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Equine infectious anaemia virus ( EIAV) is a lentivirus with an almost worldwide distribution that causes persistent infections in equids. Technical limitations have restricted genetic analysis of EIAV field isolates predominantly to gag sequences resulting in very little published information concerning the extent of inter-strain variation in pol, env and the three ancillary open reading frames ( ORFs). Here, we describe the use of long-range PCR in conjunction with next-generation sequencing ( NGS) for rapid molecular characterization of all viral ORFs and known transcription factor binding motifs within the long terminal repeat of two EIAV isolates from the 2006 Italian outbreak. These isolates were from foals believed to have been exposed to the same source material but with different clinical histories: one died 53 days post-infection ( SA) while the other ( DE) survived 5 months despite experiencing multiple febrile episodes. Nucleotide sequence identity between the isolates was 99.358% confirming infection with the same EIAV strain with most differences comprising single nucleotide polymorphisms in env and the second exon of rev. Although the synonymous:non-synonymous nucleotide substitution ratio was approximately 2:1 in gag and pol, the situation is reversed in env and ORF3 suggesting these sequences are subjected to host-mediated selective pressure. EIAV proviral quasispecies complexity in vivo has not been extensively investigated; however, analysis suggests it was relatively low in SA at the time of death. These results highlight advantages of NGS for molecular characterization of EIAV namely it avoids potential artefacts generated by traditional composite sequencing strategies and can provide information about viral quasispecies complexity. [ABSTRACT FROM AUTHOR]

Athletic performance is both a stress factor and an adaptive response to exercise that may be modulated by training, reduce inflammation and help prevent disease. Studies on the endocrinology of exercise and training have demonstrated the existence of an integrated metabolic network of hormone and cytokine regulation. Subsequent molecular studies have shown that repeated bouts of exercise may establish new basal levels of gene expression at rest. The Thoroughbred horse may be a useful 'exercise model' for inter-individual comparisons between subjects with homogeneous genetic and environmental backgrounds and similar exercise management practices. In this study, the effects of training and acute effort on gene expression were evaluated with a real time PCR approach in athletic (n = 10) and sedentary horses (n = 9), using a previously characterised panel of genes known to be highly modulated during effort (CXCL2, TLR4, ILlfi, 118, IL1RII, IU8, IL6 and CEBPfS). A 'rest comparison' was performed to evaluate a training effect in both groups while a 'race comparison' was performed in athletic horses only (before, immediately after, and 12 h after racing) to determine the effect of acute effort. The results indicated that many of the investigated genes {TLR4, ILip, IL1RII, 1L18,116 and CEBPfS) were expressed to a greater extent in athletic horses compared to sedentary animals when both were at rest. However, a time-course comparison in the athletic horses revealed that genes exhibiting the highest levels of expression at rest did not show significant changes after the race. The findings suggested that training may exert a conditioning on gene expression at rest leading to a more prompt response to exercise-induced stress in Thoroughbreds. [ABSTRACT FROM AUTHOR]

A large proportion of mammalian genomes is represented by transposable elements (TE), most of them being long interspersed nuclear elements 1 ( LINE-1 or L1). An increased expression of LINE-1 elements may play an important role in cellular stress-related conditions exerting drastic effects on the mammalian transcriptome. To understand the impact of TE on the known horse transcriptome, we masked the horse EST database, pointing out that the amount is consistent with other major vertebrates. A previously developed transcript-derived fragments (TDFs) dataset, deriving from exercise-stimulated horse peripheral blood mononuclear cells (PBMCs), was found to be enriched with L1 (26.8% in terms of bp). We investigated the involvement of TDFs in exercise-induced stress through bioinformatics and gene expression analysis. Results indicate that LINE-derived sequences are not only highly but also differentially expressed during physical effort, hinting at interesting scenarios in the regulation of gene expression in relation to exercise. [ABSTRACT FROM AUTHOR]