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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-4.0Jun 2022View details →

Still standing: the heat protection delivered by a facultative symbiont to its aphid host is resilient to repeated thermal stress

This is the dataset for the article "Still standing: the heat protection delivered by a facultative symbiont to its aphid host is resilient to repeated thermal stress". This experimental study focused on the heat-protective mutualism between the pea aphid Acyrthosiphon pisum and the facultative bacterium Serratia symbiotica. We exposed two aphid lines (5A: deprived of S. symbiotica, 5AR: infected by S. symbiotica) to a varying number of heat shocks (35°C for 2 h) applied during insect immature development: none (control), one, two, or three. We recorded aphid immature survival rate, total longevity, immature development time, lifetime fecundity and hind tibia length (body size). . Individual = identification of the individual . Line = aphid clonal line, either deprived of (5A) or infected by S. symbiotica (5AR) . Temp = thermal treatment, defined by the number of heat shocks applied during aphid juvenile life (0 = control, 1, 2 or 3) . Survival = whether (Y) or not (N) the individual survived until reproduction  . Adulthood = time elapsed between birth and first reproduction (in days) . Longevity = time elapsed between birth and death (in days) . Fecundity = total number of larvae produced by each aphid throughout lifetime . Wing = whether (Y) or not (N) the individual developed wings following imaginal moult . Tibia = hind tibia length as a proxy of body size (in mm)

Surrogate-modelling & machine learning dataset : finite element stress analysis of biaxial specimen with random elastic properties - 1000 samples

Dataset finite element stress analysis of biaxial specimen with random elastic properties Unzip and execute dataset.py to visualise data samples. PyVista is needed.

Surrogate-modelling & machine learning dataset : finite element stress analysis of biaxial specimen with random elastic properties - 100 samples

Dataset finite element stress analysis of biaxial specimen with random elastic properties Unzip and execute dataset.py to visualise data samples. PyVista is needed

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"

Graph Neural Network dataset : mechanical stress analysis in networks of spherical pores - 1000 samples

Graph Neural Network dataset : mechanical stress analysis in networks of spherical pores - 1000 samples unzip, run data_set.py to see how to interact with the dataset using PyTorch Geometric toolbox

Graph Neural Network dataset : mechanical stress analysis in networks of spherical pores - 6000 samples

Graph Neural Network dataset : mechanical stress analysis in networks of spherical pores - 6000 samples unzip, run data_set.py to see how to interact with the dataset using PyTorch Geometric toolbox

opencc-zeroJul 2022View details →

Failure and deformation characteristics of shale under true triaxial stress loading and unloading under water retention and seepage

A multifunctional true triaxial fluid-structure coupling system was used to conduct water retention and seepage tests of shale under true triaxial loading and unloading stress paths. The stress-strain evolution law of shale specimens under different experimental conditions was obtained, and the corresponding deformation and strength law was analyzed. The evolution law and failure characteristics of cracks in shale were obtained by CT scanning images before and after the experiment. The results show that under the condition of water retention, the volumetric strain of shale specimen increases first, then decreases and finally continues to increase with the increase of deviational stress, indicating that the volumetric change has experienced a process of compaction-expansion-compacting. The partial stress-maximum horizontal strain curve of the sample increases first and then decreases, while the deformation of the sample in the direction of intermediate principal stress shows the characteristics of repeated compression and expansion. In the seepage test, the permeability - maximum horizontal strain curve can be divided into two parts before and after fracture according to the deviant stress - maximum horizontal strain curve. Before fracture, the compression velocity of the specimen in the loading direction exceeds the expansion velocity in the unloading direction, resulting in a decrease in volume and a decrease in permeability. With the increase of deviatoric stress, cracks occur inside the particles and continue to spread from the tip until the cracks break through the shale specimen. In this process, the pore fissure area increases and the permeability of the sample increases rapidly. In terms of fracture evolution, for the water-retaining test, dense tensile and shear cracks appear on the failure plane perpendicular to the direction of maximum and minimum principal stress, and complex shear fracture network appears on the failure plane perpendicular to the direction of intermediate principal stress. For the seepage test, heavy shear failure occurs throughout the original fracture of the sample. With the increase of the penetration depth, the crack shape on the failure surface perpendicular to the direction of intermediate principal stress gradually changes from single type to complex type.

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.

