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238 results for “functional phenotype”
Phenotype data (composition, functionality, end-product quality) of wheat grown in Flanders, Belgium
<p>Data for the Ph.D. dissertation entitled: Outline of four degrees of diversification for understanding bread wheat (<em>Triticum aestivum</em> L.) quality. For further details on the content of the files, the meaning of abbreviations and used techniques, it is referred to the Ph.D. manuscript. </p> <p>For further details, please contact the author. </p>
Data from: Ontogenetic changes in the phenotypic integration and modularity of leaf functional traits
1.Changes in resource availability, functional demands, hormonal regulation and developmental constraints can promote differences in the expression of leaf traits during plant development and foster changes in the targets of natural selection. As a consequence, the pattern and magnitude of covariation among traits, and therefore their phenotypic integration and modularity are equally expected to change throughout ontogeny. However, these changes have not been described yet. 2.We measured leaf economic, defensive and morphological traits in plants of Turnera velutina and estimated the magnitude and pattern of foliar integration and modularity for juvenile and reproductive individuals. In addition, we assessed the relationship between plant biomass and foliar integration within and among ontogenetic stages. 3.Both the pattern and magnitude of foliar integration changed across plant ontogeny. Foliar integration was lower in juvenile than in reproductive plants, and the pattern of phenotypic integration and modularity was different between ontogenetic stages: whereas leaves from juvenile plants showed two functional modules related to plant defence and leaf economy, traits from reproductive plants had greater interconnectivity and hence lower modularity. 4.The relationship between plant biomass and foliar integration was negative within each ontogenetic stage but positive between ontogenetic stages, suggesting that processes intrinsic to plant development influenced the magnitude of foliar integration to a greater extent than plant size. 5.Our findings indicate that plants can change the patterns of covariation among leaf traits during their development. Whereas a lower foliar integration in juvenile plants could allow for greater lability to explore a multi-trait phenotypic space, canalization of leaf attributes along ontogeny should promote greater phenotypic integration, constraining the number of multi-trait combinations that plants can express. Hence, we suggest that ontogenetic changes in foliar integration allow plants to deal with changing selective dynamics and physiological priorities along their development.
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.
Life history predicts flight muscle phenotype and function in birds
<p>1. Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals' ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored.</p> <p>2. We asked how age- and sex-dependent demands on flight muscle function are reconciled in birds. The flight muscle is an essential multifunctional organ, mediating a large range of functions associated with powered flight and thermoregulation. These functions must be balanced over an individual's lifetime.</p> <p>3. We leveraged within- and between-species comparisons in a clade of small passerines (<em>Tarsiger</em> bush-robins) from the eastern edge of the Qinghai-Tibet Plateau. We integrated measurements of flight muscle physiology, morphology, behavior, phenology, and environmental data, analyzing trait data within a context of three widespread, adaptive life-history strategies – sexual dichromatism, age and sex-structured migration, and delayed plumage maturation. This approach provides a framework of the selective forces that shape functional variation within and between species.</p> <p>4. We found more variation in flight muscle traits within species than has been previously described between species of birds under 20 g. This variation was associated with the discovery of mixed muscle fiber types (i.e. both fast glycolytic and fast oxidative fibers), which differ markedly in their physiological and functional attributes. This result is surprising given that the flight muscles of small birds are generally thought to contain only fast oxidative fibers, suggesting a novel ecological context for glycolytic muscle fibers in small birds. Within each species, flight muscle phenotypes varied by age and sex, reflecting the functional demands at different life-history stages and the pressures that individuals face as a result of their multi-class identity (i.e. species, age, and sex).</p> <p>5. Our findings reveal new links between avian physiology, ecology, behavior, and life history, while demonstrating the importance of demographic-dependent selection in shaping functional phenotypic variation. </p>
