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USDA National Needs Fellowship in the Development and Application of Quantitative Methods and Tools for Animal Genomics

USDA NATIONAL NEEDS Ph.D. FELLOWSHIP IN STATISTICAL GENETICS AND GENOMICS

The USDA NATIONAL NEEDS Ph.D. FELLOWSHIP in the Development and Application of Quantiative Methods and Tools for Animal Genomics will be competitively awarded to an outstanding candidate who intends to pursue a Ph.D. degree in either GENETICS or BIOINFORMATICS AND COMPUTATIONAL BIOLOGY at Iowa State University

The USDA NATIONAL NEEDS FELLOWSHIP has the following features:

  • Stipend: $24,000 Per Year for three years
  • Full Tuition Scholarship
  • Paid Student Health Insurance
  • Nine months to spend time in up to three research laboratories before deciding on major professor
  • Educational Allowance Funds
  • Funds to Support Professional Travel
  • Funds to Support Industry Internships
  • Recruiting for Entry Spring 2007, Summer 2007, Fall 2007, and Spring 2008
Who should apply?: applicants interested in animal biological questions dealing with quantitative and population genetics, statistical genomics and bioinformatics, and molecular genetics and genomics.

Applicants can APPLY through the Interdepartmental Genetics graduate program (IG). Contact Information: Genetics, 2102 Molecular Biology, Ames, IA 50011-3260/Phone 1-800-499-1972 or 515-294-7697. FAX is 515-294-6669. genetics@iastate.edu Linda Wild, Program Coordinator

OR

Applicants can APPLY through the Bioinformatics and Computation Biology graduate program (BCB). Contact Information: Bioinformatics and Computational Biology, 2014 Molecular Biology, Ames, IA 50011-3260/Phone 515-294-5122. FAX is 515-294-6790. bcb@iastate.edu Trish Stauble, Program Assistant.

Applications: All domestic applicant applying to the Genetics and BCB programs will be considered for award of these fellowships; deadline for consideration is October 1, 2007. Students will be considered for Spring 2007, Summer 2007, Fall 2007, and Spring 2008.

BACKGROUND AND TRAINING PROGRAM OVERVIEW

PREREQUISITES FOR PROSPECTIVE FELLOWS.
Students with strong backgrounds in biology, chemistry, physics, mathematics, statistics, or genetics, and experience in research will be recruited.

BACKGROUND
Most important traits in animal agriculture are determined by multiple genes with varying levels of effects on phenotype. Mapping the location of these “QTL”, estimating their effects, and understand-ding their mode of inheritance and function are essential for the application of molecular genetic/genomics to the advancement of animal agriculture. Recent technological developments have opened great opportunities to advance the study of the genetic basis of quantitative traits on a much larger scale than previously imaginable. These include complete genome sequencing, high-throughput genotyping of large numbers of polymorphic genetic markers (SNPs), and global analysis of gene expression profiles using micro-arrays.

These technologies and their continuously decreasing costs not only allow tremendous advances in research but also put the agricultural industries in a position to capitalize on molecular genetics and genomics through marker-assisted selection, transgenics, and other strategies. These technologies capitalize on developments in molecular genetics, but it is clear that their implementation will not be successful without people highly trained in statistical genomics, quantitative genetics and bioinformatics. In fact, it is the integration of these disciplines with molecular genetics that is required for their successful application in research and industry. With much of the focus of recent training on molecular and functional genomic aspects of research problems, there currently is a lack of people that are adequately trained in the quantitative aspects of the application of molecular/genomic technologies to animal agriculture.

The proposed interdisciplinary training plan will provide breadth and depth through core training in quantitative genetics, statistics, statistical genomics, and molecular genetics, with introductory training in bioinformatics and computer science (databases), coupled with an intensive collaborative research experience.

