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Sample records for coverage pig genome

  1. Genomic analysis reveals selection in Chinese native black pig

    PubMed Central

    Fu, Yuhua; Li, Cencen; Tang, Qianzi; Tian, Shilin; Jin, Long; Chen, Jianhai; Li, Mingzhou; Li, Changchun

    2016-01-01

    Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production. PMID:27808243

  2. Swine Genome Sequencing Consortium (SGSC): A Strategic Roadmap for Sequencing The Pig Genome

    PubMed Central

    Schook, Lawrence B.; Beever, Jonathan E.; Rogers, Jane; Humphray, Sean; Archibald, Alan; Chardon, Patrick; Milan, Denis; Rohrer, Gary; Eversole, Kellye

    2005-01-01

    The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human–pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome. PMID:18629187

  3. The complete mitochondrial genome of the Yorkshire pig (Sus scrofa).

    PubMed

    Xu, Dong; Yang, Hu; Ma, Haiming

    2016-01-01

    This study aims to identify the complete nucleotide sequence of mitochondrial genome in the Yorkshire pig. Sequence analysis indicates that the genome structure is in accordance with other pig breeds, and it contains 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Yorkshire pig provides an important record set for further study on genetic mechanism.

  4. A HIGH COVERAGE GENOME SEQUENCE FROM AN ARCHAIC DENISOVAN INDIVIDUAL

    PubMed Central

    Meyer, Matthias; Kircher, Martin; Gansauge, Marie-Theres; Li, Heng; Racimo, Fernando; Mallick, Swapan; Schraiber, Joshua G.; Jay, Flora; Prüfer, Kay; de Filippo, Cesare; Sudmant, Peter H.; Alkan, Can; Fu, Qiaomei; Do, Ron; Rohland, Nadin; Tandon, Arti; Siebauer, Michael; Green, Richard E.; Bryc, Katarzyna; Briggs, Adrian W.; Stenzel, Udo; Dabney, Jesse; Shendure, Jay; Kitzman, Jacob; Hammer, Michael F.; Shunkov, Michael V.; Derevianko, Anatoli P.; Patterson, Nick; Andrés, Aida M.; Eichler, Evan E.; Slatkin, Montgomery; Reich, David; Kelso, Janet; Pääbo, Svante

    2013-01-01

    We present a DNA library preparation method that has allowed us to reconstruct a high coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans. PMID:22936568

  5. Low coverage sequencing of two Asian elephant (Elephas maximus) genomes

    PubMed Central

    2014-01-01

    Background There are three species of elephant that exist, the Asian elephant (Elephas maximus) and two species of African elephant (Loxodonta africana and Loxodonta cyclotis). The populations of all three species are dwindling, and are under threat due to factors, such as habitat destruction and ivory hunting. The species differ in many respects, including in their morphology and response to disease. The availability of elephant genome sequence data from all three elephant species will complement studies of behaviour, genetic diversity, evolution and disease resistance. Findings We present low-coverage Illumina sequence data from two Asian elephants, representing approximately 5X and 2.5X coverage respectively. Both raw and aligned data are available, using the African elephant (L. africana) genome as a reference. Conclusions The data presented here are an important addition to the available genetic and genomic information on Asian and African elephants. PMID:25053995

  6. Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa)

    PubMed Central

    Chen, Kefei; Baxter, Tara; Muir, William M.; Groenen, Martien A.; Schook, Lawrence B.

    2007-01-01

    The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health. PMID:17384734

  7. Inferring Heterozygosity from Ancient and Low Coverage Genomes

    PubMed Central

    Kousathanas, Athanasios; Leuenberger, Christoph; Link, Vivian; Sell, Christian; Burger, Joachim; Wegmann, Daniel

    2017-01-01

    While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage <1× of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence, except for the initial alignment of the sequencing data, and takes into account both variable sequencing errors and potential postmortem damage. It is thus also applicable to nonmodel organisms and ancient genomes. Since error rates as reported by sequencing machines are generally distorted and require recalibration, we also introduce a method to accurately infer recalibration parameters in the presence of postmortem damage. This method does not require knowledge about the underlying genome sequence, but instead works with haploid data (e.g., from the X-chromosome from mammalian males) and integrates over the unknown genotypes. Using extensive simulations we show that a few megabasepairs of haploid data are sufficient for accurate recalibration, even at average coverages as low as 1×. At similar coverages, our method also produces very accurate estimates of heterozygosity down to 10−4 within windows of about 1 Mbp. We further illustrate the usefulness of our approach by inferring genome-wide patterns of diversity for several ancient human samples, and we found that 3000–5000-year-old samples showed diversity patterns comparable to those of modern humans. In contrast, two European hunter-gatherer samples exhibited not only considerably lower levels of diversity than modern samples, but also highly distinct distributions of diversity along their genomes. Interestingly, these distributions were also very different between the two samples, supporting earlier

  8. Modeling genome coverage in single-cell sequencing

    PubMed Central

    Daley, Timothy; Smith, Andrew D.

    2014-01-01

    Motivation: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material. Results: We propose a method to predict the genome coverage of a deep sequencing experiment using information from an initial shallow sequencing experiment mapped to a reference genome. The observed coverage statistics are used in a non-parametric empirical Bayes Poisson model to estimate the gain in coverage from deeper sequencing. This approach allows researchers to know statistical features of deep sequencing experiments without actually sequencing deeply, providing a basis for optimizing and comparing single-cell sequencing protocols or screening libraries. Availability and implementation: The method is available as part of the preseq software package. Source code is available at http://smithlabresearch.org/preseq. Contact: andrewds@usc.edu Supplementary information: Supplementary material is available at Bioinformatics online. PMID:25107873

  9. A high utility integrated map of the pig genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genome...

  10. Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2)

    PubMed Central

    Warr, Amanda; Robert, Christelle; Hume, David; Archibald, Alan L.; Deeb, Nader; Watson, Mick

    2015-01-01

    Many applications of high throughput sequencing rely on the availability of an accurate reference genome. Variant calling often produces large data sets that cannot be realistically validated and which may contain large numbers of false-positives. Errors in the reference assembly increase the number of false-positives. While resources are available to aid in the filtering of variants from human data, for other species these do not yet exist and strict filtering techniques must be employed which are more likely to exclude true-positives. This work assesses the accuracy of the pig reference genome (Sscrofa10.2) using whole genome sequencing reads from the Duroc sow whose genome the assembly was based on. Indicators of structural variation including high regional coverage, unexpected insert sizes, improper pairing and homozygous variants were used to identify low quality (LQ) regions of the assembly. Low coverage (LC) regions were also identified and analyzed separately. The LQ regions covered 13.85% of the genome, the LC regions covered 26.6% of the genome and combined (LQLC) they covered 33.07% of the genome. Over half of dbSNP variants were located in the LQLC regions. Of copy number variable regions identified in a previous study, 86.3% were located in the LQLC regions. The regions were also enriched for gene predictions from RNA-seq data with 42.98% falling in the LQLC regions. Excluding variants in the LQ, LC, or LQLC from future analyses will help reduce the number of false-positive variant calls. Researchers using WGS data should be aware that the current pig reference genome does not give an accurate representation of the copy number of alleles in the original Duroc sow’s genome. PMID:26640477

  11. Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2).

    PubMed

    Warr, Amanda; Robert, Christelle; Hume, David; Archibald, Alan L; Deeb, Nader; Watson, Mick

    2015-01-01

    Many applications of high throughput sequencing rely on the availability of an accurate reference genome. Variant calling often produces large data sets that cannot be realistically validated and which may contain large numbers of false-positives. Errors in the reference assembly increase the number of false-positives. While resources are available to aid in the filtering of variants from human data, for other species these do not yet exist and strict filtering techniques must be employed which are more likely to exclude true-positives. This work assesses the accuracy of the pig reference genome (Sscrofa10.2) using whole genome sequencing reads from the Duroc sow whose genome the assembly was based on. Indicators of structural variation including high regional coverage, unexpected insert sizes, improper pairing and homozygous variants were used to identify low quality (LQ) regions of the assembly. Low coverage (LC) regions were also identified and analyzed separately. The LQ regions covered 13.85% of the genome, the LC regions covered 26.6% of the genome and combined (LQLC) they covered 33.07% of the genome. Over half of dbSNP variants were located in the LQLC regions. Of copy number variable regions identified in a previous study, 86.3% were located in the LQLC regions. The regions were also enriched for gene predictions from RNA-seq data with 42.98% falling in the LQLC regions. Excluding variants in the LQ, LC, or LQLC from future analyses will help reduce the number of false-positive variant calls. Researchers using WGS data should be aware that the current pig reference genome does not give an accurate representation of the copy number of alleles in the original Duroc sow's genome.

  12. Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

    PubMed

    Xie, Lei; Bourne, Philip E

    2005-08-01

    The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference frame, and integrating structure data from the Protein Data Bank (PDB), target sequences from the structural genomics projects, structure homology derived from the SUPERFAMILY database, and genome annotations from Ensembl and NCBI, we provide a quantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37% of the functional classes identified in the genome; whole structure coverage exists for 25% of the genome. If all the structural genomics targets were solved (twice the current number of structures in the PDB), it is estimated that structures of one domain would cover 69% of the functional classes identified and complete structure coverage would be 44%. Homology models from existing experimental structures extend the 37% coverage to 56% of the genome as single domains and 25% to 31% for complete structures. Coverage from homology models is not evenly distributed by protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures should be determined. Current key functional families without structure representation are highlighted here; updated information on the "most wanted list" that should be solved is available on a weekly basis from http://function.rcsb.org:8080/pdb/function_distribution/index.html.

  13. Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds.

    PubMed

    Choi, Jung-Woo; Chung, Won-Hyong; Lee, Kyung-Tai; Cho, Eun-Seok; Lee, Si-Woo; Choi, Bong-Hwan; Lee, Sang-Heon; Lim, Wonjun; Lim, Dajeong; Lee, Yun-Gyeong; Hong, Joon-Ki; Kim, Doo-Wan; Jeon, Hyeon-Jeong; Kim, Jiwoong; Kim, Namshin; Kim, Tae-Hun

    2015-08-01

    Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.

  14. The pig genome project has plenty to squeal about.

    PubMed

    Fan, B; Gorbach, D M; Rothschild, M F

    2011-01-01

    Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed.

  15. Information recovery from low coverage whole-genome bisulfite sequencing

    PubMed Central

    Libertini, Emanuele; Heath, Simon C.; Hamoudi, Rifat A.; Gut, Marta; Ziller, Michael J.; Czyz, Agata; Ruotti, Victor; Stunnenberg, Hendrik G.; Frontini, Mattia; Ouwehand, Willem H.; Meissner, Alexander; Gut, Ivo G.; Beck, Stephan

    2016-01-01

    The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future. PMID:27346250

  16. The complete mitochondrial genome of Java warty pig (Sus verrucosus).

    PubMed

    Fan, Jie; Li, Chun-Hong; Shi, Wei

    2015-06-01

    In the present study, the complete mitochondrial genome sequence of the Java warty pig was reported for the first time. The total length of the mitogenome was 16,479 bp. It contained the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region) as that of most other pigs. The overall composition of the mitogenome was estimated to be 34.9% for A, 26.1% for T, 26.0% for C and 13.0% for G showing an A-T (61.0%)-rich feature. The mitochondrial genome analyzed here will provide new genetic resource to uncover pigs' evolution.

  17. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

    PubMed Central

    2011-01-01

    Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives

  18. A unique circovirus-like genome detected in pig feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a metagenomic approach and molecular cloning methods, we identified, cloned, and sequenced the complete genome of a novel circular DNA virus, porcine stool-associated virus (PoSCV4), from pig feces. Phylogenetic analysis of the deduced replication initiator protein showed that PoSCV4 is most r...

  19. Analysis of pig genomes provide insight into porcine demography and evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For nearly 8,000 years pigs and humans have shared a close and complex relationship, and through domestication and breeding, humans have shaped the genomes of current diverse pig breeds. Here we present the assembly and analysis of the genome sequence of a female domestic pig from the European Duroc...

  20. Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17

    PubMed Central

    Hart, Elizabeth A; Caccamo, Mario; Harrow, Jennifer L; Humphray, Sean J; Gilbert, James GR; Trevanion, Steve; Hubbard, Tim; Rogers, Jane; Rothschild, Max F

    2007-01-01

    Background We describe here the sequencing, annotation and comparative analysis of an 8 Mb region of pig chromosome 17, which provides a useful test region to assess coverage and quality for the pig genome sequencing project. We report our findings comparing the annotation of draft sequence assembled at different depths of coverage. Results Within this region we annotated 71 loci, of which 53 are orthologous to human known coding genes. When compared to the syntenic regions in human (20q13.13-q13.33) and mouse (chromosome 2, 167.5 Mb-178.3 Mb), this region was found to be highly conserved with respect to gene order. The most notable difference between the three species is the presence of a large expansion of zinc finger coding genes and pseudogenes on mouse chromosome 2 between Edn3 and Phactr3 that is absent from pig and human. All of our annotation has been made publicly available in the Vertebrate Genome Annotation browser, VEGA. We assessed the impact of coverage on sequence assembly across this region and found, as expected, that increased sequence depth resulted in fewer, longer contigs. One-third of our annotated loci could not be fully re-aligned back to the low coverage version of the sequence, principally because the transcripts are fragmented over several contigs. Conclusion We have demonstrated the considerable advantages of sequencing at increased read depths and discuss the implications that lower coverage sequence may have on subsequent comparative and functional studies, particularly those involving complex loci such as GNAS. PMID:17705864

  1. Mining the pig genome to investigate the domestication process

    PubMed Central

    Ramos-Onsins, S E; Burgos-Paz, W; Manunza, A; Amills, M

    2014-01-01

    Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication. PMID:25074569

  2. Advances in Pig Genomics and Functional Gene Discovery

    PubMed Central

    2003-01-01

    Advances in pig gene identification, mapping and functional analysis have continued to make rapid progress. The porcine genetic linkage map now has nearly 3000 loci, including several hundred genes, and is likely to expand considerably in the next few years, with many more genes and amplified fragment length polymorphism (AFLP) markers being added to the map. The physical genetic map is also growing rapidly and has over 3000 genes and markers. Several recent quantitative trait loci (QTL) scans and candidate gene analyses have identified important chromosomal regions and individual genes associated with traits of economic interest. The commercial pig industry is actively using this information and traditional performance information to improve pig production by marker-assisted selection (MAS). Research to study the co-expression of thousands of genes is now advancing and methods to combine these approaches to aid in gene discovery are under way. The pig's role in xenotransplantation and biomedical research makes the study of its genome important for the study of human disease. This review will briefly describe advances made, directions for future research and the implications for both the pig industry and human health. PMID:18629119

  3. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

    PubMed Central

    Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark; Gailing, Oliver; Liang, Haiying; Romero-Severson, Jeanne; Schlarbaum, Scott; Carlson, John E.

    2015-01-01

    Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence. PMID:26698853

  4. Identification of copy number variants in whole-genome data using Reference Coverage Profiles.

    PubMed

    Glusman, Gustavo; Severson, Alissa; Dhankani, Varsha; Robinson, Max; Farrah, Terry; Mauldin, Denise E; Stittrich, Anna B; Ament, Seth A; Roach, Jared C; Brunkow, Mary E; Bodian, Dale L; Vockley, Joseph G; Shmulevich, Ilya; Niederhuber, John E; Hood, Leroy

    2015-01-01

    The identification of DNA copy numbers from short-read sequencing data remains a challenge for both technical and algorithmic reasons. The raw data for these analyses are measured in tens to hundreds of gigabytes per genome; transmitting, storing, and analyzing such large files is cumbersome, particularly for methods that analyze several samples simultaneously. We developed a very efficient representation of depth of coverage (150-1000× compression) that enables such analyses. Current methods for analyzing variants in whole-genome sequencing (WGS) data frequently miss copy number variants (CNVs), particularly hemizygous deletions in the 1-100 kb range. To fill this gap, we developed a method to identify CNVs in individual genomes, based on comparison to joint profiles pre-computed from a large set of genomes. We analyzed depth of coverage in over 6000 high quality (>40×) genomes. The depth of coverage has strong sequence-specific fluctuations only partially explained by global parameters like %GC. To account for these fluctuations, we constructed multi-genome profiles representing the observed or inferred diploid depth of coverage at each position along the genome. These Reference Coverage Profiles (RCPs) take into account the diverse technologies and pipeline versions used. Normalization of the scaled coverage to the RCP followed by hidden Markov model (HMM) segmentation enables efficient detection of CNVs and large deletions in individual genomes. Use of pre-computed multi-genome coverage profiles improves our ability to analyze each individual genome. We make available RCPs and tools for performing these analyses on personal genomes. We expect the increased sensitivity and specificity for individual genome analysis to be critical for achieving clinical-grade genome interpretation.

  5. Applying functional genomics research to the study of pig reproduction.

    PubMed

    Pomp, D; Caetano, A R; Bertani, G R; Gladney, C D; Johnson, R K

    2001-01-01

    Functional genomics is an experimental approach that incorporates genome-wide or system-wide experimentation, expanding the scope of biological investigation from studying single genes to studying potentially all genes at once in a systematic manner. This technology is highly appealing because of its high throughput and relatively low cost. Furthermore, analysis of gene expression using microarrays is likely to be more biologically relevant than the conventional paradigm of reductionism, because it has the potential to uncover new biological connections between genes and biochemical pathways. However, functional genomics is still in its infancy, especially with regard to the study of pig reproduction. Currently, efforts are centred on developing the necessary resources to enable high throughput evaluation and comparison of gene expression. However, it is clear that in the near future functional genomics will be applied on a large scale to study the biology and physiology of reproduction in pigs, and to understand better the complex nature of genetic control over polygenic characteristics, such as ovulation rate and litter size. We can look forward to generating a significant amount of new data on differences in gene expression between genotypes, treatments, or at various temporal and spatial coordinates within a variety of reproductively relevant systems. Along with this capability will be the challenge of collating, analysing and interpreting datasets that are orders of magnitude more extensive and complex than those currently used. Furthermore, integration of functional genomics with traditional genetic approaches and with detailed analysis of the proteome and relevant whole animal phenotypes will be required to make full use of this powerful new experimental paradigm as a beneficial research tool.

  6. Genome data from a sixteenth century pig illuminate modern breed relationships.

    PubMed

    Ramírez, O; Burgos-Paz, W; Casas, E; Ballester, M; Bianco, E; Olalde, I; Santpere, G; Novella, V; Gut, M; Lalueza-Fox, C; Saña, M; Pérez-Enciso, M

    2015-02-01

    Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.

  7. Genome data from a sixteenth century pig illuminate modern breed relationships

    PubMed Central

    Ramírez, O; Burgos-Paz, W; Casas, E; Ballester, M; Bianco, E; Olalde, I; Santpere, G; Novella, V; Gut, M; Lalueza-Fox, C; Saña, M; Pérez-Enciso, M

    2015-01-01

    Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds. PMID:25204303

  8. The complete sequence of the mitochondrial genome of Rongchang pig (Sus Scrofa).

    PubMed

    Wang, Ling-Yu; Xu, Dong; Ma, Hai-Ming

    2016-01-01

    Rongchang pig is one of the native breeds in Sichuan province in China. The total length of mitochondrial genome of Rongchang pig is 16,710 bp, including 34.67% A, 26.18% C, 25.82% T and 13.33% G, and in the order A > C > T > G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Rongchang pig. The mitochondrial genome of Rongchang pig subsequently provides an important information in genetic mechanism and the evolution genomes.

  9. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

    USGS Publications Warehouse

    Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

    2014-01-01

    As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

  10. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

    PubMed

    Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

    2014-01-01

    As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

  11. Genome editing revolutionize the creation of genetically modified pigs for modeling human diseases.

    PubMed

    Yao, Jing; Huang, Jiaojiao; Zhao, Jianguo

    2016-09-01

    Pigs have anatomical, physiological and genomic characteristics that make them highly suitable for modeling human diseases. Genetically modified (GM) pig models of human diseases are critical for studying pathogenesis, treatment, and prevention. The emergence of nuclease-mediated genome editing technology has been successfully employed for engineering of the pig genome, which has revolutionize the creation of GM pig models with highly complex pathophysiologies and comorbidities. In this review, we summarize the progress of recently developed genome editing technologies, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), which enable highly efficient and precise introduction of genome modifications into pigs, and tailored disease models that have been generated in various disciplines via genome editing technology. We also summarize the GM pig models that have been generated by conventional transgenic strategies. Additionally, perspectives regarding the application of GM pigs in biomedical research are discussed.

  12. Calibrating genomic and allelic coverage bias in single-cell sequencing

    PubMed Central

    Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

    2016-01-01

    Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

  13. Calibrating genomic and allelic coverage bias in single-cell sequencing.

    PubMed

    Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

    2015-04-16

    Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

  14. Sequencing the Pig Genome Using a Mapped BAC by BAC Approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have generated a highly contiguous physical map covering >98% of the pig genome in just 176 contigs. The map is localised to the genome through integration with the UIUC RH map as well BAC end sequence alignments to the human genome. Over 265k HindIII restriction digest fingerprints totalling 1...

  15. The complete sequence of the mitochondrial genome of Lantang pig (Sus scrofa).

    PubMed

    Ran, Mao-Liang; Liu, Zhen; Yang, An-Qi; Li, Zhi; Chen, Bin

    2016-01-01

    Lantang pig is a native breed of Guangzhou Province in China. It is the first time that the complete mitochondrial genome sequence of Lantang pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 conntrol region (D-loop region, Table 1). The total base composition of Lantang pig mitochondrial genome is 34.69% for A, 26.18% for C, 25.82% for T and 13.31% for G, in the order A>C>T>G. The complete mitochondrial genome of Lantang pig provides an important data in genetic mechanism and the evolution genomes.

  16. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

    PubMed Central

    2011-01-01

    Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome

  17. Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians.

    PubMed

    Shen, Hui; Li, Jian; Zhang, Jigang; Xu, Chao; Jiang, Yan; Wu, Zikai; Zhao, Fuping; Liao, Li; Chen, Jun; Lin, Yong; Tian, Qing; Papasian, Christopher J; Deng, Hong-Wen

    2013-01-01

    Whole genome sequencing studies are essential to obtain a comprehensive understanding of the vast pattern of human genomic variations. Here we report the results of a high-coverage whole genome sequencing study for 44 unrelated healthy Caucasian adults, each sequenced to over 50-fold coverage (averaging 65.8×). We identified approximately 11 million single nucleotide polymorphisms (SNPs), 2.8 million short insertions and deletions, and over 500,000 block substitutions. We showed that, although previous studies, including the 1000 Genomes Project Phase 1 study, have catalogued the vast majority of common SNPs, many of the low-frequency and rare variants remain undiscovered. For instance, approximately 1.4 million SNPs and 1.3 million short indels that we found were novel to both the dbSNP and the 1000 Genomes Project Phase 1 data sets, and the majority of which (∼96%) have a minor allele frequency less than 5%. On average, each individual genome carried ∼3.3 million SNPs and ∼492,000 indels/block substitutions, including approximately 179 variants that were predicted to cause loss of function of the gene products. Moreover, each individual genome carried an average of 44 such loss-of-function variants in a homozygous state, which would completely "knock out" the corresponding genes. Across all the 44 genomes, a total of 182 genes were "knocked-out" in at least one individual genome, among which 46 genes were "knocked out" in over 30% of our samples, suggesting that a number of genes are commonly "knocked-out" in general populations. Gene ontology analysis suggested that these commonly "knocked-out" genes are enriched in biological process related to antigen processing and immune response. Our results contribute towards a comprehensive characterization of human genomic variation, especially for less-common and rare variants, and provide an invaluable resource for future genetic studies of human variation and diseases.

  18. A 2-D guinea pig lung proteome map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Guinea pigs represent an important model for a number of infectious and non-infectious pulmonary diseases. The guinea pig genome has recently been sequenced to full coverage, opening up new research avenues using genomics, transcriptomics and proteomics techniques in this species. In order to furth...

  19. Construction of a llama bacterial artificial chromosome library with approximately 9-fold genome equivalent coverage.

    PubMed

    Airmet, K W; Hinckley, J D; Tree, L T; Moss, M; Blumell, S; Ulicny, K; Gustafson, A K; Weed, M; Theodosis, R; Lehnardt, M; Genho, J; Stevens, M R; Kooyman, D L

    2012-01-01

    The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be 2.4 × 10⁹ bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.

  20. The complete sequence of mitochondrial genome of Laiwu Black pig (Sus Scrofa).

    PubMed

    Yang, Hu; Xu, Xing-Li; Ma, Hai-Ming

    2016-01-01

    In the present study, the ear tissue of an adult Laiwu Black pig is from the Shandong province of China. The complete mitochondrial genome of Laiwu Black pig was determined by polymerase chain reaction (PCR). The complete mitochondrial genome is 16,710 bp, and it contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a control region (D-loop), with the genome organization and gene order being identical to that of the typical vertebrates.

  1. The complete mitochondrial genome sequence of Diannan small-ear pig (Sus Scrofa).

    PubMed

    Wang, Ling-Yu; Xu, Dong; Xiao, Ding-Fu; Ma, Hai-Ming

    2016-01-01

    In this study, the complete mitochondrial genome sequence of Diannan small-ear pig in Yunnan Province was firstly reported, which was determined through polymerase chain reaction (PCR) method. The total length of mitochondrial genome of Diannan small-ear pig was 16720 bp, including 34.77% A, 26.18% C, 25.81% T and 13.24% G, and in the order A > C > T > G. Mitochondrial genome contained a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. The mitochondrial genome of Diannan small-ear pig provides an important data set for the study on genetic mechanism.

  2. The complete sequence of mitochondrial genome of Wuzhishan pig (Sus Scrofa).

    PubMed

    Chai, Yu-Lan; Xu, Dong; Ma, Hai-Ming

    2016-01-01

    In the present study, we sequenced the complete mitochondrial genome of Wuzhishan pig, which was 16,741 bp in size and had a nucleotide composition in A and T (60.46%). The genome consisted of a major non-coding control region (D-loop region) and 37 genes, including 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and 22 transfer RNA (tRNA) genes. The genes in the mitochondrial genomes of Wuzhishan pig used three kinds of initiation codons (ATA, ATG, and GTG) and four kinds of termination codons (TAA, AGA, TAG, and an incomplete termination codons T-). The complete mitochondrial genome sequence of Wuzhishan pig provides an important data set for further study on genetic mechanism.

  3. A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim

    PubMed Central

    Feldman, Michal; Harbeck, Michaela; Keller, Marcel; Spyrou, Maria A.; Rott, Andreas; Trautmann, Bernd; Scholz, Holger C.; Päffgen, Bernd; Peters, Joris; McCormick, Michael; Bos, Kirsten; Herbig, Alexander; Krause, Johannes

    2016-01-01

    The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany. PMID:27578768

  4. The complete sequence of the mitochondrial genome of Duroc pig (Sus Scrofa).

    PubMed

    Wang, Ling-Yu; Chai, Yu-Lan; Ma, Hai-Ming

    2016-01-01

    In this study, the total length of mitochondrial genome of Duroc pig is 16,731 bp, including 34.66% A, 26.27% C, 25.74% T and 13.33% G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. ND2 selects ATT as the initiation codon, and ATA is chose as an initiation codon in ND3 and ND5, the nonstandard start codon is GTG in ND4L and the rest protein common start codon is ATG. The mitochondrial genome of Duroc pig provides an important data in genetic mechanism, which plays an important role in the three-way crossbred pigs.

  5. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage

    PubMed Central

    Chakraborty, Mahul; Baldwin-Brown, James G.; Long, Anthony D.; Emerson, J. J.

    2016-01-01

    Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a ‘missing manual’ that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly. PMID:27458204

  6. Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs

    PubMed Central

    Wang, Hongyang; Wang, Chao; Yang, Kui; Liu, Jing; Zhang, Yu; Wang, Yanan; Xu, Xuewen; Michal, Jennifer J.; Jiang, Zhihua; Liu, Bang

    2015-01-01

    Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs’ independent domestication, and facilitate further functional studies of CNV-associated genes. PMID:26154170

  7. A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds

    PubMed Central

    2014-01-01

    Background Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. Results We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. Conclusions In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs. PMID:24422716

  8. Identification of loci affecting teat number by genome-wide association studies on three pig populations

    PubMed Central

    Tang, Jianhong; Zhang, Zhiyan; Yang, Bin; Guo, Yuanmei; Ai, Huashui; Long, Yi; Su, Ying; Cui, Leilei; Zhou, Liyu; Wang, Xiaopeng; Zhang, Hui; Wang, Chengbin; Ren, Jun; Huang, Lusheng; Ding, Nengshui

    2017-01-01

    Objective Three genome-wide association studies (GWAS) and a meta-analysis of GWAS were conducted to explore the genetic mechanisms underlying variation in pig teat number. Methods We performed three GWAS and a meta-analysis for teat number on three pig populations, including a White Duroc×Erhualian F2 resource population (n = 1,743), a Chinese Erhualian pig population (n = 320) and a Chinese Sutai pig population (n = 383). Results We detected 24 single nucleotide polymorphisms (SNPs) that surpassed the genome-wide significant level on Sus Scrofa chromosomes (SSC) 1, 7, and 12 in the F2 resource population, corresponding to four loci for pig teat number. We highlighted vertnin (VRTN) and lysine demethylase 6B (KDM6B) as two interesting candidate genes at the loci on SSC7 and SSC12. No significant associated SNPs were identified in the meta-analysis of GWAS. Conclusion The results verified the complex genetic architecture of pig teat number. The causative variants for teat number may be different in the three populations PMID:27165028

  9. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds

    PubMed Central

    Yang, Yalan; Zhou, Rong; Mu, Yulian; Hou, Xinhua; Tang, Zhonglin; Li, Kui

    2016-01-01

    DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5′ and 3′ flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals. PMID:27444743

  10. Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data.

    PubMed

    Li, Shu-Fen; Gao, Wu-Jun; Zhao, Xin-Peng; Dong, Tian-Yu; Deng, Chuan-Liang; Lu, Long-Dou

    2014-01-01

    Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

  11. Detection of hepatitis E virus genome in pig livers in Antioquia, Colombia.

    PubMed

    Gutiérrez-Vergara, C; Quintero, J; Duarte, J F; Suescún, J P; López-Herrera, A

    2015-03-31

    Hepatitis E is a form of endemic acute hepatitis found in humans in many countries worldwide and is caused by the hepatitis E Virus (HEV). Detection of HEV in pigs indicates that they may be carriers, possibly through zoonosis. The prevalence of HEV in pigs in Colombia is unknown. Studies in the US found that 11% of pig livers sold in grocery stores are contaminated with HEV. It is also known that HEV can be inactivated when cooked, as it is labile to high temperatures. The aim of this study was to determine HEV contamination in pig livers sold in Medellín, Antioquia. A total of 150 livers from 5 slaughterhouses and 100 livers in grocery stores from different social strata of the city of Medellin analyzed to detect a segment of the HEV open reading frame-1 using reverse transcription-polymerase chain reaction. The results showed that 41.3% of pig livers from slaughterhouses and 25% of livers from grocery stores tested positive for HEV. Thus, the HEV genome is present in pig livers sold in Antioquia, revealing the presence of this virus in pigs from Colombia and the need subject entrails to proper cooking processes before consumption. Further research is required to determine the role of this virus in public health and pork production in Colombia.

  12. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.

    PubMed

    Ai, Huashui; Fang, Xiaodong; Yang, Bin; Huang, Zhiyong; Chen, Hao; Mao, Likai; Zhang, Feng; Zhang, Lu; Cui, Leilei; He, Weiming; Yang, Jie; Yao, Xiaoming; Zhou, Lisheng; Han, Lijuan; Li, Jing; Sun, Silong; Xie, Xianhua; Lai, Boxian; Su, Ying; Lu, Yao; Yang, Hui; Huang, Tao; Deng, Wenjiang; Nielsen, Rasmus; Ren, Jun; Huang, Lusheng

    2015-03-01

    Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.

  13. Identification of genomic regions associated with cryptorchidism in pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cryptorchidism, failure of one or both testes to descend into the scrotum, is a common abnormality in pigs and man. Research has shown that genetics contributes to the incidence of the defect. Unlike humans, porcine cryptorchidism is not typically associated with other physiological defects. Yet cry...

  14. Houseofficers' reactions to media coverage about the sequencing of the human genome.

    PubMed

    Geller, Gail; Tambor, Ellen S; Bernhardt, Barbara A; Rodgers, Joann; Holtzman, Neil A

    2003-05-01

    After the announcement that sequencing of the human genome was nearly complete, media coverage was extensive. In light of ample evidence that the media are a primary source of health and science information, even for health professionals, media portrayals are often inaccurate or misleading, and discoveries that emanate from sequencing the human genome are likely to influence future health care, it is important to assess physicians' interpretations of media coverage about the human genome announcement. This paper describes the reactions of a sample of new physicians in the United States to this announcement, as well as the content of the stories they read or heard. Semi-structured surveys were distributed to all incoming houseofficers during Orientation at one major academic medical center. Eighty-one percent of 190 houseofficers returned a survey; 123 completed surveys were analyzed. Fifty-four percent of respondents thought the media message was only positive and 21% thought it was negative or mixed. Participants who reported radio as their media source were less likely to recall positive messages (p<0.05). Sixty-five percent and 76%, respectively, had positive perceptions of the impact of the accomplishment on people and on the medical profession. Overall, 48% were enthusiastic and 52% were guarded about the accomplishment. Enthusiasm was related to being an adult primary care houseofficer (p=0.07) or to having heard about it on television or in the newspaper (p<0.05). Of the 36 stories analyzed, newspaper and television reports focused more on medical implications and radio reports focused more on ethical issues. The degree of enthusiasm about the accomplishment reflects the content of the media coverage, and, at least for adult primary care houseofficers, probably reflects the increasing relevance of genetic discoveries to medical practice. Since physicians obtain much of their health and science information from the media, they can play an instrumental role in

  15. Whole Genome Sequence Analysis of Pig Respiratory Bacterial Pathogens with Elevated Minimum Inhibitory Concentrations for Macrolides.

    PubMed

    Dayao, Denise Ann Estarez; Seddon, Jennifer M; Gibson, Justine S; Blackall, Patrick J; Turni, Conny

    2016-10-01

    Macrolides are often used to treat and control bacterial pathogens causing respiratory disease in pigs. This study analyzed the whole genome sequences of one clinical isolate of Actinobacillus pleuropneumoniae, Haemophilus parasuis, Pasteurella multocida, and Bordetella bronchiseptica, all isolated from Australian pigs to identify the mechanism underlying the elevated minimum inhibitory concentrations (MICs) for erythromycin, tilmicosin, or tulathromycin. The H. parasuis assembled genome had a nucleotide transition at position 2059 (A to G) in the six copies of the 23S rRNA gene. This mutation has previously been associated with macrolide resistance but this is the first reported mechanism associated with elevated macrolide MICs in H. parasuis. There was no known macrolide resistance mechanism identified in the other three bacterial genomes. However, strA and sul2, aminoglycoside and sulfonamide resistance genes, respectively, were detected in one contiguous sequence (contig 1) of A. pleuropneumoniae assembled genome. This contig was identical to plasmids previously identified in Pasteurellaceae. This study has provided one possible explanation of elevated MICs to macrolides in H. parasuis. Further studies are necessary to clarify the mechanism causing the unexplained macrolide resistance in other Australian pig respiratory pathogens including the role of efflux systems, which were detected in all analyzed genomes.

  16. Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs.

    PubMed

    Dong, Kunzhe; Yao, Na; Pu, Yabin; He, Xiaohong; Zhao, Qianjun; Luan, Yizhao; Guan, Weijun; Rao, Shaoqi; Ma, Yuehui

    2014-01-01

    High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP) that is well adapted to the high altitude and Dahe pig (DHP) that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP) as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19) for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG) for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16) were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9) were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.

  17. Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

    PubMed

    Snyder-Mackler, Noah; Majoros, William H; Yuan, Michael L; Shaver, Amanda O; Gordon, Jacob B; Kopp, Gisela H; Schlebusch, Stephen A; Wall, Jeffrey D; Alberts, Susan C; Mukherjee, Sayan; Zhou, Xiang; Tung, Jenny

    2016-06-01

    Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software ("WHODAD") are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.

  18. Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

    PubMed Central

    Snyder-Mackler, Noah; Majoros, William H.; Yuan, Michael L.; Shaver, Amanda O.; Gordon, Jacob B.; Kopp, Gisela H.; Schlebusch, Stephen A.; Wall, Jeffrey D.; Alberts, Susan C.; Mukherjee, Sayan; Zhou, Xiang; Tung, Jenny

    2016-01-01

    Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively. PMID:27098910

  19. Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations.

    PubMed

    Bosse, Mirte; Megens, Hendrik-Jan; Madsen, Ole; Frantz, Laurent A F; Paudel, Yogesh; Crooijmans, Richard P M A; Groenen, Martien A M

    2014-08-01

    The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.

  20. Multi-breed genome-wide association study reveals heterogeneous loci associated with loin eye area in pigs.

    PubMed

    He, Yuna; Ma, Junwu; Zhang, Feng; Hou, Lijuan; Chen, Hao; Guo, Yuanmei; Zhang, Zhiyan

    2016-11-01

    Numerous quantitative trait loci (QTL) for loin eye area had been identified by linkage mapping studies, but the lack of their precise position hinders their application in the pig breeding industry. To map QTL for loin eye area to a precise genomic region, we conducted a genome-wide association study (GWAS) using Illumina 60 K PorcineSNP60 Beadchip in four swine populations: 819 F2 pigs, 273 Laiwu pigs, 434 Sutai pigs, and 326 Erhualian pigs. In total, 26 single nucleotide polymorphisms (SNPs) deposited on seven chromosomes associated with loin eye area were identified, 11 of which surpassed the genome-wide significant threshold; of the 11 SNPs, seven located on SSC2 in F2 pigs and four located on SSC12 and SSC18 in Laiwu pigs. Of note, all of the identified QTL were breed specific and no common QTL was identified across the four populations in our study. These findings not only confirmed a previous QTL on SSC2 harboring the candidate gene insulin-like growth factor 2 (IGF2), but also identified some novel candidate genes, far upstream element binding protein 3 (FUBP3), myosin heavy chain (MYH) family, leucine-rich repeats and guanylate kinase domain containing (LRGUK). Our study will contribute to the further identification of the causal mutation underlying these QTL and improve our knowledge of the complex genetic architecture for loin eye area in pigs.

