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2,180 results for “Recombination”
Recombination data for Wolbachia and Spiroplasma infected flies
<p><i><span>Wolbachia pipientis </span></i><span>is an intracellular alphaproteobacterium that<i> </i>infects 40-60% of insect species and is well known for host reproductive manipulations. Although <i>Wolbachia </i>are primarily maternally transmitted, evidence of horizontal transmission can be found in incongruent host-symbiont phylogenies and recent acquisitions of the same <i>Wolbachia </i>strain by distantly related species. Parasitoids and predator-prey interactions may indeed facilitate the transfer of <i>Wolbachia </i>between insect lineages but it is likely that <i>Wolbachia </i>are acquired via introgression in many cases. Many hypotheses exist as to explain <i>Wolbachia </i>prevalence and penetrance such as nutritional supplementation, protection from parasites, protection from viruses, or straight up reproductive parasitism. Using classical genetics we show that <i>Wolbachia </i>increase recombination in infected lineages across two genomic intervals. This increase in recombination is titer dependent as the <i>w</i>MelPop variant, which infects at higher load in <i>Drosophila melanogaster, </i>increases recombination 5% more than the <i>w</i>Mel variant. In addition, we also show that <i>Spiroplasma poulsonii, </i>the other bacterial intracellular symbiont of <i>Drosophila melanogaster, </i>does not induce an increase in recombination. Our results suggest that <i>Wolbachia</i> infection specifically<i> </i>alters host recombination landscape in a dose dependent manner.</span></p>
Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
<p>While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of <i>Drosophila pseudoobscura</i> from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a Q<sub>ST</sub>-F<sub>ST</sub> analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400kb scale, recombination rate appears to vary largely genome wide, rather than in specific intervals and (3) interpopulation differences in recombination rate may be the result of local adaptation.</p>
Looking in the medicine cabinet: methods for using real-world data to assess the impact of measles, mumps and rubella (MMR) and recombinant adjuvanted varicella-zoster vaccines on coronavirus disease 2019 (COVID-19) prevention and case fatality
<p>Supplementary File S1. 20210712_vx_off_target_pubdraft_S1 (Tables, Graphs and scripts associated with publication)</p> <p>Data file 1. Basic_Analysis.R (descriptive analysis script in R, for use with cleaned data files 3, 4 and 6)<br> Data file 2. Cleaning (Script demonstrating how Cerner data was cleaned upon download)<br> Data file 3. COVID_all_cleaned (CSV file with all COVID+ subjects in Cerner institutions)<br> Data file 4. COVID_mmr_data_cleaned (CSV file with COVID+ patients between 25-64 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, MMR vaccine history and mortality outcomes)<br> Data file 5. COVID_mmr_data_matched (CSV file matching MMR vaccine-exposed cases to controls based on propensity scores)<br> Data file 6. COVID_zoster_data_cleaned (CSV file with COVID+ patients above 50 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, zoster vaccine history and mortality outcomes)<br> Data file 7. COVID_zoster_data_matched (CSV file matching zoster vaccine-exposed cases to controls based on propensity scores)<br> Data file 8. General_25_64_data_cleaned (CSV file, all patients in Cerner institutions between 25 – 64 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, MMR vaccine history, SARS-CoV-2 infection and COVID-19 mortality outcomes ).<br> Data file 9. General_over50_data_cleaned (CSV file, all patients in Cerner institutions above 50 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, zoster vaccine history, SARS-CoV-2 infection and COVID-19 mortality outcomes).<br> Data file 10. Included_tenants (CSV file, institution IDs whose contributed cases comprise at least 0.5% of the aggregate sample size).<br> Data file 11. MMR_ps (R script to run for MMR-related files analysis)<br> Data file 12. Zoster_ps (R script to run for zoster-related files analysis)</p>
Data for "Photoluminescence tells us about voltages, recombination and diode factors in solar cells"
<p>Detailed description in "Photoluminescence tells us about voltages, recombination and diode factors in solar cells"</p> <p>by</p> <p>Susanne Siebentritt, Thomas Paul Weiss, Mohit Sood, Max Hilaire Wolter, Alberto Lomuscio, Omar Ramirez</p> <p>submitted to J. Phys. Materials</p>
Impact of RbF and NaF Postdeposition Treatments on Charge Carrier Transport and Recombination in Ga-Graded Cu(In,Ga)Se2 Solar Cells
<p>Excel file with data to all figures published in our article found at <a href="https://doi.org/10.1002/adfm.202103663">https://doi.org/10.1002/adfm.202103663 </a>(Advanced Functional Materials)</p>
Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae
<p>"Synthetic recombinant" populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant <i>Saccharomyces cerevisiae</i> populations<i> </i>created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.</p>
Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes
<p>Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.</p>
Viral reference genomes to disentangle the recombinant phylogenetic history of the potyviruses
<p>Potyviruses are a large genus of plant-infecting RNA viruses in the family Potyviridae. Due to their rapid diversification and frequent recombination, reconstructing the phylogenetic history of the potyviruses has proven difficult. Phylogenies reconstructed from different protein-coding regions of the viral genome often reveal conflicing or discordant relationships. But the extent to which discordance is due to interspecific recombination versus phylogenetic noise or errors in reconstruction is unclear. </p> <p>To explore the recombinant history of the potyviruses, we assembled a dataset containing referece genomes for 131 species of potyviruses. High-quality, full-length reference genomes for all species were obtained form NCBI GenBank. Viral genomes were carefully aligned at the codon-level and screened for recombination. The full alignment was then partitioned into several sub-alignments between each detected recombination event, such that each sub-aligment corresponds to a non-recombinant block (NRB) free of detected recombination events. Local phylogenetic trees for each NRB were then reconstructed to explore how phylogenetic relationships varied across different regions of the potyvirus genome. </p> <p>We then used our program Espalier to disentangle the phylogenetic history of the potyviruses. Espalier reconciles and removes discordances between phylogenetic trees that are likely attributable to phylogenetic error while retaining recombination events that are strongly supported by the sequence data. Applying Espalier to the potyviruses revealed that most phylogenetic discordace between local trees is likely attributable to phylogenetic noise. Removing the discordance attributable to phylogenetic error allows us to much more clearly visualize the phylogenetic history of the potyviruses.</p>
Recombinant Expression and Purification of ABHD2 from E. coli
<p>α/β Hydrolase domain-containing protein 2 (ABHD2), is a member of the metabolic serine hydrolases superfamily & a progesterone membrane receptor. In sperm, it supports the activation of CatSper which leads to sperm hypermotility. ABHD2 is 425 aa and has a N-terminal transmembrane domain followed by an extracellular facing domain. Here we report the recombinant expression and purification of ABHD2 amino acids 33-435 from <em>E. coli</em>. To the best of our knowledge, we are the first to have recombinantly purified active ABHD2.</p>
Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination
<p>This repository includes the following source datasets:</p> <p><strong>1. FluorescenceAnisotropyIII.zip </strong></p> <p>This contains following files:</p> <ol> <li>The raw fluorescence anisotropy file (Excel file) showing the values for Polarization, Anisotropy, Total Intensity, Intensity (parallel) and Intensity (perpendicular) for all the samples included in the paper as separate sheets.</li> <li>The analysis files generated in the Graphpad prism.</li> <li>The details of the files.</li> </ol> <p> </p> <p><strong>2. FT-IR.zip</strong>: This contains the normalized values for the FT-IR spectroscopy of the WT RecF, WT RecR, RecF A170W and RecR A147W.</p> <p> </p> <p><strong>3. Glycerol gradient.zip</strong>: This contains the raw gel files for the three sets of independent experiments, standard protein ruler with the respective WT RecF, WT RecO and WT RecR and details regarding the loading of samples on gels.</p> <p> </p> <p><strong>4. Pull-downII.zip</strong>: This contains details of all the pull-down experiments and the raw gel files used for</p> <ol> <li>Quantification</li> <li>The major samples for all the experiments done in triplicate</li> <li>Figure preparation for paper</li> </ol> <p> </p> <p> </p>
Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly
<p>Genetic recombination is a key molecular mechanism that has profound implications on both micro- and macro-evolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly (<em>Leptidea</em> <em>sinapis</em>) shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially due to interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a negligible influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements (TEs), most notably a significant enrichment of SINEs in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination cold-spots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and has particular implications for forthcoming research in population genetics, molecular/genome evolution and speciation.</p>
The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich
<p><span>Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (<em>Struthio</em> <em>camelus</em>), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population-scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar-sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females</span><span>,</span><span> but not homogametic males. Genetic variation within the sex-linked region (SLR) (π = 0.001) was significantly lower than in the PAR, </span><span>consistent with recombination cessation. Conversely, genetic variation </span><span>across the PAR (π = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content, and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.</span></p>
