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6,234 results for “phenotypes”
Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes. In this study, we utilized RNA-seq to assess transcriptome-wide gene expression in the muscle of Atlantic killifish (Fundulus heteroclitus) from a population that contains segregating variation in mitochondrial genotype. We examined gene expression plasticity in response to 5°C acclimation and the effects of mitochondrial genotype on this plasticity. Cold acclimation resulted in changes in gene expression consistent with up-regulation of genes involved in many cellular functions, including spliceosomal and proteasomal processes, and with down-regulation of genes involved in extracellular matrix, muscle contraction and oxidative phosphorylation functions. There were few differences in gene expression between killifish with different mitochondrial genotypes: 14 genes demonstrated significant interactions between mitochondrial genotype and acclimation temperature and 3 genes demonstrated effects of mitochondrial genotype alone. These results indicate that variation in mitochondrial genotype has modest effects on gene expression; the majority of which are revealed as differences in plasticity as a result of environmental change.
Data from: Phenotypic stochasticity prevents lytic bacteriophage population from extinction during bacterial stationary phase
It is generally thought that the adsorption rate of a bacteriophage correlates positively with fitness, but this view neglects that most phages rely only on exponentially growing bacteria for productive infections. Thus, phages must cope with the environmental stochasticity that is their hosts' physiological states. If lysogeny is one alternative, it is unclear how strictly lytic phages can survive the host stationary phase. Three scenarios may explain their maintenance: (1) pseudolysogeny, (2) diversified or (3) conservative bet-hedging. In order to better understand how a strictly lytic phage survives the stationary phase of its host, and how phage adsorption rate impacts this survival, we challenged two strictly lytic phage λ, differing in their adsorption rates, with stationary phase Escherichia coli cells. Our results showed that, pseudolysogeny was not responsible for phage survival and that, contrary to our expectation, high adsorption rate was not more detrimental during stationary phase than low adsorption rate. Interestingly, this last observation was due to the presence of the "residual fraction" (phages exhibiting extremely low adsorption rates), protecting phage populations from extinction. Whether this cryptic phenotypic variation is an adaptation (diversified bet-hedging) or merely reflecting unavoidable defects during protein synthesis remains an open question.
Data from: How does mutation affect the distribution of phenotypes?
The potential for mutational processes to influence patterns of neutral or adaptive phenotypic evolution is not well understood. If mutations are directionally biased, shifting trait means in a particular direction, or if mutation generates more variance in some directions of multivariate trait space than others, mutation itself might be a source of bias in phenotypic evolution. Here, we use mutagenesis to investigate the affect of mutation on trait mean and (co)variances in zebrafish, Danio rerio. Mutation altered the relationship between age and both prolonged swimming speed and body shape. These observations suggest that mutational effects on ontogeny or aging have the potential to generate variance across the phenome. Mutations had a far greater affect on males than females, although whether this is a reflection of sex-specific ontogeny or aging remains to be determined. In males, mutations generated positive covariance between swimming speed, size and body shape suggesting the potential for mutation to affect the evolutionary covariation of these traits. Overall, our observations suggest that mutation does not generate equal variance in all directions of phenotypic space or in each sex, and that pervasive variation in ontogeny or aging within a cohort could affect the variation available to evolution.
Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions. Shape and volume can be computed for populations of nuclei, motor neurons and red blood cells. Computed cell density revealed striking individual phenotypic variation. Unlike histology, histo-tomography allows the detection of phenotypes that require millimeter scale context in multiple planes. We expect the computational and visual insights into 3D tissue architecture provided by histo-tomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
Data from: Phenotype classification of zebrafish embryos by supervised learning
Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on supervised machine learning. We show that, compared to manual classification, automatic classification results in 90 to 100% agreement with consensus voting of biological experts in nine out of eleven considered defects in 3 days old zebrafish larvae. Automation of the analysis and classification of zebrafish embryo pictures reduces the workload and time required for the biological expert and increases the reproducibility and objectivity of this classification.
