• Identifying Single Copy Orthologs in Metazoa

      Creevey, Christopher J.; Muller, Jean; Doerks, Tobias; Thompson, Julie D.; Arendt, Detlev; Bork, Peer (PLOS, 2011-12-01)
      The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.
    • Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue

      Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David A; Waters, Sinead M.; McGee, Mark; Kelly, Alan K; McCabe, Matthew S (Biomed Central, 2017-05-02)
      Background Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.
    • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

      McCabe, Matthew Sean; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M. (PLOS, 2015-07-30)
      Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
    • Impact of three inactivated bovine viral diarrhoea virus vaccines on bulk milk p80 (NS3) ELISA test results in dairy herds

      Sayers, Riona; Sayers, Gearoid; Graham, David; Arkins, Sean (Elsevier, 2015-03-25)
      Bovine viral diarrhoea virus (BVDV) is endemic in many countries and vaccines are used as a component of control and eradication strategies. Surveillance programmes to detect exposure to BVDV often incorporate the use of bulk milk (BM) testing for antibodies against BVDV p80 (NS3), but vaccination can interfere with these results. The aim of this study was to evaluate whether BVDV vaccines would confound BM testing for specific antibodies in a nationally representative group of commercial dairy farms in the Republic of Ireland. A total of 256 commercial dairy herds were included in the statistical analysis. Quarterly BM or serum samples from selected weanling heifers (unvaccinated homeborn youngstock) were assessed by ELISA for antibodies against the BVDV p80 subunit and whole virus. Wilcoxon ranksum and receiver operating characteristic (ROC) analyses were used to examine differences among groups vaccinated with one of three commercially available inactivated BVDV vaccines. Two of the three vaccines showed evidence of interference with ELISA testing of BM samples. ROC analysis highlighted that one vaccine did not reduce the discriminatory power of the BVDV p80 ELISA for identification of herds with evidence of recent BVDV circulation, when compared with unvaccinated herds; thus, administration of this vaccine would allow uncomplicated interpretation of BM ELISA test results in vaccinated seropositive herds. Seasonal differences in BM antibody results were identified, suggesting that the latter half of lactation is the most suitable time for sampling dairy herds containing predominantly spring calving cows. The results of the present study are likely to prove useful in countries allowing vaccination during or following BVDV eradication, where BM testing is required as part of the surveillance strategy.
    • Implementing biosecurity measures on dairy farms in Ireland

      Sayers, Riona; Sayers, Gearoid; Mee, John F; Good, M.; Bermingham, Mairead L; Grant, Jim; Dillon, Pat (Elsevier, 2012-12-29)
      Dairy farms in Ireland are expanding in preparation for a new era of unrestricted milk production with the elimination of the European Union (EU) production quotas in 2015. Countries experiencing a changing agricultural demographic, including farm expansion, can benefit from documenting the implementation of on-farm biosecurity. The objectives of this study were to document and describe influences on biosecurity practices and related opinions on dairy farms. A representative response rate of 64% was achieved to a nationwide telesurvey of farmers. A 20% discrepancy was found between self-declared and truly ‘closed’ herds indicating a lack of understanding of the closed herd concept. Although >72% of farmers surveyed considered biosecurity to be important, 53% stated that a lack of information might prevent them from improving their biosecurity. Logistic regression highlighted regional, age, and farm-size related differences in biosecurity practices and opinions towards its implementation. Farmers in the most dairy cattle dense region were three times more likely to quarantine purchased stock than were their equivalents in regions where dairy production was less intense (P = 0.012). Younger farmers in general were over twice as likely as middle-aged farmers to implement biosecurity guidelines (P = 0.026). The owners of large enterprises were almost five times more likely to join a voluntary animal health scheme (P = 0.003), and were over three times more likely to pay a premium price for health accredited animals (P = 0.02) than were those farming small holdings. The baseline data recorded in this survey will form the basis for more detailed sociological and demographic research which will facilitate the targeting of future training of the farming community in biosecurity.
    • The Imprinted Retrotransposon-Like Gene PEG11 (RTL1) Is Expressed as a Full-Length Protein in Skeletal Muscle from Callipyge Sheep

