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6,383 results for “isolates”
Molecular and biological characterization of an Asian-American isolate of Chikungunya Virus
<p>This is a dataset of the figures used in the development of the manuscript <strong>Molecular and biological characterization of an Asian-American isolate of Chikungunya Virus</strong></p> <p> </p>
Tree size, microhabitat diversity and landscape structure determine the value of isolated trees for bats in farmland
<p>Isolated trees are increasingly recognised as playing a vital role in supporting biodiversity in agricultural landscapes, yet their occurrence has declined substantially in recent decades. Most bats in Europe are tree-dependent species that rely on woody elements in order to persist in farmlands. However, isolated trees are rarely considered in conservation programs and landscape planning. Further investigations are therefore urgently required to identify which trees – based on both their intrinsic characteristics and their location in the landscape – are particularly important for bats. We acoustically surveyed 57 isolated trees for bats to determine the relative and interactive effects of size, tree-related microhabitat (TreM) diversity and surrounding landscape context on bat activity. Tall trees with large diameter at breast height and crown area positively influenced the activity of <em>Pipistrellus pipistrellus</em> and small Myotis bats (<em>Myotis</em> spp.) while smaller and thinner trees favoured <em>M. myotis</em> activity. The diversity of TreMs that can be used as roosts had a positive effect on (i) <em>Barbastella barbastellus</em> activity only when trees were relatively close (10% within 100 radius scale). The potential benefits of isolated trees for bats result from ecological mechanisms operating at both tree and landscape scales, underlining the crucial need for implementing a multi-scale approach in conservation programs. Maintaining the largest and most TreM-diversified trees located in the most heterogeneous agricultural landscapes will provide the greatest benefits.</p>
Transposable element annotation Rhynchosporium commune isolate UK7
<p>To obtain a consensus sequence for each TE family, RepeatModeler v. open-4.0.7 (http://www.repeatmasker.org/RepeatModeler/) was run on the <em>R. commune</em> UK7 reference genome. The classification was based on the GIRI Repbase (v. 2018) using RepeatMasker v. open-4.0.7. (Smit, Hubley, and P. 2015; Bao, Kojima, and Kohany 2015). We used WICKERsoft to finalize the classification of TE consensus sequences (Breen et al. 2010). Specifically, we used WICKERsoft to screen for copies of known consensus sequences from other fungal species with blastn filtering for sequence identity > 80% and sequence length > 80%. (Altschul et al. 1997). Then, using WICKERsoft, flanks of 10000 bp were added and visually inspected for sequence similarity and terminal repeats with dot plots. Subsequent multiple sequence alignments were performed with 10-15 sequences using ClustalW (Thompson, Higgins, and Gibson 1994). Alignment boundaries were visually inspected in WICKERsoft and trimmed if necessary. Using WICKERsoft, consensus sequences were classified according to the presence and type of terminal repeats, as well as homology of the encoded proteins based on blastx against the NCBI protein database. Consensus sequences were named according to the three-letter classification system (Wicker et al. 2007). The reference genome was annotated with the curated consensus sequences using RepeatMasker v. open-4.0.7 with a cut-off value of 250 (Smit, Hubley, and P. 2015). Simple repeats, low complexity regions and annotated elements shorter than 100 bp were filtered out and adjacent identical TEs overlapping by more than 100 bp were merged as belonging to the same TE family. Different TE families overlapping by more than 100 bp were considered as nested insertions and were renamed accordingly. Identical elements separated by less than 200 bp are indicative of interrupted elements and were grouped into a single element. TEs overlapping genes were recovered using the bedtools v. 2.27.1 suite and the “overlap” function (Quinlan and Hall 2010).</p>
NMR data of Lanostane Type Triterpenoids isolated from Leplaea mayombensis
<p>This folder contains NMR datasets of new compounds described in the publication<em> </em>entitled: <strong>Antiplasmodial and Cytotoxic Activity of Lanostane Type Triterpenoids isolated from <em>Leplaea mayombensis</em></strong></p> <p> </p> <p>NMR processing : Topspin 4.1.13</p> <p> </p>
Novel Chromobacterium sp. isolated from mosquitos in Burkina Faso, West Africa
<p>Nov. <em>Chrombacterium</em> sp. isolated in wild caught mosquitos in Burkina Faso, West Africa </p>
Fig. 1 in The Effect Of Temperature On The Development Of Adult Generations Of Entomopathogenic Nematode Steinernema Arenarium Isolate Ch
Fig. 1. Scatterplots of canonical scores for females of both generations. Legend: dots — 18 °С; squares — 22 °С; rhombs — 28 °С. Ranges of groups are ellipsed with coefficient 0.95.
