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opencc-by-4.0Dec 2018View details →

Ionosphere-Thermosphere Data Published in "Responses of the Thermosphere and Ionosphere System to Concurrent Solar Flares and Geomagnetic Storms"

This dataset supports the Journal of Geophysical Research publication "Responses of the Thermosphere and Ionosphere System to Concurrent Solar Flares and Geomagnetic Storms" by Qian et al., 2019. The data files are selected output and related analyses from the thermosphere-ionosphere-electrodynamics general circulation model (TIEGCM). The format of the data files are either IDL save files or NetCDF files or ASCII.

opencc-by-4.0Dec 2021View details →

Data for "Low- and mid-latitude ionospheric response to the 2013 St Patrick's Day geomagnetic storm in the American Sector: GITM simulation"

The dataset stores the GITM simulation results for the study "Low- and mid-latitude ionospheric response to the 2013 St Patrick's Day geomagnetic storm in the American Sector: GITM simulation"

opencc-by-4.0Oct 2024View details →

Neuroblastoma cell lines display heterogeneity in differentiation responses

Underlying and extended data for the manuscript "Neuroblastoma cell lines display heterogeneity in differentiation responses", Ferguson et al (2024). Includes Underlying data for Figures 2A-C and Figures 3A-D, and Extended data - Table S1: qRT-PCR primer sequences, Table S2 - List of genes in clusters identified in [7] (Table S2 added after version 1).

opencc-by-4.0Oct 2023View details →

Biogeochemical responses to different El Niño events in the equatorial Pacific: A case study of 1997-98 and 2015-16 El Niños

Model output used in Biogeochemical responses to different El Niño events in the equatorial Pacific: A case study of 1997-98 and 2015-16 El Niños

The phenotypic and fitness response to the combination of copper and thermal stressors strongly varies within the ciliate species, Tetrahymena thermophila

Copper pollution can alter biological and trophic functions. Organisms can set up different tolerance strategies, including accumulation mechanisms (intracellular vacuoles, external chelation, etc.) to maintain themselves in copper-polluted environments. Accumulation mechanisms can influence the expression of other phenotypic traits, allowing organisms to improve their fitness. Whether copper effects on accumulation strategies interact with other environmental stressors such as temperature and how this may differ within species are still unsolved questions. Here, we tested experimentally whether the combined effect of copper and temperature modulates traits linked to fitness, morphology, movement and accumulation in six strains of the ciliate Tetrahymena thermophila. We also explored whether copper accumulation might modulate environmental copper concentration effects on phenotypic and fitness traits. Results showed high intraspecific variability in the phenotypic and fitness response to copper, with interactive effects between temperature and copper. In addition, they suggested an attenuation effect of copper accumulation on the sensitivity of traits to copper, but with great variation between strains, temperature and copper concentration. Diversity of responses among strains and their thermal dependencies pleads for the integration of intraspecific variability and multiple stressors approaches in ecotoxicological studies, thus improving the reliability of assessments of the effects of pollutants on biodiversity.

Effects of high dietary zinc supplementation timing on the biological responses of gestating sows and their piglets

