Find research datasets worth reusing

opencc-by-4.0Dec 2023View details →

Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress

This repository provides scRNA-seq data corresponding to the manuscript "Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.

opencc-by-4.0Nov 2023View details →

The role of bottom friction in mediating the response of the Weddell Gyre circulation to changes in surface stress and buoyancy fluxes

This repository contains code to reproduce the figures in the paper titled "The role of bottom friction in mediating the response of the Weddell Gyre circulation to changes in surface stress and buoyancy fluxes" published in the Journal of Physical Oceanography (DOI: <a href="https://doi.org/10.1175/JPO-D-23-0165.1">https://doi.org/10.1175/JPO-D-23-0165.1</a>), as well as the barotropic vorticity budget terms for each of simulation in the paper.

opencc-by-4.0Dec 2023View details →

Vocalization Patterns in Laying Hens - An Analysis of Stress-Induced Audio Responses

This repository houses a comprehensive collection of data and resources from the study "Vocalization Patterns in Laying Hens - An Analysis of Stress-Induced Audio Responses." Led by Dr. Suresh Neethirajan at Mooanalytica, Department of Agriculture & Aquaculture, Faculty of Agriculture & Computer Science, Dalhousie University, this research represents a significant foray into the field of poultry ethology and welfare monitoring using advanced machine learning techniques. Key Components of the Repository <ol> <li> Experimental Audio Data <ul> <li>Control and Treatment Vocalizations: Audio recordings of laying hens under two different stress conditions – sudden umbrella opening (Treatment 1) and simulated dog barking sounds (Treatment 2), along with control groups. The processed dataset is approximately 460 MB for the control group experimental data and about 2 GB for the 2 treatment group experimental data, capturing the nuanced responses of hens to these stressors.</li> <li>Original Raw Data: The original, unprocessed audio data is around 9 GB in size. Though not included in the repository, it can be made available upon reasonable request.</li> </ul> </li> <li> Algorithm and Code Files <ul> <li>CNN Feature Extraction and Classification Algorithms Python scripts used for the extraction of features from the audio data using Convolutional Neural Networks (CNN) and subsequent classification.</li> <li>Supplementary Algorithms Additional code files that support the processing and analysis of the audio data.</li> </ul> </li> <li> MFCC Feature Dataset <ul> <li>An Excel file containing the 40 Mel Frequency Cepstral Coefficients (MFCC) features extracted from the vocalization data. This dataset provides a detailed spectral analysis of the hen's vocalizations, crucial for understanding their response to stress.</li> </ul> </li> </ol> Study Overview This study aimed to classify and analyze the vocalization patterns of laying hens subjected to different stressors. Using a CNN model, the research identified distinct vocal patterns between control and treated groups, indicating unique vocal responses to different types of stressors. This study is pivotal in understanding the impact of environmental stressors on poultry welfare and behavior. The age of the chickens and the timing of stressor application were also critical factors influencing vocalization patterns. Implications and Applications: The findings from this study have significant implications for poultry welfare monitoring and management. By providing a non-invasive method to assess the well-being of chickens, this research contributes valuable insights into enhancing poultry management practices and welfare standards. The resources in this repository are intended for researchers, academicians, and professionals in animal behavior, veterinary science, and poultry management. We encourage the use of these data and tools for further research and practical applications in the field of precision (Digital) livestock farming and animal welfare. For any queries or requests related to the raw dataset, please contact Dr. Suresh Neethirajan.

opencc-zeroDec 2023View details →

Data from: A cucumber protein, Phloem Phosphate Stress Repressed 1, rapidly degrades in response to a phosphate stress condition

Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signalling cascades. In plants, the vascular system delivers nutrients and signalling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi-stress conditions. Here, we report on the identification and characterization of a cucumber protein, Cucumis sativus Phloem Phosphate-Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation, within the sieve tube system, through the action of CsPPSR1 Kinase. Further, we discovered that CsPPSR1 Kinase was susceptible to Pi-starvation-induced degradation, in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.