Phenotypic plasticity may mediate habitat filtering in a forest edge community
A key process determining community assembly is habitat filtering, which reduces the range of trait values and thus leads to trait convergence. Habitat filtering is often assumed to involve a reduction in species richness, but such trait convergence could also result from phenotypic plasticity. By allowing more species in the community to show the "right" phenotype and pass the filter, phenotypic plasticity could maintain species richness despite trait convergence. If phenotypic plasticity plays this role, environmental changes should modify trait distribution but not species composition or richness. We tested this hypothesis in a forest edge community recently invaded by the alien shrub <i>Rubus praecox</i>. We measured functional traits beneath <i>Rubus </i>canopy (<i>Rubus</i>-invaded community) and in adjacent microsites naturally free from <i>Rubus </i>(original community), comparing trait dispersion and community structure parameters. We also characterized the microenvironments to seek functional explanations for the observed phenotypic changes. The functional dispersion parameter FDis showed habitat filtering in the <i>Rubus</i>-invaded community (trait convergence), while in the original community it did not differ from a null model. Species richness and composition did not differ between the two communities. Soil characteristics were similar in both communities but light availability was greatly reduced in the <i>Rubus</i>-invaded community. A Principal Component Analysis of community-weighted means of functional traits showed that phenotypic changes between communities were mostly consistent with functional responses to shading, including an increase in specific leaf area and a reduction in flavonoid concentration in the <i>Rubus</i>-invaded community. We verified the conditions necessary to infer that phenotypic plasticity mediates the outcome of habitat filtering driven by <i>Rubus </i>in the study system, i.e., plasticity would explain species persistence despite trait convergence. Phenotypic plasticity, often subsumed within intraspecific variation in community assembly studies, should be considered individually to improve our understanding of the causes and consequences of habitat filtering.
Phenotypic plasticity in plant defense across life stages: inducibility, transgenerational induction, and transgenerational priming in wild radish
As they develop, many plants deploy shifts in anti-herbivore defense allocation due to changing costs and benefits of their defensive traits. Plant defenses are known to be primed or directly induced by herbivore damage within generations, and across generations by long-lasting epigenetic mechanisms. However, little is known about the ontogenetic trajectories of epigenetically inducible defensive traits across generations and their consequences. To help fill this knowledge gap, we conducted a multigenerational experiment to determine whether defense induction in wild radish plants was reflected in chromatin modifications (DNA methylation); we then examined ontogenetic trajectories (seedlings to reproductive plants) of current and transgenerational plasticity in anti-herbivore chemical (glucosinolates) and physical (trichomes) defenses in this species. Herbivory triggered genome methylation both in targeted plants and their offspring. Within one generation, both defenses were highly inducible at the seedling stage but only marginally or non-inducible in reproductive plants. Across generations, herbivory experienced by mother plants caused strong direct induction of physical defenses in their progeny, with effects lasting from seedling to reproductive stages. For chemical defenses, however, this transgenerational induction was evident only in adults. Transgenerational priming was observed in physical defenses both for seedlings and adult plants. Our results show that transgenerational induction and priming in response to herbivore offense differ for physical and chemical defense and change across plant life stages.
The influence of maternal glucocorticoids on offspring phenotype in high- and low-risk environments
<p><span><span><span><span><span><span><span><span><span><span><span>Elevated maternal glucocorticoid levels during gestation can lead to phenotypic changes in offspring via maternal effects. Although such effects have traditionally been considered maladaptive, maternally derived glucocorticoids may adaptively prepare offspring for their future environment depending upon the correlation between maternal and offspring environments. Nevertheless, relatively few studies test the effects of prenatal glucocorticoid exposure across multiple environments. We tested the potential for ecologically relevant increases in maternal glucocorticoids in the eastern fence lizard (<i>Sceloporus undulatus</i>) to induce adaptive phenotypic changes in offspring exposed to high or low densities of an invasive fire ant predator. Maternal treatment had limited effects on offspring morphology and behaviour at hatching, but by 10 days of age, we found maternal treatment interacted with offspring environment to alter anti-predator behaviours. We did not detect differences in early-life survival based on maternal treatment or offspring environment. Opposing selection on anti-predator behaviours from historic and novel invasive predators may confound the potential of maternal glucocorticoids to adaptively influence offspring behaviour. Our test of the phenotypic outcomes of transgenerational glucocorticoid effects across risk environments provides important insight into the context-specific nature of this phenomenon and the importance of understanding both current and historic evolutionary pressures.</span></span></span></span></span></span></span></span></span></span></span></p>
Unidirectional response to bidirectional selection on body size. I. Phenotypic, life history and endocrine response
Anthropogenic perturbations such as harvesting often select against a large body size and are predicted to induce rapid evolution towards smaller body sizes and earlier maturation. However, body-size evolvability and, hence, adaptability to anthropogenic perturbations remain seldom evaluated in wild populations. Here, we use a laboratory experiment over 6 generations to measure the ability of wild-caught medaka fish (Oryzias latipes) to evolve in response to bidirectional size-dependent selection mimicking opposite harvest regimes. Specifically, we imposed selection against a small body size (Large line), against a large body size (Small line) or random selection (Control line), and measured correlated responses across multiple phenotypic, life-history and endocrine traits. As expected, the Large line evolved faster somatic growth and delayed maturation, but also evolved smaller body sizes at hatch, with no change in average levels of pituitary gene expressions of luteinizing, follicle-stimulating or growth (GH) hormones. In contrast, the Small medaka line was unable to evolve smaller body sizes or earlier maturation, but evolved smaller body sizes at hatch and showed marginally-significant signs of increased reproductive investment, including larger egg sizes and elevated pituitary GH production. Natural selection on medaka body size was too weak to significantly hinder the effect of artificial selection, indicating that the asymmetric body-size response to size-dependent selection reflected an asymmetry in body-size evolvability. Our results show that trait evolvability may be contingent upon the direction of selection, and that a detailed knowledge of trait evolutionary potential is needed to forecast population response to anthropogenic change.
