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opencc-zeroAug 2022View details →

Reconstruction of a soil microbial network induced by stress temperature

By applying a nonlinear time-series analysis to the metagenomic data of the soil microbiota cultured under suitable (30℃) or stressful (37℃) conditions, we show how the microbial interaction network responds to temperature stress. While the genera that persisted only under the suitable condition gave fewer positive effects, the genera that appeared only under the stressful condition received more positive effects in agreement with SGH. However, temperature changes also induce reconstruction of a community network, leading to an increased proportion of negative interactions at the whole community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities.

opencc-by-4.0Aug 2022View details →

The hydro-mechanical properties of fracture intersections: pressure dependant permeability and effective stress law

The present repository includes the raw permeability data presented in the manuscript submitted for publication in Journal of Geophysical Research: Solid Earth entitled The hydro-mechanical properties of fracture intersections: pressure-dependant permeability and effective stress law. The repository is presented as compressed folders named after the Figures of the manuscript where the data is presented.

openother-openAug 2021View details →

Heat stress at Uva Island during the 1982-83, 1997-98 and 2015-16 ENSOs

Heat stress at Uva Island during the 1982-83, 1997-98 and 2015-16 ENSOs Description: This repository obtains and analyzes SST data for Uva Island reef to compare the intensity of heat stress during the past three major ENSOs. Content: A.Temperature_DHW.Rmd: This script uses the temperature data in the B.Temperature_data folder to calculate the accumulated heat stress (DHW) at Uva Island reef, based on three different temperature data sources (OISST, CRW and In situ sensors). Figures resulting from running the script are saved in the C.Outputs folder. B.Temperature_data: Directory containing data files in .csv format with the temperature data for Uva Island reef from different sources <ul> <li> B.Temperature_data/Uva_CRW_MMM_1985-2012.csv: Coral Reef Watch MMM (5km products v3.1) for the closest pixel to Uva Island reef </li> <li> B.Temperature_data/Uva_Daily_CRW_5km_1985-2016.csv: Coral Reef Watch SST data (5km products v3.1) for the closest pixel to Uva Island reef </li> <li> B.Temperature_data/Uva_Daily_InSitu_1997-2018.csv: In situ temperature data obtained from 1997-2018 at Uva Island reef ("Gardineroseris city') ~ 3m depth </li> <li> B.Temperature_data/Uva_Daily_OISST_1982-2016.csv: Optimal Interpolation SST data (V2) for the closest pixel to Uva Island reef </li> <li> B.Temperature_data/BanderasBay_Daily_OISST_1982-2016.csv: Optimal Interpolation SST data (V2) for the closest pixel to Uva Island reef </li> </ul> C.Outputs: Directory containing figure files related with temperature and DHW included on the paper. <ul> <li>Figure 1a and 3a</li> <li>Figure S6</li> <li>Figure S7</li> <li>Figure S8</li> <li>Figure S9</li> <li>Figure S5b</li> </ul> D.SST_nc: Directory containing scripts used to download and extract OISST and CRW SST data from .nc files. You do not have to run the code in the D.SST_nc folder to produce the data analysis in the paper (this can be achieved by running A.Temperature_DHW.Rmd using the temperature data already provided in B.Temperature_data). However, you could use these scripts to retrieve and extract the SST data by yourself.The outputs of these scripts are already included in B.Temperature_data/Uva_CRW_MMM_1985-2012.csv:, B.Temperature_data/Uva_Daily_CRW_5km_1985-2016.csv" and B.Temperature_data/Uva_Daily_OISST_1982-2016.csv. By running the scripts inside this folder you will create those files again in the "D.SST_nc" folder. You would need ~ 123GB of space for CRW SST data and ~17GB for OISST data <ul> <li> D.SST_nc/1.Get_OISST_data.sh: This script downloads 1981-2016 NOAA OI SST V2 High Resolution data from ftp://ftp.cdc.noaa.gov/Datasets/noaa.oisst.v2.highres/ </li> <li> D.SST_nc/2.Get_CoralTemp_data.sh: This script downloads NOAA CRW 5km SST data (CoralTemp v3.1) (fftp://ftp.star.nesdis.noaa.gov/pub/sod/mecb/crw/data/coraltemp/v1.0/nc/) and the 1985-2012 climatology (ftp://ftp.star.nesdis.noaa.gov/pub/sod/mecb/crw/data/5km/v3.1/climatology/nc/ct5km_climatology_v3.1.nc). It could also download the already calculated DHW values (ftp://ftp.star.nesdis.noaa.gov/pub/sod/mecb/crw/data/5km/v3.1/nc/v1.0/daily/dhw/) directly from NOAA CRW 5km products. However, these lines are commented by default since we performed these calculations ourselves based on the CRW SST data (CoralTemp) and MMM. </li> <li> D.SST_nc/3.Extract_SST_Uva.Rmd: This script extracts the SST data from OISST and CRW datasets for Uva Island. It also extracts the already calculated climatology (MMM) from CRW 5km products. CRW DHW values from NOAA CRW 5km products can be extracted as well. However, these lines are commented by default since we performed these calculations ourselves based on the CRW SST data (CoralTemp) and MMM. </li> </ul>

