Brief Summary of Minutes of Annual Meeting

The NC-1010 annual meeting was held in the Pacific Salon at the Town and Country Hotel, San Diego, CA, on January 15, 2005, in conjunction with the PAG-XI meetings. Dr. Alison Van Eenennaam, 2004 Chairperson of NC-1010, organized the meeting. The following Agenda was followed: Multistate Research Project NC-1010 Annual Meeting Interpreting Cattle Genomic Data: Biology, Applications and Outreach Saturday January 15th 2005 1:40 pm - 6:20 pm Plant and Animal Genome XIII Conference Town and Country Hotel, San Diego, CA Pacific Salon 6 & 7 1:40 pm Welcome and Introduction - Alison Van Eenennaam 1:50  2:20 "Accelerated Genetics' Application of DNA Technologies." Dr. C. Michael Cowan, General Manager, Genetic Visions, Inc. 2:20  2:50 How do we move from the laboratory to the bull barn? Dr. Marjorie A. Faust, Director of External Research, ABS Global, Inc. 2:50  3:20 "Bovine single nucleotide polymorphisms: implications for animal/food identification, traceback and pedigree verification" Dr. Michael P. Heaton, Animal Health Research Unit, USDA  ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska 3:20  3:30 Wrap-up of Speaker Session 3:30- 4:00 Coffee Break 4:00- 6:00 Station Reports 6:00  6:20 Election of new officers, discussion of future plans and wrap-up 6:20 pm Adjourn A. The meeting began at 1:40pm with a series of invited speakers. Dr. Van Eenennaam started the session with an introduction The first speaker was Dr. Michael Cowan of Genetic Visions, Inc. who spoke on Accelerated Genetics' Application of DNA Technologies. Next was Dr. Marjorie Faust from ABS Global, Inc. who gave a talk on How do we move from the laboratory to the bull barn? The final speaker was Dr. Michael Heaton from USDA ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska who presented work on Bovine single nucleotide polymorphisms: implications for animal/food identification, traceback and pedigree verification. Following discussion of the three talks, we broke for coffee and resumed the meeting at 4:00 PM. Dr. Van Eenennaam called the meeting to order at 4:00 PM on Saturday, January 15 and invited participants to introduce themselves. Several Experiment Station reports were given this evening, followed by the Business meeting. Experiment Station Reports, and/or descriptions of intended areas of research by new members, were presented by: James Reecy  Iowa State University, Melissa Ashwell - North Carolina State University , Jeanne Burton  Michigan State University, Erin Connor  BARC, Yang Da  University of Minnesota, Mike Davis  Ohio State University, Clare Gill  Texas A&M University, Khatib Hasan  University of Wisconsin, David Henderson  University of Arizona, Feng-Qi Zhao University of Vermont, Sandra Rodriguez-Zas  University of Illinois, and Alison Van Eenennaam  University of California  Davis. B. Dr. Deb Hamernik (acting CSREES Administrator) of USDA-CSREES provided an update of developments at the USDA. Specifically: 1. New Secretary of Agriculture has been nominated, Gov. Mike Johanns of Nebraska. 2. CSREES plans to sunset the Animal Genome Reagent and Tools program. Discussion to occur at NRSP-8 business meeting this PAG. 3. Materials describing current research funding at USDA-CSREES for various programs, and current future proposed research budgets were distributed. C. Future Meetings A discussion of future meeting sites was held. A motion was made and accepted that the 2006 NC-1010 annual meeting would be held in the fall (in November) of 2005 at Tucson, AZ, with the 2005 NC-1010 chairperson (Dr. David Henderson, see below) and the University of Arizona acting as hosts. A poster session for the presentation of graduate student projects would be held at the meeting, as well. D. Election of Officers Dr. David Henderson (2005 secretary) was elected chairperson for 2006. Dr. Clare Gill was elected secretary for 2006. E. Web Site An informal discussion was held regarding the NC-1010 web site: 1. It was agreed that the web site would continue to be hosted by UC Davis and maintained by Dr. Alison Van Eenennaam. 2. Any additional links or new pages should be sent to Dr. Van Eenennaam. 3. Links to pages developed for other projects would be accepted, as well. The annual meeting of NC-1010 was adjourned around 9:30 PM. The Joint NRSP-8 / NC-1010 Quantitative Genomics/Proteomics Workshop was also held at PAG on Sunday, 16 January 2005 from 8:00 am-6:20 pm. The workshop was organized by Milt Thomas/Yang Da, and followed the following program

Year 2004 Milestone A: Establish gene & protein expression profiles in the 2003 model systems & initiate new experiments in at least two additional model systems each. Extensive work is ongoing to establish and refine the gene and protein expression profiles in the model systems that were being worked on in 2003. This includes microarray work using tissues from the bovine rumen, large intestine, and small intestine (IL), primary bovine mammary epithelial cells in collagen gels (AZ), mammary epithelial cells responding to an infection using live Staphylococcus aureus, or exposure to lipopolysacharide (LPS) endotoxin from Escherichia coli (VT), and ileal tissue and peripheral blood mononuclear cells from Johnes infected and non-infected cattle (MI). Additionally, a proteomic approach is being used to identifying regulatory proteins that control amino acid transport and metabolism capacity in cattle tissue has been initiated (KY). Experiments have been initiated in four new model systems. (1) An intramammary infusion technique in lactating mice has been established to examine the acute response to LPS (VT), (2) the treatment of bovine neutrophils with endogenous and exogenous glucocorticoids is being used to examine the effect on Fas gene expression (MI), (3) peripheral blood mononuclear cells from cattle experimentally infected with Trypanosoma