Data from: Evolution of cold tolerance in the highly stress tolerant samphires and relatives (Salicornieae: Amaranthaceae)"

Low temperature constitutes one of the main barriers to plant distributions, confining many clades to their ancestrally tropical biome. However, recent evidence suggests that transitions from tropical to temperate biomes may be more frequent than previously thought. Here, we study the evolution of cold and frost tolerance in the globally distributed and highly stress-tolerant Salicornieae (Salicornioideae, Amaranthaceae s.l.). We first generate a phylogenetic tree comprising almost all known species (85-90%), using newly generated (n = 106) and published nuclear-ribosomal and plastid sequences. Next, we use geographical occurrence data to document in which clades and geographical regions cold-tolerant species occur and reconstruct how cold tolerance evolved. Finally, we test for correlated evolution between frost tolerance and the annual life form. We find that frost tolerance has evolved independently in up to four Northern Hemisphere lineages but that annuals are no more likely to evolve frost tolerance than perennials, indicating the presence of different strategies for adapting to cold environments. Our findings add to mounting evidence for multiple independent out-of-the-tropics transitions among close relatives of flowering plants and raise new questions on the ecological and physiological mechanism(s) of adaptation to low temperatures in Salicornieae.

Dataset for: Locally resolved stress-state in samples during experimental deformation: insights into the effect of stress on mineral reactions

Data used for the publication: Cionoiu, S., Tajčmanová, L., Moulas, E. and Stünitz H. (under review, 2022) Locally resolved stress-state in samples during experimental deformation: insights into the effect of stress on mineral reactions, Journal of Geophysical Research: Solid Earth See details on the files in ReadMe.txt

The effect of antidepressants on genes of endoplasmic reticulum stress in human astrocyte cell line.

Many central nervous system (CNS) diseases, including major depressive disorder (MDD), are underpinned by the unfolded protein response (UPR) activated under endoplasmic reticulum (ER) stress. New, more efficient, therapeutic options for MDD are needed to avoid adverse effects and drug resistance. Therefore, the aim of the work was to determine whether UPR signalling pathway activation in astrocytes may serve as a novel target for antidepressant drugs. Among the tested antidepressants (escitalopram, amitriptyline, S-ketamine), only S-ketamine induced the expression of most ER stress-responsive genes in astrocytes. <a href="https://doi.org/10.3390/pharmaceutics14040846">https://doi.org/10.3390/pharmaceutics14040846</a>

Data of the study of Maternal temperature stress modulates acclimation and thermal biology in Octopus maya (Cephalopoda: Octopodidae) juvenile progeny

These data shows the effects of temperature and exposure time on octopus juveniles  obtained from thermal-stressed (30°C) and non-stressed (24°C) females when exposed to optimal (25°C) and high temperatures (30°C) for 20 and 30 days, respectively. Data of  survival, and oxygen consumption (MR) were obtained, also in routine (RMR) and resting conditions (SMR). The high metabolic rate (HMR) was used to obtain the thermal metabolic scope (TMS) That was defined as: TMS = HMR - SMR Data on the  antioxidant defense enzymes and radical oxygen species (ROS) were used to evaluate if transgenerational effect of temperature provoked changes in the hability of juveniles to neutralize ROS.

Data for: Temperate and tropical lizards are vulnerable to climate warming due to increased water loss and heat stress

Climate warming has imposed profound impacts on species globally. Understanding the vulnerabilities of species from different latitudinal regions to warming climates is critical for biological conservation. Using five species of Takydromus lizards as a study system, we quantified physiological and life-history responses and geography range change across latitudes under climate warming. Using integrated biophysical models and hybrid species distribution models, we found: (1) thermal safety margin is larger at high latitudes, and is predicted to decrease under climate warming for lizards at all latitudes; (2) climate warming will speed up embryonic development and increase annual activity time of adult lizards, but will exacerbate water loss of adults across all latitudes; and (3) species across latitudes are predicted to experience habitat contraction under climate warming due to different limitations: tropical and subtropical species are vulnerable due to increased extremely high temperatures, whereas temperate species are vulnerable due to both extremely high temperatures and increased water loss. This study provides a comprehensive understanding of the vulnerability of species from different latitudinal regions to climate warming in ectotherms and also highlights the importance of integrating environmental factors, behavior, physiology, and life-history responses in predicting the risk of species to climate warming.

Non-structural carbohydrates predict survival in saplings of temperate trees under carbon stress

