Graduate
Programs in Physiology or Biophysics (MA/PhD)
A.
Purpose and Background
The
Departments of Physiology and Biophysics merged on July 1, 2000 to
form the new Department of Physiology and Biophysics, under the aegis
of Dr. Donald Small, as Chairman. The goal of the new Department
is to bring together the two Programs and their Faculty under the
same administration and general Program format. Together, there
are now 24 active faculty within the new Department of Physiology
and Biophysics whose research interests span the modern areas of Cellular
Physiology and Biophysics, with strong concentrations in Structural
Biology, Vision Research and the Biology and Physical Chemistry of
Lipids. Many of the faculty are nationally and internationally
recognized as leaders in their chosen areas of research. As
part of the reorganization of the Department of Physiology and Biophysics,
it has become clear that a merger of the faculty of the two graduate
programs would offer the opportunity to set in place curricula that
represent the interests and strengths of the Department and provide
a higher quality graduate experience for students. We believe
that the merger of the two Departments results in more flexible, expanded
graduate programs with pathways either leading toward a degree in
Physiology or to Biophysics. The joint Department offers these
two programs in a strong collegila environment to encompass and promote
the diverse overlapping research of all members of the Department.
To
this end, the graduate programs within the new Department stem from
a common first year curriculum and develops into two parallel and
overlapping paths. A small group of core courses taken in the
first year are required for both programs and will lead to a level
of understanding of the two disciplines necessary to allow students
to make choices in their program paths. In this approach, all
students have flexibilty to choose the appropriate course work for
their degree, within the guidelines set out below. The courses
for first year students are chosen with the guidance of members of
the duly constituted Students Admissions and Affairs Committee (SAC),
and in the second year with input from their Masters or PhD advisor.
Students who successfully complete the program are awarded either
a Masters or PhD in Physiology or Biophysics.
B.
Admission into the Programs in Physiology and Biophysics
Student
Recruitment
Recruitment
into the departmental programs is the preferred route of entry for
a Master of Arts or PhD. All underrepresented minorites are
encouraged to apply.
Similar
Paths for PhD and MD/PhD Students
Requirements
for PhD and MD/PhD students are similar. However, MD/PhD. students
generally enter as post-masters students, and therefore have a lower
course and credit requirement (32 versus 64 total credits) and take
their Qualifiers at the end of the first year. Other students
entering into the programs with a Masters degree from within the USA
are treated similarly and take their Qualifying Examination at the
end of the first year. In both cases, post-Masters students
are able to choose a suitable set of courses tailored to their backgrounds
and research interests, with input from the SAC 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
Master of Arts Program
The
current Master of Arts Programs in Physiology or Biophysics are offered.
In some cases, a qualified MA student may proceed into a PhD program.
This decision will be handled by the SAC 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.
C.
The Path of a Graduate Student
Special
Topics Seminar Course (GMS BY 871,872: 4 credits spread over
3 semesters).
In
the first and second years, all students take a Special Topics Seminary
course, aimed at developing a student's ability to present the merits
and/or deficits of a current research paper, in front of other students
and a proctoring faculty. The student may use a blackboard,
overheads or the computer projector during their presentations.
This course will meet for 1 hour each week, as specified by the faculty
proctoring the class. Typically, all students present at least
once each semester, but possibly more often, based on the number of
enrolled students. A post- Bachelors student is required to
take 3 semesters (4 credits), whilst post-Masters, MD/PhD, M.A., Cell
and Molecular Biology (CMB), and Neuroscience students who enter into
laboratories within the Department
take
2 semesters (for a total of 2 credits). The faculty who teaches
this course is rotated after each semester, to allow a fresh viewpoint
and area of expertise to be covered. The Chairman of the SAC, with
input from the Program Steering Committee, selects 6-8fFaculty who
are interested in teaching this course on a rotating basis.
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 proposed 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
SAC, from a list of Faculty who have volunteered at act as hosts.
This list is updated yearly.
2.
Students participate in a Departmental Retreat, to be held
at the end of September, in which Faculty speak and present posters
that document the projects in their laboratories.
3.
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 3-4 hours. Scheduling is coordinated
by the SAC 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.
4.
Generally, most students participate in 3 rotations (8
weeks each), with the possibility of a 4th , if they are truly undecided
about the choice of a thesis advisor after the first 3 are completed.
The SAC strongly encourages new students to choose at least 1 rotation
in an area that is distinct from their major area of research interest.
For example, a student who chooses 2 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, then members of the
SAC meet with the student and try to work out a suitable rotation
that fulfills this requirement. Where possible, the SAC schedule
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 2
names (rank ordered) for their first fall rotation and the SAC sets
up a schedule that does not put 2 students within the same laboratory,
and honors the first choice of most students. Near the end of the
fall semester, the students provide either 2 or 3 names for their
spring rotation (s). Students choose a PhD advisor by early June,
at the end of the first year (unless a 4th rotation is required).
