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2,180 results for “Recombination”
Divergent selection in low recombination regions shapes the genomic islands in two incipient shorebird species
<p>Divergent selection in the face of gene <span>flow is usually associated with</span> a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic island. This conundrum can be solved through examination of the genomic landscapes of species pairs that are still in the early stages of evolution. In this study, population genomics analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (<em>Charadrius alexandrinus</em>) and white-faced plover (<em>C. dealbatus</em>). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on Taiwan Island<span>.</span> <span>Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and recurrent gene flow is still ongoing in mainland coastal populations</span>. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which<span> contain several genes potentially associated with disease resistance, coloration, and regulation of plumage moulting, thus may be connected to the phenotypic and ecological divergence of</span> the two nascent species<span>. Overall, our findings suggest that divergent selection in low recombination regions may be the main force in shaping the genomic islands in two incipient shorebird species.</span></p>
Data from: Male mouse recombination maps for each autosome identified by chromosome painting
<p>Linkage maps constructed from genetic analysis of gene order and crossover frequency provide few clues to the basis of the genomewide distribution of meiotic recombination, such as chromosome structure, that influences meiotic recombination. To bridge this gap, we have generated the first cytological recombination map that identifies individual autosomes in the male mouse. We prepared meiotic chromosome (synaptonemal complex [SC]) spreads from 110 mouse spermatocytes, identified each autosome by multicolor fluorescence in situ hybridization of chromosome- specific DNA libraries, and mapped 12,000 sites of recombination along individual autosomes, using immunolocalization of MLH1, a mismatch repair protein that marks crossover sites. We show that SC length is strongly correlated with crossover frequency and distribution. Although the length of most SCs corresponds to that predicted from their mitotic chromosome length rank, several SCs are longer or shorter than expected, with corresponding increases and decreases in MLH1 frequency. Although all bivalents share certain general recombination features, such as few crossovers near the centromeres and a high rate of distal recombination, individual bivalents have unique patterns of crossover distribution along their length. In addition to SC length, other, as-yet-unidentified, factors influence crossover distribution leading to hot regions on individual chromosomes, with recombination frequencies as much as six times higher than average, as well as cold spots with no recombination. By reprobing the SC spreads with genetically mapped BACs, we demonstrate a robust strategy for integrating genetic linkage and physical contig maps with mitotic and meiotic chromosome structure.</p>
Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway
<p>This is Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway.</p>
The adaptive value of recombination in resolving intralocus sexual conflict by gene duplication.
<p>Datasets and code for the study titled "The adaptive value of recombination in resolving intralocus sexual conflict by gene duplication".</p>
Specifica's recombinant Anti SARS-CoV2 antibodies
<p>These antibodies were selected against the spike protein of SARS-CoV2 from a semi-synthetic antibody library.</p>
Heterogeneous histories of recombination suppression on stickleback sex chromosomes
<p>How consistent are the evolutionary trajectories of sex chromosomes shortly after they form? Insights into the evolution of recombination, differentiation, and degeneration can be provided by comparing closely related species with homologous sex chromosomes. The sex chromosomes of the threespine stickleback (<em>Gasterosteus aculeatus</em>) and its sister species, the Japan Sea stickleback (<em>G. nipponicus)</em>, have been well characterized. Little is known, however, about the sex chromosomes of their congener, the blackspotted stickleback (<em>G. wheatlandi</em>). We used pedigrees to obtain experimentally phased whole genome sequences from blackspotted stickleback X and Y chromosomes. Using multispecies gene trees and analysis of shared duplications, we demonstrate that Chromosome 19 is the ancestral sex chromosome and that its oldest stratum evolved in the common ancestor of the genus. After the blackspotted lineage diverged, its sex chromosomes experienced independent and more extensive recombination suppression, greater X-Y differentiation, and a much higher rate of Y degeneration than the other two species. These patterns may result from a smaller effective population size in the blackspotted stickleback. A recent fusion between the ancestral blackspotted stickleback Y chromosome and Chromosome 12, which produced a neo-X and neo-Y, may have been favored by the very small size of the recombining region on the ancestral sex chromosome. We identify six strata on the ancestral and neo-sex chromosomes where recombination between the X and Y ceased at different times. These results confirm that sex chromosomes can evolve large differences within and between species over short evolutionary timescales.</p>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: validation cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the validation cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include: </p> <p>(1) SNP genotypes for the two SNPs which overlap with the discovery cohort<br> - (nicaragua_snp_genotypes_ints.tsv) -- SNP genotypes as integers<br> - (nicaragua_snp_genotypes_strings.tsv) -- SNP genotypes as allele strings <br> (2) the ancestry PCs for each individual in the validation cohort (nicaragua_snp_ancestry_PCA.tsv)<br> (3) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (4) a file including IMGT genes used for parsing TCRA repertoire data (human_vj_alleles_alpha.tsv)<br> (5) Parsed TCRA repertoire data (nicaragua_parsed_TCRA.tgz)<br> (6) Parsed TCRB repertoire data (nicaragua_parsed_TCRB.tgz) </p> <p><strong>Corresponding raw validation cohort TCR repertoire data is available here:</strong> https://www. ncbi.nlm.nih.gov/bioproject/PRJNA762269 (The BioProject database, accession number: PRJNA762269)</p> <p><strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Exploratory Landscape Analysis Feature Data of Recombinations and noiseless BBOB Instances 1-15
<p>Data presented in the paper 'Increasing Diversity of Benchmark Functions Sets by Affine Recombination' which was submitted to PPSN 2022.</p>
Post-deposition annealing and interfacial ALD buffer layers of Sb2Se3/CdS stacks for reduced interface recombination and increased open-circuit voltages
<p>Data for the article:</p> <p>Post-deposition annealing and interfacial ALD buffer layers of Sb2Se3/CdS stacks for reduced interface recombination and increased open-circuit voltages</p>
Data from: The effect of parasite infection on the recombination rate of the yellow fever mosquito Aedes aegyti
Sexual reproduction and meiotic recombination generate new genetic combinations and may thereby help an individual infected by a parasite to protect its offspring from being infected. While this idea is often used to understand the evolutionary forces underlying the maintenance of sex and recombination, it also suggests that infected individuals should increase plastically their rate of recombination. We tested the latter idea with the mosquito Aedes aegypti and asked whether females infected by the microsporidian Vavraia culicis were more likely to have recombinant offspring than uninfected females. To measure the rate of recombination over a chromosome we analysed combinations of microsatellites on chromosome 3 in infected and uninfected females, in the (uninfected) males they copulated with and in their offspring. As predicted, the infected females were more likely to have recombinant offspring than the uninfected ones. These results show the ability of a female to diversify her offspring in response to parasitic infection by plastically increasing her recombination rate.
Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers
<p><span>Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: <em>Larimichthys</em>), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (F<sub>ST</sub>) and absolute sequence divergence (<em>D</em><sub>xy</sub>), and elevated </span><span><span><em>D</em><sub>xy</sub></span> in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation. </span></p>
Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
<p><strong>Background</strong></p> <p>Human adenovirus (HAdV) infections are caused by seven mastadenovirus species (A-G) and are the source for a variety of pathologies including gastrointestinal, respiratory, neurological, and ocular disease. While HAdV-D is the most common cause of adenovirus ocular infections, human adenoviruses B and E have also been isolated from the eye. </p> <p><strong>Results</strong></p> <p>In the course of classifying three new atypical ocular adenovirus samples, taken from the vitreous humor, we found that all three isolates were HAdV-B species, with isolate BP-AdV1 sorting with the B1 clade, and isolates BP-AdV2 and BP-AdV3 grouping into the B2 clade. The three Bascom Palmer HAdV-B genomes were then combined with over 300 HAdV-B genome sequences, including 9 ocular HAdV-B genome sequences. The whole genome phylogenetic analysis showed that 9 of the 11 ocular sequences grouped into the B1 clade, forming two clusters within B1. Attempts to categorize the penton, hexon and fiber serotypes using phylogeny of the three Bascom Palmer samples were inconclusive due to incongruence between serotype and phylogeny in the dataset. Recombination analysis using a subset of HAdV-B strains to generate a hybridization network detected recombination between non-human primate and human derived strains, recombination between one HAdV-B strain and the HAdV-E outgroup and limited recombination between the B1 and B2 clades. </p> <p><strong>Conclusions</strong></p> <p>The discordance between serotype and phylogeny detected in this study suggests that the current penton/hexon/fiber-based classification mechanism does not accurately describe the natural history and phylogenetic relationships amongst adenoviruses. A new adenovirus strain classification strategy may be beneficial to the field.</p>
Data from: Rewinding the ratchet: Rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence
<p>Natural selection is less efficient in the absence of recombination. As a result, non-recombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, <em>Melanargia ines</em>, where a Z-autosome fusion has turned the homologous autosome into a non-recombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of <em>M. ines</em>, and that they arose around the time when this population split from North-African populations, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop codons and frameshift mutations, and reduced gene expression compared to the neo-Z chromosome. Surprisingly, we identified two regions of 1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.</p>
Increasing Recombinant Protein Production in E. coli via FACS-Based Selection of N-terminal Coding DNA Libraries
<p>Data for a manuscript to be deposited to the FEBS Journal. </p> <p>Abstract as deposited:</p> <p><span><span>We present a novel approach to modify N-terminal sequences of recombinant proteins to increase their production yield in <em><span>Escherichia coli</span></em>. Prior research has demonstrated a profound impact of a few nucleotides following the initiator codon (further to as N-terminal sequences) on their expression. Most of these investigations have been limited to selecting from a few rationally designed sequences. In contrast we used directed evolution-based methodology screening large numbers of diversified sequences derived from DNA libraries coding for the N-termini of investigated proteins. To facilitate the identification of cells with increasing expression of the target construct, we cloned a GFP gene at the C-terminus of the expressed genes and used fluorescent activated cell sorting (FACS) to separate cells based on their fluorescence. By following this systematic workflow, we successfully elevated the yield of soluble recombinant proteins of multiple constructs up to over 30-fold. </span></span></p>
Test data for C-QTL analysis of barley Recombinant Chromosome Substitution Lines
<p>This data shows the testing of C-QTL approach to visualise the influence of ensembles of groups of genetic markers on plant traits from a selection of Recombinant Chromosome Substitution Lines. The analysis was performed on of 29 genotypes and two traits: Heading Date and plant height. For heading date, the two major QTLs on 2H and 7H associated with heading date using the REML approach (de la Fuente Canto 2016) are also detected using the CQTL analysis, getting the highest 'rank' or score with this approach. Similarly, marker main effect for plant height at the region of the sdw1 seems to be detected with the CQTL analysis.</p>
