Find research datasets worth reusing

opencc-by-4.0Jun 2021View details →

Mechanical Stretch Inhibition Sensitizes Proprioceptors to Compressive Stresses

A repetitive gait cycle is an archetypical component within the behavioural repertoire of many if not all animals including humans. It originates from mechanical feedback within proprioceptors to adjust the motorprogram during locomotion and thus leads to a periodic orbit in a low dimensional space. Here, we investigate the mechanics, molecules and neurons responsible for proprioception in Caenorhabditis (C.) elegans to gain insight into how mechanosensation shapes the orbital trajectory to a well-defined limit cycle. We used genome editing, force spectroscopy and multiscale modeling and found that alternating tension and compression with the spectrin network of a single proprioceptor encodes body posture and informs TRP-4/NOMPC and TWK-16/TREK2 homologs of mechanosensitive ion channels during locomotion. In contrast to a widely accepted model of proprioceptive ‘stretch’ reception, we found that proprioceptors activated locally under compressive stresses in vivo and in vitro, and propose that this property leads to compartmentalized activity within long axons delimited by curvature-dependent mechanical stresses.

opencc-by-4.0Dec 2022View details →

Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches

Raw experimental data associated with the manuscript "Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches", by Sosa-Carrillo and colleagues, bioRxiv, 10.1101/2022.11.02.514931. The code to analyze this raw data and generate the figures for the manuscript is available on GitLab at https://gitlab.inria.fr/InBio/Public/yeastcybersecretion.

opencc-by-4.0Dec 2022View details →

Dataset of image processing - High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress

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.

opencc-by-4.0Jan 2023View details →

Phenotypic diversity of root architecture and genotypic variation in durum wheat under salt stress

Supplementary data consists of Principal Components values for traits detected under salt and control conditions (S1); Markers' locations onto the durum wheat reference genome associated with QTL (S2); Markers associated with genes from NCBI database (S4); PCR results and alleles distribrution

opencc-by-4.0Apr 2023View details →

Data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos

This contains the data for the manuscript Feugere et al., "Heat induces multiomic and phenotypic stress propagation in zebrafish embryos" (2023). Zebrafish embryos were exposed to thermal stress ("TS") and stress metabolites ("SM") released by heat-stressed conspecifics in a two-way factorial design ("TSxSM"). The folder includes raw molecular data (cortisol levels, HSP70 protein levels, and gene expression acquired with LAMP and RNA-seq) and raw phenotypic data (morphology, hatching, survival, and behaviour) of zebrafish Danio rerio at 1 day and 4 days of development. The .csv files contain all quantitative data, whilst the .tab files contain the gene count data required for gene expression analysis. The data were analysed in R using the code shared in the "TSxSM2.stats.Rmd" file. The "Metadata" document provides the reader with an extensive description of each file.

opencc-by-4.0May 2023View details →

Phylogenetic analyses of hub genes accompanying the study "Environmental gradients reveal stress hubs predating plant terrestrialization"

135 ML phylogenies of hub genes identified in the study "Environmental gradients reveal stress hubs predating plant terrestrialization"

opencc-by-4.0May 2024View details →

Epigenetic and transcriptional landscape of stress memory in woodland strawberry

Bedfiles of differentially methylated regions (DMRs) that were detected in stressed mother plants (M) and their (themselves unstressed) clonal daughter plants that were formed via stolon formation (St1, St2, St3). The M plants were grown and sampled in vitro and the St1, St2, St3 plants in the green house. The DMRs were called using the the EpiDiverse/dmr bioinformatic analysis pipeline (Nunn et al., 2021). Stress assays in vitro One-month-old seedlings were transferred to a fresh MS media and growth chambers at 24oC/21oC (day/night),16 h light/8 h dark, as control conditions. For heat-stress, plants were exposed to 30oC (day/night) for one week followed by 2 days of recovery (24oC/21oC) on fresh medium as well as the control plants. Then, the plates were transferred to 37oC (day/night) for 1 week with 2 recovery days (Figure 1A). We sampled aerial parts of plants for the molecular analyses. To reduce variability resulting from individual plants, three biological replicates of 5 pooled plants were collected per condition. Samples were harvested in 1.5 mL tubes between 9:00-11:00 a.m. and immediately frozen in liquid nitrogen and stored at -80oC until required. Greenhouse propagation assays In vitro plants after heat and control treatment were transferred to soil (one plant per pot) in square plastic pots (size: 12x12x10 cm) and to a greenhouse with long day conditions (24oC/21oC day/night and 60%-70% humidity). Twelve mother plants (M) from control (CM; n=12) and heat-stress (HM; n=12) conditions were used for asexual propagation. From each mother plant, the two first stolons (St) were kept for producing the daughter plants of the first asexual propagation (St1) in individual pots. After two weeks, following root formation, the stolons were cut to get independent daughter plants from their mother plant (M). This process was continued until St3. The DMRs can also be visualized here: <a href="https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub">https://jbrowse.agroscope.info/jbrowse/?data=fragaria_sub</a> And the raw bisulfite sequencing data can be found here: <a href="https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585">https://www.ebi.ac.uk/ena/browser/text-search?query=ERP135585</a>    How many daughter plants per stolon? One stolon produce a chain of daughter plants.