High dietary zinc (Zn) fed to gestating sows may have utility as a fetal imprinting strategy to decrease pre-weaning mortality of piglets. However, the biological action that Zn may work through is unknown. High Zn may modulate the microbiome of the sow and the microbial seeding of the offspring's gut microbiome. Additonally, high dietary Zn and piglet birth weight may alter gene expression in piglet whole blood. Sows (n = 267) were fed 1 of 3 dietary treatments: 1) Control: a corn-soybean meal-based diet containing 125 ppm total supplemental zinc, 2) Breed-to-Farrow: as Control + 141 ppm supplemental Zn as ZnSO4 fed from 5 days post-breeding to farrowing; and 3) Day 110-to-Farrow: as Control + 2,715 ppm supplemental Zn as ZnSO4 starting on day 110 of gestation until farrowing. A subset of third parity sows (n = 30) were selected to assess the microbiome of colostrum, milk, and rectal and vaginal surfaces of sows. At farrowing, 4 pigs per litter (n = 120) were selected based on birthweight (BiW), as 2 average BiW pigs and 2 pigs with BiW below the litter average were selected for assessing the piglet gut microbiome on the day of birth (day 0) and day 5 of age. 16S rRNA sequencing were implemented for milk and colostrum samples while all other sample types were sequenced using shotgun metagenomics to determine taxonomic and functional profiles. On a different subset of pigs, whole blood was collected from 9 LBW pigs per treatment and 8 ABW Control pigs for RNA-sequencing to evaluate differentially expressed genes (DEGs) and pathways. Only 2 to 3 genes were differentially expressed between Control LBW and LBW pigs born to sows fed high Zn. However, 262 DEGs were identified when comparing LBW and ABW pigs, mostly reflecting pathways associated with translation, ribosome biogenesis, and amino acid and protein synthesis. Measures of alpha diversity (richness and Shannon's H Index) and beta diversity (Bray-Curtis, PERMANOVA) were conducted along with indicator species analyses. Species with an indicator value of > 0.50 were confirmed with a generalized linear mixed model as each P-value was corrected for false discovery rate (FDR) to generate a Q-value. For piglet samples, the MaAsLin2 R package was used to determine multivariate associations between dietary treatment and piglet BiW. High dietary concentrations of Zn fed to gestating sows did not affect the colostrum, milk, or vaginal microbial diversity or populations of sows. Pathogenic bacteria such as Shigella flexneri and Salmonella enterica were less abundant in fecal samples from Breed-to-Farrow sows compared to Control sows. For piglets born to Breed-to-Farrow sows, their gut microbiome favored fiber fermenting, short chain fatty acid generating microbial species compared to Control pigs. Day 110-to-Farrow piglets demonstrated a lower abundance of SCFA producing bacteria compared to Control piglets. Gene families and pathways playing roles in central metabolic functions (starch, pyruvate, sucrose, amino acid metabolism) were more abundant in Breed-to-Farrow piglets compared to pigs born to Control sows. In conclusion, high Zn fed to gestating sows may influence SCFA-producing species and may reduce the abundance of potential pathogenic bacteria in the sow and piglet. Piglet birth weight may have greater effects on gene expression of neonatal pigs.

Sexual selection buffers the negative consequences of population fragmentation on adaptive plastic responses to increasing temperatures

Whether sexual selection facilitates or hampers the ability to plastically respond to novel environments might depend on population structure, via its effects on sexual interactions and associated fitness payoffs. Using experimentally evolved lines of the seed beetle Callosobruchus maculatus, we tested whether individuals evolving under different sexual selection (monogamy vs polygamy) and population spatial structure (metapopulation vs undivided populations) treatments differed in their response across developmental thermal conditions (control, hot or stressful) in a range of fitness and fitness-associated traits. We found that individuals from subdivided populations had lower lifetime reproductive success (LRS) at hot temperatures, but only in lines evolving under relaxed sexual selection, revealing a complex interaction between sexual selection, population structure, and thermal environmental stress on fitness. We also found an effect of population structure on several traits, including fertility and adult emergence success, under exposure to high thermal conditions. Finally, we found a strong negative effect of hot and stressful temperatures in fitness and associated traits. Our results show that population structure can exacerbate the impact of a warming climate, potentially leading to declines in population viability, but that sexual selection can buffer the negative influence of population subdivision on adaptation to warm temperatures.

Data from: Evaluating temporal turnover in avian species richness in a Mediterranean semiarid region: different responses to elevation and forest cover

Aim. When studying the effects of global change on biodiversity, it is far more common for the effects of climate change and land-use changes to be assessed separately rather than jointly. However, the effects of land-use changes in recent decades on species richness in areas affected by climate change have been less studied. We assess the temporal turnover in species richness of an avian community between a historical period and a modern one as a consequence of global change. Location. Semiarid Mediterranean ecosystem (Southeastern Spain). Method. We fitted a hierarchical multi-species occupancy model for each period (1991-1992, and 2012-2017), obtaining avian species-specific estimates of occupancy probability in relation to environmental covariates (elevation and forest cover). We analyze the relationships between changes in the bird community and environmental variables, analysing the temporal turnover of the species richness and the richness-based species-exchange ratio. Results. The estimated species richness accounting for detectability was higher than observed species richness, and decreased in the more recent period. Following our hypotheses, we observed a dual pattern of species richness increase associated with different elevations, showing different species turnover rates due to the joint effects of climate change and land-use change. There is a trend toward greater species richness with higher elevations that is associated with climate change, where the species turnover rate is low. Also, species richness increased towards lower elevations, but with a high turnover rate. The latter can be due to species expansions throughout new habitat configurations in bordering forest systems associated with anthropic land-use changes. Conclusions. Our study is of great interest to understand the temporal turnover of avian species richness associated with areas experiencing both climate and land-use change.

Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability

Though not often examined together, both plant-soil feedbacks (PSFs) and functional traits have important influences on plant community dynamics and could interact. For example, seedling functional traits could impact seedling survivorship responses to soils cultured by conspecific versus heterospecific adults. Furthermore, levels of functional traits could vary with soil culturing source. In addition, these relationships might shift with light availability, which can affect trait values, microbe abundance, and whether mycorrhizal colonization is mutualistic or parasitic to seedlings. To determine the extent to which functional traits mediate PSFs via seedling survival, we conducted a field experiment. We planted seedlings of four temperate tree species across a gradient of light availability and into soil cores collected beneath conspecific (sterilized and live) and heterospecific adults. We monitored seedling survival twice per week over one growing season, and we randomly selected subsets of seedlings to measure mycorrhizal colonization and phenolics, lignin, and NSC levels at three weeks. Though evidence for PSFs was limited, Acer saccharum seedlings exhibited positive PSFs (i.e., higher survival in conspecific than heterospecific soils). In addition, soil microbes had a negative effect on A. saccharum and Prunus serotina seedling survival, with reduced survival in live versus sterilized conspecific soil. In general, we found higher trait values (measured amounts of a given trait) in conspecific than heterospecific soils and higher light availability. Additionally, A. saccharum survival increased with higher levels of phenolics, which were higher in conspecific soils and high light. Quercus alba survival decreased with higher AMF colonization. We demonstrate that functional trait values in seedlings as young as three weeks vary in response to soil source and light availability. Moreover, seedling survivorship was associated with trait values for two species, despite both drought and heavy rainfall during the growing season that may have obscured survivorship-trait relationships. These results suggest that seedling traits could have an important role in mediating the effects of local soil source and light levels on seedling survivorship and thus plant traits could have an important role in PSFs.

Decoupled responses of above- and below-ground beta-diversity to nitrogen enrichment in a typical steppe

Increased atmospheric nitrogen (N) deposition affects biodiversity in terrestrial ecosystems. However, we do not know whether the effects of N on above-ground plant β-diversity are coupled with changes occurring in the soil seed bank. We conducted a long-term N-addition experiment in a typical steppe and found that above-ground β-diversity increased and then decreased with increasing N addition, whereas below-ground β-diversity decreased linearly. This suggests decoupled dynamics of plant communities and their soil seed bank under N enrichment. Species substitution determined above- and below-ground β-diversity change via an increasing role of deterministic processes with N addition. These effects were mostly driven by differential responses of the above-ground vegetation and the soil seed bank β-diversities to N-induced changes in environmental heterogeneity, increased soil inorganic N concentrations and soil acidification. Our findings highlight the importance of considering above- and below-ground processes simultaneously for effectively conserving grassland ecosystems under N enrichment.

Accompanying data for "The Response of Tropical Rainfall to Idealized Small-Scale Thermal and Mechanical Forcing", by Martin Velez-Pardo and Timothy W. Cronin

Data accompanying the manuscript "The Response of Tropical Rainfall to Idealized Small-Scale Thermal and Mechanical Forcing", by Martin Velez-Pardo and Timothy W. Cronin.

