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6,234 results for “phenotypes”
Figure 1 in Speciation, phenotypic plasticity, or ontogeny, the case of the genus Galkinius (Pyrgomatidae, Cirripedia, Crustacea)
Figure 1. Opercular valves of Galkinius extracted from Hydnophora; A, NHM-2013 798–802; host: Hydnophora exesa. B, WAM-22091; host: H. exesa. C, NHM-2013 793–797; host: H. exesa. D, TAU AR29315; host: H. exesa. E, opercular valve of Galkinius indica, after Darwin (1854: plate XIV, 6.u; Creusia spinulosa var. 11). Abbreviations: ap, adductor plate; rt, rostral tooth; sc, scutum; sp, spur; tf, tergal furrow; tg, tergum.
Figure 2 in Stability and acceleration of phenotypic evolution in spiny rats (Trinomys, Echimyidae) across different environments
Figure 2. Time-calibrated BI tree of Trinomys based on eight genes. Horizontal bars across nodes represent 95% highest posterior density (HPD) of divergence-time estimates. Letters above nodes correspond to the nodes described in Table 2. Horizontal bar at bottom represents time scale in million years ago (Mya).
Figure 1 in Stability and acceleration of phenotypic evolution in spiny rats (Trinomys, Echimyidae) across different environments
Figure 1. Skull of Trinomys. Dorsal (top), ventral (center) and lateral (bottom) views illustrating the 18 linear measurements used in the present study. GSL, greatest skull length; LN, length of nasals; LR, length of rostrum; IOC, least interorbital constriction; WZ, width of zygomatic arches; WM, width of mastoids; BAL, basilar length; LIF, length of incisive foramen; D, length of diastema; PLA, palatal length A; PLB, palatal length B; LMS, length of molar series; PPL, post-palatal length; LBu, length of auditory bulla; HB, height of braincase; WMax, width of maxillary; WR, width of rostrum; DR, depth of rostrum. Figure modified from Nicola et al. (2003).
Figure 4 in Stability and acceleration of phenotypic evolution in spiny rats (Trinomys, Echimyidae) across different environments
Figure 4. Mean estimates of pairwise rates of phenotypic change (J) along the size axis (A) and multivariate axes PC1 (B), PC2 (C) and PC3 (D), and mean estimates of pairwise rates of general phenotypic change (J0) based in Mahalanobis distances (E). Columns represent mean estimates and error bars 95% confidence intervals. AF X AF, estimates between Atlantic Forest species; AF X y, estimates between Atlantic Forest species and T. yonenagae; AF X a, estimates between Atlantic Forest species and T. albispinus.
Figure 3 in Stability and acceleration of phenotypic evolution in spiny rats (Trinomys, Echimyidae) across different environments
Figure 3. Scores of individuals of Trinomys plotted in morphospaces formed by the size axis vs. PC1 (A), PC2 vs. PC3 (B) and CV1 vs. CV2 (C). Trinomys eliasi, T. albispinus and T. yonenagae are enclosed in convex grey polygons.
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>
Allele frequency files for population genomic and phenotypic association analyses
<p>Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. One challenge in studying the genetic architecture of local adaptation is to achieve high marker density to detect candidate genes in natural populations that often have small blocks of linkage disequilibrium. Here, we used low coverage whole-genome resequencing (lcWGR) to identify genome regions involved in thermal adaptation in wild redband trout <i>Oncorhynchus mykiss gairdneri</i>, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts.</p>
Figure 2 in Repeated colonization of caves leads to phenotypic convergence in catfishes (Siluriformes: Trichomycterus) at a small geographical scale
Figure 2. Morphological variability of some species of Trichomycterus included in this study. Lateral and dorsal view of the same individual from cave localities (designated with letter C) and surface streams (designated with letter S). Sc = Coca, Guadalupe; Su = Uchuval, Zapatoca; Cb = El Berraco, Guadalupe; Cv = La Vaca, Curití; Cg = Ojo de Agua, Guapotá; Cal = La Alsacia, Zapatoca. Bar indicates 1 cm.
