Molecular and
Cellular Physiology–

MCP Student Handbook

(For best presentation of the handbook, see the pdf version)

Table of Contents

Molecular & Cellular Physiology Contact Information

Department Chair

Associate Chair

Director of Graduate Studies

Director of Graduate Admissions

Director of Finance and Administration

Asst. Director of Finance and Administration

Graduate Student Advisors (advising, PhD program policy, admissions committte)

Lab Management (health and safety training, lab/building, keys, computer, facilities orientation, glassware)

Lab Administrative Associates (lab specific needs, reimbursements)

Student Service Officer (stipend, tuition, health insurance payments, course work, grades, PhD program policy, general student related questions), postdoc administration, all postdoc related questions, seminar series/retreat administratior, HR liason)


MCP Faculty

The Department consists of 11 primary faculty, 2 faculty with joint appointments and 4 courtesy faculty.

Courtesy Appointments

Education Overview             

The Department of Molecular & Cellular Physiology offers a course of study leading to the Doctor of Philosophy (Ph.D.) degree. The program does not offer undergraduate (e.g. bachelor) degrees, and does not offer a course of study leading to a Master’s degree. The program of study is designed to prepare students for careers in research and teaching. The major emphasis is training in research. Students work closely with a dissertation adviser and members of a research group on novel and important biological problems at the cellular and molecular level. Group size averages about 10, with a maximum of about 20 students and postdocs.  

The Department maintains a series of events and policies to promote interaction among students, postdoctoral fellows, and faculty members, including a seminar series, an annual retreat, ‘Science Fridays’, a scientific and social gathering, and access to all labs and facilities. In addition to offering students access to all of the faculty members, these arrangements encourage collaboration between groups and has fostered the development of many new technologies. Predoctoral training begins in the fall of each year.

The faculty teaches courses in physiology, cell biology, neuroscience biophysics, and molecular biology, and advanced courses in specialized areas are also offered. The program of study is created in consultation with the adviser to best fulfill each student’s educational goals. Graduate students learn about teaching by assisting in the departmental teaching programs.

Academic Requirements

Following are a list of milestones that Ph.D students are expected to complete, as well as their corresponding deadline. All forms and papers must be turned into the Student Service Office in B100.

First Year

Second Year

Third Year

Fourth Year

Fifth Year

Thesis Defense 

The graduate program in the Department is highly oriented towards hands-on research; working within the group of the dissertation advisor, so required coursework is modest.  The course requirements for the program are as follows:

Required classes must be taken for a letter grade and students must earn a minimum grade of B in any individual required course.  In addition, students in the program must maintain a grade point average of at least 3.3 for their required courses as a whole.  Courses may be retaken once to improve an unsatisfactory grade.   Failure to maintain the required grades and grade point average will be taken as evidence of unsatisfactory progress in the program.

Students may, of course, take more than the required number of courses as long as they remain within their number of allowed units/quarter 10, and so long as the number of courses taken does not become excessive to the point where it interferes with satisfactory progress in other aspects of the degree program.  Students may no longer take classroom coursework after attaining TGR status (usually in the 4th year of study).

Courses:

MCP 126: Neurons and Disease

Diseases of the nervous system. First lecture of each week focuses on the clinical, epidemiological and behavioral aspects of a selected disease or syndrome. Second lecture exposes the cell biological, electrophysiological, biochemical and/or molecular biological processes that underlie each disease presented. Instructors maintain some flexibility in the diseases chosen for elucidation, but students can expect those covered to range from the relatively straightforward, for example Multiple Sclerosis (MS) or Amyotrophic Lateral Sclerosis (ALS), to the more complex, for example, Schizophrenia or Obsessive Compulsive Disorder (OCD). 3 units for lecture and discussion only; 4 units includes a paper. Prerequisite: Biology or Human Biology core.