After the 'Black Summer' fires: faunal responses to megafire depend on fire severity, proportional area burnt, and vegetation type

<ol> <li>Climate change and human activities have disrupted historical fire regimes, leading to complex and far-reaching impacts on global ecosystems. Despite extensive research in fire ecology, studies exploring vertebrate responses to megafires, and to nuanced fire characteristics, remain limited.</li> <li>We collected camera trap data 3–27 months following Australia's 2019–20 'Black Summer' megafires from 30 burnt sites and 10 unburnt sites. Our data included 14 animal species/groups, encompassing mammalian predators, small and medium-sized mammals, large herbivores, and birds. We used generalised additive mixed models to assess the influence of time-since-the-fires, burn status, fire severity, proportional area burnt, and vegetation type on species' activity.</li> <li>Models that included fire variables were well-supported for all species. The proportional cover of low-moderate or high-extreme severity fire had substantial support for five species, particularly herbivores, which generally showed a preference for burnt sites but at differing fire severities. The proportional area burnt, disregarding severity, was well supported for four species. At highly burned sites, fox activity peaked shortly after the fires, while small to medium-sized mammal activity increased more gradually. Vegetation type strongly influenced the response of four species to fire; in particular, wet forest birds preferred unburnt areas.</li> <li> Policy implications. We document variable short- to medium-term responses of a range of species to fire which could help guide management interventions. We demonstrate that animal species' responses to fire are diverse and better captured using broader landscape-scale fire variables. We found that species were strongly influenced by proportional area burnt, fire severity, and vegetation type. Introduced foxes were attracted to recently burnt areas, so timely predator control may benefit vulnerable prey species. Wet forest species were sensitive to fires and could benefit from preservation and restoration of these habitats. Some species exploited low-moderate severity burnt areas, while others preferred high-severity burns. This suggests that species will face diverse challenges and opportunities in future extreme fire events. We emphasise the importance of using multi-faceted approaches to account for the complex responses of co-occurring species to fire events.</li> </ol>

Aracena et al- Epigenetic variation impacts individual differences in the transcriptional response to influenza infection

-Inputs for Github code-Full methylation results-Full QTL results

opencc-by-4.0Oct 2023View details →

Data from Nicolle et al. LC-HRMS study of Streptomyces sp. AgN23 Culture Media Extract. Study of AgN23 exometabolome and analysis of Arabidopsis metabolomic responses to the bacteria

This archive compiles several datasets related to studies of Streptomyces sp. AgN23 interaction with Arabidopsis thaliana. Ultra-high-performance liquid chromatography-high-resolution MS (UHPLC-HRMS) analyses were performed on a Q Exactive Plus quadrupole (Orbitrap) mass spectrometer, equipped with a heated electrospray probe (HESI II) coupled to a U-HPLC Ultimate 3000 RSLC system (Thermo Fisher Scientific, Hemel Hempstead, United Kigdom). For each biological sample, the RAW file obtained in ESI+ and ESI- mode were retrieved from the Xcalibur version 4.4 software and are deposited in separate sub-folders termed "RawPos" and "RawNeg". Each experimental cohort is grouped in a folder where the biological repeats can be retrieved, as well as QC (Quality Check, pool of all samples from the cohort), Blank samples and eventual alternative control such as Bennett, the mock control media of Streptomyces sp.  AgN23. The details regarding samples preparation, analytic parameters and mass spectrometry, statistical treatment and visualization of the data will be made available in the publication relating to this archive. The folder " AgN23-WT_AgN23-pSC004" contains chromatograms related to metabolomic study of Wild-type and pSC004-1, pSC004-10, pSC004-16 and pSC004-22 mutants of Streptomyces sp. AgN23. The folder " Col-0_AgN23" contains chromatograms related to metabolomic study of Arabidopsis thaliana Col-0 responses to colonization by Streptomyces sp. AgN23-WT. The folder " Col-0_pad3-1_AgN23" contains chromatograms related to metabolomic study of Arabidopsis thaliana Col-0 and the Arabidopsis pad3-1 mutant responses to colonization by Streptomyces sp. AgN23-WT. The folder " Col-0_pSC004" contains chromatograms related to metabolomic study of Arabidopsis thaliana Col-0 responses to colonization by Streptomyces sp. AgN23-WT and the AgN23 mutants pSC004-10 and pSC004-22. It should be noted that in the publication associated with this archive, the pSC004-1, pSC004-10, pSC004-16 and pSC004-22 mutants are referred to as ΔgbnB-1, ΔgbnB-2, ΔgbnB-3 and ΔgbnB-4, respectively.