STRENGTH IN ANIMAL GENETICS AND STATISTICAL GENOMICS PROGRAMS
ISU has a long history of excellence in theoretical and applied animal genetics, due in large part to the global legacy of ISU animal quantitative genetics pioneers J.L. Lush, L.N. Hazel, and O. Kempthorne. Their efforts in the 1950s and 60s put ISU at the international forefront of quantitative genetics applied to animals. While many universities have seen a decline in faculty expertise in quantitative genetics, to the point where graduate training in quantitative genetics becomes limiting, ISU has maintained its strength in this area. In the past two decades, ISU has also steadily moved to an internationally recognized position of strength in animal molecular genetics, and now has several faculty in positions of national and international leadership in livestock genome projects, including the USDA NRSP-8 National Swine Genome Coordinator (Rothschild), and the USDA NRSP-8 National Database/Bioinformatics Coordinator (Reecy); both members of AQMSG. The strength of the ISU program is in particular the integration of quantitative and molecular genetics. This will be further strengthened by completing a recently initiated search to fill the “Lush Endowed Chair in Animal Breeding and Genetics”. The incumbent will be an internationally renowned scientist in the area of Animal Breeding and Genetics and will become a member of the AQMSG.

Complementing ISU’s expertise in animal genetics is a strong program in theoretical and applied statistics. Faculty in the Department of Statistics have long-standing collaborative efforts in statistics applied to the agricultural sciences and animal genetics. These strong ties date back to seminars in 1924 given by Henry A. Wallace, then an editor of Wallace’s Farmer and, subsequently, founder of Pioneer Hi-Bred Seed Corn Company, Secretary of Agriculture (‘33-40), and Vice President of the US (‘41-45). In 1935, the Iowa Agriculture Experiment Station formed a Statistical Section with G. Snedecor as head, and has provided support for statistics from that point to the present. This has resulted in impressive contributions to agricultural statistics and quantitative genetics from ISU statisticians such as Snedecor, Cochran, Cox, Kempthorne, and Harville. This tradition continues now, with several faculty in the Department of Statistics holding joint appointments with the College of Agriculture. Further, students continue to be trained jointly with degrees in Statistics combined with IG, BCB, or Animal Breeding and Genetics. In the past five years, the Statistics Department has strengthened its expertise in statistical genomics, with AQMSG faculty Nettleton, Dorman, Koehler, and a recent hire in a new position in statistical genomics, P. Liu.

Bioinformatics is an essential component of graduate training and research in animal genetics and genomics and will be an integral part of the proposed training plan. Efforts in bioinformatics have significantly expanded at ISU in the past 4-5 years, with extensive research and graduate training in the graduate major in Bioinformatics and Computational Biology and in the Baker Center for Bioinformatics and Biological Statistics. Dr. Les Miller from the Department of Computer Science and specializing in data base structures, is a member of the AQMSG and will, along with other members of the Bioinformatics community, provide essential expertise to the proposed program.

TRAINING PLAN
The AQMSG training group will provide interdisciplinary research training with special emphasis on using integrative approaches for development and application of quantitative methods to animal genomics. AQMSG -trained Fellows will receive doctoral degrees majoring in Genetics through IG or in Bioinformatics through BCB, and will earn this degree within any of the AQMSG departments and faculty. Upon completion of their degrees, AQMSG Fellows will have comprehensive research skills that can be applied in their future careers. This will be accomplished by requiring all AQMSG Fellows to participate in a common set of courses and training activities. These activities will add cohesiveness to the program and expose all participants to the diverse perspectives offered by each discipline. Specific training activities required of all AQMSG Fellows are described in detail below and include: i) core coursework in Quantitative and Molecular Genetics, Statistics, and Bioinformatics, ii) Research Seminar series, iii) Bioethics trainings, and iv) Additional innovative features (see section 4) Core coursework. All AQMSG Fellows will be required to complete foundation courses in Biochemistry (BBMB 404), Transmission Genetics (GDCB 510), Molecular Genetics (GDCB 511), Statistics (STAT 401), Quantitative Genetics (ANS 561), and Bioinformatics (BCB 544):

