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6,234 results for “phenotypes”
Figure 3 from: Bogutskaya NG, Diripasko OA, Zupančič P, Jelić D, Naseka A (2019) Phenotypic diversity in an endangered freshwater fish Squalius microlepis (Actinopterygii, Leuciscidae). ZooKeys 897: 115-147. https://doi.org/10.3897/zookeys.897.38768
Figure 3 Squalius microlepisA NMW 49415, lectotype, 150.8 mm SL, "Imosky" B phenotype 1: alive specimen, MNCN_ICTIO 296.096-296.097, 147.6 mm SL, Bosnia and Herzegovina: Krenica Lake at Drinovci.
Figure 1 from: Bogutskaya NG, Diripasko OA, Zupančič P, Jelić D, Naseka A (2019) Phenotypic diversity in an endangered freshwater fish Squalius microlepis (Actinopterygii, Leuciscidae). ZooKeys 897: 115-147. https://doi.org/10.3897/zookeys.897.38768
Figure 1 Map showing localities of examined specimens: S. tenellus, S. microlepis phenotype 1, and S. microlepis phenotype 2, shadowed areas showing ranges of S. tenellus (blue) and S. microlepis (yellow); 1 – Ričice Reservoir, 2 – Ričina River, Posušje, 3 – Lower Matica River, 4 – Krenica Lake, 5 – Vrgoračka Matica River system (Vrgoračko Polje, Polje Jezero), 6 – Baćina lakes.
Figure 11 from: Bogutskaya NG, Diripasko OA, Zupančič P, Jelić D, Naseka A (2019) Phenotypic diversity in an endangered freshwater fish Squalius microlepis (Actinopterygii, Leuciscidae). ZooKeys 897: 115-147. https://doi.org/10.3897/zookeys.897.38768
Figure 11 Specimen MZUF 13512 (identified as S. microlepis by Kolombatović), Cetina River. Photo credit: Saulo Bambi, Sistema Museale dell'Università degli Studi di Firenze, Sez. di Zoologia "La Specola", Italy.
Figure 10 from: Bogutskaya NG, Diripasko OA, Zupančič P, Jelić D, Naseka A (2019) Phenotypic diversity in an endangered freshwater fish Squalius microlepis (Actinopterygii, Leuciscidae). ZooKeys 897: 115-147. https://doi.org/10.3897/zookeys.897.38768
Figure 10 A locality where two phenotypes of Squalius microlepis co-occur: Tihaljina River at Tihaljina, Bosnia and Herzegovina (7 July 2011).
The main reasons for the formation of phenotypic heterogeneity of an isogenic bacterial population
<p>The main reasons for the formation of phenotypic heterogeneity of an isogenic bacterial population</p> <p>Основные причины формирования фенотипической гетерогенности изогенной бактериальной популяции</p>
Mutant phenotypes of candidate genes from Fv'/Fm' and QY max loci identified using GWAS in Arabidopsis HapMap population
<p>The phenotypes of T-DNA insertion lines and background line (Col-0), located in the loci identified using GWAS, corresponding to maximum quantum yield (QY max) and light-adapted quantum yield (Fv'/Fm') under salt stress. The data was collected using high-throughput phenotyping of plants and is part of a manuscript currently in preparation. </p>
TOADS for Computable Phenotypes
<p>Inventory of existing tools, ontologies, algorithms, data, and standards (TOADS) that makes computable phenotypes and predictive phenomics feasible now. (SW: software; HW: hardware).</p>
Fig. 8 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 8. Dendograms obtained from the (A) NJ clustering and (B) UPGMA, using Euclidean distances between group means by combining all data (shape information from dorsal, ventral and lateral views). Branch bootstrap support shown at the nodes, 10 000 replicates.
Fig. 2 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 2. Landmarks positioned on the cranium of Meriones crassus Sundevall, 1842 shown in (A) ventral (B) dorsal and (C) lateral views. The straight lines on the ventral and lateral views were used for defining semi-landmarks based on two other landmarks. Open circles on the ventral side: the most rostral and on the most caudal point of the tympanic bulla, and on the lateral side: the most rostral margin of the tympanic bulla. Short lines are drawn to highlight sutures which are unclear here and on which the landmarks have been defined.
