GRADUATE STUDENT HANDBOOK Department of Cell and Molecular Pharmacology & Experimental Therapeutics 2015-2016
OBJECTIVE OF THE PROGRAM Our objective is to train new investigators in molecular and cellular pharmacology. In the broadest sense, drugs are chemicals that affect living systems, and pharmacology is the study of how these chemicals produce their effects. The specific goals of pharmacology are: (1) to understand the interactions between chemicals (drugs) and the mechanisms that underlie normal and abnormal cell function, (2) to manipulate these processes to prevent and correct diseases and, (3) to improve the quality of life for mankind. The Pharmacology Graduate Training Program is well suited for students seeking a connection between the basic and clinical sciences. It is an integrative study that draws knowledge from several disciplines--biochemistry, molecular biology, and human physiology--to explain how drugs elicit therapeutic or toxic effects upon living organisms. Our studies are focused upon the discovery of biological mechanisms and the development of novel therapeutic agents. Pharmacology students are exposed to comprehensive training focused on critical thinking and innovation. Graduates from our program have successfully transitioned to careers in biomedical science within academia, the pharmaceutical industry, and government agencies. Departmental Research Interests: Cancer Biology Signal Transduction Regulation of Heterotrimeric G Proteins Redox Signaling Drug Discovery Drug Resistance Cancer Chemoprevention Protein Mass Spectrometry/Proteomics Cancer Biomarkers RNA splicing and Epigenetics Tumor Microenvironment OVERVIEW During the first year, students will take the Biomedical Sciences First Year Curriculum that provides a theoretical foundation in cell biology, molecular biology, and biochemistry. The students rotate through three laboratories of their choosing. During each rotation, the student works with a faculty member on a research project. From these rotations and other interactions with the faculty, the student will select a mentor and project for the dissertation. During the second year, students will take professional and graduate courses in cell and molecular pharmacology, physiology, and therapeutics, after which written and oral qualifying examinations are taken. The minimum passing grade for professional (medical) courses is set at 80, while the minimum passing grade for graduate courses is 70. In year three, a plan of research for the dissertation project is written in the form of a National Institutes of Health fellowship proposal (1 page for Specific Aims and 6 pages for Research Proposal). Upon approval by the student's Advisory Committee, the student continues dissertation research, which culminates in the dissertation and defense before the student's advisory committee and the graduate 2
faculty of the University. The publication of at least one first-authored peer reviewed manuscript is required for completion of the program. The student will also attend and participate in the Pharmacology Departmental Seminar Series and present a research seminar to the department at least once per year. Throughout the program, but especially the last two-to-three years of training, the student is encouraged to attend national meetings and present his/her research findings at these meetings. In addition to the desired scientific interaction, this allows recognition of the student as a developing investigator at a national level and facilitates the attainment of high-quality postdoctoral positions and career placement. The following provides details of the graduate program. Deviation from the requirements listed below requires approval of the Graduate Training Committee. The Graduate Training Committee is always open to suggestions from students and faculty about how to improve the program. CURRICULUM The following table shows courses required of all Ph.D. graduate students. The schedule will differ for those students in the Medical Scientist Training Program pursuing M.D. and Ph.D. degrees. The course requirements and timeline for MSTP students is on page 10. CURRICULUM First Year Fall Semester (16 hr) Spring Semester (15 hr) Summer Semester (15 hr) Common First Year Curriculum (13 hr) Foundations of Biomedical Sciences Laboratory Rotation (3 hr) Common First Year Curriculum (7 hr) Foundations of Biomedical Sciences Spring elective: PCOL 724 Drug Discovery/Molecular Pharmacology (3 hr) Laboratory Rotation (5 hr) Common First Year Curriculum Scientific Writing (2hr) Laboratory Rotation (13 hr) Second Year Fall Semester (15 hr) Spring Semester (15 hr) Summer Semester PCOL 721 Principles of Pharmacology (4 hr) PCOL 625 Physiology (4 hr) Dissertation Research (7 hr) PCOL 621G Pharmacology (4 hr) Dissertation Research (11 hr) Written Qualifying Exam (June) Dissertation Research (15 hr) Third, Fourth, Fifth Years Fall Semester Spring Semester Summer Semester Dissertation Research (15 hr) (Advisory Committee appointed by May, 3rd yr) Elective Courses Dissertation Research (15 hr) (Oral Qualifying Exam, September, 3rd yr) CGS 700 Clinical Biostatistics (4 hr) Elective Courses Dissertation Research (15 hr) (Plan of Research presented by June, 3rd yr) (Plan of Research approved by end of 3rd yr) 3