The SAC 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 seminary course
and by giving presentations in yearly research seminars, laboratory
group meetings, pre-thesis meetings, and the thesis defense seminar.
Written skills are developed in required course work 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 research proposal on their
thesis project that is patterned after an NIH grant. This exercise
should allow the adviser and student to clarify the proposed research
and provides the student with a forum to learn basic science 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 thesis, 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 prior to their first
meeting, to serve as an introduction to the student’s thesis project.
The subject of the proposal and the nature of the Faculty Advisor’s
research determine the character of the final degree (i.e., Physiology
or Biophysics).
Department
Seminar Series
The
Department of Physiology and Biophysics runs a seminar series during
the school year. This seminar program has evolved from two long
running programs in the Department of Physiology and the Department
of Biophysics. All students are required to attend these seminars
as part of their training in critical thinking and to broaden their
general knowledge of science.
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 Seminary 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 2-3m days, on either a one-to-one basis or in small
groups with other committee members, to provide feedback with the
goal of improving their presentation skills.
Student
Posters
Students
who have completed their qualifier present a poster during Student
Achievement Day in the spring of each year, to improve their organization
and presentation skills. In addition, students at the appropriate
stage (in their penultimate or final years) are encouraged to enter
their posters in the Science Day poster competition held at the Boston
University Charles River Campus.
D.
Course Requirements
Graduate
Curriculum in Physiology or Biophysics
To
address the diversity of the faculty research areas in the merged
department, a flexible curriculum for the two Programs tracks has
been developed. Thus, all students are exposed to the full breadth
of departmental research interests, while being provided with the
more specialized training required for their thesis research in either
Physiology or Biophysics. The Department recognizes that there are
many more courses available than can be fit into any individual student’s
program. Elective coursework is chosen jointly by the student and
his/her advisor or thesis committee. Toward achieving a balanced curriculum
for all students the PhD degree requirements of the Division include
a minimum of 24 credits in formal course work. It is expected, although
not required, that formal course work credits are acquired prior to
the Qualifying Examination in the second year. Beyond 32 course
work 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
Common Core Curriculum
Fall
semester, first year-all students
GMS BI 755 Biochemistry,
4 cr
GMS MS 753 Cell
Biology, 4 cr
GMS PH 741 Research Methods in Cell Physiology
& Biophysics, 2 cr
Remaining
semesters, first & second years-all students
GMS BY 871, 872 Special
Topics/ Student Seminar, 4 cr
Electives
Suggested
Electives
Department
of Physiology & Biophysics
GMS
PH 542
Human Physiology A,
4 cr
GMS
PH 543
Human Physiology B, 4 cr
GMS
PH 741
Research Methods in Cell Physiology & Biophysics,
2 cr
GMS
PH 742
Research Methods in Cell Physiology &
Biophysics, 2 cr
GMS
PH 745 746
Special Topics, 2 cr
(e.g.,
Biology of Vision, Calcium & Cell Function)
GMS
BY 760
Foundations in Biophysics & Structural Biology,
4 cr
GMS
BY 771
Biophysics of Macromolecular Assemblies,
4 cr
GMS
BY 772
NMR Spectroscopy in Biology & Biochemistry,
2 cr
GMS
BY 774
Metabolism & Cellular Function of Complex Lipids,
2 cr
GMS
PH 843
Cell Physiology, 4 cr
Courses
in other Departments
GMS
MI 713 Comprehensive
Immunology,
4 cr
GMS
PM 700 Molecular
Neurobiology and Pharmacology,
4 cr
GMS
BI 756 Biochemistry II (intermediary metabolism),
4 cr
GMS
BI 782
Molecular Biology, 4 cr
GMS
BI 783
Structure & Function of Proteins,
2 cr
GMS
BI 788
Enzyme Catalysis, 2 cr
GMS
BI 789
Physical Biochemistry, 2 cr
GMS
BI 790
Receptors and Signal Transduction, 2
cr
GMS
PM 880 Gene
Regulation and Pharmacology,
2 cr
Sample
Course Curricula
Here
are several examples of possible 24-credit curricular that may be
taken by PhD students interested in different research areas/disciplines.
The curriculum in the first year is designed by the student and the
SAC, while the student and his/her thesis committee share this responsibility
in the second year. If MD/PhD students have had previous, equivalent
coursework in Biochemistry and Physiology, they may omit these courses
after consulting with SAC. Optional courses above the 24
credits minimum that may expand the background of the studensts are
indicated in bold.
