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6,234 results for “phenotypes”
# Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease
<p>Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern target gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, it is still challenging to understand how cell type networks work abnormally under AD. To address this, we integrated single-cell multi-omics data and predicted the gene regulatory networks in AD and control for four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes. Importantly, we applied network biology approaches to analyze the changes of network characteristics across these cell types, and between AD and control. For instance, many hub TFs target different genes between AD and control (rewiring). Also, these networks show strong hierarchical structures in which top TFs (master regulators) are largely common across cell types, whereas different TFs operate at the middle levels in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell type-specific TF-TF cooperativities in gene regulation. The cell type networks are highly modular and several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes and putative targets of approved and pending AD drugs, suggesting possible cell-type genomic medicine in AD. Finally, using the cell type gene regulatory networks, we developed machine learning models to classify and prioritize additional AD genes. We found that top prioritized genes predict clinical phenotypes (e.g., cognitive impairment) with reasonable accuracy. Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals dysregulated cell type gene dysregulatory mechanisms in AD.</p>
A case-study for improved reusability of plant phenotyping data with MIAPPE
<p>Accompanying datasets for manuscript, "A case-study for improved reusability of plant phenotyping data with MIAPPE".</p> <p>The ZIP archives in this repository contain the source files and the output files that this manuscript refers to.</p>
Data and scripts for: Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping
<p>Plant phenotyping under field conditions plays an important role in agricultural research. Efficient and accurate high-throughput phenotyping strategies enable a better connection between genotype and phenotype. Unmanned aerial vehicle-based high-throughput phenotyping platforms (UAV-HTPPs) provide novel opportunities for large-scale proximal measurement of plant traits with high efficiency, high resolution, and low cost. The objective of this study was to use time series normalized difference vegetation index (NDVI) extracted from UAV-based multispectral imagery to characterize its pattern across development and conduct genetic dissection of NDVI in a large maize population. The time series NDVI data from the multispectral sensor were obtained at 5 time points across the growing season for 1,752 diverse maize accessions with a UAV-HTPP. Cluster analysis of the acquired measurements classified 1,752 maize accessions into 2 groups with distinct NDVI developmental trends. To capture the dynamics underlying these static observations, penalized-splines (P-splines) model was used to obtain genotype-specific curve parameters. Genome-wide association study (GWAS) using static NDVI values and curve parameters as phenotypic traits detected signals significantly associated with the traits. Additionally, GWAS using the projected NDVI values from the P-splines models revealed the dynamic change of genetic effects, indicating the role of gene-environment interplay in controlling NDVI across the growing season. Our results demonstrated the utility of ultra-high spatial resolution multispectral imagery, as that acquired using a UAV-based remote sensing, for genetic dissection of NDVI.</p>
Data for the Manuscript 'Phenotypic Variation from Waterlogging in Multiple Perennial Ryegrass Varieties under Climate Change Conditions'
<p>Experimental data supporting the findings of the manuscript 'Phenotypic Variation from Waterlogging in Multiple Perennial Ryegrass Varieties under Climate Change Conditions'. This dataset will be made publicly available when the manuscript has been accepted for journal publication unless exceptional conditions become apparent. </p>
Data_Figure1(A-D)_AKR1D1 knockout mice develop a sex dependent metabolic phenotype
<p>Data of Fig1 Pannel A-D, “AKR1D1 knockout mice develop a sex dependent metabolic phenotype”</p> <p>The Dataset contains the original figure 1 (Pannel A-D) as PNG-format (10.1530JOE-21-0280_Fig1A-D.PNG). Corresponding raw from LC-MS/MS measurements are provided as one file in CSV format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1.csv), all further experiment related information (meta-data) as one file in TXT format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M1.txt), one file in PDF format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M2.pdf) and one file as CSV format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M3.csv).</p>
Fig. 2 and table 3 in Phenotypic Diversities Of Four Populations Of Clarias Gariepinus (Siluriformes, Clariidae) Obtained From Ogun And Ondo State Waterbodies In South-Western Nigeria
Fig. 2 and table 3 illustrate the values of PCA loadings for the morphometrics of Clarias gariepinus obtained from the four Rivers showing Pre-ventral distance (PVD) as the trait with the highest variation.
