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6,383 results for “isolates”
Recovery from social isolation requires dopamine in males, but not the autism-related gene nlg3 in either sex
<p>Social isolation causes profound changes in social behaviour in a variety of species. However, the genetic and molecular mechanisms modulating behavioural responses to social isolation and social recovery remain to be elucidated. Here, we quantified the behavioural response of vinegar flies to social isolation using two distinct protocols (social space preference and spontaneous tendencies to form groups). We found that social isolation increased social space and reduced sociability. These effects of social isolation were reversible and could be reduced after 3 days of group housing. Flies with a loss of function of <em>neuroligin3</em> (ortholog of autism-related <em>neuroligin</em> genes) with known increased social space in a socially enriched environment, were still able to recover from social isolation. We also show that dopamine is needed for a response to social isolation and recovery in males but not in females. Furthermore, only in males, dopamine levels are reduced after isolation and are not recovered after group housing. Finally, in socially enriched flies mutant for <em>neuroligin3</em>, dopamine levels are reduced in males, but not in females. We propose a model to explain how dopamine and <em>neuroligin3</em> are involved in the behavioural response to social isolation and its recovery in a dynamic and sex-specific manner.</p>
Foliar endophyte diversity in eastern Asia-eastern North America disjunct tree species – Influences of host identity, environment, phylogeny, and geographic isolation
<p><span>The well-known eastern Asia (EA) and eastern North America (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or clades isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these disjunct lineages. In this study, we compared foliar endophytes (including both fungi and bacteria) in 17 EA-ENA disjunct species pairs from genera representing conifers and major clades of angiosperms, as well as 23 species of </span><em>Cornus</em> from the US and China. We sequenced the ITS of fungi and 16S rDNA of bacteria to understand the composition of the endophyte community and gain insights into the relative roles of geographic isolation, host identity, phylogeny, and environment in shaping endophytic diversity patterns. We detected a much richer fungal than bacterial community in leaves of all species. Beta diversity varied greatly among individuals within species, between species, among genera, and among three natural environmental conditions. Based on a principal coordinates analysis, we found no close clustering of endophyte communities in samples from the same host plant species, from the same genus, or from the same geographic origin (i.e. EA or ENA) (when plants were grown in the same common garden), but we did detect clustering of samples from plants grown in the same environment (i.e., same geographic location). We observed separation of microbes in plant samples of the same species grown in different locations/environments. However, pooled samples across all species from the common garden with the same geographic origin (EA vs. ENA) showed a moderate level of dissimilarity in fungal endophytes between EA and ENA. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance was detected among the disjunct genera but not among species of <em>Cornus</em>. However, significant correlation between order, family, and genera of endophytes and phylogenetic distance of Cornus species was observed. We also found no significant differences in Foliar Endophytic Fungal (FEF) communities between counterparts of disjunct species pairs in EA and ENA in most genera except in <em>Liriodendron</em> and <em>Cornus</em>, although the beta diversity within genera is high. Our results suggest important roles of host identity and environment (geographic locations), and a likely minor role of phylogenetic divergence and biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera, as well as in <em>Cornus</em>. The results further suggest that the sister taxa in EA and ENA are likely different in their foliar endophyte composition when growing in their native habitats due to differences in geographic locations and local environments, which is potentially a factor driving allopatric divergence of species functional features. This hypothesis can be tested by analysis of samples from native habitats.</p>
Speciation across biomes: rapid diversification with reproductive isolation in the Australian delicate mice
