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Supplementary material - Eggerthella lenta DSM 2243 alleviates bile acid stress response in Clostridium ramosum and Anaerostipes caccae by transformation of bile acids
<p>The word document is a collection of supplementary figures and tables. <br> The excel file is a collection of raw data from experiments.</p>
Data from: Understanding evolutionary rescue and parallelism in response to environmental stress
<p>Evolutionary rescue, the process by which populations facing environmental stress avoid extinction through genetic adaptation, is a critical area of study in evolutionary biology. The order in which mutations arise and get established will be relevant to the population's rescue. This study investigates the degree of parallel evolution at the genotypic level between independent populations facing environmental stress and subject to different demographic regimes. Under density regulation, two regimes exist: in the former, the population can restore positive growth rates by adjusting its population size or through adaptive mutations, whereas in the second regime, the population is doomed to extinction unless a rescue mutation occurs. Analytical approximations for the likelihood of evolutionary rescue are obtained and contrasted with simulation results. We show that the initial level of maladaptation and the demographic regime significantly affect the level of parallelism. There is an evident transition between these two regimes. Whereas in the first regime, parallelism decreases with the level of maladaptation, it displays the opposite behavior in the rescue/extinction regime. These findings have important implications for understanding population persistence and the degree of parallelism in evolutionary responses as they integrate demographic effects and evolutionary processes.</p>
Fig. 2 in Repeated stressors do not provoke habituation or accumulation of the stress response in the catfish Rhamdia quelen
Fig. 2. Plasma cortisol concentrations of R. quelen (Quoy & Gaimard) fingerlings exposed to sequential acute stressors. Comparison of responses to two similar stressors and a third different stressor in experiment "A" and comparison of responses to three sequential stressors of the same type in experiment "B." Data are expressed in terms of mean ± S.E.M. values. The different small letters above the histograms indicate statistical differences by ANOVA, followed by Tukey's range test. (n = 8-9).
Fig. 1 in Repeated stressors do not provoke habituation or accumulation of the stress response in the catfish Rhamdia quelen
Fig. 1. Schematic representation of the experimental design of both groups of experiments. In experiment "A," Rhamdia quelen (Quoy & Gaimard) fingerlings were sequentially exposed to the same stressors twice and to a different stress the third time. In experiment "B," R. quelen fingerlings were sequentially exposed as the same stressors 3 times.
Fig. 3 in Effect of beta 1,3 glucan in stress responses of the pencilfish (Nannostomus trifasciatus) during transport within the rio Negro basin
Fig. 3. Whole-body cortisol levels (mean ± SD) during transportation of pencilfish (Nannostomus trifasciatus) previously fed with different levels of beta 1,3 glucan. No significant differences between all sampling times using the Kruskal-Wallis ANOVA on ranks were observed (P>0.05).0: initial time of transport; 24: 24 hours of transport; 24 AT: 24 hours after transport (recovery time).
Fig. 2 in Effect of beta 1,3 glucan in stress responses of the pencilfish (Nannostomus trifasciatus) during transport within the rio Negro basin
Fig. 2. Net Na+ (A) and K+ (B) fluxes during transportation of pencilfish (Nannostomus trifasciatus) previously fed with different levels of beta 1,3glucan. Positive values indicate net influxes and negative values net effluxes. N = 4 boxes per treatment in each sample time. Different lower case letters indicate significant difference among times of transport within the same group and * indicate significant difference from control group within the same time of transport by Scheirer-Ray-Hare extension of the Kruskal-Wallis test followed by the Nemenyi test (P<0.05).
Figure 3 in Response and tolerance mechanism of food crops under high temperature stress: a review
Figure 3. Process of development of heat-resistant cultivars. Identify heat-resistant genes from natural genetic resources through genome wide association mapping and then study the study how these genes are operated. Select those genes which are associated with various signaling pathways and then transform them into current germplasm.
Figure 1 in Response and tolerance mechanism of food crops under high temperature stress: a review
Figure 1. Schematic representation of most sensitive phase of various crops during high temperature stress.
