the student will be informed of all the necessary actions that need to be taken to achieve a pass status. Such information must be documented in writing to avoid any subsequent confusion and misunderstanding. The student may be given a pass grade only if all the assigned taskes are accomplished. Once the student passes the Private Defense, then the Public Defense may be scheduled.

Public Thesis Defense/Oral Examination
The Public Defense should be scheduled to take place at least two weeks after the event is announced by the Graduate School. For this reason the student must contact the graduate school to schedule the Public defense as soon as he/she passes the Private Defense to minimize delays. The Public Thesis Defense will be chaired by the Chair of the Advisory Committee. Faculty members that are required to attend the Public Defense include:  all three members of the Advisory Committee, and at least two additional faculty members who can be either the Examiners or any other faculty member. Further, one member of the CB AoC executive committee should be present. The presentation will be of the format of a formal seminar, and is generally not interrupted during presentation although minor exceptions may be granted. After the seminar the student will answer any question from the audience. Immediately after the closing of the question/answer session, all attending faculty members will vote privately (without the student being present). If the majority of the attending faculty members including the Committee members the vote to accept (reject) the dissertation, the Advisory Committee will make the final decision pass (fail) the Oral Examination. If the decision is to pass the dissertation, all of the Advisory Committee members will sign the Report of the Final Examination, which should then be submitted to the Graduate School.  A copy should be also submitted to the CB AoC Director for records.

rev. 4/15
  
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