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Dr. Mazdak Salavati
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0 Cell Biology
0 Molecular & Cellular Biology
0 Bioinfomatics
0 Genomics and transcriptomics
0 Genetic analysis of complex traits of agricultural animals

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Original article
Published: 19 June 2021 in Molecular Biology Reports
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Bovine mastitis, an inflammatory disease of the mammary gland, is classified as subclinical or clinical. Circulating neutrophils are recruited to the udder to combat infection. We compared the transcriptomic profiles in circulating leukocytes between healthy cows and those with naturally occurring subclinical or clinical mastitis. Holstein Friesian dairy cows from six farms in EU countries were recruited. Based on milk somatic cell count and clinical records, cows were classified as healthy (n = 147), subclinically (n = 45) or clinically mastitic (n = 22). Circulating leukocyte RNA was sequenced with Illumina NextSeq single end reads (30 M). Differentially expressed genes (DEGs) between the groups were identified using CLC Genomics Workbench V21, followed by GO enrichment analysis. Both subclinical and clinical mastitis caused significant changes in the leukocyte transcriptome, with more intensive changes attributed to clinical mastitis. We detected 769 DEGs between clinical and healthy groups, 258 DEGs between subclinical and healthy groups and 193 DEGs between clinical and subclinical groups. Most DEGs were associated with cell killing and immune processes. Many upregulated DEGs in clinical mastitis encoded antimicrobial peptides (AZU1, BCL3, CAMP, CATHL1, CATHL2, CATHL4,CATHL5, CATHL6, CCL1, CXCL2, CXCL13, DEFB1, DEFB10, DEFB4A, DEFB7, LCN2, PGLYRP1, PRTN3, PTX3, S100A8, S100A9, S100A12, SLC11A1, TF and LTF) which were not upregulated in subclinical mastitis. The use of transcriptomic profiles has identified a much greater up-regulation of genes encoding antimicrobial peptides in circulating leukocytes of cows with naturally occurring clinical compared with subclinical mastitis. These could play a key role in combatting disease organisms.

ACS Style

Zhangrui Cheng; Laura Buggiotti; Mazdak Salavati; Cinzia Marchitelli; Sergio Palma-Vera; Alistair Wylie; Haruko Takeda; Lijing Tang; Mark A. Crowe; D. Claire Wathes; Niamh McLoughlin; Alan Fahey; Elizabeth Matthews; Andreia Santoro; Colin Byrne; Pauline Rudd; Roisin O’Flaherty; Sinead Hallinan; Claire Wathes; Ali Fouladi; Geoff Pollott; Dirk Werling; Beatriz Sanz Bernardo; Matt Bell; Mieke Vaneetvelde; Kristof Hermans; Geert Opsomer; Sander Moerman; Jenne De Koster; Hannes Bogaert; Jan Vandepitte; Leila Vandevelde; Bonny Vanranst; Johanna Hoglund; Susanne Dahl; Klaus Ingvartsen; Martin Sørensen; Leslie Foldager; Soren Ostergaard; Janne Rothmann; Mogens Krogh; Else Meyer; Charlotte Gaillard; Jehan Ettema; Tine Rousing; Federica Signorelli; Francesco Napolitano; Bianca Moioli; Alessandra Crisa; Luca Buttazzoni; Jennifer McClure; Daragh Matthews; Francis Kearney; Andrew Cromie; Matt McClure; Shujun Zhang; Xing Chen; Huanchun Chen; Junlong Zhao; Liguo Yang; Guohua Hua; Chen Tan; Guiqiang Wang; Michel Bonneau; Andrea Pompozzi; Armin Pearn; Arnold Evertson; Linda Kosten; Anders Fogh; Thomas Andersen; Matthew Lucy; Chris Elsik; Gavin Conant; Jerry Taylor; Nicolas Gengler; Michel Georges; Frederic Colinet; Marilou Ramos Pamplona; Hedi Hammami; Catherine Bastin; Aurelie Laine; Anne-Sophie Van Laere; Martin Schulze; GplusE consortium. Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis. Molecular Biology Reports 2021, 48, 4611 -4623.

AMA Style

Zhangrui Cheng, Laura Buggiotti, Mazdak Salavati, Cinzia Marchitelli, Sergio Palma-Vera, Alistair Wylie, Haruko Takeda, Lijing Tang, Mark A. Crowe, D. Claire Wathes, Niamh McLoughlin, Alan Fahey, Elizabeth Matthews, Andreia Santoro, Colin Byrne, Pauline Rudd, Roisin O’Flaherty, Sinead Hallinan, Claire Wathes, Ali Fouladi, Geoff Pollott, Dirk Werling, Beatriz Sanz Bernardo, Matt Bell, Mieke Vaneetvelde, Kristof Hermans, Geert Opsomer, Sander Moerman, Jenne De Koster, Hannes Bogaert, Jan Vandepitte, Leila Vandevelde, Bonny Vanranst, Johanna Hoglund, Susanne Dahl, Klaus Ingvartsen, Martin Sørensen, Leslie Foldager, Soren Ostergaard, Janne Rothmann, Mogens Krogh, Else Meyer, Charlotte Gaillard, Jehan Ettema, Tine Rousing, Federica Signorelli, Francesco Napolitano, Bianca Moioli, Alessandra Crisa, Luca Buttazzoni, Jennifer McClure, Daragh Matthews, Francis Kearney, Andrew Cromie, Matt McClure, Shujun Zhang, Xing Chen, Huanchun Chen, Junlong Zhao, Liguo Yang, Guohua Hua, Chen Tan, Guiqiang Wang, Michel Bonneau, Andrea Pompozzi, Armin Pearn, Arnold Evertson, Linda Kosten, Anders Fogh, Thomas Andersen, Matthew Lucy, Chris Elsik, Gavin Conant, Jerry Taylor, Nicolas Gengler, Michel Georges, Frederic Colinet, Marilou Ramos Pamplona, Hedi Hammami, Catherine Bastin, Aurelie Laine, Anne-Sophie Van Laere, Martin Schulze, GplusE consortium. Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis. Molecular Biology Reports. 2021; 48 (5):4611-4623.

