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Biochemistry and Cell Biology

The Biochemistry and Cell Biology (BCB) Graduate Program is a rigorous, interdisciplinary program that focuses on understanding fundamental biological, biochemical and molecular underpinnings of normal cellular and organ function, and how these mechanisms affect normal and abnormal (disease) biological function.

BCB COURSE REQUIREMENTS

Year 1

GS21 1017 Foundations in Biomedical Research (7 credits)

GS21 1051 Ethics Dimensions Biomedical Sciences(1 credit)

GS13 1024 Molecular Basis of Cell Signaling ( 3 credits)

Year 2

GS03 1023 Current Methods in Biochemistry and Cell Biology (3 credits)

Scientific Writing (1 credit)

GS12 1011 BCB Seminar Series (1 credit)

Weekly seminars*

Year 3+

Candidacy (Details can be found under Course Descriptions)

GS12 1011 BCB Seminar Series (1 credit)

Weekly seminars*

BCB Electives (two courses)

Defense


*All students are required to attend BCB Seminar Series GS12 1011 only post-candidacy students are required to present.

* All students should attend at least one department seminar per week

Course Descriptions

  • BCB Seminar Series
    Course Detail

    GS12 1011 (1 credits)
    Spring and Fall

    Venkatachalam, Kartik; Poulsen, Kyle. One-semester hour. Spring and Fall annually. Grading System: Pass/Fail. Audit permitted. Prerequisite: None.

    This class is a forum in which students, postdoctoral fellows and occasionally faculty present their on-going research to facilitate discussion, learning and scientific interactions. Areas of research that are discussed include both fundamental and translational cell biology and biochemistry, touching on topics in cancer, muscle and kidney physiology, neuroscience, protein structure/function, as well as cardiovascular and circadian physiology. All students will be expected to attend lectures and participate in discussions. Post-candidacy students will be expected to present a 45-minute seminar describing their thesis research

  • Current Methods in Biochemistry and Cell Biology
    Course Detail

    GS03 1023 (3 credits)
    Fall

    Putkey, John. Three semester hour. Fall, annually. Grading System: Letter Grade. Prerequisite: GS21 1017: Foundations of Biomedical Research or 2 semesters of undergraduate biochemistry.

    The goal of this course is to instruct students in cutting edge methodologies that relate to both structural and molecular biology. The class will consists of 43 1-hour lectures held on Monday, Wednesday, and Friday. Individual lecturers are chosen from multiple GSBS Graduate Programs based on their expertise in the relevant technologies.  The lectures will provide a sound foundation in the principles, appropriate applications, and limitations of a repertoire of techniques ranging from qRT-PCR to metabolomic profiling to basic recombinant protein expression and analysis.  The course is designed to act synergistically with techniques covered in the Core Course.

  • Design and Delivery of Advanced Research Seminar
    Course Detail

    GS04 1751 (1 credits)
    Fall

    Breton, Ghislain. One semester hour. Fall, annually. Grading System: Pass or Fail. Prerequisite: none

    This course has two major objectives. The first is to familiarize students with current research in regulatory biology with particular emphasis on molecular mechanisms of cell regulation and signaling. The second goal is to teach students how to give outstanding research seminars. Weekly 90-minute meetings involve alternate faculty and student presentations on current problems in regulatory biology. Faculty presentations introduce each topic and provide a broad and critical overview of approaches used to tackle research problems. Student presentations cover recent articles from leading journals on the same topic. Students are instructed in the preparation of slides/overheads, seminar organization and techniques of oral presentation and are given detailed feedback by faculty and fellow students following their presentations. Three to four topics are covered each year and the topics discussed vary annually. Students can, and often do, register for the course multiple times during their graduate careers.

  • Molecular Basis of Cell Signaling
    Course Detail

    GS13 1024 (4 credits)
    Spring

    Du, Guangwei.  Four semester hours. Spring, annually. Grading System: Letter Grade. Prerequisites: Background in biochemistry and cell biology; Consent of instructor.

