@book{merrill_2020, edition={3rd}, title={Agricultural Genetics}, ISBN={9781792425356}, publisher={Kendall-Hunt Publishing Company}, author={Merrill, M.S.}, year={2020} }
 @article{eisemann_ashwell_devine_poole_poore_linder_2020, title={Physiological response, function of sweat glands, and hair follicle cycling in cattle in response to fescue toxicosis and hair genotype}, volume={98}, ISSN={0021-8812 1525-3163}, url={http://dx.doi.org/10.1093/jas/skaa013}, DOI={10.1093/jas/skaa013}, abstractNote={AbstractFescue toxicosis is a syndrome that results when cattle consume toxic endophyte-infected tall fescue. The objective of this study was to compare the response in physiological variables, sweat gland function, hair follicle cycling, and gene expression to feeding a total mixed ration that included tall fescue haylage and tall fescue seed containing a toxic endophyte (EI) or tall fescue haylage containing a nontoxic novel endophyte (EN) in beef heifers (Angus × Senepol heifers, n = 31) with 2 different hair genotypes. Numbers in each subgroup were as follows: novel endophyte, heterozygous slick (EN-S; n = 8), novel endophyte, homozygous hairy (wild type, EN-W; n = 7), endophyte-infected, heterozygous slick (EI-S; n = 10), and endophyte-infected, homozygous hairy (wild type, EI-W; n = 6). Physiological measurements were taken weekly for 7 wk. Data were analyzed using the MIXED procedure of SAS including dietary fescue treatment (EN vs. EI) and hair genotype (S vs. W) as main effects, day as a repeated measure, and temperature–humidity index (THI) as a covariate. Skin biopsies were taken before treatment initiation and on day 37 of treatment. Average surface temperature (ST) increased as the THI increased (P < 0.0001). Average ST was greater (P < 0.01) for animals fed EI than for animals fed the EN fescue diet, and greater (P < 0.01) for animals with the W genotype compared with animals with the S genotype. The difference between heifers with the S and W genotype was greater at greater THI (genotype × day interaction, P < 0.01). Transepidermal water loss (TEWL) was greater (P < 0.05) for animals with the S genotype compared with the W genotype and greater (P < 0.05) for heifers with the S genotype than for heifers with the W genotype when fed EI (36.7, 38.5, 30.0, and 38.7 g/m2 per hour for EN-W, EN-S, EI-W, and EI-S, respectively). The fraction of follicles in telogen in plucked hair samples for heifers fed EI was greater for animals with the S genotype than the W genotype (fraction in telogen: 0.456, 0.565, 0.297, 0.702 for EN-W, EN-S, EI-W, and EI-S, respectively; diet × genotype interaction, P < 0.05). Fraction of follicles in anagen was the opposite. EI fescue resulted in increased ST, changes in hair follicle cycling that support greater hair growth, and decreased TEWL for heifers with the W genotype compared with S genotype, suggesting greater heat stress in response to EI.}, number={3}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Eisemann, J.H. and Ashwell, M.S. and Devine, T.L. and Poole, D.H. and Poore, M.H. and Linder, K.}, year={2020}, month={Mar} }
 @article{carvalho_sanglard_nascimento_moriel_sommer_merrill_poore_duarte_serao_2020, title={miRNAs explain the variation in muscle and blood transcriptomes of beef calves born from dams with or without energy restriction during late gestation}, volume={98}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skaa054.292}, abstractNote={Abstract
               Maternal energy restriction during late gestation affects the expression of genes related to energy metabolism in muscle and immune response in blood. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. The aim of this study was to identify potentials miRNA involved in the expression of differentially expressed genes (DEG) in muscle and blood following exposure to maternal gestational energy restriction. Forty days before the expected calving date, cows were assigned to one of two diets: 100% (CTRL) or 70% (REST) of the daily energy requirement. For RNA-seq analysis, muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. miRNAs were identified from the RNA-seq data based on the bovine genome annotation, with 38 and 10 miRNAs identified in blood and muscle, respectively. The expression of the miRNAs and the previously identified 160 and 450 DEGs in muscle and blood, respectively, was pre-adjusted for fixed effects before final analyses. A stepwise selection (P-value < 0.05) was used to identify miRNAs (dependent variables) explaining variation in DEGs, for each DEG at a time, and analyses performed separately for blood and muscle. The R2 of selected models ranged from 0.88 to 0.99 in muscle and 0.92 to 0.99 in blood. Of the most selected miRNA in muscle, MiR-133a and MiR-1 are known to be related to muscle hypertrophy, and MiR-143 and bta-let-7i promote adipocyte differentiation. Of the most selected miRNA in blood, MiR-21 regulates immune system by different pathways. Using RNA-seq data, we identified miRNAs explaining a large amount of the variation of DEGs, with the identification of important miRNAs related to muscle development and immune system.}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Carvalho, Elisa B. and Sanglard, Leticia P. and Nascimento, Moyses and Moriel, Philipe and Sommer, Jeffrey and Merrill, Melissa and Poore, Matthew and Duarte, Marcio and Serao, Nick}, year={2020}, month={Nov}, pages={165–165} }
 @article{mcculloch_mente_o’nan_ashwell_2018, title={Articular cartilage gene expression patterns in the tissue surrounding the impact site following applications of shear and axial loads}, volume={19}, ISSN={1471-2474}, url={http://dx.doi.org/10.1186/s12891-018-2374-2}, DOI={10.1186/s12891-018-2374-2}, abstractNote={Osteoarthritis is a degradative joint disease found in humans and commercial swine which can develop from a number of factors, including prior joint trauma. An impact injury model was developed to deliver in vitro loads to disease-free porcine patellae in a model of OA. Axial impactions (2000 N normal) and shear impactions (500 N normal with induced shear forces) were delivered to 48 randomly assigned patellae. The patellae were then cultured for 0, 3, 7, or 14 days following the impact. Specimens in the tissue surrounding the loading site were harvested and expression of 18 OA related genes was studied via quantitative PCR. The selected genes were previously identified from published work and fell into four categories: cartilage matrix, degradative enzymes, inflammatory response, and apoptosis. Type II collagen (Col2a1) showed significantly lower expression in shear vs. axial adjacent tissue at day 0 and 7 (fold changes of 0.40 & 0.19, respectively). In addition, higher expression of degradative enzymes and Fas, an apoptosis gene, was observed in the shear specimens. The results suggest that a more physiologically valid shear load may induce more damage to surrounding articular cartilage than a normal load alone.}, number={1}, journal={BMC Musculoskeletal Disorders}, publisher={Springer Nature}, author={McCulloch, R. S. and Mente, P. L. and O’Nan, A. T. and Ashwell, M. S.}, year={2018}, month={Dec} }
 @article{ashwell_freire_o’nan_benito_hash_mcculloch_lascelles_2019, title={Characterization of gene expression in naturally occurring feline degenerative joint disease-associated pain}, volume={243}, ISSN={1090-0233}, url={http://dx.doi.org/10.1016/j.tvjl.2018.11.008}, DOI={10.1016/j.tvjl.2018.11.008}, abstractNote={Degenerative joint disease (DJD) associated-pain is a clinically relevant and common condition affecting domesticated cats and other species including humans. Identification of the neurobiological signature of pain is well developed in rodent pain models, however such information is lacking from animals or humans with naturally occurring painful conditions. In this study, identification of housekeeping genes (HKG) for neuronal tissue and expression levels of genes considered associated with chronic pain in rodent models were explored in cats with naturally occurring osteoarthritic pain. Fourteen adult cats were evaluated — seven without clinical signs of osteoarthritic pain, and seven with hind limb radiographic DJD and pain. Expression of an investigator-selected set of pain signaling genes (including ASIC3, ATF3, COX2, CX3CL1, NAV1.7, NAV1.8, NAV1.9, NGF, NK1R, TNFα, TRKA) in lumbar spinal cord dorsal horn and lumbar dorsal root ganglia tissues from clinically healthy cats and cats with DJD were studied using quantitative RT-PCR (qPCR). HKG identified as the most stable across all tissue samples were many of the ribosomal protein genes, such as RPL30 and RPS19. qPCR results showed ATF3 and CX3CL1 up-regulated in DJD-affected dorsal root ganglia compared to clinically healthy controls. In spinal cord, CX3CL1 was up-regulated and NGF was down-regulated when DJD-affected samples were compared to healthy samples. Further work is needed to understand the neurobiology of pain in naturally occurring disease and what rodent models are predictive of these changes in more heterogeneous populations such as domestic cats.}, journal={The Veterinary Journal}, publisher={Elsevier BV}, author={Ashwell, M. and Freire, M. and O’Nan, A.T. and Benito, J. and Hash, J. and McCulloch, R.S. and Lascelles, B.D.X.}, year={2019}, month={Jan}, pages={42–47} }
 @inproceedings{sanglard_nascimento_moriel_sommer_ashwell_duarte_serão_2018, title={Effect of energy restriction during late gestation in the skeletal muscle and blood transcriptome of Angus calves after preconditioning}, volume={11}, url={http://www.wcgalp.org/system/files/proceedings/2018/effect-energy-restriction-during-late-gestation-skeletal-muscle-and-blood-transcriptome-angus-calves.pdf}, number={646}, booktitle={Proceedings of the World Congress on Genetics Applied to Livestock Production}, author={Sanglard, LP and Nascimento, M and Moriel, P and Sommer, J and Ashwell, M and Duarte, MS and Serão, NVL}, year={2018} }
 @article{howard_ashwell_baynes_brooks_yeatts_maltecca_2018, title={Genetic Parameter Estimates for Metabolizing Two Common Pharmaceuticals in Swine}, volume={9}, ISSN={1664-8021}, url={http://dx.doi.org/10.3389/fgene.2018.00040}, DOI={10.3389/fgene.2018.00040}, abstractNote={In livestock, the regulation of drugs used to treat livestock has received increased attention and it is currently unknown how much of the phenotypic variation in drug metabolism is due to the genetics of an animal. Therefore, the objective of the study was to determine the amount of phenotypic variation in fenbendazole and flunixin meglumine drug metabolism due to genetics. The population consisted of crossbred female and castrated male nursery pigs (n = 198) that were sired by boars represented by four breeds. The animals were spread across nine batches. Drugs were administered intravenously and blood collected a minimum of 10 times over a 48 h period. Genetic parameters for the parent drug and metabolite concentration within each drug were estimated based on pharmacokinetics (PK) parameters or concentrations across time utilizing a random regression model. The PK parameters were estimated using a non-compartmental analysis. The PK model included fixed effects of sex and breed of sire along with random sire and batch effects. The random regression model utilized Legendre polynomials and included a fixed population concentration curve, sex, and breed of sire effects along with a random sire deviation from the population curve and batch effect. The sire effect included the intercept for all models except for the fenbendazole metabolite (i.e., intercept and slope). The mean heritability across PK parameters for the fenbendazole and flunixin meglumine parent drug (metabolite) was 0.15 (0.18) and 0.31 (0.40), respectively. For the parent drug (metabolite), the mean heritability across time was 0.27 (0.60) and 0.14 (0.44) for fenbendazole and flunixin meglumine, respectively. The errors surrounding the heritability estimates for the random regression model were smaller compared to estimates obtained from PK parameters. Across both the PK and plasma drug concentration across model, a moderate heritability was estimated. The model that utilized the plasma drug concentration across time resulted in estimates with a smaller standard error compared to models that utilized PK parameters. The current study found a low to moderate proportion of the phenotypic variation in metabolizing fenbendazole and flunixin meglumine that was explained by genetics in the current study.}, number={FEB}, journal={Frontiers in Genetics}, publisher={Frontiers Media SA}, author={Howard, Jeremy T. and Ashwell, Melissa S. and Baynes, Ronald E. and Brooks, James D. and Yeatts, James L. and Maltecca, Christian}, year={2018}, month={Feb} }
 @article{sanglard_nascimento_moriel_sommer_ashwell_poore_duarte_serão_2018, title={Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning}, volume={19}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-018-5089-8}, DOI={10.1186/s12864-018-5089-8}, abstractNote={Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response.Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation.A total of 160, 164, and 346 DEG (q-value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development: SLCO3A1, ATP6V0D1, SLC2A1, GPC4, and RASD2. In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL, KLRF1, and LOC104968634.In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Sanglard, Leticia P and Nascimento, Moysés and Moriel, Philipe and Sommer, Jeffrey and Ashwell, Melissa and Poore, Matthew H and Duarte, Márcio de S and Serão, Nick V L}, year={2018}, month={Sep} }