Chicago/Turabian Style

Zhangrui Cheng; Laura Buggiotti; Mazdak Salavati; Cinzia Marchitelli; Sergio Palma-Vera; Alistair Wylie; Haruko Takeda; Lijing Tang; Mark A. Crowe; D. Claire Wathes; Niamh McLoughlin; Alan Fahey; Elizabeth Matthews; Andreia Santoro; Colin Byrne; Pauline Rudd; Roisin O’Flaherty; Sinead Hallinan; Claire Wathes; Ali Fouladi; Geoff Pollott; Dirk Werling; Beatriz Sanz Bernardo; Matt Bell; Mieke Vaneetvelde; Kristof Hermans; Geert Opsomer; Sander Moerman; Jenne De Koster; Hannes Bogaert; Jan Vandepitte; Leila Vandevelde; Bonny Vanranst; Johanna Hoglund; Susanne Dahl; Klaus Ingvartsen; Martin Sørensen; Leslie Foldager; Soren Ostergaard; Janne Rothmann; Mogens Krogh; Else Meyer; Charlotte Gaillard; Jehan Ettema; Tine Rousing; Federica Signorelli; Francesco Napolitano; Bianca Moioli; Alessandra Crisa; Luca Buttazzoni; Jennifer McClure; Daragh Matthews; Francis Kearney; Andrew Cromie; Matt McClure; Shujun Zhang; Xing Chen; Huanchun Chen; Junlong Zhao; Liguo Yang; Guohua Hua; Chen Tan; Guiqiang Wang; Michel Bonneau; Andrea Pompozzi; Armin Pearn; Arnold Evertson; Linda Kosten; Anders Fogh; Thomas Andersen; Matthew Lucy; Chris Elsik; Gavin Conant; Jerry Taylor; Nicolas Gengler; Michel Georges; Frederic Colinet; Marilou Ramos Pamplona; Hedi Hammami; Catherine Bastin; Aurelie Laine; Anne-Sophie Van Laere; Martin Schulze; GplusE consortium. 2021. "Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis." Molecular Biology Reports 48, no. 5: 4611-4623.

Preprint content
Published: 21 April 2021
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Canine Inflammatory bowel disease (IBD) is a chronic multifactorial disease, resulting from complex interactions between the intestinal immune system, microbiota and environmental factors in genetically predisposed dogs. Previously, we identified several single nucleotide polymorphisms (SNP) and regions on chromosomes (Chr) 7, 9, 11 and 13 associated with IBD in German shepherd dogs (GSD) using GWAS and FST association analyses. Here, building on our previous results, we performed a targeted next-generation sequencing (NGS) of a two Mb region on Chr 9 and 11 that included 14 of the newly identified candidate genes, in order to identify potential functional SNPs that could explain these association signals. Furthermore, correlations between genotype and treatment response were estimated. Results revealed several SNPs in the genes for canine EEF1A1, MDH2, IL3, IL4, IL13 and PDLIM, which, based on the known function of their corresponding proteins, further our insight into the pathogenesis of IBD in dogs. In addition, several pathways involved in innate and adaptive immunity and inflammatory responses (i.e. T helper cell differentiation, Th1 and Th2 activation pathway, communication between innate and adaptive immune cells and differential regulation of cytokine production in intestinal epithelial cells by IL-17A and IL-17F), were constructed involving the gene products in the candidate regions for IBD susceptibility. Interestingly, some of the identified SNPs were present in only one outcome group, suggesting that different genetic factors are involved in the pathogenesis of IBD in different treatment response groups. This also highlights potential genetic markers to predict the response in dogs treated for IBD.

ACS Style

Atiyeh Peiravan; Mazdak Salavati; Androniki Psifidi; Mellora Sharman; Andrew Kent; Penny Watson; Karin Allenspach; Dirk Werling. Targeted next-generation sequencing of Candidate Regions Identified by GWAS Revealed SNPs Associated with IBD in GSDs. 2021, 1 .

AMA Style

Atiyeh Peiravan, Mazdak Salavati, Androniki Psifidi, Mellora Sharman, Andrew Kent, Penny Watson, Karin Allenspach, Dirk Werling. Targeted next-generation sequencing of Candidate Regions Identified by GWAS Revealed SNPs Associated with IBD in GSDs. . 2021; ():1.

Chicago/Turabian Style

Atiyeh Peiravan; Mazdak Salavati; Androniki Psifidi; Mellora Sharman; Andrew Kent; Penny Watson; Karin Allenspach; Dirk Werling. 2021. "Targeted next-generation sequencing of Candidate Regions Identified by GWAS Revealed SNPs Associated with IBD in GSDs." , no. : 1.

Journal article
Published: 01 March 2021 in Journal of Dairy Science
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ACS Style

D.C. Wathes; Z. Cheng; M. Salavati; L. Buggiotti; H. Takeda; L. Tang; F. Becker; K.I. Ingvartsen; C. Ferris; M. Hostens; M.A. Crowe. Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation. Journal of Dairy Science 2021, 104, 3596 -3616.

AMA Style

D.C. Wathes, Z. Cheng, M. Salavati, L. Buggiotti, H. Takeda, L. Tang, F. Becker, K.I. Ingvartsen, C. Ferris, M. Hostens, M.A. Crowe. Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation. Journal of Dairy Science. 2021; 104 (3):3596-3616.

Chicago/Turabian Style

D.C. Wathes; Z. Cheng; M. Salavati; L. Buggiotti; H. Takeda; L. Tang; F. Becker; K.I. Ingvartsen; C. Ferris; M. Hostens; M.A. Crowe. 2021. "Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation." Journal of Dairy Science 104, no. 3: 3596-3616.

Journal article
Published: 27 January 2021 in Genome Biology and Evolution
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Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

ACS Style

Pamela Wiener; Christelle Robert; Abulgasim Ahbara; Mazdak Salavati; Ayele Abebe; Adebabay Kebede; David Wragg; Juliane Friedrich; Deepali Vasoya; David A Hume; Appolinaire Djikeng; Mick Watson; James G D Prendergast; Olivier Hanotte; Joram M Mwacharo; Emily L Clark. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biology and Evolution 2021, 13, 1 .

AMA Style

Pamela Wiener, Christelle Robert, Abulgasim Ahbara, Mazdak Salavati, Ayele Abebe, Adebabay Kebede, David Wragg, Juliane Friedrich, Deepali Vasoya, David A Hume, Appolinaire Djikeng, Mick Watson, James G D Prendergast, Olivier Hanotte, Joram M Mwacharo, Emily L Clark. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biology and Evolution. 2021; 13 (3):1.

