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2,261 results for “stress response”
Chamaecrista fasciculata Survival and Biomass in Response to Microbe Stress History and Contemporary Stress, 2018-2019
This dataset includes Chamaecrista fasciculata biomass and survival data collected as part of a greenhouse experiment that took place at Indiana University in 2018. Rhizosphere soil was collected from Chamaecrista fasciculata plants at the end of a field experiment in which plants were treated with four stress treatments: salt, herbicide, herbivory, and no stress. These field soils were used to inoculate a greenhouse experiment in which Chamaecrista fasciculata individuals from 50 manternal families were treated with these same four stress treatments in a full factorial design (4 microbe histories x 4 contemporary stress environments), plus a sterile microbial control treatment. We measured the days to first flower, noted when plants never flowered (i.e., did not survive to flower), and measured aboveground biomass.
DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
<p><strong>Genome sequence and annotation of Fragaria vesca cv. Reine des Vallées</strong></p> <p>In order to generate a reference genome for Fragaria vesca cv. Reine des Vallées, we used MinIon long-read sequencing data to substitute the <em>F. vesca</em> genome v.4.0.a2 genome. The detailed method used to obtain these results were the following:</p> <p><em>Genome sequencing and assembly NIL Fb2</em></p> <p>Genomic DNA from strawberry plants was extracted by a Hexadecyltrimethylammonium bromide (Cetrimonium bromide, CTAB) modified protocol (Healey, Furtado, Cooper, & Henry, 2014) and purified with Agencourt AMPure XP beads (cat# A63880). Long-read sequencing was performed for the genome assembly; Genomic DNA by Ligation (Oxford Nanopore, cat# SQK-LSK109) library was prepared as described by the manufacturer and sequenced on a MinION for 72 h (Oxford Nanopore).</p> <p><em>Reference genome polishing</em></p> <p>Reads obtained from nanopore were filtered with Filtlong v0.2.1 (<a href="https://github.com/rrwick/Filtlong">https://github.com/rrwick/Filtlong</a>) using --min_mean_q 80 and --min_length 200. Cleaned reads were then aligned to the most recent version of the <em>F. vesca</em> genome v4.0.a2, downloaded from the Genome Database for Rosaceae (GDR) (<a href="https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2">https://www.rosaceae.org/species/fragaria_vesca/genome_v4.0.a2</a>), using minimap2 v2.21 (H. Li, 2018) with parameters -aLx map-ont --MD -Y. The generated BAM file was then sorted and indexed with samtools v1.11 (H. Li et al., 2009). We used mosdepth v0.3.1 (Pedersen & Quinlan, 2018) to verify that coverage on chromosomic scaffolds was over 50 X. Sniffles v1.0.12a (Sedlazeck et al., 2018) with parameters -s 10 -r 1000 -q 20 --genotype -l 30 -d 1000 was used to detect structural variations larger than 30 bp. The VCF files obtained from Sniffles was sorted and filtered with BCFtools v1.14 (Danecek et al., 2021) to keep only structural variants (SV) with smaller than 200,00 bp (we observed that larger SV were most of the time false positive caused by misalignments in regions with gaps or Ns), supported by 10 or more reads and with allelic frequencies above 0.8 (we were interested in homozygous changes). The complete filtering command used is “bcftools view -q 0.8 -Oz -i '(SVTYPE = "DUP" || SVTYPE = "INS" || SVTYPE = "DEL" || SVTYPE = "TRA" || SVTYPE = "INV" || SVTYPE = "INVDUP") && %FILTER = "PASS" && FMT/DV>9 && SVLEN>29 && SVLEN<200000' “</p> <p>From the VCF listing all the structural variants that we detected in our <em>F. vesca </em>accession, we generated a substituted genome version based on the reference <em>F. vesca</em> genome v.4.0.a2. The reference genome was first indexed with samtools faidx v1.11(Danecek et al., 2021) and a sequence dictionary was generated with Picard CreateSequenceDictionary v2.25.6 (<a href="https://broadinstitute.github.io/picard">https://broadinstitute.github.io/picard</a>). The VCF containing the SV produced from our Nanopore sequencing was also indexed with gatk (Van der Auwera GA & O'Connor BD, 2020) IndexFeatureFile v4.2.0.0 (<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile">https://gatk.broadinstitute.org/hc/en-us/articles/360037262651-IndexFeatureFile</a>). FastaAlternateReferenceMaker v4.2.0.0 (<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker">https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker</a>) was then run with the reference genome and the VCF file to generate a substituted genome representative of our <em>Fragaria</em> accession.</p> <p>As substituting our genome with the detected structural variants changes genomic coordinates, we also corrected the public GFF genome annotation of <em>F. vesca</em> (Y, Pi, Gao, Liu, & Kang, 2019) using liftoff v1.6.1 (Shumate & Salzberg, 2021). Liftoff also detects and annotates duplications within the substituted genome.</p> <p>Transposable elements annotation was carried out using the EDTA transposable element annotation pipeline v. 1.9.6 (S. Ou et al., 2019) on the substituted genome using default parameters<em>.