 @article{howard_ashwell_baynes_brooks_yeatts_maltecca_2017, title={Gene co-expression network analysis identifies porcine genes associated with variation in metabolizing fenbendazole and flunixin meglumine in the liver}, volume={7}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-017-01526-5}, DOI={10.1038/s41598-017-01526-5}, abstractNote={AbstractIdentifying individual genetic variation in drug metabolism pathways is of importance not only in livestock, but also in humans in order to provide the ultimate goal of giving the right drug at the right dose at the right time. Our objective was to identify individual genes and gene networks involved in metabolizing fenbendazole (FBZ) and flunixin meglumine (FLU) in swine liver. The population consisted of female and castrated male pigs that were sired by boars represented by 4 breeds. Progeny were randomly placed into groups: no drug (UNT), FLU or FBZ administered. Liver transcriptome profiles from 60 animals with extreme (i.e. fast or slow drug metabolism) pharmacokinetic (PK) profiles were generated from RNA sequencing. Multiple cytochrome P450 (CYP1A1, CYP2A19 and CYP2C36) genes displayed different transcript levels across treated versus UNT. Weighted gene co-expression network analysis identified 5 and 3 modules of genes correlated with PK parameters and a portion of these were enriched for biological processes relevant to drug metabolism for FBZ and FLU, respectively. Genes within identified modules were shown to have a higher transcript level relationship (i.e. connectivity) in treated versus UNT animals. Investigation into the identified genes would allow for greater insight into FBZ and FLU metabolism.}, number={1}, journal={Scientific Reports}, publisher={Springer Nature}, author={Howard, Jeremy T. and Ashwell, Melissa S. and Baynes, Ronald E. and Brooks, James D. and Yeatts, James L. and Maltecca, Christian}, year={2017}, month={May} }
 @misc{merrill_2015, title={Animal Science Biotechnology in the Classroom}, author={Merrill, M.S.}, year={2015}, month={Jul} }
 @article{howard_o’nan_maltecca_baynes_ashwell_2015, title={Differential Gene Expression across Breed and Sex in Commercial Pigs Administered Fenbendazole and Flunixin Meglumine}, volume={10}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0137830}, DOI={10.1371/journal.pone.0137830}, abstractNote={Characterizing the variability in transcript levels across breeds and sex in swine for genes that play a role in drug metabolism may shed light on breed and sex differences in drug metabolism. The objective of the study is to determine if there is heterogeneity between swine breeds and sex in transcript levels for genes previously shown to play a role in drug metabolism for animals administered flunixin meglumine or fenbendazole. Crossbred nursery female and castrated male pigs (n = 169) spread across 5 groups were utilized. Sires (n = 15) of the pigs were purebred Duroc, Landrace, Yorkshire or Hampshire boars mated to a common sow population. Animals were randomly placed into the following treatments: no drug (control), flunixin meglumine, or fenbendazole. One hour after the second dosing, animals were sacrificed and liver samples collected. Quantitative Real-Time PCR was used to measure liver gene expression of the following genes: SULT1A1, ABCB1, CYP1A2, CYP2E1, CYP3A22 and CYP3A29. The control animals were used to investigate baseline transcript level differences across breed and sex. Post drug administration transcript differences across breed and sex were investigated by comparing animals administered the drug to the controls. Contrasts to determine fold change were constructed from a model that included fixed and random effects within each drug. Significant (P-value <0.007) basal transcript differences were found across breeds for SULT1A1, CYP3A29 and CYP3A22. Across drugs, significant (P-value <0.0038) transcript differences existed between animals given a drug and controls across breeds and sex for ABCB1, PS and CYP1A2. Significant (P <0.0038) transcript differences across breeds were found for CYP2E1 and SULT1A1 for flunixin meglumine and fenbendazole, respectively. The current analysis found transcript level differences across swine breeds and sex for multiple genes, which provides greater insight into the relationship between flunixin meglumine and fenbendazole and known drug metabolizing genes.}, number={9}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Howard, Jeremy T. and O’Nan, Audrey T. and Maltecca, Christian and Baynes, Ronald E. and Ashwell, Melissa S.}, editor={Kobeissy, Firas HEditor}, year={2015}, month={Sep}, pages={e0137830} }
 @misc{merrill_2015, title={Do breed and gender affect how pigs respond to drugs?}, author={Merrill, M.S.}, year={2015}, month={May} }
 @article{huang_ashwell_fry_lloyd_flowers_spears_2015, title={Effect of dietary copper amount and source on copper metabolism and oxidative stress of weanling pigs in short-term feeding}, volume={93}, ISSN={["1525-3163"]}, DOI={10.2527/jas.2014-8082}, abstractNote={Forty-eight weanling barrows were used to determine the effects of amount and source of dietary Cu on Cu metabolism, oxidative stress in the duodenum, and VFA ratios in the cecum of weanling pigs in short-term feeding. At 21 d of age, newly weaned pigs were stratified by BW (7.03 ± 1.20 kg) and equally assigned to 1 of the following dietary treatments: 1) control (5 mg supplemental Cu/kg diet from CuSO4), 2) 225 mg supplemental Cu/kg diet from CuSO4, or 3) 225 mg supplemental Cu/kg diet from tribasic Cu chloride (TBCC). Pigs were housed 2 pigs per pen and were fed a complex diet until harvest on d 11 and 12. During harvest, bile and liver were obtained for mineral analysis, and liver samples were obtained for analysis of mRNA expression of Cu regulatory proteins. Digesta of duodenum, proximal jejunum, and ileum were collected for soluble Cu analysis. Mucosal scrapings of duodenum, proximal jejunum, and ileum were obtained for analysis of mucosal Cu concentration and mRNA expression of Cu regulatory proteins. Duodenal mucosal scrapings were also collected for analysis of malondialdehyde (MDA). Pigs fed high Cu had markedly greater (P < 0.0001) Cu concentrations in the duodenal, proximal jejunal, and ileal mucosa than controls. Copper in the duodenal mucosa was greater (P = 0.003) in CuSO4 than TBCC pigs. Duodenal MDA concentrations were greater (P = 0.003) in CuSO4 vs. control pigs and tended (P = 0.06) to be greater than in TBCC pigs. Duodenal antioxidant 1 (Atox1) mRNA was downregulated (P < 0.01) in pigs fed high Cu compared to controls and was not affected by Cu source. Compared with control pigs, those fed CuSO4 and TBCC had greater (P < 0.001) liver and bile Cu concentrations. Liver Cu was also greater (P = 0.0007) in TBCC than CuSO4-fed pigs. Hepatic Cu transporting β-polypeptide ATPase (Atp7b) was upregulated (P = 0.02) in the Cu-supplemented pigs compared with controls and did not differ among Cu sources. The acetate:propionate ratio in cecal contents was much greater in pigs supplemented with 225 mg Cu/kg diet than in controls. When fed at 225 mg Cu/kg diet, TBCC may cause less oxidative stress in the duodenum than CuSO4. Feeding weanling pigs increased Cu resulted in modulation of duodenal and liver at the transcription level.}, number={6}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Huang, Y. L. and Ashwell, M. S. and Fry, R. S. and Lloyd, K. E. and Flowers, W. L. and Spears, J. W.}, year={2015}, month={Jun}, pages={2948–2955} }
 @book{merrill_2014, place={Dubuque, IA}, edition={2nd}, title={Agricultural Genetics}, ISBN={9781465252661}, publisher={Kendall Hunt Pub. Co.}, author={Merrill, M.S.}, year={2014} }
 @inproceedings{freire_o'nan_benito_hash_ashwell_lascelles_2014, title={Characterisation of gene expression in naturally occurring feline degenerative joint disease associated pain}, author={Freire, M. and O'Nan, A. and Benito, J. and Hash, J. and Ashwell, M.S. and Lascelles, B.D.X.}, year={2014} }
 @article{mckenney_ashwell_lambert_fellner_2014, title={Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong)}, volume={9}, ISSN={["1749-4869"]}, DOI={10.1111/1749-4877.12112}, abstractNote={AbstractMicrobial populations in the gastrointestinal tract contribute to host health and nutrition. Although gut microbial ecology is well studied in livestock and domestic animals, little is known of the endogenous populations inhabiting primates or carnivora. We characterized microbial populations in fecal cultures from gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong) to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding strategies. Each species was fed a distinct standardized diet for 2 weeks prior to fecal collection. All diets were formulated to reflect the species' feeding strategies in situ. Fresh fecal samples were pooled within species and used to inoculate in vitro batch cultures. Acetate, propionate, butyrate and valerate were measured after 24 h of incubation. Eubacterial DNA was extracted from individual fecal samples, pooled, and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host species. Short chain fatty acids (P < 0.001) and methane (P < 0.001) were significantly different across species. Eubacterial profiles were consistent with fermentation data and suggest an increase in diversity with dietary fiber.}, number={5}, journal={INTEGRATIVE ZOOLOGY}, publisher={Wiley-Blackwell}, author={McKenney, Erin A. and Ashwell, Melissa and Lambert, Joanna E. and Fellner, Vivek}, year={2014}, month={Nov}, pages={557–569} }
 @article{mcculloch_ashwell_maltecca_o'nan_mente_2014, title={Progression of Gene Expression Changes following a Mechanical Injury to Articular Cartilage as a Model of Early Stage Osteoarthritis}, volume={2014}, ISSN={2090-1984 2090-1992}, url={http://dx.doi.org/10.1155/2014/371426}, DOI={10.1155/2014/371426}, abstractNote={An impact injury model of early stage osteoarthritis (OA) progression was developed using a mechanical insult to an articular cartilage surface to evaluate differential gene expression changes over time and treatment. Porcine patellae with intact cartilage surfaces were randomized to one of three treatments: nonimpacted control, axial impaction (2000 N), or a shear impaction (500 N axial, with tangential displacement to induce shear forces). After impact, the patellae were returned to culture for 0, 3, 7, or 14 days.  At the appropriate time point, RNA was extracted from full-thickness cartilage slices at the impact site.  Quantitative real-time PCR was used to evaluate differential gene expression for 18 OA related genes from four categories: cartilage matrix, degradative enzymes and inhibitors, inflammatory response and signaling, and cell apoptosis.   The shear impacted specimens were compared to the axial impacted specimens and showed that shear specimens more highly expressed type I collagen (Col1a1) at the early time points. In addition, there was generally elevated expression of degradative enzymes, inflammatory response genes, and apoptosis markers at the early time points. These changes suggest that the more physiologically relevant shear loading may initially be more damaging to the cartilage and induces more repair efforts after loading.}, journal={Arthritis}, publisher={Hindawi Limited}, author={McCulloch, R. S. and Ashwell, M. S. and Maltecca, C. and O'Nan, A. T. and Mente, P. L.}, year={2014}, month={Nov}, pages={1–9} }
 @article{ashwell_howard_baynes_o’nan_brooks_yeatts_routh_maltecca_2014, title={The effect of breed and gender on drug depletion and differential gene expression associated with drug metabolism after flunixin and fenbendazole administration}, volume={8}, journal={Journal of Molecular and Genetic Medicine}, author={Ashwell, M.S. and Howard, J.T. and Baynes, R.E. and O’Nan, A.T. and Brooks, J.D. and Yeatts, J.L. and Routh, P. and Maltecca, C.}, year={2014}, pages={67} }
 @inproceedings{ashwell_howard_baynes_o’nan_brooks_yeatts_routh_maltecca_2014, title={The effect of breed and gender on drug depletion and differential gene expression associated with drug metabolism after flunixin and fenbendazole administration}, booktitle={Swine in Biomedical Research 2014 International Conference}, author={Ashwell, M.S. and Howard, J.T. and Baynes, R.E. and O’Nan, A.T. and Brooks, J.D. and Yeatts, J.L. and Routh, P. and Maltecca, C.}, year={2014}, pages={31} }
 @inproceedings{howard_ashwell_baynes_brooks_yeatts_bellis_routh_maltecca_2014, title={The effect of breed and sex on drug depletion and differential gene expression associated with drug metabolism after fenbendazole and flunixin administration}, booktitle={Plant and Animal Genome XXII Conference Proceedings}, author={Howard, J. and Ashwell, M. and Baynes, R. and Brooks, J. and Yeatts, J. and Bellis, B. and Routh, P. and Maltecca, C.}, year={2014}, pages={262} }
 @article{howard_baynes_brooks_yeatts_bellis_ashwell_routh_o'nan_maltecca_2014, title={The effect of breed and sex on sulfamethazine, enrofloxacin, fenbendazole and flunixin meglumine pharmacokinetic parameters in swine}, volume={37}, ISSN={["1365-2885"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84911423325&partnerID=MN8TOARS}, DOI={10.1111/jvp.12128}, abstractNote={Drug use in livestock has received increased attention due to welfare concerns and food safety. Characterizing heterogeneity in the way swine populations respond to drugs could allow for group‐specific dose or drug recommendations. Our objective was to determine whether drug clearance differs across genetic backgrounds and sex for sulfamethazine, enrofloxacin, fenbendazole and flunixin meglumine. Two sires from each of four breeds were mated to a common sow population. The nursery pigs generated (n = 114) were utilized in a random crossover design. Drugs were administered intravenously and blood collected a minimum of 10 times over 48 h. A non‐compartmental analysis of drug and metabolite plasma concentration vs. time profiles was performed. Within‐drug and metabolite analysis of pharmacokinetic parameters included fixed effects of drug administration date, sex and breed of sire. Breed differences existed for flunixin meglumine (P‐value<0.05; Cl, Vdss) and oxfendazole (P‐value<0.05, AUC0→∞). Sex differences existed for oxfendazole (P‐value < 0.05; Tmax) and sulfamethazine (P‐value < 0.05, Cl). Differences in drug clearance were seen, and future work will determine the degree of additive genetic variation utilizing a larger population.}, number={6}, journal={JOURNAL OF VETERINARY PHARMACOLOGY AND THERAPEUTICS}, author={Howard, J. T. and Baynes, R. E. and Brooks, J. D. and Yeatts, J. L. and Bellis, B. and Ashwell, M. S. and Routh, P. and O'Nan, A. T. and Maltecca, C.}, year={2014}, month={Dec}, pages={531–541} }