      Byrne, Keren; Colgrave, Michelle L.; Vuocolo, Tony; Pearson, Roger; Bidwell, Christopher A.; Cockett, Noelle E.; Lynn, David J; Fleming-Waddell, Jolena N.; Tellam, Ross L. (PLOS, 2010-01-08)
      Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.
    • Improved detection of biomarkers in cervico-vaginal mucus (CVM) from postpartum cattle

      Adnane, Mounir; Kelly, Paul; Chapwanya, Aspinas; Meade, Kieran G; O’Farrelly, Cliona; The Algerian Ministry for High Education and Scientific Research; University of Tiaret, Algeria; Department of Agriculture, Food and the Marine, Ireland; ofarrecl-HRB-HRA_POR/2012/37; 13/S/472 (Biomed Central, 2018-09-29)
      Background In the postpartum cow, early diagnosis of uterine disease is currently problematic due to the lack of reliable, non-invasive diagnostic methods. Cervico-vaginal mucus (CVM) is an easy to collect potentially informative source of biomarkers for the diagnosis and prognosis of uterine disease in cows. Here, we report an improved method for processing CVM from postpartum dairy cows for the measurement of immune biomarkers. CVM samples were collected from the vagina using gloved hand during the first two weeks postpartum and processed with buffer alone or buffer containing different concentrations of the reducing agents recommended in standard protocols: Dithiothriotol (DTT) or N-Acetyl-L-Cysteine (NAC). Total protein was measured using the bicinchoninic acid (BCA) assay; interleukin 6 (IL-6), IL-8 and α1-acid glycoprotein (AGP) were measured by ELISA. Results We found that use of reducing agents to liquefy CVM affects protein yield and the accuracy of biomarker detection. Our improved protocol results in lower protein yields but improved detection of cytokines and chemokines. Using our modified method to measure AGP in CVM we found raised levels of AGP at seven days postpartum in CVM from cows that went on to develop endometritis. Conclusion We conclude that processing CVM without reducing agents improves detection of biomarkers that reflect uterine health in cattle. We propose that measurement of AGP in CVM during the first week postpartum may identify cows at risk of developing clinical endometritis.
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection

      Berry, Donagh P.; Kearney, J. F. (Cambridge University Press, 2011-02)
      The objective of this study was to quantify the accuracy achievable from imputing genotypes from a commercially available low-density marker panel (2730 single nucleotide polymorphisms (SNPs) following edits) to a commercially available higher density marker panel (51 602 SNPs following edits) in Holstein–Friesian cattle using Beagle, a freely available software package. A population of 764 Holstein–Friesian animals born since 2006 were used as the test group to quantify the accuracy of imputation, all of which had genotypes for the high-density panel; only SNPs on the low-density panel were retained with the remaining SNPs to be imputed. The reference population for imputation consisted of 4732 animals born before 2006 also with genotypes on the higher density marker panel. The concordance between the actual and imputed genotypes in the test group of animals did not vary across chromosomes and was on average 95%; the concordance between actual and imputed alleles was, on average, 97% across all SNPs. Genomic predictions were undertaken across a range of production and functional traits for the 764 test group animals using either their real or imputed genotypes. Little or no mean difference in the genomic predictions was evident when comparing direct genomic values (DGVs) using real or imputed genotypes. The average correlation between the DGVs estimated using the real or imputed genotypes for the 15 traits included in the Irish total merit index was 0.97 (range of 0.92 to 0.99), indicating good concordance between proofs from real or imputed genotypes. Results show that a commercially available high-density marker panel can be imputed from a commercially available lower density marker panel, which will also have a lower cost, thereby facilitating a reduction in the cost of genomic selection. Increased available numbers of genotyped and phenotyped animals also has implications for increasing the accuracy of genomic prediction in the entire population and thus genetic gain using genomic selection.
    • Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

      Berry, Donagh P.; McParland, Sinead; Kearney, J.F.; Sargolzaei, M.; Mullen, Michael P.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; European Union; RSF-06-0353; RSF-06-0428; 1/SF/311; 09/IN.1/B2642 (Cambridge University Press, 2014-04-09)
      The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n = 3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n = 5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the withinanimal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.
    • Increased detection of mastitis pathogens by real-time PCR compared to bacterial culture

