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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic and Biological Determinants Of Respiratory Diseases Of Ruminants

Location: Genetics, Breeding, and Animal Health Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Evaluation of bovine coronavirus antibody levels, virus shedding, and respiratory disease incidence throughout the beef cattle production cycle - (Peer Reviewed Journal)

Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes - (Peer Reviewed Journal)
Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Kalbfleisch, T.S., Schuller, G., Dickey, A.M., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Brichta-Harhay, D.M., Bono, J.L., Smith, T.P.L. 2016. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. BMC Genomics. 17:982. doi: 10.1186/s12864-016-3316-8.

Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi - (Peer Reviewed Journal)
Anton, B.P., Harhay, G.P., Smith, T.P.L., Blom, J., Roberts, R.J. 2016. Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi. PLoS One. 11(8): e0161499.

Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension - (Peer Reviewed Journal)
Heaton, M.P., Smith, T.P.L., Carnahan, J.K., Basnayake, V., Qiu, J., Simpson, B., Kalbfleisch, T.S. 2016. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension. F1000Research. 5:2003. doi:10.12688/f1000research.9254.2.

Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases - (Peer Reviewed Journal)
DeDonder, K.D., Harhay, D.M., Apley, M.D., Lubbers, B.V., Clawson, M.L., Schuller, G., Harhay, G.P., White, B.J., Larson, R.L., Capik, S.F., Riviere, J.E., Kalbfleisch, T., Tessman, R.K. 2016. Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases. Veterinary Microbiology. 192:186-193.

Haptoglobin concentrations from shipping through sickness and recovery in cattle either mass-medicated with gamithromycin or sham-treated - (Abstract Only)

Complete genome sequence of highly virulent Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) variants that recently emerged in the United States - (Peer Reviewed Journal)
Workman, A.M., Smith, T.P., Osorio, F.A., Vu, H.L. 2016. Complete genome sequence of highly virulent porcine reproductive and respiratory syndrome virus variants that recently emerged in the United States. Genome Announcements. 4(4):e00772-16.

Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension - (Abstract Only)
Heaton, M.P., Smith, T.P.L., Carnahan, J.K., Basnayake, V., Qiu, J., Simpson, B., Kalbfleisch, T.S. 2016. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension [abstract]. 35th International Society for Animal Genetics (ISAG), July 23-27, 2016, Salt Lake City, UT. Poster #P6026.

Bovine coronavirus antibody titers at weaning negatively correlate with incidence of bovine respiratory disease in the feed yard - (Abstract Only)
Workman, A.M., McDaneld, T.G., Kuehn, L.A., Chitko-McKown, C.G., Loy, J.D. 2016. Bovine coronavirus antibody titers at weaning negatively correlate with incidence of bovine respiratory disease in the feed yard [abstract]. American Society for Virology 35th Annual Meeting, June 18-22, 2016, Blackburg, VA. Poster No. P9-9.

The differentiation and protective function of cytolytic CD4 T cells in influenza infection - (Review Article)
Brown, D., Lampe, A.T., Workman, A.M. 2016. The differentiation and protective function of cytolytic CD4 T cells in influenza infection. Frontiers in Immunology. 7:93. doi:10.3389/fimmu.2016.00093

Resolving bovine viral diarrhea virus subtypes from persistently infected US beef calves with complete genome sequence - (Peer Reviewed Journal)
Workman, A.M., Heaton, M.P., Harhay, G.P., Smith, T.P.L., Grotelueschen, D.M., Sjeklocha, D.B., Brodersen, B.W., Petersen, J.L., Chitko-McKown, C.G. 2016. Resolving bovine viral diarrhea virus subtypes from persistently infected U.S. beef calves with complete genome sequence. Journal of Veterinary Diagnostic Investigation. 28(5):519-528.

Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing - (Abstract Only)
De Silva, K., Heaton, M.P., Kalbfleisch, T.S. 2016. Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing. UT-KBRIN Bioinformatics Summit 2016, April 8-10, 2016, Lake Barkley State Resort Park, Cadiz, KY. Poster #16.

Whole genome sequences of the USMARC sheep diversity panel v 2.4 aligned to the ovine reference genome assembly - (Other)
Heaton, M.P., Smith, T.P., Kalbfleisch, T.S. 2016. Whole genome sequences of the USMARC sheep diversity panel v 2.4 aligned to the ovine reference genome assembly. Internet Web Page. www.ars.usda.gov/Services/Docs.htm?docid=25585 and www.ars.usda.gov/Research/docs.htm?docid=25589.

Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle Reprint Icon - (Peer Reviewed Journal)
Dickey, A.M., Loy, J.D., Bono, J.L., Smith, T.P.L., Apley, M.D., Lubbers, B.V., DeDonder, K.D., Capik, S.F., Larson, R.L., White, B.J., Blom, J., Chitko-McKown, C.G., Clawson, M.L. 2016. Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary Research. 47:31.

ß-catenin, a transcription factor activated by canonical Wnt signaling, is expressed in sensory neurons of calves latently infected with bovine herpesvirus 1 - (Peer Reviewed Journal)
Liu, Y., Hancock, M., Workman, A.M., Doster, A., Jones, C. 2016. ß-catenin, a transcription factor activated by canonical Wnt signaling, is expressed in sensory neurons of calves latently infected with bovine herpesvirus 1. Journal of Virology. 90(6):3148-3159.

A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle - (Abstract Only)
Heaton, M.P., Kalbfleisch, T.S., Carnahan, J.K., Smith, T.P.L., Harhay, G.P., Simpson, B., Qiu, J. 2015. A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle [abstract]. International Plant and Animal Genome XXIV Conference Proceedings, January 9-13, 2016, San Diego, CA. Poster #P0506.

Whole genome sequences of the USMARC beef cattle diversity panel v2.9 aligned to the bovine reference genome assembly - (Other)
Heaton, M.P., Smith, T.P., Kalbfleisch, T.S. 2015. Whole genome sequences of the USMARC beef cattle diversity panel v2.9 aligned to the bovine reference genome assembly. Internet Web Page. www.ars.usda.gov/Services/Docs.htm?docid=25585 and www.ars.usda.gov/Research/docs.htm?docid=25586.

Full-length coding sequence for 12 bovine viral diarrhea virus isolates from persistently infected cattle in a feedyard in Kansas - (Peer Reviewed Journal)
Workman, A.M., Harhay, G.P., Heaton, M.P., Grotelueschen, D.M., Sjeklocha, D.B., Smith, T.P.L. 2015. Full-length coding sequence for 12 bovine viral diarrhea virus isolates from persistently infected cattle in a feedyard in Kansas. Genome Announcements. 3(3):e00487-15. doi:10.1128/genomeA.00487-15.

Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild type parent strain - (Peer Reviewed Journal)
Heaton, M.P., Harhay, G.P., Smith, T.P.L., Bono, J.L., Chitko-McKown, C.G. 2015. Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild-type parent strain. Genome Announcements. 3(3):e00417-15. DOI: 10.1128/genomeA.00417-15.

Identification of a mannheimia haemolytica genetic subtype that causes bovine respiratory disease - (Abstract Only)
Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S., Larson, R., Lubbers, B.V., Kalbfleisch, T.S., Schuller, G., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Workman, A.M., Harhay, D.M., Bono, J.L., Smith, T.P.L. [abstract]. 2015. Identification of a mannheimia haemolytica genetic subtype that causes bovine respiratory disease. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #1410.

Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance - (Abstract Only)
Harhay, G.P., Anton, B.P., Smith, T.P.L. [abstract]. 2015. Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #3468.

A novel antimicrobial agent differentially impacts the immunological response of stimulated bovine monocytes - (Abstract Only)
Dawes, M.E., Aguilar, J.S., Chitko-Mckown, C.G. 2015. A novel antimicrobial agent differentially impacts the immunological response of stimulated bovine monocytes [abstract]. Immunology 2015, The American Association of Immunologists Annual Meeting, May 8-12, 2015, New Orleans, LA. Poster #193.12.

Design of a DNA panel for genomic studies in Russian cattle breeds - (Peer Reviewed Journal)
Yudin, N.S., Vasil'Eva, L.A., Belyavskaya, V.A., Aitnazarov, R.B., Smirnov, P.N., Heaton, M.P., Laegreid, W.W., Orlowa, G.V., Romashenko, A.G., Voevoda, M.I. 2015. Design of a DNA panel for genomic studies in Russian cattle breeds. Russian Journal of Genetics: Applied Research. 5(1):21-25.

Genetic subgroup of small ruminant lentiviruses that infects sheep homozygous for TMEM154 frameshift deletion mutation A4delta53 - (Peer Reviewed Journal)
Clawson, M.L., Redden, R., Schuller, G., Heaton, M.P., Workman, A.M., Chitko-McKown, C.G., Smith, T.P.L., Leymaster, K.A. 2015. Genetic subgroup of small ruminant lentiviruses that infects sheep homozygous for TMEM154 frameshift deletion mutation A4delta53. Veterinary Research. 46:22.