 @inbook{freire_o'nan_benito_hash_ashwell_lascelles_2013, title={Characterization of gene expression in naturally occurring feline degenerative joint disease associated pain}, author={Freire, A. and O'Nan, A. and Benito, J. and Hash, J. and Ashwell, M.S. and Lascelles, B.D.X.}, year={2013}, month={Jun} }
 @inproceedings{fry_spears_ashwell_hansen_2013, title={Exploring cellular trace mineral metabolism in bovine and porcine tissues}, author={Fry, R.S. and Spears, J.W. and Ashwell, M.S. and Hansen, S.L.}, year={2013}, month={Jul} }
 @book{ashwell_2012, place={Dubuque, IA}, edition={1st}, title={Agricultural Genetics}, ISBN={9781465204967}, publisher={Kendall-Hunt Publishing Company}, author={Ashwell, M.S.}, year={2012} }
 @article{fry_ashwell_lloyd_o'nan_flowers_stewart_spears_2012, title={Amount and source of dietary copper affects small intestine morphology, duodenal lipid peroxidation, hepatic oxidative stress, and mRNA expression of hepatic copper regulatory proteins in weanling pigs}, volume={90}, ISSN={["1525-3163"]}, DOI={10.2527/jas.2011-4403}, abstractNote={Thirty weanling, crossbred barrows (SUS SCROFA) were used to determine the effects of amount and source of dietary Cu on small intestinal morphology and lipid peroxidation, Cu metabolism, and mRNA expression of proteins involved in hepatic Cu homeostasis. At 21 d of age, pigs were stratified by BW (6.33 ± 0.23 kg) and allocated to 1 of the following dietary treatments: i) control (no supplemental Cu; 6.7 mg Cu/kg), ii) 225 mg supplemental Cu/kg diet from Cu sulfate (CuSO(4)), or iii) 225 mg supplemental Cu/kg diet from tribasic Cu chloride (TBCC). Pigs were housed 2 pigs per pen and were fed a 3-phase diet regimen until d 35 or 36 of the study. During harvest, bile and liver were obtained for mineral analysis, and liver samples were also obtained for analysis of liver glutathione (GSH) and mRNA expression of Cu regulatory proteins. Segments of duodenum, proximal jejunum, and ileum were obtained for mucosal morphology, and duodenal mucosal scrapings were collected from all pigs for analysis of malondialdehyde (MDA). Duodenal villus height was reduced in CuSO(4) pigs compared with control (P = 0.001) and TBCC (P = 0.03) pigs. Villus height in the proximal jejunum of CuSO(4) pigs was reduced (P = 0.03) compared with control pigs, but ileal villus height was not affected (P = 0.82) by treatment. Duodenal MDA concentrations were greater (P = 0.03) in CuSO(4) pigs and tended to be greater (P = 0.10) in pigs supplemented with TBCC compared with control pigs. Liver Cu was greater (P = 0.01) in CuSO(4) vs. control pigs, and tended (P = 0.07) to be greater in TBCC pigs than control pigs. Bile Cu concentrations were greater (P < 0.001) in CuSO(4) and TBCC pigs vs. controls and were also greater (P = 0.04) in TBCC vs. CuSO(4) pigs. Total liver GSH concentrations were less (P = 0.02) in pigs fed diets supplemented with CuSO(4) vs. pigs fed control diets but total liver GSH did not differ (P = 0.11) between control and TBCC pigs. Hepatic mRNA of cytochrome c oxidase assembly protein 17 was less (P = 0.01) in CuSO(4) and tended to be less (P = 0.08) in TBCC pigs vs. control pigs. Expression of antioxidant 1 mRNA was greater (P = 0.04) in TBCC pigs and tended to be greater (P = 0.06) in CuSO(4) pigs compared with control pigs. Results of this study indicated that, when fed at 225 mg Cu/kg diet, TBCC may cause less oxidative stress in the duodenum than CuSO(4). Feeding weanling pigs increased Cu resulted in modulation of certain Cu transporters and chaperones at the transcription level.}, number={9}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Fry, R. S. and Ashwell, M. S. and Lloyd, K. E. and O'Nan, A. T. and Flowers, W. L. and Stewart, K. R. and Spears, J. W.}, year={2012}, month={Sep}, pages={3112–3119} }
 @article{ashwell_gonda_gray_maltecca_audrey t. o'nan_cassady_mente_2013, title={Changes in chondrocyte gene expression following in vitro impaction of porcine articular cartilage in an impact injury model}, volume={31}, ISSN={["1554-527X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84872761673&partnerID=MN8TOARS}, DOI={10.1002/jor.22239}, abstractNote={AbstractOur objective was to monitor chondrocyte gene expression at 0, 3, 7, and 14 days following in vitro impaction to the articular surface of porcine patellae. Patellar facets were either axially impacted with a cylindrical impactor (25 mm/s loading rate) to a load level of 2,000 N or not impacted to serve as controls. After being placed in organ culture for 0, 3, 7, or 14 days, total RNA was isolated from full thickness cartilage slices and gene expression measured for 17 genes by quantitative real‐time RT‐PCR. Targeted genes included those encoding proteins involved with biological stress, inflammation, or anabolism and catabolism of cartilage extracellular matrix. Some gene expression changes were detected on the day of impaction, but most significant changes occurred at 14 days in culture. At 14 days in culture, 10 of the 17 genes were differentially expressed with col1a1 most significantly up‐regulated in the impacted samples, suggesting impacted chondrocytes may have reverted to a fibroblast‐like phenotype. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31: 385–391, 2013}, number={3}, journal={JOURNAL OF ORTHOPAEDIC RESEARCH}, author={Ashwell, Melissa S. and Gonda, Michael G. and Gray, Kent and Maltecca, Christian and Audrey T. O'Nan and Cassady, Joseph P. and Mente, Peter L.}, year={2013}, month={Mar}, pages={385–391} }
 @article{cabrera_lin_ashwell_moeser_odle_2013, title={Early postnatal kinetics of colostral immunoglobulin G absorption in fed and fasted piglets and developmental expression of the intestinal immunoglobulin G receptor}, volume={91}, ISSN={0021-8812 1525-3163}, url={http://dx.doi.org/10.2527/jas.2011-4426}, DOI={10.2527/jas.2011-4426}, abstractNote={The transport of IgG across the epithelial barrier and into the circulation is achieved in part by the neonatal Fc receptor (FcRn), and this provides passive immunity to the neonate. The objective of this study was to determine the effect of time and feeding state on IgG absorption, intestinal morphology, and expression of IgG receptors in the first 24 h postbirth. Twenty newborn pigs were obtained immediately after birth and fitted with umbilical arterial catheters. Colostrum was manually collected from 12 lactating sows and centrifuged to produce defatted colostrum. Piglets were orally gavaged with 32 mL defatted colostrum per kilogram of BW (given in 2 doses 1 h apart) either at birth (0 h) or at 12 h postbirth under either fed (milk replacer) or fasted (saline solution) condition (n=5 per treatment). A fifth reference group (n=5) was euthanized at birth. Blood was collected every hour for the first 2 h immediately after the catheter was inserted and then every 4 h until 12 h (i.e., 0, 1, 2, 4, 8, and 12 h) for the treatment in which the defatted colostrum was given right after birth. For the treatment gavaged at 12 h postbirth, the sampling schedule was at 12, 13, 14, 16, 20, and 24 h. At 12 h postgavage, pigs were euthanized and jejunum tissues were collected for measurement of villi height, width, crypt depth, and gene expression of FcRn and β2-microglobulin (β2M) via reverse transcription PCR. Pig serum IgG concentration was determined by radial immunodiffusion. Data were analyzed according to a 2×2 factorial arrangement of treatments (0 h-fed, 0 h-fasted, 12 h-fed, and 12 h-fasted). There was no interaction between the time (age) of offering defatted colostrum (0 vs. 12 h) and nutritional state (fed vs. fasted) for any of the measurements, and there were no differences between fed and fasted pigs. Serum IgG concentrations increased progressively with time. Piglets offered defatted colostrum at 0 h had greater (P<0.05) overall IgG absorption and greater (P<0.05) villi height than those offered defatted colostrum at 12 h postbirth. Abundance of mRNA of FcRn and β2M were normalized to glyceraldehyde-3-phosphate dehydrogenase. Abundance of FcRn transcript was lower (P=0.006) in pigs euthanized at birth compared with those euthanized at 12 h of age. In conclusion, the effects of delayed offering of defatted colostrum and age-dependent changes in IgG receptor were modest over the first 24 h of life.}, number={1}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Cabrera, R. and Lin, X. and Ashwell, M. and Moeser, A. and Odle, J.}, year={2013}, month={Jan}, pages={211–218} }
 @article{fry_spears_lloyd_o'nan_ashwell_2013, title={Effect of dietary copper and breed on gene products involved in copper acquisition, distribution, and use in Angus and Simmental cows and fetuses}, volume={91}, ISSN={["1525-3163"]}, DOI={10.2527/jas.2011-3888}, abstractNote={Copper (Cu) deficiency is a widespread problem in cattle across the United States and breed differences in Cu metabolism may contribute to this issue. Intracellular Cu is tightly regulated by transport and chaperone proteins, and to date, these mechanisms have not been elucidated to address breed differences in Cu metabolism, nor have these proteins been characterized in bovine fetal liver. Mature, pregnant Angus (n = 8) and Simmental (n = 8) cows (∼4 mo into gestation) were used in a 2 × 2 factorial arrangement of treatments. All cows were bred to Angus sires resulting in an Angus vs. Simmental × Angus comparison for fetuses. Cows were randomly assigned to corn silage-based diets that were either adequate (+Cu) or deficient (-Cu; 6.6 mg Cu/kg DM) in Cu. Diets were individually fed for 112 d. At the end of the study, cows were harvested to collect duodenal mucosa scrapes, liver samples, and fetal liver samples for mineral analysis and also for mRNA and protein analysis of Cu transport and chaperone proteins. Placentomes were also obtained for mineral analysis. Plasma Cu and liver Cu were affected by Cu, breed, and Cu × breed. Both of these Cu indices were less (P ≤ 0.05) in-Cu Simmentals (-CuS) than in-Cu Angus (- uA), but were similar among +Cu Simmental (+CuS) and +Cu Angus cows (+CuA). Duodenal Cu was less (P = 0.01) in-Cu vs. +Cu cows. Placentome Cu was less (P = 0.003) in-Cu vs. +Cu cows, and was also less (P = 0.03) in Simmentals vs. Angus. Fetal liver Cu was less (P = 0.002) in-Cu vs. +Cu fetuses, and was also less (P = 0.05) in Simmental × Angus vs. Angus. Abundance of Cu transporter1 (CTR1) protein and transcripts for Cu transporters and chaperones were not affected by Cu or breed in liver and were not affected by Cu in the intestine. Duodenal Ctr1 was less (P = 0.04) and CTR1 tended (P = 0.10) to be less in Simmentals vs. Angus. Expression of Atp7a tended (P = 0.08) to be less in Simmentals than in Angus. In fetal liver, expression of antioxidant 1 (Atox1), cytochrome c oxidase assembly protein 17 (Cox17), and Cu metabolism MURR1 domain 1 (Commd1) were up-regulated (P ≤ 0.05) in-Cu vs. +Cu fetuses. In conclusion, less expression of duodenal Ctr1 and a tendency for less CTR1 (P = 0.10) and Atp7a (P = 0.08) suggest that Simmentals have a lesser ability to absorb and utilize dietary Cu, and may explain why Simmentals are more prone to Cu deficiency than Angus. Up-regulation of fetal liver Atox1, Cox17, and Commd1 in-Cu fetuses may reflect the great Cu demand by the fetus.}, number={2}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Fry, R. S. and Spears, J. W. and Lloyd, K. E. and O'Nan, A. T. and Ashwell, M. S.}, year={2013}, month={Feb}, pages={861–871} }
 @article{mcculloch_ashwell_o’nan_mente_2012, title={Identification of stable normalization genes for quantitative real-time PCR in porcine articular cartilage}, volume={3}, ISSN={2049-1891}, url={http://dx.doi.org/10.1186/2049-1891-3-36}, DOI={10.1186/2049-1891-3-36}, abstractNote={Abstract
          
            Background
            Expression levels for genes of interest must be normalized with an appropriate reference, or housekeeping gene, to make accurate comparisons of quantitative real-time PCR results. The purpose of this study was to identify the most stable housekeeping genes in porcine articular cartilage subjected to a mechanical injury from a panel of 10 candidate genes.
          
          
            Results
            Ten candidate housekeeping genes were evaluated in three different treatment groups of mechanically impacted porcine articular cartilage. The genes evaluated were: beta actin, beta-2-microglobulin, glyceraldehyde-3-phosphate dehydrogenase, hydroxymethylbilane synthase, hypoxanthine phosphoribosyl transferase, peptidylprolyl isomerase A (cyclophilin A), ribosomal protein L4, succinate dehydrogenase flavoprotein subunit A, TATA box binding protein, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein—zeta polypeptide. The stability of the genes was measured using geNorm, BestKeeper, and NormFinder software. The four most stable genes measured via geNorm were (most to least stable) succinate dehydrogenase flavoprotein, subunit A, peptidylprolyl isomerase A, glyceraldehyde-3-phosphate dehydrogenase, beta actin; the four most stable genes measured via BestKeeper were glyceraldehyde-3-phosphate dehydrogenase, peptidylprolyl isomerase A, beta actin, succinate dehydrogenase flavoprotein, subunit A; and the four most stable genes measured via NormFinder were peptidylprolyl isomerase A, succinate dehydrogenase flavoprotein, subunit A, glyceraldehyde-3-phosphate dehydrogenase, beta actin.
          
          
            Conclusions
            BestKeeper, geNorm, and NormFinder all generated similar results for the most stable genes in porcine articular cartilage. The use of these appropriate reference genes will facilitate accurate gene expression studies of porcine articular cartilage and suggest appropriate housekeeping genes for articular cartilage studies in other species.