Chicago/Turabian Style

Pamela Wiener; Christelle Robert; Abulgasim Ahbara; Mazdak Salavati; Ayele Abebe; Adebabay Kebede; David Wragg; Juliane Friedrich; Deepali Vasoya; David A Hume; Appolinaire Djikeng; Mick Watson; James G D Prendergast; Olivier Hanotte; Joram M Mwacharo; Emily L Clark. 2021. "Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations." Genome Biology and Evolution 13, no. 3: 1.

Preprint content
Published: 21 January 2021
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There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We have optimised the ‘Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)’ to profile regions of open chromatin in flash frozen pig muscle tissue samples. This protocol has allowed us to identify putative regulatory regions in semitendinosus muscle from 24 male piglets. We collected samples from the smallest, average, and largest sized male piglets from each litter through five developmental time points. The ATAC-Seq data were mapped to Sscrofa11.1 using Bowtie2 and Genrich was used for post-alignment peak-calling. Of the 4,661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with down regulation of genes involved in muscle development that were present in small sized foetal piglets but absent in large foetal piglets at day 90 of gestation. The dataset that we have generated provides: i) a resource for studies of genome regulation in pigs, and ii) contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programmes.

ACS Style

Mazdak Salavati; Shernae A. Woolley; Yennifer Cortés Araya; Michelle M. Halstead; Claire Stenhouse; Martin Johnsson; Cheryl J. Ashworth; Alan L. Archibald; Francesc X. Donadeu; Musa A. Hassan; Emily L. Clark. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. 2021, 1 .

AMA Style

Mazdak Salavati, Shernae A. Woolley, Yennifer Cortés Araya, Michelle M. Halstead, Claire Stenhouse, Martin Johnsson, Cheryl J. Ashworth, Alan L. Archibald, Francesc X. Donadeu, Musa A. Hassan, Emily L. Clark. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. . 2021; ():1.

Chicago/Turabian Style

Mazdak Salavati; Shernae A. Woolley; Yennifer Cortés Araya; Michelle M. Halstead; Claire Stenhouse; Martin Johnsson; Cheryl J. Ashworth; Alan L. Archibald; Francesc X. Donadeu; Musa A. Hassan; Emily L. Clark. 2021. "Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions." , no. : 1.

Journal article
Published: 30 December 2020 in Viruses
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In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international “CoronaHack” in April 2020, we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2; n = 163), bat (bat-CoV; n = 215) and pangolin (pangolin-CoV; n = 7) available in public repositories. We have also noted the pangolin-CoV isolate MP789 to bare stronger resemblance to SARS-CoV-2 than other pangolin-CoV. Following de novo gene annotation prediction, analyses of gene–gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Last, we have characterised several high impact variants (in-frame insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.

ACS Style

Nicholas J. Dimonaco; Mazdak Salavati; Barbara B. Shih. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses 2020, 13, 49 .

AMA Style

Nicholas J. Dimonaco, Mazdak Salavati, Barbara B. Shih. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses. 2020; 13 (1):49.

Chicago/Turabian Style

Nicholas J. Dimonaco; Mazdak Salavati; Barbara B. Shih. 2020. "Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations." Viruses 13, no. 1: 49.

Preprint content
Published: 28 December 2020
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Background: Previous studies of ageing have identified many pathways which are consistently altered in humans and model organisms. Dairy cows are often culled at quite young ages due to an inability to cope adequately with metabolic and infectious diseases, resulting in reduced milk production and infertility. Improved longevity is therefore a desirable trait which would benefit both farmers and their cows. This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. Results: Samples were divided into three age groups for analysis: i) primiparous (PP, n = 53), ii) multiparous in lactations 2-3 (MP 2-3, n = 121), and iii) MP in lactations 4-7 (MP>3, n = 55). Leukocyte expression was compared between PP vs MP>3 cows with MP 2-3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). Seven modules were significantly correlated (r ≥ 0.25) to the trait age. Genes from the modules which were more highly expressed in either the PP or MP>3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. The top three clusters from modules more highly expressed in the PP cows all involved regulation of gene transcription, particularly zinc fingers. Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. Top clusters up-regulated in MP>3 cows included the terms Glycolysis/Gluconeogenesis, C-type lectin, and Immunity. Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function (CCR7, CD27, IL7R, CAMK4, CD28), mitochondrial ribosomal proteins (MRPS27, MRPS9, MRPS31), and DNA replication and repair (WRN). Those up-regulated in MP>3 cows encoded immune defence proteins (LYZ, CTSZ, SREBF1, GRN, ANXA5, ADARB1). Conclusions: Genes and pathways associated with age in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. We also detected changes in energy utilization and immune responses in leukocytes with age.

ACS Style

Laura Buggiotti; Zhangrui Cheng; Mazdak Salavati; Claire D. Wathes. Age Related Changes in the Circulating Leukocyte Transcriptome in Dairy Cows. 2020, 1 .

AMA Style

Laura Buggiotti, Zhangrui Cheng, Mazdak Salavati, Claire D. Wathes. Age Related Changes in the Circulating Leukocyte Transcriptome in Dairy Cows. . 2020; ():1.

Chicago/Turabian Style

Laura Buggiotti; Zhangrui Cheng; Mazdak Salavati; Claire D. Wathes. 2020. "Age Related Changes in the Circulating Leukocyte Transcriptome in Dairy Cows." , no. : 1.

Standard article
Published: 12 December 2020 in Journal of Veterinary Internal Medicine
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Background Minimally invasive diagnostic imaging techniques to detect intestinal inflammation in dogs are lacking. Contrast‐enhanced ultrasound (CEUS) and endoscopic narrow band imaging‐like endoscopy (Storz Professional Image Enhancement System [SPIES]) might allow quantification of intestinal mucosal perfusion and microvessel density in chronic inflammatory enteropathy (CIE) of dogs. Hypothesis/Objectives Markers of mucosal perfusion as determined by CEUS and SPIES endoscopy are potentially useful diagnostic markers to help characterize CIE and correlate with histological inflammation type and severity. Animals Thirty client‐owned dogs diagnosed with CIE at a referral hospital were prospectively enrolled. Materials and Methods Data from CEUS, SPIES, and white light (WL) endoscopy were correlated with World Small Animal Veterinary Association (WSAVA) endoscopy and histology scores and vessel density as determined by immunohistochemistry for von Willebrand factor (vWF). Automated linear modeling was used to determine predictors of endoscopic and histologic severity. Results Duodenal histology correlated with SPIES data (area percentage value, rho = 0.424, P = .04). White light endoscopy parameters correlated with SPIES parameters in the duodenum. Colonic histology correlated positively with CEUS, whereas colonic CEUS parameters correlated inversely with vWF expression. Several duodenal parameters combined predicted duodenal histology scores to a level of 73.4%. For the colon, 2 parameters contributed more than others to 73.1%. Conclusion and Clinical Importance Minimally invasive CEUS and SPIES appear feasible to assess intestinal perfusion in CIE. Use of SPIES endoscopy may be promising for assessing small intestinal inflammation, whereas CEUS could be used to assess colonic perfusion and inflammation. Both techniques need to be investigated further for their clinical utility.