      Keane, Orla M; Budd, Kathleen E; Flynn, James; McCoy, Finola (British Veterinary Association, 2013-08-23)
      Rapid and accurate identification of mastitis pathogens is important for disease control. Bacterial culture and isolate identification is considered the gold standard in mastitis diagnosis but is time consuming and results in many culture-negative samples. Identification of mastitis pathogens by PCR has been proposed as a fast and sensitive alternative to bacterial culture. The results of bacterial culture and PCR for the identification of the aetiological agent of clinical mastitis were compared. The pathogen identified by traditional culture methods was also detected by PCR in 98 per cent of cases indicating good agreement between the positive results of bacterial culture and PCR. A mastitis pathogen could not be recovered from approximately 30 per cent of samples by bacterial culture, however, an aetiological agent was identified by PCR in 79 per cent of these samples. Therefore, a mastitis pathogen was detected in significantly more milk samples by PCR than by bacterial culture (92 per cent and 70 per cent, respectively) although the clinical relevance of PCR-positive culture-negative results remains controversial. A mixed infection of two or more mastitis pathogens was also detected more commonly by PCR. Culture-negative samples due to undetected Staphylococcus aureus infections were rare. The use of PCR technology may assist in rapid mastitis diagnosis, however, accurate interpretation of PCR results in the absence of bacterial culture remains problematic.
    • Influence of feeding systems on the eating quality of beef

      Troy, Declan J.; Murray, Brendan; O'Sullivan, Aidan; Mooney, Teresa; Moloney, Aidan P; Kerry, Joseph (Teagasc, 2002-10)
      The objective was to determine pre-slaughter factors which may enhance the eating quality of beef and to assist the Irish beef production chain to exploit these factors to produce beef of higher quality and increased consumer acceptability. The effects of pre-slaughter growth rate, high energy diets, feed type and age at slaughter on beef quality were examined.
    • InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

      Breuer, Karin; Foroushani, Amir K.; Laird, Matthew R; Chen, Carol; Sribnaia, Anastasia; Lo, Raymond; Winsor, Geoffrey L.; Hancock, Robert E. W.; Brinkman, Fiona S. L.; Lynn, David J (Oxford University Press, 2012-11-24)
      InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.
    • Insemination factors affecting the conception rate in seasonal calving Holstein-Friesian cows

      Buckley, Frank; Mee, John F; O'Sullivan, Kathleen; Evans, Ross D; Berry, Donagh P.; Dillon, Pat (EDP Sciences, 2003-11)
      Differences in conception rate to first service between artificial inseminations (AI) carried out by commercial AI operators (CAI) or do-it-yourself operators (DIY), between natural service (NAT) and AI, between different AI sires, and between fresh and frozen-thawed semen, on Irish commercial dairy farms, were studied using logistic regression. The study comprised 12 933 potential first inseminations from 77 spring-calving dairy herds. The data were recorded during 1999 and 2000. Amongst the total, 4 394 cows had repeated records across the two years. Adjustment variables included: herd, year, parity, calving period, calving to service interval, herd size, proportion of North American Holstein-Friesian genes, peak milk yield, semen fresh or frozen-thawed status, AI sire and a cow history variable to account for the correlation structure that may exist between performance records of cows present in both years of the study. Interactions of interest were tested but were non-significant. No significant association was observed between the category of AI operator and the likelihood of conception rate to first service (PREG1). The variation in PREG1 observed within the category of operator (CAI and DIY) was investigated using the Levene test for homogeneity of variance. There was no difference between the level of variation observed within CAI and DIY operators. There were significant differences in the likelihood of PREG1 between different AI sires. Amongst the 40 most commonly used AI sires, 3 sires had a lower likelihood of PREG1 (P < 0.05) when compared to the reference AI sire (sire with PREG1 similar to the mean of the group). There was a tendency for a reduced likelihood of PREG1 with the use of fresh semen compared to frozen-thawed semen ( , P = 0.067). Amongst the adjustment variables in the model, those significantly associated with the likelihood of PREG1 included the herd, calving period, calving to first service interval and peak milk yield. No significant difference in the likelihood of PREG1 was observed between AI and NAT.
    • Insulin increases 17β-estradiol production by the dominant follicle of the first postpartum follicle wave in dairy cows