opencc-by-4.0Aug 2023View details →

Elevated temperature effects on animal personality: hormonal stress response underlying behavioural differences in the American bullfrog

Dataset for research paper submitted to Animal Behaviour 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). 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. 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.

opencc-by-4.0Aug 2023View details →

Distinct States in an Active Liquid Crystal of Flagella and Kinesin-Powered Microtubules under Varying Kinesin Concentrations or Active Stress

At a constant nematic elasticity (flagella concentration) and confinement (H=100μm), higher KSA (120nM) or motor concentrations induce robust active stress that disrupts nematic alignment, resulting in chaotic behavior. Conversely, lower KSA (<60nM) concentrations fail to overcome the nematic elastic background's alignment, leading to a unique state where active microtubule bundles phase-separate into lanes within a uniform flagella background. The confocal micrograph reveals this distinct phenomenon, showing uniform flagella distribution alongside microtubule segregation into lane-like structures within the channel's limited confinement.

opencc-by-4.0Jul 2023View details →

Dataset for "A new method for identifying weather-induced power system stress using shadow prices"

These are data accompanying "A new method for identifying weather-induced power system stress using shadow prices". They consist of <ul> <li>solved network files (generated with <a href="https://github.com/PyPSA/pypsa-eur/">PyPSA-Eur</a>, here v0.6.1), used for the analysis,</li> <li>necessary data to reproduce the figures in the paper and supplementary material.</li> </ul> The optimised network files are of the form `workflow_data/results/stressful-weather/optimum/{weather_year}_181_90m_c1.25_Co2L0.0-1H.nc` (for weather_years in {1980,...,2019}). Unsolved ones can be found in `workflow_data/networks/...`. The filenames in `plot_data/` indicate which figure the data are associated to (e.g. `plot_data/fig_1_hourly_costs.csv` contains the hourly electricity costs during the winter of all networks and is necessary for Figure 1). We also added weather data for all system-defining events (mean surface level pressure, 10m wind speed anomaly, 2m temperature anomaly) in .nc files. Find more information about how to use these data and how they were generated in the README of the GitHub repository: <a href="https://github.com/koen-vg/stressful-weather/tree/v0">https://github.com/koen-vg/stressful-weather/tree/v0</a>.

opencc-by-4.0Jul 2023View details →

The effect of normal stress oscillations on fault slip behavior near the stability transition from stable to unstable motion

Tectonic fault zones are subject to normal stress variations with a wide range of spatio-temporal scales. Stress perturbations cover a wide range of frequencies and amplitudes from high frequency seismic waves generated by earthquakes to low frequency transients associated with solid Earth tides. These perturbations can reactivate critically stressed faults and trigger earthquakes. Here, we describe lab experiments to illuminate the physics of such changes in friction and the mechanics of earthquake triggering and fault reactivation. Friction tests were done in a double direct shear configuration for conditions near the stability transition from stable to unstable motion. We studied simulated fault gouge composed of quartz powder and conducted experiments at reference normal stress from 10 to 13.5 MPa. After shearing to steady state sliding, we applied sinusoidal normal stress oscillations of amplitude 0.5 to 2 MPa, and period of 0.5 to 50 s. We performed numerical simulations using measured values of rate/state friction (RSF) parameters to assess our data. Our results show that low frequency stress oscillations cause a Coulomb-like response of shear strength that transitions from stable slip to slow lab earthquakes as frequency increases. At the critical frequency predicted by RSF we observe periodic stick-slip behavior. Perturbations of high amplitude and short period weaken the fault, while lower amplitudes strengthen the fault. We find that a modified RSF formulation is able to accurately match our laboratory data. Our findings highlight the complex effects of stress perturbations for fault strength and the mode of fault slip. The data are uploaded are structured as follow: 1) For each experiment a .txt file of the datafile that is recorded from the machine (raw data) and a binary file containing the elaborated data (data_rp). The experiments information are listed in experiment_info.txt 2) The folder <a href="https://zenodo.org/api/files/89fe30fb-a2cb-4fcb-b9df-db80583fc652/codes_results.zip">codes_results.zip</a> contain the codes of the data analysis and the related results  The data are analyzed using rawPy that can be found at <a href="https://github.com/marcoscuderi/rawPy">https://github.com/marcoscuderi/rawPy</a> For any additional information please do not hesitate to contact the corresponding author Federico Pignalberi at federico.pignalberi@uniroma1.it

The effects of pesticides, pH, and predatory stress in amphibians under mesocosm conditions.