  • GDCB 510 Transmission Genetics, 3 cr. An in-depth investigation of the modern research practices of transmission genetics. Designed for students interested in genetic research. Topics include: Mendelian genetic analysis, analysis of genetic pathways, mutational analysis of gene function, chromosomal mechanics, gene mapping, extranuclear inheritance, human genetic analysis.
  • GDCB 511 Molecular Genetics, 3 cr. The principles of molecular genetics: gene structure and function at the molecular level, including regulation of gene expression, genetic rearrangement, and the organization of genetic information in prokaryotes and eukaryotes.
  • Stat 401 Statistical Methods for Research Workers, 4 cr. Methods of analyzing and interpreting experimental. Statistical concepts and models; estimation; hypothesis tests with continuous and discrete data; simple and multiple linear regression and correlation; analysis of variance.
  • AnS 561 Population and Quantitative Genetics for Breeding, 4 cr. Population and quantitative genetics for plants and animals. Study of the genetic basis and analysis of variation in quantitative traits using phenotypic and molecular marker data, including estimation of heritability and other genetic parameters, linkage analysis and mapping of quantitative trait loci, and the impact of inbreeding, heterosis, and genotype-by-environment interaction
  • BBMB 404. Biochemistry I, 3 cr. General overview for graduate and advanced undergraduate students in agricultural, biological, chemical and nutritional sciences. Chemistry of amino acids, proteins, carbohydrates, lipids, vitamins; protein structure; enzymology; carbohydrate metabolism
  • BCB 544 Introduction to Bioinformatics, 4cr. Overview of bioinformatics with a problem-solving component and hands-on practice using computational tools to solve a variety of problems. Topics include: database searching, sequence alignment, gene prediction, RNA and protein structure prediction, construction of phylogenetic trees, comparative and functional genomics.

These core courses will be supplemented with at least 9 credits of advanced coursework required for IG or BCB, with primary focus on coursework related to Quantitative Genetics, Statistics, and Bioinformatics. Participating departments have certified that the AQMSG-required courses fit their curricular requirements, thus ensuring that course loads are not excessive.

Seminar courses are vital to the interdisciplinary mission of AQMSG. They effectively integrate research efforts with course work and maintain a sense of community among students and faculty. AQMSG Fellows must attend one seminar course each semester of their Fellowship:

  • GENET/BCB 690 Student Research Seminar. Students present their research progress to peers and to faculty mentors who promote group discussion of experimental procedures and analyses.
  • GENET/BCB 691. Faculty Research Seminar. This seminar series keeps faculty and students informed about genetics research at ISU and increases collaboration among faculty and students.

Training in Bioethics
Training in responsible conduct of research is a commitment of ISU. Graduate programs at ISU utilize a variety of mechanisms that provide training in bioethics, including daylong symposia, seminar presentations during graduate student orientation, and a number of bioethics course modules offered through IG or other biological sciences departments. AQMSG students will be required to attend the orientation seminar and to take a minimum of 1 credit in Bioethics coursework.

Additional Training Features.
Several training activities listed below are planned to promote interactions between AQMSG Fellows and faculty and to foster the interdisciplinary training environment.

  • IG and BCB Workshops and Targeted Symposia
  • Quarterly “potluck” dinner and research discussion
  • Summer internships in industry, government or international laboratories
  • Funded annual attendance at major national scientific meetings

Research Training.
A cornerstone of the AQMSG training plan in animal genetics, genomics and bioinformatics is an intensive, multidisciplinary research experience involving close interaction of Fellows with AQMSG faculty and their laboratory groups, and the opportunity for interactions with scientists in industry. The first step is selection of laboratories for rotation experiences. Details on rotations are given first, then the different opportunities for research in each participating laboratory.

Laboratory Rotations
The purpose of laboratory rotations is to ensure that each Fellow will have an early interdisciplinary research experience and to ensure an informed choice of dissertation project and research mentor. Each fellow will participate in three 6-8 week rotations. To ensure exposure to both quantitative/statistical and molecular/genomic aspects of the training plan, this must include at least one rotation in a quantitatively oriented lab and one rotation in a molecular lab.

Upon arrival at ISU, Fellows will attend the all-day student/faculty IG Research Retreat or BCB Faculty-student meetings where they will have the opportunity to meet AQMSG faculty and discuss choices of laboratories for rotation, which will be facilitated by their temporary advisor. To ensure adequate time for scheduling and that adequate resources and opportunities are available, Fellows will be encouraged to plan their first rotation well prior to their arrival on campus, in consultation with their temporary advisor, and their remaining rotations by the end of the first month.