MCP 199: Undergraduate Research

Students undertake investigations sponsored by individual faculty members. Prerequisite: consent of instructor

MCP 200: Cardiovascular Physiology

Offered jointly with the Department of Medicine. Lectures, small group instruction, clinical presentations, and lab demonstrations of normal and disordered human cardiovascular physiology. Prerequisite: understanding of general biochemistry.

Terms: Spr | Units: 5 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Kobilka, B. (PI

MCP 202: Advanced Immunology II (IMMUNOL 202)

Readings of immunological literature. Classic problems and emerging areas based on primary literature. Student and faculty presentations. Prerequisite: IMMUNOL 201/MI 211.

Terms: Spr | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Garcia, K. (PI)

MCP 216: Genetic Analysis of Behavior (NBIO 216)

Advanced seminar. Findings and implications of behavioral genetics as applied to invertebrate and vertebrate model systems. Topics include biological clocks, and sensation and central pattern generators. Relevant genetic techniques and historical perspective. Student presentation.

Terms: Spr | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Clandinin, T. (PI); Goodman, M. (PI)

MCP 221: Advanced Cell Biology (BIO 214, BIOC 224)

For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, compartmentalization, transport and trafficking, motility and adhesion, differentiation, and multicellularity. Current papers from the primary literature. Prerequisite for advanced undergraduates: BIO 129A,B, and consent of instructor.

Terms: Win | Units: 2-5 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Kopito, R. (PI); Nachury, M. (PI); Pfeffer, S)

MCP 222: Imaging: Biological Light Microscopy (BIO 152)

Survey of instruments which use light and other radiation for analysis of cells in biological and medical research. Topics: basic light microscopy through confocal fluorescence and video/digital image processing. Lectures on physical principles; involves partial assembly and extensive use of lab instruments. Lab. Prerequisites: some college physics, Biology core.

Terms: Spr | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Lewis, R. (PI); Smith, S. (PI)

MCP 232: Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIO 232, BIOPHYS 232)

Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.

Terms: Spr | Units: 4 | Grading: Letter or Credit/No Credit

Instructors: Block, S. (PI); Smith, S. (PI); Stearns, T. (PI)

MCP 256: How Cells Work: Energetics, Compartments, and Coupling in Cell Biology (MCP 156)

Open to graduate and medical students, and advanced undergraduates. Dynamic aspects of cell behavior and function, including cellular energetics, homeostasis, heterogeneity of membranes, structure and function of organelles, solute and water transport, signaling and motility. Emphasis is on the principles of how coupling of molecular processes gives rise to essential functions at the cellular level. Mathematical models of cell function. Student presentations.

Terms: Aut | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Goodman, M. (PI); Maduke, M. (PI)

MCP 258: Information and Signaling Mechanisms in Neurons and Circuits (NBIO 258)

How synapses, cells, and neural circuits process information relevant to a behaving organism. How phenomena of information processing emerge at several levels of complexity in the nervous system, including sensory transduction in molecular cascades, information transmission through axons and synapses, plasticity and feedback in recurrent circuits, and encoding of sensory stimuli in neural circuits.

Terms: Aut | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

Instructors: Tsien, R. (PI); Bacchus, S. (PI)

MCP 299: Directed Reading in Molecular and Cellular Physiology

Prerequisite: consent of instructor.

Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit | Grading: Medical Option (Med-Ltr-CR/NC)

MCP 370: Medical Scholars Research

Provides an opportunity for student and faculty interaction, as well as academic credit and financial support, to medical students who undertake original research. Enrollment is limited to students with approved projects.