ACS Style

Mazdak Salavati; Jorge Pérez‐Accino; Yi Lin Tan; Tiziana Liuti; Sionagh Smith; Linda Morrison; Silke Salavati Schmitz. Correlation of minimally invasive imaging techniques to assess intestinal mucosal perfusion with established markers of chronic inflammatory enteropathy in dogs. Journal of Veterinary Internal Medicine 2020, 35, 162 -171.

AMA Style

Mazdak Salavati, Jorge Pérez‐Accino, Yi Lin Tan, Tiziana Liuti, Sionagh Smith, Linda Morrison, Silke Salavati Schmitz. Correlation of minimally invasive imaging techniques to assess intestinal mucosal perfusion with established markers of chronic inflammatory enteropathy in dogs. Journal of Veterinary Internal Medicine. 2020; 35 (1):162-171.

Chicago/Turabian Style

Mazdak Salavati; Jorge Pérez‐Accino; Yi Lin Tan; Tiziana Liuti; Sionagh Smith; Linda Morrison; Silke Salavati Schmitz. 2020. "Correlation of minimally invasive imaging techniques to assess intestinal mucosal perfusion with established markers of chronic inflammatory enteropathy in dogs." Journal of Veterinary Internal Medicine 35, no. 1: 162-171.

Preprint content
Published: 24 November 2020
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In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international “CoronaHack” in April 2020 (https://www.coronahack.co.uk/), we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2;n=163), bat (bat-CoV;n=215) and pangolin (pangolin-CoV;n=7) available in public repositories. Following de novo gene annotation prediction, analysis on gene-gene similarity network, codon usage bias and variant discovery were carried out. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Lastly, we have characterised several high impact variants (inframe insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.

ACS Style

Nicholas J. Dimonaco; Mazdak Salavati; Barbara Shih. Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations. 2020, 1 .

AMA Style

Nicholas J. Dimonaco, Mazdak Salavati, Barbara Shih. Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations. . 2020; ():1.

Chicago/Turabian Style

Nicholas J. Dimonaco; Mazdak Salavati; Barbara Shih. 2020. "Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations." , no. : 1.

Original research article
Published: 23 October 2020 in Frontiers in Genetics
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The overall aim of the Ovine FAANG project is to provide a comprehensive annotation of the new highly contiguous sheep reference genome sequence (Oar rambouillet v1.0). Mapping of transcription start sites (TSS) is a key first step in understanding transcript regulation and diversity. Using 56 tissue samples collected from the reference ewe Benz2616, we have performed a global analysis of TSS and TSS-Enhancer clusters using Cap Analysis Gene Expression (CAGE) sequencing. CAGE measures RNA expression by 5′ cap-trapping and has been specifically designed to allow the characterization of TSS within promoters to single-nucleotide resolution. We have adapted an analysis pipeline that uses TagDust2 for clean-up and trimming, Bowtie2 for mapping, CAGEfightR for clustering, and the Integrative Genomics Viewer (IGV) for visualization. Mapping of CAGE tags indicated that the expression levels of CAGE tag clusters varied across tissues. Expression profiles across tissues were validated using corresponding polyA+ mRNA-Seq data from the same samples. After removal of CAGE tags with <10 read counts, 39.3% of TSS overlapped with 5′ ends of 31,113 transcripts that had been previously annotated by NCBI (out of a total of 56,308 from the NCBI annotation). For 25,195 of the transcripts, previously annotated by NCBI, no TSS meeting stringent criteria were identified. A further 14.7% of TSS mapped to within 50 bp of annotated promoter regions. Intersecting these predicted TSS regions with annotated promoter regions (±50 bp) revealed 46% of the predicted TSS were “novel” and previously un-annotated. Using whole-genome bisulfite sequencing data from the same tissues, we were able to determine that a proportion of these “novel” TSS were hypo-methylated (32.2%) indicating that they are likely to be reproducible rather than “noise”. This global analysis of TSS in sheep will significantly enhance the annotation of gene models in the new ovine reference assembly. Our analyses provide one of the highest resolution annotations of transcript regulation and diversity in a livestock species to date.

ACS Style

Mazdak Salavati; Alex Caulton; Richard Clark; Iveta Gazova; Timothy P. L. Smith; Kim C. Worley; Noelle E. Cockett; Alan Archibald; Shannon M. Clarke; Brenda M Murdoch; Emily L. Clark. Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). Frontiers in Genetics 2020, 11, 580580 .

AMA Style

Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gazova, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon M. Clarke, Brenda M Murdoch, Emily L. Clark. Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). Frontiers in Genetics. 2020; 11 ():580580.

Chicago/Turabian Style

Mazdak Salavati; Alex Caulton; Richard Clark; Iveta Gazova; Timothy P. L. Smith; Kim C. Worley; Noelle E. Cockett; Alan Archibald; Shannon M. Clarke; Brenda M Murdoch; Emily L. Clark. 2020. "Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)." Frontiers in Genetics 11, no. : 580580.

Journal article
Published: 14 September 2020 in Journal of Equine Veterinary Science
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Limited research has been undertaken to determine the impact of horse age, sex and number of riders on horse performance in British Eventing (BE) horse trials. Improved understanding of this can aid professionals in planning a competition horse’s career. To investigate the impact of age, sex and number of riders on the peak performance of horses at each of the main levels of BE competitions. The best score from each horse competing in BE horse trials in the years 2008 to 2018 were recorded, principal component and hierarchical cluster analysis was performed. Basic data analysis was used to identify variables associated with particular better-performing clusters of horses. The interplay of the combinatory variables was then used to map out the trends in career trajectory for horses competing at each level of competition in the best and worst performing clusters. s: The peak performance of mares was worse than geldings and stallions at all levels. At Novice to Advanced, stallions did not perform as consistently with multiple riders as geldings. The age at which the best performing groups peaked was similar for mares and geldings in all classes, although stallions peaked at an older age than mares and geldings at Novice and Intermediate level. All horses were a minimum of four years old at the time of competition, as per British Eventing rules.

