UF Genetics doctoral draft 9-05-05

Note: This outline and the questions pertaining to each section must be reproduced within the body of the proposal in order to ensure that all sections have been satisfactorily addressed.

Introduction

I. Program Description

Describe the degree program under consideration, including its level, emphases (including tracks or specializations), and the total number of credit hours.

Due to the fundamental nature of genetics in the life sciences, the discipline of genetics is distributed across several colleges of the University and is not in the exclusive domain of any college. The University of Florida throughout its colleges and faculty possesses world-class state-of-the-art training and research opportunities in genetics and genomics. In recognition of the importance of genetics in modern biology and the distribution of geneticists across the campus, the University of Florida Genetics Institute (UFGI) seeks to establish a university-wide Ph.D. Program in Genetics with the goal of developing a comprehensive program that will utilize the faculty resources of the University to the best advantage of its students.

The post genomic sequencing era of biology has resulted in the new discipline of genomics that has evolved from genetics. Genomics is truly multidisciplinary requiring skill sets from biology, chemistry, mathematics/statistics, engineering and computer sciences. The challenge faced by life-scientists today working in genomics is simply how to deal and make sense of the tremendous amount of data being generated by high throughput methods.

The program will be designed to train students broadly in genetics and the emerging field of genomics. The program will bring together geneticists, bioinformations, statisticians, and computer scientists from across the university to implement a comprehensive Graduate Program in Genetics that will complement existing graduate programs in the life sciences throughout the university.

The Genetics Ph.D. degree will be a research-intensive degree and will require a minimum of 90 credit hours beyond the Bachelor degree. The core course work of the proposed program will expose students to all areas of genetics with (PCB5065). The proposed program is also computationally intensive; the core includes courses in Statistics SAT6166 and in Bioinformatics CAP5510. Students in the proposed program will have dissertation projects available to them in all areas of genetics including microbial genetics, molecular genetics, plant genetics, mammalian genetics, population genetics, statistical genetics, and bioinformatics.

Graduates from the program will find employment in the biotechnology industry, the pharmaceutical industry, government regulatory agencies and in traditional academic positions.

Readiness

II. Institutional Mission and Strength

A. Is the proposed program listed in the current State University System Strategic Plan? How do the goals of the proposed program relate to the institutional mission statement as contained in the SUS Strategic Plan and the University Strategic Plan?

The UF Strategic Plan states that “UF must adopt institutional strategies unique to its position, circumstances, and strengths that will achieve maximum impact and enhance its reputation. In particular, UF must foster the following interdisciplinary research and instructional programs on an institutional level:

• Research in cancer and genetics

• Research on the brain

• Developments in biotechnology, particularly at the interface of medicine and nanoscience

• Investigation of social and medical problems associated with Aging

• Research into the status of children and families

• Research in ecology and the environment

• Internationalization of the campus and the curriculum.

The proposed genetics graduate program will directly impact and foster interactions among faculty and students across the campus in the 5 of the 7 areas enumerated specifically in genetics, cancer, brain research, biotechnology, ageing, and ecology and the environment.

B. How does the proposed program specifically relate to existing institutional strengths such as programs of emphasis, other academic programs and/or institutes and centers?

Genetics is fundamental to the life sciences. The proposed program will serve as a single, though not exclusive, entry point for students interested in the broad discipline of genetics. The proposed program will complement other life science programs which are already in existence in several colleges of the University and which may include components that touch on specialized areas of genetics. For example, the Advanced Genetics Concentration of the IDP program is focused on molecular genetics. The core course work in the IDP program is focused on biochemistry, molecular biology, molecular genetics, cell biology, immunology and pathogeneses. Students who complete the Advanced Genetics Concentration of the IDP program are extremely well trained molecular geneticists. The IDP program is focused on molecular genetics and there is limited to no exposure in population genetics, plant genetics, computational genetics, or hard core bioinformatics. In contrast to the Genetics Advanced Concentration of the IDP program, the core proposed program exposes students to all areas of genetics and is computationally intensive with required courses in statistics and bioinformatics in addition in addition to genetics. Students in the proposed program will have research opportunities that run the full gambit of genetics and genomics. The program will prepare student for the leadership positions in the emerging field of genomics with utilizes the tools of biology, mathematics, engineering and computer sciences.

It is important to recognize that while complementary to other life science programs, the genetics graduate program will not duplicate efforts of other programs rather it will work with other programs to develop courses and curriculum that will be available to students in existing programs as well as students entering the genetics graduate program directly.

C. Describe the planning process leading up to submission of this proposal. Include a chronology of activities, listing the university personnel directly involved and any external individuals who participated in planning. Provide a timetable of events for the implementation of the proposed program.

In the fall of 2003, Dr. Kenneth I. Berns, Director of the University of Florida Genetics Institute, commissioned a curriculum/planning committee to design a University-wide genetics graduate program that would pull together all of the faculty members and resources dedicated to the study of genetics at the University of Florida. The committee was chaired by Henry Baker, Interim Chair Department of Molecular Genetics and Microbiology, Director Genetics Advanced Concentration IDP Graduate program, College of Medicine, with members including Michael Miyamoto, Associate Chair, Department of Zoology, College of Arts and Sciences, George Casella, Chair, Department of Statistics, College of Arts and Sciences, John Davis, School of Forest Resources and Conservation, Institute of Food and Agricultural Sciences, Christine Chase, Department of Horticultural Sciences, Institute of Food and Agricultural Sciences.

