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Sample records for coverage pig genome

  1. 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

  2. The sequence and analysis of a Chinese pig genome

    PubMed Central

    2012-01-01

    Background The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome. Results Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes. Conclusion Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models. PMID:23587058

  3. A decade of pig genome sequencing: a window on pig domestication and evolution.

    PubMed

    Groenen, Martien A M

    2016-03-29

    Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.

  4. 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...

  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. 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. PMID:26640477

  7. 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

  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. 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.

  10. 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.

  11. Unique circovirus-like genome detected in pig feces.

    PubMed

    Cheung, Andrew K; Ng, Terry Fei-Fan; Lager, Kelly M; Alt, David P; Delwart, Eric L; Pogranichniy, Roman M

    2014-01-01

    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 related to a fur seal feces-associated circular DNA virus. PMID:24723710

  12. Genome Pool Strategy for Structural Coverage of Protein Families

    SciTech Connect

    Jaroszewski, L.; Slabinski, L.; Wooley, J.; Deacon, A.M.; Lesley, S.A.; Wilson, I.A.; Godzik, A.

    2009-05-18

    Even closely homologous proteins often have different crystallization properties and propensities. This observation can be used to introduce an additional dimension into crystallization trials by simultaneous targeting multiple homologs in what we call a 'genome pool' strategy. We show that this strategy works because protein physicochemical properties correlated with crystallization success have a surprisingly broad distribution within most protein families. There are also easy and difficult families where this distribution is tilted in one direction. This leads to uneven structural coverage of protein families, with more easy ones solved. Increasing the size of the genome pool can improve chances of solving the difficult ones. In contrast, our analysis does not indicate that any specific genomes are easy or difficult. Finally, we show that the group of proteins with known 3D structures is systematically different from the general pool of known proteins and we assess the structural consequences of these differences.

  13. Deciphering the pig genome to understand gamete production.

    PubMed

    Rohrer, G A; Wise, T H; Ford, J J

    2006-01-01

    The field of livestock genomics has made considerable advances in the past decade. In the area of pig reproduction, a number of genome scans have identified several genomic regions associated with variation in reproductive measures ranging from ovulation rate, litter size and testis size. Additionally, several candidate genes have been associated with variation in litter size. These studies primarily focused on developing genetic markers to facilitate selection decisions. To date, their results have made minor contributions to commercial pig performance and our knowledge on the inheritance of complex phenotypes. With the availability of additional resources for pig, as well as from human and mouse studies, future studies should be directed to identifying genetic variation that affects biological processes. To reach this goal, teams of diversely trained scientists need to be formed that include geneticists, physiologists, molecular biologists and bioinformaticists. A diversified team of scientists equipped with all of the available research tools (genomic sequence data, expression arrays, knowledge of gene product functions, etc.) and appropriate swine populations should be able to decode the genome's hidden secrets on how it controls reproductive processes.

  14. 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...

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

    PubMed

    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. 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

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

    PubMed

    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

    2016-06-27

    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.

  18. Mining the pig genome to investigate the domestication process.

    PubMed

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

    2014-12-01

    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.

  19. 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

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

    PubMed

    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.

  1. 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

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

    PubMed

    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

  3. 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

  4. A whole-genome association study for pig reproductive traits.

    PubMed

    Onteru, S K; Fan, B; Du, Z-Q; Garrick, D J; Stalder, K J; Rothschild, M F

    2012-02-01

    A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.

  5. 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. PMID:25741365

  6. 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.

  7. 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...

  8. Analyses of pig genomes provide insight into porcine demography and evolution

    PubMed Central

    Groenen, Martien A. M.; Archibald, Alan L.; Uenishi, Hirohide; Tuggle, Christopher K.; Takeuchi, Yasuhiro; Rothschild, Max F.; Rogel-Gaillard, Claire; Park, Chankyu; Milan, Denis; Megens, Hendrik-Jan; Li, Shengting; Larkin, Denis M.; Kim, Heebal; Frantz, Laurent A. F.; Caccamo, Mario; Ahn, Hyeonju; Aken, Bronwen L.; Anselmo, Anna; Anthon, Christian; Auvil, Loretta; Badaoui, Bouabid; Beattie, Craig W.; Bendixen, Christian; Berman, Daniel; Blecha, Frank; Blomberg, Jonas; Bolund, Lars; Bosse, Mirte; Botti, Sara; Bujie, Zhan; Bystrom, Megan; Capitanu, Boris; Silva, Denise Carvalho; Chardon, Patrick; Chen, Celine; Cheng, Ryan; Choi, Sang-Haeng; Chow, William; Clark, Richard C.; Clee, Christopher; Crooijmans, Richard P. M. A.; Dawson, Harry D.; Dehais, Patrice; De Sapio, Fioravante; Dibbits, Bert; Drou, Nizar; Du, Zhi-Qiang; Eversole, Kellye; Fadista, João; Fairley, Susan; Faraut, Thomas; Faulkner, Geoffrey J.; Fowler, Katie E.; Fredholm, Merete; Fritz, Eric; Gilbert, James G. R.; Giuffra, Elisabetta; Gorodkin, Jan; Griffin, Darren K.; Harrow, Jennifer L.; Hayward, Alexander; Howe, Kerstin; Hu, Zhi-Liang; Humphray, Sean J.; Hunt, Toby; Hornshøj, Henrik; Jeon, Jin-Tae; Jern, Patric; Jones, Matthew; Jurka, Jerzy; Kanamori, Hiroyuki; Kapetanovic, Ronan; Kim, Jaebum; Kim, Jae-Hwan; Kim, Kyu-Won; Kim, Tae-Hun; Larson, Greger; Lee, Kyooyeol; Lee, Kyung-Tai; Leggett, Richard; Lewin, Harris A.; Li, Yingrui; Liu, Wansheng; Loveland, Jane E.; Lu, Yao; Lunney, Joan K.; Ma, Jian; Madsen, Ole; Mann, Katherine; Matthews, Lucy; McLaren, Stuart; Morozumi, Takeya; Murtaugh, Michael P.; Narayan, Jitendra; Nguyen, Dinh Truong; Ni, Peixiang; Oh, Song-Jung; Onteru, Suneel; Panitz, Frank; Park, Eung-Woo; Park, Hong-Seog; Pascal, Geraldine; Paudel, Yogesh; Perez-Enciso, Miguel; Ramirez-Gonzalez, Ricardo; Reecy, James M.; Zas, Sandra Rodriguez; Rohrer, Gary A.; Rund, Lauretta; Sang, Yongming; Schachtschneider, Kyle; Schraiber, Joshua G.; Schwartz, John; Scobie, Linda; Scott, Carol; Searle, Stephen; Servin, Bertrand; Southey, Bruce R.; Sperber, Goran; Stadler, Peter; Sweedler, Jonathan V.; Tafer, Hakim; Thomsen, Bo; Wali, Rashmi; Wang, Jian; Wang, Jun; White, Simon; Xu, Xun; Yerle, Martine; Zhang, Guojie; Zhang, Jianguo; Zhang, Jie; Zhao, Shuhong; Rogers, Jane; Churcher, Carol; Schook, Lawrence B.

    2013-01-01

    For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. PMID:23151582

  9. First Genome Sequences of Porcine Parvovirus 5 Strains Identified in Polish Pigs

    PubMed Central

    Fan, Jinghui; Cui, Jin; Gerber, Priscilla F.; Biernacka, Kinga; Stadejek, Tomasz

    2016-01-01

    Porcine parvovirus type 5 (PPV5) has been recently identified. Here, we report the genome sequences of five PPV5 strains identified in serum samples from Polish pigs, which represent the first PPV5 sequences recovered from European pigs. The PPV5 strains isolated in Poland are most related to the Chinese strain HN01. PMID:27587805

  10. Genetic Diversity, Linkage Disequilibrium and Selection Signatures in Chinese and Western Pigs Revealed by Genome-Wide SNP Markers

    PubMed Central

    Ai, Huashui; Huang, Lusheng; Ren, Jun

    2013-01-01

    To investigate population structure, linkage disequilibrium (LD) pattern and selection signature at the genome level in Chinese and Western pigs, we genotyped 304 unrelated animals from 18 diverse populations using porcine 60 K SNP chips. We confirmed the divergent evolution between Chinese and Western pigs and showed distinct topological structures of the tested populations. We acquired the evidence for the introgression of Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity revealed that historical inbreeding reduced genetic variability in several Chinese breeds. We found that intrapopulation LD extents are roughly comparable between Chinese and Western pigs. However, interpopulation LD is much longer in Western pigs compared with Chinese pigs with average r20.3 values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs. The finding indicates that higher-density markers are required to capture LD with causal variants in genome-wide association studies and genomic selection on Chinese pigs. Further, we looked across the genome to identify candidate loci under selection using FST outlier tests on two contrast samples: Tibetan pigs versus lowland pigs and belted pigs against non-belted pigs. Interestingly, we highlighted several genes including ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in Tibetan pigs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports indicates that the underlying genetic basis for high-altitude adaptation in Tibetan pigs, Tibetan peoples and yaks is likely distinct from one another. Moreover, we identified the strongest signal of directional selection at the EDNRB loci in Chinese belted pigs, supporting EDNRB as a promising candidate gene for the white belt coat color in Chinese pigs. Altogether, our findings advance the understanding of the genome biology of Chinese and Western pigs. PMID:23409110

  11. Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

    PubMed Central

    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. PMID:25192061

  12. 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.

  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

    2015-01-01

    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

  14. 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...

  15. Mapping and annotating obesity-related genes in pig and human genomes.

    PubMed

    Martelli, Pier Luigi; Fontanesi, Luca; Piovesan, Damiano; Fariselli, Piero; Casadio, Rita

    2014-01-01

    Background. Obesity is a major health problem in both developed and emerging countries. Obesity is a complex disease whose etiology involves genetic factors in strong interplay with environmental determinants and lifestyle. The discovery of genetic factors and biological pathways underlying human obesity is hampered by the difficulty in controlling the genetic background of human cohorts. Animal models are then necessary to further dissect the genetics of obesity. Pig has emerged as one of the most attractive models, because of the similarity with humans in the mechanisms regulating the fat deposition. Results. We collected the genes related to obesity in humans and to fat deposition traits in pig. We localized them on both human and pig genomes, building a map useful to interpret comparative studies on obesity. We characterized the collected genes structurally and functionally with BAR+ and mapped them on KEGG pathways and on STRING protein interaction network. Conclusions. The collected set consists of 361 obesity related genes in human and pig genomes. All genes were mapped on the human genome, and 54 could not be localized on the pig genome (release 2012). Only for 3 human genes there is no counterpart in pig, confirming that this animal is a good model for human obesity studies. Obesity related genes are mostly involved in regulation and signaling processes/pathways and relevant connection emerges between obesity-related genes and diseases such as cancer and infectious diseases.

  16. A genome-wide association analysis for susceptibility of pigs to enterotoxigenic Escherichia coli F41.

    PubMed

    Ji, H Y; Yang, B; Zhang, Z Y; Ouyang, J; Yang, M; Zhang, X F; Zhang, W C; Su, Y; Zhao, K W; Xiao, S J; Yan, X M; Ren, J; Huang, L S

    2016-10-01

    Enterotoxigenic Escherichia coli (ETEC) is a type of pathogenic bacteria that cause diarrhea in piglets through colonizing pig small intestine epithelial cells by their surface fimbriae. Different fimbriae type of ETEC including F4, F18, K99 and F41 have been isolated from diarrheal pigs. In this study, we performed a genome-wide association study to map the loci associated with the susceptibility of pigs to ETEC F41 using 39454 single nucleotide polymorphisms (SNPs) in 667 F2 pigs from a White Duroc×Erhualian F2 cross. The most significant SNP (ALGA0022658, P=5.59×10-13) located at 6.95 Mb on chromosome 4. ALGA0022658 was in high linkage disequilibrium (r 2>0.5) with surrounding SNPs that span a 1.21 Mb interval. Within this 1.21 Mb region, we investigated ZFAT as a positional candidate gene. We re-sequenced cDNA of ZFAT in four pigs with different susceptibility phenotypes, and identified seven coding variants. We genotyped these seven variants in 287 unrelated pigs from 15 diverse breeds that were measured with ETEC F41 susceptibility phenotype. Five variants showed nominal significant association (P<0.05) with ETEC F41 susceptibility phenotype in International commercial pigs. This study provided refined region associated with susceptibility of pigs to ETEC F41 than that reported previously. Further works are needed to uncover the underlying causal mutation(s).

  17. A high-coverage genome sequence from an archaic Denisovan individual.

    PubMed

    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

    2012-10-12

    We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) 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.

  18. 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.

  19. Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

    PubMed Central

    Leese, Florian; Mayer, Christoph; Agrawal, Shobhit; Dambach, Johannes; Dietz, Lars; Doemel, Jana S.; Goodall-Copstake, William P.; Held, Christoph; Jackson, Jennifer A.; Lampert, Kathrin P.; Linse, Katrin; Macher, Jan N.; Nolzen, Jennifer; Raupach, Michael J.; Rivera, Nicole T.; Schubart, Christoph D.; Striewski, Sebastian; Tollrian, Ralph; Sands, Chester J.

    2012-01-01

    High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests

  20. 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

  1. 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

  2. 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.

  3. 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

    2015-01-01

    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. PMID:25867439

  4. Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

    PubMed Central

    Zhang, Chunyan; Plastow, Graham

    2011-01-01

    We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (FIS), population differentiation (FST), and Nei’s genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher FIS, and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies. PMID:21966252

  5. 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.

  6. Draft Genome Sequences of Two Brucella abortus Strains Isolated from Cattle and Pig.

    PubMed

    Sharma, Narinder Singh; Sunita, Thakhur; Arora, A K; Mudit, Chandra; Kaur, Paviter; Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2015-01-01

    We report the draft genome sequences of two Brucella abortus strains LMN1 and LMN2 isolated from cattle and pig. The LMN1 and LMN2 have the genome size of 3,395,952 bp and 3,334,792 bp, respectively. In addition to the conserved genes of Brucella, few novel regions showing similarity to the phages were identified in both strains.

  7. Draft Genome Sequences of Two Brucella abortus Strains Isolated from Cattle and Pig

    PubMed Central

    Sharma, Narinder Singh; Sunita, Thakhur; Arora, A K; Mudit, Chandra; Kaur, Paviter; Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2015-01-01

    We report the draft genome sequences of two Brucella abortus strains LMN1 and LMN2 isolated from cattle and pig. The LMN1 and LMN2 have the genome size of 3,395,952 bp and 3,334,792 bp, respectively. In addition to the conserved genes of Brucella, few novel regions showing similarity to the phages were identified in both strains. PMID:26816552

  8. Complete Genome Sequence of Leptospira interrogans Serovar Bratislava, Strain PigK151

    PubMed Central

    Alt, David P.; Bayles, Darrell O.; Cameron, Caroline; Adler, Ben; Bulach, Dieter M.; Seemann, Torsten; Lehane, Michael J.; Haines, Lee R.; Darby, Alistair C.; Hall, Neil; Radford, Alan D.; Zuerner, Richard L.

    2015-01-01

    Leptospira interrogans serovar Bratislava infection occurs in multiple domestic and wildlife species and is associated with poor reproductive performance in swine and horses. We present the complete genome assembly of strain PigK151 comprising two chromosomes, CI (4.457 Mbp) and CII (358 kbp). PMID:26112787

  9. Complete Genome Sequence of Bordetella bronchiseptica S798, an Isolate from a Pig with Atrophic Rhinitis.

    PubMed

    Okada, Keisuke; Ogura, Yoshitoshi; Hayashi, Tetsuya; Abe, Akio; Kuwae, Asaomi; Horiguchi, Yasuhiko; Abe, Hiroyuki

    2014-01-01

    Bordetella bronchiseptica colonizes the respiratory tracts of a wide variety of mammals and causes a range of diseases, from lethal pneumonia to asymptomatic chronic infection. We report the complete genome sequence of Bordetella bronchiseptica strain S798, isolated from a pig with atrophic rhinitis in Japan. PMID:24831150

  10. Complete Genome Sequence of Bordetella bronchiseptica S798, an Isolate from a Pig with Atrophic Rhinitis.

    PubMed

    Okada, Keisuke; Ogura, Yoshitoshi; Hayashi, Tetsuya; Abe, Akio; Kuwae, Asaomi; Horiguchi, Yasuhiko; Abe, Hiroyuki

    2014-01-01

    Bordetella bronchiseptica colonizes the respiratory tracts of a wide variety of mammals and causes a range of diseases, from lethal pneumonia to asymptomatic chronic infection. We report the complete genome sequence of Bordetella bronchiseptica strain S798, isolated from a pig with atrophic rhinitis in Japan.

  11. 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...

  12. A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing1

    PubMed Central

    Garaycochea, Silvia; Speranza, Pablo; Alvarez-Valin, Fernando

    2015-01-01

    Premise of the study: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. Results: From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. Discussion: We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought. PMID:26504677

  13. Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales.

    PubMed

    Hertweck, Kate L

    2013-09-01

    The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources. PMID:24168669

  14. Comparison of dimensionality reduction methods to predict genomic breeding values for carcass traits in pigs.

    PubMed

    Azevedo, C F; Nascimento, M; Silva, F F; Resende, M D V; Lopes, P S; Guimarães, S E F; Glória, L S

    2015-01-01

    A significant contribution of molecular genetics is the direct use of DNA information to identify genetically superior individuals. With this approach, genome-wide selection (GWS) can be used for this purpose. GWS consists of analyzing a large number of single nucleotide polymorphism markers widely distributed in the genome; however, because the number of markers is much larger than the number of genotyped individuals, and such markers are highly correlated, special statistical methods are widely required. Among these methods, independent component regression, principal component regression, partial least squares, and partial principal components stand out. Thus, the aim of this study was to propose an application of the methods of dimensionality reduction to GWS of carcass traits in an F2 (Piau x commercial line) pig population. The results show similarities between the principal and the independent component methods and provided the most accurate genomic breeding estimates for most carcass traits in pigs. PMID:26505370

  15. What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae)

    PubMed Central

    2009-01-01

    Background The declining cost of DNA sequencing is making genome sequencing a feasible option for more organisms, including many of interest to ecologists and evolutionary biologists. While obtaining high-depth, completely assembled genome sequences for most non-model organisms remains challenging, low-coverage genome survey sequences (GSS) can provide a wealth of biologically useful information at low cost. Here, using a random pyrosequencing approach, we sequence the genome of the scuttle fly Megaselia scalaris and evaluate the utility of our low-coverage GSS approach. Results Random pyrosequencing of the M. scalaris genome provided a depth of coverage (0.05-0.1x) much lower than typical GSS studies. We demonstrate that, even with extremely low-coverage sequencing, bioinformatics approaches can yield extensive information about functional and repetitive elements. We also use our GSS data to develop genomic resources such as a nearly complete mitochondrial genome sequence and microsatellite markers for M. scalaris. Conclusion We conclude that low-coverage genome surveys are effective at generating useful information about organisms currently lacking genomic sequence data. PMID:19689807

  16. GStream: improving SNP and CNV coverage on genome-wide association studies.

    PubMed

    Alonso, Arnald; Marsal, Sara; Tortosa, Raül; Canela-Xandri, Oriol; Julià, Antonio

    2013-01-01

    We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.

  17. GStream: Improving SNP and CNV Coverage on Genome-Wide Association Studies

    PubMed Central

    Alonso, Arnald; Marsal, Sara; Tortosa, Raül; Canela-Xandri, Oriol; Julià, Antonio

    2013-01-01

    We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method. PMID:23844243

  18. 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.

  19. 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. PMID:24810432

  20. Analysis of Transposable Elements in the Genome of Asparagus officinalis from High Coverage Sequence Data

    PubMed Central

    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. PMID:24810432

  1. Draft Genome Sequence of Megasphaera sp. Strain DJF_B143, an Isolate from Pig Hindgut Unable to Produce Skatole.

    PubMed

    Li, Xiaoqiong; Marshall, Ian P G; Schreiber, Lars; Højberg, Ole; Canibe, Nuria; Jensen, Bent Borg

    2016-01-01

    The butyrate-producing Megasphaera spp. predominate in the pig hindgut and may play important roles in gut health. Moreover, one Megasphaera isolate has been reported to produce the boar taint compound, skatole. Here, we provide a 2.58-Mbp draft genome of a pig hindgut isolate, Megasphaera sp. DJF_B143, unable to produce skatole. PMID:26950318

  2. Draft Genome Sequence of Megasphaera sp. Strain DJF_B143, an Isolate from Pig Hindgut Unable to Produce Skatole

    PubMed Central

    Marshall, Ian P. G.; Schreiber, Lars; Højberg, Ole; Canibe, Nuria; Jensen, Bent Borg

    2016-01-01

    The butyrate-producing Megasphaera spp. predominate in the pig hindgut and may play important roles in gut health. Moreover, one Megasphaera isolate has been reported to produce the boar taint compound, skatole. Here, we provide a 2.58-Mbp draft genome of a pig hindgut isolate, Megasphaera sp. DJF_B143, unable to produce skatole. PMID:26950318

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

    PubMed Central

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

    2014-01-01

    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. PMID:24863459

  4. 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. PMID:24863459

  5. 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.

