Biochemistry and Molecular Biophysics Graduate Group

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Handbook

OVERVIEW OF PROGRAM

The Biochemistry and Molecular Biophysics (BMB) graduate program is designed to prepare students for careers as independent investigators, educators and communicators in the area of modern biochemistry and molecular biophysics, and more broadly in biomedical science. The program has been designed to provide a superior graduate level education with a curriculum of depth and flexiblity that builds on the strengths of the student and that equips the student for dissertation research. This training is provided by the world class faculty members of the BMB graduate group. The faculty in the BMB Graduate Group are unified by a common interest in understanding biological phenomena at the quantitative, mechanistic or molecular level, drawing on modern biochemical, biophysical, chemical and physical methods.

A strength of the program resides in its unusually broad combination of faculty interests and disciplines. Faculty members are drawn from many departments within the Perelman School of Medicine, the Schools of Dental and Veterinary Medicine, as well as departments in the School of Arts and Science, the School of Engineering, and affiliated research institutes such as the Wistar Institute and the Fox Chase Cancer Center.

Research Areas include:

• Regulation of metabolism.
• Elucidation signaling mechanisms and pathways that result in physiological events, such as sensory transduction, cell division, death and control of the cell cycle.
• Determination of protein, RNA, DNA and virus structures.
• Protein and enzyme folding, function design and engineering.
• Regulation, transport and processing of RNA.
• Structure and function of membranes, including ion channels, gates, pumps and pores.
• Enzyme structure and function
• The mechanism of gene regulation, including transcription, replication, and recombination events, and generally the mechanism of protein recognition of specific sites on DNA.
• The molecular basis of immunology.
• Study of protein assemblies and the basis of specific protein-protein interactions.
• Molecular basis of energy transduction, including contractility, bioenergetics an photosynthesis.
• Development of novel high-resolution magnetic resonance and optical imaging methods.

Research Methods include:

Faculty in the Biochemistry and Molecular Biophysics Graduate Group typically use a combination of biochemical, biophysical, chemical and physical methods to unravel these complex biological events. These methods include:

• High resolution spectroscopies, including optical, infrared, fluorescence, phosphorescence, pump-probe spectroscopies
• X-ray diffraction
• Microscopy, including electron, optical and fluorescence microscopy
• Nuclear magnetic and electron paramagnetic spectroscopy.
• Optical and magnetic imaging.
• Theoretical methods and computer simulations.
• Quantitative kinetic measurements using radiolabels, hydrogen exchange, stop flow and other methods.
• Electrokinetic methods such as electrophoresis, conductance measurements and patch clamping
• Peptide, nucleic acid and organic synthesis methods.
• Thermodynamic analysis using calorimetry and temperature and chemical denaturation.
• Molecular biology techniques such as cloning and high level expression of proteins

Since Biochemistry and Molecular Biophysics are rapidly evolving areas and the graduate group continues to accept new faculty, students should consult the BMB website faculty pages for current information on research areas.

 

ADMISSION

Admission for Ph.D. study is offered to students with good undergraduate training in biochemistry, physics, organic chemistry, physical chemistry, biology, and mathematics. Students lacking preparation in a particular field, but otherwise qualified, may be admitted and given the opportunity to strengthen their backgrounds by taking the appropriate courses. The Graduate Record Examination (GRE) General Test is required; GRE subject tests in biology, biochemistry, chemistry, physics or mathematics are recommended but not required. The Admissions Committee screens completed applications and decisions on admissions are based on undergraduate record, including research experience, GRE scores, letters of recommendation, and personal interviews. TOEFL scores are required for foreign students whose native language is not English. The BMB program especially encourages applications from minority students. Admission decisions are usually completed by late March. On-line applications can be accessed here.

Students accepted for admission into the Ph.D. program receive tuition, and health care and insurance reimbursement, plus a twelve-month competitive stipend. Awards are renewed annually for students in good academic standing. Support for graduate students comes from a variety of sources, including Biomedical Graduate Studies, training grants, faculty research grants, and from private foundations such as the Howard Hughes Medical Institute. Applicants are urged to apply for scholarships from the National Science Foundation and other funding programs for graduate students. A limited number of fellowships are available for outstanding foreign students.


