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Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches
Download2016
Janssen, Peter H., Li, Fuyong, Sun, Xu, Cox, Faith, Guan, Leluo, Henderson, Gemma
Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of...
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Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Download2016
Ladinig, Andrea, Stothard, Paul, Bao, Hua, Hong, Linjun, Lunney, Joan K., Harding, John C. S., Wilkinson, Jamie M., Plastow, Graham S.
Background Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant pigs can result in congenital infection and ultimately fetal death. Little is known about immune responses to infection at the maternal-fetal interface and in the fetus itself, or the molecular events...
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Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: Insights on low-quality forage utilization
Download2016
Wang, Diming, Sun, Huizeng, Liu, Jianxin, Guan, Le Luo, Wang, Bing, Liang, Guanxiang
In this study, we investigated the molecular regulatory mechanisms of milk protein production in dairy cows by studying the miRNAomes of five key metabolic tissues involved in protein synthesis and metabolism from dairy cows fed high- and low-quality diets. In total, 340, 338, 337, 330, and 328...
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Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle
Download2016
Nayeri, Shadi, Stothard, Paul, Moore, Stephen S., Abo-Ismail, Mohammed K., May, Natalie, Schenkel, Flavio, Sargolzaei, Mehdi, Miller, Stephen P.
Background Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine the positions of genomic regions affecting milk production, milk components and fertility traits in...
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Whole genome sequence analysis of an alachlor and endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida
Download2016
Ewida, Ayman Y. I., Stothard, Paul, Chauhan, Ashvini, Griffiths, Zabrenna, Pathak, Ashish
We recently isolated a Pseudomonas sp. strain W15Feb9B from Ochlockonee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides - Alachlor [(2-chloro-2′,6′-diethylphenyl-N (methoxymethyl)acetanilide)] and Endosulfan...
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Differences in whole blood gene expression associated with infection time-course and extent of fetal mortality in a reproductive model of type 2 porcine reproductive and respiratory syndrome virus (PRRSV) infection
Download2016
Ladinig, Andrea, Stothard, Paul, Wilkinson, Jamie M., Kommadath, Arun, Plastow, Graham S., Harding, John C. S., Bao, Hua, Lunney, Joan K.
Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant females causes fetal death and increased piglet mortality, but there is substantial variation in the extent of reproductive pathology between individual dams. This study used RNA-sequencing to characterize the whole...
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Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)
Download2015
Moore, Stephen S., Miller, Joshua M., Coltman, David W., Liao, Xiaoping, Stothard, Paul
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction...
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Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle
Download2015
Ekine-Dzivenu, Chinyere, Basarab, John A., Li, Changxi, Chen, Liuhong, Vinsky, Michael D., Aalhus, Jennifer L., Fitzsimmons, Carolyn J., Stothard, Paul, Dugan, Mike E. R.
Background Identification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of beef fatty acid profiles through genomic selection and marker-assisted diet...
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Xylo-oligosaccharides and virginiamycin differentially modulate gut microbial composition in chickens
Download2015
Zhao, Xin, Pourabedin, Mohsen, Guan, Leluo
Background The emergence and spread of antibiotic resistance in pathogens have led to a restriction on the use of antibiotic growth promoters (AGPs) in animal feed in some countries. The potential negative after-effects of a ban on AGPs could be mitigated by improving animal intestinal health...
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The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract
Download2015
Grebiel, Philip J., Malmuthuge, Nilusha, Guan, Leluo
A diverse microbial population colonizes the sterile mammalian gastrointestinal tract during and after the birth. There is increasing evidence that this complex microbiome plays a crucial role in the development of the mucosal immune system and influences newborn health. Microbial colonization is...