Punctuational ecological changes rather than global factors drive species diversification and the evolution of wing phenotypes in Morpho butterflies
<p>Assessing the relative importance of geographical and ecological drivers of evolution is paramount to understand the diversification of species and traits at the macroevolutionary scale. Here, we use an integrative approach, combining phylogenetics, biogeography, ecology, and quantified phenotypes to investigate the drivers of both species and phenotypic diversification of the iconic Neotropical butterfly genus <i>Morpho</i>. We generated a time-calibrated phylogeny for all known species and inferred historical biogeography. We fitted models of time-dependent (accounting for rate heterogeneity across the phylogeny) and paleoenvironment-dependent diversification (accounting for global effect on the phylogeny). We used geometric morphometrics to assess variation of wing size and shape across the tree, and investigated their dynamics of evolution. We found that the diversification of <i>Morpho</i> is best explained when considering variable diversification rates across the tree, possibly associated with lineages occupying different microhabitat conditions. First, a shift from understory to canopy was characterized by an increased speciation rate partially coupled with an increasing rate of wing shape evolution. Second, the occupation of dense bamboo thickets accompanying a major host-plant shift from dicotyledons towards monocotyledons was associated with a simultaneous diversification rate shift and an evolutionary "jump" of wing size. Our study points to a diversification pattern driven by punctuational ecological changes instead of a global driver or biogeographic history.</p>
Figure 3 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 3. Box plot of centroid size for nine populations of Merodon avidus A species. The mean centroid size of populations from the central and southern Balkans is larger than that for populations from the Pannonian region (F(1,267) = 58.57, P <0.001).
Figure 8 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 8. Strict consensus of> 200 equally parsimonious trees, length 116 steps, consistency index = 0.81, retention index = 0.87. Filled circles, nonhomoplasious changes; open circles, homoplasious changes.
Data from: Reproductive tradeoffs and phenotypic selection change with body condition, but not with predation regime, across island lizard populations
<p>Tradeoffs between reproduction and survival are central to life-history theory and are expected to shape patterns of phenotypic selection, but the ecological factors structuring these tradeoffs and resultuant patterns of selection are generally unknown. We manipulated reproductive investment and predation regime in island populations of brown anole lizards (<em>Anolis sagrei</em>) to test (1) whether previously documented increases in the survival of experimentally non-reproductive females (OVX = ovariectomy) reflect the greater susceptibility of reproductive females (SHAM = control) to predation, and (2) whether phenotypic selection differs as a function of reproductive investment and predation regime. OVX females exceeded SHAM controls in growth, mass gain, and body condition, indicating pronounced energetic costs of reproduction. Although mortality was greatest in the presence of bird and snake predators, differences in survival between OVX and SHAM were unrealted to predation regime, as were patterns of natural selection on body size. Instead, we found that body condition at the conclusion of the experiment differed significantly across populations, suggesting that local environments varied in their ability to support mass gain and positive energy balance. As mean body condition improved across populations, the magnitude of the survival cost of reproduction increased, linear selection on body size shifted from positive to negative, and quadratic selection shifted from stabilizing to weakly disruptive. Our results suggest that reproductive tradeoffs and patterns of phenotypic selection in female brown anoles are more sensitive to inferred variation in environmental quality than to experimentally induced variation in predation.</p>
Figure 1 from: Ćwiek-Kupczyńska H, Krajewski P (2021) Polish network of research infrastructure for plant phenotyping. Research Ideas and Outcomes 7: e73858. https://doi.org/10.3897/rio.7.e73858
Figure 1 The results of a survey conducted among Polish units involved in plant phenotyping in the part concerning national and international cooperation (n = 32).