<p><span>Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, is a model system for reconstructing the impact of past and present environments on diversification. Here we use genomic-scale data (1310 exons and whole mitogenomes from n = 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: <em>Pseudomys</em>), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for </span><span>introgression between cryptic lineages within <em>Pseudomys</em> <em>delicatulus</em> sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist <em>P. hermannsburgensis</em>, and contraction in the semi-arid <em>P. bolami</em>. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily </span><span>young and widespread clade has </span><span>been</span><span> driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements. </span></p>
Using protein isolation on elasmobranch blood plasma for ecological research and stable isotope analysis
<p>Stable isotope analysis is a useful tool for studying the ecology of elasmobranchs. Analysis of elasmobranch blood plasma provides insight into an individual's ecology on a small temporal scale. However, plasma is a systemic transport vessel containing many dissolved constituents in variable amounts, which may bias analyses and ecological conclusions based on that data.</p> <p>In this study, we develop a new method of protein precipitation using ethanol and acetonitrile to isolate the protein fraction of plasma from Sandbar Sharks, and examine its effects on carbon and nitrogen stable isotope values. We also tested these solvent precipitations on bovine serum albumin as a control to assess the introduction of exogenous sources of C and N.</p> <p>Protein isolation resulted in a significant decrease in δ<sup>13</sup>C values and a significant increase in C:N compared to untreated plasma. Isolated proteins were not significantly different in δ<sup>15</sup>N value compared to untreated plasma. We observed no change in isotope composition in bovine serum albumin samples, indicating protein precipitation does not itself affect isotope analysis.</p> <p>These results suggest that the preparation of blood plasma is necessary for stable isotope analysis, to eliminate the biasing effects of other dissolved compounds. We find that solvent precipitation is an effective method of isolating proteins for stable isotope studies.</p>
Figure 3 in Isolation and characterization of 3D chitin from a mite species Trachytes pauperior (Parasitiformes: Uropodina)
Figure 3. Purified chitin of T. pauperior of light microscopy modus (0-60X).
Figure 1 in Isolation and characterization of 3D chitin from a mite species Trachytes pauperior (Parasitiformes: Uropodina)
Figure 1. FTIR spectrum of the 3D chitin isolate from T. pauperior.
Figure 2 in Isolation and characterization of 3D chitin from a mite species Trachytes pauperior (Parasitiformes: Uropodina)
Figure 2. SEM images of chitin isolates from T. pauperior in 3D.
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
<p>Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (<em>Bombus affinis</em>) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of <em>B. affinis</em> from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for <em>B. affinis</em> compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where <em>B. affinis</em> is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.</p>
Data from: Preparation of isolated guard cells, containing cell walls, from Vicia faba
<p>Stomatal movement, initiated by specialized epidermal cells known as guard cells (GCs), plays a pivotal role in plant gas exchange and water use efficiency. Despite protocols existing for isolating GCs through proplasting for carrying out biochemical, physiological, and molecular studies, protocols for isolating GCs with their cell walls still intact have been lacking in the literature. In this paper, we introduce a method for the isolation of complete GCs from <em>Vicia faba </em>and show their membrane to remain impermeable through propidium iodide staining. This methodology enables further in-depth analyses into the cell wall composition of GCs, facilitating our understanding of structure-function relationship governing reversible actuation within cells.</p>
Cosmic Cousins: Identification of a Subpopulation of Binary Black Holes Consistent with Isolated Binary Evolution
<p>The accompanying data release for the analyses presented in "Cosmic Cousins: Identification of a Subpopulation of Binary Black Holes Consistent with Isolated Binary Evolution". See the github paper repository at https://github.com/jaxengodfrey/CosmicCousins and the arXiv release of the paper at: https://arxiv.org/abs/2304.01288</p>
Data: A Marine Group A isolate relies on other growing bacteria for cell wall formation
<div> <p>Raw data underlying Microscopic pictures for the paper "A Marine Group A isolate relies on other growing bacteria for cell wall formation". Data is subdivided by each figure in the paper. </p> </div>
Evaluation of the immunostimulant effect of microvesicles of Lactobacillus acidophilus isolated from wild Rattus norvegicus.