Fertilization can accelerate the pace of soil microbial community response to rest-grazing duration in the Three-river Source Region of China

<div> <div> Objectives Overgrazing leads to grassland degradation and productivity decline. Rest-grazing during the regreen-up period can quickly restore grassland and fertilization is a common restoration measure. Meanwhile, soil microorganisms are more sensitive indicators. Therefore, the experiment of rest-grazing time and fertilization was carried out to explore the response of soil microorganisms to rest-grazing time and fertilization measures. Methods A field control experiment with rest-grazing time and fertilization as factors was conducted from the time when grass returned to green till the livestock moved to the summer pasture in Dawu Town of Maqin County. The primary treatment we established was the five rest-grazing times, including rest-grazing times of 20 days, 30 days, 40 days, 50 days, and traditional grazing was used as a check group. At the same time, the secondary treatment was nitrogen addition of 300 kg·hm-2 in each primary treatment. Results The results showed that: the total phospholipid fatty acid (total PLFA), actinomyces (Act) and arbuscular mycorrhizal fungi (AMF) showed an ever-increasing biomass with the increase of rest-grazing time and the highest was at 50 days of rest-grazing, and they were all significantly higher than CK. In addition, soil microbial biomass carbon-nitrogen ratio (MBC/MBN) had a great influence on the change of microbial community. Applying nitrogen fertilizer can increase the maximum value of biomass of all PLFA groups and the biomass of all PLFA groups changed in an "inverted V" shape with the increase of rest-grazing time. Besides, instead of MBC/MBN, NO3--N was positively affected by the biomass of all PLFA groups, which actively regulated the trend of microbial functions. Conclusions The longer rest-grazing time is more conducive to the biomass of all PLFA groups. However, applying nitrogen fertilizer could break this pattern, namely, the 30d rest-grazing would be beneficial to the biomass of all PLFA groups. These findings provide key information that rest-grazing during the regreen-up period is beneficial to all PLFA groups and fertilization could change the response of microorganisms to rest-grazing, which provides reference measures for the restoration of degraded alpine meadows. </div> </div>

Corticosterone and immune responses to dehydration in squamate reptiles

Many environments present some degree of seasonal water limitations; organisms that live in such environments must be adapted to survive periods without permanent water access. Often this involves the ability to tolerate dehydration, which can have adverse physiological effects and is typically considered a physiological stressor. While having many functions, the hormone corticosterone (CORT) is often released in response to stressors, yet increasing plasma CORT while dehydrated could be considered maladaptive, especially for species that experience predictable bouts of dehydration and have related coping mechanisms. Elevating CORT could reduce immunocompetence and have other negative physiological effects. Thus, such species likely have CORT and immune responses adapted to experiencing seasonal droughts. We evaluated how dehydration affects CORT and immune function in eight squamate species that naturally experience varied water limitation. We tested whether hydric state affected plasma CORT concentrations and aspects of immunocompetence (lysis, agglutination, bacterial killing ability, and white blood cell counts) differently among species based on how seasonally water limited they are and whether this is constrained by phylogeny. The species represented four familial pairs, with one species of each pair inhabiting environments with frequent access to water and one naturally experiencing extended periods (>30 days) with no access to standing water. The effects of dehydration on CORT and immunity varied among species. Increases in CORT were generally not associated with reduced immunocompetence, indicating CORT and immunity might be decoupled in some species. Interspecies variations in responses to dehydration were more clearly grouped by phylogeny than habitat type.

Climate response to vegetation removal on different continents

Data generated in this study are archived here.

opencc-by-4.0Dec 1995View details →

Oxygen consumption (VO 2) was determined from the formula in Diurnal activity, temperature responses and endothermy in three South American cicadas (Homoptera: Cicadidae: Dorisiana bonaerensis, Quesada gigas and Fidicina mannifera)

Oxygen consumption (VO 2) was determined from the formula

Community and species-specific responses of coastal birds to COVID-19 "anthropause" in the largest hypersaline lagoon of South America

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Dataset for "Takahama, M., Patil, A., Richey, G. et al. A pairwise cytokine code explains the organism-wide response to sepsis. Nat Immunol 25, 226–239 (2024)."

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