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86 results for “chemical genetics”
Soil physical and chemical properties based on genetic horizon from 4 replicate pits placed around the replicate LTER control plots sampled in 1988 and 1989.
Dataset contains the following soil properties for each genetic horizon - site, Soil pit, upper and lower boundary (cm), Mg meq/100gm, Ca meq/100gm, K meq/100gm, CEC meq/100gm, pH, %C, %sand, %silt, %clay, Total %N, Total %P, % organic matter, Mn meq/100gm, Available-P ppm, %CO3, bulk density gm/cm3, Volume wt gm/m2.
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs
<p>The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated the inner workings of RNAP, and mutations in genes encoding RNAP drive adaptation of <i>Escherichia coli</i> to many health- and industry-relevant environments, yet a paucity of systematic analyses has hampered our understanding of the fitness benefits and trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and demonstrate that some RNA polymerase mutants both decrease average cell length and confer insensitivity to killing by cell-wall targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationships <i>in vivo</i> and for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.</p>
Fig. 2 in Genetic and chemical profiling of Solenopsis spp. (Hymenoptera: Formicidae) intercepted in Hawaii
Fig. 2. The Gas Chromatography-Mass Spectrometry (GC-MS), total ion chro- matogram (TIC) of a methanol extract of a gaster from a single ant intercepted in 2019 at a port in Hawaii. The reported major venom alkaloids from Solenopsis geminata and Solenopsis xyloni are cis-2-methyl-6-undecyl-piperidine (peak 1) and trans-2-methyl-6-undecyl-piperidine (peak 3). This intercepted Solenopsis geminata worker has 2-methyl-6-undecyl-pyridine (peak 2) as its major component. The areas under peaks 1, 2, and 3 are proportional to their quantity. This is expressed on the graph as the percent composition of the 3 identified peaks. This is the first time that the pyridine (peak 2) has been reported as a major venom component of Solenopsis geminata. Components 1 and 3 have been identified in previous literature.
Fig. 1 in Genetic and chemical profiling of Solenopsis spp. (Hymenoptera: Formicidae) intercepted in Hawaii
Fig. 1. Unrooted neighbor-joining tree constructed using the matrix of absolute numbers of pairwise differences among 55 mitochondrial COX1 haplotypes from 6 Solenopsis species: S. geminata, S. xyloni, S. amblychila, S. aurea, S. invicta, and S. saevissima. All positions containing gaps and missing data were eliminated. Bootstrap values greater than 70% are located below or above nodes. The scale bar distance is shown at the top right corner of the tree indicating number of nucleotide differences. Each sequence was identified by their GenBank number and species name, except for the Oahu sample (GenBank OK071254) marked as Oahu 2018* and the haplotype from the 2019 samples (GenBank OK071253) labelled Ltu19_03**.
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs
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Data of "Investigating the potential for genetic improvement of nitrogen and phosphorus efficiency of in a Swiss Large White pigs population using chemical analysis"
<p>Data for article 'Investigating the Potential for Genetic Improvement of Nitrogen and Phosphorus Efficiency in a Swiss Large White Pig Population using Chemical Analysis' (DOI: 10.1111/JBG.12472). Dataset of 294 Swiss Large White pigs for which phenotypes of nitrogen efficiency, phosphorus efficiency (both determined by chemical analysis of N and P content of empty body and carcass as well as the feed ingested over the experiment phase), average daily gain and gain:feed ratio are available. We also provide the pedigree that was used to estimate genetic parameters in animal models and a description of the variables (metadata).</p>
A Versatile Chemical-Genetic Approach to Examine Sodium Channelopathies
<p>The voltage-gated sodium channel Na<sub>V</sub>1.5 controls cardiac excitability and is an established therapeutic target. Mutations in the <em>SCN5A</em> gene, which encodes Na<sub>V</sub>1.5, are associated with inherited arrhythmia syndromes, including Brugada and Long-QT. To advance the general understanding of Na<sub>V</sub>1.5-related conduction biology, we have developed a chemical-genetic model to achieve acute and reversible silencing of Na<sub>V</sub>1.5 <em>in vitro </em>and <em>in vivo</em>. To this end, a human Na<sub>V</sub>1.5 chimeric channel was engineered to contain a high-affinity, isoform-specific binding site for acylsulfonamide (GX) drugs. The GX drug binding site is comprised of an extracellular-facing pocket formed by the DIV voltage-sensor (VSD4) thus enabling a structure-based chimera design strategy. The Na<sub>V</sub>1.5-GX channel has WT voltage-dependent gating and, unlike WT Na<sub>V</sub>1.5, is rapidly and reversibly inhibited by nanomolar GX compound. Using CRISPR, the GX binding site has been engineered into the homologous region of the endogenous <em>Scn5a</em> locus, thus phenocopying the chimeric construct. Inheritance of the Na<sub>V</sub>1.5-GX allele follows expected Mendelian ratios, allowing for the production of a Na<sub>V</sub>1.5<sup>GX/GX </sup>homozygous strain. In the absence of GX compound, Na<sub>V</sub>1.5<sup>GX/GX </sup>hearts<sup> </sup>display normal cardiac phenotypes <em>in vivo</em> measured by EKG and echocardiography. Patch-clamped Na<sub>V</sub>1.5<sup>GX/GX </sup>sodium channels in isolated adult myocytes have WT gating but nanomolar GX compound ablates the Na<sub>V</sub>1.5 mediated current. </p>
