Valle da Gafaria, Portugal
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR475284.fastq.gz | Fastqsanger.gz | |||
| ERR475285.fastq.gz | Fastqsanger.gz | |||
| ERR475286.fastq.gz | Fastqsanger.gz | |||
| ERR475287.fastq.gz | Fastqsanger.gz | |||
| ERR475288.fastq.gz | Fastqsanger.gz |
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Project description:From the 15th to the 19th century, the Trans-Atlantic Slave-Trade influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uninhabited location ideal for investigating early admix-ture events between Europeans and Africans. We find that genetic admixture in Cabo Verde occurred primarily between Iberian and Senegambian populations, although forced and voluntary migrations to the archipelago involved numerous other populations. Inter-individual genetic and linguistic variation recapitulate geographic distribution of individuals’ birth-places across Cabo Verdean islands, suggest-ing that Kriolu language variants have developed together with genetic divergences. Furthermore, we find that admixture occurred both early in each island, long before the 18th-century massive TAST deportations triggered by the expansion of plantation economy in Africa and the Americas, and after this era mostly during the abolition of the TAST and of slavery in European colonial empires. Our results illustrate how shifting socio-cultural relationships between enslaved and non-enslaved commu-nities shaped enslaved-African descendants’ genomic diversity and structure on both sides of the At-lantic.
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Project description:Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions, demonstrating that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is highly correlated with climate of origin and associated with genetic polymorphism in trans that shows evidence of local adaptation. While genome-wide surveys of naturally occurring DNA methylation have been published previously, the degree of genetic control revealed here is unprecedented. Furthermore, the observation that DNA methylation is associated with climate, and is apparently adaptively important, is completely novel. Bisulfite sequencing of 152 Swedish Arabidobsis accessions grown at 10 C and 121 grown at 16 C
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Project description:Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.
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Project description:Heterochromatin formation and maintenance, key for epigenetic inheritance of cells and organisms, have two major unsolved problems: One is the unclear source and action mode of repeat-derived RNAs in the process and the second is distinct machineries employed by different organisms, as the siRNA and piRNA pathways respectively used in fission yeast and Drosophila germline both require RNA amplification, but such mechanism does not seem to exist in somatic cells of flies and mammals. We attack these problems by defining the origins of repeat-derived RNAs and their specific chromatin registers in Drosophila S2 cells that lack active piRNA. We demonstrate that Dicer-2 is responsible for processing diverse repeat-derived RNAs, particularly those transcribed from active Gypsy elements, which act in cis and trans to maintain pericentromeric heterochromatin. These findings suggest that somatic cells trade genome vulnerability for stable genetic inheritance while germ cells use RNA amplification to abate such trade-off.
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Project description:Background. Pneumococcus is a major human pathogen and the polysaccharide capsule is considered its main virulence factor. Nevertheless, strains lacking a capsule, named non-typeable pneumococcus (NT), are maintained in nature and frequently colonise the human nasopharynx. Interest in these strains, not targeted by any of the currently available pneumococcal vaccines, has been rising as they seem to play an important role in the evolution of the species. Currently, there is a paucity of data regarding this group of pneumococci. Also, questions have been raised on whether they are true pneumococci. We aimed to obtain insights in the genetic content of NT and the mechanisms leading to non-typeability and to genetic diversity. Methods. A collection of 52 NT isolates representative of the lineages circulating in Portugal between 1997 and 2007, as determined by pulsed-field gel electrophoresis and multilocus sequence typing, was analysed. The capsular region was sequenced and comparative genomic hybridisation (CGH) using a microarray covering the genome of 10 pneumococcal strains was carried out. The presence of mobile elements was investigated as source of intraclonal variation. Results. NT circulating in Portugal were found to have similar capsular regions, of cps type NCC2, i.e., having aliB-like ORF1 and aliB-like ORF2 genes. The core genome of NT was essentially similar to that of encapsulated strains. Also, competence genes and most virulence genes were present. The few virulence genes absent in all NT were the capsular genes, type-I and type-II pili, choline-binding protein A (cbpA/pspC), and pneumococcal surface protein A (pspA). Intraclonal variation could not be entirely explained by the presence of prophages and other mobile elements. Conclusions. NT circulating in Portugal are a homogeneous group belonging to cps type NCC2. Our observations support the theory that they are bona-fide pneumococcal isolates that do not express the capsule but are otherwise essentially similar to encapsulated pneumococci. Thus we propose that NT should be routinely identified and reported in surveillance studies.
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