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2,180 results for “ReCombine”
Probing Ion Channel Functional Architecture and Domain Recombination Compatibility by Massively Parallel Domain Insertion Profiling
<p>Supplementary Data for a large insertional profiling study described in Coyote-Maestas et al. (2021) Nature Communications.</p>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: discovery cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the discovery 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) a file mapping the SNP data subject IDs to the TCR repertoire data subject IDs (gwas_id_mapping.tsv)<br> (2) a file including the PCAir PCs, self-reported ancestry, and genomic ancestry for each subject (all_pc_air.txt)<br> (3) a file including the PCAir variance explained by each PC (all_pc_air_variance.txt)<br> (3) a file including the SNP ID, chromosome, hg19 position, allele, rsid, and quality control metrics for each SNP in the SNP array (emerson_snp_rs_data.tsv)<br> (4) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (5) a file including predicted TRBD2 allele genotypes for each subject (emerson_trbd2_alleles.tsv)<br> (6) Parsed TCRB repertoire data. These raw data were first published in Emerson et. al, <em>Nature Genetics </em>2017. (emerson_parsed_tcrb.tgz)</p> <p><strong>Corresponding discovery cohort raw TCR repertoire data is available here: </strong>https: //doi.org/10.21417/B7001Z (ImmuneACCESS database)<br> <strong>Corresponding discovery cohort SNP data is available here:</strong> https: //www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001918.v1.p1 (The database of Genotypes and Phenotypes, accession number: phs001918)<br> <br> <strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Hydrogen atom recombination on Pt(111) and Pt(332)
<p>Experimantal transient rates of HD formation, Molecular beam parameters, Experimental isotopic branching, Experimental H+H rate constants, Modeled dissociative adsorption and recombinative desorption rate constants, Coverage dependent adsorption energy, Quantum mechanical entropy of H-atoms at 598K.</p>
Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load
<p>Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive- the driver and the target- linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal, multilocus, male meiotic drive system, Segregation Distorter (SD) in the fruit fly, Drosophila melanogaster. In African populations, the predominant SD chromosome variant, SD-Mal, is characterized by two overlapping, paracentric inversions on chromosome arm 2R and nearly perfect (~100%) transmission. We study the SD-Mal system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying Sd, the main driving allele, and one or more factors within the double inversion. While most SD-Mal chromosomes are homozygous lethal, SD-Mal haplotypes can recombine with other, complementing haplotypes via crossing over, and with wildtype chromosomes via gene conversion. SD-Mal chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, SD-Mal haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of SD haplotypes in different populations around the world, and have implications for supergene evolution broadly.</p>
Recombination experiments with inversion heterozygotes
<p>Recombination suppression in chromosomal inversion heterozygotes is a well-known but poorly understood phenomenon. Surprisingly, recombination suppression extends far outside of inverted regions where there are no intrinsic barriers to normal chromosome pairing, synapsis, double-strand break formation, or recovery of crossover products. The interference hypothesis of recombination suppression proposes heterozygous inversion breakpoints possess chiasma-like properties such that recombination suppression extends from these breakpoints in a process analogous to crossover interference. This hypothesis is qualitatively consistent with chromosome-wide patterns of recombination suppression extending to both inverted and uninverted regions of the chromosome. The present study generated quantitative predictions for this hypothesis using a probabilistic model of crossover interference with gamma-distributed inter-event distances. These predictions were then tested with experimental genetic data (>40,000 meioses) on crossing-over in intervals that are external and adjacent to four common inversions of Drosophila melanogaster. The crossover interference model accurately predicted the partially suppressed recombination rates in euchromatic intervals outside inverted regions. Furthermore, assuming interference does not extend across centromeres dramatically improved model fit and partially accounted for excess recombination observed in pericentromeric intervals. Finally, inversions with breakpoints closest to the centromere had the greatest excess of recombination in pericentromeric intervals, an observation that is consistent with negative crossover interference previously documented near Drosophila melanogaster centromeres. In conclusion, the experimental data support the interference hypothesis of recombination suppression, validate a mathematical framework for integrating distance-dependent effects of structural heterozygosity on crossover distribution, and highlight the need for improved modeling of crossover interference in pericentromeric regions.</p>
Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination
<p>Extended Data S1-S2 and Tables S6-S9 corresponding to the publication entitled Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination. Data S1 contains the phylogeny analyzed in the aforementioned study, and Data S2 contains a table of all samples considered to be descendant of a recombinant node in the study, as well as the relevant recombinant node ID. Tables S6-S9 are acknowledgments tables corresponding to GISAID (Table S6), China National Center for Bioinformation (Table S7), COVID-19 Genomics UK (COG-UK) (Table S8), and National Center for Biotechnology Information database (Table S9) on which the study was based.</p>
Data set for "The ion-ion recombination coefficient α: comparison of temperature- and pressure-dependent parameterisations for the troposphere and stratosphere"
