The Department of Physiology & Biophysics at the Boston University School of Medicine offers programs leading to the MA or PhD degrees. Each program stresses laboratory training and original research performed under the direction of a faculty member, as well as satisfactory performance in graduate coursework.

In the first and second years of both the MA and PhD programs, a core curriculum of biophysics, physiology, and biochemistry is supplemented with courses in cell and molecular biology, physics, or chemistry. The course program emphasizes flexibility and individual choice. In the first year, students do research rotations in the laboratories of three or four faculty to gain firsthand knowledge of a variety of research areas.

At end of the first year, students select a degree advisor and begin laboratory research towards the PhD degree. In the second year students continue to take courses and PhD students must pass a qualifying exam. Throughout their training, students also participate in a weekly department seminar series and report their research progress annually.

Graduate Programs in Physiology and in Biophysics (MA/PhD)

I. Purpose and Background

The Department of Physiology & Biophysics, under the aegis of Dr. David Atkinson as chair, brings together 21 active faculty members to provide excellence in research and graduate education. Research interests in the department span the modern areas of cellular physiology and molecular biophysics, with strong concentrations in structural biology, vision research, muscle physiology, and the biology and physical chemistry of lipids. The faculty is nationally and internationally recognized as leaders in their chosen areas of research. The department provides flexible graduate programs with pathways either leading towards a degree in physiology or in biophysics. The department offers these two programs in a strong, collegial environment to encompass and promote the diverse overlapping research of all members of the department.

The goal of a combined program in Physiology & Biophysics is to produce graduate students who understand the thermodynamic, chemical, electrical, and structural aspects of biological systems at the atomic level and in the context of the cell and organism. This goal is particularly timely as it is in tune with the National Institutes of Health initiatives that encourage training across scientific and medical disciplines. The training will provide graduates the advantage of learning Physiology & Biophysics in the context of the regulation of homeostasis and pathogenicity of the cell, and of the organism as a whole. Graduates will be able to communicate and collaborate effectively with a broad range of disciplines ranging from medical personnel to chemists, engineers, and physicists.

A set of required core courses will be taken by the students in the first year that will lead to a level of understanding of the two disciplines necessary for a degree in Physiology & Biophysics. After completing the core course requirements, students have flexibility to choose the appropriate additional coursework for their interests, within the guidelines set out below. The courses for first year students are chosen with the guidance of members of the duly constituted Student Admissions & Affairs Committee (SAAC), and in the second year with input from their MA or PhD advisor. Students who successfully complete the program are awarded either an MA or a PhD in Physiology & Biophysics.

II. Administration of the Programs in Physiology & Biophysics

The Chair of the Department of Physiology & Biophysics is the director of the graduate programs and has the ultimate responsibility for administering the graduate programs in Physiology & Biophysics. A Program Steering Committee oversees the graduate programs and advises the Chair of the Student Admissions & Affairs Committee (SAAC) on specific needs of the programs. Steering Committee members select faculty members to serve on the SAAC and oversee the appointment of committees that deal with developing new courses along with the review and updating of existing courses. The Steering Committee and the SAAC Chair work jointly to supervise the appointment of faculty to run the departmental seminar series and plan the departmental retreat. Student Seminar Days are organized by faculty members who are running the department seminar series in a given year.

The Student Admissions and Affairs Committee (SAAC)

The SAAC oversees the day-to-day operations of the graduate programs, including: student recruitment, admissions, orientation, rotations, assignment of dissertation advisors and administering the qualifying examinations. The SAAC is comprised of 5–7 faculty members that adequately represent the diverse research interests within the department. The SAAC serves many roles in the department. Foremost is the recruitment, evaluation, and acceptance of students into the programs. The SAAC uses its experience and discretion to admit qualified students into the programs based on the criteria outlined in the next section. Prospective students are interviewed on campus or by telephone. The SAAC also handles the orientation of new students into the programs. The SAAC is charged with setting up graduate student research rotations, scheduling the Lab Fair (described below), and with administering the qualifying examination. The SAAC is also available to help with student problems and to mediate issues between students and advisors.

III. Admission into the Programs in Physiology & Biophysics

Student recruitment

Recruitment directly into the programs in Physiology & Biophysics is the preferred route of entry for master’s or PhD students. There is no strict formula for acceptance to the programs and many factors go into the Admissions Committee’s decisions. The programs seek students from a wide range of backgrounds including physics, chemistry, biochemistry, biology, and medical sciences. For acceptance into the program, students should have outstanding grades in a rigorous curriculum and applicants should have completed organic chemistry, physics, and physical chemistry courses. The GRE general test is required and the subject test is recommended. Foreign students are required to take the TOEFL. We are especially interested in candidates with research experience. Finally, the letters from the applicant’s references are extremely important, as is the applicant’s personal statement. Underrepresented minorities are encouraged to apply.