Terms: Aut, Win, Spr, Sum | Units: 4-18 | Repeatable for credit | Grading: Medical School MD Grades

MCP 399: Graduate Research

Students undertake investigations sponsored by individual faculty members. Research fields include endocrinology, neuroendocrinology, and topics in molecular and cellular physiology. Prerequisite: consent of instructor. (Staff)

Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit | Grading: Medical Option (Med-Ltr-CR/NC

MCP 801: TGR Project

Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit | Grading: TGR

MCP 802: TGR Dissertation

Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit | Grading: TGR

Lab Rotations

In addition to the course requirements detailed above, a student is expected to complete laboratory rotations of 1quarter duration.   These rotations last no more than one quarter (± 1-2 weeks) and students are required to do at least two and allowed to do no more than four rotations.  The first of these rotations must be in a laboratory within the Department, while subsequent rotations may be in any laboratory in the allied bioscience programs.   A continuation of rotations beyond the end of the first year will require the approval of the Director of Graduate Studies for the Department.  Failure to complete rotations in this timely manner may be considered as evidence of unsatisfactory progress in the program.  Following the completion of the rotations the student will join the laboratory where they will conduct their dissertation research.

Qualifying Examination

 All students in the program must take and pass a Qualifying Examination to advance to candidacy for the Ph.D.    It is expected that students will take the qualifying examination early in the second year of study.  Failure to pass the qualifying examination by the end of the second year will be taken as evidence of unsatisfactory progress in the program.

Students should form a qualifying examination committee, consisting of at least 3 faculty members (members of the academic council), at least one of who must be a member of MCP.  This committee should normally be formed by the end of the first year of study. The composition of this committee should be approved by the Director of Graduate Studies. Students should also check with the Coordinator of Student Services for the Department (Schantae Wright) to make sure to file all required paperwork in advance.  The University maintains certain deadlines for filing for candidacy, and it is the student’s responsibility to be aware of these deadlines.

The qualifying examination consists of written and oral components.  For the written portion, the student will compose a dissertation research proposal in the format of an NIH NRSA grant application.  This proposal should include a thorough treatment of the background in the field of the proposal, a detailed rationale for the topic and experiment chosen for the proposal, and a detailed proposal of the experiments themselves.  Students are not required to present preliminary data as part of the qualifying examination, However, the student should include a section arguing the feasibility of the proposed experiments.  Of course, if the student has preliminary data, it should be included, but it is not required to go forward with the examination, and the examination should and will not be postponed for lack of such data.

The student will submit the written proposal to their qualifying at least two weeks before the scheduled oral examination.   If the committee approves, the student may go forward with the oral part of the examination.

The oral portion of the examination will consist of the student giving an oral presentation of the dissertation proposal, and fielding questions about it from the qualifying exam committee.  While these questions will center on the topic of the proposal, the student is responsible for general scientific knowledge that is relevant to the field of the proposal.  The range of questions is the purvue of the examination committee.  In no case, can the oral portion of the examination last for more than three hours, per University rules.

At the end of the examination, the committee will meet briefly in private to render a decision.  There are three general possible outcomes:

If the student receives a ‘pass’, they are advanced to candidacy for the Ph.D. once required paperwork is filed.   If the student receives a ‘conditional pass’, then they will be informed by their committee of additional requirements that must be completed before they can be advanced to candidacy (for example, a student might be required to take additional coursework to make up for an area of weakness, or they may be required to re-write a portion of the written proposal).  Once the student completes the additional requirements, they can be advanced to candidacy.  They do not need to re-take the oral examination.   If a student should receive a ‘fail’, then they must re-take the oral examination (and make any improvements required in the written proposal).  Failing the qualifying examination will be taken as evidence of unsatisfactory progress in the program.   Except in cases of extenuating circumstances that must be verified and approved by the Director of Graduate Studies for the Department, the examination must be re-taken within one elapsed quarter of the first attempt (meaning, for example: if the 1st attempt was during week 3 of the fall quarter, then the second attempt must be completed by the 3rd week of the winter quarter) Failure to pass the qualifying examination on the second attempt will be grounds for terminating the student from the program.   A student thus dismissed from the program may petition for the award of a terminal Masters degree.  The qualifying examination committee, the Director of Graduate Studies for the Department, and the Department Chair, must approve this petition.  MCP does not guarantee to award of a Masters degree to students who fail the qualifying examination, and it will only be awarded in the case that the approving parties feel it has been earned.  MCP does not award Masters degrees, except for this terminal masters degree in this special circumstance.