Data from: Genetic divergence along a climate gradient shapes chemical plasticity of a foundation tree species to both changing climate and herbivore damage
<p><span>Climate change is threatening the persistence of many tree species via independent and interactive effects on abiotic and biotic conditions. In addition, changes in temperature, precipitation, and insect attacks can alter the traits of these trees, disrupting communities and ecosystems. For foundation species such as <em>Populus</em>, phytochemical traits are key mechanisms linking trees with their environment and are likely jointly determined by interactive effects of genetic divergence and variable environments throughout their geographic range. Using reciprocal Fremont cottonwood (<em>Populus</em> <em>fremontii</em>) common gardens along a steep climatic gradient, we explored how environment (garden climate and simulated herbivore damage) and genetics (tree provenance and genotype) affect both foliar chemical traits and the plasticity of these traits. We found that: 1) Constitutive and plastic chemical responses to changes in garden climate and damage varied among defense compounds, structural compounds and nitrogen. 2) For both defense and structural compounds, plastic responses to garden climate depended on the climate in which a population or genotype evolved. Specifically, trees originating from cool provenances showed higher defense plasticity in response to climate changes than trees from hotter provenances. 3) Trees from cool provenances growing in cool conditions expressed the lowest constitutive defense levels but the strongest induced (plastic) defenses. 4) The combination of hot growing conditions and simulated herbivory switched the strategy used by these genotypes, increasing constitutive defenses but erasing the capacity for induction. Because Fremont cottonwood chemistry plays a major role in shaping riparian communities and ecosystems in the southwestern US, the effects of changes in phytochemical traits can be wide-reaching. As the southwestern US is confronted with warming temperatures and insect outbreaks, these results improve our capacity to predict ecosystem consequences of climate change and inform selection of tree genotypes for conservation and restoration purposes. </span></p>
Data from: Genetic divergence along a climate gradient shapes chemical plasticity of a foundation tree species to both changing climate and herbivore damage
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Data from: Effect of plant chemical variation and mutualistic ants on the local population genetic structure of an aphid herbivore
1.Plants exhibit impressive genetic and chemical diversity, not just between species but also within species, and the importance of plant intraspecific variation for structuring ecological communities is well known. When there is variation at the local population level, this can create a spatially‐heterogeneous habitat for specialized herbivores potentially leading to non‐random distribution of individuals across host‐plants. 2.Plant variation can affect herbivores directly and indirectly via a third species, resulting in variable herbivore growth rates across different host plants. Herbivores also exhibit within‐species variation, with some genotypes better adapted to some plant variants than others. 3.We genotyped aphids collected across two years from a field site containing ~200 patchily‐distributed host plants that exhibit high chemical diversity. The distribution of aphid genotypes, their ant mutualists, and other predators was assessed across the plants. 4.We present evidence that the local distribution of aphid (Metopeurum fuscoviride) genotypes across host‐plant individuals is associated with variation in the plant volatiles (chemotypes) and non‐volatile metabolites (metabotypes) of their host plant tansy (Tanacetum vulgare). Furthermore, these interactions in the field were influenced by plant‐host preferences of aphid‐mutualist ants. 5.Our results emphasize that plant intraspecific variation can structure ecological communities not only at the species level but also at the genetic level within species, and that this effect can be enhanced through indirect interactions with a third species.