The committee adapted the concept of a core curriculum in the first-year with specialization after the first-year. In doing so the committee made distinctions between “core” vs. “applied” genetic concepts. The committee devised a core first-year curriculum appropriate for all students with space for a four credit elective to allow students the flexibility to tailor the curriculum to their individual needs in the first year. During the Spring Semester of 2004, the “core” curriculum concept was presented at a general faculty meeting of the University of Florida Genetics Institute and feedback was solicited form the faculty. At the beginning of the Fall 2004 Semester a proposal was presented to the University Florida Graduate School and shortly thereafter the Curriculum/Planning committee was given the go ahead to formulate the full proposal.

During the Fall Semester 2004, the Curriculum/Planning committee fully developed the genetics graduate program and By-Laws for the program. In December of 2004, the Genetics Graduate Program, its proposed curriculum, and by-laws were presented both orally and writing copies distributed at a general faculty meeting of the University of Florida Genetics Institute. Again input was solicited from interested faculty members.

The curriculum/planning committee chair met with and discussed the proposed program with administrators and department chairs from across the campus including:

Kenneth Gerhardt, Interim Dean University of Florida Graduate School,

Eric Triplett, Chair, Department of Microbiology and Cell Science

Charles Woods, Chair, Department of Physiology and Functional Genomics

Douglas Andersen, Chair, Department of Neuroscience

Steven Sugrue, Chair, Anatomy and Cell Biology

James Flanegan, Chair, Biochemistry and Molecular Biology

James Crawford, Chair, Pathology, Immunology and Laboratory Medicine

Steve Baker, Chair, Pharmacology

Paul Gulig, Co-director, Immunology/Microbiology IDP Advanced Concentration

Robert Burne, Chair, Oral Biology

David Evans, Chair, Zoology

George Bowes, Chair, Botany

John Dame, Chair, Pathobiology

F. Glen Hembry, Chair, Department of Animal Sciences

Richard L. Jones, IFAS Dean for Research

Allan F. Burns, Professor and Associate Dean for Faculty Affairs

Jimmy G. Cheek, Sr. VP Agriculture and Natural Resources

Wayne Smith, IFAS Interim Dean of Academic Programs

Wayne McCormack, COM Associate Dean for Graduate Studies

Presentations were also made to the IDP Advisory Board and at the faculty meetings of the Genetics IDP Advance Concentration in the College of Medicine and the Pathobiology faculty in the College of Veterinarian Medicine.

At each meeting a copy of the proposed genetics program was made available for distribution to interested parties.

III. Program Quality - Reviews and Accreditation

If there have been program reviews, accreditation visits, or internal reviews in the discipline pertinent to the proposed program, or related disciplines, provide all the recommendations and summarize the institution's progress in implementing the recommendations.

Doctoral programs in the colleges of primary interest, Medicine, Liberal Arts and Sciences, Engineering and Agricultural and Life Sciences, have not been reviewed by external agencies. The University of Florida’s Strategic Plan clearly identified the need to promote Genetics research and programs. This proposal is an outgrowth of the Strategic Plan.

The University of Florida is accredited by the Commission on Colleges of the Southern Association of Colleges and Schools (1866 Southern Lane, Decatur, Georgia 30022-4097: Telephone number 404-679-4501) to award bachelor, master, specialist and engineer, as well as doctoral and professional degrees.

IV. Curriculum

A. For all programs, provide a sequenced course of study and list the expected specific learning outcomes and the total number of credit hours for the degree. Degree programs in the science and technology disciplines must discuss how industry-driven competencies were identified and incorporated into the curriculum, as required in FS 1001.02 (6). Also indicate the number of credit hours for the required core courses, other courses, dissertation hours and the total hours for the degree.

First year curriculum

Fall Semester

Emphasis on research training begins immediately upon entry into the Genetics Program. Students will rotate through at least three labs in at least two different colleges. Each rotation will occupy a ten week block and will commence and conclude with an oral presentation using a scientific meeting format. Student research rotations expose students to different laboratory philosophies, technologies, and projects throughout the Genetics Institute and University. The Genetics Program Director and Co-Director along with the Academic Status Committee will serve as the first year supervisory committee and function primarily to ensure that the student is guided in basic course work and given the opportunity to explore different areas of research.

PCB5065 (4 credits)

The course can be divided into 5 sections covering: i) Genes and mutations, ii) Recombination, iii) Chromosomes, mapping, and positional cloning, iv) Non-Mendelian inheritance and developmental genetics, and v) population and quantitative genetics. A molecular biology background is expected, the course does not cover molecular biology extensively, but introduces it where needed to develop and enhance the topic at hand.

STA6166 (3 credits)

The STA6166 focuses on regression starting from the beginning. (More statistically orientated students may choose to take the two course sequence STA6166 and 6167).

Research Rotations (1 credit)

Genetics Seminar (1 credit)

Spring Semester

CAP 5510 - Bioinformatics (3 credits)

This course covers basic concepts of molecular biology and computer science. Sequence comparison and assembly, physical mapping of DNA, phylogenetic trees, genome rearrangements, gene identification, biomolecular cryptology, and molecular structure prediction.

Elective (3 – 4 credits)

The elective course may be any one of a number of life-science or other related courses depending on background and specific needs of the student. It is anticipated that most students will elect a molecular biology course such as BCH 6415 Advanced Molecular and Cellular Biology; however, some students may elect computationally intensive courses or computer sciences courses.

Research Rotations (1 credit)

Genetics Seminar (1 credit)

By the end of the first year, all students should have identified a major professor; however, in some cases students may elect a fourth rotation. By the end of the summer between program years 1 and 2, students in consultation with their advisor, shall choose a Supervisory Committee. The Supervisory Committee consists of the student’s major advisor/mentor and at least 3 other members of the graduate faculty. In its supervisory role the supervisory committee will comply with contemporary graduate council policies.