Following the successful completion of the qualifying examination, the student will submit their written proposal to the NIH NRSA program.

Dissertation Research

The Biosciences have a joint training program and prospective students may do their dissertation research in any Department within the allied Biosciences.  Students have the option of formally joining the graduate “home program” of that Department if they so desire, and to receive their degree from that Department.   However, they may also remain in the MCP home program, and receive their degree from MCP, even if they do their dissertation work in another department.  In either case, responsibility for funding the student falls to the dissertation advisor.

Teaching

Opportunities exist for students to gain teaching experience as teaching assistants (TA) in various courses. However, there is no formal teaching requirement that needs to be completed to earn the Ph.D. degree.

Language

There is no language requirement for earning the Ph.D. degree. However, students will be expected to be familiar with the relevant literature in their chosen field, regardless of the language of publication.

Graduate advising and policy

Students may, and are encouraged to approach any MCP faculty member for advice as appropriate.  During the first year of study, the Director of Graduate Study (DGS: currently Dan Madison) will be available to advise on programmatic matters.  After the first year, students may consider utilizing the additional resource of their qualifying exam committee for advice on matters of science.  Following the joining of a laboratory for dissertation research, the head of that laboratory will be the student's primary advisor.

For matters involving setting and enforcing policy of the graduate program, the Department has established a Graduate Studies Committee (GSC), currently made up of Dan Madison, Brian Kobilka, Max Nachury and Rich Lewis.  The committee will also include a non-voting student representative who will be enrolled in the MCP doctoral program. This representative may attend the committee meetings except at those times, in the interests of privacy and confidentiality, when the committee may be required to discuss an individual student.   This committee will be the Departmental authority on matters of Ph.D. program requirements, policy, curriculum, student performance, and other matters related to the program.  However, routine matters such as approval of particular courses in a student's program, the makeup of a qualifying examination committee, etc., can be approved by the DGS.  For less routine matters, the committee as a whole may be consulted. 

Applying to Candidacy (CAND)

Admission to candidacy acknowledges the successful completion of departmental and university

requirements for the doctoral degree. Form can be found on the registrar’s web site

(http://www.stanford.edu/dept/registrar/shared/forms.htm) and submitted to MCP Student Services Officer.

Terminal Graduate Registration (TGR)

Doctoral students are eligible for TGR status when they have been admitted to candidacy, completed all required coursework, completed 135 units, and submitted the Doctoral Dissertation Reading Committee form. Students registered in TGR status must enroll each quarter in a TGR course (#802 for doctoral programs) in their department, with their advisor as the instructor. There are zero units for this course selection and you will not be eligible to take classes for credit. TGR students also enroll in MCP 399 for 3 research units with their advisor as the instructor, unless you are in a non-MCP thesis lab. The purpose is to work on the thesis, dissertation, or other remaining requirements that must be evaluated each quarter for academic progress and graded as follows: "N" indicating satisfactory progress, "N-" for unsatisfactory progress, and "P" for a final grade when all requirements have been completed. A hold is placed on the registration of a student who receives an "N-" grade for two consecutive quarters. Further registration is contingent on approval of an agreement for completing degree requirements by the adviser and the department.

Conferral of Degrees:

The Notice of Intention to Complete Advanced Degree Requirements form is submitted to the Graduate Degree Support Section to initiate approval for conferral of all graduate degrees. It should be submitted preferably in the second week, but no later than the last day of classes of the degree quarter, as listed in the University Calendar. Requests for conferral are reviewed by the Graduate Degree Support Section and the department to verify completion of degree requirements. In Summer, Autumn, and Winter Quarters degree certificates are sent to students within two weeks of the conferral date.

The Graduate Degree Support Section should be notified in writing when conferral plans change. Students who withdraw their conferral request or who fail to complete degree requirements must file a new Notice of Intention for a subsequent quarter. A new Notice of Intention must be filed for each degree and conferral quarter.

