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6,383 results for “isolates”
Data from: Genetic and phenotypic divergence in an island bird: isolation by distance, by colonisation or by adaptation?
Discerning the relative roles of adaptive and non-adaptive processes in generating differences among populations and species, as well as how these processes interact, are fundamental aims in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonisation history and founder effects (isolation by colonisation) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northwards colonisation of this species ca 8,500 years ago resulted in genetic bottlenecks in the colonised archipelagos. We then show that high levels of genetic structure exist across archipelagos, and that these are consistent with a pattern of isolation by colonisation, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales, and suggest that they may play an important role in the early stages of speciation.
Coyote Creek Isolated Pool Habitat Data
<p>Data collected in 2015/2016 In Coyote Creek (Santa Clara County). Part of a larger ongoing research project. Uploaded for use in a class project for Reproducible and Collaborative Data Science, part of the Data Science for the 21st Century program.</p>
Rapid phagosome isolation enables unbiased multiomic analysis of human microglia phagosomes 3
<p>Metabolomic data from phagosomes, controls and whole cell fractions of human iPSC-derived microglia in monoculture.</p>
Data from: Phenotypic antimicrobial resistance in Staphylococcus sp. and Enterococcus sp. isolated from surface water – a preliminary report
<p><span>Water as a vehicle of antimicrobial resistance (AMR) is a well-known phenomenon. Therefore, One Health inspired surveillance campaign to detect circulation of antimicrobial resistance through the ecosystem are very often based on investigation of water samples. Bacteria belonging to the genera <em>Staphylococcus</em> and <em>Enterococcus</em> are good models in One Health research because of their ubiquitous occurrence and effortless isolation techniques. In this study, we aimed to compare different types of water sources as potential spreaders of AMR staphylococci and enterococci in the ecosystem. For this reason, we took water samples from the Drava River and small waterholes in a forest area. We hypothesised that rivers could collect diverse bacteria and resistance from the catchment area, while forest waterholes gather bacterial contamination from the local wildlife, thus a less diverse resistant bacterial community characterise them. From 22 and 10 water samples, collected from waterholes and the Drava River active floodplain, we isolated 21 and 13 bacterial strains, respectively. The bacterial community of the river proved more diverse, while waterhole samples contained resistant bacteria to more antimicrobials. In waterhole samples, we detected two methicillin resistant coagulase negative Staphylococcus strains. The most conspicuous difference between the two habitats was the predominance of multidrug resistant <em>S. sciuri</em> in the forest waterholes. We could conclude that water could be a good indicator of AMR contamination of the ecosystem, and large-scale sampling could reveal the exact epidemiological role of different water habitats.</span></p>
Hybrid genome assemblies for 49 natural isolates of E.coli.
<p>Hybrid genome assemblies for 49 natural isolates of <em>E.coli. </em></p> <p>Assemblies were generated using Illumina and Oxford Nanopore long read data and each of the five assemblers, Canu, Flye, Raven, Redbean and Unicycler. </p>
Figure 2 from: Fadhilah QG, Santoso I, Maryanto AE, Abdullah S, Yasman Y (2021) Evaluation of the antifungal activity of marine actinomycetes isolates against the phytopathogenic fungi Colletotrichum siamense KA: A preliminary study for new antifungal compound discovery. Pharmacia 68(4): 837-843. https://doi.org/10.3897/pharmacia.68.e72817
Figure 2 Graph of the antibiosis assay of the three marine actinomycetes isolates.
Non-freely available datasets for the following work: "Comparison of consumption data and phenotypical antimicro-bial resistance in E. coli isolates of human urinary samples and of weaning and fattening pigs from surveillance and monitor-ing systems in Germany."