PROGRAM REQUIREMENTS

Course Requirements

Required Courses
BMB 699 (Laboratory Rotation). Three semesters of Laboratory Rotations are required and are to be completed during the first year. If needed, a fourth rotation may be taken in the second half of the summer after the first year. The first rotation may be carried out in the summer before the first year if a student chooses to matriculate early.
• BIOM 600 (Cell Biology) – required (fall, first year)
• BMB 508 (Macromolecular Biophysics: Principles and Methods) – required (fall, first year)
• BMB 509 (Structural and Mechanistic Biochemistry) - required (spring, first year)
• BIOM 611 (Biological Data Analysis) - required (spring, first year)
• BMB 705 (Candidacy Exam Prep Course) – required (spring, second year)

In addition to learning through formal lecture courses, the ability to communicate scientifically through writing, oral presentations, and posters is an essential part of a scientific training and training in these areas is a required part of the BMB program.

Attendance at the weekly Biochemistry & Biophysics Department seminar and at the weekly Friday Research Discussions is also required of all students. Active participation in research seminars is an important part of the Ph.D. training, and will help students when it comes to appointments to training grants, nominations for fellowships and awards, and obtaining strong recommendation letters from faculty for future career development. Active participation in less formal scientific forums and journal clubs specific to a student's research area, e.g. RNA club and Crystal club, is strongly encouraged for the same reasons.

Elective Courses
• Four additional elective credits are required that may include formal lecture courses, tutorial or discussion type courses. Courses offered by the BMB graduate group include:

One-semester courses(1 credit each)
BMB 518 Protein Conformation Diseases
BMB 554 Macromolecular Crystallography: Methods and Applications
BMB 560 Methods of Scientific Inquiry in Biological Systems
BMB 567 Bioinorganic Chemistry
BMB 581 Techniques of Magnetic Resonance Imaging
BMB 585 Wistar Institute Cancer Biology Course: Cell Cycle Checkpoints and Cancer
BMB 590 Biological Physics
BMB 632 Probing Structure and Function of Complex RNA-Protein Machines
BMB 650 Current Biochemical Topics – Raiziss Rounds
BMB 700 Selected Topics in Chemistry

Mini-courses(1/2 semester; 1/2 credit each)
BMB 601 Fundamentals of Magnetic Resonance
BMB 602 Imaging Biomarkers
BMB 618 Applications of High Resolution NMR Spectroscopy to Problems in Structural Biology
BMB 619 Protein Folding
BMB 622 Physical Principles of Mechano-Enzymes
BMB 624 Ion Channels and Pumps
BMB 626 Mass Spectrometry and Proteomics
BMB 627 Computing Programming for Biophysicists and Biochemists
BMB 628 Principles of Scientific Instrumentation
BMB 629 Quantitative Problems in Biochemistry and Biophysics

The BMB graduate group curriculum is periodically changed to reflect scientific advances and new faculty members. Students should consult the BMB website course pages for current BMB course offerings


Lab Rotations, Independent Studies, and Tutorials

BMB 598 Tutorial (0.5 to 2 cu) (cannot be done in the same lab as BMB 699 or BMB 799 or thesis lab)
BMB 699 Lab Rotation (1 credit)
BMB 799 Independent Study (YRS 1 – 2) (may be taken for 1/2 to 4 credits)
BMB 899 Pre-Dissertation Lab Rotation (YR 2) (may be taken for 1/2 to 4 credits)

It is expected that in the first year, courses of a more general and foundational nature will be taken in order to give students a well-rounded and diverse background in the biochemical sciences. Subsequent lecture or seminar courses are designed to increase the student’s background in more specialized areas. The three laboratory rotations ensure that first year students quickly become familiar with the variety of research opportunities available within the graduate program and so can choose a suitable thesis advisor. Independent studies taken during and after the lab rotation period provide the student with an opportunity to deepen their research experience and laboratory skills in order to formulate and carry out novel, creative, yet rigorous dissertation research.  Full-time thesis research begins upon successfully passing the candidacy exam.