Spring Commencement:

Commencement ceremonies are held each June for students who have received degrees in the previous summer, autumn, winter and Spring quarters. Students who wish to receive their diplomas at June commencement must submit a Notice of Intention by February 1 to allow adequate time for preparation of the diploma. Information on Commencement activities and distribution of diplomas is sent by the Registrar's Office in early April to addresses provided on the Notice of Intention. Students who wish to participate in commencement activities in advance of conferral of their degree may obtain a Graduate Student Petition to Walk Through Commencement Exercises from the Graduate Program Office from May 1 until the day before commencement. A Walk Through petition should be requested only if there is no possibility of completing degree requirements for June conferral.

Registration Process

Graduate students are required to register for Autumn, Winter, Spring and Summer quarters at 10 units (or TGR & Research at 3 units) until the degree is received.

Access to Stanford student privileges (funding, housing, financial aid, access to courses and facilities, etc.) is contingent upon timely and accurate completion of the following:

Deadlines are set for each of these activities and can be found on the Registrar’s website, the Stanford Academic Calendar or Axess. Holds will cause a delay of payment.

Stanford Bulletin/Explore Courses

Time Schedule

The SoM Class Time Schedule is static, dated document and represents class information as reported

and known at the time of publication. Although the SoM Class Time Schedule may be used as a general

reference for a quarter's offerings, Axess is the system of record and reports most accurately the class

schedule in any given academic quarter.

Study List

Axess

Axess is a student information system available via the web. It is regular available weekdays 8:00 am to 11:59 pm and weekends 9:00 a.m. To 11:59 p.m. Using Axess, you will be able to complete the following tasks:

New students may use Axess at any time after receipt of the registration packet from the Registrar’s office. You will need a Sunet ID and password to use Axess.

Student ID Number

Your Stanford University ID is a number assigned to our academic record and is required for any inquiries you make. The ID number is printed on your registration commitment letter, your Stanford University ID card, and all enrollment/grading related documents distributed by the registrar's office. Your ID number is unique and considered directory information. The first step in obtain g your ID card is to check with your student service officer to be sure that your personnel file has been set up, and that you have been assigned and ID number. Once you have received your number, you need to bring some form of picture ID with you to the ID office located at the Student Center at Tressider Union.

University Bill

After submitting a Registration Commitment, students may receive a University bill. Tuition credits are entered on this bill. Also entered are other University charges such as rent, student fees, late fees, loans, etc. Students receiving a fellowship paid through Stanford may elect to have these charges deducted from their stipend checks and automatically applied to their bill. If your bill is incorrect or incomplete, it is your responsibility to ensure that the bill is corrected or to pay the correct amount by the payment deadline.

Health Insurance Requirements/Payment

Financial Aid Stipends:

Entering students are normally offered research assistantships, fellowships, or traineeships that include payment of a stipend and tuition. Students are strongly encouraged to apply for predoctoral fellowships from the National Science Foundation by November of their first year in residence. Applications are available in October and due in November. Check with the Graduate Support Section of Financial Aid for further details. Students are also encouraged to apply for other outside fellowships. The Awards Data Base available on Folio (a computer on-line system) contains information on over 1,200 awards of academic interest. Departmental funds are used to supplement support from all sources to the university annual required level and to pay for health insurance. Student fees, late fees, etc. are the responsibility of each student. Students may receive stipends quarterly or semi-monthly depending on their funding source.

For those students on fellowships who are paid quarterly, the stipend checks are usually issued the day before classes begin. Checks are sent to the "mailing address" listed in axess.

Students who are paid semi-monthly (RA salary) will be paid on the 7th and the 22nd of the month (or on the preceding work day if these dates fall on a weekend or holiday). Checks are sent to the department. Semi-monthly paychecks may be directly deposited in local banks upon request to the departmental business office staff.

