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6,383 results for “isolates”
Structural variants of 20 wild isolates of Caenorhabditis elegans
<p>20 VCFs of 20 <em>Caenorhabditis elegans</em> wild isolates against VC2010 reference assembly.</p> <p>Reads come Pacific Biosciences sequencing.</p> <p>Alignment was done using ngmlr.</p> <p>Variant calling was done using Sniffles.</p> <p> </p>
The past, present, and future of ecogeographic isolation between closely related Aquilegia plants
<p>Quantifying the strength of the ecogeographic barrier is an important aspect of studies of plant speciation and a practical step to understanding the evolutionary trajectory of plants under climate change. Here, we quantified the extent of ecogeographical isolation of four closely related Aquilegia species, which radiated in the Mountains of SW China and adjacent regions and often lacked intrinsic barriers. We predicted past, present and future species potential distributions using environmental niche models, then compared them to determine the degree of overlap and ecogeographic isolation. Investigated ecogeographical isolation between species pairs, we found significant ecological differentiation in all studied species pairs except A. kansuensis and A. ecalacarata. The current strengths of ecogeographic isolation are above 0.5 in most cases. Compared with current climates, most species had an expanding range in the Last Glacial Maximum, the Mid Holocene and under four future climate scenarios. Our results suggested that ecogeographic isolation contributes to the diversification and maintenance of Aquilegia species in the Mountains of northern and SW China and would act as an essential reproductive barrier in the future.</p>
Local coexistence and genetic isolation of three pollinator species on the same fig tree species
Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and several factors may lead to poor identification of species boundaries. We used a multilocus population genetics approach to show that three mtDNA-defined cryptic lineages of the fig wasp Pleistodontes imperialis Saunders, which pollinate Port Jackson figs (Ficus rubiginosa) in north-eastern Australia, represent reproductively isolated species. These species coexist locally, with about 13% of figs (where mating occurs) containing wasps from two or three species. However, there was no evidence for gene flow between them. Confirmed cases of coexisting cryptic species provide excellent opportunities for future studies of the ecological and evolutionary forces shaping both species coexistence and fig/pollinator coevolution.
Habitat isolation interacts with top-down and bottom-up processes in a seagrass ecosystem
<p>Habitat loss is accelerating at unprecedented rates, leading to the emergence of smaller, more isolated habitat remnants. Habitat isolation adversely affects many ecological processes independently, but little is known about how habitat isolation may interact with ecosystem processes such as top-down (consumer-driven) and bottom-up (resource-driven) effects. To investigate the interactive influence of habitat isolation, resource availability and consumer distribution and impact on community structure, we tested two hypotheses using invertebrate and algal epibionts on temperate seagrasses, an ecosystem of ecological and conservation importance. First, we hypothesized that habitat isolation will change the structure of the seagrass epibiont community, and isolated patches of seagrass will have lower epibiont biomass and different epibiont community composition. Second, we hypothesized that habitat isolation would mediate top-down (i.e., herbivory) and bottom-up (i.e., nutrient enrichment) control for algal epibionts. We used observational studies in natural seagrass patches, and experimental artificial seagrass to examine three levels of habitat isolation. We further manipulated top-down and bottom-up processes in artificial seagrass through consumer reductions and nutrient additions, respectively. We indeed found that habitat isolation of seagrass patches decreased epibiont biomass and modified epibiont community composition. This pattern was largely due to dispersal limitation of invertebrate epibionts that resulted in a decline in their abundance and richness in isolated patches. Further, habitat isolation reduced consumer abundances, weakening top-down control of algal epibionts in isolated seagrass patches. Nutrient additions, however, reversed this pattern, and allowed a top-down effect on algal richness to emerge in isolated habitats, demonstrating a complex interaction between patch isolation and top-down and bottom-up processes. Habitat isolation may therefore shape the relative importance of central processes in ecosystems, leading to changes in community composition and food web structure in marine habitats.</p>