Phenotypes and genotypes of brown trout used for breeding experiments in 2014
<p><span>Adult brown trout were caught via electrofishing around the beginning of the spawning season from the River Aare and its tributaries Gürbe, Worble, Giesse, Kiese, and Rotache (Bern canton, Switzerland). They were kept in the <em>Fischereistützpunkt Reutigen</em> until </span><span>eggs could be stripped from females</span><span>. Adults were </span><span>narcoticised when ready to spawn and gametes were stripped for block-wise full-factorial in vitro fertilisations (e.g. Marques da Cunha et al. 2019). Photographs were taken from all fish, standard length and wet weight were determined, and fin clips were taken for molecular analyses. All fish were then released back into the streams of origin. Samples of 24 freshly fertilized eggs per experimentally produced full-sib family were used for various laboratory experiments (e.g. Marques da Cunha et al. 2019). The remaining embryos were raised </span><span>in the <em>Fischereistützpunkt Reutigen</em> and used for stocking the streams of parental origin and various nursery streamlets, following the routine of the stocking program of the Bern canton. These stocked fish were later sampled at various stages of their life cycle, and 13 microsatellite markers could be used to assign these fish to their parents.</span></p> <p><span>Marques da Cunha L., Uppal A., Seddon E., Nusbaumer D., Vermeirssen E.L.M., Wedekind C. 2019. </span>No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout (<em>Salmo trutta</em>). Evol. Appl. 12(5), 940-950. (doi:10.1111/eva.12767).</p>
Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex
<p class="MsoNormal"><span>Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid <em>Arabidopsis suecica </em>and its parent species <em>A. arenosa</em> and <em>A. thaliana</em> were chosen as a model system to investigate relationships between phenotypic plasticity, fitness and genetic variation. Particularly, we test if <em>A. suecica</em> is more plastic, show higher genetic diversity and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water and light, while genetic diversity was assessed through analysis of AFLP markers. <em>Arabidopsis arenosa</em> showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity were found in the inbreeding <em>A. thaliana</em>. Geographic spacing of populations might explain the clear genetic structure in <em>A. arenosa</em>, while the lack of structure in <em>A. suecica </em>could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed towards <em>A. arenosa</em> having lower fitness under poor environmental conditions. <em>Arabidopsis </em><em>suecica</em>, on the other hand, showed tendencies towards keeping up fitness under different environmental conditions. </span></p>
Data and Scripts from: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa
<p>Morphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Futhermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa, but yields new insights about the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet, but serves as a general framework for predicting multivariate ecology from phenotypic traits.</p>
Data and code of "Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats"
<p>This dataset contains behavioral and transcriptomic data, and the original code related to the following article:</p> <p>Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats. Fanny Demars, Ralitsa Todorova, Gabriel Makdah, Antonin Forestier, Marie-Odile Krebs, Bill P Godsil, Thérèse M Jay, Sidney I Wiener, & Marco N Pompili (2022) Current Biology <em>32. https://doi.org/10.1016/j.cub.2022.05.050</em></p>
Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana
<p>Data and code from: "Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana" published at Annals of Botany PLANTS. This is a dataset on phenotypic traits of Arabidopsis in response to different abiotic stresses and a reproducible R script to generate all figures and tables in the publication.</p>
Long-term experimental drought alters floral scent and pollinator visits in a Mediterranean plant community despite overall limited impacts on plant phenotype and reproduction
<p>Pollinators are declining globally, with climate change implicated as an important driver. Climate change can induce phenological shifts and reduce floral resources for pollinators, but little is known about its effects on floral attractiveness and how this might cascade to affect pollinators, pollination functions and plant fitness. We used an in situ long-term drought experiment to investigate multiple impacts of reduced precipitation in a natural Mediterranean shrubland, a habitat where climate change is predicted to increase the frequency and intensity of droughts. Focusing on three insect-pollinated plant species that provide abundant rewards and support a diversity of pollinators (<em>Cistus</em> <em>albidus</em>, <em>Salvia</em> <em>rosmarinus</em> and <em>Thymus</em> <em>vulgaris</em>), we investigated the effects of drought on a suite of floral traits including nectar production and floral scent. We also measured the impact of reduced rainfall on pollinator visits, fruit set and germination in <em>S</em>. <em>rosmarinus</em> and <em>C</em>. <em>albidus</em>. Drought altered floral emissions of all three plant species qualitatively, and reduced nectar production in <em>T</em>. <em>vulgaris</em> only. <em>Apis</em> <em>mellifera</em> and <em>Bombus</em> gr. <em>terrestris</em> visited more flowers in control plots than drought plots, while small wild bees visited more flowers in drought plots than control plots. Pollinator species richness did not differ significantly between treatments. Fruit set and seed set in <em>S. rosmarinus</em> and <em>C. albidus </em>did not differ significantly between control and drought plots, but seeds from drought plots had slower germination for <em>S. rosmarinus</em> and marginally lower germination success in <em>C. albidus</em>.</p> <p><em>Synthesis</em>. Overall, we found limited but consistent impacts of a moderate experimental drought on floral phenotype, plant reproduction and pollinator visits. Increased aridity under climate change is predicted to be stronger than the level assessed in the present study. Drought impacts will likely be stronger and this could profoundly affect the structure and functioning of plant-pollinator networks in Mediterranean ecosystems.</p>