Second-year curriculum

Course selection in the second year and thereafter will follow the University of Florida Graduate Council guidelines and will largely be based on the needs of the individual student and selected in consultation with the student’s Supervisory Committee from the menu of courses in the University catalog. Several potential courses of study are listed below which serve as an example of the breath of the educational opportunities available to students matriculating through the genetics program.

All upper level students will be required to enroll and participate in the following courses while they are in residence in the program:

Genetics Journal Colloquy (1 credit)

Genetics Seminar (1 credit)

Graduate/Doctoral Research (variable credit)*

* Students will register for Graduate Research credit until they are admitted to Ph.D. candidacy after which time they will register for Doctoral Research credit.

Students will be admitted to Ph.D. candidacy based upon successful completion of written and oral qualifying exams. Students are expected to have completed these exams by the end of their fifth semester. In accordance with graduate school policy Ph.D. students cannot take qualifying examinations prior to their third semester of graduate study beyond the bachelor’s degree.

Extended Forums for interaction:

1. Journal Clubs

Weekly Journal Clubs will be organized around at least three topics each semester. Attendance in at least one Journal Club is required each fall and spring semester.

2. Research Presentations

As part of the qualifying exam, Ph.D. students will present a research proposal in seminar format to the Genetics faculty, postdoctorals, and graduate students. The student’s preliminary findings and proposed future experiments should be discussed. The purpose of this requirement is to give the student experience in publicly communicating research findings and to provide the student a chance to receive input from Genetics faculty and students regarding the research direction and experimental approach.

All Genetics Students will present a public exit seminar prior to graduation.

Sample Courses of Study Available to Students in the Genetics Program

The sample courses of study listed below represents a selection of courses and is only a sampling of courses that a student may choose to take depending on the individual student’s interests and needs. For each student, a customized program will be tailored to best suit the student. The student in consultation with his or her mentor and Supervisory Committee will recommend a specific course of study to the Academic Status Committee which will oversee the programs of each student. The Academic Status Committee will ensure that each student’s program is in conformance with all contemporary University of Florida Graduate Council polices and guidelines.

Sample Course of Study in Plant Molecular Genetics

This sample program is for students primarily interested in plant genetics.

BCH 5045 - Graduate Survey in Biochemistry (3 credits)

FOR 6934 - Plant Molecular and Cellular Biology (3 credits)

PCB 6528 - Plant Molecular Biology (3 credits)

HOS 6373 - Methods and Applications of Plant Cell and Tissue Culture (3 credits)

GMS 6014 - Applications of Bioinformatics to Genetics (1 credit) or CAP 5515 – Computational Molecular Biology (3 credits)

Sample Course of Study in Plant Molecular Genetics with an Emphasis on Breeding

This sample program is for those students interested in bringing genomics to bear on applied plant improvement.

STA 6167 Statistical Methods in Research II (3 credits)

STA 6178 Statistical Genetics and Genomics of Complex Traits (3 credits)

ZOO 6927 Evolutionary Quantitative Genetics (4 credits)

Depending on the students breeding focus at least one of the following courses:

HOS 6201 Breeding Perennial Cultivars (3 credits)

FOR 6310 Forest Genetics and Tree Improvement (3 credits)

AGR 6322 Advanced Plant Breeding (3 credits)

Sample Course of Study in Mammalian/Human Genetics

This sample program is for those students interested in mammalian genetics with an emphasis on medical aspects of human genetics.

GMS6014 - Applications of Bioinformatics to Genetics (1 credit) CAP5515 – Computational Molecular Biology (3 credits)

BCH6415 – Advanced Molecular and Cellular Biology (3 credits)

ANG6469 – Molecular Genetics of Disease (3 credits)

BCH7410 - Advanced Gene Regulation (1 credit)

GMS6011 - Mouse Genetics (1 credit)

GMS6013 - Developmental Genetics (1 credit)

GMS6012 - Human Genetics I (1 credit)

GMS6015 - Human Genetics II (1 credit)

GMS6059 - Gene Therapy from Bench to Bedside (1 credit)

PHA6449 - Pharmacogenomics (1 credit)

Sample Course of Study in Population Genetics and Molecular Evolution (or Comparative Genetics and Genomics)

This sample program is for students interested in: (1) the origins, maintenance, and change of genetic variation in populations, species, and their larger groups; and (2) in how this diversity is related to differences at the phenotypic level. Students will take courses in the three primary areas of population genetics, molecular evolution, and molecular systematics. In addition, it is strongly recommended that all students in this program apply for one or more of the summer workshops offered at the Marine Biological Laboratory or Summer Institute in Statistical Genetics.

UF graduate courses

PCB 5615 – Molecular Evolution and Systematics (4 credits)

ZOO 6927* – Evolutionary Genetics (4 credits)

ZOO 6927* – Evolutionary Developmental Genetics (4 credits)

ZOO 6927* – Seminar in Molecular Evolution (2 credits)

National/International workshops (with participating UF faculty)

Workshop in Molecular Evolution, Marine Biological Laboratory, Woods Hole, MA (http://workshop.molecularevolution.org/)
Summer Institute in Statistical Genetics, North Carolina State University (http://statgen.ncsu.edu/brcwebsite/summer_institute_ral.php)

* Currently the Zoology Department offers a number of different courses under different sections of a Special Topics Course ZOO 6927. Dr. Robert Holt has indicated that the Zoology Department is in the process of establishing separate course numbers for the three course listed above which they currently offer under ZOO 6927.

