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SELF STUDY (FALL, 2006-SPRING, 2012) GRADUATE PROGRAM IN BIOCHEMISTRY

UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO

TABLE OF CONTENTS

Page Introduction and Overview 2 Changes in the PhD program in Biochemistry since 2006 3

Current PhD program in Biochemistry 5

Typical timeline for PhD students 7

Current curriculum 8

Recent revisions made to curriculum 13 Advisement of students in Biochemistry 14

Evaluation of the program 15

Appendices:

Table 1 – Summary 21 Table 2 – Biochemistry graduates (2006-present) 22 Table 3 – Positions following PhD 26 Table 4 – IMGP matriculating classes 27 Table 5 – Student oral presentations 28

Table 6 – Faculty ranks and diversity 29 Table 7 - Faculty research interests 30 Table 8 – Faculty publications 31

Table 9 – Faculty grant support 36 Table 10 – Faculty teaching efforts 37 Table 11 – Faculty qualifications 38 Document 1 – Core Facilities and Equipment 42 Document 2 – Mission statements 45 Faculty Biosketches – as a separate file

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Overview and Introduction

As required by the Texas Higher Education Coordinating Board (THECB), Rule §5.52, this report reviews the PhD graduate training program administered by the Department of Biochemistry at the University of Texas Health Science Center San Antonio (UTHSCSA) from the fall of 2006 through the spring of 2012. This program has no free-standing master’s degree program that admits students directly, although an MS degree program is offered as a default alternative for students who have completed coursework and a substantial research project but who must leave the PhD program for academic or personal reasons.

The graduate program in Biochemistry was approved by the THECB in 1970, and was most recently

part of institutional accreditation of the Graduate School of Biomedical Sciences (GSBS) at the UTHSCSA by the Southern Association of Colleges and Schools in 2009. Since the early 1990’s, the program has admitted an average of 6-7 students per year and has an excellent record for retention and graduation of PhD and MS students. A recent drop in admissions explained under ‘Changes in the PhD Program in Biochemistry Since 2006’ is related to the introduction of an integrated recruitment process for the GSBS. We note, however, that records for graduation and placement of PhD students remain strong, and our students have steadily increased their productivity in terms of papers published and presentations made during the period of review relative to earlier years. Related changes since 2006 in core mentoring faculty and curricular issues are also summarized. The mission statement of the GSBS is: “The Graduate School of Biomedical Sciences provides an individualized, diverse and multidisciplinary learning environment for students to develop the knowledge, skills and creativity to succeed in the evolving biomedical space.”

Faculty members in the graduate program in Biochemistry are very dedicated to these missions, and have historically been very well funded by research grants to financially support graduate student education. Faculty research interests are quite varied and range from utilization of molecular genetic to biophysical approaches for investigation of important medical issues and cellular mechanisms of regulation. A major strength of the Department is structural biochemistry and the Department houses several institutional and departmental core facilities for biophysical/biochemical analyses of macromolecules. Strengths of our faculty (funding, publications, service to the institution and profession, awards, etc.) and specific research interests are illustrated in this report and supported by the biosketches that accompany this report.

The current report is organized to: (a) highlight changes since 2006 (pages 3-4), (b) describe the current graduate program in Biochemistry (pages 5-13). (c) evaluate the program (pages 14-19) in detail by addressing each of the review criteria specified by

THECB. (d) provide appendices (pages 20-44) showing data and supporting information used to address the

review criteria.

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Changes in the PhD Program in Biochemistry at the UTHSCSA Since 2006 In 2006, the PhD program in Biochemistry was a stand-alone departmental program with potential mentors being faculty and cross-appointed faculty in the department. Recruiting/admissions and student monitoring activities were respectively administered within the department by an Admissions Committee and the Committee for Graduate Studies (COGS). During the first year of the PhD program, student stipends were provided by funds from the state of Texas designated for that purpose to the Department. Degrees were awarded by the Graduate School of Biomedical Sciences (GSBS) which oversaw graduate programs in seven different basic science programs at the UTHSCSA. In 2007, the GSBS initiated an umbrella graduate program called the Integrated Multidisciplinary Graduate Program (IMGP) in which thematic graduate training tracks were organized within individual basic science programs at the UTHSCSA. Clinical faculty members were also encouraged to participate in relevant tracks and graduate training. Students are now enrolled ‘undifferentiated’ into the umbrella program, that is, without admission into a specific track. All entering students take an interdisciplinary core course in Fundamentals of Biomedical Sciences and participate in laboratory rotations in the first semester. In the second semester, students select a specific track and a dissertation supervising professor for further training through course work and research.

Initially there were eleven such thematic tracks designated ‘non-substantive’ changes to existing graduate programs at the HSC because the tracks were assigned for management to various basic sciences programs with degree programs. Two graduate tracks in the IMGP to be developed and administered by the Department of Biochemistry were the Molecular Biophysics & Biochemistry (MBB) track and the Metabolism & Metabolic Disorders (MMD) track. Membership in the thematic tracks was not limited to departmental faculty and, in fact, each UTHSCSA graduate faculty member was allowed to participate as a mentoring faculty member in as many as four different thematic tracks. The MBB and MMD tracks included a total of 14 faculty who were not primary faculty or cross-appointees in the Biochemistry Department, and our primary faculty were represented in every track offered through the IMGP.

The 2007-2008 academic year was a transition period because the basic science programs had already independently recruited graduate students for that year. Thus, students entering the Biochemistry program that year were restricted to choosing between the two tracks administered by the Department of Biochemistry. Thereafter, recruiting and admissions were handled by the GSBS, and students were free to choose mentors among the eleven (now nine) thematic tracks in the IMGP. The state funds supporting student slots during the first year of support in the original basic science programs (~seven stipend equivalents from Biochemistry) were moved to the GSBS and pooled to support initial year stipends for graduate students entering the after 2008. Student monitoring activities are now managed by the GSBS during the first semester and thereafter by the COGS in the basic science program housing the particular track of choice.

This report will thus contain information about (a) students and faculty who were in the Biochemistry

program in 2006, including students who obtained degrees that year, (b) students admitted by the Biochemistry program in 2007 and faculty in the two thematic tracks of the IMGP administered by Biochemistry, and (c) students admitted by the IMGP after 2008 and who chose to enter the graduate tracks administered by Biochemistry. We note that, in the 2007-2008 year, of six students admitted by the Biochemistry program, five chose to enter the MMD track and one chose to enter the MBB track. However, in subsequent years, no IMGP students chose to enter the MMD track (despite a change in title to the Diabetes & Metabolic Disorders track) and, in 2010, this track was discontinued, with all students and interested faculty subsequently incorporated

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into the MBB track. The MBB track also did not initially fare well in attracting new students from the IMGP although these numbers have improved this past year largely due to more focus by track leadership and faculty on recruiting. We also note that core faculty can attract PhD students from multiple tracks, so they are not limited to students recruited into the MBB track. Many faculty members have also increased recruitment of post-doctoral fellows rather than of PhD students. Notably, under the new decanal leadership, more independence in recruiting has been encouraged and a small budget provided, although as yet this same level of independence has not been extended to the admissions process, which remains undifferentiated.

The decrease in the number of PhD students in the Biochemistry graduate program since 2006 is due

to a number of factors. Firstly, the number of students enrolled in 2006-2007 was somewhat excessive and, given some difficulty in placing students in appropriate postdoctoral positions and subsequent faculty positions, the Department made an internal decision to reduce recruitment (not, however, to the current level). In recent years, the funding available from national sources has obviously declined dramatically, and the UTHSCSA has substantially increased the requirement for faculty salary recovery from grants. Both of these factors have contributed to a decrease in financial support available for graduate students. However, the IMGP has also had a major negative impact on the number of PhD students in the MBB track. In general, students admitted by the IMGP generally have exhibited weaker backgrounds in quantitative science training and are less attracted by a program stressing biophysics and biochemistry. Students adept in these areas are often more attracted to broader academic institutions with Chemistry, Physics, and computer Science Departments unless targeted efforts in recruitment and admissions are made by more generic programs like those at the UTHSCSA. The initial conscious effort to reduce foreign admission into the IMGP also had disproportionately greater effects on the more quantitative programs such as MBB. Positive directions: The IMGP has recently become more responsive to ensuring equivalent admission and distribution of students who would be attracted to the MBB program. These are among several dynamic issues that are currently being addressed. For example, several concepts for improving the effectiveness of the IMGP are actively discussion. Among these are efforts that would clearly benefit the Biochemistry program (a) to ensure appropriate distribution of students to all constituents of the graduate school, and (b) to develop curricula across tracks that are more customized to each student, with oversight at the departmental level. Also, as mentioned above, Biochemistry program faculty members have become more aggressive in recruiting students admitted by the IMGP to the MBB track, and potential mentors have become more proactive in seeking training grant or multiple PI grant support to fund PhD students.

Because of the structural changes in the Biochemistry graduate program since 2006, some of the data

(e.g. lists of faculty mentors) are shown for three representative years: 2006, when the program was departmentally based; 2009, when the program was composed of two tracks in the IMGP; and 2012, when the program was composed of one track in the IMGP. Dean, GSBS: Chair, Department of Biochemistry:

David Weiss Bruce Nicholson Members of Biochemistry COGS: MBB Track Oversight Committee:

Rui Sousa (chair) Lee McAlister-Henn and Rui Sousa (track leaders) Franco Folli Andy Hinck (chair, Recruitment Committee) Don McEwen Dmitri Ivanov (chair, Website Committee) John Hart Paul Fitzpatrick (chair, Curriculum Committee) Dmitri Ivanov Neal Robinson (previous chair of COGS) Martin Adamo

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Current PhD Program in Biochemistry (Molecular Biophysics & Biochemistry, MBB Track)

Description: The Biochemistry program and the MBB track focus on the structure and function of cellular components broadly defined and provide advanced training for graduate students in the use of a broad spectrum of biophysical, biochemical, and molecular biological methods to study these cellular components. Goals are to acquire answers to fundamental questions of the relationship between form and function, an understanding that has important ramifications for the betterment of human health.

Curriculum: During their first semester, students in the GSBS participate in an introductory IMGP course (an intense 8 credit hour course) and in laboratory rotations within any of the tracks. MBB coursework and laboratory dissertation research commence in the second semester by which time students are expected to have selected their mentor for dissertation research. By the end of the second year, students are expected to have successfully completed required track courses (there are 4 of these for a total of 7 credit hours) and most of the advanced electives (for a total of 7 credit hours). Descriptions of required and elective courses in the MBB track are presented below. Students also attend a weekly journal club commencing the second year in the program. Since 2007, all students have been expected to actively participate (with posters or talks) in an annual Biochemistry Departmental Retreat, and they are encouraged to similarly participate in other local and national/international scientific meetings as reflected by the total number of annual attendances at meetings (an average of 32 per year over the last 6 years – see Table 1).

Evaluation of Students: Each grading period, a grade of satisfactory (S), incomplete (I), or unsatisfactory (U) for research credits is given by the Supervising Professor. In addition, research progress is evaluated at semi-annual meetings of the student with their Research Supervising Committee (which later generally becomes the official Dissertation Supervising Committee). The first such meeting is held in the Fall semester of the second year. A written progress report is submitted to each member of the Supervising Committee at least one week before the Fall meeting. During the Spring semester, a written progress report is not required, although the student and the Supervising Committee are required to meet to discuss the student's progress orally. Any student who receives a grade of excellent from all members of their dissertation committee during the fall meeting will be excused from having a meeting during the spring semester. Students who receive a grade of unsatisfactory must have an additional meeting within 6 weeks to address and correct their deficiencies.

All students are required to maintain the following minimum academic standards: 1. At least a B in all Biochemistry and IMGP courses. 2. At least a 3.0 GPA in all courses Advancement to Candidacy: In order to advance to candidacy for the PhD, a student must: (a)

complete all required courses, (b) pass the advancement to candidacy examination described below; (c) resolve any probationary requirements; and (d) obtain the Supervising Professor’s certification of potential for productive and independent investigation.

Advancement to Candidacy Exam, Oral Defense of a Research Proposal: The first attempt of an oral examination based on an original, written research proposal outside the area of the student’s dissertation or PIs research area, is to be completed by June 1 of the 2nd year for students who enter the program in August. The Examination Committee consists of a total of three members from the Department of Biochemistry or the MBB track and one faculty member from outside the Department of Biochemistry. The Chair of the examination committee is appointed by agreement among three faculty members who comprise the Departmental Qualifying Examination Oversight Committee (DQEOC) for a given academic year. The members of the DQEOC are drawn from the Biochemistry COGS and are appointed by the Department Chair for 3 year rotating terms. The purpose of the DQEOC is to provide every student examination committee with a Chair, to monitor the results of examinations of all students, and to assure an adequate degree of uniformity of examinations from student to student. The Supervising Professor is responsible for submitting the names of the proposed committee members, other than the Chair, to the DQEOC for approval.