  1. Recent advances in genome editing and creation of genetically modified pigs.

    PubMed

    Butler, James R; Ladowski, Joseph M; Martens, Gregory R; Tector, Matthew; Tector, A Joseph

    2015-11-01

    The field of xenotransplantation is benefiting greatly from recent advances in genetic engineering. The efficiency and pace with which new model animals are being created has dramatically sped progress towards clinical relevance. Endonuclease-driven genome editing now allows for the efficient generation of targeted genetic alterations. Herein we review the available methods of genetic engineering that have been successfully employed to create genetically modified pigs.

  2. Detection of selection signatures of population-specific genomic regions selected during domestication process in Jinhua pigs.

    PubMed

    Li, Zhengcao; Chen, Jiucheng; Wang, Zhen; Pan, Yuchun; Wang, Qishan; Xu, Ningying; Wang, Zhengguang

    2016-12-01

    Chinese pigs have been undergoing both natural and artificial selection for thousands of years. Jinhua pigs are of great importance, as they can be a valuable model for exploring the genetic mechanisms linked to meat quality and other traits such as disease resistance, reproduction and production. The purpose of this study was to identify distinctive footprints of selection between Jinhua pigs and other breeds utilizing genome-wide SNP data. Genotyping by genome reducing and sequencing was implemented in order to perform cross-population extended haplotype homozygosity to reveal strong signatures of selection for those economically important traits. This work was performed at a 2% genome level, which comprised 152 006 SNPs genotyped in a total of 517 individuals. Population-specific footprints of selective sweeps were searched for in the genome of Jinhua pigs using six native breeds and three European breeds as reference groups. Several candidate genes associated with meat quality, health and reproduction, such as GH1, CRHR2, TRAF4 and CCK, were found to be overlapping with the significantly positive outliers. Additionally, the results revealed that some genomic regions associated with meat quality, immune response and reproduction in Jinhua pigs have evolved directionally under domestication and subsequent selections. The identified genes and biological pathways in Jinhua pigs showed different selection patterns in comparison with the Chinese and European breeds.

  3. Generation of heterozygous fibrillin-1 mutant cloned pigs from genome-edited foetal fibroblasts

    PubMed Central

    Umeyama, Kazuhiro; Watanabe, Kota; Watanabe, Masahito; Horiuchi, Keisuke; Nakano, Kazuaki; Kitashiro, Masateru; Matsunari, Hitomi; Kimura, Tokuhiro; Arima, Yoshimi; Sampetrean, Oltea; Nagaya, Masaki; Saito, Masahiro; Saya, Hideyuki; Kosaki, Kenjiro; Nagashima, Hiroshi; Matsumoto, Morio

    2016-01-01

    Marfan syndrome (MFS) is an autosomal dominant genetic disease caused by abnormal formation of the extracellular matrix with an incidence of 1 in 3, 000 to 5, 000. Patients with Marfan syndrome experience poor quality of life caused by skeletal disorders such as scoliosis, and they are at high risk of sudden death from cardiovascular impairment. Suitable animal models of MFS are essential for conquering this intractable disease. In particular, studies employing pig models will likely provide valuable information that can be extrapolated to humans because of the physiological and anatomical similarities between the two species. Here we describe the generation of heterozygous fibrillin-1 (FBN1) mutant cloned pigs (+/Glu433AsnfsX98) using genome editing and somatic cell nuclear transfer technologies. The FBN1 mutant pigs exhibited phenotypes resembling those of humans with MFS, such as scoliosis, pectus excavatum, delayed mineralization of the epiphysis and disrupted structure of elastic fibres of the aortic medial tissue. These findings indicate the value of FBN1 mutant pigs as a model for understanding the pathogenesis of MFS and for developing treatments. PMID:27074716

  4. Full-Genome Sequence of a Reassortant H1N1 Swine Influenza Virus Isolated from Pigs in Italy.

    PubMed

    Chiapponi, Chiara; Baioni, Laura; Luppi, Andrea; Moreno, Ana; Castellan, Alberto; Foni, Emanuela

    2013-10-03

    In this study, the full-genome sequence of a novel reassortant H1N1 swine influenza virus (SIV) is reported. The isolate has a hemagglutinin (HA) gene of the pandemic H1N1 influenza virus, but it carries the seven genome segments of the avian-origin H1N1 SIV currently circulating in European pig farms.

  5. Full-Genome Sequence of a Reassortant H1N1 Swine Influenza Virus Isolated from Pigs in Italy

    PubMed Central

    Chiapponi, Chiara; Baioni, Laura; Luppi, Andrea; Moreno, Ana; Castellan, Alberto

    2013-01-01

    In this study, the full-genome sequence of a novel reassortant H1N1 swine influenza virus (SIV) is reported. The isolate has a hemagglutinin (HA) gene of the pandemic H1N1 influenza virus, but it carries the seven genome segments of the avian-origin H1N1 SIV currently circulating in European pig farms. PMID:24092781

  6. Genomic regions associated with ventro-cranial chronic pleuritis in pig.

    PubMed

    Sørensen, K K; Gregersen, V R; Christensen, O F; Velander, I H; Bendixen, C

    2011-08-01

    Ventro-cranial chronic pleuritis can be a result of pleuropneumonia and enzootic pneumonia. These diseases cause severe losses in intensive pig production worldwide, but host resistance is difficult to breed for. It could be beneficial to use marker-assisted selection, and a step towards this is to identify genomic regions associated with the trait. For this purpose, 7304 pigs from 11 boar families were analysed for associations between single nucleotide polymorphisms and ventro-cranial chronic pleuritis. The pigs were genotyped by the use of the iSelect Custom 7 K porcine SNP Chip. Quantitative trait loci (QTL), significant at the chromosome-wide level, were identified on Sus scrofa chromosomes (SSC) 2, 4, 11, 12 and 13 in four different boar families. The QTL on SSC 4 in family G was also significant at the genome-wide threshold according to Bonferroni correction. We have identified a number of candidate genes, but the causative mutations still need to be identified. Markers closely associated with the resistance traits have a strong potential for use in breeding towards animals with improved characteristics concerning ventro-cranial chronic pleuritis.

  7. Genome-wide association studies for fatty acid metabolic traits in five divergent pig populations

    PubMed Central

    Zhang, Wanchang; Bin Yang; Zhang, Junjie; Cui, Leilei; Ma, Junwu; Chen, Congying; Ai, Huashui; Xiao, Shijun; Ren, Jun; Huang, Lusheng

    2016-01-01

    Fatty acid composition profiles are important indicators of meat quality and tasting flavor. Metabolic indices of fatty acids are more authentic to reflect meat nutrition and public acceptance. To investigate the genetic mechanism of fatty acid metabolic indices in pork, we conducted genome-wide association studies (GWAS) for 33 fatty acid metabolic traits in five pig populations. We identified a total of 865 single nucleotide polymorphisms (SNPs), corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes. Our findings not only confirmed seven previously reported QTL with stronger association strength, but also revealed four novel population-specific loci, showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes. We proposed a list of candidate genes at the identified loci, including three novel genes (FADS2, SREBF1 and PLA2G7). Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. These findings advance our understanding of the genetic basis of fatty acid composition in pigs. The results from European hybrid commercial pigs can be immediately transited into breeding practice for beneficial fatty acid composition. PMID:27097669

  8. Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes).

    PubMed

    Dessimoz, Christophe; Zoller, Stefan; Manousaki, Tereza; Qiu, Huan; Meyer, Axel; Kuraku, Shigehiro

    2011-09-01

    Recent development of deep sequencing technologies has facilitated de novo genome sequencing projects, now conducted even by individual laboratories. However, this will yield more and more genome sequences that are not well assembled, and will hinder thorough annotation when no closely related reference genome is available. One of the challenging issues is the identification of protein-coding sequences split into multiple unassembled genomic segments, which can confound orthology assignment and various laboratory experiments requiring the identification of individual genes. In this study, using the genome of a cartilaginous fish, Callorhinchus milii, as test case, we performed gene prediction using a model specifically trained for this genome. We implemented an algorithm, designated ESPRIT, to identify possible linkages between multiple protein-coding portions derived from a single genomic locus split into multiple unassembled genomic segments. We developed a validation framework based on an artificially fragmented human genome, improvements between early and recent mouse genome assemblies, comparison with experimentally validated sequences from GenBank, and phylogenetic analyses. Our strategy provided insights into practical solutions for efficient annotation of only partially sequenced (low-coverage) genomes. To our knowledge, our study is the first formulation of a method to link unassembled genomic segments based on proteomes of relatively distantly related species as references.

  9. Low-coverage MiSeq next generation sequencing reveals the mitochondrial genome of the Eastern Rock Lobster, Sagmariasus verreauxi.

    PubMed

    Doyle, Stephen R; Griffith, Ian S; Murphy, Nick P; Strugnell, Jan M

    2015-01-01

    The complete mitochondrial genome of the Eastern Rock lobster, Sagmariasus verreauxi, is reported for the first time. Using low-coverage, long read MiSeq next generation sequencing, we constructed and determined the mtDNA genome organization of the 15,470 bp sequence from two isolates from Eastern Tasmania, Australia and Northern New Zealand, and identified 46 polymorphic nucleotides between the two sequences. This genome sequence and its genetic polymorphisms will likely be useful in understanding the distribution and population connectivity of the Eastern Rock Lobster, and in the fisheries management of this commercially important species.

  10. Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery1

    PubMed Central

    Gardner, Elliot M.; Johnson, Matthew G.; Ragone, Diane; Wickett, Norman J.; Zerega, Nyree J. C.

    2016-01-01

    Premise of the study: We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. Methods and Results: A de novo assembly of Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of the predicted genome size. Predicted coding regions were used in a three-way orthology search with published genomes of Morus notabilis and Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333 inferred single-copy exons. Ninety-eight putative MADS-box genes were identified. Analysis of all predicted coding regions resulted in preliminary annotation of 49,089 genes. An analysis of synonymous substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A. camansi strongly suggested a lineage-specific whole-genome duplication in Artocarpus. Conclusions: This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes. PMID:27437173

  11. Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions

    PubMed Central

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.; Stensvold, Christen Rune; Nejsum, Peter

    2015-01-01

    Background The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found in primates. Methods and Findings We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes of Trichuris recovered from a human and a porcine host in China and from a françois’ leaf-monkey (China) were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from Trichuris from françois’ leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related. Conclusion and Significance Our results indicate that Trichuris species infecting humans and pigs are phylogenetically distinct across geographical regions, which might have important implications for the implementation of suitable and effective control strategies in different regions. Moreover, we provide support for the hypothesis that Trichuris infecting primates represents a complex of cryptic species with some species being able to infect both humans and non-human primates

  12. Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

    PubMed Central

    2013-01-01

    Background In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data. Results A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism. Conclusions This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data

  13. Experimental pathogenicity and complete genome characterization of a pig origin Pasteurella multocida serogroup F isolate HN07.

    PubMed

    Peng, Zhong; Liang, Wan; Wang, Yuanguo; Liu, Wenjing; Zhang, Hongfeng; Yu, Teng; Zhang, Anding; Chen, Huanchun; Wu, Bin

    2017-01-01

    Pasteurella multocida serotype F isolates are predominately prevalent in avian hosts, but rarely seen in pigs. However, we isolated several strains of P. multocida serotype F from clinical samples of pigs in China. To understand the pathogenicity of these strains, one of the serotype F isolates designated HN07, was used to challenge experimental chickens, as P. multocida of this serotype is predominately prevalent in avian hosts. However, strain HN07 could not resulted in significant clinical signs in experimental chickens even at an infective dose of ∼10(9) CFU, suggesting the isolate was avirulent to chickens and therefore raising the possibility that the porcine serotype F isolate is not transmitted by chickens. We then used HN07 to challenge experimental pigs, as this strain was isolated from pigs. As expected, the strain led to the clinical signs and the pathological lesions in experimental pigs that are similar to the pasteurellosis disease. We then determined the complete genome sequence of the pig origin serogroup F isolate HN07 for the first time. Genome comparison between HN07 and the avian serotype F P. multocida Pm70 identified a novel integrative conjugative element (ICE) ICEpmcn07 which was likely to harbor a series of genes responsible for a putative type IV secretion system (T4SS) in HN07. This is the first time that we determined an ICE carrying a T4SS in P. multocida. Besides, comparative analysis also defined a number of virulence-associated genes in HN07 but absent in Pm70 which may have a contribution to the pathogenicity of the strain. This is the first report of the pathogenicity and genome characterization of a pig origin Pasteurella multocida serogroup F isolate. The pathogenic and genomic definition of the pig origin P. multocida serogroup F in our study would have significance on the pathogenesis and genetic diversity and virulence variability of P. multocida.

  14. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

    PubMed Central

    Kumar, Sujai; Jones, Martin; Koutsovoulos, Georgios; Clarke, Michael; Blaxter, Mark

    2013-01-01

    Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment – whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species’ genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer. PMID

  15. A sequence of 'factishes': the media-metaphorical knowledge dynamics structuring the German press coverage of the human genome.

    PubMed

    Doring, Martin

    2005-12-01

    This article deals with the cultural framing of the near sequencing of the human genome and its impact on the media coverage in Germany. It investigates in particular the way in which the weekly journal Die Zeit and the daily newspaper Frankfurter Rundschau reported this media event and its aftermath between June 2000 and June 2001. Both newspapers are quality papers that played an essential role in framing the human genome debate--alongside the Frankfurter Allgemeine Zeitung--which became the most prominent genomic forum. The decoding of the human genome prompted a huge controversy concerning the ethics of human engineering, research on stem cells and Preimplantation Genetic Diagnosis. The main aim of this article is to show how this controversy was structured by metaphor. The media coverage of the genome generated DNA-factishes--a neologism designating the ambivalence of something as fact (fait) and as a fetish (fetiche)--that mostly propagated images of a new DNA-scienticism or biological determinism. Mediated by cultural experiences, the human genome became a highly artificial and social construct of a 'NatureCulture'.

  16. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

    PubMed

    Frantz, Laurent A F; Schraiber, Joshua G; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P M A; Larson, Greger; Groenen, Martien A M

    2015-10-01

    Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

  17. The complete mitochondrial genome of Juema pig Sus scrofa (Suina: Suidae) from southern Gansu.

    PubMed

    Xu, Yan-Yan; Tian, Xiao-Xiao; Chen, Lei-Lei; Pan, Hong-Chun

    2016-09-01

    Juema pig is a kind of rare and special pig which is well adapted to high altitude, cold climate and harsh natural environment. The complete mitochondrial genome of Juema pig Sus scrofa is a circular molecule of 16 532 bp in length, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 60.7% (T: 26.2%; C: 26.0%; A: 34.5%; G: 13.3%). ND4L gene begins with GTG as start codon, ND2, ND3, and ND5 genes begin with ATA as a start codon, and other nine protein-coding genes start with ATG. Cyt b gene is terminated with AGA as stop codon, ND1 and ND2 genes are terminated with TAG as stop codon, COII, COIII, ND3, and ND4 end with T, while ATP6, ATP8, COI, ND4L, ND5, and ND6 end with TAA. In addition, the phylogenetic relationships from neighbor-joining analyses based on the 13 concatenated PCGs indicated (Tylopoda (Suina (Ruminantia (Hippopotamidae, Cetacea)))).

  18. Single- and Bayesian Multi-Marker Genome-Wide Association for Haematological Parameters in Pigs

    PubMed Central

    Ponsuksili, Siriluck; Reyer, Henry; Trakooljul, Nares; Murani, Eduard

    2016-01-01

    Haematological traits are important traits that show associations with immune and metabolic status, as well as diseases in humans and animals. Mapping genome regions that affect the blood cell traits can contribute to the identification of genomic features useable as biomarkers for immune, disease and metabolic status. A genome-wide association study (GWAS) was conducted using PorcineSNP60 BeadChips. Single-marker and Bayesian multi-marker approaches were integrated to identify genomic regions and corresponding genes overlapping for both methods. GWAS was performed for haematological traits of 591 German Landrace pig. Heritability estimates for haematological traits were medium to high. In total 252 single SNPs associated with 12 haematological traits were identified (NegLog10 of p-value > 5). The Bayesian multi-marker approach revealed 102 QTL regions across the genome, indicated by 1-Mb windows with contribution to additive genetic variance above 0.5%. The integration of both methods resulted in 24 overlapping QTL regions. This study identified overlapping QTL regions from single- and multi-marker approaches for haematological traits. Identifying candidate genes that affect blood cell traits provides the first step towards the understanding of the molecular basis of haematological phenotypes. PMID:27434032

  19. Gene prediction and annotation in Penstemon (Plantaginaceae): A workflow for marker development from extremely low-coverage genome sequencing1

    PubMed Central

    Blischak, Paul D.; Wenzel, Aaron J.; Wolfe, Andrea D.

    2014-01-01

    • Premise of the study: Penstemon (Plantaginaceae) is a large and diverse genus endemic to North America. However, determining the phylogenetic relationships among its 280 species has been difficult due to its recent evolutionary radiation. The development of a large, multilocus data set can help to resolve this challenge. • Methods: Using both previously sequenced genomic libraries and our own low-coverage whole-genome shotgun sequencing libraries, we used the MAKER2 Annotation Pipeline to identify gene regions for the development of sequencing loci from six extremely low-coverage Penstemon genomes (∼0.005×–0.007×). We also compared this approach to BLAST searches, and conducted analyses to characterize sequence divergence across the species sequenced. • Results: Annotations and gene predictions were successfully added to more than 10,000 contigs for potential use in downstream primer design. Primers were then designed for chloroplast, mitochondrial, and nuclear loci from these annotated sequences. MAKER2 identified longer gene regions in all six Penstemon genomes when compared with BLASTN and BLASTX searches. The average level of sequence divergence among the six species was 7.14%. • Discussion: Combining bioinformatics tools into a workflow that produces annotations can be useful for creating potential phylogenetic markers from thousands of sequences even when genome coverage is extremely low and reference data are only available from distant relatives. Furthermore, the output from MAKER2 contains information about important gene features, such as exon boundaries, and can be easily integrated with visualization tools to facilitate the process of marker development. PMID:25506519

  20. Construction and analysis of Siberian tiger bacterial artificial chromosome library with approximately 6.5-fold genome equivalent coverage.

    PubMed

    Liu, Changqing; Bai, Chunyu; Guo, Yu; Liu, Dan; Lu, Taofeng; Li, Xiangchen; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

    2014-03-07

    Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger.

  1. Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, are known to be associated with both diseases and phenotypic traits. Deeply sequenced genomes are often u...

  2. Draft Genome Sequence of Streptococcus caviae Strain Cavy grass 6T, Isolated from Domesticated Guinea Pig Fecal Samples

    PubMed Central

    Palakawong Na Ayudthaya, Susakul; Marshall, Ian P. G.; Schreiber, Lars

    2017-01-01

    ABSTRACT Streptococcus caviae strain Cavy grass 6T, isolated from fecal samples of pet guinea pigs, can metabolize a range of plant mono- and disaccharides, as well as polymeric carbohydrates. Here, we report the draft genome sequence of this strain, which comprises 2.11 Mb. PMID:28360157

  3. Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes.

    PubMed

    Wilmott, James S; Field, Matthew A; Johansson, Peter A; Kakavand, Hojabr; Shang, Ping; De Paoli-Iseppi, Ricardo; Vilain, Ricardo E; Pupo, Gulietta M; Tembe, Varsha; Jakrot, Valerie; Shang, Catherine A; Cebon, Jonathan; Shackleton, Mark; Fitzgerald, Anna; Thompson, John F; Hayward, Nicholas K; Mann, Graham J; Scolyer, Richard A

    2015-12-01

    Whole genome sequencing (WGS) of cancer patients' tumours offers the most comprehensive method of identifying both novel and known clinically-actionable genomic targets. However, the practicalities of performing WGS on clinical samples are poorly defined.This study was designed to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large WGS analysis of human melanoma samples.WGS was performed on melanoma cell lines (n = 15) and melanoma fresh frozen tumours (n = 222). The appropriate level of coverage and the optimal mutation detection algorithm for the project pipeline were determined.An incremental increase in sequencing coverage from 36X to 132X in melanoma tissue samples and 30X to 103X for cell lines only resulted in a small increase (1-2%) in the number of mutations detected, and the quality scores of the additional mutations indicated a low probability that the mutations were real. The results suggest that 60X coverage for melanoma tissue and 40X for melanoma cell lines empower the detection of 98-99% of informative single nucleotide variants (SNVs), a sensitivity level at which clinical decision making or landscape research projects can be carried out with a high degree of confidence in the results. Likewise the bioinformatic mutation analysis methodology strongly influenced the number and quality of SNVs detected. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, simultaneous analysis should be employed on matched melanoma tissue and blood genomes to reduce errors in mutation detection.This study provided valuable insights into the accuracy of SNV with WGS at various coverage levels in human clinical cancer specimens. Additionally, we investigated the accuracy of the publicly available mutation detection algorithms to detect cancer

  4. The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons)

    PubMed Central

    Bosse, Mirte; Crooijmans, Richard P. M. A.; Madsen, Ole; Schaftenaar, Willem; Ryder, Oliver A.; Megens, Hendrik-Jan

    2016-01-01

    The list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Many endangered species are present in captivity and actively managed in breeding programs in which often little is known about the founder individuals. Recent developments in genetic research techniques have made it possible to sequence and study whole genomes. In this study we used the critically endangered Visayan warty pig (Sus cebifrons) as a case study to test the use of genomic information as a tool in conservation management. Two captive populations of S. cebifrons exist, which originated from two different Philippine islands. We found some evidence for a recent split between the two island populations; however all individuals that were sequenced show a similar demographic history. Evidence for both past and recent inbreeding indicated that the founders were at least to some extent related. Together with this, the low level of nucleotide diversity compared to other Sus species potentially poses a threat to the viability of the captive populations. In conclusion, genomic techniques answered some important questions about this critically endangered mammal and can be a valuable toolset to inform future conservation management in other species as well. PMID:27069913

  5. Validation of selection accuracy for the total number of piglets born in Landrace pigs using genomic selection

    PubMed Central

    Oh, Jae-Don; Na, Chong-Sam; Park, Kyung-Do

    2017-01-01

    Objective This study was to determine the relationship between estimated breeding value and phenotype information after farrowing when juvenile selection was made in candidate pigs without phenotype information. Methods After collecting phenotypic and genomic information for the total number of piglets born by Landrace pigs, selection accuracy between genomic breeding value estimates using genomic information and breeding value estimates of best linear unbiased prediction (BLUP) using conventional pedigree information were compared. Results Genetic standard deviation (σa) for the total number of piglets born was 0.91. Since the total number of piglets born for candidate pigs was unknown, the accuracy of the breeding value estimated from pedigree information was 0.080. When genomic information was used, the accuracy of the breeding value was 0.216. Assuming that the replacement rate of sows per year is 100% and generation interval is 1 year, genetic gain per year is 0.346 head when genomic information is used. It is 0.128 when BLUP is used. Conclusion Genetic gain estimated from single step best linear unbiased prediction (ssBLUP) method is by 2.7 times higher than that the one estimated from BLUP method, i.e., 270% more improvement in efficiency. PMID:27507181

  6. Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

    PubMed Central

    Yang, Ya; Smith, Stephen A.

    2014-01-01

    Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction. PMID:25158799

  7. Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Causal Genes and Mutations on Pig Chromosome 17

    PubMed Central

    Hu, Zhi-Liang; Ramos, Antonio M.; Humphray, Sean J.; Rogers, Jane; Reecy, James M.; Rothschild, Max F.

    2011-01-01

    The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining. PMID:22303339

  8. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs.

    PubMed

    Wang, Chao; Wang, Hongyang; Zhang, Yu; Tang, Zhonglin; Li, Kui; Liu, Bang

    2015-03-01

    Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome-wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions have been found to be involved in lipid metabolism, melanocyte differentiation, neural development and other biological processes, which coincide with the evolutionary phenotypic changes in this breed. A synonymous substitution, c.669T>C, in ESR1, which colocalizes with a major quantitative trait locus for litter size, shows extreme differences in allele frequency between Tongcheng pigs and wild boars. Notably, the variant C allele in this locus exhibits high allele frequency in most Chinese populations, suggesting a consequence of positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C) related to reproductive traits were found to have high haplotype similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are implied to shape the two-end black colour trait in Tongcheng pig. Subsequent SNP microarray studies of five Chinese white-spotted breeds displayed a concordant signature at both loci, suggesting that these two genes are responsible for colour variations in Chinese breeds. Utilizing massively parallel sequencing, we characterized the candidate sites that adapt to artificial and environmental selections during the Chinese pig domestication. This study provides fundamental proof for further research on the evolutionary adaptation of Chinese pigs.

  9. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.

    PubMed

    Shih, Patrick M; Wu, Dongying; Latifi, Amel; Axen, Seth D; Fewer, David P; Talla, Emmanuel; Calteau, Alexandra; Cai, Fei; Tandeau de Marsac, Nicole; Rippka, Rosmarie; Herdman, Michael; Sivonen, Kaarina; Coursin, Therese; Laurent, Thierry; Goodwin, Lynne; Nolan, Matt; Davenport, Karen W; Han, Cliff S; Rubin, Edward M; Eisen, Jonathan A; Woyke, Tanja; Gugger, Muriel; Kerfeld, Cheryl A

    2013-01-15

    The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

  10. Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

    PubMed Central

    Amaral, Andreia J.; Ferretti, Luca; Megens, Hendrik-Jan; Crooijmans, Richard P. M. A.; Nie, Haisheng; Ramos-Onsins, Sebastian E.; Perez-Enciso, Miguel; Schook, Lawrence B.; Groenen, Martien A. M.

    2011-01-01

    Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection

  11. Genome sequencing of Giardia lamblia genotypes A2 and B isolates (DH and GS) and comparative analysis with the genomes of genotypes A1 and E (WB and Pig).

    PubMed

    Adam, Rodney D; Dahlstrom, Eric W; Martens, Craig A; Bruno, Daniel P; Barbian, Kent D; Ricklefs, Stacy M; Hernandez, Matthew M; Narla, Nirmala P; Patel, Rima B; Porcella, Stephen F; Nash, Theodore E

    2013-01-01

    Giardia lamblia (syn G. intestinalis, G. duodenalis) is the most common pathogenic intestinal parasite of humans worldwide and is a frequent cause of endemic and epidemic diarrhea. G. lamblia is divided into eight genotypes (A-H) which infect a wide range of mammals and humans, but human infections are caused by Genotypes A and B. To unambiguously determine the relationship among genotypes, we sequenced GS and DH (Genotypes B and A2) to high depth coverage and compared the assemblies with the nearly completed WB genome and draft sequencing surveys of Genotypes E (P15; pig isolate) and B (GS; human isolate). Our results identified DH as the smallest Giardia genome sequenced to date, while GS is the largest. Our open reading frame analyses and phylogenetic analyses showed that GS was more distant from the other three genomes than any of the other three were from each other. Whole-genome comparisons of DH_A2 and GS_B with the optically mapped WB_A1 demonstrated substantial synteny across all five chromosomes but also included a number of rearrangements, inversions, and chromosomal translocations that were more common toward the chromosome ends. However, the WB_A1/GS_B alignment demonstrated only about 70% sequence identity across the syntenic regions. Our findings add to information presented in previous reports suggesting that GS is a different species of Giardia as supported by the degree of genomic diversity, coding capacity, heterozygosity, phylogenetic distance, and known biological differences from WB_A1 and other G. lamblia genotypes.

  12. Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs.

    PubMed

    Saura, María; Fernández, Almudena; Rodríguez, M Carmen; Toro, Miguel A; Barragán, Carmen; Fernández, Ana I; Villanueva, Beatriz

    2013-01-01

    Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative

  13. Accuracy of genomic prediction of purebreds for cross bred performance in pigs.

    PubMed

    Hidalgo, A M; Bastiaansen, J W M; Lopes, M S; Calus, M P L; de Koning, D J

    2016-12-01

    In pig breeding, as the final product is a cross bred (CB) animal, the goal is to increase the CB performance. This goal requires different strategies for the implementation of genomic selection from what is currently implemented in, for example dairy cattle breeding. A good strategy is to estimate marker effects on the basis of CB performance and subsequently use them to select pure bred (PB) breeding animals. The objective of our study was to assess empirically the predictive ability (accuracy) of direct genomic values of PB for CB performance across two traits using CB and PB genomic and phenotypic data. We studied three scenarios in which genetic merit was predicted within each population, and four scenarios where PB genetic merit for CB performance was predicted based on either CB or a PB training data. Accuracy of prediction of PB genetic merit for CB performance based on CB training data ranged from 0.23 to 0.27 for gestation length (GLE), whereas it ranged from 0.11 to 0.22 for total number of piglets born (TNB). When based on PB training data, it ranged from 0.35 to 0.55 for GLE and from 0.30 to 0.40 for TNB. Our results showed that it is possible to predict PB genetic merit for CB performance using CB training data, but predictive ability was lower than training using PB training data. This result is mainly due to the structure of our data, which had small-to-moderate size of the CB training data set, low relationship between the CB training and the PB validation populations, and a high genetic correlation (0.94 for GLE and 0.90 for TNB) between the studied traits in PB and CB individuals, thus favouring selection on the basis of PB data.

  14. Coordination of Programs on Domestic Animal Genomics: The Federal Framework

    DTIC Science & Technology

    2004-06-01

    including: • Large-scale sequencing to produce draft genome sequences (8-fold sequence coverage) of honeybee, chicken, dog , cattle, swine, and cat ...develop draft-quality genome sequences for the chicken, cow, honeybee, pig, dog , and cat . All were designated to be “high priority” for sequencing by...NHGRI supported sequencing centers (with the understanding that close evolutionary relationships between dog / cat and cow/pig would only allow

  15. Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination.

    PubMed

    Ito, Mika; Kuroda, Moegi; Masuda, Tsuneyuki; Akagami, Masataka; Haga, Kei; Tsuchiaka, Shinobu; Kishimoto, Mai; Naoi, Yuki; Sano, Kaori; Omatsu, Tsutomu; Katayama, Yukie; Oba, Mami; Aoki, Hiroshi; Ichimaru, Toru; Mukono, Itsuro; Ouchi, Yoshinao; Yamasato, Hiroshi; Shirai, Junsuke; Katayama, Kazuhiko; Mizutani, Tetsuya; Nagai, Makoto

    2017-02-09

    Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs.

  16. Coverage of whole proteome by structural genomics observed through protein homology modeling database

    PubMed Central

    Yamaguchi, Akihiro; Go, Mitiko

    2006-01-01

    We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. However, cases that a modeled 3D structure covers the whole part of an ORF product are rare. When portion of an ORF with 3D structure is compared in three kingdoms of life, in archaebacteria and eubacteria, approximately 60% of the ORFs have modeled 3D structures covering almost the entire amino acid sequences, however, the percentage falls to about 30% in eukaryotes. When annual differences in the number of ORFs with modeled 3D structure are calculated, the fraction of modeled 3D structures of soluble protein for archaebacteria is increased by 5%, and that for eubacteria by 7% in the last 3 years. Assuming that this rate would be maintained and that determination of 3D structures for predicted disordered regions is unattainable, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years. The 3D structures we will have at those times are not the 3D structure of the entire proteins encoded in single ORFs, but the 3D structures of separate structural domains. Measuring or predicting spatial arrangements of structural domains in an ORF will then be a coming issue of structural genomics. PMID:17146617

  17. Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.

    PubMed

    Schiavo, G; Galimberti, G; Calò, D G; Samorè, A B; Bertolini, F; Russo, V; Gallo, M; Buttazzoni, L; Fontanesi, L

    2016-04-01

    In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni  < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.

  18. Whole genome response in guinea pigs infected with the high virulence strain Mycobacterium tuberculosis TT372

    PubMed Central

    Aiyaz, Mohamed; Bipin, Chand; Pantulwar, Vinay; Mugasimangalam, Raja; Shanley, Crystal A.; Ordway, Diane J; Orme, Ian M.

    2014-01-01

    SUMMARY In this study we conducted a microarray-based whole genomic analysis of gene expression in the lungs after exposure of guinea pigs to a low dose aerosol of the Atypical Beijing Western Cape TT372 strain of Mycobacterium tuberculosis, after harvesting lung tissues three weeks after infection at a time that effector immunity is starting to peak. The infection resulted in a very large up-regulation of multiple genes at this time, particularly in the context of a “chemokine storm” in the lungs. Overall gene expression was considerably reduced in animals that had been vaccinated with BCG two months earlier, but in both cases strong signatures featuring gamma interferon [IFNγ] and tumor necrosis factor [TNFα] were observed indicating the potent TH1 response in these animals. Even though their effects are not seen until later in the infection, even at this early time point gene expression patterns associated with the potential emergence of regulatory T cells were observed. Genes involving lung repair, response to oxidative stress, and cell trafficking were strongly expressed, but interesting these gene patterns differed substantially between the infected and vaccinated/infected groups of animals. Given the importance of this species as a relevant and cost-effective small animal model of tuberculosis, this approach has the potential to provide new information regarding the effects of vaccination on control of the disease process. PMID:25621360

  19. Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.

    PubMed

    Nicod, Jérôme; Davies, Robert W; Cai, Na; Hassett, Carl; Goodstadt, Leo; Cosgrove, Cormac; Yee, Benjamin K; Lionikaite, Vikte; McIntyre, Rebecca E; Remme, Carol Ann; Lodder, Elisabeth M; Gregory, Jennifer S; Hough, Tertius; Joynson, Russell; Phelps, Hayley; Nell, Barbara; Rowe, Clare; Wood, Joe; Walling, Alison; Bopp, Nasrin; Bhomra, Amarjit; Hernandez-Pliego, Polinka; Callebert, Jacques; Aspden, Richard M; Talbot, Nick P; Robbins, Peter A; Harrison, Mark; Fray, Martin; Launay, Jean-Marie; Pinto, Yigal M; Blizard, David A; Bezzina, Connie R; Adams, David J; Franken, Paul; Weaver, Tom; Wells, Sara; Brown, Steve D M; Potter, Paul K; Klenerman, Paul; Lionikas, Arimantas; Mott, Richard; Flint, Jonathan

    2016-08-01

    Two bottlenecks impeding the genetic analysis of complex traits in rodents are access to mapping populations able to deliver gene-level mapping resolution and the need for population-specific genotyping arrays and haplotype reference panels. Here we combine low-coverage (0.15×) sequencing with a new method to impute the ancestral haplotype space in 1,887 commercially available outbred mice. We mapped 156 unique quantitative trait loci for 92 phenotypes at a 5% false discovery rate. Gene-level mapping resolution was achieved at about one-fifth of the loci, implicating Unc13c and Pgc1a at loci for the quality of sleep, Adarb2 for home cage activity, Rtkn2 for intensity of reaction to startle, Bmp2 for wound healing, Il15 and Id2 for several T cell measures and Prkca for bone mineral content. These findings have implications for diverse areas of mammalian biology and demonstrate how genome-wide association studies can be extended via low-coverage sequencing to species with highly recombinant outbred populations.

  20. The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity.

    PubMed

    Bianco, E; Soto, H W; Vargas, L; Pérez-Enciso, M

    2015-05-01

    The history of domestic species and of their wild ancestors is not a simple one, and feral processes can clarify key aspects of this history, including the adaptive processes triggered by new environments. Here, we provide a comprehensive genomic study of Isla del Coco (Costa Rica) feral pigs, a unique population that was allegedly founded by two individuals and has remained isolated since 1793. Using SNP arrays and genome sequencing, we show that Cocos pigs are hybrids between Asian and European pigs, as are modern international pig breeds. This conclusively shows that, as early as the 18th century, British vessels were loading crossbred pigs in Great Britain and transporting them overseas. We find that the Y chromosome has Asian origin, which has not been reported in any international pig breed. Chinese haplotypes seem to have been transmitted independently between Cocos and other pig breeds, suggesting independent introgression events and a complex pattern of admixing. Although data are compatible with a founder population of N = 2, variability levels are as high in Cocos pigs as in international pig breeds (~1.9 SNPs/kb) and higher than in European wild boars or local breeds (~1.7 SNPs/kb). Nevertheless, we also report a 10-Mb region with a marked decrease in variability across all samples that contains four genes (CPE, H3F3C, SC4MOL and KHL2) previously identified as highly differentiated between wild and domestic pigs. This work therefore illustrates how feral population genomic studies can help to resolve the history of domestic species and associated admixture events.

  1. Full-length genome sequence and genetic relationship of two paramyxoviruses isolated from bat and pigs in the Americas.

    PubMed

    Wang, L-F; Hansson, E; Yu, M; Chua, K B; Mathe, N; Crameri, G; Rima, B K; Moreno-López, J; Eaton, B T

    2007-01-01

    Mapuera virus (MPRV) was isolated from a fruit bat in Brazil in 1979, but its host range and disease-causing potential are unknown. Porcine rubulavirus (PoRV) was identified as the aetiological agent of disease outbreaks in pigs in Mexico during early 1980s, but the origin of PoRV remains elusive. In this study, the completed genome sequence of MPRV was determined, and the complete genome sequence of PoRV was assembled from previously published protein-coding genes and the non-coding genome regions determined from this study. Comparison of sequence and genome organization indicated that PoRV is more closely related to MPRV than to any other members of the genus Rubulavirus. In the P gene coding region of both viruses, there is an ORF located at the 5' end of the P gene overlapping with the P protein coding region, similar to the C protein ORF present in most viruses of the subfamily Paramyxovirinae, but absent in other known rubulaviruses. Based on these findings, we hypothesise that PoRV may also originate from bats, and spillover events from bats to pigs, either directly or via an intermediate host, were responsible for the sporadic disease outbreaks observed in Mexico.

  2. Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes.

    PubMed

    Nirea, K G; Meuwissen, T H E

    2017-04-01

    We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross-breed. Elite nucleus herds had access to high-quality feed, and production herds were fed low-quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (rg  = 0.2), medium (rg  = 0.5) and high (rg  = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high-density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40-115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high-quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43-104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population.