  6. 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

  7. 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

  8. Genome-wide association QTL mapping for teat number in a purebred population of Duroc pigs.

    PubMed

    Arakawa, A; Okumura, N; Taniguchi, M; Hayashi, T; Hirose, K; Fukawa, K; Ito, T; Matsumoto, T; Uenishi, H; Mikawa, S

    2015-10-01

    Because of increasing litter size in Western pig breeds, additional teats are desirable to increase the capacity for nursing offspring. We applied genome-wide SNP markers to detect QTL regions that affect teat number in a Duroc population. We phenotyped 1024 animals for total teat number. A total of 36 588 SNPs on autosomes were used in the analysis. The estimated heritability for teat number was 0.34 ± 0.05 on the basis of a genomic relationship matrix constructed from all SNP markers. Using a BayesC method, we identified a total of 18 QTL regions that affected teat number in Duroc pigs; 9 of the 18 regions were newly detected.

  9. Comparison of Gene Expression and Genome-Wide DNA Methylation Profiling between Phenotypically Normal Cloned Pigs and Conventionally Bred Controls

    PubMed Central

    Li, Shengting; Li, Jian; Lin, Lin; Nielsen, Anders Lade; Sørensen, Charlotte Brandt; Vajta, Gábor; Wang, Jun; Zhang, Xiuqing; Du, Yutao; Yang, Huanming; Bolund, Lars

    2011-01-01

    Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions. PMID:22022462

  10. Genome-wide association studies for hematological traits in Chinese Sutai pigs

    PubMed Central

    2014-01-01

    Background It has been shown that hematological traits are strongly associated with the metabolism and the immune system in domestic pig. However, little is known about the genetic architecture of hematological traits. To identify quantitative trait loci (QTL) controlling hematological traits, we performed single marker Genome-wide association studies (GWAS) and haplotype analysis for 15 hematological traits in 495 Chinese Sutai pigs. Results We identified 161 significant SNPs including 44 genome-wide significant SNPs associated with 11 hematological traits by single marker GWAS. Most of them were located on SSC2. Meanwhile, we detected 499 significant SNPs containing 154 genome-wide significant SNPs associated with 9 hematological traits by haplotype analysis. Most of the identified loci were located on SSC7 and SSC9. Conclusions We detected 4 SNPs with pleiotropic effects on SSC2 by single marker GWAS and (or) on SSC7 by haplotype analysis. Furthermore, through checking the gene functional annotations, positions and their expression variation, we finally selected 7 genes as potential candidates. Specially, we found that three genes (TRIM58, TRIM26 and TRIM21) of them originated from the same gene family and executed similar function of innate and adaptive immune. The findings will contribute to dissection the immune gene network, further identification of causative mutations underlying the identified QTLs and providing insights into the molecular basis of hematological trait in domestic pig. PMID:24674592

  11. Evaluation of genome coverage and fidelity of multiple displacement amplification from single cells by SNP array.

    PubMed

    Ling, Jiawei; Zhuang, Guanglun; Tazon-Vega, Barbara; Zhang, Chenhui; Cao, Baoqiang; Rosenwaks, Zev; Xu, Kangpu

    2009-11-01

    The scarce amount of DNA contained in a single cell is a limiting factor for clinical application of preimplantation genetic diagnosis mainly due to the risk of misdiagnosis caused by allele dropout and the difficulty in obtaining copy number variations in all 23 pairs of chromosomes. Multiple displacement amplification (MDA) has been reported to generate large quantity of products from small amount of templates. Here, we evaluated the fidelity of whole-genome amplification MDA from single or a few cells and determined the accuracy of chromosome copy number assessment on these MDA products using an Affymetrix 10K 2.0 SNP Mapping Array. An average coverage rate (86.2%) from single cells was obtained and the rates increased significantly when five or more cells were used as templates. Higher concordance for chromosome copy number from single cells could be achieved when the MDA amplified product was used as reference (93.1%) than when gDNA used as reference (82.8%). The present study indicates that satisfactory genome coverage can be obtained from single-cell MDA which may be used for studies where only a minute amount of genetic materials is available. Clinically, MDA coupled with SNP mapping array may provide a reliable and accurate method for chromosome copy number analysis and most likely for the detection of single-gene disorders as well. PMID:19671595

  12. 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

  13. 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. PMID:27098910

  14. Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries.

    PubMed

    Akanno, E C; Schenkel, F S; Sargolzaei, M; Friendship, R M; Robinson, J A B

    2014-10-01

    Genetic improvement of pigs in tropical developing countries has focused on imported exotic populations which have been subjected to intensive selection with attendant high population-wide linkage disequilibrium (LD). Presently, indigenous pig population with limited selection and low LD are being considered for improvement. Given that the infrastructure for genetic improvement using the conventional BLUP selection methods are lacking, a genome-wide selection (GS) program was proposed for developing countries. A simulation study was conducted to evaluate the option of using 60 K SNP panel and observed amount of LD in the exotic and indigenous pig populations. Several scenarios were evaluated including different size and structure of training and validation populations, different selection methods and long-term accuracy of GS in different population/breeding structures and traits. The training set included previously selected exotic population, unselected indigenous population and their crossbreds. Traits studied included number born alive (NBA), average daily gain (ADG) and back fat thickness (BFT). The ridge regression method was used to train the prediction model. The results showed that accuracies of genomic breeding values (GBVs) in the range of 0.30 (NBA) to 0.86 (BFT) in the validation population are expected if high density marker panels are utilized. The GS method improved accuracy of breeding values better than pedigree-based approach for traits with low heritability and in young animals with no performance data. Crossbred training population performed better than purebreds when validation was in populations with similar or a different structure as in the training set. Genome-wide selection holds promise for genetic improvement of pigs in the tropics. PMID:24628765

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

    PubMed

    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

  16. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

    PubMed Central

    Bosse, Mirte; Megens, Hendrik-Jan; Frantz, Laurent A. F.; Madsen, Ole; Larson, Greger; Paudel, Yogesh; Duijvesteijn, Naomi; Harlizius, Barbara; Hagemeijer, Yanick; Crooijmans, Richard P. M. A.; Groenen, Martien A. M.

    2014-01-01

    The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds. PMID:25025832

  17. 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

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

    PubMed

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

    2016-04-21

    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.

  19. Genomic Selection for Adjacent Genetic Markers of Yorkshire Pigs Using Regularized Regression Approaches

    PubMed Central

    Park, Minsu; Kim, Tae-Hun; Cho, Eun-Seok; Kim, Heebal; Oh, Hee-Seok

    2014-01-01

    This study considers a problem of genomic selection (GS) for adjacent genetic markers of Yorkshire pigs which are typically correlated. The GS has been widely used to efficiently estimate target variables such as molecular breeding values using markers across the entire genome. Recently, GS has been applied to animals as well as plants, especially to pigs. For efficient selection of variables with specific traits in pig breeding, it is required that any such variable selection retains some properties: i) it produces a simple model by identifying insignificant variables; ii) it improves the accuracy of the prediction of future data; and iii) it is feasible to handle high-dimensional data in which the number of variables is larger than the number of observations. In this paper, we applied several variable selection methods including least absolute shrinkage and selection operator (LASSO), fused LASSO and elastic net to data with 47K single nucleotide polymorphisms and litter size for 519 observed sows. Based on experiments, we observed that the fused LASSO outperforms other approaches. PMID:25358359

  20. 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

  1. Factor analysis applied to genome prediction for high-dimensional phenotypes in pigs.

    PubMed

    Teixeira, F R F; Nascimento, M; Nascimento, A C C; E Silva, F F; Cruz, C D; Azevedo, C F; Paixão, D M; Barroso, L M A; Verardo, L L; de Resende, M D V; Guimarães, S E F; Lopes, P S

    2016-01-01

    The aim of the present study was to propose and evaluate the use of factor analysis (FA) in obtaining latent variables (factors) that represent a set of pig traits simultaneously, for use in genome-wide selection (GWS) studies. We used crosses between outbred F2 populations of Brazilian Piau X commercial pigs. Data were obtained on 345 F2 pigs, genotyped for 237 SNPs, with 41 traits. FA allowed us to obtain four biologically interpretable factors: "weight", "fat", "loin", and "performance". These factors were used as dependent variables in multiple regression models of genomic selection (Bayes A, Bayes B, RR-BLUP, and Bayesian LASSO). The use of FA is presented as an interesting alternative to select individuals for multiple variables simultaneously in GWS studies; accuracy measurements of the factors were similar to those obtained when the original traits were considered individually. The similarities between the top 10% of individuals selected by the factor, and those selected by the individual traits, were also satisfactory. Moreover, the estimated markers effects for the traits were similar to those found for the relevant factor. PMID:27323029

  2. Mechanisms of regulation of litter size in pigs on the genome level.

    PubMed

    Distl, O

    2007-09-01

    Improvement in litter size has become of great interest in pig industry as good fecundity is directly related to a sow's productive life. Genetic regulation of litter size is complex and the main component traits so far defined are ovulation rate, embryonic survival, uterus capacity, foetal survival and pre-weaning losses. Improvements using concepts of the quantitative genetics let expect only slow genetic progress due to its low heritability of approximately 0.09 for number of piglets born alive. Marker assisted selection allows to dissect litter size in its component traits and using molecular genetic markers for the components of litter size traits promises more progress and advantages in optimum balancing of the different physiological mechanisms influencing litter size. In this review, efforts being made to unravel the genetic determinants of litter size are accounted and discussed. For litter size traits, more than 50 quantitative trait loci (QTL) were mapped and in more than 12 candidate genes associations confirmed. The number of useful candidate genes is much larger as shown by expression profiles and in addition, much more QTL can be assumed. These functional genomic approaches, both QTL mapping and candidate gene analysis, have to be merged for a better understanding of a wider application across different pig breeds and lines. Newly developed tools based on microarray techniques comprising DNA variants or expressed tags of many genes or even the whole genome appear useful for in depth understanding of the genetics of litter size in pigs.

  3. 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

  4. SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs.

    PubMed

    Do, D N; Janss, L L G; Jensen, J; Kadarmideen, H N

    2015-05-01

    The study investigated genetic architecture and predictive ability using genomic annotation of residual feed intake (RFI) and its component traits (daily feed intake [DFI], ADG, and back fat [BF]). A total of 1,272 Duroc pigs had both genotypic and phenotypic records, and the records were split into a training (968 pigs) and a validation dataset (304 pigs) by assigning records as before and after January 1, 2012, respectively. SNP were annotated by 14 different classes using Ensembl variant effect prediction. Predictive accuracy and prediction bias were calculated using Bayesian Power LASSO, Bayesian A, B, and Cπ, and genomic BLUP (GBLUP) methods. Predictive accuracy ranged from 0.508 to 0.531, 0.506 to 0.532, 0.276 to 0.357, and 0.308 to 0.362 for DFI, RFI, ADG, and BF, respectively. BayesCπ100.1 increased accuracy slightly compared to the GBLUP model and other methods. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP groups. Genomic prediction has accuracy comparable to observed phenotype, and use of genomic prediction can be cost effective by replacing feed intake measurement. Genomic annotation had less impact on predictive accuracy traits considered here but may be different for other traits. It is the first study to provide useful insights into biological classes of SNP driving the whole genomic prediction for complex traits in pigs.

  5. 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

  6. First report of Metastrongylus pudendotectus by the genetic characterization of mitochondria genome of cox1 in pigs from Tibet, China.

    PubMed

    Li, Kun; Luo, Houqiang; Zhang, Hui; Lan, Yanfang; Han, Zhaoqing; Shahzad, Muhammad; Wang, Xiaoqiang; Qiu, Gang; Huang, Shucheng; Jiang, Wenteng; Li, Jiakui

    2016-06-15

    Lungworms, a world wild distributed parasites cause serious respiratory diseases to the pigs. A high infection rate of Metastrongylus lungworms has been found in Tibetan pigs being slaughtered in different slaughter houses of Tibet autonomous region. The main aim of our study was to detect and confirm the lungworm parasite by the genetic characterization of mitochondrial cox1genome isolated from the lungs of Tibetan pig. The adult lungworms were collected from the lungs of slaughtered pigs and identification was done through morphological examinations. Total genomic DNA of the extracted worms was performed and a fragment (∼450bp) of the cox1 of mitochondrial (mt) gene was amplified. Amplicons were cloned into PGEM(®)-T Easy vector and the positive clones were sequenced from a commercial company. Sequence and phylogenetic analysis were performed by software of DNAMAN and MEGA respectively. The results revealed that the lungworms infecting the Tibetan pigs were Metastrongylus pudendotectus (M. pudendotectus). To our knowledge, this is the first report for the isolation and identification for the genetic characterization of mitochondria (mt) genome of cox1 of M. pudendotectus derived from Tibetan pigs in Tibet, China. PMID:27198783

  7. First report of Metastrongylus pudendotectus by the genetic characterization of mitochondria genome of cox1 in pigs from Tibet, China.

    PubMed

    Li, Kun; Luo, Houqiang; Zhang, Hui; Lan, Yanfang; Han, Zhaoqing; Shahzad, Muhammad; Wang, Xiaoqiang; Qiu, Gang; Huang, Shucheng; Jiang, Wenteng; Li, Jiakui

    2016-06-15

    Lungworms, a world wild distributed parasites cause serious respiratory diseases to the pigs. A high infection rate of Metastrongylus lungworms has been found in Tibetan pigs being slaughtered in different slaughter houses of Tibet autonomous region. The main aim of our study was to detect and confirm the lungworm parasite by the genetic characterization of mitochondrial cox1genome isolated from the lungs of Tibetan pig. The adult lungworms were collected from the lungs of slaughtered pigs and identification was done through morphological examinations. Total genomic DNA of the extracted worms was performed and a fragment (∼450bp) of the cox1 of mitochondrial (mt) gene was amplified. Amplicons were cloned into PGEM(®)-T Easy vector and the positive clones were sequenced from a commercial company. Sequence and phylogenetic analysis were performed by software of DNAMAN and MEGA respectively. The results revealed that the lungworms infecting the Tibetan pigs were Metastrongylus pudendotectus (M. pudendotectus). To our knowledge, this is the first report for the isolation and identification for the genetic characterization of mitochondria (mt) genome of cox1 of M. pudendotectus derived from Tibetan pigs in Tibet, China.

  8. Expanded microbial genome coverage and improved protein family annotation in the COG database

    PubMed Central

    Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

    2015-01-01

    Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the

  9. 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.

  10. Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

    PubMed Central

    Diaz, Andres; Enomoto, Shinichiro; Romagosa, Anna; Sreevatsan, Srinand; Nelson, Martha; Culhane, Marie

    2015-01-01

    To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n = 10). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis. PMID:26251306

  11. Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs.

    PubMed

    Diaz, Andres; Enomoto, Shinichiro; Romagosa, Anna; Sreevatsan, Srinand; Nelson, Martha; Culhane, Marie; Torremorell, Montserrat

    2015-10-01

    To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n = 10). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis. PMID:26251306

  12. 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

  13. 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.

  14. 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.

  15. Enhancing Genome-Wide Copy Number Variation Identification by High Density Array CGH Using Diverse Resources of Pig Breeds

    PubMed Central

    Wang, Jiying; Jiang, Jicai; Wang, Haifei; Kang, Huimin; Zhang, Qin; Liu, Jian-Feng

    2014-01-01

    Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs. PMID:24475311

  16. Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs.

    PubMed

    Zhou, Zhong-Yin; Li, Ai-Min; Adeola, Adeniyi C; Liu, Yan-Hu; Irwin, David M; Xie, Hai-Bing; Zhang, Ya-Ping

    2014-06-02

    Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in the human and mouse genomes, some of which play important roles in fundamental biological processes. The pig is an important domesticated animal, however, pig lincRNAs remain poorly characterized and it is unknown if they were involved in the domestication of the pig. Here, we used available RNA-seq resources derived from 93 samples and expressed sequence tag data sets, and identified 6,621 lincRNA transcripts from 4,515 gene loci. Among the identified lincRNAs, some lincRNA genes exhibit synteny and sequence conservation, including linc-sscg2561, whose gene neighbor Dnmt3a is associated with emotional behaviors. Both linc-sscg2561 and Dnmt3a show differential expression in the frontal cortex between domesticated pigs and wild boars, suggesting a possible role in pig domestication. This study provides the first comprehensive genome-wide analysis of pig lincRNAs.

  17. 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

  18. The complete mitochondrial genome of Southern pig-tailed macaque, Macaca nemestrina, and comparative mitochondrial genomics of Macaca species.

    PubMed

    Chen, Chen; Mei, Huixian; Luo, Xueting

    2016-07-01

    In this study, we report the complete mitochondrial genome sequence of Southern pig-tailed, Macaca nemestrina for the first time. The genome is found to be 16,560 bp in length and has a base composition of A (32.25%), G (12.31%), C (30.51%), and T (24.93%), indicating that the percentage of A + T (57.18%) was higher than G + C (42.82%). Similar to other monkeys, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes were located on the H-strand except for the ND6 gene and 8 tRNA genes. To obtain a more complete understanding of the evolutionary history of Macaca genus, 11 mitochondrial genomes were used for phylogenetic analysis. This mitochondrial sequence reported here would be useful to uncover the monkey's evolution and add a new genetic resource for the genus Macaca.

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

    PubMed

    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.

  20. Sire evaluation for total number born in pigs using a genomic reaction norms approach.

    PubMed

    Silva, F F; Mulder, H A; Knol, E F; Lopes, M S; Guimarães, S E F; Lopes, P S; Mathur, P K; Viana, J M S; Bastiaansen, J W M

    2014-09-01

    In the era of genome-wide selection (GWS), genotype-by-environment (G×E) interactions can be studied using genomic information, thus enabling the estimation of SNP marker effects and the prediction of genomic estimated breeding values (GEBV) for young candidates for selection in different environments. Although G×E studies in pigs are scarce, the use of artificial insemination has enabled the distribution of genetic material from sires across multiple environments. Given the relevance of reproductive traits, such as the total number born (TNB) and the variation in environmental conditions encountered by commercial dams, understanding G×E interactions can be essential for choosing the best sires for different environments. The present work proposes a two-step reaction norm approach for G×E analysis using genomic information. The first step provided estimates of environmental effects (herd-year-season, HYS), and the second step provided estimates of the intercept and slope for the TNB across different HYS levels, obtained from the first step, using a random regression model. In both steps, pedigree ( A: ) and genomic ( G: ) relationship matrices were considered. The genetic parameters (variance components, h(2) and genetic correlations) were very similar when estimated using the A: and G: relationship matrices. The reaction norm graphs showed considerable differences in environmental sensitivity between sires, indicating a reranking of sires in terms of genetic merit across the HYS levels. Based on the G: matrix analysis, SNP by environment interactions were observed. For some SNP, the effects increased at increasing HYS levels, while for others, the effects decreased at increasing HYS levels or showed no changes between HYS levels. Cross-validation analysis demonstrated better performance of the genomic approach with respect to traditional pedigrees for both the G×E and standard models. The genomic reaction norm model resulted in an accuracy of GEBV for

  1. Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs.

    PubMed

    Lukić, B; Pong-Wong, R; Rowe, S J; de Koning, D J; Velander, I; Haley, C S; Archibald, A L; Woolliams, J A

    2015-12-01

    Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (≥0.3 μg/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62 153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross-validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome-wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h(2) , were 0.54-0.56 and 0.75-0.94 for androstenone and skatole respectively. The whole-genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole. PMID:26449733

  2. 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'. PMID:16610132

  3. Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

    PubMed Central

    Young, Jennifer M.; Garrick, Dorian J.; Dekkers, Jack C. M.; Rothschild, Max F.

    2013-01-01

    Background Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency. Methodology/Principal findings Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping. Conclusions/significance Important genomic regions associated with RFI related traits were identified for future

  4. Application of single-step genomic evaluation for crossbred performance in pig.

    PubMed

    Xiang, T; Nielsen, B; Su, G; Legarra, A; Christensen, O F

    2016-03-01

    Crossbreding is predominant and intensively used in commercial meat production systems, especially in poultry and swine. Genomic evaluation has been successfully applied for breeding within purebreds but also offers opportunities of selecting purebreds for crossbred performance by combining information from purebreds with information from crossbreds. However, it generally requires that all relevant animals are genotyped, which is costly and presently does not seem to be feasible in practice. Recently, a novel single-step BLUP method for genomic evaluation of both purebred and crossbred performance has been developed that can incorporate marker genotypes into a traditional animal model. This new method has not been validated in real data sets. In this study, we applied this single-step method to analyze data for the maternal trait of total number of piglets born in Danish Landrace, Yorkshire, and two-way crossbred pigs in different scenarios. The genetic correlation between purebred and crossbred performances was investigated first, and then the impact of (crossbred) genomic information on prediction reliability for crossbred performance was explored. The results confirm the existence of a moderate genetic correlation, and it was seen that the standard errors on the estimates were reduced when including genomic information. Models with marker information, especially crossbred genomic information, improved model-based reliabilities for crossbred performance of purebred boars and also improved the predictive ability for crossbred animals and, to some extent, reduced the bias of prediction. We conclude that the new single-step BLUP method is a good tool in the genetic evaluation for crossbred performance in purebred animals.

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

    PubMed

    Nuijten, Rascha J M; Bosse, Mirte; Crooijmans, Richard P M A; Madsen, Ole; Schaftenaar, Willem; Ryder, Oliver A; Groenen, Martien A M; 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

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

    PubMed

    Nuijten, Rascha J M; Bosse, Mirte; Crooijmans, Richard P M A; Madsen, Ole; Schaftenaar, Willem; Ryder, Oliver A; Groenen, Martien A M; 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.

  7. 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

  8. 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

  9. 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.

  10. Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

    PubMed Central

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

    2014-01-01

    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. PMID:24608928

  11. 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...