congolense is being used to help understand bovine trypanosomiasis and trypanotolerance (MI), and (4) serial analysis of bovine viral diarrhea virus (BVDV)-infected cells is being used to investigate the mechanism of immunosuppression in BVDV2-infected cattle (USDA/ARS/NADC). Year 2004 Milestone B: SNP analysis and mapping of ~ 50 candidate genes from model systems in 2003 Expression profiles of 302 genes on a bovine total leukocyte array were found to be influenced by parturition. Predominant clusters of genes with changed expression at parturition were involved in neutrophil, transendothelial migration, and extracellular matrix degradation, but not phagocytosis or killing. Genome sequence trace files encompassing the differentially expressed genes are being analyzed for SNP discovery (MI). Representational Difference Analysis (RDA), was performed using genomic DNA from bulls with high and low EPDs for marbling. Sequence homology analysis indicated that some of the difference products had homology with known genes from bovine, human or mouse, while most had no significant match. Genotype tests were generated for SNPs identified by RDA. Of these, six SNPs are associated with marbling, retail product yield, or back fat in purebred American Angus cattle (IA). In addition to SNP analysis, other type of follow up work is being done on numerous leads/candidate genes obtained from the genomic studies on the model systems outlined above, in addition to other livestock resource populations. Three bovine glucose transporters were cloned and studied for their tissue distributions and developmental regulation in the mammary gland (VT), four genes in mammary epithelial cells were shown to be rapidly and robustly induced by LPS (VT), somatostatin and somatostatin receptor genes are currently being examined for polymorphisms (OH), two cytoskeleton-associated proteins were down-regulated in liver tissue of chlortetracycline-fed but not Synovex-S-treated finishing steers, whereas two amino acid transporters, two anti-oxidant enzymes, and one transcriptional factor were found to be up-regulated (KY). Over 400 genes were identified as differentially expressed in bovine mammary epithelial cells in response to heat stress. Genes involved in trafficking and remodeling, as well as temperature-responsive genes, were among the most significant up-regulated genes. Downregulated genes included those involved in glycolysis, peptide metabolism, and cell morphology. Also of interest were a large number of differentially expressed genes related to G-protein signaling (AZ). Expression profiles of at least 42 genes were found to have inherently different expression profiles in freshly isolated peripheral blood mononuclear cells from M. paratuberculosis infected cattle when compared to similar cells from uninfected controls (MI). Polymorphisms in the protease inhibitor gene associated with milk and fat yields, productive life, and somatic cell score (WI). Year 2004 Milestone C: Intron/exon boundary and promoter analyses of ~10 candidate genes from model systems studied in 2003. Promoter analysis on the bovine somatostatin gene is ongoing in the Angus cattle from the IGF-I selection lines revealed an A to C transversion. Two alleles, E and F, and three genotypes, EE, EF, and FF were observed (OH). A number of other studies meet the objectives and/or achieve the goals of Objective 1. (1) Putative quantitative trait loci affecting conformation traits and calving ease were identified using the merged DBDR genotypic data generated at the University of Illinois and USDA-Beltsville. Regression interval mapping was used to detect QTL affecting 22 conformation traits, including body, udder, feet and legs, and dairy conformation as well as calving ease. Two genome-wise significant QTL influencing calving ease were detected on two chromosomes. Comparison of these results with other published reports identifies many common QTL affecting conformation traits (NC). (2) Putative marker-trait associations between two regions of bovine chromosome 27 and the conformation trait, dairy form were evaluated. There was some evidence of associations with milk fat percentage in the same region (BARC). (3) A cattle genome database and browser compiling QTL and sequence information as a tool for comparative mapping and gene discovery was developed. The database contains 580 QTL entries for 109 traits and 295 molecular markers compiled from 131 literature references (CA). (4) Transgenic modification of the composition of fatty acids in milk fat is being evaluated in transgenic mice. In a complementary study that seeks to modify the triacylglyceride structure of milk fat, the echidna mammary lysophosphatidic acid acyltransferase gene is being cloned (CA). (5) Research is ongoing to evaluate the effect of individual kappa-casein (k-CN) and beta-lactoglobulin (b-LG) genotypes on milk production, milk composition, reproductive performance, disease susceptibility, overall cow performance, and cost/benefits to the producer and industry (CA). IMPACTS OF OBJECTIVE 1: Members of NC1010 are using genomic approaches to identify the candidate genes associated with a variety of traits of importance to cattle production such as skeletal muscle growth, carcass and meat quality, milk production, conformation traits, milking rate, milk quality, digestion/nutrient utilization, female reproduction, stress susceptibility/adaptation, and susceptibility to infectious diseases (mastitis, Bovine viral diarrhea virus, trypanosomiasis, and Johnes disease). Genomic tools have yielded many candidate genes or leads, and researchers are now working to identify functionality and polymorphisms associated with these genes. If markers are derived from this work and found to be associated with the trait of interest in commercial cattle populations, then they may be incorporated into marker-assisted selection