Next-Generation Sequencing in Equine Genomics

Next-generation sequencing of both DNA and RNA represents a second revolution in equine genetics following publication of the equine genome sequence. Technological advancements have resulted in a wide selection of next-generation sequencing platforms capable of completing small targeted experiments or resequencing complete genomes. DNA and RNA sequencing have applications in clinical and research environments. Standards for the validation and sharing of next-generation sequencing data are critical for the widespread application of the technology and applications discussed herein. As researchers and clinicians develop a better understanding of how genetic variation and phenotypic variation are linked, next-generation sequencing could help pave the way to personalized and precision management of horses

Integrated control of vector-borne diseases of livestock--pyrethroids: panacea or poison?

Tick- and tsetse-borne diseases cost Africa approximately US$4-5 billion per year in livestock production-associated losses. The use of pyrethroid-treated cattle to control ticks and tsetse promises to be an increasingly important tool to counter this loss. However, uncontrolled use of this technology might lead to environmental damage, acaricide resistance in tick populations and a possible exacerbation of tick-borne diseases. Recent research to identify, quantify and to develop strategies to avoid these effects are highlighted

The joint US/UK 1990 epoch world magnetic model

A detailed summary of the data used, analyses performed, modeling techniques employed, and results obtained in the course of the 1990 Epoch World Magnetic Modeling effort are given. Also, use and limitations of the GEOMAG algorithm are presented. Charts and tables related to the 1990 World Magnetic Model (WMM-90) for the Earth's main field and secular variation in Mercator and polar stereographic projections are presented along with useful tables of several magnetic field components and their secular variation on a 5-degree worldwide grid

Evaluation of the School Administration Manager Project

Examines the results to date of a Wallace-supported project to help principals delegate some administrative and managerial tasks to school administration managers and spend more time interacting with teachers, students and others on instructional matters

Public engagement in local government: the voice and influence of citizens in online communicative spaces

The communications and engagement strategies of local councils play an important role in contributing to the public's understanding of local democracies, and their engagement with local issues. Based on a study of the local authority in the third largest city in the UK, Leeds, this article presents an empirically based analysis of the impact of new opportunities for public engagement afforded by digital media on the Council's communication with citizens. Drawing on over 20 face-to-face semi-structured interviews with elected politicians, Council strategists, Council communications specialists, mainstream journalists, and citizen journalists, the article explores perceptions of the Council's engagement and communication with citizens from the perspective of a range of actors involved in the engagement process. The research asks what the differing motivations behind the Council's communications and engagement strategies mean for the way that digital media are and might be used in the future to enhance the role of citizens in local governance. The research suggests that while there are no grounds for expecting digital media to displace existing channels of public engagement, digital media are beginning to play an important role in defining and reconfiguring the role of citizens within local governance

Analysis of equine protein-coding gene structure and expression by RNA-sequencing

RNA-sequencing (RNA-seq) data from eight equine tissue samples (34-day whole embryo, full term placental villous, adult testes, adult cerebellum, adult articular cartilage, adult LPS-stimulated articular cartilage, adult synovial membrane, and adult LPS-stimulated synovial membrane) were used to refine the structural annotation of protein-coding genes in the horse and for a preliminary assessment of tissue-specific expression patterns

Ultraviolet HST Observations of the Jet in M87

We present new ultraviolet photometry of the jet in M87 obtained from HST WFPC2 imaging. We combine these ultraviolet data with previously published photometry for the knots of the jet in radio, optical, and X-ray, and fit three theoretical synchrotron models to the full data set. The synchrotron models consistently overpredict the flux in the ultraviolet when fit over the entire dataset. We show that if the fit is restricted to the radio through ultraviolet data, the synchrotron models can provide a good match to the data. The break frequencies of these fits are much lower than previous estimates. The implied synchrotron lifetimes for the bulk of the emitting population are longer than earlier work, but still much shorter than the estimated kinematic lifetimes of the knots. The observed X-ray flux cannot be successfully explained by the simple synchrotron models that fit the ultraviolet and optical fluxes. We discuss the possible implications of these results for the physical properties of the M87 jet. We also observe increased flux for the HST-1 knot that is consistent with previous results for flaring. This observation fills in a significant gap in the time coverage early in the history of the flare, and therefore sets constraints on the initial brightening of the flare.Comment: 14 pages, 2 figures, Accepted for publication in ApJ, changed lightcurve and caption in Figure

The Pelvic Flexure Separates Distinct Microbial Communities in the Equine Hindgut

As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine

Analysis of unannotated equine transcripts identified by mRNA sequencing

Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific

Non-Coding RNA Sequencing of Equine Endometrium During Maternal Recognition of Pregnancy.

Maternal recognition of pregnancy (MRP) in the mare is not well defined. In a non-pregnant mare, prostaglandin F2α (PGF) is released on day 14 post-ovulation (PO) to cause luteal regression, resulting in loss of progesterone production. Equine MRP occurs prior to day 14 to halt PGF production. Studies have failed to identify a gene candidate for MRP, so attention has turned to small, non-coding RNAs. The objective of this study was to evaluate small RNA (<200 nucleotides) content in endometrium during MRP. Mares were used in a cross-over design with each having a pregnant and non-mated cycle. Each mare was randomly assigned to collection day 11 or 13 PO (n = 3/day) and endometrial biopsies were obtained. Total RNA was isolated and sequencing libraries were prepared using a small RNA library preparation kit and sequenced on a HiSeq 2000. EquCab3 was used as the reference genome and DESeq2 was used for statistical analysis. On day 11, 419 ncRNAs, representing miRNA, snRNA, snoRNA, scaRNA, and vaultRNA, were different between pregnancy statuses, but none on day 13. Equine endometrial ncRNAs with unknown structure and function were also identified. This study is the first to describe ncRNA transcriptome in equine endometrium. Identifying targets of these ncRNAs could lead to determining MRP