Find research datasets worth reusing

opencc-zeroAug 2021View details →

Context-dependent effects of Trichoderma seed inoculation on anthracnose disease and seed yield of bean (Phaseolus vulgaris): ambient conditions override cultivar-specific differences

Root colonizing Trichoderma fungi can stimulate plant immunity, but net effects are strain × cultivar-specific and changing ambient conditions further contribute to variable outcomes. Here, we used four Trichoderma spp. to inoculate seeds of four common bean (Phaseolus vulgaris) cultivars and explored in three different experimental setups the effects on fungal anthracnose after leaf inoculation with Colletotrichum lindemuthianum. Plants growing in pots with field soil under greenhouse conditions exhibited the highest and those in the open field the lowest overall levels of disease. Among 48 Trichoderma strain × bean cultivar × setup combinations, Trichoderma-inoculation enhanced disease in six and decreased disease in ten cases, but with the exception of T. asperellum B6-inoculated Negro San Luis beans, the strain × cultivar-specific effects on anthracnose severity differed among the setups, and anthracnose severity did not predict seed yield in the open field. In the case of Flor de Mayo beans, Trichoderma even reduced yield in anthracnose-free field plots, although this effect was counterbalanced in anthracnose-infected plots. We consider our work as a case study that calls for stronger emphasis on field experiments in the early phases of screenings of Trichoderma inoculants as plant biostimulants.

opencc-zeroAug 2021View details →

FGF-2-dependent signaling activated in aged human skeletal muscle promotes intramuscular adipogenesis

Aged skeletal muscle is markedly affected by fatty muscle infiltration and strategies to reduce the occurrence of intramuscular adipocytes are urgently needed. Here, we show that fibroblast growth factor-2 (FGF-2) not only stimulates muscle growth, but also promotes intramuscular adipogenesis. Using multiple screening assays upstream and downstream of microRNA (miR)-29a signaling, we located the secreted protein and adipogenic inhibitor SPARC to an FGF-2 signaling pathway that is conserved between skeletal muscle cells from mice and humans and that is activated in skeletal muscle of aged mice and humans. FGF-2 induces the miR-29a/SPARC axis through transcriptional activation of FRA-1, which binds and activates an evolutionary conserved AP-1 site element proximal in the miR-29a promoter. Genetic deletions in muscle cells and AAV-mediated overexpression of FGF-2 or SPARC in mouse skeletal muscle revealed that this axis regulates differentiation of fibro/adipogenic progenitors in vitro and intramuscular adipose tissue (IMAT) formation in vivo. Skeletal muscle from human donors aged > 75 years versus < 55 years showed activation of FGF-2-dependent signaling and increased IMAT. Thus, our data highlights a disparate role of FGF-2 in adult skeletal muscle and reveals a novel pathway to combat fat accumulation in aged human skeletal muscle.

opencc-by-4.0Jul 2017View details →

Fig. 1 in Dependence of daily oviposition activity and total fecundity on body mass in the house cricket Acheta domesticus (L.) (Insecta: Orthoptera)

Fig. 1: Biological traits demonstrably influenced by body mass in orthopterans (WITHMAN 2008).

opencc-zeroSep 2021View details →

Mycorrhizal effects on decomposition and soil CO2 flux depend on changes in nitrogen availability during forest succession

Mycorrhizal fungi play a central role in plant nutrition and nutrient cycling, yet our understanding on their effects on free-living microbes, soil carbon (C) decomposition and soil CO2 fluxes remains limited. Here we used trenches lined with mesh screens of varying sizes to isolate mycorrhizal hyphal effects on soil C dynamics in subtropical successional forests. We found that the presence of mycorrhizal hyphae suppressed soil CO2 fluxes by 17% in early-successional forests, but enhanced CO2 losses by 20% and 32% in mid- and late-successional forests, respectively. The inhibitory effects of mycorrhizal fungi on soil CO2 fluxes in the young stands were associated with changes in soil nitrogen (N) mineralization and microbial activities, suggesting that competition between mycorrhizae and saprotrophs for N likely suppressed soil C decomposition. In the mid- and late-successional stands, mycorrhizal enhancement of CO2 release from soil likely resulted from both hyphal respiration and mycorrhizal-induced acceleration of organic matter decay. Synthesis. Our results highlight the sensitivity of mycorrhizal fungi-saprotroph interactions to shifts in nutrient availability and demand, with important consequences for soil carbon dynamics particularly in ecosystems with low nutrient conditions. Incorporating such interactions into models should improve the simulations of forest biogeochemical cycles under global change.