programs to accelerate the rate of genetic improvement. Representative examples include the polymorphisms found in the IGF-I, growth hormone, growth hormone receptor, calpain, calpastatin, Pit-1, GHRH-R, IGF-II, somatostatin, and somatostatin receptor 2 loci may be useful in marker assisted selection programs designed to improve growth rates and carcass characteristics of beef cattle (OH), and the QTL and/or candidate genes identified for pregnancy rate and conformation traits (NC, BARC) may be useful for marker-assisted selection for these sustainability traits in dairy cattle. OBJECTIVE 2. Interpret and apply genomics and proteomics information by developing statistical/bioinformatics methods and utilizing molecular tools in cattle. ACCOMPLISHMENTS Year 2004 Milestone A: Recommendations for optimal gene mapping and functional genomics study designs. Several groups are working in this area including studies on (1) the influence of different normalization and parametric models in the detection of genes differentially expressed across conditions using cDNA microarrays was evaluated (IL), (2) the repeatability of the Affymetrix bovine GeneChip (IA), (3) power and sample size calculations for two color microarray experiments with biological and technical replication (MI), and (4) assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models (MI). Year 2004 Milestone B: Establish statistical methods for mapping QTL with non-additive effects Statistical methods are being developed to detect imprinted QTL with gender specific recombination frequencies (MN), and to determine the statistical power for detecting epistasis QTL effects under the F-2 Design (MN). This statistical methods research will provide new tools for mapping genes with complex inheritance, for planning experiment to map QTLs with imprinted effects, gender-specific marker-QTL recombination frequencies, and epistasis effects. Other work that meets the goal of utilizing molecular tools in cattle includes research to identify an approach to increase the efficiency of the creation of transgenic animals. This project seeks to find a more rapid way to determine the rate of homologous recombination. Strategies to quantify rates and type of DNA repair among individual cells so as to enable the selection of individuals that support the highest rates of gene targeting are being investigated (MA). Project members have also developed statistical software including a program which was written in R and that performs a global normalization analysis with a linear model simultaneously with assessing significance of gene specific treatment contrasts through bootstrapping of residuals. The software also scales the bootstrap p-value to control the dependent false discovery rate at a user defined level. A developmental version of Stochastic Search Variable Selection has also been performed with the statistical package R (AZ). Two computer packages, Pedigraph 2.0 and MiniInbred, have been developed with the support from Cargill. These programs allow graphical visualization gene flow in a large and complex pedigrees and minimization of inbreeding in animal breeding plans. Trial versions of these programs are available from http://animalgene.umn.edu. (MN). IMPACTS OF OBJECTIVE 2: The successful use of cDNA microarrays to elucidate biological phenomena depends on adequate control of experimental-induced error and characterization of animal-to-animal variation. Therefore, the development and validation of appropriate spotting patterns and hybridization schemes for microarray construction, and establishment of statistical models to provide adequate levels of confidence to identify false positive and negative results, represent major accomplishments. Similarly, the continued development of appropriate statistical methods and software to support QTL analyses and marker-assisted selection are of tremendous importance to the cattle industry. The impact of this objective will be an accelerated rate of productive leads from microarray experiments, and more expeditious analysis of the data. OBJECTIVE 3. Develop and deliver educational materials about bovine genomics research to consumers and stakeholders ACCOMPLISHMENTS Year 2004 Milestone A: Web site contents fully developed Progress on objective three during the past year includes maintenance of the NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology). This website has links to the North Central Regional Association of Agricultural Experiment Station Directors website, NC1010 goals, participant contact links, bovine and other species genomic databases, cattle extension webpages, breed associations, and outreach. Producer-targeted publications on the use of DNA-based markers in dairy and beef cattle selection programs were made available on the outreach section of the website as .pdf downloadable documents. Year 2004 Milestone B: Quantitative Genomics/Proteomics Workshop The Joint NRSP-8 / NC-1010 Quantitative Genomics/Proteomics Workshop was held at the 2005 Plant and Animal Genome Conference on Sunday, 16 January 2005. The workshop was organized by Milt Thomas/Yang Da and had excellent attendance and lively discussions. A number of other outreach events meet the objectives and/or achieve the goals of Objective 3. Two workshops on microarrays were offered at The University of Arizona in 2004. These workshops cover array laboratory techniques and statistical methodology for the analysis of array data. Statistical Analysis course developed at The University of Arizona that covers the analysis of molecular laboratory data (AZ). An article was written for the Michigan Dairy Review (MI) Multiple presentations were made to cattle producers and allied industry throughout California on the use of markers in cattle breeding programs (CA). IMPACTS OF OBJECTIVE 3: The NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology) has been established. Producer-targeted publications on the use of DNA-markers in dairy and beef cattle selection programs have been made available on the outreach section of the website. Members have been involved in various outreach activities including events aimed at both scientific (workshops on microarray analysis, animal functional genomics, quantitative genomics/proteomics) and producer audiences (e.g. use of markers in cattle breeding programs).

