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231 results for “Natural Products”
Agriculture - General: Natural Resources and Environment, Plant Production and Protection
<p>Original data comes from a project which takes or took place as part of the DFG priority program “Exploratories for large-scale and long-term functional biodiversity research”. The data is stored together with descriptive metadata, in combination called a dataset, in the project repository (<a href="https://www.bexis.uni-jena.de">https://www.bexis.uni-jena.de</a>). Species information was extracted from that original dataset. The second paragraph is part of the metadata of the original <a href="<a href="http://dataset.in/">http://dataset.in/</a>">dataset.In this project we investigate seed bank and bryophyte propagule content in top soil in grasslands. Müller J (2016). Seed bank grassland. Biodiversity Exploratories. Occurrence dataset <a href="https://doi.org/10.15468/jax26w">https://doi.org/10.15468/jax26w</a> accessed via GBIF.org</p>
Interspecific social interactions shape public goods production in natural microbial communities
<p>The R code (Hesse_etal.R) descibes step by step how metal polution affects the ecology and evolution of a community-wide public good – the production of metal-detoxifying siderophores. This code accompanies the manuscript "Interspecific interactions shape public goods production in natural microbial communities" (https://www.biorxiv.org/content/10.1101/710715v1).</p> <p>The R code is divided into different sections per figure (1-5 and supplementary Figure S1). Each section first starts with reading in the appropriate data files (cvs files) and continues with statistics and plotting of figures.</p>
The Natural Products Atlas - data download
<p>Download files from the Natural Products Atlas (<a href="https://www.npatlas.org/joomla/">npatlas.org</a>).</p> <p>van Santen, J. A.; Poynton, E. F.; Iskakova, D.; McMann, E.; Alsup, T. A.; Clark, T. N.; Fergusson, C. H.; Fewer, D. P.; Hughes, A. H.; McCadden, C. A.; Parra Villalobos, J.; Soldatou, S.; Rudolf, J. D.; Janssen, E. M.-L.; Duncan, K. R.; Linington, R. G.* "The Natural Products Atlas 2.0: A Database of Microbially-Derived Natural Products", <em>Nucleic Acids Research</em>, <strong>2022</strong>, 50, D1, 11, D1317-D1323. <a href="https://doi.org/10.1093/nar/gkab941">10.1093/nar/gkab941</a></p> <p>van Santen, J. A.; Jacob, G.; Leen Singh, A.; Aniebok, V.; Balunas, M. J.; Bunsko, D.; Carnevale Neto, F.; Castaño-Espriu, L.; Chang, C.; Clark, T. N.; Cleary Little, J. L.; Delgadillo, D. A.; Dorrestein, P. C.; Duncan, K. R.; Egan, J. M.; Galey, M. M.; Haeckl, F. P. J.; Hua, A.; Hughes, A. H.; Iskakova, D.; Khadilkar, A.; Lee, J.-H.; Lee, S.; LeGrow, N.; Liu, D. Y.; Macho, J. M.; McCaughey, C. S.; Medema, M. H.; Neupane, R. P.; O’Donnell, T. J.; Paula, J. S.; Sanchez, L. M.; Shaikh, A. F.; Soldatou, S.; Terlouw, B. R.; Tran, T. A.; Valentine, M.; van der Hooft, J. J. J.; Vo, D. A.; Wang, M.; Wilson, D.; Zink, K. E.; Linington, R. G.* "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery”, <em>ACS Central Science</em>, <strong>2019</strong>, 5, 11, 1824-1833. <a href="https://doi.org/10.1021/acscentsci.9b00806">10.1021/acscentsci.9b00806</a></p> <p> </p> <p>Now includes ontological data from:</p> <p>NP Classifier - <a href="https://npclassifier.ucsd.edu/">https://npclassifier.ucsd.edu/</a></p> <p>ClassyFire - <a href="http://classyfire.wishartlab.com/">http://classyfire.wishartlab.com/</a></p> <p>Including archived versions, extra data download types, and new MIBiG and GNPS IDs</p> <p>Includes dump of compounds deemed out of scope and removed from DB on May 19, 2021.</p> <p>The latest versions (v2021_08 onward) include the ontological data in the full JSON download.</p> <p>Starting in v2024_09 - compounds with exclusions are included as a separate file but kept in the database for reference.</p>
Fingerprint Matrix Files for "Machine Learning-based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics"
<p>These files are the necessary dataset to reproduce the observed machine learning metrics in the paper "Machine Learning-based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics" in review at the Journal of Natural Products. </p> <ul> <li>Multiclassifier_23_Drug_Class_Train-Test_Fingerprint_Matrix.tsv is the accumulated positive training set for the 23 different classes demonstrated in the training and testing sets.</li> <li>Negative_Train-Test_Fingerprint_Matrix.tsv is the negatives training and testing examples derived from the RIKEN NP Depo which represent a diverse set of natural product compounds that serve as the counter points to the positive examples.</li> <li>GNPS_23_Drug_Class_Fingerprints_Matrix.tsv is the dataset of fingerprints generated from the publically available GNPS MSMS dataset. These training examples serve to confirm the ability of the machine learning model to generalize to experimental data. </li> <li> Negative_Train-Test_Fingerprint_Matrix.tsv is the dataset of negative training examples derived from the publically available spectra from the GNPS dataset. It is composed of nearly 2,800 random MSMS spectra to compose a diverse negative evaluation set. </li> <li>Random_GNPS_Fingerprints.tsv is the dataset of fingeprints of 9,443 random spectra from GNPS used to evaluate the false positive rate of each model.</li> </ul>