Intraspecific variation of Phragmites australis: Clinal adaption of functional traits and phenotypic plasticity vary with latitude of origin
<p>1. Widespread plant species generally have high intraspecific variation in functional traits, which is reflected in their great variety of phenotypes. This variety can result from both genetic differences due to local adaptation and phenotypic plasticity. With high intraspecific variation and nearly global distribution, the common reed <i>Phragmites australis</i> is a suitable model species for studying the underlying mechanisms of intraspecific trait variation. </p> <p>2. In this study, 71 genotypes of <i>P. australis</i> from seven phylogeographic groups were transplanted into two replicate common gardens located in very different climates: northern Europe and mid-east Asia. We measured seven functional traits of all these genotypes over the growing season, including shoot height, maximum biomass per shoot, shoot density, node number per stem, leaf lifespan, flowering occurrence and flowering date. Our aim was to assess the relative effects of genetic (phylogeographic origin) and environmental (common garden) status, and interactions between them, on intraspecific variation in functional traits of <i>P. australis</i>. </p> <p>3. We found common garden having the strongest influence on most functional traits studied. All traits except flowering occurrence varied significantly across gardens, revealing the important role of phenotypic plasticity on trait variation of <i>P. australis</i>. We also found significant differences in trait variation among the different phylogeographic groups of <i>P. australis</i> and, thus, evidence for genetically determined intraspecific variation in the morphological and life-history traits addressed in this study. All functional traits showed significant (p≤0.0054), albeit minor to moderately explained (<i>R</i><sup>2</sup> ≤0.57), latitudinal patterns in both gardens. Covariation of multiple traits was similar in the two gardens. Phenotypic plasticity was trait-specific, and the plasticity of shoot height and maximum biomass per shoot increased towards higher latitude of genotypic origin. Our results indicate that the latitude of origin affects the evolution of functional traits, as well as their phenotypic plasticity. </p> <p>4. Since phenotypic plasticity is a crucial mechanism for acclimation and evolution, our findings support the role of gene-based adaptive phenotypic plasticity in plant evolution. The intraspecific spatial variation of functional traits and their phenotypic plasticity can help predict species distribution, persistence and invasion under global climate change.</p>
Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions - behavior data
<p>Processed behavior data for all zebrafish behavior runs included in manuscript. This includes data such as bouts / minute. The raw data used to generate this processed output is available upon request (too large for any public repository). These files can be used to generate all statistics and graphs using the script statsandgraphs.py (https://github.com/sthyme/ZFSchizophrenia/tree/master/BehaviorAnalysis). Each directory also contains scripts used, genotyping information, and output files for the statistical analyses presented in the manuscript.</p>
Dynamic loading of human engineered heart tissue enhances contractile function and drives a desmosome-linked disease phenotype (TEM data)
<p>This is the TEM imaging data for the desmosome analysis as reported in the manuscript titled "Dynamic loading of human engineered heart tissue enhances contractile function and drives a desmosome-linked disease phenotype."</p>
Figure 6 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 6. Dorsal view of third-instar larval head capsule (left half) of Chrysoperla bolti sp. nov. The drawing represents the typical condition seen in 18 individuals from two populations in northern Kyrgyzstan. The colour insert is a typical mature third-instar larva of the species.
Figure 3 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 3. Frequency distributions of volley period measured in solo vibrational songs recorded at 25 ± 1° C from individuals of Chrysoperla shahrudensis sp. nov. (red/grey bars), Chrysoperla bolti sp. nov. (blue/ dark grey bars), and Chrysoperla adamsi (green/light grey bars). Measurements were calculated as individual averages; N = number of individuals from which individual averages were calculated.
Figure 5 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 5. Dorsal view of third-instar larval head capsule (left half) of Chrysoperla shahrudensis sp. nov. The drawing represents the typical condition seen in 24 individuals from two populations in Iran. The colour insert is a typical mature third-instar larva of the species.
