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Doctoral Programs In Pharmacology And Physiology

Year 1

Students are admitted into the CMPP program on a provisional basis for the first year. After successful completion of the first year of study- which includes required coursework, laboratory rotations (including written and oral reports), and selection of a thesis advisor, students formally enter the graduate studies program of the Department of Pharmacology and Physiology. During the first year, students will be advised directly by the CMPP program director.

Coursework

The following courses, or acceptable equivalents as determined by the Graduate Studies Committee, are required of all Ph. D. candidates:

Required courses (26 credit hour, total):

  • IND 408 Adv. Biochemistry (5 credit hours, fall course)* IND 409 Cell Biology (4 credit hours, fall course)*
  • IND 410 Molecular Biology (4 credit hours, spring course)*
  • IND 501 Ethics in Research (1 credit hour, fall course)*
  • PHP 403 Human Cell Physiology (4 credit hours, fall course) * PHP 502 Seminar (4 credit hours, fall/spring course)*§
  • PHP 404 Principles of Pharmacology (4 credit hours, spring course)*

*These courses are typically taken in the first year; requests to take these courses after the first year require approval of the Graduate Studies Committee.

†Elective courses (6 credit hours, total):

  • IND 447/PHP 447 Signal Transduction (4 credit hours, spring course) PHP 405 Effective Scientific Communication (2 credit hours, spring course)
  • PHP 550 Ion Channels and Disease (2 credit hours, spring course)
  • MBI 473 Immunology (3 credit hours, fall course)
  • NSC 525 Biology of Neurological Diseases (3 credit hours, spring course) BST 463 Introduction to Biostatistics (4 credit hours, fall course)
  • PTH 507 Cancer Biology (3 credit hours, spring course)
  • PTH 509 Pathways to Human Disease I (4 credit hours, fall course)
  • PTH 510 Pathways to Human Disease II (4 credit hours, spring course) PTH 571 Molecular Basis of Disease (3 credit hours, fall course)
  • CVS 401 Cardiovascular Biology and Disease (3 credit hours, fall course)

†Selection of appropriate elective courses that complement the student’s research area should be done in conjunction with the student’s thesis advisor in consultation with the Director of Graduate Studies. Elective courses can be taken at any time during the student’s period of study, though most students prefer to complete all course requirements within the first year. Requests to take elective courses that are not on the recommended list require approval of the Graduate Studies Committee. Requests for approval should be made prior to the semester in which the course is held.

§ Attendance at all Department of Pharmacology and Physiology seminars and lectures is required until the requirements for the Ph.D. are completed. Each student is also required to formally enroll in PHP 502 each semester through their years of graduate study; however, a total of 4 credits are required. The student must present a seminar in this series at least 4 times prior to graduation. Seminar topics may consist of research areas in pharmacology and physiology, and dissertation progress reports. Topics will be chosen by the course director or by the student with approval of the course director. Students are encouraged to attend research seminars of local and visiting scientists hosted by other departments. In addition, students are strongly encouraged to join one of several journal clubs run by faculty within the department.

Assessment

All required courses, with the exception of PHP 405 and 502, and IND 501 must be taken on the A/E system; Rotations, PHP 405, 502 and IND 501 are taken on the S/E system. Minimum passing grades for courses and research carrying credit are C or S, although C is considered a failure for any student on probation.  Students who receive a grade of C in any two courses will be terminated from the program. Those students with a GPA less than 3.0 at the end of the academic year and/or those who have received a grade of ‘C’ in any course may be dropped from the program. Alternatively, the student may be permitted to undergo a first-year examination (discussed in detail below).

A/E System

  • A - Excellent
  • A-
  • B+
  • B-
  • C - Poor
  • E - Failure
  • I - Incomplete
  • IE - Incomplete and Failure
  • W - Withdrawn
  • No Report

S/E System

  • S - Satisfactory
  • E - Failure
  • I - Incomplete
  • IE - Incomplete and Failure
  • W - Withdrawn
  • No Report

Laboratory Rotations

All first-year students must successfully complete at least three laboratory rotations before formally entering the program in Pharmacology or Physiology. Under most cases, these rotations will have been completed during the student’s first year of study.  These laboratory rotations provide an opportunity to gain a broader perspective of the sciences of pharmacology and physiology and, at the same time, allow the student to become familiar with the diverse investigative activities being pursued within the University of Rochester Medical Center. Typically, faculty who are interested in having students rotate in their laboratory present brief overviews of their research projects at the beginning of the semester to highlight ongoing studies. However, students are encouraged to contact faculty directly to determine whether the faculty member is accepting students. The duration of each rotation is 10 weeks, and students are expected to spend at least 10-12 hours per week in the lab.