    This course provides a detailed exploration of the molecular basis of cell signaling with emphasis on recent developments, structure-function, and quantitation.  The course will include both the regulation of second messenger systems (GPCRs, G proteins, cAMP, IP3 and lipid), ion channels, growth factor-regulated tyrosine kinases, small G proteins (ras, GEFs, Gaps), kinase/phosphatase pathways, steroid hormones/transcription, and the modeling of these systems. 

  • Scientific Writing for Grant Proposals
    Course Detail

    GS03 1111 (1 credits)
    Summer Session

    Frost, Jeffrey. One semester hour. Summer annually. Grading System: Letter Grade. Prerequisite: GSBS Core Course.

    The goal of this mini-course will be to learn how to write an effective grant proposal. There will be formal lectures on the components of an NIH grant followed by writing workshops. The course will also include a mock study section with peer review of the written proposals.

    This course fulfills the GSBS writing requirements.

     

  • Topics in Molecular Medicine
    Course Detail

    GS21 1611 (1 credits)
    All Semesters

    Milewicz, Dianna. One semester hour. Fall, Spring, and Summer, annually. Grading System: Pass or Fail. Prerequisite: MD/PhD students only; consent of instructor (Pass/Fail only)

    The seminar will use selected topics in molecular medicine as a vehicle to introduce students to basic ideas of biomedical research, to the skills involved in evaluating the research literature and presenting data, and to the interplay between the research laboratory and the problems of clinical medicine. Students will be expected to conduct literature reviews, make oral presentations of research papers, and participate in the discussions of each topic. The course is offered in the Fall, Spring, and Summer semester, and MD/PhD students are required to register for the course throughout their tenure in the Program except during the third and fourth years of Medical School when schedules for clinical rotations conflict with the weekly seminar.

CANDIDACY EXAM DESCRIPTION

Approved by the BCB Steering Committee 01/05/21; updated 1/07/21

BCB students are required to take an on-topic candidacy exam in which the research proposal is based on the student’s intended dissertation project. Significant preliminary data is not expected and should not be a reason for delaying the qualifying examination.

1. Candidacy Examination Timing
The BCB Program will follow GSBS guidelines with respect to timing of the candidacy exam. Ph.D. students who matriculated in a Fall semester must submit the candidacy exam petition to the GSBS Academic Standards Committee by August 31 of the first term of the third year. The exam must be completed by the end of the first term of the student’s third year. M.D./ Ph.D. students must petition by the end of the Fall Term of GS2 and complete their exam by the end of Spring term of GS2. The Program will honor extensions granted by GSBS. All students must take their candidacy exam within 8 weeks of the approval of their Specific Aims page by the Academic Standards Committee (ASC). The final exam proposal is due to the student’s Candidacy Exam Committee and to GSBS for Turnitin analysis three weeks prior to the exam date. Students should consult the GSBS website for form submission requirements and plan accordingly. Students are encouraged to begin making arrangements for the exam 4-5 months in advance, as described in the following sections.

2. Formation of the Candidacy Exam Committee
The Program Director will appoint a Program Examination Committee (PEC). This shall consist of approximately 10 BCB program faculty who are representative of the diverse interests of the program. Committee members are to be available for service on BCB student candidacy exams. BCB students are required to choose 4 of their 5 examination committee members from this roster (including the Chair). The 5th member must be from outside the BCB Program. A maximum of two members of the student’s Candidacy Exam Committee may also be members of the student’s Advisory Committee. One member of the student’s Exam Committee must have significantly different expertise than the topic of the proposal; this member can be the person from outside the program or one of the PEC members.

The PEC Chair serves for the academic year and must chair all BCB student exams for that academic year unless a conflict of interest or scheduling exists, in which case an Alternate Chair will serve. The committee is responsible for ensuring consistency and high standards of both the written and oral portions of the candidacy exam. Students are strongly encouraged to consult with the Program Director and/ or the PEC Chairperson while selecting committee members, prior to requesting that individual faculty serve on the exam committee in order to ensure adequate diversity and expertise. If the student and mentor feel strongly that particular critical expertise is not represented by the faculty listed on the PEC roster to permit a thorough and fair examination, the student should contact the Program Director to determine whether ad hoc PEC members should be appointed.