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When the committee members approve the written proposal, they sign the Petition for Oral Examination form. At this time, the student schedules the oral examination, which must occur within two weeks of approval of the written proposal. Following the oral examination, all members of the Examination Committee complete an evaluation form, and the Committee makes the final pass/fail decision at the time of the examination. The student’s Supervising Professor is present during the examination but does not participate and does not vote. In case of failure, the student is allowed to repeat the examination with the same committee once. The chair of the examination committee gives the student a written explanation for the basis of the failure and provides guidelines to prepare for the re-examination. Failing the re-examination will be cause for dismissal from the PhD program, at which time the student may petition COGS for admission to the Master’s degree program.

Following successful completion of the advancement to candidacy oral exam, the Supervising Professor must certify that the student has potential for productive and independent investigation.

Dissertation Research Proposal and Proposal Seminar: By November 1 of the third year, the student submits a draft of a proposal for dissertation research to the Supervising Professor for review. The student presents a departmental seminar based on his/her dissertation research proposal early in the sixth semester (end of the third year). The student submits the research proposal to the Research Supervising Committee one week prior to the seminar and meets with the Supervising Committee within three weeks after the seminar. The student submits the dissertation research proposal, revised if necessary, to the Research Supervising Committee for approval prior to submission to COGS. At this time, the student and mentor name the members of the formal Dissertation Supervising committee; normally this committee is comprised of the previous Research Supervising Committee, with the addition of an external member outside the UTHSCSA.

The Dissertation Supervising Committee is composed of (a) the Supervising Professor, who chairs this committee, (b) two member of the MBB track, at least one of whom has a primary appointment in the Department of Biochemistry, (c) one faculty member in another IMGP track, but who does not have an appointment in the Department of Biochemistry, and (d) one member, designated as the external reviewer, must be from outside the UTHSCSA and an expert in the field of the proposed dissertation.

Dissertation: At least twice a year, the student meets with the Dissertation Supervising Committee to report progress of the research. The role of the external reviewer is to evaluate the scientific merit of the completed dissertation and is only involved in the Final Oral Examination.

When the student seeks permission to stop experimental work and to write the dissertation, the student submits a copy of the dissertation outline and data, in the form of figures and tables, to members of the Dissertation Supervising Committee as a progress report. The student will review the data at a committee meeting. The Dissertation Supervising Committee shall determine whether all experimental work has been completed and whether the data are of sufficient quality and quantity to constitute an acceptable dissertation. If permission is given to stop experimental work, the student may do so and initiate writing the dissertation. The Supervising Professor must approve a draft of the complete dissertation before the student submits it to the other members of the Dissertation Supervising Committee.

Final Oral Examination: When the Dissertation Supervising Committee judges the dissertation to be suitable for defense, the student schedules a seminar and defense date. After the public presentation, the Dissertation Supervising Committee meets with the candidate in executive session to administer an intensive and detailed oral defense of the dissertation. The Dissertation Supervising Committee members vote on the candidate’s success or failure on the Final Oral Examination; more than one vote for failure signifies failure on the examination. The Dissertation Supervising Committee members also vote for approval or disapproval of the final version of the dissertation. When the dissertation meets the approval of the Dissertation Supervising Committee, the student submits the dissertation approval page to the Office of the Graduate Dean for signature by the Dean. Approval of these recommendations by the Graduate Faculty Council is required before the degree is awarded.

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Typical Timeline

[Example for students entering in 2012 and alternate years thereafter] Year 1 Fall semester Spring Semester INTD 5000 (8 CH) Fundamentals of Biomedical Sciences INTD 5008 (2 CH) Laboratory Rotations

BIOC 6037 (2 CH) Integration of Metabolic Pathways BIOC 5087 (1 CH) Molecular Genetics and Biotechnology INTD 5008 (2 CH) Laboratory Rotations INTD 6002 (0.5 CH) Ethics in Research Electives (3.5 CH)

Year 2

Fall Semester Spring Semester BIOC 6029 (1 CH) MBB Journal Club BIOC 6097 (5-6 CH) Research Electives (2-3 CH)

BIOC 6036 (2 CH) Macromolecules I: Structure and Mechanism

BIOC 5085 (2 CH) Macromolecules II: Biophysical Methods in Biology (2nd half of the semester)

BIOC 6029 (1 CH) MBB Journal Club BIOC 6097 (2 CH) Research Electives (2 CH) May: Advancement to PhD Candidacy Exam

Year 3

Fall semester Spring Semester BIOC 6097 (8 CH) Research BIOC 6029 (1 CH) MBB Journal Club

BIOC 6097 (8 CH) Research BIOC 6029 (1 CH) MBB Journal Club Dissertation Research Proposal

Years 4-6

Fall semester Spring Semester BIOC 6097 (8 CH) Research BIOC 6029 (1 CH) MBB Journal Club

BIOC 6097 (8 CH) Research BIOC 6029 (1 CH) MBB Journal Club Dissertation Defense

In addition to the formal coursework described above, all MBB students are required to attend and actively participate in all weekly departmental seminars, and are expected to attend and actively participate in annual departmental retreats.

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Current Curriculum – Molecular Biophysics and Biochemistry Track Core Courses

FIRST YEAR:

BINTD 5000 Fundamentals of Biomedical Sciences Credit Hours: 8.0 This course is required of all students in the IMGP. It covers the fundamentals of biochemistry, molecular biology, cell biology, organismal and systems biology, and microbiology and immunology. The design of the course centers on weekly “topics” that form a nucleus for discussion of “core concepts” of biomedical sciences. Each topic will be covered in 1 week by interdisciplinary faculty teams, led by a faculty team leader. The course includes independent learning, didactic lectures, and primary literature discussion. 31INTD 5008 Laboratory Rotations Credit Hours: 2.0 This course is required of all students in the IMGP. It provides an opportunity for students to participate in research activities in the laboratories of faculty members in different tracks to learn laboratory skills and to gain an introduction to the research fields of faculty members. Students participate in 4 six-week rotations. INTD 6002 Ethics in Research Credit Hours: 0.5 This course is required of all students in the IMGP. It covers topics relevant to ethics in scientific research. The course is 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. This course is required of all doctoral graduate students.

These courses are completed as part of the IMGP during the fall semester. In the spring semester of the first year, students proceed with advanced courses offered by the MBB track (page 9). The following are general standing requirements of the program.

SECOND – FIFTH YEAR BIOC 6029 Journal Club (current director – Dr. Shiio) Credit Hours: 1 Taken by all MBB students in and after their second year, recent literature is presented and discussed. The goal is to expose student to advanced topics and provide experience in presentation of research results and critical evaluation of the literature. The course meets weekly during the semester. Direction of the journal club rotates among MBB faculty. BBIOC 6097 Research Credit Hours: 1.0–9.0 This course consists of independent, original research under the direction of a faculty advisor.

FINAL GRADUATION EVENTS

BIOC 6098 Thesis Credit Hours: 1.0–9.0 Registration for a least one term is required of MS candidates. Semester Prerequisites: admission to candidacy for the MS degree BIOC 7099 Dissertation Credit Hours: 1.0–9.0 Registration for at least two terms is required for PhD candidates. Semester Prerequisites: admission to candidacy for the PhD degree

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Advanced Biochemistry Courses Students enrolled in the Molecular Biophysics & Biochemistry Track must take 14 semester credit hours of Advanced Biochemistry Courses: four required courses (7.0 semester credit hours), and additional advanced elective courses (7.0 semester credit hours). One advanced elective course must be a course offered by a track other than MBB. The courses listed below are approved advanced biochemistry courses. The required advanced courses are designed to insure that all students have strong basic backgrounds in biochemistry, biophysics, metabolism, and molecular genetics since these are common important themes in all avenues of research in such a program. The elective and special topics courses offer different options for students who may be more generally focused on macromolecular structure/function areas or on cellular regulatory functions. Along with electives offered by other tracks, these selections allow broad flexibility in planning the curriculum for individual students.

REQUIRED ADVANCED COURSES: BIOC 5085 Biophysical Methods in Biology: 2 credit hours BIOC 5087 Molecular Genetics and Biotechnology: 1 credit hour BIOC 6036 Macromolecular Structure & Mechanism: 2 credit hours BIOC 6037 Integration of Metabolic Pathways: 2 credit hour MBB Elective Courses: BIOC 6010 Gene Expression 2 credit hours INTD 6033 Cell Signaling Mechanisms 2 credit hours BIOC 6035 Biochemistry of Multimolecular Complexes 2 credit hours INTD 6043 Structure and Function of Membrane Proteins 2 credit hours The following more specialized elective courses focus on specific methods. They include hands-on experience with instrumentation and a significant didactic component. (credit hours based on course hours) BIOC 5083 Hydrodynamic Methods BIOC 5091 Nuclear Magnetic Resonance Spectroscopy for Biochemists BIOC 5091 Data Analysis in Biochemistry and Biophysics Proposed courses: [BIOC 5091 Protein Structure Analysis by X-Ray Diffraction Methods] [BIOC 5091 Applications of Surface Plasmon Resonance in Biochemistry] [BIOC 5091 Applications of Mass Spectrometry in Biochemistry]

Advanced Courses in other Tracks: Also available to students in the MBB track are numerous advanced courses offered by the other eight thematic tracks. MBB students are required to take at least one advanced course in another track, and may substitute other advanced courses for those offered in Biochemistry upon approval of COGS. Conversely, the advanced MBB courses are open to students in other tracks. In fact, the elective courses INTD 6033 and INTD 6043 have INTD rather than BIOC designations because students from tracks other that MBB frequently enroll in these courses.

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Descriptions of Advanced MBB Courses (offered every other year)

Required BIOC 5085 Biophysical Methods in Biology (current director – Dr. Borries Demeler) This course covers modern biophysical methods for studying biological macromolecules in sufficient detail to understand the current literature. Topics to be covered include: Macromolecular structure determination by X-ray crystallography and NMR spectroscopy; absorbance, fluorescence, and EPR spectroscopy; circular dichroism; light scattering; mass spectrometry; and hydrodynamics, including diffusion, electrophoresis, sedimentation velocity, and sedimentation equilibrium. Semester Credit Hours: 2.0 BIOC 5087 Molecular Genetics and Biotechnology (current director – Dr. Steve Hardies) The objective of this course it to provide comprehensive treatment of the exploration of genes and proteins through molecular biological techniques tailored towards experimental biochemistry. Topics to be covered include: the theory and practice of PCR including real-time PCR, PCR mutagenesis, and clone construction by PCR; problems in the preparation of large quantities of recombinant proteins in E. coli; site-specific and saturation mutagenesis; the bioinformatics of protein families; and molecular genetic systems used to explore gene expression and protein interactions in bacteria, yeast, Drosophila, and mammals. Semester Credit Hours: 1.0 BIOC 6036 Macromolecular Structure & Mechanism (current director – Dr. Rui Sousa) This course covers the fundamentals of protein and nucleic acid structure and of enzyme catalysis. The course is required for students in the Molecular Biochemistry and Biophysics track. The topics to be covered include: DNA and RNA structure, protein structure, protein folding, ligand binding by proteins, and enzyme catalysis. Semester Credit Hours: 2.0

BIOC 6037 Integration of Metabolic Pathways (current director – Dr. Lee Henn) The objective of this course is to provide an understanding of the individual reactions in intermediary metabolism and how the reactions are integrated by regulatory mechanisms. The topics to be covered include carbohydrate, lipid, and nitrogen metabolism and mechanisms of regulation of individual enzymes and metabolic pathways. Semester Credit Hours: 2.0

Electives BIOC 6010 Gene Expression (current director – Dr. Martin Adamo) The course covers gene expression focusing on regulation at the levels of transcription, RNA processing, transport and stability, epigenetics, and translation. Proteins and other regulatory molecules involved in these processes will also be covered. Particular emphasis will be placed on transcriptional control mechanisms including: RNA polymerases, chromatin remodeling, methylation and other epigenetic modifications, families of transcription factors including their DNA binding properties, protein-protein interaction domains, trans-activation mechanisms, regulation by ligand binding, phosphorylation and other signaling mechanisms and nuclear-cytoplasmic transport; posttranscriptional mechanisms including: mechanisms of RNA splicing, nuclear-cytoplasmic transport of RNA, RNA localization and targeting, RNA stability; and translational control. Post-transcriptional and translational control mechanisms will highlight the roles of RNA binding proteins and their modifications