      Butler, Stephen T.; Pelton, S.H.; Butler, W.R. (Bioscientifica on behalf of Society for Reproduction and Fertility, 2004-05-01)
      Prolonged anovulation following parturition has a negative impact on fertility in dairy cows. Insulin plays an important role in ovarian function in many species, and is profoundly depressed in dairy cows during early lactation. We hypothesized that hypoinsulinemia during early lactation represents a key indicator of nutritional status, resulting in delayed ovulation. Holstein cows (n = 10) were subjected to either a hyperinsulinemic–euglycemic clamp (INS) or saline infusion (CTL) for 96 h, beginning on day 10 after parturition during the first postpartum follicular wave. Insulin was infused continuously (0.3 μg/kg body weight per h) via a jugular catheter, and euglycemia was maintained by infusion of glucose. Circulating insulin concentrations were elevated 2.6-fold in INS cows compared with CTL cows (0.73 ± 0.026 vs 0.28 ± 0.026 ng/ml; P < 0.001). Insulin treatment did not affect (P > 0.05) luteinizing hormone (LH) pulse frequency, pulse amplitude or mean circulating LH. Circulating estradiol was elevated in INS cows (P < 0.01) and circulating testosterone also tended to be higher. The ratio of testosterone to estradiol was not different between treatments for the initial 30 h of infusion, but was significantly reduced thereafter in response to insulin (P < 0.01), suggesting that hyperinsulinemia increased follicular aromatase activity. Insulin treatment also resulted in reduced circulating nonesterified fatty acids, and increased circulating total and free insulin-like growth factor-I concentrations. Insulin infusion increased estradiol secretion by the dominant follicle of the first postpartum follicular wave in dairy cows, and this effect appears not to be mediated through changes in pulsatile LH release.
    • Insulin restores GH responsiveness during lactation-induced negative energy balance in dairy cattle: effects on expression of IGF-I and GH receptor 1A

      Butler, Stephen T.; Marr, A.L.; Pelton, S.H.; Radcliff, R.P.; Lucy, Matt C.; Butler, W.R. (Bioscientifica, 2003-02-01)
      Early lactation in dairy cattle is a period of severe negative energy balance (NEB) characterized by reduced blood glucose and insulin concentrations and elevated blood growth hormone (GH) concentrations. The liver is refractory to GH during NEB and this uncoupling of the GH-insulin-like growth factor (IGF) axis results in diminished plasma concentrations of IGF-I. Our objectives were to examine the effects of insulin administration during the immediate postpartum period on plasma IGF-I and GH concentrations and to examine the hepatic expression of total GH receptor (all GH receptor transcripts), GH receptor 1A (GHR 1A) and IGF-I. In addition, we examined adipose tissue for total GH receptor and IGF-I mRNA levels to establish the effects of chronic hyperinsulinemia on an insulin-responsive peripheral tissue. Holstein cows (n = 14) were subjected to either a hyperinsulinemic-euglycemic clamp (insulin; INS) or saline infusion (control; CTL) for 96 hours starting on day 10 postpartum. Insulin was infused intravenously (1µg • kg BW-1 • h-1), blood samples were collected hourly, and euglycemia was maintained by infusion of glucose. Insulin concentrations during the infusions were increased 8-fold in INS cows compared with CTL cows (2.33 ± 0.14 vs. 0.27 ± 0.14 ng/ml; P < 0.001) while blood glucose concentrations were not different between treatments (45.3 ± 2.2 vs. 42.5 ± 2.2 mg/dl; P > 0.1). Plasma IGF-I increased continuously during the insulin infusion, and reached the highest concentrations at the end of the clamp, being almost four-fold higher in INS compared with CTL cows (117 ± 4 vs. 30 ± 4 ng/ml; P < 0.001). Hepatic expression of GHR 1A and IGF-I mRNA was low in CTL cows, but was increased 3.6-fold (P < 0.05) and 6.3-fold (P < 0.001) respectively in INS cows. By contrast, in adipose tissue the changes in gene expression in response to insulin were reversed with decreases in both total GHR and IGF-I mRNA. The expression of GHR 1A and IGF-I mRNA in liver tissue were correlated in INS (r = 0.86; P < 0.05), but not CTL cows (r = 0.43; P > 0.1). Insulin appears to be a key metabolic signal in coupling the GH-IGF axis, thus orchestrating a marked elevation in circulating IGF-I concentrations.
    • Intake, growth and carcass traits in male progeny of sires differing in genetic merit for beef production

