Comparative genomics of worldwide Brucella canis with a focus on Brazil
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB22763 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: Not available
| S-EPMC6114238 | biostudies-literature
Project description:WTCCC2 Visceral Leishmaniasis samples from Brazil using Illumina 670k
| EGAD00010000636 | EGA
Project description:Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis and public release of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with geographic distance from Africa, as expected under a serial founder effect for an out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected—including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas—the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations. Keywords: High Density SNP array
2008-02-05 | GSE10331 | GEO
Project description:The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.
2024-01-31 | GSE253912 | GEO
Project description:Interventions: Participants will take 6 brazil nuts a day for four weeks.
This four week intervention will be preceded by a 4 week run-in / wash out phase
participants will be advised to exclude any selenium rich foods or green tea during the study
This Pilot study will confirm the amount of Brazil Nuts we will use in the study comparing with green tea. This follow up study (Effects of combining Selenium (Se) and green tea on biomarkers for colorectal cancer prevention in human subjects). will be registered with ANZCTR in the near future’
At the initial interview dietary advice will be given. This will give an understanding of the nature of the volunteers diet and the likely influence of Se to the diet and suitability to become involved in the study
(if intolerant to nuts volunteers will not participate in the study)
We will ask participants not to consume, whenever possible, throughout the study:-
Any selenium supplement
Any selenium enriched foods, such as nuts, sea food (such as tuna or octopus)
The Brazil nut is a large nut that comes from the castanheiro de para tree in Brazil’s rainforests. Each serving of about six to eight nuts contains 4 g of protein and 7 grams each of monosaturated and polysaturated fat.
Brazil nuts (Berholletia excelas, family Lecythidaceae) are the richest known food source of selenium, with mean concentrations reported in the literature between 8-83 micrograms Se/g
6 Brazil nuts daily provides 48 micrograms Se/day - 53 micrograms Se/day
Primary outcome(s): If supplementation of 6 Brazil nuts/day increases plasma Selenium (Se) levels
A blood sample (5mls of whole blood taken on 2 occasions) will be collected at baseline and after intervention, testing for plasma Selenium levels[Blood samples collected at commencement of intervention (week 0) and at end of intervention (wk 4)]
Study Design: Purpose: Prevention; Allocation: Non-randomised trial; Masking: Open (masking not used);Assignment: Single group;Type of endpoint: Safety
| 2458510 | ecrin-mdr-crc
Project description:To understand roles of PEA15 in HCC, expression of PEA15 was depleted in FOCUS cells.
2024-01-01 | GSE198993 | GEO
Project description:Rickettsia rickettsii str. Brazil Genome sequencing
| PRJNA75023 | ENA
Project description:Plasmodium vivax Brazil I genome sequencing
| PRJNA67065 | ENA
Project description:Animal and Plant viruses in sewage water in Brazil
| PRJEB19795 | ENA