Pesticides are applied throughout the world often with unintended consequences on ecological communities. In some regions, pesticides are associated with declining amphibians, but we have a poor understanding of the underlying mechanisms. Pesticides break down more slowly under low pH conditions and become more lethal to amphibians when combined with predatory stress, but these phenomena have not been tested outside of the laboratory. I examined how pH, predatory stress, and a single application of an insecticide (carbaryl) affected the survival and growth of larval bullfrogs (Rana catesbeiana) and green frogs (R. clamitans) in outdoor mesocosms. Decreased pH had no effect on survival, but caused greater tadpole growth. Low concentrations of carbaryl had no effect on either species, but high concentrations caused lower survival and greater growth in bullfrogs. Predatory stress and reduced pH did not make carbaryl more lethal likely due to the rapid breakdown rate of carbaryl in outdoor mesocosms. Thus, whereas the stress of pH and predators can make carbaryl (and other pesticides) more lethal under laboratory conditions using repeated applications of carbaryl, these stressors did not interact under mesocosm conditions using a single application of carbaryl.

Synergistic impacts of malathion and predatory stress on six species of North American tadpoles.

The decline of many amphibian populations is associated with pesticides, but for most pesticides we know little about their toxicity to amphibians. Malathion is a classic example; it is sprayed over aquatic habitats to control mosquitoes that carry malaria and the West Nile virus, yet we know little about its effect on amphibians. I examined the survival of six species of tadpoles (wood frogs, Rana sylvatica; leopard frogs, R. pipiens; green frogs, R. clamitans; bullfrogs, R. catesbeiana; American toads, Bufo americanus; and gray tree frogs, Hyla versicolor) for 16 d in the presence or absence of predatory stress and six concentrations of malathion. Malathion was moderately toxic to all species of tadpoles (median lethal concentration [LC50] values, the concentration estimated to kill 50% of a test population, ranged from 1.25–5.9 mg/L). These values are within the range of values reported for the few amphibians that have been tested (0.2–42 mg/L). In one of the six species, malathion became twice as lethal when combined with predatory stress. Similar synergistic interactions have been found with the insecticide carbaryl, suggesting that the synergy may occur in many carbamate and organophosphate insecticides. While malathion has the potential to kill amphibians and its presence is correlated with habitats containing declining populations, its actual role in amphibian declines is uncertain given the relatively low concentration in aquatic habitats.

The lethal impacts of Roundup and predatory stress on six species of North American tadpoles.

The decline in amphibians across the globe has sparked a search for the causes, and recent evidence suggests a connection with pesticides. However, for most pesticides, tests on amphibians are rare and conducted only for short durations (1 to 4 days) and without natural stressors. Recent studies have discovered that the stress of predator cues in the water can make insecticides much more lethal to larval amphibians, but it is unknown whether this phenomenon can be generalized to other types of pesticides. Using six species of North American amphibian larvae (Rana sylvatica, R. pipiens, R. clamitans, R. catesbeiana, Bufo americanus, and Hyla versicolor), I examined the impact of a globally common herbicide (Roundup) on the survival of tadpoles for 16days with and without the chemical cues emitted by predatory newts (Notophthalmus viridescens). LC5016-d estimates varied from 0.55 to 2.52 mg of active ingredient (AI)/L, which was considerably lower than the few previous studies using Roundup (1.5 to 15.5 mg AI/L). Moreover, in one of the six species tested (R. sylvatica), the addition of predatory stress made Roundup twice as lethal. This discovery suggests that synergistic interactions between predatory stress and pesticides may indeed be a generalizable phenomenon in amphibians that occurs with a wide variety of pesticides.

Relyea, R. A., and N. Mills. 2001. Predator-induced stress makes the pesticide carbaryl more deadly to grey treefrog tadpoles (Hyla versicolor). PNAS 98:2491-2496.

