The University of Texas Health Science Center at San Antonio

The University of Texas Health Science Center at San Antonio

Integrated Multidisciplinary Graduate Program (IMGP)

GENETICS, GENOMICS, AND DEVELOPMENT (GGD) TRACK GUIDELINES

August 2010

I. Description

II. The Faculty

III. Track Governance Committee

IV. Acceptance into the GGD Track

V. Course Requirements for Ph.D. Candidates

A. Required Courses

B. Elective Courses

C. GGD Track Curriculum Summary and Schedule

VI. Grade Requirements

VII. Requirements for Admission to Ph.D. Candidacy

A. Selection of Dissertation Advisor

B. Qualifying Exam

C. Dissertation Committee

D. Dissertation Proposal

E. Admission to Candidacy

VIII. Student Evaluations

IX. Awarding of Ph.D. Degree

A. Dissertation Defense

B. The Dissertation

C. Awarding of the Degree

X. Exceptions to the Guidelines

XI. Attachments

Attachment A: GGD Track Credentialing Request and Approval Forms

Attachment B: Guidelines for Credentialing of Faculty in GGD Track

Attachment C: GGD Track Faculty

Attachment D: GGD Track Governance Guidelines

Attachment E: Mentor and Track Selection Form

Attachment F: Recommended Elective Courses

Attachment G: Approval Form for Dissertation Proposal

Attachment H: Student Evaluation Forms for Year 2 to Year 5

Attachment I: Graduate School of Biomedical Science Forms

I. Description

The Genetics, Genomics & Development Track embraces three complementary disciplines to provide students with a solid foundation of training that will prepare them for careers in some of the most exciting areas of modern biomedical research. The track has a strong emphasis in interdisciplinary approaches to graduate education and training to provide students with a broad foundation for future career development. Research and training opportunities within the program include molecular genetics of human disease, genetics of complex disorders, use of genetic animal models, genomics, proteomics, stem cell biology and reproductive and developmental biology. Students have the opportunity for exposure to a wide range of research approaches including molecular, cellular and whole organism methodologies as well as current high-throughput “omics” technologies and bioinformatics.

II. The Faculty

GGD Track faculty members are diverse and represent numerous departments and schools of the UTHSCSA including the Graduate School, Medical School, and Dental School. Faculty members in the GGD track have Ph.D., M.D., D.D.S. or equivalent degrees and are appointed as Assistant Professor, Associate Professor, or Professor. The forms for credentialing request and approval are in Attachment A, and the guidelines for credentialing of faculty participants in the GGD track are provided in Attachment B. A list of current GGD track faculty members is appended in Attachment C. Faculty rosters in the GGD Track will be reviewed by the Track Credentialing Committee according to the guidelines outlined in Attachment B. The majority of the faculty have active research programs in their laboratories, which are funded by extramural and intramural grants.

III. Track Governance Committee

The operation of the GGD Track is governed by the Track Governance Committee, which is composed of the track leader (chair of the Governance Committee), the Co-leader, the Curriculum Committee Chair, the Recruitment Committee Chair, the Qualifying Exam Chair, the Credentialing Committee Chair, the Student Advisor, the IMGP Admissions Committee Representatives, and a Student Representative. The functions of each committee and individuals are described in Attachment D.

IV. Acceptance into the GGD Track

Students for the Genetics, Genomics and Development Track come from the IMGP. The IMGP recruits and admits students into the program using the general qualifications for the graduate program. Until the student chooses a track, he/she is under the guidelines of the IMGP. During this time, they will fulfill the following requirements.

IMGP Core Course: Fundamentals of Biomedical Sciences INTD 5000 (8 credits, Fall 1st year).

The IMGP core course (INTD 5000) will expose a diverse group of students to a range of multidisciplinary topics. The focus of the core course is to promote the development of independent, critical and creative thinking skills, to teach students how to use information they learn, and to foster the development of skills in experimental design and data analysis. The course will accomplish these tasks by having students be active participants in their education. Active learning methods include, independent learning (assignments outside class), in-class participation, and small group discussions of concepts and the primary scientific literature. INTD 5000 core course centers around weekly “topics” that form a nucleus for presentation and discussion of “core concepts”. The course is designed for first-year graduate students matriculating into the integrated multidisciplinary graduate program.

