HuGER

a.    Epidemiology Study Design and Power Estimation
b.    Statistically Guided Environmental Sampling
c.    Environmental Transport and Transformation of Toxicants
d.    Deposition/Delivery of Toxicant to Target
e.    Foundations of Modeling
f.    Application of Statistics to Exposure Assessment
g.    Interventional Studies in Environmental Exposure

a.    Environmental Diversity (Outdoor, Indoor, Home, Workplace…)
b.    Media Diversity (Air, Water, Soil, Particulates, Residues from Plants and Animals)
c.    Media Collection, Storage, Processing
d.    Measurement Technology Platforms
e.    Analytical/Statistical Challenges

a.    Sample Diversity (Blood, Urine, Hair, Tissue, Toenails…)
b.    Sample Collection, Storage, Processing
c.    Measurement Technology Platforms
d.    Analytical/Statistical Challenges

a.    Sample Diversity
b.    Sample Collection, Storage, Processing
c.    Molecular Biology of Perturbed Systems (Acute vs. Chronic Changes)
d.    Measurement Technology Platforms:  Perturbation at the Molecular Level

i.    Gene Expression
ii.    Epigenetic Status
iii.    Protein Measurement

e.    Analytical/Statistical Challenges

a.    Factors That Shape Genetic Variation in Populations

i.    Demographics, Natural Selection, Drift
ii.    Measuring the Signatures of Selection

b.    Contrasting Mendelian Vs. Non Mendelian Genetics

i.    Genetic Heterogeneity, Phenotypic Heterogeneity

c.    Environmental Exposures as Phenotype Modulators
d.    Epigenetic Influences on Phenotype

i.    Interaction Between DNA Sequence Variation and Epigenetic Regulation of Gene Expressioin

a.    Sequencing Based

i.    Conventional, Massive Throughput

b.    Genotyping Based

i.    Affymetrix, Illumina

a.    Epidemiology
b.    Family Based

i.    Linkage, TDT

c.    Association

i.    Candidate Gene
ii.    Genome-Wide

a.    Single-point Vs. Multi-Point
b.    Haplotypes, Haplotype Blocks
c.    Tagging Strategies
d.    Gene by Gene Interactions

a.    Cell Based
b.    Animal Based

General and Systems Toxicology PCOL 602                  Drug Metabolism PCOL 550
Molecular and Cellular Toxicology PCOL 610                Genomics and Proteomics PCOL 601
Pharmacogenetics/Pharmacogenomics    PCOL 631       Clinical Toxicology PCOL 574                   Fundamentals of Industrial & Environ. Health CPH 584  Cellular Commun. & Signal Trans. PCOL 630A&B
Measurement & Data Analysis in Biomed Eng BME 517   Bioprocess Engineering Applications ABE 581B
Air Pollution II:Aerosols CHEE 569B                            Biosensors and Controls ABE 547

 Topics in Gene Regulation BIOC 569                      Human Genetics GENE 533
 Molecular Mechanisms of Development MCB 555      Nucleic Acid BIOC 568
 Applied Molecular Genetics BIOC 571                     Advances in Mammalian Genetics BIOC 574              Advanced Genetics PLS 627                                 Biological Structure BIOC 585                              Population Genetics GENE 526                             Methods in Cell Biology and Genomics PLS 539        Concepts in Genetic Analysis MCB 545                   Molecular Mechanisms of Carcinogenesis CBIO 551      Cancer Genetics CBIO 589

• Ph.D. students in participating programs are required to undertake three research rotations, usually completed in laboratories of faculty within their department. HuGER students will adapt the research rotation requirements of their degree program in order to acquire multidisciplinary research experiences.
• In particular, all HuGER students will be required to perform one research rotation in each of our three core areas, thus ensuring exposure to fundamentally new perspectives. Each rotation will be one half-semester long and will occur on a fixed schedule. Rotation reports, from both the trainee and the hosting faculty member, will be submitted to the HuGER Executive Committee within one week of completing each rotation.
• Such reports will assist in monitoring internal quality control. Following the completion of the third rotation, the trainee will again meet with the HuGER Executive Committee and select their dissertation advisor and thesis committee. The rationale for this selection will be explored to ensure the appropriate student/mentor match is achieved.
• Following completion of all three rotations, HuGER trainees will also be required to present an overview of their rotations. Trainees will be expected to articulate an appreciation of the inter-dependency of the various experimental approaches, methodologies, and scientific concepts that they were exposed to during the rotations. Trainees will be asked to reflect on the strengths and weaknesses inherent to each research area when considered as acting independently rather than collaboratively.
• At the end of each cycle of rotations there will be 4 trainees scheduled to make a presentation, in the format of a colloquium (see above).