Similar paths for PhD and MD/PhD students

Requirements for PhD and MD/PhD students are similar. Students in the PhD program take their qualifying examination in their second year. MD/PhD students enter after completing the second year Medical Curriculum and are therefore treated as post-master’s students with a lower course and credit requirement (32 versus 64 total credits), and take their qualifying exam at the end of their first year in the program. Other students entering into the programs with a master’s degree from within the U.S. are treated similarly and take their qualifying examination at the end of the first year. In both cases, post-master’s students are able to choose a suitable set of courses tailored to their backgrounds and research interests, with input from the SAAC during the first year and from their advisor in following years. Transfer students are handled on a case-by-case basis, but may be able to take the qualifying examination at the end of their first year.

The MA programs

Master’s programs in Physiology & Biophysics are offered. In some cases, a qualified MA student may proceed into the PhD program. This decision will be handled by the SAAC on a case-by-case basis. An MA requires 32 credit hours (paid for by the student) and requires either a literature-based thesis or a short laboratory-based thesis with two readers from within the department.

IV. The Path of a Graduate Student

Special Topics Seminar course (GMS BY 871, 872: 8 credits spread over 4 semesters)

In the first and second years, all students take the Special Topics Seminar course aimed at developing the student’s ability to read the scientific literature and present the merits and/or deficits of a current research paper in front of other students and a proctoring faculty member. The students use a blackboard and computer projector during their presentations. This component of the course meets for 1 hour each week, as specified by the faculty member proctoring the class. Typically, all students present at least once each semester, and possibly more often, based on the number of enrolled students. An important complement to the student presentations is attendance at the weekly Physiology & Biophysics Seminar Series, where the students are exposed to cutting-edge research by outstanding speakers. Post-bachelor’s students take 3 semesters (6 credits), while post-master’s, MD/PhD, MA, Cell & Molecular Biology (CMB), and Neuroscience students who enter into laboratories within the department take 2 semesters (for a total of 4 credits). The faculty member who teaches this course is rotated after each semester to allow a fresh viewpoint and area of expertise to be covered. The Chair of the SAAC, with input from the Program Steering Committee, selects 6–8 faculty members who are interested in teaching this course on a rotating basis.

Laboratory rotations

The rotation program seeks to broaden the scientific and laboratory experience of new graduate students, while also providing the opportunity to evaluate possible PhD advisors. The guidelines for this process are presented in a natural sequence or timeline for the first year in graduate school:

1. Students are assigned a temporary desk within an appropriate laboratory that may be used as a home base during their initial 6–8 weeks in the program. Laboratories are selected carefully by the SAAC from a list of faculty who have volunteered to act as hosts. This list is updated yearly.
2. To facilitate interactions between faculty and new students, a Laboratory Fair is held within the first 6–8 weeks of the fall semester. The fair starts in September and groups of faculty (2–4) meet with the entire class of students for 1 to 2 hours. Scheduling is coordinated by the SAAC and the entire fair takes place over a period of 4–6 weeks, with 1–2 meetings per week. September and October are an intensive time for the students, as they will be attending classes and the fair simultaneously. Thus, there is no formal rotation during the first half of the fall semester.
3. Students participate in a Departmental Retreat, held at the end of September or beginning of October, in which faculty, students and post-docs from individual laboratories give oral presentations and present posters that highlight the projects in their laboratories.
4. Generally, students participate in three rotations (8 weeks each), with the possibility of a fourth if they are undecided about the choice of a thesis advisor after the first three rotations are completed. The SAAC strongly encourages new students to choose at least one rotation in an area that is distinct from their major area of research interest. For example, a student who chooses two rotations in structural biology laboratories (such as X-ray crystallography, EM, or NMR) is encouraged to choose another rotation from an entirely different area within the department. If this does not happen, members of the SAAC meet with the student and try to work out a suitable rotation that fulfills this requirement. Where possible, the SAAC schedules rotations such that only one student is rotating in a laboratory in a given rotation slot.

Upon completion of the Laboratory Fair, students are asked to submit three names (rank ordered) for their first fall rotation to the SAAC, which then sets up a schedule that attempts to honor the first choice of most students. Near the end of the fall semester, the students provide either two or three names for their spring rotation(s). Students choose a PhD advisor by early June, at the end of the first year (unless a fourth rotation is required). The SAAC oversees this process.