Sample Course of Study in Statistical Genetics

This sample program is for those students interested in the computationally intensive aspects of genetic and genomics and is mathematically rigorous. Students electing this course of study would substitute STA 6201 for STA 6166 in their first semester in the program.

STA 6207 - Applied Statistics (3 credits)

STA 6208 – Regression Analysis (3 credits)

STA 5325 - Mathematical Statistics 1 (3 credits)

STS 5328 – Mathematical Statistics 2 (3 credits)

STA 6329 – Matrix Computing (2 credits)

BCH 5045 - Graduate Survey in Biochemistry (3 credits)

STA 6178 - Statistical Genetics and Genomics of Complex Traits (3 credits)

STA 6934 - Techniques in Microarray Data Analysis (1-3 credits)

GMS 6014 - Application of Bioinformatics in Genetics Research (1 credit)

Sample Course of Study in Bioinformatics

This sample program is for those students interested in bioinformatics, such as (1) building large genomic and proteomic databases, (2) developing networked computer systems for high throughput biological technology, and (3) data analysis using data mining and knowledge discovery techniques. Students electing this course of study are recommended to take COP 5725 Database Management Systems as their elective in the second semester of the first-year of the program.

COT 5405 - Analysis of Algorithms (3 credits)

CAP 5515 - Computational Molecular Biology (3 credits)

CAP 5805 - Simulation (3 credits)

CAP 6610 - Machine Learning (3 credits)

CIS 6930 - Special Topics (3 credits)

B. Describe the admission standards and graduation requirements for the program.

A recognized baccalaureate from a regionally accredited (e.g. SACS) college or university, or an international equivalent based on a four-year curriculum. Applicants to the genetics program may have undergraduate majors in anyone of a number of life-science majors or in computationally intensive majors such as statistics or computer sciences. The genetics program’s admissions committee will be charged with determining the acceptability of the content and quality of specific undergraduate majors.

Applicants with bachelor’s degrees only must present a minimum grade point average of B (3.0) for all 3000 – 4000 level course work and a combined verbal and quantitative score of 1000 on the Graduate Record Examination (GRE).

A minimum score of 550 on the paper test or 213 on the computer version of the Test of English as a Foreign Language (TOEFL), if required.

A satisfactory conduct record.

Proof of immunization for measles and rubella, and a tuberculosis skin test if required, prior to registering at UF

Course Requirements and Examinations

All requirements for a Ph.D. degree at the University of Florida must be fulfilled. Requirements in the Graduate Catalog Genetics Program will be followed.

All members of the Graduate Faculty who are also members of the University of Florida Genetics Institute are eligible to serve as chair or member of the student’s supervisory committee. The outside member will be established in consultation with the Academic Status Committee.

Ph.D. Degree: The Genetics Ph.D. degree is a research intensive degree and requires a minimum of 90 credit hours beyond the Bachelor of Science degree.

1. Written Examinations:

The written portion of the qualifying examination will consist of a written examination centered on, but not limited to, basic material covered in the first-year curricula. The examination will be administered to all students in June of their third semester following completion of the first-year curricula. Performance on the written examination along with the student’s performance during the first-year will be evaluated by the Academic Status Committee. The Academic Status Committee will communicate one of three evaluations to the student: i. Pass – Ph.D. level, ii. Pass – Masters level, or iii. Fail. Students who receive: Pass – Ph.D. level evaluation will continue on in the Ph.D. program. Students who receive: Pass – Masters level may elect to take a second written exam in August prior to the start of their second year. Students earning Pass – Ph.D. level at this time will continue on in the Ph.D. program. Students not achieving Pass – Ph.D. level at this time will have the option of completing a second year of approved course work and upon successful completion will be awarded a Masters Degree. Students receiving a failing evaluation will be dismissed from the program.

2. Oral Exam:

The oral exam will be conducted after the written portion of the exam is successfully completed, during the fall semester at the beginning of their third year of participation in the program. If the student has not completed the oral exam by the end of the fall semester during their third year in the program, they will be flagged and not allowed to register for the next semester. In preparation for the oral examination, the student will prepare a NIH or NSF-style written proposal for the committee and present a public seminar covering their program of work. The public seminar will typically occur during the Genetics Institute’s Seminar Series time-slot. The proposal will serve as the starting point for the oral examination, but the questions need not be limited to the contents of the proposal and may cover any aspect of science chosen by the committee members. The External member of the committee from outside the Genetics faculty will chair the oral exam. This person will clarify questions when necessary, and will ensure that all members of the committee receive approximately equal time for questioning. The oral examination is expected to last from 2 to 3 hours.

3. Dissertation Defense:

The dissertation defense will be comprised of a formal public oral presentation followed by a closed oral examination by the student’s Supervisory Committee.

C. List the accreditation agencies and learned societies that would be concerned with corresponding bachelor’s or master’s programs associated with the proposed program. Are the programs accredited? If not, why?

Doctoral programs are generally not accredited by professional societies. However, the University of Florida is accredited by the Commission on Colleges of the Southern Association of Colleges and Schools to award doctoral degrees.

D. Provide a one or two sentence description of each required or elective course.

AGR 6322 - Advanced Plant Breeding (3 credits)

This course focuses on the theory and use of biometrical genetic models for analytical evaluation of qualitative and quantitative characteristics, with procedures applicable to various types of plant species.