      Clarke, A. M.; Drennan, Michael J; McGee, Mark; Kenny, David A.; Evans, Ross D; Berry, Donagh P. (Cambridge University Press, 2009-06)
      Validation of economic indexes under a controlled experimental environment, can aid in their acceptance and use as breeding tools to increase herd profitability. The objective of this study was to compare intake, growth and carcass traits in bull and steer progeny of high and low ranking sires, for genetic merit in an economic index. The Beef Carcass Index (BCI; expressed in euro (€) and based on weaning weight, feed intake, carcass weight, carcass conformation and fat scores) was generated by the Irish Cattle Breeding Federation as a tool to compare animals on genetic merit for the expected profitability of their progeny at slaughter. A total of 107 male suckler herd progeny, from 22 late-maturing ‘continental’ beef sires of high (n = 11) or low (n = 11) BCI were compared under either a bull or steer production system, and slaughtered at approximately 16 and 24 months of age, respectively. All progeny were purchased after weaning at approximately 6 to 8 months of age. Dry matter (DM) intake and live-weight gain in steer progeny offered grazed grass or grass silage alone, did not differ between the two genetic groups. Similarly, DM intake and feed efficiency did not differ between genetic groups during an ad libitum concentrate-finishing period on either production system. Carcasses of progeny of high BCI sires were 14 kg heavier (P < 0.05) than those of low BCI sires. In a series of regression analyses, increasing sire BCI resulted in increases in carcass weight (P < 0.01) and carcass conformation (P = 0.051) scores, and decreases in carcass fat (P < 0.001) scores, but had no effect on weaning weight or DM intake of the progeny. Each unit increase in sire expected progeny difference led to an increase in progeny weaning weight, DM intake, carcass weight, carcass conformation score and carcass fat score of 1.0 (s.e. = 0.53) kg, 1.1 (s.e. = 0.32) kg, 1.3 (s.e. = 0.31) kg, 0.9 (s.e. = 0.32; scale 1 to 15) and 1.0 (s.e. = 0.25; scale 1 to 15), respectively, none of which differed from the theoretical expectation of unity. The expected difference in profitability at slaughter between progeny of the high and low BCI sires was €42, whereas the observed phenotypic profit differential of the progeny was €53 in favour of the high BCI sires. Results from this study indicate that the BCI is a useful tool in the selection of genetically superior sires, and that actual progeny performance under the conditions of this study is within expectations for both bull and steer beef production systems.
    • Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis

      Foley, Cathriona; Chapwanya, Aspinas; Callanan, John J; Whiston, Ronan; Miranda-CasoLuengo, Raúl; Lu, Junnan; Meijer, Wim G; Lynn, David J; O’ Farrelly, Cliona; Meade, Kieran G (Biomed Central, 2015-10-19)
      Background The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility postpartum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the postpartum dairy cow. Methods Endometrial biopsy RNA was extracted from 15 cows at 7 and 21 days postpartum (DPP), using the Qiagen RNeasy® Plus Mini kit and quality determined using an Agilent 2100 bioanalyser. Disease status was determined by histpathology based on inflammatory cell infiltrate. RNA-seq of both mRNA and miRNA libraries were performed on an Illumina® HiSeq™ 2000. Paired reads were aligned to the bovine genome with Bowtie2 and differentially expressed genes were identified using EdgeR. Significantly over-represented Gene Ontology terms were identified using GO-seq, and pathway analysis was performed using KEGG. Quanititative real-time PCR was also performed for validation (ABI 7500 fast). Haematology was assessed using an automated ADVIA 2120 analyser. Serum proteins were evaluated by ELISA and metabolite analysis was performed using a Beckman Coulter AU 400 clinical analyser. Terminal-restriction fragment length polymorphism (T-RFLP) was used to obtain fingerprints of the microbial communities present. Results Next-generation sequencing from endometrial biopsies taken at 7 DPP identified significant induction of inflammatory gene expression in all cows. Despite the common inflammatory profile and enrichment of the Toll-like receptor and NFκB pathways, 73 genes and 31 miRNAs were significantly differentially expressed between healthy cows (HC, n = 9) and cows which subsequently developed CE at 7 DPP (n = 6, FDR < 0.1). While significant differential expression of 4197 genes in the transcriptome of healthy cows between 7 and 21 DPP showed the transition from a proinflammatory to tissue profliferation and repair, only 31 genes were differentially expressed in cows with CE (FDR < 0.1), indicating the arrest of such a transition. A link betwene the dysregulated inflammatory response and the composition of the uterine microbial communities was suggested by the presence of significant differences in uterine bacterial tRFLP profiles between HC and CE groups. Furthermore, inflammatory activity was not confined to the uterus; decreased circulating granulocytes and increased Acute Phase Protein (SAA and HP) expression levels were detected in plasma at 7 DPP in cows that developed CE. Conclusion Our data suggests that the IL1 and IL17 inflammatory cascade activated early postpartum is resolved thereby restoring homeostasis in healthy cows by 21 DPP, but this transition fails to occur in cows which develop CE. Despite a common early inflammatory profile, elevated and differential expression of specific immune genes may identify cows at risk of prolonged inflammation and the development of CE postpartum.
    • Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis

