Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
231
datasets available to search
ShareScore release 0.9.0
Dataset results
231 results for “Natural Products”
Data from: Expanding the described metabolome of the marine cyanobacterium Moorea producens JHB through orthogonal natural products workflows
Moorea producens JHB, a Jamaican strain of tropical filamentous marine cyanobacteria, has been extensively studied by traditional natural products techniques. These previous bioassay and structure guided isolations led to the discovery of two exciting classes of natural products, hectochlorin (1) and jamaicamides A (2) and B (3). In the current study, mass spectrometry-based 'molecular networking' was used to visualize the metabolome of Moorea producens JHB, and both guided and enhanced the isolation workflow, revealing additional metabolites in these compound classes. Further, we developed additional insight into the metabolic capabilities of this strain by genome sequencing analysis, which subsequently led to the isolation of a compound unrelated to the jamaicamide and hectochlorin families. Another approach involved stimulation of the biosynthesis of a minor jamaicamide metabolite by cultivation in modified media, and provided insights about the underlying biosynthetic machinery as well as preliminary structure-activity information within this structure class. This study demonstrated that these orthogonal approaches are complementary and enrich secondary metabolomic coverage even in an extensively studied bacterial strain.
Data from: The link between host density and egg production in a parasitoid insect: comparison between agricultural and natural habitats
1. Theory predicts that organisms should invest in overcoming a factor that may limit their reproductive success in direct proportion to their probability of being limited by it. The occurrence of egg limitation (where female insects deplete their eggs while oviposition opportunities are still available) is predicted to impose selection for increased fecundity at the expense of other fitness components. 2. We tested the hypothesis that the fecundity of a proovigenic parasitoid (where females emerge with their full egg load) should be positively correlated with the mean expectation for oviposition opportunities in the environment. More specifically, we tested whether females from agricultural systems, where hosts are often relatively abundant, emerge with more eggs than those from natural habitats. 3. We studied the proovigenic parasitoid wasp Anagrus daanei, which parasitizes eggs of leafhoppers of the genus Erythroneura. Erythroneura spp. leafhoppers feed on Vitis spp. (grapes) and are major pests of commercial vineyards as well as common herbivores of wild Vitis californica, which grows in riparian habitats. We sampled leafhoppers and parasitoids from eight vineyards and eight riparian habitats in central California. 4. We found that leafhopper density was higher at vineyards than in riparian habitats, whereas leafhopper egg size and parasitoid body size did not differ among these habitat types. Parasitoids from vineyards had higher egg loads than parasitoids from wild grapes, and fecundity was positively related to host density across field sites. Parasitoid egg volume was larger in natural sites; however, this variation was not significantly correlated with host density across field sites. Within a single population of parasitoids collected from a vineyard, parasitoid egg load was negatively correlated with longevity, suggesting a trade-off between reproduction and lifespan. 5. The results may be explained by a rapid evolution of reproductive traits in response to oviposition opportunities; or alternatively, by the occurrence of maternal effects on the fecundity of daughters based on the foraging experience of their mothers. 6. The ability of parasitoid fecundity to track mean host availability may strengthen the ability of parasitoids to suppress the population densities of their hosts, and hence may represent an important ecological or eco-evolutionary feedback.
Data from: Towards smarter harvesting from natural palm populations by sparing the individuals that contribute most to population growth or productivity
1. Natural populations deliver a wide range of products that provide income for millions of people and need to be exploited sustainably. Large heterogeneity in individual performance within these exploited populations has the potential to improve population recovery after exploitation and thus help sustaining yields over time. 2. We explored the potential of using individual heterogeneity to design smarter harvest schemes, by sparing individuals that contribute most to future productivity and population growth, using the understorey palm Chamaedorea elegans as a model system. Leaves of this palm are an important non-timber forest product and long-term inter-individual growth variability can be evaluated from internode lengths. 3. We studied a population of 830 individuals, half of which was subjected to a 67 % defoliation treatment for three years. We measured effects of defoliation on vital rates and leaf size – a trait that determines marketability. We constructed integral projection models in which vital rates depended on stem length, past growth rate, and defoliation, and evaluated transient population dynamics to quantify population development and leaf yield. We then simulated scenarios in which we spared individuals that were either most important for population growth or had leaves smaller than marketable size. 4. Individuals varying in size or past growth rate responded similarly to leaf harvesting in terms of growth and reproduction. By contrast, defoliation-induced reduction in survival chance was smaller in large individuals than in small ones. Simulations showed that harvest-induced population decline was much reduced when individuals from size and past growth classes that contributed most to population growth were spared. Under this scenario cumulative leaf harvest over 20 years was somewhat reduced, but long-term leaf production was sustained. A three-fold increase in leaf yield was generated when individuals with small leaves are spared. 5. Synthesis and applications This study demonstrates the potential to create smarter systems of palm leaf harvest by accounting for individual heterogeneity within exploited populations. Sparing individuals that contribute most to population growth ensured sustained leaf production over time. The concepts and methods presented here are generally applicable to exploited plant and animal species which exhibit considerable individual heterogeneity.