</em></p> <p><strong>Differentially methylated regions</strong></p> <p>The file Stress_vs_control_DMRs.zip file contains the DMRs that were called using the reads submitted to ENA (ERP135585) and obtained as follows:</p> <p>First, bedGraph files from wgbs pipeline were pre-filtered for a minimum coverage of 5 reads using awk command. These output files were then used as input for the EpiDiverse/dmr bioinformatics analysis pipeline for non-model plant species to define DMRs (Nunn <em>et al</em>., 2021) with default parameters (minimum coverage threshold 5; maximum q-value 0.05; minimum differential methylation level 10%; 10 as minimum number of Cs; Minimum distance (bp) between Cs that are not to be considered as part of the same DMR is 146 bp). The pipeline uses metilene v.0.2.6.1 (<a href="https://www.bioinf.uni-leipzig.de/Software/metilene/">https://www.bioinf.uni-leipzig.de/Software/metilene/</a>) for pairwise comparison between groups and R-packages ggplot2 v.3.3.5 and gplots v.3.1.1, for visualization results (Fig. S1). Based on our <em>F. vesca</em> genome transcript annotation and methylation data (overlapped regions with DNA methylation cytosines and DMRs), we detected the methylated genes, promoters, 3’ UTRs, 5’UTR and transposable elements in strawberry. Global DNA methylation and DMR plots were performed with R-package ggplot2. Gene analyses by methylation patterns and analysis of per-family TE DNA methylation profiles were performed with deepTools v.3.5.0 (Ramírez <em>et al</em>., 2014). DMRs comparison between treatments were done by the Venn diagram v.1.7.0 R-package.</p> <p>We produced several genome browsers tracks with DMRs that we integrated in our local instance of JBrowse available at the following url: <a href="https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub">https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub</a></p>
Dataset-Response strategies to acute and chronic environmental stress in the arctic breeding Lapland longspur (Calcarius lapponicus)
<p>This is the dataset presenting the phenotypic measurements in the paper Response strategies to acute and chronic environmental stress in the arctic breeding Lapland longspur (<em>Calcarius lapponicus</em>).</p>
Dataset of image processing - High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress
<p>The data set contains the analysis data files from the image analysis workflow developed to quantify cortical microtubules rearrangements in the case of tensile stress (<a href="https://github.com/VergerLab/MT_Angle2Ablation_Workflow">https://github.com/VergerLab/MT_Angle2Ablation_Workflow</a>), generated form a specific dataset (https://doi.org/10.5878/17te-jg54). The files include the intermediary images processed at each step of the image analysis workflow in imageJ, the log files produced by the imageJ macro describing the input and the output images and the text files containing the quantified values. </p>
Elevated temperature effects on animal personality: hormonal stress response underlying behavioural differences in the American bullfrog
<p>Dataset for research paper submitted to Animal Behaviour</p> <p>Behavioural_data.csv: raw data for how individual bullfrogs performed in six different trials on an 8-arm maze before and after they were submitted to thermal stress. Behaviours analyzed: movements against the wall of the maze, posture changes, total ambulatory distance (m), and time on the centre of the arena (s).</p> <p>Hormone_data.csv: raw hormone (corticosterone and testosterone) data collected from individual bullfrogs in four different time points: baseline, 12 hours after stress, 24 days after stress, and 47 days after stress.</p> <p>Mass_data.csv: raw mass data collected from individual bullfrogs at the beginning and end of the experiment. SVL = snout-vent length. Body index is calculated as the residuals of a linear regression between mass as dependent variable and SVL as independent variable.</p>
Natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The data of Arabidopsis thaliana accessions which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic. </p>
Spatially corrected dataset for natural variation across Arabidopsis diversity panel in early responses to salt stress
<p>The spatially corrected data of Arabidopsis thaliana accessions, which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic.</p> <p>The spatial correction was done using the asreml package. The data was subsequently used for the Genome-Wide Association Study. </p>
Light micrographs on the morphological response to heat stress in the filamentous Zygnematophyceae Mougeotia sp. and Spirogyra pratensis
<p>Herein are the light micrographs of <em>Mougeotia</em> sp. and <em>Spirogyra pratensis</em> that were used to obtain the quantitative information for Figure 1 in the article "Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits" published in The Plant Journal, doi: 10.1111/tpj.14782</p>
Reduced stress defense responses contribute to the higher toxicity of a pesticide under warming
<p>There is a pressing need to identify the molecular mechanisms underlying the, often magnifying, interactive effects between contaminants and natural stressors. We here test our hypothesis that lower general stress defense responses contribute to synergistic interactions between stressors. We focus on the widespread pattern that many contaminants are more toxic at higher temperatures. Specifically, we tested the effects of an environmentally realistic low-effect and high-effect concentration of the pesticide chlorpyrifos under warming at the gene expression level in the Northern house mosquito <em>Culex pipiens molestus</em> (Forskal, 1775). By applying the independent action model for combined stressors on RNA-seq data, we identified interactive gene expression patterns under combined exposure to chlorpyrifos and warming for general stress defense responses: protection of macromolecules, antioxidant processes, detoxification, and energy metabolism/allocation. Most of these general stress defense response genes showed upregulated antagonistic interactions, i.e. were less upregulated than expected under the independent action model. This indicates that when pesticide exposure was combined with warming the general stress defense responses were no longer buffering increased stress levels, which may contribute to a higher sensitivity to toxicants under warming. These upregulated antagonistic interactions were stronger for the high-effect chlorpyrifos concentration, indicating that exposure to this concentration under warming was most stressful. Our results highlight that quantitative analysis of the frequency and strength of the interaction types of general stress defense response genes, specifically focusing on antagonistic upregulations and synergistic downregulations, may advance understanding of how natural stressors modify the toxicity of contaminants.</p>