Figure 7 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters
Figure 7. Geographical distribution of tridentate Euglossa dilemma sp. nov. (black) and predominantly bidentate Euglossa viridissima (white) as inferred from recent baiting assays (circles) as well as museum material (diamonds). Note lack of E. viridissima in the south-eastern part (Costa Rica) of the range. Museum material included paratypes of E. dilemma and additional specimens of one or both species in the collections of D. W. Roubik, T. Eltz (CTE), G. Gerlach (CGG), the Zoologische Staatssammlung München (ZSM), the Smithsonian Institution (SI), and the Snow Entomological Collection (SEC). Only unambiguous and non-redundant localities were plotted. Localities of baiting assays are (from west to east): Chamela (Jalisco, Mexico), El Chote (Veracruz, Mexico), Ayozinthepec (Oaxaca, Mexico), Monte Pio and Poza Azul (both Veracruz, Mexico), Tuxtla Gutiérrez, Esquintla, Tapachula, Ocosingo and Palenque (all Chiapas, Mexico), Atasta (Campeche, Mexico), Retalhuleu (Guatemala), Lacanjá (Chiapas, Mexico), Escarcega (Campeche, Mexico), El Remate (Campeche, Mexico), Chablekal, Xmatkuil (Yucatán, Mexico), Tikal (Guatemala), San Crisanto (Yucatán, Mexico), Chetumal and Coba (both Quintana Roo, Mexico), Chinandega, Chacocente, Escameca Grande, Jinotega, Ometepe and Las Pampas (all Nicaragua), and Area de Conservación Guanacaste (Costa Rica).
Figure 6 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters
Figure 6. Chronogram showing divergence times and phylogenetic relationships of selected lineages in the genus Euglossa and the sibling species Euglossa dilemma sp. nov. and E. viridissima. The tree topology corresponds to that obtained via Bayesian methods. Bayesian posterior probabilities and parsimony bootstrap values are shown for the sister species only. Divergence times were obtained via penalized likelihood using the fossil-calibrated molecular clock procedures described in Ramírez et al. (2010b). The maximum and minimum age estimates for the MRCA of E. dilemma and E. viridissima correspond to the molecular clock analyses in which the MRCA of the genus Euglossa was assigned a fossil calibration of 20 and 15 Myr, respectively.
Figure 2 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters
Figure 2. Allele size distribution of Euglossa viridissima- like males from the Yucatán peninsula, Mexico, at the microsatellite locus ann02. Overall, bidentate males (grey bars) had significantly smaller allele sizes than tridentate individuals (black bars), and there was little overlap in allele size. The seven individuals indicated as red circles were also tridentate, but had been clustered with bidentate males in the analysis of perfume similarity (see Fig. 1), lacking HNDB. These seven individuals had the third (central) mandibular tooth significantly displaced towards the tip of the mandible (nearer to the distal tooth, see Fig. 3B), unlike in other tridentate males. Their ann02 allele size suggests that they in fact belong to the bidentate lineage. See text for further explanation.
Figure 4 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters
Figure 4. Results of a PCA of 15 morphological variables measured in male Euglossa viridissima and Euglossa dilemma sp. nov. Components 1 and 3, which showed significant differences between the species, are used for this two-dimensional representation. Note that E. dilemma shows slightly less variability and is essentially nested within E. viridissima morphospace. Centroids of distributions are shown.