A written thesis proposal

Success in science requires that students be able to express their thoughts both verbally and in written form. The necessary verbal skills are developed through participation in the Special Topics seminar course and by giving presentations in yearly research seminars at the Student Seminar Day(s), laboratory group meetings, pre-thesis meetings, and the thesis defense seminar. Written skills are developed in required coursework and in the writing of papers and the thesis. However, the latter may occur rather late in a student’s research project when time is at a premium. Thus, students are required to prepare an 8–10 page research proposal on their thesis project using the NIH National Research Service Award (NRSA) or American Heart Association Research Training Grants and Fellowship format and forms, as appropriate. This exercise should allow the advisor and student to clarify the proposed research and provides the student with a forum to learn basic scientific and grant writing skills, with input from the advisor. This proposal should be completed during the summer and/or early fall, after passing the qualifying examination, and is intended to help prepare the student for future writing of the dissertation, related papers, fellowships, and grants. When the proposal is completed to the satisfaction of the advisor, it is given to members of the pre-thesis committee not less than two weeks prior to their first meeting, to serve as an introduction to the student’s thesis project. A copy of the proposal is also submitted to the SAAC.

Student Seminars

In years 3–5, or starting with the spring term after the qualifying examination has been completed, all graduate students will present a 20–30 minute seminar on their thesis research. These seminars form a logical extension of the departmental Seminar Series and the Special Topics course and take place on a specified Student Seminar Day (or days) scheduled in April or May. Pre-thesis committee members for a presenting student take notes on the quality of the presentation and meet with the student within 2–3 days, on either a one-to-one basis or in small groups with other committee members, to provide feedback with the goal of improving the student’s presentation skills.

Student Posters Presentations

Students who have completed their qualifying exams present a poster during Russek Day in the spring of each year, to improve their organization and presentation skills. These students also present their posters at the Departmental Retreat held each fall. In addition, students are encouraged to enter their posters in the Science Day poster competition held at the Boston University Charles River Campus.

V. Course Requirements

Incoming PhD and MA students are required to take two semesters of Biochemistry (BI 755 & BI 756, 8 credits total) and four semesters of the Special Topics Seminar course (BY 871 & 872, 8 credits total). To allow flexibility for the breadth of the fields of physiology and biophysics, yet ensure a working knowledge of both, students are required to take a minimum of one physiology course and one biophysics course. The acceptable physiology courses are: Cell Physiology (PH 842, 4 cr), or Human Physiology A and B (PH 730 and PH 731, 3 cr each, total of 6 cr). The acceptable biophysics courses are: Biophysics of Macromolecular Assemblies (PH 771, 4 cr) or Foundations of Biophysics and Structural Biology (BY 760, 4 cr).

Elective coursework is chosen jointly by the student and their advisor or thesis committee. To achieve a balanced curriculum for all students, the PhD degree requirements of the Division of Graduate Medical Sciences include a minimum of 24 credits in formal coursework. It is expected, although not required, that the formal course work credits are acquired prior to the qualifying examination at the end of the second year. Beyond 32 coursework credits, students are encouraged to informally audit courses following consultation with their thesis committee. Students who have already taken an appropriate graduate-level course in the core curriculum are permitted to substitute an elective or electives in the first semester, as long as the total semester course credits remain 10.

A sample curriculum

Fall semester, first year—all students

• Biochemistry A (BI 755, 4 cr)
• Cell Physiology (PH 842, 4 cr) or Human Physiology A (PH 731, 3 cr)
• Special Topics Seminar Course (BY 871, 2 cr)

Spring semester, first year

• Biochemistry B (BI 756, 4 cr)
• Foundations in Biophysics and Structural Biology (BY 760, 4 cr) or Human Physiology B (PH 732, 3 cr)*
• Special Topics Seminar Course (BY 871, 2 cr)

*Students fulfilling their physiology requirement with Human Physiology A and B would fulfill their biophysics requirement in their second year.

Remaining semesters, first and second years—all students

• Special topics/student seminar (BY 871, 872, 4 cr total)
• Electives

Suggested electives:

Department of Physiology & Biophysics

• Cell Physiology (PH 843) 4 cr
• Human Physiology A (PH 542) 4 cr
• Human Physiology B (PH 543) 4 cr
• Foundations in Biophysics and Structural Biology (BY 760) 4 cr
• Biophysics of Macromolecular Assemblies (BY 771) 4 cr
• NMR Spectroscopy in Biology and Biochemistry (BY 772) 2 cr
• Metabolism and Cellular Function of Complex Lipids (BY 774) 2 cr
• Special Topics (PH 745, 746) 2 cr (e.g. Biology of Vision, Calcium, and Cell Function)