Reduction in the metabolic levels due to phenotypic plasticity in the Pyrenean newt, Calotriton asper, during cave colonization
According to theories on cave adaptation, cave organisms are expected to develop a lower metabolic rate compared to surface organisms as an adaptation to food scarcity in the subterranean environments. To test this hypothesis, we compared the oxygen consumption rates of the surface and subterranean populations of a surface-dwelling species, the newt Calotriton asper, occasionally found in caves. In this study, we designed a new experimental setup in which animals with free movement were monitored for several days in a respirometer. First, we measured the metabolic rates of individuals from the surface and subterranean populations, both maintained for eight years in captivity in a natural cave. We then tested individuals from these populations immediately after they were caught and one year later while being maintained in the cave. We found that the surface individuals that acclimated to the cave significantly reduced their oxygen consumption, whereas individuals from the subterranean population maintained in the cave under a light/dark cycle did not significantly modify their metabolic rates. Second, we compared these metabolic rates to those of an obligate subterranean salamander (Proteus anguinus), a surface aquatic Urodel (Ambystoma mexicanum), and a fish species (Gobio occitaniae) as references for surface organisms from different phyla. As predicted, we found differences between the subterranean and surface species, and the metabolic rates of surface and subterranean C. asper populations were between those of the obligate subterranean and surface species. These results suggest that the plasticity of the metabolism observed in surface C. asper was neither directly due to food availability in our experiments nor the light/dark conditions, but due to static temperatures. Moreover, we suggest that this adjustment of the metabolic level at a temperature close to the thermal optimum may further allow individual species to cope with the food limitations of the subterranean environment.
CircNRIP1 drives the malignant phenotypes in gastric cancer through mediating the miR-148b-5p/CYR61 axis
<p><b>Background: </b>Gastric cancer (GC) is a frequent disease with a poor prognosis worldwide. Circular RNAs (circRNAs) are considered to be important regulators that mediate the occurrence and development of cancers, including GC. However, the regulatory mechanism of circRNAs in GC progression is not fully understood.</p> <p><b>Methods: </b>The expression of circular RNA nuclear receptor-interacting protein 1 (circNRIP1), microRNA (miR)-148b-5p and Cysteine-rich 61 (CYR61) was gauged using quantitative real-time polymerase chain reaction (qRT-PCR). The stability of circNRIP1 was determined by Ribonuclease R (RNase R) assay.</p> <p><b>Results:</b> CircNRIP1 was upregulated in GC tissues and cells, and it was a stable circular RNA. CircNRIP1 overexpression facilitated cell proliferation, cycle progression, colony formation, invasion, migration and angiogenesis, while circNRIP1 knockdown exhibited opposite effects in GC cells. Mechanistically, miR-148b-5p could mediate the regulation of circNRIP1 on GC cell progression by serving as a target of circNRIP1. Furthermore, miR-148b-5p inhibited GC cell malignant behaviors by sponging CYR61. Meanwhile, circNRIP1 could regulate CYR61 expression via downregulating miR-148b-5p. Besides, circNRIP1 knockdown suppressed tumor growth in xenograft models.</p> <p><b>Conclusion:</b> CircNRIP1 contributed to GC progression through regulating the miR-148b-5p/CYR61 axis, hinting that circNRIP1 might be a new target for GC treatment.</p>
Figure 31 from: Mullins P, Kawada R, Balhoff J, Deans A (2012) A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38. https://doi.org/10.3897/zookeys.223.3572
Figure 31 - Most parsimonious tree from exhaustive search in PAUP*. Numbers above nodes show bootstrap support and numbers below nodes show jackknife support from the maximum parsimony analysis.
Figures 13-18 from: Mullins P, Kawada R, Balhoff J, Deans A (2012) A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38. https://doi.org/10.3897/zookeys.223.3572
Figures 13-18 - Brightfield images of Evaniscus rufithorax Enderlein. 13, 14 Lateral habitus 15, 16 Dorsal habitus 17 Anterior oblique 18 Anterior face.
Figures 7-12 from: Mullins P, Kawada R, Balhoff J, Deans A (2012) A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38. https://doi.org/10.3897/zookeys.223.3572
Figures 7-12 - Brightfield images of Evaniscus rafaeli Kawada sp. n. 7, 8 Lateral habitus 9, 10 Dorsal habitus 11 Anterior oblique 12 Anterior face.
Figures 1-6 from: Mullins P, Kawada R, Balhoff J, Deans A (2012) A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38. https://doi.org/10.3897/zookeys.223.3572
Figures 1-6 - Brightfield images of Evaniscus lansdownei Mullins sp. n. 1, 2 Lateral habitus 3, 4 Dorsal habitus 5 Anterior oblique 6 Anterior face.
ScienceDex guides
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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.