Candidate High-Resolution Mass Spectrometry-Based Reference Method for the Quantification of Procalcitonin in Human Serum Using a Characterized Recombinant Protein as a Primary Calibrator
<p>Dataset related to Huu-Hien Huynh, Vincent Delatour, Maxence Derbez-Morin, Qinde Liu, Amandine Boeuf, and Joëlle Vinh, (2022) Candidate High-Resolution Mass Spectrometry-Based Reference Method for the Quantification of Procalcitonin in Human Serum Using a Characterized Recombinant Protein as a Primary Calibrator. Anal. Chem. 2022, 94, 10, 4146–4154.</p>
Codes for: A numerical model supports the evolutionary advantage of recombination plasticity in shifting environments
<p><span>Numerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions.</span> <span>Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario – when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination </span><span>in individuals developing in a different environment than their parents and optionally, also in offspring of such individuals. </span><span>We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may appear beneficial also when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared to the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms such as chromatin epigenetics remodeling.</span></p>
Exploring the effect of microstructure and surface recombination on hydrogen effusion in Zn-Ni coated martensitic steels by advanced computational modelling
<p>Raw data pertaining to the publication "Exploring the effect of microstructure and surface recombination on hydrogen effusion in Zn-Ni coated martensitic steels by advanced computational modelling".</p>
Theory and optimisation of radiative recombination in broken-gap InAs/GaSb superlattices
<p>Raw data and plotting scripts associated with the paper:<br><br>Cónal Murphy, Eoin P. O'Reilly and Christopher A. Broderick, "Theory and optimisation of radiative recombination in broken-gap InAs/GaSb superlattices", <em>J. Phys. D: Appl. Phys.</em> <strong>57</strong> 035103 (2023) (DOI: 10.1088/1361-6463/ad015d)</p>
PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells-Dataset
<p><span> PHRF1 is an E3 ligase that promotes TGF-</span><span>B</span><span> signaling by ubiquitinating a homeodomain repressor TG-interacting factor (TGIF). The suppression of PHRF1 activity by PML-RAR</span><span> facilitates the progression of acute promyelocytic leukemia (APL). PHRF1 also contributes to non-homologous end-joining in response to DNA damage by linking H3K36me3 and NBS1 with DNA repair machinery. However, its role in class switch recombination (CSR) is not well understood. In this study, we report the importance of PHRF1 in IgA switching in CH12F3-2A cells and CD19-Cre mice. Our studies revealed that Crispr-Cas9 mediated PHRF1 knockout and shRNA-silenced CH12F3-2A cells reduced IgA production, as well as decreased the amounts of PARP1, NELF-A, and NELF-D. The introduction of PARP1 could partially restore IgA production in PHRF1 knockout cells. Intriguingly, IgA, as well as IgG1, IgG2a, and IgG3, switchings were not significantly decreased in PHRF1 deficient splenic B lymphocytes isolated from CD19-Cre mice. The levels of PARP1 and NELF-D were not decreased in PHRF1-depleted primary splenic B cells. Overall, our findings suggest that PHRF1 may modulate IgA switching in CH12F3-2A cells.</span></p>
Data from: High-resolution crossover maps for each bivalent of Zea mays using recombination nodules
<p>Recombination nodules (RNs) mark sites of crossing over along pachytene synaptonemal complexes (SCs). Thus, RNs provide the highest resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes because they are observed by electron microscopy. Using the maize inbred line KYS, we have prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4272 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. Average RN frequency per bivalent is closely correlated with SC length. The total length of the RN map is about two-fold shorter than most linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents.</p>
Assess Incidence of Deep Vein Thrombosis(DVT)Following Administration of Recombinant Human Antithrombin (rhAT) to Hereditary Antithrombin(AT) Deficient Patients in High Risk Situations.
ClinicalTrials.gov study NCT00056550. IPD Sharing: Not stated. Countries: 6. Publications: 1.
A Phase I Study of Quadrivalent Human Papilloma Virus (HPV) (Types 6, 11, 16, 18) Recombinant Vaccine in HIV-Infected and HIV-Negative Pre-Adolescents, Adolescents, and Young Adults
ClinicalTrials.gov study NCT00798265. IPD Sharing: YES. Countries: 1. Publications: 3.
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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.
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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.