IMGP Laboratory Rotation INTD 5008 (2 credits, Fall 1st year; 2 credits, Spring 1st year)

During the first year of graduate study, each predoctoral student will participate in research in the laboratories of potential mentors. Each rotation will last a minimum of six weeks (no longer than 12 weeks) and will typically be conducted in the fall and spring semesters of the first year. Ideally, the student will have selected a laboratory in which to complete his/her dissertation research before or during the spring semester of the first year. A student can combine two consecutive 6-week rotations to generate one 12-week rotation provided this is mutually agreeable between the student and the faculty member. Thus, a student could complete: four 6-week rotations, or two 6-week rotations plus one 12-week rotation, or two 12-week rotations. However, a student cannot complete more than two 6-week rotations or one 12-week rotation in the same laboratory. Rotations are intended to: a) acquaint the student with specific research topics in the graduate program, b) introduce students to technique(s) which may prove useful in their dissertation research, c) allow an opportunity for the student to assess whether he/she is compatible with the mentor and his/her laboratory personnel, and d) allow the faculty member to decide if the student is compatible with his/her lab. Choice of the laboratories for rotation should be made based upon the student's specific research interests and in consultation with IMGP Student Advisors. The policies for the evaluation and grading of laboratory rotations will be established by the Rotation Course director. An electronic copy of the grade and evaluation forms will be forwarded to the track student advisor once the student chooses a track.

In the Spring of the first year, the student will choose a mentor and a track. The student will submit the mentor selection form to the Dean’s office (see Attachment E). After joining the Genetics, Genomics and Development Track, the student will follow these specific GGD guidelines. The supervisor must be a GGD track mentoring faculty member conducting funded biomedical research. The supervisor must sign the Mentor Selection Form to indicate his/her willingness to support the student’s stipend, benefits, and dissertation research expenditures and must provide an account from which funds for the stipend and benefits will be taken beginning September 1st of the second year.

V. Course Requirements for Ph.D. Candidates

A. Required Courses

1) IMGP Core Course: Fundamentals of Biomedical Sciences INTD 5000 (8 credits, Fall 1st year)

2) IMGP Laboratory Rotation INTD 5008 (2 credits, Fall 1st year; 2 credits, Spring 1st year)

3) INTD 6002 Ethics in Research. This course will deal with topics relevant to ethics in scientific research. The course will be taught on a "case study" basis, dealing with real and hypothetical situations relevant to the conduct of scientific research. Topics discussed will include, but will not be limited to: data management, peer review, recognizing scientific misconduct, authorship, and The University of Texas regulations relevant to human and animal research. (0.5 Semester Credit Hours, Spring 1st year)

4) CSBL 6064 Genes and Development (the GGD Track core course consisting of four units (4 credits, Spring 1st year):

Genetics (also offered individually as CSBL 5025, 1 credit)

Course Description: This unit is designed to provide an overview of genetic research. Topics to be covered include: cytogenetics, mitochondrial genetics, cancer genetics, linkage analysis, complex traits, population genetics, animal models, sex determination, and epigenetics. (1.0 credit)

Genomics (also offered individually as CSBL 5024, 1 credit)

Course Description: The Genomics unit covers historical aspects of the Genomic project and high throughput methods (microarray, SAGE, proteomics, etc.) to perform global analysis of gene expression; the course provides also an overview of new biological fields like systems biology, functional genomics, and comparative genomics. The students will become familiarized with tools, methods, databases, and approaches used to extract biological information from global analyses. Hands on training on biological databases and classes covering examples of the use of genomics to answer questions related to cancer and diseases is an important part of the course, helping the students to visualize how genomics can be used in their own research projects. (1.0 credit)

Development (also offered individually as CSBL 5023, 1 credit)

Course Description: This unit provides a survey of concepts in developmental biology (induction, cell-cell interactions, morphogen gradients, morphogenetic movements, transcriptional regulation, organogenesis) using experimental examples from both invertebrate and vertebrate embryos. The first set of lectures will focus on gametogenesis, fertilization, and early developmental events, such as cleavage, midblastula transition, gastrulation, and axis formation. The second set of lectures will explore the fates of germ layers in the contexts of cell type-specific differentiation, and cell-cell interactions during organogenesis. (1.0 credit)

Stem Cell Biology (also offered individually as CSBL 5026, 1 credit)

Course Description: This unit provides students with an up-to-date overview on current topics in stem cell biology. It is intended for the future basic scientist who is interested in studying the regulatory mechanisms of stem cells as well as for the future clinician who is interested in how stem cell biology will continue to impact patient’s care. Topics that will be discussed are (1) basic biology of stem cells, including embryonic stem cells, adult stem cells, stem cells in different tissues and model systems, (2) microenvironment-mediated and (3) epigenetic regulators of stem cells, (4) stem cells in medicine, including regenerative medicine, cancer and aging, and (5) ethics. (1.0 credit)

5) INTD 6097 Research (Beginning summer 1st year). Independent, original research under the direction of one of the mentors listed with the Genetics, Genomics and Development Program. The trainee will learn how to design and execute scientific experiments as well as be trained in methodology. The trainees will carry out original research for their dissertation.

