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1,168 results for “metabolites”
Development and validation of a novel plasmid chassis system for screening of metabolite-responsive transcription factors
<p>This dataset contains the raw data that lie at the basis of the results discussed in <strong>Chapter 3: Development and validation of a novel plasmid chassis system for screening of metabolite-responsive transcription factors </strong>of the PhD thesis of Amber Bernauw. The README.txt file provides more information on the different data files.</p>
Fungicides Cuprozin Progress and SWITCH Modulate Primary and Specialized Metabolites of Strawberry Fruits
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Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
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Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
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Datasets and code for manuscript: Age, breed, sex, and diet influence serum metabolite profiles of 2000 pet dogs
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Data from: Plant host traits mediated by foliar fungal symbionts and secondary metabolites
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Data and code for: Previous assessments of faecal glucocorticoid metabolites in Cape Mountain zebra (Equus zebra zebra) were flawed
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Climate Change Across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest; concentrations of foliar metabolites: polyamines, amino acids, chlorophyll, carotenoids, soluble proteins, soluble elements, sugars, and total nitrogen and carbon in red maple (Acer rubrum) trees.
Foliage was collected in 2015 and 2017 from red maple trees at the Climate Change Across Seasons Experiment (CCASE) as part of the Hubbard Brook Ecosystem Study (HBES). Analyses of foliar metabolites include polyamines, amino acids, chlorophylls, carotenoids, soluble proteins, soluble inorganic elements, sugars, and total nitrogen and carbon. There are six (11 x 14m) plots in total in this study; two control (plots 1 and 2), two warmed 5 degrees (°) Celsius (C) above ambient throughout the growing season (plots 3 and 4), and two warmed 5 °C in the growing season, with snow removal during the winter to induce soil freezing and then warmed with buried heating cables to create a subsequent thaw (plots 5 and 6). Each soil freeze/thaw cycle includes 72 hours of soil freezing followed by 72 hours of thaw. Four kilometers (km) of heating cable are buried in the soil to warm these four plots. Together, these treatments led to warmer growing season soil temperatures and an increased frequency of soil freeze-thaw cycles (FTCs) in winter. Our goal was to determine how these changes in soil temperature affect foliar nitrogen (N) and carbon metabolism of red maple trees. These data were gathered as a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Ensminger et al 2020 - Fecal glucocorticoid metabolites in harvested elk
<p>Raw data for modeling fecal glucocorticoid metabolites in Ensminger et al. 2020.</p>
Data from - Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal
<p>Data from "Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal" published in <em>Ecology </em>in 2020. doi.org/10.1002/ecy.3192</p>
Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires
<p><strong>Background </strong>The dieback epidemic decimating common ash (<em>Fraxinus excelsior</em>) in Europe is caused by the invasive fungus <em>Hymenoscyphus fraxineus</em>. In this study we analyzed the genomes of <em>H. fraxineus</em> and <em>H. albidus</em>, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of <em>Helotiales</em>. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of <em>H. fraxineus</em> and displacement of <em>H. albidus</em>.</p> <p><strong>Results</strong> The genomes of <em>H. fraxineus</em> and <em>H. albidus </em>showed a high level of synteny and identity. The assembly of <em>H. fraxineus </em>is 13 Mb longer than that of <em>H. albidus’, </em>most of this difference can be attributed to higher dispersed repeat content ((i.e transposable elements [TEs]) in <em>H. fraxineus</em>. In general, TE families in <em>H. fraxineus</em>showed more signals of repeat-induced point mutations (RIP) than in <em>H. albidus</em>, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those that did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the <em>H. fraxineus-</em>specific, <em>hymenosetin </em>biosynthetic gene cluster (BGC).</p> <p><strong>C</strong><strong>onclusion </strong>The genomes of <em>H. fraxineus</em> and <em>H. albidus</em> show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that <em>H. albidus</em> may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment. </p> <p><strong>Data included</strong></p> <p>This post contains the alternate structural and functional annotations of the genomes of Helotealean fungi used in the study.</p>
Feeding black soldier fly larva to replace soybean meal in growing pigs – responses in the amine metabolites in blood
<p>Insect meals from black soldier fly (<em>Hermetia illucens</em>; BSF) larvae as dietary protein source have the ability to deliver nutrients, particularly dietary amino acids (AA) and could provide functional properties that positively supports animal health and productivity. More knowledge, however, is needed to assess the impact of BSF based diet on gut and animal health. Sixteen male pigs with an average initial body weight of 34.9 ± 3.4 kg were randomly assigned to groups fed for three weeks with iso-caloric and iso-proteinaceous experimental diets prepared with either soybean meal (SBM) as reference protein source or with BSF, as single source of dietary protein. At the end of the feeding trial, blood plasma were collected to study the changes at systemic level in plasma amine metabolites as an effect of the experimental diet.</p>
Data from: Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals
The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.
Mass spectrometry imaging of metabolites in symbiont containing tissues of Bathymodiolus sp. mussels from a hydrothermal vent
<p>Molecules in <em>Bathymodiolus </em>sp. tissue. Distribution of five lipid metabolites in symbiont containing gill tissues was visualized using MALDI mass spectrometry imaging (red: high amounts, blue: low amounts of lipids).</p>
Imaging of metabolites in symbiont containing tissues of Bathymodiolus sp. mussels from a hydrothermal vent
<p>MALDI-MS laser spot size directly influences the resolution of ion-maps generated by MALDI-MS imaging. Here we show from top to bottom different ion maps from <em>Bathymodiolus sp</em>. tissue acquired with decreasing spot sizes (laser spot diameter indicated in each image). Details relevant to the scale of the bacterial symbionts become visible by using laser settings under 10 µm spot size.</p>
Metabolite dataset on LED effects
<p>Dataset containing metabolite data from samples taken on Arabidopsis thaliana plants cultivated under different light sources. LIMS-Sample = unique sample identifier , Treat = treatment (phy = fluorescent light, ldr = LED light (Roschwege), ldv ( LED light, Valoya), cgw = natural light + metal halide lamps + SonT lamps), Age = age in days after sowing, time = time of harvest (EN last hour of the dark phase, ED = last hour of the light phase), id =identifier in MS run</p>
Database specific for the pesticide active substance and their metabolites, comprising the main genotoxicity endpoints
<p>In 2014, EFSA has commissioned the compilation of a database specific for the pesticide residues including active substances and their metabolites, which comprises different genotoxicity endpoints, i.e. point mutations, structural and numerical chromosome aberrations, and DNA damage.</p> <p>Data collection on individual genotoxicity studies has been retrieved from regulatory toxicological reports (Draft or Renewal Assessment Reports, i.e. DARs or RARs, respectively) as provided by the Rapporteur Member State (RMS) during the pesticide peer review process at European Level. The final EFSA conclusion on the overall genotoxic potential of active substance or metabolites taking into account all available information is not included in the database. </p> <p>The database contains identity and genotoxicity information on more than 290 active substances and some of their metabolites.</p> <p>The database represents a practical tool to complement in-silico tools i.e. QSAR (Quantitative structure–activity relationship models), grouping and read across for prediction of the genotoxicity hazard of the pesticides residues, and it supposes to enlarge the chemical domains for their application.</p> <p><strong>Format: xls; contact: data.collection@efsa.europa.eu, pesticides.ppr@efsa.europa.eu </strong></p> <p><br> <strong>DISCLAIMER</strong><br> Without prejudice to the legal notice applicable to EFSA's website available here, the following legal notice applies to the Pesticide genotoxicity database and any documents, data or information contained therein. Users are advised to read this legal notice carefully before accessing, using or reading any document, data or information made available in this context, or making any other use of the Database.<br> The Pesticide genotoxicity database is a compilation of chemical and genotoxicity information on active substances and some of their metabolites. The database contains the results of individual studies as initially assessed by the Rapporteur member state (RMS) and reported in the respective Draft assessment reports (DARs) or Renewal Assessment Reports (RARs). The final EFSA Conclusions on the respective active substances are available to the public on the EFSA Journal. The database includes the data that was available at the moment of compilation of the database (December 2016) and will be updated on a regular basis by including or deleting of information as a result of renewal procedure of active substances (Regulation (EU) No 1107/2009). <br> EFSA makes no representations or warranties about the accuracy or suitability of any document, information, data provided in the Database. In case of discrepancy between the data provided in the original scientific output (DARs/RARs) and that in this database, preference shall be given to the former.<br> This database does not disclose any commercially sensitive or otherwise confidential information. Unless otherwise stated, the owners of the data compiled in this database are the applicants under Regulation (EU) No 1107/2009, and by acceiding the Database you acknowledge that agreement for reuse of these data should be sought from them.<br> The information provided in the Database and related materials are not intended to constitute advice of any kind or the rendering of consulting, or other professional services of any kind. Acceding the Database does not establish any contractual relationship with EFSA. Users are advised to consult with an attorney, food consultant or other professional to determine what may be best for your individual needs.<br> By acceding the Database, you also acknowledge that the documents, data or information made available by EFSA may contain inaccuracies or errors. The content of the information provided is for your information and use only. It may be subject to change at any time and without prior notice by EFSA.</p>
