USDA NATIONAL NEEDS Ph.D. FELLOWSHIP IN ANIMAL MOLECULAR BIOLOGY
The USDA NATIONAL NEEDS Ph.D. FELLOWSHIP in Animal Molecular Biology
with an emphasis in Genomics and Bioinformatics 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: $22,000 for three years
- Tuition Scholarship
- Paid Student Health Insurance
- Nine months to spend time in up to three research laboratories
before deciding on major professor
Who should apply: applicants interested in biological questions dealing with animal and microbial
genomics, food safety and disease resistance, and growth and development of animals.
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 February 1, 2006.
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.
STRENGTH IN ANIMAL MOLECULAR BIOLOGY, GENETICS AND BIOINFORMATICS
Iowa State University (ISU) has a long history of excellence in theoretical and applied animal molecular biology and genetics, due in large part to the global legacy of ISU animal genetics pioneers J.L. Lush and L.N. Hazel. In the past two decades, ISU has steadily moved to a nationally and 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 position of USDA National Research Support Program-8 (NRSP-8) National Swine Genome Coordinator (M. Rothschild), and the position of USDA NRSP-8 National Database/Bioinformatics Coordinator (J. Reecy); both these faculty are participating in AMBGB. Efforts in bioinformatics at ISU in the past 3-4 years have significantly expanded, with extensive research and graduate training interactions within the graduate major in Bioinformatics and Computational Biology and with the Baker Center for Bioinformatics and Biological Statistics. Furthermore, the Ames research community is a world leader in animal disease research. In addition to Iowa State University, there are two other premier animal health institutions located in the Ames area. The USDA ARS National Animal Disease Center (NADC) is the principal USDA research center for investigating diseases of domestic livestock and poultry, while the USDA APHIS National Veterinary Services Laboratories (NVSL) is responsible for the evaluation and licensing of veterinary biologics. Several USDA scientists have faculty appointments at ISU, and AMBGB faculty members have active collaborations with NADC and NVSL scientists.
RESEARCH
A cornerstone of the AMBGB training plan in animal molecular biology, genomics and bioinformatics is an intensive,
multidisciplinary research experience involving close interaction of Fellows with AMBGB faculty and their
laboratory groups, and the opportunity for interactions with scientists in industry and Federal laboratories.
The first step is the selection of laboratories for rotation experiences to select the dissertation laboratory.
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 in at least two of the four participating departments. Upon their arrival at ISU, Fellows will attend the all-day student/faculty IG Research Retreat or BCB Faculty-student meetings where they will have the important opportunity to meet AMBGB faculty and discuss choices of laboratories for rotation. A temporary advisor (see p.6) assigned by the AMBGB Executive Committee will further facilitate this process. Fellows will be mentored to choose rotations from at least two research disciplines within the AMBGB, such as to enhance the breadth of the training experience.
• AMBGB Faculty Research Programs. There are three major biological research emphases within AMBGB, with Bioinformatics integrating all of these areas. These biological focus areas are: animal and microbial genomics, food safety and disease resistance, and growth and development of animals. Many questions of basic research are involved, but the overall emphasis of this work continues to be the study of animal biology with an emphasis toward biotechnological, genomic, and genetic improvement of animals and animal products, an important area of national need. AMBGB faculty members are conducting research within and across these focus areas, and examples of these research projects follow.