AQMSG FACULTY RESEARCH PROGRAMS
AQMSG comprises three major research areas: 1) Quantative and Population Genetics, 2) Statistical Genomics and Bioinformatics, and 3) Molecular Genetics and Genomics. Many questions of basic research are involved, but the overall emphasis is the study of animal genetics and genomics, with an emphasis toward biotechnological, genomic, and genetic improvement of animals and animal products, an important area of national need. AQMSG faculty are conducting research within and across these focus areas. In the following, faculty are grouped in these three research areas but it should be noted that they have much overlap and most faculty conduct work in more than one area and/or actively collaborate with faculty in other areas.

Quantitative and Population Genetics
J. Dekkers studies the integration of quantitative and molecular genetics, with application to genetic improvement of livestock. His research includes statistical aspects of QTL detection (in collaboration with Fernando, Rothschild, Lamont, and Koehler) and its integration with gene expression data (in collaboration with Nettleton and Carriquiry), genetics and functional genomics of feed efficiency in pigs (in collaboration with Tuggle, Honavar and Nettleton), and the design and optimization of breeding programs, including marker-assisted selection, for livestock. R. Fernando develops statistical and computational methods for QTL mapping QTL and marker-assisted selection. Recent research includes comparison of approaches for combined disequilibrium and co-segregation analyses for fine mapping QTL in complex pedigrees, Markov Chain Monte Carlo methods for computing haplotype and genotype probabilities, and non- parametric methods for genetic evaluation and selection using genome-wide dense marker data. Collaborations are with Dekkers, Lamont, Rothschild, Carriquiry, and Nettleton. K. Stalder has research on swine production traits, particularly sow longevity. In collaboration with Rothschild, he will be using QTL and candidate genes in the evaluation of sow longevity and associated traits. His primary Extension appointment leads to direct application of results of his research program by the industry. Additionally, he has an active research program evaluating pork quality and its effects on further processed products. He collaborates with numerous other faculty on a variety of projects. Dr. Dorian Garrick is currently a professor at Colorado State University, but will be appointed as the first Lush Chair in Animal Breeding and Genetics at Iowa State University, starting the fall of 2007. Dr. Garrick’s research focuses on the portfolio of endeavors that are involved in the design, enhancement, implementation and monitoring of genetic improvement programs. These include aspects of genetics, economics, statistics and biology. Attention is directed at variance component estimation, prediction of breeding values, development of breeding objectives and breeding industry structure, primarily in regard to their application to the national improvement of beef cattle, but other species are also considered. Dr. Garrick expects to collaborate with many other faculty.

Additional Information on the faculty and their research can be found through the departmental ISU websites. Animal Science (Dekkers, Fernando, Garrick, Stalder)

Statistical Genomics and Bioinformatics
A Carriquiry is a statistician with expertise and interest in animal breeding and genetics and biological statistics. Recent research includes 1) developing and fitting a hierarchical generalized linear model to pseudo-replicated gene expression measurements and 2) use of a generalization of Kullback-Leibler distances to cluster posterior distributions of gene expression. She collaborates with Fernando, Dekkers, and Nettleton. K. Dorman is a mathematical biologist with two main biological interest areas: 1) comparative genomics and 2) persistent infectious disease. Recent projects include development of better methods to analyze recombinant sequences especially to predict recombination hotspots, a new method to detect historical selection shifts, and statistical analysis of a cellular automata model of the immune system to identify important determinants of Leishmania persistence. K. Koehler has extensive experience in the design and analysis of experiments in biological sciences. Recent projects include development of stillbirth and disease incidence models for dairy cattle, statistical procedures for quantitative trait detection for genes affecting various traits in pigs, cattle and poultry (with Dekkers and Lamont). P. Liu is currently completing her Ph.D. in Statistics at Cornell and will join ISU in August 2006 in a new faculty position in Statistical Genomics. Her research focuses on development and application of statistical inferences for genomic data. Current collaborative projects include detecting differentially expressed genes in different cell types and modeling and analyzing gene expression profiles in yeast that accompany alterations in phospholipid metabolism induced by environmental changes. L. Miller studies data modeling, data search strategies, tools for collecting and analyzing data, database systems, and data warehouses. He collaborates with Reecy and other faculty that work in bioinformatics and animal genetics/genomics. D. Nettleton develops statistical methods for the design and analysis of experiments in the biological sciences. He collaborates with many Dekkers, Lamont, Reecy, Tuggle, and Fernando on expression profiling and QTL mapping. Recent statistical research has focused on estimating false discovery rates in high-throughput genomics experiments and using selective transcriptional profiling to identify loci that control expression of one or more genes.