          }, number={1}, journal={Journal of Animal Science and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={McCulloch, Ryan S and Ashwell, Melissa S and O’Nan, Audrey T and Mente, Peter L}, year={2012}, month={Nov} }
 @article{maltecca_gray_weigel_cassady_ashwell_2011, title={A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations}, volume={42}, ISSN={["0268-9146"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80255123496&partnerID=MN8TOARS}, DOI={10.1111/j.1365-2052.2011.02188.x}, abstractNote={Direct gestation length influences economically important traits in dairy cattle that are related to birth and peri-natal survival of the calf. The objective of this study was to identify single nucleotide polymorphisms (SNPs) that are significantly associated with direct gestation length through a genome-wide association study. Data used in the analysis included 7,308,194 cow gestation lengths from daughters of 4743 United States Holstein sires in the Cooperative Dairy DNA Repository population and 580,157 gestation lengths from 749 sires in the Italian Brown population. Association analysis included 36,768 and 35,082 SNPs spanning all autosomes for Holstein and Brown Swiss, respectively. Multiple shrinkage Bayesian was employed. Estimates of heritability for both populations were moderate, with values of 0.32 (±0.03) and 0.29 (±0.02) for Holstein and Brown Swiss, respectively. A panel of SNPs was identified, which included SNPs that have significant effects on direct gestation length, of which the strongest candidate region is located on chromosome 18. Two regions not previously linked to direct calving ease and calf survival were identified on chromosome 7 and 28, corresponding to regions that contain genes related to embryonic development and foetal development. SNPs were also identified in regions that have been previously mapped for calving difficulty and longevity. This study identifies target regions for the investigation of direct foetal effects, which are a significant factor in determining the ease of calving.}, number={6}, journal={ANIMAL GENETICS}, author={Maltecca, C. and Gray, K. A. and Weigel, K. A. and Cassady, J. P. and Ashwell, M.}, year={2011}, month={Dec}, pages={585–591} }
 @inproceedings{mcculloch_ashwell_o’nan_maltecca_mente_2011, title={Articular cartilage chondrocyte gene expression alterations following shear and axial impactions}, author={McCulloch, R.S. and Ashwell, M.S. and O’Nan, A.T. and Maltecca, C. and Mente, P.L.}, year={2011} }
 @misc{merrill_2010, title={Animal functional genomics at NC State University}, author={Merrill, M.S.}, year={2010}, month={Feb} }
 @article{fry_spears_hansen_ashwell_2010, title={Dietary iron affects mRNA expression of porcine copper transporters}, volume={24}, ISSN={0892-6638 1530-6860}, url={http://dx.doi.org/10.1096/fasebj.24.1_supplement.229.7}, DOI={10.1096/fasebj.24.1_supplement.229.7}, abstractNote={Weanling male pigs (21 days of age) were fed diets deficient (20 mg Fe/kg; L‐Fe), adequate (120 mg Fe/kg; A‐Fe) or high (520 mg Fe/kg; H‐Fe) in iron (Fe) for 32 days to evaluate the effects of dietary Fe level on copper (Cu) transporters and chaperones. Increasing dietary Fe increased Fe in proximal duodenum and liver. Liver Cu was lower in A‐Fe than in L‐Fe and H‐Fe pigs and did not differ among pigs fed L‐Fe and H‐Fe diets. Expression of liver copper transporter 1 (Ctr1) was higher in L‐Fe vs. A‐Fe pigs. Liver Atp7b was lower in both L‐Fe and H‐Fe pigs vs. A‐Fe pigs. Ceruloplasmin (Cp) expression in liver was up‐regulated in L‐Fe and H‐Fe pigs vs. A‐Fe pigs. Cp was also increased in pigs fed L‐Fe vs. H‐Fe diets. Feeding a L‐Fe diet tended to decrease Commd1 compared to feeding an A‐Fe diet. Liver cytochrome c oxidase assembly protein 17 (Cox17), antioxidant 1 (Atox1), copper chaperone for Cu/Zn superoxide dismutase (CCS), Cu/Zn superoxide dismutase (Sod1), and metallothionein 1a (Mt1a) were unaffected by dietary Fe. Duodenal Cu concentration and expression of duodenal Ctr1, Atox1, Cox17, CCS, Sod1, Atp7a, or Mt1a were not affected by dietary Fe. These data indicate that dietary Fe affects cellular Cu transporters involved in import and export of Cu to a greater extent in the liver than in duodenum. Reduced hepatic expression of Atp7b in both L‐Fe and H‐Fe pigs may explain the increased liver Cu seen in these pigs relative to A‐Fe.Grant Funding Source: Micronutrients}, number={S1}, journal={The FASEB Journal}, publisher={Wiley}, author={Fry, Robert Scott and Spears, Jerry W and Hansen, Stephanie L and Ashwell, Melissa S}, year={2010}, month={Apr} }
 @inproceedings{mcculloch_ashwell_o’nan_mente_2010, title={Differential gene expression of chrondocytes from a porcine impact injury model using suitable reference genes}, booktitle={Transactions of the 56th annual meeting of the Orthopedic Research Society}, author={McCulloch, R.S. and Ashwell, M.S. and O’Nan, A.T. and Mente, P.L.}, year={2010} }
 @article{fry_ashwell_spears_2010, title={Duodenal copper transporters in cattle are affected by breed}, volume={88}, number={Supplement 2}, journal={Journal of Animal Science}, author={Fry, R.S. and Ashwell, M.S. and Spears, J.W.}, year={2010}, pages={11} }
 @article{fry_ashwell_flowers_stewart_spears_2010, title={Effect of level and source of dietary copper on copper metabolism in the small intestine of weanling pigs}, volume={88}, number={Supplement 1}, journal={Journal of Animal Science}, author={Fry, R.S. and Ashwell, M.S. and Flowers, W.L. and Stewart, K.R. and Spears, J.W.}, year={2010}, pages={499} }
 @article{fry_spears_hansen_liu_ashwell_2010, title={Effects of dietary iron and age on cellular copper metabolism in liver of weanling pigs}, volume={88}, number={Supplement 1}, journal={Journal of Animal Science}, author={Fry, R.S. and Spears, J.W. and Hansen, S.L. and Liu, H.C. and Ashwell, M.S.}, year={2010}, pages={499} }
 @inproceedings{mckenney_o’nan_fellner_ashwell_2010, title={Evaluating the QiaAMP DNA stool kit for metagenomic studies in Arctictis binturong}, author={McKenney, E.A. and O’Nan, A.T. and Fellner, V. and Ashwell, M.S.}, year={2010}, month={Aug} }
 @article{hansen_ashwell_moeser_fry_knutson_spears_2010, title={High dietary iron reduces transporters involved in iron and manganese metabolism and increases intestinal permeability in calves}, volume={93}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2009-2341}, abstractNote={A 56-d experiment was designed to examine the effect of high dietary Fe on metal transporters involved in Fe and Mn metabolism. Fourteen weaned Holstein calves were stratified by weight and randomly assigned to 1 of 2 treatments: 1) no supplemental Fe (normal Fe) or 2) 750mg of supplemental Fe/kg of dry matter (high Fe). Jugular blood was collected on d 0, 35, and 56. At the end of the trial, 6 calves per treatment were humanely killed and duodenal scrapings, liver, and heart were collected for analysis. Additionally, proximal duodenum was mounted on Ussing chambers to assess intestinal barrier integrity. Calves receiving high dietary Fe displayed decreased transepithelial resistance and increased apical-to-basolateral flux of radiolabeled mannitol, suggesting that high Fe created increased intestinal permeability. Feeding calves a diet high in Fe decreased average daily gain, dry matter intake, and feed efficiency. Hemoglobin and serum Fe concentrations did not differ due to dietary treatment. High dietary Fe increased concentrations of Fe in the liver, but did not affect heart or duodenal Fe concentrations. Duodenal Mn concentrations were lowered by feeding a high Fe diet, but liver and heart Mn concentrations were not affected. As determined by real-time reverse transcription PCR, relative hepatic expression of the gene that encodes the Fe regulatory hormone hepcidin was 5-fold greater in calves fed high dietary Fe. Hepcidin is released in response to increased Fe status and binds to the Fe export protein ferroportin causing ferroportin to be degraded, thereby reducing dietary Fe absorption. Confirmation of this result was achieved through Western blotting of duodenal protein, which revealed that ferroportin was decreased in calves fed high dietary Fe. Duodenal protein expression of divalent metal transporter 1 (DMT1), a Fe import protein that can also transport Mn, tended to be reduced by high dietary Fe. Transcript levels of several genes involved in Fe metabolism in liver and duodenum were unchanged by treatment. In summary, feeding calves a diet high in Fe induced a signal cascade (hepcidin) designed to reduce absorption of Fe (via reduced protein expression of ferroportin and DMT1) in a manner similar to that reported in rodents. Additionally, reduced levels of DMT1 protein appeared to decrease duodenal Mn, suggesting that Mn may also be a substrate for DMT1 in cattle.}, number={2}, journal={JOURNAL OF DAIRY SCIENCE}, author={Hansen, S. L. and Ashwell, M. S. and Moeser, A. J. and Fry, R. S. and Knutson, M. D. and Spears, J. W.}, year={2010}, month={Feb}, pages={656–665} }
 @article{ashwell_fry_spears_o'nan_maltecca_2011, title={Investigation of breed and sex effects on cytochrome P450 gene expression in cattle liver}, volume={90}, ISSN={["0034-5288"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79951771053&partnerID=MN8TOARS}, DOI={10.1016/j.rvsc.2010.05.029}, abstractNote={Many cytochrome P450 enzymes are involved in xenobiotic metabolism and elimination. In humans, genetic variation in some of these enzymes contributes to inter-individual drug responses, sometimes having significant clinical effects. Transcript levels of eight P450 genes were evaluated in liver to investigate potential differences in breed and sex in cattle. In Angus calves, heifers appeared to have higher gene expression than steers for two of the eight genes. In Angus and Simmental pregnant cows, Angus appeared to have higher gene expression for three of the eight genes. Transcript evaluation is just the first step toward determining if differences exist between breeds and sexes in enzyme catalytic activity. However, others (Giantin et al., 2008) have shown correlations between transcript levels and catalytic activity in other cattle breeds. Therefore breed and/or sex of an animal may need to be considered before administering a dose of a xenobiotic due to the potential for harmful drug residues in foodstuffs as well as improper treatment of disease conditions.}, number={2}, journal={RESEARCH IN VETERINARY SCIENCE}, author={Ashwell, M. S. and Fry, R. S. and Spears, J. W. and O'Nan, A. T. and Maltecca, C.}, year={2011}, month={Apr}, pages={235–237} }
 @inproceedings{mcculloch_ashwell_mente_2009, title={Differential chondrocyte gene expression following in vitro shear and axial impactions to porcine articular cartilage}, booktitle={BMES 2009 Annual Fall Meeting}, author={McCulloch, R.S. and Ashwell, M.S. and Mente, P.L.}, year={2009}, pages={134} }
 @article{fry_ashwell_hansen_engle_han_spears_2009, title={Effects of a long-term copper deficiency on gene expression profiles of copper transporters and chaperones in the intestine and liver of cattle}, volume={87}, number={Supplement 2}, journal={Journal of Animal Science}, author={Fry, R.S. and Ashwell, M.S. and Hansen, S.L. and Engle, T.E. and Han, H. and Spears, J.W.}, year={2009}, pages={561} }
 @article{oviedo-rondon_ashwell_wineland_2009, title={Gene expression in chicken and turkey tibia growth plates is affected by oxygen concentrations during the plateau stage of incubation}, volume={88}, number={Suppl 1}, journal={Journal of Poultry Science}, author={Oviedo-Rondon, E.O. and Ashwell, M.S. and Wineland, M.J.}, year={2009}, pages={61} }
 @article{hansen_ashwell_fry_spears_2009, title={High dietary iron negatively impacts gene products important in iron and manganese metabolism in young calves}, volume={87}, number={Suppl 2}, journal={Journal of Animal Science}, author={Hansen, S.L. and Ashwell, M.S. and Fry, R.S. and Spears, J.W.}, year={2009}, pages={516} }
 @article{hansen_trakooljul_liu_hicks_ashwell_spears_2010, title={Proteins involved in iron metabolism in beef cattle are affected by copper deficiency in combination with high dietary manganese, but not by copper deficiency alone}, volume={88}, ISSN={["1525-3163"]}, DOI={10.2527/jas.2009-1846}, abstractNote={A 493-d study was conducted to determine the impact of a severe, long-term Cu deficiency on Fe metabolism in beef cattle. Twenty-one Angus calves were born to cows receiving one of the following treatments: 1) adequate Cu (+Cu), 2) Cu deficient (-Cu), and 3) Cu deficient plus high Mn (-Cu+Mn). Copper deficiency was induced through the addition of 2 mg of Mo/kg of DM. After weaning, calves remained on the same treatment as their dam through growing (basal diet analyzed 7 mg of Cu/kg of DM) and finishing (analyzed 4 mg of Cu/kg of DM) phases. Plasma Fe concentrations were positively correlated (P < 0.01; r = 0.49) with plasma Cu concentrations. Liver Fe concentrations were greater (P = 0.05) in -Cu vs. +Cu calves and further increased (P = 0.07) in -Cu+Mn vs. -Cu calves. There was a negative relationship (P < 0.01; r = -0.31) between liver Cu and Fe concentrations. This relationship is likely explained by less (P < 0.01) plasma ceruloplasmin activity in -Cu than +Cu calves. As determined by real-time reverse transcription-PCR, relative expression of hepatic hepcidin was significantly downregulated (>1.5 fold) in -Cu compared with +Cu calves (P = 0.03), and expression of hepatic ferroportin tended (P = 0.09) to be downregulated in -Cu vs. +Cu. In the duodenum, ferritin tended to be upregulated in -Cu. vs. +Cu calves (P < 0.06). No significant change (P > 0.2) due to Cu-deficiency was detected at the transcriptional level for either isoform of divalent metal transporter 1 (DMT1 mRNA with or without an iron responsive element; dmt1IRE and dmt1-nonIRE) in liver or intestine. Duodenal expression of hephaestin and ferroportin protein was not affected by dietary treatment (P > 0.20). However, duodenal expression of DMT1 protein was less (P = 0.04) in -Cu+Mn steers vs. -Cu steers. In summary, Cu deficiency alone did affect hepatic gene expression of hepcidin and ferroportin, but did not affect duodenal expression of proteins important in Fe metabolism. However, the addition of 500 mg of Mn/kg of DM to a diet low in Cu reduced duodenal expression of the Fe import protein DMT1.}, number={1}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Hansen, S. L. and Trakooljul, N. and Liu, H. -C. S. and Hicks, J. A. and Ashwell, M. S. and Spears, J. W.}, year={2010}, month={Jan}, pages={275–283} }