ELECTIVE COURSE WORK: Upon passing the Qualifying Exams and Admission to Candidacy, the student is required to choose and take two advanced courses with approval of the choices by the student s mentor. Advanced courses are offered by multiple training programs in the College of Graduate Studies including Pharmacology. The electives chosen should align with the student s research interests. These may be taken at any time prior to defense of the dissertation. EVALUATION OF STUDENT PROGRESS Before the Advisory Committee is formed, the Pharmacology Graduate Training Committee and/or Graduate Training Coordinator is responsible for monitoring the progress of the student. The Graduate Training Committee evaluates the academic performance of students in their course work at the end of each semester. Once an advisory committee is formed the student s progress is monitored at least once a year using the Annual Evaluation of Student (Committee Meeting Form). In addition, the Graduate Training Committee meets with all mentors once a year to discuss the progress and development of each student as an investigator. If a student has a problem with any aspect of their graduate training experience they may seek help from their Graduate Training Program coordinator. If the issue cannot be discussed with the Graduate Training Coordinator, then the student should go to the chairperson of the department or the chairperson s designee for resolution of the problem. After following the above protocol for problem resolution, the student may seek the advice of the Dean of the College of Graduate Studies. The student may also appeal any decisions made by the Graduate Training Committee or Chairperson. If the student disagrees with the decision of the Dean of the College of Graduate Studies he/she may appeal to the Provost. LABORATORY ROTATIONS: The students are expected to rotate through three laboratories of their choosing. During each rotation, the student works with a senior investigator on a research project. This requires reading and discussion of background material and participation in experimental design, data collection and analysis of results. The purposes of these rotations are four-fold: 1) to orient the student to scientific investigation per se and to various investigative approaches; 2) to allow the student to learn laboratory techniques in a hands-on manner; 3) to allow the student and faculty to get to know each other well; and 4) to provide the student with the information necessary for the selection of a dissertation project. WRITTEN QUALIFYING EXAM: After completing all required course work, the student will take the Written Qualifying Exam offered in June of each year. The exam, given as a take home assignment over a 1 week period, covers course work, and assesses the ability of the student to interpret data, form hypotheses and design experiments to test the hypotheses. The passing grade is 70%. If the student fails this exam, it may be retaken at the discretion of the faculty. A minimum of three months between the first and second exam is usually required by the faculty. 4
ORAL QUALIFYING EXAM: Upon passing the Written Qualifying Exam, the student, with input from his/her mentor, selects a research topic to work up and present for the Oral Qualifying Exam (to be held in September following the Written Exam). The topic must be approved by the student s mentor. It is suggested that the student at this time select members for the Dissertation Committee. This Committee consists of 5 members, with 2 members outside of the student s department (see below). The student is encouraged to devise hypotheses and Aims with the approval of their mentor and input from the Dissertation Committee. In the event that the Dissertation Committee is not formed, the student may consult with members of the Graduate Training Committee. The student should deliver a 30-40 minute presentation, addressing 2 to 3 specific aims, along the following lines: 1. overview of the problem 2. hypothesis or hypotheses to be tested 3. experimental design 4. description of the predicted results 5. interpretation of the data 6. limitations of the experimental approach 7. estimate of time required to complete experiments and analyze data The presentation will be used as a framework for the exam by the faculty. The student s depth of knowledge will be explored. The student is expected to be able to explain common laboratory techniques and more specialized techniques to be used in the experiments, to be fluent with the literature relevant to the problem, and to be able to suggest and deal with alternative hypotheses and approaches. In addition, broader questions may be asked as well as questions relating to any areas of weakness detected by the Written Qualifying Exam. The faculty recognize that the Oral Qualifying Exam may be the first exam of this type taken by the student. The student is encouraged to consult with more senior students about their experience with the exam. However, it should be recognized that every oral exam is different because the research topic and strategy differ. Further, the student is encouraged to use the exam as a first opportunity to present hypotheses and strategies being considered for the dissertation project to a group of scientists for feedback regarding level of enthusiasm, potential problems, and alternative approaches that might be considered. Evaluation of the student s performance in course work, in the laboratory and on the qualifying exams provides the basis for the faculty to decide whether the student should be admitted to candidacy for the Ph.D. degree. The entire Pharmacology faculty is invited to participate in both exams and in the decision on admission to candidacy. 5