ANG 6469 - Molecular Genetics of Disease (3 credits)

This course examines the molecular genetics of disease in humans. The completion of the human genome sequence and a database of genetic variants have greatly accelerated the discovery of genes involved in disease, leading to breakthroughs in diagnosis and treatment. We will discuss the range of genetic-based disorders from single-gene recessive defects (eg. cystic fibrosis) to complex diseases (eg. diabetes and alcoholism). Methods to isolate genes involved in disease (eg. whole genome scans and linkage disequilibrium) and types of treatment (eg. gene therapy) will also be discussed.

BCH 6415 – Advanced Molecular and Cellular Biology (3 credits)

This course covers the molecular biology of pro- and eukaryotic organisms, emphasis on understanding experimental approaches which led to recent developments. Chromosome structure and organization, advances in recombinant DNA technology, DNA replication, RNA transcription and protein synthesis, and selected aspects of molecular regulation of gene expression.

BCH 7410 - Advanced Gene Regulation (1 credit)

A literature-based assessment of most recent advances in factors governing eukaryotic gene regulation.

CAP 5510 - Bioinformatics (3 credits)

CAP 5515 - Computational Molecular Biology (3 credits)

This course focuses on algorithms related to molecular biology, including sequence comparisons, pattern matching, pattern extraction, graph techniques in phylogeny construction, secondary structure prediction, multiple sequence alignment, contig search, DNA computing, computational learning theory, and genetic algorithms.

CAP 5805 - Simulation (3 credits)

This provides an introduction to concepts in continuous and discrete simulation with an emphasis on fundamental concepts and methodology, using practical examples from a wide variety of disciplines.

CAP 6610 - Machine Learning (3 credits)

The subject matter of this course reviews attempts, within the artificial intelligence community, to construct computer programs that learn. Topics covered include statistical pattern recognition with its applications to such areas as optical character recognition, inductive learning, and automated discovery.

CIS 6930 - Special Topics (3 credits; max 9)

Prereq: vary depending on topics.

COT 5405 - Analysis of Algorithms (3 credits)

Course provides an introduction and illustration of basic techniques for designing efficient algorithms and analyzing algorithm complexity.

FOR 6310 - Forest Genetics and Tree Improvement (3 credits)

Review of Mendelian, population, and quantitative genetics as important in natural forests and breeding programs of forest trees. Principles of tree improvement programs, gene conservation, and breeding strategy development for wide variety of tree species are covered.

FOR 6934 - Plant Molecular and Cellular Biology (3 credits)

Selected topics in forestry and natural resources.

GMS 6011 - Mouse Genetics (1 credit)

This course provides a theoretical framework for understanding fundamentals of mouse genetics and use of mouse model for study of human disease as well as advanced technical tools used for research and their application to novel problems.

GMS 6012 - Human Genetics I (1 credit)

This course provides a theoretical framework for understanding fundamentals of human genetics as well as advanced technical tools used for research.

GMS 6013 - Developmental Genetics (1 credit)

This course provides a theoretical framework for understanding fundamental developmental genetics. Advantages and limitations of several model systems and their application to the study

of development.

GMS 6014 - Applications of Bioinformatics to Genetics (1 credit)

This course provides students with basic tools for the storage, retrieval, and analysis of information related to genetics.

GMS 6015 - Human Genetics II (1 credit)

This course is an extension of GMS 6012 Human Genetics I and provides a more in depth examination of the theoretical framework, emphasizing functional genomics and bioinformatics as well as advanced technical tools used for research and development in these areas.

GMS 6059 - Gene Therapy from Bench to Bedside (1 credit)

This course investigates the design and use of gene transfer vectors for treating a variety of diseases and provides a practical understanding of successes and hurdles in gene therapy.

HOS 6201 - Breeding Perennial Cultivars (3 credits)

This course covers the methods of breeding perennial fruit and ornamental cultivars using mutations, cell and tissue culture, polyploidy, wide hybridization, and recurrent selection. The conservation and domestication of wild plants are also covered.

HOS 6373 - Methods and Applications of Plant Cell and Tissue Culture (3 credits)

Course covers current techniques of plant cell and tissue culturing methods.

PCB 5065 - Advanced Genetics (4 credits)

Examination of genetic principles including gene and gene function; recombination and linkage; molecular markers, multipoint linkage analysis, and positional cloning; quantitative, population, developmental, and non-Medalian genetics. The course can be divided into 5 sections covering: i) Genes and mutations, ii) Recombination, iii) Chromosomes, mapping, and positional cloning, iv) Non-Mendelian inheritance and developmental genetics, and v) population and quantitative genetics. A molecular biology background is expected, the course does not cover molecular biology extensively, but introduces it where needed to develop and enhance the topic at hand.

PCB 5615 – Molecular Evolution and Systematics (4 credits)

This course investigates the patterns and processes of change at the molecular level in populations, species, and higher taxonomic groups and their systematic implications.

PCB 6528 - Plant Molecular Biology (3 credits)

The course focuses on the structure, function, and analysis of plant genomes, genes, and gene products using a lecture format with frequent discussion of recent papers featuring studies of genome structure, transformation, gene tagging, transcription, signal transduction, organelles, protein trafficking.

PHA 6449 - Pharmacogenomics (1 credit)

This course provides an introduction to basic concepts and methodology of genome mapping and functional genomics applied in field of pharmacogenomics. Examples are chosen from current reviews and primary literature.

STA 5325 - Mathematical Statistics 1 (3 credits)

This course covers topics in probability and statistics, particularly discrete and continuous random variables, sampling distributions, estimation, and hypothesis testing.