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in these processes. Semester Credit Hours: 2.0 BIOC 6035 Biochemistry of Multimolecular Complexes (current director – Dr. John Hart) This course covers the assembly and biochemistry of several multimolecular complexes including those of transcription, cell motion, cell permeation, cell signaling, apoptosis, viral assembly and protein assembly-related processes of conformational diseases such as ALS, Huntington, Alzheimer, and Parkinson diseases. The techniques used to obtain information about these multimolecular complexes are also to be covered. The biochemical aspects of these studies will address both simple enzymatic activities and the more complex activities of biological motors. Semester Credit Hours: 2.0

Drug Discovery and Design (BIOC 6035) This new course, currently under development, will be offered in the fall of 2013 in lieu of BIOC 6035. Semester Credit Hours: 2.0 INTD 6033 Cell Signaling Mechanisms (current director – Dr. Jean Jiang) This course covers the molecular mechanisms of action of various extracellular mediators including hormones, neurotransmitters, growth factors, cytokines, etc., and cell signaling events. Several areas will be discussed including: (1) mechanisms of mediator synthesis; (2) interaction of mediators with specific receptors; (3) modulation by mediators of various second messenger systems including cyclic nucleotides, inositol phospholipids, calcium, protein phosphorylation, ion flux, etc.; and (4) intra- and intercellular mechanism for regulating mediator action. Semester Credit Hours: 2.0

INTD 6043 Structure & Function of Membrane Proteins (current director – Dr. Bruce Nicholson) This is a course targeted at students within any of the Graduate Tracks. The objective of the course is to provide a broad view, allowing for in depth consideration in selected areas, of the structure and diverse functions of proteins within a membrane environment. Specific topics to be covered include: ion selective channels, large membrane pores, membrane transporters, membrane pumps, and membrane receptors. The format of the course will be didactic lecture followed by student presentations of relevant topics. Semester Credit Hours: 2

BIOC 5091 Special Topics in Biochemistry: Quantitative Biochemistry (current director – Dr. Neal Robinson) This course covers statistical and mathematical analysis of typical biochemical data. Topics to be discussed include: enzyme kinetics, first and second order chemical reactions, ligand binding, scintillation counting of radioactivity, UV-VIS difference and derivative spectra, analytical ultra-sedimentation, and solution of multiple simultaneous equations using matrix algebra. Emphasis is placed upon the use of computers to analyze experimental data using programs running under Windows, or Linux platforms. Students will also become familiar with file transfers between these two platforms and the use of VNC viewer to enable their PC computers to be used as a Linux terminal. Semester Credit Hours: 1.0

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BIOC 5092 Nuclear Magnetic Resonance Spectroscopy for Biochemists (current director – Dr. Andy Hinck) This course is designed to provide students with a working knowledge of the basic underlying theory of modern pulsed Nuclear Magnetic Resonance methods used to study the structures and internal dynamics of biological macromolecules in solution. The theoretical concepts covered will include an overview of pulse excitation, digital sampling, and fourier tranformation. The product operator formalism will be used to describe how modern multinuclear multidimensional pulse methods function to yield the desired signals. The practical concepts covered will include an overview of modern methods for obtaining sequential resonance assignments, determining high-resolution three-dimensional structures, and analyzing internal dynamics. Semester Credit Hours: 2.0 BIOC 5083 Hydrodynamic Methods (current director - Dr. Bo Demeler) This course is intended to provide a solid understanding of hydrodynamics and macromolecular transport processes, such as sedimentation and diffusion. The focus will be on hydrodynamic methods involving analytical ultracentrifugation and light scattering. Topics in sedimentation velocity, sedimentation equilibrium, buoyant density sedimentation, as well as static- and dynamic light scatter-ing and the complementarity of these approaches will be discussed. Macromolecular interactions involving mass action, concentration dependent nonideality and reaction rates are covered. This course will also cover a range of data analysis approaches including the van Holde - Weischet method, the second moment method, direct boundary fitting by finite element modeling, the C(s) method, the 2-dimensional spectrum analysis, genetic algorithm optimization, nonlinear least squares fitting approaches to user-defined models. Also covered will be statistical analysis using Monte Carlo and bootstrap methods. The course will be offered in the spring/summer.

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Recent Revisions Made to Curriculum as a Result of Internal Assessment 2010-2011 A. To ensure that students in all PhD programs at the UTHSCSA have experience in reading and interpreting research literature, the common introductory IMGP course was revised at the end of 2010 academic year. In subsequent years, students have worked in small groups on a weekly basis to read, interpret, review, and present results of a significant publication related to the scientific area presented in lectures during each week. The lecture format of the course was also changed so that a small group of faculty covers various aspects of a different biomedical subject each week. B. The Diabetes and Metabolic Disorders track was merged with the Molecular Biophysics and Biochemistry (MBB) track to attract more qualified PhD students and to ensure that faculty efforts would be more focused on insuring the effectiveness of the PhD program in Biochemistry. 2011-2012 A. To ensure that all students entering the MBB track have a solid and advanced understanding of basic concepts in the area of biochemistry (because biochemistry is not required for applicants to the IMGP, and because these concepts are no longer presented in the common introductory IMGP course), two new required courses were introduced into the curriculum. One (BIOC 6036) focuses on analyses of protein and enzyme chemistry; the other (BIOC 6037) focuses on major concepts in cellular metabolic pathways and regulation. B. To ensure that all MBB students get additional practice interpreting and presenting research literature, a new weekly journal club for all students was developed and will commence in the Fall of 2012. Previously as a free standing course, but now as part of the journal club, to ensure a teaching opportunity, students are required to make one departmental presentation (called the Biochemistry Student Review) in the form of a lecture on a topic outside their dissertation research. C. A new elective advanced course on the biochemical/biophysical bases for drug discovery and improvement is under development.

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Advisement of Students in Biochemistry For students in the Biochemistry graduate program (specifically the MBB track): Advisement on student time-to-degree: The chair of the Committee of Graduate Studies meets with students who have chosen to enter the MBB track to describe the PhD curriculum. He/she informs them that it is possible to complete all degree requirements and be awarded a PhD within 4-5 years, and we have examples of students who have achieved this timeline. However, this assumes that all academic requirements are met on time, that a substantial research project is developed and completed, and that the student successfully presents and defends dissertation research. On average, students in the program have required 5.5 to 6 years to complete all requirements for the PhD. Advisement on career counseling: On one level, advisement in this area is conducted on a personal basis for each student by the student’s PhD mentor and by members of the student’s research dissertation committee. The mentor and this committee often suggest particular areas for postdoctoral studies or alternative paths if the student is not interested in pursuing such studies. On another level, in terms of introducing all students to alternative applications of their PhD degrees to future career plans, the program makes an effort to expose students, generally through the departmental seminar program, to individuals with PhD degrees in the area of Biochemistry who have chosen different types of career paths. These individuals may have academic appointments (involving different emphases on research and/or teaching) in professional schools or in undergraduate schools, or they may have various positions in scientific companies including biotechnology, development, or entrepreneurial endeavors. The graduate students in the department are provided the opportunity (and urged) to participate in informal lunches following presentations by these seminar speakers. In this way, they can pose their own questions about different career opportunities to knowledgeable individuals. Our faculty members also participate in various career counseling workshops and courses organized by the GSBS for graduate students and postdoctoral fellows. Along these lines, a new office of Postdoctoral Affairs in the GSBS was recently inaugurated.

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EVALUATION OF THE PROGRAM The criteria and areas to consider for review of graduate programs according to the Texas Adminstrative Code, Rule §5.52, have been summarized in an Evaluation Table provided by the UTHSCSA office of the Vice President for Academic, Faculty, and Student Affairs (VPAFSA). These areas include the 18 Characteristics of Texas Doctoral Programs as well as nine areas specified by the VPAFSA. Summary responses to requested measures are shown in this Table on the following page. Details of data collected and utilized to support these responses are elaborated in tables and documents in the Appendix section. This report is also part of a response to Chancellor Cigarroa’s “Framework for Advancing Excellence throughout The University of Texas System.” His action plan calls for (a) strengthened criteria for review and continuation of Ph.D. programs, (b) actions to strengthen and develop innovative plans to improve Ph.D. student advising to shorten time to degree, and to provide career advising, and (c) plans to incentivize students and programs regarding time-to-completion of degrees.

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Evaluation of Doctoral/Master Programs in Biochemistry, UTHSCSA

Measure (fall, 2006 - spring, 2012) Operational Definition or Description Value or Comment

Number of Degrees Per Year Six year average of PhD and MS degrees awarded. (See Table 1 for details.)

Average of 6.3 PhD degrees per year and 0.3 MS degrees per year.

Graduation Rates Six year total for students in the Biochemistry graduate program. (See Table 2 for details.)

39 students received PhD degrees and 2 students received MS degrees. 3 other students (or 6.5 %) withdrew from the program and 2 (4.3%) were dismissed.

Average Time to Degree Six year average for PhD students. (See Table 1 for details.)

Average of 6.0 years/PhD degree with a reduction in this average to 5.4 years/PhD degree in the current year.

Employment Profile (in field within one year of graduation)

Profile since 2006 of employment within one year of completion of PhD or MS degree. (See Table 3 for details.)

Of 39 students gaining PhDs in the Biochemistryprogram from 2006-2012, in the year following graduation:

23 chose postdoctoral positions outside the HSC, 12 remained at the UTHSCSA for postdoctoral work, 2 chose jobs – both in research areas, and the positions of 2 are unknown.

Of 2 students receiving MS degrees in the Biochemistry Program during this time, both held research-related positions in local companies following graduation.

Admission Criteria Current IMGP requirements and previous Biochemistry program requirements.

Current IMGP requirements: Applicants are required to have a minimum of a Bachelor’s degree (GPA >3) and credit for courses taken in Biology (2 years), Chemistry (1 year general and organic chemistry), Physics (1 year), and Mathematics (minimum of 1 semester of Calculus). The Biology and Chemistry courses should include laboratory experience. All applicants must take the GREs (with scores generally >1200) and international applicants must take the TOEFL exam (with scores >68 on the internet-based exam). The GRE must be taken within the last 5 years and the TOEFL within the last 2 years. These are similar to earlier Biochemistry program requirements in 2006 and 2007, except that Physical Chemistry was also a required prerequisite.

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Measure (fall, 2006 - spring, 2012) Operational Definition or Description Value or Comment

Percentage Full-time Students (FTS) with Financial Support

Six year survey of financial support.

From fall 2006 to fall 2008, the Biochemistry program provided full-time support for students during their first year in the program. From fall 2008 to the present, the GSBS provided the first year of support. After the first year, support is provided to PhD students through grants to the mentors or by the Department. Support for MS students is provided by the mentor.

Average Financial Support Provided Graduate stipends in 2006 and 2012.

Current support is $26,000 annually, with resident tuition, fees and basic student health insurance paid on behalf of the student. Annual support has increased incrementally since 2006 when the stipend was set at $22,800 and students were expected to cover other fees.

Percentage Full-Time Students Six year survey of full-time students. All students seeking PhD or MS degrees were/are full-time students.

Student Enrollment Average of student enrollment over the previous six-year period. (See Table 1 for details.)

An average of 30 students was enrolled in the PhD program/year, with this number falling to 18 in the previous year.

Student Retention Rates Six year survey of student retention rates. (See Table 2 for details.)

39 students received PhD degrees and 2 students received MS degrees. 3 other students (or 6.5 %) withdrew from the program and 2 (4.3%) were dismissed.

Student Diversity

Summary of all students in the Biochemistry program from 2006-present. (A summary of students in the entire IMGP is shown in Table 4.)

Of 50 previous and current PhD students, ethnicity numbers are 32 Asian, 10 Caucasian, 4 Hispanic, 1 Hispanic/American Indian, 1 American Indian, 1 African American, and 1 Pacific Islander. Of 3 MS students, 2 are Hispanic and 1 is African American. Of 50 PhD students, 28 are male and 22 female. MS students are 2 male and 1 female.

Student Publications/Presentations

Six year survey – numbers of publications and presentations by PhD graduate students. (See Tables 2 and 3 for details.)

The average numbers per PhD graduate from 2006-2012 were 4.2 publications, 7.2 oral or poster presentations, 2.5 departmental seminars, and 3.3 awards (for travel, posters, scholarships or other achievements).