Figure 1 in Repeated colonization of caves leads to phenotypic convergence in catfishes (Siluriformes: Trichomycterus) at a small geographical scale
Figure 1. Type localities of cave species of Trichomycterus in the Neotropical region (top left), a photograph showing an example of habitats occupied by fishes in this system (Las Sardinas Cave, the type locality of T. rosablanca; photo by Felipe Villegas) and map of the Department of Santander showing the collection sites of specimens of Trichomycterus analysd in this study (bottom). Triangles correspond to caves, circles to surface streams. Orange triangles correspond to cave localities where fishes show reduced eyes and coloration, and blue triangles to caves where fishes have regular eyes and coloration. Cave localities are designated with letter C and surface streams with the letter S. The type localities of cave species T. rosablanca (Cs) and T. sandovali (Cal) are indicated with asterisks. Photograph (El Peñón, Santander) by Felipe Villegas-Instituto Humboldt.
Imaging Mass Cytometry of human normal colon mucosa (CLN1-6) from: A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially resolved tissue phenotyping at single-cell resolution.
<p>Four µm-thick sections were cut from each block of samples CLN1-CLN6 with a microtome and used for staining with a panel of 26 antibodies targeting the main immune, stromal and epithelial cell populations of the gastrointestinal tract (Supplementary Table 2). The optimal dilution of each antibody in the panel was identified by staining and ablating FFPE appendix sections. The resulting images were reviewed by a mucosal immunologist (J.S.) and the dilution giving the best signal to background ratio was selected for each antibody (Supplementary Table 2). To perform the staining for IMC, slides were dewaxed after a one-hour incubation at 60°C, rehydrated and heat-induced antigen retrieval was performed with a pressure cooker in Antigen Retrieval Reagent-Basic (R&D Systems). Slides were incubated in a 10% BSA (Sigma), 0.1% Tween (Sigma), and 2% Kiovig (Shire Pharmaceuticals) Superblock Blocking Buffer (Thermo Fisher) blocking solution at room temperature for two hours. Each antibody was added to a primary antibody mix at the selected concentration in blocking solution and incubated overnight at 4°C. After two washes in PBS and PBS-0.1% Tween, the slides were treated with the DNA intercalator Cell-ID™ Intercalator-Ir (Fluidigm) (containing the two iridium isotopes 191Ir and 193Ir) 1.25 mM in a PBS solution. After a 30-minute incubation, the slides were washed once in PBS and once in MilliQ water and air-dried. The stained slides were then loaded in the Hyperion Imaging System (Fluidigm) imaging module to obtain light-contrast high resolution images of approximately four mm<sup>2</sup>. These images were used to select the ROI in each slide. For CLN1-CLN6, 1 mm<sup>2 </sup>ROIs were selected to contain the full thickness of the colon mucosa, with epithelial crypts in longitudinal orientation. ROIs were ablated at a o µm/pixel resolution and 200 Hz frequency.</p> <p>Twenty-eight images from 26 antibodies (Supplementary Table 2) and two DNA intercalators were obtained from the raw .txt files of the ablated regions in CLN1-CLN6 using the data extraction process.</p>
An extended epiphenotype for an extended phenotype in Toxoplasma gondii infected feral house mice
<p>Parasitism of mice by Toxoplasma gondii reduces the host's aversion to cat odors, likely increasing predation and transmission of the parasite to its definitive host. This behavioral change suggests a parasitic manipulation where host behavior becomes an extended phenotype of the parasite. Independently, epigenetic changes within an organism are now known to create behavioral change. The results described here provide an experimental connection between these disparate strands of extended phenotypes and the role of epigenetics in behavioral diversity. Using mice captured on Kangaroo Island in Australia, we demonstrate that Toxoplasma gondii infection leads to specific DNA hypomethylation events in the host brain. Previous laboratory studies have shown that these epigenetic changes underlie the central processing of cat odors. We posit that the concept of extended phenotype can be expanded to extended epiphenotype, thus linking parasite genes to host behavior through epigenesis. This phenomenon has broad implications for inter-species relationships.</p>
Label-free imaging of M1 and M2 macrophage phenotypes in the human dermis in vivo using two-photon excited FLIM