STA 5328 – Mathematical Statistics 2 (3 credits)

This course provides the mathematical foundations of point estimation, confidence intervals, tests of hypotheses, linear models, and analysis of variance.

STA 61XX (3 credits)

New statistics course modeled on STA6166 but tailored to genetics. The STA6166 focuses on regression starting from the beginning. (More statistically orientated students may choose to take the two course sequence STA6166 and 6167).

STA 6166 - Statistical Methods in Research I (3 credits)

This course covers statistical methods based on t, F, and Chi-squared tests, analysis of variance for basic experimental designs, factorial experiments, regression analysis and analysis of covariance.

STA 6167 - Statistical Methods in Research II (3 credits)

This course provides an in depth examination of analysis of covariance, general linear model, factorial, nested, split-plot, incomplete block designs and an analysis of count data.

STA 6178 - Statistical Genetics and Genomics of Complex Traits (3 credits)

This course covers the biological and molecular basis and uses of likelihood ratio test, multinomial distribution and Bailey’s theorem, linkage analysis of qualitative traits, twin and sibling studies, computation of kinship coefficient by matrix method. Principals of mapping of quantitative trait loci by EM algorithm, heritability, breeding value prediction using flanking markers with variance component analysis, linkage disequilibrium analysis for gene mapping are also covered. In addition to forensic genetics using Bayes’ formula, genetic counseling, and gene pattern matching and construction of evolutionary trees by cluster analysis.

STA 6207- Applied Statistics (3 credits)

Principles of experimental design, completely randomized design (analysis, contrasts, diagnostics), random effects models, factorial experiments (fixed, random, and mixed effect), block designs, Latin squares, split plots, and full and fractional factorial experiments are covered in this course.

STA 6208 – Regression Analysis (3 credits)

This courses focuses on simple linear regression; multiple regression; model selection residual analysis; influence diagnostics; multicollinearity; ANOVA and regression; generalized linear models; nonlinear regression.

STA 6329 - Matrix Algebra and Statistical Computing (3 credits)

This course covers basic theory of determinants, inverses and generalized inverses, eigenvalues and eigenvectors; applications of partitioned matrices; diagonalization and decomposition theorems; applications in least squares.

STA 6934 - Techniques in Microarray Data Analysis (1-3 credits; max: 8)

This course focuses on statistical methods employed in the analysis of large datasets resulting from gene expression profiling studies.

ZOO 6927 – Special Topics in Zoology: Evolutionary Genetics (4 credits; max: 15)

ZOO 6927 – Special Topics in Zoology: Evolutionary Developmental Genetics (4 credits; max: 15)

ZOO 6927 – Special Topics in Zoology: Seminar in Molecular Evolution (2 credits; max: 15)

ZOO 6927 - Special Topics in Zoology: Evolutionary Quantitative Genetics (4 credits; max: 15)

E. Describe briefly the anticipated delivery system for the proposed program as it may relate to resources e.g., traditional delivery on main campus; traditional delivery at branches or centers; or nontraditional instruction such as instructional technology (distance learning), self-paced instruction, and external degrees. Include an assessment of the potential for delivery of the proposed program through collaboration with other universities, both public and private. Cite specific queries made of other institutions with respect to the feasibility of shared courses utilizing distance learning technologies, and joint-use facilities for research or internships.

This program will be offered in a traditional format to on-campus, full-time students. Only Graduate Faculty will be eligible to serve on the student’s supervisory committee. The residency requirement will be enforced and the student will be enrolled full-time for a minimum of four years.

However, in the future, the Graduate council may be asked to consider proposals to jointly confer this degree with other institutions, particularly Scripps Florida and International Universities.

V. Assessment of Current and Anticipated Faculty

A. Use DCU Table One to provide information about each existing faculty member who is expected to participate in the proposed program by the fifth year. Append to the table the number of master's theses directed, number of doctoral dissertations directed, and the number and type of professional publications for each faculty member.

Appendices A and B include the Graduate Faculty who are members of the Genetics Institute who would be eligible to serve on a Genetics student’s supervisory committee. The external member would be selected from any of the more than 2700 Graduate Faculty members at the University of Florida.

B. Also, use DCU Table One to indicate whether additional faculty will be needed to initiate the program, their faculty code (i.e., A, B, C, D, or E as detailed in the lower portion of Table One), their areas of specialization, their proposed ranks, and when they would be hired. Provide in narrative the rationale for this plan; if there is no need for additional faculty, explain.

No additional faculty will be required to offer this program. Educating graduate students is a requirement of the Graduate Faculty. The faculty will consider working with students enrolled in the Genetics Graduate program as an opportunity to advance a rapidly evolving discipline and enhance their research endeavors. The cross-pollination of ideas will be an important corollary of the academic process.

C. Use DCU Table One to estimate each existing and additional faculty member's workload (in percent person-years) that would be devoted to the proposed program by the fifth year of implementation, assuming that the program is approved. (Note: this total will carry over to DCU Table Four's fifth year summary of faculty positions.)

The average faculty member spends about four hours per week with each doctoral student they supervise (an effort of 10%). Assuming the average salary in person-years for Graduate Faculty members is $85,000 and further assuming an enrollment of ten students in the Genetics Graduate Program, the first-year cost of the program would be $85,000, excluding fringe benefits.

It is anticipated that the program will enroll 10 new students each year of the first four years then increasing to 20 students and they will take five years to graduate. Thus, the total enrollment during the fifth year is projected to be 60 students for a cost of $510,000, excluding fringe benefits.

