Dataset Information

Prion gene (PRNP) haplotype variation in United States goat breeds (Open Access publication).

ABSTRACT: Scrapie eradication efforts cost 18 million dollars annually in the United States and rely heavily upon PRNP genotyping of sheep. Genetic resistance might reduce goat scrapie and limit the risk of goats serving as a scrapie reservoir, so PRNP coding sequences were examined from 446 goats of 10 breeds, 8 of which had not been previously examined at PRNP. The 10 observed alleles were all related to one of two central haplotypes by a single amino acid substitution. At least five of these alleles (M142, R143, S146, H154, and K222) have been associated with increased incubation time or decreased odds of scrapie. To the best of our knowledge, neither S146 nor K222 has been found in any goats with scrapie, though further evaluation will be required to demonstrate true resistance. S146 was more common, present in several breeds at widely varying frequencies, while K222 was observed only in two dairy breeds at low frequency. Overall, this study provides frequency data on PRNP alleles in US goats, shows the pattern of relationships between haplotypes, and demonstrates segregation of multiple scrapieassociated alleles in several breeds not examined before at PRNP.

SUBMITTER: White S

PROVIDER: S-EPMC2674890 | biostudies-other | 2008 Sep-Oct

REPOSITORIES: biostudies-other

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Prion gene (PRNP) haplotype variation in United States goat breeds (Open Access publication).

White Stephen S Herrmann-Hoesing Lynn L O'rourke Katherine K Waldron Daniel D Rowe Joan J Alverson Janet J

Genetics, selection, evolution : GSE 20080812 5

Scrapie eradication efforts cost 18 million dollars annually in the United States and rely heavily upon PRNP genotyping of sheep. Genetic resistance might reduce goat scrapie and limit the risk of goats serving as a scrapie reservoir, so PRNP coding sequences were examined from 446 goats of 10 breeds, 8 of which had not been previously examined at PRNP. The 10 observed alleles were all related to one of two central haplotypes by a single amino acid substitution. At least five of these alleles (M ...[more]

PMID: 18694550

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Project description:Scrapie is a neurodegenerative disease that impacts sheep and goats, characterized by gradual and progressive changes in neurological function. Recent research shows that the scrapie incubation period is significantly influenced by specific variations in amino acids within the prion protein gene (PRNP). The objective of this study was to estimate the national prevalence of caprine PRNP genetic variability at codons 146, 211, and 222 in goat populations across the United States. A total of 3052 blood, ear tissue, and brain tissue samples were collected from goats from 50 states. The participating states were categorized into four Veterinary Service (VS) district regions. The samples underwent DNA extraction, and the PRNP variants corresponding to codons 146, 211, and 222 were amplified and sequenced. The analysis of PRNP variants, when compared to the PRNP reference sequence, revealed seven alleles in twelve genotypes. The homozygous 146NN, 211RR, and 222QQ alleles, which have been linked to an increased risk of scrapie, were found to be the most prevalent among all the goats. The heterozygous 222QK, 211RQ, 146SD, 146ND, and 146NS alleles and the homozygous 222KK, 146SS, and 146DD alleles, known to be associated with reduced scrapie susceptibility and a prolonged incubation period after experimental challenge, were found in 1.098% (222QK), 2.33% (211RQ), 0.58% (146SD), 3.13% (146ND), 20.68% (146NS), 0.005% (222KK), 3.31% (146SS), and 0.67% (146DD) of goats, respectively. The 222QK allele was found most frequently in goats tested from the east (VS District 1, 1.59%) and southwest (VS District 4, 1.08%) regions, whereas the 211RQ allele was found most often in goats tested from the Midwest (VS District 2, 8.03%) and east (VS District 1, 6.53%) regions. The 146NS allele was found most frequently in goats tested from the northwest (VS District 3, 29.02%) and southwest (VS District 4, 20.69%) regions. Our results showed that the prevalence of less susceptible genotypes at PRNP codon 146 may be sufficient to use genetic susceptibility testing in some herds. This may reduce the number of goats removed as part of a herd clean-up plan and may promote the selective breeding goats for less susceptible alleles in high-risk herds at the national level.

Project description:Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK revealed that German universities and research organisations primarily funded articles in fully open access journals. By contrast, articles in hybrid journal accounted for the largest share of spending according to the Austrian and UK data. Fees paid for hybrid journals were on average more expensive than those paid for fully open access journals.

Project description:Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records from the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). We aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov-Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. This comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.

Dataset Information

Prion gene (PRNP) haplotype variation in United States goat breeds (Open Access publication).

Publications

Prion gene (PRNP) haplotype variation in United States goat breeds (Open Access publication).

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