Rotation Assessment

The Program Director will meet with students at the beginning of their first academic year to discuss faculty expectations of student performance during the rotation period. To obtain a satisfactory grade for a rotation, a student must participate in the activities of the lab (such as journal clubs and lab meetings), complete experimental activities agreed upon, and be able to demonstrate proper documentation, analysis, and presentation of acquired data. Rotations will be assessed through a combination of evaluations, and written and oral reports.

  1. At the end of each rotation, both the student and mentor will each complete a written evaluation. Forms for these evaluations can be found on the graduate forms website. The mentor is expected to discuss their written evaluation with the student and submit following the instructions on the bottom of the form.
  2. In addition, the student must complete three written reports on their rotation experiences. These entail a two-page report on each of their 1st and 2nd laboratory rotations, and a five-page report on any one of their rotations (most likely from the lab that has been joined). The reports will describe the research problem encountered during the rotation and include the following subsections: background, significance/rationale, approach, future directions, figures as appropriate, and references (figures and references not included in page limit). The two-page reports should be completed with the input of the rotation advisor, and the final document submitted to the CMPP Program director and Year 1 program coordinator within 1 week of the end of the rotation. The five-page report is due June 30th. This report will follow the same format as the two-page interim reports, but it will be evaluated by two members of the CMPP Committee. The students will work with their assigned CMPP committee member to revise the document as needed, with a final due date of July 31st. The overall evaluation of these three writing exercises will be considered one part of each student’s end of first year evaluation. Students selected to take the first-year exam will be exempt from writing the five-page report.
  3. First-year students will also present a 30-minute talk on a selected rotation at the end of the semester as part of the student colloquium.

Faculty Review of Student Performance

At the conclusion of the academic year, the Graduate Studies Committee meets to discuss the academic performance of first-year students. Coursework grades and laboratory rotation evaluations are used to assess student performance. Students are expected to have an overall GPA of at least 3.0, and rotation evaluations of “meets expectations” or “exceeds expectations” (scale = Exceeds Expectations/ Meets Expectations/Needs Improvement/Unacceptable) for lab rotation performance. Those students with a GPA less than 3.0 and/or those who have received a grade of ‘C’ in any course may be dropped from the program. Alternatively, the student may be permitted to undergo a first-year examination (discussed in detail below). Students must receive a grade of “Pass” on this exam to remain in the program. At the conclusion of the first academic year, a summary of student performance and recommendations of the Graduate Studies Committee are presented to the Department Faculty by the Director of Graduate Studies. Students who have successfully completed their first year of studies receive a letter from the Director of Graduate Studies indicating admittance into the Doctoral Program in Pharmacology and Physiology. The Director of Graduate Studies meets individually with those students who did not meet the performance criteria in order to convey performance deficiencies and concerns of the faculty and discuss remediation.

First-year Examination

Students receiving a "C" in a course and/or having an overall grade point average of less than 3.0 after the first year are required to take the first-year exam. The purpose of the exam is to evaluate a student's critical thinking skills in both written and oral formats, in order to identify those students who appear capable of completing all requirements for the doctoral program. The subject of the first-year exam is a recent article from the literature. Faculty members from the Department of Pharmacology and Physiology submit recent articles to the Director of Graduate Studies. A group of papers that align with the background and interests of the student is assembled by the Graduate Studies Committee. Students taking this exam meet with the Director of Graduate Studies, who reviews the instructions for completing the exam and explains the expectations for passing the exam to the student(s). Written instructions and expectations are provided to those students and faculty participating in the exam. Students are not allowed to retake this exam. Failure results in termination from the program. Students who pass the examination receive verbal feedback on their performance immediately after the exam.