Fig. 5 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 5. Box-and-whisker plots of (A) skull size and (B) relative bulla size of the ventral cranium. The boxes indicate the 25–75 % quartiles; the whiskers represent the minimal and maximal values.
Data from: Gene editing to induce FOXP3 expression in human CD4+ T cells leads to a stable regulatory phenotype and function.
<p>Thymic regulatory T cells (tTreg) are potent inhibitors of autoreactive immune responses and loss of tTreg function results in fatal autoimmune disease. Defects in Treg number or function are also implicated in multiple autoimmune diseases, leading to growing interest in use of Treg as cell therapies to establish immune tolerance. Because tTreg are present at low numbers in circulating blood and may be challenging to purify and expand, and also inherently defective in some subjects, we designed an alternative strategy to creating autologous Treg-like cells from bulk CD4+ T cells. We utilized homology-directed-repair (HDR)-based gene-editing to enforce FOXP3 expression. Targeted insertion of a robust enhancer/promoter proximal to the first coding exon bypassed epigenetic silencing, permitting stable, high level endogenous FOXP3 expression. HDR-edited T cells, edTreg, manifested a transcriptional program leading to sustained expression of canonical markers and suppressive activity of tTreg. Both human and murine edTreg mediated immunosuppression in vivo in models of inflammatory disease. Further, this engineering strategy permitted generation of antigen-specific edTreg with robust in vitro and in vivo functional activity. Finally, edTreg could be enriched and expanded at scale using clinically-relevant methods. Together, these finding suggest edTreg production may permit broad future clinical application.</p>
Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)
<p>Spatial patterns of intraspecific variation are shaped by factors such as geographic distance among populations, historical changes in gene flow and interactions with local environments. Although these factors are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation. We address this question by exploring the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits marked geographic variation in body size across its range. We combined a comprehensive SNP and phenotypic dataset to test whether genome-wide genetic and phenotypic differentiation are best explained by (a) isolation by distance, (b) isolation by history, or (c) isolation by environment. We find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow, phenotypic diversity can be best predicted by contemporary environmental heterogeneity. Our genomic analyses reveal strong phylogeographic structure coinciding with the Chivela Pass at the Isthmus of Tehuantepec and was formed in the Pleistocene, when populations were isolated in north-south refugia. In contrast, we found a strong association between body size and environmental variables, such as temperature and precipitation. The relationship between body size and local climate is consistent with a pattern produced by either natural selection or environmental plasticity. Overall, these results provide empirical evidence for why phenotypic and genomic data are often in conflict in taxonomic and phylogeographic studies.</p>
Desert-like badlands and surrounding (semi-)dry grasslands of Central Germany promote small-scale phenotypic and genetic differentiation in Thymus praecox
Environmental heterogeneity among sites can generate phenotypic and genetic variation facilitating differentiation and microevolution of plant populations. Badlands are desert-like, predominantly vegetation-poor habitats often embedded in (semi-)dry grasslands. The desert-like conditions of badlands demand extreme adaptation of plants, i.e., phenotypic modifications in short-term and/or natural adaptation in long-term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation in this unique and widely occurring habitat type. The present study focused on the largest known badlands systems in Central Europe located in the 'Drei Gleichen' region, a designated nature conservation area in Central Germany. Locations were suitable for this study in terms of having co-occurring badlands and (semi-)dry grassland habitats (sites) occupied by the pioneer plant Thymus praecox. Here, we studied the environmental preferences, morphological and functional trait variation, and genetic variation using microsatellite markers of T. praecox. Results revealed significant, mainly site-dependent environmental, phenotypic and genetic differentiation. In general, individuals in badlands are shorter in height, have lower patch sizes (length x width), relative growth rates, and smaller stomata. The PCA additionally unveiled slightly increased leaf robustness, trichome density, decreased stomatal conductance, fewer females, and earlier phenology in badlands. We interpret differentiation patterns as adaptive responses to light, temperature, drought and nutrient stress conditions supported by reviewed literature. Genetic differentiation was strongest between local badlands and grassland sites, and clearly weaker among locations and between sites (in total) as indicated by GST, AMOVA, PCoA and population structure. Our study supports the importance of small-scale microhabitat conditions as a driver of microevolutionary processes, and the population´s need for sufficient phenotypic plasticity and genetic resources to deal with environmental changes. We demonstrated that badlands are an appropriate model system for testing plant response to extreme habitats and that more research is needed on these fascinating landscapes.