Data from: Dynamics of reproductive isolation in stick insects at the transition between populations and species
<p>Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in `fits and bursts', rather than being uniform and gradual. We show in <em>Timema</em> stick insects that one form of reproductive isolation indeed evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that the evolution of habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum. The results show different evolutionary dynamics for different components of reproductive isolation, indicate sudden transitions between phases of speciation, and highlight a special relevance for species status in the evolution of reproductive isolation.</p>
Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species
<p>Raw data sets for the microbiologyOpen research article "Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species" including ClustalW Trees and the respective input file; canB 3.0 results; TYGS phylogenetic tree results; PGAP genome annotation files and Canu 2.0 assembly reports of the two genomes.</p>
Leishmanicidal and healing effects of 3β,6β,16β-trihydroxy lup-20 (29)-ene isolated from Combretum leprosum on Leishmania braziliensis infection in vitro and in vivo
<p>Treatment of cutaneous leishmaniasis depends on drugs that potentially cause serious side effects and resistance. Thus, topical therapies are attractive alternatives to the drugs currently used. 3β, 6β, 16β-trihydroxylup-20 (29)-ene is a lupane triterpene isolated from Combretum leprosum Mart. leaves (CLF-1), with reports of in vitro antileishmanial effect against L. amazonensis and to promote lesion healing in animal model. Herein, we evaluated the in vitro and in vivo antileishmanial and healing effects of CLF-1 against L. braziliensis. CLF-1 treatment showed low toxicity in macrophages and significantly reduced parasite load in vitro. CLF-1 induced higher IL-12 and TNF-α production and more discrete IL-4 and IL-10 production. For in vivo evaluation, a CLF-1 cream formulation was prepared to treat hamsters infected with L. braziliensis. CLF-1 treatment was able to reduce parasite load on the infected skin and lymph node more efficiently than the conventional treatment. Histopathological analysis indicated a strong inflammatory response accompanied by an important healing response. Data from this study indicate that topical CLF-1 treatment was effective and non-toxic in L. braziliensis infected hamsters suggesting its potential for further development as a future therapeutic intervention.</p>
Lipidomics of mitochondria isolated from human fibroblasts
<p>Mitochondrial trifunctional protein (TFP) has a monolysocardiolipin-acyltransferase (MLCL-AT) activity and therefore establishes a link between fatty acid oxidation and cardiolipin remodelling. We hypothesized that TFP deficiency produced changes in cardiolipin and other phospholipid content and composition in mitochondria of TFP cultured fibroblasts. The data showed that phospholipid profiles varied among patient fibroblasts. There was a correlation between genotype and the phospholipid profiles. Two profiles were found when cardiolipin, monolysocardiolipin, and oxidized cardiolipin and other phospholipids were considered, one of them similar to Barth syndrome. We concluded that cardiolipin remodeling may play a role in the pathogenesis of at least some patients with TFP/LCHAD deficiency.</p> <p>A previously described protocol was employed for the identification and quantification of mitochondrial phospholipids (including CL) and oxidized phospholipids by LC-MS/MS [1]. Briefly, lipids were extracted using the Folch method, total phosphate content was quantified, and samples were then analyzed using a LC-MS/MS system. The identification and quantification of the lipid species were achieved with an optimized workflow using SIEVE 2.2 software, and an in-house database.<br> [1]. Chao H, Anthonymuthu TS, Kenny EM, Amoscato AA, Cole LK, Hatch GM et al. Disentangling oxidation/hydrolysis reactions of brain mitochondrial cardiolipins in pathogenesis of traumatic injury. JCI Insight 2018;3(21).</p>
Data for: Isolation of targeted hypothalamic neurons for studies of hormonal, metabolic, and electrical regulation