Year 2

Students formally enter the graduate studies program of the Department of Pharmacology and Physiology following completion of their first-year of study in one of the first-year program areas. Students must designate a thesis advisor and Ph.D. track (Pharmacology or Physiology). The selection of a thesis advisor requires approval by the Director of Graduate Studies and the Graduate Studies Committee. A faculty member may not be able to accept a student for some of the following reasons: (1) insufficient laboratory space or facilities; (2) lack of funds to support research; (3) commitments that prevent the faculty member from devoting sufficient time to the student’s training and education; and (4) plans for a sabbatical leave. Students wishing to make a change in their selection of thesis advisor must petition the Director of Graduate Studies and provide the Graduate Studies Committee with the rationale for electing a different advisor.

Thesis Advisor

Full-time, tenure-track faculty members at the University holding primary or secondary appointments in Pharmacology and Physiology, as well as full- time, tenure-track faculty members of the Aab Cardiovascular Research Institute may serve as a Ph.D. thesis advisor to graduate students in the Pharmacology and Physiology programs. A thesis advisor should be selected by June 1 of the first academic year. Selection of the Thesis Advisor requires approval by the Director of Graduate Studies in Pharmacology and Physiology. Expectations of graduate students and of thesis advisors can be found at the graduate forms site

Thesis Advisory Committee

The thesis advisory committee performs several functions during the student’s time at the University. It serves as the basis for the qualifying examination committee, reviews the student’s progress on an annual basis, provides advice during the development and progression of the research project, and serves (along with an appointed Chair) as the examination committee for the thesis defense. The Thesis Advisory Committee should be consulted during conception of the thesis problem, execution of the thesis research, and the writing of the thesis. A faculty member does not need to be performing similar scientific research to be a valuable committee member. Often, those with peripheral knowledge of the student’s research area can see important avenues of study because of their different perspectives.

Students are expected to assemble their thesis advisory committee by the end of their second academic year. Students, after consultation with their faculty advisor, should submit the list of prospective committee members to the Director of Graduate Studies in Pharmacology and Physiology for approval. The Department of Pharmacology and Physiology requires that the thesis advisory committee be composed of three faculty members in addition to the student’s thesis advisor, for a total of four committee members. The University requires that the final thesis committee be composed of at least three faculty members (including the student’s advisor) - two faculty members with primary appointments in Pharmacology and Physiology and one faculty member with a primary appointment in another department. Therefore, to satisfy both requirements…

… if the student’s thesis advisor holds a primary appointment in Pharmacology or Physiology, the student should choose one more primary faculty for the committee to satisfy the requirements of the Dean’s office. The third member should hold a primary appointment in another department. The fourth committee member can hold either a primary or secondary appointment in Pharmacology and Physiology.

…if the student’s thesis advisor does not have a primary appointment in Pharmacology and Physiology, the student should select two committee members with primary appointments in this department. The fourth committee member should have a primary appointment in another department.

At any time, the student and his/her thesis advisor may petition the Director of Graduate Studies and the Graduate Studies Committee to alter the composition of the Thesis Advisory Committee in order to reflect changing needs of the student’s research project.

Seminar

Second-year students will present two seminars during the year – one in the fall and one in the spring.  In the fall semester, second-year students will present a literature review of his/her choice. During the spring semester, students will present a research/literature seminar designed to incorporate some of their preliminary laboratory research in conjunction with relevant recent literature.

Teaching (TA) Requirement

Students are required to act as a teaching assistant in one or more courses prior to completion of their degree. Typically, this requirement is fulfilled during the second year, but can be fulfilled at any time. A minimum of 8 student contact hours are required. Students may TA more than one course, or more than one semester, to satisfy this requirement. Students are strongly recommended to contact the course director for the course that they wish to TA far in advance of the semester the course will be offered. Upon completion of a teaching assistantship, the student must submit a TA Requirement Certification form, signed by the course director, to the Graduate Program Administrator. Below is a list of courses in which there are opportunities to TA. Students who wish to TA courses not on this list will require prior approval from the Graduate Committee.