The Department endeavors to provide tuition and stipend support to its doctoral students as needed through the completion of their degree, provided that student maintains satisfactory progress toward the degree.  The Department/Advisor (as appropriate) cannot however guarantee such support beyond the middle of the 5th year of study.

Outside employment is discouraged.

Tax

Tuition

Tuition is fully covered by research assistantships or traineeships at 10 units. Tuition paid by the department is paid directly to the University. Students will receive tuition credit on their University bill

Health and Safety

Stanford University's health and safety mission is to provide a safe and healthy environment for faculty, students and staff and to assure compliance with federal, state and local regulations. The University Environmental Health and Safety (EH&S) office manages health and safety programs for the School of Medicine such as:

Each person working in a lab is required to be trained in the specific hazards of his or her job. Laboratory safety is a component of the orientation to a research lab. It is the Principal Investigator's responsibility to provide training for lab equipment, procedures and chemicals. EH&S provides two mandatory training sessions.

EH&S, through the Health Physics Department, provides mandatory training for use of radioisotopes as part of Stanford's licensing agreement with the State of California. New students need to contact Health Physics and complete the following before they can work with any radioactive material:

In conjunction with the Medical School's Health and Safety Program office, EH&S provides mandatory Lab Safety Training. The office also assists in resolving safety problems and provides each department Safety Team with safety information and regulatory compliance strategies. EH&S provides a variety of environmental health and safety services:

The Department has developed a Building Response Team made up of representatives of the research and administrative staffs and students. Their initial goals will focus on compliance issues, education and training, disaster preparedness and accident reporting. They also maintain copies of the Radiation Safety Manual, Stanford Biohazardous Materials Guidelines, Stanford Safety Manual and Material Safety Data Sheets (MSDS) and department training records.

Transportation

Cars:   Permits are required for parking on campus. Three types are available: “Resident” permits that allow you to park at your campus dorm or apartment. “A” stickers entitle you to park in any lot. “C” stickers enable you to park only in “C” lots which are further away. Both A&C permits are available to commuters (students not living on campus). Carpool and vanpools permits are also available to eligible persons. For more information call the Parking & Transportation office at 723-9637 or visit their website http://transportation.stanford.edu/

Bicycles: The California Vehicle Code requires registration bicycles to aid in identification and recovery if stolen. Tressider Recreation center registers bicycles Mon-Thur afternoons. Call 723-4361 for information. Engravers are available at the Police Station to engrave a license number or Stanford student ID number on bicycle frames. Stolen bicycles should be reported to the Police station (723-9633).

Marguerite Shuttle: The Marguerite is the main campus public transport and is free. It operates Mon- Fri all year except on University holidays.

Caltrain: This train has many convenient stops from San Francisco to Gilroy. The marguerite can shuttle from both Palo Alto stations into Stanford. See website for updated schedule: http://www.caltrain.com/site3.aspx

Departmental Facilities

The Department of Molecular & Cellular Physiology, located on the main floor of the Beckman Center, is part of the Medical Center Complex. Most lab space and equipment is shared and members of different laboratory groups are intermingled. This is a popular and efficient way to promote collaboration and intellectual interaction. The Beckman Center houses a Protein and Nucleic (PAN) core facility equipped for the synthesis and characterization of macromolecules. The Fluorescence Activated Cell Sorter Facility is located on the ground floor along with Munzer Auditorium, PAN facility, Cell Sciences Imaging Facility and the Bistro Café.

Computer Resources:

Mail

Pantry

Located in B100. It includes Microwave, refrigerator, toaster oven and sink and cabinets.

Card Key Security System

Department Library/Conference Rooms

RESERVATIONS: See any admin or Schantae

Outside of Department Resources

Post Office

Banking

Tresidder Memorial Union

Bechtel International Center

Stanford Bookstore

Lane Medical Library

Fleischmann Learning Resource Center

Resource Links:


Stanford Medicine Resources:

Footer Links: