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3,576 results for “strain”
Data from: Conservation of a domestic metapopulation structured into related and partly admixed strains
Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronised maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenisation process. This study collected and evaluated samples, data and genome-wide information and developed genome-assisted cross-border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semi-private alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.
Data from: Genome assembly and annotation of a Drosophila simulans strain from Madagascar
Drosophila simulans is a closely relative of the genetic model D. melanogaster. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252 provides a clear improvement with alternative splicing for 52% of the multiple-exon genes, UTRs for 70% of the genes, 225 novel genes and 781 pseudogenes being reported. We anticipate that the M252 genome will be a valuable resource for many research questions.
Data from: Estimating costs of aphid resistance to parasitoids conferred by a protective strain of the bacterial endosymbiont Regiella insecticola
Heritable bacterial endosymbionts are common in aphids (Hemiptera: Aphididae), and they can influence ecologically important traits of their hosts. It is generally assumed that their persistence in a population is dependent on a balance between the costs and benefits they confer. A good example is Hamiltonella defensa Moran et al., a facultative symbiont that provides a benefit by strongly increasing aphid resistance to parasitoid wasps, but becomes costly to the host in the absence of parasitoids. Regiella insecticola Moran et al. is another common symbiont of aphids and generally does not influence resistance to parasitoids. In the green peach aphid, Myzus persicae (Sulzer), however, one strain (R5.15) was discovered that behaves like H. defensa in that it provides strong protection against parasitoid wasps. Here we compare R5.15-infected and uninfected lines of three M. persicae clones to test whether this protective symbiont is costly as well, i.e., whether it has any negative effects on aphid life-history traits. Furthermore, we transferred R5.15 to two other aphid species, the pea aphid, Acyrthosiphon pisum (Harris), and the black bean aphid, Aphis fabae Scopoli, where this strain is also protective against parasitoids and where we could compare its effects with those of additional, non-protective strains of R. insecticola. Negative effects of R5.15 on host survival and lifetime reproduction were limited and frequently non-significant, and these effects were comparable or in one case weaker than those of R. insecticola strains that are not protective against parasitoid wasps. Unless the benefit of protection is counteracted by detrimental effects on traits that were not considered in this study, R. insecticola strain R5.15 should have a high potential to spread in aphid populations.
Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges
Background: The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared. Results: The strains from each pathotype form monophyletic clades, with a short branch shared by the Aw and A pathotypes. Pathotype-specific recombination was detected in seven regions of the alignment. Using Ancestral Character Estimation, 426 SNPs were mapped to the four branches at the base of the A, A*, Aw and A/Aw clades. Several genes containing pathotype-specific nonsynonymous mutations have functions related to pathogenicity. The A pathotype is enriched for SNP-containing genes involved in defense mechanisms, while A* is significantly depleted for genes that are involved in transcription. The pathotypes differ by four gene islands that largely coincide with regions of recombination and include genes with a role in virulence. Both A* and Aw are missing genes involved in defense mechanisms. In contrast to a recent study, we find that there are an extremely small number of pathotype-specific gene presences and absences. Conclusions: The three pathotypes of X. citri pv. citri that differ in their host ranges largely show genomic differences related to recombination, horizontal gene transfer and single nucleotide polymorphism. We detail the phylogenetic relationship of the pathotypes and provide a set of candidate genes involved in pathotype-specific evolutionary events that could explain to the differences in host range and pathogenicity between them.