 @inproceedings{mente_gonda_ashwell_2009, title={Temporal differences in chondrocyte gene expression following an in vitro cartilage injury}, author={Mente, P.L. and Gonda, M.G. and Ashwell, M.S.}, year={2009} }
 @article{ashwell_ceddia_house_cassady_eisen_eling_collins_grissom_odle_2010, title={Trans-10, cis-12-conjugated linoleic acid alters hepatic gene expression in a polygenic obese line of mice displaying hepatic lipidosis}, volume={21}, ISSN={["1873-4847"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77955844665&partnerID=MN8TOARS}, DOI={10.1016/j.jnutbio.2009.06.013}, abstractNote={The trans-10, cis-12 isomer of conjugated linoleic acid (CLA) causes a rapid reduction of body and adipose mass in mice. In addition to changes in adipose tissue, numerous studies have reported alterations in hepatic lipid metabolism. Livers of CLA-fed mice gain mass, partly due to lipid accumulation; however, the precise molecular mechanisms are unknown. To elucidate these mechanisms, we examined fatty acid composition and gene expression profiles of livers from a polygenic obese line of mice fed 1% trans-10, cis-12-CLA for 14 days. Analysis of gene expression data led to the identification of 1393 genes differentially expressed in the liver of CLA-fed male mice at a nominal P value of .01, and 775 were considered significant using a false discovery rate (FDR) threshold of .05. While surprisingly few genes in lipid metabolism were impacted, pathway analysis found that protein kinase A (PKA) and cyclic adenosine monophosphate (cAMP) pathways signaling pathways were affected by CLA treatment and 98 of the 775 genes were found to be regulated by hepatocyte nuclear factor 4α, a transcription factor important in controlling liver metabolic status.}, number={9}, journal={JOURNAL OF NUTRITIONAL BIOCHEMISTRY}, author={Ashwell, Melissa S. and Ceddia, Ryan P. and House, Ralph L. and Cassady, Joseph P. and Eisen, Eugene J. and Eling, Thomas E. and Collins, Jennifer B. and Grissom, Sherry F. and Odle, Jack}, year={2010}, month={Sep}, pages={848–855} }
 @inproceedings{fry_ashwell_hansen_engle_han_spears_2008, title={Effects of long-term copper deficiency on gene profiles of copper transporters and chaperones in the liver of cattle}, booktitle={Proceedings of the 13th International Symposium on Trace Elements in Man and Animals}, author={Fry, R.S. and Ashwell, M.S. and Hansen, S.L. and Engle, T.E. and Han, H. and Spears, J.W.}, year={2008}, pages={79–80} }
 @article{ashwell_o'nan_gonda_mente_2008, title={Gene expression profiling of chondrocytes from a porcine impact injury model}, volume={16}, ISSN={["1522-9653"]}, DOI={10.1016/j.joca.2007.12.012}, abstractNote={ObjectiveTo identify differentially expressed genes between axially impacted and control articular cartilage taken from porcine patellae maintained in organ culture for 14 days.MethodsPorcine patellae were impacted perpendicular to the articular surface to create an impact injury. Intact patellae (control and impacted) were maintained in culture for 14 days. Total RNA was then extracted from the articular cartilage beneath the impaction and used to prepare two Serial Analysis of Gene Expression (SAGE) libraries. Approximately 42,500 SAGE long tags were sequenced from the libraries. The expression of select genes was confirmed by quantitative real-time PCR analysis.ResultsThirty-nine SAGE tags were significantly differentially expressed in the impacted and control libraries, representing 30 different annotated pig genes. These genes represented gene products associated with matrix molecules, iron and phosphate transport, protein biosynthesis, skeletal development, cell proliferation, lipid metabolism and the inflammatory response. Twenty-three of the 30 genes were down-regulated in the impacted library and five were up-regulated in the impacted library. Quantitative real-time PCR follow-up of four genes supported the results found with SAGE.ConclusionWe have identified 30 putative genes differentially expressed in a porcine impact injury model and validated these findings for four of these genes using real-time PCR. Results using this impact injury model have contributed further evidence that damaged chondrocytes may de-differentiate into fibroblast-like cells and proliferate in an attempt to repair themselves. Additional work is underway to study these genes in further detail at earlier time points to provide a more complete story about the fate of chondrocytes in articular cartilage following an injury.}, number={8}, journal={OSTEOARTHRITIS AND CARTILAGE}, author={Ashwell, M. S. and O'Nan, A. T. and Gonda, M. G. and Mente, P. L.}, year={2008}, month={Aug}, pages={936–946} }
 @article{hansen_ashwell_legleiter_fry_lloyd_spears_2009, title={The addition of high manganese to a copper-deficient diet further depresses copper status and growth of cattle}, volume={101}, ISSN={["1475-2662"]}, DOI={10.1017/S0007114508057589}, abstractNote={A study was conducted evaluating the effect of long-term Cu deficiency, with or without high Mn, on growth, gene expression and Cu status of beef cattle. Twenty-one Angus calves were born to cows receiving one of the following treatments: (1) 10 mg supplemental Cu/kg DM (+Cu); (2) no supplemental Cu and 2 mg Mo/kg DM ( − Cu); (3) − Cu diet plus 500 mg supplemental Mn/kg DM ( − Cu+Mn). Calves were weaned at approximately 183 d of age and individually fed throughout the growing and finishing phases. Plasma Cu was lower (P < 0·01) in − Cu calves compared with +Cu calves while high dietary Mn further depressed (P < 0·01) plasma Cu in − Cu+Mn calvesv.− Cu calves. Liver Cu concentrations in +Cu calves were greater (P < 0·01) than in − Cu calves, with no differences between − Cu and − Cu+Mn calves. The daily body-weight gain of +Cu calves was greater (P < 0·01) than − Cu calves during the period from birth to weaning, but did not differ during the growing phase. − Cu+Mn calves gained less (P < 0·05) than − Cu calves during the growing phase. DM intake was lower (P < 0·01) in − Cu+Mn calvesv.− Cu calves, and did not differ among +Cu and − Cu calves. The relative gene expression of cytochrome c oxidase in the liver was lower (P < 0·05) in − Cu calves compared with +Cu or − Cu+Mn calves. In conclusion, feeding a Cu − deficient diet in combination with high Mn negatively affected the growth and Cu status of beef cattle.}, number={7}, journal={BRITISH JOURNAL OF NUTRITION}, author={Hansen, Stephanie L. and Ashwell, Melissa S. and Legleiter, Leon R. and Fry, Robert S. and Lloyd, Karen E. and Spears, Jerry W.}, year={2009}, month={Apr}, pages={1068–1078} }
 @misc{merrill_2007, title={Using genomic tools to improve health and reproduction traits}, author={Merrill, M.S.}, year={2007}, month={Sep} }
 @article{blowe_boyette_ashwell_eisen_robison_cassady_2006, title={Characterization of a line of pigs previously selected for increased litter size for RBP4 and follistatin}, volume={123}, ISSN={["1439-0388"]}, DOI={10.1111/j.1439-0388.2006.00620.x}, abstractNote={SummaryThe objective of this study was to determine if selection response for increased litter size in pigs could be partially attributed to three type 1 marker loci coding for genes known to affect litter size: oestrogen receptor (ESR), retinol‐binding protein 4 (RBP4) and follistatin (FS). In the high litter size line (LS), pigs from the largest litters, based on number of pigs born alive (NBA), were retained to parent the next generation. A randomly selected control line (LC) was maintained. Gilts were reared in litters of 10 pigs or less to minimize maternal effects. Pigs were measured at generations 10–12. Additional traits scored were number of fully formed pigs (NFF) and number of mummified fetuses (MUM). Breeding values for NFF and NBA were greater (p < 0.05) in LS than LC in generations 11 and 12, but no significant line differences were found for MUM. The A allele of the ESR locus was fixed in both lines. After adjustment for effects of genetic drift, frequency of the two alleles segregating for the FS and RBP4 loci did not differ significantly between lines. No significant additive or dominance effects of the FS markers were detected for NFF, NBA and MUM in either LS or LC. Response to selection for increased litter size could not be attributed to effects at the ESR, RBP4 or FS loci.}, number={6}, journal={JOURNAL OF ANIMAL BREEDING AND GENETICS}, author={Blowe, C. D. and Boyette, K. E. and Ashwell, M. S. and Eisen, E. J. and Robison, O. W. and Cassady, J. P.}, year={2006}, month={Dec}, pages={389–395} }
 @article{muncie_cassady_ashwell_2006, title={Refinement of quantitative trait loci on bovine chromosome 18 affecting health and reproduction in US Holsteins}, volume={37}, ISSN={["1365-2052"]}, DOI={10.1111/j.1365-2052.2006.01425.x}, abstractNote={SummarySelection for increased milk yield is associated with decreased fertility in US Holsteins. Previously, a putative quantitative trait locus (QTL) on chromosome 18 affecting daughter pregnancy rate (DPR) was identified in one family. Our aim was to determine the validity of the QTL using additional markers and an extended pedigree. Twelve markers were genotyped in 940 descendants of the original sire in which the QTL was identified. Analysis of the extended pedigree detected significant and suggestive QTL for DPR, productive life and somatic cell score. Further analysis is underway to refine the QTL region so that positional candidate genes can be identified.}, number={3}, journal={ANIMAL GENETICS}, author={Muncie, S. A. and Cassady, J. P. and Ashwell, M. S.}, year={2006}, month={Jun}, pages={273–275} }
 @misc{merrill_2006, title={Transcript profiling of chondrocytes in a porcine impact injury model of osteoarthritis}, author={Merrill, M.S.}, year={2006}, month={Aug} }
 @article{connor_ashwell_schnabel_williams_2006, title={Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle}, volume={112}, ISSN={["1424-859X"]}, DOI={10.1159/000087519}, abstractNote={In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order on the comparative map near the 40 cM region of the BTA27 linkage map where a QTL affecting dairy form had previously been identified. The resulting map identified <i>ADRB3</i> as a positional candidate gene for the QTL contributing to the dairy form trait based on its estimated position between 40 and 45 cM on the linkage map. It is also a functional candidate gene due to its role in fat metabolism, and polymorphisms in the <i>ADRB3</i> gene associated with obesity and metabolic disease in humans, as well as, carcass fat in sheep. Further studies are underway to investigate the existence of polymorphisms in the bovine <i>ADRB3</i> gene and their association with traits related to fat deposition in cattle.   }, number={1-2}, journal={CYTOGENETIC AND GENOME RESEARCH}, author={Connor, EE and Ashwell, MS and Schnabel, R and Williams, JL}, year={2006}, pages={98–102} }
 @article{ashwell_heyen_weller_ron_sonstegard_van tassell_lewin_2005, title={Detection of quantitative trait loci influencing conformation traits and calving ease in Holstein-Friesian cattle}, volume={88}, ISSN={["0022-0302"]}, DOI={10.3168/jds.S0022-0302(05)73095-2}, abstractNote={An extension of our previous genome scan of a North American Holstein-Friesian population was conducted to identify quantitative trait loci (QTL) affecting conformation traits. Resource families consisted of 1404 sons of 10 elite sires. Genome coverage was estimated to be 2713.5 cM (90%) for 406 markers using a granddaughter design. 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. Analysis of the families jointly identified 41 chromosome-wise significant QTL influencing conformation traits and 3 significant QTL influencing calving ease on 20 chromosomes. The false discovery rate method was used to account for multiple testing and 3/4 of the suggestive and 5/6 of significant QTL should be real effects. Fourteen of the 44 QTL were significant at the genome-wise level. Comparison of these results with other published reports identifies common QTL affecting conformation traits. Regions on 10 chromosomes appear to affect multiple traits, including conformation, milk production, and somatic cell score, within these particular US Holstein families. Additional work is needed to determine the precise locations of the QTL and select positional candidate genes influencing these traits.}, number={11}, journal={JOURNAL OF DAIRY SCIENCE}, author={Ashwell, MS and Heyen, DW and Weller, JI and Ron, M and Sonstegard, TS and Van Tassell, CP and Lewin, HA}, year={2005}, month={Nov}, pages={4111–4119} }
 @article{schnabel_kim_ashwell_sonstegard_van tassell_connor_taylor_2005, title={Fine-mapping milk production quantitative trait loci on BTA6: Analysis of the bovine osteopontin gene}, volume={102}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0502398102}, DOI={10.1073/pnas.0502398102}, abstractNote={
            Bovine chromosome six (BTA6) harbors up to six quantitative trait loci (QTL) influencing the milk production of dairy cattle. In stark contrast to human, there is long-range linkage disequilibrium in dairy cattle, which has previously made it difficult to identify the mutations underlying these QTL. Using 38 microsatellite markers in a pedigree of 3,147 Holstein bulls, we fine mapped regions of BTA6 that had previously been shown to harbor QTL. Next, we sequenced a 12.3-kb region harboring Osteopontin, a positional candidate for the statistically most significant of the identified QTL. Nine mutations were identified, and only genotypes for the
            OPN3907
            indel were concordant with the QTL genotypes of eight bulls that were established by segregation analysis. Four of these mutations were genotyped, and a joint linkage/linkage disequilibrium mapping analysis was used to demonstrate the existence of only two functionally distinct clusters of haplotypes within the QTL region, which were uniquely defined by
            OPN3907
            alleles. We estimate a probability of 0.40 that no other mutation within this region is concordant with the QTL genotypes of these eight bulls. Finally, we demonstrate that the motif harboring
            OPN3907
            , which is upstream of the promoter and within a region known to harbor tissue-specific osteopontin regulatory elements, is moderately conserved among mammals. The motif was not retrieved from database queries and may be a novel regulatory element.