BCB Program Examination Committee 9/1/2021-8/31/2022

Kristin Eckel-Mahan, Chair
Askar Akimzhanov, Alternate Chair
Shane Cunha, Regular Member
Vihang Narkar, Regular Member
Catherine Denicourt, Regular Member
Danielle Wu, Regular Member
Mikhail Kolonin, Regular Member
Zheng Chen, Regular Member
Guangwei Du, Regular Member
Scott Evans, Regular Member
Xiangli Yang, Regular Member
Liuqing Yang, Regular Member 

3. Format of the Candidacy Examination
The examination consists of a written 6-page “inside” research proposal related to the student’s planned thesis project and a live oral examination by the committee. The oral examination will consist of a brief oral presentation of the proposal by the student, followed by a question/ answer session conducted by the committee. At the end of the oral exam, the committee will evaluate the student’s performance and make a determination of the outcome, which will be communicated to the student at that time.

4. Preparation of the written proposal
a. Proposal Conception. As the first step in writing the research proposal, the student must write a Specific Aims page. The topic of the research proposal will be related to the student’s anticipated thesis project. The aims must be reviewed and approved by the student’s Advisory Committee before being forwarded to the GSBS Academic Standards Committee for final approval. Ideally this should be presented and discussed in an Advisory Committee meeting. The student then prepares a full research proposal based on the approved aims to be defended in the Oral Examination.

b. Writing the Proposal. A BCB Candidacy Exam Proposal should describe a novel hypothesis supported by rigorous prior research, either from the literature or the student’s own preliminary data. The student should propose to test this novel hypothesis in specific aims developed by the student using suitable experimental approaches. Preliminary data is not necessary for the development of the specific aims or any aspect of the proposal. The student is not required to propose Aims that he/she plans to actually undertake, but they may do so. The proposal will follow the format of an NIH Individual Predoctoral Fellowship application.

The full proposal is due to the Candidacy Exam Committee via email at least three weeks prior to the oral examination date. The committee will review the proposal and determine whether it is suitable for an oral examination. If the proposal is not of sufficient depth or quality, the committee may ask the student to rewrite a portion or the entirety (rarely) of the proposal.

Consultation and academic conduct. All portions of the proposal must be written independently by the student. Although the specific aims of the student’s proposal may be similar to aims developed in consultation with the advisor for other purposes, the text must be composed entirely of the student's writing and not that of any other person. The student’s thesis advisor will be asked to verify that the proposal is an original contribution that is distinct from the mentor’s existing written proposals. The student may seek feedback on the written exam proposal from others, including fellow students, postdocs, at-large faculty, and the thesis advisor(s). Members of the current BCB Program Examining Committee, including those on the student’s committee, are not permitted to provide feedback or edits on the written proposal, with the exception of the student’s own thesis advisor(s).

It is permissible for a student to submit for the candidacy examination some or all of an individual fellowship proposal s/he previously submitted in their own name for funding consideration to NIH or another agency. Utilization of such proposals, or sections thereof, is permissible even if the mentor had provided input. Students are strongly encouraged to review such previous fellowship proposals to determine suitability for an examination by a diverse scientific group.

c. Proposal format. For details on formatting requirements, please consult the PHS SF424(R&R) Fellowship Instructions on the NIH website. Generally, proposals are single-spaced with minimum 0.5” margins and 11 pt font; several fonts are allowable. Arial is suggested.

-Title Page: Title, student name, faculty advisor’s name, date of exam

-Abstract (350 words max): Provide an overview of the project, hypothesis, significance and approach

-Specific Aims (1 page): State concisely and realistically what the research is intended to accomplish and/or what hypothesis is to be tested.

- Research Strategy (6 pages)
 Significance: Briefly sketch the background to the proposal, critically evaluate existing knowledge, and specifically identify gaps which the research is intended to fill. State concisely the importance of the research by relating the Specific Aims to long-term objectives. (suggested 1-2 pages of the 6 allowed for Research Strategy).