Other Courses

Many of the courses available to BMB students are taught in collaboration with other graduate programs or departments. Topics covered by these courses include molecular genetics of prokaryotes and eukaryotes, the structure and function of proteins and nucleic acids, molecular cell biology, biophysics of macromolecules, regulation of cell growth, membrane structure and function, virology, gene therapy, x-ray diffraction, and spectroscopy. Students may also take other graduate group courses at the 500 level and above, with approval of the BMB graduate group. A listing of all courses offered at the University is described in the University’s Course Register, which is online athttp://www.upenn.edu/registrar


Combined Degree Programs

Students in theMD/PhD programfollow the same guidelines and curriculum for the Ph.D. portion of their coursework, except for the differences listed here:

Year 1 Medical School (spring) - One graduate course
Year 1 Medical School (summer) - One laboratory rotation
Year 2 Medical School (fall) - One graduate course or laboratory rotation
Year 3 (fall & spring) - Full time graduate program and Candidacy Exam
Years 4 - 6 - Full time dissertation

Eleven to fourteen credits may be transferred from the School of Medicine to complete the required elective credits.

Students in theVMD/PhD programgenerally follow the same guidelines as those in the MD/PhD program, although the full time graduate program for these students usually begins in the spring of Year 3.

For combined degree students the third lab rotation is optional.

 

ACADEMIC ADVISING

Course advising is the responsibility of the Advising Committee. In view of the diversity of the students in the program, the Committee reviews the background of each student, and in consultation with the student, decides on his or her curriculum. The goal is to provide a flexible yet structured program so students of diverse backgrounds will receive the appropriate training for their research interests.

Each incoming student meets individually with the Advising Committee during orientation week to select his or her fall courses, and at the end of December to select spring courses. A group meeting is held in early May to discuss summer lab rotations. Rising second year students meet individually with the Advising Committee mid-July to discuss fall courses and at the end of December to select spring courses, although some students may not need this second meeting if they have fulfilled all course requirements.

Students are assigned a student mentor as soon as they are accepted into the program. The role of the mentor is to provide informal advice on more general aspects of graduate education, such as adjustment to graduate life, guidance in career paths, and to advise a student in choosing a Thesis Advisor.

In addition to the regular advising provided by the Advising Committee, the BMB Graduate Group and its umbrella organization, Biomedical Graduate Studies (BGS) provides support and training for other practical issues of being a Ph.D student. These include topics such as scientific writing, applying for fellowships, how to get the most out of your thesis committee.

Career Services provides a wealth of career information on its website. It works with all Penn students to help them define career goals through individual counseling and workshops on a wide range of topics from resume writing to interview to networking. It also sponsors on-campus recruiting sessions and maintains lists of job opportunities.

 

CANDIDACY EXAM

All graduate students affiliated with BGS (Biomedical Graduate Studies) are required to pass a Candidacy Examination in the spring of the second year. In BMB, this examination consists of both a written research proposal (in the style of an NIH fellowship application) and an oral defense of the proposal. Only students in good academic standing are eligible to take the Candidacy Examination. Click here for more information.

 

DISSERTATION STATUS

A. Composition of Thesis Committees

Working Thesis Committee

After passing the Candidacy Exam, the student must form a Working Thesis Committee and fill out the "Working Thesis CommitteeApproval Form." The Working Thesis Committee will be comprised of three faculty members; at least two must be members of the BMB Graduate Group. The Chair of the Working Thesis Committee must be a member of the BMB Graduate Group. The thesis advisor is not a member of the committee, but is expected to attend committee meetings.

Final Thesis Committee

The Final Thesis Committee includes all members of the Working Thesis Committee plus one external examiner. The External Examiner is someone from outside the BMB Graduate Group who is brought in as an additional examiner for the thesis defense. The external examiner may be a member of another graduate group in BGS, a standing faculty member at U. Penn, or from outside the university. The BMB graduate group chair must approve the choice of external examiner in writing. If it is not possible for the External Examiner to attend the oral defense, he or she will be asked to provide a written report to the Chair of the student's thesis committee prior to the defense.

The Working and Final Thesis Committees should be constituted to include breadth as well as expertise in the particular research area of thesis work. The student and his or her advisor shall jointly select the members of the thesis committees. The student should submit in writing a list of potential committee members, indicating which faculty will serve as Committee Chair, to his or her Thesis Advisor and the Graduate Group Chair. The Graduate Group Chair will respond in writing to approve the composition of the Committee, or make recommendations for other candidates. The Graduate Group Chair will adjudicate any disagreement on the composition of the thesis committee. The student must register the composition of his or her thesis committees with the Graduate Group Office after approval by the Graduate Group Chair. Once the student obtains approval, they must fill out the "Final Thesis Committee Approval Form."