Data from: Evolution of fungal phenotypic disparity
<p><span>Organismal grade multicellularity has been achieved only in animals, plants, and fungi. All three kingdoms manifest phenotypically disparate body plans, but their evolution has only been considered in detail for animals. Here we seek to test the general relevance of hypotheses on the evolution of animal body plans by characterising the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated, zygomycetous, sac-bearing, and club-bearing. The discontinuity between morphotypes is a consequence of the extinction of phylogenetic intermediates, indicating that a complete record of fungal disparity would present a much more homogeneous distribution of form. Fungal phenotypic variety gradually expands through time for the most part but sharply increases with the emergence of multicellular body plans. Simulations show these temporal trends to be decidedly non-random, and at least partially shaped by hierarchical contingency. Fungal phenotypic distance is decoupled from changes in gene number, genome size, and taxonomic diversity. Only differences in organismal complexity, the number of traits that constitute an organism, at the cellular and multicellular levels present a meaningful relationship with fungal disparity. Both animals and fungi exhibit a gradual increase in disparity through time, resulting in distributions of form made discontinuous by the extinction of phylogenetic intermediates. These congruences hint at a common mode of multicellular body plan evolution.</span></p>
The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia
<p>Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Both effects are likely to depend on prior selection on phenotypic and transcriptional plasticity in response to hypoxia, and may therefore show signs of local adaptation. Here we report the lifespan effects of chronic, mild, intermittent hypoxia (CMIH) and short-term survival in acute severe hypoxia (ASH) in four clones of <em>Daphnia magna</em> originating from either permanent or intermittent habitats, the latter regularly drying up with frequent hypoxic conditions. We show that CMIH extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to ASH. Exposure to CMIH did not protect against ASH; to the contrary, <em>Daphnia</em> from the CMIH treatment had lower ASH tolerance than normoxic controls. Few transcripts changed their abundance in response to the CMIH treatment in any of the clones. After 12 hours of ASH treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in mitochondrial and respiratory metabolism, oxygen transport, and, unexpectedly, gluconeogenesis showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to ASH than those from permanent habitats, there were no significant hypoxia-by-habitat of origin or CMIH-by-ASH interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.</p>
Direct and indirect phenotypic effects on sociability indicate potential to evolve
<p class="MsoNormal">The decision to leave or join a group is important as group size influences many aspects of organisms' lives and their fitness. This tendency to socialise with others, sociability, should be influenced by genes carried by focal individuals (direct genetic effects) and by genes in partner individuals (indirect genetic effects), indicating the trait's evolution could be slower or faster than expected. However, estimating these genetic parameters is difficult. Here, in a laboratory population of the cockroach <em>Blaptica dubia</em>, I estimate phenotypic parameters for sociability: repeatability (<em><span>R</span></em>) and repeatable influence (<em><span>RI</span></em>), which indicate whether direct and indirect genetic effects respectively are likely. I also estimate the interaction coefficient (<em><span>Ψ</span></em><em>)</em>, which quantifies how strongly a partner's trait influences the phenotype of the focal individual and is key in models for the evolution of interacting phenotypes. Focal individuals were somewhat repeatable for sociability across a three-week period (<em><span>R</span></em> = 0.080), and partners also had marginally consistent effects on focal sociability (<em><span>RI</span></em> = 0.053). The interaction coefficient was non-zero, although in the opposite sign for the sexes; males preferred to associate with larger individuals (<em><span>Ψ</span></em><sub>male </sub>= -0.129) while females preferred to associate with smaller individuals (<em><span>Ψ</span></em><sub>female</sub><strong><sub> </sub></strong>= 0.071). Individual sociability was consistent between dyadic trials and in social networks of groups. These results provide phenotypic evidence that direct and indirect genetic effects have limited influence on sociability, with perhaps the most evolutionary potential stemming from heritable effects of the body mass of partners. Sex-specific interaction coefficients may produce sexual conflict and the evolution of sexual dimorphism in social behaviour.</p>