opencc-by-4.0Dec 2023View details →

Carmichael_etal_Data_Analysis_All_Stress_Responses

Data for the submission "Reconciling variability in multiple stressor effects using environmental performance curves". This includes growth rate data for 12 bacterial taxa exposed to gradients of temperature, pH and salinity.  The R script for the data analysis pipeline is included, as well as a README file describing the data layout.

opencc-by-4.0Nov 2021View details →

Distinct and essential roles of bZIP transcription factors in stress response and pathogenesis in Alternaria alternata

The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata un- der metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We determined the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A. alternata by analyzing targeted gene deletion mutants. Morphological analysis provides evidence that bZIPs including Gcn4, MeaB, Atf1, Hac1 and Ada1 are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover, the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings identified many crucial transcription factor genes and pathways related to cell development, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.

opencc-by-4.0Jan 2022View details →

GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)

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>.

Supplementary Table S5 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S5. Repository data showing genes identified by MapMan in Giza 178 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose.  E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S4 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S4. Repository data showing genes identified by MapMan in Giza 177 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose. E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S2 - Article:Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S2. Repository data for the global analysis produced for cv Giza 177.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 177 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 177 up regulated genes.    D, GOEA results for Giza 177 down regulated genes.

Supplementary Table S3 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S3. Repository data for the global analysis produced for cv Giza 178.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 178 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 178 up regulated genes.    D, GOEA results for Giza 178 down regulated genes.

Role of Alkylhydroperoxidase Rv2159c in the Oxidative Stress Response and Virulence of Mycobacterium tuberculosis

Mycobacterium tuberculosis, which causes tuberculosis, is one of the leading infectious agents worldwide with a high rate of mortality. Following aerosol inhalation, M. tuberculosis primarily infects the alveolar macrophages, which results in a host immune response that gradually activates various antimicrobial mechanisms, including the production of reactive oxygen species (ROS), within the phagocytes to neutralize the bacteria. OxyR is the master regulator of oxidative stress response in several bacterial species. However, due to the absence of a functional oxyR locus in M. tuberculosis, the peroxidase stress is controlled by alkylhydroperoxidases. M. tuberculosis expresses alkylhydroperoxide reductase to counteract the toxic effects of ROS. In the current study, we report the functional characterization of an ortholgue of alkylhydroperoxidase family member, Rv2159c, a conserved protein with putative peroxidase activity, during stress response and virulence of M. tuberculosis. We generated a gene knockout mutant of M. tuberculosis Rv2159c (MtbΔ2159) by specialized transduction. The MtbΔ2159 was sensitive to oxidative stress and exposure to toxic transition metals. In a human monocyte (THP-1) cell infection model, MtbΔ2159 showed reduced intracellular survival and increased expression of pro-inflammatory molecules, includingIL-1β, IP-10 and MIP-1α, compared to the wild type M. tuberculosis and Rv2159c-complemented MtbΔ2159 strains. Similarly, in a guinea pig model of pulmonary infection, MtbΔ2159 displayed growth attenuation in the lungs, compared to the wild type M. tuberculosis and Rv2159c-complemented MtbΔ2159 strains. Our study suggests that Rv2159c has a significant role in maintaining the cellular homeostasis during stress and virulence of M. tuberculosis.

opencc-zeroApr 2022View details →

Network analysis reveals that acute stress exacerbates gene regulatory responses of the gill to seawater in Atlantic salmon