Global declines in amphibians likely have multiple causes, including widespread pesticide use. Our knowledge of pesticide effects on amphibians is largely limited to short-term (4-d) toxicity tests conducted under highly artificial conditions to determine lethal concentrations (LC50). We found that if we used slightly longer exposure times (10–16 d), low concentrations of the pesticide carbaryl (3–4% of LC504-d) killed 10–60% of gray treefrog (Hyla versicolor) tadpoles. If predatory cues also were present, the pesticide became 2–4 times more lethal, killing 60–98% of tadpoles. Thus, under more realistic conditions of increased exposure times and predatory stress, current application rates for carbaryl can potentially devastate gray treefrog populations. Further, because predator-induced stress is ubiquitous in animals and carbaryl’s mode of action is common to many pesticides, these negative impacts may be widespread in nature.

openCC (other)Jul 2024View details →

Data and code from: A mixture of grass-legume cover crop species may ameliorate water stress in a changing climate, a greenhouse experiment at Dickinson College in Carlisle, PA, USA, 2021.

Data and R code associated with a greenhouse study investigating the influence of water stress on growth, root traits, and biomass of rye and crimson clover seedlings grown separately or together. Data were collected in the Dr. Inge P. Stafford Greenhouse of Dickinson College (Carlisle PA, USA) in June 2021.

openOpenAug 2021View details →

SGS-LTER Ecosystem Stress Area - long-term density dataset following nutrient enrichment stress on the Central Plains Experimental Range in Nunn, Colorado, USA 1975-2011, ARS Study Number 3 (Reformatted to a Darwin Core Archive)

This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/330/3, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/520/8. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Water, nitrogen, and water-plus-nitrogen at levels beyond the range normally experience by shortgrass steppe communities were applied from 1971 through 1975, plant densities were sampled through 1977, and then sampling resumed in 1982, with sampling frequencies changing from annually to every other year. The initial sampling from 1970 to 1974 showed that the water and water plus nitrogen treatments had the strongest effect on plant community structure, both treatments increased biomass, and exotic weed species were noted on the water plus nitrogen treatment. Later sampling from 1982 to 1991 showed a ten-fold increase in exotic weed species on the water plus nitrogen plots as compared to the controls (Milchunas and Lauenroth 1995), a community change that has persiste

openOpenAug 2021View details →

SGS-LTER Ecosystem Stress Area - long-term point-frame (percent basal cover) dataset following nutrient enrichment stress on the Central Plains Experimental Range in Nunn, Colorado, USA 1982-2011, ARS Study Number 3 (Reformatted to a Darwin Core Archive)

This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/331/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/521/7. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Water, nitrogen, and water-plus-nitrogen at levels beyond the range normally experience by shortgrass steppe communities were applied from 1971 through 1975, plant densities were sampled through 1977, and then sampling resumed in 1982, with sampling frequencies changing from annually to every other year. The initial sampling from 1970 to 1974 showed that the water and water plus nitrogen treatments had the strongest effect on plant community structure, both treatments increased biomass, and exotic weed species were noted on the water plus nitrogen treatment. Later sampling from 1982 to 1991 showed a ten-fold increase in exotic weed species on the water plus nitrogen plots as compared to the controls (Milchunas and Lauenroth 1995), a community change that has persiste

openCC (other)Feb 2025View details →

Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits

Climate change will increase soil drying, altering microbial communities via increasing water stress and decreasing resource availability. The responses of these microbial communities to changing environments is likely governed by physiological tradeoffs between high yield, resource acquisition, and stress tolerance (Y-A-S framework). We leveraged a unique field experiment that manipulates both drought and carbon availability across two years and three land uses, and we used both metagenomic and bioassay indicators of the three microbial community traits to test the following hypotheses: 1. Drought increases microbial allocation to stress tolerance functions, at the expense of growth and resource acquisition. 2. Because microbes are resource-limited under drought, increased carbon will enable greater expression of stress tolerance. 3. All three key life history traits described in the YAS framework will trade off, especially when resources are limited. Drought did increase microbial physiological investment in stress tolerance (measured via trehalose production), but we saw few other changes in microbial communities under drought. Carbon addition increased resource acquisition (measured via enzyme activity and resource acquisition gene abundance) and stress tolerance (trehalose assay), but did so in both drought and average rainfall environments. We found no evidence of trait tradeoffs, as we found no significant negative correlations between traits (measured via bioassay and metagenomics). In summary, we found C addition, and to a lesser extent, drought, both altered microbial community function and functional genes. However, resources did not alter drought response in a way that was consistent with theory of life history tradeoffs.