Find research datasets worth reusing

opencc-zeroDec 2012View details →

Data from: Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

We used whole transcriptome microarrays to assess changes in gene expression and monitored mortality rates and epicuticular hydrocarbons (CHCs) in response to desiccation stress in four natural populations of Drosophila mojavensis from Baja California and mainland Mexico. Desiccation had the greatest effect on gene expression, followed by biogeographical variation at regional and population levels. Genes involved in environmental sensing and cuticular structure were up-regulated in dry conditions, while genes involved in transcription itself were down-regulated. Flies from Baja California had higher expression of reproductive and mitochondrial genes, suggesting that these populations have greater fecundity and higher metabolic rates. Host plant differences had a surprisingly minor effect on the transcriptome. In most cases, desiccation-caused mortality was greater in flies reared on fermenting cactus tissues than laboratory media. Water content of adult females and males was significantly different, and was lower in Baja California males. Different groups of CHCs simultaneously increased and decreased in amounts due to desiccation exposure of 9 and 18 hr and were population-specific and dependent on larval rearing substrates. Overall, we observed that changes in gene expression involved a coordinated response of metabolic, behavioral, and cuticular genes. Together with differential expression of cuticular hydrocarbons, this study revealed some of the mechanisms that have allowed D. mojavensis to exploit its harsh desert conditions. Certainly, for D. mojavensis that uses different host plants, population-level understanding of responses to stressors associated with future climate change in desert regions must be evaluated across geographical and local ecological scales.

opencc-zeroDec 2016View details →

Data from: Water-borne pharmaceuticals reduce phenotypic diversity and response capacity of natural phytoplankton communities

Chemical micropollutants occur worldwide in the environment at low concentrations and in complex mixtures, and how they affect the ecology of natural systems is still uncertain. Dynamics of natural communities are driven by the interaction between individual organisms and their growth environment, which is mediated by the organisms' expressed phenotypic traits. We tested whether exposure to a mixture of 12 pharmaceuticals and personal care products (PPCP) influences phenotypic trait diversity in lake phytoplankton communities and their ability to regulate biomass production to fit environmental changes (response capacity). We exposed natural phytoplankton assemblages to three mixture levels in permeable microcosms maintained at three depths in a eutrophic lake for one week, during which the environmental conditions were fluctuating. We studied individual-level traits, phenotypic diversity and community biomass. PPCP reduced individual-level trait variance and overall community phenotypic diversity, but maintained higher standing phytoplankton biomass compared to untreated controls. Estimated effect sizes of PPCP on traits and community properties were very large (partial Eta-squared > 0.15). The PPCP mixture antagonistically interacted with the natural environmental gradient in habitats offered by different depths and, at concentrations comparable to those in waste-water effluents, prevented communities from converging to the same phenotypic structure and total biomass of unexposed controls. We show that micropollutants can alter individual-level trait diversity of lake phytoplankton communities and therefore their capacity to respond to natural environmental gradients, potentially affecting aquatic ecosystem processes.

opencc-zeroJun 2021View details →

Setaria viridis images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.