FORMATION OF ADVISORY COMMITTEE: For incoming students, their Advisory Committee is the Graduate Training Committee which consists of: Jennifer Isaacs, Ph.D., Chair Lauren E. Ball, Ph.D. Joe Blumer, Ph.D. Scott T. Eblen, Ph.D. Mariana Pehar, Ph.D. Steven A. Rosenzweig, Ph.D. Kenneth D. Tew, Ph.D., D.Sc. ex offici Official approval of the student s Advisory Committee must be obtained by the Chair of the Graduate Training Committee, the Chairman of the Department, and the Dean of the College of Graduate Studies by the first of May in the student s third year. The Committee will include the mentor, two additional faculty from Pharmacology, and two faculty from outside the department. In those cases where the mentor does not hold a primary appointment in Pharmacology, the student must select three members of the Pharmacology Department to serve on the advisory committee. The Committee may have additional members if desired. A major criterion for selection of faculty for the Committee is that the investigator can effectively interact with and help the student on his/her dissertation project. Further, the Advisory Committee can be modified if the changes are justified (e.g., major change in dissertation topic). The student must meet with the Advisory Committee at least once a year. PLAN OF RESEARCH: The Plan of Research is written in the format of a training fellowship, comprised of a Specific Aims page and a 6 page Research Strategy, with references limited to 4 pages. In June of the third year, the student will present a 50-minute seminar on the Plan of Research to students, fellows and faculty including the student s Advisory Committee. Two weeks prior to the seminar, copies of the Plan of Research must be distributed to the Advisory Committee. Following the seminar, the student and Advisory Committee will meet to discuss the Plan of Research in more detail. The Plan of Research must be approved by the Advisory Committee no later than the end of the third year in the program. The seminar on the Plan of Research can, of course, be presented earlier as desired by the student and the mentor. The Plan of Research is not a binding document or contract between the student and mentor which, when completed, leads to granting of the Ph.D. degree. Rather, it is the best plan that the student, with help from the mentor, Advisory Committee and others, can formulate to address a set of specific questions. Deviations from the plan, with consent of the Advisory Committee, are allowable and expected. Following a successful proposal defense, the Advisory Committee certifies admission to candidacy by signing the Plan of Research and Admission to Candidacy forms, which are subsequently submitted to the Dean of the College of Graduate Studies. All Ph.D. students must be admitted to candidacy at least one year prior to submission and defense of the Dissertation. 6
Subsequently, each student will submit an Annual Report two weeks prior to their departmental seminar. This report, provided to the Advisory Committee and to Graduate Coordinator, will include: The original Aims of the project and any changes thereof. A description of the progress made since the last presentation to the department. This includes honors and awards received, publications, and abstracts presented locally, and nationally or internationally. SEMINARS: 1. Graduate students are required to attend a seminar series of interest. The Pharmacology Department offers a Research Seminar Series held on alternating Mondays at 1:00. 2. Students in the second year will present a 45-minute seminar on their research to the Pharmacology Department in May. 3. Students in the third year will present a 50-minute seminar on their Plan of Research to the Advisory Committee and the Pharmacology Department (see above). 4. Subsequently, the student will present a 50-minute seminar on their research each year to the Advisory Committee and the Pharmacology Department. 5. The student s final seminar will be on his/her dissertation as part of the defense (see below). STUDENT RESEARCH DAY: After completion of the first year, the student is expected to participate annually in the Medical University s Student Research Day held in November. Students are expected to present a poster or an oral presentation describing their research. Exceptions to this participation require approval of the Co- Chairs of the Graduate Training Committee. STUDENT TEACHING: Upon passing the Qualifying Exams (or for M.D.-Ph.D. students, upon completing the second year of medical school), students may prepare and deliver a lecture on either a general concept of pharmacology or a particular drug class. These lectures are given to second year graduate students in the program (as part of the Principles of Pharmacology course) and serve two purposes: 1) they provide overview or tutorial lectures in pharmacology for the second year students; 2) they provide the more senior students with the opportunity to develop and evolve their skills in communication and teaching. 7
