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6,383 results for “isolates”
Draft Genome Sequences of Pseudomonas sp. Strain MWU13-2924, Isolated from a Wild Cranberry Bog in Truro, MA
<p>Annotated genome of Pseudomonas sp. MWU13.2924.</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>
Parkinson's disease-related brain metabolic patterns and neurodegeneration in isolated REM sleep behavior disorder
<p><span><b>Objective</b>: To elucidate the role of Parkinson's disease (PD)-related brain metabolic patterns as a biomarker in isolated rapid-eye-movement sleep behavior disorder (iRBD) for future disease conversion.</span></p> <p><span><b>Method</b>: This is a prospective cohort study consisting of 30 iRBD patients, 25 de novo PD patients with a premorbid history of RBD, 21 long-standing PD patients on stable treatment and 24 healthy controls. iRBD group was longitudinally followed up. All participants underwent <sup>18</sup>F-Fluorodeoxyglucose (FDG) PET and were evaluated with olfaction, cognition, and the Movement disorders society-Unified PD Rating Scale (MDS-UPDRS) at baseline. From FDG-PET scans, we derived metabolic patterns from the long-standing PD group (PD-RP) and de novo PD group with RBD (dnPDRBD-RP). Subsequently, we calculated the PD-RP and dnPDRBD-RP scores in iRBD patients. We validated the metabolic patterns in each PD group and separate iRBD cohort (<i>n</i>=14).</span></p> <p><span><b>Result</b>: The two patterns significantly correlated with each other and were spatially overlapping yet distinct. The MDS-UPDRS motor scores significantly correlated with PD-RP (<i>p</i> = 0.013) but not with dnPDRBD-RP (<i>p</i> = 0.076). In contrast, dnPDRBD-RP correlated with olfaction in butanol threshold test (<i>p</i> = 0.018) in iRBD subjects, but PD-RP did not (<i>p</i> = 0.21). High dnPDRBD-RP in iRBD patients predicted future phenoconversion with all cut-off ranges from 1.5 to 3 standard deviations of the control value, whereas predictability of PD-RP was only significant in a partial range of cut-off.</span></p> <p><b>Conclusion:</b> The dnPDRBD-RP is an efficient neuroimaging biomarker that reflects prodromal features of PD and predicts phenoconversion in iRBD that can be applied individually.</p>
Distribution. Coastal SE South Africa, with isolated populations in C South Africa. in Bovidae
Distribution. Coastal SE South Africa, with isolated populations in C South Africa.
Distribution. SE Chad, W Sudan, and isolated populations in extreme N Central African Republic. in Bovidae
Distribution. SE Chad, W Sudan, and isolated populations in extreme N Central African Republic.
Distribution. Two isolated populations, in W & S Kenya and N Zimbabwe. in Molossidae
Distribution. Two isolated populations, in W & S Kenya and N Zimbabwe.
Distribution. Known only from isolated records in SW Nicaragua and WC Costa Rica. in Cricetidae
Distribution. Known only from isolated records in SW Nicaragua and WC Costa Rica.
Data from: The neuropeptide Drosulfakinin regulates social isolation-induced aggression in Drosophila
Social isolation strongly modulates behavior across the animal kingdom. We utilized the fruit fly Drosophila melanogaster to study social isolation-driven changes in animal behavior and gene expression in the brain. RNA-seq identified several head-expressed genes strongly responding to social isolation or enrichment. Of particular interest, social isolation downregulated expression of the gene encoding the neuropeptide Drosulfakinin (Dsk), the homologue of vertebrate cholecystokinin (CCK), which is critical for many mammalian social behaviors. Dsk knockdown significantly increased social isolation-induced aggression. Genetic activation or silencing of Dsk neurons each similarly increased isolation-driven aggression. Our results suggest a U-shaped dependence of social isolation-induced aggressive behavior on Dsk signaling, similar to the actions of many neuromodulators in other contexts.
Data from: Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate
[No abstract entered]
Data from: Isolation and characterization of fifteen polymorphic microsatellite loci for the citrus mealybug, Planococcus citri (Hemiptera: Pseudococcidae), and cross-amplification in two other mealybug species
[No abstract filled]
Distribution. Restricted to a few isolated localities in Western Cape Province of South Africa. in Muridae
Distribution. Restricted to a few isolated localities in Western Cape Province of South Africa.
Distribution. Recorded from two isolated regions in N & C Sulawesi, at elevations of 75-1005 m. in Muridae
Distribution. Recorded from two isolated regions in N & C Sulawesi, at elevations of 75-1005 m.