Fig. 2 in The Effect Of Temperature On The Development Of Adult Generations Of Entomopathogenic Nematode Steinernema Arenarium Isolate Ch
Fig. 2. Scatterplots of canonical scores for males of both generations. Legend: dots — 18 °С; squares — 22 °С; rhombs — 28 °С. Ranges of groups are ellipsed with coefficient 0.95.
Extracellular Vesicles Analysis in the COVID-19 Era: Insights on Serum Inactivation Protocols towards Downstream Isolation and Analysis
<p>Representative AFM images of the samples analyzed in the relative manuscript. Raw data just imported from the AFM multimode native format to the Gwyddion Open source data analysis software</p>
Meta-omics-aided isolation of elusive anaerobic arsenic-methylating soil bacteria
<p>Data pertaining to the manuscript "<strong>Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium"</strong> by Karen Viacava, Jiangtao, Qiao, Andrew Janowczyk, Suresh Poudel, Nicolas Jacquemin, Karin Lederballe Meibom, Him K. Shrestha, Matthew C. Reid, Robert L. Hettich and Rizlan Bernier-Latmani published in ISME journal.</p>
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.
<p>Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of the antibiotic resistant phenotype. To that end, we leveraged fully resolved <em>Enterococcus faecium</em> and <em>Enterococcus faecalis</em> genomes of isolates collected over five days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of <em>E. faecium</em> isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in <em>E. faecalis</em> isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in <em>liaSR</em> genes and a putative composite transposon in<em> E. faecium</em>, offering a new paradigm for the study of daptomycin resistance and novel insights into the dissemination of daptomycin resistance. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.</p>
Alterations of antimicrobial resistance genes in the clinical multi-drug resistance Acinetobacter baumannii isolates in Vietnam
<p><strong>FIGURE 1 </strong>List of antibiotic resistance gene expression.</p> <p><strong>TABLE 1 </strong>Primers used in this study.</p> <p><strong>TABLE 2 </strong>Clinical characteristics of 30 patients with <em>A. baumannii </em>isolates.</p> <p><strong>TABLE 3 </strong>Antimicrobial resistance values of <em>A. baumannii</em> isolated during 2017 to 2019 year in the Military Hospital 103.</p> <p><strong>TABLE 4 </strong>Relationship between genotype and phenotype antimicrobial resistance of isolates in this study.</p> <p><strong>TABLE 5 </strong>List of altered antibiotic resistance genes expression in isolates of <em>A. baumannii</em> (up or down two-fold changes of related genes compare with <em>16S rRNA</em> gene).</p> <p><strong>TABLE 6 </strong>The multiple antimicrobial resistance gene profile of 30 <em>A. baumannii</em> isolates.</p> <p> </p>
An isolated mass gap black hole or neutron star detected with astrometric microlensing
<p>This repository contains data, models, and simulations associated with the ApJ Letter "An isolated mass gap black hole or neutron star detected with astrometric microlensing" and its corresponding Supplement.</p>
Scanning electron microscope images of Dunaliela tertiolecta and Phaeodactylum tricornutum cultures and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media
<p>Scanning electron microscope images of cultures of microalgae<em> Dunaliela</em><em> </em><em>tertiolecta</em><em> </em>and <em>Phaeodactylum</em><em> </em><em>tricornutum</em><em> </em>and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and Anna Romolo, University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics.</p> <p> </p> <p> </p>
Weekly Standardized Counts of Influenza Positive Isolates in 4 Region in China Mainland
<p><strong>The data include weekly standardized counts of influenza positive isolates in 4 region in China mainland that covers 30 provinces.More details about the method of standardization and division of regions can be seen in "Characterization of influenza seasonality in China, 2010-2018: implications for seasonal influenza vaccination timing".</strong></p>
Genome and annotation files for Blumeria graminis f. sp. tritici isolate ISR_7 (genome assembly: Bgt_ISR7_genome_v1_4)
<p>Genome and annotation files for Blumeria graminis f. sp. tritici isolate ISR_7 (genome assembly: Bgt_ISR7_genome_v1_4)</p>
Isolated Ballistic Non-Abelian Interface Channel
<p>Dataset for B. Dutta et al., "Isolated Ballistic Non-Abelian Interface Channel".</p> <p>The following datafiles are used for the figures in main text and supplementary materials.</p>
A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities
<p>This file contains the data that was used in the paper titled "A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities" which will be published in Frontiers of Pharmacology.</p>
The Supplementary Material for the article entitled "Comparative analysis of global transcriptomes in nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after infecting human intestinal epithelium in vitro"
<p>The Supplementary Material (Additional files 1-5, including Table S1-S4 and Figure S1) for this article.</p> <p> </p> <p><strong>Table S1.</strong> Upregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S2.</strong> Downregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S3. </strong>The enriched GO terms in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S4. </strong>The enriched KEGG pathways in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Figure S1. </strong>The enriched GO terms and KEGG pathways in Group B relative to Group A. Bar charts show the enriched GO terms (A) and the enriched KEGG pathways (B) by significance power. Color of bars indicate power of significance and length in x axes of bar indicate number of annotated genes in the particular term of pathway. Cnetplots show the relationship between GO term (C) and KEGG pathways (D). Dot size representing GO terms and KEGG pathways indicates number of significantly changed and its annotated genes. The GO terms or KEGG pathways connected through their common and annotated genes. </p>
Genome of the isolates: Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
<p>The draft genome of the isolates in Mouse Intestinal Bacteria Collection (miBC)</p> <p> </p> <p>Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. Due to host-specific features of the gut microbiota, it is sound to establish collections of isolates from single host species. Hence, this project established a collection of bacterial strains isolated from the intestine of mice.</p> <p>The original version of the collection published in 2016 (Lagkouvardos, et. al. 2016.<em> Nat. Microbiol.</em>). was doubled by the addition of 112 strains, representing a total of 141 species across 6 phyla and 35 families for the entire collection. As we aimed to create a well-curated resource, all bacterial species within miBC have been taxonomically described and are publicly available.</p> <p> </p>
Text-fig. 12. Paramblypterus cf. rohani. Arrows indicate directio cranialis. a, b: photograph and drawing of four ridge scales in front of the dorsal fin base, locality Otovice "Chmelnice", P 80178, scale bars 5 mm; c: scale rows from the area between the pectoral and pelvic fins, outer surfaces of the scales bear fine ridges terminating as denticles on the posterior edge of the scales, locality Otovice "Chmelnice", NM-M 4916, scale bar 5 mm; d: isolated scale, from anterior area of the lateral side of the body, with denticulated posterior edge, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; e: isolated scale from the pelvic area of the body, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; f, g: drawing and photograph of the postcleithrum and the scales behind the pectoral girdle (the scales bear conspicuous ridges on their outer surface; well preserved large postcleithrum is without ridges.), locality Otovice "Chmelnice", NM-M 4915, scale bars 5 mm. Abbreviations: Cl – cleithrum, Pcl – postcleithrum, Scl – supracleithrum. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 12. Paramblypterus cf. rohani. Arrows indicate directio cranialis. a, b: photograph and drawing of four ridge scales in front of the dorsal fin base, locality Otovice "Chmelnice", P 80178, scale bars 5 mm; c: scale rows from the area between the pectoral and pelvic fins, outer surfaces of the scales bear fine ridges terminating as denticles on the posterior edge of the scales, locality Otovice "Chmelnice", NM-M 4916, scale bar 5 mm; d: isolated scale, from anterior area of the lateral side of the body, with denticulated posterior edge, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; e: isolated scale from the pelvic area of the body, locality Otovice "Chmelnice", P 30945, scale bar 2 mm; f, g: drawing and photograph of the postcleithrum and the scales behind the pectoral girdle (the scales bear conspicuous ridges on their outer surface; well preserved large postcleithrum is without ridges.), locality Otovice "Chmelnice", NM-M 4915, scale bars 5 mm. Abbreviations: Cl – cleithrum, Pcl – postcleithrum, Scl – supracleithrum.
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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.