6) CSBL 5089 Graduate Colloquium. This course is designed to provide graduate students with training in evaluating the scientific literature and in presentation of research in a seminar or journal club format. The course will focus on critical thinking, including evaluation of existing literature, interpretation of experimental results, and comparison of alternative models and interpretations. These tools are essential both for oral presentations and for writing grant proposals and manuscripts. Emphasis will be placed on evaluation of the science, organization of the manuscript, and on oral presentation skills. (2 Semester Credit Hours, Spring 1st year).

7) CSBL 5077 Scientific Writing. This course will develop skills in scientific writing and presentation of research results. It will emphasize learning-by-doing-and-redoing. Students will write something every week. The capstone project for the students will be writing a grant proposal and defending it in front of the class. Topics to be covered include: (1) fundamentals of writing clearly; (2) principles of revision;(3) effective presentation of data; (4) fundamentals of oral presentation; (5) writing/presenting to the appropriate audience; (6) how to write background/introductory sections; (7) how to write materials and methods; (8) how to write the discussion section; (9) how to constructively critique one’s own and other’s writing. (2 Semester Credit Hours, Fall 2nd year)

8) CSBL 5095 Experimental Design and Data Analysis. The purpose of the course is to provide an introduction to experimental design and statistical analysis. The emphasis of the course will be on the selection and application of proper tests of statistical significance. Practical experience will be provided in the use of both parametric and nonparametric methods of statistical evaluation. Among the topics to be covered are: data reduction, types of distributions, hypothesis testing, scales of measurement, chi square analysis, the special case of the comparison of two groups, analysis of variance, a posteriori multiple range tests, tests of the assumptions of parametric analyses, advanced forms of the analysis of variance, linear regression and correlation analysis. (2 Semester Credit Hours, Fall 2nd year)

9) CSBL 6090 Seminar. The GGD track is under the umbrella of the Cellular & Structural Biology Ph.D. graduate program (CSBL), therefore the student is required to register for and attend the Seminar Course (CSBL 6090, 1 credit) every semester starting in the fall semester of the second year. The course is organized by Student Seminar Chair and Journal Club Chair, two faculty members elected by CSBL Graduate Faculty. The policies for the evaluation and grading of CSBL 6090 will be established by the Course Directors, who are Student Seminar Chair and Journal Club Chair, in a format approved by CSBL COGS. The course requires attendance at the departmental seminar, student journal club, and student research seminar, which are currently scheduled two times per week. In addition to attending the seminars, each student is required to make presentations. First, each student must give two Journal Club presentations according to the policy outlined by the Course Director in the course syllabus. Second, starting in the third year, each student must present a seminar based on their research conducted at this institution annually. The Student Seminar Chair is responsible for scheduling the student presentations throughout the Fall and Spring semesters. Student research seminars are designed to ensure that students receive adequate opportunity to communicate and defend their research results.

10) CSBL 6071 Supervised Teaching. Doctoral candidates are required to register for and receive a grade of “Satisfactory” (S) for Supervised Teaching once during their tenure in the Graduate Program. It is suggested that this be done during the second year of graduate study. Fulfillment of this requirement is obtained through active participation (lecturing, laboratory teaching, etc.) in one of the graduate or professional school courses. A student must have first satisfactorily completed the course in which he/she intends to teach or obtain approval from the course instructor.

11) INTD 7099 Dissertation. Prerequisite: Admission to candidacy for Doctor of Philosophy degree. Registration for at least two terms is required of Ph.D. candidates.

B. Elective Courses

In addition to the mandatory course work described above, the GGD track students are required to take elective courses totaling at least 6 credits. Various advanced-level courses are currently offered by faculty in the IMGP of the Graduate School. Electives aligned with the student’s research and career choice are recommended. See Attachment F for a current list of approved electives.