Structures of FDA-approved drugs and their active metabolites and data sets of experimental PD and PK properties
<p>Data sets are extracted from the 2024 release of the e-Drug3D Database (2118 FDA-approved drug structures)</p> <ol> <li><strong>e-Drug3D_2118.zip </strong>(contains e-Drug3D_2118.sdf)<strong> -</strong> <strong>Chemical Structures</strong> - The e-Drug3D collection in SDF format file - one 3D conformer; ionization of carboxylic acid, phosphate, phosphonate, phosphonoamide, amidinium and guanidinium groups. The datablock contains the ID, name (INN), CAS number and Status.</li> <li><strong>e-Drug3D_2118_PK.csv - </strong><strong>Pharmacokinetics</strong> - Column/field value is separated by a semicolon. It contains the e-Drug3D ID, INN (drug name), CAS number, year of approval, Status, is_or_has a metabolite, routes of administration, Volume of distribution (VD), Clearance (Cl), Plasma Protein Binding (PPB), Half-life (t1/2), Bioavailability (F), Cmax/Tmax, comment on solubility.</li> <li><strong>e-Drug3D_2118_PD.csv -</strong> <strong>Pharmacodynamics</strong> - Column/field value is separated by a semicolon. It contains the e-Drug3D ID, INN (drug name), CAS number, year of approval, Status, Primary target, ATC code(s), PDB codes and main list of drug targets.</li> <li><strong>e-Drug3D_2118_RD.csv -</strong> <strong>FDA Registration Data</strong> - Column/field value is separated by a semicolon. It contains the ID, name (INN), CAS number, First year of approval, Status, <a href="http://www.knapsackfamily.com/knapsack_core/top.php">KNApSAcK</a> or <a href="https://www.npatlas.org">NPAtlas</a> Id if natural product, all associated NDA numbers [FDA approval number, name of the label file in PDF format, company name, year of approval and commercial name of the drug] and the Indication/Therapeutic class information.</li> <li><strong>labels.tar.gz</strong> - The drug label files in PDF format (compressed directory). A label file is named with the NDA number. The NDA number is the approval number assigned by the FDA. A drug may possess several NDA numbers (see the above e-Drug3D-RD data set).</li> </ol>
Plasma metabolites of three migrant bird species during nocturnal endurance flight
<p>Plasma metabolites of the fat-, protein and carbohydrate metabolism were analysed in European robins, garden warblers and pied flycatchers during their nocturnal migration on a Swiss Alpine pass, Col de Bretolet. Birds were caught in high mist nets out of their nocturnal flight; hence the plasma metabolites reflect the metabolism of a flying, fasting bird.</p>
Quantification of phosphorylated metabolites, organic acids, and intermediates of the TCA cycle using capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) following treatment of Escherichia coli with ciprofloxacin
<p>Capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) was used to quantify phosphorylated metabolites, organic acids, and intermediates of the TCA cycle of Escherichia coli treated with ciprofloxacin, BTP-001 (a novel antimicrobial peptide), and a combination of the two . Metabolite extracts were analyzed with a Xevo TQ-XS triple quadrupole mass spectrometer (Waters, USA).</p><p>Samples were gathered from E. coli cultures grown in batch cultivations using 1 liter bioreactors. Briefly, intracellular metabolites were extracted by cycling samples between −20 °C EtOH and N2 (<i>l</i>) in three consecutive freeze–thaw cycles, with vortexing every 10 min during the thawing phase. Filters were removed and the cell debris was pelleted (4500 rcf, 10 min, -9 °C). The supernatants were transferred to a new tube, snap frozen in N2 (<i>l</i>), and lyophilized. Lyophilized extracts were reconstituted in 500 µL cold Milli-Q H2O and cleared by spin-filtration with a 10 kDa molecular cutoff (20817 rcf, 10 min, 0 °C). A mix of 80 µL centrifuged sample and 20 µL 13C-labeled ISTD extract from yeast was sent to analysis. </p><p>Data processing and absolute quantification was performed as earlier described using the TargetLynx application manager of MassLynx v 4.1 (Waters) to interpolate calibration curves made with appropriate dilutions of analytical grade standards (Sigma-Aldrich). The response factor of the corresponding U13C-isotopologues were used to correct the standard and sample extract response factors. Extract concentrations were normalized to the CDW, which was calculated from interpolation of the OD600 vs. CDW (g/L) curve. </p><p>Further statistical analysis in MetaboAnalyst v 5.0 replaced missing values with 1/5 of the minimum value of the respective metabolite. An unpaired T-test with unequal variance determined differential enriched metabolites with a false discovery rate (FDR) < 0.05 which are presented as log2 fold-change compared to control. </p>
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.