  12. Genome-wide DNA methylation profiles changes associated with constant heat stress in pigs as measured by bisulfite sequencing

    PubMed Central

    Hao, Yue; Cui, Yanjun; Gu, Xianhong

    2016-01-01

    Heat stress affects muscle development and meat quality in food animals; however, little is known regarding its regulatory mechanisms at the epigenetic level, such as via DNA methylation. In this study, we aimed to compare the DNA methylation profiles between control and heat-stressed pigs to identify candidate genes for skeletal muscle development and meat quality. Whole-genome bisulfite sequencing was used to investigate the genome-wide DNA methylation patterns in the longissimus dorsi muscles of the pigs. Both groups showed similar proportions of methylation at CpG sites but exhibited different proportions at non-CpG sites. A total of 57,147 differentially methylated regions were identified between the two groups, which corresponded to 1,422 differentially methylated genes. Gene ontogeny and KEGG pathway analyses indicated that these were mainly involved in energy and lipid metabolism, cellular defense and stress responses, and calcium signaling pathways. This study revealed the global DNA methylation pattern of pig muscle between normal and heat stress conditions. The result of this study might contribute to a better understanding of epigenetic regulation in pig muscle development and meat quality. PMID:27264107

  13. Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

    PubMed Central

    Hoffmann, Thomas J.; Kvale, Mark N.; Hesselson, Stephanie E.; Zhan, Yiping; Aquino, Christine; Cao, Yang; Cawley, Simon; Chung, Elaine; Connell, Sheryl; Eshragh, Jasmin; Ewing, Marcia; Gollub, Jeremy; Henderson, Mary; Hubbell, Earl; Iribarren, Carlos; Kaufman, Jay; Lao, Richard Z.; Lu, Yontao; Ludwig, Dana; Mathauda, Gurpreet K.; McGuire, William; Mei, Gangwu; Miles, Sunita; Purdy, Matthew M.; Quesenberry, Charles; Ranatunga, Dilrini; Rowell, Sarah; Sadler, Marianne; Shapero, Michael H.; Shen, Ling; Shenoy, Tanushree R.; Smethurst, David; Van den Eeden, Stephen K.; Walter, Larry; Wan, Eunice; Wearley, Reid; Webster, Teresa; Wen, Christopher C.; Weng, Li; Whitmer, Rachel A.; Williams, Alan; Wong, Simon C.; Zau, Chia; Finn, Andrea; Schaefer, Catherine; Kwok, Pui-Yan; Risch, Neil

    2011-01-01

    The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies. PMID:21565264

  14. Accuracy of Predicted Genomic Breeding Values in Purebred and Crossbred Pigs

    PubMed Central

    Hidalgo, André M.; Bastiaansen, John W. M.; Lopes, Marcos S.; Harlizius, Barbara; Groenen, Martien A. M.; de Koning, Dirk-Jan

    2015-01-01

    Genomic selection has been widely implemented in dairy cattle breeding when the aim is to improve performance of purebred animals. In pigs, however, the final product is a crossbred animal. This may affect the efficiency of methods that are currently implemented for dairy cattle. Therefore, the objective of this study was to determine the accuracy of predicted breeding values in crossbred pigs using purebred genomic and phenotypic data. A second objective was to compare the predictive ability of SNPs when training is done in either single or multiple populations for four traits: age at first insemination (AFI); total number of piglets born (TNB); litter birth weight (LBW); and litter variation (LVR). We performed marker-based and pedigree-based predictions. Within-population predictions for the four traits ranged from 0.21 to 0.72. Multi-population prediction yielded accuracies ranging from 0.18 to 0.67. Predictions across purebred populations as well as predicting genetic merit of crossbreds from their purebred parental lines for AFI performed poorly (not significantly different from zero). In contrast, accuracies of across-population predictions and accuracies of purebred to crossbred predictions for LBW and LVR ranged from 0.08 to 0.31 and 0.11 to 0.31, respectively. Accuracy for TNB was zero for across-population prediction, whereas for purebred to crossbred prediction it ranged from 0.08 to 0.22. In general, marker-based outperformed pedigree-based prediction across populations and traits. However, in some cases pedigree-based prediction performed similarly or outperformed marker-based prediction. There was predictive ability when purebred populations were used to predict crossbred genetic merit using an additive model in the populations studied. AFI was the only exception, indicating that predictive ability depends largely on the genetic correlation between PB and CB performance, which was 0.31 for AFI. Multi-population prediction was no better than within

  15. 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

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

    PubMed

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

    2014-12-01

    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.

  17. A genomic variant in IRF9 is associated with serum cytokine levels in pig.

    PubMed

    Wang, Wenwen; Liu, Yang; Wang, Haifei; Ding, Xiangdong; Liu, Jianfeng; Yu, Ying; Zhang, Qin

    2016-01-01

    The interferon regulatory factor 9 (IRF9) gene is a member of the IRF family and has been shown to play functionally diverse roles in the regulation of the immune system. Previous study revealed the IRF9 gene resides within the reported quantitative trait locus (QTLs) for cytokine levels. The aims of this study were to identify genomic variants in IRF9 and to test the association between the variants and cytokine levels in pig. A synonymous single-nucleotide polymorphism (c.459A>G) was identified in exon 4 of the IRF9 gene. Association analysis in 300 piglets (Landrace, n=68; large white, n=158; and Songliao black, n=74) showed that this variant was significantly associated with the level of interferon (IFN)-γ and the ratio of IFN-γ to IL-10 in serum (P<0.05). Relative quantification of messenger RNA (mRNA) revealed that spleen had the highest expression level and individuals with genotype AA had higher expression than those with genotype AG. Transfection-based mRNA stability assay analysis further showed that the mutant allele G could reduce the RNA stability of IRF9. These findings suggest that the SNP (c.459A>G) could be a causative mutation for the association between IRF9 and the serum cytokine levels in swine. PMID:26518782

  18. 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.

  19. Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

    PubMed Central

    Sun, Yaqi; Wang, Hongyang; Wang, Chao; Yu, Shaobo; Liu, Jing; Zhang, Yu; Fan, Bin; Li, Kui; Liu, Bang

    2014-01-01

    Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs. PMID:25198154

  20. 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.

  1. Genomic selection in a pig population including information from slaughtered full sibs of boars within a sib-testing program.

    PubMed

    Samorè, A B; Buttazzoni, L; Gallo, M; Russo, V; Fontanesi, L

    2015-05-01

    Genomic selection is becoming a common practise in dairy cattle, but only few works have studied its introduction in pig selection programs. Results described for this species are highly dependent on the considered traits and the specific population structure. This paper aims to simulate the impact of genomic selection in a pig population with a training cohort of performance-tested and slaughtered full sibs. This population is selected for performance, carcass and meat quality traits by full-sib testing of boars. Data were simulated using a forward-in-time simulation process that modeled around 60K single nucleotide polymorphisms and several quantitative trait loci distributed across the 18 porcine autosomes. Data were edited to obtain, for each cycle, 200 sires mated with 800 dams to produce 800 litters of 4 piglets each, two males and two females (needed for the sib test), for a total of 3200 newborns. At each cycle, a subset of 200 litters were sib tested, and 60 boars and 160 sows were selected to replace the same number of culled male and female parents. Simulated selection of boars based on performance test data of their full sibs (one castrated brother and two sisters per boar in 200 litters) lasted for 15 cycles. Genotyping and phenotyping of the three tested sibs (training population) and genotyping of the candidate boars (prediction population) were assumed. Breeding values were calculated for traits with two heritability levels (h 2=0.40, carcass traits, and h 2=0.10, meat quality parameters) on simulated pedigrees, phenotypes and genotypes. Genomic breeding values, estimated by various models (GBLUP from raw phenotype or using breeding values and single-step models), were compared with the classical BLUP Animal Model predictions in terms of predictive ability. Results obtained for traits with moderate heritability (h 2=0.40), similar to the heritability of traits commonly measured within a sib-testing program, did not show any benefit from the

  2. Draft Genome Sequences of a Unique t324-ST541-V Methicillin-Resistant Staphylococcus aureus Strain from a Pig.

    PubMed

    Moon, Dong Chan; Kim, Byung-Yong; Nam, Hyang-Mi; Jang, Geum-Chan; Jung, Suk-Chan; Lee, Hee-Soo; Park, Yong-Ho; Lim, Suk-Kyung

    2016-04-28

    Methicillin-resistant Staphylococcus aureus (MRSA), the major causative agent of nosocomial infection, has also been reported from non-human sources. A sequence type (ST) 541 MRSA isolate designated K12PJN53 was isolated from a healthy pig in 2012. The genome of K12PJN53 consists of 44 contiguous sequences (contigs), totalling 2,880,108 bases with 32.88% GC content. Among the annotated contigs, 14, 17, and 18 contained genes related to antimicrobial resistance, adherence, and toxin genes, respectively. The genomic distance of strain K12PJN53 was close to the ST398 strains. This is the first report of the draft genome sequence of a novel livestock-associated MRSA ST541 strain.

  3. 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

  4. Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population

    PubMed Central

    Yan, Hua; Liu, Xin; Li, Na; Liang, Jing; Pu, Lei; Zhang, Yuebo; Shi, Huibi; Zhao, Kebin; Wang, Lixian

    2014-01-01

    As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS) in 605 pigs of the F2 generation derived from a Large White × Minzhu intercross. Traits under study were abdominal circumference (AC), body height (BH), body length (BL), cannon bone circumference (CBC), chest depth (CD), chest width (CW), rump circumference (RC), rump width (RW), scapula width (SW), and waist width (WW). A total of 138 SNPs (the most significant being MARC0033464) on chromosome 7 were found to be associated with BH, BL, CBC, and RC (P-value  = 4.15E-6). One SNP on chromosome 1 was found to be associated with CD at genome-wide significance levels. The percentage phenotypic variance of these significant SNPs ranged from 0.1–25.48%. Moreover, a conditional analysis revealed that the significant SNPs were derived from a single quantitative trait locus (QTL) and indicated additional chromosome-wide significant association for 25 SNPs on SSC4 (BL, CBC) and 9 SNPs on SSC7 (RC). Linkage analysis revealed two complete linkage disequilibrium haplotype blocks that contained seven and four SNPs, respectively. In block 1, the most significant SNP, MARC0033464, was present. Annotations from pig reference genome suggested six genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in block 1 (495 kb), and one gene (SCUBE3) in block 3 (124 kb). Functional analysis indicated that HMGA1 and SCUBE3 genes are the potential genes controlling BH, BL, and RC in pigs, with an application in breeding programs. We screened several candidate intervals and genes based on SNP location and gene function, and predicted their function using bioinformatics analyses. PMID:25090094

  5. High coverage of the complete mitochondrial genome of the rare Gray's beaked whale (Mesoplodon grayi) using Illumina next generation sequencing.

    PubMed

    Thompson, Kirsten F; Patel, Selina; Williams, Liam; Tsai, Peter; Constantine, Rochelle; Baker, C Scott; Millar, Craig D

    2016-01-01

    Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genome of Gray's beaked whale (Mesoplodon grayi) to an average coverage of 152X. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome length to be 16,347 bp. The nucleotide composition was asymmetric (33.3% A, 24.6% C, 12.6% G, 29.5% T) with an overall GC content of 37.2%. The gene organization was similar to that of other cetaceans with 13 protein-coding genes, 2 rRNAs (12S and 16S), 22 predicted tRNAs and 1 control region or D-loop. We found no evidence of heteroplasmy or nuclear copies of mitochondrial DNA in this individual. Beaked whales within the genus Mesoplodon are rarely seen at sea and their basic biology is poorly understood. These data will contribute to resolving the phylogeography and population ecology of this speciose group.

  6. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

    PubMed Central

    Lachance, Joseph; Vernot, Benjamin; Elbers, Clara C.; Ferwerda, Bart; Froment, Alain; Bodo, Jean-Marie; Lema, Godfrey; Fu, Wenqing; Nyambo, Thomas B.; Rebbeck, Timothy R.; Zhang, Kun; Akey, Joshua M.; Tishkoff, Sarah A.

    2012-01-01

    Summary To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole-genomes of five individuals in each of three different hunter-gatherer populations at > 60x coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height. PMID:22840920

  7. 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. PMID:27376238

  8. 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.

  9. Association and Haplotype Analyses of Positional Candidate Genes in Five Genomic Regions Linked to Scrotal Hernia in Commercial Pig Lines

    PubMed Central

    Du, Zhi-Qiang; Zhao, Xia; Vukasinovic, Natascha; Rodriguez, Fernanda; Clutter, Archie C.; Rothschild, Max F.

    2009-01-01

    Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully. Using a family-based analysis we found that four regions surrounding ELF5, KIF18A, COL23A1 on chromosome 2, and NPTX1 on chromosome 12, respectively, may contain the genetic variants important for the development of the scrotal hernia in pigs. These findings were replicated in another case-control dataset. The SNPs around the ELF5 region were in high linkage disequilibrium with each other, and a haplotype containing SNPs from ELF5 and CAT was highly significantly associated with hernia development. Extensive re-sequencing work focused on the KIF18A gene did not detect any further SNPs with extensive association signals. These genes may be involved in the estrogen receptor signaling pathway (KIF18A and NPTX1), the epithelial-mesenchymal transition (ELF5) and the collagen metabolism pathway (COL23A1), which are associated with the important molecular characteristics of hernia pathophysiology. Further investigation on the molecular mechanisms of these genes may provide more molecular clues on hernia development in pigs. PMID:19287495

  10. Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

    PubMed

    Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

    2016-08-01

    Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality. PMID:27287925

  11. A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6

    PubMed Central

    2010-01-01

    Background In many countries, male piglets are castrated shortly after birth because a proportion of un-castrated male pigs produce meat with an unpleasant flavour and odour. Main compounds of boar taint are androstenone and skatole. The aim of this high-density genome-wide association study was to identify single nucleotide polymorphisms (SNPs) associated with androstenone levels in a commercial sire line of pigs. The identification of major genetic effects causing boar taint would accelerate the reduction of boar taint through breeding to finally eliminate the need for castration. Results The Illumina Porcine 60K+SNP Beadchip was genotyped on 987 pigs divergent for androstenone concentration from a commercial Duroc-based sire line. The association analysis with 47,897 SNPs revealed that androstenone levels in fat tissue were significantly affected by 37 SNPs on pig chromosomes SSC1 and SSC6. Among them, the 5 most significant SNPs explained together 13.7% of the genetic variance in androstenone. On SSC6, a larger region of 10 Mb was shown to be associated with androstenone covering several candidate genes potentially involved in the synthesis and metabolism of androgens. Besides known candidate genes, such as cytochrome P450 A19 (CYP2A19), sulfotransferases SULT2A1, and SULT2B1, also new members of the cytochrome P450 CYP2 gene subfamilies and of the hydroxysteroid-dehydrogenases (HSD17B14) were found. In addition, the gene encoding the ß-chain of the luteinizing hormone (LHB) which induces steroid synthesis in the Leydig cells of the testis at onset of puberty maps to this area on SSC6. Interestingly, the gene encoding the α-chain of LH is also located in one of the highly significant areas on SSC1. Conclusions This study reveals several areas of the genome at high resolution responsible for variation of androstenone levels in intact boars. Major genetic factors on SSC1 and SSC6 showing moderate to large effects on androstenone concentration were identified in

  12. Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing

    PubMed Central

    2013-01-01

    Background Reduced representation bisulfite sequencing (RRBS) was developed to measure DNA methylation of high-CG regions at single base-pair resolution, and has been widely used because of its minimal DNA requirements and cost efficacy; however, the CpG coverage of genomic regions is restricted and important regions with low-CG will be ignored in DNA methylation profiling. This method could be improved to generate a more comprehensive representation. Results Based on in silico simulation of enzyme digestion of human and mouse genomes, we have optimized the current single-enzyme RRBS by applying double enzyme digestion in the library construction to interrogate more representative regions. CpG coverage of genomic regions was considerably increased in both high-CG and low-CG regions using the double-enzyme RRBS method, leading to more accurate detection of their average methylation levels and identification of differential methylation regions between samples. We also applied this double-enzyme RRBS method to comprehensively analyze the CpG methylation profiles of two colorectal cancer cell lines. Conclusion The double-enzyme RRBS increases the CpG coverage of genomic regions considerably over the previous single-enzyme RRBS method, leading to more accurate detection of their average methylation levels. It will facilitate genome-wide DNA methylation studies in multiple and complex clinical samples. PMID:23324053

  13. 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.

  14. 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. PMID:27051344

  15. Coincidental detection of genomes of porcine parvoviruses and porcine circovirus type 2 infecting pigs in Japan.

    PubMed

    Saekhow, Prayuth; Kishizuka, Shingo; Sano, Natsuha; Mitsui, Hiroko; Akasaki, Hajime; Mawatari, Takahiro; Ikeda, Hidetoshi

    2016-01-01

    The infection status of 15 viruses in 120 pigs aged about 6 months was investigated based on tonsil specimens collected from a slaughterhouse. Only 5 species of porcine parvoviruses and porcine circovirus type 2 (PCV2) were detected at high frequencies; 67% for porcine parvovirus (PPV) (PPV-Kr or -NADL2 as the new abbreviation), 58% for PPV2 (CnP-PARV4), 39% for PPV3 (P-PARV4), 33% for PPV4 (PPV4), 55% for PBo-likeV (PBoV7) and 80% for PCV2. A phylogenetic analysis of PPV3 suggested that Japanese PPV3s showed a slight variation, and possibly, there were farms harboring homogeneous or heterogeneous PPV3s. Statistical analyses indicated that the detection of PCV2 was significantly coincidental with each detection of PPV, PPV2 and PPV3, and PPV and PPV4 were also coincidentally detected. The concurrent infection with PCV2 and porcine parvoviruses in the subclinically infected pigs may resemble the infection status of pigs with the clinical manifestations of porcine circovirus associated disease which occurs in 3-5 months old pigs and is thought to be primarily caused by the PCV2 infection. PMID:26166811

  16. 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

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

    PubMed

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

    2015-12-01

    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

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

    PubMed

    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

  19. 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

  20. 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.

  1. 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. PMID:27296164

  2. A Quantitative Analysis of the Mass Media Coverage of Genomics Medicine in China: A Call for Science Journalism in the Developing World

    PubMed Central

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

    2014-01-01

    Abstract 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

  3. 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

  4. 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.

  5. Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds

    PubMed Central

    2012-01-01

    Background Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. Results Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL), 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 μg/g). In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. Conclusions Despite the small sample size, a total of 25 haplotypes and three single markers were identified

  6. 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

  7. 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. PMID:16706918

  8. Accuracy of genomic prediction using deregressed breeding values estimated from purebred and crossbred offspring phenotypes in pigs.

    PubMed

    Hidalgo, A M; Bastiaansen, J W M; Lopes, M S; Veroneze, R; Groenen, M A M; de Koning, D-J

    2015-07-01

    Genomic selection is applied to dairy cattle breeding to improve the genetic progress of purebred (PB) animals, whereas in pigs and poultry the target is a crossbred (CB) animal for which a different strategy appears to be needed. The source of information used to estimate the breeding values, i.e., using phenotypes of CB or PB animals, may affect the accuracy of prediction. The objective of our study was to assess the direct genomic value (DGV) accuracy of CB and PB pigs using different sources of phenotypic information. Data used were from 3 populations: 2,078 Dutch Landrace-based, 2,301 Large White-based, and 497 crossbreds from an F1 cross between the 2 lines. Two female reproduction traits were analyzed: gestation length (GLE) and total number of piglets born (TNB). Phenotypes used in the analyses originated from offspring of genotyped individuals. Phenotypes collected on CB and PB animals were analyzed as separate traits using a single-trait model. Breeding values were estimated separately for each trait in a pedigree BLUP analysis and subsequently deregressed. Deregressed EBV for each trait originating from different sources (CB or PB offspring) were used to study the accuracy of genomic prediction. Accuracy of prediction was computed as the correlation between DGV and the DEBV of the validation population. Accuracy of prediction within PB populations ranged from 0.43 to 0.62 across GLE and TNB. Accuracies to predict genetic merit of CB animals with one PB population in the training set ranged from 0.12 to 0.28, with the exception of using the CB offspring phenotype of the Dutch Landrace that resulted in an accuracy estimate around 0 for both traits. Accuracies to predict genetic merit of CB animals with both parental PB populations in the training set ranged from 0.17 to 0.30. We conclude that prediction within population and trait had good predictive ability regardless of the trait being the PB or CB performance, whereas using PB population(s) to predict

  9. Genome-Wide Association Analysis for Blood Lipid Traits Measured in Three Pig Populations Reveals a Substantial Level of Genetic Heterogeneity.

    PubMed

    Yang, Hui; Huang, Xiaochang; Zeng, Zhijun; Zhang, Wanchang; Liu, Chenlong; Fang, Shaoming; Huang, Lusheng; Chen, Congying

    2015-01-01

    Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.

  10. Genome-Wide Association Analysis for Blood Lipid Traits Measured in Three Pig Populations Reveals a Substantial Level of Genetic Heterogeneity

    PubMed Central

    Yang, Hui; Huang, Xiaochang; Zeng, Zhijun; Zhang, Wanchang; Liu, Chenlong; Fang, Shaoming; Huang, Lusheng; Chen, Congying

    2015-01-01

    Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption. PMID:26121138

  11. 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

  12. Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces

    PubMed Central

    Højberg, Ole; Canibe, Nuria; Jensen, Bent Borg

    2016-01-01

    Olsenella scatoligenes SK9K4T is a strictly anaerobic bacterium isolated from pig feces that produces the malodorous compounds 3-methylindole (skatole) and 4-methylphenol (p-cresol). Here, we report the 2.47 Mbp draft genome sequence of SK9K4T, exploring pathways for the synthesis of skatole and p-cresol from the amino acids tryptophan and tyrosine, respectively. PMID:26950328

  13. Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces.