Drivers of intraspecific differentiation of the alpine cold tolerant herb Notopterygium oviforme: the roles of isolation by distance and ecological factors
<p>Determining the driver mechanisms of phenotypic and genetic divergence of species have long been the central topic in evolutionary biology. However, the relative roles of isolation by distance (IBD) and environment factors in contributing to species divergence is largely undetermined in perennial herbs in East Asia. In this study, we collected population genetic samples of a cold-tolerant perennial herb <i>Notopterygium oviforme</i> in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping-by-sequencing, microsatellite markers and ecological environment factors to determine the relative contributions of geography, climatic and soil factors on genetic, chemical and phenotypic trait divergence. The clearly genetic distinction was identified between the west Qinling (WQ) and east Qinling Mountains (EQ) geographical groups within<i> N. oviforme</i>. Interestingly, the two groups have existed the obviously niche conservatism, which might have caused the similarity of most leaf functional traits. Multiple matrix regression with randomization analysis showed that the spatial pattern of intraspecific divergence mainly resulted from effect of IBD, not isolation by environment. Meanwhile, transcriptomic expression divergence and some ecological factors have played the key roles in differentiation of intraspecific lineage. Approximate Bayesian Computation showed that both lineages have experienced the historically population expansion, and the recent range contraction. Molecular dating suggested that the intraspecific divergence was closely associated with the dramatically uplifts of the Qinling Mountains in East Asia. These results demonstrated that the geography, geological and environmental factors together shaped the cryptic intraspecific diversification and population dynamics shifts of<i> </i>perennial cold tolerant herb.</p>
Antibiotic tolerance indicative for persistence is pervasive among clinical Streptococcus pneumoniae isolates and shows strong condition dependence - dataset
<p>The dataset is linked to the article entitled 'Antibiotic tolerance indicative for persistence is pervasive among clinical <em>Streptococcus pneumoniae</em> isolates and shows strong condition dependence' with following abstract. </p> <p><em>Streptococcus pneumoniae</em> is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in <em>S. pneumoniae</em> is an emerging problem as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet, in <em>S. pneumonia</em>e little is known about antibiotic-tolerant persisters and robust experimental means are lacking. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. Here, we set out to identify and characterize persistence in <em>S. pneumoniae. </em>Specifically, we followed different strategies to overcome the self-limiting nature of<em> S. pneumoniae </em>as confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. In optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of <em>S. pneumoniae</em> clinical isolates, which assumes that a high natural diversity in persistence is widely present in <em>S. pneumoniae</em>. Collectively, this proof-of-concept significantly progresses the understanding of the importance of antibiotic persistence in<em> S. pneumoniae</em> infections which will set stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research.</p>
UNL Pseudomonas isolates
<p>Raw reads of <em>Pseudomonas </em>spp. isolates from ground turkey meat. </p>
Figure 2 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Figure 2 - Phylogenetic tree of Calonectria species in the Sphaero-Naviculate group based on maximum likelihood (ML) analysis of combined DNA dataset of tef1, his3, cmdA and tub2 gene sequences. ML and MP (maximum parsimony) bootstrap values (ML/MP) are shown above branches, with bootstrap values below 60 % marked with an *, and absent analysis values are marked with -. Isolates representing ex-type material are marked with "T", isolates highlighted in bold were sequenced in this study and novel species were covered in orange. The tree was rooted to Ca. pauciramosa (CMW 5683 and CMW 30823).
Figure 4 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Figure 4 - Calonectria montana. a–c Macroconidiophores d–f Sphaeropedunculate vesicles g–h Conidiogenous apparatus with conidiophore branches and doliiform to reniform phialides i–j Macroconidia Scale bars: a–c = 20 μm; d–j = 10 μm.
Figure 3 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Figure 3 - Calonectria lichi. a–c Macroconidiophore d–f Clavate vesicles g–i Conidiogenous apparatus with conidiophore branches and doliiform to reniform phialides j–k Macroconidia Scale bars: a–c = 50 μm; d–f = 5 μm; g–k = 10 μm.
Figure 1 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688
Figure 1 - Phylogenetic tree of Calonectria species in the Prolate group based on maximum likelihood (ML) analysis of combined DNA dataset of tef1, his3, cmdA and tub2 gene sequences. ML and MP (maximum parsimony) bootstrap values (ML/MP) are shown above branches, with bootstrap values below 60 % marked with an *, and absent analysis values are marked with -. Isolates representing ex-type material are marked with "T", isolates highlighted in bold were sequenced in this study and novel species were covered in blue. The tree was rooted to Ca. hongkongensis (CBS 114711 and CBS 114828).
Figure 2 from: Kaňuch P, Dorková M, Mikhailenko AP, Polumordvinov OA, Jarčuška B, Krištín A (2017) Isolated populations of the bush-cricket Pholidoptera frivaldszkyi (Orthoptera, Tettigoniidae) in Russia suggest a disjunct area of the species distribution. ZooKeys 665: 85-92. https://doi.org/10.3897/zookeys.665.12339
Figure 2 - Maximum-likelihood (ML) phylogenetic tree for 16 haplotypes of Pholidoptera frivaldszkyi (pf1–pf16; GenBank accession numbers KF706416–KF706428, KY554960–KY554962) with outgroup species (KC852400, KY554963–KY554966) based on a 778 bp fragment of the mtDNA COI gene. Tree topology and branch lengths of Bayesian inference were congruent with ML analysis. Nodes with significant support values are indicated (upper, ML bootstrap > 50%; lower, Bayesian posterior probability > 0.90).
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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.