  3. Genome wide association of changes in feeding behavior due to heat stress in pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heat stress negatively impacts pork production. Grow-finish production losses include decreased growth, reduced feed intake, and mortality. Pigs change their feeding behavior to decrease heat production when temperatures are elevated. Identification of pigs that are more tolerant of warmer temperatu...

  4. A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

    PubMed Central

    2009-01-01

    Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA) and total number of piglets born (TNB) in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P < 0.001) and SSC17 (P < 0.01) with effects on both traits. This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis. As much as 18 epistatic QTL were found for NBA (four at P < 0.01 and five at P < 0.05) and TNB (three at P < 0.01 and six at P < 0.05), respectively. These epistatic QTL were distributed in multiple genomic regions, which covered 13 of the 18 pig autosomes, and they had small individual effects that ranged between 3 to 4% of the phenotypic variance. Different patterns of interactions (a × a, a × d, d × a and d × d) were found amongst the epistatic QTL pairs identified in the current work. Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17), dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the

  5. Full-length genomic analysis of porcine rotavirus strains isolated from pigs with diarrhea in Northern Italy.

    PubMed

    Monini, Marina; Zaccaria, Guendalina; Ianiro, Giovanni; Lavazza, Antonio; Vaccari, Gabriele; Ruggeri, Franco M

    2014-07-01

    Group A rotaviruses (RVA) cause acute dehydrating diarrhea in young of man and many animal species, including pigs. Swine RVA has an important economic impact on the farming industry, and pigs represent a potential reservoir for zoonotic transmission of RVA to humans. To investigate the genetic diversity of porcine RVA strains in Italy and identify their possible zoonotic characteristics, 25 RVA-positive feces were collected from diarrheic pigs in Northern Italy, in 2009-2010; all viral strains were characterized by G and P genotyping RT-PCR. Three samples were selected for full genome sequencing. Sequencing of the NSP3 genes of all samples was also performed. Rotavirus diagnosis was carried out by ELISA and electron microscopy. RT-PCR and Sanger sequencing were performed in a one-tube format, using primer sets specific for each of the 11 genome segments. Analysis of the G (VP7) and P (VP4) genotypes showed that all strains identified were typical porcine RVAs (G4, G5, G9; P[6], P[13], P[23]). Full-length genome sequencing was performed on selected G9 isolates. Most segments belonged to the genotype constellation 1 (Wa-like), which is shared by most human RVA strains, but gene types such as I5 (VP6) and A8 (NSP1), which are typical of porcine and rare among human RVAs, were also detected. We identified RVA strains showing the T7 genotype, an NSP3 gene type that was previously reported in unusual strains of possible porcine or bovine origin from children with diarrhea. Recent reports suggested that G9 RVA may have been introduced from swine to human populations involving gene reassortment events. The observation that some of the RVA genotypes from swine in Italy were similar to viruses characterized in children underlines the importance of animal RVA surveillance, to clarify and monitor the role of animals as genetic reservoirs of emerging RVA strains pathogenic for humans.

  6. Gradual development of a genome-wide H3-K9 trimethylation pattern in paternally derived pig pronucleus.

    PubMed

    Jeong, Young Sun; Yeo, Seungeun; Park, Jung Sun; Lee, Kyung-Kwang; Kang, Yong-Kook

    2007-06-01

    The cytoplasm of a mature oocyte contains many protein complexes that are programmed to restructure incoming sperm chromatins on fertilization. Of the complicated biochemical events that these functional machineries control, the most impressive and important is epigenetic reprogramming. Despite its importance in epigenetic resetting, or "de-differentiation," of gamete genomes back to an incipient status, the mechanisms of epigenetic reprogramming do not seem to be conserved among mammals. Here, we report that, unlike in the mouse, the pig sperm-derived pronucleus is markedly trimethylated at lysine 9 of histone H3 (H3-m(3)K9), which might be associated with preservation of paternally derived cytosine methylation in pig zygotes. The male H3-m(3)K9 pattern is gradually established during pronucleus development, and this process occurs independently of DNA replication. Considering these unique epigenetic features, the pig zygote is, we believe, suited to serve as another model of epigenetic reprogramming that is antithetical to the well-characterized mouse model.

  7. CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing

    PubMed Central

    Lambirth, Kevin C.; Whaley, Adam M.; Schlueter, Jessica A.; Bost, Kenneth L.; Piller, Kenneth J.

    2015-01-01

    Transgenic crops have become a staple in modern agriculture, and are typically characterized using a variety of molecular techniques involving proteomics and metabolomics. Characterization of the transgene insertion site is of great interest, as disruptions, deletions, and genomic location can affect product selection and fitness, and identification of these regions and their integrity is required for regulatory agencies. Here, we present CONTRAILS (Characterization of Transgene Insertion Locations with Sequencing), a straightforward, rapid and reproducible method for the identification of transgene insertion sites in highly complex and repetitive genomes using low coverage paired-end Illumina sequencing and traditional PCR. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications. Using whole genome sequencing of in-house transgenic Glycine max, a legume with a highly repetitive and complex genome, we used CONTRAILS to successfully identify the location of a single T-DNA insertion to single base resolution. PMID:26697366

  8. Complete genome sequence and pathogenicity of two swine parainfluenzavirus 3 isolates from pigs in the United States.

    PubMed

    Qiao, Dan; Janke, Bruce H; Elankumaran, Subbiah

    2010-01-01

    Two novel paramyxoviruses, 81-19252 (Texas81) and 92-7783 (ISU92), isolated from the brains of pigs in the United States in the 1980s and 1990s, were characterized. The complete genome of Texas81 virus was 15,456 nucleotides (nt) in length, that of ISU92 was 15,480 nt, and both genomes consisted of six nonoverlapping genes, predicted to encode nine proteins, with conserved and complementary 3' leader and 5' trailer regions and conserved gene starts, gene stops, and trinucleotide intergenic sequences similar to those in paramyxoviruses. The corresponding genes from these two viruses were similar in length, except for the F genes, of which the ISU92 form had an additional 24-nt U-rich 3' untranslated region. The P genes of swine viruses were predicted to produce V and D mRNAs by RNA editing (one to four G insertions in Texas81 and one to nine G insertions in ISU92) or C mRNA by alternative translation initiation. Sequence-specific features related to virus replication and host-specific amino acid signatures indicated that these viruses originated from bovine parainfluenzavirus 3 (bPIV3). Phylogenetic analysis of individual genes suggested that these viruses are novel members of the genus Respirovirus of the Paramyxovirinae subfamily and may be grouped into two subgenotypes of genotype A of bPIV3. Our comprehensive studies revealed that these swine PIV3 are variants of bPIV3 and were possibly transferred from cattle to pigs but failed to establish an active enzootic state. These two viruses were mildly pathogenic to conventionally reared pigs, and results from a limited enzyme-linked immunosorbent assay-based serosurvey of swine farms in Minnesota and Iowa in 2007 and 2008 were negative.

  9. A quantitative analysis of the mass media coverage of genomics medicine in China: a call for science journalism in the developing world.

    PubMed

    Zhao, Feifei; Chen, Yan; Ge, Siqi; Yu, Xinwei; Shao, Shuang; Black, Michael; Wang, Youxin; Zhang, Jie; Song, Manshu; Wang, Wei

    2014-04-01

    Science journalism is a previously neglected but rapidly growing area of scholarship in postgenomics medicine and socio-technical studies of knowledge-based innovations. Science journalism can help evaluate the quantity and quality of information flux between traditional scientific expert communities and the broader public, for example, in personalized medicine education. Newspapers can play a crucial role in science and health communication, and more importantly, in framing public engagement. However, research on the role of newspaper coverage of genomics-related articles has not been readily available in resource-limited settings. As genomics is rapidly expanding worldwide, this gap in newspaper reportage in China is therefore an important issue. In order to bridge this gap, we investigated the coverage of genomics medicine in eight major Chinese national newspapers, using the China Core Newspapers Full-text Database (CCND) and articles in scientific journals in PubMed from 2000 to 2011. Coverage of genomics medicine in these eight official government Chinese newspapers has remained low, with only 12 articles published per newspaper per year between 2000 and 2011. Between 2000 and 2011, over a 40-fold difference was observed in the number of genomics medicine-related articles in PubMed, as compared to that in newspapers. The numbers of genomics-related articles among the eight major newspapers from 2000 to 2011 were significantly different (p=0.001). Commentary/mini reviews and articles about gene therapy for specific diseases were most frequently published in 2006 and 2011. In parallel, we observed that "cancer gene therapy," "new susceptibility gene locus," and "gene technology revolution" were the top three thematic strands addressed in the newspapers, even though their volume remained low. This study reports on the under-representation of newspaper coverage of genomics medicine in China, despite the vast growth of scientific articles in journals in this

  10. Genome-wide scans to detect positive selection in Large White and Tongcheng pigs.

    PubMed

    Li, Xiuling; Yang, Songbai; Tang, Zhonglin; Li, Kui; Rothschild, Max F; Liu, Bang; Fan, Bin

    2014-06-01

    Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient FST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.

  11. Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs.

    PubMed

    Liu, Guo-Hua; Wu, Chang-Yi; Song, Hui-Qun; Wei, Shu-Jun; Xu, Min-Jun; Lin, Rui-Qing; Zhao, Guang-Hui; Huang, Si-Yang; Zhu, Xing-Quan

    2012-01-15

    Ascaris lumbricoides and Ascaris suum are parasitic nematodes living in the small intestine of humans and pigs, and can cause the disease ascariasis. For long, there has been controversy as to whether the two ascaridoid taxa represent the same species due to their significant resemblances in morphology. However, the complete mitochondrial (mt) genome data have been lacking for A. lumbricoides in spite of human and animal health significance and socio-economic impact globally of these parasites. In the present study, we sequenced the complete mt genomes of A. lumbricoides and A. suum (China isolate), which was 14,303 bp and 14,311 bp in size, respectively. The identity of the mt genomes was 98.1% between A. lumbricoides and A. suum (China isolate), and 98.5% between A. suum (China isolate) and A. suum (USA isolate). Both genomes are circular, and consist of 36 genes, including 12 genes for proteins, 2 genes for rRNA and 22 genes for tRNA, which are consistent with that of all other species of ascaridoid studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T (71.7% for A. lumbricoides and 71.8% for A. suum). The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. Phylogenetic analyses of A. lumbricoides and A. suum using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (Bayesian analysis, maximum likelihood and maximum parsimony) all clustered in a clade with high statistical support, indicating that A. lumbricoides and A. suum was very closely related. These mt genome data and the results provide some additional genetic evidence that A. lumbricoides and A. suum may represent the same species. The mt genome data presented in this study are also useful novel markers for studying the molecular epidemiology and population genetics of Ascaris.

  12. Production of α1,3-galactosyltransferase targeted pigs using transcription activator-like effector nuclease-mediated genome editing technology.

    PubMed

    Kang, Jung-Taek; Kwon, Dae-Kee; Park, A-Rum; Lee, Eun-Jin; Yun, Yun-Jin; Ji, Dal-Young; Lee, Kiho; Park, Kwang-Wook

    2016-03-01

    Recent developments in genome editing technology using meganucleases demonstrate an efficient method of producing gene edited pigs. In this study, we examined the effectiveness of the transcription activator-like effector nuclease (TALEN) system in generating specific mutations on the pig genome. Specific TALEN was designed to induce a double-strand break on exon 9 of the porcine α1,3-galactosyltransferase (GGTA1) gene as it is the main cause of hyperacute rejection after xenotransplantation. Human decay-accelerating factor (hDAF) gene, which can produce a complement inhibitor to protect cells from complement attack after xenotransplantation, was also integrated into the genome simultaneously. Plasmids coding for the TALEN pair and hDAF gene were transfected into porcine cells by electroporation to disrupt the porcine GGTA1 gene and express hDAF. The transfected cells were then sorted using a biotin-labeled IB4 lectin attached to magnetic beads to obtain GGTA1 deficient cells. As a result, we established GGTA1 knockout (KO) cell lines with biallelic modification (35.0%) and GGTA1 KO cell lines expressing hDAF (13.0%). When these cells were used for somatic cell nuclear transfer, we successfully obtained live GGTA1 KO pigs expressing hDAF. Our results demonstrate that TALEN-mediated genome editing is efficient and can be successfully used to generate gene edited pigs.

  13. Study of a chimeric foot-and-mouth disease virus DNA vaccine containing structural genes of serotype O in a genome backbone of serotype Asia 1 in guinea pigs.

    PubMed

    Chockalingam, A K; Thiyagarajan, S; Govindasamy, N; Patnaikuni, R; Garlapati, S; Golla, R R; Joyappa, D H; Krishnamshetty, P; Veluvarti, V V S; Veluvati, V V S

    2010-01-01

    Since foot-and-mouth disease virus (FMDV) serotypes display a great genetic and antigenic diversity, there is a constant requirement to monitor the performance of FMDV vaccines in the field with respect to their antigenic coverage. To avoid possible antigenic changes in field FMDV isolates during their adaptation to BHK-21 cells, a standard step used in production of conventional FMDV vaccines, the custom-made chimeric conventional or DNA vaccines, in which antigenic determinants are replaced with those of appropriate field strains, should be constructed. Using this approach, we made a plasmid-based chimeric FMDV DNA vaccine containing structural genes of serotype O in the genome backbone of serotype Asia 1, all under the control of Human cytomegalovirus (HCMV) immediate early gene promoter. BHK-21 cells transfected with the chimeric DNA vaccine did not show cytopathic effect (CPE), but expressed virus-specific proteins as demonstrated by 35S-methionine labeling and immunoprecipitation. Guinea pigs immunized with the chimeric DNA vaccine produced virus-specific antibodies assayed by ELISA and virus neutralization test (VNT), respectively. The chimeric DNA vaccine showed a partial protection of guinea pigs challenged with the virulent FMDV. Although the chimeric DNA vaccine, in general, was not as effective as a conventional one, this study encourages further work towards the development of genetically engineered custom-made chimeric vaccines against FMDV.

  14. Somatic Cell Nuclear Transfer Followed by CRIPSR/Cas9 Microinjection Results in Highly Efficient Genome Editing in Cloned Pigs.

    PubMed

    Sheets, Timothy P; Park, Chi-Hun; Park, Ki-Eun; Powell, Anne; Donovan, David M; Telugu, Bhanu P

    2016-12-03

    The domestic pig is an ideal "dual purpose" animal model for agricultural and biomedical research. With the availability of genome editing tools such as clustered regularly interspaced short palindromic repeat (CRISPR) and associated nuclease Cas9 (CRISPR/Cas9), it is now possible to perform site-specific alterations with relative ease, and will likely help realize the potential of this valuable model. In this article, we investigated for the first time a combination of somatic cell nuclear transfer (SCNT) and direct injection of CRISPR/Cas ribonucleoprotein complex targeting GRB10 into the reconstituted oocytes to generate GRB10 ablated Ossabaw fetuses. This strategy resulted in highly efficient (100%) generation of biallelic modifications in cloned fetuses. By combining SCNT with CRISPR/Cas9 microinjection, genome edited animals can now be produced without the need to manage a founder herd, while simultaneously eliminating the need for laborious in vitro culture and screening. Our approach utilizes standard cloning techniques while simultaneously performing genome editing in the cloned zygotes of a large animal model for agriculture and biomedical applications.

  15. Somatic Cell Nuclear Transfer Followed by CRIPSR/Cas9 Microinjection Results in Highly Efficient Genome Editing in Cloned Pigs

    PubMed Central

    Sheets, Timothy P.; Park, Chi-Hun; Park, Ki-Eun; Powell, Anne; Donovan, David M.; Telugu, Bhanu P.

    2016-01-01

    The domestic pig is an ideal “dual purpose” animal model for agricultural and biomedical research. With the availability of genome editing tools such as clustered regularly interspaced short palindromic repeat (CRISPR) and associated nuclease Cas9 (CRISPR/Cas9), it is now possible to perform site-specific alterations with relative ease, and will likely help realize the potential of this valuable model. In this article, we investigated for the first time a combination of somatic cell nuclear transfer (SCNT) and direct injection of CRISPR/Cas ribonucleoprotein complex targeting GRB10 into the reconstituted oocytes to generate GRB10 ablated Ossabaw fetuses. This strategy resulted in highly efficient (100%) generation of biallelic modifications in cloned fetuses. By combining SCNT with CRISPR/Cas9 microinjection, genome edited animals can now be produced without the need to manage a founder herd, while simultaneously eliminating the need for laborious in vitro culture and screening. Our approach utilizes standard cloning techniques while simultaneously performing genome editing in the cloned zygotes of a large animal model for agriculture and biomedical applications. PMID:27918485

  16. Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs

    PubMed Central

    Welzenbach, Julia; Neuhoff, Christiane; Heidt, Hanna; Cinar, Mehmet Ulas; Looft, Christian; Schellander, Karl; Tholen, Ernst; Große-Brinkhaus, Christine

    2016-01-01

    The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein “phosphoglycerate mutase 2” and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes. PMID:27589727

  17. A genome-wide association study in large white and landrace pig populations for number piglets born alive.

    PubMed

    Bergfelder-Drüing, Sarah; Grosse-Brinkhaus, Christine; Lind, Bianca; Erbe, Malena; Schellander, Karl; Simianer, Henner; Tholen, Ernst

    2015-01-01

    The number of piglets born alive (NBA) per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS) were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3), Austria (1) and Switzerland (1). The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

  18. Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

    PubMed Central

    2013-01-01

    Background Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations. A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history. Results The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ─ including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ─, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds. Conclusions High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the

  19. Genome-wide association study for the level of serum electrolytes in Italian Large White pigs.

    PubMed

    Bovo, S; Schiavo, G; Mazzoni, G; Dall'Olio, S; Galimberti, G; Calò, D G; Scotti, E; Bertolini, F; Buttazzoni, L; Samorè, A B; Fontanesi, L

    2016-10-01

    Calcium, magnesium and phosphorus are essential electrolytes involved in a large number of biological processes. Imbalance of these minerals in blood may indicate clinically relevant conditions and are important in inferring acute or chronic pathologies in humans and animals. In this work, we carried out a genome-wide association study (GWAS) for the level of these three electrolytes in the serum of 843 performance-tested Italian Large White pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip, and GWAS was carried out using genome-wide efficient mixed-model association. For the level of Ca(2+) , eight single nucleotide polymorphisms (SNPs) were significant, considering a false discovery rate (FDR) < 0.05, and another eight were above the moderate association threshold (Pnominal value  < 5.00E-05). These SNPs are distributed in four porcine chromosomes (SSC): SSC8, SSC11, SSC12 and SSC13. In particular, a few putative different signals of association detected on SSC13 and one on SSC12 were in genes or close to genes involved in calcium metabolism (P2RY1, RAP2B, SLC9A9, C3orf58, TSC22D2, PLCH1 and CACNB1). Only one SNP (on SSC7) and six SNPs (on SSC2 and SSC7) showed moderate association with the level of magnesium and phosphorus respectively. The association signals for these two latter minerals might identify genes not known thus far for playing a role in their biological functions and regulations. In conclusion, our GWAS contributed to increased knowledge on the role that calcium, magnesium and phosphorus may play in the genetically determined physiological mechanisms affecting the natural variability of mineral levels in mammalian blood.

  20. Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue.

    PubMed

    Kader, Tanjina; Goode, David L; Wong, Stephen Q; Connaughton, Jacquie; Rowley, Simone M; Devereux, Lisa; Byrne, David; Fox, Stephen B; Mir Arnau, Gisela; Tothill, Richard W; Campbell, Ian G; Gorringe, Kylie L

    2016-11-15

    Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.

  1. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data.

    PubMed

    Wang, Hongyang; Li, Rui; Zhou, Xiang; Xue, Liyao; Xu, Xuewen; Liu, Bang

    2016-11-04

    Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3' end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3'UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.

  2. Genome-wide association study reveals regions associated with gestation length in two pig populations.

    PubMed

    Hidalgo, A M; Lopes, M S; Harlizius, B; Bastiaansen, J W M

    2016-04-01

    Reproduction traits, such as gestation length (GLE), play an important role in dam line breeding in pigs. The objective of our study was to identify single nucleotide polymorphisms (SNPs) that are associated with GLE in two pig populations. Genotypes and deregressed breeding values were available for 2081 Dutch Landrace-based (DL) and 2301 Large White-based (LW) pigs. We identified two QTL regions for GLE, one in each population. For DL, three associated SNPs were detected in one QTL region spanning 0.52 Mbp on Sus scrofa chromosome (SSC) 2. For LW, four associated SNPs were detected in one region of 0.14 Mbp on SSC5. The region on SSC2 contains the heparin-binding EGF-like growth factor (HBEGF) gene, which promotes embryo implantation and has been described to be involved in embryo survival throughout gestation. The associated SNP can be used for marker-assisted selection in the studied populations, and further studies of the HBEGF gene are warranted to investigate its role in GLE.

  3. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data

    PubMed Central

    Wang, Hongyang; Li, Rui; Zhou, Xiang; Xue, Liyao; Xu, Xuewen; Liu, Bang

    2016-01-01

    Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS. PMID:27812017

  4. Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network, and pathway analyses

    PubMed Central

    Kogelman, Lisette J. A.; Pant, Sameer D.; Fredholm, Merete; Kadarmideen, Haja N.

    2014-01-01

    Obesity is a complex condition with world-wide exponentially rising prevalence rates, linked with severe diseases like Type 2 Diabetes. Economic and welfare consequences have led to a raised interest in a better understanding of the biological and genetic background. To date, whole genome investigations focusing on single genetic variants have achieved limited success, and the importance of including genetic interactions is becoming evident. Here, the aim was to perform an integrative genomic analysis in an F2 pig resource population that was constructed with an aim to maximize genetic variation of obesity-related phenotypes and genotyped using the 60K SNP chip. Firstly, Genome Wide Association (GWA) analysis was performed on the Obesity Index to locate candidate genomic regions that were further validated using combined Linkage Disequilibrium Linkage Analysis and investigated by evaluation of haplotype blocks. We built Weighted Interaction SNP Hub (WISH) and differentially wired (DW) networks using genotypic correlations amongst obesity-associated SNPs resulting from GWA analysis. GWA results and SNP modules detected by WISH and DW analyses were further investigated by functional enrichment analyses. The functional annotation of SNPs revealed several genes associated with obesity, e.g., NPC2 and OR4D10. Moreover, gene enrichment analyses identified several significantly associated pathways, over and above the GWA study results, that may influence obesity and obesity related diseases, e.g., metabolic processes. WISH networks based on genotypic correlations allowed further identification of various gene ontology terms and pathways related to obesity and related traits, which were not identified by the GWA study. In conclusion, this is the first study to develop a (genetic) obesity index and employ systems genetics in a porcine model to provide important insights into the complex genetic architecture associated with obesity and many biological pathways that underlie

  5. Genomic regions affecting backfat thickness and cannon bone circumference identified by genome-wide association study in a Duroc pig population.

    PubMed

    Okumura, Naohiko; Matsumoto, Toshimi; Hayashi, Takeshi; Hirose, Kensuke; Fukawa, Kazuo; Itou, Tetsuya; Uenishi, Hirohide; Mikawa, Satoshi; Awata, Takashi

    2013-08-01

    We performed a genome-wide association study using the porcine 60K SNP array to detect QTL regions for nine traits in a three-generational Duroc samples (n = 651), viz. generations 1, 2 and 3 from a population selected over five generations using a closed nucleus breeding scheme. We applied a linear mixed model for association mapping to detect SNP effects, adjusting for fixed effects (sex and season) and random polygenic effects (reflecting genetic relatedness), and derived a likelihood ratio statistic for each SNP using the efficient mixed-model association method. We detected a region on SSC6 for backfat thickness (BFT) and on SSC7 for cannon bone circumference (CANNON), with a genome-wide significance of P < 0.01 after Bonferroni correction. These regions had been detected previously in other pig populations. Six genes are located in the BFT-associated region, while the CANNON-associated region includes 66 genes. In the future, significantly associated SNPs, derived by sequencing the coding regions of the six genes in the BFT region, can be used in marker-assisted selection of BFT, whereas haplotypes constructed from the SSC7 region with strong LD can be used to select for the CANNON trait in our resource family.

  6. Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold?

    PubMed

    Grapes, L; Rudd, S; Fernando, R L; Megy, K; Rocha, D; Rothschild, M F

    2006-06-01

    Gene-to-gene variation in the frequency of single nucleotide polymorphisms (SNPs) has been observed in humans, mice, rats, primates and pigs, but a relationship across species in this variation has not been described. Here, the frequency of porcine coding SNPs (cSNPs) identified by in silico methods, and the frequency of murine cSNPs, were compared with the frequency of human cSNPs across homologous genes. From 150,000 porcine expressed sequence tag (EST) sequences, a total of 452 SNP-containing sequence clusters were found, totalling 1394 putative SNPs. All the clustered porcine EST annotations and SNP data have been made publicly available at http://sputnik.btk.fi/project?name=swine. Human and murine cSNPs were identified from dbSNP and were characterized as either validated or total number of cSNPs (validated plus non-validated) for comparison purposes. The correlation between in silico pig cSNP and validated human cSNP densities was found to be 0.77 (p < 0.00001) for a set of 25 homologous genes, while a correlation of 0.48 (p < 0.0005) was found for a primarily random sample of 50 homologous human and mouse genes. This is the first evidence of conserved gene-to-gene variability in cSNP frequency across species and indicates that site-directed screening of porcine genes that are homologous to cSNP-rich human genes may rapidly advance cSNP discovery in pigs.

  7. Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola.

    PubMed

    Svartström, Olov; Mushtaq, Memoona; Pringle, Märit; Segerman, Bo

    2013-01-01

    Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.

  8. Genome-wide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons

    PubMed Central

    Wall, Jeffrey D; Schlebusch, Stephen A; Alberts, Susan C; Cox, Laura A; Snyder-Mackler, Noah; Nevonen, Kimberly; Carbone, Lucia; Tung, Jenny

    2017-01-01

    Naturally occurring admixture has now been documented in every major primate lineage, suggesting its key role in primate evolutionary history. Active primate hybrid zones can provide valuable insight into this process. Here, we investigate the history of admixture in one of the best-studied natural primate hybrid zones, between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in the Amboseli ecosystem of Kenya. We generated a new genome assembly for yellow baboon and low coverage genome-wide resequencing data from yellow baboons, anubis baboons, and known hybrids (n=44). Using a novel composite likelihood method for estimating local ancestry from low coverage data, we found high levels of genetic diversity and genetic differentiation between the parent taxa, and excellent agreement between genome-scale ancestry estimates and a priori pedigree, life history, and morphology-based estimates (r2=0.899). However, even putatively unadmixed Amboseli yellow individuals carried a substantial proportion of anubis ancestry, presumably due to historical admixture. Further, the distribution of shared versus fixed differences between a putatively unadmixed Amboseli yellow baboon and an unadmixed anubis baboon, both sequenced at high coverage, are inconsistent with simple isolation-migration or equilibrium migration models. Our findings suggest a complex process of intermittent contact that has occurred multiple times in baboon evolutionary history, despite no obvious fitness costs to hybrids or major geographic or behavioral barriers. In combination with the extensive phenotypic data available for baboon hybrids, our results provide valuable context for understanding the history of admixture in primates, including in our own lineage. PMID:27145036

  9. Transgenesis for pig models

    PubMed Central

    Yum, Soo-Young; Yoon, Ki-Young; Lee, Choong-Il; Lee, Byeong-Chun

    2016-01-01

    Animal models, particularly pigs, have come to play an important role in translational biomedical research. There have been many pig models with genetically modifications via somatic cell nuclear transfer (SCNT). However, because most transgenic pigs have been produced by random integration to date, the necessity for more exact gene-mutated models using recombinase based conditional gene expression like mice has been raised. Currently, advanced genome-editing technologies enable us to generate specific gene-deleted and -inserted pig models. In the future, the development of pig models with gene editing technologies could be a valuable resource for biomedical research. PMID:27030199

  10. Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

    PubMed Central

    Bosse, Mirte; Megens, Hendrik-Jan; Madsen, Ole; Crooijmans, Richard P.M.A.; Ryder, Oliver A.; Austerlitz, Frédéric; Groenen, Martien A.M.; de Cara, M. Angeles R.

    2015-01-01

    Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs. PMID:26063737

  11. Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population.

    PubMed

    Uemoto, Y; Soma, Y; Sato, S; Ishida, M; Shibata, T; Kadowaki, H; Kobayashi, E; Suzuki, K

    2012-02-01

    The fatty acid composition and melting point of fatty tissue are among the most important economic traits in pig breeding because of their influence on the eating quality of meat. Identifying the quantitative trait locus (QTL) of these traits may help reveal the genetic structure of fatty acid composition and the melting point of fatty tissue and improve meat-quality traits by marker-assisted selection. We conducted whole-genome QTL analysis for fatty acid composition and melting point of inner and outer subcutaneous fat and inter- and intramuscular fat in a purebred Duroc population. A total of 129 markers were genotyped and used for QTL analysis. For fatty acid compositions of inner and outer subcutaneous fat, three significant QTL and 17 suggestive QTL were detected on SSC2, 4, 6, 8, 9, 10, 11, 12, 14 and 18. For the melting point of inner and outer subcutaneous fat, two significant QTL were detected on the same region of SSC14. For fatty acid compositions of inter- and intramuscular fat, five significant QTL and 13 suggestive QTL were detected on SSC2, 4, 6, 8, 9, 10, 14 and 15. On SSC14, significant QTL for C18:0 and C18:1 of outer subcutaneous fat and intramuscular fat, and melting point of subcutaneous fat, which had high likelihood of odds (LOD) scores (2.67-5.78), were detected in the same region. This study determined QTL affecting fatty acid composition and melting point of different fat tissues in purebred Duroc pigs.

  12. Full-length genomic analysis of porcine G9P[23] and G9P[7] rotavirus strains isolated from pigs with diarrhea in South Korea.

    PubMed

    Kim, Ha-Hyun; Matthijnssens, Jelle; Kim, Hyun-Jeong; Kwon, Hyung-Jun; Park, Jun-Gyu; Son, Kyu-Yeol; Ryu, Eun-Hye; Kim, Deok-Song; Lee, Woo Song; Kang, Mun-Il; Yang, Dong-Kun; Hyun, Bang-Hun; Park, Sang-Ik; Park, Su-Jin; Cho, Kyoung-Oh

    2012-10-01

    Group A rotaviruses (RVAs) are agents causing severe gastroenteritis in infants and young animals. G9 RVA strains are believed to have originated from pigs. However, this genotype has emerged as the fifth major human RVA genotype worldwide. To better understand the relationship between human and porcine RVA strains, complete RVA genome data are needed. For human RVA strains, the number of complete genome data have grown exponentially. However, there is still a lack of complete genome data on porcine RVA strains. Recently, G9 RVA strains have been identified as the third most important genotype in diarrheic pigs in South Korea in combinations with P[7] and P[23]. This study is the first report on complete genome analyses of 1 G9P[7] and 3 G9P[23] porcine RVA strains, resulting in the following genotype constellation: G9-P[7]/P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. By comparisons of these genotype constellations, it was revealed that the Korean G9P[7] and G9P[23] RVA strains possessed a typical porcine RVA backbone, similar to other known porcine RVA strains. However, detailed phylogenetic analyses revealed the presence of intra-genotype reassortments among porcine RVA strains in South Korea. Thus, our data provide genetic information of G9 RVA strains increasingly detected in both humans and pigs, and will help to establish the role of pigs as a source or reservoir for novel human RVA strains.

  13. Performance Evaluation of NIPT in Detection of Chromosomal Copy Number Variants Using Low-Coverage Whole-Genome Sequencing of Plasma DNA

    PubMed Central

    Lin, Linhua; Yin, Xuyang; Wang, Jun; Chen, Dayang; Chen, Fang; Jiang, Hui; Ren, Jinghui; Wang, Wei

    2016-01-01

    Objectives The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method. Method A total of 919 archived maternal plasma samples with karyotyping/microarray results, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated. Results 33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively. Conclusion Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs. PMID:27415003

  14. Zearalenone Mycotoxin Affects Immune Mediators, MAPK Signalling Molecules, Nuclear Receptors and Genome-Wide Gene Expression in Pig Spleen

    PubMed Central

    Pistol, Gina Cecilia; Braicu, Cornelia; Motiu, Monica; Gras, Mihail Alexandru; Marin, Daniela Eliza; Stancu, Mariana; Calin, Loredana; Israel-Roming, Florentina; Berindan-Neagoe, Ioana; Taranu, Ionelia

    2015-01-01

    The toxicity of zearalenone (ZEA) was evaluated in swine spleen, a key organ for the innate and adaptative immune response. Weaned pigs were fed for 18 days with a control or a ZEA contaminated diet. The effect of ZEA was assessed on wide genome expression, pro- (TNF-α, IL-8, IL-6, IL-1β, IFN-γ) and anti-inflammatory (IL-10, IL-4) cytokines, other molecules involved in inflammatory processes (MMPs/TIMPs), as well as signaling molecules, (p38/JNK1/JNK2-MAPKs) and nuclear receptors (PPARγ/NFkB/AP-1/STAT3/c-JUN). Microarray analysis showed that 46% of total number of differentially expressed genes was involved in cellular signaling pathway, 13% in cytokine network and 10% in the inflammatory response. ZEA increased expression and synthesis of pro- inflammatory (TNF-α, IL-8, IL-6, IL-1β) and had no effect on IFN-γ, IL-4 and IL-10 cytokines in spleen. The inflammatory stimulation might be a consequence of JNK pathway activation rather than of p-38MAPK and NF-kB involvement whose gene and protein expression were suppressed by ZEA action. In summary, our findings indicated the role of ZEA as an immune disruptor at spleen level. PMID:26011631

  15. A chimeric porcine circovirus (PCV) with the immunogenic capsid gene of the pathogenic PCV type 2 (PCV2) cloned into the genomic backbone of the nonpathogenic PCV1 induces protective immunity against PCV2 infection in pigs.

    PubMed

    Fenaux, M; Opriessnig, T; Halbur, P G; Elvinger, F; Meng, X J

    2004-06-01

    Porcine circovirus type 2 (PCV2) is associated with postweaning multisystemic wasting syndrome in pigs, whereas PCV1 is nonpathogenic. We previously demonstrated that a chimeric PCV1-2 virus (with the immunogenic capsid gene of PCV2 cloned into the backbone of PCV1) induces an antibody response to the PCV2 capsid protein and is attenuated in pigs. Here, we report that the attenuated chimeric PCV1-2 induces protective immunity to wild-type PCV2 challenge in pigs. A total of 48 specific-pathogen-free piglets were randomly and equally assigned to four groups of 12 pigs each. Pigs in group 1 were vaccinated by intramuscular injection with 200 microg of the chimeric PCV1-2 infectious DNA clone. Pigs in group 2 were vaccinated by intralymphoid injection with 200 microg of a chimeric PCV1-2 infectious DNA clone. Pigs in group 3 were vaccinated by intramuscular injection with 10(3.5) 50% tissue culture infective doses (TCID(50)) of the chimeric PCV1-2 live virus. Pigs in group 4 were not vaccinated and served as controls. By 42 days postvaccination (DPV), the majority of pigs had seroconverted to PCV2 capsid antibody. At 42 DPV, all pigs were challenged intranasally and intramuscularly with 2 x 10(4.5) TCID(50) of a wild-type pathogenic PCV2 virus. By 21 days postchallenge (DPC), 9 out of the 12 group 4 pigs were viremic for PCV2. Vaccinated animals in groups 1 to 3 had no detectable PCV2 viremia after challenge. At 21 DPC the lymph nodes in the nonvaccinated pigs were larger (P < 0.05) than those of vaccinated pigs. The PCV2 genomic copy loads in lymph nodes were reduced (P < 0.0001) in vaccinated pigs. Moderate amounts of PCV2 antigen were detected in most lymphoid tissues of nonvaccinated pigs but in only 1 of 36 vaccinated pigs. Mild-to-severe lymphoid depletion and histiocytic replacement were detected in lymphoid tissues in the majority of nonvaccinated group 4 pigs but in only a few vaccinated group 1 to 3 pigs. The data from this study indicated that when given

  16. Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping.

    PubMed

    Do, Duy Ngoc; Strathe, Anders Bjerring; Ostersen, Tage; Jensen, Just; Mark, Thomas; Kadarmideen, Haja N

    2013-01-01

    This study was aimed at identifying genomic regions controlling feeding behavior in Danish Duroc boars and its potential implications for eating behavior in humans. Data regarding individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV) and mean feed intake rate (FR) were available for 1130 boars. All boars were genotyped using the Illumina Porcine SNP60 BeadChip. The association analyses were performed using the GenABEL package in the R program. Sixteen SNPs were found to have moderate genome-wide significance (p<5E-05) and 76 SNPs had suggestive (p<5E-04) association with feeding behavior traits. MSI2 gene on chromosome (SSC) 14 was very strongly associated with NVD. Thirty-six SNPs were located in genome regions where QTLs have previously been reported for behavior and/or feed intake traits in pigs. The regions: 64-65 Mb on SSC 1, 124-130 Mb on SSC 8, 63-68 Mb on SSC 11, 32-39 Mb and 59-60 Mb on SSC 12 harbored several signifcant SNPs. Synapse genes (GABRR2, PPP1R9B, SYT1, GABRR1, CADPS2, DLGAP2 and GOPC), dephosphorylation genes (PPM1E, DAPP1, PTPN18, PTPRZ1, PTPN4, MTMR4 and RNGTT) and positive regulation of peptide secretion genes (GHRH, NNAT and TCF7L2) were highly significantly associated with feeding behavior traits. This is the first GWAS to identify genetic variants and biological mechanisms for eating behavior in pigs and these results are important for genetic improvement of pig feed efficiency. We have also conducted pig-human comparative gene mapping to reveal key genomic regions and/or genes on the human genome that may influence eating behavior in human beings and consequently affect the development of obesity and metabolic syndrome. This is the first translational genomics study of its kind to report potential candidate genes for eating behavior in humans.