Pathways
Leading to a Degree in Physiology
Cellular Physiology/Electrophysiology:
Fall,
first year (10 cr):
| GMS
BI 755 |
Biochemistry
|
4
cr |
| GMS
MS 753 |
Cell
Biology |
4
cr |
| GMS
PH 741 |
Research
Methods in Cell Physiology & Biophysics |
4 cr |
Spring,
first year (8 cr):
| GMS
BI 756 |
Biochemistry
II |
4
cr |
GMS
PH 742
|
Research
Methods in Cell Physiology & Biophysics |
2
cr |
| GMS
BY 871, 872 |
Special
Topics/ Student Seminar |
4
cr |
Fall,
second year ( 6 cr):
| GMS
PH 842 |
Cell
Physiology
|
4
cr |
| GMS
BY 871, 872 |
Special
Topics/ Student Seminar |
4
cr |
Spring,
second year (2 cr):
| GMS
PH 745 |
Special
Topics in Physiology
|
2
cr |
|
GMS
BY 871, 872 |
Special Topics/ Student Seminar |
4 cr |
General
Physiology (including
those students with clinical research orientation):
Fall,
first year (10 cr):
| GMS
BI 755 |
Biochemistry
I |
4
cr |
| GMS
MS 753 |
Cell
Biology |
4
cr |
| GMS
PH 741 |
Research
Methods in Cell Physiology & Biophysics |
2
cr |
Spring,
first year (8 cr):
| GMS
BI 756 |
Biochemistry
II
|
4
cr |
|
GMS
PH 742 |
Research
Methods in Cell Physiology & Biophysics II |
2 cr |
| GMS
BY 871 |
Special Topics/ Student Seminar |
2 cr |
Fall, second year (6 cr):
| GMS
PH 542 |
Human Physiology A |
4 cr |
| GMS
BY 871 |
Special
Topics/Student Seminar |
2
cr |
Spring,
second year (4 cr):
| GMS
PH 543 |
Human
Physiology B |
4
cr |
| GMS
BY 774 |
Metabolism
& Cellular Function of Complex Lipids |
2
cr |
| GMS
BY 871 |
Special
Topics Seminar/Student Seminar |
2 cr |
Pathways
Leading to a Degree in Biophysics
Structural
Biology and/or Molecular or Cellular Biophysics
Fall,
first year (10 cr)
| GMS
BI 755 |
Biochemistry
I |
4
cr |
| GMS
MS 753 |
Cell
Biology |
4
cr |
| GMS
PH 741 |
Research
Methods in Cell Physiology & Biophysics I |
2
cr |
Spring,
first year (6 cr)
| GMS
BI 760 |
Foundations
of Biophysics & Structural Biology |
4
cr |
| GMS
PH 843 |
Cellular
Physiology |
4
cr |
| GMS
BY 871 |
Special
Topics Seminar/Student Seminar |
2
cr |
Fall,
second year (6 cr):
| GMS
BY 771 |
Biophysics
of Macromolecular Assemblies |
4
cr |
| GMS
BI 789 |
Physical
Biochemistry |
2
cr |
| GMS
BY 871 |
Special
Topics Seminar/Student Seminar |
2
cr |
Spring,
second year (2 cr):
| GMS
BY 772 |
NMR
Spectroscopy in Biology & Biochemistry |
2
cr |
| GMS
BI 783 |
Structure
& Function of Proteins |
2
cr |
| GMS
BY 871 |
Special
Topics Seminar/Student Seminar |
2
cr |
The
Qualifying Examination
The
Qualifying Examination is given at the end of the second semester
within the 2nd year for the PhD students. Moreover, MD/PhD, post-Masters
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 Qualifier will be overseen by
the SAC. Program faculty serve on the Qualifier Examination committees
on a rotating basis.
1.
A written Qualifying Examination with 4-6 thought questions is given,
based on the relevant course taken by the students.
2.
The oral examination consists of the student being assigned
3 current research papers to read and subsequently, being tested on
their understanding of the material in front of an examining committee.
This committee is comprised of 5 Program faculty. Papers are chosen
by the committee and given to the students 2-3 weeks in advance of
the oral examination. Thesis advisers will not participate in the
oral defense of students who are pursuing a PhD in their laboratory.
Pre-thesis
Meetings
After
the student has passed the qualifier, a pre-thesis committee of 4
members must be established in the fall of that year and submitted
to the SAC. 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.
E.
Resources for the Programs
All
faculty of the Department of Physiology and Biophysics participate
in the graduate programs in Physiology and 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 X-ray crystallography, NMR and Structural Electron Microscopy that
will be used by students carrying out their research in Structural
Biology (see Departmental Web pages). Overall, 16 Faculty currently
participate in an NIH funded Pre-doctoral Training Grant in Structural
Biology within the Department, that is currently in its 20th year
of funding. An in- depth review of each faculty's research can be
obtained form the Department Web pages at: http://biophysics.bumc.bu.edu