B. Evaluation of Student’s Progress

The Working Thesis Committee meets to monitor the students' progress every 6 months. A one-page summary of progress and plans should be prepared by the student and submitted to the committee at least 2 days prior to the meeting. The Thesis Committee is permitted and indeed encouraged to interview the student in the absence of the Thesis Advisor andvice versa. A written summary will be prepared after each meeting by the Thesis Committee Chair and will be placed in the student’s academic file.

If the Committee and/or the Thesis Advisor are not satisfied with the student's productivity, a written report will be prepared by the Committee outlining a proposed course of action. A copy of the report will be forwarded to the Graduate Group Chair, the student and the Thesis Advisor. The student will have the opportunity to reply to the written report of the Committee. Within 6 months, an additional meeting of the Thesis Committee will take place to determine the progress. In the event that the student does not make sufficient progress, he or she will be placed on academic probation. If progress is not apparent by the next Committee meeting, the student will be asked to petition for a terminal Master’s degree.

C. Preparation of Dissertation

The Thesis Committee will give written approval for the student to begin to schedule the defense, but this does not automatically mean that experimental work is completed. The student should be prepared to continue experiments while writing and to rewrite or do additional experiments after the thesis defense if deemed necessary by the committee. If the student has not already done so, at this point he or she should, in conjunction with the Thesis Advisor, select the external examiner to form the Final Thesis Committee. A draft of the dissertation must be submitted at least two weeks in advance of the defense to minimize the possibility of unexpected problems. The Graduate School of Arts and Sciences (GAS) requires a dissertation to represent a definite contribution to scientific knowledge and to show that a student possesses "power of independent research." The Graduate Group requires that the dissertation contain original work that answers a well formulated scientific question or questions and that the dissertation display a logical progression of scientific thought. It is expected, although not required, that this caliber of work will result in one or more peer reviewed scientific publications with the student as a first or lead author, either already published or under review by the time of the defense. Note that publication of a paper with the student as an author does not automatically indicate sufficient quality and quantity of work to constitute a defensible thesis.

D. Thesis Defense

The thesis defense will take the form of a public lecture. The private portion of the defense will be conducted solely by members of the Thesis Committee and the Graduate Group Chair, and in the absence of the Thesis Advisor. The decision on approval of the thesis will be made solely by a consensus of the Thesis Committee in the absence of the student and the Thesis Advisor.

If a Thesis Committee member cannot attend the Defense, the student must meet with the Chair of the Graduate Group to discuss the circumstances and decide on a course of action. One possible outcome is that the missing Committee member must review the student's written dissertation and submit a critique to the chair of the Committee before the thesis defense, so that those comments and any questions can be included during the private portion of the defense and addressed in any revisions that may be made to the dissertation.

Students who are defending their theses must inform the Graduate Group Office at least two weeks in advance of the defense date, and supply the title of the thesis and place and time of the defense, as well as an abstract and a figure for the monitors announcing the defense. The Graduate Group Office will announce the thesis defense to the University community. The Graduate Group Office is responsible for completing the forms indicating that the thesis has been successfully defended. Before a student makes the appointment to deposit the thesis, he or she must provide the Graduate Group Office with a copy of the abstract page, a signed copy of the title page, and postdoctoral appointment information, if available.

Students should consult the"Graduation Checklist"as soon the Thesis Committee formally grants permission to write.



OTHER PROGRAM INFORMATION

Academic Standards

The University standard for satisfactory academic progress is a 3.0 grade point average (B). The minimum standard for final course grades in the BMB Graduate Group is a "B". BMB student who do not achieve the minimum grade for courses will be referred to the Biomedical Graduate Studies Academic Standards Committee. The Academic Standards Committee will, in concert with the BMB Academic Review Committee's recommendations, impose sanctions such as academic probation. In addition, the Academic Review Committee may ask a student to retake a course, continue course work towards the terminal Master's Degree, or withdraw from the program. The Academic Review Committee will review each case on an individual basis.