  17. Genome-Wide Association Study Reveals Genetic Architecture of Eating Behavior in Pigs and Its Implications for Humans Obesity by Comparative Mapping

    PubMed Central

    Do, Duy Ngoc; Strathe, Anders Bjerring; Ostersen, Tage; Jensen, Just; Mark, Thomas; Kadarmideen, Haja N

    2013-01-01

    This study was aimed at identifying genomic regions controlling feeding behavior in Danish Duroc boars and its potential implications for eating behavior in humans. Data regarding individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV) and mean feed intake rate (FR) were available for 1130 boars. All boars were genotyped using the Illumina Porcine SNP60 BeadChip. The association analyses were performed using the GenABEL package in the R program. Sixteen SNPs were found to have moderate genome-wide significance (p<5E-05) and 76 SNPs had suggestive (p<5E-04) association with feeding behavior traits. MSI2 gene on chromosome (SSC) 14 was very strongly associated with NVD. Thirty-six SNPs were located in genome regions where QTLs have previously been reported for behavior and/or feed intake traits in pigs. The regions: 64–65 Mb on SSC 1, 124–130 Mb on SSC 8, 63–68 Mb on SSC 11, 32–39 Mb and 59–60 Mb on SSC 12 harbored several signifcant SNPs. Synapse genes (GABRR2, PPP1R9B, SYT1, GABRR1, CADPS2, DLGAP2 and GOPC), dephosphorylation genes (PPM1E, DAPP1, PTPN18, PTPRZ1, PTPN4, MTMR4 and RNGTT) and positive regulation of peptide secretion genes (GHRH, NNAT and TCF7L2) were highly significantly associated with feeding behavior traits. This is the first GWAS to identify genetic variants and biological mechanisms for eating behavior in pigs and these results are important for genetic improvement of pig feed efficiency. We have also conducted pig-human comparative gene mapping to reveal key genomic regions and/or genes on the human genome that may influence eating behavior in human beings and consequently affect the development of obesity and metabolic syndrome. This is the first translational genomics study of its kind to report potential candidate genes for eating behavior in humans. PMID:23977060

  18. Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limite...

  19. Genome-wide association of multiple complex traits in outbred mice by ultra low-coverage sequencing

    PubMed Central

    Nicod, Jérôme; Davies, Robert W.; Cai, Na; Hassett, Carl; Goodstadt, Leo; Cosgrove, Cormac; Yee, Benjamin K; Lionikaite, Vikte; McIntyre, Rebecca E; Remme, Carol Ann; Lodder, Elisabeth M.; Gregory, Jennifer S.; Hough, Tertius; Joynson, Russell; Phelps, Hayley; Nell, Barbara; Rowe, Clare; Wood, Joe; Walling, Alison; Bopp, Nasrin; Bhomra, Amarjit; Hernandez-Pliego, Polinka; Callebert, Jacques; Aspden, Richard M.; Talbot, Nick P; Robbins, Peter A; Harrison, Mark; Fray, Martin; Launay, Jean-Marie; Pinto, Yigal M.; Blizard, David A.; Bezzina, Connie R.; Adams, David J; Franken, Paul; Weaver, Tom; Wells, Sara; Brown, Steve DM; Potter, Paul K; Klenerman, Paul; Lionikas, Arimantas; Mott, Richard; Flint, Jonathan

    2016-01-01

    Two bottlenecks impeding the genetic analysis of complex traits in rodents are access to mapping populations able to deliver gene-level mapping resolution, and the need for population specific genotyping arrays and haplotype reference panels. Here we combine low coverage sequencing (0.15X) with a novel method to impute the ancestral haplotype space in 1,887 commercially available outbred mice. We mapped 156 unique quantitative trait loci for 92 phenotypes at 5% false discovery rate. Gene-level mapping resolution was achieved at about a fifth of loci, implicating Unc13c and Pgc1-alpha at loci for the quality of sleep, Adarb2 for home cage activity, Rtkn2 for intensity of reaction to startle, Bmp2 for wound healing, Il15 and Id2 for several T-cell measures and Prkca for bone mineral content. These findings have implications for diverse areas of mammalian biology and demonstrate how GWAS can be extended via low-coverage sequencing to species with highly recombinant outbred populations. PMID:27376238

  20. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

    PubMed Central

    Viennas, Emmanouil; Komianou, Angeliki; Mizzi, Clint; Stojiljkovic, Maja; Mitropoulou, Christina; Muilu, Juha; Vihinen, Mauno; Grypioti, Panagiota; Papadaki, Styliani; Pavlidis, Cristiana; Zukic, Branka; Katsila, Theodora; van der Spek, Peter J.; Pavlovic, Sonja; Tzimas, Giannis; Patrinos, George P.

    2017-01-01

    FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications. PMID:27924022

  1. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies.

    PubMed

    Viennas, Emmanouil; Komianou, Angeliki; Mizzi, Clint; Stojiljkovic, Maja; Mitropoulou, Christina; Muilu, Juha; Vihinen, Mauno; Grypioti, Panagiota; Papadaki, Styliani; Pavlidis, Cristiana; Zukic, Branka; Katsila, Theodora; van der Spek, Peter J; Pavlovic, Sonja; Tzimas, Giannis; Patrinos, George P

    2017-01-04

    FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications.

  2. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications.

    PubMed

    Buckley, Patrick G; Mantripragada, Kiran K; Benetkiewicz, Magdalena; Tapia-Páez, Isabel; Diaz De Ståhl, Teresita; Rosenquist, Magnus; Ali, Haider; Jarbo, Caroline; De Bustos, Cecilía; Hirvelä, Carina; Sinder Wilén, Birgitta; Fransson, Ingegerd; Thyr, Charlotte; Johnsson, Britt-Inger; Bruder, Carl E G; Menzel, Uwe; Hergersberg, Martin; Mandahl, Nils; Blennow, Elisabeth; Wedell, Anna; Beare, David M; Collins, John E; Dunham, Ian; Albertson, Donna; Pinkel, Daniel; Bastian, Boris C; Faruqi, A Fawad; Lasken, Roger S; Ichimura, Koichi; Collins, V Peter; Dumanski, Jan P

    2002-12-01

    We have constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number variation. This chromosome 22 array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb. To demonstrate the utility of the array, we have applied it to profile acral melanoma, dermatofibrosarcoma, DiGeorge syndrome and neurofibromatosis 2. We accurately diagnosed homozygous/heterozygous deletions, amplifications/gains, IGLV/IGLC locus instability, and breakpoints of an imbalanced translocation. We further identified the 14-3-3 eta isoform as a candidate tumor suppressor in glioblastoma. Two significant methodological advances in array construction were also developed and validated. These include a strictly sequence defined, repeat-free, and non-redundant strategy for array preparation. This approach allows an increase in array resolution and analysis of any locus; disregarding common repeats, genomic clone availability and sequence redundancy. In addition, we report that the application of phi29 DNA polymerase is advantageous in microarray preparation. A broad spectrum of issues in medical research and diagnostics can be approached using the array. This well annotated and gene-rich autosome contains numerous uncharacterized disease genes. It is therefore crucial to associate these genes to specific 22q-related conditions and this array will be instrumental towards this goal. Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array.

  3. Development of a Novel Oligonucleotide Array for Genomic Screening of Chemical Warfare Agent Exposure in Guinea Pigs and Swine

    DTIC Science & Technology

    2004-04-01

    respectively. To address this gap in research tools, we have developed an oligonucleotide microarray that contains representative genes from guinea pig...To address this gap in research tools, we have developed an oligonucleotide microarray that contains representative genes from guinea pig...toxicogenomics. Toxicogenomics is focused on identifying changes in gene expression in response to a toxic chemical and then using that information to

  4. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.

    PubMed

    Ammiraju, Jetty S S; Luo, Meizhong; Goicoechea, José L; Wang, Wenming; Kudrna, Dave; Mueller, Christopher; Talag, Jayson; Kim, HyeRan; Sisneros, Nicholas B; Blackmon, Barbara; Fang, Eric; Tomkins, Jeffery B; Brar, Darshan; MacKill, David; McCouch, Susan; Kurata, Nori; Lambert, Georgina; Galbraith, David W; Arumuganathan, K; Rao, Kiran; Walling, Jason G; Gill, Navdeep; Yu, Yeisoo; SanMiguel, Phillip; Soderlund, Carol; Jackson, Scott; Wing, Rod A

    2006-01-01

    Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%-4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed.

  5. Genome-wide identification, classification and functional analyses of the bHLH transcription factor family in the pig, Sus scrofa.

    PubMed

    Liu, Wuyi

    2015-08-01

    The basic helix-loop-helix (bHLH) transcription factors are one of the largest families of gene regulatory proteins and play crucial roles in genetic, developmental and physiological processes in eukaryotes. Here, we conducted a survey of the Sus scrofa genome and identified 109 putative bHLH transcription factor members belonging to super-groups A, B, C, D, E, and F, respectively, while four members were orphan genes. We identified 6 most significantly enriched KEGG pathways and 116 most significant GO annotation categories. Further comprehensive surveys in human genome and other 12 medical databases identified 72 significantly enriched biological pathways with these 113 pig bHLH transcription factors. From the functional protein association network analysis 93 hub proteins were identified and 55 hub proteins created a tight network or a functional module within their protein families. Especially, there were 20 hub proteins found highly connected in the functional interaction network. The present study deepens our understanding and provided insights into the evolution and functional aspects of animal bHLH proteins and should serve as a solid foundation for further for analyses of specific bHLH transcription factors in the pig and other mammals.

  6. Intragenic and extragenic disruptions of FOXL2 mapped by whole genome low-coverage sequencing in two BPES families with chromosome reciprocal translocation.

    PubMed

    Yang, Yongjia; Yang, Chuanchun; Zhu, Yimin; Chen, Haixiao; Zhao, Rui; He, Xinyu; Tao, Lijuan; Wang, Pin; Zhou, Lijun; Zhao, Liu; Tu, Ming; Dong, Zirui; Chen, Hui; Xie, Zhiguo

    2014-09-01

    Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is a rare autosomal dominant disorder that affects craniofacial development and ovarian function. FOXL2 is the only gene known to be responsible for BPES. The majority of BPES patients show intragenic mutations of FOXL2. Recently, a 7.4 kb sequence disruption, which was 283 kb upstream of FOXL2, was identified to independently contribute to the BPES phenotype. Several breakpoints nearing FOXL2 (0 Mb to 1.2 Mb, several of which were distant from the 7.4 kb sequence disruption) have been mapped or deduced through a traditional method in BPES patients with chromosome reciprocal translocation. In this study, two BPES families with chromosome reciprocal translocation were investigated. Intragenic mutations of FOXL2 or pathogenic copy number variations were excluded for the two BPES families. All of the four breakpoints were identified at a base-precise manner using Giemsa banding and whole genome low-coverage sequencing (WGLCS). In family 01, the breakpoints were found at chr1:95,609,998 and chr3:138,879, 114 (213,132 bp upstream of FOXL2). In family 02, the breakpoints were located at chr3:138,665,431 (intragenic disruptions of FOXL2) and chr20:56,924,609. Results indicate that the intragenic and extragenic interruptions of FOXL2 can be accurately and rapidly detected using WGLCS. In addition, both the 213 kb upstream and intragenic interruptions of FOXL2 can cause BPES phenotype.

  7. A gene expression atlas of the domestic pig

    PubMed Central

    2012-01-01

    Background This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering. Results The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development. Conclusions As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas. PMID:23153189

  8. Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs

    PubMed Central

    Ros-Freixedes, Roger; Gol, Sofia; Pena, Ramona N.; Tor, Marc; Ibáñez-Escriche, Noelia; Dekkers, Jack C. M.; Estany, Joan

    2016-01-01

    Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork. PMID:27023885

  9. Complete genome analyses of the first porcine rotavirus group H identified from a South African pig does not provide evidence for recent interspecies transmission events.

    PubMed

    Nyaga, Martin M; Peenze, Ina; Potgieter, Christiaan A; Seheri, L Mapaseka; Page, Nicola A; Yinda, Claude K; Steele, A Duncan; Matthijnssens, Jelle; Mphahlele, M Jeffrey

    2016-03-01

    Rotaviruses (RVs) are classified into eight species/groups (RVA-RVH) according to the migration patterns of their 11 genome segments, as well as by serological and molecular properties of Viral Protein 6 (VP6). In 1997 a new unclassified RV was reported infecting adults in Bangladesh and China. This virus was initially named novel adult diarrhoea rotavirus (ADRV-N), but later renamed as RVH. Since then, RVH has been detected in humans only very sporadically. However, RVH is increasingly being detected in pig populations in the USA, Brazil and Japan, but not yet in Africa. Unfortunately, whole genome sequence data of porcine RVH strains in GenBank is currently restricted to a single strain (SKA-1) from Japan. Porcine diarrhoeic samples were collected in South Africa and analysed for rotavirus using an RVA ELISA and electropherotyping by PAGE. One sample displayed a 4:2:1:1:1:1:1 migration pattern, typical for RVH. In order to further investigate this strain, sequence-independent amplification followed by random sequencing using the 454/Roche GS FLX Sequencer was performed, resulting in the second complete porcine RVH strain (MRC-DPRU1575) available in databases. Phylogenetically, all segments of MRC-DPRU1575 clustered closely with the SKA-1 strain and in some segments with known porcine RVH strains from Brazil and the USA. In contrast, the porcine RVH strains were only distantly related to human RVH strains from Asia and a partial RVH-like strain recently detected in bats from Cameroon. Overall, strain MRC-DPRU1575 is the first complete genome of a porcine RVH from Africa and allows for the development of improved RVH screening methods. Our analyses indicate that RVH strains cluster according to their host species, not suggesting any evidence of recent interspecies transmission events. However, more RVH genomes from a wider host range are needed to better understand their evolutionary pathways and zoonotic potential.

  10. A Whole Genome Association Study on Meat Quality Traits Using High Density SNP Chips in a Cross between Korean Native Pig and Landrace.

    PubMed

    Lee, K-T; Lee, Y-M; Alam, M; Choi, B H; Park, M R; Kim, K-S; Kim, T-H; Kim, J-J

    2012-11-01

    A whole genome association (WGA) study was performed to detect significant polymorphisms for meat quality traits in an F2 cross population (N = 478) that were generated with Korean native pig sires and Landrace dams in National Livestock Research Institute, Songwhan, Korea. The animals were genotyped using Illumina porcine 60k SNP beadchips, in which a set of 46,865 SNPs were available for the WGA analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water holding capacity, drip loss, shear force, CIE L, CIE a and CIE b. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model, after adjusting for sex, sire and slaughter stage as fixed effects. With the significant SNPs for each trait (p<0.001), a stepwise regression procedure was applied to determine the best set of SNPs with the additive and/or dominance effects. A total of 106 SNPs, or quantitative trait loci (QTL) were detected, and about 32 to 66% of the total phenotypic variation was explained by the significant SNPs for each trait. The QTL were identified in most porcine chromosomes (SSCs), in which majority of the QTL were detected in SSCs 1, 2, 12, 13, 14 and 16. Several QTL clusters were identified on SSCs 12, 16 and 17, and a cluster of QTL influencing crude protein, crude lipid, drip loss, shear force, CIE a and CIE b were located between 20 and 29 Mb of SSC12. A pleiotropic QTL for drip loss, CIE L and CIE b was also detected on SSC16. These QTL need to be validated in commercial pig populations for genetic improvement in meat quality via marker-assisted selection.

  11. P-TEFb Kinase Activity Is Essential for Global Transcription, Resumption of Meiosis and Embryonic Genome Activation in Pig

    PubMed Central

    Oqani, Reza K.; Lin, Tao; Lee, Jae Eun; Choi, Ki Myung; Shin, Hyun Young; Jin, Dong Il

    2016-01-01

    Positive transcription elongation factor b (P-TEFb) is a RNA polymerase II carboxyl-terminal domain (Pol II CTD) kinase that phosphorylates Ser2 of the CTD and promotes the elongation phase of transcription. Despite the fact that P-TEFb has role in many cellular processes, the role of this kinase complex remains to be understood in mammalian early developmental events. In this study, using immunocytochemical analyses, we found that the P-TEFb components, CDK9, Cyclin T1 and Cyclin T2 were localized to nuclear speckles, as well as in nucleolar-like bodies in pig germinal vesicle oocytes. Using nascent RNA labeling and small molecule inhibitors, we showed that inhibition of CDK9 activity abolished the transcription of GV oocytes globally. Moreover, using fluorescence in situ hybridization, in absence of CDK9 kinase activity the production of ribosomal RNAs was impaired. We also presented the evidences indicating that P-TEFb kinase activity is essential for resumption of oocyte meiosis and embryo development. Treatment with CDK9 inhibitors resulted in germinal vesicle arrest in maturing oocytes in vitro. Inhibition of CDK9 kinase activity did not interfere with in vitro fertilization and pronuclear formation. However, when in vitro produced zygotes were treated with CDK9 inhibitors, their development beyond the 4-cell stage was impaired. In these embryos, inhibition of CDK9 abrogated global transcriptional activity and rRNA production. Collectively, our data suggested that P-TEFb kinase activity is crucial for oocyte maturation, embryo development and regulation of RNA transcription in pig. PMID:27011207

  12. Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake.

    PubMed

    Do, Duy N; Strathe, Anders B; Ostersen, Tage; Pant, Sameer D; Kadarmideen, Haja N

    2014-01-01

    Residual feed intake (RFI) is a complex trait that is economically important for livestock production; however, the genetic and biological mechanisms regulating RFI are largely unknown in pigs. Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genome-wide association (GWA) and pathway analyses. A total of 596 Yorkshire boars with phenotypes for two different measures of RFI (RFI1 and 2) and 60k genotypic data was used. GWA analysis was performed using a univariate mixed model and 12 and 7 SNPs were found to be significantly associated with RFI1 and RFI2, respectively. Several genes such as xin actin-binding repeat-containing protein 2 (XIRP2),tetratricopeptide repeat domain 29 (TTC29),suppressor of glucose, autophagy associated 1 (SOGA1),MAS1,G-protein-coupled receptor (GPCR) kinase 5 (GRK5),prospero-homeobox protein 1 (PROX1),GPCR 155 (GPR155), and FYVE domain containing the 26 (ZFYVE26) were identified as putative candidates for RFI based on their genomic location in the vicinity of these SNPs. Genes located within 50 kbp of SNPs significantly associated with RFI and RFI2 (q-value ≤ 0.2) were subsequently used for pathway analyses. These analyses were performed by assigning genes to biological pathways and then testing the association of individual pathways with RFI using a Fisher's exact test. Metabolic pathway was significantly associated with both RFIs. Other biological pathways regulating phagosome, tight junctions, olfactory transduction, and insulin secretion were significantly associated with both RFI traits when relaxed threshold for cut-off p-value was used (p ≤ 0.05). These results implied porcine RFI is regulated by multiple biological mechanisms, although the metabolic processes might be the most important. Olfactory transduction pathway controlling the perception of feed via smell, insulin pathway controlling food intake might be important

  13. Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd.

    PubMed

    Xu, Pei; Xu, Shizhong; Wu, Xiaohua; Tao, Ye; Wang, Baogen; Wang, Sha; Qin, Dehui; Lu, Zhongfu; Li, Guojing

    2014-02-01

    Restriction site-associated DNA sequencing (RAD-Seq), a next-generation sequencing-based genome 'complexity reduction' protocol, has been useful in population genomics in species with a reference genome. However, the application of this protocol to natural populations of genomically underinvestigated species, particularly under low-to-medium sequencing depth, has not been well justified. In this study, a Bayesian method was developed for calling genotypes from an F₂ population of bottle gourd [Lagenaria siceraria (Mol.) Standl.] to construct a high-density genetic map. Low-depth genome shotgun sequencing allowed the assembly of scaffolds/contigs comprising approximately 50% of the estimated genome, of which 922 were anchored for identifying syntenic regions between species. RAD-Seq genotyping of a natural population comprising 80 accessions identified 3226 single nuclear polymorphisms (SNPs), based on which two sub-gene pools were suggested for association with fruit shape. The two sub-gene pools were moderately differentiated, as reflected by the Hudson's F(ST) value of 0.14, and they represent regions on LG7 with strikingly elevated F(ST) values. Seven-fold reduction in heterozygosity and two times increase in LD (r²) were observed in the same region for the round-fruited sub-gene pool. Outlier test suggested the locus LX3405 on LG7 to be a candidate site under selection. Comparative genomic analysis revealed that the cucumber genome region syntenic to the high FST island on LG7 harbors an ortholog of the tomato fruit shape gene OVATE. Our results point to a bright future of applying RAD-Seq to population genomic studies for non-model species even under low-to-medium sequencing efforts. The genomic resources provide valuable information for cucurbit genome research.

  14. Sideline Coverage

    PubMed Central

    Gould, Sara J.; Cardone, Dennis A.; Munyak, John; Underwood, Philipp J.; Gould, Stephen A.

    2014-01-01

    Context: Sidelines coverage presents unique challenges in the evaluation of injured athletes. Health care providers may be confronted with the question of when to obtain radiographs following an injury. Given that most sidelines coverage occurs outside the elite level, radiographs are not readily available at the time of injury, and the decision of when to send a player for radiographs must be made based on physical examination. Clinical tools have been developed to aid in identifying injuries that are likely to result in radiographically important fractures or dislocations. Evidence Acquisition: A search for the keywords x-ray and decision rule along with the anatomic locations shoulder, elbow, wrist, knee, and ankle was performed using the PubMed database. No limits were set regarding year of publication. We selected meta-analyses, randomized controlled trials, and survey results. Our selection focused on the largest, most well-studied published reports. We also attempted to include studies that reported the application of the rules to the field of sports medicine. Study Design: Retrospective literature review. Level of Evidence: Level 4. Results: The Ottawa Foot and Ankle Rules have been validated and implemented and are appropriate for use in both pediatric and adult populations. The Ottawa Knee Rules have been widely studied, validated, and accepted for evaluation of knee injuries. There are promising studies of decision rules for clinically important fractures of the wrist, but these studies have not been validated. The elbow has been evaluated with good outcomes via the elbow extension test, which has been validated in both single and multicenter studies. Currently, there are no reliable clinical decision tools for traumatic sports injuries to the shoulder to aid in the decision of when to obtain radiographs. Conclusion: Clinical decision tools have been developed to aid in the diagnosis and management of injuries commonly sustained during sporting events

  15. Full-Genome Sequence of a Reassortant H1N2 Influenza A Virus Isolated from Pigs in Brazil.

    PubMed

    Schmidt, Candice; Cibulski, Samuel Paulo; Muterle Varela, Ana Paula; Mengue Scheffer, Camila; Wendlant, Adrieli; Quoos Mayer, Fabiana; Lopes de Almeida, Laura; Franco, Ana Cláudia; Roehe, Paulo Michel

    2014-12-18

    In this study, the full-genome sequence of a reassortant H1N2 swine influenza virus is reported. The isolate has the hemagglutinin (HA) and neuraminidase (NA) genes from human lineage (H1-δ cluster and N2), and the internal genes (polymerase basic 1 [PB1], polymerase basic 2 [PB2], polymerase acidic [PA], nucleoprotein [NP], matrix [M], and nonstructural [NS]) are derived from human 2009 pandemic H1N1 (H1N1pdm09) virus.

  16. NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

    PubMed

    Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

    2016-11-01

    For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs.

  17. Genome-wide association study for ham weight loss at first salting in Italian Large White pigs: towards the genetic dissection of a key trait for dry-cured ham production.

    PubMed

    Fontanesi, L; Schiavo, G; Gallo, M; Baiocco, C; Galimberti, G; Bovo, S; Russo, V; Buttazzoni, L

    2017-02-01

    Protected designation of origin dry-cured hams are the most important productions of the Italian heavy pig industry. Hams capable of minimal seasoning losses produce better quality dry-cured hams. Ham weight loss during the first 7 days in brine (first salting) is highly correlated with the total loss of weight up to the end of seasoning, and it has quite high heritability (0.30-0.61). For these reasons, ham weight loss at first salting has been included as a meat quality trait in the Italian heavy pig selection program. In this work, we carried out a genome-wide association study for this parameter in the Italian Large White pig breed by genotyping 1365 animals with the Illumina BeadChip PorcineSNP60 chip. A total of 44 single nucleotide polymorphisms (SNPs) had a Pnominal value below 5.0E-04, five of which were below 5.0E-05 and one of them (ALGA0057985 on chromosome 10) was associated with this trait at a PBonferroni threshold of 0.10. These SNPs identified a total of at least 29 putative QTLs that were located on most porcine autosomal chromosomes. This study provides genomic information that could be useful in dissecting this complex trait by identifying potential candidate genes whose function could contribute to understanding the biological mechanisms affecting meat quality for seasoning aptitude.

  18. Exome Capture with Heterologous Enrichment in Pig (Sus scrofa).

    PubMed

    Guiatti, Denis; Pomari, Elena; Radovic, Slobodanka; Spadotto, Alessandro; Stefanon, Bruno

    2015-01-01

    The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6% mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY® system confirms that this "human-on-pig" approach offers new potentiality for the identification of DNA variants in protein-coding genes.

  19. Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs.

    PubMed

    Li, Mingzhou; Jin, Long; Ma, Jideng; Tian, Shilin; Li, Ruiqiang; Li, Xuewei

    2016-01-01

    Selection in genomic regions is prevalent in mammals; however, the effects of selection on the mitogenome are not clearly understood. We determined the complete mitochondrial DNA (mtDNA) sequences from six wild Tibetan pigs from the Tibetan plateau and four domestic pig breeds from the lowland of neighboring southwest China. Nucleotide diversity analysis using the sliding window method showed that the nucleotide diversity of wild Tibetan pigs in most regions of the mitogenome was higher than that of domestic pigs. The 12 s ribosomal RNA showed relatively lower nucleotide diversity in Tibetan pigs, suggesting purifying selection of these genes during high-altitude adaptation. More non-synonymous nucleotide substitutions in the ATP6 were found in wild Tibetan pigs, indicating adaptive selection in Tibetan pigs. The results suggested distinct impacts of natural selection and artificial selection upon the mitogenome, especially the mitochondrial signatures of adaptive evolution in wild Tibetan pigs under natural selection.

  20. Pigs taking wing with transposons and recombinases

    PubMed Central

    Clark, Karl J; Carlson, Daniel F; Fahrenkrug, Scott C

    2007-01-01

    Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, including the addition of exogenous genetic material or manipulation of the endogenous genome, holds great promise for changing pig phenotypes for agricultural and medical applications. Although the first transgenic pigs were described in 1985, poor survival of manipulated embryos; inefficiencies in the integration, transmission, and expression of transgenes; and expensive husbandry costs have impeded the widespread application of pig genetic engineering. Sequencing of the pig genome and advances in reproductive technologies have rejuvenated efforts to apply transgenesis to swine. Pigs provide a compelling new resource for the directed production of pharmaceutical proteins and the provision of cells, vascular grafts, and organs for xenotransplantation. Additionally, given remarkable similarities in the physiology and size of people and pigs, swine will increasingly provide large animal models of human disease where rodent models are insufficient. We review the challenges facing pig transgenesis and discuss the utility of transposases and recombinases for enhancing the success and sophistication of pig genetic engineering. 'The paradise of my fancy is one where pigs have wings.' (GK Chesterton). PMID:18047690

  1. Precision engineering for PRRSV resistance in pigs: Macrophages from genome edited pigs lacking CD163 SRCR5 domain are fully resistant to both PRRSV genotypes while maintaining biological function.

    PubMed

    Burkard, Christine; Lillico, Simon G; Reid, Elizabeth; Jackson, Ben; Mileham, Alan J; Ait-Ali, Tahar; Whitelaw, C Bruce A; Archibald, Alan L

    2017-02-01

    Porcine Reproductive and Respiratory Syndrome (PRRS) is a panzootic infectious disease of pigs, causing major economic losses to the world-wide pig industry. PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 has been described as a fusion receptor for PRRSV, whereby the scavenger receptor cysteine-rich domain 5 (SRCR5) region was shown to be an interaction site for the virus in vitro. CD163 is expressed at high levels on the surface of macrophages, particularly in the respiratory system. Here we describe the application of CRISPR/Cas9 to pig zygotes, resulting in the generation of pigs with a deletion of Exon 7 of the CD163 gene, encoding SRCR5. Deletion of SRCR5 showed no adverse effects in pigs maintained under standard husbandry conditions with normal growth rates and complete blood counts observed. Pulmonary alveolar macrophages (PAMs) and peripheral blood monocytes (PBMCs) were isolated from the animals and assessed in vitro. Both PAMs and macrophages obtained from PBMCs by CSF1 stimulation (PMMs) show the characteristic differentiation and cell surface marker expression of macrophages of the respective origin. Expression and correct folding of the SRCR5 deletion CD163 on the surface of macrophages and biological activity of the protein as hemoglobin-haptoglobin scavenger was confirmed. Challenge of both PAMs and PMMs with PRRSV genotype 1, subtypes 1, 2, and 3 and PMMs with PRRSV genotype 2 showed complete resistance to viral infections assessed by replication. Confocal microscopy revealed the absence of replication structures in the SRCR5 CD163 deletion macrophages, indicating an inhibition of infection prior to gene expression, i.e. at entry/fusion or unpacking stages.

  2. Precision engineering for PRRSV resistance in pigs: Macrophages from genome edited pigs lacking CD163 SRCR5 domain are fully resistant to both PRRSV genotypes while maintaining biological function

    PubMed Central

    Jackson, Ben; Mileham, Alan J.; Ait-Ali, Tahar; Whitelaw, C. Bruce A.

    2017-01-01

    Porcine Reproductive and Respiratory Syndrome (PRRS) is a panzootic infectious disease of pigs, causing major economic losses to the world-wide pig industry. PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 has been described as a fusion receptor for PRRSV, whereby the scavenger receptor cysteine-rich domain 5 (SRCR5) region was shown to be an interaction site for the virus in vitro. CD163 is expressed at high levels on the surface of macrophages, particularly in the respiratory system. Here we describe the application of CRISPR/Cas9 to pig zygotes, resulting in the generation of pigs with a deletion of Exon 7 of the CD163 gene, encoding SRCR5. Deletion of SRCR5 showed no adverse effects in pigs maintained under standard husbandry conditions with normal growth rates and complete blood counts observed. Pulmonary alveolar macrophages (PAMs) and peripheral blood monocytes (PBMCs) were isolated from the animals and assessed in vitro. Both PAMs and macrophages obtained from PBMCs by CSF1 stimulation (PMMs) show the characteristic differentiation and cell surface marker expression of macrophages of the respective origin. Expression and correct folding of the SRCR5 deletion CD163 on the surface of macrophages and biological activity of the protein as hemoglobin-haptoglobin scavenger was confirmed. Challenge of both PAMs and PMMs with PRRSV genotype 1, subtypes 1, 2, and 3 and PMMs with PRRSV genotype 2 showed complete resistance to viral infections assessed by replication. Confocal microscopy revealed the absence of replication structures in the SRCR5 CD163 deletion macrophages, indicating an inhibition of infection prior to gene expression, i.e. at entry/fusion or unpacking stages. PMID:28231264

  3. Experimental evidence of hepatitis A virus infection in pigs.

    PubMed

    Song, Young-Jo; Park, Woo-Jung; Park, Byung-Joo; Kwak, Sang-Woo; Kim, Yong-Hyeon; Lee, Joong-Bok; Park, Seung-Yong; Song, Chang-Seon; Lee, Sang-Won; Seo, Kun-Ho; Kang, Young-Sun; Park, Choi-Kyu; Song, Jae-Young; Choi, In-Soo

    2016-04-01

    Hepatitis A virus (HAV) is the leading cause of acute viral hepatitis worldwide, with HAV infection being restricted to humans and nonhuman primates. In this study, HAV infection status was serologically determined in domestic pigs and experimental infections of HAV were attempted to verify HAV infectivity in pigs. Antibodies specific to HAV or HAV-like agents were detected in 3.5% of serum samples collected from pigs in swine farms. When the pigs were infected intravenously with 2 × 10(5) 50% tissue culture infectious dose (TCID50 ) of HAV, shedding of the virus in feces, viremia, and seroconversion were detected. In pigs orally infected with the same quantity of HAV, viral shedding was detected only in feces. HAV genomic RNA was detected in the liver and bile of intravenously infected pigs, but only in the bile of orally infected pigs. In further experiments, pigs were intravenously infected with 6 × 10(5) TCID50 of HAV. Shedding of HAV in feces, along with viremia and seroconversion, were confirmed in infected pigs but not in sentinel pigs. HAV genomic RNA was detected in the liver, bile, spleen, lymph node, and kidney of the infected pigs. HAV antigenomic RNA was detected in the spleen of one HAV-infected pig, suggesting HAV replication in splenic cells. Infiltration of inflammatory cells was observed in the livers of infected pigs but not in controls. This is the first experimental evidence to demonstrate that human HAV strains can infect pigs.

  4. Genetically modified pig models for human diseases.

    PubMed

    Fan, Nana; Lai, Liangxue

    2013-02-20

    Genetically modified animal models are important for understanding the pathogenesis of human disease and developing therapeutic strategies. Although genetically modified mice have been widely used to model human diseases, some of these mouse models do not replicate important disease symptoms or pathology. Pigs are more similar to humans than mice in anatomy, physiology, and genome. Thus, pigs are considered to be better animal models to mimic some human diseases. This review describes genetically modified pigs that have been used to model various diseases including neurological, cardiovascular, and diabetic disorders. We also discuss the development in gene modification technology that can facilitate the generation of transgenic pig models for human diseases.

  5. Genome-wide study refines the quantitative trait locus for number of ribs in a Large White × Minzhu intercross pig population and reveals a new candidate gene.

    PubMed

    Zhang, Long-Chao; Yue, Jing-Wei; Pu, Lei; Wang, Li-Gang; Liu, Xin; Liang, Jing; Yan, Hua; Zhao, Ke-Bin; Li, Na; Shi, Hui-Bi; Zhang, Yue-Bo; Wang, Li-Xian

    2016-10-01

    In China, sparerib is one of the most valuable parts of the pork carcass. As a result, candidate gene mining for number of ribs has become an interesting study focus. To examine the genetic basis for this major trait, we genotyped 596 individuals from an F2 Large White × Minzhu intercross pig population using the PorcineSNP60 Genotyping BeadChip. The genome-wide association study identified a locus for number of ribs in a 2.38-Mb region on Sus scrofa chromosome 7 (SSC7 of Sus scrofa genome assembly, Sscrofa10.2). We identified the top significant SNP ASGA0035536, which explained 16.51 % of the phenotypic variance. A previously reported candidate causal mutation (g.19034 A>C) in vertebrae development-associated gene VRTN explained 8.79 % of the phenotypic variation on number of ribs and had a much lower effect than ASGA0035536. Haplotype sharing analysis in F1 boars localized the rib number QTL to a 951-kb interval on SSC7. This interval encompassed 17 annotated genes in Sscrofa10.2, including the previously reported VRTN candidate gene. Of the 17 candidate genes, LTBP2, which encodes a latent transforming growth factor beta binding protein, was previously reported to indirectly regulate the activity of growth differentiation factor Gdf11, which has been shown to increase the number of ribs in knock-out mice. Thus, we propose LTBP2 as a good new candidate gene for number of ribs in the pig population. This finding advances our understanding of the genetic architecture of rib number in pigs.

  6. Drug Plan Coverage Rules

    MedlinePlus

    ... Medication Therapy Management programs Drug plan coverage rules , current page Using your drug plan for the first time Filling a prescription without your new plan card Costs for Medicare drug coverage Joining a health or ...

  7. Genetically modified pig models for neurodegenerative disorders.

    PubMed

    Holm, Ida E; Alstrup, Aage Kristian Olsen; Luo, Yonglun

    2016-01-01

    Increasing incidence of neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease has become one of the most challenging health issues in ageing humans. One approach to combat this is to generate genetically modified animal models of neurodegenerative disorders for studying pathogenesis, prognosis, diagnosis, treatment, and prevention. Owing to the genetic, anatomic, physiologic, pathologic, and neurologic similarities between pigs and humans, genetically modified pig models of neurodegenerative disorders have been attractive large animal models to bridge the gap of preclinical investigations between rodents and humans. In this review, we provide a neuroanatomical overview in pigs and summarize and discuss the generation of genetically modified pig models of neurodegenerative disorders including Alzheimer's diseases, Huntington's disease, Parkinson's disease, amyotrophic lateral sclerosis, spinal muscular atrophy, and ataxia-telangiectasia. We also highlight how non-invasive bioimaging technologies such as positron emission tomography (PET), computer tomography (CT), and magnetic resonance imaging (MRI), and behavioural testing have been applied to characterize neurodegenerative pig models. We further propose a multiplex genome editing and preterm recloning (MAP) approach by using the rapid growth of the ground-breaking precision genome editing technology CRISPR/Cas9 and somatic cell nuclear transfer (SCNT). With this approach, we hope to shorten the temporal requirement in generating multiple transgenic pigs, increase the survival rate of founder pigs, and generate genetically modified pigs that will more closely resemble the disease-causing mutations and recapitulate pathological features of human conditions.

  8. Identification of essential and non-essential genes of the guinea pig cytomegalovirus (GPCMV) genome via transposome mutagenesis of an infectious BAC clone.

    PubMed

    McGregor, Alistair; Liu, Fenyong; Schleiss, Mark R

    2004-05-01

    We report application of a transposition methodology that allows the easy characterization and mutation of genes encoded on an infectious bacterial artificial chromosome (BAC) clone. We characterized mutants generated by transposome (Tn) mutagenesis of a BAC clone of guinea pig cytomegalovirus (GPCMV). A pool of Tn mutant GPCMV BACs were screened initially by restriction profile analysis to verify they were full-length, and subsequently GPCMV BAC DNA from individual mutants was transfected onto guinea pig lung fibroblast cells in order to generate virus. Tn GPCMV BAC mutants were classed as either essential or non-essential gene insertions, depending upon their ability to regenerate viable, replication-competent virus. Representative mutants were more fully characterized. Analysis by sequencing the Tn insertion site on the mutated BACs, and by regeneration of virus using transfection of guinea pig fibroblasts (GPL), demonstrated that a recombinant with a Tn insertion in the UL35 homolog gene (GP35) was a non-essential gene for viral replication in tissue culture. A mutant with an insertion in the UL46 homolog (GP46) was nonviable, a phenotype which could be rescued by homologous recombination of BAC DNA with wild-type UL46 sequences, suggesting an essential role of this putative capsid gene in virus replication.

  9. Medicare Prescription Drug Coverage

    MedlinePlus

    ... people also have to pay an additional monthly cost. Private companies provide Medicare prescription drug coverage. You choose the drug plan you like best. Whether or not you should sign up depends on how good your current coverage is. You need to sign up as ...