<p>All original data used in the study published in the Journal of Visualized Experiments entitled: "Isolation of Targeted Hypothalamic Neurons for Studies of Hormonal, Metabolic, and Electrical Regulation" by Kathera-Ibarra-Forzisi et al. are provided in this dataset. </p> <p>Data are organized in sub-folders containing either confocal or bright-field images of primary hypothalamic neurons. The dataset does not contain analyses or measurements. For each figure of the paper, the data are organized in sub-folders corresponding to a specific experimental condition. The sub-folders are labeled with the corresponding figure number and the salient experimental conditions. For example, the sub-folder labeled "confocal images figure 3" contains all the original confocal images from which the representative images of the figure were chosen from. Likewise, the folder "LepR+ figure 3" contains all the images of neurons immunolabeled with LepR antibody. Data can be used by a third party for verification purposes but cannot be used for publication.</p> <p><em>Abstract of the study</em>: The hypothalamus regulates fundamental metabolic processes by controlling functions as varied as food intake, body temperature, and hormone release. As the functions of the hypothalamus are controlled by specific subsets of neuronal populations, the ability to isolate them provides a major tool for studying metabolic mechanisms. In this regard, the neuronal complexity of the hypothalamus poses exceptional challenges. For these reasons, new techniques, such as Magnetic-Activated Cell Sorting (MACS), have been explored. This paper describes a new application of magnetic-activated cell sorting (MACS) using microbead technology to isolate a targeted neuronal population from prenatal mice brains. The technique is simple and guarantees a highly pure and viable primary hypothalamic neuron culture with high reproducibility. The hypothalamus is gently dissociated, neurons are selectively isolated and separated from glial cells, and finally, using a specific antibody for a cell surface marker, the population of interest is selected. Once isolated, targeted neurons can be used to investigate their morphological, electrical, and endocrine characteristics and their responses in normal or pathological conditions. Furthermore, given the variegated roles of the hypothalamus in regulating feeding, metabolism, stress, sleep, and motivation, a closer look at targeted and region-specific neurons may provide insight into their tasks in this complex environment.</p>
Energetic Particle Injection during Short Isolated Bubble as seen in RCM Simulation and Spacecraft Observations in the Flow Braking Region
<p>The names of the RCM simulation output files specify the simulation time in a format of "hhmmss". The stored quantities are, "I","J","COLAT","ALOCT","MLT","BNDLOC","XMIN","YMIN","FTV","BMIN","V", "BIRK_fromV(NH)","P(RCM),nPa", "PV_gamma","Vtotx", "Vtoty","Vx_exb","Vy_exb","vel_x","vel_y","Ey","PEDLAM", "PEDPSI", "HALL", "RCM_T_p","RCM_T_e","RCM_N_e","EFLUX","EAVG","f_i_50-75","f_i_75-125","f_i_125-200","f_i_200-300","f_e_50-75","f_e_75-125","f_e_125-200","f_e_200-300","Vm","dbxdz","dbydz","dbrdz","dbzdx","dbzdy".<br> For the first hour of substorm-growth-phase-like quasi-steady convection, we uploaded the RCM simulation output files at 1-minute intervals. Then, the RCM output files were uploaded at 20-second intervals for the next 7 minutes of bubble injection, and at 1-minute intervals for the rest of the simulation.</p>
The isolation of novel species expands the genomic diversity of Lachnospiraceae
<p>A comprehensive understanding of the diversity of <em>Lachnospiraceae</em>, one of the most promising next-generation probiotics, is currently lacking, which limits the selection of strains for subsequent applications. To address this, we performed an in-depth genomic and functional analysis of 1,868 high-quality isolated genomes by integrating data from public databases and our new isolates, representing 387 colonization selective species-level clusters, of which 9 genera represent multi-lineage clusters. Pan-genome analysis, single nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography shape the functional diversity of <em>Lachnospiraceae</em>. Finally, analyses of associations with atherosclerotic cardiovascular disease (ACVD) indicated that many strains of the potentially novel species can reduce the abundance of opportunistic pathogens. Together, the large-scale genomics diversity analysis of <em>Lachnospiraceae </em>highlights the importance of potentially novel species and provides the ability for strain-level metagenomic association analysis to guide the selection of strains for the next-generation probiotics.</p>
Fig. 1 in Genotype diversity, phylogenetic analysis and seasonality of isolates of Acanthamoeba spp. in swimming pools in Kafrelsheikh, Egypt
Fig. 1. Fresh unstained trophozoites (A) and cysts (B–D) of Acanthamoeba spp.