• AMBGB Faculty Research Programs. 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 R. Fernando, M. Rothschild, and S. Lamont) and its integration with gene expression data (in collaboration with D. Nettleton), genetics and functional genomics of feed efficiency in pigs (in collaboration with C. Tuggle, V. Honavar and D. Nettleton), and the design and optimization of breeding programs, including marker-assisted selection, for livestock. S. Lamont studies molecular genetics and genomics of poultry as it relates to disease resistance, immunity, growth and composition traits. She utilizes genomic scans, SNPs, microarrays, and quantitative PCR to associate variation in DNA structure or gene expression with biological traits. Several projects are collaborative with AMBGB faculty (Dekkers, Nettleton), and include cooperation with poultry genetics companies. D. Moody is a new faculty member initiating studies on the genetic regulation of energy utilization in dairy cattle. Her projects will include candidate gene and QTL analyses, microarray investigation of differential gene expression, and defining physiological effects of long-term selection for milk production in dairy cattle. She also studies the genetic regulation of osteoporosis in laying hens through similar methods. M. Rothschild is co-director of the Center for Integrated Animal Genomics (with S. Carpenter). His research involves quantitative and molecular genetics in the pig, with an emphasis on identifying genes of economic value to pork industry. Recent research projects have included gene mapping and comparative genomics (with Dekkers and Tuggle), and quantitative trait detection of genes influencing reproductive, growth, obesity, longevity (with Nilsen-Hamilton), and health traits. Rothschild is also conducting collaborative projects in nutrigenomics, identifying disease genes in the dog and growth genes in shrimp. 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 D. Nettleton and J. 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 J. Dekkers, V. Honavar and D. Nettleton).
In the area of microbial genomics, C. Minion is studying virulence factors of animal Mycoplasma pathogens using genomic sequencing and functional genomics. He and G. Phillips are using transcriptional profiling to identify genes induced as a result of associations of pathogenic bacteria with their mammalian hosts.
Growth and Development
Funded collaborations are ongoing with the Nilsen-Hamilton and Honovar labs. N.M. Ellinwood is a new faculty member
in Animal Science (AS) who works on canine models of neuropathic lysosomal storage disease models of the human
genetic disesases mucopolysaccharidoses types I and IIIB. His work incorporates medical and molecular genetics,
pathology, lipid and glycosaminoglycan biochemisty, and enzymology, to better understand the processes of
central nervous system pathology and to develop central nervous system targeted therapy in large animal as
a preclinical tool. C. Komar is another new Animal Science faculty member who studies the regulation of gene
expression in the ovary. Recent projects include investigating a family of transcription factors that are hormonally regulated during the ovarian cycle, and looking at the effects of environmental factors on ovarian gene expression. Studies also focus on how the mammalian ovary develops, and how the structure of the ovary allows for its cyclic function. M. Nilsen-Hamilton studies two growth factor-regulated genes in reproduction and tissue remodeling. The first is a growth
and angiogenesis factor expressed in the embryonic spinal cord, by the placenta and in wound healing.
Another factor is an acute phase protein that stimulates apoptosis in neutrophils. She has identified the
bovine gene for this protein and is also investigating its role in Johne’s disease and mastitis. 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, double muscling in cattle, microarray analysis of gene expression in beef cattle, heart development, and candidate gene analysis.
Food Safety and Infectious Disease
N. Cornick focuses on pre-harvest food safety, bacterial colonization mechanisms, zoonotic transmission of bacterial
pathogens, pathogenesis of enteric E. coli diseases and the microbial ecology of gastrointestinal systems.
Currently projects include defining colonization mechanisms used by E. coli O157:H7 in ruminants with
C. Minion and understanding the pathogenesis of Shiga toxin-producing E. coli (STEC) disease using an edema
disease model in piglets. C. Minion investigates the molecular basis of bacterial pathogenesis. Ongoing projects
include the molecular basis for persistence of the food safety pathogens Salmonella enteritidis (poultry) and E.
coli O157:H7 (ruminants). Many projects involve collaboration with AMBGB faculty (Phillips, Tuggle). L. Nolan uses
genomic approaches to elucidate virulence mechanisms of enteric bacteria, including those causing disease in
production animals and food-borne illness in human beings. One such study involves sequencing the avian
pathogenic Escherichia coli (APEC) genome and several megaplasmids. These sequences are used to identify new ORFs
for their contribution to virulence. She is also examining the evolution of APEC virulence and antimicrobial
resistance, testing potential vaccines for their ability to prevent colibacillosis, and developing enhanced methods
for detection and tracking of Salmonella spp. G. Phillips studies membrane biogenesis in gram-negative bacteria.