Data archive for Gott et al. 'Chronological age, biological age, and individual variation in the stress response in the European starling: A follow-up study'
<p>Data archive for Gott et al. 'Chronological age, biological age, and individual variation in the stress response in the European starling: A follow-up study'.</p> <p>Revised version of September 4 2018.</p> <p>Contains one data file and one R script to reproduce the analyses in the paper.</p>
Data archive for 'Cognitive bias in relation to developmental history and stress response in European starlings (Sturnus vulgaris)'
<p>Data files and R code for Gott et al. 'Cognitive bias in relation to developmental history and stress response in European starlings (Sturnus vulgaris)'.</p> <p>One .csv file gives the trial-by-trial data from the cognitive bias experiment. The other gives individual-level summary variables. Both are used by the R script.</p> <p>Uploaded 9th September 2018</p>
The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress
<p>This repository contains the modeling files and the analysis related to the article <a href="https://www.ncbi.nlm.nih.gov/pubmed/28821611">"The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress"</a> by Wang et al. in J Biol Chem 2017.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/ecm29/">Sali lab website</a> or the README file.</p>
Salt stress responses in 9 Arabidopsis accessions
<p>The dataset is used as an example dataset for the MVApp, previously published the results in Awlia et al., 2016 Frontiers in Plant Science.</p>
Processed data for "Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses"
<p>tar.gz of processed data in the form of compressed R files (rds) of SingleCellExperiment (<a href="https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html">https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html</a>) objects and a metadata csv for the data in the publication <em>Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses </em>(O'Flanagan et al. 2019).</p>
Drought stress triggers differential survival and functional trait responses in the establishment of Arnica montana seedlings
<ul> <li>The establishment and survival of seedlings are critical stages in the life cycle of plants and therefore usually well timed to humid and favourable conditions. Climate projections suggest that the threatened mountain grassland species <em>Arnica montana</em> may be increasingly exposed to drought stress. However, studies that focus on the species’ early development are missing. We evaluated impacts of drought-induced stress on <em>A. montana</em> seedlings in their early establishment phase and identified traits for the species’ fitness decline.</li> <li>In a greenhouse experiment, we tested the response of <em>A. montana</em> seedlings to different drought levels (moderate, strong, extreme). To assess their fitness under increasing drought, we evaluated the survival of the seedlings based on four senescence stages and measured the performance of above- and belowground morphological and physiological functional traits.</li> <li><em>Arnica montana</em> seedlings showed high resistance to drought. Senescence accelerated and survival declined only under strong and extreme drought conditions. However, the seedlings’ vegetative performance decreased even with moderate drought, as indicated by smaller values of most leaf traits and some root traits. Physiological trait response was less sensitive.</li> <li>Drought stress hinders the establishment and survival of <em>A. montana</em> seedlings. Following the functional trait responses to drought and their associations with survival, we suggest declining leaf length, leaf width, and leaf number as sensitive traits that can lead to a decline performance.</li> </ul>
Plastic responses of survival and fertility following heat stress in pupal and adult Drosophila virilis
<p>The impact of rising global temperatures on survival and reproduction is putting many species at risk of extinction. In particular, it has recently been shown that thermal effects on reproduction, particularly limits to male fertility, can underpin species distributions in insects. However, the physiological factors influencing fertility at high temperatures are poorly understood. Key factors that affect somatic thermal tolerance such as hardening, the ability to phenotypically increase thermal tolerance after a mild heat shock, and the differential impact of temperature on different life stages, are largely unexplored for thermal fertility tolerance. Here, we examine the impact of high temperatures on male fertility in the cosmopolitan fruit fly <i>Drosophila virilis</i>. We first determined whether temperature stress at either the pupal or adult life-history stage impacts fertility. We then tested the capacity for heat-hardening to mitigate heat-induced sterility. We found that thermal stress reduces fertility in different ways in pupae and adults. Pupal heat stress delays sexual maturity, whereas males heated as adults can reproduce initially following heat stress, but lose the ability to produce offspring. We also found evidence that while heat-hardening in <i>D. virilis </i>can improve high temperature survival, there is no significant protective impact of this same hardening treatment on fertility. These results suggest that males may be unable to prevent the costs of high temperature stress on fertility through heat-hardening which limits a species' ability to quickly and effectively reduce fertility loss in the face of short-term high temperature events.</p>
Photophysiology and molecular responses of the soft coral Sarcophyton cf glaucum exposed to heat and high light stress
<p>An experiment testing different temperatures (26 vs 32 ºC) and light intensities (high light HL and low light LL, ∼662 and 253 µmol photons m<sup>-2</sup> s<sup>-1</sup>) was carried out using the soft coral <em>Sarcophyton</em> cf <em>glaucum</em> (leather coral) as model species.</p> <p>In summary, corals were exposed to the different light intensities for 30 days (Photoacclimation, time-point 1) and a subsequent marine heatwave simulation was carried out for 10 days (Marine heatwave, time-point 2). Subsequently, corals were returned to control temperature and allowed to recover for 30 days (Recovery, time-point 3). Photophysiological performance (maximum quantum yield of photosystem II (Fv/Fm), a measure of photosynthetic activity; dark-level fluorescence (F<sub>0</sub>), as a proxy of chlorophyll <em>a</em> content; and zooxanthellae density) and stress biomarkers (total protein, catalase - CAT, superoxide dismutase - SOD, glutathione-S-transferase - GST, total antioxidant capacity - TAC, lipid peroxidation - LPO, ubiquitin - UBI, and heat shock protein 70 - Hsp70) were assessed in corals at these three time-points.</p>
Figure 1 in Alfalfa responses to drought, salinity, and herbivory by Tetranychus urticae (Acari: Tetranychidae) and performance of the pest on water-stressed plants
Figure 1. Effects of drought stress on proline content of alfalfa plants before and after Tetranychus urticae feeding. Within each column mean (± SE) followed by the same letter(s) are not significantly different. Capital letters show the effect of drought.
Figure 2 in Alfalfa responses to drought, salinity, and herbivory by Tetranychus urticae (Acari: Tetranychidae) and performance of the pest on water-stressed plants
Figure 2. Effects of salinity stress on proline content of alfalfa plants before and after Tetranychus urticae feeding. Within each column mean (± SE) followed by the same letter(s) are not significantly different. Capital letters show the effect of salinity.
Dataset: A quantitative 1H NMR approach for evaluating the metabolic response of Saccharomyces cerevisiae to mild heat stress
<p>In this study, the effect of growth temperature on the yeast (<em>Saccharomyces cerevisiae</em>) metabolome has been analyzed by one-dimensional proton NMR spectroscopy (<sup>1</sup>H NMR).</p> <p>Yeast cells were grown either at 30 or 37°C. A non-targeted chemometric evaluation of the spectra was performed in order to detect potential biomarkers. Moreover, an exhaustive assignment for most of the detected NMR signals was carried out, corresponding to 38 identified metabolites. Resonances from these identified metabolites were integrated, and univariate and multivariate data analyses were applied on the matrices of these relative concentrations. Observed changes in metabolite concentrations were consistent with the expected process of temperature acclimation, showing alterations in amino acid cellular pools, nucleotide metabolism and lipid composition.</p>
Data from: Understanding evolutionary rescue and parallelism in response to environmental stress
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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.
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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.
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