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Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Identifying COVID-19 Vaccine Deserts Using Machine Learning and Geospatial Analyses to Target Community-engaged Testing for Vulnerable Rural Populations to Prevent Localized Outbreaks

ABSTRACT: Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Identifying COVID-19 Vaccine Deserts Using Machine Learning and Geospatial Analyses to Target Community-engaged Testing for Vulnerable Rural Populations to Prevent Localized Outbreaks

PROVIDER: PRJNA876356 | ENA |

REPOSITORIES: ENA

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Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Identifying COVID-19 Vaccine Deserts Using Machine Learning and Geospatial Analyses to Target Community-engaged Testing for Vulnerable Rural Populations to Prevent Localized Outbreaks

Project description:Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Identifying COVID-19 Vaccine Deserts Using Machine Learning and Geospatial Analyses to Target Community-engaged Testing for Vulnerable Rural Populations to Prevent Localized Outbreaks

| PRJNA876357 | ENA

Rapid Acceleration of Diagnostics - Underserved Populations(RADx-UP): Community Engaged Research on COVID-19 Testing Among Underserved and/or Vulnerable Populations

Project description:Rapid Acceleration of Diagnostics - Underserved Populations(RADx-UP): Community Engaged Research on COVID-19 Testing Among Underserved and/or Vulnerable Populations

| PRJNA772350 | ENA

Rapid Acceleration of Diagnostics - Underserved Populations(RADx-UP): Community Engaged Research on COVID-19 Testing Among Underserved and/or Vulnerable Populations

Project description:Rapid Acceleration of Diagnostics - Underserved Populations(RADx-UP): Community Engaged Research on COVID-19 Testing Among Underserved and/or Vulnerable Populations

| PRJNA772351 | ENA

Epigenetic variation between urban and rural populations of Darwin’s finches

Project description:The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in evolutionary change. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. In the current study we explored variation between populations of Darwin’s finches living in adjacent “urban” and “rural” environments on Santa Cruz Island in the Galápagos. We tested for morphological, genetic, and epigenetic differences between the urban and rural populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find genetic differences between populations of either species, based on comparisons of copy number variation (CNV). In contrast, we did find epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially methylated regions (DMR), as well as their possible functional significance. In summary, our study documents local population epigenetic variation within species of Darwin’s finches.

2017-01-07 | GSE87825 | GEO

DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts

Project description:High concentration of NaCl increases DNA breaks both in cell culture and in vivo. The breaks remain elevated as long as NaCl concentration remains high and are rapidly repaired when the concentration is lowered. Repair of the breaks after NaCl is reduced is accompanied by formation of foci containing phosphorylated H2AX (γH2AX), which occurs around DNA double-strand breaks and contributes to their repair. By chromatin immunoprecipitation using anti-γH2AX antibody, followed by massive parallel sequencing (ChIP-Seq), we find that during repair of double–strand breaks induced by high NaCl, γH2AX is predominantly localized to regions of the genome devoid of genes (“gene deserts”), indicating that the high NaCl-induced double-strand breaks are located there. Localization to gene deserts helps explain why the DNA breaks are less harmful than are the random breaks induced by genotoxic agents such as UV radiation, ionizing radiation and oxidants. We propose that the universal presence of NaCl around animal cells has directly influenced the evolution of the structure of their genomes.

2011-11-21 | GSE32882 | GEO

Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Community-engaged Approaches to Testing in Community and Healthcare Settings for Underserved Populations (CATCH-UP)

Project description:Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Community-engaged Approaches to Testing in Community and Healthcare Settings for Underserved Populations (CATCH-UP)

| PRJNA783112 | ENA

Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Community-engaged Approaches to Testing in Community and Healthcare Settings for Underserved Populations (CATCH-UP)

| PRJNA783113 | ENA

Regional Epigenetic Variation in Asexual Snail Populations among Urban and Rural Lakes

Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.

2019-09-27 | GSE133502 | GEO

Mitotic Transcriptional Clearance of Actively Engaged Pol II Through Transcriptional Elongation Control

Project description:Chromatin is highly condensed and transcriptionally repressed during mitosis. Although it is established that some general transcription factors are inactivated by phosphorylation at mitosis, many details of mitotic transcriptional repression and its underlying mechanisms are largely unknown. Here, we provide evidence that as cells enter mitosis, genes with transcriptionally engaged RNA Polymerase II (Pol II) can continue transcription until the end of the gene to clear Pol II from mitotic chromatin. Using ChIP-Seq, we find that the transcriptional reinitiation process is globally impaired in early mitosis (prophase/prometaphase), with loss of TFIIB occupancy and nucleosome-free regions at promoters. Pretreatment of nocodazole-arrested mitotic cells with the P-TEFb inhibitor flavopiridol prevents the release of promoter-proximal engaged Pol II. Global nascent RNA sequencing and RNA fluorescence in situ hybridization (FISH) of individual genes demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Chemical and mutational inhibition of P-TEFb in mitosis leads to delays in the progression of cell division. Together, our study reveals a novel mechanism for mitotic transcriptional repression whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. ChIP-Seq of Pol II of different forms, TFIIB, H3K4me3 in human HeLa cells at different cell cycle stages. ChIP-Seq of Pol II in HeLa mitotic cells with or without CDK9 inhibitor flavopiridol pretreatment. Nascent RNA-seq in asynchronous and arrested mitotic cells.

2015-10-30 | E-GEOD-71848 | biostudies-arrayexpress

Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Community-engaged Research to Improve the COVID-19 Testing Cascade Among Underserved Populations in the US Caribbean Territories

Project description:Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): Community-engaged Research to Improve the COVID-19 Testing Cascade Among Underserved Populations in the US Caribbean Territories

| PRJNA789647 | ENA

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