Setaria viridis images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX

restrictedcc-by-4.0Mar 2024View details →

Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses

Rscript for figure generation and data analysis: GenerateFigures.R   Seurat objects containing processed data after quality control: <a href="../api/records/10867209/draft/files/NCCS_For_Zenodo.RDS/content" target="_blank" rel="noopener noreferrer">NCCS_For_Zenodo.RDS</a> - NCCS discovery cohort. <a href="../api/records/10867209/draft/files/Pavia_For_Zenodo.RDS/content" target="_blank" rel="noopener noreferrer">Pavia_For_Zenodo.RDS</a> - Pavia validation cohort.   RDS files containing DEGs or differentially abundant surface markers: TestResults2Groups.rds - Cell type specific LTR vs Non Responder DEG  TestResults2GroupsADT.rds - Cell type specific LTR vs Non Responder differential surface markers TestResults2GroupsLungOnly.rds - Cell type specific LTR vs Non Responder DEG on lung samples only TestResults2GroupsLungOnlyADT.rds - Cell type specific LTR vs Non Responder differential surface markers on lung samples only TestResults3Groups.rds - Cell type specific LTR vs R vs Non Responder differential DEG TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers TestResults2GroupsGeneralRNA.rds - Across cell type LTR vs Non Responder DEG  TestResults2GroupsGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers TestResults2GroupsLungOnlyGeneralRNA.rds - Across cell type LTR vs Non Responder DEG on lung samples only TestResults2GroupsLungOnlyGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers on lung samples only TestResults3GroupsGeneralRNA.rds - Across cell type LTR vs R vs Non Responder differential DEG TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers   Logistic regression models trained on the NCCS discovery cohort: PerCellPredictions <CellType> * - Celltype specific models predicting either LTR, R or control group trained on all NCCS samples PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only. PerCellPredictions_2Groups_<CellType> * - Celltype specific models predicting either LTR or NonResponder trained on all NCCS samples

opencc-zeroJan 2022View details →

Phenotypic data for M. edulis responses to warming and ocean acidification

1. In mosaic marine habitats, such as intertidal zones, ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO2 production. The non-linear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation. 2. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of the Gulf of Maine (GOM), USA for this study. GOM is a hot spot of global climate change (average Sea Surface Temperature (SST) increasing by > 0.2 °C y−1 ) with > 60% decline in mussel population over the past 40 years. 3. Here, we utilize bioenergetic underpinnings to identify limits of stress tolerance in M. edulis from GOM exposed to warming and OA. We have measured whole-organism oxygen consumption rates and metabolic biomarkers in mussels exposed to control and elevated temperatures (10 vs. 15 °C, respectively) and current and moderately elevated PCO2 levels (~ 400 vs. 800 µatm, respectively). 4. Our study demonstrates that adult M. edulis from GOM are metabolically resilient to the moderate OA scenario but responsive to warming as seen in changes in metabolic rate, energy reserves (total lipids), metabolite profiles (glucose and osmolyte dimethyl amine) and enzyme activities (carbonic anhydrase and calcium-ATPase). 5. Our results are in agreement with recent literature that OA scenarios for the next 100-300 years do not affect this species, possibly as a consequence of maintaining its in vivo acid−base balance.

opencc-zeroMar 2022View details →

Meta-analysis of phenotypic plasticity in response to thermal treatments in invertebrates

Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity—particularly in traits with modest-to-low cross-sex genetic correlations— typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception—cold resistance—is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.

opencc-zeroSep 2022View details →

Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

To predict how widely distributed species will perform under future climate change it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate-change scenario for central Europe and revealed the population structure through whole genome sequencing. Plants were grown under two temperature (18°C, 21°C) and three precipitation regimes (65 mm, 75 mm, 90 mm) to measure their response in biomass and fecundity related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations and another cluster containing Central European populations. Population genetic diversity decreased with increasing latitude and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.

opencc-by-4.0Oct 2022View details →

Drug Response Phenotype Terms

Data and code for "Leveraging a Pharmacogenomics Knowledge-base to Formulate a Drug Response Phenotype Terminology for Genomic Medicine" published in Bioinformatics

opencc-by-4.0Apr 2019View details →

High-throughput phenotyping of salt-stress responses of the selected Arabidopsis hormone mutants

This data was collected using Hight Throughput Phenotyping machine (psi.cz) purchased by KAUST in January 2018. The plants were germinated and grown under 12/12 light/dark light regime, 22C, 60% humidity for two weeks. After two weeks, half of the plants were exposed to approximately 100 mM NaCl (protocol described in Awlia et al., 2016, Frontiers in Plant Sci, <a href="https://doi.org/10.3389/fpls.2016.01414">https://doi.org/10.3389/fpls.2016.01414</a>). The rosettes of the plants were subsequently phenotyped using the Thermal Camera, RGB, and Chlorophyll Fluorescence camera (in this order). Chlorophyll fluorescence was measured after 15 minutes of dark adaptation using the "LightCurve2" protocol.  The description of the traits is available in the notebook available at <a href="https://github.com/mmjulkowska/PSI_notebook">https://github.com/mmjulkowska/PSI_notebook</a>

opencc-zeroDec 2012View details →

Data from: Morphological change and phenotypic plasticity in native and non–native pumpkinseed sunfish in response to sustained water velocities

