108 research outputs found
Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep.
No full textSupplementary data for publication: Lifan Zhang, Michelle R. Mousel, Xiaolin Wu, Jennifer J. Michal, Xiang Zhou, Bo Ding, Gregory S. Lewis and Zhihua Jiang. (2013). Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep. PLoS ONE, 2013 Jun 10;8(6):e65942. doi: 10.1371
Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep.
No full textSupplementary data for publication: Lifan Zhang, Michelle R. Mousel, Xiaolin Wu, Jennifer J. Michal, Xiang Zhou, Bo Ding, Gregory S. Lewis and Zhihua Jiang. (2013). Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep. PLoS ONE, 2013 Jun 10;8(6):e65942. doi: 10.1371
Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep.
No full textSupplementary data for publication: Lifan Zhang, Michelle R. Mousel, Xiaolin Wu, Jennifer J. Michal, Xiang Zhou, Bo Ding, Gregory S. Lewis and Zhihua Jiang. (2013). Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep. PLoS ONE, 2013 Jun 10;8(6):e65942. doi: 10.1371
Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent
No full textSupplementary data for publication: Michelle R. Mousel, Stephen N White, David R. Herndon, James O. Reynolds, Michael V. Gonzalez, Wendell C. Johnson, Massaro W. Ueti, J. Bret Taylor, Donald P. Knowles (2015). Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent Anim Genet. 2016 Feb;47(1):136-7. doi: 10.1111/age.1238
Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent
No full textSupplementary data for publication: Michelle R. Mousel, Stephen N White, David R. Herndon, James O. Reynolds, Michael V. Gonzalez, Wendell C. Johnson, Massaro W. Ueti, J. Bret Taylor, Donald P. Knowles (2015). Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent Anim Genet. 2016 Feb;47(1):136-7. doi: 10.1111/age.1238
Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent
No full textSupplementary data for publication: Michelle R. Mousel, Stephen N White, David R. Herndon, James O. Reynolds, Michael V. Gonzalez, Wendell C. Johnson, Massaro W. Ueti, J. Bret Taylor, Donald P. Knowles (2015). Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent Anim Genet. 2016 Feb;47(1):136-7. doi: 10.1111/age.1238
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GENETIC STRUCTURE OF ROCKY MOUNTAIN ELK FROM WIND CAVE NATIONAL PARK
No full textElk (Cervus canadensis) play an integral role in balancing ecosystems, have significant economic value, and hold cultural value across diverse groups. Diseases such as chronic wasting disease (CWD), a fatal prion disease of cervids, threaten elk populations. Improved understanding of elk genetics can contribute to disease management, may provide information integral for determining genetic trends and future directions, and may lead to identification of trait associated variants, opening the door to selection desirable for production or even disease resistance. To advance the field and provide a foundation for elk conservation genomics, sequencing and genotyping of elk is necessary. This study employed the first reported genotype-by-sequencing in elk. Single nucleotide polymorphism (SNPs) discovery was undertaken in 306 Rocky Mountain elk (Cervus canadensis nelsoni) from Wind Cave National Park (WICA), South Dakota, USA. Genetic diversity and population structure of WICA elk were analyzed as one single population and as three subpopulations, as designated by geospatial analysis in a previous study. Effective population size (Ne) was determined to range from 36-316 and tests identified 3,251 variants out of Hardy-Weinberg equilibrium. Pairwise differentiation (Fst) indicated little difference in the genetic structure between WICA subpopulations (Fst≈0.003), but principal component analysis showed weak population structure when analyzed as a total population. Analysis that included 38,583 alleles private to the subpopulations revealed distinct genetic structure by geographical location, confirming previous field observations. Measurements of observed heterozygosity indicated subpopulation A (Ho=0.645) and subpopulation B (Ho=0.658) had the higher heterozygosity compared to subpopulation C (Ho=0.60). All subpopulation heterozygosity’s were higher than the total population average (Ho=0.53). The genetic structure seen in these subpopulations is likely due to the design of the park fence. Low areas of the fence and elk dropdown gates at the western and southwestern boarder of the park allowed elk to freely cross near regions A and B, but not region C, until renovations completely enclosed the park after 2013. This recent enclosure, along with other park geographical features and efforts to reduce WICA elk population density, will require managers employ periodic genetic monitoring to ensure that genetically differentiated subpopulations do not lose standing genetic diversity
