Duration: 10/01/2007 to 09/30/2009

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

During the past five years, researchers with strong and long-lasting research programs on various aspects of bovine health and well being from several SAES (i.e. IL, MSU, WI, MN, KY, CA, NC) have formally collaborated or informally discussed joint research projects at national meetings and annual multi-state research project gatherings. We have identified commonalities and complementaries in our respective areas and are committed to collaborate on projects aimed at better understanding the genomic and proteomic basis of health and well being in cattle. A key problem that we have identified is a lack of a satisfactory gene expression database available for the bovine species, leading to duplication and redundancy in costly genomic- and proteomic-level experiments being performed. Furthermore, there is lack of agreement or consistency in the platforms and protocols to be used to identify, measure, statistically analyze, and document gene and protein expression changes, protein networks that regulate them, and corresponding cell or animal phenotypes obtained through our high-dimensional bovine health and well being studies. This NCDC seeks to remedy this problem.

Objective:

The main objective of this NCDC is to bring together a critical mass of colleagues eager to develop a cattle database framework for annotation with gene/protein expression and regulation information. We envision that this cattle database will complement existing human and mouse Gene Expression Atlas databases (http://symatlas.gnf.org/SymAtlas/). A second objective is to collate the collection of existing gene/protein expression and regulation data with development of new data to annotate and test the database. The initial focus of this effort would be on traits of bovine health and well being (e.g., immunocompetence, host-pathogen interaction, fertility, and metabolic capacity) for which we already have published substantial data. Once the blueprint for the database framework has been developed, we will launch it with password protection (for use by our NCDC group) on one of our existing EST database web sites (e.g., http://www.cafg.msu.edu) and try annotating it with our own published gene and protein expression data and with any new data we generate over the 2 year NCDC project. Thus, the ultimate goal of this NCDC is to develop a critical mass of researchers who will use and contribute data to the same database so it becomes the standard for bovine genomics and proteomics workers (regardless of traits of interest). Clearly, a lot of past and recent data are available from other groups that could be integrated into this database, and retrieval of these data for further annotation of our database will be the foundation of a new NC project proposal written and submitted by this NCDC (by December 1, 2008). Also, it will take a core of people monitoring/measuring gene and protein expression profiles with agreed upon platforms and protocols and using the same terminology to move this database concept forward. Our thinking is that we would basically formulate the bones of a database system that would meld with existing Atlas databases and do our best to populate it with our available gene and protein expression data as a start, as well as set some platform and methodological standards so that others can contribute standardized data to the database in the future.

Commitment to the NCDC:

A concrete example of how this NCDC will work together is the integration of effort and know-how already planned by the University of Illinois at Urbana-Champaign (UIUC) and Michigan State University (MSU). MSU has developed substantial gene expression profiling platforms and protocols, as well as a large amount of bovine health and well being related gene and protein expression data from them to share with UIUC. In turn, UIUC has in place the statistical and bioinformatics expertise and tools to support analysis of these high-dimensional datasets and to extract the maximum amount of important information from them. In addition, MSU will provide wet lab training to all NCDC colleagues seeking this expertise, and an existing web site for initial Bovine Atlas database launch and test annotation in support of this NCDC. Likewise, UIUC will provide ongoing statistical and bioinformatics expertise needed to support this work of NCDC. Also, MSU (Michigan and Mississippi) are currently generating new information on protein networks that regulate gene expression in bovine immune cells subjected to stress hormones and pathogens, two models of novel gene expression regulation information in cattle that will be made available to UIUC for statistical and bioinformatics analyses and available for use by NCDC collaborators to apply for joint extramural grants. Additional pieces that will contribute to this NCDC are that the CA member has a bank of bovine samples suitable for studying specific genes or gene pathways, a member from WI has characterized gene variants associated with dairy production and reproduction traits, a member from NCSU has an extensive list of quantitative trait loci influencing production and health traits in dairy cattle, members from MN are generating microarray and genome-wide association data to study genes and DNA variations associated with mastitis resistance and fertility, a member from KY has mastered techniques to effectively measure altered expression of gene products (mRNA/protein) to study alteration of metabolic capacity in metabolically-stressed cattle, another member from WI can provide the statistical expertise to adequately model the measurements, and another member from IL can help with the bioinformatics tools to facilitate the interpretations of the results from the analyses.

Supporting NCDC Activities:

Participants of the NCDC will formally meet at least once a year at one of the collaborating SAES and follow-up with informal monthly e-mails and bimonthly conference calls during the two years of the project. All participants of the NCDC are committed to contribute to the writing of the NC proposal. Once the NCDC participants have developed sufficient preliminary data and agreed on the language of the objectives and methods of the future NC document, three NCDC members will take the lead compiling a draft of the NC proposal. All participants will be responsible for describing their corresponding roles and methods to ensure the timely and successful accomplishment of the overarching NC objectives. The NCDC will have a Wiki website where participants can contribute to the NC project proposal in a synchronous and asynchronous manner.

Impact:

The development of a NC proposal, which seeks to support studies that explore genomic and proteomic underpinnings of key bovine traits by providing a publicly available and interactive Bovine Gene Expression Atlas database, will facilitate sustainability of animal agriculture in the US and globally by ensuring that results of such studies will be readily accessible for use by biopharmaceutical and cattle-related industries and research institutions.

Verbal agreement for this NCDC has been obtained from:

Jeanne Burton (Michigan) burtonj@msu.edu
Sandra Rodriguez-Zas (Illinois) rodrgzzs@uiuc.edu
Melissa Ashwell (North Carolina) melissa_ashwell@ncsu.edu
Jamie Matthew (Kentucky) jmatthew@uky.edu
Yang Da (Minnesota) yda@umn.edu
Guilherme Rosa (Wisconsin) grosa@wisc.edu
Juan Medrano (California) jfmedrano@ucdavis.edu
Hasan Khatib (Wisconsin) hkhatib@wisc.edu
Erdogan Memili (Mississippi) em149@ads.msstate.edu>

Objectives

Procedures and Activities

Expected Outcomes and Impacts

Projected Participation

View Appendix E: Participation

Educational Plan

Organization/Governance

Literature Cited

Attachments

Land Grant Participating States/Institutions

CA, IL, KY, MD, MI, MN, NC, NY, SD, WI

Non Land Grant Participating States/Institutions