Biodiversity-productivity relationships in a natural grassland community vary under diversity loss scenarios
<p>Understanding the biodiversity-productivity relationship and underlying mechanisms in natural ecosystems under realistic diversity loss scenarios remains a major challenge for ecologists despite its importance for predicting impacts of rapid loss of biodiversity worldwide. Here we report the results of a plant functional group (PFG) removal experiment conducted on the Mongolian Plateau, the largest remaining natural grassland in the world.</p> <p>Our results demonstrated that the biodiversity-productivity relationship varied among positive linear, neutral, and unimodal forms under different PFG loss patterns. Moreover, the form of this relationship with the same PFG loss pattern sometimes changed through time.</p> <p>The abundance of the remaining PFG(s) before removal and their compensation following the loss of other PFGs were two major mechanisms affecting the biodiversity-productivity relationship under diversity loss scenarios. The abundance effect promoted positive responses of productivity to biodiversity, but the compensation effect caused several biodiversity-productivity relationships, hinging on its direction (positive or negative) and strength. As indicated by the values of the compensation index, negative, zero and partial compensations contributed to the positive relationships, while full compensation resulted in a neutral relationship. Over-compensation at intermediate PFG richness levels created a unimodal curve in our system, but it could also lead to a negative linear relationship.</p> <p><i>Synthesis</i>. Our experiment provides a vivid picture of how the form of the biodiversity-productivity relationship varies among different diversity loss patterns in a natural ecosystem. We argue that compensation by the remaining species, which is not revealed by synthesized biodiversity experiments, plays a critical role in shaping the form of this relationship when diversity is lost from existing systems. The direction and strength of compensation are highly dependent on extirpation scenarios. Thus, impacts of biodiversity loss on natural ecosystems are likely more complex than predicted by the canonical positive saturating curve obtained from the synthesized biodiversity experiments. We suggest that models forecasting the consequences of biodiversity declines on natural ecosystems should take into account diversity loss patterns and the ensuing compensation.</p>
Evaluation of Ion Mobility Spectrometry for Improving Constitutional Assignment in Natural Products Mixtures - cytoscape files
<p>Cytoscape files associated with Figure 5 from the manuscript: Evaluation of Ion Mobility Spectrometry for Improving Constitutional Assignment in Natural Products Mixtures</p>
Genome sequences of Rhizopogon roseolus, Mariannaea elegans, Myrothecium verrucaria, and Sphaerostilbella broomeana and the identification of biosynthetic gene clusters for fungal peptide natural products
<p>Data to accompany the paper, detailed in manifest.txt</p>
Plant responses to ramet density and herbivory under natural field conditions: Impacts on volatile organic compound emissions and seed production
Open the record for dataset details and reuse information.