Data and script for: A marker of biological age explains individual variation in the strength of the adult stress response
<p>Data and script for: A marker of biological age explains individual variation in the strength of the adult stress response.</p> <p>Comprises 2 CSV data files and one R script.</p>
Data for "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis"
<p>Raw data associated with the publication "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis". Temperature profile, daily measurements, physiological measurements, elemental analysis, NanoSIMS data, and cell density data are included as individual tabs in the Excel file. </p>
Dataset for the submitted manuscript titled 'Response of Southern Ocean Resource Stress in a Changing Climate'
<p>Netcdf output files of Primary Production, carbon export, Fe and Mn limitations, and deficiencies from PISCES-QUOTA model with Mn limitation (described in Anugerahanti and Tagliabue, 2023) forced by historical IPSL CM5A climate model simulation (1850-2005) and RCP8.5 high emission IPSL CM5A simulation (2005-2100) on the ORCA2 grid, as described and discussed in Anugerahanti and Tagliabue, in the manuscript submitted for Geophysical Research Letters. Due to the large size of the files, this has been collated to only contain surface/ upper 100m south of 40S. </p>
Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism
<p>The mutualism between the thioautotrophic bacterial ectosymbiont <em>Candidatus</em> Thiobius zoothamnicola and the giant ciliate <em>Zoothamnium niveum</em> thrives in a variety of shallow-water marine environments with highly fluctuating sulfide emissions. To persist over time, both partners must reproduce and ensure the transmission of symbionts before the sulfide stops, which enables carbon fixation of the symbiont and nourishment of the host. We experimentally investigated the response of this mutualism to depletion of sulfide. We found that colonies released some initially present but also newly produced macrozooids until death, but in fewer numbers than when exposed to sulfide. The symbionts on the colonies proliferated less without sulfide, and became larger and more rod-shaped than symbionts from freshly collected colonies that were exposed to sulfide and oxygen. The symbiotic monolayer was severely disturbed by growth of other microbes and loss of symbionts. We conclude that the response of both partners to the termination of sulfide emission was remarkably quick. The development and the release of swarmers continued until host died and thus this behavior contributed to the continuation of the association.</p>
Manhattan and QQ plots of GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)
<p>The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>. The raw GWAS outputs can be found <a href="https://zenodo.org/badge/DOI/10.5281/zenodo.5856310.svg">here</a>. This dataset represents Manhattan plots and QQ plots made out of the data. </p>
Characterization of the nuclear proteome of Chlamydomonas in response to salt stress
<p><strong>Supplementary Files and Figures for the manuscript </strong></p> <p><strong>"Characterization of the nuclear proteome of Chlamydomonas in response to salt stressCharacterization of the nuclear proteome of Chlamydomonas in response to salt stress"</strong></p>
Survival, wet weight and muscle cellular stress responses of Palaemon varians shrimps exposed to combined temperature and salinity variations
<p>Shrimps were exposed to a full factorial experiment combining different temperatures (20, 23 and 26 ºC) and salinities (20, 40). Cellular stress response biomarkers were assessed in the shrimps muscle at several time-points, namely the 7th, 14th, 21st and 28th days of exposure. Wet weight (as proxy for growth) and survival were also assessed during the experiment. These datasets refer to the publication of an article in STOTEN (<a href="https://doi.org/10.1016/j.scitotenv.2022.158732">https://doi.org/10.1016/j.scitotenv.2022.158732</a>).</p> <p>Note: the biomarker dataset contained 3.2% of missing values, which were replaced by group averages for the purpose of the statistical analyses in the article.</p>
Figure 4 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)
Figure 4. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus
Figure 3 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)
Figure 3. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus
Figure 2 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)
Figure 2. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus
Figure 1 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)
Figure 1. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus
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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.