          }, number={19}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Schnabel, R. D. and Kim, J.-J. and Ashwell, M. S. and Sonstegard, T. S. and Van Tassell, C. P. and Connor, E. E. and Taylor, J. F.}, year={2005}, month={May}, pages={6896–6901} }
 @article{schnabel_sonstegard_taylor_ashwell_2005, title={Whole-genome scan to detect QTL for milk production, conformation, fertility and functional traits in two US Holstein families}, volume={36}, ISSN={["1365-2052"]}, DOI={10.1111/j.1365-2052.2005.01337.x}, abstractNote={SummaryA genome scan was conducted in two US Holstein half‐sib families to identify quantitative trait loci (QTL) affecting milk production and conformation traits using the granddaughter design. The sires of the two studied families were related as sire and son and had 96 and 212 sons respectively. A total of 221 microsatellite loci were scored in both families. Statistical analysis was performed using two different analytical methods; half‐sib least squares regression and Bayesian Monte Carlo Markov Chain. Traits analysed included five traditional milk production traits, somatic cell count, daughter pregnancy rate, male fertility and 20 conformation traits. A total of 47 tests achieved at least genome‐wise significance. However, results from the two methods of analysis were only concordant for QTL location and level of significance in eight instances.}, number={5}, journal={ANIMAL GENETICS}, author={Schnabel, RD and Sonstegard, TS and Taylor, JF and Ashwell, MS}, year={2005}, month={Oct}, pages={408–416} }
 @article{connor_sonstegard_ashwell_bennett_williams_2004, title={An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions}, volume={35}, ISSN={0268-9146 1365-2052}, url={http://dx.doi.org/10.1111/j.1365-2052.2004.01151.x}, DOI={10.1111/j.1365-2052.2004.01151.x}, abstractNote={SummaryAt present, the density of genes on the bovine maps is extremely limited and current resolution of the human–bovine comparative map is insufficient for selection of candidate genes controlling many economic traits of interest in dairy cattle. This study describes the chromosomal mapping of 10 selected gene‐associated markers to bovine linkage and radiation hybrid maps to improve the breakpoint resolution in the human–bovine comparative map near two previously identified quantitative trait loci for the linear type trait, dairy form. Two regions of conserved synteny not previously described are reported between the telomeric region of bovine chromosome 27 (BTA27) and human chromosome 3 (HSA3) p24 region and between the HSA4q34.1 region and BTA8. These data increase the number of genes positioned on the bovine gene maps, refine the human–bovine comparative map, and should improve the efficiency of candidate gene selection for the dairy form trait in cattle.}, number={4}, journal={Animal Genetics}, publisher={Wiley}, author={Connor, E. E. and Sonstegard, T. S. and Ashwell, M. S. and Bennett, G. L. and Williams, J. L.}, year={2004}, month={Aug}, pages={265–269} }
 @article{ashwell_heyen_sonstegard_van tassell_da_vanraden_ron_weller_lewin_2004, title={Detection of Quantitative Trait Loci Affecting Milk Production, Health, and Reproductive Traits in Holstein Cattle}, volume={87}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(04)73186-0}, DOI={10.3168/jds.s0022-0302(04)73186-0}, abstractNote={We report putative quantitative trait loci affecting female fertility and milk production traits using the merged data from two research groups that conducted independent genome scans in Dairy Bull DNA Repository grandsire families to identify quantitative trait loci (QTL) affecting economically important traits. Six families used by both groups had been genotyped for 367 microsatellite markers covering 2713.5 cM of the cattle genome (90%), with an average spacing of 7.4 cM. Phenotypic traits included PTA for pregnancy rate and daughter deviations for milk, protein and fat yields, protein and fat percentages, somatic cell score, and productive life. Analysis of the merged dataset identified putative quantitative trait loci that were not detected in the separate studies, and the pregnancy rate PTA estimates that recently became available allowed detection of pregnancy rate QTL for the first time. Sixty-one putative significant marker effects were identified within families, and 13 were identified across families. Highly significant effects were found on chromosome 3 affecting fat percentage and protein yield, on chromosome 6 affecting protein and fat percentages, on chromosome 14 affecting fat percentage, on chromosome 18 affecting pregnancy rate, and on chromosome 20 affecting protein percentage. Within-family analysis detected putative QTL associated with pregnancy rate on six chromosomes, with the effect on chromosome 18 being the most significant statistically. These findings may help identify the most useful markers available for QTL detection and, eventually, for marker-assisted selection for improvement of these economically important traits.}, number={2}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Ashwell, M.S. and Heyen, D.W. and Sonstegard, T.S. and Van Tassell, C.P. and Da, Y. and VanRaden, P.M. and Ron, M. and Weller, J.I. and Lewin, H.A.}, year={2004}, month={Feb}, pages={468–475} }
 @article{van tassell_sonstegard_ashwell_2004, title={Mapping Quantitative Trait Loci Affecting Dairy Conformation to Chromosome 27 in Two Holstein Grandsire Families}, volume={87}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(04)73184-7}, DOI={10.3168/jds.s0022-0302(04)73184-7}, abstractNote={Preliminary marker association results for quantitative trait loci affecting conformation traits using the granddaughter design and 8 large US Holstein grandsire families revealed strong associations in two families between the predicted transmitting abilities for dairy conformation and marker genotypes on bovine chromosome 27. Those results were based on single marker-trait associations in a genome-scan to identify broad chromosomal regions potentially containing genes affecting traits of interest. Results presented here describe continued study of quantitative trait loci on chromosome 27 for eventual incorporation into a marker-assisted selection program. Tests of marker associations for family 8 (91 sons) indicated an association with a microsatellite marker located near the telomere of chromosome 27. Interval analysis performed using additional marker genotypes generated for family 8 yielded further evidence for a quantitative trait locus in this region. No evidence was found for associations with milk production traits in this family in this region. An association was also detected in family 2 (240 sons) with a microsatellite marker located approximately 21 cM from the centromere of chromosome 27. Interval analysis performed for family 2 yielded evidence for a quantitative trait locus for dairy conformation near BMS689 with evidence of associations with fat percentage in the same region. Identification of quantitative trait loci affecting dairy conformation and fat components supports results reported by other groups, providing additional evidence that genes affecting fat metabolism are located on bovine chromosome 27.}, number={2}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Van Tassell, C.P. and Sonstegard, T.S. and Ashwell, M.S.}, year={2004}, month={Feb}, pages={450–457} }
 @article{vallejo_li_rogers_ashwell_2003, title={Genetic Diversity and Background Linkage Disequilibrium in the North American Holstein Cattle Population}, volume={86}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(03)74028-4}, DOI={10.3168/jds.s0022-0302(03)74028-4}, abstractNote={The objectives of this study were to 1) identify highly heterozygous Holstein bulls that are as unrelated as possible and widely used in the US dairy industry; 2) quantify the level of genetic diversity in US Holsteins; and 3) determine the extent of background linkage disequilibrium (BLD) and disease trait associated linkage disequilibrium (DLD) in the US Holstein population. Twenty-three Holstein bulls that are not closely related but were widely used in the US dairy industry were genotyped for 54 microsatellite loci. The genotyping was performed on automated DNA sequencers (PE Applied Biosystems, CA), following polymerase chain reaction amplification with fluorescent dye-labeled primers. The heterozygosity for the sampled population ranged from 0.43 to 0.80. This wide range of heterozygosity allows selection of the most heterozygous bulls to develop informative families for gene mapping studies. The degree of genetic diversity in this population is significant and allows selection for traits of economic importance. As expected, there is extensive linkage disequilibrium (LD) in the US Holstein population. About half of the syntenic marker pairs presented a typical pattern of LD produced by DLD. Most of the nonsyntenic marker pairs had a typical pattern of LD arising from BLD. These results suggest that the observed LD is not purely due to genetic drift and migration and that a portion might be due to DLD. This raises our hopes of successful fine-localization of genes for complex traits using LD mapping.}, number={12}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Vallejo, R.L. and Li, Y.L. and Rogers, G.W. and Ashwell, M.S.}, year={2003}, month={Dec}, pages={4137–4147} }
 @misc{merrill_2003, title={Genetic approaches to improving health and reproduction in cattle}, author={Merrill, M.S.}, year={2003}, month={Nov} }
 @article{connor_sonstegard_keele_bennett_williams_papworth_van tassell_ashwell_2004, title={Physical and linkage mapping of mammary-derived expressed sequence tags in cattle}, volume={83}, ISSN={0888-7543}, url={http://dx.doi.org/10.1016/S0888-7543(03)00218-0}, DOI={10.1016/S0888-7543(03)00218-0}, abstractNote={This study describes the physical and linkage mapping of 42 gene-associated markers developed from mammary gland-derived expressed sequence tags to the cattle genome. Of the markers, 25 were placed on the USDA reference linkage map and 37 were positioned on the Roslin 3000-rad radiation hybrid (RH) map, with 20 assignments shared between the maps. Although no novel regions of conserved synteny between the cattle and the human genomes were identified, the coverage was extended for bovine chromosomes 3, 7, 15, and 29 compared with previously published comparative maps between human and bovine genomes. Overall, these data improve the resolution of the human-bovine comparative maps and will assist future efforts to integrate bovine RH and linkage map data.}, number={1}, journal={Genomics}, publisher={Elsevier BV}, author={Connor, E.E and Sonstegard, T.S and Keele, J.W and Bennett, G.L and Williams, J.L and Papworth, R and Van Tassell, C.P and Ashwell, M.S}, year={2004}, month={Jan}, pages={148–152} }
 @article{ashwell_sonstegard_kata_womack_2002, title={A radiation hybrid map of bovine chromosome 27}, volume={33}, ISSN={0268-9146}, url={http://dx.doi.org/10.1046/j.1365-2052.2002.0742c.x}, DOI={10.1046/j.1365-2052.2002.0742c.x}, abstractNote={Animal GeneticsVolume 33, Issue 1 p. 75-76 A radiation hybrid map of bovine chromosome 27 Melissa S. Ashwell, Melissa S. Ashwell USDA, ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.,Search for more papers by this authorTad S. Sonstegard, Tad S. Sonstegard USDA, ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.,Search for more papers by this authorSrinivas Kata, Srinivas Kata Department of Veterinary Pathobiology, Texas A & M University, College Station, TX, USASearch for more papers by this authorJames E. Womack, James E. Womack Department of Veterinary Pathobiology, Texas A & M University, College Station, TX, USASearch for more papers by this author Melissa S. Ashwell, Melissa S. Ashwell USDA, ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.,Search for more papers by this authorTad S. Sonstegard, Tad S. Sonstegard USDA, ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.,Search for more papers by this authorSrinivas Kata, Srinivas Kata Department of Veterinary Pathobiology, Texas A & M University, College Station, TX, USASearch for more papers by this authorJames E. Womack, James E. Womack Department of Veterinary Pathobiology, Texas A & M University, College Station, TX, USASearch for more papers by this author First published: 05 March 2002 https://doi.org/10.1046/j.1365-2052.2002.0742c.xCitations: 5 Melissa S. Ashwell, (e-mail: mashwell@anri.barc.usda.gov) Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume33, Issue1February 2002Pages 75-76 RelatedInformation}, number={1}, journal={Animal Genetics}, publisher={Wiley}, author={Ashwell, Melissa S. and Sonstegard, Tad S. and Kata, Srinivas and Womack, James E.}, year={2002}, month={Feb}, pages={75–76} }
 @article{connor_ashwell_dahl_2002, title={Characterization and expression of the bovine growth hormone-releasing hormone (GHRH) receptor}, volume={22}, ISSN={0739-7240}, url={http://dx.doi.org/10.1016/s0739-7240(02)00129-7}, DOI={10.1016/s0739-7240(02)00129-7}, abstractNote={The hypothalamic hormone, growth hormone-releasing hormone (GHRH) and its pituitary receptor are principal regulators of pituitary growth hormone (GH) synthesis and release. In the present study, we cloned and sequenced a complete bovine pituitary GHRH receptor cDNA in order to study its expression in cattle. The lengths of the exons in the bovine GHRH receptor gene were determined by comparison of the cloned cDNA with genomic sequences obtained from a bovine genomic library clone. As in other species, the bovine cDNA sequence encodes a 423-amino acid protein containing seven hydrophobic domains characteristic of a G protein-coupled receptor. The predicted bovine amino acid sequence shares 93, 90, 89, 87, and 85% identity with the ovine, porcine, human, rat and mouse sequences, respectively. Expression of the receptor in bovine ileum, ovary, anterior pituitary, testis, hypothalamus, pancreas and liver was examined by RT-PCR. Of those tissues examined, GHRH receptor expression was detected in the anterior pituitary gland and hypothalamus. To gain a better understanding of GHRH receptor gene regulation in ruminants, we examined the effect of bovine somatotropin (bST) treatment on pituitary GHRH receptor expression in dairy heifers using relative and real-time RT-PCR. In the present study, bST treatment of dairy heifers resulted in no significant decline in pituitary GHRH receptor expression.}, number={4}, journal={Domestic Animal Endocrinology}, publisher={Elsevier BV}, author={Connor, E.E. and Ashwell, M.S. and Dahl, G.E.}, year={2002}, month={Jun}, pages={189–200} }
 @inproceedings{ashwell_schnabel_sonstegard_van tassell_2002, title={Fine-mapping of QTL affecting protein percent and fat percent on BTA6 in a popular U.S. Holstein family.}, volume={31}, booktitle={World Congress of Genetics Applied to Livestock Production Proceedings}, author={Ashwell, M.S. and Schnabel, R.D. and Sonstegard, T.S. and Van Tassell, C.P.}, year={2002}, pages={123–126} }
 @inbook{van tassell_sonstegard_ashwell_connor_kappes_2002, place={New York}, title={Genetics, Cattle Genomics}, volume={2}, url={http://dx.doi.org/10.1016/b0-12-227235-8/00178-4}, DOI={10.1016/b0-12-227235-8/00178-4}, booktitle={Encyclopedia of Dairy Sciences}, publisher={Elsevier}, author={Van Tassell, C.P. and Sonstegard, T.S. and Ashwell, M.S. and Connor, E. and Kappes, S.M.}, editor={Roginski, H. and Fuquay, J.W. and Fox, P.F.Editors}, year={2002}, pages={1219–1224} }