Graduate Licensure Rate (If Applicable) Not applicable.

Student-Core Faculty Ratio #Graduate students/#mentoring faculty in a given year – 3 representative years. (See Tables 1 and 4 for details.)

2006 2009 2012 AVG 1.4 0.7 0.5 0.9

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Measure (fall, 2006 - spring, 2012) Operational Definition or Description Value or Comment

Number of Core Faculty Numbers in three representative years. (See introductory text and Table 6 for details.)

26 in 2006; 41 in 2009; 37 in 2012

Faculty Diversity

Comparison of three representative years. (See Table 6.) The wide diversity of faculty research interests is summarized in Table 7.

2006 2009 2012 Total# 26 42 37 Male 81% 76% 81% Female 19% 24% 19% Asian 23% 24% 19% Hispanic 4% 5% 5% Caucasian 73% 71% 76% Professors 62% 68% 65% Assoc Profs 19% 20% 22% Asst Profs 19% 12% 13%

Core Faculty Publications Annual averages of peer reviewed publications for 7 years. (See Table 8 for details.)

2006 2007 2008 2009 2010 2011 2012 AVG 3.2 3.2 3.7 3.6 4.0 3.3 3.5 3.5

Core Faculty External Grants Annual averages of RO1 equivalents per faculty member for 7 years. (See Table 9 for details.)

2006 2007 2008 2009 2010 2011 2012 AVG 1.4 1.6 1.6 1.8 2.0 1.9 1.6 1.7

Faculty Teaching Load

Annual averages over previous 4 academic years for Department of Biochemistry faculty (teaching loads for faculty in the MBB track but outside the Department are not accessible). (See Table 10 for details.)

For the years 2008-2009, 2009-2010, 2010-2011, and 2011-2012 (when records of teaching efforts were assessed on a biannual basis), Biochemistry faculty averaged 18.1 contact didactic teaching hours and 5.1 other student service hours. Individual mentoring included an average of 1.2 graduate students/faculty member and an average of 1.4 postdoctoral fellows (the latter number is for 2009-2012 only).

Faculty Qualifications

Biosketches for 35 of the 37 current faculty members of the Biochemistry graduate program are provided in a separate file. Examples of service activities and awards to some individual faculty members are provided in Table 11. The diversity of faculty research interests is illustrated in Table 7.

Mentoring faculty all have PhD and/or MD degrees, and years of experience in academia ranging from 4 to 40. All faculty members participate in didactic teaching and service activities (to the department, to the university, and/or to national organizations) as well as the mentoring of graduate students associated with their individual research efforts or with the program in Biochemistry.

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Measure (fall, 2006 - spring, 2012) Operational Definition or Description Value or Comment

Program Curriculum and Duration in Comparison to Peer Programs

Comparison with other programs at the UTHSCSA and with programs at UT Southwestern

The program curriculum is described in detail above. Comparable to other programs, most didactic activities are completed within 2 years. Our average over the past six years was 6.0 years/PhD degree. This number was reduced to 5.4 years/PhD degree in the current year, a number comparable to the UTHSCSA-wide number of 5.5 years given on the institution’s website and to 5.3 years/PhD degree for the Department of Biological Chemistry at UT Southwestern.

Program Facilities and Equipment Departmental Cores and other facilities and equipment (See Document 1.)

The Department houses several Core Facilities: Bioinformatics, Macromolecular Interactions [Analytical Ultracentrifugation, Surface Plasmon Resonance, and Light Scattering], NMR Spectroscopy, Mass Spectrometry, X-ray Crystallography, and Protein Expression and Purification. These facilities and other equipment are described in more detail in Document 1.

Program Finance and Resources Student stipend support

First year stipends were provided by the program in Biochemistry until the Fall of 2008 and thereafter were provided by the GSBS. The expectation is that, after the first year, graduate student stipends are provided by grant support to the mentor. In cases of a loss or hiatus in funding to the mentor, the Department ensures continued stipend support. Over the 6 year review period, this coverage accounted for 10% of the total support for graduate student stipends.

Program Administration Departmental and GSBS roles

As described in the introduction (Changes in the PhD Program in Biochemistry at the UTHSCSA since 2006), the GSBS has been responsible for recruiting and admissions since 2008 (with contributions from each track), and oversees the curriculum for the first semester. Thereafter, MBB students follow the curriculum designed by the track and are academically monitored by the Biochemistry COGS. Members of the MBB executive committee and of COGS are listed in the introduction.

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Measure (fall, 2006 - spring, 2012) Operational Definition or Description Value or Comment

Alignment of Program with Stated Program and Institutional Goals and Purposes Institutional Goals (See Document 2.)

The mission of The University of Texas Health Science Center at San Antonio is to make lives better through excellence in education, research, health care and community engagement. As a Department of the UTHSCSA in the School of Medicine with graduate studies oversight by the Graduate School of Biomedical Sciences, we adhere to the missions and goals of these entities. As an equal employment opportunity and affirmative action employer, it is the policy of The University of Texas Health Science Center at San Antonio to promote and ensure equal employment opportunity for all individuals without regard to race, color, religion, sex, national origin, age, sexual orientation, disability, or veteran status. The University is committed to the Affirmative Action Program in compliance with all government requirements to ensure nondiscrimination.

Date of Last External Review Submitted 2008

External Program Accreditation Southern Association of Colleges and Schools, January, 2009

One year monitoring report submitted in 2008 and approved in 2009.

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APPENDICES

TABLE 1: Summary of data presented in Table 2For PhD graduates in each year:

fall-spring #PhDs #PhDs Avg yrs/ #PhDs Publications: Meeting Presen*: Dept Pres** Awards***:in program awarded PhD admitted Avg#/PhD Total/yr Avg#/PhD Total/yr Total/yr Avg#/PhD Total/yr

2006-2007 37 4 5.6 6 5 20 5.8 23 2 42007-2008 39 5 6.1 6 3.7 22 6.2 37 2.3 72008-2009 33 5 6.6 0 4 20 6.6 33 5 102009-2010 29 9 6.2 1 4.7 42 8.7 78 20 3.2 162010-2011 21 4 6.3 1 4.5 18 5.3 21 14 1.5 4.52011-2012 18 11 5.4 4 3 31 10.5 115 20 6 54

averages: 30 6.3 6 3 4.2 26 7.2 51 18 3.3 16(36 in prep)

fall-spring #MSs * Types of meetings (national or local) and presentations (oral or poster)awarded are described in Table 2.

2006-2007 **Types of oral presentations (dissertation proposals and defenses,2007-2008 or reviews) are described in Table 4.2008-2009 1 ***Types of awards (travel, poster, honors, fellowships) are described2009-2010 in Table 2.2010-2011 12011-2012

averages 0.3

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TABLE 2: Biochemistry Graduates (2006-present) [Data obtained from Committee on Graduate Studies and from student CVs or mentors.]

PhD Grad Supervising Sex, Entered Graduation Years to # pubs #present #awards Yrs of pubs (200X)fall-spring (student#) Professor ethnicity Program Date Complete PhD (*1st author)2006-2007 1 Lafer M,A 2001 2006 5 7 9 2 3*,5*,6*,7*,8,9*,12

2 Henn M,A 2000 2006-May 5.7 6 3 5*,6-3*,7*,83 Lafer M,A 2001 2007 6.0 1 3 10*4 Hinck M,H 2001 2007-May(Apr) 5.7 6 9 2 5,5*,6,8*,10*,11*

2007-2008 5 Nicholson F,A TF-Buffalo 2007-1Jun incomplete info 2 3 2 4*,6, two** in prep6 Jiang M,AA 2002 2007-2Aug 5.0 3 1 1 7*,9*,107 Jiang F,C 2001 2007-2Aug 6.0 5 2,5,7,8*,118 Liu M,A 2001 2007-3Dec 6.3 6 4 4 3,5*,6-2,7,9-from pubmed9 Lee F,A 2001 2007-3Dec 6.3 3 5*,7*,8*

10 Luduena M,A 2001 2008-1Jun 6.7 3 10 8,8*,9*2008-2009 11 Robinson F,C 2000 2008-2Aug 8.0 2 7*,8*-from pubmed

12 Venkatachalam F,A, 2002 2008-3Dec 6.3 5 4 8,9*,10,10-2*,one in prep13 Barnes M,H 2001 2009-1Jan 7.4 1 5 9*14 Adamo M,C 2002 2009-May 6.7 8 9 8,9-4all*,10,10-2*15 Sousa M,A 2004 2009-May 4.7 4 6 5,7,8,9

2009-2010 16 Hart M,A 2002 2009-Aug 7.0 4 10 3 7*,9*,10,11,2 in prep17 Hart M,A 2003 2009-Aug 6.0 4 9 1 8,9,9*,10*,2** in prep18 Hart M,C 2004 2009-Dec(Sept) 5.3 4 5 3 9,9*,10,10*19 Henn F,A 2003 2009-Dec(Nov) 6.2 2 5 8*,10*20 Liu M,A 2004 2009-Dec(Dec) 5.3 10 10 6,8,9-2**,10-2**,10,11-2,1221 Jiang F,A 2002 2010-Jan 7.4 7 9 4 7,8,9*,10-2**,11*,12, 3 in prep22 Kim M,A 2004 2010-Apr 5.5 5 4 8,10,10*,11*,1223 Jiang M,A 2003 2010-Apr 6.5 4 2 8,9,10*,11*24 Nicholson M,A 2003 2010-Apr 6.5 2 4 5 10*,11*,2 in prep

2010-2011 25 Naski (Masters) M,A 2003 2010-Sept 7.0 5 1 5,11-3***,12*26 Hinck M,A 2005 2011-Jan 5.4 6 2 8,9,10-2,11,11*27 Luduena F,A 2004 2011-May 6.7 2 8 1 10-2**28 Jiang F,A 2005 2011-July 5.9 5 9,10-2,11-2

2011-2012 29 Asmis M,A 2006 2011-Sept 5.1 3 14 11 9,10*,11,2 in prep**

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30 Merry Lindsey F,A 2007 2011-Oct 4.2 8 13 11 10-3,10*,11-2,11*,12*,2 in prep

31 McEwen M,A 2006 2011-Nov 5.3 2 2 2 8*,12*32 Jiang F,A 2006 2011-Nov 5.3 2 10 11,12*,4 in prep-3*33 Jiang F,A 2006 2012-Jun 5.7 4 11 3 10,11*,12,12*,3** in prep34 Hinck M,A 2006 2012-Jun 5.7 2 8 2 11,12*,1* in prep35 Naski (Boyer) M,A 2005 2012-Jun 6.7 1 1 12*36 Nicholson M,C 2005 2012-Mar 5.7 3 4 2 10-3***,4inprep(3*)37 Adamo F,A 2007 2012-July 5.0 3 16 11 10,11,11*,3inprep(2*)38 Musi F,A 2007 2012-July 5.0 2 7 6 9,10,4-all*inprep39 Hinck M,C 2003 2012-Aug 9 - LOA* 1 3 6 5,2**inprep

future 40 Hart F,C 2006 changed labs 1 13 2 10,1*inprep41 Liu M,A 2007 3 2 6 9,10,1242 Asmis F,C 2007 4 14 4 11*,12-2,12*,2inprep43 Hinck F,H 2007 2 3 4 9,1044 Kim F,H 2009 1 7 6 1245 Ivanov M,C 201046 Kim M,AI,H 2011 1 5 4 1247 Shapiro F,AI,H 201248 Masters F,C 201249 Ivanov F,PI 201250 Musi M,A 2012

Master's 51 Henn M,H 2005 2009-Aug(Jun) 3.8-cg labs 1 952 Lafer M,H 2004 2011-May 6.7 - LOA* 2 4 5 7,1253 Lindsey F,AA 2009 In progress

Withdrew 54 Kim F,A Withdrew 200755 Ahuja F,A Withdrew 200756 Serwer M,A Withdrew 2008

Dismissed 57 Hinck M,C 2004 Dismissed 201058 Serwer M,A 2007 Dismissed 2012 1

LOA*=leave of absence, M=male, F=female TF=transfer A=Asian, C=Caucasian,

AA=African American, AI=American Indian,

PI=Pacific IslanderH=Hispanic

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Yrs of presentations (200X) Yrs of awards (200X)Student # natl local* oral poster travel other fellowship

1 5-3,6-2 (4,5,6)6 5,6 5-3,6-3 6 six2 6 (4,5,6) 4,5,6-23 3,9-2 (5,6,7) 3,5,6,7,9-24 5,6 (4,5,6) 4,5-2,6-2 4,95 3,5,6 (5,6,7) 3,5-2,6-2,7 6 56 5 (5,6,7) 5-2,6,7 77 (5,6,7) 5,6,78 6-2,7-2 (5,6,7) 5,6-3,7-3 6,7 6,79 (5,6,7) 5,6,7