Approach: Briefly summarize the experimental design and the procedures to be used to accomplish the specific aims of this research. Include a description of the types of data to be obtained and how they will be analyzed to accomplish the specific aims, as well as (optional) preliminary results that bear directly on the rationale and Specific Aims of the proposal. Alternatively, the student may cite published work by the student or others.

References Cited
 
(not counted toward page limit)

5. Preparation for the oral examination
a. Oral examination format. The oral examination is comprised of an opening presentation of the research proposal by the student (20-25 min). Visual aids are permitted, and the presentation will not be interrupted. The committee will then conduct an oral examination (up to 3 hours) covering the proposal, directly related areas, general and background information, breadth questions, and other questions as the committee deems appropriate. No questions will be provided to the student in advance of the exam.

-Assessing Depth. During the oral exam, the committee will examine the student’s understanding of the intellectual basis for the research proposal, pertinent background, details of the technical approaches and experimental strategy, interpretation of results, potential pitfalls and alternative approaches. The Examination Committee will carefully assess the student’s responses to determine whether the student has adequate depth of understanding to carry forward as a post-candidacy student and, in part, as confirmation that the student made original and substantial contributions to the overall conception of the proposal.

-Assessing Breadth. After receiving the written portion of the exam but before the oral exam, the Examination Committee will confer in order to devise a cohesive and fair plan to evaluate the breadth of the student’s knowledge. Breadth questions and topics will be related to the proposal but will also effectively examine the student’s breadth of knowledge. The Examination Committee will choose the most effective questions (usually ~2-3 per committee member) to be used during the examination. These questions are not provided to the student in advance. The Examination Committee Chair will be responsible for ensuring that breadth is assessed in a fair manner among all student exams that year.

b. Preparation for the oral examination. Students are encouraged to review the relevant literature and be able to explain and defend their proposed studies to an intelligent, not necessarily expert, group of scientists. Students are also encouraged to review content from coursework, as the committee will be informed about the prior academic work of the student. The presentation slides and presentation should be rehearsed for timing and clarity. Practice fielding live questions is strongly encouraged. A successful Ph.D. candidate will know the difference between “It is not known” and “I do not know” and will be ready to discuss what is and is not known in the relevant literature or the student’s own work, as well as to propose new or alternative experiments in real time to address gaps in scientific knowledge.

Consultation and academic conduct. The student may seek feedback on the visual aids and presentation for the oral examination from others, including fellow students, postdocs and at-large faculty. The student is encouraged to schedule mock (also termed “practice”) exams. The thesis mentor and faculty currently serving on the Program Examining Committee are not permitted to attend or participate in mock/practice exams or Q/A sessions that are for the specific purpose of practicing for the candidacy examination. Routine Q/A during scientific discussions or lab meetings are permitted, whether or not the discussions pertain to aims or experiments that are also included in the candidacy exam proposal. Students may always ask questions of the mentor, or any other faculty, regarding background, techniques, experimental design or interpretation of their data, as part of normal scientific discourse and training. Students are not expected to change the nature or content of their scientific interactions, rather asked to exclude their mentor and PEC faculty from mock exams.

6. Performance Assessment
After the exam, the committee will confer privately without the student present. Performance on the written proposal, depth and breadth components is graded separately as unconditional pass, conditional pass, re-examination, or fail. All parts must be passed, but each can be remediated separately. The exam outcome and mechanism of remediation, if necessary, will be determined by the Examination Committee and conveyed to the student, the Program Director and GSBS in writing by the Examination Committee Chair. The Examination Committee will also make a recommendation to the Academic Standards Committee about whether the student should be permitted to bypass the M.S. degree. The GSBS rubric will also be submitted by the Chair to GSBS. In outcomes of re-examination or fail, the student is encouraged to meet with the Exam Chair and committee members to discuss suggestions for improvement. In an outcome of fail, the student’s advisor, Advisory Committee and GSBS Dean for Academic Affairs will determine whether the student should be granted the opportunity to complete a terminal M.S. degree.