ARIZONA Henderson, D.A. 2005. A Bayesian Statistical Method for the Detection of Differential Gene Expression and Control of Multiple Hypothesis Testing With Gene Expression Microarray Data. 2005 ENAR Meeting, Austin, TX Henderson, D.A. 2005. Stochastic Search Variable Selection For The Detection Of Differential Gene Expression. Intl. PAG XIII, San Diego, CA Henderson, D.A. 2004. Microarray Data Analysis. In Bioinformatics. David Mount, Ed. Cold Spring Harbor Press. Stiening CM, Hoying JB, Abdallah MB, Coussens PM, Collier RJ. 2005. Effects of heat stress on morphology and gene expression of bovine mammary epithelial cells (BMEC) in collagen gel culture. J. Dairy Sci. submitted abstract. CALIFORNIA Kao, B. T., E. J. DePeters, and A. L. Van Eenennaam. 2005. Endogenous Production of Omega-3 Fatty Acids in the Mammary Gland of Transgenic Mice. Abstract # P763. Final program and abstract guide. XIII International Plant & Animal Genome Meeting, San Diego, CA, Jan.15-19, 2005. http://www.intl-pag.org/pag/13/abstracts/PAG13_P763.html Morimoto, K.C. 2004. transgenic expression of C. elegans omega-3 and delta-12 desaturases in mammalian cells. M.S. thesis in Animal Science, UC Davis. Morimoto, K.C., A. L. Van Eenennaam, E. J. DePeters and J. F. Medrano 2005. Endogenous Production of Omega-3 and Omega-6 Fatty Acids in Mammalian Cells. J. Dairy Science 88(3) 1142-1146. Van Eenennaam, A. L. 2004. Genetic Engineering in California Agriculture. 30 minute UC peer-reviewed video. ANRUCTV 04-06, University of California, Division of Agriculture and Natural Resources. 6502V (VHS) or 6502D (DVD) http://groups.ucanr.org/anronuctv/Video_Program_Sales_Information/ Van Eenennaam, A. L. 2004. DNA-based Marker-Assisted Selection in Beef Cattle. Chapter in Cow-Calf Management Guide & Cattle Producers Library. University of Idaho Moscow, ID. (In press.) Van Eenennaam, A. L. 2005. DNA-based Biotechnologies. Chapter in Beef Sire Selection Manual, National Beef Cattle Evaluation Consortium Educational Committee. Submitted. Van Eenennaam, A. L. 2005. What is the future of animal biotechnology ? California Agriculture. Submitted. Van Eenennaam, A. L. NC1010 website (http://animalscience.ucdavis.edu/LivestockBiotechnology) Van Eenennaam, A. L. UC Davis Animal Genomics and Biotechnology Cooperative Extension Program website (http://animalscience.ucdavis.edu/animalbiotech) Wong, M.I. and J.F. Medrano 2005. A Primer on Real Time PCR for mRNA Quantitation. (Review) BioTechniques (in press). ILLINOIS Loor, J. J., J. K. Drackley, H. M. Dann, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin. 2004. Gene expression patterns in liver of dairy cows from dry-off through early lactation using a bovine cDNA microarray. Federation of American Societies for Experimental Biology Experimental Biology April 2004, Abstract # 822.4 (http://select.biosis.org/faseb/eb2004_data/FASEB004847.html) Loor, J. J., H. M. Dann, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin, and J. K. Drackley. 2004. Mammary and hepatic gene expression analysis in peripartal dairy cows using a bovine cDNA microarray. Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1):103, T134. Loor, J. J., D. B. Carlson, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin, and J. K. Drackley. 2004. Gene expression profiles in liver of dairy cows in response to feed restriction using a bovine cDNA microarray. Annual Meeting of the American Society of Dairyl Sciences. J. Dairy Sci. 87(Suppl. 1):103, T136. Loor, J. J., N. A. Janovick, R. E. Everts, S. L. Rodriguez-Zas, H. A. Lewin, and J. K. Drackley. 2004. Adipose, mammary, and hepatic gene expression profiling in lactating dairy cows using a bovine cDNA microarray. Annual Meeting of the American Society of Dairy Sciences. J. Dairy Sci. 87(Suppl. 1):103, T135. Rodriguez-Zas, S. L., M. R. Band, R. E. Everts, B. R. Southey, Z. L. Liu, H. A. Lewin. 2004. Comparison of normalization and models for the analysis of gene expression data. Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1):377, W256. Rodriguez-Zas, S. L., J. J. Loor, J. K. Drackley, and H. A. Lewin. 2004. Application of a random regression model to gene expression profiling. Annual Meeting of the American Society of Animal Sciences. J. Anim. Sci. 82(Suppl. 1): 242, abs. 365. IOWA Hu, Z.-L., K. Glenn, A.M. Ramos, C.J. Otieno, J.M. Reecy, and M.F. Rothschild. 2005. Expeditor: A pipeline for designing primers Using Human Gene Structure and Livestock Animal EST Information. Journal of Heredity 96:1-3. Soller, M. and J.M. Reecy. 2004. QTL mapping and cloning in beef cattle. AgBioTechNet Proceedings 004 paper 3:1-8. Max F. Rothschild, Susan J. Lamont, James M. Reecy. Current Status of Animal Genomics. Proceedings Annual AAAS meeting, Washintgon DC Feb 17-19, 2005 KENTUCKY M. Z. Fan, J. C. Matthews, N. M. P. Etienne, D. G. Burrin, and B. Stoll. 2004. Expression of Apical Membrane L-glutamate Transporters in Neonatal Porcine Epithelial Cells Along the Small Intestinal Crypt-villus Axis. American Journal of Physiology- Gastrointestinal and Liver Physiology 287:G385-G398. Novak, D., F. Quiggle, and J. C. Matthews. 2004. Androgen Secretion by Rcho-1 Cells is Independent of Extracellular Glutamate Concentration. Placenta 25:548-552. J. C. Matthews. Expression and Function of Non-Organelle Glutamate Transporters To Support Peripheral Tissue Function. 