A complex genomic architecture underlies reproductive isolation in a North American Oriole hybrid zone
<p>Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species--the Baltimore (<em>Icterus galbula</em>) and Bullock's (<em>I. bullockii</em>) orioles--to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic baseline, a large putative inversion on the Z chromosome, and complex interactions between melanogenesis-pathway candidate genes. Concordant and coincident clines for these different genomic regions further suggest the coupling of pre- and post-mating barriers. Our findings of complex and coupled interactions between pre- and post-mating barriers suggest a relatively rapid accumulation of barriers between these species, and they demonstrate the complexities of the speciation process.</p>
Data for: Annotation resource for seven Botrytis cinerea isolates from greenhouses in Michigan
<p>Fungal plant pathogen <em>Botrytis cinerea</em> affects a variety of important agricultural systems, including greenhouse production. Seven isolates of B. cinerea were whole-genome sequenced to provide an additional resource providing insight regarding host specificity, fungicide resistance, and geographic relatedness in pathogen populations. Fasta files of each genome assembly, raw reads (fastq), and more information can be found under NCBI BioProject PRJNA984325. Annotation data is included here.</p>
Warmer springs increase potential for temporal reproductive isolation among habitat patches in subalpine flowering plants
<ol> <li>Flowering phenology can vary considerably even at fine spatial scales, potentially leading to temporal reproductive isolation among habitat patches. Climate change could alter flowering synchrony, and hence temporal isolation, if plants in different microhabitats vary in their phenological response to climate change. Despite the importance of temporal isolation in determining patterns of gene flow, and hence population genetic structure and local adaptation, little is known about how changes in climate affect temporal isolation within populations.</li> <li>Here, we use flowering phenology and floral abundance data of 50 subalpine plant species over 44 years to test whether temporal isolation between habitat patches is affected by spring temperature. For each species and year, we analyzed temporal separation in peak flowering and flowering overlap between habitat patches separated by 5 to 950 m.</li> <li>Across our study species, warmer springs were associated with more temporal differentiation in flowering peaks among habitat patches, and less flowering overlap, increasing potential for temporal isolation within populations.</li> <li> <em>Synthesis</em>. By reducing opportunities for mating among plants in nearby habitat patches, our results suggest that warmer springs may reduce opportunities for gene flow within populations, and, consequently, the capacity of plant populations to adapt to environmental changes.</li> </ol>
Bearing database - Evaluation of isolated cases
<p><strong>Induced failure test data on outer race, inner race and rolling elements of a spherical roller bearing (FAG 22205E1KC3)</strong><br> This site allows access to vibration records of a bearing, in normal state and under localized induced faults in outer race (OR), inner race (IR) and rolling elements (RE). The experiment is developed in a test bench, to validate the performance of a low-cost data acquisition system proposed by the Technological Research Group of Railways (CITEF) of the Polytechnic University of Madrid. The characteristics of the developed database are specified in the attached document "READ_ME.docx".</p> <p>The article link is available at: <a href="https://doi.org/10.3390/math11163498">https://doi.org/10.3390/math11163498</a></p>
Lipidomic data of macrophages isolated from adult fruit flies (Drosophila melanogaster) 24 hours post-infection
<p>The immune response is an energy-demanding process that must be coordinated with systemic metabolic changes redirecting nutrients from stores to the immune system. Although this interplay is fundamental for the function of the immune system, the underlying mechanisms remain elusive. </p> <p>Our data show that the pro-inflammatory polarization of <em>Drosophila</em> macrophages is coupled to the production of the insulin antagonist <em>ImpL2</em> through the activity of the transcription factor HIF1α. <em>ImpL2</em> production, reflecting nutritional demands of activated macrophages, subsequently impairs insulin signaling in the fat body, thereby triggering FOXO-driven mobilization of lipoproteins. This metabolic adaptation is fundamental for the function of the immune system and an individual's resistance to infection.</p> <p>We demonstrated that analogically to <em>Drosophila</em>, mammalian immune-activated macrophages produce <em>ImpL2</em> homolog IGFBP7 in a HIF1α-dependent manner and that enhanced IGFBP7 production by these cells induces mobilization of lipoproteins from hepatocytes.</p> <p>Hence, the production of <em>ImpL2</em>/IGFBP7 by macrophages represents an evolutionarily conserved mechanism by which macrophages alleviate insulin signaling in the central metabolic organ to secure nutrients necessary for their function upon bacterial infection.</p>