The transition from freshwater to seawater represents a physiological challenge for Atlantic salmon smolts preparing for downstream migration. Stressors occurring during downstream migration to the ocean impair the ability of smolts to maintain osmotic/ionic homeostasis in seawater. The molecular mechanisms underlying this interaction are not fully understood, especially at the organ level. We combined RNA-Seq with measures of whole-animal homeostasis to examine gene expression dynamics in the gills of smolts associated with impaired seawater tolerance after an aquaculture-related stressor. Smolts were given a 24 h seawater tolerance test before and after exposure to an acute handling/confinement stress. RNA-Seq followed by differential expression and weighted gene correlation network analysis (WGCNA) was used to quantify the transcriptional response of the gill to handling/confinement stress, seawater and their interaction. Exposure to acute stress was associated with a general stress response and impaired osmotic/ionic homeostasis in seawater. We identified gene networks in the gill exhibiting response to acute stress alone, seawater alone, and others exhibiting combined effects of both stress and seawater. Our findings indicate that acute handling/ confinement stress increases the intensity of seawater-related gene expression and suggest that increased investment in mechanisms related to ion transport may be part of a compensatory response to impaired seawater tolerance in smolts.

opencc-zeroJun 2022View details →

Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - albeit significant - effect of strain × environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.

opencc-by-4.0Jul 2022View details →

Obesity and acute stress modulate appetite and neural responses in food word reactivity task

Data used in "Carnell S, Benson L, Papantoni A, Chen L, Huo Y, Wang Z, Peterson BS, Geliebter A. Obesity and acute stress modulate appetite and neural responses in food word reactivity task. PloS one"

opencc-by-4.0Jul 2022View details →

OMA1-mediated integrated stress response protects against ferroptosis in mitochondrial cardiomyopathy

Cardiomyopathy and heart failure are common manifestations in mitochondrial disease caused by deficiencies in the oxidative phosphorylation system of mitochondria (OXPHOS). Here, we demonstrate that the cardiac-specific loss of the assembly factor Cox10 of the cytochrome c oxidase causes mitochondrial cardiomyopathy in mice, which is associated with OXPHOS deficiency, lysosomal defects and an aberrant mitochondrial morphology. Activation of the mitochondrial peptidase Oma1 in Cox10-/- mice results in mitochondrial fragmentation and induction of the integrated stress response (ISR) along the Oma1-Dele1-Atf4 signalling axis. Ablation of Oma1 or Dele1 in Cox10-/- mice aggravates cardiomyopathy. ISR inhibition impairs the cardiac glutathione metabolism, limits the selenium-dependent accumulation of the glutathione peroxidase Gpx4 and increases lipid peroxidation in the heart, ultimately culminating in ferroptosis. Our results demonstrate a protective role of the Oma1-Dele1-mediated ISR in mitochondrial cardiomyopathy and link ferroptosis to OXPHOS deficiency and mitochondrial disease.

opencc-zeroSep 2022View details →

A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes

Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in non-coding elements near genes involved in environmental response pathways as well as losses of transcriptions factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.

opencc-by-4.0Sep 2022View details →

Poroelastic response of water level in Tengchong well aquifer to dynamic stress

Data used in manuscript named "Poroelastic response of water level in Tengchong well aquifer to dynamic stress"

opencc-zeroOct 2022View details →

Sexual selection moderates heat stress response in males and females

1. A widespread effect of climate change is the displacement of organisms from their thermal optima. The associated thermal stress imposed by climate change has been argued to have a particularly strong impact on male reproduction but evidence for this postulated sex-specific stress response is equivocal. 2. One important factor that may explain intra- and interspecific variation in stress responses is sexual selection, which is predicted to magnify negative effects of stress. Nevertheless, empirical studies exploring the interplay of sexual selection and heat stress are still scarce. 3. We tested experimentally for an interaction between sexual selection and thermal stress in the red flour beetle Tribolium castaneum by contrasting heat responses in male and female reproductive success between setups of enforced monogamy versus polygamy. 4. We found that polygamy magnifies detrimental effects of heat stress in males but relaxes the observed negative effects in females. Our results suggest that sexual selection can reverse sex differences in thermal sensitivity, and may therefore alter sex-specific selection on alleles associated with heat tolerance. 5. Assuming that sexual selection and natural selection are aligned to favour the same genetic variants under environmental stress, our findings support the idea that sexual selection on males may promote the adaptation to current global warming.