Data from: Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains
Background: Present study focuses on diversity and distribution analysis of endophytic fungi associated with different tissues of Eugenia jambolana. The influence of season and geographical location on diversity and distribution of endophytic fungi has been analyzed. Antibacterial activity of isolated fungal species has also been investigated against MDR bacterial strains. Result: A total of 1896 endophytic fungal isolates were obtained from healthy, surface sterilized tissues of leaf, stem and petiole tissues during summer, monsoon and winter season. Out of 24 fungal species isolated, 20 species belong to class Ascomycetes, 2 to Basidiomycetes and 2 to Zygomycetes. Maximum species diversity was in rainy season whereas colonization frequency was in winter. All the diversity indices showed maximum species diversity at site 5 (Yamunanager), rainy among the seasons and leaf among the tissues studied. Aspergillus genus was most frequently isolated. Aspergillus niger and Alternaria alternata were most dominant species. Three way ANOVA results showed that effect of season was highly significant on species diversity in relation to sites and tissues. 60% endophytic fungal extracts showed significant antibacterial activity against one or more than one MDR bacterial strain. Conclusion: Different fungal species were recovered from different sites but the inter-site comparisons were not significant according to Jaccard similarity coefficient. Diversity of such fungal endophytes indicates that Eugenia jambolana plant acts as an ecosystem facilitating survival of many microbes with impressive antibacterial potential.
Data from: Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets
Background: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. Results: The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. Conclusion: The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
Data from: Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattle
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular interest as the occurrence of such lineage in Europe is demonstrated for the first time, filling an historical gap within the phylogeography of the lineage. Comparative genome analyses of these strains with 41 isolates from other parts of the world revealed that the two Danish A.Br.008/011 strains were related to the heroin-associated strains responsible for outbreaks of injection anthrax in drug users in Europe. Eight novel diagnostic SNPs that specifically discriminate the different sub-groups of Danish strains were identified and developed into PCR-based genotyping assays.
Data from: Functional genotypes are associated with commensal Escherichia coli strain abundance within host individuals and populations
The selective pressures that determine genotype abundance and distribution frequently vary between ecological levels. Thus, it is often unclear whether the same functional genotypes will become abundant at different levels and how selection acting at these different scales are linked. In this study, we examined whether particular functional genotypes, defined by the presence or absence of 34 genes, of commensal E. coli strains were associated with within-host abundance and/or host population abundance in a wild population of 54 adult mountain brushtail possums (Trichosurus cunninghami). Our results revealed that there was a positive correlation between a strain's relative abundance within individuals and the strain's abundance in the host population. We also found that strain abundance at both ecological levels was predicted by the same group of functional genes (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated patterns of occurrence. We propose that direct selection on the same functional genes at both levels may in part be responsible for the observed correlation between the ecological levels. However, a potential link between abundance within the host and excretion rate may also contribute.
Taxonomic profiles of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness
<p>Taxonomic profiles including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness.</p> <p>See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.</p>
Taxonomic binnings of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness
<p>Taxonomic binnings including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness.</p> <p>See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.</p>
Upper-limb rehabilitation exercises acquired through 29 elastomer strain sensors placed on fabric
<p>A multivariate dataset obtained recording the stretch of various segments of the fabric of a sensorized garment while executing several rehabilitation exercises.</p> <p>Full description in P. Tormene, T. Giorgino, S. Quaglini, M. Stefanelli. <em>Matching incomplete time series with dynamic time warping: an algorithm and an application to post-stroke rehabilitation.</em> Artificial Intelligence in Medicine, Volume 45, Issue 1, Pages 11-34, http://dx.doi.org/10.1016/j.artmed.2008.11.007 and in enclosed Readme file.</p>
Borrelia strain diversity
<p>Simulated sequence data for testing Bb strain diversity method, all in FASTQ format.</p> <ul> <li>Included are read sets from 3 whole genomes (B31, JD1, N40) x 10 replicates of each. B31_01_R1.fq.bz1 (Genome B31, replicate 1, read 1). These files are compressed with http://www.linfo.org/bzip2.html and can be decompressed with bzip2 -d <em>file.bz2 . </em></li> <li>Also included are reads from all 32 ospC types and subtypes (single replicate of each, uncompressed).</li> <li>Mixes of reads from ospC types are also included. They are named according to the genotypes and fractions they contain: BA.01.99_ospC_1.fq is 1% ospC type B, 99% ospC type A for example, and contains the 1st read pair of the paired FASTQ reads (the paired reads are in the file BA.01.99_ospC_2.fq).</li> </ul>
FIGURE 10. Chromaphyosemion omega, male from the strain C 89 in Description of three new species of the genus Chromaphyosemion Radda, 1971 (Cyprinodontiformes: Nothobranchiidae) from the coastal plains of Cameroon with a preliminary review of the Chromaphyosemion splendopleure complex
FIGURE 10. Chromaphyosemion omega, male from the strain C 89/35, not preserved. Photo by W. Eigelshofen
Fluorescence microscopy of Chlamydomonas reinhardtii for mCherry detection: secretion peptides strains.
