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2,180 results for “Recombination”
Figure 1 in Recombinant - and -tubulin from Echinococcus granulosus: expression, purification and polymerization
Figure 1. The cloning and expression of α9- and β4-tubulin. (a) The expression of α9- and β4-tubulin in E. coli BL21 (DE3). M: standard protein molecular weight marker, lane 1: negative control without induction, lane 2: induced control, lane 3: the supernatant after sonication, lane 4: the pellet after sonication, and lane 5: purified recombinant tubulin. (b) Western blot analysis. M: standard protein molecular weight marker, lane 1: α-tubulin, lane 2: β-tubulin.
Figure 3 in Recombinant - and -tubulin from Echinococcus granulosus: expression, purification and polymerization
Figure 3. The sequence alignment of Echinococcus granulosus β4-tubulin and corresponding sequences from humans and parasites. Symbol meanings are as in Figure 2. EgB4, E. granulosus β4-tubulin; EmB1, E. multilocularis Tub-1 gene (7838198); EmB2, E. multilocularis Tub-2 gene (7838200); EmB3, E. multilocularis Tub-3 gene (7838202); HuB3, human B3 (50592996); HuB4, human B4a (574584803); HmB2C, H. microstoma beta 2C (674589300); HcB1, H. contortus beta tubulin isotype 1 (124244617); SjB2, S. japonicum beta 2 (226467271); PfB, P. falciparum beta (160732).
Figure 5 in Recombinant - and -tubulin from Echinococcus granulosus: expression, purification and polymerization
Figure 5. The polymerization of Echinococcus granulosus α9- and β4-tubulin. (a) Spectrophotometric analysis of polymerization of E. granulosus α9- and β4-tubulin at different concentrations. (b) Confocal scanning laser micrographs of the polymerization product of recombinant tubulin showing immune reactivity to anti-α-tubulin/Alexa-Fluor 488 antibody and anti-β-tubulin/Alexa-Fluor 647 antibody. (I): Phase contrast view, (II): α-tubulin immuno-reactivity, (III): β-tubulin immune-reactivity. (c) The microtubule-like structure resulting from polymerization of pure expressed α9- and β4-tubulin under appropriate conditions in vitro.
Figure 4 in Recombinant - and -tubulin from Echinococcus granulosus: expression, purification and polymerization
Figure 4. Modelled structure of the polymerized Echinococcus granulosus α9- and β4-tubulin dimer based on PDB ID 4f6r.
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan
Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 known complete genomes of AlYVV from databank and two complete genomes determined in this study (indicated in black boxes). The tree was rooted on ToLCNDV (AB613826) as an out-group. The schematic representation of recombination events detected by RDP4. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: pre-coat protein (AV2), coat protein (CP), replication-associated proteins (Rep and REn), transcriptional protein (TrAP), and AC4 region. AlYVV from different countries were colored differently. The colors of blocks represent the different ALYVV species and strains. Numbers at nodes indicate bootstrap confidence scores (1000 replicates).
Figure 5. 3D in Studies on the recombinant production and anticancer activity of thermostable L- asparaginase I from Pyrococcus abyssi
Figure 5. 3D structure of L-asparaginase, α-helices are shown in red, β-pleated sheets in yellow. The interaction of enzyme and L-asparagine is shown, ligand atoms are shown in balls at active site.
Figure 4 in Studies on the recombinant production and anticancer activity of thermostable L- asparaginase I from Pyrococcus abyssi
Figure 4. Lineweaver-Burk plot indicating used for the calculation of KM and Vmax of recombinant L-asparaginase.
Figure 3 in Studies on the recombinant production and anticancer activity of thermostable L- asparaginase I from Pyrococcus abyssi
Figure 3. Effect of pH on the enzyme activity. The pH value for optimum enzyme activity was found 8.
Figure 6 in Studies on the recombinant production and anticancer activity of thermostable L- asparaginase I from Pyrococcus abyssi
Figure 6. ConSurf generated conserved sequences of L-asparaginase gene, the active site residues associated with interaction of ligand are shown in boxes.
Figure 1. SDS-PAGE photograph. M in Studies on the recombinant production and anticancer activity of thermostable L- asparaginase I from Pyrococcus abyssi
Figure 1. SDS-PAGE photograph. M, Protein marker; E, cellular extract from experimental culture; F1 and F2, purified enzyme fractions collected from chromatography colum; C, negative control experiment (extract of cells transformed with plasmid without gene of interest).