Magnesium Hydroxide Nanoparticles Production from Natural Bitterns
<p>Magnesium hydroxide nanoparticles are widely employed in numerous industrial applications. Several preparation methods have been proposed using mainly synthetic Mg<sup>2+</sup> containing solutions. In the present work, the possibility of producing Mg(OH)<sub>2</sub> nanoparticles from real bitterns, the by-product of sea salt production, is investigated. Bitterns are highly concentrated Mg<sup>2+</sup> containing solutions whose exploitation can turn a waste into valuable products embracing the circular economy idea. Two bitterns collected from Galia and Margi saltworks of the district of Trapani (Italy) were studied. Galia and Margi bitterns had a 1 M and 2.5 M Mg<sup>2+</sup> concentration, respectively. A 2 mm diameter circular-cross sectional T-mixer was adopted to ensure fast reactant mixing. NaOH solutions were employed as precipitant agents. Mg(OH)<sub>2</sub> nanoparticles characterized by cationic and mass purity higher than 99 % and 90 %, respectively, were successfully produced when treating Galia bitterns, while the excessive Margi Mg<sup>2+</sup> concentration yielded stronger micrometer Mg(OH)<sub>2</sub> agglomerates.</p>
The LOTUS Initiative for Open Natural Products Research: wikidata query results
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p> <p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p> <p>This dataset is constituted of 4 tables.</p> <ol> <li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li> <li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li> <li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li> <li>compound_reference_taxon.tsv - the documented structure-organism pairs</li> </ol> <p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p> <p> </p> <p><br> </p>
The LOTUS Initiative for Open Natural Products Research: frozen dataset
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
DBsimilarity of Natural Products to aid compound identification on MS and NMR pipelines, similarity networking and more
<p>DBsimilarity is proposed for organizing structure databases into Similarity Networks to assist researchers with analyzing and making sense of chemical data available. It converts SDF files into CSV files when needed, adds chemoinformatics data, constructs a MZMine custom database file and a NMRfilter candidate list of compounds for rapid dereplication of MS and 2D NMR data, calculates similarities, and constructs CSV files for Similarity Networks using Cytoscape. DBsimilarity aims to bridge chemoinformatics to laboratory-focused natural products researchers and students. </p>
Plant species percent cover data: The influence of natural enemies on plant community composition and productivity
The purpose of this experiment is to determine the influences of natural enemies, including plant pathogenic fungi and insect pests, influence plant community composition, productivity, and diversity over time. The experiment is being conducted in an old field that is burned every other year. Within the old field, there are 8 blocks, and within each block there are 6 treatments: foliar fungicide, soil drench fungicide, foliar insecticide, mammal exclosure, the combination of all enemy suppression tactics (pesticides and mammal exclosure), and a nontreated control. The pesticides are applied repeatedly throughout the growing season. Within the plots, community productivity, species composition, percent cover, and pest damage are being quantified over time.
Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings: To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage PacBio long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions: In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
Fig. 2 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest
Fig. 2. Two pairs of females with infants drink the seepage water at a natural-lick.
Fig. 6 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest
Fig. 6. Visitation time of each orangutan class to the naturallicks.
Fig. 4 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest
Fig. 4. Visiting proportion of each orangutan class: flanged male, female with infant, and others.
Fig. 3 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest
Fig. 3. Proportion of visitation frequency of top 3 species among the natural-licks.
Fig. 5 in Natural-Licks Use By Orangutans And Conservation Of Their Habitats In Bornean Tropical Production Forest
Fig. 5. Duration of the visit of each orangutan class to the naturallicks.