Figure 3. A in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters
Figure 3. A, Euglossa viridissima-like males attracted to a bait dish at Xmatkuil, Yucatán, Mexico. B, mandibular morphology of males of tridentate Euglossa dilemma sp. nov., and tridentate and bidentate males of E. viridissima. The position of the central mandibular tooth in tridentate individuals is expressed as the ratio of the distance between the distal and the central tooth to the distance between the central and the basal tooth. Means and standard deviations are given.
Figure 1 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters
Figure 1. Differences in the chemical composition of tibial perfumes between tridentate (black circles) and bidentate (grey circles) Euglossa viridissima-like males as revealed by a multidimensional scaling (MDS) analysis. Only tridentate males contained HNDB. Tridentate males without HNDB are highlighted (red symbols).
Transcriptome dataset to: Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development
<p>This collection contains RNA-seq data obtained from young flower buds of <em>Silene latifolia </em>for each sample in the main manuscript in triplicate (male, female, two generations of hermaphrodites). The RNA was isolated from adult plants of U15 population and two subsequent generations, made by full-sib mating (U15=15 generations, U16=16 generations, U17=17 generations). The petals and sepals were removed before RNA-isolation. To avoid the bias made by sampling of old flower buds, only the first flowers were always sampled. The deposited RNA-seq data were not processed. </p>
Fig. 6 in Multivariate analysis of chemical and genetic diversity of wild Humulus lupulus L. (hop) collected in situ in northern France
Fig. 6. Heatmap highlighting variation of volatile compounds across the 63 hop accessions from Northern France. This heatmap has been generated with normalized data for the top 51 molecules responsible for differences between the chemical profiles. Red and green colors indicate lowest and highest performance of the traits, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Multivariate analysis of chemical and genetic diversity of wild Humulus lupulus L. (hop) collected in situ in northern France
Fig. 5. Identification of population genetic structure of the 63 accessions of Humulus lupulus L. sampled in Northern France (Hauts-de-France region) using 11 microsatellites. A. Bar plot showing the distribution of individual assignations estimated for K = 2 and K = 6 clusters, from Bayesian inference cluster analysis performed with the 53 Humulus lupulus haplotypes sampled from the 14 locations (from A to K). Each vertical line represents an individual and the length of each colored line corresponds to the membership coefficient (scale at the left of the bar plot) for each cluster. Individuals are grouped according to their sampling locations. B. Frequencies of the 6 clusters (represented by colors) within each sampled location. Colors are same than on Fig. 5A. C. Principle Component Analysis (PCoA) based on genetic distances between each accession. Individuals were colored according to their sample site collection. D. Dendrogram underlying genetic clustering of the 63 hop accessions, including 10 commercial varieties (samples 1 to 10), 3 heirloom varieties (samples 11 to 13) and 50 wild sampled from 11 geographical locations (cf Table 1). 1: Nugget, 2: Strisselspalt, 3: Golding, 4: Challenger, 5: Brewers Gold, 6: Cascade, 7: Magnum, 8: Northern Brewer, 9: Target, 10: Fuggle, 11: Groene Bel, 12: Star, 13: Coigneau, Location A: 14 to 18; Location B: 19 to 23; Location C: 24 to 28; Location D: 29 to 32; Location E: 33 and 34; Location F: 34 and 35; Location G: 37 and 38; Location H: 39 to 42; Location I: 43 to 52; Location J: 53 to 58; Location K: 59 to 63. The tree was constructed using the unweighted neighbor-joining method based on genetic dissimilarity among the haplotypes according to microsatellite markers. Each branch corresponds to a hop genotype and the colors of branches indicate locations from which the genotypes were sampled. The color code is the same as the one on Fig. 5C.
Fig. 2 in Multivariate analysis of chemical and genetic diversity of wild Humulus lupulus L. (hop) collected in situ in northern France
Fig. 2. Analysis of volatile compounds in hop cones by GC-MS. A. Chemical structure of main volatile compounds found in hop cones. B. GC-MS total ion chromatogram of a hop cone sample (cv. Nugget). Compounds identified correspond to the following compounds: (1) β-myrcene; (2) β-caryophyllene; (3) linalool; (4) 2- undecanone; (5) copaene; (6) α-humulene; (7) γ-muurolene.
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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.