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1,812 results for “dissection”
Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing
<p>Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (<em>Pungitius pungitius</em>) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components, and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogenous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.</p>
The dissection of a despotic society: exploration, dominance and hormonal traits
<p>Naked mole-rats (<em>Heterocephalus glaber</em>) live in large colonies with one breeding female (queen), one to three breeding males, and the remainder are non-reproductive subordinates. We investigated how the dominance ranking position in naked mole-rats differs with exploration (the propensity to explore a novel environment), and endocrine related markers. Faecal progestagen metabolite (fPM), glucocorticoid metabolite (fGCM), androgen metabolite (fAM) metabolite, and plasma prolactin concentrations were quantified in breeding, high, middle and low ranked females and males. There were no significant differences between the dominance ranking positions and exploration behaviour. Interestingly, the queens and high-ranking females had higher fGCM and fAM concentrations compared to middle and low ranked females; possibly due to an increased possibility of conflict with each other. The queen had significantly higher fPM concentrations than all other ranked females since she is responsible for procreation. In the males, the breeding males had higher fGCM concentrations compared to high and low ranked males. However, breeding males and middle-ranking males had overall higher prolactin levels than all other ranked males and these individuals may indirectly contribute to greater cooperative care and burrow maintenance. We suggest that high-ranking females exhibit higher fGCM and fAM concentrations possibly due to competition with the queen.</p>
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment
<p>All processed data used in the manuscript 'A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment'. For more detail please refer to the manuscript. If there is any question please contact Bokai Zhu via email: BZHU0@MGH.HARVARD.EDU.</p> <p>Data folder structure:</p> <p>Main data (eg. presented in main figures etc): Please see .zip file 'data_submission.zip'.</p> <p>Additional data (eg. during revision, or other misc files): Please see .zip file 'data_submission_part2.zip'.</p>
Standard methods for dissection of Varroa destructor females supplementary videos
<p>These three videos present methodological steps to perform Varroa destructor females dissection either ventrally (Video S1) or dorsally (Video S2 and S3)</p>
Comparative analysis of patient-specific aortic dissections through computational fluid dynamics suggests increased likelihood of degeneration in partially thrombosed aorta
<p>Aortic dissection is a life-threatening cardiovascular disease associated with high rates of morbidity and mortality, especially in medically under-served communities. It compromises the hemodynamics of the arteries that originate from the aorta, and its outcomes include visceral ischemia and aortic rupture in the acute phase and aneurysmatic degeneration in the chronic phase. Understanding patients’ blood flow patterns is pivotal for non-invasive evidence-based treatment as they greatly influence both the disease onset and its outcome. In this paper, we combine diagnostic imaging techniques and computational fluid dynamics to analyze the flow patterns of three aorta dissections (fully perfused, partially thrombosed, and fully thrombosed), and compare them to a healthy aorta. Besides flow kinematics, we focus on time averaged wall shear stress and oscillatory shear index that are recognized risk factors for aneurysm and rupture. Our analysis shows that partially thrombosed dissection is the most prone to false lumen degeneration. In all dissections, the arteries connected to the false lumen are generally poorly supplied with blood. Further, both true and false lumens present higher turbulence levels than the healthy aorta, and critical stagnation points. Mesh sensitivity and a thorough comparison against literature data together support the methodology robustness.</p>
Coloc summary results for "Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets"
<p>Text files containing coloc results between MS GWAS loci and CD4 T and B cell cis-eQTLs from DICE. These results accompany the paper "<strong>Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets"</strong></p>
Figure 8. Dissected S7 in A new species of Epeolus Latreille, 1802 (Hymenoptera: Apidae) from western North America
Figure 8. Dissected S7 (left) and S8 (right), ventral view, of male Epeolus
Dataset for "Pan-cancer integrative analyses dissect the remodeling of endothelial cells in human cancers"
<p>This is the dataset for "Pan-cancer integrative analyses dissect the remodeling of endothelial cells in human cancers".</p> <p> </p> <p>File "NSR.panE.exprs.all.h5ad.gz" contains processed expression .h5ad data.</p> <p>File "NSR.panE.obs.meta.csv" contains the meta data for this study.</p> <p>File "umap.zip" contains the .csv files for umap coordinates.</p> <p> </p> <p> </p>
From Fear to Love: Dissecting Political Trust in China
<p>The data is about the paper "From Fear to Love: Dissecting Political Trust in China"</p>
Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans data
<p>Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the <em>Caenorhabditis elegans</em> mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in <em>C. elegans</em>, a 499 bp deletion in <em>ctb-1</em> rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in <em>nd5</em>, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the <em>nd5 </em>mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original <em>ctb-1</em> deletion by unknown mechanisms. </p>
Cyanoacrylate glue in breast surgery: the GLUBREAST Trial Can cyanoacrylate glue reduce seroma after axillary dissection?
