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2,180 results for “Recombination”
RNA-Seq of chicken embryonic feather/scale recombination skin explants
GEO Series GSE111099. Gallus gallus. 16 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic profile of three-dimensional tissue-engineered human skeletal muscle model of Pompe disease and recombinant protein therapy
GEO Series GSE159062. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Tcrd rearrangement redirects a processive Tcra recombination program to expand the Tcra repertoire
GEO Series GSE95826. Mus musculus. 28 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Recombination initiation maps of individual human genomes
GEO Series GSE59836. Homo sapiens. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Lp(a) and 17K recombinant apo(a) treatment of THP-1 macrophages
GEO Series GSE226759. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of HeLa cells infected with YK410, a recombinant strain of HSV-1
GEO Series GSE240449. Human alphaherpesvirus 1. 18 samples. Type: Expression profiling by high throughput sequencing.
Meiotic recombination cold spots in chromosomal cohesion sites [ChIP-chip]
GEO Series GSE52858. Schizosaccharomyces pombe. 2 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Recombination between SARS-CoV-2 "strains": The possibility of the emergence of more or less virulent "strains" of the virus
<p>To explore the possibility of genomic recombination a total of 2,611 SARS-CoV-2 sequences were mined from the NCBI Virus resource. Multiple sequence alignment and recombination analysis of these sequences were performed using MAFFET and Recombination detection program (RDP) respectively, to determine the emergence of new SARS-CoV-2 viral sequences. We report for the first time, 3 novel recombination events between SARS-CoV-2 sequences, with one event having occurred in 65% of the sequences analysed<em>.</em> Bearing in mind that the prerequisite for recombination is the occurrence of two or more viral sequences in the same reservoir, biological niche or host at the same time, we hypothesized that there was co-infection and or superinfection facilitating recombination in the primary hosts prior to infection of the secondary hosts with the recombinant sequences. Recombination between the SARS-CoV-2 sequences poses the likelihood of the emergence of new more or less virulent “strains” of the virus. We believe that the future of science lies in our ability to be able to use computational based methods to predict the genetic sequences of infectious agents of the next epidemics. The addition of more SARS-CoV-2 sequences has a bearing on our understanding of its origin, hence more SARS-CoV-2 sequences in public databases are needed to elucidate our understanding of this family of viruses.</p>
Recombinant human ACE2 protein production and purification
<p>Recombinant human ACE2 protein production and purification</p>
The MRN complex promotes DNA repair by homologous recombination and restrains antigenic variation in African trypanosomes
<p>Sanger sequencing of PCR products to determine MMEJ repair junctions.</p>
Data from: Impact of deleterious mutations, sexually antagonistic selection and mode of recombination suppression on transitions between male and female heterogamety.
Deleterious mutations accumulating on non-recombining Y chromosomes can drive XY to XY turnovers, as they allow to replace the old mutation-loaded Y by a new mutation-free one. The same process is thought to prevent XY to ZW turnovers, because the latter requires fixation of the ancestral Y, assuming dominance of the emergent feminizing mutation. Using individual-based simulations, we explored whether and how an epistatically dominant W allele can spread in a young XY system that gradually accumulates deleterious mutations. We also investigated how sexually antagonistic (SA) polymorphism on the ancestral sex chromosomes and the mechanism controlling X-Y recombination suppression affect these transitions. In contrast with XY to XY turnovers, XY to ZW turnovers cannot be favored by Y chromosome mutation load. If the arrest of X-Y recombination depends on genotypic sex, transitions are strongly hindered by deleterious mutations, and totally suppressed by very small SA cost, because deleterious mutations and female-detrimental SA alleles would have to fix with the Y. If, however, the arrest of X-Y recombination depends on phenotypic sex, X and Y recombine in XY ZW females, allowing for the purge of Y-linked deleterious mutations and loss of the SA polymorphism, causing XY to ZW turnovers to occur at the same rate as in the absence of deleterious and sex-antagonistic mutations. We generalize our results to other types of turnovers (e.g., triggered by non-dominant sex-determining mutations) and discuss their empirical relevance.