    PubMed

    Li, Xiaoqiong; Højberg, Ole; Noel, Samantha Joan; Canibe, Nuria; Jensen, Bent Borg

    2016-01-01

    Olsenella scatoligenes SK9K4(T) is a strictly anaerobic bacterium isolated from pig feces that produces the malodorous compounds 3-methylindole (skatole) and 4-methylphenol (p-cresol). Here, we report the 2.47 Mbp draft genome sequence of SK9K4(T), exploring pathways for the synthesis of skatole and p-cresol from the amino acids tryptophan and tyrosine, respectively. PMID:26950328

  14. Genome-wide association study of meat quality traits in a White Duroc×Erhualian F2 intercross and Chinese Sutai pigs.

    PubMed

    Ma, Junwu; Yang, Jie; Zhou, Lisheng; Zhang, Zhiyan; Ma, Huanban; Xie, Xianhua; Zhang, Feng; Xiong, Xinwei; Cui, Leilei; Yang, Hui; Liu, Xianxian; Duan, Yanyu; Xiao, Shijun; Ai, Huashui; Ren, Jun; Huang, Lusheng

    2013-01-01

    Thousands of QTLs for meat quality traits have been identified by linkage mapping studies, but most of them lack precise position or replication between populations, which hinder their application in pig breeding programs. To localize QTLs for meat quality traits to precise genomic regions, we performed a genome-wide association (GWA) study using the Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality traits, including pH, color, drip loss, moisture content, protein content and intramuscular fat content (IMF), marbling and firmness scores in the M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on the two populations. In total, 127 chromosome-wide significant SNPs for these traits were identified. Among them, 11 SNPs reached genome-wise significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28 genomic regions of approximately 10 Mb or less. Most of these regions corresponded to previously reported QTL regions and spanned smaller intervals than before. The loci on SSC3 and SSC7 appeared to have pleiotropic effects on several related traits. Besides them, a few QTL signals were replicated between the two populations. Further, we identified thirteen new candidate genes for IMF, marbling and firmness, on the basis of their positions, functional annotations and reported expression patterns. The findings will contribute to further identification of the causal mutation underlying these QTLs and future marker-assisted selection in pigs.

  15. Mitochondrial genome polymorphisms associated with longissimus muscle composition in Iberian pigs.

    PubMed

    Fernández, A I; Alves, E; Fernández, A; de Pedro, E; López-García, M A; Ovilo, C; Rodríguez, M C; Silió, L

    2008-06-01

    We carried out a study to investigate the associations between mitochondrial DNA polymorphisms and meat quality traits (intramuscular fat and protein content of the longissimus) in an Iberian porcine line named Torbiscal. The studied pigs (n = 319) belong to 9 maternal lineages and were previously assigned to 6 mitochondrial haplotypes (H1 to H6), based on Cytochrome b and Dloop sequences. Statistical analyses, following a bivariate mixed model, show a greater fat content and lower protein content in H3 haplotype carriers than H1, H2, H4, H5, and H6 haplotype carriers. The magnitudes of these differences are close to 1 g of fat and -0.5 g of protein per 100 g of muscle. To identify the causative mutation of these effects on intramuscular fat and protein contents, the complete mitochondrial DNA sequence of 6 individuals was determined, each one carrying a different mitochondrial haplotype. The alignments of these 6 complete mitochondrial sequences allowed identification of 32 substitutions and 2 indels. Two polymorphic positions were exclusively detected in H3 carriers: a synonymous transition 9104C > T in the gene-coding region of Cytochrome c oxidase subunit III and a substitution 715A > G in 12S rRNA. Genotyping results of a larger number of Torbiscal samples showed the exclusive presence of 9104T and 715G alleles in H3 carriers. The detected candidate substitutions are located in essential mitochondrial genes, and although they do not change the amino acid composition, we cannot disregard a potential change in the secondary structure of their corresponding mRNA. The usefulness of these polymorphisms as markers in selection programs requires validation of the consistency of these results in other Iberian pig lines. PMID:18344306

  16. Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

    PubMed Central

    2013-01-01

    Background Obesity, excess fat tissue in the body, can underlie a variety of medical complaints including heart disease, stroke and cancer. The pig is an excellent model organism for the study of various human disorders, including obesity, as well as being the foremost agricultural species. In order to identify genetic variants associated with fatness, we used a selective genomic approach sampling DNA from animals at the extreme ends of the fat and lean spectrum using estimated breeding values derived from a total population size of over 70,000 animals. DNA from 3 breeds (Sire Line Large White, Duroc and a white Pietrain composite line (Titan)) was used to interrogate the Illumina Porcine SNP60 Genotyping Beadchip in order to identify significant associations in terms of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs). Results By sampling animals at each end of the fat/lean EBV (estimate breeding value) spectrum the whole population could be assessed using less than 300 animals, without losing statistical power. Indeed, several significant SNPs (at the 5% genome wide significance level) were discovered, 4 of these linked to genes with ontologies that had previously been correlated with fatness (NTS, FABP6, SST and NR3C2). Quantitative analysis of the data identified putative CNV regions containing genes whose ontology suggested fatness related functions (MCHR1, PPARα, SLC5A1 and SLC5A4). Conclusions Selective genotyping of EBVs at either end of the phenotypic spectrum proved to be a cost effective means of identifying SNPs and CNVs associated with fatness and with estimated major effects in a large population of animals. PMID:24225222

  17. 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

  18. Genome-wide association study of periweaning failure-to-thrive syndrome (PFTS) in pigs.

    PubMed

    Zanella, R; Morés, N; Morés, M A Z; Peixoto, J O; Zanella, E L; Ciacci-Zanella, J R; Ibelli, A M G; Gava, D; Cantão, M E; Ledur, M C

    2016-06-25

    Porcine periweaning-failure-to-thrive syndrome (PFTS) is a condition that affects newly weaned piglets. It is characterised by a progressive debilitation leading to death, in the absence of infectious, nutritional, management or environmental factors. In this study, we present the first report of PFTS in South America and the results of a genome-wide association study to identify the genetic markers associated with the appearance of this condition in a crossbred swine population. Four chromosomal regions were associated with PFTS predisposition, one located on SSCX, one on SSC8, and the two other regions on SSC14. Regions on SSC8 and SSC14 harbour important functional candidate genes involved in human depression and might have an important role in PFTS. Our findings contribute to the increasing knowledge about this syndrome, which has been investigated since 2007, and to the identification of the aetiology of this disease. PMID:27162284

  19. 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

  20. Genome-Wide DNA Methylation Changes between the Superficial and Deep Backfat Tissues of the Pig

    PubMed Central

    Li, Mingzhou; Wang, Tao; Wu, Honglong; Zhang, Jie; Zhou, Chaowei; Jiang, Anan; Li, Ruiqiang; Li, Xuewei

    2012-01-01

    Adipose tissue is not only a storage organ involved in fuel metabolism, but also an endocrine organ involved in the regulation of insulin sensitivity, thermogenesis, immunity, and inflammation. There are anatomical, cellular, molecular and physiological differences among adipose tissues deposited in different body sites. However, current understanding of the intrinsic differences between the sub-compartments of the subcutaneous adipose tissue remains rudimentary. Here, we analyzed the genome-wide DNA methylation differences between the porcine superficial and deep backfat tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing. We show that the genes with differentially methylated regions in their promoter are mainly involved in the processes of “lipid metabolism” and “regulation of immune-related cytokines”. Compared with the deep backfat tissue, the promoters of genes related to the ‘positive regulation of cytokine production’ were significantly hypermethylated in the superficial backfat tissue, which reflects the intrinsic functional and metabolic differences between the sub-compartments of the subcutaneous adipose tissue. This study provides epigenetic evidence for functionally relevant methylation differences between different layers of porcine backfat tissues. PMID:22837681

  1. Development and Characterization of Simple Sequence Repeat Markers Providing Genome-Wide Coverage and High Resolution in Maize

    PubMed Central

    Xu, Jie; Liu, Ling; Xu, Yunbi; Chen, Churun; Rong, Tingzhao; Ali, Farhan; Zhou, Shufeng; Wu, Fengkai; Liu, Yaxi; Wang, Jing; Cao, Moju; Lu, Yanli

    2013-01-01

    Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study. PMID:23804557

  2. An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2

    PubMed Central

    2012-01-01

    Background Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biology of the phenotype under investigation. Our combined strategy of comparative genomics and chromosomal heritability estimate analysis of obesity traits, subscapular skinfold thickness and back-fat thickness in Korean cohorts and pig (Sus scrofa), may overcome the limitations of candidate gene analysis and allow us to better understand genetic predisposition to human obesity. Results We found common genes including FTO, the fat mass and obesity associated gene, identified from significant SNPs by association studies of each trait. These common genes were related to blood pressure and arterial stiffness (P = 1.65E-05) and type 2 diabetes (P = 0.00578). Through the estimation of variance of genetic component (heritability) for each chromosome by SNPs, we observed a significant positive correlation (r = 0.479) between genetic contributions of human and pig to obesity traits. Furthermore, we noted that human chromosome 2 (syntenic to pig chromosomes 3 and 15) was most important in explaining the phenotypic variance for obesity. Conclusions Obesity genetics still awaits further discovery. Navigating syntenic regions suggests obesity candidate genes on chromosome 2 that are previously known to be associated with obesity-related diseases: MRPL33, PARD3B, ERBB4, STK39, and ZNF385B. PMID:23253381

  3. 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...

  4. Cytotoxic Effects during Knock Out of Multiple Porcine Endogenous Retrovirus (PERV) Sequences in the Pig Genome by Zinc Finger Nucleases (ZFN).

    PubMed

    Semaan, Marwan; Ivanusic, Daniel; Denner, Joachim

    2015-01-01

    Xenotransplantation has been proposed as a solution to the shortage of suitable human donors for transplantation and pigs are currently favoured as donor animals. However, xenotransplantation may be associated with the transmission of zoonotic microorganisms. Whereas most porcine microorganisms representing a risk for the human recipient may be eliminated by designated pathogen free breeding, multiple copies of porcine endogenous retroviruses (PERVs) are integrated in the genome of all pigs and cannot be eliminated this way. PERVs are released as infectious particles and infect human cells. The zinc finger nuclease (ZFN) technology allows knocking out specifically cellular genes, however it was not yet used to eliminate multiple integrated proviral sequences with a strong conservation in the target sequence. To reduce the risk of horizontal PERV transmission and to knock out as many as possible proviruses, for the first time the powerful tool of the ZFN technology was used. ZFN were designed to bind specifically to sequences conserved in all known replication-competent proviruses. Expression and transport of the ZFN into the nucleus was shown by Western blot analysis, co-localisation analysis, PLA and FRET. Survival of transfected cells was analysed using fluorescent ZFN and cell counting. After transfection a strong expression of the ZFN proteins and a co-localisation of the expressed ZFN proteins were shown. However, expression of the ZFN was found to be extremely toxic for the transfected cells. The induced cytotoxicity was likely due to the specific cutting of the high copy number of the PERV proviruses, which is also commonly observed when ZFN with low specificity cleave numerous off-target sites in a genome. This is the first attempt to knock out multiple, nearly identical, genes in a cellular genome using ZFN. The attempt failed, and other strategies should be used to prevent PERV transmission.

  5. Cloning. Pigs is pigs.

    PubMed

    Prather, R S

    2000-09-15

    Since the first report of a cloned animal (Dolly the sheep) 3 years ago, cloning mammals has become something of a cottage industry. As Prather discusses in his Perspective, pigs can now be added to the august list of cloned animals, which includes cows, goats, and mice. This is a particularly spectacular achievement because pig cloning has turned out to be notoriously difficult. The pig is also a valuable domestic animal to have cloned because, being physiologically close to humans, its organs can be used in xenotransplantation.

  6. Cloning. Pigs is pigs.

    PubMed

    Prather, R S

    2000-09-15

    Since the first report of a cloned animal (Dolly the sheep) 3 years ago, cloning mammals has become something of a cottage industry. As Prather discusses in his Perspective, pigs can now be added to the august list of cloned animals, which includes cows, goats, and mice. This is a particularly spectacular achievement because pig cloning has turned out to be notoriously difficult. The pig is also a valuable domestic animal to have cloned because, being physiologically close to humans, its organs can be used in xenotransplantation. PMID:11012362

  7. Genomic relatedness among Actinobacillus pleuropneumoniae field strains of sterotypes 1 and 5 isolated from healthy and diseased pigs.

    PubMed Central

    Chatellier, S; Harel, J; Dugourd, D; Chevallier, B; Kobisch, M; Gottschalk, M

    1999-01-01

    Forty-four Actinobacillus pleuropneumoniae isolates recovered from both healthy and diseased pigs were characterized by random amplified polymorphic DNA analysis (RAPD), pulsed field gel electrophoresis (PFGE) and apx toxin gene typing. Nine RAPD types and 14 PFGE patterns were identified. No common RAPD or PFGE patterns were found between strains of serotype 1 and those of serotype 5. The RAPD analysis indicated that the 15 serotype 1 strains isolated from diseased pigs were assigned to 4 RAPD types, with 66% of strains characterized by the same RAPD type. By contrast, the 5 strains of serotype 1 isolated from healthy carriers were dispersed in 4 RAPD types. These data suggest that the diversity of strains isolated from healthy pigs could be higher than that of strains recovered from diseased pigs. In addition, all serotype 5 strains exhibited a unique RAPD type. Unlike RAPD, PFGE analysis allowed discrimination among isolates of serotype 1 and among those of serotype 5. All but 3 isolates showed the same apx genotype as their respective serotype reference strain. These data indicate that RAPD analysis is a valuable rapid tool for routine subtyping of strains of serotype 1. For strains of serotype 5, a combination of several typing methods, such as PFGE and apx gene typing, is needed to provide useful information on the molecular epidemiology of swine pleuropneumonia. Images Figure 1. Figure 3. PMID:10480458

  8. Genomic, Tissue Expression, and Protein Characterization of pCLCA1, a Putative Modulator of Cystic Fibrosis in the Pig

    PubMed Central

    Plog, Stephanie; Mundhenk, Lars; Klymiuk, Nikolai; Gruber, Achim D.

    2009-01-01

    Recent studies have identified members of the CLCA (chloride channels, calcium-activated) gene family as potential modulators of the cystic fibrosis (CF) phenotype, but differences between the human and murine CLCA genes and proteins may limit the use of murine CF models. Recently established pig models of CF are expected to mimic the human disease more closely than the available mouse models do. Here, we characterized the porcine CLCA gene locus, analyzed the expression pattern and protein processing of pCLCA1, and compared it to its human ortholog, hCLCA1. The porcine CLCA gene family is located on chromosome 4q25, with a broad synteny with the human and murine clca gene loci, except for a pig-specific gene duplication of pCLCA4. Using pCLCA1-specific antibodies, the protein was immunohistochemically localized in mucin-producing cells, including goblet cells and mucinous glands in the respiratory and alimentary tracts. Similar to hCLCA1, biochemical characterization of pCLCA1 identified a secreted soluble protein that could serve as an extracellular signaling molecule or functional constituent of the protective mucous layers. The results suggest that pCLCA1 shares essential characteristics of hCLCA1, supporting the pig model as a promising tool for studying the modulating role of pCLCA1 in the complex pathology of CF. (J Histochem Cytochem 57:1169–1181, 2009) PMID:19755716

  9. 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

  10. 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. PMID:26658066

  11. Immunization Coverage

    MedlinePlus

    ... underused vaccines is increasing. Immunization currently averts an estimated 2 to 3 million deaths every year. An ... avoided, however, if global vaccination coverage improves. An estimated 19.4 million infants worldwide are still missing ...

  12. 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 Central

    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. PMID:16344555

  13. 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

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

    PubMed

    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.

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

    PubMed

    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

  16. Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs

    PubMed Central

    2014-01-01

    Background Feed efficiency is one of the major components determining costs of animal production. Residual feed intake (RFI) is defined as the difference between the observed and the expected feed intake given a certain production. Residual feed intake 1 (RFI1) was calculated based on regression of individual daily feed intake (DFI) on initial test weight and average daily gain. Residual feed intake 2 (RFI2) was as RFI1 except it was also regressed with respect to backfat (BF). It has been shown to be a sensitive and accurate measure for feed efficiency in livestock but knowledge of the genomic regions and mechanisms affecting RFI in pigs is lacking. The study aimed to identify genetic markers and candidate genes for RFI and its component traits as well as pathways associated with RFI in Danish Duroc boars by genome-wide associations and systems genetic analyses. Results Phenotypic and genotypic records (using the Illumina Porcine SNP60 BeadChip) were available on 1,272 boars. Fifteen and 12 loci were significantly associated (p < 1.52 × 10-6) with RFI1 and RFI2, respectively. Among them, 10 SNPs were significantly associated with both RFI1 and RFI2 implying the existence of common mechanisms controlling the two RFI measures. Significant QTL regions for component traits of RFI (DFI and BF) were detected on pig chromosome (SSC) 1 (for DFI) and 2 for (BF). The SNPs within MAP3K5 and PEX7 on SSC 1, ENSSSCG00000022338 on SSC 9, and DSCAM on SSC 13 might be interesting markers for both RFI measures. Functional annotation of genes in 0.5 Mb size flanking significant SNPs indicated regulation of protein and lipid metabolic process, gap junction, inositol phosphate metabolism and insulin signaling pathway are significant biological processes and pathways for RFI, respectively. Conclusions The study detected novel genetic variants and QTLs on SSC 1, 8, 9, 13 and 18 for RFI and indicated significant biological processes and metabolic pathways involved in RFI. The

  17. Comparative assessment of the pig, mouse, and human genomes: A structural and functional analysis of genes involved in immunity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A detailed analysis was conducted on portions of the porcine, murine, and human genome associated with the immune response. It was found that non-protein coding RNA/DNA that potentially interact and regulate gene expression, nucleotide similarity, isochore type, and the similarity of 5’ and 3’ UTR ...

  18. Identification of a 1.6 kb genome locus of guinea pig cytomegalovirus required for efficient viral growth in animals but not in cell culture.

    PubMed

    Nozawa, Naoki; Yamamoto, Yumiko; Fukui, Yoshiko; Katano, Harutaka; Tsutsui, Yoshihiro; Sato, Yuko; Yamada, Souichi; Inami, Yuhki; Nakamura, Kohnosuke; Yokoi, Masayuki; Kurane, Ichiro; Inoue, Naoki

    2008-09-15

    Guinea pig cytomegalovirus (GPCMV) provides a useful model for studies of congenital CMV infection. During characterization of the GPCMV genome sequence, we identified two types of strains in a virus stock purchased from ATCC. One of them, GPCMV/del, lacks a 1.6 kb locus that positionally corresponds to murine CMV (MCMV) M129-M133. Growth of GPCMV/del in cell culture was marginally better than that of the other strain, GPCMV/full, which harbors the 1.6 kb locus. However, in animals infected intraperitoneally with virus stocks containing both strains, GPCMV/full disseminated more efficiently than GPCMV/del, including 200-fold greater viral load in salivary glands. Viral DNA, transcripts of the immediate-early 2 gene homolog, and viral antigens were more abundant in animals infected with GPCMV/full than in those infected with GPCMV/del. Although the observed phenomena have some similarity with the growth properties of MCMV strains defective in mck-1/mck-2(M129/131) and those defective in sgg(M132), no M129-M132 homologs were found in the 1.6 kb locus. Since one of the ORFs in the locus has a weak sequence similarity with HCMV UL130, which relates to cell tropism, further studies will be required to learn the mechanism for efficient GPCMV growth in animal. PMID:18656220

  19. A genome-wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines.

    PubMed

    Preissler, Regine; Tetens, Jens; Reiners, Kerstin; Looft, Holger; Kemper, Nicole

    2013-08-01

    Postpartum dysgalactia syndrome (PDS) in sows is an important disease after parturition with a relevant economic impact, affecting the health and welfare of both sows and piglets. The genetic background of this disease has been discussed and its heritability estimated, but further genetic analyses are lacking in detail. The aim of the current study was to detect loci affecting the susceptibility to PDS through a genome-wide association approach. The study was designed as a family-based association study with matched sampling of affected sows and healthy half- or full-sib control sows on six farms. For the study, 597 sows (322 affected vs. 275 healthy control sows) were genotyped on 62 163 single nucleotide polymorphisms (SNPs) using the Illumina PorcineSNP60 BeadChip. After quality control, 585 sows (314 affected vs. 271 healthy control sows) and 49 740 SNPs remained for further analysis. Statistics were performed mainly with the r package genabel and included a principal component analysis. A statistically significant genome-wide associated SNP was identified on porcine chromosome (SSC) 17. Further promising results with moderate significance were detected on SSC 13 and on an unplaced scaffold with an older annotation on SSC 15. The PRICKLE2 and NRP2 genes were identified as candidate genes near associated SNPs. Several quantitative trait loci (QTL) have been previously described in these genomic regions, including QTL for mammary gland condition, as teat number and non-functional nipples QTL, as well as QTL for body temperature and gestation length.

  20. Accounting for genetic architecture in single- and multipopulation genomic prediction using weights from genomewide association studies in pigs.

    PubMed

    Veroneze, R; Lopes, P S; Lopes, M S; Hidalgo, A M; Guimarães, S E F; Harlizius, B; Knol, E F; van Arendonk, J A M; Silva, F F; Bastiaansen, J W M

    2016-06-01

    We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions.