<p>The uploaded data are related to the publication "The ion–ion recombination coefficient <span class="math-tex">\(\alpha\)</span>: comparison of temperature- and pressure-dependent parameterisations for the troposphere and stratosphere" in Atmospheric Chemistry and Physics (ACP). The data are the same as shown in the figures of the publication. The naming of the uploaded files indicates the figure (e.g., "Fig_2" indicates Figure 2 of the publication). </p>
Fig. 5 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 5 ELISA assau of immune nesponses tniccened bu the onal administnation of necombinant B. subtilis spones. Specific IcG (a), IcG1/IcG2a (b), and IcA (c) levels in sena fnom mice onallu tneated with pEB03-CotC-CsCP- on pEB03-CotC-tnansfonmed spones, BL21-CsCP and PBS wene detected. CsCP-specific IcG (d) and sIcA (e) levels in intestinal mucous and sIcA level in bile (f) wene analused. Data ane expnessed as the mean ± SD. Statistical sicnificance was analused bu the Student's t-test (*P <0.05; **P <0.01). Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 containinc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP
Fig. 3 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 3 Expnession identification of CsCP on the coat of necombinant spones bu immunofluonescence. The B. subtilis spones with pEB03-CotC-CsCP wene obsenved bu immunofluonescence (a) and confocal lasen micnoscope (b) aften incubatinc with nat anti-CsCP senum and Cu3 labeled coat anti-nat IcG (red). The nucleus was stained with DAPI (blue). Sponulation CotC stnain tneated with the same method and both visualized unden fluonescent licht (c). All spones above wene obsenved unden bnicht field (BF) as well. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC. Scale-bars: a, c, 50 μm; b, 2 μm
Fig. 4 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 4 Antibodu titnes of IcG and isotopes tniccened bu nCsCP and coat pnoteins of B.s-CotC-CsCP spones via subcutaneous immunization noute. ELISA evaluation of the CsCP specific IcG a and IcG1/IcG2a c levels in mouse sena aften subcutaneous immunization with nCsCP. b Antibodu titnes of IcG induced bu nCsCP at week 6. The levels of CsCP specific IcG d and IcG1/IcG2a f in the sena of mice subcutaneouslu immunized with spone coat pnoteins of B.s-CotC-CsCP. Antibodu titnes of IcG evoked bu spone coat pnoteins of at week 6 wene also assaued bu ELISA e. Data wene displaued as the mean ± SD. *P <0.05; **P <0.01; ***P <0.001. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 containinc pEB03-CotC; nCP, punified nCsCP
Fig. 7 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 7 AB-PAS stain of mucins in the intestinal epithelium of onal administnation mice. Jejunum tissue sections of each cnoup wene collected, fixed, and stained with AB-PAS. Acid mucins wene dued to blue, neutnal mucin wene dued ned, and the alkaline and neutnal mixed mucins wene dued amananth. Panels a-b, c-d, e-f and g-h indicate PBS, B.s-CotC, BL21-CsCP and B.s-CotC-CsCP onallu administened cnoups at week 4, nespectivelu. Panels (i) and (j) show the B.s-CotC-CsCP cnoup tneated at week 6. Scale-bars: a, c, e, g, i, 200 μm; b, d, f, h, j, 50 μm. The annows indicate acidic mucins secneted bu coblet cells
Fig. 2 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 2 Expnession and identification of nCsCP and CotC-CsCP. a SDS-PAGE analusis of CsCP expnessed in E. coli BL21 and B. subtilis spones. The moleculan mass of CotC-CsCP fusion pnotein was appnoximatelu 43.8 kDa. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP; nCP, punified nCsCP. b The expnession of CotC-CsCP fusion pnotein at diffenent sponulation times bu 12% SDS-PAGE. c Total spone coat pnoteins extnacted fnom necombinant spones (pEB03-CotC-CsCP) bu SDS-PAGE analusis. d Identification of CotC-CsCP fusion pnotein bu MS. e MALDI-TOF/TOF-MS analusis of punified nCsCP. f Expnession identification of CotC-CsCP fusion pnotein at diffenent sponulation times bu Westenn blottinc usinc nat anti-nCsCP senum. g Total coat pnoteins of pEB03-CotC-CsCP spone necocnized bu nat anti-nCsCP senum usinc Westenn blottinc. Abbreviations: P, pnecipitation; S, supennatant
Fig. 6 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 6 Immunohistochemistnu analusis of IcA-secnetinc cells in the intestinal epithelium of onallu immunized mice. IcA-secnetinc cells wene stained dank bnown. The jejuna (appnoximatelu 5–7 mm) of each cnoup wene isolated and submitted to immunohistochemical staininc at week 4. Panels (a) and (b) nepnesent PBS-tneated mice. Panels (c) and (d) nepnesent B.s-CotC onallu administened mice. Panels (e) and (f) nepnesent BL21-CsCP cavaced mice. Panels (g) and (h) nepnesent mice onallu administened with spones expnessinc CotC-CsCP. Scale-bars: a, c, e, g, 200 μm; b, d, f, h, 50 μm. The annows indicate IcA-secnetinc cells. i Intecnated option densitu (IOD) of IcA-secnetinc cells. ***P <0.001
Fig. 1 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 1 Schematic of the tneatment necimen. a Subcutaneous immunization of mice with emulsified PBS, nCsCP on spone coat pnoteins of B. s-CotCCsCP administened thnee times. Senum samples wene collected at 2, 4, 6 and 8 weeks. b Onal administnation of mice with PBS, spones of B.s-CotC on B.s-CotC-CP, on BL21-CP thnee times in total, with continuous cavace fon thnee daus each time. Senum, intestine and bile samples wene collected evenu 2 weeks. Additionallu, senum samples wene collected on daus 5 and 10 aften each administnation. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP
Figure 5 in Improved diagnostic sensitivity of human strongyloidiasis using point-of-care mixed recombinant antigen-based immunochromatography
Figure 5. The intensity values of NIE (a), SsIR (b), and NIE-SsIR (c) ICT kits were evaluated using an in-house strip reader (red line indicates cut-off intensity value). Groups I, II, and III represented healthy controls, proven strongyloidiasis, and other parasitic infections, respectively. Any value above the cut-off value (red horizontal lines) is negative. Receiver operator characteristic (ROC) area analyses of the NIE, SsIR, and NIE-SsIR ICT kits to compare accuracy of all kits with gold standard methods (d).