  • PHP 403 Human Cell Physiology – Fall
  • PHP 404 Principles of Pharmacology – Spring
  • IND 447/PHP 447 Signal Transduction – Spring
  • HSF 110 Human Structure and Function, First-year medical school course – Fall (CV/BP and Pulmonary Physiology labs) *Commitment is 2 consecutive years* PHP 100 Medical Pharmacology, First-year medical school course – Spring (Small Group Facilitator) *Commitment is 2 consecutive years*

Qualifying Examination Preparation

Students are strongly encouraged to meet with their thesis advisory committee prior to scheduling their Qualifying Examination. During this meeting, the student and committee members should discuss the student’s emerging research proposal. The Director of Graduate Studies meets with second-year students to provide students with the rules and expectations of the qualifying examination. A written summary of rules and expectations will be provided at the meeting. The Qualifying Examination may be scheduled as early as the spring of the second year of study, but must be completed no later than October 1st of the third academic year.

Year 3

The third year of study is marked by the completion of the Qualifying Examination in the fall. Students must also maintain a 3.0 GPA throughout their years of study, attend departmental seminars, and continue full-time research. 

The Qualifying Examination

Exams may be scheduled as early as the spring of the second year of study, but must be completed no later than October 1st of the third academic year. An examination grade of “Fail” is recorded for those students who have not taken the exam by the deadline. Whether the student is permitted to take the exam at a later date is left to the discretion of the Graduate Studies Committee. A second failing grade results in termination from the program. The Qualifying Examination is administered by members of the student’s Thesis Advisory Committee, plus two ad hoc faculty members appointed by the Director of Graduate Studies. The appointed faculty members serve for the Qualifying Examination only, and are not permanent members of the student’s Thesis Advisory Committee. Students must schedule the exam at least one month prior to the actual date of the exam and inform both the Director of Graduate Studies and the Graduate Studies Coordinator of the date, time, and location of the exam. The exam consists of an "open" seminar, followed by a "closed" session, during which time the student is questioned by committee members. The closed portion of the exam typically lasts between two and three hours.  The thesis advisor is not present during the closed examination. The student will submit the required paperwork and research proposal (ten-page maximum) in the NIH grant-proposal format to all members of the Qualifying Examination committee at least 15 work days prior to the examination. Failure to distribute the written document by the deadline, without prior approval from the Graduate Studies Committee, will result in cancellation of both the examination and seminar, and the exam will be recorded as ‘Fail’. The student will be given an opportunity to retake the exam once. Details of the format of the written portion of the exam are listed below. Failure to follow the formatting guidelines will result in the proposal being returned to the student and may result in a recorded grade of “Fail” for the exam.

Written Exam Specifications

Students are expected to propose a logical series of experiments designed to test a stated hypothesis and to defend their proposed ideas and approaches. The examination is not intended to be an abridged thesis defense, and therefore, limited preliminary data is required.

  1. Students must use the current NIH-style format for their proposal.
    References are not included in the 10-page limit. All print (including figure axes and legends) must be clear and legible.
  2. Font: Use an Arial or Helvetica typeface and a font size of 11 points or larger. A symbol font may be used to insert Greek letters or special characters; the font size requirement still applies. Type density, including characters and spaces must be no more than 15 characters per inch. Type may be no more than 6 lines per inch
  3. Page Size and Margins: Use standard size (8 ½” x 11”) sheets of paper.
    Use at least one-half inch margins (top, bottom, left, and right) for all pages. Use single column format. The proposal must be single-sided and single-spaced.
  4. Number pages consecutively. Do not use suffixes (e.g. 5a, 5b, etc.). Do not include unnumbered pages.

Oral Examination

The aim of the research proposal/qualifying examination is to assess the student’s general knowledge of the broad aspects of pharmacology and physiology and to test the student’s ability to apply this knowledge to the solution of research problems. Students must deliver a 60 minute (50-minute presentation, 10 minutes for questions) open proposal seminar prior to the closed examination. During this seminar, students should clearly state the hypothesis to be tested by the specific aims of the proposed project, provide justification for the research through consideration of published literature and/or preliminary data, and clearly outline the proposed line of experiments and anticipated results. Students should make every attempt to schedule their open seminar during the Student Colloquium Series (PHP 502). However, in some instances scheduling constraints may require the open seminar and exam to be scheduled at an alternate time.