ACS Style

Katherine Hanousek; Mazdak Salavati; Bettina Dunkel. The impact of horse age, sex and number of riders on horse performance in British Eventing horse trials. Journal of Equine Veterinary Science 2020, 94, 103250 .

AMA Style

Katherine Hanousek, Mazdak Salavati, Bettina Dunkel. The impact of horse age, sex and number of riders on horse performance in British Eventing horse trials. Journal of Equine Veterinary Science. 2020; 94 ():103250.

Chicago/Turabian Style

Katherine Hanousek; Mazdak Salavati; Bettina Dunkel. 2020. "The impact of horse age, sex and number of riders on horse performance in British Eventing horse trials." Journal of Equine Veterinary Science 94, no. : 103250.

Preprint content
Published: 06 July 2020
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The overall aim of the Ovine FAANG project is to provide a comprehensive annotation of the new highly contiguous sheep reference genome sequence (Oar rambouillet v1.0). Mapping of transcription start sites (TSS) is a key first step in understanding transcript regulation and diversity. Using 56 tissue samples collected from the reference ewe Benz2616 we have performed a global analysis of TSS and TSS- Enhancer clusters using Cap Analysis Gene Expression (CAGE) sequencing. CAGE measures RNA expression by 5’ cap-trapping and has been specifically designed to allow the characterization of TSS within promoters to single-nucleotide resolution. We have adapted an analysis pipeline that uses TagDust2 for clean-up and trimming, Bowtie2 for mapping, CAGEfightR for clustering and the Integrative Genomics Viewer (IGV) for visualization. Mapping of CAGE tags indicated that the expression levels of CAGE tag clusters varied across tissues. Expression profiles across tissues were validated using corresponding polyA+ mRNA-Seq data from the same samples. After removal of CAGE tags with < 10 read counts, 39.3% of TSS overlapped with 5’ ends of 31,113 transcripts that had been previously annotated by NCBI (out of a total of 56,308 from the NCBI annotation). For 25,195 of the transcripts, previously annotated by NCBI, no TSS meeting stringent criteria were identified. A further 14.7% of TSS mapped to within 50bp of annotated promoter regions. Intersecting these predicted TSS regions with annotated promoter regions (±50bp) revealed 46% of the predicted TSS were ‘novel’ and previously un-annotated. Using whole genome bisulphite sequencing data from the same tissues we were able to determine that a proportion of these ‘novel’ TSS were hypo-methylated (32.2%) indicating that they are likely to be reproducible rather than ‘noise’. This global analysis of TSS in sheep will significantly enhance the annotation of gene models in the new ovine reference assembly. Our analyses provide one of the highest resolution annotations of transcript regulation and diversity in a livestock species to date.

ACS Style

Mazdak Salavati; Alex Caulton; Richard Clark; Iveta Gazova; Timothy P. L. Smith; Kim C. Worley; Noelle E. Cockett; Alan L. Archibald; Shannon M. Clarke; Brenda M. Murdoch; Emily Louise Clark; on behalf of The Ovine FAANG Project Consortium. Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0). 2020, 1 .

AMA Style

Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gazova, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan L. Archibald, Shannon M. Clarke, Brenda M. Murdoch, Emily Louise Clark, on behalf of The Ovine FAANG Project Consortium. Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0). . 2020; ():1.

Chicago/Turabian Style

Mazdak Salavati; Alex Caulton; Richard Clark; Iveta Gazova; Timothy P. L. Smith; Kim C. Worley; Noelle E. Cockett; Alan L. Archibald; Shannon M. Clarke; Brenda M. Murdoch; Emily Louise Clark; on behalf of The Ovine FAANG Project Consortium. 2020. "Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)." , no. : 1.

Journal article
Published: 01 July 2020 in Journal of Dairy Science
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The aim of this study was to detect the genomic region or regions associated with metabolic clusters in early-lactation Holstein cows. This study was carried out in 2 experiments. In experiment I, which was carried out on 105 multiparous Holstein cows, animals were classified through k-means clustering on log-transformed and standardized concentrations of blood glucose, insulin-like growth factor I, free fatty acids, and β-hydroxybutyrate at 14 and 35 d in milk (DIM), into metabolic clusters, either balanced (BAL) or other (OTR). Forty percent of the animals were categorized in the BAL group, and the remainder were categorized as OTR. The cows were genotyped for a total of 777,962 SNP. A genome-wide association study was performed, using a case-control approach through the GEMMA software, accounting for population structure. We found 8 SNP (BTA11, BTA23, and BTAX) associated with the predicted metabolic clusters. In experiment II, carried out on 4,267 second-parity Holstein cows, milk samples collected starting from the first week until 50 DIM were used to determine Fourier-transform mid-infrared (FT-MIR) spectra and subsequently to classify the animals into the same metabolic clusters (BAL vs. OTR). Twenty-eight percent of the animals were categorized in the BAL group, and the remainder were classified in the OTR category. Although daily milk yield was lower in BAL cows, we found no difference in daily fat- and protein-corrected milk yield in cows from the BAL metabolic cluster compared with those in the OTR metabolic cluster. In the next step, a single-step genomic BLUP was used to identify the genomic region(s) associated with the predicted metabolic clusters. The results revealed that prediction of metabolic clusters is a highly polygenic trait regulated by many small-sized effects. The region of 36,258 to 36,295 kb on BTA27 was the highly associated region for the predicted metabolic clusters, with the closest genes to this region (ANK1 and miR-486) being related to hematopoiesis, erythropoiesis, and mammary gland development. The heritability for metabolic clustering was 0.17 (SD 0.03), indicating that the use of FT-MIR spectra in milk to predict metabolic clusters in early-lactation across a large number of cows has satisfactory potential to be included in genetic selection programs for modern dairy cows.

ACS Style

H. Atashi; M. Salavati; J. De Koster; M.A. Crowe; G. Opsomer; M. Hostens. Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows. Journal of Dairy Science 2020, 103, 6392 -6406.