opencc-by-4.0Sep 2021View details →

Cleaned data from Supplementary Table S1 from "Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method"

This data is derived from <a href="https://doi.org/10.5281/zenodo.5277805">https://doi.org/10.5281/zenodo.5277805</a>. As of 2021-09-08, <a href="https://doi.org/10.5281/zenodo.5277805">https://doi.org/10.5281/zenodo.5277805</a> contained an Excel file with md5:8907e7444f49d02d58fdef9fb2a1089a and filename "TableS1.xlsx"; the file was licensed under <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a>. In "TableS1.xlsx" there were, among others, worksheets with the names "Table S1. TECRDB Keqs" and "Table S2. TECRDB ΔrH data". Worksheet "Table S1. TECRDB Keqs" was exported as a csv with filename "TableS1_Keq.csv". A column "id" was added with a persistent identifier created in w3id.org. Worksheet "Table S2. TECRDB ΔrH data"" was exported as a csv with filename "TableS1_deltaH.csv". A column "id" was added with a persistent identifier created in w3id.org. No other corrections were made.

opencc-zeroSep 2021View details →

Associations between metabolic traits and growth rate in brown trout (Salmo trutta) depend on thermal regime

Metabolism defines the energetic cost of life, yet we still know relatively little about why intraspecific variation in metabolic rate arises and persists. Spatiotemporal variation in selection potentially maintains differences, but relationships between metabolic traits (standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic scope) and fitness across contexts are unresolved. We show that associations between SMR, MMR, and growth rate (a key fitness-related trait) vary depending on thermal regime (a potential selective agent) in offspring of wild-sampled brown trout from two populations reared for ~15 months in either a cool or warm (+ 1.8°C) regime. SMR was positively related to growth in the cool, but negatively related in the warm regime. The opposite patterns were found for MMR and growth associations (positive in warm, negative in cool regime). Mean SMR, but not MMR, was lower in warm regimes within both populations (i.e., basal metabolic costs were reduced at higher temperatures), consistent with an adaptive acclimation response that optimises growth. Metabolic phenotypes thus exhibited a thermally sensitive metabolic 'floor' and a less flexible metabolic 'ceiling'. Our findings suggest a role for growth-related fluctuating selection in shaping patterns of metabolic variation that is likely important in adapting to climate change.

opencc-zeroSep 2021View details →

Relatedness modulates density-dependent cannibalism rates in Drosophila

1. Cannibalism is taxonomically widespread, and can have large impacts on individual fitness and population-level processes. As such, identifying how cannibalism rates vary in response to ecological cues is important for predicting species evolution and population dynamics. 2. In this study, we aimed to identify several eco-evolutionary factors that affect cannibalism rate and measure how they interacted with one another. 3. To do this, we conducted two experiments using complimentary methods to measure how cannibalism rates varied among larval Drosophila melanogaster and Drosophila simulans in response to changes in conspecific relatedness, social familiarity and density. 4. We found that larvae were more likely to cannibalise non-related larval victims in both species, and that this effect increased at high densities in D. simulans. We found no evidence that Drosophila larvae use social familiarity to assess relatedness. Finally, in D. melanogaster, cannibalistic larvae prefer to cannibalise larvae that are being attacked by a greater number of conspecifics, implying that cues linked to conspecific abundance encourage cooperative cannibalism. 5. By showing that cannibalism frequency in Drosophila spp. is sensitive to relatedness and several other factors, we reveal the complex relationship between cannibalism frequency and species ecology. Also, by showing that the effect of relatedness on cannibalism frequency is density-dependent, we advance the current understanding of how ecological variables interact to affect kin selection. ANALYSIS CODE IS WRITTEN IN R.