Impact of dispersion correction in DFT-enhanced anisotropic NMR for stereochemical elucidation of flexible marine natural products
<p><strong>Supplementary Data of the article "Impact of dispersion correction in DFT-enhanced anisotropic NMR for stereochemical elucidation of flexible marine natural products."</strong></p> <p> </p>
Chemical Diversity of Cyanobacterial Natural Products (2010-2023)
<p>Cyanobacterial natural products reported from 2010 to 2023.</p> <p> </p>
Synthetic natural gas (SNG) production with higher carbon recovery from biomass: Techno-economic assessment
<p>Dataset for the paper: Synthetic natural gas (SNG) production with higher carbon recovery from biomass: Techno-economic assessment</p>
3D electron diffraction dataset of natural product Beauveriolide Q
<p><span>3D ED data was recorded using EPU-D, with the original dataset saved in MRC format. The PETS2 processing file contains all the dataset’s metadata. Structure analysis and refinement data are also included.</span></p>
Switchable Synthesis of Natural-Product-Like Lawsones and Indenopyrazoles through Regioselective Ring-Expansion of Indantrione
<p>Lawsones and indenopyrazoles are the prevalent structural motifs and building blocks in pharmaceuticals and bioactive molecules, but their synthesis has always remained challenging as no comprehensive protocol has been outlined to date. Herein, a new metal-free, ring-expansion reaction of indantrione with diazomethanes, generated in situ from the N-tosylhydrazones, has been developed for the synthesis of lawsone and indenopyrazole derivatives in acetonitrile and alcohol solvents, respectively. It provides these valuable lawsone and pyrazole skeletons in good yields and high levels of diastereoselectivity from simple and readily available starting materials. DFT calculations were used to explore the mechanism in different solutions. The synthetic application example also showed the prospects of this method for the preparation of valuable compounds.</p>
Dataset for Disordered dolomite as an unusual biomineralization product found in the center of a natural Cassis pearl
<p>Natural pearls are produced without human intervention, mainly due to various irritations from the surrounding environment to their mantle tissues. Pearls usually possess similar mineral compositions to the host shells, which means they are also dominated by aragonite and calcite. In this study, we report a natural pearl from a <em>Cassis</em> species mollusk containing granular central structures. Raman spectroscopy, laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS), energy dispersive X-ray spectroscopy (EDS) coupled with scanning electron microscope (SEM), and X-ray diffraction (XRD) analyses were carried out in order to characterize the mineral composition in the center region of this pearl. Our results showed that this pearl's center was made of mostly disordered dolomite (Ca<sub>0.53</sub>Mg<sub>0.47</sub>CO<sub>3</sub>) mixing with small amount of aragonite and high magnesium-calcite. To the best of our knowledge, this is the first time disordered dolomite was conclusively identified inside of a natural pearl and such information expanded our knowledge on internal growth structures and formation of natural pearls.</p>
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
Identification of disinfection by‑product precursors by natural organic matter fractionation: a review - Full Data
<p>Data gathered for the meta-analysis performed in the review paper.</p> <p>Full references to the used data is found in the review paper itself.</p>
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 9</a> .</p> <p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p> <p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p> <p>File 220916_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/7085063">the LOTUS database version 9</a> and the SMILES chains of the compounds were collected.</p> <p>The SMILES chains were translated to 2D chemical structures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p> <p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p> <p>Each compound was also supplemented with metadata from file 220916_frozen_metadata.csv .</p> <p>Archive file acd_lotusv9.sdf.zip contains acd_lotusv9.sdf with 218,478 compound descriptions inside.</p> <p>Archive file acd_lotusv9.NMRUDB.zip is a compressed version of acd_lotusv9.NMRUDB, itself created by importation of file acd_lotusv9.sdf in an ACD/Labs database file (new with version 0.0.4).</p> <p>The description of the first compound was copied in file firstmolv9.sdf and is provided for a quick inspection of the database content.</p> <p>The title line in firstmolv9.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220916_frozen_metadata.csv .</p> <p>Files acd_lotusv9.sdf acd_lotusv9.NMRUDB contain biological taxonomy data from file 220916_frozen_metadata.csv that were not exploited in acd_lotusv7. Sub-files dealing with a particular taxon can be easily produced now.</p> <p>Chemical shift calculations for <sup>13</sup>C nuclei using the HOSE code approach are available <a href="https://zenodo.org/record/7047760">here</a> for the compounds in acd_lotusv7.</p> <p> </p>
Fig. 8 in Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease
Fig. 8. (a) The general structure of a flavonoid. (b) Chemical structures of the flavonoids – quercetin (14), kaempferol-3-O-rutinoside (16), rutin (17), hyperoside (18), the chromanone derivative (20), myricetin (23), apigenin (24), and luteolin (25), (c) pongamol (15), (d) epicatechin (19), catechin (27), EGCG (29), hesperetin (32), and hesperidin (33), (e) amentoflavone (21), (f) curcumin (22), (g) delphinidin (26), and (h) rotenone (30).
Fig. 1 in Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease
Fig. 1. An illustration of dengue virus structure showing the lipid bilayer, the structural proteins, and the positive RNA strand.
Fig. 7 in Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease
Fig. 7. Chemical structures of ganodermanontriol (10), lucidumol A (11), ganoderic acid C2 (12), and ganosporeric acid A (13). Wherein, () indicates a wedged bond; (- - -) indicates a hashed bond.
Fig. 9 in Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease
Fig. 9. Chemical structures of the phenolic compounds (a) gallic acid (31), methyl orsellinate (34), resveratrol (35), gingerol (36), anacardic acid (37), and cardol triene (38), (b) tatanan A (39).
ScienceDex guides
Understand access before you commit
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.