AMA Style

H. Atashi, M. Salavati, J. De Koster, M.A. Crowe, G. Opsomer, M. Hostens. Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows. Journal of Dairy Science. 2020; 103 (7):6392-6406.

Chicago/Turabian Style

H. Atashi; M. Salavati; J. De Koster; M.A. Crowe; G. Opsomer; M. Hostens. 2020. "Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows." Journal of Dairy Science 103, no. 7: 6392-6406.

Original research article
Published: 30 June 2020 in Frontiers in Microbiology
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Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic zoonotic disease where host genetics is thought to contribute to susceptibility or resistance. One of the genes implicated is the SLC11A1 gene, that encodes for the natural resistance-associated macrophage protein 1 (NRAMP1). The aim of this study was to identify SLC11A1 polymorphisms and to investigate any resulting functional differences in NRAMP1 expression that might be correlated with resistance/susceptibility to M. bovis infection. Sequencing of the SLC11A1 gene in cDNA isolated from Brown Swiss, Holstein Friesian, and Sahiwal cattle identified five single nucleotide polymorphisms (SNPs) in the coding region, but only one of these (SNP4, c.1066C>G, rs109453173) was present in all three cattle breeds and therefore warranted further investigation. Additionally, variations of 10, 11, and 12 GT repeats were identified in a microsatellite (MS1) in the SLC11A1 3′UTR. Measurement of NRAMP1 expression in bovine macrophages by ELISA showed no differences between cells generated from the different breeds. Furthermore, variations in the length of the MS1 microsatellite did not impact on NRAMP1 protein expression as analyzed by luciferase reporter assay. However, further analysis of the ELISA data identified that the presence of the alternative G allele at SNP4 was associated with increased expression of NRAMP1 in bovine macrophages. Since NRAMP1 has been shown to influence the survival of intracellular pathogens such as M. bovis through the sequestering of iron, it is possible that cattle expressing the alternative G allele might have an increased resistance to bTB through increased NRAMP1 expression in their macrophages.

ACS Style

Angela Holder; Rachel Garty; Charlotte Elder; Paula Mesnard; Celine Laquerbe; Marie-Christine Bartens; Mazdak Salavati; Muhammad Zubair Shabbir; Thomas Tzelos; Timothy Connelly; Bernardo Villarreal-Ramos; Dirk Werling. Analysis of Genetic Variation in the Bovine SLC11A1 Gene, Its Influence on the Expression of NRAMP1 and Potential Association With Resistance to Bovine Tuberculosis. Frontiers in Microbiology 2020, 11, 1420 .

AMA Style

Angela Holder, Rachel Garty, Charlotte Elder, Paula Mesnard, Celine Laquerbe, Marie-Christine Bartens, Mazdak Salavati, Muhammad Zubair Shabbir, Thomas Tzelos, Timothy Connelly, Bernardo Villarreal-Ramos, Dirk Werling. Analysis of Genetic Variation in the Bovine SLC11A1 Gene, Its Influence on the Expression of NRAMP1 and Potential Association With Resistance to Bovine Tuberculosis. Frontiers in Microbiology. 2020; 11 ():1420.

Chicago/Turabian Style

Angela Holder; Rachel Garty; Charlotte Elder; Paula Mesnard; Celine Laquerbe; Marie-Christine Bartens; Mazdak Salavati; Muhammad Zubair Shabbir; Thomas Tzelos; Timothy Connelly; Bernardo Villarreal-Ramos; Dirk Werling. 2020. "Analysis of Genetic Variation in the Bovine SLC11A1 Gene, Its Influence on the Expression of NRAMP1 and Potential Association With Resistance to Bovine Tuberculosis." Frontiers in Microbiology 11, no. : 1420.

Journal article
Published: 01 May 2020 in Journal of Dairy Science
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Improving nitrogen use efficiency (NUE) at both the individual cow and the herd level has become a key target in dairy production systems, for both environmental and economic reasons. Cost-effective and large-scale phenotyping methods are required to improve NUE through genetic selection and by feeding and management strategies. The aim of this study was to evaluate the possibility of using mid-infrared (MIR) spectra of milk to predict individual dairy cow NUE during early lactation. Data were collected from 129 Holstein cows, from calving until 50 d in milk, in 3 research herds (Denmark, Ireland, and the UK). In 2 of the herds, diets were designed to challenge cows metabolically, whereas a diet reflecting local management practices was offered in the third herd. Nitrogen intake (kg/d) and nitrogen excreted in milk (kg/d) were calculated daily. Nitrogen use efficiency was calculated as the ratio between nitrogen in milk and nitrogen intake, and expressed as a percentage. Individual daily values for NUE ranged from 9.7 to 81.7%, with an average of 36.9% and standard deviation of 10.4%. Milk MIR spectra were recorded twice weekly and were standardized into a common format to avoid bias between apparatus or sampling periods. Regression models predicting NUE using milk MIR spectra were developed on 1,034 observations using partial least squares or support vector machines regression methods. The models were then evaluated through (1) a cross-validation using 10 subsets, (2) a cow validation excluding 25% of the cows to be used as a validation set, and (3) a diet validation excluding each of the diets one by one to be used as validation sets. The best statistical performances were obtained when using the support vector machines method. Inclusion of milk yield and lactation number as predictors, in combination with the spectra, also improved the calibration. In cross-validation, the best model predicted NUE with a coefficient of determination of cross-validation of 0.74 and a relative error of 14%, which is suitable to discriminate between low- and high-NUE cows. When performing the cow validation, the relative error remained at 14%, and during the diet validation the relative error ranged from 12 to 34%. In the diet validation, the models showed a lack of robustness, demonstrating difficulties in predicting NUE for diets and for samples that were not represented in the calibration data set. Hence, a need exists to integrate more data in the models to cover a maximum of variability regarding breeds, diets, lactation stages, management practices, seasons, MIR instruments, and geographic regions. Although the model needs to be validated and improved for use in routine conditions, these preliminary results showed that it was possible to obtain information on NUE through milk MIR spectra. This could potentially allow large-scale predictions to aid both further genetic and genomic studies, and the development of farm management tools.

ACS Style

C. Grelet; E. Froidmont; L. Foldager; M. Salavati; M. Hostens; C.P. Ferris; K.L. Ingvartsen; M.A. Crowe; M.T. Sorensen; J.A. Fernandez Pierna; A. Vanlierde; N. Gengler; F. Dehareng. Potential of milk mid-infrared spectra to predict nitrogen use efficiency of individual dairy cows in early lactation. Journal of Dairy Science 2020, 103, 4435 -4445.

