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240 results for “molecular phenotype”
Classification of Matching Molecular Series on the Basis of SAR Phenotypes and Structural Relationships
<p>A database comprising a total of 13,236 pairs of MMS with different SAR characteristics is provided. For each pair the corresponding MMS-cores are provided as SMILES. In addition, for each MMS-core the number of compounds and the SAR phenotype are given. ChEMBL target IDs (CHEMBLID_Target) designate target sets from which the MMS pairs originate. </p>
Figure 2 in Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine
Figure 2. Median-joining network of GyrA (A), ParC (B) and ParE (C) of the haplotypes of fluoroquinolone resistant P. aeruginosa isolates. Each haplotype is represented by a circle. The asterisk (*) denotes the founder haplotype. The size of circle is relative to haplotype frequency. Bars indicate the number of nucleotide substitutions for GyrA (A), ParC (B) and ParE (C) sequences from fluoroquinolone resistant P. aeruginosa isolates recovered in Palestine.
Figure 3 in Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine
Figure 3. Nucleotide variation positions of GyrA (A), ParC (B) and ParE (C) genes among the studied fluoroquinolone resistant P. aeruginosa isolates according to the references from GenBank. Parsimony informative sites are shaded in light grey, while InDels are shaded in dark gray.
Figure 1 in Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine
Figure 1. Molecular phylogenetic analysis by Maximum Likelihood method based on the GyrA (A), ParC (B) and ParE (C) sequence from fluoroquinolone resistant P. aeruginosa isolated in Palestine. Reference sequences retrieved from Genbank for the GyrA (A), ParC (B) and ParE (C) genes were denoted by asterisks (*). Sequences from Palestine and reference sequences were used to construct the phylogenetic tree. Evolutionary analyses were conducted in MEGA6.
Merging metabolomics and genomics provides a catalog of genetic factors that infuence molecular phenotypes in pigs linking relevant metabolic pathways
<h3>Content</h3> <p>Metabolites included in the study. Summary statistics of metabolite levels for the Large White and Duroc pig populations are provided.</p>
Figure 6 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 6. Scatterplot of individual scores from the canonical variate analysis (CVA) of female specimens of: A, sympatric populations of Merodon avidus A and M. avidus B from Dubašnica Mt (ADUB, BDUB) and Greece (AGRE, BGRE) (Wilks' L = 0.003; F(48,30) = 3.64; P <0.001); B, allopatric populations of M. avidus A from FYR MACEDONIA (AMKD), Morinj (AMOR), and the Pannonian region (APAN) (Wilks' L = 0.09; F(32,48) = 3.59; P <0.0001); C, allopatric populations of M. avidus B from Durmitor Mt (BDUR), Stara Mt (BSPL), Kopaonik Mt (BKOP), and FYR MACEDONIA (BMKD) (Wilks' L = 0.36; F(32,32) = 0.66; P <0.879); D, allopatric populations of M. avidus A and M. avidus B (Wilks' L = 0.09; F(80,245) = 1.94; P <0.0001). The amount of variation explained by each canonical axis is in parentheses.
Figure 5 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 5. Scatterplot of individual scores from the canonical variate analysis (CVA) of all specimens (both sexes) of metapopulations: A, Merodon avidus A from Dubašnica Mt (ADUB) (Wilks' L = 0.04; F(48,72) = 3.06; P <0.000); B, M. avidus B from Dubašnica Mt (BDUB) (Wilks' L = 0.10; F(64,174) = 2.18; P <0.000); C, M. avidus B from Durmitor Mt (BDUR) (Wilks' L = 0.10; F(64,174) = 2.21; P <0.000); D, M. avidus A from FYR MACEDONIA (AMKD) (Wilks' L = 0.002; F(112,171) = 2.40; P <0.000); E, M. avidus A from Greece (AGRE) (Wilks' L = 0.009; F(64,53) = 1.93; P <0.007). The amount of variation explained by each canonical axis is in parentheses. The number of misclassified specimens/total number of analysed
Figure 1 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 1. Origin of the analysed populations using wing geometric morphometrics from the Balkan Peninsula: 1, Pannonian Plain (PAN, Serbia); 2, Dubašnica Mt, E 21°59′, N 44°01′ (DUB, Serbia); 3, Stara Mt, E 22°41′, N 43°20′ (SPL, Serbia); 4, Kopaonik Mt, E 20°40′, N 43°15′ (KOP, Serbia); 5, Durmitor Mt, E 19°00′, N 43°11′ (DUR, Montenegro); 6, Morinj, E 18°40′, N 43°29′30″ (MOR, Montenegro); 7, Former Yugoslav Republic of Macedonia (MKD); 8, Greece (GRE). (Numbers within region are noted sampling sites of populations).
Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data
<p>GWAS summary statistics for Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data published in Molecular Psychiatry by Quintero Reis A, Newton BA, Kessler R, Polimanti R, and Wendt FR.</p>
FIG. 3 in A new species and a new record of the genus Phaeophyscia Moberg (Lecanorales, Physciaceae) from Pakistan supported by phenotypic and molecular phylogenetic analyses
FIG. 3. — Phaeophyscia microspora Aptroot & Schumm: A, foliose thallus of type specimen (holo-, LAH[LAH37622]); B, apothecia; C, lobe with rhizines; D, section of an apothecium; E, ascus; F, ascospores. Scale bars: A, 1 cm; B, 3 mm; C, 1.5 mm; D, 80 μm; E, 13 μm; F, 8 μm.
FIG. 2 in A new species and a new record of the genus Phaeophyscia Moberg (Lecanorales, Physciaceae) from Pakistan supported by phenotypic and molecular phylogenetic analyses
FIG. 2. — Phaeophyscia kaghanensis Niazi, Nadeem, Afshan & Khalid, sp. nov.: A, foliose thallus of type specimen (holo-, LAH[LAH37615]); B, apothecia; C, section of an apothecium; D, E, ascus; F, ascospores. Scale bars: A, 1 cm; B, 3 mm; C, 100 μm; D, 28 μm; E, 24 μm; F, 14 μm.
FIG. 1 in A new species and a new record of the genus Phaeophyscia Moberg (Lecanorales, Physciaceae) from Pakistan supported by phenotypic and molecular phylogenetic analyses
FIG. 1. — Phylogeny of Phaeophyscia Moberg and related species based on a maximum likelihood (ML) analysis of the ITS region. Phaeophyscia kaghanensis Niazi, Nadeem, Afshan & Khalid, sp. nov. and P. microspora Aptroot & Schumm are shown in bold.
Repository Information PB260 x PB266 Molecular and Phenotypic
<p>This data refer to:</p> <p>Mendes-Moreira P, Alves ML, Satovic Z, Pacheco dos Santos J, Santos JN, Souza JC, Pêgo SE, Hallauer AR and Vaz Patto MC. 2015. <strong>Genetic Architecture of Ear Fasciation in Maize (<em>Zea mays</em>) under QTL Scrutiny. PLOS ONE.</strong></p> <p><strong>Files were used to obtain the results expressed in the paper refered above</strong></p> <p>Repository Information PB260 x PB266 Molecular.</p> <p>Repository Information PB260 x PB266 Phenotypic</p>
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
<p>Supplementary Tables and Supplementary Methods for the research article "Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes" published in Database.</p>
Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species
<p>The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in <i>Primula vulgaris </i>and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (<i>CYPᵀ</i>), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in <i>CYPᵀ</i>. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in <i>P. vulgaris</i>. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.</p>
Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism
<p>Locusts exhibit one of nature's most spectacular examples of complex phenotypic plasticity, in which changes in density cause solitary and cryptic individuals to transform into gregarious and conspicuous locusts forming large migrating swarms. We investigated how these coordinated alternative phenotypes might have evolved by studying the Central American locust and three closely related non-swarming grasshoppers in a comparative framework. By experimentally isolating and crowding during nymphal development, we induced density-dependent phenotypic plasticity and quantified the resulting behavioural, morphological, and molecular reaction norms. All four species exhibited clear plasticity, but the individual reaction norms varied among species and showed different magnitudes. Transcriptomic responses were species-specific, but density-responsive genes were functionally similar across species. There were modules of co-expressed genes that were highly correlated with plastic reaction norms, revealing a potential molecular basis of density-dependent phenotypic plasticity. These findings collectively highlight the importance of studying multiple reaction norms from a comparative perspective.</p>
Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (Lepus spp., Lagomorpha: Leporidae)