Phenotypic plasticity can contribute to the proliferation and invasion success of nonindigenous species by promoting phenotypic changes that increase fitness, facilitate range expansion and improve survival. In this study, differences in phenotypic plasticity were investigated using young-of-year pumpkinseed sunfish from colonies established with lentic and lotic populations originating in Canada (native) and Spain (non-native). Individuals were subjected to static and flowing water treatments for 80 days. Inter- and intra-population differences were tested using ancova and discriminant function analysis, and differences in phenotypic plasticity were tested through a manova of discriminant function scores. Differences between Iberian and North American populations were observed in dorsal fin length, pectoral fin position and caudal peduncle length. Phenotypic plasticity had less influence on morphology than genetic factors, regardless of population origin. Contrary to predictions, Iberian pumpkinseed exhibited lower levels of phenotypic plasticity than native populations, suggesting that canalization may have occurred in the non-native populations during the processes of introduction and range expansion.

opencc-zeroDec 2016View details →

Data from: Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells - like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a "climate change" common garden, where we raised temperature 3°C, decreased pH by 0.2 units, and limited food supply by filtering out planktonic particles > 5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170,000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2-10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of > 90% when effective sample size is 900.

opencc-zeroJul 2021View details →

Associations among cotyledon developmental stability, canalization and phenotypic plasticity in response to shading and burial depth in five herbaceous species at early seedling stage

Premise of research. Cotyledons have important functions in early seedling stage and have important effects on later stages, but we know little about the relationships among developmental stability, canalization and phenotypic plasticity in cotyledons. Methodology. We conducted a field experiment with five herbaceous species, by subjecting them to contrasting light conditions and burial depths and measuring their cotyledon size and fluctuating asymmetry (random deviation from perfect bilateral symmetry, indicating developmental stability or instability), coefficient of variation and plasticity of cotyledon size, to investigate the relationships among cotyledon developmental stability, canalization and plasticity in response to shading and deep burial. Pivotal results. Pharbitis purpurea, Convolvulus arvensis and Carpesium abrotanoides had increased cotyledon size in response to shading at both burial depths; Abutilon theophrasti showed reduced cotyledon size in response to shading vs. full light at shallow depth, but greater cotyledon size in response to both shading and deep burial. Shading increased cotyledon fluctuating asymmetry of P. purpurea and C. abrotanoides, while deep burial decreased it. Cotyledon fluctuating asymmetry had positive correlations with coefficient of variation and plasticity in response to shade in shading, with little correlation between coefficient of variation and plasticity. Conclusions. Results suggested A. theophrasti may have greater tolerance for multiple stresses than the other species, and deep burial may improve shade tolerance of cotyledons through moderate level of stress selection. Both developmental instability and decreased canalization may indicate the state of faster growth. Developmental instability can facilitate more-active response to shading in cotyledon, while the relationship between canalization and plasticity should be more complex.

opencc-zeroNov 2022View details →

Metabolic phenotype mediates the outcome of competitive interactions in a response-surface field experiment

Competition and metabolism should be linked. Intraspecific variation in metabolic rates and, hence, resource demands covary with competitive ability. The effects of metabolism on conspecific interactions, however, have mostly been studied under laboratory conditions. We used a trait-specific response-surface design to test for the effects of metabolism on pairwise interactions of the marine colonial invertebrate, Bugula neritina in the field. Specifically, we compared the performance (survival, growth, and reproduction) of focal individuals, both in the presence and absence of a neighbour colony, both of which had their metabolic phenotype characterised. Survival of focal colonies depended on the metabolic phenotype of the neighbouring individual, and on the combination of both the focal and neighbour colony metabolic phenotypes that were present. Surprisingly, we found pervasive effects of neighbour metabolic phenotypes on focal colony growth and reproduction, though the sign and strength of these effects showed strong microenvironmental variability. Overall, we find that the metabolic phenotype changes the strength of competitive interactions, but these effects are highly contingent on local conditions. We suggest future studies explore how variation in metabolic rate affects organisms beyond the focal organism alone, particularly under field conditions.

opencc-zeroMar 2023View details →

Data from: Intra-specific variation in responses to habitat restoration: Could artificial reefs increase spatiotemporal segregation between migratory phenotypes of lake sturgeon?