Supplementary material 2 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Raw morphometric data and collection information
Supplementary material 1 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Tables S1, S2, S3. Sampling, genbank sequences and sequences of primers
Figure 1 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 1 Geographic distribution and morphotypes of Euphonia affinis, sampling, phylogeny, and haplotype networks. A geographic distribution of E. affinis: in blue E. a. godmani, in yellow E. a. affinis, and in red E. a. olmecorum (Geographic distribution modified from NatureServe shapefile in ArcGIS, ArcMAP 10.2.2; Esri, Redlands, CA, USA). Tissue sampling locations are indicated by circles in the map. Plumage morphotypes of E. a. godmani (female and male) with white undertail coverts, and E. a. affinis (female and male) with yellow undertail coverts. The previously proposed subspecies E. a. olmecorum (not shown) is similar to E. a. affinis, but paler plumage in females and a purple-blue back in males have been reported. B haplotype networks obtained for the mitochondrial gene ND2 and the nuclear genes ODC, MUSK, GAPDH intron 11, and BRM intron 15. Samples from the western distribution, assigned as E. a. godmani, are shown in blue and from the eastern distribution, assigned as E. a. affinis are indicated in yellow, E. a. olmecorum in red. C bayesian Inference concatenated phylogeny of E. a. godmani (west) and E. a. affinis-E. a. olmecorum (eastern Mexico, Central America).
Figure 4 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 4 Vocalization analysis. Boxplot of note emission rate A and PCA of measured vocal characters B Calls differ between the two groups in temporal structure, but not in frequency or number of notes.
Figure 6 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 6 Equivalence and similarity tests in environmental space for E. a. affinis and E. a. godmani. A PCA of Ecological niche for of E. affinis lineages and the variables contribution to the analyses. The gray gradient indicates the density of the occurrences of the lineages, and the dashed and solid line indicates the 50% and 100% of the environmental background B graphical results of the equivalency tests comparing the two lineages. For both tests (equivalence and similarity) we only presented values for the D metrics. For all graphs the D observed values of the overlap niche analyses are present with the black diamond. The p value is showing in each graphic, all of them not significant for these analyses C graphical results of the similarity test comparing the two lineages in both directions (E. a. affinis vs. E. a. godmani and vice versa), ns = Not significant, p > 0.05.
Figure 5 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 5 Ecological niche modelling and its projection in the geographic areas for E. a. affinis (yellow) and E. a. godmani (blue). In all four panels (a-d), the contribution values of each environmental variable of ENM's is illustrated in the left and the projection of the Ecological niche conditions in the geographic distribution area is shown in the maps. a Ecological Niche projected in the current geographic distribution area of E. affinis and E. a. godmani. b ENM's projected into the geography for each lineage. c ENM of E. a. affinis and E. a. godmani projected in the Last Maximum Glacial ecological conditions. d ENM of E. a. affinis and E. a. godmani projected in the Last Inter Glacial ecological conditions.
Figure 3 from: Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE (2020) Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). ZooKeys 952: 129-157. https://doi.org/10.3897/zookeys.952.51785
Figure 3 Morphometric analyses results. A) Females boxplots and PCA for WC, TLE, and BD morphometric characters. B) Males boxplot and PCA for WC, TLE, and BD morphometric characters. C) Boxplot and PCA for TL, BL, and BW. WC, TLE, and BD characters were analyzed by separated sex, because the analyses indicated sexual dimorphism (see results and Table 3). Bill length (BL, from the upper base of the bill to the tip of the upper mandible), bill width (BW), bill depth (BD, from the upper mandible to the base of the bill at the distal edge of the nostrils), wing chord (WC, distance from the carpal joint the tip of the longest primary), tarsus length (TL), and tail length (TLE, distance from the uropygial gland to the tip of the longest rectrix).
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.