<p>Macrophages (ΜΦs) are important immune effector cells that promote (M1 ΜΦs) or inhibit (M2 ΜΦs) inflammation and are involved in numerous physiological and pathogenic immune responses. Their precise role and relevance, however, are not fully understood for lack of non-invasive quantification methods. Here, we show that two-photon excited fluorescence lifetime imaging (TPE-FLIM), a label-free non-invasive method, can visualize ΜΦs in the human dermis in vivo. We demonstrate in vitro that human dermal ΜΦs exhibit specific TPE-FLIM properties that distinguish them from the main components of the extracellular matrix and other dermal cells. We visualized ΜΦs, their phenotypes and phagocytosis in the skin of healthy individuals in vivo using TPE-FLIM. Additionally, machine learning identified M1 and M2 MФs with a sensitivity of 0.88±0.04 and 0.82±0.03 and a specificity of 0.89±0.03 and 0.90±0.03, respectively. In clinical research, TPE-FLIM can advance the understanding of the role of MФs in health and disease.</p>
Images of H9 cell colonies and code for phenotype classification
<p>The dataset and code are part of the following manuscript submitted for publication in International Journal of Molecular Sciences (MDPI):</p> <p>"Quality Control of Human Pluripotent Stem Cell Colonies by Computational Image Analysis using Convolutional Neural Networks" by Anastasiya Mamaeva, Olga Krasnova, Konstantin Kozlov, Vitaly Gursky, Maria Samsonova and Irina Neganova</p>
Genome-wide association study of polygenic risk score-defined phenotype suffers from inflated test-statistics
<p>Simulation results from running the following script 100 times: https://github.com/euffelmann/paper-ad_prs_extremes/blob/main/scripts/ad_prs_extremes_simulation.R.</p> <p>These files can be used to reproduce tables and figures in: https://github.com/euffelmann/paper-ad_prs_extremes</p>
Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito
<p>Climatic variation is a key driver of genetic differentiation and phenotypic traits evolution, and local adaptation to temperature is expected in widespread species. We investigated phenotypic and genomic changes in the native range of the Asian tiger mosquito, <em>Aedes</em> <em>albopictus</em>. We first refine the phylogeographic structure based on genome-wide regions (1,901 double-digest restriction-site associated DNA single nucleotide polymophisms [ddRAD SNPs]) from 41 populations. We then explore the patterns of cold adaptation using phenotypic traits measured in common garden (wing size and cold tolerance) and genotype–temperature associations at targeted candidate regions (51,706 exon-capture SNPs) from nine populations. We confirm the existence of three evolutionary lineages including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and Okinawa), and C (South Korea and Japan). We identified temperature-associated differentiation in 15 out of 221 candidate regions but none in ddRAD regions, supporting the role of directional selection in detected genes. These include genes involved in lipid metabolism and a circadian clock gene. Most outlier SNPs are differently fixed between clades A and C, whereas clade B has an intermediate pattern. Females are larger at higher latitudes yet produce no more eggs, which might favor the storage of energetic reserves in colder climates. Nondiapausing eggs from temperate populations survive better to cold exposure than those from tropical populations, suggesting they are protected from freezing damages but this cold tolerance has a fitness cost in terms of egg viability. Altogether, our results provide strong evidence for the thermal adaptation of <em>A</em>. <em>albopictus</em> across its wide temperature range.</p>
Metabolic phenotype mediates the outcome of competitive interactions in a response-surface field experiment
<p>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.<b> </b>We used a trait-specific response-surface design to test for the effects of metabolism on pairwise interactions of the marine colonial invertebrate, <i>Bugula neritina</i> 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.<b> </b>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.<b> </b>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.</p>
Phenotypic plasticity in desiccation physiology of closely related, range restricted and broadly distributed fruit fly species