2004. In: S. Gill and O. Pulido (Eds.) Glutamate Receptors in Peripheral Tissues: Excitatory Transmission Outside the Central Nervous System. Chapter 1, pp. 1-30. Kluwer Academc/Plenum Press, New York. G. L. Sipe, S. E. Kitts, K. R. McLeod, and J. C. Matthews. 2004. Chlortetracycline, but not Synovex-S, Differentially Affects Tissue Expression of High-Affinity Glutamate Transporters in Fattening Steers. Journal of Animal Science 82 (suppl. 1):42. S. E. Kitts, J. C. Matthews, G. L. Sipes, T. S. Rumsey, T. H. Elasser, R. L. Baldwin, and K. R. McLeod. 2004. Effects of Chlortetracycline (CTC) and Steroidal Implant on Growth and Plasma Growth Hormone (GH) and Thyroid-Stimulating Hormone (TSH) After Challenge with Thyroid-Releasing Hormone (TRH) and GH-Releasing Hormone (GHR) on Finishing Beef Steers. Journal of Animal Science 82 (suppl. 1):41. MASSACHUSETTS Blackburn, A.C., McLary, S.C., Naeem, R., Luszcz, J., Stockton, D.W., Donehower, L.A., Mohammed, M., Mailhes, J.B., Soferr, T., Naber, S.P., Otis, C.N., and Jerry, D.J. 2003. Loss of heterozygosity occurs via mitotic recombination in Trp53+/- mice and associates with mammary tumor susceptibility of the BALB/c strain. Cancer Res. 64:5140-5147. MICHIGAN Abdel-Azim, G.A., A.E. Freeman, M.E. Kehrli, Jr., S.C. Kelm, J.L. Burton, A.L. Kuck, and S. Schnell. 2005. Genetic basis and risk factors for infectious and noninfectious diseases in US Holsteins. I. Estimation of genetic parameters for single diseases and general health. J. Dairy Sci. 88 (in press, to appear in the March 2005 issue). Burton, J.L. 2003. Functional Genomics of the Stress-Immune Axis. International Agriculture Biotechnology Short Course. Michigan State University. May, July, and August, 2003. (three invited lectures). Burton, J.L. 2003. Animal Functional Genomics Research at Michigan State University: Connecting Animal Agriculture With Mainstream Biology. Department of Biology seminar series, Hope College, Michigan. Nov 21, 2003. Burton, J.L. 2004. Stress-Immune Interactions in Dairy Cattle: New Understanding From a Functional Genomics Perspective. In: Proceedings of the Prince Agri Products, Inc. 24th Annual Feed Ingredients Conference. Held at the West Des MoinesMarriot Hotel, Des Moines, IA, August 17-18, 2004 (CD available from Prince Agri, Inc.). Burton, J.L, P. Coussens, M. VandeHaar, M. Allen, G. Smith, and J. Ireland. 2004. From Genes to Dairy Farms. Michigan Dairy Review 9(1): 12-15 (see Jan 2004 issue of the MDR at http://www.msu.edu/user/mdr/). Burton, J.L., S.A. Madsen, L-C. Chang, P.S.D. Weber, G.J.M. Rosa, L.K. Matukumalli, and T.S. Sonstegard. 2005. Expression Profiles and SNP Analysis of Genes That Regulate Neutrophil Apoptosis, Endothelial Adhesion, and Extracellular Matrix Remodeling at Parturition in Dairy Cows. Proceedings of the Plant and Animal Genome conference, Jan 2005. San Diego, Ca. Confirmation String: jeanneburton_100404_1839 (poster P694). Burton, J.L., S.A. Madsen, L-C. Chang, P.S.D. Weber, K.R. Buckham, and L. Neuder. 2004. Gene Expression Changes During Glucocorticoid Challenge of Bovine Neutrophils and Implications for Immune Cell Function. Session on Genetic and Genomic Techniques in the Study and Management of Production Diseases. 12th International Conference on Production Diseases. Michigan State University. July, 2004 [invited abstract and oral presentation]. Burton, J.L., S.A. Madsen, L-C. Chang, P.S.D. Weber, K.R. Buckham, and P.M. Coussens. 2004. Parturition-Induced Changes in Neutrophil Gene Expression: Implications for Cell Function. FASS annual joint ADSA/ASAS/PSA Animal Health Program Symposium: Integrative aspects of immunity, nutrient metabolism, and production in livestock. St. Louis, MO. July, 2004 [abstract and invited oral presentation]. Burton, J.L, S.A. Madsen, L-C. Chang, P. S.D. Weber, K.R. Buckham, R. van Dorp, M-C. Hickey, and B. Earley. 2005. Gene Expression Signatures in Neutrophils Exposed to Glucocorticoids: a New Paradigm to Explain Neutrophil Dysfunction in Parturient Dairy Cows. Invited Review, Vet. Immunol. Immunopathol. (in press). Burton, J.L., S.A. Madsen, L.-C. Chang, K.R. Buckham, L.E. Neuder, and P.S.D. Weber. 2005. Microarray analysis of bovine neutrophils around parturition: implications for mammary gland and reproductive tract health. Invited paper in the Proceedings of the 12th International Conference on Production Diseases (ICPD) in Farm Animals. Held at the Kellogg Center, Michigan State University, East Lansing. MI, July 19-22, 2004 (in press). Chang, L-C, P.S.D. Weber, S.A. Madsen, T. Toeboell, and J.L. Burton. 2004. Fas gene expression is transcriptionally regulated by glucocorticoids in bovine blood neutrophils. Proceedings of the 85th Annual Meeting of the Conference of Research Workers in Animal Diseases. Chicago, IL. Nov. 14-16, 2004. (abstract 127 and oral presentation). Chang, L-C., R. van Dorp, P.S.D. Weber, K.R. Buckham, and J.L. Burton. 2004. Parturition-induced gene expression signatures in bovine peripheral blood mononuclear cells. Session on Genetic and Genomic Techniques in the Study and Management of Production Diseases. 12th International Conference on Production Diseases. Michigan State University. July, 2004 [abstract and oral presentation]. Chang, L.-C., S.A. Madsen, T. Toelboell, P.S.D. Weber, and J.L. Burton. 2004. Effects of glucocorticoids on Fas gene expression in bovine blood neutrophils. J. Endocrinol. 183:569-583. Coussens, P.M. 2004. A Model for Immune Responses to Mycobacterium paratuberculosis. Infect. Immunity (Minireviews), 72:3089-3096. Coussens, P.M. 2004. Development of gene expression signatures for chronic infectious diseases, a bovine model. International Conference on Immunogenomics, Budaphest Hungary October 11-14, 2004. Coussens, P.M. 2004. Use of Host Genomics to Elucidate Immune Effector Mechanisms. International Veterinary Immunology Symposium, Quebec City, Quebec. July 25-30, 2004. Coussens, P.M., C. B. Pudrith, X. Ren, S. P. Suchyta, J. R. Stabel, K. Skovgaard, and P.M.H. Heegaard. 