The “Intensive PERL for Life Sciences Researchers” Workshop provides a 6 hour (Intensive) or 9 hour (recommended for those less comfortable with computers) introduction to Perl Scripting geared towards Life Sciences Research. HuGER trainees will learn to use the Perl scripting language to parse data and extract selected features and subsets of data. These Introductory Perl Workshops will also enable HuGER trainees to write simple scripts tailored to their specific data analysis needs.

The “Introduction to High Throughput Computing for Life Sciences Researchers” Workshop provides a 6 hr introduction to UNIX/ EMBOSS/HPC/Grid. HuGER trainees will gain proficiency on the Unix command line and learn to use the UA campus super-computing and Grid Computing resources to accelerate their computational analyses. The High Throughput Computing Workshops will introduce HuGER trainees to the options available for more rapid processing of substantive quantities of data or running large numbers of computing jobs.

Successful scientists must be competent and effective communicators. This will be especially important for the new generation of scientists who will need to communicate effectively across disciplinary boundaries. A two-credit “Scientific Writing Strategies and Ethics” class will be upgraded into a comprehensive three-credit Communication Skills class for the Fall of 2009.

The course will assist trainees in developing both written and verbal communication skills. Trainees will be taught to write clear and concise manuscripts and grants, and instructed in how to become an accomplished reviewer of grants and journal articles. Trainees must prepare a manuscript and a short grant for the course. Trainees are also taught grantsmanship, hypothesis-driven research, adequate preliminary information, presentation of results, and directing the grant to the appropriate audience.

The verbal skills component will focus on how to reduce fear of speaking, how to design visual aids, and how to prepare and present a professional presentation. Trainees will present their first HuGER program seminar in this class and be evaluated by their peers during the semester.

During the course of their studies, HuGER trainees will be required to present five HuGER training program seminars. The first seminar will be presented to fellow graduate students in the Scientific Communications Skills course (PCOL595B) and will focus on a Literature Review on a topic of the trainees choosing, with input from the Course Coordinator. The second seminar will be the “Rotation Seminar” (see below) and take place in the setting of a colloquium. The third seminar will require the student to present a “Famous Scientist”.

Trainees will be allowed to select either a famous contemporary (living) scientist in any area of science, or a scientist they consider to be making seminal contributions within the overall goals of the HuGER TG initiative. Trainees will be required to directly communicate with a scientist of their choice, and obtain professional and personal information pertaining to the career path of the selected individual. The fourth seminar will take the format of a “Lay Audience” seminar, in which the trainee will present a synopsis of their own research in a manner that a lay audience can readily understand. The fifth seminar will be a “Research Seminar” in which the trainee will present a summary of their dissertation project to faculty and trainees.

The HuGER training program will host a half-day Fall and Spring Colloquium, organized by HuGER trainees, with the assistance of the Curriculum Coordinator, the Seminar Coordinator, and one or two HuGER post-doctoral trainees.

The Fall Colloquium will take the format of a Roundtable Discussion/debate on contemporary issues identified by trainees as significantly impacting research on gene:environment interactions. These may be scientific (intellectual or technological), sociological, ethical or legal issues. HuGER trainees will identify two invited speakers and two appropriate University of Arizona faculty to participate on the program.

The Spring Colloquium will require a 30 min presentation of the “Rotation Seminar” from each of 4 pre-doctoral HuGER trainees, presentations from 2 post-doctoral HuGER trainees, and one member of the HuGER training faculty. The program will be concluded with a Panel-hosted (all 7 speakers) question/answer discussion session. HuGER trainees will be responsible (with oversight) for all aspects of the Colloquium, including the selection of invited speakers, reserving meeting rooms, coordinating audio-visual support, introducing speakers etc. This endeavor will contribute to the personal and professional skills of the trainees.

A fundamental aspect of science is the responsibility of investigators to conduct experiments in an ethical and responsible way. As training faculty, we recognize that it is essential to teach the principles of the ethical conduct of science to all HuGER trainees. This is accomplished primarily through a one credit hour course "Science, Society, and Ethics" provided by the Department of Molecular and Cellular Biology (MCB 695E).  Various ethical issues, such as ownership of genetic information, genetic profiling of humans and its social implications, genetic manipulation of humans, genetic manipulation of other species, are specifically relevant to genomics and are very active areas of research and discussion. 

Appropriate training in ethical issues is of critical importance in science and is required of all Graduate Research Assistants and Teaching Assistants at the University of Arizona. In addition to this formal course, discussions of ethical considerations will also be discussed when appropriate during weekly laboratory meetings organized by each HuGER training faculty member for their own research group. Such discussions will focus on ethical and technical considerations as they pertain specifically to the conduct of research in the HuGER faculty member's own research group, and will be organized in such a way as to encourage highly focused issues that can be discussed in considerable detail.