10 2,3-2,4,5-2,8-4 (5,6,7) 2,3-2,4,5-3,6,7,8-411 (6,7,8) 6,7,812 6,7,9,10 (6,7,8) 6-2,7-2,8,9,1013 (6,7,8) 6,7,8 4,5,6,7,814 6,7-4,8-2,9 7 (6,8) 6-2,7-5,8-3,915 7,8-2,9-3 (6,7,8) 6,7-2,8-3,9-316 11,10-2,8,7,5,4 11,10,7 11-2,10-3,9,8,7-2,5,4 7,10,1117 8-2,7-2,6-2,5,4-2 (7,8,9) 8,7,6,4 7-2,8-2,6,5,4 918 8-2,7-2,5 (7,8,9) 9,8-3,7-3,5 7,8 9 AFAR19 7 9-3,8, 9 7,8,9-220 9-2.8,7 8-2,7-3,6 9-2,8-3,7-4,621 11,10,7-2,6-2,5,4 (7,8,9) 10 11,9,8,7-3,6-2,5,4 12,9,7,422 8 6,7,9 6,7,8,923 nine-2 (7,8,9) 7,8,9-224 9,7 (7,8,9),9 7-2,8,9-3 9,7 11,9,725 8 (8,9,10) 8-2,9,1026 (8,9,10) 8,9,10 2in1027 7,8-2,9,10-2,11-2 (8,9,10) 7,8-3,9-2,10-3,11-2 1128 (8,9,10) 8,9,1029 11-6,10-3,9-4,8 (9,10,11) 9-2,10,11 11-6,10-3,9-2,2,8 11-2,10-2 9-2,10-2 10,11,12 AHA

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30 9,10-3,11-6 9-2,11 11-4,10,9-2,8 11-3,10-2,9 10 11-6,10,9 9,10 TS TG31 9,11 9,11 2 in 2012 CPRIT32 10 8,9-3,10-4,11 8,9-3,10-5,1133 10 9-3,10-3,11-4 9-3,10-4,11-4 9,9,1034 8,11 8,9,10,11-3 8-2,9,10,11-4 9,1035 8 (9,10,11) 8,9,10,1136 9,10 10,11 9,10-2,11 9,1137 9,10-2,11-2 9-4,10-2,11-3,12-2 10,12 9-5,10-3,11-5,12 10-2,11-2 9,10-2,12 10,11,12 TSTG+cert38 9,10,11-4,12 (9,10,11) 11 9-2,10-2,11-4,12 10,11-2 10,11,12 TSTG+cett39 8 9,10 8,9,10 5,6,7,8,9,1040 10,11,12-3 9-2,10-2,11-2,12-2 11,12-2 9-2,10-3,11-2,12-3 12,1141 10,10 10,10 10,11-2,12,1342 12,11-3,10-2,9-4,8-2 12,11,9 12,9 12,11-3,10-2,9-4,8-2 11 12 10,11 TSTG43 12-2,11 (9,11,12) 9,12-3,11-2 12 10 8-10,10-12 NIH,CPRIT44 11-2,12 10,11-2,12 10,11-4,12-2 9,11,12-24546 9,11-2 11,12 9,11-3,12 11 11-2,12474849505152 7-2,8,9 7,8,9,10,11 NIH535455565758

*parentheses indicate years added for students who failedto include dept retreat and recruitment presentations in CVs.

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TABLE 3: Biochemistry Program - Positions Following PhD (by student number) PD = postdoctoral position

One Year After PhD Current Fall, 2006 – Spring, 2007

1 PD-UTHSCSA Res Sci-UTHSCSA 2 PD-Univ of Illinois 2ndPD-Univ Kansas 3 PD-UTHSCSA Res Assoc – Rutgers Univ 4 PD-Stanford Scientist – Teranos Inc, CA

Fall, 2007 – Spring, 2008 5 PD-UC San Diego same 6 PD-US Army Inst of Surg Res Contractor Henry Jackson Found 7 PD-US Army Inst of Surg Res Prog MGR, Sci Appls Air Force 8 PD-Univ of Utah School of Med same 9 Job-DPT labs* – San Antonio same 10 PD-Rutgers Business Sch Bristol-Myers, Squibb

Fall, 2008 – Spring, 2009 11 Unknown Unknown 12 PD-UTHSCSA 2ndPD-HSC Barshop Inst 13 PD-Southwest Found, San Antonio Res Sci, XBiotech Corp, Austin 14 PD-Army Res Inst of Env Med Job-same Inst in Natick, MA 15 PD-Univ of Wisconsin, Madison same

Fall, 2009 – Spring, 2010 16 PD-UTHSCSA Asst Prof, St. Mary’s Univ, SA 17 PD-Yale same 18 PD-Col St Univ (HHMI) same (seeking fac position) 19 PD-UTHSCSA Chicago School of Business 20 PD-UTHSCSA 2ndPD-TX A&M HSC 21 PD-MD Anderson same 22 PD-Sloan Kettering Cancer Ctr (HHMI) same 23 PD-Wash Univ (St. Louis) same 24 PD-UTHSCSA same

Fall, 2010 – Spring, 2011 25 PD-Maine Med Ctr Res Inst same 26 PD-NCI, NIH same 27 unknown unknown 28 PD-UTHSCSA same

Fall, 2011 – Spring, 2012 29 PD-U Wash same 30 PD-U Wash same 31 PD-UTHSCSA same 32 PD-UTHSCSA same 36 PD-UTHSCSA same 33 PD-NIH same 34 PD-Harvard Med same 35 PD-Harvard Med same 39 PD-UTHSCSA same 37 PD-Harvard Med same 38 PD-Harvard Med same

Biochemistry Program - Positions Following MS (by student number) Fall, 2009

51 Translational Sci and Clinical Trials - Southwest Oncology Group, San Antonio

Fall, 2011 52 Res Assoc – RMS Clinical Research Consultants, Austin

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TABLE 4: IMGP matriculating Class

Matriculating

Class 2007 2008 2009 2010 2011 2012

Total 38 45 42* 35 33 33 Domestic 19 30 35 27 28 18 international 19 14 7 8 5 15 male 16 12 15 11 13 14 female 22 32 27 24 20 19 Average UG GPA 3.5 3.4 3.4 3.5 3.4 3.4**

Average GRE 1074 1204 1193 1182 1197 1284** Asian 1 4 2 2 5 1 White 8 21 19 15 8 10 Unreported 4 1 1 0 0 0 URM 6 8 13 10 14 7

*includes 2 deferrals matriculating from 2008

** data not official Note: 2007 was a transition year with recruitment and admission activities conducted by

basic science programs, and with students limited to choices of tracks administered by that program. After 2007, recruitment and admission of students was conducted by the GSBS.

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TABLE 5: Oral Departmental Presentations (by student number)

Fall, 2009 – Spring, 2010 Summary: 6/24 31 Proposal 9 Dissertation Defenses 7/14 16 Defense 9 Dissertation Proposals 7/15 17 Defense 2 Student Reviews 7/15 33 Proposal 8/28 18 Defense 9/2 20 Review 11/15 19 Defense 11/19 20 Defense 12/2 32 Proposal 12/18 34 Proposal 1/26 21 Defense 2/23 40 Proposal 3/8 22 Review 4/5 22 Defense 4/29 23 Defense 4/30 24 Defense 5/13 41 Proposal 6/2 30 Proposal 6/17 38 Proposal 7/22 37 Proposal Fall, 2010 – Spring, 2011 Summary: 8/19 43 Proposal 4 Dissertation Defenses 8/23 25 Defense 3 Dissertation Proposals 11/1 42 Proposal 7 Student Reviews 11/30 26 Review 12/15 26 Defense 3/7 28 Review 3/29 27 Review 4/11 27 Defense 5/12 58 Proposal 6/27 32 Review 7/19 28 Defense 7/27 33 Review 8/11 31 Review 8/16 29 Review Fall, 2011 – Spring, 2012 Summary: 9/7 29 Defense 11 Dissertation Defenses 9/13 40 Review 1 Dissertation Proposal 9/19 34 Review 8 Student Reviews 9/27 30 Review 11/11 30 Defense 11/9 31 Defense 11/16 32 Defense 3/29 36 Defense 4/3 33 Defense 4/5 35 Review 4/5 34 Defense 4/12 36 Review 4/30 35 Defense 6/29 39 Defense 7/5 37 Defense. 7/5 44 Proposal 7/9 38 Defense 7/27 37 Review 8/3 38 Review 8/30 43 Review

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TABLE 6: Faculty Ranks and Diversity in Three Representative Years

BIOCHEMISTRY FACULTY IN 2006 DEPARTMENT OF BIOCHEMISTRY: OTHER DEPARTMENTS: Professors: Merle Olson (previous Chair, Cross-appointed Faculty

Dean of the GSBS, now retired emeritus) Feng Liu, Pharmacology Larry Barnes (became Associate Dean Bjorn Steffensen, Dental School

of the GSBS in 2008, now retired) Manjeri Venkatachalam, Pathology Eileen Lafer Michael Naski, Pathology John Lee Richard Luduena Bettie Sue Masters Lee McAlister-Henn Bruce Nicholson (Chair since 2004) Neal Robinson Phil Serwer Rui Sousa Sue Weintraub Associate Professors: Martin Adamo (to professor in 2008) Steve Hardies John Hart (to professor in 2007) Andrew Hinck (to professor in 2008) Jean Jiang (to professor in 2008) Assistant Professors: Borries Demeler (to associate professor

with tenure in 2009) Chongwoo Kim Don McEwen Yuzuru Shiio Jens Wohnert (left the department in 2007) Faculty Diversity (total 26): Males - 21 Asian - 6 Professors - 16 Females - 5 Hispanic - 1 Associate Professors - 5 Caucasian - 19 Assistant Professors – 5

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BIOCHEMISTRY FACULTY IN 2009 MBB TRACK: DEPARTMENT OF BIOCHEMISTRY: OTHER DEPARTMENTS: Professors: Martin Adamo James Stockand, Physiology John Hart David Weiss, Physiology, Dean GSGMS Andrew Hinck Jean Jiang Cross-appointed Faculty Gregg Fields (arrived 2008, departed 2010) Feng Liu, Pharmacology Paul Fitzpatrick (since 2009) Bjorn Stefensen, Dental School Eileen Lafer Manjeri Venkatachalam, Pathology John Lee Richard Luduena Bettie Sue Masters Lee McAlister-Henn Bruce Nicholson (Chair since 2004) Neal Robinson Phil Serwer Rui Sousa Sue Weintraub Joint Faculty Phil Loverde (since 2008) Associate Professors: Borries Demeler Robert Brenner, Physiology Steve Hardies Maria Gaczynska, Molecular Medicine Mark Shapiro, Physiology

Cross-appointed Faculty Ricardo Aguiar, Medicine

Assistant Professors: Dmitri Ivanov (since 2008) Chongwoo Kim Don McEwen Yuzuru Shiio DMD TRACK [Mentoring Faculty Only]: DEPARTMENT OF BIOCHEMISTRY: OTHER DEPARTMENTS: Professors: Martin Adamo Lily Dong, Cell & Structural Biology Paul Fitzpatrick (since 2009) Feng Liu, Physiology Bettie Sue Masters Holly VanRemman, Physiology Lee McAlister-Henn Merry Lindsey, Cardiology Sue Weintraub Ralph DeFronzo, Medicine Franco Folli, Medicine Nicholas Musi, Medicine Bandana Chatterjee, Molecular Medicine Associate Professors: Yidong Bai, Cell & Structural Biology Lu, Xin-Yun, Pharmacology Assistant Professors: Shane Rea, Physiology Faculty Diversity (total 42): Males - 32 Asian - 10 Professors - 29 Females - 10 Hispanic - 2 Associate Professors - 8 Caucasian - 30 Assistant Professors – 5

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BIOCHEMISTRY FACULTY IN 2012