2005. Johnes disease in cattle is associated with enhanced expression of genes encoding IL-5, GATA-3, tissue inhibitors of matrix metalloproteinases 1 and 2, and factors promoting apoptosis in peripheral blood mononuclear cells. Vet. Immunol. Immunopathol. (in press). Coussens, P.M., M.J. Coussens, B.R. Tooker, and W. Nobis. 2004. Structure of the bovine NRAMP1 gene and identification of novel polymorphisms. DNA Sequence. 15:15-25. Coussens, P.M., N. Verman, M.A. Coussens, M.D. Elftman, and A.M. McNulty. 2004. Cytokine Gene Expression in Peripheral Blood Mononuclear Cells and Tissues of Cattle Infected with Mycobacterium avium subspecies paratuberculosis: Evidence for an Inherent Pro-inflammatory Gene Expression Pattern. Infect. Immunity 72:1409-1422. Eicher, S., and J.L. Burton. 2005. Immune System: Stress Effects. Encyclopedia of Animal Science. Ed. W.C. Pond and A.W. Bell. Marcel Dekker Publisher, New York, NY (in press; see www.dekker.com). Evans, A.C.O., J.L.H. Ireland, M.E. Winn, P. Lonergan, G.W. Smith, P.M. Coussens, and J.J. Ireland. 2004. Identification of candidate estradiol target genes involved in apoptosis and selection of dominant follicles during follicular waves. Biol. Reprod. 70:1475-1484. Glass, E., and P.M. Coussens. 2005. Functional genomics of host  pathogen interactions in species of veterinary importance. Vet. Immunol. Immunopathol. (in press). Hill, E.W., G. M. OGorman, M. Agaba, J.P. Gibson, O. Hanotte, S.J. Kemp, J. Naessens, P.M. Coussens, and D.E. MacHugh. 2005. Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics. Vet. Immunol. Immunopathol. (in press). Kobayashi, Y., F. Jimenez-Krassel, Q Li, J.Yao, R. Huang, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2004. Evidence that Cocaine- and Amphetamine- Regulated Transcript is a Novel Intraovarian Regulator of Follicular Atresia. Endocrinol. 145:5373-5383. Madsen, S.A., L-C. Chang, and , J.L. Burton. 2004. Glucocorticoid modulation of Bcl-2 family members A1 and Bak in bovine blood neutrophils. Proceedings of the 85th Annual Meeting of the Conference of Research Workers in Animal Diseases. Chicago, IL. Nov. 14-16, 2004. (abstract 136 and oral presentation). Placed 1st in the American Association of Veterinary Immunologists graduate student oral competition. Madsen, S.A., L-C. Chang, M-C. Hickey, G.J. M. Rosa, P.M. Coussens, and J.L. Burton. 2004. Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiol. Genomics 16:212-221. Madsen, S.A. M-C. Hickey, and J.L. Burton. 2003. Glucocorticoids in parturient serum activate steroid receptors to modulate apoptosis in bovine blood neutrophils. Proc. 84th Annual Meeting of the Conference of Research Workers in Animal Diseases. Nov. 12-14, 2003. Chicago, IL (abstract 100 and oral presentation; 2nd place award in the American Association of Veterinary Immunologists graduate student oral competition; also see the AAVI On-line Newsletter at: http://www.cvm.missouri.edu/aavi/newsletter_3_04/newsletter_3_04.htm#StudentAwards. Ortiz-Colón, G., A.C. Grant, J.L. Burton, M.E. Doumit and D.D. Buskirk. 2004. Dexamethasone Downregulates Glucocorticoid Receptor Expression in Cultured Bovine Preadipocytes. FASS annual joint ADSA/ASAS/PSA meeting. St. Louis, MO. July, 2004 (abstract and oral presentation). Patel, O.V., S.P. Suchyta, S.S. Sipkovsky, J. Yao, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2005. Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression. Vet. Immunol. Immunopathol. (in press). Rhoads, R.P., J.D. Sampson, R.J. Tempelman, S.S. Sipkovsky, P.M. Coussens, M.C. Lucy, J.N. Spain, and D.E. Speiers. 2004. Hepatic gene expression profiling in lactating dairy cows during an initial period of hyperthermia. Presented at the Joint ADSA-ASAS Meetings, St. Louis, MO, July 24-28,2004. Saama, P.M., J. B. Jacob, M.E. Kehrli, Jr., A. E. Freeman, S.C. Kelm, A.L. Kuck, R. J. Tempelman, and J.L. Burton. 2004. Genetic Variation in Bovine Mononuclear Leukocyte Responses to Dexamethasone. J. Dairy Sci. 87:3928-3937. Steibel, J. P., Tempelman, R. J., Rosa, G. J. M. Power and sample size calculations for two color microarray experiments with biological and technical replication. J. Anim. Sci. 82 (Suppl. 1): 415, 2004. Steibel, J. P., Rosa, G. J. M., Tempelman, R. J. Thick-tailed and heteroskedastic linear models for the analysis of cDNA microarray data. Presented at the Joint Statistical Meetings 2004 Abstracts, Toronto - Canada, 2004. Suchyta, S.P., Sipkovsky S., Halgren, R.G., Kruska, R.,Elftman, M., Weber-Nielsen, M., Vandehaar, M.J., Xiao, L., Tempelman, R.J., and Coussens, P.M. 2003. Bovine Mammary Gene Expression Profiling Using A cDNA Microarray Enhanced For Mammary Specific Transcripts Physiological Genomics 16: 8-18. Tempelman, R.J. 2005. Assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models. Veterinary Immunology and Immunopathology (in press). Tempelman, R.J. 2004. Experimental Design for Gene Expression Microarrays. 2004. Presented at the Second Long OligoNucleotide Microarray Workshop, University of Arizona, Tuscon, May 14, 2004. http://ag.arizona.edu/microarray/workshopMay2004.html . Tempelman, R.J. 2004. Experimental Design for Gene Expression Microarrays. 2004. Presented at the Third Long OligoNucleotide Microarray Workshop, University of Arizona, Tuscon, December 16, 2004. http://ag.arizona.edu/microarray/workshopDec2004.html . Tempelman, R.J., L. D. Douglass, and B.A. Craig. 2004. Mixed Model Workshop. A 2-day workshop presented at the ASAS-ADSA Joint Meetings, St. Louis, MO July 27-28, 2004. Tempelman, R.J. and G.J.M. Rosa. 2004. Design and Analysis of Gene Expression Studies Using Microarrays (1-Day Continuing Education Course), Presented at the Joint Statistical Meetings, Toronto - Canada, 2004. Tooker, B.C., and P.M. Coussens. 2004. Phagocytosis of M. paratuberculosis fails to Activate Expression of NADH Dehydrogenase and Nucleolin-Related Protein in Bovine Macrophages. FEMS Immunol. Lett. 93:137-142. Weber, P.S.D., L.