Cytokine profiles from shipping through sickness and recovery in cattle either mass-medicated with gamithromycin or sham-treated - (Abstract Only)
Chitko-McKown, C.G., DeDonder, K.D., Bennett, G.L., Apley, M.D., Harhay, G.P., Kuehn, L.A., White, B.J., Larson, R.L., Capik, S.F., Lubbers, B.V., Workman, A.M. 2014. Cytokine profiles from shipping through sickness and recovery in cattle either mass-medicated with gamithromycin or sham-treated [abstract]. Conference on Research Workers in Animal Disease, December 7-9, 2014, Chicago, Illinois. Paper No. 148.

Pathogen variation across time and space: sequencing to characterize Mannheimia haemolytica diversity - (Proceedings)

Association of TMEM154 missense mutations with lentiviral infection and virus subtypes in sheep - (Proceedings)
Heaton, M.P., Leymaster, K.A., Clawson, M.L. 2014. Association of TMEM154 missense mutations with lentiviral infection and virus subtypes in sheep. In: Proceedings of the 10th World Congress of Genetics Applied to Livestock Production, August 17-22, 2014, Vancouver, BC, Canada. Available. Paper No. 352. https://asas.org/wcgalp-proceedings

SNPs for parentage testing and traceability in globally diverse breeds of sheep - (Peer Reviewed Journal)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One. 9(4):e94851. DOI: 10.1371/JOURNAL.PONE.0094851.

Sequencing a North American yak genome - (Other)
Heaton, M.P. 2014. Sequencing a North American yak genome. International Yak Association. Online available. IYAK.org. http://0101.nccdn.net/1_5/11e/372/14c/HeatonIYAK2014_ARSapproved.pdf.

Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever - (Peer Reviewed Journal)
Harhay, G.P., Murray, R.W., Lubbers, B., Griffin, D., Koren, S., Phillippy, A.M., Harhay, D.M., Bono, J.L., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P. 2014. Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever. Genome Announcements. 2(1):e00088-14.

Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever - (Peer Reviewed Journal)
Harhay, G.P., McVey, D.S., Koren, S., Phillippy, A.M., Bono, J.L., Harhay, D.M., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Korlach, J., Smith, T.P. 2014. Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever. Genome Announcements. 2(1):e00084-14.

SNPs for parentage testing and traceability in globally diverse breeds of sheep - (Abstract Only)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep [Abstract]. Proceedings Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster P614.

Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes - (Peer Reviewed Journal)
Kalbfleisch, T.S., Heaton, M.P. 2014. Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes. F1000 Research 2:244. doi: 10.12688/f1000research.2-244.v2.

Reducing assembly complexity of microbial genomes with single-molecule sequencing - (Peer Reviewed Journal)
Koren, S., Harhay, G.P., Smith, T.P.L., Bono, J.L., Harhay, D.M., McVey, D.S., Radune, D., Bergman, N.H., Phillippy, A.M. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14:R101. DOI: 10.1186/GB-2013-14-9-R101.

Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes - (Peer Reviewed Journal)
Sider, L.H., Heaton, M.P., Chitko-Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A., Laegreid, W.W., and Clawson, M.L. 2013. Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes. Veterinary Research. 44:64. DOI: 10.1186/1297-9716-44-64.

The methylome and virulence of bovine respiratory disease bacterial pathogens - (Other)
Harhay, G.P. 2013. The methylome and virulence of bovine respiratory disease bacterial pathogens. American Society for Microbiology. Presentation in WS-24, Studying Whole-Genome Microbial Epigenetics.

Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle - (Peer Reviewed Journal)
Harhay, G.P., Koren, S., Phillippy, A.M., McVey, D.S., Kuszak, J., Clawson, M.L., Harhay, D.M., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P.L. 2013. Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle. Genome Announcements. 1(3):e00188-13. DOI: 10.1128/GENOMEA.00188-13.

Characterization of ovine Nectin-4, a novel peste des petits ruminants virus (PPRV) receptor - (Peer Reviewed Journal)
Birch, J., Juleff, N., Heaton, M.P., Kalbfleisch, T., Kijas, J., Bailey, D. 2013. Characterization of ovine Nectin-4, a novel peste des petits ruminants virus (PPRV) receptor. Journal of Virology. 87(8):4756-4761.