  10. Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

    PubMed Central

    Knight, Daniel R.; Squire, Michele M.; Collins, Deirdre A.; Riley, Thomas V.

    2017-01-01

    Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large “open” pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3

  11. Prolactin Family of the Guinea Pig, Cavia porcellus

    PubMed Central

    Alam, S. M. Khorshed; Konno, Toshihiro; Rumi, M. A. Karim; Dong, Yafeng; Weiner, Carl P.; Soares, Michael J.

    2010-01-01

    Prolactin (PRL) is a multifunctional hormone with prominent roles in regulating growth and reproduction. The guinea pig (Cavia porcellus) has been extensively used in endocrine and reproduction research. Thus far, the PRL cDNA and protein have not been isolated from the guinea pig. In the present study, we used information derived from the public guinea pig genome database as a tool for identifying guinea pig PRL and PRL-related proteins. Guinea pig PRL exhibits prominent nucleotide and amino acid sequence differences when compared with PRLs of other eutherian mammals. In contrast, guinea pig GH is highly conserved. Expression of PRL and GH in the guinea pig is prominent in the anterior pituitary, similar to known expression patterns of PRL and GH for other species. Two additional guinea pig cDNAs were identified and termed PRL-related proteins (PRLRP1, PRLRP2). They exhibited a more distant relationship to PRL and their expression was restricted to the placenta. Recombinant guinea pig PRL protein was generated and shown to be biologically active in the PRL-responsive Nb2 lymphoma cell bioassay. In contrast, recombinant guinea pig PRLRP1 protein did not exhibit PRL-like bioactivity. In summary, we have developed a new set of research tools for investigating the biology of the PRL family in an important animal model, the guinea pig. PMID:20534723

  12. Women's Health Insurance Coverage

    MedlinePlus

    ... to be updated by the end of 2016. Abortion services are explicitly prohibited from being included as ... 25 states have laws banning coverage of most abortions from the plans available through the state Marketplaces, ...

  13. Identification and Complete Genome of Seneca Valley Virus in Vesicular Fluid and Sera of Pigs Affected with Idiopathic Vesicular Disease, Brazil.

    PubMed

    Vannucci, F A; Linhares, D C L; Barcellos, D E S N; Lam, H C; Collins, J; Marthaler, D

    2015-12-01

    Numerous, ongoing outbreaks in Brazilian swine herds have been characterized by vesicular lesions in sows and acute losses of neonatal piglets. The complete genome of Seneca Valley virus (SVV) was identified in vesicular fluid and sera of sows, providing evidence of association between SVV and vesicular disease and viraemia in affected animals.

  14. Pig lacks functional NLRC4 and NAIP genes.

    PubMed

    Sakuma, Chisato; Toki, Daisuke; Shinkai, Hiroki; Takenouchi, Takato; Sato, Mitsuru; Kitani, Hiroshi; Uenishi, Hirohide

    2017-02-01

    The NLRC4 inflammasome, which recognizes flagellin and components of the type III secretion system, plays an important role in the clearance of intracellular bacteria. Here, we examined the genomic sequences carrying two genes encoding key components of the NLRC4 inflammasome-NLR family, CARD-containing 4 (NLRC4), and NLR apoptosis inhibitory protein (NAIP)-in pigs. Pigs have a single locus encoding NLRC4 and NAIP. Comparison of the sequences thus obtained with the corresponding regions in humans revealed the deletion of intermediate exons in both pig genes. In addition, the genomic sequences of both pig genes lacked valid open reading frames encoding functional NLRC4 or NAIP protein. Additional pigs representing multiple breeds and wild boars also lacked the exons that we failed to find through genome sequencing. Furthermore, neither the NLRC4 nor the NAIP gene was expressed in pigs. These findings indicate that pigs lack the NLRC4 inflammasome, an important factor involved in monitoring bacterial proteins and contributing to the clearance of intracellular pathogens. These results also suggest that genetic polymorphisms affecting the molecular functions of TLR2, TLR4, TLR5, and other pattern recognition receptors associated with the recognition of bacteria have a more profound influence on disease resistance in pigs than in other species.

  15. Immunisation coverage, 2012.

    PubMed

    Hull, Brynley P; Dey, Aditi; Menzies, Rob I; Brotherton, Julia M; McIntyre, Peter B

    2014-09-30

    This, the 6th annual immunisation coverage report, documents trends during 2012 for a range of standard measures derived from Australian Childhood Immunisation Register (ACIR) data, and National Human Papillomavirus (HPV) Vaccination Program Register data. These include coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP) and coverage in adolescents and adults. The proportion of Australian children 'fully vaccinated' at 12, 24 and 60 months of age was 91.7%, 92.5% and 91.2%, respectively. For vaccines available on the NIP but not assessed during 2012 for 'fully vaccinated' status or for eligibility for incentive payments (rotavirus and pneumococcal at 12 months and meningococcal C and varicella at 24 months) coverage varied. Although pneumococcal vaccine had similar coverage at 12 months to other vaccines, coverage was lower for rotavirus at 12 months (83.6%) and varicella at 24 months (84.4%). Although 'fully vaccinated' coverage at 12 months of age was lower among Indigenous children than non-Indigenous children in all jurisdictions, the extent of the difference varied, reaching a 15 percentage point differential in South Australia but only a 0.4 percentage point differential in the Northern Territory. Overall, Indigenous coverage at 24 months of age exceeded that at 12 months of age nationally and for all jurisdictions, but as receipt of varicella vaccine at 18 months is excluded from calculations, this represents delayed immunisation, with some contribution from immunisation incentives. The 'fully vaccinated' coverage estimates for vaccinations due by 60 months of age for Indigenous children exceeded 90% at 91% in 2012. Unlike in 2011, at 60 months of age, there was no dramatic variation in coverage between Indigenous and non-Indigenous children for individual jurisdictions. As previously documented, vaccines recommended for Indigenous children only, hepatitis A and pneumococcal vaccine, had

  16. A GWAS of teat number in pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Number of functional teats is an important trait in commercial swine production. As litter size continues to increase, the number of teats must also increase to supply nutrition to all piglets. The pig displays considerable variation for number of teats; therefore, a genome-wide association (GWA) an...

  17. The search for coverage

    SciTech Connect

    Laseter, W.S.

    1993-06-01

    Anyone involved with the purchase or management of corporate liability insurance is familiar with the onerous pollution exclusions'' that accompany virtually all liability and property policies issued in recent years. As a result of these provisions, many businesses mistakenly presume their insurance program provides no coverage for environmental losses. Most companies, however, already own substantial sums of environmental coverage in the form of old comprehensive general liability (CGL) and first party, all risks'' property insurance policies issued before the introduction of pollution exclusions in the early 1970s. Unfortunately, due to records destruction policies, office moves, changes in ownership and other opportunities to lose files, most businesses have a difficult time reconstructing their past coverage.

  18. The Coverage Issue

    ERIC Educational Resources Information Center

    Yoshinobu, Stan; Jones, Matthew G.

    2012-01-01

    A significant issue mathematics instructors face is how to cover all the material. Mathematics teachers of all levels have some external and internal pressures to "get through" all the required material. The authors define "the coverage issue" to be the set of difficulties that arise in attempting to cover a lengthy list of topics. Principal among…

  19. Coverage That Counts.

    ERIC Educational Resources Information Center

    Moss, Nancy

    1990-01-01

    As the shrinking pool of applicants forces colleges to adapt new approaches to recruiting, media campaigns are emerging as an effective way to send key messages to target audiences. Media relations can lend credibility (news coverage is considered more credible than advertising); save money; reach targeted areas; and communicate key themes. (MLW)

  20. Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs

    PubMed Central

    Yang, Jie; Huang, Lusheng; Yang, Ming; Fan, Yin; Li, Lin; Fang, Shaoming; Deng, Wenjiang; Cui, Leilei; Zhang, Zhen; Ai, Huashui; Wu, Zhenfang; Gao, Jun; Ren, Jun

    2016-01-01

    Vertnin (VRTN) variants have been associated with the number of thoracic vertebrae in European pigs, but the association has not been evidenced in Chinese indigenous pigs. In this study, we first performed a genome-wide association study in Chinese Erhualian pigs using one VRTN candidate causative mutation and the Illumina Porcine 60K SNP Beadchips. The VRTN mutation is significantly associated with thoracic vertebral number in this population. We further show that the VRTN mutation has pleiotropic and desirable effects on teat number and carcass (body) length across four diverse populations, including Erhualian, White Duroc × Erhualian F2 population, Duroc and Landrace pigs. No association was observed between VRTN genotype and growth and fatness traits in these populations. Therefore, testing for the VRTN mutation in pig breeding schemes would not only increase the number of vertebrae and nipples, but also enlarge body size without undesirable effects on growth and fatness traits, consequently improving pork production. Further, by using whole-genome sequence data, we show that the VRTN mutation was possibly introgressed from Chinese pigs into European pigs. Our results provide another example showing that introgressed Chinese genes greatly contributed to the development and production of modern European pig breeds. PMID:26781738

  1. Aspects of coverage in medical DNA sequencing

    PubMed Central

    Wendl, Michael C; Wilson, Richard K

    2008-01-01

    Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations. Results We address the medical sequencing coverage problem via an extension of the standard mathematical theory of haploid coverage. The expected diploid multi-fold coverage, as well as its generalization for aneuploidy are derived and these expressions can be readily evaluated for any project. The resulting theory is used as a scaling law to calibrate performance to that of standard BAC sequencing at 8× to 10× redundancy, i.e. for expected coverages that exceed 99% of the unique sequence. A differential strategy is formalized for tumor/normal studies wherein tumor samples are sequenced more deeply than normal ones. In particular, both tumor alleles should be detected at least twice, while both normal alleles are detected at least once. Our theory predicts these requirements can be met for tumor and normal redundancies of approximately 26× and 21×, respectively. We explain why these values do not differ by a factor of 2, as might intuitively be expected. Future technology developments should prompt even deeper sequencing of tumors, but the 21× value for normal samples is essentially a constant. Conclusion Given the assumptions of standard coverage theory, our model gives pragmatic estimates for required redundancy. The differential strategy should be an efficient means of identifying potential somatic mutations for further study. PMID:18485222

  2. Integrating the USMARC genetic map for the pig with the pig physical map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A comprehensive genetic linkage map containing 3418 markers and spanning 2,326 cM of the autosomal genome was generated and integrated with the available physical maps for the pig. Marker types consisted of 1531 microsatellites and 1887 markers based on single feature polymorphisms, insertion/delet...

  3. Coverage Metrics for Model Checking

    NASA Technical Reports Server (NTRS)

    Penix, John; Visser, Willem; Norvig, Peter (Technical Monitor)

    2001-01-01

    When using model checking to verify programs in practice, it is not usually possible to achieve complete coverage of the system. In this position paper we describe ongoing research within the Automated Software Engineering group at NASA Ames on the use of test coverage metrics to measure partial coverage and provide heuristic guidance for program model checking. We are specifically interested in applying and developing coverage metrics for concurrent programs that might be used to support certification of next generation avionics software.

  4. Comparison of gene coverage of mouse oligonucleotide microarray platforms

    PubMed Central

    Verdugo, Ricardo A; Medrano, Juan F

    2006-01-01

    Background The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. Results A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis): Affymetrix430 2.0 (75.6%), ABI Genome Survey (81.24%), Agilent (79.33%), Codelink (78.09%), Sentrix (90.47%); and four array-ready oligosets: Sigma (47.95%), Operon v.3 (69.89%), Operon v.4 (84.03%), and MEEBO (84.03%). The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. Conclusion The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here reveals that the

  5. Increasing immunization coverage.

    PubMed

    Hammer, Lawrence D; Curry, Edward S; Harlor, Allen D; Laughlin, James J; Leeds, Andrea J; Lessin, Herschel R; Rodgers, Chadwick T; Granado-Villar, Deise C; Brown, Jeffrey M; Cotton, William H; Gaines, Beverly Marie Madry; Gambon, Thresia B; Gitterman, Benjamin A; Gorski, Peter A; Kraft, Colleen A; Marino, Ronald Vincent; Paz-Soldan, Gonzalo J; Zind, Barbara

    2010-06-01

    In 1977, the American Academy of Pediatrics issued a statement calling for universal immunization of all children for whom vaccines are not contraindicated. In 1995, the policy statement "Implementation of the Immunization Policy" was published by the American Academy of Pediatrics, followed in 2003 with publication of the first version of this statement, "Increasing Immunization Coverage." Since 2003, there have continued to be improvements in immunization coverage, with progress toward meeting the goals set forth in Healthy People 2010. Data from the 2007 National Immunization Survey showed that 90% of children 19 to 35 months of age have received recommended doses of each of the following vaccines: inactivated poliovirus (IPV), measles-mumps-rubella (MMR), varicella-zoster virus (VZB), hepatitis B virus (HBV), and Haemophilus influenzae type b (Hib). For diphtheria and tetanus and acellular pertussis (DTaP) vaccine, 84.5% have received the recommended 4 doses by 35 months of age. Nevertheless, the Healthy People 2010 goal of at least 80% coverage for the full series (at least 4 doses of DTaP, 3 doses of IPV, 1 dose of MMR, 3 doses of Hib, 3 doses of HBV, and 1 dose of varicella-zoster virus vaccine) has not yet been met, and immunization coverage of adolescents continues to lag behind the goals set forth in Healthy People 2010. Despite these encouraging data, a vast number of new challenges that threaten continued success toward the goal of universal immunization coverage have emerged. These challenges include an increase in new vaccines and new vaccine combinations as well as a significant number of vaccines currently under development; a dramatic increase in the acquisition cost of vaccines, coupled with a lack of adequate payment to practitioners to buy and administer vaccines; unanticipated manufacturing and delivery problems that have caused significant shortages of various vaccine products; and the rise of a public antivaccination movement that uses the

  6. After-hours coverage

    PubMed Central

    Bordman, Risa; Wheler, David; Drummond, Neil; White, David; Crighton, Eric

    2005-01-01

    OBJECTIVE To determine the prevalence and content of existing or developing policies and guidelines of medical associations and colleges regarding after-hours care by family physicians and general practitioners, especially legal requirements. DESIGN Telephone survey in fall 2002, updated in fall 2004. SETTING Canada. PARTICIPANTS All national and provincial medical associations, Colleges of Family Physicians, Colleges of Physicians and Surgeons, local government offices for the north, and the Canadian Medical Protective Association (CMPA). MAIN OUTCOME MEASURE Response to the question: “Does your agency have a policy in place regarding after-hours health care coverage by FPs/GPs, or are there active discussions regarding such a policy?” RESULTS The College of Physicians and Surgeons of British Columbia was the first to institute a policy, in 1995, requiring physicians to make “specific arrangements” for after-hours care of their patients. The College of Physicians and Surgeons of Alberta adopted a similar policy in 1996 along with a guideline to aid implementation. In 2002, the College of Physicians and Surgeons of Nova Scotia approved a guideline on the Availability of Physicians After Hours. The Saskatchewan Medical Association and the College of Physicians and Surgeons of Saskatchewan formulated a joint policy on medical practice coverage that was released in 2003. Many agencies actively discussed the topic. Provincial and national Colleges of Family Physicians did not have any policies in place. The CMPA does not generate guidelines but released in an information letter in May 2000 a section entitled “Reducing your risk when you’re not available.” CONCLUSION There is increasing interest Canada-wide in setting policy for after-hours care. While provincial Colleges of Physicians and Surgeons have traditionally led the way, a trend toward more collaboration between associations was identified. The effect of policy implementation on physicians

  7. Antenna Beam Coverage Concepts

    NASA Technical Reports Server (NTRS)

    Estabrook, Polly; Motamedi, Masoud

    1990-01-01

    The strawman Personal Access Satellite System (PASS) design calls for the use of a CONUS beam for transmission between the supplier and the satellite and for fixed beams for transmission between the basic personal terminal and the satellite. The satellite uses a 3 m main reflector for transmission at 20 GHz and a 2 m main reflector for reception at 30 GHz. There are several types of spot beams under consideration for the PASS system besides fixed beams. The beam pattern of a CONUS coverage switched beam is shown along with that of a scanning beam. A switched beam refers to one in which the signal from the satellite is connected alternatively to various feed horns. Scanning beams are taken to mean beams whose footprints are moved between contiguous regions in the beam's coverage area. The advantages and disadvantages of switched and/or scanning beams relative to fixed beams. The consequences of using switched/scanning in lieu of fixed beams in the PASS design and attempts are made to evaluate the listed advantages and disadvantages. Two uses of switched/scanning beams are examined. To illustrate the implications of switched beams use on PASS system design, operation at two beam scan rates is explored.

  8. Genetic differences in recombination frequency in the pig (Sus scrofa).

    PubMed

    Ollivier, L

    1995-10-01

    A comparison has been performed on 3 recently published linkage maps of the pig, hereafter designated as the American (A), European (E), and Swedish (S) maps. The cumulated distances between common markers in these 3 maps were in the ratio 1.00 (A):0.88 (E):0.77 (S), in keeping with the ratio of the percentages of domestic genome in the reference families used to build the corresponding maps, i.e., 1.00 (A):0.81 (E):0.50 (S). From further recombination frequencies reported in wild boars (in the S report), the wild pig genome length (in centimorgans) is expected to represent 66% of the domestic pig genome length. These observations tend to confirm a general result of Burt and Bell (Nature (London), 326: 803-805 (1987)), showing higher chiasma frequencies in domestic mammalian species compared with wild species. Consequences for mapping studies are discussed.

  9. Immunisation coverage annual report, 2009.

    PubMed

    Hull, Brynley; Dey, Aditi; Mahajan, Deepika; Menzies, Rob; McIntyre, Peter B

    2011-06-01

    This, the third annual immunisation coverage report, documents trends during 2009 for a range of standard measures derived from Australian Childhood Immunisation Register data, including overall coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). Coverage by Indigenous status and mapping by smaller geographic areas as well as trends in timeliness is also summarised according to standard templates. With respect to overall coverage, the Immunise Australia Program targets have been reached for children at 12 and 24 months of age but not for children at 5 years of age. Coverage at 24 months of age exceeds that at 12 months of age, but as receipt of varicella vaccine at 18 months is excluded from calculations of 'fully immunised' this probably represents delayed immunisation, with some contribution from immunisation incentives. Similarly, the decrease in coverage estimates for immunisations due at 4 years of age from March 2008 is primarily due to changing the assessment age from 6 years to 5 years of age from December 2007. With respect to individual vaccines, a number of those available on the NIP are not currently assessed for 'fully immunised' status or for eligibility for incentive payments. These include pneumococcal conjugate and meningococcal C conjugate vaccines, for which coverage is comparable with vaccines that are assessed for 'fully immunised' status, and rotavirus and varicella vaccines for which coverage is lower. Coverage is also suboptimal for vaccines recommended for Indigenous children only (i.e. hepatitis A and pneumococcal polysaccharide vaccine) as previously reported for other vaccines for both children and adults. Delayed receipt of vaccines is an important issue for vaccines recommended for Indigenous children and has not improved among non-Indigenous children despite improvements in coverage at the 24-month milestone. Although Indigenous children in Australia have coverage levels

  10. Pig in the Middle.

    ERIC Educational Resources Information Center

    Mills, Sophie

    2000-01-01

    Explores themes relating to human transition as they appear in "Charlotte's Web" and four other stories using pigs as a subject. Discusses the motifs common to all these texts that recur in the film "Babe." Considers how the cycle of life and death is ceaseless, and pigs symbolize the necessary transitions that people must all…

  11. Cysticercosis in the pig.

    PubMed

    de Aluja, A S

    2008-01-01

    Taenia solium cysticercosis is still an important parasitosis in rural pigs in many developing countries, México among them. The main causes for the persistence of this condition are lack of hygiene in the rural communities, lack of education of the animal owners, lack of control in the trade of pigs and their meat and lack of conscientious meat inspection. The pig production systems in the marginated areas of Mexico are briefly mentioned and it is stressed that among the important reasons for the persistence of the reproductive cycle of Taenia solium is the fact that appropriate toilet facilities in village dwellings are not mandatory. The diagnostic methods of cysticercosis in the living pigs and in their meat are discussed and the degenerative stages of the larvae as well as methods to test their viability are explained. The treatment of infected pigs and their meat is discussed. Recommendations for control programmes are given.

  12. A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans

    PubMed Central

    Romanenko, Svetlana A.; Perelman, Polina L.; Trifonov, Vladimir A.; Serdyukova, Natalia A.; Li, Tangliang; Fu, Beiyuan; O’Brien, Patricia C. M.; Ng, Bee L.; Nie, Wenhui; Liehr, Thomas; Stanyon, Roscoe; Graphodatsky, Alexander S.; Yang, Fengtang

    2015-01-01

    The domesticated guinea pig, Cavia porcellus (Hystricomorpha, Rodentia), is an important laboratory species and a model for a number of human diseases. Nevertheless, genomic tools for this species are lacking; even its karyotype is poorly characterized. The guinea pig belongs to Hystricomorpha, a widespread and important group of rodents; so far the chromosomes of guinea pigs have not been compared with that of other hystricomorph species or with any other mammals. We generated full sets of chromosome-specific painting probes for the guinea pig by flow sorting and microdissection, and for the first time, mapped the chromosomal homologies between guinea pig and human by reciprocal chromosome painting. Our data demonstrate that the guinea pig karyotype has undergone extensive rearrangements: 78 synteny-conserved human autosomal segments were delimited in the guinea pig genome. The high rate of genome evolution in the guinea pig may explain why the HSA7/16 and HSA16/19 associations presumed ancestral for eutherians and the three syntenic associations (HSA1/10, 3/19, and 9/11) considered ancestral for rodents were not found in C. porcellus. The comparative chromosome map presented here is a starting point for further development of physical and genetic maps of the guinea pig as well as an aid for genome assembly assignment to specific chromosomes. Furthermore, the comparative mapping will allow a transfer of gene map data from other species. The probes developed here provide a genomic toolkit, which will make the guinea pig a key species to unravel the evolutionary biology of the Hystricomorph rodents. PMID:26010445

  13. Serological and Molecular Investigation of Swine Hepatitis E Virus in Pigs Raised in Southern Italy.

    PubMed

    Costanzo, Nicola; Sarno, Eleonora; Peretti, Vincenzo; Ciambrone, Lucia; Casalinuovo, Francesco; Santoro, Adriano

    2015-11-01

    Hepatitis E virus (HEV) infection is a common acute hepatitis transmitted by the fecal-oral route. In developed countries, the virus has a zoonotic potential, and domestic pigs and wild boars are considered main reservoirs. To assess the prevalence of HEV-positive animals in the Calabria region (southern Italy) on a serological and molecular level, a total of 216 autochthonous healthy pigs (Apulo-Calabrese breed) were sampled. Both sera and feces were collected. Pigs were grouped based on age: 117 pigs <6 months and 99 pigs >6 months. By using a commercial enzyme-linked immunosorbent assay system, a total of 173 (80%) of the 216 pigs tested seropositive. In all sampled farms (n = 8), pigs with antibodies (immunoglobulin G) against HEV were detected at a level higher than 60%, with a significant difference among age groups (P < 0.0001). Moreover, 16 fattening pigs were found to be nested reverse transcription PCR positive and thus to shed viral genomes in their feces. These positive findings resulted in a prevalence of 48.4% on the farm level (16 of 35 pigs) and an overall prevalence of 7.4% at the animal level (16 of 216 pigs). Based on the present study, HEV seems to circulate among the autochthonous domestic pig population of southern Italy with a low sharing rate. Further studies exploring the origin of infection are needed to minimize the risk of human exposure and to reduce consequences for public health.

  14. Effective coverage: a metric for monitoring Universal Health Coverage.

    PubMed

    Ng, Marie; Fullman, Nancy; Dieleman, Joseph L; Flaxman, Abraham D; Murray, Christopher J L; Lim, Stephen S

    2014-09-01

    A major challenge in monitoring universal health coverage (UHC) is identifying an indicator that can adequately capture the multiple components underlying the UHC initiative. Effective coverage, which unites individual and intervention characteristics into a single metric, offers a direct and flexible means to measure health system performance at different levels. We view effective coverage as a relevant and actionable metric for tracking progress towards achieving UHC. In this paper, we review the concept of effective coverage and delineate the three components of the metric - need, use, and quality - using several examples. Further, we explain how the metric can be used for monitoring interventions at both local and global levels. We also discuss the ways that current health information systems can support generating estimates of effective coverage. We conclude by recognizing some of the challenges associated with producing estimates of effective coverage. Despite these challenges, effective coverage is a powerful metric that can provide a more nuanced understanding of whether, and how well, a health system is delivering services to its populations.

  15. Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family

    PubMed Central

    2008-01-01

    Background The first step of GPI anchor biosynthesis is catalyzed by PIG-A, an enzyme that transfers N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol. This protein is present in all eukaryotic organisms ranging from protozoa to higher mammals, as part of a larger complex of five to six 'accessory' proteins whose individual roles in the glycosyltransferase reaction are as yet unclear. The PIG-A gene has been shown to be an essential gene in various eukaryotes. In humans, mutations in the protein have been associated with paroxysomal noctural hemoglobuinuria. The corresponding PIG-A gene has also been recently identified in the genome of many archaeabacteria although genes of the accessory proteins have not been discovered in them. The present study explores the evolution of PIG-A and the phylogenetic relationship between this protein and other glycosyltransferases. Results In this paper we show that out of the twelve conserved motifs identified by us eleven are exclusively present in PIG-A and, therefore, can be used as markers to identify PIG-A from newly sequenced genomes. Three of these motifs are absent in the primitive eukaryote, G. lamblia. Sequence analyses show that seven of these conserved motifs are present in prokaryote and archaeal counterparts in rudimentary forms and can be used to differentiate PIG-A proteins from glycosyltransferases. Using partial least square regression analysis and data involving presence or absence of motifs in a range of PIG-A and glycosyltransferases we show that (i) PIG-A may have evolved from prokaryotic glycosyltransferases and lipopolysaccharide synthases, members of the GT4 family of glycosyltransferases and (ii) it is possible to uniquely classify PIG-A proteins versus glycosyltransferases. Conclusion Besides identifying unique motifs and showing that PIG-A protein from G. lamblia and some putative PIG-A proteins from archaebacteria are evolutionarily closer to glycosyltransferases, these studies

  16. Enterobacter cloacae inhibits human norovirus infectivity in gnotobiotic pigs

    PubMed Central

    Lei, Shaohua; Samuel, Helen; Twitchell, Erica; Bui, Tammy; Ramesh, Ashwin; Wen, Ke; Weiss, Mariah; Li, Guohua; Yang, Xingdong; Jiang, Xi; Yuan, Lijuan

    2016-01-01

    Human noroviruses (HuNoVs) are the leading cause of epidemic gastroenteritis worldwide. Study of HuNoV biology has been hampered by the lack of an efficient cell culture system. Recently, enteric commensal bacteria Enterobacter cloacae has been recognized as a helper in HuNoV infection of B cells in vitro. To test the influences of E. cloacae on HuNoV infectivity and to determine whether HuNoV infects B cells in vivo, we colonized gnotobiotic pigs with E. cloacae and inoculated pigs with 2.74 × 104 genome copies of HuNoV. Compared to control pigs, reduced HuNoV shedding was observed in E. cloacae colonized pigs, characterized by significantly shorter duration of shedding in post-inoculation day 10 subgroup and lower cumulative shedding and peak shedding in individual pigs. Colonization of E. cloacae also reduced HuNoV titers in intestinal tissues and in blood. In both control and E. cloacae colonized pigs, HuNoV infection of enterocytes was confirmed, however infection of B cells was not observed in ileum, and the entire lamina propria in sections of duodenum, jejunum, and ileum were HuNoV-negative. In summary, E. cloacae inhibited HuNoV infectivity, and B cells were not a target cell type for HuNoV in gnotobiotic pigs, with or without E. cloacae colonization. PMID:27113278

  17. Enterobacter cloacae inhibits human norovirus infectivity in gnotobiotic pigs.

    PubMed

    Lei, Shaohua; Samuel, Helen; Twitchell, Erica; Bui, Tammy; Ramesh, Ashwin; Wen, Ke; Weiss, Mariah; Li, Guohua; Yang, Xingdong; Jiang, Xi; Yuan, Lijuan

    2016-04-26

    Human noroviruses (HuNoVs) are the leading cause of epidemic gastroenteritis worldwide. Study of HuNoV biology has been hampered by the lack of an efficient cell culture system. Recently, enteric commensal bacteria Enterobacter cloacae has been recognized as a helper in HuNoV infection of B cells in vitro. To test the influences of E. cloacae on HuNoV infectivity and to determine whether HuNoV infects B cells in vivo, we colonized gnotobiotic pigs with E. cloacae and inoculated pigs with 2.74 × 10(4) genome copies of HuNoV. Compared to control pigs, reduced HuNoV shedding was observed in E. cloacae colonized pigs, characterized by significantly shorter duration of shedding in post-inoculation day 10 subgroup and lower cumulative shedding and peak shedding in individual pigs. Colonization of E. cloacae also reduced HuNoV titers in intestinal tissues and in blood. In both control and E. cloacae colonized pigs, HuNoV infection of enterocytes was confirmed, however infection of B cells was not observed in ileum, and the entire lamina propria in sections of duodenum, jejunum, and ileum were HuNoV-negative. In summary, E. cloacae inhibited HuNoV infectivity, and B cells were not a target cell type for HuNoV in gnotobiotic pigs, with or without E. cloacae colonization.

  18. Vaccination coverage rates for 1986.

    PubMed

    1987-10-01

    This article sets forth data on vaccination coverage rates in children under 1 year of age in the individual countries of Latin America and the Caribbean in 1986. In the Region of the Americas as a whole, the 1986 coverage rate was 80% for oral poliovaccine, 54% for DPT, 55% for measles, and 63% for BCG. Vaccination coverage rates increased over 1985 levels for all but measles, which showed a 5% decline due to decreases in Brazil and Mexico. In the Caribbean subregion, the majority of country coverage rates for DPT and oral poliovirus vaccine are equal to or above 80%, while measles coverage rates are generally below 50%. In Central America, vaccine coverage rates with all antigens except BCG showed significant increases between 1985 and 1986. In Central America, coverage ranged from above 80% for oral poliovirus vaccine and DPT in Belize, Costa Rica, and Nicaragua, to below 40% in Guatemala. In general, countries in the region are improving vaccination performance as a result of establishment of vaccination days or campaigns and acceleration of the Expanded Program on Immunization. However, much work remains to be done if the goal of 100% immunization of children and women of childbearing age by 1990 is to be met.

  19. Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20.

    PubMed

    Gertz, E Michael; Schäffer, Alejandro A; Agarwala, Richa; Bonnet-Garnier, Amélie; Rogel-Gaillard, Claire; Hayes, Hélène; Mage, Rose G

    2013-10-01

    We report on the analyses of genes encoding immunoglobulin heavy and light chains in the rabbit 6.51× whole genome assembly. This OryCun2.0 assembly confirms previous mapping of the duplicated IGK1 and IGK2 loci to chromosome 2 and the IGL lambda light chain locus to chromosome 21. The most frequently rearranged and expressed IGHV1 that is closest to IG DH and IGHJ genes encodes rabbit VHa allotypes. The partially inbred Thorbecke strain rabbit used for whole-genome sequencing was homozygous at the IGK but heterozygous with the IGHV1a1 allele in one of 79 IGHV-containing unplaced scaffolds and IGHV1a2, IGHM, IGHG, and IGHE sequences in another. Some IGKV, IGLV, and IGHA genes are also in other unplaced scaffolds. By fluorescence in situ hybridization, we assigned the previously unmapped IGH locus to the q-telomeric region of rabbit chromosome 20. An approximately 3-Mb segment of human chromosome 14 including IGH genes predicted to map to this telomeric region based on synteny analysis could not be located on assembled chromosome 20. Unplaced scaffold chrUn0053 contains some of the genes that comparative mapping predicts to be missing. We identified discrepancies between previous targeted studies and the OryCun2.0 assembly and some new BAC clones with IGH sequences that can guide other studies to further sequence and improve the OryCun2.0 assembly. Complete knowledge of gene sequences encoding variable regions of rabbit heavy, kappa, and lambda chains will lead to better understanding of how and why rabbits produce antibodies of high specificity and affinity through gene conversion and somatic hypermutation.

  20. Your Medicare Coverage: Durable Medical Equipment (DME) Coverage

    MedlinePlus

    ... Search Medicare.gov for covered items Durable medical equipment (DME) coverage How often is it covered? Medicare ... B (Medical Insurance) covers medically necessary durable medical equipment (DME) that your doctor prescribes for use in ...

  1. Experimental pig-to-pig transmission dynamics for African swine fever virus, Georgia 2007/1 strain.

    PubMed

    Guinat, C; Gubbins, S; Vergne, T; Gonzales, J L; Dixon, L; Pfeiffer, D U

    2016-01-01

    African swine fever virus (ASFV) continues to cause outbreaks in domestic pigs and wild boar in Eastern European countries. To gain insights into its transmission dynamics, we estimated the pig-to-pig basic reproduction number (R 0) for the Georgia 2007/1 ASFV strain using a stochastic susceptible-exposed-infectious-recovered (SEIR) model with parameters estimated from transmission experiments. Models showed that R 0 is 2·8 [95% confidence interval (CI) 1·3-4·8] within a pen and 1·4 (95% CI 0·6-2·4) between pens. The results furthermore suggest that ASFV genome detection in oronasal samples is an effective diagnostic tool for early detection of infection. This study provides quantitative information on transmission parameters for ASFV in domestic pigs, which are required to more effectively assess the potential impact of strategies for the control of between-farm epidemic spread in European countries.

  2. Annual immunisation coverage report, 2010.

    PubMed

    Hull, Brynley; Dey, Aditi; Menzies, Rob; McIntyre, Peter

    2013-03-31

    This, the fourth annual immunisation coverage report, documents trends during 2010 for a range of standard measures derived from Australian Childhood Immunisation Register (ACIR) data. These include coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). For the first time, coverage from other sources for adolescents and the elderly are included. The proportion of children 'fully vaccinated' at 12, 24 and 60 months of age was 91.6%, 92.1% and 89.1% respectively. For vaccines available on the NIP but not currently assessed for 'fully immunised' status or for eligibility for incentive payments (rotavirus and pneumococcal at 12 months and meningococcal C and varicella at 24 months) coverage varied. Although pneumococcal vaccine had similar coverage at 12 months to other vaccines, coverage was lower for rotavirus at 12 months (84.7%) and varicella at 24 months (83.0%). Overall coverage at 24 months of age exceeded that at 12 months of age nationally and for most jurisdictions, but as receipt of varicella vaccine at 18 months is excluded from calculations, this represents delayed immunisation, with some contribution from immunisation incentives. The 'fully immunised' coverage estimates for immunisations due by 60 months increased substantially in 2009, reaching almost 90% in 2010, probably related to completed immunisation by 60 months of age being introduced in 2009 as a requirement for GP incentive payments. As previously documented, vaccines recommended for Indigenous children only (hepatitis A and pneumococcal polysaccharide vaccine) had suboptimal coverage at around 57%. Delayed receipt of vaccines by Indigenous children at the 60-month milestone age improved from 56% to 62% but the disparity in on-time vaccination between Indigenous and non-Indigenous children at earlier age milestones did not improve. Coverage data for human papillomavirus (HPV)from the national HPV register are consistent with high

  3. Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

    PubMed Central

    Bosse, Mirte; Lopes, Marcos S.; Madsen, Ole; Megens, Hendrik-Jan; Crooijmans, Richard P. M. A.; Frantz, Laurent A. F.; Harlizius, Barbara; Bastiaansen, John W. M.; Groenen, Martien A. M.

    2015-01-01

    Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs. PMID:26702043

  4. Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.

    PubMed

    Bosse, Mirte; Lopes, Marcos S; Madsen, Ole; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Frantz, Laurent A F; Harlizius, Barbara; Bastiaansen, John W M; Groenen, Martien A M

    2015-12-22

    Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.

  5. Immunisation coverage annual report, 2008.

    PubMed

    Hull, Brynley P; Mahajan, Deepika; Dey, Aditi; Menzies, Rob I; McIntyre, Peter B

    2010-09-01

    This, the 2nd annual immunisation coverage report, documents trends during 2008 for a range of standard measures derived from Australian Childhood Immunisation Register data, including overall coverage at standard age milestones and for individual vaccines included on the National Immunisation Program (NIP). Coverage by indigenous status and mapping by smaller geographic areas as well as trends in timeliness are also summarised according to standard templates. With respect to overall coverage, Immunise Australia Program targets have been reached for children at 12 and 24 months of age but not for children at 5 years of age. Coverage at 24 months of age exceeds that at 12 months of age, but as receipt of varicella vaccine at 18 months is excluded from calculations of 'fully immunised' this probably represents delayed immunisation, with some contribution from immunisation incentives. Similarly, the decrease in coverage estimates for immunisations due at 4 years of age from March 2008, is primarily due to changing the assessment age from 6 years to 5 years of age from December 2007. A number of individual vaccines on the NIP are not currently assessed for 'fully immunised' status or for eligibility for incentive payments. These include pneumococcal conjugate and meningococcal C conjugate vaccines for which coverage is comparable to vaccines which are assessed for 'fully immunised' status, and rotavirus and varicella vaccines for which coverage is lower. Coverage is also suboptimal for vaccines recommended for Indigenous children only (i.e. hepatitis A and pneumococcal polysaccharide vaccine) as previously reported for other vaccines for both children and adults. Delayed receipt of vaccines is an important issue for vaccines recommended for Indigenous children and has not improved among non-Indigenous children despite improvements in coverage at the 24-month milestone. Although Indigenous children in Australia have coverage levels that are similar to non

  6. Medicare coverage for oncology services.

    PubMed

    Bagley, G P; McVearry, K

    1998-05-15

    Medicare's mission is to assure health care security for our beneficiaries. Title XVIII of the Social Security Act (the Act) provides the Health Care Financing Administration (HCFA) with the authority to fulfill this mission. Although Medicare is considered a defined benefit program, the Act vested Medicare with the discretionary authority to make specific policy decisions when necessary. HCFA's discretionary authority, which is found at section 1862(a)(1)(A) of the Act, enables HCFA to provide coverage for services that are reasonable and necessary for the treatment and diagnosis of illness or injury or to improve the functioning of a malformed body member. To determine whether a service is reasonable and necessary, HCFA relies on authoritative evidence. This evidence includes, but is not limited to, approvals from appropriate federal agencies, such as the Food and Drug Administration, and systematic evaluations of scientific literature via technology assessments. HCFA also may decide that a service warrants a unique type of coverage policy, which is referred to as coverage with conditions. This form of coverage is a middle ground between strict noncoverage and general coverage for a medical service that appears promising, but still is evolving. All these policy specifications effect Medicare coverage of oncology services. This means that reasonable and necessary diagnostic and therapeutic cancer-related services that are not otherwise prohibited by Medicare's statute, regulations, and manual instructions are covered and paid for by the program. Prior to the Balanced Budget Act of 1997 (BBA '97), Medicare provided coverage for some beneficiaries to undergo mammography and Papanicolaou smear screening. As a result of BBA '97, Congress has mandated expanding coverage for these services as well as adding coverage for pelvic examinations, prostate cancer screening, colorectal screening, and antiemetic drugs used as part of an anticancer chemotherapy regimen. Other

  7. Pig production in the Solomon Islands. I. Village pig production.

    PubMed

    de Fredrick, D F

    1977-05-01

    In 181 villages in the Solomon Islands the pig: human ratio was 1:5-8 and the annual per capita pork consumption was 4-2 kg. Some communities did not keep pigs or eat pig meat. Sows weaned an average of 5-5 piglets per year and mean liveweight at 12 months of age was 28-4 kg. Most pigs were kept on the ground but some were housed in pens over the sea and very few lived in their owner's houses. Pigs were important in the social life of the people but proportionally fewer pigs were raised than in neighbouring Pacific countries.