(MBB TRACK) DEPARTMENT OF BIOCHEMISTRY: OTHER DEPARTMENTS: Professors: Martin Adamo Franco Folli, Medicine John Hart James Stockand, Physiology Andrew Hinck David Weiss, Physiology, Dean GSGMS Jean Jiang Paul Fitzpatrick Cross-appointed Faculty Eileen Lafer Feng Liu, Pharmacology John Lee Leslie Myatt, Medicine, OB/Gyn Richard Luduena Bjorn Stefensen, Dental School Bettie Sue Masters Manjeri Venkatachalam, Pathology Lee McAlister-Henn Bruce Nicholson Neal Robinson Phil Serwer Rui Sousa Sue Weintraub Joint Faculty Reto Asmis (since 2011) Phil Loverde Associate Professors: Borries Demeler Robert Brenner, Physiology Steve Hardies Maria Gaczynska, Molecular Medicine Merry Lindsey, Medicine

Nicolas Musi, Medicine Mark Shapiro, Physiology Cross-appointed Faculty Ricardo Aguiar, Medicine

Assistant Professors: Dmitri Ivanov Shane Rea, Physiology Chongwoo Kim Don McEwen Yuzuru Shiio Faculty Diversity (total 37): Males - 30 Asian - 7 Professors - 24 Females - 7 Hispanic - 2 Associate Professors - 8 Caucasian - 28 Assistant Professors - 5

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Table 7: Research Interests – Current Faculty Members of the Molecular Biophysics and Biochemistry Track

Martin L. Adamo, Professor of Biochemistry; PhD, University of Houston, 1986. Research interests: Regulation of insulin-like growth factor-I biosynthesis and signaling in conditions of normal and pathological growth. Ricardo T. Aguiar, Department of Medicine, Assistant Professor (Cross appointment in Biochemistry); M.D. Federal University Paraiba, Brazil, 1987; PhD, Univ. of Sao Paulo, Brazil, 1994. Research interests: Molecular pathogenesis of hematological malignancies: basis for the rational design of targeted therapeutics; Intersection of the cAMP signals with survival pathways in normal and malignant B-lymphocytes. Reto Asmis, Professor of Biochemistry; PhD, University of Fribourg, Switzerland, 1989. Research interests: Role of thiol Antioxidant Systems in Macrophage Dysfunction Associated with Cardiovascular Disease and Diabetic Complications Robert Brenner, Department of Physiology Associate Professor; PhD, University of Texas at Austin, 1997. Research interests: Large conductance (BK-type) calcium-activated potassium channels that are gated to open by micromolar calcium concentrations and voltage. Borries Demeler, Department of Biochemistry, Associate Professor; PhD, Oregon State University, 1992. Research interests: Development, testing and implementation of user-friendly analysis software tools for the hydrodynamic modeling of biological macromolecules. Integration of multiple biophysical techniques for global analysis of complex systems. Gregg Fields, Department of Biochemistry, Professor; PhD, Department of Chemistry, Florida State University, 1988. Research interests: extracellular matrix biochemistry, synthetic protein design and construction, proteases of the extracellular matrix, cancer chemical biology, biomimetic biomaterials for drug delivery, tumor cell biology/signal transduction, and solid-phase peptide synthesis methodology Paul F. Fitzpatrick, Professor of Biochemistry; PhD University of Michigan. 1981. Research interests: Catalytic and regulatory mechanisms of enzymes with focus on two classes of enzymes, the tetrahydropterin-dependent aromatic amino acid hydroxylases and the flavoprotein oxidases. Franco Folli, Professor of Medicine; M.D. Universita di Milano, 1990, PhD Universita di Milano e Padova, 1996, Research interests: Regulation of protein expression in diabetes mellitus and associated disease states, tyrosine kinases and mechanisms of intracellular signal transduction, biology of regulated secretion in the endocrine pancreas and central nervous system, pathogenesis of insulin-dependent diabetes mellitus (T1DM) and Stiff-man syndrome, mechanisms of insulin action and resistance, pathogenesis of non-insulin-dependent diabetes mellitus (T2DM) Maria Gaczynska, Department of Molecular Medicine, Associate Professor; PhD, University of Lodz, Poland, 1989. Research interests: The role of the proteasome, a multifunctional macromolecular assembly, in cell cycle progression, signal transduction pathways, immune response and general “housekeeping” in the human cell to better understand its role in cancer and aging. Stephen C. Hardies, Department of Biochemistry, Associate Professor; PhD, University of Wisconsin, Madison, 1979. Molecular genetics of a mammalian transposon; genome mapping. P. John Hart, Professor of Biochemistry; PhD, University of Texas at Austin, 1993. Research interests: Metalloprotein structure, action, and redesign; role of copper-zinc superoxide dismutase in Lou Gehrig’s disease, structural biology of metal trafficking; blue copper proteins; protein crystallography. Andrew P. Hinck, Professor of Biochemistry; PhD, University of Wisconsin, 1993. Research interests: Solution NMR spectroscopy of proteins and nucleic acids; transforming growth factor β and its interaction with the ligand binding domain of the TFG-β type I and type II receptors; protein-RNA interactions. Dmitri Ivanov, Department of Biochemistry, Assistant Professor- CPRIT Scholar in Cancer Research; PhD, Brandeis University, 2001. Research interests: Solution NMR spectroscopy to probe how physical interactions at

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protein interfaces determine biological outcomes with particularly emphasis in the assembly of higher-order macromolecular structures such as viral shells or multi-subunit cellular machines. Jean X. Jiang, Professor of Biochemistry; PhD, State University of New York at Stony Brook, 1991. Research interests: Gap junction mediated cell-to-cell communication and intercellular signaling mechanisms. Chongwoo A. Kim, Department of Biochemistry, Assistant Professor; PhD Johns Hopkins University, 1996. Research interests: Structure- function of polycomb group proteins. Eileen Lafer, Professor of Biochemistry; PhD, Tufts University, 1983. Research interests: The basic biology of the synapse and basic mechanisms underlying neurotransmission. John C. Lee, Professor of Biochemistry; PhD, Purdue University, 1966. Research interests: Structure, function, and regulation of assembly RNA-protein complexes; regulation of eukaryotic gene expression by peptide growth factors. Merry Lindsey Department of Medicine, Associate Professor; PhD Baylor College of Medicine, 1999. Research Interests: cardiovascular-oriented research that involves developing multidimensional approaches to examine the mechanisms whereby the left ventricle responds to injury and applying the knowledge gained to develop therapeutic strategies to prevent, slow, or reverse the progression to heart failure Feng Liu, Professor of Pharmacology (Cross appointment in Biochemistry); PhD, Iowa State University, 1990. Research interests: Receptor tyrosine kinase signal transduction and regulation.Structure and function studies of protein kinases and signaling molecules. Richard F. Ludueña, Professor of Biochemistry; PhD, Stanford University, 1973. Research interests: Structure of tubulin; biochemistry of microtubules; tubulin isotypes. Bettie Sue Siler Masters, Professor of Biochemistry and The Robert A. Welch Foundation Professor in Chemistry; PhD, Duke University, 1963. Research interests: Structure-function studies of FAD- and FMN-containing enzymes, specifically NADPH-cytochrome P450 reductase and the three isoforms of nitric oxide synthase: neuronal, endothelial, and inducible. The studies include various biophysical techniques, including rapid reaction kinetics, EPR, ENDOR, NMR, and x-ray crystallography. Donald G. McEwen, Assistant Proessor of Biochemistry; PhD, Washington University School of Medicine, 1997. Research interests: Characterization of key signaling molecules and pathways. Lee McAlister-Henn, Professor and Deputy Chair; PhD, The University of Texas Southwestern Medical Center, 1980. Research interests: Molecular genetic analysis of central metabolic pathways in eukaryotic cells. Nicolas Musi, Associate Professor of Medicine and Director of Center for Healthy Aging; M.D. Universidad Anahuac Mexico City, 1995. Research interests: Molecular mechanisms of insulin action and insulin resistance in skeletal muscle. Leslie Myatt, Professor OB/Gyn; PhD Charing Cross Hospital Medical School, University of London, 1979. Research interests: Regulation of placental blood flows and the role of oxidative and nitrative stress in placental function. Bruce J. Nicholson, Chair and Professor of Biochemistry; PhD California Institute of Technology, 1983. Research interests: Structure and function of gap junctions; connexins; gap junctions as tumor suppressors. Shane Rea, Assistant Professor Physiology; PhD, University of Queensland, 2000. Research Interests”: To understand the causes of human aging at a molecular genetic level using the C. elegans as a model system. Neal C. Robinson, Professor of Biochemistry; PhD, University of Washington, 1971. Research interests: Structure and function of mitochondrial electron transport complexes and the role of phospholipids in stabilizing their structures.

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Philip Serwer, Professor of Biochemistry; PhD, Harvard, 1973. Research interests: Genetics of the assembly of multimolecular particles (bacteriophages); dynamics of DNA conformation; fluorescence microscopy of single event-metabolism. Mark Shapiro, Department of Physiology, Associate Professor; PhD, Rush University Medical Center, 1991. Research interests: Physiology and regulation of ion channels of excitable cells. Yuzuru Shiio, Department of Biochemistry, Assistant Professor; M.D. University of Tokyo, 1989, PhD University of Tokyo, 1993. Research interests: Quantitative Proteomic Analysis of Proteins Important in Cancer. Rui J. Sousa, Professor of Biochemistry; PhD, University of Pittsburgh, 1991. Research interests: Structures and mechanisms of nucleic acid polymerases. Bjorn Steffensen, Professor of Periodontics (Cross appointment in Biochemistry); PhD, University of British Columbia, 1997. Research interests: Molecular and structural basis for interactions of matrix metalloproteinases and extracellular matrix molecules in health and disease. James Stockand, Professor of Physiology; PhD, Univ. of Texas Health Science Center at Houston, 1996. Research interests: The use of contemporary methodologies, including electrophysiology, molecular biology, biochemistry, genomics and proteomics, and fluorescence microscopy to investigate regulation of ENaC and aldosterone signaling. Manjeri A. Venkatachalam, Professor of Pathology (Cross appointment in Biochemistry); M.B., B.S., Calcutta Medical College and Calcutta University, 1962. Research interests: Molecular pathology of cell death; acute renal failure; glomerular structure and function. Susan T. Weintraub, Professor of Biochemistry; PhD, The University of Texas Health Science Center at San Antonio, 1979. Research interests: Structure, elucidation and quantification of natural and synthetic compounds of biological interest, in particular, phospholipids, peptides, proteins, transition metal complexes and anti-inflammatory agents derived from plants. David Weiss, Department of Physiology, Dean GSGMS; PhD, Baylor College of Medicine, 1987. Research interests: Understanding how GABA receptors function, e.g., how GABA binding results in opening of the chloride-selective pore, the mechanism by which allosteric compounds alter channel function, and how the GABAergic neuron regulates the number of postsynaptic GABA receptors on the cell surface.

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TABLE 8: Faculty Publication Numbers2006 2007 2008 2009 2010 2011 2012 source

Adamo, Martin 3 1 1 5 5 4 1 his listAguiar, Ricardo 2 1 1 4 4 2 1 pubmedAsmis, Reto 6 3 2 3 3 1 9 his listBrenner, Andrew 4 2 1 3 0 3 3 his listDemeler, Borries 6 6 13 6 14 4 4 his listFields, Gregg 11 10 4 9 CVFitzpatrick, Paul 6 6 2 8 10 4 2 pubmedFolli, Franco 3 4 6 11 4 12 3 his listGaczynska, Maria 2 0 3 1 3 1 2 pubmedHardies, Stephen 0 4 1 1 1 0 3 his listHart, P John 3 3 4 10 7 3 3 his listHinck, Andrew 1 3 5 5 5 5 5 pubmedIvanov, Dmitri 1 3 0 0 0 0 1 pubmedJiang, Jean 1 3 4 3 10 8 11 CVKim, Chongwoo 0 0 1 0 3 1 2 CVLafer, Eileen 5 3 4 2 4 1 2 pubmedLee, John 1 1 2 1 4 2 2 his listLindsey, Merry 6 5 8 4 9 7 15 her listLiu, Feng 1 2 1 4 4 4 5 CVLoVerde, Phil 11 12 5 5 0 2 4 his listLuduena, Richard 6 2 7 3 3 3 2 his listMasters, Bettie Sue 4 2 3 3 1 4 2 pubmedMcAlister-Henn, Lee 3 1 3 2 3 2 1 her listMcEwen, Donald 0 0 0 1 2 1 3 CVMusi, Nicolas 6 7 6 6 4 10 3 pubmedMyatt, Leslie 12 6 6 11 11 4 8 his listNicholson, Bruce 1 0 2 3 2 2 2 his listRea, Shane 3 2 2 2 2 1 2 pubmedRobinson, Neal 1 0 1 1 1 2 2 pubmedSerwer, Philip 0 8 3 1 3 2 3 his listShapiro, Mark 3 4 6 3 1 5 2 his listShiio, Yuzuru 3 0 0 0 0 3 2 his listSousa, Rui 4 3 6 2 1 1 4 his listSteffensen, Bjorn 0 1 2 2 2 4 1 his listStockand, James 3 6 5 4 4 4 5 his listVenkatachalam, Manje 1 0 0 3 4 0 5 pubmedWeintraub, Susan 4 6 10 11 8 7 7 pubmedWeiss, David 2 0 3 1 2 0 0 his list

annual average 3.2 3.2 3.7 3.6 4 3.3 3.5

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TABLE 9: Faculty Grant Support - RO1 equivalents2006 2007 2008 2009 2010 2011 20121.2 1.4 1.4 2.4 2 1.4 1.91.6 1.8 2.2 1.8 2.9 3.5 3.51.5 2.1 2.1 2 1.9 2.5 2.11.1 1.7 1 1 1.2 1.7 1.50 1 1 1.7 1.7 1.7 1.7