-C. Chang, T. Toelboell, and J.L. Burton. 2004. Mechanisms of glucocorticoid-induced L-selectin (CD62L) down-regulation in bovine blood neutrophils. Session on Genetic and Genomic Techniques in the Study and Management of Production Diseases. 12th International Conference on Production Diseases. Michigan State University. July, 2004 [abstract and oral presentation]. Weber, P.S.D., T. Toelboell, L-C. Chang, J. Durrett Tirrell, P.M. Saama, G.W. Smith, and J.L. Burton. 2004. Mechanisms of glucocorticoid-induced down regulation of neutrophil L-selectin: Evidence for effects at the gene expression level and primarily on blood neutrophils. J. Leuk. Biol. 75:815-827. Weber, P.S.D., T. Toeboell, L-C Chang, and J.L. Burton. 2003. Glucocorticoid-induced down-regulation of L-selectin (CD62L) gene expression in bovine blood neutrophils is mediated by the glucocorticoid receptor (GR). Proc. 84th Annual Meeting of the Conference of Research Workers in Animal Diseases. Nov. 12-14, 2000. Chicago, IL (abstract 99 and oral presentation). Yao, J., X. Ren, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2004. Generation of a Bovine Oocyte cDNA Library and Microarray: Resources for Identification of Genes Important for Follicular Development and Early Embryogenesis. Physiol. Genomics 19:84-92. Yao,J., X. Ren, J.J. Ireland, P.M. Coussens, and G.W. Smith. 2004. Generation of a bovine oocyte cDNA library: a valuable resource for identification of key oocyte-specific genes. Plant and Animal Genome Meeting San Diego, CA January 11-14, 2004. MINNESOTA Garbe, J. R. and Y. Da. (2004) Pedigraph 2.0, a software tool for the graphing and analysis of large complex pedigrees. Abstract book, p. 242, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Garbe, J. R. and Y. Da. (2004) A computerized approach to minimize inbreeding of breeding plans. Abstract book, p. 376, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Garbe, J. R. and Y. Da. (2004) Graphical visualization of two large complex populations using Pedigraph 2.0. Abstract book, p. 377, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Liu, W., C.W. and F. A. Ponce de León. 2004. Assignement of SRY, ANT3 and CSF2RA to the Bovine Y Chromosome by FISH and RH mapping. Animal Biotechnology, 15: 103-109. London, N.R. (2004) Statistical theory and methods for mapping gender-affected genes and quantitative trait loci. Ph.D. Thesis. Department of Animal Science and Program in Molecular Veterinary Bioscience, University of Minnesota. London, N. R. and Y. Da (2004) Statistical methods to detect imprinted QTL with gender specific recombination frequencies. Abstract book, p. 416, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. London, N. R. and Y. Da (2004) Linkage analysis and experimental design for mapping imprinted genes. Final Abstracts Guide, page 254. Plant and Animal Genome XI, San Diego, USA, January 11 15, 2003. Mao, Y. a and Y. Da. (2004) Statistical power for detecting epistasis QTL effects under the F-2 Design. Abstract book, p. 414, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. Mizoshita, K., N. Ihara, C.M. Carpio, G.L. Bennett, F.A. Ponce de León, C.W. Beattie and Y. Sugimoto. Chromosomal mapping of 65 microsatellites developed from microdissected BTA14 and BTA20 chromosome-specific genomic libraries. Animal Genetics 35:408-410. Xu, J. (2004) Statistical analysis for mapping linked quantitative trait loci. Ph.D. Thesis. Department of Animal Science, University of Minnesota. Xu, J., J.R. Garbe, N.R. London, Y. Mao and Y. Da. (2004) Evaluation of three statistical methods for QTL analysis. Abstract book, p. 243, ADSA-ASAS-PSA Joint Annual Meeting, St. Louis, July 25-29, 2004. MISSISIPPI None reported NORTH CAROLINA Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P. and Lewin, H.A. (2004) Detection of quantitative trait loci affecting conformation traits in Holstein cattle. Journal of Dairy Science. 87 (Suppl. 1): 414. Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P., Da, Y. VanRaden, P.M., Ron, M. Weller, J.I. and Lewin, H.A. (2004) Detection of quantitative trait loci affecting female fertility and milk production in ten Dairy Bull DNA Repository families. Journal of Dairy Science. 87: 468-475. Connor, E.E., Sonstegard, T.S., Ashwell, M.S., Bennett, G.L. and Williams, J.L. (2004) Chromosomal mapping of 12 gene-associated markers in cattle identified novel regions of conserved synteny between the human and bovine genomes. Plant and Animal Genome XII: P630. Connor, E.E., Sonstegard, T.S., Ashwell, M.S., Bennett, G.L. and Williams, J.L. (2004) An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions. Animal Genetics. 35: 265-269. Connor, E.E., Sonstegard, T.S., Keele, J.W., Bennett, G.L., Williams, J.L., Papworth, R., Van Tassell, C.P. and Ashwell, M.S. (2004) Physical and linkage mapping of mammary-derived expressed sequence tags in cattle. Genomics. 83: 148-152. Van Tassell, C.P., Sonstegard, T.S. and Ashwell, M.S. (2004) Mapping quantitative trait loci for dairy form in regions of chromosome 27 in two families of Holstein. Journal of Dairy Science. 87: 450-457. OHIO Pagan, M., M.E. Davis, D.A. Stick, R.C.M. Simmen, N.E. Raney, R.J. Tempelman, and C.W. Ernst. 2003. Evaluation of serum insulin-like growth factor binding proteins (IGFBP) in Angus cattle divergently selected for serum IGF-I concentration. Domestic Anim. Endocrin. 25:345-358. Yilmaz, A., M.E. Davis, and R.C.M. Simmen. 2004. Estimation of (co)variance components for reproductive traits in Angus beef cattle divergently selected for blood serum IGF-I concentration. J. Anim. Sci. 82:2285-2292. Zhao, Q., M.E. Davis, and H.C. Hines. 