<p>Human and animal databases used for the creation of the work "Comparison of consumption data and phenotypical antimicrobial resistance in E. coli isolates of human urinary samples and of weaning and fattening pigs from surveillance and monitoring systems in Germany."</p>
Phylogenetic characterization of a microsporidium (Nosema sp.HA) isolated from the mulberry pest, Hemerophila atrilineata
<p>The research involved study of Lentil a nutritious and affordable historical plant. The research question was can the gene be classified according to the lentil and its relatives. The method involved using either phylogenetic or physiological characteristics of mesophilic bacteria isolated from a field-scale sludge composter were determined by 16S rDNA and phenotype analysis. The research used 34 mesophilic isolates of 5 (15%), 16 (47%) and 3 (9%) displayed amylase, protease activity. The result showed the binding proteins were stored in multigenes. The development was a resistance to environmental conditions. It concluded the information was known regarding microbial inhabitants of the ecosystem. In the study the 16S-DGGE approach estimated bacterial species and showed changes in the environment. </p>
Data from: Toxic diffuse isolated cerebellar edema from over-the-counter health supplements
[No abstract entered]
Fig. 1 in PREVALENCE OF NOSEMA CERANAE (MICROSPORIDIA) IN THE APIS MELLIFERA MELLIFERA BEE COLONIES FROM LONG TIME ISOLATED APIARIES OF SIBERIA
Fig. 1. The map of localization of the Yenisei population and studied apiaries (dots 1–6)
Isolation Creation XI: Travel Souvenirs
Creativity Challenge during the Covid-19 pandemic: 3D museum of random items found around the house. This (modern reconstruction) Phoenician glass vessel was gifted to me in 2018 by a coworker when we were both working as archaeological illustrators in Israel. I sometimes use it to practice drawing, while I wait for the time when we can get back in the field, see more beautiful places, and study their material culture. Source: Objaverse 1.0 / Sketchfab
Datasets for paper "Global biochemical profiling of fast-growing Antarctic bacteria isolated from meltwater ponds by high-throughput FTIR spectroscopy"
<p><span>Fourier transform infrared (FTIR) spectroscopy is a biophysical techniq</span><span>u<span>e used for non-destructive biochemical profiling of biological samples. It can provide comprehensive information about the total cellular biochemical profile of microbial cells. In this study, FTIR spectroscopy was used to perform biochemical characterization of twenty-nine bacterial strains isolated from the Antarctic meltwater ponds. The bacteria were grown on two forms of brain heart infusion (BHI) medium: agar at six different temperatures </span>(4, 10, 18, 25, 30, and 37 °C) and on broth at 18 °C. Multivariate data analysis approaches such as principal component analysis (PCA) and correlation analysis were used to study the difference in biochemical profiles induced by the cultivation conditions.</span> <span>The observed results indicated a strong correlation between FTIR spectra and the phylogenetic relationships among the studied bacteria. The most accurate taxonomy-aligned clustering was achieved with bacteria cultivated on agar</span><span>. Cultivation on two forms of BHI medium provided biochemically different bacterial biomass. The impact of temperature on the total cellular biochemical profile of the studied bacteria was </span><span>species-specific</span><span>, however, similarly for all bacteria, lipid spectral region was the least affected while polysaccharide region was the most affected by different temperatures. <span>T</span>he biggest temperature-triggered changes of the cell chemistry were detected for bacteria with a wide temperature tolerance such <em><span>Pseudomonas lundensis </span></em><span>strains<em> </em>and<em> Acinetobacter lwoffii </em>BIM B-1558. </span></span></p>
Gut microbiome strain-sharing within isolated village social networks
Open the record for dataset details and reuse information.
Isolation of 6-chlorodamirone A and 6-bromodamirone A from Latrunculia sp.