Additional Information on the faculty and their research can be found through the departmental ISU websites. Statistics (Carriquiry, Dorman, Koehler, Liu, Miller, Nettleton)

Molecular Genetics and Genomics
H. Harris’ research focuses on infectious diseases of swine and shrimp and has expertise in pathogenic microbiology, nomenclature and classification of bacteria and viruses, bacteriophage therapy, vaccinology, infectious agent elimination techniques, antibiotic alternatives, and xenotransplantation. S. Lamont studies molecular genetics and genomics of poultry with reference to disease resistance, immunity, growth and resource-allocation traits. She utilizes SNPs (in candidate genes and genome-wide), microarrays, and quantitative PCR to associate variation in DNA structure or gene expression with biological traits. Several projects are collaborative with AQMSG faculty (Dekkers, Nettleton), and include cooperation with poultry genetics companies. J. Reecy focuses on the effects of transcription factors on the growth and development of skeletal and cardiac muscle. He also studies molecular genetics in beef cattle, with an emphasis on identifying genes of economic value to the industry. Research projects include studies on work overload hypertrophy (Nettleton), double muscling (Nettleton), microarray analysis of gene expression in beef cattle, candidate gene analysis, and identification of epistatic alleles (Dekkers). M. Rothschild is Director of the Center for Integrated Animal Genomics and a director for the International Swine Genome sequencing project. His research involves quantitative and molecular genetics in the pig, with emphasis on identifying genes of economic value. Recent research included gene mapping and comparative genomics (with Dekkers) and detection of genes influencing reproductive, growth, obesity, longevity (with Stalder) and health traits, and collaborative projects in nutrigenomics, on disease genes in the dog and on growth genes in shrimp. D. Spurlock conducts research on genetic regulation of energy utilization in dairy cattle, including candidate gene analyses, microarray gene expression, and defining physiological effects of long-term selection for milk production in dairy cattle. C. Tuggle is using structural and functional genomics to study how gene expression controls mammalian growth, reproduction and resistance to disease. Tuggle has collaborative projects in transcriptional profiling: a) to study the reproductive-immune interplay of maternal-fetal interactions, using the pig as a model (with Nettleton and Reecy) and b) to study genes and pathways that control pig feed intake and develop a comparative gene expression database between pigs, human and mouse (with Dekkers and Nettleton).

Additional Information on the faculty and their research can be found through the departmental ISU websites. Animal Science (Harris, Lamont, Reecy, Rothschild, Spurlock, Tuggle).

DEVELOPMENT OF CRITICAL THINKING AND COMMUNICATION SKILLS
AQMSG faculty mentors will provide strong guidance to aid continued development of skills in critical thinking and oral and written communication, which will be honed through several special features of the program (see Section 4). These will include informal seminar presentations to student peers and faculty advisors, presentations given during the quarterly AQMSG research meetings, opportunities to present research findings at national conferences, and through mentoring of gifted college students from underrepresented groups. Writing skills will be specifically developed by requiring grant proposals as part of the Preliminary Examination, and in preparation of manuscripts that result from student research activities. Examinations. Examination requirements for completion of the Ph.D. are the responsibility of the Fellow's graduate major (IG or BCB), the home department, the advisory committee, and the AQMSG Executive Committee. Minimum requirements for AQMSG Fellows are completion of a comprehensive written and oral Preliminary Examination to establish Ph.D. candidacy, and a final defense of the dissertation. The written component of the Preliminary Examination will include the preparation of a grant proposal on the Fellow's research project. The oral portion will include formal questions in the areas relevant to the Fellow's training. The dissertation defense will consist of a public lecture and an oral examination by the Fellow's dissertation committee. Time to Degree. Following completion of their laboratory rotations, Fellows will select a dissertation advisor in consultation with their temporary advisor and the AQMSG Executive Committee. The role of the AQMSG Executive Committee will be to encourage representation of Fellows across the disciplines within AQMSG. Fellows will assemble a thesis advisory committee in the first year and meet with the thesis committee annually. Early in the second year, they will present a research proposal of the intended thesis research project to their thesis committee. Fellows will complete their required common-core lecture courses by the end of the second year. The preliminary examination will also be completed by the end of the second year. Completion of dissertation research will probably require approximately four years beyond the first year of research in laboratory rotations. The research advisor will be financially responsible for the Ph.D. candidate after the Fellowship ends.