Fig. 1 in Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex
Fig. 1 Species tree inferred by the DISSECT module of *BEAST based on six nuclear loci. Clades containing conspecific samples have been shown as triangles. Six clades and three singletons comprise the nine species discussed in the text. Numbers above branches are the clade
Fig. 5 in Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex
Fig. 5 Proposed model of the introgression and recombination between the S. atocioides (pink) and S. aegyptiaca (yellow) S. aegyptiaca lineages. Event A is a hybridisation episode leading to the introgression of a S. atocioides (pink) allele of EST09 into the S. aegyptiaca (yellow) population. This would have occurred at ca. 0.026 relative time units. Event B is recombination among alleles in the S. aegyptiaca (yellow) population over time since introgression to produce several combinations between the single S. atocioides (pink) allele lineage from the source population and several S. aegyptiaca (yellow) allele lineages present in the S. atocioides (pink) population. We presuppose that a recombination hotspot is present to generate approx. the same breakpoint in each case. This results in alelle combinations with monophyletic S. atocioides (pink) alleles (all derived from pink allele 1) in the recombinants, but more diverse S. aegyptiaca (yellow) alleles (derived from yellow alleles 1, 2 and 3) in the recombinants, consistent with the gene tree observations. Alternatively, two independent recombinations (rather than three) and subsequent divergence of one S. aegyptiaca (yellow) allele lineage in the recombinants could explain the gene trees
Fig. 4 in Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex
Fig. 4 Maximum clade credibility chronogram inferred using BEAST of the 3′ partition of EST09. Numbers above branches are the clade posterior probabilities. The putatively recombined sequences are marked by red
Recombinant PNGaseF production and deglycosylation assays
<p>Recombinant PNGaseF production and deglycosylation assays. Open Lab notebook.</p> <p>1.5 L of BL21 E.coli cells harbouring the pOPH6:EmPNGaseF vector encoding a His-tagged construct of Elizabethkingia miricola PNGase F (EmPNGaseF, Uniprot P21163, PNGF_ELIMR) were used to express the protein. EmPNGAse F was purified from the E.coli lysate by immobilised metal affinity and size exclusion chromatography and its activity assayed against 5 distinct glycoproteins.</p>
Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)
<p>Data sets and files for linkage map construction and for inferring recombination rate variation in <em>Populus tremula</em>. Associated scripts for analyses can be found at <a href="https://github.com/parkingvarsson/Recombination_rate_variation">https://github.com/parkingvarsson/Recombination_rate_variation</a> </p>
Data and code relating to Becher, Jackson & Charlesworth. Patterns of genetic variability in genomic regions with low rates of recombination.
<p>Data and code relating to Becher, Jackson & Charlesworth. Patterns of genetic variability in genomic regions with low rates of recombination.</p> <p>Contains genotype data, R code for analysis and visualisation, a SLiM simulation script, README, etc.</p>
Data and code for: Recombinant venom proteins in insect seminal fluid reduces female lifespan
<p>Publication: https://doi.org/10.1101/2024.01.14.575309</p> <p>This repository contains all the data as well as the scripts used for the analysis and visualisation. </p> <table> <tbody> <tr> <td><strong>File</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>TMT.ipynb</td> <td>The Jupyter notebook containing the Python code for statistical analysis and figure generation. Scripts are sectioned in the order that results are presented in the study, with sub-headings and figure numbers where appropriate.</td> </tr> <tr> <td>actingal4.csv</td> <td>Offspring phenotype data from the UAS:venom x Act5C-GAL4 assay (Results: Testing functional expression of recombinant venoms).</td> </tr> <tr> <td>femalelifespan_1-1.csv</td> <td>Female lifespan data from the 1:1 male:female mating assay (Results: TMT males reduce the lifespan of mated females). Time = days since initial male exposure until death. Status: 1 = death observed; 0 = censored. </td> </tr> <tr> <td>femalelifespan_3-1.csv</td> <td>Female lifespan data from the 3:1 male:female mating assay (Results: TMT males reduce the lifespan of mated females). Time = days since initial male exposure until death. Status: 1 = death observed; 0 = censored. </td> </tr> <tr> <td>singlemating.csv</td> <td>Data from the single-pair courtship assay. 1 = successful courtship observed; 0 = successful courtship not observed.