Figure 7 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 7. Maximum likelihood phylogram of the cryptic species of the Chrysoperla carnea- group, based on 4630 bp of mitochondrial DNA sequence from the protein-coding genes ND2, COI, COII and ND5. The tree was inferred under the General Time Reversible model, using a discrete gamma distribution to model evolutionary rate variation while allowing some sites to remain invariant (GTR+G + I as implemented in MEGA v.7.0, Kumar et al. 2016). Numbers at the branch points are support values from 150 bootstrap replicates; branch lengths are proportional to the number of substitutions per site. Specimen numbers and geographical locations are shown for each operational taxonomic unit (twig) on the tree. The three songconvergent species discussed in the text are highlighted in colour: Chrysoperla shahrudensis in red, Chrysoperla bolti in blue and Chrysoperla adamsi in green. Thumbnail oscillographs of 12 s of song phenotype for 13 common species are placed on the figure at their approximate vertical positions on the phylogram.
Figure 4 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 4. Adult of (a) Chrysoperla. shahrudensis sp. nov., non-diapausing green form; (b) C. shahrudensis, diapausing sandy-brown form, and (c) Chrysoperla bolti sp. nov., all-season green form.
Figure 2 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 2. Oscillographs of duetting interactions. (a) 12 s of a typical duet between a male and a female of Chrysoperla shahrudensis sp. nov., showing the partners politely exchanging single volleyplus-rumble units or shortest repeated units (SRUs). (b) 12 s of a typical duet between a male and a female of Chrysoperla bolti sp. nov., showing the partners politely exchanging single SRUs. (c) 71 s oscillograph showing a female of C. shahrudensis duetting with a conspecific for the first 24 s, with C. bolti for the next 25 s, and with Chrysoperla adamsi (North America) for the last 22 s. In each of those three duets, the female being tested is capable of synchronizing precisely with the prerecorded playback signal. As discussed in the text, C. shahrudensis shows no such duetting response to playbacks of songs of any carnea-group species other than C. bolti and C. adamsi. All duets were recorded at 25 ± 1°C.
Figure 1 in Distinctive but functionally convergent song phenotypes characterize two new allopatric species of the Chrysoperla carnea-group in Asia, Chrysoperla shahrudensis sp. nov. and Chrysoperla bolti sp. nov. (Neuroptera: Chrysopidae)
Figure 1. Oscillographs (lower of each pair of traces) and sonographs (upper traces) of (a) a solo vibrational song of Chrysoperla shahrudensis sp. nov. from northern Iran and (b) a solo vibrational song of Chrysoperla bolti sp. nov. from Kyrgyzstan, Asia, illustrating convergent song phenotypes in these two Asian species. Each song was recorded at 25 ± 1°C and is drawn to the same time scale of 12 s. Start, middle, end, and rumble sections of an individual volley are marked by the arrows, while duration and period of the primary volley are bracketed.
Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function - data bundle
<p>This bundle is an archive of data files, configuration files, and scripts related to the manuscript "Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function".</p> <p> </p>
Dataset: Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture
<p>Dataset for Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture manuscript submitted to Plant Phenomics. The dataset contains raw and processed root architecture images, RhizoVision trait outputs, and the associated R scripts for statistical analysis and model parameterization.</p>
Biofilm Modified Macrophage Phenotype and Function in Diabetic Wound Healing
ClinicalTrials.gov study NCT03271580. IPD Sharing: NO. Countries: 1. Publications: 7.
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.
The Effect of Polycystic Ovary Syndrome Phenotypes on Quality of Life and Sexual Function
ClinicalTrials.gov study NCT06428786. IPD Sharing: NO. Countries: 1. Publications: 2.
Investigating a Von Willebrand Factor (VWF) Functional Screening Assay for Assigning the Phenotypic Variants of Von Willebrand Disease (VWD)
ClinicalTrials.gov study NCT02466789. IPD Sharing: Not stated. Countries: 1. Publications: 10.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.