  1. 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.

  2. Genome-Wide Gene Expression Profiles in Lung Tissues of Pig Breeds Differing in Resistance to Porcine Reproductive and Respiratory Syndrome Virus

    PubMed Central

    Zhang, Chenhua; Zhang, Yujie; Wang, Nan; Li, Yanping; Yang, Lijuan; Jiang, Chenglan; Zhang, Chaoyang; Wen, Changhong; Jiang, Yunliang

    2014-01-01

    Porcine reproductive and respiratory syndrome (PRRS) caused by PRRS virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, typical respiratory symptoms in piglets, and high mortality rate of piglets. In this study, we employed an Affymetrix microarray chip to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited a range of clinical features that typify the disease, whereas the DPL pigs showed only mild signs of the disease. Overall, the DPL group had a lower percentage of CD4+ cells and lower CD4+/CD8+ratios than the DLY group (p<0.05). For both IL-10 and TNF-α, the DLY pigs had significantly higher levels than the DPL pigs (p<0.01). The DLY pigs have lower serum IFN-γ levels than the DPL pigs (p<0.01). The serum IgG levels increased slightly from 0 dpi to 7 dpi, and peaked at 14 dpi (p<0.0001). Microarray data analysis revealed 16 differentially expressed (DE) genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The mRNA expression levels of 10 out of the 16 DE genes were validated by real-time quantitative RT-PCR and their fold change was consistent with the result of microarray data analysis. We further analyzed the mRNA expression level of 8 differentially expressed genes between the DPL and DLY pigs for both uninfected and infected groups, and found that TF and USP18 genes were important in underlying porcine resistance or susceptibility to PRRSV. PMID:24465897

  3. 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

  4. 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. PMID:24320550

  5. 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.

  6. 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.

  7. Molecular Genetic Maps in Wild Emmer Wheat, Triticum dicoccoides: Genome-Wide Coverage, Massive Negative Interference, and Putative Quasi-Linkage

    PubMed Central

    Peng, Junhua; Korol, Abraham B.; Fahima, Tzion; Röder, Marion S.; Ronin, Yefim I.; Li, Youchun C.; Nevo, Eviatar

    2000-01-01

    The main objectives of the study reported here were to construct a molecular map of wild emmer wheat, Triticum dicoccoides, to characterize the marker-related anatomy of the genome, and to evaluate segregation and recombination patterns upon crossing T. dicoccoides with its domesticated descendant Triticum durum (cultivar Langdon). The total map length exceeded 3000 cM and possibly covered the entire tetraploid genome (AABB). Clusters of molecular markers were observed on most of the 14 chromosomes. AFLP (amplified fragment length polymorphism) markers manifested a random distribution among homologous groups, but not among genomes and chromosomes. Genetic differentiation between T. dicoccoides and T. durum was attributed mainly to the B genome as revealed by AFLP markers. The segregation-distorted markers were mainly clustered on 4A, 5A, and 5B chromosomes. Homeoalleles, differentially conferring the vigor of gametes, might be responsible for the distortion on 5A and 5B chromosomes. Quasilinkage, deviation from free recombination between markers of nonhomologous chromosomes, was discovered. Massive negative interference was observed in most of the chromosomes (an excess of double crossovers in adjacent intervals relative to the expected rates on the assumption of no interference). The general pattern of distribution of islands of negative interference included near-centromeric location, spanning the centromere, and median/subterminal location. [An appendix describing the molecular marker loci is available as an online supplement at http://www.genome.org.] PMID:11042150

  8. Genome-wide identification of allele-specific expression in response to Streptococcus suis 2 infection in two differentially susceptible pig breeds.

    PubMed

    Wu, Huayu; Gaur, Uma; Mekchay, Supamit; Peng, Xianwen; Li, Lianghua; Sun, Hua; Song, Zhongxu; Dong, Binke; Li, Mingbo; Wimmers, Klaus; Ponsuksili, Siriluck; Li, Kui; Mei, Shuqi; Liu, Guisheng

    2015-11-01

    Although allele expression imbalance has been recognized in many species, and strongly linked to diseases, no whole transcriptome allele imbalance has been detected in pigs during pathogen infections. The pathogen Streptococcus suis 2 (SS2) causes serious zoonotic disease. Different pig breeds show differential susceptibility/resistance to pathogen infection, but the biological insight is little known. Here we analyzed allele-specific expression (ASE) using the spleen transcriptome of four pigs belonging to two phenotypically different breeds after SS2 infection. The comparative analysis of allele specific SNPs between control and infected animals revealed 882 and 1096 statistically significant differentially expressed allele SNPs (criteria: ratio ≧ 2 or ≦ 0.5) in Landrace and Enshi black pig, respectively. Twenty nine allelically imbalanced SNPs were further verified by Sanger sequencing, and later six SNPs were quantified by pyrosequencing assay. The pyrosequencing results are in agreement with the RNA-seq results, except two SNPs. Looking at the role of ASE in predisposition to diseases, the discovery of causative variants by ASE analysis might help the pig industry in long term to design breeding programs for improving SS2 resistance.

  9. 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. PMID:26446984

  10. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe.

    PubMed

    Wahls, Wayne P; Davidson, Mari K

    2008-09-01

    In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4(+) gene for positive and negative selection, an origin of replication (ars1) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS(+). These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization. PMID:18613214

  11. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe

    PubMed Central

    Wahls, Wayne P.; Davidson, Mari K.

    2011-01-01

    In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4+ gene for positive and negative selection, an origin of replication (ars1 ) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS+. These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization. PMID:18613214

  12. Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation.

    PubMed

    Tomazetto, Geizecler; Hahnke, Sarah; Maus, Irena; Wibberg, Daniel; Pühler, Alfred; Schlüter, Andreas; Klocke, Michael

    2014-12-20

    The bacterium Peptoniphilus sp. strain ING2-D1G (DSM 28672), a mesophilic and obligate anaerobic bacterium belonging to the order Clostridiales was isolated from a biogas-producing lab-scale completely stirred tank reactor (CSTR) optimized for anaerobic digestion of maize silage in co-fermentation with pig and cattle manure. In this study, the whole genome sequence of Peptoniphilus sp. strain ING2-D1G, a new isolate potentially involved in protein breakdown and acidogenesis during biomass degradation, is reported. The chromosome of this strain is 1.6Mb in size and encodes genes predicted to be involved in the production of acetate, lactate and butyrate specifying the acidogenic metabolism of the isolate.

  13. Air traffic coverage

    SciTech Connect

    George, L.L.

    1988-09-16

    The Federal Aviation Administration plans to consolidate several hundred air traffic control centers and TRACONs into area control facilities while maintaining air traffic coverage. This paper defines air traffic coverage, a performance measure of the air traffic control system. Air traffic coverage measures performance without controversy regarding delay and collision probabilities and costs. Coverage measures help evaluate alternative facility architectures and help schedule consolidation. Coverage measures also help evaluate protocols for handling one facility's air traffic to another facility in case of facility failure. Coverage measures help evaluate radar, communications and other air traffic control systems and procedures. 4 refs., 2 figs.,

  14. A Genetic Analysis of Taoyuan Pig and Its Phylogenetic Relationship to Eurasian Pig Breeds

    PubMed Central

    Li, Kuan-Yi; Li, Kuang-Ti; Cheng, Chun-Chun; Chen, Chia-Hsuan; Hung, Chien-Yi; Ju, Yu-Ten

    2015-01-01

    Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan’s early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high FST values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes. PMID:25656199

  15. Insurance Coverage Policies for Personalized Medicine

    PubMed Central

    Hresko, Andrew; Haga, Susanne B.

    2012-01-01

    Adoption of personalized medicine in practice has been slow, in part due to the lack of evidence of clinical benefit provided by these technologies. Coverage by insurers is a critical step in achieving widespread adoption of personalized medicine. Insurers consider a variety of factors when formulating medical coverage policies for personalized medicine, including the overall strength of evidence for a test, availability of clinical guidelines and health technology assessments by independent organizations. In this study, we reviewed coverage policies of the largest U.S. insurers for genomic (disease-related) and pharmacogenetic (PGx) tests to determine the extent that these tests were covered and the evidence basis for the coverage decisions. We identified 41 coverage policies for 49 unique testing: 22 tests for disease diagnosis, prognosis and risk and 27 PGx tests. Fifty percent (or less) of the tests reviewed were covered by insurers. Lack of evidence of clinical utility appears to be a major factor in decisions of non-coverage. The inclusion of PGx information in drug package inserts appears to be a common theme of PGx tests that are covered. This analysis highlights the variability of coverage determinations and factors considered, suggesting that the adoption of personal medicine will affected by numerous factors, but will continue to be slowed due to lack of demonstrated clinical benefit. PMID:25562360

  16. Insurance coverage policies for personalized medicine.

    PubMed

    Hresko, Andrew; Haga, Susanne B

    2012-10-30

    Adoption of personalized medicine in practice has been slow, in part due to the lack of evidence of clinical benefit provided by these technologies. Coverage by insurers is a critical step in achieving widespread adoption of personalized medicine. Insurers consider a variety of factors when formulating medical coverage policies for personalized medicine, including the overall strength of evidence for a test, availability of clinical guidelines and health technology assessments by independent organizations. In this study, we reviewed coverage policies of the largest U.S. insurers for genomic (disease-related) and pharmacogenetic (PGx) tests to determine the extent that these tests were covered and the evidence basis for the coverage decisions. We identified 41 coverage policies for 49 unique testing: 22 tests for disease diagnosis, prognosis and risk and 27 PGx tests. Fifty percent (or less) of the tests reviewed were covered by insurers. Lack of evidence of clinical utility appears to be a major factor in decisions of non-coverage. The inclusion of PGx information in drug package inserts appears to be a common theme of PGx tests that are covered. This analysis highlights the variability of coverage determinations and factors considered, suggesting that the adoption of personal medicine will affected by numerous factors, but will continue to be slowed due to lack of demonstrated clinical benefit.

  17. Constellation Coverage Analysis

    NASA Technical Reports Server (NTRS)

    Lo, Martin W. (Compiler)

    1997-01-01

    The design of satellite constellations requires an understanding of the dynamic global coverage provided by the constellations. Even for a small constellation with a simple circular orbit propagator, the combinatorial nature of the analysis frequently renders the problem intractable. Particularly for the initial design phase where the orbital parameters are still fluid and undetermined, the coverage information is crucial to evaluate the performance of the constellation design. We have developed a fast and simple algorithm for determining the global constellation coverage dynamically using image processing techniques. This approach provides a fast, powerful and simple method for the analysis of global constellation coverage.

  18. [Coverage of health services].

    PubMed

    Martínez-Narváez, G

    1992-01-01

    In this paper the concepts and criteria related to health coverage are discussed in the context of the organization of national health systems. The main international agreements based on WHO/PAHO proposals are also described. The relationship between primary health care and health coverage is analyzed and the evolution of the programs for the extension of health coverage in Mexico are discussed, with emphasis on the problems of overlap and definition of the universe in the several institutions of the health sector. Finally, the author reviews the problems to measure coverage in order to guarantee social and operative efficiency of the Mexican health system. PMID:1411776

  19. 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. PMID:26347296

  20. 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.

  1. 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...

  2. Cloning pigs: advances and applications.

    PubMed

    Polejaeva, I A

    2001-01-01

    Although mouse embryonic stem cells have been used widely for over a decade as an important tool for introducing precise genetic modification into the genome, demonstrating the great value of this technology in a range of biomedical applications, similar technology does not exist for domestic animals. However, the development of somatic cell nuclear transfer has bypassed the need for embryonic stem cells from livestock. The production of offspring from differentiated cell nuclei provides information and opportunities in a number of areas including cellular differentiation, early development and ageing. However, the primary significance of cloning is probably in the opportunities that this technology brings to genetic manipulation. Potential applications of gene targeting in livestock species are described with particular emphasis on the generation of pigs that can be used for xenotransplantation, and the production of improved models for human physiology and disease. The development of techniques for somatic cell nuclear transfer in pigs and the challenges associated with this technology are also reviewed.

  3. Identification of Copy Number Variations in Xiang and Kele Pigs

    PubMed Central

    Xie, Jian; Li, Rongrong; Li, Sheng; Ran, Xueqin; Wang, Jiafu; Jiang, Jicai; Zhao, Pengju

    2016-01-01

    Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds. PMID:26840413

  4. 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 ...

  5. De novo assembly of the carrot mitochondrial genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Organelle genome sequence data are a valuable tool to study phylogenetic relationships and genome evolution. Low coverage whole genome shot gun sequencing provides good coverage of organelle genomes making genome-sequencing projects possible for any plant species. Despite its power, features of mito...

  6. Current transcriptomics in pig immunity research.

    PubMed

    Schroyen, Martine; Tuggle, Christopher K

    2015-02-01

    Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig's robustness and resilience against pathogens through selection, a better understanding of the genetic and epigenetic factors in the immune response is required. This review highlights results from the most recent transcriptome research, and the meta-analyses performed, in the context of pig immunity. A technological overview is given including wholegenome microarrays, immune-specific arrays, small-scale high-throughput expression methods, high-density tiling arrays, and next generation sequencing (NGS). Although whole genome microarray techniques will remain complementary to NGS for some time in domestic species, research will transition to sequencing-based methods due to cost-effectiveness and the extra information that such methods provide. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review. With emphasis on the insights obtained from transcriptomic analyses for porcine immunity, we also discuss the experimental design in pig immunity research and the value of the newly published porcine genome assembly in using the pig as a model for human immune response. We conclude by discussing the importance of establishing community standards to maximize the possibility of integrative computational analyses, such as was clearly beneficial for the human ENCODE project.

  7. Drug Plan Coverage Rules

    MedlinePlus

    ... works with other insurance Find health & drug plans Drug plan coverage rules Note Call your Medicare drug ... shingles vaccine) when medically necessary to prevent illness. Drugs you get in hospital outpatient settings In most ...

  8. 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...

  9. Next-generation sequence analysis of the genome of RFHVMn, the macaque homolog of Kaposi's sarcoma (KS)-associated herpesvirus, from a KS-like tumor of a pig-tailed macaque.

    PubMed

    Bruce, A Gregory; Ryan, Jonathan T; Thomas, Mathew J; Peng, Xinxia; Grundhoff, Adam; Tsai, Che-Chung; Rose, Timothy M

    2013-12-01

    The complete sequence of retroperitoneal fibromatosis-associated herpesvirus Macaca nemestrina (RFHVMn), the pig-tailed macaque homolog of Kaposi's sarcoma-associated herpesvirus (KSHV), was determined by next-generation sequence analysis of a Kaposi's sarcoma (KS)-like macaque tumor. Colinearity of genes was observed with the KSHV genome, and the core herpesvirus genes had strong sequence homology to the corresponding KSHV genes. RFHVMn lacked homologs of open reading frame 11 (ORF11) and KSHV ORFs K5 and K6, which appear to have been generated by duplication of ORFs K3 and K4 after the divergence of KSHV and RFHV. RFHVMn contained positional homologs of all other unique KSHV genes, although some showed limited sequence similarity. RFHVMn contained a number of candidate microRNA genes. Although there was little sequence similarity with KSHV microRNAs, one candidate contained the same seed sequence as the positional homolog, kshv-miR-K12-10a, suggesting functional overlap. RNA transcript splicing was highly conserved between RFHVMn and KSHV, and strong sequence conservation was noted in specific promoters and putative origins of replication, predicting important functional similarities. Sequence comparisons indicated that RFHVMn and KSHV developed in long-term synchrony with the evolution of their hosts, and both viruses phylogenetically group within the RV1 lineage of Old World primate rhadinoviruses. RFHVMn is the closest homolog of KSHV to be completely sequenced and the first sequenced RV1 rhadinovirus homolog of KSHV from a nonhuman Old World primate. The strong genetic and sequence similarity between RFHVMn and KSHV, coupled with similarities in biology and pathology, demonstrate that RFHVMn infection in macaques offers an important and relevant model for the study of KSHV in humans. PMID:24109218

  10. 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

  11. The use of nuclear transfer to produce transgenic pigs.

    PubMed

    Macháty, Zoltán; Bondioli, Kenneth R; Ramsoondar, Jagdeece J; Fodor, William L

    2002-01-01

    Manipulation of the pig genome has the potential to improve pig production and offers powerful biomedical applications. Genetic manipulation of mammals has been possible for over two decades, but the technology available has proven both difficult and inefficient. The development of new techniques to enhance efficiency and overcome the complications of random insertion is of importance. Nuclear transfer combined with homologous recombination provides a possible solution: precise genetic modifications in the pig genome may be induced via homologous recombination, and viable offspring can be produced by nuclear transfer using cultured transfected cell lines. The technique is still ineffective, but it is believed to have immense potential. One area that would benefit from the technology is that of xenotransplantation: transgenic pigs are expected to be available as organ donors in the foreseeable future. PMID:12006153

  12. 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.

  13. A reference gene catalogue of the pig gut microbiome.

    PubMed

    Xiao, Liang; Estellé, Jordi; Kiilerich, Pia; Ramayo-Caldas, Yuliaxis; Xia, Zhongkui; Feng, Qiang; Liang, Suisha; Pedersen, Anni Øyan; Kjeldsen, Niels Jørgen; Liu, Chuan; Maguin, Emmanuelle; Doré, Joël; Pons, Nicolas; Le Chatelier, Emmanuelle; Prifti, Edi; Li, Junhua; Jia, Huijue; Liu, Xin; Xu, Xun; Ehrlich, Stanislav D; Madsen, Lise; Kristiansen, Karsten; Rogel-Gaillard, Claire; Wang, Jun

    2016-09-19

    The pig is a major species for livestock production and is also extensively used as the preferred model species for analyses of a wide range of human physiological functions and diseases(1). The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized(2). Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue(3,4). Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome(5). By deep metagenome sequencing of faecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Of the functional pathways found in the human catalogue, 96% are present in the pig catalogue, supporting the potential use of pigs for biomedical research. We show that sex, age and host genetics are likely to influence the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems.

  14. A reference gene catalogue of the pig gut microbiome.

    PubMed

    Xiao, Liang; Estellé, Jordi; Kiilerich, Pia; Ramayo-Caldas, Yuliaxis; Xia, Zhongkui; Feng, Qiang; Liang, Suisha; Pedersen, Anni Øyan; Kjeldsen, Niels Jørgen; Liu, Chuan; Maguin, Emmanuelle; Doré, Joël; Pons, Nicolas; Le Chatelier, Emmanuelle; Prifti, Edi; Li, Junhua; Jia, Huijue; Liu, Xin; Xu, Xun; Ehrlich, Stanislav D; Madsen, Lise; Kristiansen, Karsten; Rogel-Gaillard, Claire; Wang, Jun

    2016-01-01

    The pig is a major species for livestock production and is also extensively used as the preferred model species for analyses of a wide range of human physiological functions and diseases(1). The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized(2). Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue(3,4). Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome(5). By deep metagenome sequencing of faecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Of the functional pathways found in the human catalogue, 96% are present in the pig catalogue, supporting the potential use of pigs for biomedical research. We show that sex, age and host genetics are likely to influence the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems. PMID:27643971

  15. When pigs fly, UCP1 makes heat.

    PubMed

    Jastroch, Martin; Andersson, Leif

    2015-05-01

    Brown and beige adipose tissue may represent important therapeutic targets for the treatment of diabetes and obesity as these organs dissipate nutrient energy as heat through the thermogenic uncoupling protein 1 (UCP1). While mice are commonly used to mimic the potential effects of brown/beige adipose tissue that may act in human metabolism, new animal models are edging into the market for translational medicine. Pigs reflect human metabolism better than mice in multiple parameters such as obesity-induced hyperglycemia, cholesterol profiles and energy metabolism. Recently, it was reported that energy expenditure and body temperature in pigs is induced by the hormone leptin, and that leptin's action is mediated by UCP1 in adipose tissue. Given the tremendous importance of identifying molecular mechanisms for targeting therapeutics, we critically examine the evidence supporting the presence of UCP1 in pigs and conclude that methodological shortcomings prevent an unequivocal claim for the presence of UCP1 in pigs. Despite this, we believe that leptin's effects on energy expenditure in pigs are potentially more transformative to human medicine in the absence of UCP1, as adult and obese humans possess only minor amounts of UCP1. In general, we propose that the biology of new animal models requires attention to comparative studies with humans given the increasing amount of genomic information for various animal species.

  16. Current Progress of Genetically Engineered Pig Models for Biomedical Research

    PubMed Central

    Gün, Gökhan

    2014-01-01

    Abstract The first transgenic pigs were generated for agricultural purposes about three decades ago. Since then, the micromanipulation techniques of pig oocytes and embryos expanded from pronuclear injection of foreign DNA to somatic cell nuclear transfer, intracytoplasmic sperm injection-mediated gene transfer, lentiviral transduction, and cytoplasmic injection. Mechanistically, the passive transgenesis approach based on random integration of foreign DNA was developed to active genetic engineering techniques based on the transient activity of ectopic enzymes, such as transposases, recombinases, and programmable nucleases. Whole-genome sequencing and annotation of advanced genome maps of the pig complemented these developments. The full implementation of these tools promises to immensely increase the efficiency and, in parallel, to reduce the costs for the generation of genetically engineered pigs. Today, the major application of genetically engineered pigs is found in the field of biomedical disease modeling. It is anticipated that genetically engineered pigs will increasingly be used in biomedical research, since this model shows several similarities to humans with regard to physiology, metabolism, genome organization, pathology, and aging. PMID:25469311

  17. 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…

  18. Cleaning pipelines: a pigging primer

    SciTech Connect

    Kipin, P.