<p>NMR data pertaining to the isolation of 6-chlorodamirone A and 6-bromodamirone A from Latrunculia sp.</p>
Dataset related to the article "Isolated Valve Amyloid Deposition in Aortic Stenosis: Potential Clinical and Pathophysiological Relevance"
<p>This record contains raw data related to the article "Isolated Valve Amyloid Deposition in Aortic Stenosis: Potential Clinical and Pathophysiological Relevance"</p> <p>Abstract: Amyloid deposition within stenotic aortic valves (AVs) also appears frequent in the absence of cardiac amyloidosis, but its clinical and pathophysiological relevance has not been investigated. We will elucidate the rate of isolated AV amyloid deposition and its potential clinical and pathophysiological significance in aortic stenosis (AS). In 130 patients without systemic and/or cardiac amyloidosis, we collected the explanted AVs during cardiac surgery: 57 patients with calcific AS<br>and 73 patients with AV insufficiency (41 with AV sclerosis and 32 without, who were used as controls). Amyloid deposition was found in 21 AS valves (37%), 4 sclerotic AVs (10%), and none of the controls. Patients with and without isolated AV amyloid deposition had similar clinical and echocardiographic characteristics and survival rates. Isolated AV amyloid deposition was associated with higher degrees of AV fibrosis (p = 0.0082) and calcification (p < 0.0001). Immunohistochemistry analysis suggested serum amyloid A1 (SAA1), in addition to transthyretin (TTR), as the protein possibly involved in AV amyloid deposition. Circulating SAA1 levels were within the normal range<br>in all groups, and no difference was observed in AS patients with and without AV amyloid deposition. In vitro, AV interstitial cells (VICs) were stimulated with interleukin (IL)-1β which induced increased SAA1-mRNA both in the control VICs (+6.4 ± 0.5, p = 0.02) and the AS VICs (+7.6 ± 0.5, p = 0.008). In conclusion, isolated AV amyloid deposition is frequent in the context of AS, but it does not appear to have potential clinical relevance. Conversely, amyloid deposition within AV leaflets, probably promoted by local inflammation, could play a role in AS pathophysiology.</p>
Figure 1 in EVALUATION OF THE EFFECTIVENESS OF USING A UNIVERSAL METHOD FOR ISOLATING GENOMIC dsDNA BY SALTING OUT TECHNIQUE ACCORDING TO THE S.M. ALJANABI AND I. MARTINEZ PROTOCOL FOR YEAST SACCHAROMYCES CEREVISIAE
Figure 1. UVVis Spectrophotometry, scan profile of extracted Saccharomyces cerevisiae dsDNA.
Figures 1-4 from: Jordal BH (2018) The smallest known species of Afrotropical Scolytoplatypus Schaufuss (Curculionidae, Scolytinae) – with unique features and an isolated phylogenetic position. ZooKeys 749: 125-130. https://doi.org/10.3897/zookeys.749.24199
Figures 1-4 Habitus, head and elytral declivity of Scolytoplatypus unipilus sp. n.
Proteome annotation of Phytophthora oleae, isolate VK10A, causative agent of rot of olive drupes.
<p>The proteome of Phytophthora oleae, isolate VK10A, causative agent of rot of olive drupes was predicted by using the genomic sequence (AUGUSTUS/GeneMark-ES) as described before (<a href="https://doi.org/10.5281/zenodo.11092245">https://doi.org/10.5281/zenodo.11092245</a>) and <em>de novo</em> mRNA assembly carried out by Trinity and GeneMark. Here, we present the proteome annotation of both genomic CDS and ORF, these latter derived from sense and antisense orientation of <em>de novo</em> mRNA. </p>
Four genome assemblies of legacy Xanthomonas oryzae pv. oryzae isolated from Indian rice fields
<p>This dataset contains sequencing data for <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> strain M24, including Illumina reads (SRR30576374) and PacBio HiFi reads (SRR30576370) from a genome announcement titled, "Four genome assemblies of legacy <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> isolated from Indian rice fields."</p>
Data from: Ecological speciation in sympatric palms: 2. pre- and post-zygotic isolation
We evaluated reproductive isolation in two species of palms (Howea) that have evolved sympatrically on Lord Howe Island (LHI, Australia). We estimated the strength of some pre- and post-zygotic mechanisms in maintaining current species boundaries. We found that flowering time displacement between species is consistent across in and ex situ common gardens and is thus partly genetically determined. On LHI, pre-zygotic isolation due solely to flowering displacement was 97% for H. belmoreana and 80% for H. forsteriana; this asymmetry results from H. forsteriana flowering earlier than H. belmoreana and being protandrous. As expected, only a few hybrids (here confirmed by genotyping) at both juvenile and adult stages could be detected in two sites on LHI, in which the two species grow intermingled (The Far Flats) or adjacently (Transit Hill). Yet, the distribution of hybrids was different between sites. At Transit Hill we found no hybrid adult trees, but 13.5% of younger palms examined there were of late hybrid classes. In contrast we found four hybrid adult trees, mostly of late hybrid classes, and only one juvenile F1 hybrid in the Far Flats. This pattern indicates that selection acts against hybrids between the juvenile and adult stages. An in situ reciprocal seed transplant between volcanic and calcareous soils also shows that early fitness components (up to 36 months) were affected by species and soil. These results are indicative of divergent selection in reproductive isolation, although it does not solely explain the current distribution of the two species on LHI.
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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.