Ethics Training

The training program in Responsible Conduct of Research (RCR) has three major educational components: web-based training, program literature, and small group discussion workshops. Participation in all phases of the training program is mandatory for all graduate students in the Biomedical Graduate Studies programs. The training program begins with a brief faculty presentation to incoming students at the BGS new student orientation, which provides an overview of responsible conduct of research and appropriate behavior in the classroom and lab. New students are also given a copy of the Cold Spring Harbor publication,At the Bench(Kathy Barker, author) which covers some aspects of RCR. See the BGS website for further information:http://www.med.upenn.edu/bgs/rcr.shtml

Individual Development Plan (IDP)

Biomedical Graduate Studies (BGS) has implemented a required an annual Individual Development Plan (IDP) for all predoctoral students, the goals of which are to make sure students and mentors are communicating openly and that students are working proactively toward developing the skills they will need to succeed. All BMB students will be meeting with either the Advising Committee (first and second year students) or their mentors (dissertation students) once a year to discuss their achievements in the past year and their plans for the following year. Guidelines for these meetings for each group of students can be found here.

Transfer of Credits

Students who enter the program having taken similar courses at the graduate level at other institutions with a B grade or better, may petition the Graduate Group for transfer of credits. The decision to approve transfer of credits will be made in writing by the Graduate Group Chair. Up to eight courses may be transferred. Students who have taken graduate courses at Penn through the College of General Studies (CGS) may apply to transfer up to four course units toward the Ph.D. degree. Combined degree students may transfer as many as 14 course units from another Penn professional or graduate program, but are required to take 8 course units of Ph.D. lecture courses and seminars. It is recommended that incoming students review any courses that may be transferable at their meetings with the Advising Committee in September.

Transfer from Other Programs

University of Pennsylvania students who are currently enrolled in another graduate group within BGS may be considered for transferring into the BMB Graduate Group. Students should express their interest in joining the BMB Graduate Group by writing a letter of intent to the Graduate Group Chair. The student will then meet with the Chair to review his or her academic record and establish a plan for meeting the BMB requirements. Students who wish to transfer from graduate groups outside of BGS need to follow the same procedures as regular applicants to the program.

Terminal Master's Degree

The BMB Graduate Group does not offer study towards a Master's degree. However, the Graduate Group may award a terminal Master's degree to students who choose not to continue in the Ph.D. program. In certain instances, the Graduate Group Chair may recommend that students who have not performed satisfactorily in course work, the Candidacy Examination, or dissertation research leave the program with a terminal Master's degree. The University requires a minimum of 8 course units for the terminal Master's degree. A final paper may also be required, as determined by the Graduate Group Chair and Academic Review Committee.

Leave of Absence

The University allows graduate students to take a leave of absence with the permission of the Graduate Group Chair and the graduate dean. Students must write to the graduate group requesting the leave; if the chair approves, the request will be forwarded to the graduate dean (i.e., the BGS Director) for approval. The main types of leave are medical, family, and paid time off for the birth or adoption of a child. Under medical and unpaid family leaves, stipends are suspended during the leave period and are guaranteed upon return from leave under the conditions of the original award guarantee, i.e., as long as the student remains in good academic standing. Note that students who have passed the candidacy exam may need to arrange fellowship support from a mentor in order to return; there is no guarantee that the original mentor will be able to provide financial support when the student returns from leave. Students receiving NIH NRSA support in the form of a training grant appointment or individual fellowship must also obtain permission for a leave from NIH.

Students who wish to take a medical leave are expected to arrange for a letter from the treating professional(s) justifying the leave. The letter should be sent to the BGS Director. Students on medical leave are expected to seek and follow the advice of the graduate group chair or his/her designate to remediate any work and to devise a course of study for re-enrollment. Such students are also expected to make appropriate financial arrangements to continue any necessary treatment during the leave (e.g., payment for the Student Health Insurance plan), to continue treatment, and to arrange for an appropriate support system. In order to return from medical leave, students must arrange for treating professional(s) to provide documentation of treatment and progress. Students who take a leave for psychological reasons are expected to arrange evaluation with Counseling and Psychological Services (CAPS) four weeks prior to the sought return date.

BGS abides by the University’s policies for Family Leave and Time Off for Childbirth or Adoption. The University policies can be found here.