Background Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of... more
Background Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by...
Research Interests: Functional Analysis, Biology, Gene expression, Biological Sciences, Humans, and 15 moreFemale, Animals, Gene ontology, KEGG, Horses, Gene, Feeding Functional Response, Functional Group, Gene expression profiling, Differential expression, Functional Response, BMC, Gluteus medius, Fatty acid metabolism, and Exercise training
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Research Interests: Computational Biology, Biology, Health, Medicine, Multidisciplinary, and 15 moreDendritic Cells, Transcriptome, Identification, Mycobacterium tuberculosis, Mutations, Classification, Discovery, Expression, Lung, Mycobacterium bovis, Neuroendocrine Tumors, Nature Communications, Cell Lung Cancer, Innate Immune System, and Pathway
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Research Interests: Biology and Ancient DNA
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Coordinated regulation of gene expression is essential for pathogen adaptation in vivo. Understanding the control of these virulence circuits in the TB pathogen Mycobacterium tuberculosis is a key challenge if we are to increase our basic... more
Coordinated regulation of gene expression is essential for pathogen adaptation in vivo. Understanding the control of these virulence circuits in the TB pathogen Mycobacterium tuberculosis is a key challenge if we are to increase our basic understanding of how this organism establishes infection. In this study we focused on the transcriptional regulator Rv1404 that shows similarity to the MarR family of transcriptional repressors. Rv1404 derepresses a set of genes in vivo that have been implicated in virulence and may therefore allow adaptation of M. tuberculosis to the intracellular environment. We used a combination of ChIP-qPCR and Electromobility Band Shift Assays (EMSA) to show that Rv1404 coordinates gene expression in response to stresses such as low pH in M. tuberculosis. Two genes regulated by Rv1404, rv1403c and rv1405c, encode putative SAM-dependent methyltransferases. To elucidate gene function, M. tuberculosis rv1403c and rv1405c mutants were constructed. The mutants showed attenuated growth in response to in vitro stress conditions that mimic the intracellular milieu. Our data sheds new light on the function of a novel regulon controlled by Rv1404 that coordinates adaptation of M. tuberculosis to the in vivo environment and reveals the Rv1405c and Rv1403c methyltransferases as playing a role in this adaptive process.
Research Interests: Biology, Transcription Factors, Medicine, Virulence, Tuberculosis, and 12 moreMycobacterium tuberculosis, Mutation, Polymerase Chain Reaction, Gene, Phenotype, Genotype, Chromatin Immunoprecipitation, Host Pathogen Interactions, Hydrogen-Ion Concentration, DNA binding proteins, Stress Physiological, and Medical and Health Sciences
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Mycobacterial infections still represent a major burden on human and animal health, particularly in the context of human and bovine tuberculosis caused by infection with Mycobacterium tuberculosis and M. bovis, respectively. It is now... more
Mycobacterial infections still represent a major burden on human and animal health, particularly in the context of human and bovine tuberculosis caused by infection with Mycobacterium tuberculosis and M. bovis, respectively. It is now well understood that differentiation of immune cells into their various lineages is influenced by microRNA transcriptional regulatory networks, and that dynamic and orchestrated control of miRNA and mRNA expression profiles is critical in mounting an effective host immune response to infection. In this chapter, we review studies that demonstrate how mycobacterial infections alter host miRNA expression profiles to evade immune responses and promote pathogen survival. We also discuss the potential diagnostic and therapeutic applications of miRNAs for mycobacterial infections.
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Research Interests: Reproduction, Biology, Fertility, Medicine, Microarray, and 15 moreOmega-3 fatty acids, Female, Animals, PUFA, Dietary Supplements, Dairy Cow, Medical Physiology, Early Pregnancy, Cattle, Endometrium, Corpus Luteum, Estrous cycle, Physiological Genomics, Microarray technology, and In Vitro Techniques
Microsatellite markers offer great potential for genetic comparisons within and between populations. We report the analysis of 12 microsatellite loci in six breeds of European cattle. This yielded a wide spectrum of variability with... more
Microsatellite markers offer great potential for genetic comparisons within and between populations. We report the analysis of 12 microsatellite loci in six breeds of European cattle. This yielded a wide spectrum of variability with observed heterozygosities ranging from 0.00 to 0.91. Deviations from Hardy-Weinberg equilibrium were noted for some locus-population combinations, particularly at a microsatellite located within the prolactin gene. Also, significant linkage disequilibrium was detected between two microsatellite loci located within the bovine major histocompatibility complex, and this association was maintained across breeds, providing evidence for marker stability during short-term evolution. The mode of mutation was investigated by comparing the observed data with that expected under the infinite alleles model of neutral mutation, and six of the microsatellite loci were found to deviate significantly, suggesting that a stepwise mutation model may be more appropriate. One indication of marker utility is that, when genetic distance estimates were computed, the resultant dendrogram showed concordance with known breed histories.