Data from: Efficient inference of recombination hot regions in bacterial genomes
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of "hotspots" of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here we focus in particular on identifying "hot regions" of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed "chromosome painting" algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site which additionally reflects the specific deviations at the site due to recombination. Using simulated data, we show that hot regions have consistently higher deviations from the genome wide average than normal regions. We applied our approach to previously analysed Escherichia coli genomes, and revealed that the new method is highly correlated with the number of recombination events affecting each site inferred by ClonalOrigin, a method that is only applicable to small numbers of genomes. Furthermore, we analysed recombination hot regions in Campylobacter jejuni by using 200 genomes. We identified three recombination hot regions which are enriched for genes related to membrane proteins. Our approach and its implementation, which is downloadable from https://github.com/bioprojects/orderedPainting, will help to develop a new phase of population genomic studies of recombination in prokaryotes.
Data from: Population-specific recombination sites within the human MHC region
Genetic rearrangement by recombination is one of the major driving forces for genome evolution and recombination are known to occur in non-random, discreet recombination sites within the genome. Mapping of recombination sites have proved difficult particularly in the human MHC region that is complicated by both population variation and highly polymorphic HLA genes. To overcome these problems, HLA typed individuals from three representative populations: Asian, European and African were used to generate phased HLA haplotypes. Extended haplotype homozygosity (EHH) plots constructed from the phased haplotype data revealed discreet EHH drops corresponding to recombination events and these signatures were observed to be different for each population. Surprisingly, the majority of recombination sites detected are unique to each population rather than being common. Unique recombination sites account for 56.8% (21/37 of total sites) in the Asian cohort, 50.0% (15/30 sites) in Europeans and 63.2% (24/38 sites) in Africans. Validation carried out at a known sperm typing recombination site of 45kb (HLA-F Telomeric) showed that EHH was an efficient method to narrow the recombination region to 826bp and this was further refined to 660bp by re-sequencing. This approach significantly enhanced mapping of the genomic architecture within the human MHC will be useful in studies to identify disease risk genes.
Data from: The role of recombination, niche-specific gene pools and flexible genomes in the ecological speciation of bacteria
Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche‐specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that (a) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect and (b) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche‐specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche‐specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.
Data and script for "rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers."
Open the record for dataset details and reuse information.
Structural variants in the HXB/BXH recombinant inbred panel
<p>Whole genome lined-read sequencing data of the HXB/BXH recombinant inbred panel was mapped using Longranger. Structural variants were merged using SURVIVOR.</p>
Figure 1 from: Shkondrov A, Kondeva-Burdina M, Stambolov I, Krasteva I (2024) Activity of an oleanane-type tritrepenoid saponin from A. glycyphyllos on human recombinant MAO enzymes. Pharmacia 71: 1-6. https://doi.org/10.3897/pharmacia.71.e114786
Figure 1 Chromatograms of Sg in the negative (a) and positive (b) ionization modes.
Figure 2 from: Shkondrov A, Kondeva-Burdina M, Stambolov I, Krasteva I (2024) Activity of an oleanane-type tritrepenoid saponin from A. glycyphyllos on human recombinant MAO enzymes. Pharmacia 71: 1-6. https://doi.org/10.3897/pharmacia.71.e114786
Figure 2 HRESIMS spectrum of compound Sg in the (a) negative and (b) positive modes.
Combining mutation and recombination statistics to infer clonal families in antibody repertoires
<p>All data used for the benchmark of HILARy. The benchmark procedure is described here https://github.com/statbiophys/HILARy/tree/main/data_with_scripts </p>
Data from: Random-sequence genetic oligomer pools display an innate potential for ligation and recombination
Recombination, the exchange of information between different genetic polymer strands, is of fundamental importance in biology for genome maintenance and genetic diversification mediated by dedicated recombinase enzymes. Here, we describe a pervasive non-enzymatic capacity for recombination (and ligation) in random-sequence genetic oligomer pools. Specifically, we examine random and semi-random eicosamer (N20) pools of RNA, DNA and the unnatural genetic polymers ANA (arabino-), HNA (hexitol-) and AtNA (altritol-nucleic acids). While DNA, ANA and HNA pools proved inert, RNA and AtNA pools displayed diverse modes of spontaneous intermolecular recombination, connecting recombination mechanistically to the vicinal ring cis-diol configuration shared by RNA and AtNA. Thus, the chemical constitution that renders both susceptible to hydrolysis emerges as the fundamental determinant of an innate capacity for recombination, which is shown to enable a concomitant increase in compositional, informational and structural pool complexity and hence evolutionary potential.
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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.