Evaluation

During the closed examination, students will be evaluated by their ability to satisfactorily answer questions raised by committee members that focus primarily on the following issues:

  1. Does the proposed research project address a valid and important scientific question?
  2. Has a central hypothesis been clearly stated? Is the hypothesis supported by published literature and/or preliminary data?
  3. Does the student have a broad and firmly based knowledge of the literature related to the area of research?
  4. Do the proposed methods appropriately address the hypothesis? Are the questions likely to be answered by the proposed approach?
  5. Are the proposed methods feasible? Does the student understand the limitations of the proposed techniques and possible technical obstacles? Does the student have alternate approaches in mind?
  6. Can the student clearly describe the predicted results and competently interpret the multiple possible outcomes of the experiments?
  7. Is it likely that the project could be completed within the requisite time frame?
  8. Is the scientific significance/importance of the question clearly stated? Is the relevance of this information to human health/disease clearly expressed?

Re-Taking the Exam

If a student fails the examination, he/she may be given an opportunity to retake the exam once. According to the U of R Regulations and University Policies Concerning Graduate Studies, “A second qualifying examination after failure, if permitted, may be taken after a period of five calendar months.” Given scheduling constraints, students should allow plenty of time to arrange with their Qualifying Examination Committee the date, time, and location of the Qualifying Examination. In addition, the student must submit two forms (available from the graduate program coordinator) along with an Abstract and Title Page to the Senior Associate Dean for Graduate studies requesting that the examination be scheduled. This form must be sent no later than 15 work days before the scheduled examination.

Seminar

During the third year of graduate work, a seminar is delivered in conjunction with the Qualifying Examination and is the only seminar required for the year.

The Remaining Years

The remaining years of graduate study are spent on full-time research developing the research project that will be described in the Ph.D. thesis. The research advisor and thesis advisory committee play key roles during these years.

Annual Assessment

Following successful completion of the Qualifying Examination, students must meet with their thesis advisory committee at least once yearly. During these meetings, the committee will discuss the student’s progress and clarify research problems. A written report of the student’s progress must be approved by the committee and then submitted to the Director of Graduate Studies and Senior Associate Dean for Graduate Studies, by June 1 of each academic year. If the annual progress report is not submitted by this deadline, stipend funding may be terminated. The form for this report can be found on the Graduate forms website(Evaluation- Annual).

The annual committee meeting is typically done in conjunction with the student’s required seminar. Prior to the committee meeting, students will work with their research advisor(s) to fill out the annual progress report and then distribute the report to committee members. Students who receive an overall performance evaluation of ‘good’, ‘fair’, or ‘poor’ (scale = poor/fair/good/very good/excellent/outstanding) will be asked to schedule bi-annual committee meetings to provide more feedback to the student. The Director of Graduate Studies will meet with students who receive a grade of ‘fair’ or ‘poor’ and their advisor to discuss potential ways to improve performance. The completed annual progress report (signed by all committee members) should be submitted after this meeting.

Additional Requirements

Students are encouraged to work closely with their thesis advisor to submit a predoctoral grant application in year 3 or 4. Students are expected to submit at least one first author peer-reviewed manuscript for publication before their doctoral defense.

Dissertation Preparation and Defense

The dissertation (thesis) is written after the student's Thesis Advisory Committee and advisor have approved the completion of the thesis research. The expectation of the CMPP program is that each dissertation shall be a report on independent research, consist of a body of work of suitable scope and depth, and be formulated in a manner worthy of publication. All collaborations and other contributors to the student’s thesis should be clearly indicated and defined in the written document and public presentation.

When the student is ready to write the thesis, the appropriate form should be signed and delivered to the graduate program coordinator. He or she should go to the following website to print out a copy of the booklet "Preparing your Thesis, A Manual for Graduate Students”- http://www.rochester.edu/theses. This booklet outlines the University's requirements for format, documentation, and the physical form of the thesis. The student must prepare the

thesis to meet the requirements set forth in this booklet.  Students should also consult the “Regulations and University Policies Concerning Graduate Studies” for additional instructions. The student should reach an agreement about the format and content of the thesis with their advisor prior to writing the thesis. The advisor has the ultimate responsibility and authority to determine the format of the student's thesis.