Research Interests: Genetics, Biology, Medicine, Biological Sciences, Europe, and 15 moreAnimals, Male, Microsatellite, Cattle, Major histocompatibility complex, Linkage Disequilibrium, Genetic variation, Base Sequence, Microsatellite DNA, Genetic distance, Genetic Markers, alleles, microsatellite loci, Gene frequency, and Medical and Health Sciences
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Objectives Improved bovine tuberculosis (bTB) diagnostics with higher sensitivity and specificity are urgently required. A better understanding of the peripheral blood transcriptional response of Mycobacterium bovis-infected animals after... more
Objectives Improved bovine tuberculosis (bTB) diagnostics with higher sensitivity and specificity are urgently required. A better understanding of the peripheral blood transcriptional response of Mycobacterium bovis-infected animals after bovine purified protein derivative (PPD-b) stimulation of whole blood—an important component of current bTB diagnostics—will provide new information for development of better diagnostics. Methods RNA sequencing (RNA-seq) was used to study the peripheral blood transcriptome after stimulation with PPD-b across four time points (-1 wk pre-infection, and +1 wk, +2 wk, and +10 wk post-infection) from a 14-week M. bovis infection time course experiment with ten age-matched Holstein-Friesian cattle. Results In vitro PPD-b stimulation of peripheral blood from M. bovis-infected and non-infected cattle elicited a strong transcriptional response. Comparison of PPD-b stimulated, and unstimulated samples revealed higher expression of genes encoding cytokine receptors, transcription factors, and interferon-inducible proteins. Lower expression was seen for genes encoding proteins involved in antimicrobial activity, C-type lectin receptors, inhibition of signal transduction, and genes encoding metal ion transporters. Conclusions A transcriptional signature associated with the peripheral blood response to PPD-b stimulation consisting of 170 genes was identified exclusively in the post-infection time points. Therefore, this represents a panel of potential biomarkers of M. bovis infection.
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Research Interests: Microbiology, Biology, Cytokines, Innate immunity, Medicine, and 15 moreVirulence, Tuberculosis, Mycobacterium tuberculosis, Animals, Male, Bovine Tuberculosis, Cattle, Immune system, Mycobacterium bovis, Gene Expression Regulation, Gene expression profiling, Alveolar Macrophage, Innate Immune System, TLR, and Medical and Health Sciences
Research Interests: Computational Biology, Biology, Medicine, Signal Transduction, Cats, and 15 moreTranscriptome, Animals, Male, Bovine Tuberculosis, Gene, Cattle, Immune system, Reproducibility of Results, Host Pathogen Interactions, Lysosomes, Mycobacterium bovis, Gene Expression Regulation, Gene expression profiling, Alveolar Macrophage, and Innate Immune System
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SummaryOwing to increasing scientific and agricultural interest in the disease‐resistant (trypanotolerant), indigenous cattle breeds of West and Central Africa, there is a need for a rational genetically based description of populations... more
SummaryOwing to increasing scientific and agricultural interest in the disease‐resistant (trypanotolerant), indigenous cattle breeds of West and Central Africa, there is a need for a rational genetically based description of populations in the region. The greatest threat to the invaluable genetic resource represented by these animals is that of extensive genetic introgression of distantly related zebu cattle from northern populations which do not share their inherited tolerances. Southern blotting with a chromosome Y‐specific probe, btDYZ‐1 (locus DYZ1) is shown to be a sensitive assay to detect such introgression. Evidence of historical crossbreeding is reported in two important N'Dama populations previously classed as purely taurine.
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RT-qPCR can be used to accurately determine expression levels of genes following RNA extraction from tissue samples. If blood is the source of total RNA, it is often desirable to process the samples immediately following collection... more
RT-qPCR can be used to accurately determine expression levels of genes following RNA extraction from tissue samples. If blood is the source of total RNA, it is often desirable to process the samples immediately following collection because delays in processing for RNA extraction may influence mRNA expression estimates obtained from RT-qPCR analyses. However, this may not be feasible if the site of blood collection is distant from the processing laboratory. In the present study, the effects of delays in the processing of blood samples on mRNA expression data was investigated using a panel of 23 functionally diverse genes from five different gene ontology (GO) categories in peripheral blood sampled from ten age-matched healthy cattle. Venous blood was collected in Tempus™ Blood RNA tubes, which contain reagents that lyse blood cells immediately and stabilise the RNA signature (T(0)). Blood was also collected in conventional lithium heparin collection tubes, and stored at ambient temperature for T(4), T(6) and T(8)h, prior to total RNA extraction. The mRNA expression profiles of these 23 genes were determined by RT-qPCR and compared across the time course. Thirteen genes showed significant up- or down-fold changes in mRNA expression over the 8h time course. Among the GO categories, genes in the Immune response category showed the most differential expression. These results also demonstrated that the changes in mRNA expression for the IFNG gene, which encodes the cytokine IFN-γ, did not correspond to IFN-γ protein levels estimated using ELISA.
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Variation at the myostatin (MSTN) gene locus has been shown to influence racing phenotypes in Thoroughbred horses, and in particular, early skeletal muscle development and the aptitude for racing at short distances. Specifically, a single... more
Variation at the myostatin (MSTN) gene locus has been shown to influence racing phenotypes in Thoroughbred horses, and in particular, early skeletal muscle development and the aptitude for racing at short distances. Specifically, a single nucleotide polymorphism (SNP) in the first intron of MSTN (g.66493737C/T) is highly predictive of best race distance among Flat racing Thoroughbreds: homozygous C/C horses are best suited to short distance races, heterozygous C/T horses are best suited to middle distance races, and homozygous T/T horses are best suited to longer distance races. Patent applications for this gene marker association, and other linked markers, have been filed. The information contained within the patent applications is exclusively licensed to the commercial biotechnology company Equinome Ltd, which provides a DNA-based test to the international Thoroughbred horse racing and breeding industry. The application of this information in the industry enables informed decision making in breeding and racing and can be used to assist selection to accelerate the rate of change of genetic types among distinct populations (Case Study 1) and within individual breeding operations (Case Study 2).