1. Non-structural carbohydrates (NSCs) mediate plant survival when the plant's carbon (C) balance is negative, suggesting that NSCs could predict plant survival under C stress. To examine this possibility, we exposed saplings of six temperate tree species to diverse levels of C stress created by the combination of two light conditions (full light availability and deep shade) and two defoliation levels (severe defoliation and non-defoliation). We then measured survival, biomass, and total NSCs and soluble sugar (SSs) concentrations in different organs of both dead and live saplings. 2. We estimated mean NSCs and SSs contents and concentrations per sapling and fitted logistic generalized mixed-effects models to determine if NSCs and SSs predict survival. Using inverse prediction modelling, we also determined whether there is a common NSCs and SS threshold across species at the time of sapling's death. 3. Defoliation and shade reduced the mean sapling's NSCs and SSs contents, indicating C stress. Mean sapling NSCs and SSs contents and concentrations predicted survival and the robustness of the models improved with the inclusion of species. At death, saplings of the exotic deciduous tree species Acer pseudoplatanus exhibited significantly lower mean NSCs and SSs contents than saplings of the evergreen conifer species Podocarpus nubigenus and lower stem NSCs and SSs concentrations than the broadleaf evergreen species Drimys winteri. 4. The energetic role that NSCs and SSs play in plants under C stress was evidenced by the capacity of these compounds to predict sapling survival under C stress. No common threshold of NSCs and SSs contents or concentrations for sapling survival amongst species was found, indicating that the level of these compounds may not be good proxies for interspecific comparisons of tolerance to C stress. Presumably, there are species-specific limits for the mobilization and use of NSCs and SSs in metabolism. 5. Our results anticipate that the inclusion of NSCs and SSs in modelling will improve predictions regarding tree responses to ongoing climate change. Nonetheless, a better understanding of the many roles that carbohydrates play in plant survival under C stress is required to scale predictions up to the community level.

3D locations of the radiators and the details of Coulomb stress about the Mw 7.3 East Cape earthquake

This is part of the supplementary material of the paper " The 2021 Mw 7.3 East Cape earthquake: Triggered Rupture in Complex Faulting Revealed by Multi-Array Back-projections". The 3D locations of the radiators are in the file ‘S1.xlsx’. The details of Coulomb stress calculation are in the file ‘S2.xlsx to S9.xlsx’.

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-zeroSep 2022View details →

Data from: Climatic stress decreases tick survival but increases rate of host-seeking behavior

Ticks are vectors of many diseases and are expanding in geographic distribution. However, how ticks will fare in their new environments where they may experience stressful climatic conditions at the expansion front remains unclear. Since there is a trade-off in ticks between behaviors that promote longevity and behaviors that promote reproduction, we hypothesized that extreme climatic stress reduces the survivorship of ticks but increases the frequency of tick host-seeking behavior or questing. Here, we used a novel method to simulate climatic stress on individual ticks of three species – Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis – to evaluate their survival, physiology, and questing behavior. The first experiment involved placing 144 adult ticks of each species in two temperature ranges (15-25 °C and 25-35 °C) and three relative humidity treatments (32% RH, 58% RH, and 84% RH). We assessed the ticks daily for survivorship and questing, and we measured water loss by comparing the mass of each tick when it died to when it was fully hydrated. In this first experiment, ticks in warmer and less humid conditions generally died faster than in cooler and more humid conditions. Ticks of all three species were more likely to quest shortly before their death and consistently died after losing approximately 50-56% of total body water content, but Ixodes reached that threshold much faster than the other two species. The second experiment involved placing 18 ticks of each species at 35 °C and 32% RH. We assessed the ticks every three hours for survivorship, questing, and water loss. Ticks again were more likely to quest shortly before their death. With frequent checks, we were able to measure the dehydration tolerance more accurately and the rate of water loss. Ticks of all three species consistently died after losing approximately 51% of total body water content. However, Ixodes lost water approximately 5× faster than Amblyomma and 11× faster than Dermacentor. These results demonstrate that severe climatic stress tilts the trade-off toward higher questing rates, but not higher overall questing time because of reduced survival rates. Further investigations of ticks' behavioral and physiological responses to abiotic stress are necessary to develop robust models of how climate change will affect the transmission of tick-borne diseases.

Nutritional stress exacerbates impact of a novel insecticide on solitary bees' behaviour, reproduction and survival

Pesticide exposure and food stress are major threats to bees, but their potential synergistic impacts under field-realistic conditions remain poorly understood and are not considered in current pesticide risk assessments. We conducted a semi-field experiment to examine the single and interactive effects of the novel insecticide flupyradifurone (FPF) and nutritional stress on fitness proxies in the solitary bee Osmia bicornis. Individually marked bees were released into flight cages with monocultures of either buckwheat, wild mustard or purple tansy, which were assigned to an insecticide treatment (FPF or control) in a crossed design. Nutritional stress, which was high in bees foraging on buckwheat, intermediate on wild mustard and low on purple tansy, modulated the impact of insecticide exposure. Within the first day after application of FPF, mortality of bees feeding on buckwheat was 29 times higher compared to control treatments, while mortality of FPF exposed and control bees was similar in the other two plant species. Moreover, we found negative synergistic impacts of FPF and nutritional stress on offspring production, flight activity, flight duration, and flower visitation frequency. These results reveal that environmental policies and risk assessment schemes that ignore interactions among anthropogenic stressors will fail to adequately protect bees and the pollination services they provide.