    1985-02-04

    The ''pig'', a cleaning device currently used to clear out pipes, is discussed here. Types of pigs are described and include styrofoam, rubber, and soft foam. The limitations to the use of pigs are discussed. Unless all valves are fully open, a pig can get stuck. Ball-type tees may cause a short pig to drop and bypass. Generally, no pig is able to traverse a one-cut miter.

  19. 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 make. (NH)

  20. Tail biting in pigs.

    PubMed

    Schrøder-Petersen, D L; Simonsen, H B

    2001-11-01

    One of the costly and welfare-reducing problems in modern pig production is tail biting. Tail biting is an abnormal behaviour, characterized by one pig's dental manipulation of another pig's tail. Tail biting can be classified into two groups: the pre-injury stage, before any wound on the tail is present, and the injury stage, where the tail is wounded and bleeding. Tail biting in the injury stage will reduce welfare of the bitten pig and the possible spread of infection is a health as well as welfare problem. The pigs that become tail biters may also suffer, because they are frustrated due to living in a stressful environment. This frustration may result in an excessive motivation for biting the tails of pen mates. This review aims to summarize recent research and theories in relation to tail biting. PMID:11681870

  1. Molecular approaches in pig breeding to improve meat quality.

    PubMed

    Davoli, Roberta; Braglia, Silvia

    2007-12-01

    This article reviews the advances in molecular genetics that have led to the identification of genes and markers associated with meat quality in pig. The development of a considerable number of annotated livestock genome sequences represents an incredibly rich source of information that can be used to identify candidate genes responsible for complex traits and quantitative trait loci effects. In pig, the huge amount of information emerging from the study of the genome has helped in the acquisition of new knowledge concerning biological systems and it is opening new opportunities for the genetic selection of this specie. Among the new fields of genomics recently developed, functional genomics and proteomics that allow considering many genes and proteins at the same time are very useful tools for a better understanding of the function and regulation of genes, and how these participate in complex networks controlling the phenotypic characteristics of a trait. In particular, global gene expression profiling at the mRNA and protein level can provide a better understanding of gene regulation that underlies biological functions and physiology related to the delivery of a better pig meat quality. Moreover, the possibility to realize an integrated approach of genomics and proteomics with bioinformatics tools is essential to obtain a complete exploitation of the available molecular genetics information. The development of this knowledge will benefit scientists, industry and breeders considering that the efficiency and accuracy of the traditional pig selection schemes will be improved by the implementation of molecular data into breeding programs. PMID:18208864

  2. 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.

  3. 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.

  4. 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

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

    PubMed

    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.

  6. A GPS coverage model

    NASA Technical Reports Server (NTRS)

    Skidmore, Trent A.

    1994-01-01

    The results of several case studies using the Global Positioning System coverage model developed at Ohio University are summarized. Presented are results pertaining to outage area, outage dynamics, and availability. Input parameters to the model include the satellite orbit data, service area of interest, geometry requirements, and horizon and antenna mask angles. It is shown for precision-landing Category 1 requirements that the planned GPS 21 Primary Satellite Constellation produces significant outage area and unavailability. It is also shown that a decrease in the user equivalent range error dramatically decreases outage area and improves the service availability.

  7. 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

  8. Comparative analysis of monocyte subsets in the pig.

    PubMed

    Fairbairn, Lynsey; Kapetanovic, Ronan; Beraldi, Dario; Sester, David P; Tuggle, Chris K; Archibald, Alan L; Hume, David A

    2013-06-15

    Human and mouse monocyte can be divided into two different subpopulations based on surface marker expression: CD14/16 and Ly6C/CX3CR1, respectively. Monocyte subpopulations in the pig were identified based on reciprocal expression of CD14 and the scavenger receptor CD163. The two populations, CD14(hi)-CD163(low) and CD14(low)-CD163(hi), show approximately equal abundance in the steady-state. Culture of pig PBMCs in CSF1 indicates that the two populations are a maturation series controlled by this growth factor. Gene expression in pig monocyte subpopulations was profiled using the newly developed and annotated pig whole genome snowball microarray. Previous studies have suggested a functional equivalence between human and mouse subsets, but certain genes such as CD36, CLEC4E, or TREM-1 showed human-specific expression. The same genes were expressed selectively in pig monocyte subsets. However, the profiles suggest that the pig CD14(low)-CD163(high) cells are actually equivalent to intermediate human monocytes, and there is no CD14(-) CD16(+) "nonclassical" population. The results are discussed in terms of the relevance of the pig as a model for understanding human monocyte function. PMID:23667115

  9. 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.

  10. Pathway analysis in blood cells of pigs infected with classical swine fever virus: comparison of pigs that develop a chronic form of infection or recover.

    PubMed

    Hulst, Marcel; Loeffen, Willie; Weesendorp, Eefke

    2013-02-01

    Infection of pigs with CSFV can lead to either acute disease, resulting in death or recovery, or chronic disease. The mechanisms by which CSFV manipulates the pig's first line of defence to establish a chronic infection are poorly understood. Therefore, pigs were infected with moderately virulent CSFV, and whole blood was collected on a regular basis during a period of 18 days. Using whole-genome microarrays, time-dependent changes in gene expression were recorded in blood cells of chronically diseased pigs and pigs that recovered. Bioinformatics analysis of regulated genes indicated that different immunological pathways were regulated in chronically diseased pigs compared to recovered pigs. In recovered pigs, antiviral defence mechanisms were rapidly activated, whereas in chronically diseased pigs, several genes with the potential to inhibit NF-κB- and IRF3/7-mediated transcription of type I interferons were up-regulated. Compared to recovered pigs, chronically diseased pigs failed to activate NK or cytotoxic T-cell pathways, and they showed decreased gene activity in antigen-presenting monocytes/macrophages. Remarkably, in chronically diseased pigs, genes related to the human autoimmune disease systemic lupus erythematosus (SLE) were up-regulated during the whole period of 18 days. CSFV pathology in kidney and skin resembles that of SLE. Furthermore, enzymes involved in the degradation of 1,25-dihydroxyvitamin D3 and of tryptophan to kynurenines were expressed at different levels in chronically diseased and recovered pigs. Both of these chemical processes may affect the functions of T helper/regulatory cells that are crucial for tempering the inflammatory response after a viral infection.

  11. Genome-wide DNA Methylation Profiles of Small Intestine and Liver in Fast-growing and Slow-growing Weaning Piglets

    PubMed Central

    Kwak, Woori; Kim, Jin-nam; Kim, Daewon; Hong, Jin Su; Jeong, Jae Hark; Kim, Heebal; Cho, Seoae; Kim, Yoo Yong

    2014-01-01

    Although growth rate is one of the main economic traits of concern in pig production, there is limited knowledge on its epigenetic regulation, such as DNA methylation. In this study, we conducted methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) to compare genome-wide DNA methylation profile of small intestine and liver tissue between fast- and slow-growing weaning piglets. The genome-wide methylation pattern between the two different growing groups showed similar proportion of CpG (regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence) coverage, genomic regions, and gene regions. Differentially methylated regions and genes were also identified for downstream analysis. In canonical pathway analysis using differentially methylated genes, pathways (triacylglycerol pathway, some cell cycle related pathways, and insulin receptor signaling pathway) expected to be related to growth rate were enriched in the two organ tissues. Differentially methylated genes were also organized in gene networks related to the cellular development, growth, and carbohydrate metabolism. Even though further study is required, the result of this study may contribute to the understanding of epigenetic regulation in pig growth. PMID:25358311

  12. 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

  13. Newspaper Coverage of Racial Injustices.

    ERIC Educational Resources Information Center

    Martindale, Carolyn

    Noting that the press was criticized during the 1960s for failing to convey to white readers the problems and injustices experienced by black Americans, a study analyzed the nature and amount of civil rights coverage in five newspapers from 1963 through 1980. News coverage concerning blacks was examined in 66 issues from four major newspapers in…

  14. Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

    PubMed Central

    Dalrymple, Brian P; Kirkness, Ewen F; Nefedov, Mikhail; McWilliam, Sean; Ratnakumar, Abhirami; Barris, Wes; Zhao, Shaying; Shetty, Jyoti; Maddox, Jillian F; O'Grady, Margaret; Nicholas, Frank; Crawford, Allan M; Smith, Tim; de Jong, Pieter J; McEwan, John; Oddy, V Hutton; Cockett, Noelle E

    2007-01-01

    Background Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? Results A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser. Conclusion We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited. PMID:17663790

  15. 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.

  16. 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

    2016-01-01

    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. PMID:26650334

  17. Senecavirus A: An Emerging Vesicular Infection in Brazilian Pig Herds.

    PubMed

    Leme, R A; Zotti, E; Alcântara, B K; Oliveira, M V; Freitas, L A; Alfieri, A F; Alfieri, A A

    2015-12-01

    Vesicular diseases are clinically and economically important infections that affect farm animals. North American studies have suggested that Senecavirus A infection might be associated with a vesicular disease in pigs known as porcine idiopathic vesicular disease (PIVD). In the beginning of 2015, outbreaks of porcine vesicular disease have occurred in six Brazilian states from three geographical regions. Official diagnostic tests were performed with negative results for classical vesicular diseases of compulsory reporting. This study investigated Senecavirus A infection in PIVD outbreaks in which other aetiological agents were ruled out. A primer set was designed to amplify a 542-bp product size of VP3/VP1 region of Senecavirus A genome in RT-PCR assay. Primer specificity was analysed in silico and in porcine biological specimens. For this, clinical specimens were collected from eight pig herds affected with PIVD, including vesicular fluid (n = 4) and swabs (n = 7) and scrapings of ruptured vesicles and ulcerative lesions (n = 5) from weaned and adult pigs. Clinically healthy animals (n = 52) of PIVD-affected and non-affected pig herds also were evaluated for Senecavirus A infection. The 16 samples from PIVD-affected animals were positive for Senecavirus A in the RT-PCR assay, while none of the clinically healthy pigs were detected with the virus. Sequencing analysis revealed high nucleotide (87.6-98.5%) and amino acid (95-99.4%) similarities to SVV-01 prototype and other Senecavirus A strains from North American pigs. Primer set presented herein was suitable for molecular characterization of Senecavirus A. The results suggest that Senecavirus A was the aetiological agent of the vesicular disease outbreaks in the evaluated pig herds. This is the first study to report the Senecavirus A infection in clinically affected pigs outside of North America. Senecavirus A was considered a novel emerging pathogen associated with an important vesicular disease in Brazil

  18. Mapping of 195 genes in cattle and updated comparative map with man, mouse, rat and pig.

    PubMed

    Hayes, H; Elduque, C; Gautier, M; Schibler, L; Cribiu, E; Eggen, A

    2003-01-01

    Our on-going goal is to improve and update the comparative genome organization between cattle and man but also among the most detailed mammalian species genomes i.e. cattle, mouse, rat and pig. In this work, we localized 195 genes in cattle and checked all human/bovine non-concordant localizations found in the literature. Next, we compiled all the genes mapped in cattle, goat, sheep and pig (2,166) for which the human ortholog with its chromosomal position is known, added corresponding data in mouse and rat, and ordered the genes relatively to the human genome sequence. We estimate that our compilation provides bovine mapping information for about 89% of the human autosomes. Thus, a near complete, overall and detailed picture of the number, distribution and extent of bovine conserved syntenies (regardless of gene order) on human R-banded autosomes is proposed as well as a comparison with mouse, rat and pig genomes. PMID:14970673

  19. Global routine vaccination coverage, 2014.

    PubMed

    Subaiya, Saleena; Dumolard, Laure; Lydon, Patrick; Gacic-Dobo, Marta; Eggers, Rudolf; Conklin, Laura

    2015-11-13

    The year 2014 marked the 40th anniversary of the World Health Organization’s (WHO) Expanded Program on Immunization, which was established to ensure equitable access to routine immunization services (1). Since 1974, global coverage with the four core vaccines (Bacille Calmette- Guérin vaccine [BCG; for protection against tuberculosis], diphtheria-tetanus-pertussis [DTP] vaccine, poliovirus vaccine, and measles vaccine) has increased from <5% to ≥85%, and additional vaccines have been added to the recommended schedule. Coverage with the 3rd dose of DTP vaccine (DTP3) by age 12 months is an indicator of immunization program performance because it reflects completion of the basic infant immunization schedule; coverage with other vaccines, including the 3rd dose of poliovirus vaccine (polio3); the 1st dose of measles-containing vaccine (MCV1) is also assessed. Estimated global DTP3 coverage has remained at 84%–86% since 2009, with estimated 2014 coverage at 86%. Estimated global coverage for the 2nd routine dose of measles-containing vaccine (MCV2) was 38% by age 24 months and 56% when older age groups were included, similar to levels reported in 2013 (36% and 55%, respectively). To reach and sustain high immunization coverage in all countries, adequate vaccine stock management and additional opportunities for immunization, such as through routine visits in the second year of life, are integral components to strengthening immunization programs and reducing morbidity and mortality from vaccine preventable diseases. PMID:26562454

  20. 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

  1. 7 CFR 1437.5 - Coverage period.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Coverage period. 1437.5 Section 1437.5 Agriculture... Provisions § 1437.5 Coverage period. (a) The coverage period is the time during which coverage is available against loss of production of the eligible crop as a result of natural disaster. (b) The coverage...

  2. 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…

  3. 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)

  4. 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.

  5. Global routine vaccination coverage, 2013.

    PubMed

    Harris, Jennifer B; Gacic-Dobo, Marta; Eggers, Rudolf; Brown, David W; Sodha, Samir V

    2014-11-21

    In 1974, the World Health Organization (WHO) established the Expanded Program on Immunization to ensure that all children have access to routinely recommended vaccines. Since then, global coverage with the four core vaccines (Bacille Calmette-Guérin vaccine [for protection against tuberculosis], diphtheria-tetanus-pertussis vaccine [DTP], polio vaccine, and measles vaccine) has increased from <5% to ≥84%, and additional vaccines have been added to the recommended schedule. Coverage with the third dose of DTP vaccine (DTP3) by age 12 months is a key indicator of immunization program performance. Estimated global DTP3 coverage has remained at 83%-84% since 2009, with estimated 2013 coverage at 84%. Global coverage estimates for the second routine dose of measles-containing vaccine (MCV2) are reported for the first time in 2013; global coverage was 35% by the end of the second year of life and 53% when including older age groups. Improvements in equity of access and use of immunization services will help ensure that all children are protected from vaccine-preventable diseases. PMID:25412062

  6. 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

  7. 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. PMID:24430555

  8. Genes, genome and Gestalt.

    PubMed

    Grisolia, Cesar Koppe

    2005-01-01

    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.

  9. Extending Medicare immunosuppressive medication coverage.

    PubMed

    Beaubrun, Anne Christine

    2012-02-01

    African Americans and the poor are at a high risk of suffering from kidney disease and are at an extreme disadvantage when it comes to obtaining the resources needed to maintain a functioning kidney post-transplant. Medicare currently covers 80% of the cost of immunosuppressive therapy for up to three years following a Medicare-covered transplant for patients whose Medicare entitlement was based solely on their end-stage renal disease diagnosis. Adequate insurance coverage has the potential to prevent graft failure and retransplantation resulting from cost-related immunosuppressive medication nonadherence. Given the multifactorial nature of medication nonadherence, extending insurance coverage in an attempt to reduce graft failures should be coupled with intensive interventions to prevent the socioeconomic and various other factors associated with medication nonadherence. Lifetime Medicare coverage for all kidney-transplant recipients, coupled with medication adherence promotion, has the potential to minimize poor outcomes associated with graft failure, especially among minorities and the impoverished.

  10. 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

  11. 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...

  12. 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... trucks. Other levels of coverage may be approved if the necessary emission reductions are...

  13. 5 CFR 847.415 - OASDI coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false OASDI coverage. 847.415 Section 847.415...) ELECTIONS OF RETIREMENT COVERAGE BY CURRENT AND FORMER EMPLOYEES OF NONAPPROPRIATED FUND INSTRUMENTALITIES Elections of Coverage Under the Retroactive Provisions Elections of Csrs Or Fers Coverage Based on A...

  14. 5 CFR 837.301 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Coverage. 837.301 Section 837.301...) REEMPLOYMENT OF ANNUITANTS Coverage and Contributions § 837.301 Coverage. (a) When annuity terminates on, or is suspended during, reemployment. Retirement coverage under either CSRS or FERS is governed by subpart B...

  15. 5 CFR 837.301 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Coverage. 837.301 Section 837.301...) REEMPLOYMENT OF ANNUITANTS Coverage and Contributions § 837.301 Coverage. (a) When annuity terminates on, or is suspended during, reemployment. Retirement coverage under either CSRS or FERS is governed by subpart B...

  16. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 4 2013-01-01 2013-01-01 false Minimum coverage. 205.5 Section 205.5... REGULATIONS AIRCRAFT ACCIDENT LIABILITY INSURANCE § 205.5 Minimum coverage. (a) Insurance contracts and self... maintain the following coverage: (1) Third-party aircraft accident liability coverage for bodily injury...

  17. 5 CFR 837.301 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Coverage. 837.301 Section 837.301...) REEMPLOYMENT OF ANNUITANTS Coverage and Contributions § 837.301 Coverage. (a) When annuity terminates on, or is suspended during, reemployment. Retirement coverage under either CSRS or FERS is governed by subpart B...

  18. 5 CFR 837.301 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Coverage. 837.301 Section 837.301...) REEMPLOYMENT OF ANNUITANTS Coverage and Contributions § 837.301 Coverage. (a) When annuity terminates on, or is suspended during, reemployment. Retirement coverage under either CSRS or FERS is governed by subpart B...

  19. 5 CFR 847.415 - OASDI coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false OASDI coverage. 847.415 Section 847.415...) ELECTIONS OF RETIREMENT COVERAGE BY CURRENT AND FORMER EMPLOYEES OF NONAPPROPRIATED FUND INSTRUMENTALITIES Elections of Coverage Under the Retroactive Provisions Elections of Csrs Or Fers Coverage Based on A...

  20. 14 CFR 205.5 - Minimum coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 4 2012-01-01 2012-01-01 false Minimum coverage. 205.5 Section 205.5... REGULATIONS AIRCRAFT ACCIDENT LIABILITY INSURANCE § 205.5 Minimum coverage. (a) Insurance contracts and self... maintain the following coverage: (1) Third-party aircraft accident liability coverage for bodily injury...

  1. 42 CFR 457.470 - Prohibited coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 4 2012-10-01 2012-10-01 false Prohibited coverage. 457.470 Section 457.470 Public... Requirements: Coverage and Benefits § 457.470 Prohibited coverage. A State is not required to provide health benefits coverage under the plan for an item or service for which payment is prohibited under title...

  2. 5 CFR 837.301 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false Coverage. 837.301 Section 837.301...) REEMPLOYMENT OF ANNUITANTS Coverage and Contributions § 837.301 Coverage. (a) When annuity terminates on, or is suspended during, reemployment. Retirement coverage under either CSRS or FERS is governed by subpart B...

  3. 42 CFR 457.470 - Prohibited coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 4 2013-10-01 2013-10-01 false Prohibited coverage. 457.470 Section 457.470 Public... Requirements: Coverage and Benefits § 457.470 Prohibited coverage. A State is not required to provide health benefits coverage under the plan for an item or service for which payment is prohibited under title...

  4. 42 CFR 457.470 - Prohibited coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Prohibited coverage. 457.470 Section 457.470 Public... Requirements: Coverage and Benefits § 457.470 Prohibited coverage. A State is not required to provide health benefits coverage under the plan for an item or service for which payment is prohibited under title...

  5. 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...

  6. 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...

  7. 32 CFR 199.8 - Double coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 2 2013-07-01 2013-07-01 false Double coverage. 199.8 Section 199.8 National... CIVILIAN HEALTH AND MEDICAL PROGRAM OF THE UNIFORMED SERVICES (CHAMPUS) § 199.8 Double coverage. (a... insurance plans do not exceed the total charges. (b) Double coverage plan. A double coverage plan is one...

  8. 32 CFR 199.8 - Double coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 2 2014-07-01 2014-07-01 false Double coverage. 199.8 Section 199.8 National... CIVILIAN HEALTH AND MEDICAL PROGRAM OF THE UNIFORMED SERVICES (CHAMPUS) § 199.8 Double coverage. (a... insurance plans do not exceed the total charges. (b) Double coverage plan. A double coverage plan is one...

  9. 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

  10. Monitoring Intervention Coverage in the Context of Universal Health Coverage

    PubMed Central

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

    2014-01-01

    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

  11. 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

  12. 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.

  13. The Pig--Pet, Pork or Sacrifice?

    ERIC Educational Resources Information Center

    Arnold, Arthur

    1988-01-01

    Discusses the various roles of the pig in children's books, including E. B. White's CHARLOTTE'S WEB and Nina Bawden's PEPPERMINT PIG. Notes that, although pigs are often used as metaphors for greed, gluttony, and squalor, the portrayal of pigs in children's literature is typically positive. (MM)

  14. Rapid DNA extraction of pig ear tissues.

    PubMed

    Kunhareang, S; Zhou, H; Hickford, J G H

    2010-07-01

    A single-step DNA isolation procedure from pig tissues was developed and the product used directly for polymerase chain reaction (PCR) amplification, single-strand conformational polymorphism (SSCP) analysis and sequencing. The procedure consists of proteinase K digestion of 2-10mg of fresh tissue, at 55 degrees C for 1h, followed by application of the products of digestion to filter paper. A 1.2mm-diameter punch of that paper has sufficient DNA to act as a template for PCR amplification. The quality of the genomic DNA appeared to be high as the PCR amplicons produced sharp banding patterns on both agarose gel electrophoresis and on SSCP analysis, and they could be used for DNA sequencing following cloning. The dried genomic DNA on filter paper can be kept at room temperature. The procedure is considered effective as it is simple, fast and inexpensive. It would be useful for large-scale genotyping and could be used to obtain genomic DNA from various tissues.