<p><span>Lactic acid bacteria are components of the microbiota of the gastrointestinal tract in both humans and animals and are widely used as probiotics. The bacterial strain <em>Lactobacillus sp</em>. is the most related to probiotic activity and released<span> </span>membrane microvesicles (MVs). Some of their primary functions are to carry and transmit antigens to the host tissues and modulate the host defense responses. In the present study, <em>Lactobacillus acidophilus</em> was isolated from the ileum of free-living <em>Rattus norvegicus</em> to evaluate the immunostimulant effect of their MVs in two biological models. MVs from <em>L. acidophilus</em> were characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, electron microscopy</span><span>, and nanoparticle tracking analysis. The immunostimulant effect of</span><span> MVs</span><span> from </span><em><span>L. acidophilus</span></em><span> on ovine abomasal explants, previously stimulated with 30 µg/1h of MVs and subsequently challenged with third-stage larvae (L3) of <em>Haemonchus contortus</em>, was probed, demonstrating a decrease in the percentage of larvae association, and favoring the migration of inflammatory cells to the infection site. In contrast, cells line of the RAW 264.7 were stimulated by 10 µg/3h of MVs from <em>L. acidophilus</em> to evaluate their activation through the expression of transcripts coding for IL-1β and TNF-α. In both cases, the immunostimulatory effect</span><span>s of </span><span>MVs<em> </em><span>from <em>L. acidophilus</em></span> isolated from free-living <em>R. norvegicus</em> were verified, demonstrating that these structures are capable of immunostimulated the </span><span>evaluated biological models and </span><span>could carried important antigen that can be considerate in a formulation to promote the intestinal health in livestock production.<span> </span>The present study is the first report of MVs secreted by <em>L. acidophilus</em> isolated from free-living <em>R. norvegicus </em>caring that this rodent is resistant to many bacterial pathogens that normally affect the gastrointestinal tract of other mammals.</span></p> <p><span>In the atachment file we present the data obtained of the porcentage of asocciation and porcentage of mortality of L3 stage larvae from <em>H. contort</em></span><span><em>u</em>s in abomasal tissue stimulated with microvesicles from <em>L. acidophilus</em>. In the other hand the expression of IL-1</span><span>β</span><span> and TNF</span><span>α. </span><span> mRNA from RAW 264.7 cells stimulated with microvesicles from <em>L. acidophilus.</em> </span></p>
PfRH5-induced human monoclonal antibodies show broadly neutralizing activity in P. falciparum clinical isolates
<p>Vaccines to the <em>Plasmodium falciparum </em>reticulocyte binding-like protein homolog 5 (PfRH5) target the blood stage of the parasite's life cycle. PfRH5 has the potential to trigger the production of strain-transcendent antibodies and has proven its efficacy both in pre-clinical and early clinical studies. Vaccine-induced monoclonal antibodies (mAbs) to PfRH5 showed promising outcomes in cultured <em>P. falciparum </em>strains from distinct geographic areas. Here, we assessed the functional impact of vaccine-induced mAbs to PfRH5 on the genetically more complex <em>P. falciparum </em>clinical isolates. We used mAbs isolated from single-cell sorted B-cells of volunteers enrolled in the phase 1a (NCT02181088) clinical trial of the viral-vectored PfRH5 vaccine and used ex-vivo growth inhibition assays (GIA) to assess their efficacy in <em>P. falciparum </em>clinical isolates. Next-generation sequencing (NGS) was used to assess the breadth of genetic diversity in <em>P. falciparum </em>clinical isolates and to infer the genotype/phenotype relationship involved in antibody susceptibility. We showed a dose-dependent inhibition of clinical isolates with three main GIA groups, high, medium, and low. Except for one isolate, our data shows no significant differences in antibody GIA profile between the <em>P. falciparum </em>clinical isolates and the 3D7 reference strain, which harbours the vaccine allele. We observed an additive relationship, where the combination of GIA-low and GIA-medium antibodies resulted in increased GIA activities, having important implications for the contribution of specific monoclonal antibodies in polyclonal IgG responses. While our NGS analysis showed the occurrence of novel mutations in the <em>pfrh5 </em>gene, these mutations were predicted to have little or no functional impact on the antigen's structure or recognition by known mAbs. Our present findings complement earlier reports on the strain transcendent potential of mAbs to PfRH5 and constitute, to our knowledge, the first report on the susceptibility of <em>P. falciparum </em>clinical isolates from natural infections to vaccine-induced mAbs to PfRH5.</p>