Rhodotorula minuta fungemia in a ewe lamb - (Peer Reviewed Journal)
Chitko-McKown, C.G., Leymaster, K.A., Heaton, M.P., Griffin, D.D., Veatch, J.K., Jones, S., Clawson, M.L. 2013. Rhodotorula minuta fungemia in a ewe lamb. Transboundary and Emerging Diseases. doi:10.1111/tbed.12062. [Epub ahead of print].

Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep - (Peer Reviewed Journal)
Heaton, M.P., Kalbfleisch, T.S., Petrik, D.T., Simpson, B., Kijas, J.W., Clawson, M.L., Chitko MckKown, C.G., Harhay, G.P., Leymaster, K.A. 2013. Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep. PLoS One. 8(2):e55490. doi:10.1371/journal.pone.0055490.

Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle - (Abstract Only)
Harhay, G.P., McVey, D.S., Korlach, J., Roberts, R., Chitko-McKown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L., Anton, B.P. 2013. Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 99.

Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep - (Abstract Only)
Heaton, M.P., Kalbfleisch, T., Petrik, D.T., Simpson, B., Kijas, J., Clawson, M.L., Chitko-McKown, C.G., Leymaster, K.A., Harhay, G.P. 2013. Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep [abstract]. International Plant & Animal Genome XXI Conference. No. P0625.

The kinetics of white blood cell counts during vaccination against bovine respiratory disease pathogens and their correlations with lung lesions, diagnosis and average daily gain - (Abstract Only)

Porcine macrophage Cdelta2+ and Cdelta2- cell lines support influenza virus infection and replication and Cdelta2+ cells mount innate immune responses to influenza virus infection - (Abstract Only)
Joseph, J., Zhu, L., Chitko Mckown, C.G., Li, F., Kaushik, R. 2012. Porcine macrophage Cdelta2+ and Cdelta2- cell lines support influenza virus infection and replication and Cdelta2+ cells mount innate immune responses to influenza virus infection [abstract]. In: Proceedings Research Workers in Animal Diseases Conference, December 2-4, 2012, Chicago, Illinois. Poster 70P.

Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species - (Peer Reviewed Journal)
Miller, J.M., Kijas, J.W., Heaton, M.P., McEwan, J.C., Coltman, D.W. 2012. Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species. Molecular Ecology Resources. 12(6):1145-1150. doi:10.1111/1755-0998.12017.

Identification and evolution of Shiga Toxin-producing Escherichia coli O157 genetic subtypes - (Abstract Only)
Clawson, M.L. 2012. Identification and evolution of Shiga Toxin-producing Escherichia coli O157 genetic subtypes. International Dairy Federation, World Dairy Summit. C0402, http://wds2012.com/ScientificProgramme/Abstracts/WDS2012_0216.pdf.

Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes - (Abstract Only)
Sider, L.H., Clawson, M.L., Heaton, M.P., Chitko Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A. 2012. Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes. The 58th Genomic Congress, September 11-14, 2012. Foz de Iguacu, Brazil. Poster No. GM001.

Reduced OPP susceptibility in naturally exposed lambs with homozygous TMEM154 K35 genotypes - (Abstract Only)
Chitko Mckown, C.G., Leymaster, K.A., Heaton, M.P., Clawson, M.L., Harhay, G.P. 2012. Reduced OPP susceptibility in naturally exposed lambs with homozygous TMEM154 K35 genotypes [abstract]. Immunology 2012. The 99th Annual Meeting of the American Association for Immunology, May 4-8, 2012, Boston, Massachusetts. Page 275. Abstract No. 170.3. Poster No. P1246.

Development of a SNP panel for parentage assignment in sheep - (Abstract Only)
Kijas, J.W., Mcewan, J., Clarke, S.M., Maddox, J.F., Mcculloch, R., Driver, F., Ilic, K., Heaton, M.P. 2012. Development of a SNP panel for parentage assignment in sheep [abstract]. Plant & Animal Genome XX Conference, January 14-18, 2012, San Diego, California. Poster #P0577.

Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle - (Abstract Only)
Harhay, G.P., Mcvey, D.S., Kitzmiller, A., Clamp, M., Osborne, B., Dwan, C., Zhang, J., Sisneros, N., Wang, S., Peluso, P., Bono, J.L., Chitko Mckown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L. [abstract]. 2012. Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle. Advances in Genome Biology and Technology, February 15-18, 2012, Marco Island, Florida. Poster No. 129.

Enabling next-gen sequencing and analysis at the USDA-ARS U.S. Meat Animal Research Center with MiniLIMS - (Abstract Only)

Last Modified: 2/23/2016
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