      Foley, Cathriona; Chapwanya, Aspinas; Callanan, John J; Whiston, Ronan; Miranda-CasoLuengo, Raúl; Lu, Junnan; Meijer, Wim G; Lynn, David J; O’ Farrelly, Cliona; Meade, Kieran G (Biomed Central, 2015-10-19)
      Background The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility postpartum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the postpartum dairy cow. Methods Endometrial biopsy RNA was extracted from 15 cows at 7 and 21 days postpartum (DPP), using the Qiagen RNeasy® Plus Mini kit and quality determined using an Agilent 2100 bioanalyser. Disease status was determined by histpathology based on inflammatory cell infiltrate. RNA-seq of both mRNA and miRNA libraries were performed on an Illumina® HiSeq™ 2000. Paired reads were aligned to the bovine genome with Bowtie2 and differentially expressed genes were identified using EdgeR. Significantly over-represented Gene Ontology terms were identified using GO-seq, and pathway analysis was performed using KEGG. Quanititative real-time PCR was also performed for validation (ABI 7500 fast). Haematology was assessed using an automated ADVIA 2120 analyser. Serum proteins were evaluated by ELISA and metabolite analysis was performed using a Beckman Coulter AU 400 clinical analyser. Terminal-restriction fragment length polymorphism (T-RFLP) was used to obtain fingerprints of the microbial communities present. Results Next-generation sequencing from endometrial biopsies taken at 7 DPP identified significant induction of inflammatory gene expression in all cows. Despite the common inflammatory profile and enrichment of the Toll-like receptor and NFκB pathways, 73 genes and 31 miRNAs were significantly differentially expressed between healthy cows (HC, n = 9) and cows which subsequently developed CE at 7 DPP (n = 6, FDR < 0.1). While significant differential expression of 4197 genes in the transcriptome of healthy cows between 7 and 21 DPP showed the transition from a proinflammatory to tissue profliferation and repair, only 31 genes were differentially expressed in cows with CE (FDR < 0.1), indicating the arrest of such a transition. A link betwene the dysregulated inflammatory response and the composition of the uterine microbial communities was suggested by the presence of significant differences in uterine bacterial tRFLP profiles between HC and CE groups. Furthermore, inflammatory activity was not confined to the uterus; decreased circulating granulocytes and increased Acute Phase Protein (SAA and HP) expression levels were detected in plasma at 7 DPP in cows that developed CE. Conclusion Our data suggests that the IL1 and IL17 inflammatory cascade activated early postpartum is resolved thereby restoring homeostasis in healthy cows by 21 DPP, but this transition fails to occur in cows which develop CE. Despite a common early inflammatory profile, elevated and differential expression of specific immune genes may identify cows at risk of prolonged inflammation and the development of CE postpartum.
    • Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis

      Foley, Cathriona; Chapwanya, Aspinas; Callanan, John J; Whiston, Ronan; Miranda-CasoLuengo, Raul; Lu, Junnan; Meijer, Wim G; Lynn, David J; O’ Farrelly, Cliona; Meade, Kieran G (Biomed Central, 2015-10-19)
      Background The regulation of endometrial inflammation has important consequences for the resumption of bovine fertility postpartum. All cows experience bacterial influx into the uterus after calving; however a significant proportion fail to clear infection leading to the development of cytological endometritis (CE) and compromised fertility. We hypothesised that early immunological changes could not only act as potential prognostic biomarkers for the subsequent development of disease but also shed light on the pathogenesis of endometritis in the postpartum dairy cow. Methods Endometrial biopsy RNA was extracted from 15 cows at 7 and 21 days postpartum (DPP), using the Qiagen RNeasy® Plus Mini kit and quality determined using an Agilent 2100 bioanalyser. Disease status was determined by histpathology based on inflammatory cell infiltrate. RNA-seq of both mRNA and miRNA libraries were performed on an Illumina® HiSeq™ 2000. Paired reads were aligned to the bovine genome with Bowtie2 and differentially expressed genes were identified using EdgeR. Significantly over-represented Gene Ontology terms were identified using GO-seq, and pathway analysis was performed using KEGG. Quanititative real-time PCR was also performed for validation (ABI 7500 fast). Haematology was assessed using an automated ADVIA 2120 analyser. Serum proteins were evaluated by ELISA and metabolite analysis was performed using a Beckman Coulter AU 400 clinical analyser. Terminal-restriction fragment length polymorphism (T-RFLP) was used to obtain fingerprints of the microbial communities present. Results Next-generation sequencing from endometrial biopsies taken at 7 DPP identified significant induction of inflammatory gene expression in all cows. Despite the common inflammatory profile and enrichment of the Toll-like receptor and NFκB pathways, 73 genes and 31 miRNAs were significantly differentially expressed between healthy cows (HC, n = 9) and cows which subsequently developed CE at 7 DPP (n = 6, FDR < 0.1). While significant differential expression of 4197 genes in the transcriptome of healthy cows between 7 and 21 DPP showed the transition from a proinflammatory to tissue profliferation and repair, only 31 genes were differentially expressed in cows with CE (FDR < 0.1), indicating the arrest of such a transition. A link betwene the dysregulated inflammatory response and the composition of the uterine microbial communities was suggested by the presence of significant differences in uterine bacterial tRFLP profiles between HC and CE groups. Furthermore, inflammatory activity was not confined to the uterus; decreased circulating granulocytes and increased Acute Phase Protein (SAA and HP) expression levels were detected in plasma at 7 DPP in cows that developed CE. Conclusion Our data suggests that the IL1 and IL17 inflammatory cascade activated early postpartum is resolved thereby restoring homeostasis in healthy cows by 21 DPP, but this transition fails to occur in cows which develop CE. Despite a common early inflammatory profile, elevated and differential expression of specific immune genes may identify cows at risk of prolonged inflammation and the development of CE postpartum.
    • The integration of ‘omic’ disciplines and systems biology in cattle breeding

      Berry, Donagh P.; Meade, Kieran G; Mullen, Michael Paul; Butler, Stephen T.; Diskin, Michael G.; Morris, Dermot G.; Creevey, Christopher J. (Cambridge University Press, 2010-10)
      Enormous progress has been made in the selection of animals, including cattle, for specific traits using traditional quantitative genetics approaches. Never the less, considerable variation in phenotypes remains unexplained, and therefore represents potential additional gain for animal production. In addition, the paradigm shift in new disciplines now being applied to animal breeding represents a powerful opportunity to prise open the ‘black box’ underlying the response to selection and fully understand the genetic architecture controlling the traits of interest. A move away from traditional approaches of animal breeding toward systems approaches using integrative analysis of data from the ‘omic’ disciplines represents a multitude of exciting opportunities for animal breeding going forward as well as providing alternatives for overcoming some of the limitations of traditional approaches such as the expressed phenotype being an imperfect predictor of the individual’s true genetic merit, or the phenotype being only expressed in one gender or late in the lifetime of an animal. This review aims to discuss these opportunities from the perspective of their potential application and contribution to cattle breeding. Harnessing the potential of this paradigm shift also poses some new challenges for animal scientists – and they will also be discussed