Source: UNIV OF MINNESOTA submitted to NRP
GRADUATE STUDIES IN ANIMAL HEALTH AND MICROBIAL GENOMICS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
0203689
Grant No.
2005-38420-15765
Cumulative Award Amt.
(N/A)
Proposal No.
2005-02313
Multistate No.
(N/A)
Project Start Date
Sep 1, 2005
Project End Date
Aug 31, 2010
Grant Year
2005
Program Code
[KK]- National Needs Graduate Fellowships Program
Recipient Organization
UNIV OF MINNESOTA
(N/A)
MINNEAPOLIS,MN 55455
Performing Department
VETERINARY BIOMEDICAL SCIENCES
Non Technical Summary
Advances in the genome projects of agriculturally important animals and pathogens has created a critical need for a new generation of scientists trained in the forefront of genomics, and computer-based quantitative skills. The objective of this training program is to train students to meet the demand in food and agricultural sciences to harness the benefits of this growing genomic information.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
90360993020100%
Knowledge Area
903 - Communication, Education, and Information Delivery;

Subject Of Investigation
6099 - People and communities, general/other;

Field Of Science
3020 - Education;
Goals / Objectives
The purpose of the proposed Ph.D. fellowship program in microbial and animal health genomics is to provide multidisciplinary training for future generations of scientists that will serve the national need for the continued improvement in animal health and well-being. It is well recognized that the future of animal agriculture in the United States, as well as the public perception of the wholesomeness of the food we produce, is intimately tied to advances in our understanding of the mechanisms by which pathogenic microorganisms cause disease. In addition, the realization of the impact of zoonotic infections on the ever increasing human population, and the growing awareness and political realities of agroterrorism, biosecurity and food-borne illnesses further emphasized the importance of training scientists with the scientific skills and leadership abilities to address these critical areas. The objective of this training program is to train students to meet the demand that has been created for a new generation of scientists able to harness the benefits of the vast and growing amount of genomic information. The most important indication of the impact and success of this fellowship program in will be the type of employment offers received by Fellows upon graduation; we anticipate that graduates of this NNF program will be highly sought after by academic institutions and companies that are leaders in the genomics field. As a quantitative measure, we anticipate that the research projects completed by Fellows will result in numerous publications in top-rated peer-reviewed journals, and that they will have a significant scientific impact.
Project Methods
The goal of this NNF training program is to provide students with sufficient broad based knowledge, quality communication skills, and the advanced research training in mechanisms of animal health and disease essential for careers as independent investigators and teachers in biological sciences. This program provides students with training in state-of-the-art methodology in critical areas of animal and microbial genomics and bioinformatics. The proposed program consists of a number of unique features that are designed to ensure the long-term success of the program. These include: (a) a focused and rigorous program of education and research experiences with an emphasis on microbial and animal health genomics; (b) the formal training of students in the area of bioinformatics and genomics by participation in the Biomedical Genomics Center minor program in Bioinformatics; (c) the formal training of students in teaching approaches by participation in mentored teaching exercises offered within the Department of Education and required classroom/laboratory teaching; (d) the selection of program faculty with active and well-funded research programs in genetics, genomics, pathogenomics, infectious disease and bioinformatics, (e) representation and support from numerous related Centers, core facilities, and programs at the University of Minnesota with a focus on microbial and animal genomics and bioinformatics so as to provide students with intellectual multidisciplinary interactions and state-of-the-art genomics and computational biology resources; and, (f) a stimulating and creative institutional environment and infrastructure designed to enhance learning and the application of genomics and bioinformatic tools to solving problems related to animal agriculture. A web site describing this NNF program will be developed which will be will be linked with the Comparative and Molecular Biosciences graduate program, Animal Biotechnology Center, Biomedical Genomics Center, and the University of Minnesota Graduate School. This web site will not only be used for recruitment, but will serve and the conduit to disseminated the results of the fellows and program throughout the entire training period. This will include describing the progress of the fellows in the program, their research accomplishments including publications and scientific presentations, and updates on their placement and scientific accomplishments following completion of the training program. Ultimately, this proposed training program will meets the need for training of future scientists in genomic and bioinformatic approaches to address key aspects of food and agricultural sciences.

Progress 09/01/05 to 08/31/10

Outputs
OUTPUTS: This award funded two PhD trainees in the area of animal health and microbial genomics. Two students were recruited to the Comparative and Molecular Biosciences graduate program in the College of Veterinary Medicine, University of Minnesota. After a series of three, 8-week lab rotations in selected training grant faculty labs, the students selected their advisors and research projects. The first student working with Dr. M. Rutherford on Cryptosporidium parvum, a zoonotic parasitic pathogen of cattle and humans. Her work utilized a whole genome transcriptome approach to identify genes associated with life cycle progression during a 72 h in vitro culture model. She completed her graduate program requirements, completed the Masters of Public Health degree, and successfully defended her PhD thesis in August, 20011. The second student is working with Dr. K Reed on health immunogenetics of the turkey. Specifically she is cloning and sequencing the major histocompatibility complex region of the turkey genome to identify expressed class I and class I genes. She has completed her core graduate program courses and the required minor degree courses in bioinformatics. She will defend her PhD thesis in January 2012. PARTICIPANTS: Two PhD graduates trained in animal health and microbial genomics, including formal minor training in bioinformatics. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: No changes to original aims of the proposal.