He is also interested in determining the molecular mechanisms as to how subpopulations of bacteria under persist
exposure to antibiotics, i.e., how they survive
exposure to antibiotics without becoming fully resistant. Q. Zhang recently moved to ISU and his research
focuses on Campylobacter jejuni, one of the most prevalent bacterial foodborne human pathogens in the US and other
developed countries. He conducts research to i) elucidate the ecology of C. jejuni in food animal reservoirs, ii)
examine the mechanisms associated with the development and persistence of antibiotic resistance in this pathogen, iii) define the genetic elements required for C. jejuni to colonize the various animal hosts, and iv) characterize outer membrane proteins that are involved in pathogen-host interactions and immune protection. The goals of these studies are to develop effective intervention strategies to control foodborne pathogens in animal reservoirs and the human host.
Bioinformatics
K. Dorman uses computational tools in genetics and evolution to study infectious disease, particularly those caused by rapidly evolving RNA viruses that result in persistent infections. Projects include developing better tools for detecting and analyzing recombinant viral sequences (with S. Carpenter), differential equation and cellular automata models of the pathogen/host interactions leading to persistent infection (with S. Carpenter), and models of drug resistance evolution in viruses. R. Fernando develops statistical and computational methods for mapping QTL and marker assisted selection. Recent research in this area include: comparison of alternative approaches for combined disequilibrium and co-segregation analyses for fine mapping QTL with complex pedigrees, Markov chain Monte Carlo methods for computing haplotype and genotype probabilities, and computational strategies for marker and genotype assisted selection with large pedigrees. Collaborations using these methods are with Rothschild, Nettleton, and Dekkers. V. Honavar focuses on the development of algorithms and software for information integration and data-driven knowledge acquisition problems that arise in comparative genomics, macromolecular sequence-structure-function-interaction-expression analysis, and discovery of genetic regulatory networks from gene expression data. Honavar collaborates with Tuggle and Dekkers on integration of quantitative genetics and gene expression analysis, with Buss on the study of retinal development using proteomics techniques, and with structural and molecular biologists on development of data mining approaches to prediction of protein-protein interactions, protein localization, and gene function. K. Koehler is a statistician with 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), Brownian models for gene expression divergence, modeling effects of nutrition on tumor incidence, and in modeling effects of isoflavones on preventing bone loss in women. D. Nettleton develops statistical methods for the design and analysis of experiments in the biological sciences. He collaborates with many AMBGB faculty members (Dekkers, Lamont, Reecy, Tuggle, Fernando) on expression profiling and QTL mapping experiments.
Additional Information on the faculty and their research can be found through the departmental ISU websites.
Animal Science (Tuggle, Reecy,
Dekkers, Ellinwood, Fernando, Komar, Lamont, Moody, Rothschild)
Computer Science (Honavar)
Statistics (Dorman, Koehler, Nettleton)
Veterinary Microbiology
and Preventive Medicine (Cornick, Minion, Nolan, Phillips, Zhang)
Development of Critical Thinking and Communication Skills.
AMBGB faculty mentors will provide strong guidance to aid continued development of skills in critical thinking and oral and written communication. Critical thinking and oral communication skills 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 monthly AMBGB 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), their home department, their dissertation advisory committee, and the AMBGB Executive Committee. Minimum requirements for AMBGB 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 written grant proposal on the Fellow's research project. The oral portion of the Preliminary Examination will include formal questions in the area of animal molecular biology, genomics, bioinformatics, and in other areas relevant to the Fellow's training, such as food safety, growth, development, or disease resistance. 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 AMBGB Executive Committee. The role of the AMBGB Executive Committee will be to encourage representation of Fellows across the disciplines within AMBGB. 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.
Publications
Graduate students of AMBGB faculty have published 218 papers in refereed journals in the past five years. The natural cohesiveness of the AMBGB faculty group will contribute to successful mentoring of Fellows. Interactions among the AMBGB faculty are strong, with many collaborative papers and grants. The AMBGB faculty members clearly have the funding necessary to maintain a supportive research environment.