Trainees will not only be mentored by HuGER faculty but also through a network of very successful alumni and visiting scientists, who will assist in providing multiple perspectives on career opportunities and pathways to career success. Experts and alumni from academia, industry and government will participate in the HuGER seminar program, and host meetings with trainees that will focus on career preparation and opportunities. Trainees will meet with visiting “Professors” to learn about “life after graduate school”. Development of supervisory skills will be assisted by coordinating campus training of high school/undergraduate students with the HuGER training program, HuGER trainees will be required to mentor at least one high school or undergraduate student during the final three years of their training.

In addition, it is expected that senior HuGER graduate students (year 4/5) will establish a trainee/apprentice relationship with incoming graduate students (not restricted to HuGER trainees). HuGER trainees will be required to establish membership in at least one scientific/professional organization. Attendance at scientific conferences will provide networking opportunities for trainees. HuGER faculty will provide introductions at such meetings, and instruct trainees in how to maximize the benefits from frequently formidable scientific programs. Confidence in framing and asking questions during scientific sessions, developed within the Communication Skills course, will increase the visibility of HuGER trainees. Trainees will be nominated for positions on local and national graduate student advisory committees, providing both networking and leadership opportunities.

Currently, Ph.D. students in participating programs are required to undertake three research rotations, usually completed in laboratories of faculty within their department. HuGER students will adapt the research rotation requirements of their degree program in order to acquire multidisciplinary research experiences. In particular, all HuGER students will be required to perform one research rotation in each of our three core areas, thus ensuring exposure to fundamentally new perspectives.

Each rotation will be one half-semester long and will occur on a fixed schedule. Rotation reports, from both the trainee and the hosting faculty member, will be submitted to the HuGER Executive Committee within one week of completing each rotation. Such reports will assist in monitoring internal quality control. Following the completion of the third rotation, the trainee will again meet with the HuGER Executive Committee and select their dissertation advisor and thesis committee. The rationale for this selection will be explored to ensure the appropriate student/mentor match is achieved.

Following completion of all three rotations, HuGER trainees will also be required to present an overview of their rotations. Trainees will be expected to articulate an appreciation of the inter-dependency of the various experimental approaches, methodologies, and scientific concepts that they were exposed to during the rotations. Trainees will be asked to reflect on the strengths and weaknesses inherent to each research area when considered as acting independently rather than collaboratively. At the end of each cycle of rotations there will be 4 trainees scheduled to make a presentation, in the format of a colloquium (see above).

During the summer linking the first and second years of the program, trainees will have the opportunity to spend 10-12 weeks training in the laboratory of an “industrial” partner. We have received enthusiastic commitments from two partners (see Appendix Vi), both of whom offer truly unique training opportunities for HuGER trainees.

The first, Translational Genomics Research Institute (TGen; http://www.tgen.org/) is a non-profit 501(c)(3) organization located in Phoenix. TGen is on the cutting edge of translational research where investigators are unraveling the genetic components of common and complex diseases. TGen's vision is of a world where an understanding of genomic variation can be rapidly translated to the diagnosis and treatment of disease in a manner tailored to individual patients.

The second partner is High Throughput Genomics (HTG; http://www.htgenomics.com/) based in Tucson. In addition to HTG’s own laboratory, they are initiating a laboratory setting at Bio5, under the auspices of a new Chemical Genomics and Translational Research Center, where some of the HuGER trainees could also receive training. Rotation projects will be designed by the host coordinators (Mike Berens, TGen; Bruce Seligmann, HTG) in consultation with the HuGER Executive Committee. Two HuGER trainees will be placed at each site each year. Based upon initial success with these partnerships we will carefully add additional industrial rotation sites.

All University of Arizona graduate students are required to form a dissertation committee by the time of Advancement to Candidacy. Some departments require earlier committee formulation. Candidates must be able to develop a proposal of sufficient academic merit and on a topic to satisfy their committee. Dissertation research proposals of all graduate student recipients of a HuGER pre-doctoral fellowship will be reviewed by the Executive Committee to ensure the proposal reflects the mission of the HuGER TG.

The Graduate College requires a minimum of three dissertation committee members, all of whom must be University of Arizona tenured, tenure-track, or approved as equivalent. If a committee has only three members, all must approve the dissertation. Some departments require four or five members, who may be tenured or tenure-track, or a special approved member. Special members must be pre-approved by the Dean of the Graduate College. Any members beyond the fourth can also be tenured or tenure-track, or special approved members.

For all HuGER trainees, the dissertation committee must appoint a HuGER faculty member from each of the three core research areas (environmental and public health sciences and engineering, population and functional genetics/ genomics, and computational biology and statistics/ bioinformatics).

Remaining within departmental guidelines, we will encourage the Dissertation Committees to become more active participants in advising HuGER trainees. Indeed, the multi-disciplinary nature of HuGER trainee research will necessitate a more vigorous team-based approach in guiding these students. Since we anticipate that practical challenges to HuGER dissertation research will emerge from within each of the contributory core research areas, we envision the relationship between HuGER trainees and their Dissertation Committees should evolve into one that challenges not only the trainee but also the faculty.