  15. Toward universal coverage in Massachusetts.

    PubMed

    Blumberg, Linda J; Holahan, John; Weil, Alan; Clemans-Cope, Lisa; Buettgens, Matthew; Blavin, Fredric; Zuckerman, Stephen

    2006-01-01

    This paper presents several options designed to help the Commonwealth of Massachusetts move to universal health insurance coverage. The alternatives all build upon a common base that includes an expansion of the Medicaid program, income-related tax credits, a purchasing pool, and government-sponsored reinsurance. These measures in themselves would not yield universal coverage, nor would an employer mandate by itself. We show that an individual mandate, and an employer mandate combined with an individual mandate, both would yield universal coverage with a relatively small increase in government costs relative to state gross domestic product and current health spending. The cost of an employer mandate--with a "pay or play" design--is sensitive to the payroll tax rate and base, the number and kind of exemptions, and whether workers whose employers "pay" receive discounts when they purchase health insurance. The development of these alternatives and their analyses contributed to the eventual health care compromise that emerged in Massachusetts in April 2006. PMID:17004641

  16. Production of the mouse whey acidic protein in transgenic pigs during lactation.

    PubMed

    Shamay, A; Solinas, S; Pursel, V G; McKnight, R A; Alexander, L; Beattie, C; Hennighausen, L; Wall, R J

    1991-11-01

    The mouse whey acidic protein (WAP) gene was introduced into the genome of pigs and its expression was analyzed in the mammary gland. Mouse WAP was detected in milk of lactating females from five lines at levels between .5 and 1.5 g/liter, thereby representing as much as 2% of the total milk proteins. The corresponding mRNA was expressed in mammary tissue at levels similar to those of pig beta-lactoglobulin and beta-casein. The pattern of WAP secretion in three pigs over a period of 6 wk was quantitatively similar to that of pig beta-lactoglobulin. From the eight transgenic pigs analyzed, three successfully completed one lactational period, but five pigs stopped lactating a few days after parturition. Our results show that it is possible to produce large quantities of a foreign protein in milk of pigs over a full lactational period. However, expression of WAP can compromise the mammary gland and render it nonfunctional. PMID:1721617

  17. Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus

    PubMed Central

    2012-01-01

    Background The rising demand for pork has resulted in a massive expansion of pig production in Uganda. This has resulted in increased contact between humans and pigs. Pigs can act as reservoirs for emerging infectious diseases. Therefore identification of potential zoonotic pathogens is important for public health surveillance. In this study, during a routine general surveillance for African swine fever, domestic pigs from Uganda were screened for the presence of RNA and DNA viruses using a high-throughput pyrosequencing method. Findings Serum samples from 16 domestic pigs were collected from five regions in Uganda and pooled accordingly. Genomic DNA and RNA were extracted and sequenced on the 454 GS-FLX platform. Among the sequences assigned to a taxon, 53% mapped to the domestic pig (Sus scrofa). African swine fever virus, Torque teno viruses (TTVs), and porcine endogenous retroviruses were identified. Interestingly, two pools (B and C) of RNA origin had sequences that showed 98% sequence identity to Ndumu virus (NDUV). None of the reads had identity to the class Insecta indicating that these sequences were unlikely to result from contamination with mosquito nucleic acids. Conclusions This is the first report of the domestic pig as a vertebrate host for Ndumu virus. NDUV had been previously isolated only from culicine mosquitoes. NDUV therefore represents a potential zoonotic pathogen, particularly given the increasing risk of human-livestock-mosquito contact. PMID:23006778

  18. Preclinical electrogastrography in experimental pigs

    PubMed Central

    Květina, Jaroslav; Varayil, Jithinraj Edakkanambeth; Ali, Shahzad Marghoob; Kuneš, Martin; Bureš, Jan; Tachecí, Ilja; Rejchrt, Stanislav; Kopáčová, Marcela

    2010-01-01

    Surface electrogastrography (EGG) is a non-invasive means of recording gastric myoelectric activity or slow waves from cutaneous leads placed over the stomach. This paper provides a comprehensive review of preclinical EGG. Our group recently set up and worked out the methods for EGG in experimental pigs. We gained our initial experience in the use of EGG in assessment of porcine gastric myoelectric activity after volume challenge and after intragastric administration of itopride and erythromycin. The mean dominant frequency in pigs is comparable with that found in humans. EGG in experimental pigs is feasible. Experimental EGG is an important basis for further preclinical projects in pharmacology and toxicology. PMID:21217873

  19. 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.

  20. Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1

    PubMed Central

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

    2014-01-01

    Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today. PMID:25601878

  1. 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...

  2. 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...

  3. 5 CFR 351.202 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 351.202 Section 351.202... Provisions § 351.202 Coverage. (a) Employees covered. Except as provided in paragraph (b) of this section... administrative body to be covered hereunder. Coverage includes administrative law judges except as modified...

  4. 5 CFR 430.202 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 430.202 Section 430.202... Performance Appraisal for General Schedule, Prevailing Rate, and Certain Other Employees § 430.202 Coverage..., coverage includes, but is not limited to, senior-level and scientific and professional employees paid...

  5. 5 CFR 530.303 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 530.303 Section 530.303...) Special Rate Schedules for Recruitment and Retention General Provisions § 530.303 Coverage. (a) Under 5 U... coverage criteria specifically state otherwise. OPM will establish special rate schedules...

  6. 29 CFR 1975.4 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 9 2012-07-01 2012-07-01 false Coverage. 1975.4 Section 1975.4 Labor Regulations Relating...) COVERAGE OF EMPLOYERS UNDER THE WILLIAMS-STEIGER OCCUPATIONAL SAFETY AND HEALTH ACT OF 1970 § 1975.4 Coverage. (a) General. Any employer employing one or more employees would be an “employer engaged in...

  7. 5 CFR 430.202 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 430.202 Section 430.202... Performance Appraisal for General Schedule, Prevailing Rate, and Certain Other Employees § 430.202 Coverage..., coverage includes, but is not limited to, senior-level and scientific and professional employees paid...

  8. 5 CFR 530.303 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 530.303 Section 530.303...) Special Rate Schedules for Recruitment and Retention General Provisions § 530.303 Coverage. (a) Under 5 U... coverage criteria specifically state otherwise. OPM will establish special rate schedules...

  9. 5 CFR 530.303 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 530.303 Section 530.303...) Special Rate Schedules for Recruitment and Retention General Provisions § 530.303 Coverage. (a) Under 5 U... coverage criteria specifically state otherwise. OPM will establish special rate schedules...

  10. 5 CFR 530.303 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 530.303 Section 530.303...) Special Rate Schedules for Recruitment and Retention General Provisions § 530.303 Coverage. (a) Under 5 U... coverage criteria specifically state otherwise. OPM will establish special rate schedules...

  11. 5 CFR 890.804 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Coverage. 890.804 Section 890.804... EMPLOYEES HEALTH BENEFITS PROGRAM Benefits for Former Spouses § 890.804 Coverage. (a) Type of enrollment. A former spouse who meets the requirements of § 890.803 may elect coverage for self only or for self...

  12. 5 CFR 890.1106 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...(5) and who meets any applicable requirements of 5 CFR 890.302 of this part. (2) For a former spouse... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Coverage. 890.1106 Section 890.1106... EMPLOYEES HEALTH BENEFITS PROGRAM Temporary Continuation of Coverage § 890.1106 Coverage. (a) Type...

  13. 5 CFR 351.202 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 351.202 Section 351.202... Provisions § 351.202 Coverage. (a) Employees covered. Except as provided in paragraph (b) of this section... administrative body to be covered hereunder. Coverage includes administrative law judges except as modified...

  14. 5 CFR 880.303 - FEHBP coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false FEHBP coverage. 880.303 Section 880.303... FEHBP coverage. (a) If the missing annuitant had a family enrollment, the enrollment will be transferred... she disappeared, subject to the temporary extension of coverage for conversion. (c) If the...

  15. 5 CFR 9901.503 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 3 2011-01-01 2011-01-01 false Coverage. 9901.503 Section 9901.503... (NSPS) Staffing and Employment General § 9901.503 Coverage. (a) At his or her sole and exclusive... in DoD organizational and functional units are eligible for coverage under this subpart:...

  16. 42 CFR 423.566 - Coverage determinations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 3 2014-10-01 2014-10-01 false Coverage determinations. 423.566 Section 423.566... (CONTINUED) MEDICARE PROGRAM (CONTINUED) VOLUNTARY MEDICARE PRESCRIPTION DRUG BENEFIT Grievances, Coverage Determinations, Redeterminations, and Reconsiderations § 423.566 Coverage determinations. (a) Responsibilities...

  17. 5 CFR 890.1106 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...(5) and who meets any applicable requirements of 5 CFR 890.302 of this part. (2) For a former spouse... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Coverage. 890.1106 Section 890.1106... EMPLOYEES HEALTH BENEFITS PROGRAM Temporary Continuation of Coverage § 890.1106 Coverage. (a) Type...

  18. 7 CFR 1806.3 - Coverage requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 12 2010-01-01 2010-01-01 false Coverage requirements. 1806.3 Section 1806.3... REGULATIONS INSURANCE Real Property Insurance § 1806.3 Coverage requirements. The County Supervisor should..., the County Supervisor will see that the coverage is obtained on one or more of the most...

  19. 5 CFR 9701.505 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 3 2012-01-01 2012-01-01 false Coverage. 9701.505 Section 9701.505... MANAGEMENT SYSTEM Labor-Management Relations § 9701.505 Coverage. (a) Employees covered. This subpart applies....S.C. chapter 71 are eligible for coverage under this subpart. In addition, this subpart applies...

  20. 5 CFR 430.202 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 430.202 Section 430.202... Performance Appraisal for General Schedule, Prevailing Rate, and Certain Other Employees § 430.202 Coverage..., coverage includes, but is not limited to, senior-level and scientific and professional employees paid...

  1. 42 CFR 423.566 - Coverage determinations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 3 2013-10-01 2013-10-01 false Coverage determinations. 423.566 Section 423.566... (CONTINUED) MEDICARE PROGRAM (CONTINUED) VOLUNTARY MEDICARE PRESCRIPTION DRUG BENEFIT Grievances, Coverage Determinations, Redeterminations, and Reconsiderations § 423.566 Coverage determinations. (a) Responsibilities...

  2. 5 CFR 351.202 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 351.202 Section 351.202... Provisions § 351.202 Coverage. (a) Employees covered. Except as provided in paragraph (b) of this section... administrative body to be covered hereunder. Coverage includes administrative law judges except as modified...

  3. 5 CFR 351.202 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 351.202 Section 351.202... Provisions § 351.202 Coverage. (a) Employees covered. Except as provided in paragraph (b) of this section... administrative body to be covered hereunder. Coverage includes administrative law judges except as modified...

  4. 5 CFR 890.1203 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Coverage. 890.1203 Section 890.1203... Hostages Captured in Lebanon § 890.1203 Coverage. (a) An individual is covered under this subpart when the U.S. Department of State determines that the individual is eligible for coverage under section...

  5. 5 CFR 430.202 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 430.202 Section 430.202... Performance Appraisal for General Schedule, Prevailing Rate, and Certain Other Employees § 430.202 Coverage..., coverage includes, but is not limited to, senior-level and scientific and professional employees paid...

  6. 5 CFR 880.303 - FEHBP coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false FEHBP coverage. 880.303 Section 880.303... FEHBP coverage. (a) If the missing annuitant had a family enrollment, the enrollment will be transferred... she disappeared, subject to the temporary extension of coverage for conversion. (c) If the...

  7. 5 CFR 890.1106 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...(5) and who meets any applicable requirements of 5 CFR 890.302 of this part. (2) For a former spouse... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Coverage. 890.1106 Section 890.1106... EMPLOYEES HEALTH BENEFITS PROGRAM Temporary Continuation of Coverage § 890.1106 Coverage. (a) Type...

  8. 5 CFR 530.303 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 530.303 Section 530.303...) Special Rate Schedules for Recruitment and Retention General Provisions § 530.303 Coverage. (a) Under 5 U... coverage criteria specifically state otherwise. OPM will establish special rate schedules...

  9. 5 CFR 890.1106 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...(5) and who meets any applicable requirements of 5 CFR 890.302 of this part. (2) For a former spouse... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false Coverage. 890.1106 Section 890.1106... EMPLOYEES HEALTH BENEFITS PROGRAM Temporary Continuation of Coverage § 890.1106 Coverage. (a) Type...

  10. 5 CFR 317.301 - Conversion coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Conversion coverage. 317.301 Section 317... THE SENIOR EXECUTIVE SERVICE Conversion to the Senior Executive Service § 317.301 Conversion coverage... statutory action extending coverage under 5 U.S.C. 3132(a)(1) to that agency. Except as otherwise...

  11. 5 CFR 430.202 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 430.202 Section 430.202... Performance Appraisal for General Schedule, Prevailing Rate, and Certain Other Employees § 430.202 Coverage..., coverage includes, but is not limited to, senior-level and scientific and professional employees paid...

  12. 5 CFR 351.202 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 351.202 Section 351.202... Provisions § 351.202 Coverage. (a) Employees covered. Except as provided in paragraph (b) of this section... administrative body to be covered hereunder. Coverage includes administrative law judges except as modified...

  13. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 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...

  14. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 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...

  15. 5 CFR 300.603 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 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...

  16. 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...

  17. 40 CFR 51.356 - Vehicle coverage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  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. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  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. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  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. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 34 CFR 74.31 - Insurance coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 1 2012-07-01 2012-07-01 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  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, 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. JGI Genomic Single-cell Assembly Workflow

    SciTech Connect

    Trong, S.

    2011-09-16

    JIGSAW is a software package disigned to quality control and assemble genomic DNA sequences from single-cell bacterial and archaeal genomes. Amplification of singel-cell genomes using multiple displacement amplification technology presents challenges that magnify the amount of contaminants in the sample and produce non uniform depth of sequence coverage. these factors pose problems whan assembling the genomic data using currently availible short read assembles. The software addresses these problems by removing contaminants and normalizing the sequence read coverage prior to assemble. A hybrid assembly approach using two different open source genome assembly tools is then applied to piece together the DNA fragments. Additional reporting of QC metrics for the input sample and the genome assembly is provided for further analysis.

  6. JGI Genomic Single-cell Assembly Workflow

    2011-09-16

    JIGSAW is a software package disigned to quality control and assemble genomic DNA sequences from single-cell bacterial and archaeal genomes. Amplification of singel-cell genomes using multiple displacement amplification technology presents challenges that magnify the amount of contaminants in the sample and produce non uniform depth of sequence coverage. these factors pose problems whan assembling the genomic data using currently availible short read assembles. The software addresses these problems by removing contaminants and normalizing the sequencemore » read coverage prior to assemble. A hybrid assembly approach using two different open source genome assembly tools is then applied to piece together the DNA fragments. Additional reporting of QC metrics for the input sample and the genome assembly is provided for further analysis.« less

  7. Guinea pig models of asthma.

    PubMed

    McGovern, Alice E; Mazzone, Stuart B

    2014-01-01

    Described in this unit are methods for establishing guinea pig models of asthma. Sufficient detail is provided to enable investigators to study bronchoconstriction, cough, airway hyperresponsiveness, inflammation, and remodeling. PMID:25446291

  8. MICROSATELLITE DIVERSITY AND CROSSOVER REGIONS WITHIN HOMOZYGOUS AND HETEROZYGOUS SLA HAPLOTYPES OF DIFFERENT PIG BREEDS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our aim was to investigate microsatellite (MS) diversity and find crossover regions at 42 polymorphic MS loci in the SLA genomic region of 72 pigs with different homozygous and heterozygous well-defined SLA haplotypes. We analyzed the genetic polymorphisms of the 42 MS markers in 23 SLA homozygous/h...

  9. 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...

  10. Eradication of Taenia solium cysticercosis: a role for vaccination of pigs.

    PubMed

    Lightowlers, M W

    1999-06-01

    Neurocysticercosis due to Taenia solium is an important cause of human morbidity and mortality, particularly in Latin America and parts of Africa and Asia. The disease has been recognised as potentially eradicable. Emphasis has been placed on control of the parasite through mass chemotherapy of human populations to remove tapeworm carriers. This strategy does not control the source of tapeworm infections, cysticercosis in pigs, and parasite transmission may continue due to incomplete chemotherapy coverage of human tapeworm carriers or because of immigration of tapeworm carriers into control areas. Exceptionally effective, practical vaccines have been developed against cysticercosis in sheep and cattle and a recent trial has proved recombinant antigens to be effective against Taenia solium cysticercosis in pigs. A new strategy for eradication of Taenia solium is proposed, based principally on a combined approach of chemotherapy of human tapeworm carriers and vaccination of all pigs at risk of infection.

  11. Review: influenza virus in pigs.

    PubMed

    Crisci, Elisa; Mussá, Tufária; Fraile, Lorenzo; Montoya, Maria

    2013-10-01

    Influenza virus disease still remains one of the major threats to human health, involving a wide range of animal species and pigs play an important role in influenza ecology. Pigs were labeled as "mixing vessels" since they are susceptible to infection with avian, human and swine influenza viruses and genetic reassortment between these viruses can occur. After the H1N1 influenza pandemic of 2009 with a swine origin virus, the most recent research in "influenzology" is directed at improving knowledge of porcine influenza virus infection. This tendency is probably due to the fact that domestic pigs are closely related to humans and represent an excellent animal model to study various microbial infectious diseases. In spite of the role of the pig in influenza virus ecology, swine immune responses against influenza viruses are not fully understood. Considering these premises, the aim of this review is to focus on the in vitro studies performed with porcine cells and influenza virus and on the immune responses of pigs against human, avian and swine influenza viruses in vivo. The increased acceptance of pigs as suitable and valuable models in the scientific community may stimulate the development of new tools to assess porcine immune responses, paving the way for their consideration as the future "gold standard" large-animal model in immunology.

  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. 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.

  14. 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

  15. AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.

    PubMed

    Chen, Junfang; Lutsik, Pavlo; Akulenko, Ruslan; Walter, Jörn; Helms, Volkhard

    2014-12-01

    Whole-genome bisulfite sequencing (WGBS) is an approach of growing importance. It is the only approach that provides a comprehensive picture of the genome-wide DNA methylation profile. However, obtaining a sufficient amount of genome and read coverage typically requires high sequencing costs. Bioinformatics tools can reduce this cost burden by improving the quality of sequencing data. We have developed a statistical method Ajusted Local Kernel Smoother (AKSmooth) that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data. We demonstrate the AKSmooth performance on the low-coverage (~ 4 ×) DNA methylation profiles of three human colon cancer samples and matched controls. Under the best set of parameters, AKSmooth-curated data showed high concordance with the gold standard high-coverage sample (Pearson 0.90), outperforming the popular analogous method. In addition, AKSmooth showed computational efficiency with runtime benchmark over 4.5 times better than the reference tool. To summarize, AKSmooth is a simple and efficient tool that can provide an accurate human colon methylome estimation profile from low-coverage WGBS data. The proposed method is implemented in R and is available at https://github.com/Junfang/AKSmooth. PMID:25553811

  16. 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.

  17. Whitecap coverage from aerial photography

    NASA Technical Reports Server (NTRS)

    Austin, R. W.

    1970-01-01

    A program for determining the feasibility of deriving sea surface wind speeds by remotely sensing ocean surface radiances in the nonglitter regions is discussed. With a knowledge of the duration and geographical extent of the wind field, information about the conventional sea state may be derived. The use of optical techniques for determining sea state has obvious limitations. For example, such means can be used only in daylight and only when a clear path of sight is available between the sensor and the surface. However, sensors and vehicles capable of providing the data needed for such techniques are planned for the near future; therefore, a secondary or backup capability can be provided with little added effort. The information currently being sought regarding white water coverage is also of direct interest to those working with passive microwave systems, the study of energy transfer between winds and ocean currents, the aerial estimation of wind speeds, and many others.

  18. Sideline coverage of youth football.

    PubMed

    Rizzone, Katie; Diamond, Alex; Gregory, Andrew

    2013-01-01

    Youth football is a popular sport in the United States and has been for some time. There are currently more than 3 million participants in youth football leagues according to USA Football. While the number of participants and overall injuries may be higher in other sports, football has a higher rate of injuries. Most youth sporting events do not have medical personnel on the sidelines in event of an injury or emergency. Therefore it is necessary for youth sports coaches to undergo basic medical training in order to effectively act in these situations. In addition, an argument could be made that appropriate medical personnel should be on the sideline for collision sports at all levels, from youth to professional. This article will discuss issues pertinent to sideline coverage of youth football, including coaching education, sideline personnel, emergency action plans, age and size divisions, tackle versus flag football, and injury prevention.

  19. 45 CFR 148.124 - Certification and disclosure of coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... days of creditable coverage before a significant break in coverage as defined in § 146.113(b)(2)(iii... (for example, family coverage or individual-plus-spouse coverage). (B) Certificates provided on...

  20. 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.