<p><strong>Overview</strong></p> <p>Life-cell imaging was performed with a confocal fluorescence microscopy to observe mCherry in the secretion vacuoles. mCherry fluorescence compartmentalization was observed by a Confocal Zeiss LSM 780-NLO, using an argon laser 543 nm to excite mCherry and a spectral detector set approximately to 610-650 nm range. For chlorophyll, we used a laser at 405 nm for excitation, and spectral detector set to 680 nm region. All pictures were taken with the same system configuration and analyzed by Fiji, an ImageJ distribution software. Cells images were acquired in bundles of 0.4 μm afar photos per channel in the z-axis. </p> <p> </p> <p><strong>Files info:</strong></p> <p>Each file is the raw image obtained from fluorescent microscopy.</p> <p> </p> <p><strong>Organization</strong></p> <p>Construct_name.czi - Ex: "pAH04mCherry.czi"</p> <p>pAH04mCherry -> construct without signal peptide</p> <p>pJP22mCherry -> construct with signal peptide from arylsulfatase 1 (<em>Chlamydomonas </em><em>reinhardtii</em>)</p> <p>pJP26mCherry -> construct with signal peptide from binding protein 1 (<em>C. </em><em>reinhardtii</em>)</p> <p>pJP28mCherry -> construct with signal peptide from carbonic anhydrase 1 (<em>C. </em><em>reinhardtii</em>)</p> <p>pJP29 mCherry -> construct with signal peptide from ice-binding protein 1 (Artic <em>Chlamydomonas sp</em>)</p> <p>pJP30-35mCherry -> construct with signal peptide from in silico identified list (DOI 10.5281/zenodo.556792).</p> <p>Wildtype cc1690 -> parental strain used for transformation.</p> <p> </p> <p>For more information on the constructs, check our paper. </p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433</p> <p> </p>
Isolation and characterization of cell wall and extracellular polysaccharides from cultures of the mycoparasitic strain Tirochoderma koningiopsis
<p>The results obtained are part of the Miniatura 6 (2022/06/X/NZ9/00569) project</p>
Benchmarking datasets used in the manuscript "Strain-level metagenomic profiling using pangenome graphs with PanTax"
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Predictive Design of Ultrastretchable Electrodes with Strain-Insensitive Performance via Robotics- and Machine Learning-Integrated Workflow
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Assemblies for 'Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients'
<p>Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen <i>P. aeruginosa</i>. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.</p>
Data of "Effects of bacteria-embedded polylactic acid (PLA) capsules on fracture properties of strain hardening cementitious composite (SHCC)"
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Data set for "Reconciling High-resolution Strain Rate of Continental China from GNSS Data with the Spherical Spline Interpolation"
<p>Data set for "Reconciling High-resolution Strain Rate of Continental China from GNSS Data with the Spherical Spline Interpolation". And This database contains GNSS velocity and strain rate field data for mainland China obtained by the spherical spline method. Also, we include the sub-graph data for each graph of the manuscript "Reconciling High-resolution Strain Rate of Continental China from GNSS Data with the Spherical Spline Interpolation". We have detailed the meaning and format of each data in the "readme.txt", and a separate "readme.txt" is included in each zip.</p>
ScienceDex guides
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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.
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.