Isolation drives species gains and losses of insect metacommunities over time in a mountaintop forest archipelago
<p><strong>Aim: </strong>We evaluated the effects of forest island size, isolation, and area in the landscape driving temporal changes of insect biodiversity in a mountaintop forest archipelago. We tested the following hypotheses: (i) changes in insect species composition is higher and dominated by species gains through time in smaller but less isolated forest islands; (ii) larger amounts of forest in the landscape result in higher gains of more vagile species over time, regardless of their size and isolation; (iii) heterogenization processes will prevail in less vagile groups, while homogenization processes will dominate in highly vagile groups due to differences in dispersal capability.</p> <p><strong>Location:</strong> Espinhaço Range Biosphere Reserve, Brazil.</p> <p><strong>Taxon:</strong> Insects.</p> <p><strong>Methods:</strong> We used ants, dung beetles, bees, wasps, and butterflies as study models to represent a gradient of low-to-high dispersal capability. We evaluated the colonization- and extirpation-resultant components of temporal β-diversity using area- and isolation-related variables as predictors.</p> <p><strong>Results:</strong> We found distinct colonization- and extirpation-resultant homogenization and heterogenization processes acting according to each insect group, likely due to different dispersal capabilities. Ants were dominated by species losses, with widespread and rare species being lost. Butterflies gained species, represented mainly by widespread species, leading to an increased colonization-resultant homogenization. Distance to neighboring forest islands was the underlying predictor affecting the temporal β-diversity of insect groups and on species gains and losses but differed according to the survey period. Effects of the forest amount in the landscape increased the temporal β-diversity of bees and butterflies but decreased that of ants, dung beetles, and wasps.</p> <p><strong>Main Conclusions:</strong> We recommend conserving the forest amount in the landscape and keeping forest connectivity among forest islands since the temporal dynamics of local colonization and extirpation can depend on the organisms' dispersal capability. Fragmentation and habitat loss-related hypotheses will benefit from incorporating colonization-extirpation processes into their predictions.</p>
Column size for direct displacement based design of base-isolated RC frame buildings
<p>In this paper, a method of computer-added program-based algorithm is introduced to evaluate the possible floor-wise column size for direct displacement-based design of base-isolated reinforced concrete frame buildings. The design storey drifts are kept low as base isolated buildings are mostly intended to achieve low storey drift fully-operational performance level under spectrum-compatible ground motions. Lead rubber bearing is used as base isolator and designed according to the UBC-97 maximum vertical load method. The frame deformation components considered in the algorithm are column tip displacement due to flexure, average column displacement due to shear, and joint rotation due to flexure and shear. It was observed that the proposed method effectively determines the storey-wise column size for various building plans, heights upto 9-storey and base displacement upto 350mm for target storey drift upto 0.25%.</p>
Impact of prolonged chronic social isolation stress on behavior and multifractal complexity of metabolic rate in Octodon degus
<p>We investigated the effects of prolonged chronic social isolation stress on behavioral, cognitive, and physiological performance in the social, long-lived rodent <em>Octodon degus</em>. Degu pups were separated into two social stress treatments: control (CTRL) and chronically isolated (CI) individuals from post-natal and post-weaning until adulthood. We quantified anxiety-like behavior and cognitive performance with behavioral tests. Additionally, we measured their basal metabolic rate (BMR). Data include behavioral tests and physiological traits (body mass and Basal Metabolic Rate).</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.