Overview of Thesis Defense Process and Registration of Defense:

Important Due Dates

  1. At least 6 months prior to scheduling a defense – meet with your advisory committee to request approval to begin writing thesis.
  2. At least 4 months prior to scheduling a defense – notify your graduate program coordinator of the three faculty members to nominate to serve as Chair for your defense.
  3. At least 2 months prior to the date of defense – arrange date, time, and location of defense with committee and poll your defense chair and advisory committee to determine their preference for thesis format (hard copy/pdf). Notify the Registrar and graduate program coordinator of defense date. Your graduate program coordinator will start your defense record in an online SharePoint, PhD Completion Site. You will work with your graduate program coordinator to provide other documents to complete the online defense record. Check with your graduate program coordinator to determine when these documents must be submitted. 
  4. At least 25 work days prior to the date of defense – provide thesis to your graduate program coordinator to upload to online system and make hard copies as needed.
  5. At least 15 work days prior to the date of defense – graduate program coordinator will confirm thesis and all paperwork is uploaded to online system and approve. This generates an email to your advisor, advisory committee and program director to request online approval of the thesis submitted for defense.
  6. At least 10 full work days prior to the date of defense – advisor, advisory committee and program director have approved your thesis for defense. The thesis and defense record is reviewed and approved by SMD Senior Associate Dean for Graduate Studies.
  7. At least 5 full work days prior to the date of defense – registration of thesis for defense. The University Dean for Graduate Studies reviews and approves the thesis and defense record. This generates an email to your defense chair, advisor and advisory committee announcing the date, time, and location of defense. The defense chair receives instructions for the defense, forms and for reporting the exam outcome.

Nomination of Defense Chair

A Chair is appointed for each Ph.D. oral defense exam to monitor and promote fairness and rigor in the conduct of the defense. The Chair’s status as a nonmember of the advisor’s and student’s working group, program, or department enables distance from previously established judgments on the candidate’s work. The outsider status also limits the Chair’s and member’s’ ability to use department administrative influence in the defense process. The candidate and advisor will nominate three individuals to serve as Chair using the Request for PhD Chairperson form prepared by the graduate program coordinator and submitted to the Senior Associate Dean for Graduate Studies. You will be notified of the Chair selection and the selected chair and will be included in the planning for specific defense dates.

Registration for Defense

At least 15 full work days prior to the date of defense, the final thesis and required forms must be uploaded to the online system. Work with the Registrar and graduate program coordinator to ensure completion of forms.

Final Oral Examination

The Final Oral Examination will be taken after completion of all other requirements for the degree, but not earlier than six months after passing the cumulative and oral qualifying examinations. The examination consists of two parts: the first part is a public seminar that describes the work presented in the dissertation. The second part of the examination takes place immediately after the seminar and after all questions have been satisfactorily answered. The student will then meet privately with the Dissertation Advisory Committee to defend the dissertation.

After your Defense

After a successful defense, the student must make the corrections requested by the advisory committee as well as corrections from the University Dean for Graduate Studies.  The University Graduate Studies (UGS) office may also notate required corrections to the format of your thesis. This annotated copy, along with the original thesis, will be stored in the PhD Completion Site for you to reference after your defense. Log into https://phdprocess.ur.rochester.edu to access this document; in most cases your graduate program coordinator will download and provide it for you. If required, a final signed form from the student’s advisor indicating that all changes have been made will be submitted to the UGS.

  1. Once all corrections/revisions are completed, all PhD students must attach a pdf of their final abstract (350 words or less) and attach a pdf of their final dissertation to the UR ProQuest site (http://www.etdadmin.com/rochester. You will receive instructions for the ProQuest publishing process from the University Graduate Studies (UGS) office. In addition, you will receive instructions from UGS for other forms to complete that are required for the completion of the degree.
  2. After your final thesis is submitted to ProQuest, provide a PDF version to your graduate program coordinator who will have hard cover bound copies made - one for the student, one for your advisor, and one for the department library. This is a courtesy paid for by the Department of Pharmacology and Physiology. You can have additional copies bound, at your expense. Do not request bound copies through ProQuest.

Note: Please be sure that the graduate program coordinator receives a copy of any correspondence between your advisor and the Senior Associate Dean for Graduate Studies Office that concerns your qualifying examinations and thesis registration. It is important that accurate records be kept within the department on the status of each student.