<p>In 2018, the National Cancer Institute of Naples has launched the GLUBREAST Trial to verify the efficacy of cyanoacrylate sealing glue to reduce seroma after axillary dissection in breast surgery. The glue is a synthetic sealant, CE approved for internal human uses and surgical procedures. The assumed mechanism of action in breast surgery is that the glue create a seal coating in the operative field to occlude lymphatic leaks and limit seroma formation. Methods The trial included one hundred-eighty patients scheduled for breast conserving surgery or total mastectomy without reconstruction.Ninety-one were randomized to receive suction drain and sealant glue after axillary dissection (Experimental Arm), whereas eighty-nine patients (Control Arm) received suction drain without glue. Statistics A multivariable mixed effect model on presence of liquid drained and volume drained were calculated. Stratified models by visits were performed. Results The trial ended in June 2022. Older age was associated with a higher volume of seroma drained per day (β 0.30; 95% CI: 0.00‐0.60). 5‐U increase in Body Mass Index was associated with higher daily drained seroma volume in patients underwent breast conserving surgery (β 5.0; 95% CI: 0.62‐9.4), but not in patients underwent<br>mastectomy (β 2.5; 95% CI: ‐3.6‐8.6). We did not find statistically significant differences in presence of liquid drained and volume<br>drained among the study groups. An advantage for the Experimental Arm was observed from 3 th and 4 th to 5 th outpatient<br>visits without reaching a statistical significance (p=0.069 and p=0.072, respectively), so far 5% of patients in the Experimental<br>Group had clinical benefit from the glue.Conclusions. Data in the literature come from case series, and surgeons need higher level<br>of evidence to drive surgical decision-making and choose proper devices to increase patient quality of life. GLUBREAST randomized trial tested the efficacy of cyanoacrylate sealing glue to prevent post-operative seroma in breast surgery. Although only a small number of patients benefited from sealant application, we regret to say this trial has some limitation, i.e. the prolonged presence of suction drain. Further research is warranted to better clarify the benefit of cyanoacrylate glue in breast surgery.</p>
Scans of leaves dissected in phyllotactic order: complementation of ago7 mutant A. thaliana plants with truncated promoter transgenes
<p>This transgenic complementation experiment is described in a paper by Hoyer et al. (2019): <a href="https://doi.org/10.1002/pld3.102">https://doi.org/10.1002/pld3.102</a></p> <p>Adaxial (ad) and abaxial (ab) surfaces of rosettes were photographed in between removal of leaves, to enable checking that leaves were removed in the correct phyllotactic order.<strong> </strong>A manifest file with file SHA-1 sums is included.</p> <p>Metadata and LeafJ measurements have been made available separately, to facilitate updates -- see <a href="https://github.com/jshoyer/raspi-photo-and-leaf-scan-metadata">https://github.com/jshoyer/raspi-photo-and-leaf-scan-metadata</a>, archived as <a href="https://doi.org/10.5281/zenodo.1340636">https://doi.org/10.5281/zenodo.1340636</a></p> <p>Seed was plated and growth started on 2016-08-26. Leaves were dissected and scanned 33 and 35 days post-stratification (2016-09-28 and 30).</p>
Dataset for "Dissecting abdominal aortic aneurysm in Ang II-infused mice: suprarenal branch ruptures and apparent luminal dilatation"
<p>This dataset contains histology, synchrotron and ultrasound data for the manuscript "Dissecting abdominal aortic aneurysm<br> in Ang II-infused mice: suprarenal branch ruptures and apparent luminal dilatation", published in Cardiovascular Research in 2014.</p> <p>Histology data are zipped and to be opened using the Olympus-software OlyVIA, or with the BIOP-tool called VSI-reader, which is a plugin to the open-source software Fiji. Imaging data are saved in .mcs format and can be opened with the commercial software Mimics (Materialise, Leuven, Belgium). Filenames correspond to the mouse ID as it was used in the study.</p>
Genomic dissection of 43 serum urate-associated loci provides multiple insights into molecular mechanisms of urate control
<p>Summary statistics for trans-ancestral analysis presented in "Genomic dissection of 43 serum urate-associated loci provides multiple insights into molecular mechanisms of urate control" by Boocock et al.</p> <p>Columns in order with descriptions are:</p> <p>SNP(rsid) CHROM POS(genome position) REF(reference allele) ALT(alternative allele) Z_EUR(zscore european) Z_EAS(zscore east asian) P_META(p-value from trans-ancestral meta-analysis) </p>
CRISPRi with barcoded expression reporters dissects regulatory networks in human cells
<p>Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.</p>
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
Hybrid zones provide unique opportunities to examine reproductive isolation and introgression in nature. We utilized 45,384 Single Nucleotide Polymorphism (SNP) loci to perform association mapping of 14 floral, vegetative, and ecological traits that differ between Iris hexagona and Iris fulva, and to investigate, using a Bayesian Genomic Cline (BGC) framework, patterns of genomic introgression in a large and phenotypically diverse hybrid zone in southern Louisiana. Many loci of small effect-size were consistently found to be associated with phenotypic variation across all traits, and several individual loci were revealed to influence phenotypic variation across multiple traits. Patterns of genomic introgression were quite heterogeneous throughout the Louisiana Iris genome, with I. hexagona alleles tending to be favored over those of I. fulva. Loci that were found to have exceptional patterns of introgression were also found to be significantly associated with phenotypic variation in a small number of morphological traits. However, this was the exception rather than the rule, as most loci that were associated with morphological trait variation were not significantly associated with excess ancestry. These findings provide insights into the complexity of the genomic architecture of phenotypic differences and are a first step towards identifying loci that are associated with both trait variation and reproductive isolation in nature.