opencc-by-4.0Oct 2021View details →

Heightened condition dependent expression of structural colouration in the faces, but not wings, of male and female flies

Data from White et al. (2021): Heightened condition dependent expression of structural colouration in the faces, but not wings, of male and female flies

opencc-by-4.0Jun 2021View details →

Dependency Management Bots in Open-Source Systems - Prevalence and Adoption

This is a re-analysis package for the paper: Dependency Management Bots in Open-Source Systems - Prevalence and Adoption. The package includes scripts and processed data collected from GitHub about five investigated dependency management bots: Dependabot, Depfu, Greenkeeper, Pyup and Renovate.

opencc-by-4.0May 2019View details →

Raw Data supporting Promoters adopt distinct dynamic manifestations depending on transcription factor context

All source data is provided as MAT-files, which can be opened in Matlab. In total, the source data contain 270 core data files and 540 processed data files. The data for each individual promoter is stored in a different directory and the 9 promoters are: <ul> <li> ALD3 </li> <li> DCS2 </li> <li> DDR2 </li> <li> HXK1 </li> <li> RTN2 </li> <li> TKL2 </li> <li> SIP18 </li> <li> pSIP18_mut6 (also referred to as mutant A4) </li> <li> pSIP18_mut21 (also referred to as mutant D6) </li> </ul> The data for the first 7 promoters was previously reported in (Hansen and O’Shea, 2013), though in an unnormalized form. That is, it was previously reported as a concentration per cell in arbitrary fluorescence units (AU). In the present manuscript, we have calibrated the data to obtain absolute abundances, such that the MAT-files now contain both the old AU concentration as well as absolute abundances, i.e. number of YFP molecules per cell. The calibration was performed as described in (Huang et al., 2016). Similarly, the data for the last 2 promoters (A4 and D6) was previously reported in its unnormalized form in (Hansen and O’Shea, 2015) and it is here also reported in the form of absolute abundances.   The MAT-files containing the raw data have the suffix “_size.mat”. The name of the MAT files describes the experiment. If the file name contains “DM”, then it is a single pulse. Thus, “SIP18_DM_40min_275nM_size.mat” refers to a single 40 min pulse with 275 nM 1-NM-PP1 for the SIP18 promoter. Similarly if the file name contains “FM”, e.g. “RTN2_FM_8_5min_690nM_size.mat” then it refers to eight 5 min pulses separated by 5 min intervals at 690 nM for the RTN2 promoter. Finally, if the file name contains “FM4”, e.g.  “TKL2_FM4_15minINT_690nM_size.mat” then the experiment was four 5 min pulses separated by 15 min intervals at 690 nM for the TKL2 promoter. The concentration is the concentration of 1-NM-PP1 that was used and 100 nM, 275 nM, 690 nM and 3mM refers to approximately, 25%, 50%, 75% and 100% Msn2 activation. For full experimental details please see (Hansen and O’Shea, 2013; Hansen et al., 2015).   The “_size.mat” MAT-files contain the following variables: <ul> <li> cell_size_pixels</li> <li> CFP</li> <li> CFP_molecules</li> <li> CFP_raw</li> <li> inhibitor_conc</li> <li> MSN2_raw</li> <li> MSN2_RFP</li> <li> pulse_parameters • time</li> <li> YFP</li> <li> YFP_molecules</li> <li> YFP_raw</li> </ul> CFP, CFP_molecules, CFP_raw and YFP, YFP_molecules, YFP_raw are Nx64 matrices, where each row N correspond to a different cell and the 64 columns correspond to the 64 experimentally measured timepoints corresponding to the “time” vector running from -5 min to 152.5 min in increments of 2.5 min and the 1NM-PP1 inhibitor was added at time 0. “CFP_raw” and “YFP_raw” contains raw, uncorrected data, so without photobleaching correction and background subtraction. “CFP” and “YFP” contain corrected data in arbitrary fluorescence units (AU) and report on the concentration (i.e. size normalized). Finally, “CFP_molecules” and “YFP_molecules” contains the total number of CFP and YFP molecules per cell (i.e. this is not a concentration, but the absolute abundance). The area of each cell at each timepoint can be found in the matrix “cell_size_pixels”. Since the cells are live and growing, this will tend to increase during the experiments. Occasionally large fluctuations can occur due to errors in cell segmentation or due to division. For full details on the image analysis and cell segmentation, please see (Hansen and O’Shea, 2013; Hansen et al., 2015).   The variables “inhibitor_conc” and “pulse_parameters” refer to the type of experiment and is also given by the name. “inhibitor_conc”  gives the 1NMPP1 concentration: 100 nM, 275 nM, 690 nM or 3000 nM. “pulse_parameters” contains either 2 or 3 elements and given the dynamical pulse sequence parameters. Column 1 contains the number of pulses and column 2 the duration of the pulses. Column 3 gives the interval between the pulses if more than one pulse is used – otherwise column 3 is zero.   Moreover, on a more technical note it should be noted that the signal-to-noise of the CFP reporter is worse than the YFP reporter. Therefore, we always use the YFP reporter for quantitative analysis. Furthermore, the two other MAT-files “…MSN2.mat” and “…YFP.mat” contain processed data. Please see the ReadMe file on the code for a full description and how these were derived.   Finally, Supplementary Table 1 contains the model-inferred parameters for each promoter and condition.     References Hansen, A.S., and O’Shea, E.K. (2013). Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol. Syst. Biol. Hansen, A.S., and O’Shea, E.K. (2015). Cis Determinants of Promoter Threshold and Activation Timescale. Cell Rep. Hansen, A.S., Hao, N., and OShea, E.K. (2015). High-throughput microfluidics to control and measure signaling dynamics in single yeast cells. Nat. Protoc. Huang, L., Pauleve, L., Zechner, C., Unger, M., Hansen, A.S., and Koeppl, H. (2016). Reconstructing dynamic molecular states from single-cell time series. J. R. Soc. Interface.