Draft genomes of 972 carbapenem-resistant Pseudomonas aeruginosa isolates (shovill assemblies of Reyes et al 2023 dataset raw reads)
<p>This dataset contains shovill assemblies of raw reads released under NCBI BioProject PRJNA824880 generated in Reyes J et al (The Lancet Microbe. Volume 4 Issue 3 Pages e159-e170 (March 2023); DOI: 10.1016/S2666-5247(22)00329-9)</p> <p> </p>
Threatened endemic arthropods and vertebrates partition their diets with non-native ants in an isolated island ecosystem - binary diet dataset and stats code
<p>The dietary dataset associated to <strong>"Threatened endemic arthropods and vertebrates partition their diets with non-native ants in an isolated island ecosystem"</strong>. We also provide the novel code (in R) used for the statistical analyses.</p>
Compatible interaction experiment with Aegilops cylindrica infected with Zymoseptoria tritici isolate Zt 469 - CSLM images and videos
<p>Microscopic images and videos from convocal laser scanning microscopy (CLSM) analysis using maximum projections of confocal z-stacks. Cell nuclei and plant tissue are visible in purple, fungal hyphae in green.</p>
Habitat fragmentation induces rapid phenotypic divergence of migratory and isolated sticklebacks
<p>The adaptive capacity of many organisms is seriously challenged by human-imposed environmental change, which currently happens at unprecedented rates and magnitudes. For migratory fish, habitat fragmentation is a major challenge that can compromise their survival and reproduction. Therefore, it is important to study if fish populations can adapt to such modifications of their habitat. Here, we study whether originally anadromous three-spined stickleback populations (Gasterosteus aculeatus; 'migrants') changed in behavior and morphology in response to human-induced isolation. We made use of a natural field-experiment, where the construction of pumping stations and sluices in the 1970s unintendedly created replicates of land-locked stickleback populations ('resident') in the Netherlands. For two years, we systematically tested populations of residents and migrants for differences in morphology and behavioral traits (activity, aggressiveness, exploration, boldness and shoaling) in lab-based assays. We detected differences between migrant and resident populations in virtually all phenotypic traits studied: compared to the ancestral migrants, residents were smaller in size, had fewer and smaller plates and were significantly more active, aggressive, exploratory and bolder and shoaled less. Despite large ecological differences between 2018 and 2019, results were largely consistent across the two years. Our study shows that human-induced environmental change has led to the rapid and consistent morphological and behavioral divergence of stickleback populations in about 50 generations. Such changes may be adaptive but this remains to be tested.</p>
Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes
<p>The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verify the existence of the two coexisting demes using a 96-SNP fluidigm array. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity is higher in Deme I than in Deme II. Furthermore, strong genetic divergence is observed with genome-wide <i>F</i><sub>ST</sub>≈0.2. Comparing with similar data from other lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in Deme II vs. Deme I, indicating different degree of isolation. Finally, we located two gene-copies for LDH-A<i> </i>and find divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.</p>
Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in plantae
<p>Transcription profiles were generated from the <em>Rhynchosporium commune</em> isolate UK7. RNA-seq experiments were conducted <em>in plantae</em> on the barley cultivar Beatrix (Viskosa 9 Pasadena, Saaten Union, breeders’ Reference NS01/2449). Leaves were collected at 9 and at 13 days post infection (dpi). All experiments were conducted in triplicates. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.</p>
Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in vitro
<p>Transcription profiles were generated from the <em>Rhynchosporium commune</em> isolate UK7. Cultures were grown either on Luria-Bertani (LBA) or Potato Dextrose Broth (PDB) media. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. Experiments were conducted in triplicates. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.</p>
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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.