AMA Style

C. Grelet, E. Froidmont, L. Foldager, M. Salavati, M. Hostens, C.P. Ferris, K.L. Ingvartsen, M.A. Crowe, M.T. Sorensen, J.A. Fernandez Pierna, A. Vanlierde, N. Gengler, F. Dehareng. Potential of milk mid-infrared spectra to predict nitrogen use efficiency of individual dairy cows in early lactation. Journal of Dairy Science. 2020; 103 (5):4435-4445.

Chicago/Turabian Style

C. Grelet; E. Froidmont; L. Foldager; M. Salavati; M. Hostens; C.P. Ferris; K.L. Ingvartsen; M.A. Crowe; M.T. Sorensen; J.A. Fernandez Pierna; A. Vanlierde; N. Gengler; F. Dehareng. 2020. "Potential of milk mid-infrared spectra to predict nitrogen use efficiency of individual dairy cows in early lactation." Journal of Dairy Science 103, no. 5: 4435-4445.

Preprint content
Published: 26 April 2020
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Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding Bos taurus cattle for increased resistance to bTB is feasible. The utility of such an approach is still unknown for the Bos indicus cattle population. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture in Bos indicus breeds in Cameroon.We conducted a cross-sectional study of slaughter cattle in Cameroon and genotyped a sample of 213 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci.Previous studies had found that breed was an important factor in explaining the epidemiology of bTB, with Fulani cattle appearing to be more susceptible than mixed breeds. However, we show that the apparent phenotypic differences in visual appearance between the breeds was not reflected by clear genomic differences. At the genetic level, cattle belonging to different hierarchical genomic clusters differed in their susceptibility to bTB. There was evidence of a genomic association between M. bovis infection status with specific SNPs.We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production.

ACS Style

Rebecca Callaby; Robert F Kelly; Stella Mazeri; Franklyn Egbe; Lindert Benedictus; Emily Louise Clark; Andrea Doeschl-Wilson; Barend Mark De Clare Bronsvoort; Mazdak Salavati; Adrian Muwonge. A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis. 2020, 1 .

AMA Style

Rebecca Callaby, Robert F Kelly, Stella Mazeri, Franklyn Egbe, Lindert Benedictus, Emily Louise Clark, Andrea Doeschl-Wilson, Barend Mark De Clare Bronsvoort, Mazdak Salavati, Adrian Muwonge. A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis. . 2020; ():1.

Chicago/Turabian Style

Rebecca Callaby; Robert F Kelly; Stella Mazeri; Franklyn Egbe; Lindert Benedictus; Emily Louise Clark; Andrea Doeschl-Wilson; Barend Mark De Clare Bronsvoort; Mazdak Salavati; Adrian Muwonge. 2020. "A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis." , no. : 1.

Journal article
Published: 21 April 2020 in Preventive Veterinary Medicine
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Blood biomarkers may be used to detect physiological imbalance and potential disease. However, blood sampling is difficult and expensive, and not applicable in commercial settings. Instead, individual milk samples are readily available at low cost, can be sampled easily and analysed instantly. The present observational study sampled blood and milk from 234 Holstein dairy cows from experimental herds in six European countries. The objective was to compare the use of three different sets of milk biomarkers for identification of cows in physiological imbalance and thus at risk of developing metabolic or infectious diseases. Random forests was used to predict body energy balance (EBAL), index for physiological imbalance (PI-index) and three clusters differentiating the metabolic status of cows created on basis of concentrations of plasma glucose, β-hydroxybutyrate (BHB), non-esterified fatty acids (NEFA) and serum IGF-1. These three metabolic clusters were interpreted as cows in balance, physiological imbalance and “intermediate cows” with physiological status in between. The three sets of milk biomarkers used for prediction were: milk Fourier transform mid-IR (FT-MIR) spectra, 19 immunoglobulin G (IgG) N-glycans and 8 milk metabolites and enzymes (MME). Blood biomarkers were sampled twice; around 14 days after calving (days in milk (DIM)) and around 35 DIM. MME and FT-MIR were sampled twice weekly 1−50 DIM whereas IgG N-glycan were measured only four times. Performances of EBAL and PI-index predictions were measured by coefficient of determination (R2cv) and root mean squared error (RMSEcv) from leave-one-cow-out cross-validation (cv). For metabolic clusters, performance was measured by sensitivity, specificity and global accuracy from this cross-validation. Best prediction of PI-index was obtained by MME (R2cv = 0.40 (95 % CI: 0.29−0.50) at 14 DIM and 0.35 (0.23−0.44) at 35 DIM) while FT-MIR showed a better performance than MME for prediction of EBAL (R2cv = 0.28 (0.24−0.33) vs 0.21 (0.18−0.25)). Global accuracies of predicting metabolic clusters from MME and FT-MIR were at the same level ranging from 0.54 (95 % CI: 0.39−0.68) to 0.65 (0.55−0.75) for MME and 0.51 (0.37−0.65) to 0.68 (0.53−0.81) for FT-MIR. R2cv and accuracies were lower for IgG N-glycans. In conclusion, neither EBAL nor PI-index were sufficiently well predicted to be used as a management tool for identification of risk cows. MME and FT-MIR may be used to predict the physiological status of the cows, while the use of IgG N-glycans for prediction still needs development. Nevertheless, accuracies need to be improved and a larger training data set is warranted.

ACS Style

Leslie Foldager; Charlotte Gaillard; Martin T. Sorensen; Torben Larsen; Elizabeth Matthews; Roisin O’Flaherty; Fiona Carter; Mark A. Crowe; Clément Grelet; Mazdak Salavati; Miel Hostens; Klaus L. Ingvartsen; Mogens A. Krogh. Predicting physiological imbalance in Holstein dairy cows by three different sets of milk biomarkers. Preventive Veterinary Medicine 2020, 179, 105006 .

AMA Style

Leslie Foldager, Charlotte Gaillard, Martin T. Sorensen, Torben Larsen, Elizabeth Matthews, Roisin O’Flaherty, Fiona Carter, Mark A. Crowe, Clément Grelet, Mazdak Salavati, Miel Hostens, Klaus L. Ingvartsen, Mogens A. Krogh. Predicting physiological imbalance in Holstein dairy cows by three different sets of milk biomarkers. Preventive Veterinary Medicine. 2020; 179 ():105006.