FIG. 1. — Dominique Luizet vers l in Les Saxifraga L. de l'herbier Luizet: informatisation et numérisation des types et dissections
FIG. 1. — Dominique Luizet vers l'âge de 75 ans (Guétrot 1931).
Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat
<p>The study material in the GWAS panel with 193 bread wheat genotypes from Indian and exotic collections was selected to map the genomic regions responsible for grain iron and Zinc content under drought and heat stress treatments.</p> <p>Phenotypic data:</p> <p>The GWAS panel was evaluated at IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m) under Irrigated (IR), Restricted Irrigated (RI) and Late sown (LS) treatment conditions over 2 years i.e. 2020 and 2021 with augmented RCBD design. Data was collected on Grain Iron and Grain zinc content along with thousand-grain weight. Around 20 g of grain sample from each of 282 genotypes from the GWAS panel under all three conditions were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance.</p> <p>Genotypic data:</p> <p>Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >10%, and heterozygote frequency >50% were removed from the analysis. The remaining set of 13,947 high-quality SNPs was used in GWAS analysis.</p>
Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
<p><span>Mungbean (<em>Vigna radiata</em> (L) Wizcek) is an important pulse crop, increasingly used as a source of protein, fiber, low fat, carbohydrates, minerals, and bioactive compounds in human diets. Mungbean is a dicot plant with trifoliate leaves. Leaves are central to various plant processes like photosynthesis, light interception, and overall canopy structure. The objectives were to study leaf morphological traits, use image analysis to extract leaf traits from images from the Iowa Mungbean Diversity (IMD) panel, develop a regression model for the prediction of leaflet area, and conduct association mapping for leaf morphological traits. We collected more than 5000 leaf images of the IMD panel consisting of 484 accessions over two years (2020 and 2021) with two replications per experiment. Leaf traits were extracted using image analysis, analyzed, and used for association mapping. Morphological diversity included leaflet type (oval or lobed), leaflet size (small, medium, large), lobed angle (shallow, deep), and vein coloration (green, purple). A regression model was developed to predict each ovate leaflet's area (adjusted R<sup>2</sup> = 0.97; residual standard errors of <= 1.10). The candidate genes <em>Vradi01g07560</em>, <em>Vradi05g01240</em>, <em>Vradi02g05730</em>, and <em>Vradi03g00440</em>, are associated with multiple traits (length, width, perimeter, and area) across the leaflets (left, terminal, and right). These are suitable candidate genes for further investigation in their role in leaf development, growth, and function. Future studies will be needed to correlate the observed traits discussed here with yield or important agronomic traits for use as phenotypic or genotypic markers in marker-aided selection methods for mungbean crop improvement.</span></p>
Genetic dissection of triplicated chromosome 21 orthologs yields varying skeletal traits in Down syndrome model mice
<p><span class="normaltextrun">Down syndrome (DS) phenotypes result from triplicated genes, but effects of three copy genes are not well known. A mouse mapping panel genetically dissecting human chromosome 21 (Hsa21) syntenic regions was used to investigate the contributions and interactions of triplicated Hsa21 orthologous genes on mouse chromosome 16 (Mmu16) on skeletal phenotypes. Skeletal structure and mechanical properties were assessed in femurs of male and female Dp9Tyb, Dp2Tyb, Dp3Tyb, Dp4Tyb, Dp5Tyb, Dp6Tyb, Ts1Rhr, and Dp1Tyb;<em>Dyrk1a</em><sup>+/+/-</sup> mice. Dp1Tyb mice, with the entire Hsa21 homologous region of Mmu16 triplicated, display bone deficits similar to those of humans with DS and served as a baseline for other strains in the panel. Bone phenotypes varied based on triplicated gene content, sex, and bone compartment. Three copies of <em>Dyrk1a</em> played a sex-specific, essential role in trabecular deficits and may interact with other genes to influence cortical deficits related to DS. Triplicated genes in Dp9Tyb and Dp2Tyb mice improved some skeletal parameters. As triplicated genes can both improve and worsen bone deficits, it is important to understand the interaction between and molecular mechanisms of skeletal alterations affected by these genes.</span></p>
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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.
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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.
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