  8. Global Routine Vaccination Coverage, 2015.

    PubMed

    Casey, Rebecca M; Dumolard, Laure; Danovaro-Holliday, M Carolina; Gacic-Dobo, Marta; Diallo, Mamadou S; Hampton, Lee M; Wallace, Aaron S

    2016-11-18

    In 1974, the World Health Organization (WHO) established the Expanded Program on Immunization* to provide protection against six vaccine-preventable diseases through routine infant immunization (1). Based on 2015 WHO and United Nations Children's Fund (UNICEF) estimates, global coverage with the third dose of diphtheria-tetanus-pertussis vaccine (DTP3), the first dose of measles-containing vaccine (MCV1) and the third dose of polio vaccine (Pol3) has remained stable (84%-86%) since 2010. From 2014 to 2015, estimated global coverage with the second MCV dose (MCV2) increased from 39% to 43% by the end of the second year of life and from 58% to 61% when older age groups were included. Global coverage was higher in 2015 than 2010 for newer or underused vaccines, including rotavirus vaccine, pneumococcal conjugate vaccine (PCV), rubella vaccine, Haemophilus influenzae type b (Hib) vaccine, and 3 doses of hepatitis B (HepB3) vaccine. Coverage estimates varied widely by WHO Region, country, and district; in addition, for the vaccines evaluated (MCV, DTP3, Pol3, HepB3, Hib3), wide disparities were found in coverage by country income classification. Improvements in equity of access are necessary to reach and sustain higher coverage and increase protection from vaccine-preventable diseases for all persons.

  9. Genetically Engineered Pig Models for Human Diseases

    PubMed Central

    Prather, Randall S.; Lorson, Monique; Ross, Jason W.; Whyte, Jeffrey J.; Walters, Eric

    2015-01-01

    Although pigs are used widely as models of human disease, their utility as models has been enhanced by genetic engineering. Initially, transgenes were added randomly to the genome, but with the application of homologous recombination, zinc finger nucleases, and transcription activator-like effector nuclease (TALEN) technologies, now most any genetic change that can be envisioned can be completed. To date these genetic modifications have resulted in animals that have the potential to provide new insights into human diseases for which a good animal model did not exist previously. These new animal models should provide the preclinical data for treatments that are developed for diseases such as Alzheimer's disease, cystic fibrosis, retinitis pigmentosa, spinal muscular atrophy, diabetes, and organ failure. These new models will help to uncover aspects and treatments of these diseases that were otherwise unattainable. The focus of this review is to describe genetically engineered pigs that have resulted in models of human diseases. PMID:25387017

  10. A panel of VNTR markers in pigs.

    PubMed

    Signer, E N; Gu, F; Jeffreys, A J

    1996-06-01

    By cloning tandemly repeated sequences from the pig genome by use of non-porcine minisatellite probes for library screening, five novel polymorphic VNTR loci were isolated: three minisatellites and two satellite-like loci. Four of them could be mapped onto chromosomes by linkage analysis and/or in situ hybridization. They were assigned to Chromosomes (Chrs) 5, 6, 14, and 16. Physical mapping on both presumed satellites and on one of the minisatellites revealed that the former resided near or at the centromere and the latter towards the chromosome ends. The location of the minisatellite is of particular interest since, together with data on three other minisatellites previously isolated, it supports the idea that, as in humans, minisatellites may preferentially be subtelomeric also in pigs.

  11. Mycotoxic nephropathy in pigs*

    PubMed Central

    Elling, F.; Møller, T.

    1973-01-01

    In Denmark a nephropathy in pigs characterized by tubular atrophy and interstitial fibrosis has been identified frequently during the last 5 decades in the course of meat inspection in slaughterhouses. The disease was first described by Larsen, who recognized the connexion between feeding mouldy rye to pigs and the development of the nephropathy. In this study kidneys were examined from 19 pigs coming from a farm with an outbreak of nephropathy. The barley fed to the pigs was contaminated with the mycotoxin ochratoxin A. Histological examination revealed different degrees of change ranging from slight regressive changes in the tubular epithelium and periglomerular and interstitial fibrosis to tubular atrophy, thickened basement membranes, glomerular sclerosis, and marked fibrosis. These differences were considered to be due to differences in the length of time of exposure to the mouldy barley and differences in the amount of mycotoxin consumed by the individual pig. However, it will be necessary to carry out experiments using crystalline ochratoxin A in order to prove such a relationship. Mycotoxins have also been suggested as etiological factors in Balkan nephropathy in man, which in the initial stages is characterized by tubular lesions similar to those seen in mycotoxic nephropathy in pigs. ImagesFig. 1Fig. 2Fig. 7Fig. 8Fig. 9Fig. 3Fig. 4Fig. 5Fig. 6Fig. 10Fig. 11 PMID:4546872

  12. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions fr...

  13. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The availability of a high-density SNP chip and a reference genome sequence of the pig have enabled the construction of a high-density linkage map. A high density linkage map is an essential tool for the further fine-mapping of QTL for a variety of traits in the pig and for a better und...

  14. Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces.

    PubMed

    Ma, Liping; Xia, Yu; Li, Bing; Yang, Ying; Li, Li-Guan; Tiedje, James M; Zhang, Tong

    2016-01-05

    The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.

  15. Use of a Guinea Pig-Specific Transcriptome Array for Evaluation of Protective Immunity against Genital Chlamydial Infection following Intranasal Vaccination in Guinea Pigs.

    DTIC Science & Technology

    2014-12-11

    2008) Guinea pig model of Mycobacterium tuberculosis latent/dormant infection . Microbes and Infection 10: 1469–1476. 54. Smith DW, Balasubramanian V...RESEARCH ARTICLE Use of a Guinea Pig-Specific Transcriptome Array for Evaluation of Protective Immunity against Genital Chlamydial Infection ...Center for Emerging Infectious Diseases and Center of Excellence in Infection Genomics, University of Texas at San Antonio, One UTSA Circle, San Antonio

  16. Immunogenomics for identification of disease resistance genes in pigs: a review focusing on Gram-negative bacilli

    PubMed Central

    2012-01-01

    Over the past years, infectious disease has caused enormous economic loss in pig industry. Among the pathogens, gram negative bacteria not only cause inflammation, but also cause different diseases and make the pigs more susceptible to virus infection. Vaccination, medication and elimination of sick pigs are major strategies of controlling disease. Genetic methods, such as selection of disease resistance in the pig, have not been widely used. Recently, the completion of the porcine whole genome sequencing has provided powerful tools to identify the genome regions that harboring genes controlling disease or immunity. Immunogenomics, which combines DNA variations, transcriptome, immune response, and QTL mapping data to illustrate the interactions between pathogen and host immune system, will be an effective genomics tool for identification of disease resistance genes in pigs. These genes will be potential targets for disease resistance in breeding programs. This paper reviewed the progress of disease resistance study in the pig focusing on Gram-negative bacilli. Major porcine Gram-negative bacilli and diseases, suggested candidate genes/pathways against porcine Gram-negative bacilli, and distributions of QTLs for immune capacity on pig chromosomes were summarized. Some tools for immunogenomics research were described. We conclude that integration of sequencing, whole genome associations, functional genomics studies, and immune response information is necessary to illustrate molecular mechanisms and key genes in disease resistance. PMID:23137309

  17. Immunisation coverage annual report, 2011.

    PubMed

    Hull, Brynley P; Dey, Aditi; Menzies, Rob I; Brotherton, Julia M; McIntyre, Peter B

    2013-12-31

    This, the 5th annual immunisation coverage report, documents trends during 2011 for a range of standard measures derived from Australian Childhood Immunisation Register data, and National Human Papillomavirus (HPV) Vaccination Program Register data. The proportion of children 'fully vaccinated' at 12, 24 and 60 months of age was 91.4%, 92.2% and 89.5% respectively. Although pneumococcal vaccine had similar coverage at 12 months to other vaccines, coverage was lower for rotavirus at 12 months (83.8%) and varicella at 24 months (83.9%). By late 2011, the percentage of children who received the 1st dose of DTPa vaccine dose at less than 8 weeks of age was greater than 50% in 3 jurisdictions, the Australian Capital Territory, Victoria, and Queensland and at 70% for New South Wales and Tasmania. Although coverage at 12 months of age was lower among Indigenous children than non-Indigenous children in all jurisdictions, the extent of the difference varied. Overall, coverage at 24 months of age exceeded that at 12 months of age nationally. At 60 months of age, there was dramatic variation between individual jurisdictions, ranging from coverage 8% lower in Indigenous children in South Australia to 6% higher in the Northern Territory. As previously documented, vaccines recommended for Indigenous children only (hepatitis A and pneumococcal polysaccharide vaccine) had suboptimal coverage at 60% and 68%, respectively. On-time receipt (before 49 months of age) of vaccines by Indigenous children at the 60-month milestone age improved between 2010 (18%) and 2011 (19%) but the disparity in on-time vaccination between Indigenous and non-Indigenous children increased at all 3 age milestones. The percentage of vaccine objectors in 2011 (1.7%) has increased from 2007 when it was 1.1%. Coverage data for the 3rd dose of HPV from the national HPV register in the school catch up program was 71% but was substantially lower for the catch-up program for women outside school (39

  18. Advances in Swine Biomedical Model Genomics

    PubMed Central

    Lunney, Joan K.

    2007-01-01

    This review is a short update on the diversity of swine biomedical models and the importance of genomics in their continued development. The swine has been used as a major mammalian model for human studies because of the similarity in size and physiology, and in organ development and disease progression. The pig model allows for deliberately timed studies, imaging of internal vessels and organs using standard human technologies, and collection of repeated peripheral samples and, at kill, detailed mucosal tissues. The ability to use pigs from the same litter, or cloned or transgenic pigs, facilitates comparative analyses and genetic mapping. The availability of numerous well defined cell lines, representing a broad range of tissues, further facilitates testing of gene expression, drug susceptibility, etc. Thus the pig is an excellent biomedical model for humans. For genomic applications it is an asset that the pig genome has high sequence and chromosome structure homology with humans. With the swine genome sequence now well advanced there are improving genetic and proteomic tools for these comparative analyses. The review will discuss some of the genomic approaches used to probe these models. The review will highlight genomic studies of melanoma and of infectious disease resistance, discussing issues to consider in designing such studies. It will end with a short discussion of the potential for genomic approaches to develop new alternatives for control of the most economically important disease of pigs, porcine reproductive and respiratory syndrome (PRRS), and the potential for applying knowledge gained with this virus for human viral infectious disease studies. PMID:17384736

  19. 24 CFR 203.205 - Plan coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Plan coverage. 203.205 Section 203... Protection Plans (plan) § 203.205 Plan coverage. (a) Plan coverage must take effect at closing or settlement following the initial sale of the property to the homeowner. (b) During the first year of coverage, a...

  20. 24 CFR 203.205 - Plan coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 2 2014-04-01 2014-04-01 false Plan coverage. 203.205 Section 203... Protection Plans (plan) § 203.205 Plan coverage. (a) Plan coverage must take effect at closing or settlement following the initial sale of the property to the homeowner. (b) During the first year of coverage, a...

  1. 24 CFR 203.205 - Plan coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Plan coverage. 203.205 Section 203... Protection Plans (plan) § 203.205 Plan coverage. (a) Plan coverage must take effect at closing or settlement following the initial sale of the property to the homeowner. (b) During the first year of coverage, a...

  2. Monitoring intervention coverage in the context of universal health coverage.

    PubMed

    Boerma, Ties; AbouZahr, Carla; Evans, David; Evans, Tim

    2014-09-01

    Monitoring universal health coverage (UHC) focuses on information on health intervention coverage and financial protection. This paper addresses monitoring intervention coverage, related to the full spectrum of UHC, including health promotion and disease prevention, treatment, rehabilitation, and palliation. A comprehensive core set of indicators most relevant to the country situation should be monitored on a regular basis as part of health progress and systems performance assessment for all countries. UHC monitoring should be embedded in a broad results framework for the country health system, but focus on indicators related to the coverage of interventions that most directly reflect the results of UHC investments and strategies in each country. A set of tracer coverage indicators can be selected, divided into two groups-promotion/prevention, and treatment/care-as illustrated in this paper. Disaggregation of the indicators by the main equity stratifiers is critical to monitor progress in all population groups. Targets need to be set in accordance with baselines, historical rate of progress, and measurement considerations. Critical measurement gaps also exist, especially for treatment indicators, covering issues such as mental health, injuries, chronic conditions, surgical interventions, rehabilitation, and palliation. Consequently, further research and proxy indicators need to be used in the interim. Ideally, indicators should include a quality of intervention dimension. For some interventions, use of a single indicator is feasible, such as management of hypertension; but in many areas additional indicators are needed to capture quality of service provision. The monitoring of UHC has significant implications for health information systems. Major data gaps will need to be filled. At a minimum, countries will need to administer regular household health surveys with biological and clinical data collection. Countries will also need to improve the production of

  3. Fine mapping and single nucleotide polymorphism effects estimation on pig chromosomes 1, 4, 7, 8, 17 and X

    PubMed Central

    Hidalgo, André M.; Lopes, Paulo S.; Paixão, Débora M.; Silva, Fabyano F.; Bastiaansen, John W.M.; Paiva, Samuel R.; Faria, Danielle A.; Guimarães, Simone E.F.

    2013-01-01

    Fine mapping of quantitative trait loci (QTL) from previous linkage studies was performed on pig chromosomes 1, 4, 7, 8, 17, and X which were known to harbor QTL. Traits were divided into: growth performance, carcass, internal organs, cut yields, and meat quality. Fifty families were used of a F2 population produced by crossing local Brazilian Piau boars with commercial sows. The linkage map consisted of 237 SNP and 37 microsatellite markers covering 866 centimorgans. QTL were identified by regression interval mapping using GridQTL. Individual marker effects were estimated by Bayesian LASSO regression using R. In total, 32 QTL affecting the evaluated traits were detected along the chromosomes studied. Seven of the QTL were known from previous studies using our F2 population, and 25 novel QTL resulted from the increased marker coverage. Six of the seven QTL that were significant at the 5% genome-wide level had SNPs within their confidence interval whose effects were among the 5% largest effects. The combined use of microsatellites along with SNP markers increased the saturation of the genome map and led to smaller confidence intervals of the QTL. The results showed that the tested models yield similar improvements in QTL mapping accuracy. PMID:24385854

  4. Light-RCV: a lightweight read coverage viewer for next generation sequencing data

    PubMed Central

    2015-01-01

    Background Next-generation sequencing (NGS) technologies has brought an unprecedented amount of genomic data for analysis. Unlike array-based profiling technologies, NGS can reveal the expression profile across a transcript at the base level. Such a base-level read coverage provides further insights for alternative mRNA splicing, single-nucleotide polymorphism (SNP), novel transcript discovery, etc. However, to our best knowledge, none of existing NGS viewers can timely visualize genome-wide base-level read coverages in an interactive environment. Results This study proposes an efficient visualization pipeline and implements a lightweight read coverage viewer, Light-RCV, with the proposed pipeline. Light-RCV consists of four featured designs on the path from raw NGS data to the final visualized read coverage: i) read coverage construction algorithm, ii) multi-resolution profiles, iii) two-stage architecture and iv) storage format. With these designs, Light-RCV achieves a < 0.5s response time on any scale of genomic ranges, including whole chromosomes. Finally, a case study was performed to demonstrate the importance of visualizing base-level read coverage and the value of Light-RCV. Conclusions Compared with multi-functional genome viewers such as Artemis, Savant, Tablet and Integrative Genomics Viewer (IGV), Light-RCV is designed only for visualization. Therefore, it does not provide advanced analyses. However, its backend technology provides an efficient kernel of base-level visualization that can be easily embedded to other viewers. This viewer is the first to provide timely visualization of genome-wide read coverage at the base level in an interactive environment. The software is available for free at http://lightrcv.ee.ncku.edu.tw. PMID:26680734

  5. Urolithiasis in finishing pigs.

    PubMed

    Maes, D G D; Vrielinck, J; Millet, S; Janssens, G P J; Deprez, P

    2004-11-01

    Urolithiasis in sows and neonatal pigs is well-known, but information on its occurrence and impact in finishing pigs is sparse. This study reports three outbreaks of urolithiasis in finishing pigs. In one herd, no symptoms were observed, whereas in the other herds the presence of calculi caused obstruction of the urinary tract resulting in death. Using infra-red spectroscopy, the predominant mineral-type found in the uroliths was calcium carbonate (calcite). Only small amounts of calcium oxalate (< 1%) could be detected. A high urinary pH, small abnormalities in the mineral composition of the feed and insufficient drinking water were the most important risk factors identified. To prevent urolithiasis, it is important to ensure adequate water intake, to provide a balanced mineral diet, and to avoid urinary tract infections.

  6. Crime News Coverage in Perspective.

    ERIC Educational Resources Information Center

    Graber, Doris A.

    According to one sociological model, news is a product of socially determined notions of who and what is important and the organizational structures that result for routinizing news collection; events that deviate from these notions are ignored. This report describes a study of crime news coverage in the media that used this model to examine the…

  7. Is Crime News Coverage Excessive?

    ERIC Educational Resources Information Center

    Graber, Doris A.

    1979-01-01

    Reports on the frequency and manner in which various crime and noncrime news topics were presented in selected newspapers and television newscasts in 1976. Examines news flow data to determine whether news output was inflexible, and whether crime news coverage distorted the amount of real-life crime. (PD)

  8. Immunisation coverage annual report, 2014.

    PubMed

    Hull, Brynley P; Hendry, Alexandra J; Dey, Aditi; Beard, Frank H; Brotherton, Julia M; McIntyre, Peter B

    2017-03-31

    This 8th annual immunisation coverage report shows data for 2014 derived from the Australian Childhood Immunisation Register and the National Human Papillomavirus Vaccination Program Register. This report includes coverage data for 'fully immunised' and by individual vaccines at standard age milestones and timeliness of receipt at earlier ages according to Indigenous status. Overall, 'fully immunised' coverage has been mostly stable at the 12- and 24-month age milestones since late 2003, but at 60 months of age, it has increased by more than 10 percentage points since 2009. As in previous years, coverage for 'fully immunised' at 12 months of age among Indigenous children was 3.7% lower than for non-Indigenous children overall, varying from 6.9 percentage points in Western Australia to 0.3 of a percentage point in the Australian Capital Territory. In 2014, 73.4% of Australian females aged 15 years had 3 documented doses of human papillomavirus vaccine (jurisdictional range 67.7% to 77.4%), and 82.7% had at least 1 dose, compared with 71.4% and 81.5%, respectively, in 2013. The disparity in on-time vaccination between Indigenous and non-Indigenous children in 2014 diminished progressively from 20.2% for vaccines due by 12 months to 11.5% for those due by 24 months and 3.0% at 60 months of age.

  9. ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants.

    PubMed

    Chen, Feng-Chi; Chuang, Trees-Juen

    2005-05-15

    ESTviewer is a web application for interactively visualizing human gene structures, with emphasis on mammalian and avian expressed sequence tags (ESTs) that are conserved in the human genome and alternatively spliced (AS) variants. AS variants from the UCSC, Vega and PSEP annotations are presented in this application for comparison. EST data from six species, human, mouse, rat, cattle, pig and chicken, are mapped to the human genome to show cross-species EST conservation in annotated exonic and intronic regions. Cross-species EST conservation is evolutionarily and functionally important because it represents the effects of selection pressure on genic regions and transcriptome over evolutionary time. Emphatically, ESTviewer provides a convenient tool to compare highly conserved non-human ESTs and human AS variants. The application takes human gene accession Ids or coordinates of genomic sequences as inputs and presents annotated gene structures and their AS variants. In addition, the lengths and percentages of human genic regions covered by ESTs are displayed to show the level of EST coverage of different species. The percentages of the UCSC, Vega and PSEP annotated exons covered by ESTs of the six studied species are also displayed in the interface.

  10. Genes, genome and Gestalt.

    PubMed

    Grisolia, Cesar Koppe

    2005-03-31

    According to Gestalt thinking, biological systems cannot be viewed as the sum of their elements, but as processes of the whole. To understand organisms we must start from the whole, observing how the various parts are related. In genetics, we must observe the genome over and above the sum of its genes. Either loss or addition of one gene in a genome can change the function of the organism. Genomes are organized in networks of genes, which need to be well integrated. In the case of genetically modified organisms (GMOs), for example, soybeans, rats, Anopheles mosquitoes, and pigs, the insertion of an exogenous gene into a receptive organism generally causes disturbance in the networks, resulting in the breakdown of gene interactions. In these cases, genetic modification increased the genetic load of the GMO and consequently decreased its adaptability (fitness). Therefore, it is hard to claim that the production of such organisms with an increased genetic load does not have ethical implications.

  11. The effects of feeder adjustment and trough space on growth performance of finishing pigs.

    PubMed

    Myers, A J; Goodband, R D; Tokach, M D; Dritz, S S; DeRouchey, J M; Nelssen, J L

    2012-12-01

    Two studies were conducted to determine the effects of feeder adjustment and trough space on growth performance of finishing pigs. In Exp. 1, 234 pigs (initial BW 41.5 kg) were used in an 89-d trial. Pigs were randomly allotted to 1 of 3 treatments with 9 replications of 8 pigs/pen and 1 replicate with 6 pigs/pen. Treatments consisted of a minimum feeder gap setting of 1.27, 1.91, or 2.54 cm. Feeders were adjusted to a minimum gap setting, but the agitation plate could be moved upward to a maximum opening of 1.91, 2.54, or 3.18 cm, respectively. Feeder adjustments of 1.27, 1.91, and 2.54 cm averaged 28, 58, and 75% pan coverage, respectively. From d 0 to 58, increasing feeder gap improved (linear; P ≤ 0.04) ADG and ADFI, but decreased (linear; P < 0.05) G:F. Although the response was linear for ADG, no increase occurred (quadratic; P = 0.15) beyond the 1.91-cm feeder gap setting. From d 58 to 89, increasing feeder gap setting tended (linear; P = 0.08) to worsen G:F. Overall (d 0 to 89), pigs fed with increasing feeder gap had decreased (linear; P <0.03) G:F due to increased (linear; P <0.02) ADFI. In Exp. 2, 288 pigs (initial BW 41.3 kg) were used in a 91-d study to evaluate the effects of feeder trough space (4.45 vs. 8.9 cm/pig) and minimum feeder gap opening of 1.27 cm (narrow) vs. 2.54 cm (wide). The treatments were arranged in a 2 × 2 factorial with 6 replications per treatment. Feeder trough space was altered by having pens of either 8 to 16 pigs per pen with all pigs provided 0.74 m(2) floor space per pig. From d 0 to 56 and 56 to 91, no adjustment × space interactions or effects of trough space were observed. From d 0 to 56, pigs with the wide feeder gap setting had decreased (P < 0.02) G:F compared with those that had the narrow feeder gap setting. From d 56 to 91, pigs with the wider feeder gap setting had increased (P < 0.001) ADFI, but consequently had decreased (P < 0.01) G:F. Overall (d 0 to 91), no trough space × feeder adjustment interactions

  12. St. Paul's Pig Pack.

    ERIC Educational Resources Information Center

    Miller, Penny Folley

    1982-01-01

    Describes a guinea pig (cavy) breeding and management program developed as part of an elementary school science curriculum. Includes comments on show competitions (sponsored by the American Rabbit Breeders Association) to measure the success of the breeding program and to enable children to experience the business world. (Author/JN)

  13. A Simple "Pig" Game

    ERIC Educational Resources Information Center

    Johnson, Roger W.

    2008-01-01

    Our pig game involves a series of tosses of a die with the possibility of a player's score improving with each additional toss. With each additional toss, however, there is also the chance of losing the entire score accumulated so far. Two different strategies for deciding how many tosses a player should attempt are developed and then compared in…

  14. Generation of germline ablated male pigs by CRISPR/Cas9 editing of the NANOS2 gene.

    PubMed

    Park, Ki-Eun; Kaucher, Amy V; Powell, Anne; Waqas, Muhammad Salman; Sandmaier, Shelley E S; Oatley, Melissa J; Park, Chi-Hun; Tibary, Ahmed; Donovan, David M; Blomberg, Le Ann; Lillico, Simon G; Whitelaw, C Bruce A; Mileham, Alan; Telugu, Bhanu P; Oatley, Jon M

    2017-01-10

    Genome editing tools have revolutionized the generation of genetically modified animals including livestock. In particular, the domestic pig is a proven model of human physiology and an agriculturally important species. In this study, we utilized the CRISPR/Cas9 system to edit the NANOS2 gene in pig embryos to generate offspring with mono-allelic and bi-allelic mutations. We found that NANOS2 knockout pigs phenocopy knockout mice with male specific germline ablation but other aspects of testicular development are normal. Moreover, male pigs with one intact NANOS2 allele and female knockout pigs are fertile. From an agriculture perspective, NANOS2 knockout male pigs are expected to serve as an ideal surrogate for transplantation of donor spermatogonial stem cells to expand the availability of gametes from genetically desirable sires.

  15. Generation of germline ablated male pigs by CRISPR/Cas9 editing of the NANOS2 gene

    PubMed Central

    Park, Ki-Eun; Kaucher, Amy V.; Powell, Anne; Waqas, Muhammad Salman; Sandmaier, Shelley E.S.; Oatley, Melissa J.; Park, Chi-Hun; Tibary, Ahmed; Donovan, David M.; Blomberg, Le Ann; Lillico, Simon G.; Whitelaw, C. Bruce A.; Mileham, Alan; Telugu, Bhanu P.; Oatley, Jon M.

    2017-01-01

    Genome editing tools have revolutionized the generation of genetically modified animals including livestock. In particular, the domestic pig is a proven model of human physiology and an agriculturally important species. In this study, we utilized the CRISPR/Cas9 system to edit the NANOS2 gene in pig embryos to generate offspring with mono-allelic and bi-allelic mutations. We found that NANOS2 knockout pigs phenocopy knockout mice with male specific germline ablation but other aspects of testicular development are normal. Moreover, male pigs with one intact NANOS2 allele and female knockout pigs are fertile. From an agriculture perspective, NANOS2 knockout male pigs are expected to serve as an ideal surrogate for transplantation of donor spermatogonial stem cells to expand the availability of gametes from genetically desirable sires. PMID:28071690

  16. Coverage-adjusted entropy estimation.

    PubMed

    Vu, Vincent Q; Yu, Bin; Kass, Robert E

    2007-09-20

    Data on 'neural coding' have frequently been analyzed using information-theoretic measures. These formulations involve the fundamental and generally difficult statistical problem of estimating entropy. We review briefly several methods that have been advanced to estimate entropy and highlight a method, the coverage-adjusted entropy estimator (CAE), due to Chao and Shen that appeared recently in the environmental statistics literature. This method begins with the elementary Horvitz-Thompson estimator, developed for sampling from a finite population, and adjusts for the potential new species that have not yet been observed in the sample-these become the new patterns or 'words' in a spike train that have not yet been observed. The adjustment is due to I. J. Good, and is called the Good-Turing coverage estimate. We provide a new empirical regularization derivation of the coverage-adjusted probability estimator, which shrinks the maximum likelihood estimate. We prove that the CAE is consistent and first-order optimal, with rate O(P)(1/log n), in the class of distributions with finite entropy variance and that, within the class of distributions with finite qth moment of the log-likelihood, the Good-Turing coverage estimate and the total probability of unobserved words converge at rate O(P)(1/(log n)(q)). We then provide a simulation study of the estimator with standard distributions and examples from neuronal data, where observations are dependent. The results show that, with a minor modification, the CAE performs much better than the MLE and is better than the best upper bound estimator, due to Paninski, when the number of possible words m is unknown or infinite.

  17. Medical coverage of gymnastics competitions.

    PubMed

    Hecht, Suzanne S; Burton, Monique S

    2009-01-01

    Medical coverage of gymnastics competitions can be a challenging task for the sports medicine physician and other medical personnel because of the complexity and aerial nature of the sport. A broad understanding of the six gymnastics disciplines, along with the type of competitions, injury epidemiology, and the common acute gymnastics injuries will help sports medicine professionals in planning and delivering optimal care to the injured or ill gymnast.

  18. First survey and functional annotation of prohormone and convertase genes in the pig

    PubMed Central

    2012-01-01

    Background The pig is a biomedical model to study human and livestock traits. Many of these traits are controlled by neuropeptides that result from the cleavage of prohormones by prohormone convertases. Only 45 prohormones have been confirmed in the pig. Sequence homology can be ineffective to annotate prohormone genes in sequenced species like the pig due to the multifactorial nature of the prohormone processing. The goal of this study is to undertake the first complete survey of prohormone and prohormone convertases genes in the pig genome. These genes were functionally annotated based on 35 gene expression microarray experiments. The cleavage sites of prohormone sequences into potentially active neuropeptides were predicted. Results We identified 95 unique prohormone genes, 2 alternative calcitonin-related sequences, 8 prohormone convertases and 1 cleavage facilitator in the pig genome 10.2 assembly and trace archives. Of these, 11 pig prohormone genes have not been reported in the UniProt, UniGene or Gene databases. These genes are intermedin, cortistatin, insulin-like 5, orexigenic neuropeptide QRFP, prokineticin 2, prolactin-releasing peptide, parathyroid hormone 2, urocortin, urocortin 2, urocortin 3, and urotensin 2-related peptide. In addition, a novel neuropeptide S was identified in the pig genome correcting the previously reported pig sequence that is identical to the rabbit sequence. Most differentially expressed prohormone genes were under-expressed in pigs experiencing immune challenge relative to the un-challenged controls, in non-pregnant relative to pregnant sows, in old relative to young embryos, and in non-neural relative to neural tissues. The cleavage prediction based on human sequences had the best performance with a correct classification rate of cleaved and non-cleaved sites of 92% suggesting that the processing of prohormones in pigs is similar to humans. The cleavage prediction models did not find conclusive evidence supporting the

  19. Molecular cloning and expression of the IL-10 gene from guinea pigs.

    PubMed

    Dirisala, Vijaya R; Jeevan, Amminikutty; Bix, Gregory; Yoshimura, Teizo; McMurray, David N

    2012-04-25

    The Guinea pig (Cavia porcellus) is one of the most relevant small animals for modeling human tuberculosis (TB) in terms of susceptibility to low dose aerosol infection, the organization of granulomas, extrapulmonary dissemination and vaccine-induced protection. It is also considered to be a gold standard for a number of other infectious and non-infectious diseases; however, this animal model has a major disadvantage due to the lack of readily available immunological reagents. In the present study, we successfully cloned a cDNA for the critical Th2 cytokine, interleukin-10 (IL-10), from inbred Strain 2 guinea pigs using the DNA sequence information provided by the genome project. The complete open reading frame (ORF) consists of 537 base pairs which encodes a protein of 179 amino acids. This cDNA sequence exhibited 87% homology with human IL-10. Surprisingly, it showed only 84% homology with the previously published IL-10 sequence from the C4-deficient (C4D) guinea pig, leading us to clone IL-10 cDNA from the Hartley strain of guinea pig. The IL-10 gene from the Hartley strain showed 100% homology with the IL-10 sequence of Strain 2 guinea pigs. In order to validate the only published IL-10 sequence existing in Genbank reported from C4D guinea pigs, genomic DNA was isolated from tissues of C4D guinea pigs. Amplification with various sets of primers showed that the IL-10 sequence reported from C4D guinea pigs contained numerous errors. Hence the IL-10 sequence that is being reported by us replaces the earlier sequence making our IL-10 sequence to be the first one accurate from guinea pig. Recombinant guinea pig IL-10 proteins were subsequently expressed in both prokaryotic and eukaryotic cells, purified and were confirmed by N-terminal sequencing. Polyclonal anti-IL-10 antibodies were generated in rabbits using the recombinant IL-10 protein expressed in this study. Taken together, our results indicate that the DNA sequence information provided by the genome project

  20. Sequencing the maize genome.

    PubMed

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  1. Generation of GGTA1 biallelic knockout pigs via zinc-finger nucleases and somatic cell nuclear transfer.

    PubMed

    Bao, Lei; Chen, HaiDe; Jong, UiMyong; Rim, CholHo; Li, WenLing; Lin, XiJuan; Zhang, Dan; Luo, Qiong; Cui, Chun; Huang, HeFeng; Zhang, Yan; Xiao, Lei; Fu, ZhiXin

    2014-02-01

    Genetically modified pigs are valuable models of human disease and donors of xenotransplanted organs. Conventional gene targeting in pig somatic cells is extremely inefficient. Zinc-finger nuclease (ZFN) technology has been shown to be a powerful tool for efficiently inducing mutations in the genome. However, ZFN-mediated targeting in pigs has rarely been achieved. Here, we used ZFNs to knock out the porcine α-1, 3-galactosyl-transferase (GGTA1) gene, which generates Gal epitopes that trigger hyperacute immune rejection in pig-to-human transplantation. Primary pig fibroblasts were transfected with ZFNs targeting the coding region of GGTA1. Eighteen mono-allelic and four biallelic knockout cell clones were obtained after drug selection with efficiencies of 23.4% and 5.2%, respectively. The biallelic cells were used to produce cloned pigs via somatic cell nuclear transfer (SCNT). Three GGTA1 null piglets were born, and one knockout primary fibroblast cell line was established from a cloned fetus. Gal epitopes on GGTA1 null pig cells were completely eliminated from the cell membrane. Functionally, GGTA1 knockout cells were protected from complement-mediated immune attacks when incubated with human serum. This study demonstrated that ZFN is an efficient tool in creating gene-modified pigs. GGTA1 null pigs and GGTA1 null fetal fibroblasts would benefit research and pig-to-human transplantation.

  2. Coverage Evaluation of Academic Libraries Survey (ALS).

    ERIC Educational Resources Information Center

    Marston, Christopher C.

    1999-01-01

    Evaluates universe coverage, data coverage, and response rates of the Academic Libraries Survey. Includes examination of survey design and data collection, perceptions of regional survey coordinators, and reporting by public versus private institutions. (Author)

  3. Bundled automobile insurance coverage and accidents.

    PubMed

    Li, Chu-Shiu; Liu, Chwen-Chi; Peng, Sheng-Chang

    2013-01-01

    This paper investigates the characteristics of automobile accidents by taking into account two types of automobile insurance coverage: comprehensive vehicle physical damage insurance and voluntary third-party liability insurance. By using a unique data set in the Taiwanese automobile insurance market, we explore the bundled automobile insurance coverage and the occurrence of claims. It is shown that vehicle physical damage insurance is the major automobile coverage and affects the decision to purchase voluntary liability insurance coverage as a complement. Moreover, policyholders with high vehicle physical damage insurance coverage have a significantly higher probability of filing vehicle damage claims, and if they additionally purchase low voluntary liability insurance coverage, their accident claims probability is higher than those who purchase high voluntary liability insurance coverage. Our empirical results reveal that additional automobile insurance coverage information can capture more driver characteristics and driving behaviors to provide useful information for insurers' underwriting policies and to help analyze the occurrence of automobile accidents.

  4. Closing the Prescription Drug Coverage Gap

    MedlinePlus

    ... coverage gap discount work for brand-name drugs? Companies that make brand-name prescription drugs must sign ... Coverage Gap Discount Program. This program requires the companies to offer discounts on brand-name drugs to ...

  5. Transcriptome profiling identifies differentially expressed genes in postnatal developing pituitary gland of miniature pig.

    PubMed

    Shan, Lei; Wu, Qi; Li, Yuli; Shang, Haitao; Guo, Kenan; Wu, Jiayan; Wei, Hong; Zhao, Jianguo; Yu, Jun; Li, Meng-Hua

    2014-01-01

    In recent years, Tibetan pig and Bama pig are popularly used as animal models for medical researches. However, little genomic information is available for the two breeds, particularly regarding gene expression pattern at the whole-transcriptome level. In this study, we characterized the pituitary transcriptome profile along their postnatal developmental stages within and between the two breeds in order to illustrate the differential dynamics and functions of differentially expressed genes. We obtained a total of ∼300 million 80-bp paired-end reads, detected 15 715 previously annotated genes. Most of the genes (90.33%) were shared between the two breeds with the main functions in metabolic process. Four hormone genes (GH, PRL, LHB, and FSHB) were detected in all samples with extremely high levels of expression. Functional differences between the three developmental stages (infancy, puberty and adulthood) in each breed were dominantly presented by the gene expressions at the first stage. That is, Bama pig was over-represented in the genes involved in the cellular process, while Tibetan pig was over-represented in the genes represented by the reproductive process. The identified SNPs indicated that the divergence between the miniature pig breeds and the large pig (Duroc) were greater than that between the two miniature pig breeds. This study substantially expands our knowledge concerning the genes transcribed in the pig pituitary gland and provides an overview of pituitary transcriptome dynamics throughout the period of postnatal development.