Impacts
The outcome of this program is the training and graduation of two scientists with strong bioinformatics capabilities to complement rigorous molecular biology and animal health research skills. Both graduates are seeking positions in higher education that will allow them to both continue animal health research and to teach.

Publications

  • Reed KM, Bauer MM, Monson MS, Benoit B, Chaves LD, O'Hare TH, Delany ME, 2011. Defining the turkey MHC: identification of expressed class I- and class IIB-like genes independent of the MHC-B. Immunogenetics 63(11):753-71. PMID: 21710346
  • Bauer MM, Reed KM, 2011 Extended sequence of the turkey MHC B-locus and sequence variation in the highly polymorphic B-G loci. Immunogenetics63(4):209-21. PMID: 21207020
  • Chaves LD, Krueth SB, Bauer MM, Reed KM, 2011. Sequence of a turkey BAC clone identifies MHC Class III orthologs and supports ancient origins of immunological gene clusters. Cytogenet Genome Res. 132(1-2):55-63. PMID: 20733277
  • Reed KM, Bauer MM, Mendoza KM, Armien AG, 2010. A candidate gene for choanal atresia in alpaca. Genome 53(3):224-30. PMID: 20237599
  • Kim JE, Bauer MM, Mendoza KM, Reed KM, Coulombe RA Jr, 2010. Comparative genomics identifies new alpha class genes within the avian glutathione S-transferase gene cluster. Gene 452(2):45-53. PMID: 19913078
  • Mauzy, MJ, Enomoto S, Lancto CA, Abrahamsen MS, and Rutherford MS, 2012. The Cryptosporidium parvum transcriptome during in vitro development. PLoS One, in press.


Progress 09/01/07 to 08/31/08

Outputs
Both trainees are making outstanding progress. One is completing the final (4th) year of her research and plans to defend in Summer 2010. She has completed 4 courses for the Bioinformatics minor program. Research focuses on whole genome expression cluster analysis to identify genes in Cryptosporidium that relate to host species specificity and to life cycle progression. The second student is starting her third year of training and is working in the area of turkey immunogenetics. Specifically, her PhD thesis work centers on completing the genomic analysis of the turkey MHC region, characterization of class I and class II gene expression, and determining if a unique cluster of related genes are novel antigen presenting molecules. PRODUCTS: No products are expected of this project. OUTCOMES: Outcomes are expected to be two PhD scientists trained at the interface of genomics and bioinformatics with focus on agriculturally important animals or their pathogens. DISSEMINATION ACTIVITIES: The PI has created a website highlighting the training grant, and the students recognize the NNF support on their research posters. FUTURE INITIATIVES: We plan to submit an updated, expanded version of this training program in the next USDA cycle.

Impacts
The immediate impact of this project is the support for specialized training of two PhD students.

Publications

  • No publications reported this period


Progress 09/01/06 to 08/31/07

Outputs
We now have both of our funded students in the training program. One student has begun her second year of study, has completed research laboratory rotations, and has selected an advisor/research project. The focus of her studies will be whole genome transcriptional profiling of Cryptosporidium parvum during in vitro infection of human intestinal epithelial cells. Data will be used to pattern expression of genes for identifying common promoter elements and for developmental stage-specific genes. Her GPA for first year studies was 3.78, including one of the required bioinformatics minor courses. She is completing an MPH project simultaneously, and will complete her additional required minor courses by Summer 2008. Her Ph.D. thesis committee has been selected, and she will submit for preliminary oral examinations in Spring 2008. A second student has matriculated in Fall 2007 and is completing research rotations. PRODUCTS: No products generated. OUTCOMES: Outcomes cannot be determined at this time. DISSEMINATION ACTIVITIES: P.I. will attend the Food and Agricultural Sciences NNF Grants Program and Higher Education Multicultural Scholars Program Conference in October, 2007. FUTURE INITIATIVES: To mentor completion of Ph.D. studies for the two trainees, and to renew support for the program.

Impacts
This NNF program has supported two Ph.D. trainees who will gain expertise in the junction of genomic biology and bioinformatics.

Publications

  • No publications reported this period


Progress 09/01/05 to 09/01/06

Outputs
(N/A)

Impacts
No tangible impacts are noted as yet.

Publications

  • No publications reported this period