D. In the case of PhD programs, use DCU Table Two to compare the number of faculty, research productivity and projected number of students to at least three peer programs, two of which must be outside Florida. For those disciplines that are included in the National Research Council (NRC) Research-Doctorate Programs in the United States and the National Science Foundation (NSF), please utilize the data from these two sources. NRC data is available on CD ROM and the NSF data is available on-line at www.nsf.gov/sbe/srs/profiles/. For disciplines that are not included in these two sources, please utilize alternate sources to provide comparable data. Universities may choose to provide additional peer data comparisons that are not available from NRC or NSF, such as percent of graduate students supported by contracts and grants, and total contracts and grants for the most recent year.

The University of Florida throughout its colleges and faculty possesses world-class state-of-the-art training and research opportunities in genetics and genomics. In DCU table two comparisons are made between University of Florida and the genetics training programs at North Carolina State University, Harvard University, Stanford University and Yale University.

VI. Assessment of Current and Anticipated Resources

A. In narrative form, assess current facilities and resources available for the proposed program in the following categories:

1. Library volumes (Provide the total number of volumes available in this discipline and related fields.)

According to the library statistics for 2003-2004 maintained in Institutional Research, the total number of bound volumes in the UF library is 4,075,290. This includes 348,046 volumes in the Health Science Library and 678,913 volumes in the Science Library. The total library expenditures for 2003-2004 were $25,112,380 with $10,167,169 of that budgeted for library materials.

2. Serials (Provide the total number available in this discipline and related fields, and list those major journals which are available at your institution.)

According to the library statistics for 2003-2004 maintained in Institutional Research, the total number of journal and serial subscriptions is 25,320. Between the Marston Science Library and the Health Science Library the University of Florida subscribes to all major journals covering genetics and genomics including but not limited to: Science, Nature, Cell, Genetics, Genes and Development, Molecular and General Genomics, and Bioinformatics.

3. Describe classroom, teaching laboratory, research laboratory, office, and any other type of space, which is necessary and currently available for the proposed program.

	UF TOTAL	MEDICINE	LIBERAL ARTS & SCIENCES	AGRICULTURAL & LIFE SCIENCES	ENGINEERING
CLASSROOMS	382,633	3,122	9,946	8,723	10,900
INSTRUCTIONAL LAB	530,757	8,325	78,448	39,286	68,659
RESEARCH LAB	2,631,843	241,008	257,262	476,207	274,349
OFFICES	2,793,800	352,709	280,129	235,036	216,254
SUPPORT SPACE	2,405,985	10,242	405	44,872	5,711

In the spring of 2006, the University of Florida Genetics Cancer building will open. In addition to seminar and conference rooms this building contains 76,298 sq ft of additional research space in addition to 19,766 sq ft of core laboratory space. When completed the genetics cancer building will be the largest research building on the campus and will house the administrative offices of the University of Florida Genetics Institute. The new building will likely serve as a hub for public activities of the proposed Genetics Ph.D. program. As such many seminars and research conferences will likely occur in the new building. While the building may serve as a focal point for the proposed Genetics Ph.D. graduate program, the program will be distributed across the entire campus. Only a small handful of participating faculty members and students will be located in the genetics cancer building.

4. Equipment, focusing primarily on instructional and research requirements

All major equipment is available to support the proposed degree program. No new equipment will be requested.

5. Fellowships, scholarships, and graduate assistantships (List the number and amount allocated to the academic unit in question for the past year.)

The University of Florida supports over 200 new doctoral students each year on alumni fellowships through the Provost’s Office. Over 95% of our doctoral students are funded either through research grants, fellowships, or teaching assistantships.

6. Internship sites if appropriate

B. Describe additional facilities and resources required for the initiation of the proposed program (e.g., library volumes, serials, space, assistantships, specialized equipment, other expenses, OPS time, etc.). If a new capital expenditure for instructional or research space is required, indicate where this item appears on the university's capital outlay priority list. The provision of new resources will need to be reflected in the budget table (DCU Table Four), and the source of funding indicated. DCU Table Four only includes I&R costs. If non-I&R costs, such as indirect costs affecting libraries and student services, are expected to increase as a result of the program, describe and estimate those expenses in narrative form. It is expected that high enrollment programs in particular would necessitate increased costs in non- I&R activities.

All of the resources necessary to offer the proposed Genetics Ph.D. program are currently available. In the future should faculty, laboratory facilities, library holdings, courses, or financial support not be available then the admissions committee in consultation with the director would actively manage the number of students admitted into the program to match resources available.

Accountability

VII. Assessment of Need and Demand

A. What national, state, or local data support the need for more people to be prepared in this program at this level? (This may include national, state, or local plans or reports that support the need for this program; demand for the proposed program which has emanated from a perceived need by agencies or industries in your service area; and summaries of prospective student inquiries.) Indicate potential employment options for graduates for the program. If similar programs (either private of public) exist in the state, provide data that support the need for an additional program. Summarize the outcome of communication with such programs.

In a November 2003 speech to the state legislature, Governor Jeb Bush said that Scripps’ impact could be similar to what NASA and the space industry brought to Florida. “Forty years ago, Florida had a once in a lifetime opportunity to be on the leading edge of technology that would revolutionize the world”. “Today, the Scripps Florida project gives this generation of Floridians that same opportunity to leap to the forefront of emerging technology and scientific discovery.” The proposed Genetics Ph.D. is aimed at training the next generation of scientists to take advantage of the great wealth of information that has been made available as a result of sequencing the human genome and the genomes of other economically important and model species.