Courses in other departments

• Biochemistry II (intermediary metabolism) (BI 756) 4 cr
• Molecular Biology (BI 782) 4 cr
• Comprehensive Immunology (MI 713) 4 cr
• Molecular Neurobiology and Pharmacology (PM 700) 4 cr
• Structure & Function of Proteins (BI 783) 2 cr
• Enzyme Catalysis (BI 788) 2 cr
• Receptors and Signal Transduction (BI 790) 2 cr
• Physical Biochemistry (BI 789) 2 cr
• Gene Regulation and Pharmacology (PM 880) 2 cr
• Mass Spectrometry, Proteomics, and Functional Genomics (BI 793) 2 cr
• Principles of Genetics and Genomics (GE 701) 4 cr
• Biostatistics (MS 700) 2 cr
• Molecules to Molecular Therapeutics (MM 710) 4 cr

The qualifying examination

The qualifying examination is given at the end of the second semester within the 2nd year for PhD students. MD/PhD, post-master’s, and some transfer students in the PhD program have the option of taking the qualifying examination at the end of the second semester of the first year. Administration of the qualifying examination will be overseen by the SAAC. Program faculty members serve on the qualifying examination committees on a rotating basis. The two-part exam consists of:

1. A written qualifying examination with thought-provoking questions that span topics in biophysics, physiology, biochemistry, and cell biology. Students choose and answer four of the eight questions in four hours.
2. An oral examination where the student is assigned 3 current research papers to read and is subsequently tested on their understanding of the material in front of an examining committee. This committee is comprised of 5 program faculty members. Papers are chosen by the committee and given to the students 2–3 weeks in advance of the oral examination. Thesis advisors will not participate in the oral defense of students who are pursuing a PhD in their laboratory.

Both the written and oral portion of the qualifying exam must be passed in order for a student to continue in the PhD program. Students who fail either the oral or the written portion of the exam (or both) can retake that portion of the exam once in order to achieve a passing score. Master’s students do not take the qualifying examination.

Pre-thesis meetings

After the student has passed the qualifying exam, a pre-thesis committee of at least five members must be established in the fall of that year and submitted to the SAAC. Students submit their thesis proposal in grant form to the members of the committee 2 weeks before the first pre-thesis committee meeting. At least one member from outside the department, and preferably from a different institution, should be included in the final thesis committee. An external committee member is not required for pre-thesis meetings, which will be held about every 10–12 months or 3 times prior to graduation.

Thesis defense

The PhD thesis defense consists of a public seminar followed by a closed door thesis defense with a minimum of 5 committee members, including 1 member from outside the department

VI. Resources for the Programs

All faculty of the Department of Physiology & Biophysics participate in the graduate programs in Physiology & Biophysics. The faculty have well funded research programs and extensively equipped individual laboratories for carrying out research in cellular physiology and biophysics. In addition, the department maintains core facilities in molecular biology, spectroscopy, X-ray crystallography, NMR, and structural electron microscopy that will be used by students carrying out their research.

Donald M. Small, MD, Lipids, Lipoproteins, and Disease

Christopher W. Akey, PhD, Structural Biology of Channels and Chaperones

David Atkinson, PhD, Plasma Lipoproteins: Structure and Biology

Esther Bullitt, PhD, Bacterial Adhesion and Viral Replication

M. Carter Cornwall, PhD, Visual Transduction and Adaptation

Christopher Gabel, PhD, Neural Regeneration and Neurocircuitry in C. elegans

J. Fernando Garcia-Diaz, PhD, Expression and Modulation of Ion Channels

Hwai-Chen Guo, PhD, Protein Crystallography and Molecular Function

Olga Gursky, PhD, Protein Conformation, Structure, and Energetics

James A. Hamilton, PhD, Structural Biology of Membranes in Native and Pathological States

James F. Head, PhD, Structural Studies of Protein-Protein and Protein-Ligand Interactions

Haya Herscovitz, PhD, Assembly, Chaperone-Assisted Folding, and Secretion of Lipoproteins

William J. Lehman, PhD, Electron Microscopy and 3D Reconstruction of Actin Thin Filaments

Simon Levy, PhD, Calcium Signaling in Nerve Cells

Assen Marintchev, PhD, Eukaryotic Translation Initiation and NMR

C. James McKnight, PhD, Protein Structure, Function, Folding, and NMR Spectroscopy

Jeffrey R. Moore, PhD., Cell Motility and Motor Proteins

Judith D. Saide, PhD, Structural Proteins of Drosophila Flight Muscle

Barbara A. Seaton, PhD, X-ray Crystallography and Protein-Membrane Interactions

G. Graham Shipley, PhD, D. Sc., Membrane and Receptor Biology

Raphael A. Zoeller, PhD, Functional Roles of Lipids in Cell and Membrane Biology