Fields, Gregg 1 2 2 3 52 2 2.5 2.5 2.5 3.5 3.5

Folli, Franco 0 1 1.2 2.2 2.4 2.6 1.6Gaczynska, Maria NA*Hardies, Stephen 1 1 1 1.1 1.1 0 0Hart, P John 1.4 2.8 2.4 2.6 3.4 2.7 2.7Hinck, Andrew 1 1 1.2 1.4 1.4 0.4 0.4Ivanov, Dmitri 0 0.5 0.5 1 2 1.5 1Jiang, Jean 2.1 2.1 1.7 2.4 2.4 2.2 2.1Kim, Chongwoo 0 0 1.1 1.1 0.9 0.9 0.5Lafer, Eileen 1 1 1 1.2 1.2 2 2Lee, John 0.7 0.7 0 0 0.7 1.2 1.5Lindsey, Merry 1.7 1.8 2.8 3.9 8.7 7.8 5.6Liu, Feng 2 2 2 2.2 2.2 1 2LoVerde, Phil 1 1 1 1 1 1.9 1.5Luduena, Richard 0.5 0.5 0.5 0.5 1.5 1.5 1Masters, Bettie Sue 1 1 2 2 2 2 2McAlister-Henn, Lee 2 2 2 2 2 1 1McEwen, Donald na*Musi, Nicolas 0.9 2.4 1.7 1.5 2.5 2.5 2Myatt, Leslie 3.8 3.9 3.3 3.3 2.3 3 2Nicholson, Bruce (a) 2 2 2.2 2 1 1.2 0.2Rea, Shane NA*Robinson, Neal 0.5 0.5 0 1 1 1 1Serwer, Philip 3.5 3.5 2.7 2.7 0.7 0.2 0.2Shapiro, Mark 1.2 1 1 2 2 2.2 2.1Shiio, Yuzuru 0 1.4 1.4 1.8 1.8 1.4 1.6Sousa, Rui 1.2 1.2 1 2.4 1.4 1.4 1Steffensen, Bjorn (b) 2.5 1.5 1.5 1.5 1.5 1 2Stockand, James 2.9 2.9 2.9 2.2 3.4 2.2 2.2Venkatachalam, Manjeri 1 1 1 1 1 0 0Weintraub, Susan 1.4 1.4 1.2 1.8 1.8 1.8 1.4Weiss, David 3 2.5 2.5 1.5 1 1 1

annual averages 1.4 1.6 1.6 1.8 2 1.9 1.6Data based on a list or a CV provided by the individual: NA* - data not available

RO1 or equivalent funding ($250,000+/yr) = 1 na* - not applicable due to health issuePOI projects or funding of about $100,000-150,000/yr = 0.5R21, etc., type awards (about $75,000/yr)= 0.4Welch or equivalent (about $50,000/yr) = 0.2small awards = 0.1

Note: Numbers are for research grants to faculty. Not included are numerous other grants including, for example (a) several recruiting and training grants obtained by Nicholson and (b) several training grants obtained by Steffensen.

Fitzpatrick, Paul

Adamo, MartinAguiar, RicardoAsmis, RetoBrenner, AndrewDemeler, Borries

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TABLE 10: Faculty Teaching Activities - Averages over two year periods

2008-2009 and 2009-2010 2010-2011 and 2011-2012Didactic Other Total # grad stu Didactic Other Total #grad stu #postdocs

Adamo 26 17 43 1.5 16 11.5 27.5 1 0Asmis 9 4 13 3 0

Demeler 38 3 41 0 41 0.5 41.5 0 1Fields 6 0 6 0 (departed)Fitzpatrick 14 3 17 4.5 21 0 21 1 5Hardies 28 2.5 30.5 0 45 3 48 0 0Hart 14.5 10 24.5 2.5 11.3 3 14.3 2 5.5Hinck 37 6 43 5 22.5 2.5 25 3 1.5

Ivanov 8.3 5.5 13.8 0.5 2Jiang 14 14 28 5 14.5 7.5 22 3.5 3.5Kim 16 5.5 21.5 1 12 8 20 2 0Lafer 18 3 21 1 14 5 19 0.5 1.5Lee 30 4.5 34.5 0 24 4.5 28.5 0 1Loverde 5 3 8 0 19 3.5 22.5 1 0.5Luduena 25.5 1.5 27 1 30.3 0 30.3 0.5 1Masters 4 2 6 0 4.5 1.5 6 0.5 3.5McAlister-H 15 15.5 30. 5 1.5 14 10 24 0.5 1.5McEwen 16.5 5 21.5 1 14.5 4 18.5 1.5 0Nicholson 10 12 22 3 8.5 5.5 14 2 0Robinson 17.5 9.5 27 0 23.5 0 23.5 0 1.5Serwer 27 3.5 30.5 1 22 2 24 1 0Shiio 10.5 2.5 13 0.5 9.8 2 11.8 0 1Sousa 12.5 10 22.5 1 12 2.5 14.5 0 2.5Weintraub 19 3.5 22.5 0 12 7 19 0 0

avg 18.4 6.2 24.3 1.3 17.8 4 21.8 1 1.4

Didactic: actual contact lecture hours in introductory graduate, medical, or dental biochemistry courses and in advancedgraduate courses; points for course directorships.

Other: service on student committees (research, dissertation, rotations, qualifying exams), track leadership, etc.Total: didactic hours plus other student service.#Graduate or #postdoctoral students: actual #students supervised. Note: numbers in these columns should

be multiplied by some substantial figure to express the hours spent on individual mentoring efforts.Data from faculty members, CVs, course syllabi.

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TABLE 11: Examples of Faculty Qualifications2006 2007 2008 2009 2010 2011 2012 OTHER ACTIVITIES/AWARDS

Adamo Study Secs AHA USMLE exam comm 2009-2012NIH Pres-Elect, Soc for Exp Biol & Med 2009-2011

Aguilar Ed Boards Micro RNA, Scholar – Amer Soc of Hematology 2006-09Frontiers in Young Investigator – Voelcker Fund 2009-14

non-coding RNA

Asmis Study Secs AHANIH

Ed Boards J Nut Bioc,Atheroscler

J Pharm& Exp Ther

Fields Ed Boards J. Biomol.Tech Welch Chair 2008-2010Intl J Peptide Res Pres, Amer Peptide Soc 2009-2011

J Biol Chem PepCon Advisory Comm 2008Biopolymers Key Note Speaker: PepCon 2008, 2nd World

Curr Prot and Pep Cancer Congress 2009, Chem & Biol ofChem Biol & Drug Des Peptides 2008, Modern Solid Phase

Syn & Applications 2009Commencement speaker UTHSCSA 2009BIT Life Science Lifetime Membership 2008

Fitzpatrick Study Secs NIH Fellow, AAAS, 2010Ed Boards Arch B & B

[exec ed]

Gaczynska Study Secs NIHEd Boards Ubiquitin

Hart Study Secs ACS Ewing Halsell, Pres’s Coun Dist Prof of Biochem, 2006-present

Director, X-ray Crystallography Core Lab

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Jiang Study Secs NIHEd Boards Front Biosci

[mg edit]JBC

Opthal JCurrChemBioIntJBCand MB

WorldJBCBMC Cel Bio

JBoneMinResLafer Study Secs NIH Dir, Ctr for Surface Plasmon Resonance

Ed Boards Fac 1000 Co-Dir, Ctr for Macromolecular InteractionsBrain Cel Biol

Lindsey Study Secs NIH Dir, Cardiovascular Fxn Core, Barshop Inst.Ed Boards JMolCelCard

JCardFailureCirc Res

HypertensionAmJPhys

Liu Study Secs VA, AHADiabetes Assoc

LoVerde Ed Boards Microb Path 1995-2015 WHO Panel on Parasitic Diseases MolBiolParasit 2002-pres WHO Com on ResParasitology 2002-pres Sci Advisory Comm for NIAIDParasit Res Ext Contract Schistosomiasis Res

AmJTropMed 2008 Pres, Assn of Parasitologist

Luduena Ed Board J Biol Chem 2007 UTHSCSA Distinguished Teaching AwdStudy Secs DOD 2010 UT Regents Outstanding Teaching Awd

Masters Welch Found Dist Prof in Chemistry, 2002-presFellow of the AAAS since 2001President of the ASBMB, 2002-4Chair, Public Affairs Adv Comm of the Amer Soc

for Bioc and Mol Biol, 2011-2013Membership Comm, Inst of Med Nat Acas of Sci

member 2008-12; chair 2010-12

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Shapiro Study Secs NIH

Shiio Study Secs AHA

Steffensen Study Secs 23 as ad hoc and full member since 1998 2006-pres: Castella Dist Prof in Gerodontology2012: Irwin Mandel Dist Mentor, ADA Res2012-pres: Fellow, Amer Dean Edu Assn

Leadership Inst.

Stockand Study Secs AHA 2006 Established Investigator Award, AHANIH 2007 Henry Pickering Bowditch Award,

Ed BoardsAmJPhyisiol Amer. Physiol. Soc.JExpBiolMedBMCPhysiol

FrontMembPhysioBiophys

Weintraub Study Secs see CV for extensive service here 2012: Pres of the Amer Soc of Mass Spec.Ed Boards J Chrom A

J Amer Soc Mass SpecJ Proteome Res

Weiss Study Secs NIH 2005-2010 Chairman, Physiology, UTHSCSAEd BoardsMolecPharm 2011-2012 Vice Dean of Basic Sci Res, Med

Cell Sci. 2010-pres Dean, Grad School of Biomed SciBiophys J 2010-pres Dielmann Chr in Basic Biomed Inve

JBC 2011-pres Vice President for Research

STUDY SECTIONS = FULL MEMBERSHIP (AD HOC SERVICES OF ALMOST ALL FACULTY ARE NOT SHOWN). The year of the column entry signifies the first year of service on a study sections or an editorial board.

OTHER CORE FACILITY DIRECTORS:BORIES DEMELER: HYDRODYNAMICSANDREW HINCK: NMRRUI SOUSA: PROTEIN PURIFICATION

OTHER SIGNIFICANT AWARDS IN THIS REVIEW PERIOD:JOHN LEE - UTHSCSA - DISTINGUISHED TEACHING AWARDRICHARD LUDUENA - UTHSCSA AND STATE OF TEXAS DISTINGUISHED TEACHING AWARDSDMITRI IVANOV - CPRIT SCHOLAR 2010-2014

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Document 1: UTHSCSA CORE FACILITITES AND OTHERS HOUSED IN THE DEPARTMENT OF BIOCHEMISTRY

Bioinformatics Core Facility (BCF) - Borries Demeler, Director

The BCF primarily provides computational support for investigators at UTHSCSA, but also provides

services to administrative and departmental offices on campus. The BCF supports a wide range of scientific applications, software packages, and computing platforms, with an emphasis on Unix/Linux/X11 architectures. The BCF offers assistance gaining access to national resources like XSEDE and TeraGrid, and provides programming services for websites, database applications and custom scientific software. Our programmers are well versed in numerous programming languages, including C/C++, Java, php, MySQL, and shell programming. We assist with backup solutions for your laboratory, high performance parallel and supercomputing applications, visualization, and next generation sequence analysis, and specialize in the implementation of demanding network solutions for your laboratory and workplace. We also offer poster printing services for formats up to 42 inches in height (arbitrary width).