The National Research Council has identified emerging fields in the taxonomy for their 2005 Assessing Research Doctorate Programs study. The NRC has identified the following emerging fields for doctoral programs: Life Sciences – Biotechnology, Systems Biology; Arts and Humanities – Race, Ethnicity and Post colonial Studies, Film Studies, Feminist, Gender, and Sexuality Studies; Physical, Mathematical Sciences and Engineering – Nanoscience and Nanotechnology, Information Science; Social and Behavioral Sciences – Science and Technology Studies, Organizations, Occupations, and Work.

The University of Florida must be able to respond to various needs of its students, to evolving disciplines, and to new directions in technology and science. It is clear from national and state agendas that new knowledge and applied technologies are critical for continued advancement of society and for the safety and welfare of U.S. citizens. The University of Florida must be positioned to respond rapidly to the educational needs of its students. The proposed Genetics Ph.D. program is on its way to accomplish this goal.

B. Use DCU Table Three-B to indicate the number of students (headcount and FTE) you expect to major in the proposed program during each of the first five years of implementation, categorizing them according to their primary sources. In the narrative following Table Three, the rationale for enrollment projections should be provided and the estimated headcount to FTE ratio explained. If, initially, students within the institution are expected to change majors to enroll in the proposed program, describe the shifts from disciplines, which will likely occur.

The headcount of graduate students in doctoral programs at the University of Florida will increase slightly as a result of this program. In the first year ten students will be recruited and at maturity the target is to recruit ten students per year. At maturity the program will likely have 100 doctoral students in residence assuming admittance rate and graduation rate are equal at maturity and that the average length of time to degree is five years for the average student.

All students enrolled in the program will be funded on either a fellowship or an assistantship. The typical registration for a student on a fellowship is 12 credits during the academic year and 8 credits during the summer, for a total of 32 credit hours per year. Thus, on average, one graduate student headcount equals 0.87 FTE. The typical registration on an assistantship is 9 credits per semester during the academic year and 6 credits during the summer, for a total of 24 credit hours per year.

From the faculty perspective, there will be very little added effort if the program is approved. In large-part the proposed Genetics Ph.D. program represents a reorganization across the campus of intellectual efforts already accruing focused on both genetics research and teaching arenas. Given the wealth of talent at the University of Florida in the area of genetics and genomics, it is expected that the program will not only draw students from the State of Florida, but from the entire Nation as well as international students.

C. For all programs, indicate what steps will be taken to achieve a diverse student body in this program. Please create a place for signature at the end of section (VII) (C) and have your university’s Equal Opportunity officer read, sign, and date this section of the proposal.

The University of Florida Graduate School is actively engaged in recruiting and retaining students who typically are underrepresented in graduate programs. Specifically, the Office of Graduate Minority Programs (OGMP) is responsible for developing recruitment strategies including Campus Visitation Programs conducted during the fall and spring of each academic year; and for participation in recruitment opportunities at selected colleges and universities throughout the United States. Each year, during the recruitment season, the staff of OGMP makes contact with approximately 3,000 highly qualified underrepresented students. Additionally, OGMP administers the Summer Board of Education Program (BOE), which is an early-start admission program beginning in the summer preceding the fall term. The BOE consists of academic programming (e.g., 6-week mentored research experience, cultural and social programming that is designed to acclimate underrepresented graduate students to the campus and surrounding communities.

Apart from the specific programming outlined above, OGMP also works with academic units across the university to promote racial/ethnic diversity in graduate recruitment and retention. For example, OGMP has worked closely with the College of Engineering in their AGEP and GEM programs that encourage underrepresented students to pursue graduate studies in Engineering. Further, OGMP has provided various forms of support for the College of Dentistry, Medicine, Liberal Arts & Sciences, and Journalism. As an example, OGMP participated in a recent Chemistry Department research poster presentation day for undergraduate students who participated in the Research Experience for Undergraduates (REU). During these sessions, OGMP staff gave presentations on UF graduate programs.

VIII. Budget

A. Assuming no special appropriation for initiation of the program, how would resources within the institution be shifted to support the new program?

The Academic Status Committee of the University of Florida Genetics Institute will assure that participating departments and faculty members have the necessary resources in terms of equipment, space, and library holdings required to mentor genetics doctoral students.

It is expected the chair of the student’s supervisory committee will devote 10% effort to the student. Assistance in the laboratory and exploring new ideas are often seen as two popular advantages of supervising doctoral students.

B. Use DCU Table Four to display dollar estimates of both current and new resources for the proposed program for the first and the fifth years of the program. In narrative form, identify the source of both current and any new resources to be devoted to the proposed program. If other programs will be negatively impacted by a reallocation of resources for the proposed program, identify the program and provide a justification.

The figures in table four were derived as an estimate of effort faculty members would devote to the new genetics Ph.D. graduate program. Individuals who serve as chair of student supervisory committees will devote on average 10% of their efforts in service as mentor. Faculty members who do not serve as mentor will devote considerably less of their efforts to the program. On average for purposes of this calculation, the assumption was made that each member of the University of Florida Genetics Institute and are also members of the graduate faculty would devote 5% of their efforts to the program. It is recognized that some faculty members will devote more while others will devote considerably less effort to the program.

C. Describe what steps have been taken to obtain information regarding resources available outside the institution (businesses, industrial organizations, governm


Vice President for Academic Affairs		Date		President		Date

		Projected Student Enrollment
	Total Estimated Costs	Headcount	FTE
First Year of Implementation	$	10	8.6
Second Year of Implementation		20	17.2
Third Year of Implementation		30	25.8
Fourth Year of Implementation		50	43
Fifth Year of Implementation	$	60	51.6