  6. Transcriptome Profiling Identifies Differentially Expressed Genes in Postnatal Developing Pituitary Gland of Miniature Pig

    PubMed Central

    Shan, Lei; Wu, Qi; Li, Yuli; Shang, Haitao; Guo, Kenan; Wu, Jiayan; Wei, Hong; Zhao, Jianguo; Yu, Jun; Li, Meng-Hua

    2014-01-01

    In recent years, Tibetan pig and Bama pig are popularly used as animal models for medical researches. However, little genomic information is available for the two breeds, particularly regarding gene expression pattern at the whole-transcriptome level. In this study, we characterized the pituitary transcriptome profile along their postnatal developmental stages within and between the two breeds in order to illustrate the differential dynamics and functions of differentially expressed genes. We obtained a total of ∼300 million 80-bp paired-end reads, detected 15 715 previously annotated genes. Most of the genes (90.33%) were shared between the two breeds with the main functions in metabolic process. Four hormone genes (GH, PRL, LHB, and FSHB) were detected in all samples with extremely high levels of expression. Functional differences between the three developmental stages (infancy, puberty and adulthood) in each breed were dominantly presented by the gene expressions at the first stage. That is, Bama pig was over-represented in the genes involved in the cellular process, while Tibetan pig was over-represented in the genes represented by the reproductive process. The identified SNPs indicated that the divergence between the miniature pig breeds and the large pig (Duroc) were greater than that between the two miniature pig breeds. This study substantially expands our knowledge concerning the genes transcribed in the pig pituitary gland and provides an overview of pituitary transcriptome dynamics throughout the period of postnatal development. PMID:24282060

  7. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  8. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 20 Employees' Benefits 2 2013-04-01 2013-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  9. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  10. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  11. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 1 2012-10-01 2012-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  12. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 28 Judicial Administration 2 2013-07-01 2013-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  13. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  14. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  15. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 2 Grants and Agreements 1 2013-01-01 2013-01-01 false Insurance coverage. 215.31 Section 215.31... A-110) Post Award Requirements Property Standards § 215.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired...

  16. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 1 2014-10-01 2014-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  17. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 1 2012-10-01 2012-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  18. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  19. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 1 2014-07-01 2014-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  20. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  1. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  2. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  3. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  4. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  5. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  6. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  7. 2 CFR 200.310 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 2 Grants and Agreements 1 2014-01-01 2014-01-01 false Insurance coverage. 200.310 Section 200.310... REQUIREMENTS FOR FEDERAL AWARDS Post Federal Award Requirements Property Standards § 200.310 Insurance coverage. The non-Federal entity must, at a minimum, provide the equivalent insurance coverage for real...

  8. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 1 2014-07-01 2014-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  9. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 2 2013-04-01 2009-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  10. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 1 2013-10-01 2013-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  11. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  12. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 1 2012-07-01 2012-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  13. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 4 2014-01-01 2014-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  14. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 2 2012-04-01 2009-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  15. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 1 2013-07-01 2013-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  16. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  17. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  18. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 20 Employees' Benefits 2 2014-04-01 2014-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  19. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  20. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 1 2013-07-01 2013-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  1. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 1 2014-10-01 2014-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  2. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  3. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  4. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  5. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 2 Grants and Agreements 1 2012-01-01 2012-01-01 false Insurance coverage. 215.31 Section 215.31... A-110) Post Award Requirements Property Standards § 215.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired...

  6. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  7. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 4 2013-01-01 2013-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  8. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  9. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 1 2014-07-01 2014-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  10. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  11. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 1 2013-07-01 2013-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  12. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 1 2012-07-01 2012-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  13. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  14. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  15. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 5 2012-01-01 2012-01-01 false Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  16. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 28 Judicial Administration 2 2014-07-01 2014-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  17. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  18. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 2 2014-04-01 2014-04-01 false Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  19. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 28 Judicial Administration 2 2012-07-01 2012-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  20. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  1. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  2. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  3. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  4. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  5. 29 CFR 801.3 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... POLYGRAPH PROTECTION ACT OF 1988 General § 801.3 Coverage. (a) The coverage of the Act extends to “any... coverage to be coextensive with the full scope of the Congressional power to regulate commerce. See, for example, Godwin v. Occupational Safety and Health Review Commission, 540 F. 2d 1013, 1015 (9th Cir....

  6. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a...

  7. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 300.603 Section 300.603 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Time-In-Grade Restrictions § 300.603 Coverage. (a) Coverage. This subpart applies to advancement to a...

  8. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  9. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  10. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  11. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  12. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  13. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  14. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  15. 40 CFR 30.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Insurance coverage. 30.31 Section 30.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 30.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  16. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  17. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  18. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  19. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 1 2011-07-01 2011-07-01 false Insurance coverage. 74.31 Section 74.31 Education... Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided to property...

  20. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  1. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 1 2011-10-01 2011-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  2. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  3. 45 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Insurance coverage. 74.31 Section 74.31 Public..., AND COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 74.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  4. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  5. 10 CFR 600.131 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Insurance coverage. 600.131 Section 600.131 Energy... Nonprofit Organizations Post-Award Requirements § 600.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with DOE funds...

  6. 45 CFR 2543.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Insurance coverage. 2543.31 Section 2543.31 Public... ORGANIZATIONS Post-Award Requirements Property Standards § 2543.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  7. 15 CFR 14.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Insurance coverage. 14.31 Section 14... COMMERCIAL ORGANIZATIONS Post-Award Requirements Property Standards § 14.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  8. 22 CFR 518.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 2 2011-04-01 2009-04-01 true Insurance coverage. 518.31 Section 518.31... Requirements Property Standards § 518.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  9. 32 CFR 32.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 1 2011-07-01 2011-07-01 false Insurance coverage. 32.31 Section 32.31 National... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 32.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  10. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  11. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  12. 24 CFR 84.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Insurance coverage. 84.31 Section 84.31 Housing and Urban Development Office of the Secretary, Department of Housing and Urban... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  13. 24 CFR 35.1140 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Insurance coverage. 35.1140 Section... § 35.1140 Insurance coverage. For the requirements concerning the obligation of a PHA to obtain reasonable insurance coverage with respect to the hazards associated with evaluation and hazard...

  14. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 2 Grants and Agreements 1 2011-01-01 2011-01-01 false Insurance coverage. 215.31 Section 215.31... A-110) Post Award Requirements Property Standards § 215.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired...

  15. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  16. 28 CFR 70.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Insurance coverage. 70.31 Section 70.31...-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 70.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  17. 36 CFR 1210.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Insurance coverage. 1210.31 Section 1210.31 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL....31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage...

  18. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  19. 20 CFR 435.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Insurance coverage. 435.31 Section 435.31... ORGANIZATIONS Post-Award Requirements Property Standards § 435.31 Insurance coverage. Recipients must, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with...

  20. 38 CFR 49.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Insurance coverage. 49.31... NON-PROFIT ORGANIZATIONS Post-Award Requirements Property Standards § 49.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and...

  1. 49 CFR 19.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Insurance coverage. 19.31 Section 19.31... Requirements Property Standards § 19.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment acquired with Federal funds as provided...

  2. 22 CFR 226.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Insurance coverage. 226.31 Section 226.31...-GOVERNMENTAL ORGANIZATIONS Post-award Requirements Property Standards § 226.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property and equipment...

  3. 22 CFR 145.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Insurance coverage. 145.31 Section 145.31 Foreign Relations DEPARTMENT OF STATE CIVIL RIGHTS GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  4. 14 CFR 1260.131 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Insurance coverage. 1260.131 Section 1260... Higher Education, Hospitals, and Other Non-Profit Organizations Property Standards § 1260.131 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for real property...

  5. 2 CFR 215.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Insurance coverage. 215.31 Section 215.31 Grants and Agreements OFFICE OF MANAGEMENT AND BUDGET CIRCULARS AND GUIDANCE Reserved UNIFORM... Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance coverage for...

  6. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 2 2014-07-01 2014-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  7. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 2 2013-07-01 2013-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  8. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 2 2011-07-01 2011-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  9. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 2 2012-07-01 2012-07-01 false Vehicle coverage. 51.356 Section 51.356....356 Vehicle coverage. The performance standard for enhanced I/M programs assumes coverage of all 1968 and later model year light duty vehicles and light duty trucks up to 8,500 pounds GVWR, and...

  10. Xenotransplantation and pig endogenous retroviruses.

    PubMed

    Magre, Saema; Takeuchi, Yasuhiro; Bartosch, Birke

    2003-01-01

    Xenotransplantation, in particular transplantation of pig cells, tissues and organs into human patients, may alleviate the current shortage of suitable allografts available for human transplantation. This overview addresses the physiological, immunological and virological factors considered with regard to xenotransplantation. Among the issues reviewed are the merits of using pigs as xenograft source species, the compatibility of pig and human organ physiology and the immunological hindrances with regard to the various types of rejection and attempts at abrogating rejection. Advances in the prevention of pig organ rejection by creating genetically modified pigs that are more suited to the human microenvironment are also discussed. Finally, with regard to virology, possible zoonotic infections emanating from pigs are reviewed, with special emphasis on the pig endogenous retrovirus (PERV). An in depth account of PERV studies, comprising their discovery as well as recent knowledge of the virus, is given. To date, all retrospective studies on patients with pig xenografts have shown no evidence of PERV transmission, however, many factors make us interpret these results with caution. Although the lack of PERV infection in xenograft recipients up to now is encouraging, more basic research and controlled animal studies that mimic the pig to human xenotransplantation setting more closely are required for safety assessment.

  11. Medical male circumcision coverage in Rakai, Uganda.

    PubMed

    Kong, Xiangrong; Kigozi, Godfrey; Ssekasanvu, Joseph; Nalugoda, Fred; Nakigozi, Gertrude; Chang, Larry W; Latkin, Carl; Serwadda, David; Wawer, Maria J; Gray, Ronald H

    2017-03-13

    We assessed medical male circumcision (MMC) scale-up in Rakai, Uganda using population-based surveys during 2007-2014. MMC coverage increased from 28.5 to 52.0%. Coverage was initially lower in 15-19-year-olds but increased in 2014, was higher in married men and in trading communities, and lowest in the sexually inactive. Coverage did not vary by self-perceived risk of HIV or HIV serostatus. Increasing generalized coverage suggested that MMC became normative, but coverage falls short of WHO/Joint United Nations Programme on HIV and AIDS (UNAIDS) 80% targets, indicating the need for demand generation.

  12. Insurance coverage for employment-related claims

    SciTech Connect

    Scheuermann, J.E.

    1993-12-31

    This article analyzes the principal coverage issues arising under CGL policies for employment-related claims. Section I discusses the bases of the duty to defend and the duty to idemnify in the key CGL policy provisions at issue, including the bodily injury and personal injury coverages. Section II examines the three provisions in CGL policies typically raised as defenses to coverage for employment-related claims and two public policy considerations that may affect claims for coverage. The duty to defend is given closer crutiny in section III. Finally, in section IV the effects of settlement on coverage are discussed. 106 refs.

  13. 42 CFR 422.68 - Effective dates of coverage and change of coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... continuity of health benefits coverage. (e) Special election period for individual age 65. For an election of... HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM MEDICARE ADVANTAGE PROGRAM Eligibility, Election, and Enrollment § 422.68 Effective dates of coverage and change of coverage. (a) Initial coverage election...

  14. Porcine rubulavirus LPMV RNA persists in the central nervous system of pigs after recovery from acute infection.

    PubMed

    Wiman, A C; Hjertner, B; Linné, T; Herron, B; Allan, G; McNeilly, F; Adair, B; Moreno-López, J; Berg, M

    1998-10-01

    In order to study persistence of the porcine rubulavirus LPMV, we examined tissue samples collected from pigs 53 days after experimental infection. These pigs survived the initial infection and could clinically be considered to have recovered from the infection. Two of the pigs used in this study were chemically immunosuppressed during the last 4 days before necropsy. No infectious virus or viral antigen could be detected in any tissue using standard methods for virus isolation and detection. However, the presence of viral genomic RNA and mRNA could be demonstrated in the mid brain of the convalescent pig using an optimised RT-nested PCR. Mid brain, forebrain and lung were all shown to contain LPMV RNA in the immunosuppressed convalescent pigs. In addition we examined the P-gene editing in the recovered pigs and conclude that the viral genome is transcriptionally active in these pigs. The relevance of the persistence of LPMV for maintenance and spread within and/or between pig populations is discussed.

  15. Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

    PubMed

    García-López, Rodrigo; Vázquez-Castellanos, Jorge Francisco; Moya, Andrés

    2015-01-01

    Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological, or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges, such as the formation of chimerical structures and intra-species variability. Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different operational taxonomic units (OTUs), sometimes remaining inadvisably unrelated. Thus

  16. Generation of RUNX3 knockout pigs using CRISPR/Cas9-mediated gene targeting.

    PubMed

    Kang, J-T; Ryu, J; Cho, B; Lee, E-J; Yun, Y-J; Ahn, S; Lee, J; Ji, D-Y; Lee, K; Park, K-W

    2016-12-01

    Pigs are an attractive animal model to study the progression of cancer because of their anatomical and physiological similarities to human. However, the use of pig models for cancer research has been limited by availability of genetically engineered pigs which can recapitulate human cancer progression. Utilizing genome editing technologies such as CRISPR/Cas9 system allows us to generate genetically engineered pigs at a higher efficiency. In this study, specific CRISPR/Cas9 systems were used to target RUNX3, a known tumour suppressor gene, to generate a pig model that can induce gastric cancer in human. First, RUNX3 knockout cell lines carrying genetic modification (monoallelic or biallelic) of RUNX3 were generated by introducing engineered CRISPR/Cas9 system specific to RUNX3 into foetal fibroblast cells. Then, the genetically modified foetal fibroblast cells were used as donor cells for somatic cell nuclear transfer, followed by embryo transfer. We successfully obtained four live RUNX3 knockout piglets from two surrogates. The piglets showed the lack of RUNX3 protein in their internal organ system. Our results demonstrate that the CRISPR/Cas9 system is effective in inducing mutations on a specific locus of genome and the RUNX3 knockout pigs can be useful resources for human cancer research and to develop novel cancer therapies.

  17. Technology And Pregnant Pigs

    NASA Technical Reports Server (NTRS)

    1978-01-01

    One of the interesting things about aerospace spinoff is the way it keeps cropping up in uncommon applications unimaginably remote from the original technology. For example, the pig pregnancy detector. The pig pregnancy detector? City folk may be surprised to learn that there is such a thing-and wonder why. The why is because it is a sow's job to produce piglets and farmers can't afford to keep those who don't; it costs about a half-dollar a day in feed, labor and facilities, and even in small herds that's intolerable. So the barren sow must go. Until recently, the best method of determining pig pregnancy was "eyeballing," daily visual examination over a period of time. The problem with eyeballing is that pregnancy is not evident until well advanced; when there is no pregnancy, the farmer learns too late that he has been feeding a sow that won't give him a litter. Advancing technology provided an answer: the quick, easy-to-use, accurate automatic detector for early evaluation of pregnancy status. Among the most popular of these devices are Scanopreg and Scanoprobe, to whose development NASA technology contributed. Scanopreg is an ultrasonic system which detects pregnancy about 30 days after breeding, long before eyeballing can provide an answer. The companion Scanoprobe is a dual-function unit which not only determines pregnancy but also gives farmers an analysis of a hog's meat-fat ratio, an important factor in breeding. Only a short time on the market, Scanopreg and Scanoprobe have already found wide acceptance among meat producers because they rapidly repay their cost.

  18. The ecoresponsive genome of Daphnia pulex

    SciTech Connect

    Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Caceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Frohlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V; Kültz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

    2011-02-04

    This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.

  19. Draft Genome Sequence of Hypervirulent and Vaccine Candidate Streptococcus suis Strain SC19

    PubMed Central

    Teng, Lin; Dong, Xingxing; Zhou, Yang; Li, Zhiwei; Deng, Limei; Chen, Huanchun; Wang, Xiaohong

    2017-01-01

    ABSTRACT Streptococcus suis, a zoonotic bacterium found primarily in pigs, has been recognized recently as an emerging pathogen of humans. Herein, we describe the genome of Streptococcus suis strain SC19, a hypervirulent and vaccine candidate strain isolated from a pig amid the 2005 outbreak in China. PMID:28104658

  20. Meta-analysis of genome wide association studies for pork quality traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Given the importance of pork quality in the meat processing industry, genome-wide association studies were performed for eight meat quality traits and also, a meta-analysis (MA) of GWA was implemented combining independent results from pig populations. Data from three pig datasets (USMARC, Commercia...

  1. Soft tissue coverage in abdominal wall reconstruction.

    PubMed

    Baumann, Donald P; Butler, Charles E

    2013-10-01

    Abdominal wall defects requiring soft tissue coverage can be either partial-thickness defects or full-thickness composite defects. Soft tissue flap reconstruction offers significant advantages in defects that cannot be closed primarily. Flap reconstruction is performed in a single-stage procedure obviating chronic wound management. If the defect size exceeds the availability of local soft tissue for coverage, regional pedicled flaps can be delivered into the abdominal wall while maintaining blood supply from their donor site. Microsurgical free tissue transfer increases the capacity to provide soft tissue coverage for abdominal wall defects that are not amenable to either local or regional flap coverage.

  2. Enhanced sequencing coverage with digital droplet multiple displacement amplification

    PubMed Central

    Sidore, Angus M.; Lan, Freeman; Lim, Shaun W.; Abate, Adam R.

    2016-01-01

    Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing. PMID:26704978

  3. Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain W25K.

    PubMed

    Ren, Wenkai; Liu, Gang; Yin, Jie; Chen, Shuai; Li, Tiejun; Kong, Xiangfeng; Peng, Yuanyi; Yin, Yulong; Hardwidge, Philip R

    2014-06-26

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in humans and newly weaned pigs. Here, we report the draft genome sequence of ETEC strain W25K, which causes diarrhea in piglets.

  4. Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain W25K

    PubMed Central

    Ren, Wenkai; Liu, Gang; Yin, Jie; Chen, Shuai; Li, Tiejun; Kong, Xiangfeng; Peng, Yuanyi; Hardwidge, Philip R.

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in humans and newly weaned pigs. Here, we report the draft genome sequence of ETEC strain W25K, which causes diarrhea in piglets. PMID:24970825

  5. ASFV in Tanzania: asymptomatic pigs harbor virus of molecular similarity to Georgia 2007.

    PubMed

    Uttenthal, Å; Braae, U C; Ngowi, H A; Rasmussen, T B; Nielsen, J; Johansen, M V

    2013-07-26

    In 2011 African swine fever virus (ASFV) genome was detected in asymptomatic pigs in field samples in Mbeya, Tanzania. The aim of this paper is to partly characterize the virus that was harbored in these pigs and furthermore to confirm, by a second sampling, the latest occurrence of ASFV in the study area. ASFV genome was detected in serum from 10 out of 127 healthy European/crossbreed pigs. ASFV DNA was polymerase chain reaction (PCR) amplified and sequenced from sera with high viral loads using primers targeting p54 or p72. Both p54 and p72 had total identity to ASFV Genotype II (Georgia 2007/1). The ASFV epidemiology in Mbeya was studied in a new collection of 804 pig sera obtained in 2012. The antibody prevalence in four age groups (3-6 months.; 7-12 months; 13-18 months or 19-36 months) was 3-5%; all antibody positive sera were analyzed by PCR with negative results. The presence of antibodies in 3-month-old pigs confirms the circulation of ASFV in Mbeya several months after our detection of ASFV in asymptomatic pigs. The initial blood samples were obtained on Whatman FTA filter papers as dried blood samples. The samples were stored under field conditions and ASFV could be sequenced in DNA eluted 10 months later, showing the use of FTA samples. Studies on the genetic breed of the pigs are needed as well as sequence studies including the variable region of ASFV to elucidate why asymptomatic pigs with high viral loads were detected.

  6. Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations

    PubMed Central

    García-López, Rodrigo; Vázquez-Castellanos, Jorge Francisco; Moya, Andrés

    2015-01-01

    Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological, or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges, such as the formation of chimerical structures and intra-species variability. Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different operational taxonomic units (OTUs), sometimes remaining inadvisably unrelated. Thus

  7. Field experiences with intelligent pigs

    SciTech Connect

    Smith, S.N.; Duvivier, J.P.; Lefevre, D.E.; Robb, G.A.

    1996-08-01

    Oil and gas production operations use intelligent pigs for corrosion inspection of gathering systems and pipelines worldwide. The authors have been involved with intelligent pig inspections which have been conducted on over 155 different pipelines owned by one international corporation. A variety of intelligent pig vendors have been used with tools ranging from standard first generation magnetic flux leakage (MFL) to high-resolution MFL to standard and custom made ultrasonic (UT) tools. Experiences encountered during these inspections are discussed and resolutions to many of the problems are described.

  8. Ascaris suum draft genome.

    PubMed

    Jex, Aaron R; Liu, Shiping; Li, Bo; Young, Neil D; Hall, Ross S; Li, Yingrui; Yang, Linfeng; Zeng, Na; Xu, Xun; Xiong, Zijun; Chen, Fangyuan; Wu, Xuan; Zhang, Guojie; Fang, Xiaodong; Kang, Yi; Anderson, Garry A; Harris, Todd W; Campbell, Bronwyn E; Vlaminck, Johnny; Wang, Tao; Cantacessi, Cinzia; Schwarz, Erich M; Ranganathan, Shoba; Geldhof, Peter; Nejsum, Peter; Sternberg, Paul W; Yang, Huanming; Wang, Jun; Wang, Jian; Gasser, Robin B

    2011-10-26

    Parasitic diseases have a devastating, long-term impact on human health, welfare and food production worldwide. More than two billion people are infected with geohelminths, including the roundworms Ascaris (common roundworm), Necator and Ancylostoma (hookworms), and Trichuris (whipworm), mainly in developing or impoverished nations of Asia, Africa and Latin America. In humans, the diseases caused by these parasites result in about 135,000 deaths annually, with a global burden comparable with that of malaria or tuberculosis in disability-adjusted life years. Ascaris alone infects around 1.2 billion people and, in children, causes nutritional deficiency, impaired physical and cognitive development and, in severe cases, death. Ascaris also causes major production losses in pigs owing to reduced growth, failure to thrive and mortality. The Ascaris-swine model makes it possible to study the parasite, its relationship with the host, and ascariasis at the molecular level. To enable such molecular studies, we report the 273 megabase draft genome of Ascaris suum and compare it with other nematode genomes. This genome has low repeat content (4.4%) and encodes about 18,500 protein-coding genes. Notably, the A. suum secretome (about 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissues, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and underpins the development of new and urgently needed interventions (drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.

  9. Investigation of the disposal of dead pigs by pig farmers in mainland China by simulation experiment.

    PubMed

    Wu, Linhai; Xu, Guoyan; Li, Qingguang; Hou, Bo; Hu, Wuyang; Wang, Jianhua

    2017-01-01

    Dead pigs are a major waste by-product of pig farming. Thus, safe disposal of dead pigs is important to the protection of consumer health and the ecological environment by preventing marketing of slaughtered and processed dead pigs and improper dumping of dead pigs. In this study, a probability model was constructed for the disposal of dead pigs by pig farmers by selecting factors affecting disposal. To that end, we drew on the definition and meaning of behavior probability based on survey data collected from 654 pig farmers in Funing County, Jiangsu Province, China. Moreover, the role of influencing factors in pig farmers' behavioral choices regarding the disposal of dead pigs was simulated by simulation experiment. The results indicated that years of farming had a positive impact on pig farmers' choice of negative disposal of dead pigs. Moreover, there was not a simple linear relationship between scale of farming and pig farmers' behavioral choices related to the disposal of dead pigs. The probability for farmers to choose the safe disposal of dead pigs increased with the improvement of their knowledge of government policies and relevant laws and regulations. Pig farmers' behavioral choice about the disposal of dead pigs was also affected by government subsidy policies, regulation, and punishment. Government regulation and punishment were more effective than subsidy. The findings of our simulation experiment provide important decision-making support for the governance in preventing the marketing of dead pigs at the source.

  10. Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA, 2014.

    PubMed

    Wang, Leyi; Byrum, Beverly; Zhang, Yan

    2014-07-01

    In Ohio, United States, in early 2014, a deltacoronavirus was detected in feces and intestine samples from pigs with diarrheal disease. The complete genome sequence and phylogenetic analysis of the virus confirmed that the virus is closely related to a porcine deltacoronavirus (porcine coronavirus HKU15) reported in Hong Kong in 2012.

  11. A divergent clade of circular single-stranded DNA viruses from pig feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using metagenomics and molecular cloning methods, we characterized five novel small circular viral genomes from pig feces distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a new, highly divergent, clade...

  12. Helminth parasites in pigs: new challenges in pig production and current research highlights.

    PubMed

    Roepstorff, A; Mejer, H; Nejsum, P; Thamsborg, S M

    2011-08-04

    , the heredity of host resistance to A. suum and T. suis is so high that breeding for resistant pigs may be a possibility. Experimental studies have demonstrated that fermentable dietary carbohydrates have an antagonistic effect on Oesophagostomum and to a lesser extent on T. suis and A. suum, whereas egg-destroying microfungi may be used to inactivate the hard-shelled A. suum and T. suis eggs in the environment. Helminth control in Denmark has previously relied solely on anthelmintic treatment in herds with low helminth transmission. When indoor transmission rates increase, or in outdoor herds with high pasture contamination levels, medication may advantageously be combined with sustainable control measures, such as selected pig genomes, bioactive forages, and egg-destroying microfungi.

  13. Computational Methods for Analyzing Health News Coverage

    ERIC Educational Resources Information Center

    McFarlane, Delano J.

    2011-01-01

    Researchers that investigate the media's coverage of health have historically relied on keyword searches to retrieve relevant health news coverage, and manual content analysis methods to categorize and score health news text. These methods are problematic. Manual content analysis methods are labor intensive, time consuming, and inherently…

  14. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  15. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  16. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  17. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  18. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... or death of persons, including nonemployee cargo attendants, other than passengers, and for damage to... accident liability insurance coverage for bodily injury to or death of aircraft passengers, with minimum... death of aircraft passengers, with a minimum coverage of $75,000 for any one passenger and a total...

  19. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 2 2010-01-01 2010-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  20. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 2 2012-01-01 2012-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  1. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 2 2014-01-01 2014-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  2. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 2 2013-01-01 2013-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  3. 12 CFR 205.3 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 2 2011-01-01 2011-01-01 false Coverage. 205.3 Section 205.3 Banks and Banking... this paragraph (c)(7) remain subject to § 205.10(e) regarding compulsory use and sections 915 and 916... (REGULATION E) § 205.3 Coverage. (a) General. This part applies to any electronic fund transfer...

  4. 5 CFR 9701.202 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Coverage. 9701.202 Section 9701.202... MANAGEMENT SYSTEM Classification General § 9701.202 Coverage. (a) This subpart applies to eligible DHS... covered by a prevailing rate system established under 5 U.S.C. chapter 53, subchapter IV; (3) Employees...

  5. 5 CFR 9701.402 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Coverage. 9701.402 Section 9701.402 Administrative Personnel DEPARTMENT OF HOMELAND SECURITY HUMAN RESOURCES MANAGEMENT SYSTEM (DEPARTMENT OF... MANAGEMENT SYSTEM Performance Management § 9701.402 Coverage. (a) This subpart applies to eligible...

  6. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 2 2013-04-01 2013-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  7. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  8. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  9. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 15 2013-01-01 2013-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  10. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  11. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 2 2014-04-01 2014-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  12. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  13. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 1 2013-07-01 2013-07-01 false Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  14. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 1 2012-07-01 2012-07-01 false Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  15. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  16. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 15 2012-01-01 2012-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  17. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  18. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  19. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  20. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 1 2014-07-01 2013-07-01 true Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  1. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  2. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  3. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  4. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  5. 5 CFR 550.181 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 550.181 Section 550.181 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Law Enforcement Availability Pay § 550.181 Coverage. (a) Each employee meeting the...

  6. Abstract Journals: A Survey of Patent Coverage.

    ERIC Educational Resources Information Center

    Rimmer, Brenda M.

    1988-01-01

    Describes a survey of 33 British, French, German, and U.S. abstract journals that examined their coverage of patent specifications. The standards for the identification of patent documents developed by the World Intellectual Property Organization are discussed, and an appendix provides a listing of the patent coverage by the country of each…

  7. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage....

  8. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage....

  9. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage....

  10. 77 FR 16453 - Student Health Insurance Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES 45 CFR Parts 144, 147, and 158 CMS-9981-F RIN 0938-AQ95 Student Health Insurance Coverage... establishes requirements for student health insurance coverage under the Public Health Service (PHS) Act...

  11. 76 FR 7767 - Student Health Insurance Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-11

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES 45 CFR Parts 144 and 147 RIN 0950-AA20 Student Health Insurance Coverage AGENCY: Centers... proposed regulation that would establish rules for student health insurance coverage under the...

  12. 5 CFR 430.302 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 430.302 Section 430.302 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PERFORMANCE MANAGEMENT Managing Senior Executive Performance § 430.302 Coverage. (a) This subpart applies to all senior...

  13. 5 CFR 430.302 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 430.302 Section 430.302 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PERFORMANCE MANAGEMENT Managing Senior Executive Performance § 430.302 Coverage. (a) This subpart applies to all senior...

  14. 32 CFR 2001.71 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Coverage. 2001.71 Section 2001.71 National Defense Other Regulations Relating to National Defense INFORMATION SECURITY OVERSIGHT OFFICE, NATIONAL... Training § 2001.71 Coverage. (a) General. Each department or agency shall establish and maintain a...

  15. 32 CFR 2001.71 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Coverage. 2001.71 Section 2001.71 National Defense Other Regulations Relating to National Defense INFORMATION SECURITY OVERSIGHT OFFICE, NATIONAL... Training § 2001.71 Coverage. (a) General. Each department or agency shall establish and maintain a...

  16. 32 CFR 2001.71 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Coverage. 2001.71 Section 2001.71 National Defense Other Regulations Relating to National Defense INFORMATION SECURITY OVERSIGHT OFFICE, NATIONAL... Training § 2001.71 Coverage. (a) General. Each department or agency shall establish and maintain a...

  17. HEALTH INSURANCE COVERAGE FOR WORKERS ON LAYOFF.

    ERIC Educational Resources Information Center

    KOLODRUBETZ, WALTER W.

    ESTIMATES OF GROUP HEALTH INSURANCE COVERAGE BY INDUSTRY INDICATE THAT EXTENDED PROTECTION DURING LAYOFF IS GUARANTEED TO NO MORE THAN A TENTH OF THE APPROXIMATELY 50 MILLION WORKERS COVERED BY GROUP HEALTH INSURANCE PLANS. THIS COVERAGE HAS LARGELY DEVELOPED DURING THE PAST 15 YEARS. FRAGMENTARY DATA SUGGEST THAT INCREASED COST ATTRIBUTABLE TO…

  18. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  19. 24 CFR 1006.330 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Insurance coverage. 1006.330... DEVELOPMENT NATIVE HAWAIIAN HOUSING BLOCK GRANT PROGRAM Program Requirements § 1006.330 Insurance coverage. (a) In general. As a condition to receiving NHHBG funds, the DHHL must require adequate...

  20. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  1. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  2. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  3. 7 CFR 3019.31 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Insurance coverage. 3019.31 Section 3019.31 Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... Standards § 3019.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  4. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  5. 29 CFR 95.31 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 1 2011-07-01 2011-07-01 false Insurance coverage. 95.31 Section 95.31 Labor Office of the Secretary of Labor GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER NON... § 95.31 Insurance coverage. Recipients shall, at a minimum, provide the equivalent insurance...

  6. 43 CFR 12.931 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Insurance coverage. 12.931 Section 12.931 Public Lands: Interior Office of the Secretary of the Interior ADMINISTRATIVE AND AUDIT REQUIREMENTS AND... Requirements § 12.931 Insurance coverage. Recipients shall, at a minimum, provide the equivalent...

  7. 24 CFR 320.11 - Insurance coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Insurance coverage. 320.11 Section...-BACKED SECURITIES Pass-Through Type Securities § 320.11 Insurance coverage. The issuer shall maintain, for the benefit of the Association, insurance, errors and omissions, fidelity bond and other...

  8. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage....

  9. 5 CFR 315.903 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 315.903 Section 315.903 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS CAREER AND CAREER-CONDITIONAL EMPLOYMENT Probation on Initial Appointment to a Supervisory or Managerial Position § 315.903 Coverage....

  10. 5 CFR 831.1612 - Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity computations. 831.1612 Section 831.1612...) RETIREMENT Customs and Border Protection Officers § 831.1612 Elections of Retirement Coverage,...

  11. 5 CFR 831.1612 - Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity computations. 831.1612 Section 831.1612...) RETIREMENT Customs and Border Protection Officers § 831.1612 Elections of Retirement Coverage,...

  12. 5 CFR 831.1612 - Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Elections of Retirement Coverage, exclusions from retirement coverage, and proportional annuity computations. 831.1612 Section 831.1612...) RETIREMENT Customs and Border Protection Officers § 831.1612 Elections of Retirement Coverage,...

  13. Hepatitis E Virus of Subtype 3a in a Pig Farm, South-Eastern France.

    PubMed

    Colson, P; Saint-Jacques, P; Ferretti, A; Davoust, B

    2015-12-01

    Hepatitis E virus (HEV) has emerged during the past decade as a causative agent of autochthonous hepatitis and is a clinical concern in Western developed countries. It has been increasingly recognized that pigs are a major reservoir of HEV of genotypes 3 and 4 worldwide and pig-derived food items represent a potential source of infections by these viruses in humans. Hepatitis E virus RNA testing was performed here on faeces from rectal swabs sampled in 2012 from 50 3-month-old farm pigs from the same farm located in south-eastern France than in a previous work conducted in 2007. Pig HEV sequences corresponding to genomic fragments of ORF2 and ORF1 genes were obtained after RT-PCR amplification with in-house protocols. Hepatitis E virus genotype was determined by phylogenetic analysis. Prevalence was similar to that determined 5 years earlier (68% versus 62%). Two robust phylogenetic clusters of HEV subtypes 3a and 3f were identified, and these sequences obtained in 2012 largely differ compared with those obtained in 2007. Notably, HEV sequences obtained in 2012 from a majority (62%) of the infected pigs belonged to subtype 3a, which was not previously described in France, including not being found in any of humans, pigs or wild boars. Further studies are needed to assess the circulation of HEV-3a in pigs and humans in this country. In addition, along with previous findings, this study supports the need for increased information to the public on the risk of HEV infection through contacts with pigs or consumption of pig-derived products in France.

  14. Expressed sequence tag analysis of guinea pig (Cavia porcellus) eye tissues for NEIBank

    PubMed Central

    Simpanya, Mukoma F.; Wistow, Graeme; Gao, James; David, Larry L.; Giblin, Frank J.

    2008-01-01

    Purpose To characterize gene expression patterns in guinea pig ocular tissues and identify orthologs of human genes from NEIBank expressed sequence tags. Methods RNA was extracted from dissected eye tissues of 2.5-month-old guinea pigs to make three unamplified and unnormalized cDNA libraries in the pCMVSport-6 vector for the lens, retina, and eye minus lens and retina. Over 4,000 clones were sequenced from each library and were analyzed using GRIST for clustering and gene identification. Lens crystallin EST data were validated using two-dimensional electrophoresis (2-DE), matrix assisted laser desorption (MALDI), and electrospray ionization mass spectrometry (ESIMS). Results Combined data from the three libraries generated a total of 6,694 distinctive gene clusters, with each library having between 1,000 and 3,000 clusters. Approximately 60% of the total gene clusters were novel cDNA sequences and had significant homologies to other mammalian sequences in GenBank. Complete cDNA sequences were obtained for many guinea pig lens proteins, including αA/αAinsert-, γN-, and γS-crystallins, lengsin and GRIFIN. The ratio of αA- to αB-crystallin on 2-DE gels was 8: 1 in the lens nucleus and 6.5: 1 in the cortex. Analysis of ESTs, genome sequence, and proteins (by MALDI), did not reveal any evidence for the presence of γD-, γE-, and γF-crystallin in the guinea pig. Predicted masses of many guinea pig lens crystallins were confirmed by ESIMS analysis. For the retina, orthologs of human phototransduction genes were found, such as Rhodopsin, S-antigen (Sag, Arrestin), and Transducin. The guinea-pig ortholog of NRL, a key rod photoreceptor-specific transcription factor, was also represented in EST data. In the ‘rest-of-eye’ library, the most abundant transcripts included decorin and keratin 12, representative of the cornea. Conclusions Genomic analysis of guinea pig eye tissues provides sequence-verified clones for future studies. Guinea pig orthologs of many human

  15. Characterization of an influenza A virus isolated from pigs during an outbreak of respiratory disease in swine and people during a county fair in the United States.

    PubMed

    Vincent, Amy L; Swenson, Sabrina L; Lager, Kelly M; Gauger, Phillip C; Loiacono, Christina; Zhang, Yan

    2009-05-28

    In August 2007, pigs and people became clinically affected by an influenza-like illness during attendance at an Ohio county fair. Influenza A virus was identified from pigs and people, and the virus isolates were characterized as swine H1N1 similar to swine viruses currently circulating in the U.S. pig population. The swine isolate, A/SW/OH/511445/2007 (OH07), was evaluated in an experimental challenge and transmission study reported here. Our results indicate that the OH07 virus was pathogenic in pigs, was transmissible among pigs, and failed to cross-react with many swine H1 anti-sera. Naturally exposed pigs shed virus as early as 3 days and as long as 7 days after contact with experimentally infected pigs. This suggests there was opportunity for exposure of people handling the pigs at the fair. The molecular analysis of the OH07 isolates demonstrated that the eight gene segments were similar to those of currently circulating triple reassortant swine influenza viruses. However, numerous nucleotide changes leading to amino acid changes were demonstrated in the HA gene and throughout the genome as compared to contemporary swine viruses in the same genetic cluster. It remains unknown if any of the amino acid changes were related to the ability of this virus to infect people. The characteristics of the OH07 virus in our pig experimental model as well as the documented human transmission warrant close monitoring of the spread of this virus in pig and human populations.