By integrating high-performance computing into current research, we hope to facilitate leading-edge research and help investigators at UTHSCSA to be computationally competitive in a broad spectrum of research applications. The facility is equipped with a modern 230 processor supercomputer for parallel computation, and offers mass storage for database and data mining application. We further support popular bioinformatics and genomics software packages, including next generation sequence analysis. Trained staff are available to address security, programming, web development, and other computational tasks, and to help you with your custom programming needs. Our goal is to foster collaborations and provide assistance with grant writing for proposals seeking to integrate modern computational techniques in research activities.

Center for Macromolecular Interactions – Three Facilities

(1) The Center for Analytical Ultracentrifugation of Macromolecular Assemblies (CAUMA) - Borries Demeler, Director

The CAUMA provides analytical ultracentrifugation (AUC) service for local and national investigators. Research projects conducted at CAUMA include the study of biological macromolecules, nanoparticles, and material science applications. For each study, we assist the investigator by developing a custom experimental design, performing the data acquisition, and by analyzing the resulting data using the popular UltraScan software, which provides unsurpassed resolution and accuracy. We also offer training on our AUC instruments, and teach a workshop on AUC data analysis with UltraScan.

AUC is a first principle separation method. It allows the investigator to perform all studies in a physiological solution state, where ionic strength, pH, solute concentration, buffer conditions, temperature, etc. can be modulated to investigate dynamic effects in the experimental system, and to replicate physiological conditions as closely as possible. AUC does not require any standards and provides composition information by resolving all dissolved solutes into size, shape or density distributions. Studies performed at CAUMA include, but are not limited to, research into protein/DNA/small molecule interactions, oligomerization of proteins, aggregation studies, composition analysis, particle sizing, anisotropy determination, particle density measurement, drug interactions, molecular weight determination, and macromolecular assembly.

(2) The UTHSCSA Center for Surface Plasmon Resonance - Eileen Lafer, Director This center provides expertise and instrumentation in Surface Plasmon Resonance. The Center has two

BIAcore 3000s and one T100 instruments. We offer fee-for-service or individual/group training and provide help with experimental design, applications, and data analysis as well as assistance in grant and manuscript preparation.

The Technical section provides information on sensor chips, chemical compatibility, injection information, and maintenance/washing procedures. It also contains a restricted site for software and GE/BIAcore user manuals.

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The Protocols sections contains information on basic procedures for pre-conditioning, pH scouting, minimal biotinylation, and activation/capture. There is also a Rmax calculator available, a procedure for calculating peptide concentration based on absorbance, and tables for preparing commonly used reagents.

A Training section contains the procedure for conducting a well characterized small molecule study using SPR. The training guides the user through reagents, preparation of the instrument and preparation of the sensor chip, capture of the ligand, and analyte preparation. Users are required to download Scrubber® software and obtain a license for its use. Also download the tutorials.

(3) The UTHSCSA Center for Light Scattering – Eileen Lafer/Borries Demeler/Rui Sousa, co-directors

This center provides instrumentation and expertise in light scattering and isothermal titration calorimetry. Instrumentation includes the following.

The DynaPro NanoStar from Wyatt Technologies is available for Dynamic Light Scattering (DLS). It is capable of measuring samples ranging in size from 0.5 nm to 1000 nm at concentrations as low as 0.1 mg/ml. Sample volumes as small as 1 uL may be tested. Operation is performed through the easy to use DYNAMICS® Software and data may be exported to MS Word or other programs. The NanoStar also has a dedicated Static Light Scattering (SLS) detector so not only can it measure hydrodynamic radii, but absolute molecular weights as well.

The VP-ITC from GE/Microcal permits: (a) Simultaneous determination of all binding parameters in a single experiment - information unobtainable from more limited binding assays by characterization of molecular interactions of small molecules, proteins, antibodies, nucleic acids, lipids and other biomolecules, lead optimization, enzyme kinetics, assessment of the effect of molecular structure changes on binding mechanisms, and assessment of biological activity. (b) Direct measurement of sub-millimolar to nanomolar binding constants (102 to 109 M-1). Measure nanomolar to picomolar binding constants (109 to 1012 M-1) using the competitive binding technique. (c) Investigation of any biomolecular interaction with high sensitivity. No labeling or immobilization is required. There are no buffer restrictions and turbid solutions are easily handled. The instrument provides unattended operation after sample loading and no reagents are required.

Center for Biomolecular NMR Spectroscopy – Andrew Hinck, Director

This facility offers state-of-the-art high field NMR instrumentation for structural studies of biological macromolecules. The instrumentation presently available includes four-channel Bruker Avance 500, 600, and 700 MHz NMR spectrometers. The facility also has available an ultrahigh sensitivity 5mm 1H-13C-15N triple-resonance cold probe for the 600 MHz spectrometer. The resources of the facility can be accessed either on a fee-for-service or on a collaborative use basis. The types of analyses conducted on a fee-for-service basis include acquisition and analysis of the required spectra for elucidation of small molecule structures (includes synthetic molecules, natural products, cofactors, lipids, and short peptides (30 amino acids or less)). The types of projects conducted collaboratively include the determination of three-dimensional structures of biological macromolecules, including proteins and nucleic acids, both alone and as complexes with various ligands. The instrumentation available in the Center was purchased through funds provided by the NIH National Center for Research Resources, the Houston Endowment, the UTHSCSA Children's Cancer Research Center, and the U. Texas Permanant University Fund. The operational costs of the facility are supported by the Macromolecular Shared Resource of the Cancer Therapy & Research Center (CTRC), the UTHSCSA Core Facilities Committee, and User Fees.

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Center for Mass Spectrometry – Susan Weintraub, Director

This center is equipped with the following Mass Spectrometers:

LTQ-Orbitrap Velos H/ETD MS (Thermo Fisher) LTQ ion trap MS (Thermo Fisher) Voyager-DE STR MALDI-TOF/MS (Applied Biosystems) Quantum triple quadrupole MS (Thermo Fisher) TRACE DSQ EI/CI GC/MS (Thermo Fisher)

And with the following equipment for gel analysis and handling:

FX Pro Plus Imager (Bio-Rad) GS-800 calibrated densitometer (BIo-Rad) ProteomeWorks spotcutter (Bio-Rad) PDQuest gel analysis software (Bio-Rad) Progenesis SameSpots software (Nonlinear Dynamics)

Services provided include: Molecular mass determination Protein identification In-gel digestion Sequence characterization of peptides Localization of sites of posttranslational modification Electron impact and chemical ionization mass spectral analysis Gas chromatography/mass spectral analysis (GC/MS) 1-D and 2-D gel electrophoresis Robotic gel spot excision

Center for X-ray Crystallography – John Hart, Director

The mission of the X-ray Crystallography Core Laboratory is to provide state-of-the-art resources to researchers at the University of Texas Health Science Center at San Antonio, and to external users, enabling the detailed 3-D analyses of biological macromolecules that play important roles in human health. This is a full service core in that it not only offers access to sophisticated equipment and technologies but also offers advice and technical assistance in sample preparation. Services are also provided to investigators without funding to facilitate the development of pilot data for new potentially fundable projects, as core resources permit.

Technology:

The X-ray Crystallography Core Laboratory at the University of Texas Health Science Center at San Antonio offers state-of-the-art macromolecular X-ray crystallographic instrumentation operating on a collaborative use basis. The equipment infrastructure of the facility presently includes two complete X-ray crystallography systems:

1) Rigaku R-AXIS HTC imaging plate area detector with VariMax HighFlux optics mounted on a high-flux MIcroMax 007HF generator with an X-STREAM cryogenic crystal cooling system

2) Rigaku R-AXIS HTC imaging plate area detector with VariMax HighRes optics mounted on a high-flux MIcroMax 007HF generator with an X-STREAM cryogenic crystal cooling system

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The improved brilliance of the 007HF equipped with VariMax optics relative to conventional home lab X-ray sources gives researchers the in-house capability to work with very small or poorly diffracting crystals. Computational hardware (Intel Quad-core Linux workstations) and software (CNS, CCP4, COOT, d*TREK, HKL-2000, PHENIX, SHARP, SHELX, etc.) are also in place enabling the complete protein structure determination and refinement process to be accomplished in relatively short order.

Protein Expression and Purification Core (PEPcore) – Rui Sousa, Director

The PEPCore helps to produce highly purified recombinant proteins for functional and structural

studies. At this point, we mainly use bacteria as the expression host. In the future, other systems such as yeast, insect and mammalian cells shall also be available.

For protein production in E. coli, different conditions (e.g., induction temperature, IPTG concentration and incubation time) will be tested and various strategies will be used to achieve optimal expression and keep the target protein in the soluble portion. The expressed target protein will be first purified using affinity chromatography. Other purification methods (e.g., ion exchange and size exclusion chromatography) will be applied if deemed necessary. Protein is normally expressed in 1-5 L scale and milligrams of final purified protein can be expected.

UTHSCSA CORE FACILITITES HOUSED OUTSIDE THE DEPARTMENT OF BIOCHEMISTRY

The UTHSCSA houses 15 different core facilities. Clearly, the six facilities in the Department of Biochemistry described above are likely to be most useful for core faculty and students in the graduate program, and many of our students receive hands-on training in techniques available from one or more of these core facilities. Other core facilities that are heavily used by individuals in our program include: Flow Cytometry Imaging Genomics Nucleic Acid (sequence analyses and DNA oligonucleotide synthesis)

OTHER INSTRUMENTATION AND FACILITIES HOUSED IN THE DEPARTMENT OF BIOCHEMISTRY

Within the Department of Biochemistry are numerous common rooms and equipment available to all faculty and students in the program. These include:

Dishwashing facility and two autoclaves Cold rooms and warm rooms (the latter at 37oC and 30oC, equipped with incubator shakers) Centrifuges (ultra, high performance, and general purpose Circular dichroism spectrometer Fluorometers (general purpose, life-time, high pressure) Gel imaging systems (fluorescent, chemiluminescent) and a plate reader qRT-PCR system Scintillation counter Sonicator and lyophilizer X-ray developer In addition, many laboratories are equipped with other types of instruments including spectrometers,

FPLC and HPLC systems, tissue culture hoods, etc. These are generally available by request to the principal investigators.

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Document 2: As a Department of the UTHSCSA in the School of Medicine with graduate student oversight by the Graduate School of Biomedical Sciences, the Department of Biochemistry adheres to elements (in blue) of the following mission statements and goals (from entity websites).

UTHSCSA Mission Statement The mission of The University of Texas Health Science Center at San Antonio is to make lives better through excellence in education, research, health care and community engagement. Strategies for achieving this mission are:

• Educating a diverse student body to become excellent health care providers and scientists. • Engaging in research to understand health and disease. • Commercializing discoveries, as appropriate, to benefit the public. • Providing compassionate and culturally proficient health care. • Engaging our community to improve health. • Influencing thoughtful advances in health policy.

UTHSCSA School of Medicine We are a young institution with the passion to excel. When the history of our School is written, it will be noted this was "our time." We are on the threshold of an historic and transformational era of growth and achievement for our School, and our University that will change the future of health. We seek the pursuit of scientific truth at our School of Medicine - the clinical bridge from the laboratory to the bedside. Ours is a unique care experience that brings the latest discoveries to benefit our patients and our students.

Mission

The mission of the School of Medicine is to provide responsive and comprehensive education, research and service of the highest quality in order to meet the health-related needs of the citizens of Texas. In all aspects of fulfilling this mission, the School of Medicine is committed to fostering the broadest diversity and inclusion that ensures successful achievement of the institutional priorities to:

• Cultivate a pervasive, adaptive and respectful environment promoting diversity, inclusion, equity, professionalism, humanism and opportunity

• Provide exemplary medical education and training to a diverse body of health career professionals at all levels while fostering a commitment to scholarship, leadership and life-long learning across the educational continuum.

• Build and sustain recognized leadership and advance scholarship excellence across the biomedical and health-related research spectrum

• Deliver exemplary and compassionate health care to enhance every patient's quality of life • Serve as a responsive resource to address community health needs whether local or global • Attain health equity for the diverse patient population of South Texas

UTHSCSA Graduate School of Biomedical Sciences The Graduate School of Biomedical Sciences provides an individualized, diverse and multidisciplinary learning environment for students to develop the knowledge, skills and creativity to succeed in the evolving biomedical space.

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Faculty and Academic Equal Opportunity/Affirmative Action Office The mission of the Faculty and Academic EO/AA Office is to insure that every member of the Health Science Center (HSC) community, individuals seeking employment or an education, and individuals who wish to participate in a benefit from programs and activities offered by the HSC are afforded equal opportunity and freedom from all forms of discrimination that may violate their civil rights and other protections afforded them by the State of Texas, The University of Texas System and The University of Texas Health Science Center at San Antonio (UTHSCSA).