2004. Associations of polymorphisms in the Pit-1 gene with growth and carcass traits in Angus beef cattle. J. Anim. Sci. 82:2229-2233. TEXAS Bryan, T.M., Abbey, C.A., Raudsepp, T., Chowdhary, B.P., Gill, C.A., Ing, N.H., Blanchard, T. and Welsh, T.H., Jr (2004) Chromosome assignment of an equine glucorticoid receptor gene (GR) using fluorescence in situ hybridization (FISH) and radiation hybrid (RH) mapping. Anim. Genet. (accepted). Dikeman, M.E., Pollak, E.J., Zhang, Z., Moser, D.W., Gill, C.A. and Dressler, E.A. (2004) Phenotypic ranges and relationships among carcass and meat palatability traits for fourteen cattle breeds, and heritabilities and expected progeny differences for Warner-Bratzler shear force in three beef cattle breeds. J. Anim. Sci. (submitted). Fluharty, F.L., Gill, C.A., Raudsepp, T., Chowdhary, B.P. and Jackwood, D.L. (2004) Identification of a sequence characterized, amplified DNA marker associated with the potential for marbling in steers. Anim. Genet. (submitted). Gill, C.A., Herring, A.D., Lunt, D.K., and Sanders, J.O. (2004) An overview of the McGregor Genomics Project: Mapping genes for production efficiency. Proceedings of the 50th annual Beef Cattle Short Course, August 2-4, College Station, TX. pp. H1-H8. Herring, A. D. and Gill, C.A. (2004) Genetic Markers and Marker Assisted Selection in Beef Cattle. Proceedings of Ovagenix Customer Information Field Day, July 31, College Station, TX. Amen, T.S., Herring, A.D., Gill, C.A. and Sanders, J.O. (2004) Investigation of birth weight and gestation length in Bos indicus-Bos taurus reciprocal cross calves produced through embryo transfer. 2004 Beef Cattle Research in Texas, pp. 1-3. Moser, D.W., Thallman, R.M., Pollak, E.J., Dikeman, M.E., Gill, C.A., Koontz, S.R., Holm, T.R. and Dressler, E.W. (2004) Meeting consumer demands through genetic selection: the NCBA Carcass Merit Project. Proceedings of the 36th annual meeting of the Beef Improvement Federation, Sioux Falls, SD. pp. 42-44. Rakowitz, K.R., Abbey, C.A., Schein, J., Adelson, D.L. and Gill, C.A. (2004) A 3Mb BAC contig and STS content map of the POLL critical interval on bovine chromosome one. (Abstract) Proceedings of the 29th International Conference on Animal Genetics, Tokyo, Japan, Sept. 11-16. Amen, T.S., Herring, A.D., Gill, C.A. and Sanders, J.O. (2004) Investigation of gestation length in Bos indicus-Bos taurus reciprocal backcross calves produced through embryo transfer. J. Anim. Sci. 82 (Suppl. 1): 449 (Abstract #882). Amen, T.S., Herring, A.D., Gill, C.A. and Sanders, J.O. (2004) Investigation of birth weight in Bos indicus-Bos taurus reciprocal backcross calves produced through embryo transfer. J. Anim. Sci. 82 (Suppl. 1): 449 (Abstract #882). Chiu, R., Bosdet, I., Mathewson, C., Wye, N., Lee, D., Barber, S., Yang, G., Stott, J., Abbey, C., Motta de Carmo Costa, M., Gill, C., Hansen, C., Keele, J., Larkin, D., Meng, Y., Osoegawa, K., Schibler, L., Siddiqui, A., Snelling, W., Williams, J.L., Adelson, D., Archibald, A., Benkel, B., Caetano, A.R., Eggen, A., Holt, R., Jones, S., de Jong, P.J., Lewin, H., McEwan, J.C., Moore, S., Tellam, R., Zhao, S., Kappes, S., Marra, M. and Schein, J. (2004) A BAC physical map of the bovine genome. (Abstract) Proceedings of Plant and Animal Genome XII, San Diego, California, USA. USDA-ARS-BARC Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P., Da, Y., VanRaden, P.M., Ron, M., Weller, J.I., Lewin, H.A. Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle. J. Dairy Sci. 2004. v. 87. pp. 468-475. Connor, E.E., Sonstegard, T.S. Ashwell, M.S., Bennett, G.L., Williams, J.L. An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions. Anim. Genet. 2004. v. 35. pp. 265-269. Van Tassell, C.P., Sonstegard, T.S., Ashwell, M.S. Mapping quantitative trait loci affecting dairy conformation to chromosome 27 in two Holstein grandsire families. J. Dairy Sci. 2004. v. 87. pp. 450-457. USDA-ARS-NADC Neill, J.D. and J.F. Ridpath. 2004. Remodeling of cellular functions following infection with bovine viral diarrhea virus type 2 as indicated using Serial Analysis of Gene Expression. American Society for Virology. Montreal , Quebec, Canada Neill, J.D. 2004. Functional genomics analysis of bovine viral diarrhea virus-infected cells: unraveling an enigma. International Conference on Production Diseases in Farm Animals, East Lansing, Michigan. Neill, J.D., 2004. Functional genomics analysis of infection by bovine viral diarrhea virus type 2 in a bovine B-cell lymphosarcoma cell line. Conference of Research Workers in Animal Disease, Chicago, Illinois. VERMONT Wellnitz, O. and D.E. Kerr. 2004. Cryopreserved bovine mammary cells to model epithelial response to infection. Veterinary Immunology and Immunopathology 101:191-202. Zhao, F.-Q., Zheng, Y.-C., Wall, E.H., and McFadden, T.B. 2005. Cloning and expression of bovine sodium/glucose cotransporters. J. Dairy Sci. 88, 182-194. Zhao , F.-Q., Miller, P. J., Wall, E. H., Zheng, Y.-C., Dong, B. Neville, M. C., and McFadden, T. B. 2004. Bovine glucose transporter GLUT8: cloning, expression, and developmental regulation in mammary gland. Biochim. Biophys. Acta, 1680, 103-113. Kerr, D.E. and O. Wellnitz. 2004. Cryopreserved bovine mammary cells to model epithelial response to infection. 7th International Veterinary Immunology Symposium. Quebec City, Canada. Wellnitz, O. and D.E. Kerr. 2004. Mammary epithelial cell response to infection with differentbacteria. 55th Annual Meeting of the European Association for Animal Production. Bled, Slovenia. Zheng, J., J.L. Ather, and D.E. Kerr. 2004. Functional characterization of the bovine lactoferrin gene promoter. 7th International Veterinary Immunology Symposium. Quebec City, Canada. WISCONSIN Khatib H. (2004) Imprinting of Nesp55 gene in cattle. Mamm Genome 15:663-667. Khatib H. (2005). Monoallelic expression of the protease inhibitor gene in humans, sheep, and cattle. Mamm Genome 16:1-9 (in press). Khatib H., Heifetz E., and Dekkers J. (2004). Association of the Protease Inhibitor Gene with Economic Traits in Holstein Dairy Cattle. J Dairy Sci. (in press).