INTERDISCIPLINARY RESEARCH TRAINING
One of the foremost values of this training program is its interdisciplinary nature, which is fundamental to both the IG and BCB graduate programs. Founded in 1992, the educational philosophy of IG was formally stated in the 1990 Policy Statement of the Council of Graduate Schools that "some of the most interesting and challenging questions arise at the boundaries of existing disciplines" and that "such interdisciplinary questions are most appropriately addressed by cooperative efforts such as interdisciplinary programs". As well, the BCB program is inherently interdisciplinary, being composed of faculty trained in biology, chemistry, physics, mathematics, engineering, statistics and computer science who have significant collaborations that span research groups and integrate students being trained and funded through interdisciplinary training grants (NSF-IGERT and USDA-MGET). An NSF-sponsored external review in the Fall of 2002 concluded that the enthusiasm and involvement of a growing number of ISU faculty, the demonstrated commitment of ISU administration to support BCB, the successful leveraging of financial support for students, the successful attraction of research funding, and the administrative skill of the leadership all contribute its success: "At ISU, they appear to be well on the road to developing a new paradigm for interdisciplinary graduate education.". All aspects of the AQMSG training plan are deeply rooted in these interdisciplinary ideas. Programmatic features that cultivate this educational philosophy are discussed below.

Group Research Meetings.
Intensive experience in collaborative, multidisciplinary research will be provided to Fellows through informal quarterly meetings of students from ongoing training programs. Fellows will provide leadership for coordination of this series of meetings. These meetings, held in the evening, include informal presentations of research and/or discussion of recent journal articles, preceded by a communal dinner to encourage informal discussions. Critical analysis of experimental design and data in this setting will help develop Fellows' analytical skills.

Workshops and Seminar Series.
Both IG and BCB offer a multi-seminar Workshop in Current Topics. The IG Workshops are accompanied by a seminar-style lecture and discussion short course that meets before the Workshop. Students prepare for the Workshop by participating in a seminar course (GENET591/BCB593) where they read and actively discuss papers suggested by the visiting speakers. In a unique aspect of the Workshop (one highly valued by the attending students), Workshop speakers give an informal “chalk-talk” only to the students in a relaxed setting, which allows for significant student participation. Almost every year, the BCB Program holds a Workshop in Bioinformatics with the University of Iowa Bioinformatics Program, which provides opportunities to exchange ideas and information between groups focused on bioinformatics. The Baker Center for Bioinformatics and Biological Statistics also conducts a Seminar Series that offers a complementary opportunity to hear of interdisciplinary bioinformatics research at leading laboratories across the nation and world.

Targeted Symposia.
AQMSG faculty members have a history of organizing Symposia targeted toward animal genetics and genomics. Recently, several faculty garnered Federal, industrial, and local funding for two Symposia held in Ames in 2005: Genetics of Animal Health (July 2005) (http://www.ans .iastate.edu/GAH2005.html); and Integration of Structural and Functional Genomics (Sept 2005) (http://www.bb.iastate.edu/%7Egfst/homepg.html). For 2007, a Symposium on Epistatic Interactions for Animal and Plant Genetics will be held, with Dekkers as co-organizer. Similar future symposia will provide Professional Development opportunities for AQMSG Fellows. Graduate students are involved in many aspects of Symposium organization, including hosting of speakers, transportation, entertainment, mailings and other preparation activities. Students may also present their work as a poster or orally.