Habitat restoration is an important tool used to conserve biodiversity and restore species, but its effects are notoriously difficult to predict. Although outcomes of restoration projects are usually assessed using indices of species abundance and diversity, phenotypic differences among individuals within species are likely associated with differing responses to restored habitats. Here, we use lake sturgeon (Acipenser fulvescens) as a case study to illustrate how responses to habitat restoration can differ between phenotypes and potentially lead to unanticipated effects on populations. North America's St. Clair River supports one of the largest remaining populations of lake sturgeon but has lost much spawning habitat due to its role as a major industrial corridor between the Laurentian Great Lakes Erie and Huron. Two artificial reefs were recently built in the lower and middle segments of the river to increase the available sturgeon spawning habitat. Interestingly, lake sturgeon in the St. Clair River express different migratory phenotypes that may be associated with different likelihoods of colonizing artificial reefs. Acoustic telemetry revealed that artificial reefs were more likely to be used by sturgeon that migrated downstream to overwinter in Lake St. Clair than those that migrated upstream to overwinter in Lake Huron. Furthermore, increasing time spent at the artificial reefs by Lake St. Clair migrants was associated with later arrival to and shorter occupancy of the river's only natural spawning site, the primary location where the two phenotypes have opportunity to interbreed. Additional research is necessary to determine the ultimate impacts of the artificial reefs on lake sturgeon populations; nevertheless, our study showed phenotype-specific opportunity to colonize restored habitat and a mechanism through which this could lead to changes in gene flow. Our results illustrate the importance of considering intra-specific diversity when planning restoration projects and assessing the effects on populations.

opencc-zeroAug 2023View details →

Data from: Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes

Geographic access to isolated ecosystems is an important catalyst of adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and volcanic lakes from surrounding rivers. We test the "lake effect" on the phenotypic rate and state across 253 cichlid species. The rate of evolution was consistently higher (~10-fold) in lakes, and consistent across different dimensions of the phenotype. Rate shifts tended to occur coincident with or immediately following river-to-lake transitions, generally resulting in 2- to 5-fold faster rates than in the founding riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit considerable overlap in phenotypes, generally with less disparity in lakes, but often different evolutionary optima. Taken together, these results suggest that lake radiations rapidly expand into niches largely already represented by ancestral riverine lineages, albeit in different frequencies. Lakes may provide ecological opportunity via ecological release (e.g., from predators/competitors), but need not be coupled with access to novel ecological niches.

Double-method Comparative Study in Order to Predict the Use of Co-receptors From Type 1 HIV: Phenotypic Study (Trofile ESTA®) and Virologic Response to a CCR5 Antagonist in the Short Term

ClinicalTrials.gov study NCT01060618. IPD Sharing: Not stated. Countries: 1. Publications: 2.

Relationship of Haptoglobin Phenotype to Vascular Function and Response to Vitamin E Supplementation in Patients With Diabetes Mellitus Type 2: The EVAS Trial

ClinicalTrials.gov study NCT02776397. IPD Sharing: Not stated. Countries: 1. Publications: 5.

ECG-I Phenotyping of Persistent AF Based on Driver Distribution to Predict Response to Pulmonary Vein Isolation

ClinicalTrials.gov study NCT03394404. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.

PAM50 HER2-enriched Phenotype as a Predictor of Response to Dual HER2 Blockade in HER2-positive Early Breast Cancer

ClinicalTrials.gov study NCT01973660. IPD Sharing: Not stated. Countries: 1. Publications: 7.