Contrasting soil- and canopy-nurse effects on dependent species in metalliferous systems may be explained by dominant plant functional strategies

Plant-plant interaction studies in metalliferous systems have focused either on the role of facilitation or on the negative effects of elemental allelopathy. However, no studies have investigated both of these effects in the same system, and their relationships with the functional strategy of the nurse species, although this is crucial for the ecological restoration of polluted sites. We assessed the effects of two dominant nurse species, with apparent contrasting strategies, on two target species on a slag heap in the Pyrenees (France). We quantified both long-term soil-engineering and short-term canopy effects on the growth of two target species. We also measured morphological traits and leaf metal concentration of the two nurse species and their effects on air moisture, temperature, and vapour pressure deficit. Nurse functional strategies, as inferred from morphological traits and leaf metal concentration seem to drive their long-term soil engineering effects on target species: Gypsophila repens, the relatively larger and more exploitative species with high leaf metal concentration, had negative long-term effects likely due to elemental allelopathy, whereas Minuartia verna, the relatively smaller and more conservative species with a lower amount of metals in leaves, had neutral long-term effects. Although Gypsophila repens had a slightly stronger positive effect on microclimate than Minuartia verna, this did not turn into higher short-term effects for the target species. Our study highlights the possible role of the nurse's functional strategies in driving the relative importance of long and short-term effects on target species in metalliferous systems. This knowledge is key to increasing our understanding of plant-plant interaction outcomes in metalliferous systems and our ability to restore polluted environments.

