What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms

Grid site testing for ATLAS with Hammer Cloud

With the exponential growth of LHC (Large Hadron Collider) data in 2012, distributed computing has become the established way to analyze collider data. The ATLAS grid infrastructure includes more than 130 sites worldwide, ranging from large national computing centers to smaller university clusters. HammerCloud was previously introduced with the goals of enabling virtual organisations (VO) and site-administrators to run validation tests of the site and software infrastructure in an automated or on-demand manner. The HammerCloud infrastructure has been constantly improved to support the addition of new test workflows. These new workflows comprise e.g. tests of the ATLAS nightly build system, ATLAS Monte Carlo production system, XRootD federation (FAX) and new site stress test workflows. We report on the development, optimization and results of the various components in the HammerCloud framework

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

Spatial Data Infrastructures for environmental e-government services: The case of water abstractions authorisations

Environment-related authorisations are a relevant issue for environmental management. They require a considerable effort by the authorities, and this might result in substantial delays for the citizens. Implementing those authorisation processes by means of e-government services would improve efficiency and, consequently, citizen satisfaction. Environment-related authorisations usually require a variety of geospatial information, and have to deal with administrative areas which do not match physical and ecological ones. They also have to integrate heterogeneous information in different formats, data models and languages, and provided by distinct organisations, even from different countries. This paper discusses how Spatial Data Infrastructures (SDIs) can deal with these problems in the environmental domain, while improving the level of service provision in terms of e-government applications. This is even more relevant within the European Union where there is a legal mandate to establish an SDI to support environmental policies and activities with an impact on the environment. As a proof-of-concept, an application to request and manage water abstraction authorisations, based on an SDI, is demonstrated. This application is part of SDIGER, a cross-border inter-administration SDI to support the water framework directive information access for the Adour–Garonne and Ebro River basins, that was a pilot project for the EU INSPIRE Directive. The introduction of this transactional e-government service modifies the administrative process of granting authorisations: it allows to re-use the effort in data capture made by the applicants in their requests, facilitates the submission of more feasible applications and reduces the workload of the office staff

RNA-seq analysis of single bovine blastocysts

Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results: We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions: This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.EEA BalcarceFil: Chitwood, James L. University of California Davis. Department of Animal Science; Estados UnidosFil: Rincon, Gonzalo. University of California Davis. Department of Animal Science; Estados UnidosFil: Kaiser, German Gustavo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Medrano, Juan F. University of California Davis. Department of Animal Science; Estados UnidosFil: Ross, Pablo J. University of California Davis. Department of Animal Science; Estados Unido

Exploring the views on total quality human resources management between public and private educational units

The aim of the present study is to identify the attitudes of the directors of different types of educational units regarding the practices of Total Quality of Human Resources Management (TQHRM) in Greece. The specific objectives of the survey are the exploration and analysis of the following issues: a) The philosophy applied by each director on the unit they manage and the position of the HR in it; b) the directors’ opinion about the TQHRM Practices; and c) the difference in the approach of these practices between the public and private educational unit directors.The data is collected using a questionnaire that was sent electronically to Greek schools of various levels in 2018 and the number of responses is 70, of which 53% are from the private and 47% from the public sector directors. To process responses and draw conclusions, both one-dimensional and multidimensional analysis were performed. The results of this survey show that the HRM practices followed by the directors do not have a clear orientation. This highlights the need for training those who run an educational institution on TQHRM and the understanding of the importance of Human Resources on achieving the goals of an organization

Improving the geospatial consistency of digital libraries metadata

Consistency is an essential aspect of the quality of metadata. Inconsistent metadata records are harmful: given a themed query, the set of retrieved metadata records would contain descriptions of unrelated or irrelevant resources, and may even not contain some resources considered obvious. This is even worse when the description of the location is inconsistent. Inconsistent spatial descriptions may yield invisible or hidden geographical resources that cannot be retrieved by means of spatially themed queries. Therefore, ensuring spatial consistency should be a primary goal when reusing, sharing and developing georeferenced digital collections. We present a methodology able to detect geospatial inconsistencies in metadata collections based on the combination of spatial ranking, reverse geocoding, geographic knowledge organization systems and information-retrieval techniques. This methodology has been applied to a collection of metadata records describing maps and atlases belonging to the Library of Congress. The proposed approach was able to automatically identify inconsistent metadata records (870 out of 10,575) and propose fixes to most of them (91.5%) These results support the ability of the proposed methodology to assess the impact of spatial inconsistency in the retrievability and visibility of metadata records and improve their spatial consistency