opencc-zeroSep 2022View details →

Data from: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks

Ticks are the most important vectors of zoonotic disease-causing pathogens in North America and Europe. Many tick species are expanding their geographic range. Although correlational evidence suggests that climate change is driving the range expansion of ticks, experimental evidence is necessary to develop a mechanistic understanding of ticks' response to a range of climatic conditions. Previous experiments used simulated microclimates, but these protocols require hazardous salts or expensive laboratory equipment to manipulate humidity. We developed a novel, safe, stable, convenient, and economical method to isolate individual ticks and manipulate their microclimates. The protocol involves placing individual ticks in plastic tubes, and placing six tubes along with a commercial two-way humidity control pack in an airtight container. We successfully used this method to investigate how humidity affects survival and host-seeking (questing) behavior of three tick species: the lone star tick (Amblyomma americanum), American dog tick (Dermacentor variabilis), and black-legged tick (Ixodes scapularis). We placed 72 adult females of each species individually into plastic tubes and separated them into three experimental relative humidity (RH) treatments representing distinct climates: 32% RH, 58% RH, and 84% RH. We assessed the survival and questing behavior of each tick for 30 days. In all three species, survivorship significantly declined in drier conditions. Questing height was negatively associated with RH in Amblyomma, positively associated with RH in Dermacentor, and not associated with RH in Ixodes. The frequency of questing behavior increased significantly with drier conditions for Dermacentor but not for Amblyomma or Ixodes. This report demonstrates an effective method for assessing the viability and host-seeking behavior of tick vectors of zoonotic diseases under different climatic conditions.

opencc-by-4.0Sep 2022View details →

Nicaragua Upper-Plate Earthquake Inversion and Static Stress Change

This data set contains GPS time series and displacements (in tabular form) for the April 10 2014 and Sept 15 & 28 2016 M>5 upper-plate earthquakes in Nicaragua. The data set also contains configuration files for GBIS code, used in determining fault kinematics and Coulomb 3.3, used for calculating static stress change following the earthquakes. A README.txt file is in each folder and details what configuration files do and format of data.

opencc-by-4.0Sep 2022View details →

ETV6 represses Tumor Necrosis Factor During Stress Hematopoiesis to Regulate Mouse Stem Cell Function