Figure 3 in Improved diagnostic sensitivity of human strongyloidiasis using point-of-care mixed recombinant antigen-based immunochromatography
Figure 3. The purified NIE (a) and SsIR (b) fusion-tagged proteins visualized following electrophoresis through 12% and 10% SDS–PAGE, respectively. The gels were stained with Coomassie Brilliant Blue. Representative dot ELISAs (c) using NIE (1–2), SsIR (3–4), and mixed NIE and SsIR (5–6) proteins as the antigens probed with pooled positive (1, 3, 5) and negative (2, 4, 6) sera. M indicates molecular mass maker.
Figure 1 in Improved diagnostic sensitivity of human strongyloidiasis using point-of-care mixed recombinant antigen-based immunochromatography
Figure 1. Flow diagram of study design for the NIE, SsIR, and NIE-SsIR ICT kits. The SsIR ICT kit procedure was performed as previously described by Boonroumkaew et al. [4].
Figure 2 in Improved diagnostic sensitivity of human strongyloidiasis using point-of-care mixed recombinant antigen-based immunochromatography
Figure 2. The parts of an ICT kit (left) and reference colour card (right) (a). An ICT kit showing a positive result (b) with a band at both control (C) and test (T) lines. An ICT kit showing a negative result (c) with a band only at the C line. The intensity value of the colour image is specified by the red, green, and blue parameters as separate integers from 0 to 255 with the 8-bit representation of a pixel in the image. The intensity values were plotted for C and T lines of the positive (d) and negative (e) ICT kits. The intensity values (d and e) were related to colour band intensity of C and T lines in the strips. S indicates sample hole.
Figure 4 in Improved diagnostic sensitivity of human strongyloidiasis using point-of-care mixed recombinant antigen-based immunochromatography
Figure 4. Representative results of the NIE, SsIR, and NIE-SsIR ICT kits, Positive, positive pooled serum samples; Negative, negative pooled serum samples; Hc, healthy control; Ss, proven strongyloidiasis; Gl, giardiasis; Eh, amoebiasis; Bh, blastocystosis; Ov, opisthorchiasis; Fg, fascioliasis; Ph, paragonimiasis; Tn, taeniasis; Cc, cysticercosis; Se, sparganosis; Hw, hookworm infections; Al, ascariasis; Tt, trichuriasis; Ts, trichinellosis; Ac, angiostrongyliasis; Gs, gnathostomiasis; Cp, capillariasis. The intensity cut-off levels for a positive result of the NIE, SsIR, and NIE-SsIR ICT kits were 1, 1, and>0.5, respectively by the naked eye and <164, <164, and <167, respectively by the in-house strip reader. The "+" and "—" symbols indicated positive and negative results.
Figure 2 in Recombinant - and -tubulin from Echinococcus granulosus: expression, purification and polymerization
Figure 2. Sequence alignment of Echinococcus granulosus α9-tubulin and corresponding sequences from humans and parasites. The symbol ''*'' denotes the positions of amino acids that have a single, fully conserved amino acid residue; the symbol '':'' denotes conservation between groups of amino acids with strongly similar properties; the symbol ''.'' denotes conservation between groups of amino acids with weakly similar properties; and the symbol ''–'' denotes gaps inserted to maximize sequence alignment. EgA9, E. granulosus α9; HuA6, human alpha 6 (119578461); HmA5, H. microstoma alpha 5 (674586714); HcA, H. contortus alpha tubulin (159155); SjA1, S. japonicum alpha 1–3 (226478902); and TgA, T. gondii alpha (161937).
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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.