 @misc{merrill_2002, title={Genomic tools and techniques used in livestock species}, author={Merrill, M.S.}, year={2002}, month={May} }
 @inproceedings{ashwell_2002, title={Genomic tools and techniques used in livestock species}, volume={20}, booktitle={American College of Veterinary Internal Medicine Forum Proceedings}, author={Ashwell, M.S.}, year={2002}, pages={261–263} }
 @inproceedings{sadler_anderson_ashwell_2002, title={Isolation of DNA from buccal and vaginal samples using the BuccalAmp kit}, volume={9}, booktitle={Epicentre Forum}, author={Sadler, R.S. and Anderson, M.A. and Ashwell, M.S.}, year={2002}, pages={13} }
 @inproceedings{ashwell_sonstegard_van tassell_2002, title={Mapping genes related to disease resistance and milk production in Holsteins}, volume={20}, booktitle={American College of Veterinary Internal Medicine Forum Proceedings}, author={Ashwell, M.S. and Sonstegard, T.S. and Van Tassell, C.P.}, year={2002}, pages={264–266} }
 @misc{merrill_2002, title={Mapping genes related to disease resistance and milk production in US Holsteins}, author={Merrill, M.S.}, year={2002}, month={May} }
 @misc{merrill_2002, title={Molecular approaches to improved disease resistance in dairy cattle}, author={Merrill, M.S.}, year={2002}, month={Nov} }
 @article{ashwell_van tassell_sonstegard_2001, title={A Genome Scan To Identify Quantitative Trait Loci Affecting Economically Important Traits in a US Holstein Population}, volume={84}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(01)74705-4}, DOI={10.3168/jds.s0022-0302(01)74705-4}, abstractNote={Quantitative trait loci affecting economically important traits were studied for eight large US Holstein grandsire families by using the granddaughter design. A total of 155 microsatellite markers located throughout the bovine genome were selected for the scan. The data analyzed include genotypes for 50 markers not previously reported. Results analyses of 105 marker genotypes reported previously were updated. Effects of marker alleles were analyzed for 38 traits including traits for milk production, somatic cell score, productive life, conformation, calving ease, and 16 canonical traits derived from conformation and production traits. Permutation tests were used to calculate empirical traitwise error rates. A traitwise critical value of P = 0.1 was used to determine significance. Ten putative quantitative trait loci associated with seven of the new markers were identified within specific families. One marker on chromosome 14 was associated with differences in fat yield, fat percentage, and a canonical production trait in two families. Markers on chromosomes 18 and 22 were associated with differences in rump angle in the same family. Markers were associated with differences in udder depth and fore udder attachment on chromosomes 16 and 20, respectively. One marker on chromosome 27 was associated with a difference in the dairy capacity composite index, and another marker on chromosome 13 was associated with a difference in a canonical conformation trait. These additional markers complete our genome scan to identify quantitative trait loci affecting economically important traits in a selected commercial Holstein population. The quantitative trait loci identified in this genome scan may be useful for marker-assisted selection to increase the rate of genetic improvement on traits such as disease resistance and conformation traits associated with fitness while accelerating genetic improvement for production.}, number={11}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Ashwell, M.S. and Van Tassell, C.P. and Sonstegard, T.S.}, year={2001}, month={Nov}, pages={2535–2542} }
 @article{sonstegard_van tassell_ashwell_2001, title={Dairy cattle genomics: Tools to accelerate genetic improvement?}, volume={79}, ISSN={0021-8812}, url={http://dx.doi.org/10.2527/jas2001.79e-supple307x}, DOI={10.2527/jas2001.79e-supple307x}, abstractNote={Traditional selection based on genetic merit calculated from phenotypic and pedigree informa- tion has been tremendously effective at improving pro- duction in dairy cattle. Hypothetically, genetic improve- ment could be accelerated even further for yield and other economically important traits by directly select- ing upon the genetic differences underlying the pheno- types. To elucidate these genetic differences, research strategies based on genomic science have been devel- oped to identify economic trait loci (ETL). Once resolved with respect to position in the genome, DNA marker- based tests that identify ETL can be practically applied to enhance selection in a commercial setting. To date, most dairy-related ETL have been detected in Holstein grandsire families using the granddaughter design. Be- cause the marker intervals identifying these ETL are not resolved well enough for accurate selection in cur- rent populations, ETL analyses have been or are being extended to include ancestral animals that connect fam- ily pedigrees and current generations of nonprogeny- tested animals from within the founder animal pedi- gree. Increasing genotypic and phenotypic information}, number={E-Suppl}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Sonstegard, T. S. and Van Tassell, C. P. and Ashwell, M. S.}, year={2001}, pages={E307} }
 @misc{merrill_2001, title={Identification of QTL affecting milk production traits on bovine chromosome 6}, author={Merrill, M.S.}, year={2001}, month={Mar} }
 @article{ashwell_ashwell_garrett_bennett_2001, title={Isolation, characterization and mapping of the bovine signal peptidase subunit 18 gene}, volume={32}, ISSN={0268-9146}, url={http://dx.doi.org/10.1046/j.1365-2052.2001.0769b.x}, DOI={10.1046/j.1365-2052.2001.0769b.x}, abstractNote={Animal GeneticsVolume 32, Issue 4 p. 232-233 Isolation, characterization and mapping of the bovine signal peptidase subunit 18 gene M. S. Ashwell, M. S. Ashwell USDA–ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.Search for more papers by this authorC. M. Ashwell, C. M. Ashwell USDA–ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.Search for more papers by this authorW. M. Garrett, W. M. Garrett USDA–ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.Search for more papers by this authorG. L. Bennett, G. L. Bennett USDA–ARS, US Meat Animal Research Center, Clay Center, NE, USASearch for more papers by this author M. S. Ashwell, M. S. Ashwell USDA–ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.Search for more papers by this authorC. M. Ashwell, C. M. Ashwell USDA–ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.Search for more papers by this authorW. M. Garrett, W. M. Garrett USDA–ARS, Beltsville Agricultural Research Center, Beltsville, MD, USA.Search for more papers by this authorG. L. Bennett, G. L. Bennett USDA–ARS, US Meat Animal Research Center, Clay Center, NE, USASearch for more papers by this author First published: 20 December 2001 https://doi.org/10.1046/j.1365-2052.2001.0769b.xCitations: 1 M. S. Ashwell, (e-mail: mashwell@anri.barc.usda.gov) Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume32, Issue4August 2001Pages 232-233 RelatedInformation}, number={4}, journal={Animal Genetics}, publisher={Wiley}, author={Ashwell, M. S. and Ashwell, C. M. and Garrett, W. M. and Bennett, G. L.}, year={2001}, month={Aug}, pages={232–233} }
 @misc{merrill_2001, title={Mapping genes related to disease resistance and milk production in dairy cattle}, author={Merrill, M.S.}, year={2001}, month={Oct} }
 @misc{merrill_2000, title={A genome scan to identify QTL affecting economically important traits in dairy cattle}, author={Merrill, M.S.}, year={2000}, month={Dec} }
 @article{sonstegard_garrett_ashwell_bennett_kappes_van tassell_2000, title={Comparative map alignment of BTA27 and HSA4 and 8 to identify conserved segments of genome containing fat deposition QTL}, volume={11}, ISSN={0938-8990 1432-1777}, url={http://dx.doi.org/10.1007/s003350010130}, DOI={10.1007/s003350010130}, abstractNote={Quantitative trait loci (QTL) associated with fat deposition have been identified on bovine Chromosome 27 (BTA27) in two different cattle populations. To generate more informative markers for verification and refinement of these QTL-containing intervals, we initiated construction of a BTA27 comparative map. Fourteen genes were selected for mapping based on previously identified regions of conservation between the cattle and human genomes. Markers were developed from the bovine orthologs of genes found on human Chromosomes 1 (HSA1), 4, 8, and 14. Twelve genes were mapped on the bovine linkage map by using markers associated with single nucleotide polymorphisms or microsatellites. Seven of these genes were also anchored to the physical map by assignment of fluorescence in situ hybridization probes. The remaining two genes not associated with an identifiable polymorphism were assigned only to the physical map. In all, seven genes were mapped to BTA27. Map information generated from the other seven genes not syntenic with BTA27 refined the breakpoint locations of conserved segments between species and revealed three areas of disagreement with the previous comparative map. Consequently, portions of HSA1 and 14 are not conserved on BTA27, and a previously undefined conserved segment corresponding to HSA8p22 was identified near the pericentromeric region of BTA8. These results show that BTA27 contains two conserved segments corresponding to HSA8p, which are separated by a segment corresponding to HSA4q. Comparative map alignment strongly suggests the conserved segment orthologous to HSA8p21-q11 contains QTL for fat deposition in cattle.}, number={8}, journal={Mammalian Genome}, publisher={Springer Science and Business Media LLC}, author={Sonstegard, Tad S. and Garrett, Wes M. and Ashwell, Melissa S. and Bennett, Gary L. and Kappes, Steven M. and Van Tassell, Curtis P.}, year={2000}, month={Aug}, pages={682–688} }
 @article{van tassell_ashwell_sonstegard_2000, title={Detection of Putative Loci Affecting Milk, Health, and Conformation Traits in a US Holstein Population Using 105 Microsatellite Markers}, volume={83}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(00)75058-2}, DOI={10.3168/jds.s0022-0302(00)75058-2}, abstractNote={Quantitative trait loci affecting milk yield, health, and conformation traits were studied for eight large US Holstein grandsire families by using the granddaughter design. A total of 105 microsatellite markers, located throughout the bovine genome, were selected for the scan. The data analyzed include genotypes for 35 markers in eight families not previously reported and genotypes for 70 markers reported previously in seven of those families. Analyses of markers previously reported were updated. Effects of marker alleles were analyzed for 38 traits, including traits for milk production, somatic cell score, productive life, conformation, calving ease, and 16 canonical traits derived from conformation and production traits. Permutation tests were used to calculate empirical trait-wise error rates. A trait-wise critical value of P = 0.1 was used to determine significance. Eight putative quantitative trait loci associated with 7 of the 35 new markers were identified within specific families. Two of these markers were associated with differences in strength and rump angle on chromosomes 4 and 9, respectively. Different markers were associated with protein percentage, milk yield, and somatic cell score on chromosomes 6, 7, and 10 in different families. Differences in the canonically transformed traits were associated with markers on chromosomes 5, 6, and 9. Additional marker-trait combinations were identified in the across-family tests, including effects on chromosomes 3, 4, and 9 for protein percentage, body depth, and canonical conformation traits, respectively. Additional markers are being added to allow interval analysis for putative quantitative trait loci that have been identified and to increase marker density.}, number={8}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Van Tassell, C.P. and Ashwell, M.S. and Sonstegard, T.S.}, year={2000}, month={Aug}, pages={1865–1872} }
 @article{ashwell_van tassell_1999, title={Detection of Putative Loci Affecting Milk, Health, and Type Traits in a US Holstein Population Using 70 Microsatellite Markers in a Genome Scan}, volume={82}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(99)75501-3}, DOI={10.3168/jds.s0022-0302(99)75501-3}, abstractNote={Quantitative trait loci affecting milk yield, health, and type traits were studied for seven large U.S. Holstein grandsire families using the granddaughter design. Seventy microsatellite markers located throughout the genome were selected for the quantitative trait loci scan. Effects of marker alleles were analyzed for 30 traits (21 type traits, 5 milk traits, 2 calving ease triats, and somatic cell score and productive life) and 16 canonical traits derived from type and production traits. Previously we reported results from 36 of these markers but have re-evaluated those results using a more robust analysis method. We report results from all 70 markers using permutation tests to calculate experiment-wise significance values, replacing the less stringent comparison-wise values previously reported. With this new methodology we detected 9 putative quantitative trait loci within specific families. Four markers were associated with effects on type traits on chromosomes 4, 5, 14, and 23. Two markers were associated with effects on protein percentage on chromosomes 6 and 14, and 3 markers were associated with effects on productive life on chromosomes 2, 21, and 23. Although these initial 70 microsatellite markers have been completed in the 7 Holstein families, additional markers will need to be added to allow interval analysis of areas where putative QTL have been identified and to increase marker density where needed.}, number={11}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Ashwell, M.S. and Van Tassell, C.P.}, year={1999}, month={Nov}, pages={2497–2502} }
 @article{connor_ashwell_kappes_dahl_1999, title={Mapping of the bovine growth hormone-releasing hormone receptor (GHRH-R) gene to chromosome 4 by linkage analysis using a novel PCR-RFLP.}, volume={77}, ISSN={0021-8812}, url={http://dx.doi.org/10.2527/1999.773793x}, DOI={10.2527/1999.773793x}, abstractNote={Journal Article Rapid communication: mapping of the bovine growth hormone-releasing hormone receptor (GHRH-R) gene to chromosome 4 by linkage analysis using a novel PCR-RFLP Get access E. E. Connor, E. E. Connor *Department of Animal and Avian Sciences, University of Maryland, College Park 20742-2311, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar M. S. Ashwell, M. S. Ashwell †ARS, USDA, Beltsville, MD 20705 Search for other works by this author on: Oxford Academic PubMed Google Scholar S. M. Kappes, S. M. Kappes ‡USDA, Meat Animal Research Center, Clay Center, NE 68933 Search for other works by this author on: Oxford Academic PubMed Google Scholar G. E. Dahl G. E. Dahl *Department of Animal and Avian Sciences, University of Maryland, College Park 20742-2311, USA 2To whom correspondence should be addressed (phone: (301) 405-1374, fax: (301) 314-9059, E-mail: gd38@umail.umd.edu). Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Animal Science, Volume 77, Issue 3, March 1999, Pages 793–794, https://doi.org/10.2527/1999.773793x Published: 01 March 1999 Article history Received: 28 September 1998 Accepted: 06 January 1999 Published: 01 March 1999}, number={3}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Connor, E E and Ashwell, M S and Kappes, S M and Dahl, G E}, year={1999}, pages={793} }