<p>1. Variation in geographic range size among closely related species may result from differences in physiological traits, such as desiccation tolerance, that enable these species to interact with their environment or adapt to new surroundings.</p> <p>2. We tested the hypothesis that insect species with a broader geographic range have either a higher basal desiccation tolerance or mount a more plastic response than more narrowly distributed species by exposing four fruit fly species (Ceratitis capitata, Ceratitis rosa, Ceratitis cosyra and Ceratitis podocarpi) to one of three acclimation treatments (control: standard relative humidity and temperature; desiccation: standard temperature and low humidity; and temperature: low relative humidity and high temperature) and measuring metabolic rate, activity, water loss rates and survival.</p> <p>3. The targeted physiological responses differed between species and acclimation treatments. Survival of the widely distributed C. capitata improved by up to 43% after short term exposure to high temperature and desiccation (35°C; 0% RH) treatment, while survival in the more narrowly distributed species only improved by 4-30% after a desiccation treatment (25°C; 0% RH).</p> <p>4. Less water was lost by broadly distributed C. capitata through excretion after both high temperature and desiccation treatments, but only activity and respiratory water loss were reduced after the temperature treatment, and total water loss and cuticular water loss declined after the desiccation treatment. The narrowly distributed C. rosa also lost less water through excretion after both acclimation treatments but showed reduced cuticular and respiratory water loss only after desiccation. While basal tolerance in C. cosyra was high, acclimation responses in this species and C. podocarpi were insignificant in that they did not produce a measurable survival benefit.</p> <p>5. Broadly distributed species successfully employed unique combinations of physiological strategies, with some having highly flexible responses to stressful environmental conditions, which ultimately results in beneficial acclimation to enhance survival during dry conditions. By contrast, range restricted species showed limited responses to desiccation stress. Flexible desiccation responses likely contribute to species geographic ranges in changing climate conditions.</p>
Phenotypic stability in scalar calcium of freshwater fish across a wide range of aqueous calcium availability in nature
<div> <p>Spatial environmental gradients can promote adaptive differences among conspecific populations as a result of local adaptation or phenotypic plasticity. Such divergence can be opposed by various constraints, including gene flow, limited genetic variation, temporal fluctuations, or developmental constraints. We focus on the constraint that can be imposed when some populations are found in locations characterized by low levels of an essential nutrient. We use scales of wild fish to investigate phenotypic effects of spatial variation in a potentially limiting nutrient – calcium. If scale calcium (we use "scalar" calcium for consistency with the physiology literature) simply reflects environmental calcium availability, we expect higher levels of scalar calcium in fish from calcium-rich water, compared to fish from calcium-poor water. To consider this "passive response" scenario, we analysed scalar calcium concentrations from three native fish species (<em>Lepomis gibbosus</em>, <em>Percina caprodes</em>, and <em>Perca flavescens</em>) collected at multiple sites across a dissolved calcium gradient in the Upper St. Lawrence River. Contradicting the "passive response" scenario, we did not detect strong or consistent relationships between scalar calcium and water calcium. Instead, for a given proportional increase in water calcium across the wide environmental gradient, the corresponding proportional change in scalar calcium was much smaller. We thus favor the alternative "active homeostasis" scenario, wherein fish from calcium-poor water are better able to uptake, mobilize, and deposit calcium than are fish from calcium-rich water. We further highlight the importance of studying functional traits, such as scales, in their natural setting as opposed to only laboratory studies.</p> </div>
Influenza phenotype-genotype database beta version
<p>Beta version of a data base of genetic mutations in influenzaA viruses linked to phenotypic changes in the literature with references. Not exclusive and sources should be checked before use.</p>
Open Plant Phenotyping Database Seedling Images
<p>The Open Plant Phenotyping Database [OPPD] is a public dataset for visual recognition tasks on images of plant seedlings. The dataset consists of 7,590 images with 315,038 plant objects, representing 64,292 individual plants from 47 different species. Each plant species has been cultivated using three growth conditions (ideal, drought and natural) and tracked temporally to achieve high intra-species variability.</p> <p>This is a subset of the .jpg images available at https://gitlab.au.dk/AUENG-Vision/OPPD/-/archive/master/OPPD-master.zip in the folder: /DATA/images_plants/1COMF/</p>
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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.