</td> </tr> <tr> <td>competitivemating.csv</td> <td>Offspring genotype data from the competitive mating assay. Female = group of offspring from a given mother. white = positive result from gDNA PCR using the 'white' primers (supplementary table S2). TMT = positive result from gDNA PCR using the 'UAS' primers (supplementary table S2).</td> </tr> <tr> <td>malelifespan.csv</td> <td>TMT male lifespan data from the male longevity assay. Time = days since eclosion. Status: 1 = death observed; 0 = censored. </td> </tr> </tbody> </table> <p> </p> <p>TMT-GAMA.db and TMT-lethality.db contains data from the GAMA model (doi:10.5281/zenodo.11439089), which is accessed by the Jupyter notebook.</p> <table> <tbody> <tr> <td><strong>Table</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>TMT_step_output</td> <td>Each simulation will write key values to this table each cycle once transgenic males have begun to be released.</td> </tr> <tr> <td>TMT_female_output</td> <td>Each female will write key values to this table upon their death once transgeni males have begun to be released.</td> </tr> <tr> <td>TMT_PR50</td> <td>Each simulation will write to this table when/if the female population reaches 50% of its initial size.</td> </tr> <tr> <td>TMT_PR95</td> <td>Each simulation will write to this table when/if the female population reaches 95% of its initial size.</td> </tr> </tbody> </table>
Recombination and In-silico protein modelling and functional characterization of copLAB genes from Trinidadian Xanthomonas campestris and melonis isolates
<p>RDP, GARD, RaptorX and InterProScan outputs relating to the publication tentatively titled "Heavy metal resistance islands associated with a putative Tn in Trinidadian copper resistant <em>Xanthomonas campestris </em>and <em>melonis </em>strains are strongly linked to homologs from the <em>Stenotrophomonas </em>genus"</p>
Diagnostic accuracy of a novel enzyme‑linked immunoassay for the detection of IgG and IgG4 against Strongyloides stercoralis based on the recombinant antigens NIE/SsIR.
<p>Background: The diagnosis of strongyloidiasis is challenging. Serological tests are acknowledged to have high sensitivity, but issues due to cross-reactions with other parasites, native parasite antigen supply and intrinsic test variability do occur. Assays based on recombinant antigens could represent an improvement. The aim of this study was to assess the sensitivity and specificity of two novel immunoglobulin (Ig)G and IgG4 enzyme-linked immunosorbent assays (ELISAs) based on the recombinant antigens NIE/SsIR for the diagnosis of strongyloidiasis.</p> <p>Methods: This was a retrospective diagnostic accuracy study. We included serum samples collected from immigrants from strongyloidiasis endemic areas for whom there was a matched result for Strongyloides stercoralis on agar plate culture and/or PCR assay, or a positive microscopy for S. stercoralis larvae. For the included samples, results were also available from an in-house indirect fluorescent antibody test (IFAT) and a commercial (Bordier ELISA; Bordier Affinity Products SA) ELISA. We excluded: (i) samples with insufficient serum volume; (ii) samples from patients treated with ivermectin in the previous 6 months; and (iii) sera from patients for whom only routine coproparasitology was performed after formol–ether concentration, if negative for S. stercoralis larvae. The performance of the novel assays was assessed against: (i) a primary reference standard, with samples classified as negative/positive on the basis of the results of fecal tests; (ii) a composite reference standard (CRS), which also considered patients to be positive who had concordant positive results for the IFAT and Bordier ELISA or with a single “high titer” positive result for the IFAT or Bordier ELISA. Samples with a single positive test, either for the IFAT or Bordier ELISA, at low titer, were considered to be “indeterminate,” and analyses were carried out with and without their inclusion.</p> <p>Results: When assessed against the primary reference standard, the sensitivities of the IgG and IgG4 ELISAs were 92% (95% confidence interval [CI]: 88–97%) and 81% (95% CI: 74–87%), respectively, and the specificities were 91% (95% CI: 88–95%) and 94% (95% CI: 91–97%), respectively. When tested against the CRS, the IgG ELISA performed best, with 78% sensitivity (95% CI: 72–83%) and 98% specificity (95% CI: 96–100%), when a cut-off of 0.675 was applied and the indeterminate samples were excluded from the analysis.</p> <p>Conclusion: The NIE-SsIR IgG ELISA demonstrated better accuracy than the IgG4 assay and was deemed promising particularly for serosurveys in endemic areas.</p>
COJO ARG variants from "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits"
<p>These are COJO ARG variants accompanying the manuscript "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits". For more details, view the README.md file and refer to our manuscript.</p>
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