 @article{zegeye_ashwell_ogg_rexroad_mather_1999, title={RFLP markers in the bovine butyrophilin gene}, volume={30}, ISSN={0268-9146}, url={http://dx.doi.org/10.1046/j.1365-2052.1999.00526-4.x}, DOI={10.1046/j.1365-2052.1999.00526-4.x}, abstractNote={Animal GeneticsVolume 30, Issue 5 p. 385-386 RFLP markers in the bovine butyrophilin gene A Zegeye, A Zegeye Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;Search for more papers by this authorM Ashwell, M Ashwell Gene Evaluation and Mapping Laboratory, USDA, Beltsville, MD, 20705, USASearch for more papers by this authorS Ogg, S Ogg Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;Search for more papers by this authorC Rexroad, C Rexroad Gene Evaluation and Mapping Laboratory, USDA, Beltsville, MD, 20705, USASearch for more papers by this authorI H Mather, I H Mather Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;Search for more papers by this author A Zegeye, A Zegeye Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;Search for more papers by this authorM Ashwell, M Ashwell Gene Evaluation and Mapping Laboratory, USDA, Beltsville, MD, 20705, USASearch for more papers by this authorS Ogg, S Ogg Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;Search for more papers by this authorC Rexroad, C Rexroad Gene Evaluation and Mapping Laboratory, USDA, Beltsville, MD, 20705, USASearch for more papers by this authorI H Mather, I H Mather Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;Search for more papers by this author First published: 11 September 2003 https://doi.org/10.1046/j.1365-2052.1999.00526-4.xCitations: 4Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Citing Literature Volume30, Issue5October 1999Pages 385-386 RelatedInformation}, number={5}, journal={Animal Genetics}, publisher={Wiley}, author={Zegeye, A and Ashwell, M and Ogg, S and Rexroad, C and Mather, I H}, year={1999}, month={Oct}, pages={385–386} }
 @article{ashwell_da_vanraden_rexroad_miller_1998, title={Detection of Putative Loci Affecting Conformational Type Traits in an Elite Population of United States Holsteins Using Microsatellite Markers}, volume={81}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(98)75674-7}, DOI={10.3168/jds.s0022-0302(98)75674-7}, abstractNote={Quantitative trait loci affecting conformational type traits were studied in seven large grandsire families of US Holsteins using the granddaughter design and 16 microsatellite markers on 10 chromosomes. The most significant marker effect was marker BM203 (chromosome 27) for dairy form in a single grandsire family. A multivariate analysis for dairy form and milk yield was also conducted, and the result was highly significant, indicating that a segregating quantitative trait locus or loci affecting dairy form and milk yield could exist near BM203 on chromosome 27. Marker BM1258 (chromosome 23) had a significant effect on udder depth. A multivariate analysis on udder depth and somatic cell score was conducted for markers 513 and BM1258, and both markers showed significant effects on these two traits, indicating that one or several quantitative trait loci affecting udder depth and mastitis might exist on chromosome 23. Marker BM4204 (chromosome 9) had a significant effect on foot angle and on the composite index of traits pertaining to feet and legs, indicating that one or several quantitative trait loci affecting traits pertaining to feet and legs might exist on chromosome 9. Selection on these markers could increase genetic progress within these families.}, number={4}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Ashwell, M.S. and Da, Y. and Vanraden, P.M. and Rexroad, C.E., Jr. and Miller, R.H.}, year={1998}, month={Apr}, pages={1120–1125} }
 @article{ashwell_da_van tassell_vanraden_miller_rexroad_1998, title={Detection of Putative Loci Affecting Milk Production and Composition, Health, and Type Traits in a United States Holstein Population}, volume={81}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.s0022-0302(98)75896-5}, DOI={10.3168/jds.s0022-0302(98)75896-5}, abstractNote={Quantitative trait loci affecting milk yield and composition, health, and type traits were studied for seven large grandsire families of US Holstein using the granddaughter design. The families were genotyped at 20 microsatellite markers on 15 chromosomes, and the effects of the marker alleles were analyzed for 28 traits (21 type traits, 5 milk yield and composition traits, somatic cell score, and productive herd life). Markers BM415 on chromosome 6 and BM6425 on chromosome 14 were associated with effects on protein percentage in a single grandsire family. The latter marker had a lower probability of being associated with changes in milk yield and fat percentage in the same family. Increases in productive herd life were associated with an allele at marker BM719 on chromosome 16 in one grandsire family.}, number={12}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Ashwell, M.S. and Da, Y. and Van Tassell, C.P. and Vanraden, P.M. and Miller, R.H. and Rexroad, C.E., Jr.}, year={1998}, month={Dec}, pages={3309–3314} }
 @article{ashwell_rexroad_miller_vanraden_da_1997, title={Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers}, volume={28}, ISSN={0268-9146 1365-2052}, url={http://dx.doi.org/10.1111/j.1365-2052.1997.00115.x}, DOI={10.1111/j.1365-2052.1997.00115.x}, abstractNote={Quantitative trait loci (QTL) affecting health and milk production traits were studied in seven large half‐sib US Holstein families by using the granddaughter design. Genotyping for 16 markers was completed and marker allele differences within and pooled‐across families were analysed. Potential QTL were identified for somatic cell score (SCS), fat yield, fat percentage, protein yield and protein percentage. Three markers (BM203, BM4505 and BM2078) were associated with significant effects for different traits and, after further analysis, may be useful in marker‐assisted selection in specific families. Comparisons between these data and previously identified QTL support the location of a QTL for milk yield and protein yield on chromosome 21.}, number={3}, journal={Animal Genetics}, publisher={Wiley}, author={Ashwell, M S and Rexroad, C E, Jr and Miller, R H and VanRaden, P M and Da, Y}, year={1997}, month={Jun}, pages={216–222} }
 @article{ashwell_rexroad_miller_vanraden_1996, title={Mapping economic trait loci for somatic cell score in Holstein cattle using microsatellite markers and selective genotyping}, volume={27}, ISSN={0268-9146 1365-2052}, url={http://dx.doi.org/10.1111/j.1365-2052.1996.tb00484.x}, DOI={10.1111/j.1365-2052.1996.tb00484.x}, abstractNote={SummaryMarker‐assisted selection (MAS) uses genetic marker genotypes to predict an animal's production potential and will provide additional selection information for progeny testing. With the discovery of highly polymorphic microsatellite markers, the tools now exist to begin the search for economic trait loci (ETL), which is the first step toward MAS. The objective of this study was to identify ETL for somatic cell score in an existing Holstein population. Using the granddaughter design, sons from seven grandsire families were genotyped with 20 autosomal microsatellites from five chromosomes (4, 8, 13, 17, 23), with an emphasis on chromosome 23, which is the location of the bovine major histocompatibility complex (BoLA). Selective genotyping was used to reduce the number of genotypes required, in which the 10 highest and 10 lowest sons from the phenotypic distribution curve were tested (140 sons in seven families). One marker (513), located near BoLA, showed evidence of an ETL in three of five polymorphic families. Additional sons were genotyped from the five families to estimate the effect and to compare selective and ‘complete’ genotyping. Both methods detected an ETL at marker 513, but in different families. This study provides evidence of the usefulness of microsatellite markers and the granddaughter design in the detection of ETL; however, additional markers need to be evaluated to determine the usefulness of selective genotyping. Based on the results from the 20 studied markers, the most likely position of a somatic cell score ETL lies near marker 513, located on chromosome 23.}, number={4}, journal={Animal Genetics}, publisher={Wiley}, author={Ashwell, M. S. and Rexroad, C. E., Jr and Miller, R. H. and VanRaden, P. M.}, year={1996}, month={Aug}, pages={235–242} }
 @misc{merrill_1996, title={State of the art in animal genome mapping}, author={Merrill, M.S.}, year={1996} }
 @article{ashwell_ogg_mather_1996, title={The bovine butyrophilin gene maps to chromsome 23}, volume={27}, ISSN={0268-9146 1365-2052}, url={http://dx.doi.org/10.1111/j.1365-2052.1996.tb00945.x}, DOI={10.1111/j.1365-2052.1996.tb00945.x}, abstractNote={SummaryChromosomal assignment of the bovine butyrophilin gene (BTN) was performed by analysis of DNA from somatic hybrid cell lines using the polymerase chain reaction. The gene was assigned to bovine chromosome 23 using two sets of primers specific for bovine BTN.}, number={3}, journal={Animal Genetics}, publisher={Wiley}, author={Ashwell, M S and Ogg, S L and Mather, I H}, year={1996}, month={Jun}, pages={171–173} }
 @misc{merrill_1995, title={Current techniques used in gene mapping}, author={Merrill, M.S.}, year={1995} }
 @article{schuster_bowden_1994, title={D10S681, a microsatellite polymorphism near the RET locus}, volume={3}, ISSN={0964-6906 1460-2083}, url={http://dx.doi.org/10.1093/hmg/3.4.677}, DOI={10.1093/hmg/3.4.677}, number={4}, journal={Human Molecular Genetics}, publisher={Oxford University Press (OUP)}, author={Schuster, M.K. and Bowden, D.W.}, year={1994}, pages={677–677} }
 @article{zheng_ma_dorman_wang_braunschweiger_soares_schuster_rothschild_bowden_torrey_et al._1994, title={Development of 124 Sequence-Tagged Sites and Cytogenetic Localization of 217 Cosmids for Human Chromosome 10}, volume={22}, ISSN={0888-7543}, url={http://dx.doi.org/10.1006/geno.1994.1345}, DOI={10.1006/geno.1994.1345}, abstractNote={A total of 124 new chromosome 10-specific sequence-tagged sites (STSs) were derived from two sources: (1) DNA sequences obtained from anonymous clones in new libraries enriched for human chromosome 10 inserts, and (2) published sequences of genes and other loci already known to map to chromosome 10. Libraries were constructed from a somatic cell hybrid carrying human chromosomes 10 and Y. A cosmid library was made from total DNA of the hybrid and probed with labeled total human DNA to identify clones with human DNA inserts. Two hundred seventeen cosmids were mapped to regions of human chromosome 10 by fluorescence in situ hybridization. Twenty-five cosmids represent probes that have been placed on the genetic map previously. One hundred ninety-two cosmids represent new probes that have not been mapped previously. Cosmids carrying inserts with CA repeats were identified by hybridization with a labeled poly(dC-dA)-poly(dG-dT) probe and subcloned to yield microsatellite STS markers. Two small insert plasmid libraries were made, the first by subcloning inserts from a chromosome 10-enriched lambda phage library (LL10NS01) and the second by cloning Alu element-mediated PCR products amplified from hybrid DNA. STSs were generated from the DNA sequences of clone inserts. Chromosome 10-specific STSs were distinguished from Y chromosome STSs by one or both of the following criteria: (1) successful PCR amplification from a template consisting of DNA from another chromosome 10-containing cell line, NA10926B, or (2) FISH localization to chromosome 10 of the source cosmid or of YACs isolated by PCR screening with the STS. These libraries were the source of 90 new chromosome 10-specific STSs, 42 of which contain CA repeats.}, number={1}, journal={Genomics}, publisher={Elsevier BV}, author={Zheng, Chuang-jie and Ma, Nancy Shui-Fong and Dorman, Thomas E. and Wang, Mei-Tai and Braunschweiger, Karen and Soares, Lorena and Schuster, Melissa K. and Rothschild, Cynthia B. and Bowden, Donald W. and Torrey, Dana and et al.}, year={1994}, month={Jul}, pages={55–67} }
 @article{xue_yu_maurer_memoll_nutile-mcmenemy_schuster_bowden_mao_noll_1994, title={Germline RET mutations in MEN 2A and FMTC and their detection by simple DNA diagnostic tests}, volume={3}, ISSN={0964-6906 1460-2083}, url={http://dx.doi.org/10.1093/hmg/3.4.635}, DOI={10.1093/hmg/3.4.635}, abstractNote={Multiple endocrine neoplasia type 2A (MEN 2A) and familial medullary thyroid carcinoma (FMTC) are two closely related cancer syndromes inherited in an autosomal dominant manner. Mutations in the RET proto-oncogene were found in MEN 2A and FMTC families. In this study we report seven different germline mutations in the RET proto-oncogene in five of five MEN 2A and five of six FMTC families. Each of the mutations involves a cysteine residue in the extracellular cysteine-rich domain of the RET receptor tyrosine kinase. We developed simple polymerase chain reaction based diagnostic tests for all seven mutations in these families.}, number={4}, journal={Human Molecular Genetics}, publisher={Oxford University Press (OUP)}, author={Xue, Feiyu and Yu, Hong and Maurer, L.Herbert and Memoll, Vincent A. and Nutile-McMenemy, Nancy and Schuster, Melissa K. and Bowden, Donald W. and Mao, Jen-I and Noll, Walter W.}, year={1994}, pages={635–638} }
 @article{rothschild_noll_gravius_schuster_nutile-mcmenemy_jones_bowden_1992, title={Characterization of radiation/fusion hybrids containing parts of human chromosome 10 and their use in mapping chromosome 10-specific probes}, volume={13}, ISSN={0888-7543}, url={http://dx.doi.org/10.1016/0888-7543(92)90197-z}, DOI={10.1016/0888-7543(92)90197-z}, abstractNote={We have characterized a panel of somatic cell hybrid cell lines which contain different portions of human chromosome 10. Genomic DNA from the somatic cell hybrids was tested for hybridization with each of an ordered set of probes used previously to construct a genetic map of chromosome 10, as well as several additional probes, previously localized by in situ hybridization. Hybridization of an unmapped probe to the cell line DNAs can be used to determine its most likely position on the chromosome relative to the mapped set of probes. Genomic DNA from two of the cell lines has been used to construct region-specific cosmid and bacteriophage libraries, and clones derived from these libraries were localized by hybridization to the panel of hybrid cell lines. Several of these probes reveal restriction fragment length polymorphisms which have been genetically mapped. Three of the probes map near the locus for multiple endocrine neoplasia type 2A, and one of these probes, BG-JC353 (D10S167), maps between RBP3 and TB14.34 (D10S34). Another probe, CRI-J282 (D10S104), is close to the FNRB locus. The panel of hybrid cell lines is thus useful for rapidly localizing unmapped probes and as a source of DNA for the construction of recombinant libraries derived from specific regions of the chromosome.}, number={1}, journal={Genomics}, publisher={Elsevier BV}, author={Rothschild, Cynthia B. and Noll, Walter W. and Gravius, Thomas C. and Schuster, Melissa K. and Nutile-McMenemy, Nancy and Jones, Carol and Bowden, Donald W.}, year={1992}, month={May}, pages={25–34} }