Animal Breeding and Genetics Summer Short Courses.
Since 2001, AQMSG faculty (Dekkers, Fernando, Lamont, Nettleton) have been active in organizing post-graduate short-courses on specialized topics relevant to Animal Breeding and Genetics and Statistical Genomics. These short-courses involve intensive training during 2 to 10 days by specialists on the respective topics from within or external to ISU and are open to students, faculty and staff from ISU and to members from other universities, institutes and industry. During the past five years, seven such short courses have been offered. Plans are to continue offering these short courses, which will be ideal opportunities for Fellows to update their knowledge from experts in the field, and to interact with students, faculty and staff from other universities, institutes and industry.

IG Research Retreat/BCB Faculty-Student Meetings.
At the beginning of each academic year, IG holds an all-day multidisciplinary Research Retreat at a recreational area near Ames. Faculty and advanced graduate students give short research talks and present posters. The day includes two meals and recreational activities. The BCB Program holds similar meetings on campus between new students and faculty, who give short research presentations, with opportunities for informal discussions.

Interdisciplinary Seminars.
In GENET690 and BCB690, all Fellows present research results to their peers. IG majors represent 14 different home departments and BCB majors 10; thus, these presentations provide exposure to a wide variety of current research projects. The annual IG and BCB faculty seminar series (GENET691 and BCB691) also expose students to a broad overview of research conducted by the programs’ experienced scientists (see list of seminars in Appendix, pp.43-50).

OTHER INNOVATIVE FEATURES

Travel to National Scientific Meetings.
As an essential part of their training, Fellows will attend a national or international scientific conference each year, using funds provided by the College of Agriculture (Appendix, letter p.145), supplemented by individual faculty research grants. There are multiple benefits to early and frequent attendance of scientific conferences. In their early years, the excitement of the meetings will contribute to the student's enthusiasm for their own research work. As well, personal contacts made will enhance the Fellows' resources and independence.

Professional Skills Development. In addition to the opportunities for professional development discussed above, the following experiences will develop specific professional skills:

  • Additional Mentoring Opportunities. Because their future careers will involve communication, continuing education, and mentoring of colleagues, we believe this is a crucial aspect of graduate student training. We, therefore, further describe the mentoring opportunities available to AQMSG Fellows. Peer mentoring is discussed above in Section 2. The College of Agriculture has a strong history in attracting undergraduate and high school students from under-represented groups to do summer research internships. Examples include the Summer Internship for Minority Students Program (discussed in Section 2) and the Program for Women in Science and Engineering. Another opportunity for mentoring lies in the NIH-NSF Summer Institute in Bioinformatics and Computational Biology at ISU (SIBCB), which provides advanced undergraduates and beginning graduate students with interdisciplinary bioinformatics research and education experiences. SIBCB students participate in a 2-week short course, which provides intensive iinstructional reviews of fundamental methods in computational biology and applications to research problems, with lectures by internationally renowned faculty in programming for bioinformatics and computer laboratory sessions devoted to practical applications. After completing the short course, students work with individual faculty on specialized research projects. Students also attend seminars by invited speakers and prepare final presentations about their research projects. AQMSG students may participate through teaching in SIBCB laboratory courses or mentoring SIBCB student research projects. Finally, nearly every faculty member involves undergraduate students in their lab through Work-Study or Undergraduate Research Assistantships. These students are often eager to learn and can provide additional, more informal, mentoring opportunities for AQMSG Fellows Grantsmanship Workshops. A highly practical training opportunity for professional scientists are the grantsmanship Workshops hosted by the Vice provost for research. In these Workshops, biotechnology faculty who have been successful in obtaining USDA-NRI or other external funding discuss their experiences and give specific details on grant preparation, targeting agricultural and related research funding opportunities. Advanced students can gain skills that will be useful for future fund-raising efforts in their own labs or companies.
  • Preparing Future Faculty Program. ISU offer a program in Preparing Future Faculty (PFF), a national movement sponsored by the Association of American Colleges and Universities and the Council of Graduate Schools. The goal of PFF is to better prepare graduates for faculty careers through a combination of seminars, mentoring, and practical classroom and departmental service experiences. The ISU PFF program supplements Departmental graduate preparation by offering two seminar and workshop courses covering such diverse topics as grant and proposal writing, intellectual property, learning styles, researching employers, and promotion and tenure. The PFF helps participants learn about the full range and balance of faculty life in research, teaching, and service and provides important credentials for the competitive academic job market. AQMSG students will be strongly encouraged to take advantage of this opportunity.
  • Symposia Organization. As discussed above, AQMSG Fellows will have the opportunity to help organize and actively participate in the running of Symposia.