Chicago/Turabian Style

Leslie Foldager; Charlotte Gaillard; Martin T. Sorensen; Torben Larsen; Elizabeth Matthews; Roisin O’Flaherty; Fiona Carter; Mark A. Crowe; Clément Grelet; Mazdak Salavati; Miel Hostens; Klaus L. Ingvartsen; Mogens A. Krogh. 2020. "Predicting physiological imbalance in Holstein dairy cows by three different sets of milk biomarkers." Preventive Veterinary Medicine 179, no. : 105006.

Journal article
Published: 17 March 2020 in Animals
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The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.

ACS Style

Hadi Atashi; Mazdak Salavati; Jenne De Koster; Mark A. Crowe; Geert Opsomer; Miel Hostens; the GplusE consortium. A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach. Animals 2020, 10, 500 .

AMA Style

Hadi Atashi, Mazdak Salavati, Jenne De Koster, Mark A. Crowe, Geert Opsomer, Miel Hostens, the GplusE consortium. A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach. Animals. 2020; 10 (3):500.

Chicago/Turabian Style

Hadi Atashi; Mazdak Salavati; Jenne De Koster; Mark A. Crowe; Geert Opsomer; Miel Hostens; the GplusE consortium. 2020. "A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach." Animals 10, no. 3: 500.

Journal article
Published: 01 January 2020 in Animal
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Both blood- and milk-based biomarkers have been analysed for decades in research settings, although often only in one herd, and without focus on the variation in the biomarkers that are specifically related to herd or diet. Biomarkers can be used to detect physiological imbalance and disease risk and may have a role in precision livestock farming (PLF). For use in PLF, it is important to quantify normal variation in specific biomarkers and the source of this variation. The objective of this study was to estimate the between- and within-herd variation in a number of blood metabolites (β-hydroxybutyrate (BHB), non-esterified fatty acids, glucose and serum IGF-1), milk metabolites (free glucose, glucose-6-phosphate, urea, isocitrate, BHB and uric acid), milk enzymes (lactate dehydrogenase and N-acetyl-β-D-glucosaminidase (NAGase)) and composite indicators for metabolic imbalances (Physiological Imbalance-index and energy balance), to help facilitate their adoption within PLF. Blood and milk were sampled from 234 Holstein dairy cows from 6 experimental herds, each in a different European country, and offered a total of 10 different diets. Blood was sampled on 2 occasions at approximately 14 days-in-milk (DIM) and 35 DIM. Milk samples were collected twice weekly (in total 2750 samples) from DIM 1 to 50. Multilevel random regression models were used to estimate the variance components and to calculate the intraclass correlations (ICCs). The ICCs for the milk metabolites, when adjusted for parity and DIM at sampling, demonstrated that between 12% (glucose-6-phosphate) and 46% (urea) of the variation in the metabolites’ levels could be associated with the herd-diet combination. Intraclass Correlations related to the herd-diet combination were generally higher for blood metabolites, from 17% (cholesterol) to approximately 46% (BHB and urea). The high ICCs for urea suggest that this biomarker can be used for monitoring on herd level. The low variance within cow for NAGase indicates that few samples would be needed to describe the status and potentially a general reference value could be used. The low ICC for most of the biomarkers and larger within cow variation emphasises that multiple samples would be needed - most likely on the individual cows - for making the biomarkers useful for monitoring. The majority of biomarkers were influenced by parity and DIM which indicate that these should be accounted for if the biomarker should be used for monitoring.

ACS Style

M. A. Krogh; M. Hostens; M. Salavati; C. Grelet; M. T. Sorensen; D. C. Wathes; C. P. Ferris; C. Marchitelli; F. Signorelli; F. Napolitano; F. Becker; T. Larsen; E. Matthews; F. Carter; A. Vanlierde; G. Opsomer; N. Gengler; F. Dehareng; M. A. Crowe; K. L. Ingvartsen; L. Foldager. Between- and within-herd variation in blood and milk biomarkers in Holstein cows in early lactation. Animal 2020, 14, 1067 -1075.

AMA Style

M. A. Krogh, M. Hostens, M. Salavati, C. Grelet, M. T. Sorensen, D. C. Wathes, C. P. Ferris, C. Marchitelli, F. Signorelli, F. Napolitano, F. Becker, T. Larsen, E. Matthews, F. Carter, A. Vanlierde, G. Opsomer, N. Gengler, F. Dehareng, M. A. Crowe, K. L. Ingvartsen, L. Foldager. Between- and within-herd variation in blood and milk biomarkers in Holstein cows in early lactation. Animal. 2020; 14 (5):1067-1075.

Chicago/Turabian Style

M. A. Krogh; M. Hostens; M. Salavati; C. Grelet; M. T. Sorensen; D. C. Wathes; C. P. Ferris; C. Marchitelli; F. Signorelli; F. Napolitano; F. Becker; T. Larsen; E. Matthews; F. Carter; A. Vanlierde; G. Opsomer; N. Gengler; F. Dehareng; M. A. Crowe; K. L. Ingvartsen; L. Foldager. 2020. "Between- and within-herd variation in blood and milk biomarkers in Holstein cows in early lactation." Animal 14, no. 5: 1067-1075.

Journal article
Published: 04 November 2019 in Frontiers in Genetics
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Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics, we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 17 transcriptionally rich tissues and 3 cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis, we grouped genes according to their expression patterns and assigned those groups of coexpressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

ACS Style

Charity Muriuki; Stephen J. Bush; Mazdak Salavati; Mary E.B. McCulloch; Zofia M. Lisowski; Morris Agaba; Appolinaire Djikeng; David A. Hume; Emily L. Clark. A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus). Frontiers in Genetics 2019, 10, 1080 .

AMA Style

Charity Muriuki, Stephen J. Bush, Mazdak Salavati, Mary E.B. McCulloch, Zofia M. Lisowski, Morris Agaba, Appolinaire Djikeng, David A. Hume, Emily L. Clark. A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus). Frontiers in Genetics. 2019; 10 ():1080.

Chicago/Turabian Style

Charity Muriuki; Stephen J. Bush; Mazdak Salavati; Mary E.B. McCulloch; Zofia M. Lisowski; Morris Agaba; Appolinaire Djikeng; David A. Hume; Emily L. Clark. 2019. "A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)." Frontiers in Genetics 10, no. : 1080.