From weeds to natural enemies: Implications of weed cultivation and bio-pesticides for organic onion production
<p>Weed management is challenging for vegetable crops highly sensitive to weed competition, such as onions. Thrips (<em>Thysanoptera</em>: <em>Thripidae</em>) are major insect pests of onion, causing damage through feeding, and vector bacterial pathogens causing rot. Both thrips and their associated pathogens are known to survive on many weed species in onion growing regions. Combining weeding with bio-pesticides may synergistically manage thrips and disease by reducing disease prevalence and indirectly increasing onion yield. However, disturbances from weeding may negatively impact natural enemies. We estimate the effects of organic weed management and bio-pesticides on weed density, thrips and natural enemy activity, disease severity, and yield. The experiment was a randomized complete block design, with four replications of each weeding (control, tine-weeded 2x, tine-weeded 4x, and hand-weeded) and bio-pesticide (control, OxiDate 2.0, Serenade) combination. Arthropods were monitored using yellow sticky cards, and weed counts, marketable yield, and bulb rot prevalence were estimated. Hand-weeding resulted in the lowest weed density and thrips abundance. Additionally, hand-weeding produced 9x higher yield compared to all other treatments. Significant interactions were observed between tine-weeding and bio-pesticide treatments. Natural enemy abundance was slightly negatively impacted by weeding, dependent on year. DNA metabarcoding results show high parasitoid diversity in onion systems and strong reads for multiple genera containing important known biological control agents. Our study suggests hand-weeding is necessary in the southeast for maximum onion yield. Future research should focus on exploring the impact of management on natural enemy communities in onion systems at a large scale.</p>
Supplementary dataset for Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes
<p>Supplementary files for the paper: Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes</p> <p>23777967_protease.fasta.xz:<br> A fasta file (compressed by xz) containing 23777967 protease sequences obtained from 161954 bacterial genomes<br> 23777967_protease_cluster.csv.xz:<br> A csv file (compressed by xz) containing MMseqs2 cluster information of 23777967 proteases<br> This csv file has 5 columns: rep (representative sequence name), mem (member sequence name), number of members in cluster, cluster No.<br> Fig1C_cytoscape.zip:<br> Cytoscape file corresponding to Fig.1C, as well as its node and edge tables<br> Fig2C_cytoscape.zip:<br> Cytoscape file corresponding to Fig.2C, as well as its node and edge tables<br> FigS2_cytoscape.zip:<br> Cytoscape file corresponding to Supplementary Fig.2, as well as its node and edge tables. Size was differently scaled for very large nodes containing more than 1000 precursors/proteases</p>
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
Flower strips and remnant semi-natural vegetation have different impacts on pollination and productivity of sunflower crops
<p>Intensification of agricultural landscapes to fulfil increased global food demands has dramatically impacted biodiversity and ecosystem services. Several pollinator groups, which are vital for the maintenance of pollinator-dependent crops, have been severely affected by this intensification process. Management tools, such as the implementation of agri-environmental schemes, have been widely proposed to improve pollinator's communities and pollination services, although the effectiveness of wildflower strips in comparison to existing natural or semi-natural habitats and the impact on yield has not been fully demonstrated.</p> <p><span>Here, we aimed to assess the effect of flower strips implementation near sunflower fields in two intensive agricultural regions and to quantify their impact on visitation rates and sunflower productivity. Data were obtained in two regions in Spain (Burgos and Cuenca) in sunflower fields with associated semi-natural vegetation (SNVs), with implemented wildflower strips (WFSs) and without vegetation structures (NonVs). Visitation rates were monitored over two years by direct observations, and both sunflower seed production and weight were assessed in 52 fields per year.</span></p> <p><span>Our results revealed regional and inter-annual variation in visitation rates, likely driven by structural differences in the landscapes studied. In Cuenca, characterized by more heterogeneous and floral resources-richer landscapes, the effects of WFSs were significant in the second year of implementation, with higher visitation rates and higher productivity values in fields with implemented wildflower strips compared to those without. In contrast, in Burgos, no consistent effects among field treatments across years were observed.</span></p> <p><span>Synthesis and applications. T</span><span>he implementation of flower strips or maintenance of remnant semi-natural habitats adjacent to sunflower fields, showed context-dependent effects on visitation rates and crop yield. In highly simplified agroecosystems, these interventions may be insufficient or may need longer times to produce significant effects. Yet, in regions where natural and semi-natural patches were already present, the implementation of flower strips was a successful strategy to promote pollinators and sunflower <a>productivity.</a></span></p>
Crystal structure of natural product Argyrin-D determined by 3D electron diffraction
<p>360° rotation of the Argyrin D model (stick mode with carbon, yellow; nitrogen, blue; oxygen, red; sulfur, gold and hydrogen, white) defined by a 2Fo-Fc map contoured at 1.2 sigma (grey mesh). The model was refined at a resolution of 1.1Å in Phenix using implemented electron scattering factors and restraints to R and Rfree values of 17.3 and 18.6%, respectively.</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.