Training in Bioethics.
ISU has developed a nationally recognized Bioethics Program organized by the Department of Philosophy. Its mission is to nurture discussion of ethical issues in science and technology and to formally train faculty members to introduce such issues to their students. All IG and BCB students attend a concentrated Scientific Ethics Orientation or a ˝ credit course entitled "Professional Practice in Research ". Additionally, all BCB students must take two BCB-approved bioethics course modules; these include Professional Practices in Research, Intellectual Property and Industry Interactions, and Ethical Arguments and Agricultural Biotechnology. All IG students have the opportunity to participate in a 2 credit course in the spring "Issues in Biology". The intent of the course is to introduce graduate students in the life sciences to contemporary issues in bioethics - especially issues that interrelate biology, biomedical sciences, and society.

Industrial Interactions and International Research Travel (IRTA).
To round out the thorough preparation of Fellows for future careers in animal genetics and biotechnology with an emphasis on agricultural applications, and to provide an international research experience, AQMSG will provide the Fellows with opportunities for active participation in joint research projects funded by animal biotechnology and genetics companies and/or to conduct part of their thesis research at Wageningen Agricultural University (WAU) in the Netherlands. In addition, internship opportunities in the research divisions of leading animal genetics companies have been arranged. Each Fellow may elect to take a three- to six-month internship in a research group at these companies or at WAU. The industry internships will provide a top-quality, first-hand experience with applied agricultural animal genetics and biotechnology that will supplement ISU’s traditional focus on “Science with Practice”. An internship at WAU, with which members of the AQMSG have ongoing collaborations and student exchange programs, will provide Fellows with the opportunity to interact with faculty and students from one of the leading research groups in Animal Breeding and Genetics in Europe. It is anticipated that these internships may in some cases lead to or be part of dissertation research which is jointly mentored by a researcher from the host organization and an AQMSG faculty member.

Relationships with the industry companies are based upon fruitful, long-term collaborations with AQMSG faculty and contacts that range from formal to informal. For example, Dr. Archie Clutter, a senior research scientist in the Animal Genetics Division of Monsanto Co., has collaborating faculty status in the Department of Animal Science and has been an active member of the advisory committee of several students. In addition, AQMSG faculty have been the major advisor of multiple students that now work in animal genetics companies, including Dr. Laura Grapes, a National Needs Fellow co-advised by Fernando and Rothschild, and currently is a geneticist at Monsanto Co. The scope of the industry collaborations of AQMSG faculty are documented by grants, contracts, joint publications and licensing of ISU patents. A specific example is the close collaboration with two poultry genetics companies of Joe McElroy, a National Needs Fellow who was co-advised by Lamont and Dekkers and completed his degree in 2005. Aviagen and Hy-Line Int. each provided access to real-world data for analyses which formed the majority of Joe’s Ph.D. dissertation. Two peer-reviewed papers first-authored by Joe included industry geneticists as co-authors (see McElroy et al. publications on p.36 and letters from Aviagen and Hy-Line on p.151 and p.154). As exemplified by the letters, the ability of Fellows to participate in research projects that address scientific topics of interest to the animal genetics industries will give them unique opportunities and experience.

Selection:
Selected Fellows will participate in 3 to 4 research lab rotations during their first year of graduate study with animal molecular biology faculty. The three areas of animal molecular biology with emphasis in genomics and bioinformatics (AMBGB) are Animal and Microbial Genomics, Animal Growth and Development, and Food Safety and Disease Resistance.

Training Plan: The proposed interdisciplinary training plan will provide breadth and depth through core training in molecular genetics, statistics and introductory bioinformatics, coupled with an intensive experience in collaborative research in one of the four above areas. Future scientists trained under the proposed program will have a sound understanding of molecular biology and will also have considerable appreciation of the quantitative or bioinformatic aspects of their area of expertise. The resulting pre-doctoral experience will provide scientists with an excellent preparation for innovative future careers in animal molecular biology, genomics, and/or bioinformatics in the food/agricultural sciences.