At the root of the blood system lies a heterogenous population of hematopoietic stem and progenitor cells (HSPCs), which reside in the bone marrow (BM) and give rise to diverse blood lineages. Maintaining this pool of self-renewing HSPCs is critical to uphold hematopoiesis during period of stress such as bleeding or infection1. ETS Variant Transcription Factor 6 (ETV6) is a transcriptional repressor that is highly expressed in HSPCs2 where it is essential for development and maintenance of the adult hematopoiesis 3. In 2015, our group4 and others5-7  identified germline pathogenic ETV6 variants in families with predisposition to B-acute lymphoblastic leukemia (B-ALL) and thrombocytopenia, defining a new genetic syndrome known as Thrombocytopenia 5 (T5). Subsequently, we performed targeted germline ETV6 sequencing of remission blood samples from over 4,000 children with B-ALL and identified germline ETV6 variants in ~1% of cases7. In vitro studies revealed that ETV6 variant proteins exhibit impaired repressor activity, reduced DNA binding, and aberrant subcellular localization4,5,7,8. Overall, these studies indicated that T5-associated germline ETV6 variants negatively impact the repressor activity of ETV6. In support of this notion, transcriptional profiling of peripheral blood cells from T5 patients has revealed upregulation of interferon response genes9. Nevertheless, little remains known about the mechanisms by which ETV6 regulates the HSPC compartment and how T5-associated ETV6 variants contribute to disease.   To address these questions, we used CRISPR-Cas9 gene editing to generate a novel mouse model harboring a pathogenic heterozygous germline Etv6 variant, R355X, the murine equivalent to the human T5-associated variant R359X10. Through the comprehensive study of this model, we describe a novel role for ETV6 during aging and regenerative hematopoiesis and show that the heterozygous Etv6R355X variant impairs HSC function in vitro and in vivo. Using genomic approaches to interrogate mouse and human HSCs, we identify new ETV6 targets, including the gene encoding Tumor Necrosis Factor (TNF) and genes involved in TNF signaling. Further, we show increased TNF production and cell cycling in Etv6R355X/+ mouse HSPCs post-BM transplantation. Finally, we demonstrate that genetic ablation of Tnf restores the long-term potential of Etv6R355X/+ cells in serial replating assays in vitro. Together, these findings provide novel insights into the pathways regulated by ETV6 and demonstrate how a pathogenic variant impacts ETV6 function in the context of hematopoietic stress. All bulk RNAseq, Cut&Run, ATACseq, and Hi-C data has been submitted to in the Gene Expression Omnibus (accession number GSE213597) and Sequence Read Archive (BioProject number PRJNA880871). Due to the journal’s limitation on submitted supplementary data  as an Excel file, all post-analysis supplemental data files are deposited in Dryad data repository to be made available with this manuscript.

opencc-by-4.0Sep 2022View details →

Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)

This vcf file constitute underlying raw data material for the manuscript "Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)".  The SNP genotype data came from a whole-genome resequencing and were called using the Nipponbare IRGSP 1.0 rice reference genome. SNPs with a miss rate greater than 30% and minor allele frequency (MAF) less than 5% were removed. Heterozygous alleles were also excluded. Finally, 160,498 SNPs were selected and used in the GWAS analysis.

opencc-by-4.0Jul 2022View details →

Supplementary Materials of Bacillus subtilis Protects the Ducks from Oxidative Stress Induced by Escherichia coli: Efficacy and Molecular Mechanism

Figure S1: The KEGG classification of DEGs; Table S1: Analysis composition of basal diets and nutrient level (air-dry basis, %); Table S2: Primers used for the RT-qPCR in this study.

opencc-by-3.0Sep 2022View details →

Survival, wet weight and muscle cellular stress responses of Palaemon varians shrimps exposed to combined temperature and salinity variations

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>). 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.

opencc-by-4.0Jun 2022View details →

Transcriptome data of social defeat stress of various durations

Data of meta-analysis of transcriptomic changes in the PFC after SDS of various durations. This analysis enabled us to identify clusters of the most reproducible changes in gene expression after 10 and 30 days of SDS and to determine which genes are associated with susceptibility and resistance to SDS after 10 days. Furthermore, we compared such changes in mice after SDS of various durations with data from a meta-analysis of postmortem transcriptomes of the dorsolateral PFC from depressed patients and data of the transcriptomic study on the PFC from patients with PTSD.

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

opencc-by-4.0Jul 2022View details →

Supplementary material - Eggerthella lenta DSM 2243 alleviates bile acid stress response in Clostridium ramosum and Anaerostipes caccae by transformation of bile acids

The word document is a collection of supplementary figures and tables.  The excel file is a collection of raw data from experiments.

opencc-by-4.0Jun 2010View details →

Figure 2: Variation of the shear stress depending on the speed rate 54-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES

The evaluation of photodegradation was carried out through the variation of photoprotective factor of the studied product kept 60 minutes under UV radiation at 65±C. The tests revealed the preservation or even a slight increase in the SPF. The use of screen substances in the formulation of photoprotective products results in undesirable sensory characteristics: visible white ¯lm on the skin surface, unpleasant sensation, dry or oily skin after application.

opencc-zeroApr 2024View details →

Evolutionary potential under heat and drought stress at the southern range edge of North American Arabidopsis lyrata

The warm edges of species' distributions are vulnerable to global warming. Evidence is the recent range retraction from there found in many species. It is unclear why populations cannot easily adapt to warmer, drier, or combined hot and dry conditions and locally persist. Here, we assessed the ability to adapt to these stressors in the temperate species Arabidopsis lyrata. We grew plants from replicate seed families of a central population with high genetic diversity under a temperature and precipitation regime typical of the low-latitude margin or under hotter and/or drier conditions within naturally occurring amplitudes. We then calculated genetic variance-covariance (G-) matrices of traits depicting growth and allocation as well as selection vectors to compare the predicted adaptation potential under the different climate-stress regimes. We found that the sum of genetic variances and genetic correlations were not significantly different under stress as compared to benign conditions. However, under drought and heat drought, the predicted ability to adapt was severely constrained due to strong selection and selection pointing in a direction with less multivariate genetic variation. The much-reduced ability to adapt to dry and hot-dry conditions is likely to reduce the persistence of populations at the low-latitude margin of the species' distribution and contribute to the local extinction of the species under further warming.

opencc-by-4.0Nov 2023View details →

Data supporting the manuscript entitled: 'Intermittent soil water stress history favors microbial traits that better mitigate wheat biomass losses during subsequent water stress.'

Data living in this data repository supports the scientific article entitled: Intermittent soil water stress history favors microbial traits that better mitigate wheat biomass losses during subsequent water stress.

opencc-by-4.0Apr 2024View details →

Supplementary Materials of "Elementary mathematics helps to shed light on the transpiration budget under water stress"

This directory contains the Jupyter notebook used to do complete analysis from our paper "Elementary mathematics sheds light on the transpiration budget under water stress" submitted to the Ecohydrology Journal at the Special Issues "ECOHYDROLOGY OF INLAND AND COASTAL WATERS in honor of Ignacio Rodriguez-Iturbe". These materials are referenced in the main text and supplemental text of the publication. The purpose of this repository is to facilitate replication of our analysis by any interested parties.  Specifically, this directory contains ten files: <ul> <li>From 0 to 5, Jupyter Notebook prepared and used for the analysis (please execute the notebooks in numerical sequence). </li> <li>"Table_S1.xlsx" Data From: Kröber, W., H. Heklau, and H. Bruelheide. 2015. “Leaf Morphology of 40 Evergreen and Deciduous Broadleaved Subtropical Tree Species and Relationships to Functional Ecophysiological Traits.” Plant Biology  17 (2): 373–83. <a href="https://doi.org/10.1111/plb.12250">https://doi.org/10.1111/plb.12250</a>.</li> <li>"Richards_VG.csv" contains Van Genuchten Parameters for various soils.</li> <li>"The_Rosetta_Stone_of_the_Darcy_Buckingham_law.pdf" addresses the challenge of converting water flux units between Darcy-like soil and plant descriptions, where hydrologists use "head" units (meters) and plant physiologists use pressure potential (MPa). The aim is to clarify and perform the necessary unit conversions, with detailed explanations available in the relevant section on <a href="https://abouthydrology.blogspot.com/2022/10/my-water-management-in-agricolture.html">this webpage</a>.</li> </ul>