Fitness landscapes reveal context-dependent benefits of oviposition behaviour

Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Do such context-dependent behaviours reflect maladaptive variation, or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behaviour reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating female egg allocation across patches, which allowed us to assess behaviours not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce significantly more (but slower-developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts.

opencc-by-4.0Nov 2022View details →

Sampling time-dependent artifacts in single-cell genomics studies: scRNA-seq data

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention. This repository contains the expression matrices and Seurat objects associated with the scRNA-seq data of the manuscript: "Sampling time-dependent artifacts in single-cell genomics studies" published in Genome Biology in 2020. The purpose of this repo is to share processed files and metadata for immediate access and reproducibility. The code to analyze it is thoroughly documented at the associated Github repository (https://github.com/massonix/sampling_artifacts).

Data from: eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin-antitoxin system

In their natural environment, most bacteria preferentially live as complex surface-attached multicellular colonies called biofilms. Biofilms begin with a few cells adhering to a surface, where they multiply to form a mature colony. When conditions deteriorate, cells can leave the biofilm. This dispersion is thought to be an important process that modifies the overall biofilm architecture and that promotes colonization of new environments. In Caulobacter crescentus biofilms, extracellular DNA (eDNA) is released upon cell death and prevents newborn cells from joining the established biofilm. Thus, eDNA promotes the dispersal of newborn cells and the subsequent colonization of new environments. These observations suggest that eDNA is a cue for sensing detrimental environmental conditions in the biofilm. Here we show that the toxin-antitoxin system (TAS) ParDE4 stimulates cell death in areas of a biofilm with decreased O2 availability. In conditions where O2 availability is low, eDNA concentration is correlated with cell death. Cell dispersal away from biofilms is decreased when parDE4 is deleted, probably due to the lower local eDNA concentration. Expression of parDE4 is positively regulated by O2 and the expression of this operon is decreased in biofilms where O2 availability is low. Thus, a programmed cell death mechanism using an O2-regulated TAS stimulates dispersal away from areas of a biofilm with decreased O2 availability and favors colonization of a new, more hospitable environment.

Time-dependent benefits of camouflage strategies on heterogeneous backgrounds

Background-matching camouflage is a well-established strategy to reduce detection, but implementing this on heterogeneous backgrounds is challenging. For prey with fixed colour patterns, solutions include specialising on a particular visual microhabitat or adopting a compromise or generalist appearance, matching multiple backgrounds imperfectly. Existing studies suggest both approaches can succeed, but most consider relatively simple scenarios, where artificial prey appear against two backgrounds differing in a single visual characteristic. Here, we used computer-based search tasks with human participants to test the relative benefits of specialising and generalising for complex targets, displayed on either two or four types of naturalistic backgrounds. Overall, across two background types, specialisation was beneficial, though its success varied with search duration, such that generalist targets could outperform specialists in the first seconds of each search event. Against four different backgrounds, the initial cost to specialisation was greater, so specialists and generalists ultimately experienced similar survival. Generalists performed better when their patterning was a compromise between backgrounds that were more similar to each other than when backgrounds were more different, with similarity in luminance more relevant than pattern differences. Time-dependence in the relative success of these strategies suggests that predator search behaviour may affect optimal camouflage in real-world situations.

Poison frog dietary preference depends on prey type and alkaloid load

The ability to acquire chemical defenses through the diet has evolved across several major taxa. Chemically defended organisms may need to balance chemical defense acquisition and nutritional quality of prey items. However, these dietary preferences and potential trade-offs are rarely considered in the framework of diet-derived defenses. Poison frogs (Family Dendrobatidae) acquire defensive alkaloids from their arthropod diet of ants and mites, although their dietary preferences have never been investigated. We conducted prey preference assays with the Dyeing Poison frog (Dendrobates tinctorius) to test the hypothesis that alkaloid load and prey traits influence frog dietary preferences. We tested size preferences (big versus small) within each of four prey groups (ants, beetles, flies, and fly larvae) and found that frogs preferred interacting with smaller prey items of the fly and beetle groups. Frog taxonomic prey preferences were also tested as we experimentally increased their chemical defense load by feeding frogs decahydroquinoline, an alkaloid compound similar to those naturally found in their diet. Contrary to our expectations, overall preferences did not change during alkaloid consumption, as frogs across groups preferred fly larvae over other prey. Finally, we assessed the protein and lipid content of prey items and found that small ants have the highest lipid content while large fly larvae have the highest protein content. Our results suggest that consideration of toxicity and prey nutritional value are important factors in understanding the evolution of acquired chemical defenses and niche partitioning as a whole.

