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622 results for “Genomic integrity”
Fig. 2 in Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)
Fig. 2. (A) Maximum likelihood consensus tree of 2443 SNPs for 156 individuals. Branches with <50% UFBoot support are collapsed and support of> 75% is indicated on branches. (B) STRUCTURE analyses of 1,477 SNPs with individuals aligned to SNP tree. (C) Membership in haplotype groups (Wahlberg et al. 2003a) from ML analysis of 633 bp of COI (Supplementary Fig. S2), with individuals aligned to SNP tree. Butterflies images are courtesy of Norbert Kondla.
Fig. 1 in Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)
Fig. 1. Range map for the Phyciodes tharos group of butterflies. Distributions shown are based on Layberry et al. (1998), Wahlberg et al. (2003a), Brock and Kaufman (2006), iNaturalist (2020) (research grade data only), and Lotts and Naberhaus (2020). White dots show sampling locations (details in Supplementary Table S1). Map on right shows expansion of Alberta, the region with the most intensive sampling, with black stars for locations of major cities: Edmonton and Calgary. Butterfly images are courtesy of Norbert Kondla.
Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture
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QIBC code: "NEAT1 Modulates the TIRR/53BP1 Complex to Maintain Genome Integrity"
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Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle
<p><em><span>Mycobacterium bovis</span></em><span> causes bovine tuberculosis (bTB), an infectious disease of cattle that represents a zoonotic threat to humans. Research has shown that the peripheral blood (PB) transcriptome is perturbed during bTB disease but the genomic architecture underpinning this transcriptional response remains poorly understood.</span> Here, we analyse PB transcriptomics data from 63 control and 60 confirmed <em>M. bovis </em>infected animals and detect 2,592 differently expressed genes perturbing multiple immune response pathways. Leveraging imputed genome-wide SNP data, we characterise thousands of <em>cis­</em>-expression quantitative trait loci (eQTLs) and show that the PB transcriptome is substantially impacted by intrapopulation genomic variation during <em>M. bovis</em> infection. Integrating our <em>cis-</em>eQTL data with bTB susceptibility GWAS summary statistics, we perform a transcriptome-wide association study and identify 132 functionally relevant genes (including <em>RGS10</em>, <em>GBP4</em>, <em>TREML2</em>, and <em>RELT</em>) and provide important new omics data for understanding the host response to mycobacterial infections that cause tuberculosis in mammals.</p> <p> </p>
Dataset for "Moving towards genome-wide data integration for patient stratification with Integrate Any Omics"
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Data from: Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning
Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multi-species approaches. We used an interdisciplinary, multi-species, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
Supplemental data for: Classification of the Celastrales based on integration of genomic, morphological, and Sanger-sequence characters
<p>We present the best sampled phylogenetic analysis of Celastrales, with respect to both character and taxon sampling, and use it to present a natural classification of the order. Parnassiaceae are highly supported as sister to Celastraceae; we recognize both families as distinct. <em>Pottingeria</em> is highly supported as a member of an early derived lineage within Celastraceae. We recognize and circumscribe 13 subfamilies in Celastraceae, including the new subfamilies Crossopetaloideae, Maytenoideae, Microtropioideae, Monimopetaloideae, and Salaciopsioideae. We identified five genera that likely require generic recircumscriptions: <em>Cassine</em>, <em>Elachyptera</em>, <em>Gymnosporia</em>, <em>Salacia</em>, and <em>Semialarium</em>. Genera that had not been previously sampled in Sanger-sequence-based studies are resolved as follows: <em>Arnicratea</em> is sister to <em>Reissantia</em>, <em>Bequaertia</em> is in a clade with <em>Campylostemon</em> and <em>Tristemonanthus</em>, <em>Goniodiscus</em> is sister to <em>Wilczekra</em>, <em>Ptelidium</em> is nested within <em>Elaeodendron</em>, and <em>Tetrasiphon</em> is most closely related to <em>Gyminda</em>.</p>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
Integrating Whole Genome Sequencing and Digital Twins Into the Management of Hypercholesterolemia in Emiratis
ClinicalTrials.gov study NCT06535542. IPD Sharing: YES. Countries: 1. Publications: 6.
Discovering Patterns in the Gut Microbiota Associated With the Risk of Stroke and the Outcome After a Stroke and Integration of These Data With Genomic Information to Find New Drug Targets and New Tre
ClinicalTrials.gov study NCT04795687. IPD Sharing: YES. Countries: 1. Publications: 1.
Ramucirumab/Paclitaxel as Second-line Treatment in Metastatic Gastric or Gastroesophageal Junction Adenocarcinoma With Integrative Genomic Analysis
ClinicalTrials.gov study NCT02628951. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Hereditary Gastric Cancer Syndromes: An Integrated Genomic and Clinicopathologic Study of the Predisposition to Gastric Cancer
ClinicalTrials.gov study NCT03030404. IPD Sharing: YES. Countries: 1. Publications: 9.
Integrated Whole-Genome Analysis of Hematologic Disorders
ClinicalTrials.gov study NCT01108159. IPD Sharing: Not stated. Countries: 1. Publications: 1.
BostonGene-Integrated Genomic Registry (BIGR)
ClinicalTrials.gov study NCT04991922. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution
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Data from: Integrative approaches to guide conservation decisions: using genomics to define conservation units and functional corridors
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Data from: Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources
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Data from: Integrated genome-scale analysis identifies novel genes and networks underlying senescence in maize
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.