Interaction of hypertensive rat serum immunoglobulin with recombinant human proteins
<p><strong>Microsoft Excel file: “HuProt supplemental data.xlsx”</strong></p> <p><em>Description of supplementary material : HuProt array v3.1 IgM and IgG signals from rat serum pools.</em></p> <p><strong>Sheet 1</strong>: “Array Z scores” Z scores for all array features for all sample pools used in the study detected with anti-IgM and anti-IgG reporter antibodies</p> <p><strong>Sheet 2</strong>: “IgM Z scores top 35” Z scores for the 35 array features that had highest scores detected with anti-IgM reporter in 28 week old salt loaded SHR-A3 and the corresponding scores for 16 week old SHR-A3 and 28 week old SHR-A3(<em>IgH</em>-B2) congenics.</p> <p><strong>Sheet 3</strong>: “IgM Z scores higher at 28 wks” Refinement of Sheet 2 to eliminate array features in which IgM Z scores were greater in 16 week old SHR-A3 prior to salt loading compared with 28 week old salt-loaded SHR-A3.</p> <p><strong>Sheet 4</strong>: “IgM Z scores congenics down” Refinement of Sheet 3 to include only array features in which IgM Z scores were reduced in 28 week old salt-loaded SHR-A3(<em>IgH</em>-B2) compared with 28 week old salt-loaded SHR-A3.</p> <p><strong>Sheet 5</strong>: “IgG Z scores top 35” Z scores for the 35 array features that had highest scores detected with anti-IgG reporter in 28 week old salt loaded SHR-A3 and the corresponding scores for 16 week old SHR-A3 and 28 week old SHR-A3(<em>IgH</em>-B2) congenics.</p> <p><strong>Sheet 6</strong>: “IgG Z scores higher at 28 wks” Refinement of Sheet 2 to eliminate array features in which IgG Z scores were greater in 16 week old SHR-A3 prior to salt loading compared with 28 week old salt-loaded SHR-A3.</p> <p><strong>Sheet 7</strong>: “IgG Z scores congenics down” Refinement of Sheet 3 to include only array features in which IgG Z scores were reduced in 28 week old salt-loaded SHR-A3(<em>IgH</em>-B2) compared with 28 week old salt-loaded SHR-A3.</p> <p><strong>Sheet 8: </strong>“Table 1 IgM IgG concordance” This data is presented as Table 1 in the manuscript and identifies those array features that are common to both Sheet 4 and Sheet 7, representing array features for which both IgM and IgG reactivity were reduced in 28 week old salt-loaded SHR-A3(<em>IgH</em>-B2) compared with 28 week old salt-loaded SHR-A3.</p>
Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor SlCYS8 in Nicotiana benthamiana
<p>Complete dataset (MS Label-free quantification) for the publication 'Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor <em>Sl</em>CYS8 in <em>Nicotiana benthamiana</em>'</p> <p>DOI: 10.1111/pbi.13092</p> <p> </p>
Photophysical and Spectroscopic dataset for Carrier Dynamics and Recombination in Ag-In-Zn-S Quantum Dots
<p>(1) HR-TEM images of alloyed AgIn<sub>1.5</sub>Zn<sub>1.9</sub>S<sub>3.6</sub> (A1) and AgIn<sub>1.5</sub>Zn<sub>4.4</sub>S<sub>6.8</sub> (A2) nanocrystals.</p> <p>(2) Energy-dispersive spectra of alloyed AgIn<sub>1.5</sub>Zn<sub>1.9</sub>S<sub>3.6</sub> (A1) and AgIn<sub>1.5</sub>Zn<sub>4.4</sub>S<sub>6.8</sub> (A2) nanocrystals.</p> <p>(3) UV-vis-NIR spectra of A1 nanocrystals and A1-MV, where the nanocrystals are conjugated with methyl viologen (MV2+) molecules.</p> <p>(4) (a) Normalized PL decays of A1 nanocrystals measured at various detection wavelengths, (b and c) PL decays measured at room temperature for A1 and A2 nanocrystals, (d and e) PL decays measured at various temperatures for A1 and A2 nanocrystals.</p> <p>(5) Transient absorption (TA) spectra for A1 nanocrystals for various pump-probe delays.</p> <p> </p> <p>This work was supported by National Science Centre Poland Grant No. 2019/35/B/ST3/04235.</p> <p>P.K., P.B., and A.P. acknowledge the financial support from the National Science Centre of Poland, Grant No. 2022/45/B/ST5/02120.</p>
Downstream data for recombination inferrence in the barn owl (Tyto alba)
<p>Downstream data for the publication "<strong>The recombination landscape of the barn owl, from families to populations</strong>". </p> <p>Use with <a href="https://github.com/topalw/Recombination_barn_owl">https://github.com/topalw/Recombination_barn_owl</a></p>
Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.
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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.
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.