<p>Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological as well as behavioral differences. Each species has had its own evolutionary trajectory, formed by many types of selection pressures and random drift, making it extremely complicated to associate genetic differences between the species with the phenotypic differences. In the present study, we have used an in vitro model to analyze in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, arctic/subarctic mountain hare (Lepus timidus Linnaeus) and a temperate, steppe-like climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1,623 genes, manifesting in differences in cell growth, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest speciation acts on fundamental processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.</p>
Dataset 2. Variant Distribution of Majority Molecular Phenotype Classifications Relative to All Classifications
<p>A variant may occur in multiple individuals, tissue types, or splice sites. A consensus (majority) molecular phenotype classification for the variant is displayed on ValidSpliceMut, generated by observing all affected cases and associated classifications. For each expression validated variant, the phenotypes are classified as per Figure 2 of Shirley et al. 2019 (<a href="https://doi.org/10.12688/f1000research.17204.3" target="_blank" rel="noopener">https://doi.org/10.12688/f1000research.17204.3</a>). The bins on the horizontal axis of these histograms represent the count of splicing variants with the most frequent classification divided by the total number of cases affected by a variant. Bar height represents the number of variants having the majority classification within the appropriate bin. </p> <p>Below each histogram is a table that describes the distribution of majority molecular phenotypes in each bin. The three bins consist of mutations designated as variants that cause allele-specific alternative splicing (category 1), those that are likely aberrant (category 2) and mutations that are aberrant (category 3). For a full description of how these molecular phenotype classifications are determined, see Shirley <em>et al. </em>2019. Figure 2 of the paper describes the algorithm we use to ensure that variants with no effect on splicing have been eliminated previous to this analysis.</p> <p>To gain more information about the mutations in a particular bin, an data file has been provided for each of these figures. To identify which mutations occur in each bin, sort the data file in order of the <em>`%Mol_Phenotype`</em> column which was used to designate histogram bins. Once a mutation of interest has been found, download <a href="../records/3522192">Dataset 1 on Zenodo</a> (Filename: ‘ValidSpliceMut_TabDelimited_v4.txt’) and search for the mutation (mutation names will be identical). The mutation will appear in Dataset for however many patients the mutation was identified in (from the TCGA and ICGC Cancer Projects). From Dataset 1, users can acquire the mutation’s associated gene, its position within a gene, the Information-Theory based prediction that the mutation would have on splicing, and the given evidence of splicing using the <a href="https://f1000research.com/articles/3-8">Veridical algorithm</a>. The latter provides how many reads were found in RNAseq data that supported an aberrant splicing event (exon skipping, intron inclusion, etc).</p> <p>Files/archives provided:</p> <p>1 Supplementary figure to Shirley et al. <em>F1000Research</em> 2019, <strong>7</strong>:1908. Dataset 2 contains six histograms and supporting tables (generated with GraphPad Prism v6.0). A variant may occur in multiple individuals, tissue types, or splice sites. Histogram bins show the fraction of splicing molecular phenotype classifications relative to the major consensus phenotype among all cases for variants that are present in at least 2, 3, 5, 10, 15, and 20 different tissue types.</p> <p>2. Aggregated variant data/consensus phenotypes used to generate histograms, including tissue types.</p> <p>3. Software to generate histograms from variants validated in Dataset 1 (DOI <a href="../doi/10.5281/zenodo.1488210">10.5281/zenodo.1488210</a>).</p>
Figure 4 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 4. Wing centroid size in male and female Merodon avidus A and M. avidus B.
Figure 2 in High molecular and phenotypic diversity in the Merodon avidus complex (Diptera, Syrphidae): cryptic speciation in a diverse insect taxon
Figure 2. Positions of the wing landmarks used in the geometric morphometric analyses.
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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.