DISSERTATION and DEFENSE: Students preparting to defend will need to submit the Thesis Defense Notification Form at least 3 weeks prior to the official defense date. The dissertation typically consists of an introductory chapter followed by chapters consisting of published, submitted or to-be-submitted manuscripts. The final chapter discusses the findings more generally and should provides insight into where future studies on the problem might be directed. The dissertation will then be given to the student s Advisory Committee for evaluation. Four weeks later, the student presents a 60-minute seminar on work in the dissertation followed by questions from the floor. This seminar is open to all who wish to attend. After a short break, the student, Advisory Committee and other faculty will meet in closed session for a discussion of the dissertation. Final changes agreed upon by the student and the Advisory Committee are incorporated into the dissertation followed by signing of the dissertation by the Advisory Committee. The following represents the minimum standard for a dissertation submitted by a graduate student enrolled in the Department of Cell and Molecular Pharmacology graduate program. This minimum is based on the perceived expectations of the faculty of the Department of Cell and Molecular Pharmacology. General Format Table of Contents Abstract Chapters List of references Specific Instructions on Chapter Format A. CHAPTER 1: Introduction It is expected that Chapter 1 will represent a comprehensive overview of the field(s) comprising the dissertation research. All of the essential studies leading up to the work proposed in the dissertation should be evaluated in this chapter. This includes the historical perspective of the field. Ideally, this chapter should be written in a fashion that could be submitted as a review to an appropriate journal. The literature review is then followed by a statement of the: Hypothesis Objective(s) Specific Aims B. SUBSEQUENT CHAPTER FORMAT 1. Introduction Each Chapter should have its own Introduction providing a brief background and overview of the pertinent studies. This section should present the goals/aim of the work detailed, equivalent to the introductory section of a manuscript. In referring to previous chapters within the dissertation, one should state as discussed in Chapter rather than, we previously reported as in a publication. This makes the dissertation a stand-alone document. 8
2. Methods The Methods should be comprehensive, stand-alone descriptions of how experiments were performed. If new techniques were developed, appropriate space should be devoted to the characterization of the method. This will likely include many details that do not end up in a journal publication. As an alternative, a separate Methods chapter can be included if the same methods are used in all of the following chapters. 3. Results 4. Discussion 5. Conclusion C. FINAL CHAPTER FORMAT Conclusion It is expected that the final chapter of the dissertation will represent a comprehensive overview of the work carried out, detailing the conclusions made in the context of the field. This chapter should include a sub-heading, Future Directions, which describes where the work accomplished would logically lead and the kinds of experiments which might be performed next. Course Requirements of MSTP students in the Pharmacology Training Program During the first year of graduate training, MSTP students are required to take the following components of the College of Graduate Studies First Year Curriculum: Essentials of Scientific Practice, I, II, III-CGS 710, 711, 712; Important Unanswered Questions in the Biomedical Sciences-CGS 760; and Foundations of Biomedical Science: Receptors and Signaling Unit-CGS 701G. During the fall of the first year of graduate training, Principles of Pharmacology (PCOL 721) is required. Clinical Biostatistics MCR-700 is required by the graduate school and can be taken any time during graduate training. Exemption of this course may be allowed, upon demonstration of competency in statistics. In addition to the courses required by the College of Graduate Studies, 12 hours of advanced coursework is required for the Ph.D. degree. Completion of these credits may be satisfied by enrollment in Principles of Pharmacology PCOL 721 (4 hr), the Receptors and Signaling Unit-CGS 701G (2hr), a Spring Selective of your choosing (3hr), and elective courses within your area of research interest. Timeline for MSTP students: Summer after Med Year 2 Selection of Mentor (May) Part 1 of the USMLE Essentials of Scientific Practice III (CGS 712, 2 hr) Research in your lab area of interest (13 hr) Fall of Year 3, first year of graduate training Essentials of Scientific Practice I (CGS 710, 2 hr) Diversity in Science (CGS 711, 1 hr) 9
Important Unanswered Questions in the Biomedical Sciences (CGS 760, 1 hr) Foundations of Biomedical Science: Receptors and Signaling Unit (CGS 701G, 2 hr) Principles of Pharmacology (PCOL 721, 4 hr) Research in your lab area of interest (5 hr) Selection of Dissertation Advisory Committee Spring of Year 3 Important Unanswered Questions in the Biomedical Sciences (CGS 760, 1 hr) Spring Selective in your area of interest (3 hr) Research in your lab area of interest (11 hr) Summer of Year 3 Written Qualifying Exam (June) Fall of Year 4 Oral Qualifying Exam (September) - Presentation of a research project likely to evolve into a dissertation project. Spring of Year 4 Plan of Research Years 3 and above Clinical Biostatistics CGS700 (Offered in the fall, 4 hr) 2 Electives in your area of interest Participation in a Journal Club Annual presentation of a research seminar in the Department of Pharmacology Attendance to a seminar series of interest 10