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Sheep Cis-Regulatory Element Polymorphisms Confer Resilience in Ovine Lentivirus Infection
No full textOvine progressive pneumonia is an incurable, slowly fatal infection that affects up to half of all flocks in the United States, caused by ovine lentivirus. Sheep suffer debilitating pneumonia, arthritis, encephalitis, and mastitis. Infection causes significant losses to all aspects of sheep production endangering supply of meat, milk, and wool products for human consumption. Identification of host factors that decrease susceptibility to infectious disease is a key step in combating ovine lentivirus and other retroviruses such as human immunodeficiency virus. We built upon previous work that detected a genomic region at four zinc finger genes ZNF389, ZNF192, ZSCAN16, and ZNF165 as strongly associated with 50% reduction in proviral load. Since proviral load is correlated with severity of disease and lifespan in production flocks, the aim was to find genetic variants to predict this resilient phenotype and that may be causal mutations. DNA regulatory elements in sheep macrophages were annotated because most mutations responsible for phenotypic consequences are found within these elements. Alveolar macrophages function in innate and adaptive immunity as well as wound healing in the lungs dependent on tissue-specific gene expression under epigenetic regulation. The functional diversity of tissue-resident macrophages highlights the need to study tissue-specific regulatory elements that control gene expression. This study reported the first genome-wide survey of regulatory elements in any sheep immune cell, specifically those enriched for H3K4me3 (active promoters), H3K27ac (active enhancers), H3K4me1 (enhancers), CTCF (domain anchors), and H3K27me3 (silencers) which allowed assignment of putative biological function to 12% of the sheep genome. This annotation of transcriptional regulatory elements in target tissues will aid researchers in identifying genetic mutations of immunological consequence for many infectious diseases. A haplotype cluster of at least ten small DNA polymorphisms within the active cis-regulatory elements for ZNF389 were significantly associated with the resilient phenotype to ovine lentivirus in multiple sheep populations. Other zinc finger transcription factors, like ZAP, have been implicated in restriction of retroviral replication from several host species. These data will empower research into functional mutations at sheep regulatory elements and development of marker-assisted selection schemes to develop disease-resilient production flocks
Text, Medium, Afterlife: Intertextuality and Intermediality in the Works of Yoko Tawada
No full textText, Medium, Afterlife: Intertextuality and Intermediality in the Works of Yoko Tawada examines the roles of personal and mass media technologies in the works of contemporary German-language author Yoko Tawada. The study analyses the author\u27s prose fiction, wherein
the possibility of limitless textual permutations - an afterlife of the text - is accessed through a web of intertextual and intermedial associations. The expression of an individual voice against a
dominant culture\u27s mass media mobilizes a discourse of networks which emerges from the creative gaps and apertures revealed by the author\u27s deconstructive approach to language and literatures
Additional Analysis Files
No full textThe data provided here are supplementary files for "Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages." Alisha T. Massa, Michelle R. Mousel, Maria K. Herndon, David R. Herndon, Brenda M Murdoch, Stephen N. White. Front. Genet., 07 January 2021. https://doi.org/10.3389/fgene.2020.612031
The compressed file contains BED format locations for promoters, enhancers, insulators, and silencer DNA regulatory elements as determined by ChIP-seq for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Further metadata and protocol details are available on the FAANG data portal at https://data.faang.org/api/fire_api/assays/WSU_SOP_Native_ChIP-seq_Protocol_2019.pdf and https://data.faang.org/api/fire_api/analysis/WSU_SOP_ChIP-seq_Bioinformatic_Analysis_Protocol_2020.pdf
This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact the FAANG Data Coordination Centre and FAANG consortium (email [email protected] and cc [email protected]) to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle
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