  16. Multi-Locus Analysis Reveals A Different Pattern of Genetic Diversity for Mitochondrial and Nuclear DNA between Wild and Domestic Pigs in East Asia

    PubMed Central

    Ji, Yin-Qiu; Wu, Dong-Dong; Wu, Gui-Sheng; Wang, Guo-Dong; Zhang, Ya-Ping

    2011-01-01

    Background A major reduction of genetic diversity in mtDNA occurred during the domestication of East Asian pigs. However, the extent to which genetic diversity has been lost in the nuclear genome is uncertain. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationships and demographic history of domestic pigs and their ancestors, wild boars, we investigated 14 nuclear markers (including 8 functional genes, 2 pseudogenes and 4 intergenic regions) from 11 different chromosomes in East Asia-wide samples and pooled them with previously obtained mtDNA data for a combined analysis. Principal Findings The results indicated that domestic pigs and wild boars possess comparable levels of nucleotide diversity across the nuclear genome, which is inconsistent with patterns that have been found in mitochondrial genome. Conclusions This incongruence between the mtDNA and nuclear genomes is suggestive of a large-scale backcross between male wild boars and female domestic pigs in East Asia. Our data reveal the impacts of founder effects and backcross on the pig genome and help us better understand the complex demographic histories of East Asian pigs, which will be useful for future work on artificial selection. PMID:22065995

  17. Establishment of a novel, eco-friendly transgenic pig model using porcine pancreatic amylase promoter-driven fungal cellulase transgenes.

    PubMed

    Lin, Y S; Yang, C C; Hsu, C C; Hsu, J T; Wu, S C; Lin, C J; Cheng, W T K

    2015-02-01

    Competition between humans and livestock for cereal and legume grains makes it challenging to provide economical feeds to livestock animals. Recent increases in corn and soybean prices have had a significant impact on the cost of feed for pig producers. The utilization of byproducts and alternative ingredients in pig diets has the potential to reduce feed costs. Moreover, unlike ruminants, pigs have limited ability to utilize diets with high fiber content because they lack endogenous enzymes capable of breaking down nonstarch polysaccharides into simple sugars. Here, we investigated the feasibility of a transgenic strategy in which expression of the fungal cellulase transgene was driven by the porcine pancreatic amylase promoter in pigs. A 2,488 bp 5'-flanking region of the porcine pancreatic amylase gene was cloned by the genomic walking technique, and its structural features were characterized. Using GFP as a reporter, we found that this region contained promoter activity and had the potential to control heterologous gene expression. Transgenic pigs were generated by pronuclear microinjection. Founders and offspring were identified by PCR and Southern blot analyses. Cellulase mRNA and protein showed tissue-specific expression in the pancreas of F1 generation pigs. Cellulolytic enzyme activity was also identified in the pancreas of transgenic pigs. These results demonstrated the establishment of a tissue-specific promoter of the porcine pancreatic amylase gene. Transgenic pigs expressing exogenous cellulase may represent a way to increase the intake of low-cost, fiber-rich feeds.

  18. Analyzing the test process using structural coverage

    NASA Technical Reports Server (NTRS)

    Ramsey, James; Basili, Victor R.

    1985-01-01

    A large, commercially developed FORTRAN program was modified to produce structural coverage metrics. The modified program was executed on a set of functionally generated acceptance tests and a large sample of operational usage cases. The resulting structural coverage metrics are combined with fault and error data to evaluate structural coverage. It was shown that in the software environment the functionally generated tests seem to be a good approximation of operational use. The relative proportions of the exercised statement subclasses change as the structural coverage of the program increases. A method was also proposed for evaluating if two sets of input data exercise a program in a similar manner. Evidence was provided that implies that in this environment, faults revealed in a procedure are independent of the number of times the procedure is executed and that it may be reasonable to use procedure coverage in software models that use statement coverage. Finally, the evidence suggests that it may be possible to use structural coverage to aid in the management of the acceptance test processed.

  19. Comparative proteomic analysis of lung tissue from guinea pigs with Leptospiral Pulmonary Haemorrhage Syndrome (LPHS) reveals a decrease in abundance of host proteins involved in cytoskeletal and cellular organization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The recent completion of the complete genome sequence of the guinea pig (Cavia porcellus) provides innovative opportunities to apply proteomic technologies to an important animal model of disease. In this study, a 2-D guinea pig proteome lung map was used to investigate the pathogenic mechanisms of ...

  20. Identification of quantitative trait loci affecting reproduction in pigs.

    PubMed

    Cassady, J P; Johnson, R K; Pomp, D; Rohrer, G A; Van Vleck, L D; Spiegel, E K; Gilson, K M

    2001-03-01

    The objective of this research was to identify chromosomal regions harboring QTL affecting reproduction in pigs. A three-generation resource population was developed by crossing low-indexing pigs from a randomly selected control line (C) with high-indexing pigs of a line selected for increased index of ovulation rate and embryonic survival (I). Differences between Lines I and C at Generation 10 were 6.7 ova and 3.3 fetuses at 50 d of gestation and 3.1 fully formed and 1.6 live pigs at birth. Phenotypic data were collected on F2 females, born in three replicates, for ovulation rate (n = 423), age at puberty (n = 295), litter size (n = 370), and number of nipples (n = 428). Litter-size data included number of fully formed, live, stillborn, and mummified pigs. Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers distributed across all 18 autosomes and the X chromosome. Genotypic data were available on 423 F2 females. Average spacing between markers was 19.3 Kosambi centimorgans. Calculations of logarithms of odds (LOD) scores were by least squares, and fixed effects for sire-dam combination and replicate were included in the models. Genome-wide significance level thresholds of 5% and 10% were calculated using a permutation approach. There was evidence (P < 0.05) for QTL affecting ovulation rate on SSC9, age at puberty on SSC7 and SSC8, number of nipples on SSC8 and SSC11, number of stillborn pigs on SSC5 and SSC13, and number of fully formed pigs on SSC11. There was evidence (P < 0.10) for additional QTL affecting age at puberty on SSC7, SSC8, and SSC12, number born live on SSC11, and number of nipples on SSC1, SSC6, and SSC7. Litter size is lowly heritable and sex-limited. Therefore, accuracy of selection for litter size may be enhanced by marker-assisted selection. Ovulation rate and age at puberty are laborious to measure, and thus marker-assisted selection may provide a practical and efficient method of selection.

  1. Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.

    PubMed

    Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C; Fiser, Andras

    2014-03-11

    The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins--including proteins for which reliable homology models can be generated--on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long.

  2. Insights from Human/Mouse genome comparisons

    SciTech Connect

    Pennacchio, Len A.

    2003-03-30

    Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish (Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestry of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.

  3. Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology

    PubMed Central

    Song, Kai; Li, Li; Zhang, Guofan

    2016-01-01

    Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies. Here, we used high-coverage reference data sets from Crassostrea gigas to simulate sequencing data with different coverage, and we evaluate the influence of genotype calling rate and accuracy as a function of coverage. Having initially identified the appropriate parameter settings for filtering to ensure genotype accuracy, we used two different single-nucleotide polymorphism (SNP) calling pipelines, single-sample and multi-sample. We found that a coverage of 15× was suitable for obtaining sufficient numbers of SNPs with high accuracy. Our work provides guidelines for the selection of sequence coverage when using NGS to investigate species with a high degree of heterozygosity and rapid decay of linkage disequilibrium. PMID:27760996

  4. Widespread detection and characterization of porcine parainfluenza virus 1 in pigs in the USA.

    PubMed

    Palinski, Rachel M; Chen, Zhenhai; Henningson, Jamie N; Lang, Yuekun; Rowland, Raymond R R; Fang, Ying; Prickett, John; Gauger, Phillip C; Hause, Ben M

    2016-02-01

    Porcine parainfluenza virus 1 (PPIV1) was first identified in 2013 in slaughterhouse pigs in Hong Kong, China. Here, two near-complete genomes were assembled from swine exhibiting acute respiratory disease that were 90.0-95.3% identical to Chinese PPIV1. Analysis of the HN gene from ten additional PPIV1-positive samples found 85.0-95.5% identity, suggesting genetic diversity between strains. Molecular analysis identified 17 out of 279 (6.1%) positive samples from pigs with respiratory disease. Eleven nursery pigs from a naturally infected herd were asymptomatic; however, nasal swabs from six pigs and the lungs of a single pig were quantitative reverse transcriptase (qRT)-PCR positive. Histopathology identified PPIV1 RNA in the nasal respiratory epithelium and trachea. Two serological assays demonstrated seroconversion of infected pigs and further analysis of 59 swine serum samples found 52.5% and 66.1% seropositivity, respectively. Taken together, the results confirm the widespread presence of PPIV1 in the US swine herd.

  5. Insulinoma in 2 guinea pigs (Cavia porcellus)

    PubMed Central

    2005-01-01

    Abstract This paper describes an insulinoma in 2 guinea pigs (Cavia porcellus). Both guinea pigs presented with neurologic signs and low blood glucose readings. The neurologic signs resolved with dextrose administration. Insulinoma was confirmed on postmortem examination. PMID:15943120

  6. Experimental aerosolized guinea pig-adapted Zaire ebolavirus (variant: Mayinga) causes lethal pneumonia in guinea pigs.

    PubMed

    Twenhafel, N A; Shaia, C I; Bunton, T E; Shamblin, J D; Wollen, S E; Pitt, L M; Sizemore, D R; Ogg, M M; Johnston, S C

    2015-01-01

    Eight guinea pigs were aerosolized with guinea pig-adapted Zaire ebolavirus (variant: Mayinga) and developed lethal interstitial pneumonia that was distinct from lesions described in guinea pigs challenged subcutaneously, nonhuman primates challenged by the aerosol route, and natural infection in humans. Guinea pigs succumbed with significant pathologic changes primarily restricted to the lungs. Intracytoplasmic inclusion bodies were observed in many alveolar macrophages. Perivasculitis was noted within the lungs. These changes are unlike those of documented subcutaneously challenged guinea pigs and aerosolized filoviral infections in nonhuman primates and human cases. Similar to findings in subcutaneously challenged guinea pigs, there were only mild lesions in the liver and spleen. To our knowledge, this is the first report of aerosol challenge of guinea pigs with guinea pig-adapted Zaire ebolavirus (variant: Mayinga). Before choosing this model for use in aerosolized ebolavirus studies, scientists and pathologists should be aware that aerosolized guinea pig-adapted Zaire ebolavirus (variant: Mayinga) causes lethal pneumonia in guinea pigs.

  7. Measuring populations to improve vaccination coverage

    NASA Astrophysics Data System (ADS)

    Bharti, Nita; Djibo, Ali; Tatem, Andrew J.; Grenfell, Bryan T.; Ferrari, Matthew J.

    2016-10-01

    In low-income settings, vaccination campaigns supplement routine immunization but often fail to achieve coverage goals due to uncertainty about target population size and distribution. Accurate, updated estimates of target populations are rare but critical; short-term fluctuations can greatly impact population size and susceptibility. We use satellite imagery to quantify population fluctuations and the coverage achieved by a measles outbreak response vaccination campaign in urban Niger and compare campaign estimates to measurements from a post-campaign survey. Vaccine coverage was overestimated because the campaign underestimated resident numbers and seasonal migration further increased the target population. We combine satellite-derived measurements of fluctuations in population distribution with high-resolution measles case reports to develop a dynamic model that illustrates the potential improvement in vaccination campaign coverage if planners account for predictable population fluctuations. Satellite imagery can improve retrospective estimates of vaccination campaign impact and future campaign planning by synchronizing interventions with predictable population fluxes.

  8. Measuring populations to improve vaccination coverage

    PubMed Central

    Bharti, Nita; Djibo, Ali; Tatem, Andrew J.; Grenfell, Bryan T.; Ferrari, Matthew J.

    2016-01-01

    In low-income settings, vaccination campaigns supplement routine immunization but often fail to achieve coverage goals due to uncertainty about target population size and distribution. Accurate, updated estimates of target populations are rare but critical; short-term fluctuations can greatly impact population size and susceptibility. We use satellite imagery to quantify population fluctuations and the coverage achieved by a measles outbreak response vaccination campaign in urban Niger and compare campaign estimates to measurements from a post-campaign survey. Vaccine coverage was overestimated because the campaign underestimated resident numbers and seasonal migration further increased the target population. We combine satellite-derived measurements of fluctuations in population distribution with high-resolution measles case reports to develop a dynamic model that illustrates the potential improvement in vaccination campaign coverage if planners account for predictable population fluctuations. Satellite imagery can improve retrospective estimates of vaccination campaign impact and future campaign planning by synchronizing interventions with predictable population fluxes. PMID:27703191

  9. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  10. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  11. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  12. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  13. 5 CFR 550.1402 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...) Compensatory Time Off for Travel § 550.1402 Coverage. This subpart applies to an employee as defined in 5 U.S.C... employee whose pay is fixed and adjusted from time to time in accordance with prevailing rates...

  14. Universal prescription drug coverage in Canada

    PubMed Central

    Boothe, Katherine

    2016-01-01

    Canada’s universal public healthcare system is unique among developed countries insofar as it does not include universal coverage of prescription drugs. Universal, public coverage of prescription drugs has been recommended by major national commissions in Canada dating back to the 1960s. It has not, however, been implemented. In this article, we extend research on the failure of early proposals for universal drug coverage in Canada to explain failures of calls for reform over the past 20 years. We describe the confluence of barriers to reform stemming from Canadian policy institutions, ideas held by federal policy-makers, and electoral incentives for necessary reforms. Though universal “pharmacare” is once again on the policy agenda in Canada, arguably at higher levels of policy discourse than ever before, the frequently recommended option of universal, public coverage of prescription drugs remains unlikely to be implemented without political leadership necessary to overcome these policy barriers. PMID:27744279

  15. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... DEVELOPMENT GENERAL INTRODUCTION TO FHA PROGRAMS Requirements for Application, Commitment, and Endorsement... Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The mortgage shall cover the entire property included in the project....

  16. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... DEVELOPMENT GENERAL INTRODUCTION TO FHA PROGRAMS Requirements for Application, Commitment, and Endorsement... Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The mortgage shall cover the entire property included in the project....

  17. An Exploration into Fern Genome Space.

    PubMed

    Wolf, Paul G; Sessa, Emily B; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J; Sigel, Erin M; Gitzendanner, Matthew A; Visger, Clayton J; Banks, Jo Ann; Soltis, Douglas E; Soltis, Pamela S; Pryer, Kathleen M; Der, Joshua P

    2015-08-26

    Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

  18. An Exploration into Fern Genome Space

    PubMed Central

    Wolf, Paul G.; Sessa, Emily B.; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J.; Sigel, Erin M.; Gitzendanner, Matthew A.; Visger, Clayton J.; Banks, Jo Ann; Soltis, Douglas E.; Soltis, Pamela S.; Pryer, Kathleen M.; Der, Joshua P.

    2015-01-01

    Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants. PMID:26311176

  19. Simplified DGS procedure for large-scale genome structural study.

    PubMed

    Jung, Yong-Chul; Xu, Jia; Chen, Jun; Kim, Yeong; Winchester, David; Wang, San Ming

    2009-11-01

    Ditag genome scanning (DGS) uses next-generation DNA sequencing to sequence the ends of ditag fragments produced by restriction enzymes. These sequences are compared to known genome sequences to determine their structure. In order to use DGS for large-scale genome structural studies, we have substantially revised the original protocol by replacing the in vivo genomic DNA cloning with in vitro adaptor ligation, eliminating the ditag concatemerization steps, and replacing the 454 sequencer with Solexa or SOLiD sequencers for ditag sequence collection. This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously.

  20. Thiamphenicol disposition in pigs.

    PubMed

    Castells, G; Prats, C; El Korchi, G; Pérez, B; Arboix, M; Cristòfol, C; Martì, G

    1999-06-01

    Pharmacokinetic parameters of thiamphenicol (TAP) were determined after intravenous (i.v.) and intramuscular (i.m.) administration of 30 mg kg-1 of TAP in pigs. Plasma drug concentrations were determined by high performance liquid chromatography (HPLC) Intravenous TAP kinetics were fitted to a bi-exponential equation, with a first rapid disposition phase followed by a slower disposition phase. Elimination half-life was short, at 59.3 (29.4) minutes; volume of distribution at steady state was 0.62 (0.24) 1 kg-1; and plasma clearance was 13.4 (4.5) ml min-1 kg-1. After i.m. administration, the peak plasma concentration (Cmax= 4.1 microg ml-1) was reached in about 60 minutes; these concentrations are lower than those reported in other species. The TAP elimination half-life after i.m. administration, 250.2 (107.1) minutes was longer after than i.v. administration, probably due to the slow rate of absorption from the muscle. The mean bioavailability value for i.m. administration was 76 (12) per cent.

  1. 45 CFR 800.107 - Levels of coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... to offer an MSP pursuant to a contract with OPM. (b) Bronze or platinum metal levels of coverage... coverage or the platinum level of coverage, or both, on any Exchange or SHOP in any State. (c)...

  2. 45 CFR 800.107 - Levels of coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... to offer an MSP pursuant to a contract with OPM. (b) Bronze or platinum metal levels of coverage... coverage or the platinum level of coverage, or both, on any Exchange or SHOP in any State. (c)...

  3. 78 FR 217 - Shared Responsibility for Employers Regarding Health Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-02

    ... Shared Responsibility for Employers Regarding Health Coverage; Proposed Rule #0;#0;Federal Register / Vol... Health Coverage AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice of proposed rulemaking... employers regarding employee health coverage. These proposed regulations would affect only employers...

  4. Development of Advanced Technologies for Complete Genomic and Proteomic Characterization of Quantized Human Tumor Cells

    DTIC Science & Technology

    2014-07-01

    biomarker discovery . To complete this aim, we need blood and PBMC cells from both patients and their family members. Our clinical collaborators at...selection and family history of samples submitted to Complete Genomics for WGS analysis. Table 2. CGI quality control template for 12 genomic DNA...from a few kb long to entire chromosomes – based on comparison of the genome coverage signal to a pre-computed “median coverage profile” of many

  5. Guinea-pig reaginic antibody

    PubMed Central

    Margni, R. A.; Hajos, Silvia E.

    1973-01-01

    The methods for isolation and purification of a guinea-pig serum protein with homocytotropic antibody activity and characteristics of IgE are described. By precipitation in the equivalence zone or immunoadsorption and chromatography on DEAE-cellulose, we isolated an homocytotropic antibody, that was not able to give a precipitin line when it was reacted directly with the antigen. It was capable of sensitizing guinea-pig skin for PCA after a latent period of 24–48 hours but not after 3 hours; it was sensitive to treatment with mercaptoethanol. It had antigenic determinants present in the other guinea-pig immunoglobulins and particular antigenic determinants. All these properties make us believe that this protein belongs to an immunoglobulin different from γ1 and similar to the reaginic antibody (IgE) described in other species. ImagesFIG. 3FIG. 4FIG. 5 PMID:4126261

  6. Guinea-pig reaginic antibody

    PubMed Central

    Margni, R. A.; Hajos, Silvia E.

    1973-01-01

    The physicochemical and biological properties of purified guinea-pig reaginic antibody were studied. It is a labile protein different to γ1. Its antibody activity is completely destroyed by heating at 56° for 6 hours and by treatment with mercaptoethanol. The capacity to give PCA is decreased by repeated freezing and thawing. It is a bivalent antibody, haemagglutinating, does not fix complement and is capable of sensitizing guinea-pig skin for PCA reaction after a latent period of a week but not after 3 hours. Reaginic antibody appears on day 7–8 after the first inoculation and the higher levels (PCA reaction) are obtained at the eleventh to thirteenth days. After the fifteenth to seventeenth days the PCA is negative. The reaginic antibody does not pass the placenta. Higher levels of reaginic antibody were obtained when the guinea-pigs were inoculated with the antigen in saline with simultaneous inoculation, intraperitoneally, of killed Bordetella pertussis, phase I. PMID:4354828

  7. Sequencing and genome annotation of honey bee microsporidia parasite, Nosema apis and comparative genome analysis with its sympatric congener, N. ceranae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we present a draft genome sequence and annotation of the honey bee microsporidian parasite, Nosema apis. We applied the whole-genome shotgun (WGS) sequencing approach to sequence and assemble the genome of N. apis to 22-fold sequence coverage. We predicted 2927 protein-coding genes in the N. ...

  8. RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes.

    PubMed

    Buza, Krisztian; Wilczynski, Bartek; Dojer, Norbert

    2015-01-01

    Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

  9. Dietary aluminosilicate supplement enhances immune activity in mice and reinforces clearance of porcine circovirus type 2 in experimentally infected pigs.

    PubMed

    Jung, Bock-Gie; Toan, Nguyen Tat; Cho, Sun-Ju; Ko, Jae-hyung; Jung, Yeon-Kwon; Lee, Bong-Joo

    2010-07-14

    Aluminosilicate is the major component of clay minerals such as zeolite, bentonite and clinoptilolite. The minerals possess a number of beneficial activities, especially in regulating the immune system. The aims of the present study were to evaluate immune enhancing effects of dietary aluminosilicate supplement (DAS) in mice, and to demonstrate clearance effects of DAS against porcine circovirus type 2 (PCV2) in experimentally infected pigs as an initial step towards the development of an antibiotic substitute for use in pigs. Relative messenger RNA expression levels of interferon-gamma, interleukin-4 and tumor necrosis factor-alpha, phagocytic activities of polymorphonuclear leucocytes, serum antibody production level and spleen B cell ratio were significantly increased in the DAS groups of mice compared with the control group (each feeding group had three replications with 5 mice each). The results indicated that general immune activity including cellular and humoral immunity could be enhanced by DAS in mice. In experimentally PCV2-infected pigs, the load of viral genome in nasal swab, serum and lung of the DAS group of pigs was significantly decreased compared with the control group at 28 days post-infection (each group three pigs). Corresponding histopathological analyses demonstrated that pigs in the DAS group displayed mild and less severe abnormal changes compared with the control group, indicating that DAS reinforces clearance of PCV2 in experimentally infected pigs. This may relate to general immune enhancing effects of DAS in mice. Therefore DAS will help the health of animal, especially in swine.

  10. Draft genome sequence of Phomopsis longicolla MSPL 10-6

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phomopsis longicolla T.W. Hobbs is the primary cause of Phomopsis seed decay in soybean. We report the de novo assembled draft genome sequence of P. longicolla isolate MSPL10-6 with a 54.8-fold depth of coverage. The resulting draft genome was estimated to be approximately 64 Mb in size with an over...

  11. Efficient production by sperm-mediated gene transfer of human decay accelerating factor (hDAF) transgenic pigs for xenotransplantation

    PubMed Central

    Lavitrano, Marialuisa; Bacci, Maria Laura; Forni, Monica; Lazzereschi, Davide; Di Stefano, Carla; Fioretti, Daniela; Giancotti, Paola; Marfé, Gabriella; Pucci, Loredana; Renzi, Luigina; Wang, Hongjun; Stoppacciaro, Antonella; Stassi, Giorgio; Sargiacomo, Massimo; Sinibaldi, Paola; Turchi, Valeria; Giovannoni, Roberto; Della Casa, Giacinto; Seren, Eraldo; Rossi, Giancarlo

    2002-01-01

    A large number of hDAF transgenic pigs to be used for xenotransplantation research were generated by using sperm-mediated gene transfer (SMGT). The efficiency of transgenesis obtained with SMGT was much greater than with any other method. In the experiments reported, up to 80% of pigs had the transgene integrated into the genome. Most of the pigs carrying the hDAF gene transcribed it in a stable manner (64%). The great majority of pigs that transcribed the gene expressed the protein (83%). The hDAF gene was transmitted to progeny. Expression was stable and found in caveolae as it is in human cells. The expressed gene was functional based on in vitro experiments performed on peripheral blood mononuclear cells. These results show that our SMGT approach to transgenesis provides an efficient procedure for studies involving large animal models. PMID:12393815

  12. Polar constellations design for discontinuous coverage

    NASA Astrophysics Data System (ADS)

    Sarno, Salvatore; Graziano, Maria Daniela; D'Errico, Marco

    2016-10-01

    A novel constellation design method is developed for discontinuous coverage of the globe and polar caps. It integrates and extends the applicability of the coverage regions and mitigates the limitations of the existing techniques based on streets-of-coverage (SOC) theory. In particular, the visibility conditions of the targets are mapped in the (Ω, u)-domain to identify the number of satellites per plane and the distance between successive orbits, whereas the planes are arranged around the equator exploiting satellites both in ascending and descending phase. The proposed approach is applied to design potential space segments in polar LEO supporting the existing maritime surveillance services over the globe and on the future polar routes. Results show they require a smaller total number of satellites with respect to the SOC-based configurations for revisit times less than one hour and wide range of swaths. In details, it is observed a reduction between 6% and 22% for global coverage and between 24% and 33% for the coverage of polar caps.

  13. Identification of G protein-coupled estrogen receptor in human and pig spermatozoa.

    PubMed

    Rago, V; Giordano, F; Brunelli, E; Zito, D; Aquila, S; Carpino, A

    2014-06-01

    Estrogens are known to influence functional properties of mammalian spermatozoa inducing rapid responses through the classical estrogen receptors (ERα and ERβ). Recently, the G protein-coupled estrogen receptor (GPER) has been identified as mediator of fast non-genomic estrogen effects in different cells. This work investigated the expression of GPER in human and pig spermatozoa using immunofluorescence, Western blot analysis and RT-PCR. GPER was found to be confined to the mid-piece of human sperm cells, whereas it was detected in the acrosomal region, the equatorial segment and the mid-piece of pig spermatozoa. Furthermore, in the male gametes of both species, the immunoblots of sperm extracts revealed a band at ~42 kDa, consistent with the GPER molecular weight, and RT-PCR detected the GPER transcripts. This is the first report demonstrating the expression of GPER in human and pig mature sperm cells and evidencing its species-specific cellular localization.

  14. 42 CFR 422.68 - Effective dates of coverage and change of coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 3 2011-10-01 2011-10-01 false Effective dates of coverage and change of coverage. 422.68 Section 422.68 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM MEDICARE ADVANTAGE PROGRAM Eligibility, Election,...

  15. 5 CFR 842.1009 - Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity computations. 842.1009 Section 842.1009... EMPLOYEES RETIREMENT SYSTEM-BASIC ANNUITY Customs and Border Protection Officers § 842.1009 Elections...

  16. 5 CFR 842.1009 - Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity computations. 842.1009 Section 842.1009... EMPLOYEES RETIREMENT SYSTEM-BASIC ANNUITY Customs and Border Protection Officers § 842.1009 Elections...

  17. 5 CFR 842.1009 - Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Elections of retirement coverage, exclusions from retirement coverage, and proportional annuity computations. 842.1009 Section 842.1009... EMPLOYEES RETIREMENT SYSTEM-BASIC ANNUITY Customs and Border Protection Officers § 842.1009 Elections...

  18. Perplexity analysis of obesity news coverage.

    PubMed

    McFarlane, Delano J; Elhadad, Noémie; Kukafka, Rita

    2009-11-14

    An important task performed during the analysis of health news coverage is the identification of news articles that are related to a specific health topic (e.g. obesity). This is often done using a combination of keyword searching and manual encoding of news content. Statistical language models and their evaluation metric, perplexity, may help to automate this task. A perplexity study of obesity news was performed to evaluate perplexity as a measure of the similarity of news corpora to obesity news content. The results of this study showed that perplexity increased as news coverage became more general relative to obesity news (obesity news approximately 187, general health news approximately 278, general news approximately 378, general news across multiple publishers approximately 382). This indicates that language model perplexity can measure the similarity news content to obesity news coverage, and could be used as the basis for an automated health news classifier.

  19. Learning Time-Varying Coverage Functions

    PubMed Central

    Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

    2015-01-01

    Coverage functions are an important class of discrete functions that capture the law of diminishing returns arising naturally from applications in social network analysis, machine learning, and algorithmic game theory. In this paper, we propose a new problem of learning time-varying coverage functions, and develop a novel parametrization of these functions using random features. Based on the connection between time-varying coverage functions and counting processes, we also propose an efficient parameter learning algorithm based on likelihood maximization, and provide a sample complexity analysis. We applied our algorithm to the influence function estimation problem in information diffusion in social networks, and show that with few assumptions about the diffusion processes, our algorithm is able to estimate influence significantly more accurately than existing approaches on both synthetic and real world data. PMID:25960624

  20. Fermented liquid feed for pigs.

    PubMed

    Missotten, Joris A M; Michiels, Joris; Ovyn, Anneke; De Smet, Stefaan; Dierick, Noël A

    2010-12-01

    Since the announcement of the ban on the use of antibiotics as antimicrobial growth promoters in the feed of pigs in 2006 the investigation towards alternative feed additives has augmented considerably. Although fermented liquid feed is not an additive, but a feeding strategy, the experimental work examining its possible advantages also saw a rise. The use of fermented liquid feed (FLF) has two main advantages, namely that the simultaneous provision of feed and water may result in an alleviation of the transition from the sow milk to solid feed and may also reduce the time spent to find both sources of nutrients, and secondly, that offering FLF with a low pH may strengthen the potential of the stomach as a first line of defence against possible pathogenic infections. Because of these two advantages, FLF is often stated as an ideal feed for weaned piglets. The results obtained so far are rather variable, but in general they show a better body weight gain and worse feed/gain ratio for the piglets. However, for growing-finishing pigs on average a better feed/gain ratio is found compared to pigs fed dry feed. This better performance is mostly associated with less harmful microbiota and better gut morphology. This review provides an overview of the current knowledge of FLF for pigs,dealing with the FLF itself as well as its effect on the gastrointestinal tract and animal performance.

  1. Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduc...

  2. The nature of newspaper coverage of homicide

    PubMed Central

    Taylor, C; Sorenson, S

    2002-01-01

    Objectives: Previous research has shown that some homicides are more likely than others to receive newspaper coverage (for example, homicides by strangers). The present investigation examined whether, once the decision has been made to report on a homicide, the nature of the coverage (that is, how much visibility is given to a story, what information is included, and how a story is written) differs according to two key variables, victim ethnicity, and victim-suspect relationship. Setting: Los Angeles, California (USA). Methods: Homicide articles from the 1990–94 issues of the Los Angeles Times were stratified according to the predictors of interest (victim ethnicity and victim-suspect relationship) and a sample was drawn. Data that characterized two primary aspects of newspaper coverage, prominence and story framing (including background information, story focus, use of opinions, story tone, and "hook" or leading introductory lines) were abstracted from the articles. Descriptive statistics and cross tabulations were generated. Multivariate analyses were conducted to examine the predictive value of victim ethnicity and victim-suspect relationship on the nature of the newspaper coverage. Results: Newspaper coverage of homicide was generally factual, episodic, and unemotional in tone. Victim-suspect relationship, but not victim ethnicity, was related to how a story was covered, particularly the story frame. Homicides by intimates were covered consistently differently from other types of homicides; these stories were less likely to be opinion dominated, be emotional, and begin with a "hook". Conclusion: Victim-suspect relationship was related to the nature of coverage of homicides in a large, metropolitan newspaper. Given the agenda setting and issue framing functions of the news media, these findings have implications for the manner in which the public and policy makers perceive homicides and, consequently, for the support afforded to various types of solutions for

  3. Comparative carcass and tissue nutrient composition of transgenic Yorkshire pigs expressing phytase in the saliva and conventional Yorkshire pigs.

    PubMed

    Forsberg, C W; Meidinger, R G; Ajakaiye, A; Murray, D; Fan, M Z; Mandell, I B; Phillips, J P

    2014-10-01

    A transgenic line of Yorkshire (YK) pigs named the Cassie (CA) line was produced with a low copy number phytase transgene inserted in the genome. The transgenic line efficiently digests P, Ca, and other major minerals of plant dietary origin. The objectives of this study were to 1) compare carcass and tissue nutrient composition and meat quality traits for third generation hemizygous CA line market BW finisher pigs (n = 24) with age-matched conventional YK finisher pigs (n = 24) and 2) examine effects of outbreeding with high-index conventional YK boars on modifying carcass leanness from the third to sixth generations in CA line finisher boars (n = 73) and gilts (n = 103). Cassie boars (n = 12) and CA gilts (n = 12) were fed diets without supplemental P and comparable numbers of age-matched YK boars and gilts fed diets containing supplement P were raised throughout the finisher phase. The pigs were slaughtered and then fabricated into commercial pork primals before meat composition and quality evaluation. Proximate and major micronutrient composition was determined on tissues including fat, kidney, lean, liver, and skin. The main difference observed was greater (P = 0.033) crude fat content in CA boar carcasses and increased (P < 0.04) leaf lard in both CA boars and gilts but no differences were observed (P = 0.895 and P = 0.223, respectively) in carcass backfat thickness as compared with YK pigs. There were no substantive differences in tissue composition, except for CA boar kidneys. Numerous changes in the mineral, fatty acid, and indispensable AA composition for CA boar kidneys were not apparent in CA gilts. These changes may point to adaptive physiological changes in the boar kidney necessary for homeostatic regulation of mineral retention related to phytase action rather than to insertion of the transgene. However, from a meat composition perspective, transgenic expression of phytase in the CA line of YK pigs had little overall effect on meat composition

  4. Genome edited sheep and cattle.

    PubMed

    Proudfoot, Chris; Carlson, Daniel F; Huddart, Rachel; Long, Charles R; Pryor, Jane H; King, Tim J; Lillico, Simon G; Mileham, Alan J; McLaren, David G; Whitelaw, C Bruce A; Fahrenkrug, Scott C

    2015-02-01

    Genome editing tools enable efficient and accurate genome manipulation. An enhanced ability to modify the genomes of livestock species could be utilized to improve disease resistance, productivity or breeding capability as well as the generation of new biomedical models. To date, with respect to the direct injection of genome editor mRNA into livestock zygotes, this technology has been limited to the generation of pigs with edited genomes. To capture the far-reaching applications of gene-editing, from disease modelling to agricultural improvement, the technology must be easily applied to a number of species using a variety of approaches. In this study, we demonstrate zygote injection of TALEN mRNA can also produce gene-edited cattle and sheep. In both species we have targeted the myostatin (MSTN) gene. In addition, we report a critical innovation for application of gene-editing to the cattle industry whereby gene-edited calves can be produced with specified genetics by ovum pickup, in vitro fertilization and zygote microinjection (OPU-IVF-ZM). This provides a practical alternative to somatic cell nuclear transfer for gene knockout or introgression of desirable alleles into a target breed/genetic line.

  5. Rodeo medicine: considerations in event coverage.

    PubMed

    Young, Eliot J; Markey, Keith L

    2010-01-01

    Rodeo is an increasingly popular but dangerous sport, with injury rates higher than any other sport. While there are several organizations that oversee many of the rodeo competitions in the U.S., most events are non-sanctioned. Several factors contribute to the risk for injury, and medical coverage is usually volunteer-based. This article describes the common events that occur in most rodeo competitions, highlights the injuries most often documented in rodeo injury reporting, and suggests guidelines for preparation of medical coverage of a typical rodeo event.

  6. Extreme sports: injuries and medical coverage.

    PubMed

    Young, Craig C

    2002-10-01

    Extreme sports (including in-line skating, snowboarding, mountain bicycling, extreme skiing, rock climbing, indoor tackle football, kickboxing, skateboarding, and ultra-endurance racing) are growing in popularity. Often these sports are designed to expose athletes to greater thrills and risks than are found in traditional sporting activities. Despite this increased risk of injury, athletes competing in these sports often have little or no formal medical coverage. This article reviews what is known about this emerging area of sports medicine to assist physicians in preparing for medical coverage of these athletes and their competitions.

  7. Controlling the coverage area of a microcell

    NASA Astrophysics Data System (ADS)

    Arowojolu, A. A.; Turkmani, A. M. D.

    A theoretical computer-based study has been undertaken to investigate potential mechanisms for controlling the coverage area of a typical urban microcell. These mechanisms, effected at the base station, include antenna height variation, the use of a directional antenna and antenna downtilt. A signal strength prediction algorithm which is based on geometrical optics and the geometrical theory of diffraction and which makes use of the three-dimensional radiation patterns of antennas has been employed in the study. Results obtained in the form of signal strength profiles demonstrate the effectiveness, in particular, of beam tilting for controlling the microcell coverage area.

  8. 20 CFR 404.1412 - Compensation quarters of coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false Compensation quarters of coverage. 404.1412... the Railroad Retirement Program § 404.1412 Compensation quarters of coverage. As used in this subpart, a compensation quarter of coverage is any quarter of coverage computed with respect to...

  9. 20 CFR 404.1412 - Compensation quarters of coverage.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Compensation quarters of coverage. 404.1412... the Railroad Retirement Program § 404.1412 Compensation quarters of coverage. As used in this subpart, a compensation quarter of coverage is any quarter of coverage computed with respect to...

  10. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 11 2012-01-01 2012-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  11. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 11 2010-01-01 2010-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  12. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 11 2013-01-01 2013-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  13. 7 CFR 1737.31 - Area Coverage Survey (ACS).

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 11 2011-01-01 2011-01-01 false Area Coverage Survey (ACS). 1737.31 Section 1737.31... Studies-Area Coverage Survey and Loan Design § 1737.31 Area Coverage Survey (ACS). (a) The Area Coverage Survey (ACS) is a market forecast of service requirements of subscribers in a proposed service area....

  14. 42 CFR 457.1010 - Purchase of family coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Purchase of family coverage. 457.1010 Section 457... Waivers: General Provisions § 457.1010 Purchase of family coverage. A State may purchase family coverage... family coverage is cost-effective under the standards described in § 457.1015; (b) The State does...

  15. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  16. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 4 2013-10-01 2013-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  17. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 4 2014-10-01 2014-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  18. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 4 2012-10-01 2012-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  19. 42 CFR 440.330 - Benchmark health benefits coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Benchmark health benefits coverage. 440.330 Section 440.330 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Benchmark-Equivalent Coverage § 440.330 Benchmark health benefits coverage. Benchmark coverage is...

  20. 46 CFR 154.1155 - Hand hose line: Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Hand hose line: Coverage. 154.1155 Section 154.1155... Firefighting System: Dry Chemical § 154.1155 Hand hose line: Coverage. The coverage for the area for a hand hose line under § 154.1150 must not exceed the length of the hand hose line except the coverage for...