opencc-by-4.0Dec 2022View details →

Code and data for manuscript: Is phase-dependent stability related to phase-dependent gait robustness?

Code and code data for manuscript: Is phase-dependent stability related to phase-dependent gait robustness?

opencc-zeroDec 2022View details →

Dataset from: Warming effects on grassland productivity depend on plant diversity

Aim: Climate warming and biodiversity loss both alter plant productivity, yet we lack an understanding of how biodiversity regulates the responses of ecosystems to warming. In this study, we examine how plant diversity regulates the responses of grassland productivity to experimental warming using meta-analytic techniques. Location: Global Major taxa studied: Grassland ecosystems Methods: Our meta-analysis is based on warming responses of 40 different plant communities obtained from 20 independent studies on grasslands across five continents. Results: Our results show that plant diversity and its responses to warming were the most important factors regulating the warming effects on plant productivity, among all the factors considered (plant diversity, climate and experimental settings). Specifically, warming increased plant productivity when plant diversity (indicated by effective number of species) in grasslands was lesser than 10, whereas warming decreased plant productivity when plant diversity was greater than 10. Moreover, the structural equation modelling showed that the magnitude of warming enhanced plant productivity by increasing the performance of dominant plant species in grasslands of diversity lesser than 10. The negative effects of warming on productivity in grasslands with plant diversity greater than 10 were partly explained by diversity-induced decline in plant dominance. Main Conclusions: Our findings suggest that the positive or negative effect of warming on grassland productivity depends on how biodiverse a grassland is. This could mainly owe to differences in how warming may affect plant dominance and subsequent shifts in interspecific interactions in grasslands of different plant diversity levels.

opencc-zeroDec 2022View details →

Data for: Context dependency in interference competition among birds in an endangered woodland ecosystem

Aim Much research has quantified species responses to human-modified ecosystems. However, there has been relatively limited work on how human-modified ecosystems may reshape competitive interactions between species. Using extensive data gathered over 19 years across an area exceeding three million ha, we asked: Are levels of interference competition between bird species context-dependent and influenced by habitat structure and productivity? We focussed on the hyper-aggressive behaviour of the Noisy Miner, which has been recognised as a Key Threatening Process for other woodland bird species. Location Temperate woodlands of south-eastern Australia Methods We constructed Bayesian multi-species occupancy/detection models of bird species in woodland patches and tested the fixed and interactive effects of Noisy Miner presence, the amount of tree cover, net primary productivity, and time. We quantified the responses of 31 species, many with known interactions with the Noisy Miner documented in previous studies at fine spatial scales. However, whether environmental conditions such as amount of forest cover and net primary productivity mediate the impact of Noisy Miners remains untested at large spatial scales and over decadal time scales. Results We identified negative associations between the Noisy Miner and 18 bird species, including, unexpectedly, both small- and large-bodied taxa. Site occupancy in some species was influenced by interactions between Noisy Miner presence and increasing amounts of tree cover or productivity. Our results suggest that for some species, interference competition by the Noisy Miner is context-dependent and mitigated by increasing tree cover and/or increasing net primary productivity Main conclusions Areas of high productivity or tree cover may be important refugia for some species of woodland birds. Vegetation clearing that reduces tree cover could likely strengthen interference competition by the Noisy Miner on parts of the remaining woodland bird community, including species of conservation concern.