Egg size and offspring phenotype data at early life stages in seven Arctic charr morphs
<p>Maternal effects have the potential to alter early developmental processes of offspring and contribute to adaptive diversification. Egg size is a major contributor to offspring phenotype, which can influence developmental trajectories and potential resource use. However, to what extent intraspecific variation in egg size facilitates evolution of resource polymorphism is poorly understood. We studied multiple resource morphs of Icelandic Arctic charr, ranging from an anadromous morph – with a phenotype similar to the proposed ancestral phenotype – to sympatric morphs that vary in their degree of phenotypic divergence from the ancestral anadromous morph. We characterised variation in egg size and tested whether egg size influenced offspring phenotype at early-life stages (i.e. timing of- and size at- hatching and first feeding [FF]). We predicted that egg size would differ among morphs and be less variable as morphs diverge away from the ancestral anadromous phenotype. We also predicted that egg size would correlate with offspring size and developmental timing. We found morphs had different egg size, developmental timing and size at hatching and FF. Egg size increased as phenotypic proximity to the ancestral anadromous phenotype decreased, with larger eggs generally giving rise to larger offspring, especially at FF, but egg size had no effect on developmental rate. The interaction between egg size and the environment may have a profound impact on offspring fitness, where the resulting differences in early-life history traits may act to initiate and/or maintain resource morphs diversification. </p>
Dataset for: Phenotyping single-cell motility in microfluidic confinement
<p>Associated dataset and simulation codes for the publication "Phenotyping single-cell motility in microfluidic confinement" (2022), by Samuel A. Bentley, Hannah Laeverenz-Schlogelhofer, Vasileios Anagnostidis, Jan Cammann, Marco G. Mazza, Fabrice Gielen, Kirsty Y. Wan. </p>
Mitochondrial influence on sex-specific phenotypes within natural populations
<p>Data and scripts for the manuscript entitled "Mitochondrial influence on sex-specific phenotypes within natural populations" submitted to <em>Evolution</em><em>. </em></p>
Data for: Associations between leaf developmental stability, canalization and phenotypic plasticity in an architectural perspective
<p class="MsoNormal"><span>Associations between developmental stability, canalization and phenotypic plasticity have been predicted, but rarely supported by direct evidence. Architectural analysis may provide a more powerful approach to finding correlations among these mechanisms in plants. T</span><span>o investigate the relationships among the three mechanisms in architectural perspective, w</span><span>e </span><span>subjected plants of </span><em><span>Abutilon theophrasti</span></em><span> to three densities, measured and calculated </span><span>fluctuating asymmetry (FA), coefficients of variation (CV)</span><span> and </span><span>plasticity (PI) of three leaf traits, to analyze the </span><span>correlations among these variables.</span><span> As density increased, mean leaf size, petiole length and angle of most layers and mean leaf FA of some layers decreased (at both stages), CV of petiole angle increased (at day 50), and PI of petiole length and angle across all layers decreased (at day 70); leaf FA and CV of traits generally increased with higher layers at all densities. At both stages, there were more positive correlations between FA and CV at lower vs. high densities; at day 50, little correlation of plasticity with FA or CV was found; at day 70, more positive correlations between FA and PI occurred for response to high vs. low density than for response to medium vs. low density, and more positive correlations between CV and PI occurred at lower vs. high densities. Results suggested that developmental instability, decreased canalization and plasticity can be cooperative and the relationships between decreased canalization and plasticity are more likely to be positive if decreased canalization is due to vibrant growth rather than stressful effects. The relationships of plasticity with developmental instability differed from its relationship with decreased canalization in the way of variation. Decreased canalization should be more beneficial for possible plasticity in the future, while canalization may result from already-expressed plasticity.</span></p>
Phenotypic data from: from buds to shoots: insights into grapevine development from the Witch's Broom bud sport
<p><strong>Background </strong></p> <p>Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch's Broom bud sport occurs occasionally in various grapevine (<em>Vitis vinifera</em>) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch's Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch's Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets.</p> <p><strong>Results</strong></p> <p>The Dakapo and Merlot cases of Witch's Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch's Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968–974 unique genetic mutations in our two Witch's Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch's Broom impacting the gene GSVIVG01008260001.</p> <p><strong>Conclusions</strong></p> <p>The Witch's Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch's Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.</p>
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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.