  1. Mapping full-length porcine endogenous retroviruses in a large white pig.

    PubMed

    Herring, C; Quinn, G; Bower, R; Parsons, N; Logan, N A; Brawley, A; Elsome, K; Whittam, A; Fernandez-Suarez, X M; Cunningham, D; Onions, D; Langford, G; Scobie, L

    2001-12-01

    Xenotransplantation may bridge the widening gap between the shortage of donor organs and the increasing number of patients waiting for transplantation. However, a major safety issue is the potential cross-species transmission of porcine endogenous retroviruses (PERV). This problem could be resolved if it is possible to produce pigs that do not contain replication-competent copies of this virus. In order to determine the feasibility of this, we have determined the number of potentially replication-competent full-length PERV proviruses and obtained data on their integration sites within the porcine genome. We have screened genomic DNA libraries from a Large White pig for potentially intact proviruses. We identified six unique PERV B proviruses that were apparently intact in all three genes, while the majority of isolated proviruses were defective in one or more genes. No intact PERV A proviruses were found in this pig, despite the identification of multiple defective A proviruses. Genotyping of 30 unrelated pigs for these unique proviruses showed a heterogeneous distribution. Two proviruses were uncommon, present in 7 of 30 and 3 of 30 pigs, while three were each present in 24 of 30 pigs, and one was present in 30 of 30 animals examined. Our data indicate that few PERV proviruses in Large White pigs are capable of productive infection and suggest that many could be removed by selective breeding. Further studies are required to determine if all potentially functional proviruses could be removed by breeding or whether gene knockout techniques will be required to remove the residuum. PMID:11711616

  2. Genetic variations associated with six-white-point coat pigmentation in Diannan small-ear pigs

    PubMed Central

    Lü, Meng-Die; Han, Xu-Man; Ma, Yun-Fei; Irwin, David M.; Gao, Yun; Deng, Jia-Kun; Adeola, Adeniyi C.; Xie, Hai-Bing; Zhang, Ya-Ping

    2016-01-01

    A common phenotypic difference among domestic animals is variation in coat color. Six-white-point is a pigmentation pattern observed in varying pig breeds, which seems to have evolved through several different mechanistic pathways. Herein, we re-sequenced whole genomes of 31 Diannan small-ear pigs from China and found that the six-white-point coat color in Diannan small-ear pigs is likely regulated by polygenic loci, rather than by the MC1R locus. Strong associations were observed at three loci (EDNRB, CNTLN, and PINK1), which explain about 20 percent of the total coat color variance in the Diannan small-ear pigs. We found a mutation that is highly differentiated between six-white-point and black Diannan small-ear pigs, which is located in a conserved noncoding sequence upstream of the EDNRB gene and is a putative binding site of the CEBPB protein. This study advances our understanding of coat color evolution in Diannan small-ear pigs and expands our traditional knowledge of coat color being a monogenic trait. PMID:27270507

  3. 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.

  4. 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 ...

  5. Accurate and comprehensive sequencing of personal genomes.

    PubMed

    Ajay, Subramanian S; Parker, Stephen C J; Abaan, Hatice Ozel; Fajardo, Karin V Fuentes; Margulies, Elliott H

    2011-09-01

    As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of ∼30× coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAII(x) and HiSeq 2000, to a very high depth (126×). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a "sequencing guide" for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported.

  6. 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

  7. Enhanced sequencing coverage with digital droplet multiple displacement amplification.

    PubMed

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

    2016-04-20

    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.

  8. 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

  9. 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

  10. Virus load in pigs affected with different clinical forms of classical swine fever.

    PubMed

    Rout, M; Saikumar, G

    2012-04-01

    Classical swine fever (CSF) is an endemic disease in India, but the real magnitude of the problem is not known as only outbreaks of acute CSF are reported and many cases of chronic and clinically inapparent forms of the disease, which manifest a confusing clinical picture, remain undiagnosed. The real status of classical swine fever virus (CSFV) infection can only be known by testing pigs with highly specific and sensitive diagnostic assays. To obtain the baseline prevalence of CSFV infection among pigs in an endemic region where no vaccination was being performed, a real-time PCR assay was used to detect viral genetic material in tissue samples collected from a slaughterhouse in the northern state of Uttar Pradesh in India. In total, 1120 slaughtered pigs were examined for the presence of CSF suggestive pathological lesions and tissues from suspected cases were tested for the presence of CSFV antigen and nucleic acids by indirect immuno-peroxidase test and real-time PCR, respectively. Based on the detection of viral genetic material in the tonsils, the prevalence of CSFV infection among slaughtered pigs was found to be 7.67%. Pigs detected positive for viral genome by quantitative real-time PCR assay when categorized into different forms of CSF, depending upon the pathological lesions observed, the viral load in the tonsils of some of the pigs with chronic or clinically inapparent form of the disease was similar to that detected in pigs with acute CSF. The results of the study suggested that the risk posed by pigs with chronic disease or those infected but showing no clinical disease may be relatively higher as they can transmit the virus to new susceptible hosts over a longer period of time.

  11. Coccidiosis in guinea-pigs.

    PubMed

    Ellis, P A; Wright, A E

    1961-07-01

    The attention of laboratory workers is drawn to the possibility of coccidiosis as a cause of death in guinea-pigs. The purchase of a number of guinea-pigs infected with this protozoon was followed by 12 deaths when these animals were injected with material for diagnostic purposes. No deaths occurred in the laboratory stock herd, as these were kept separate from the newcomers and were not infected. The life history of the parasite is described, together with the post-mortem findings in our series of animals.

  12. 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…

  13. 43 CFR 3933.51 - Bond coverage.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Bond coverage. 3933.51 Section 3933.51 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT... Assignments and Subleases § 3933.51 Bond coverage. Before the BLM will approve an assignment, the...

  14. 7 CFR 1735.11 - Area coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... effect this requirement. See 7 CFR 1737.11(a), Preapplication Determinations: Area to be Served. ... 7 Agriculture 11 2014-01-01 2014-01-01 false Area coverage. 1735.11 Section 1735.11 Agriculture... Policies § 1735.11 Area coverage. Borrowers must make adequate telephone service available to the...

  15. 7 CFR 1710.103 - Area coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 11 2010-01-01 2010-01-01 false Area coverage. 1710.103 Section 1710.103 Agriculture... Basic Policies § 1710.103 Area coverage. (a) Borrowers shall make a diligent effort to extend electric service to all unserved persons within their service area who: (1) Desire electric service; and (2)...

  16. 7 CFR 1710.103 - Area coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 11 2014-01-01 2014-01-01 false Area coverage. 1710.103 Section 1710.103 Agriculture... Basic Policies § 1710.103 Area coverage. (a) Borrowers shall make a diligent effort to extend electric service to all unserved persons within their service area who: (1) Desire electric service; and (2)...

  17. 7 CFR 1735.11 - Area coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... effect this requirement. See 7 CFR 1737.11(a), Preapplication Determinations: Area to be Served. ... 7 Agriculture 11 2010-01-01 2010-01-01 false Area coverage. 1735.11 Section 1735.11 Agriculture... Policies § 1735.11 Area coverage. Borrowers must make adequate telephone service available to the...

  18. 5 CFR 430.302 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 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...

  19. 5 CFR 752.201 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false Coverage. 752.201 Section 752.201 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) ADVERSE ACTIONS Regulatory Requirements for Suspension for 14 Days or Less § 752.201 Coverage. (a) Adverse...

  20. 5 CFR 430.302 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 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...

  1. 5 CFR 9701.704 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... an administrative grievance procedure, whichever is applicable. (c) The appeal rights in 5 CFR 315... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Coverage. 9701.704 Section 9701.704... MANAGEMENT SYSTEM Appeals § 9701.704 Coverage. (a) Subject to a determination by the Secretary or...

  2. 5 CFR 610.101 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 610.101 Section 610.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS HOURS OF DUTY Weekly and Daily Scheduling of Work § 610.101 Coverage. This subpart applies to each employee to whom subpart A of part...

  3. 5 CFR 339.101 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 339.101 Section 339.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS MEDICAL QUALIFICATION DETERMINATIONS General § 339.101 Coverage. This part applies to all applicants for and employees in...

  4. 5 CFR 300.402 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 300.402 Section 300.402 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Use of Commercial Recruiting Firms and Nonprofit Employment Services § 300.402 Coverage. This part applies...

  5. 5 CFR 339.101 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 339.101 Section 339.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS MEDICAL QUALIFICATION DETERMINATIONS General § 339.101 Coverage. This part applies to all applicants for and employees in...

  6. 5 CFR 359.901 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... CFR 752.601(c)(2). ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 359.901 Section 359.901... Appointees and Reemployed Annuitants § 359.901 Coverage. (a) This subpart covers the removal from the SES...

  7. 45 CFR 73.735-1001 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 1 2012-10-01 2012-10-01 false Coverage. 73.735-1001 Section 73.735-1001 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION STANDARDS OF CONDUCT Provisions Relating to Experts, Consultants and Advisory Committee Members § 73.735-1001 Coverage. (a) For purposes...

  8. 22 CFR 513.610 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 2 2012-04-01 2009-04-01 true Coverage. 513.610 Section 513.610 Foreign Relations BROADCASTING BOARD OF GOVERNORS GOVERNMENT DEBARMENT AND SUSPENSION (NONPROCUREMENT) AND... Coverage. (a) This subpart applies to any grantee of the Board. (b) This subpart applies to any...

  9. 7 CFR 1710.103 - Area coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 11 2011-01-01 2011-01-01 false Area coverage. 1710.103 Section 1710.103 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE... Basic Policies § 1710.103 Area coverage. (a) Borrowers shall make a diligent effort to extend...

  10. 5 CFR 534.601 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 534.601 Section 534.601 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER OTHER SYSTEMS Pay for Administrative Appeals Judge Positions § 534.601 Coverage. (a) This subpart implements 5 U.S.C. 5372b and...

  11. 5 CFR 730.103 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Coverage. 730.103 Section 730.103 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) NOTIFICATION OF POST-EMPLOYMENT RESTRICTIONS § 730.103 Coverage. (a) The following individuals are subject...

  12. 5 CFR 610.101 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 610.101 Section 610.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS HOURS OF DUTY Weekly and Daily Scheduling of Work § 610.101 Coverage. This subpart applies to each employee to whom subpart A of part...

  13. 5 CFR 730.103 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false Coverage. 730.103 Section 730.103 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) NOTIFICATION OF POST-EMPLOYMENT RESTRICTIONS § 730.103 Coverage. (a) The following individuals are subject...

  14. 49 CFR 209.303 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 4 2011-10-01 2011-10-01 false Coverage. 209.303 Section 209.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RAILROAD SAFETY ENFORCEMENT PROCEDURES Disqualification Procedures § 209.303 Coverage....

  15. 41 CFR 302-17.2 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true Coverage. 302-17.2 Section 302-17.2 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES MISCELLANEOUS ALLOWANCES 17-RELOCATION INCOME TAX (RIT) ALLOWANCE § 302-17.2 Coverage....

  16. 5 CFR 550.702 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 550.702 Section 550.702 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Severance Pay § 550.702 Coverage. Except as provided in 5 U.S.C. 5595(a)(2) (i) through (viii), this...

  17. 5 CFR 300.502 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 300.502 Section 300.502 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EMPLOYMENT (GENERAL) Use of Private Sector Temporaries § 300.502 Coverage. (a) These regulations apply to the competitive service...

  18. 49 CFR 209.303 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Coverage. 209.303 Section 209.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RAILROAD SAFETY ENFORCEMENT PROCEDURES Disqualification Procedures § 209.303 Coverage....

  19. 5 CFR 752.201 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 2 2011-01-01 2011-01-01 false Coverage. 752.201 Section 752.201 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) ADVERSE ACTIONS Regulatory Requirements for Suspension for 14 Days or Less § 752.201 Coverage. (a) Adverse...

  20. 5 CFR 550.802 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 550.802 Section 550.802 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Back Pay § 550.802 Coverage. (a) Except as provided in paragraph (b) of this section, this...

  1. 7 CFR 1710.103 - Area coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 11 2012-01-01 2012-01-01 false Area coverage. 1710.103 Section 1710.103 Agriculture Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE... Basic Policies § 1710.103 Area coverage. (a) Borrowers shall make a diligent effort to extend...

  2. 5 CFR 534.601 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 534.601 Section 534.601 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER OTHER SYSTEMS Pay for Administrative Appeals Judge Positions § 534.601 Coverage. (a) This subpart implements 5 U.S.C. 5372b and...

  3. 5 CFR 304.101 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 304.101 Section 304.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EXPERT AND CONSULTANT APPOINTMENTS § 304.101 Coverage. These regulations apply to the appointment of experts and consultants...

  4. 5 CFR 610.304 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 610.304 Section 610.304 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS HOURS OF DUTY Administrative Dismissals of Daily, Hourly, and Piecework Employees § 610.304 Coverage. This subpart applies to...

  5. 38 CFR 8a.4 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Coverage. 8a.4 Section 8a.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS VETERANS MORTGAGE LIFE INSURANCE § 8a.4 Coverage. (a) The amount of VMLI in force on his or her life at any one time shall...

  6. 29 CFR 1603.101 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 4 2013-07-01 2013-07-01 false Coverage. 1603.101 Section 1603.101 Labor Regulations Relating to Labor (Continued) EQUAL EMPLOYMENT OPPORTUNITY COMMISSION PROCEDURES FOR PREVIOUSLY EXEMPT... GOVERNMENT EMPLOYEE RIGHTS ACT OF 1991 Administrative Process § 1603.101 Coverage. Section 304 of...

  7. 5 CFR 532.103 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 532.103 Section 532.103 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PREVAILING RATE SYSTEMS General Provisions § 532.103 Coverage. The provisions of this part shall apply to prevailing rate employees...

  8. 5 CFR 9701.704 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... an administrative grievance procedure, whichever is applicable. (c) The appeal rights in 5 CFR 315... 5 Administrative Personnel 3 2012-01-01 2012-01-01 false Coverage. 9701.704 Section 9701.704... MANAGEMENT SYSTEM Appeals § 9701.704 Coverage. (a) Subject to a determination by the Secretary or...

  9. 5 CFR 630.701 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 630.701 Section 630.701 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Shore Leave § 630.701 Coverage. This subpart applies to an employee as defined in section 6301 of title 5,...

  10. 5 CFR 630.602 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 630.602 Section 630.602 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Home Leave § 630.602 Coverage. An employee who meets the requirements of section 6304(b) of title 5, United...

  11. 5 CFR 752.201 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 2 2013-01-01 2013-01-01 false Coverage. 752.201 Section 752.201 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) ADVERSE ACTIONS Regulatory Requirements for Suspension for 14 Days or Less § 752.201 Coverage. (a) Adverse...

  12. 5 CFR 610.304 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 610.304 Section 610.304 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS HOURS OF DUTY Administrative Dismissals of Daily, Hourly, and Piecework Employees § 610.304 Coverage. This subpart applies to...

  13. 5 CFR 550.1001 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 550.1001 Section 550.1001 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Adjustment of Work Schedules for Religious Observances § 550.1001 Coverage. This subpart applies to...

  14. 45 CFR 73.735-1001 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Coverage. 73.735-1001 Section 73.735-1001 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION STANDARDS OF CONDUCT Provisions Relating to Experts, Consultants and Advisory Committee Members § 73.735-1001 Coverage. (a) For purposes...

  15. 24 CFR 200.17 - Mortgage coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 2 2013-04-01 2013-04-01 false Mortgage coverage. 200.17 Section 200.17 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued... Eligibility Requirements for Existing Projects Eligible Mortgage § 200.17 Mortgage coverage. The...

  16. 5 CFR 1320.4 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 3 2014-01-01 2014-01-01 false Coverage. 1320.4 Section 1320.4 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES CONTROLLING PAPERWORK BURDENS ON THE PUBLIC § 1320.4 Coverage. (a) The requirements of this part apply to all agencies as defined in §...

  17. 29 CFR 9.3 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 1 2014-07-01 2013-07-01 true Coverage. 9.3 Section 9.3 Labor Office of the Secretary of Labor NONDISPLACEMENT OF QUALIFIED WORKERS UNDER SERVICE CONTRACTS General § 9.3 Coverage. This part applies to all service contracts and their solicitations, except those excluded by § 9.4 of this...

  18. 7 CFR 1735.11 - Area coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... effect this requirement. See 7 CFR 1737.11(a), Preapplication Determinations: Area to be Served. ... 7 Agriculture 11 2013-01-01 2013-01-01 false Area coverage. 1735.11 Section 1735.11 Agriculture... Policies § 1735.11 Area coverage. Borrowers must make adequate telephone service available to the...

  19. 5 CFR 550.802 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false Coverage. 550.802 Section 550.802 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Back Pay § 550.802 Coverage. (a) Except as provided in paragraph (b) of this section, this...

  20. 49 CFR 209.303 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 4 2013-10-01 2013-10-01 false Coverage. 209.303 Section 209.303 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RAILROAD SAFETY ENFORCEMENT PROCEDURES Disqualification Procedures § 209.303 Coverage....

  1. 5 CFR 9701.704 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... an administrative grievance procedure, whichever is applicable. (c) The appeal rights in 5 CFR 315... 5 Administrative Personnel 3 2011-01-01 2011-01-01 false Coverage. 9701.704 Section 9701.704... MANAGEMENT SYSTEM Appeals § 9701.704 Coverage. (a) Subject to a determination by the Secretary or...

  2. 5 CFR 880.304 - FEGLI coverage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 2 2012-01-01 2012-01-01 false FEGLI coverage. 880.304 Section 880.304 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED... FEGLI coverage. (a) FEGLI premiums will not be collected during periods when an annuitant is a...

  3. 24 CFR 51.4 - Program coverage.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Program coverage. 51.4 Section 51.4 Housing and Urban Development Office of the Secretary, Department of Housing and Urban Development ENVIRONMENTAL CRITERIA AND STANDARDS General Provisions § 51.4 Program coverage. Environmental standards...

  4. 5 CFR 304.101 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 304.101 Section 304.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EXPERT AND CONSULTANT APPOINTMENTS § 304.101 Coverage. These regulations apply to the appointment of experts and consultants...

  5. 5 CFR 752.201 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Coverage. 752.201 Section 752.201 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) ADVERSE ACTIONS Regulatory Requirements for Suspension for 14 Days or Less § 752.201 Coverage. (a) Adverse...

  6. 5 CFR 890.601 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Coverage. 890.601 Section 890.601 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) FEDERAL... Coverage. An annuitant (a retired employee or survivor under part 891 of this chapter) who is enrolled,...

  7. 5 CFR 352.502 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 352.502 Section 352.502 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS REEMPLOYMENT RIGHTS....502 Coverage. This subpart applies to any of the following serving in a position in the...

  8. 5 CFR 550.1001 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 550.1001 Section 550.1001 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Adjustment of Work Schedules for Religious Observances § 550.1001 Coverage. This subpart applies to...

  9. 5 CFR 412.101 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 412.101 Section 412.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS SUPERVISORY, MANAGEMENT, AND EXECUTIVE DEVELOPMENT General Provisions § 412.101 Coverage. This part applies to all incumbents of,...

  10. 5 CFR 412.101 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 412.101 Section 412.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS SUPERVISORY, MANAGEMENT, AND EXECUTIVE DEVELOPMENT General Provisions § 412.101 Coverage. This part applies to all incumbents of,...

  11. 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...

  12. 38 CFR 8a.4 - Coverage.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Coverage. 8a.4 Section 8a.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS VETERANS MORTGAGE LIFE INSURANCE § 8a.4 Coverage. (a) The amount of VMLI in force on his or her life at any one time shall...

  13. 25 CFR 700.505 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 2 2013-04-01 2013-04-01 false Coverage. 700.505 Section 700.505 Indians THE OFFICE OF NAVAJO AND HOPI INDIAN RELOCATION COMMISSION OPERATIONS AND RELOCATION PROCEDURES Employee Responsibility and Conduct § 700.505 Coverage. The regulations contained in this part apply to all...

  14. 5 CFR 752.601 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 2 2014-01-01 2014-01-01 false Coverage. 752.601 Section 752.601 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS (CONTINUED) ADVERSE... Coverage. (a) Adverse actions covered. This subpart applies to suspensions for more than 14 days...

  15. 5 CFR 304.101 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 304.101 Section 304.101 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS EXPERT AND CONSULTANT APPOINTMENTS § 304.101 Coverage. These regulations apply to the appointment of experts and consultants...

  16. 5 CFR 534.601 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 534.601 Section 534.601 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER OTHER SYSTEMS Pay for Administrative Appeals Judge Positions § 534.601 Coverage. (a) This subpart implements 5 U.S.C. 5372b and...

  17. 5 CFR 550.702 - Coverage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Coverage. 550.702 Section 550.702 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Severance Pay § 550.702 Coverage. Except as provided in 5 U.S.C. 5595(a)(2) (i) through (viii), this...

  18. 5 CFR 630.802 - Coverage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Coverage. 630.802 Section 630.802 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Funeral Leave § 630.802 Coverage. This subpart applies to: (a) An employee as defined in section 2105 of title...

  19. 5 CFR 630.802 - Coverage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Coverage. 630.802 Section 630.802 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Funeral Leave § 630.802 Coverage. This subpart applies to: (a) An employee as defined in section 2105 of title...

  20. 5 CFR 591.302 - Coverage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Coverage. 591.302 Section 591.302 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ALLOWANCES AND DIFFERENTIALS Allowance Based on Duty at Remote Worksites § 591.302 Coverage. (a) Agencies. This subpart applies...