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159 results for “terpenoids”
GC-MS data set for Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>RAW GC/MS data set for characterization of class II terpene synthases from <em>Callicarpa americana </em></p>
Data from: Geographic distribution of terpenoid chemotypes in Tanacetum vulgare mediates tansy aphid occurrence but not abundance
<p>Intraspecific variation of specialized metabolites in plants, such as terpenoids, are used to determine chemotypes. Tansy (<em>Tanacetum vulgare</em> L.) exhibits diverse terpenoid profiles that affect insect communities. However, it is not fully known whether patterns of their chemical composition and associated insects vary beyond the community scale. Here, we investigated the geographic distribution of mono- and sesquiterpenoid chemotypes in tansy leaves and their relationships with specific insect communities across Germany. We sampled tansy leaves from ten plants with and five plants without aphids in each of 26 sites along a north-south and west-east transect in Germany. Hexane-extracted metabolites from leaf tissues were analyzed by gas chromatography-mass spectrometry (GC-MS). Plant morphological traits, aphid occurrence and abundance, and occurrence of ants were recorded locally. The effect of plant chemotype, plant morphological parameters, and abiotic site parameters such as soil types, temperature and precipitation on insect occurrences were analyzed. Plants clustered into four monoterpenoid and four sesquiterpenoid chemotype classes. Monoterpene classes differed in their latitudinal distribution, whereas sesquiterpenes were more evenly distributed across the transect. Aphid and ant occurrence was influenced by monoterpenoids. Plants of monoterpenoid class 1 were colonized by aphids and ants significantly more often than expected by chance, whereas in other classes there were no significant differences. Aphid abundance was affected by soil type, and average annual temperature positively correlated with the occurrence of ants. We found significant geographic patterns in the distribution of tansy chemodiversity and show that monoterpenoids affect aphid and ant occurrence, while the soil type can influence aphid abundance. We show that geographic variation in plant chemistry influences insect community assembly on tansy plants.</p>
Selected Simple Natural Antimicrobial Terpenoids as Additives to Control Biodegradation of Polyhydroxy Butyrate
<p><strong>Abstract</strong></p> <div>In this experimental research, different types of essential oils (EOs) were blended with polyhydroxybutyrate (PHB) to study the influence of these additives on PHB degradation. The blends were developed by incorporating three terpenoids at two concentrations (1 and 3%). The mineralization rate obtained from CO<sub>2</sub> released from each sample was the factor that defined biodegradation. Furthermore, scanning electron microscope (SEM), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA) were used in this research. The biodegradation percentages of PHB blended with 3% of eucalyptol, limonene, and thymol after 226 days were reached 66.4%, 73.3%, and 76.9%, respectively, while the rate for pure PHB was 100% after 198 days, and SEM images proved these results. Mechanical analysis of the samples showed that eucalyptol had the highest resistance level, even before the burial test. The other additives showed excellent mechanical properties although they had less mechanical strength than pure PHB after extrusion. The samples’ mechanical properties improved due to their crystallinity and decreased glass transition temperature (Tg). DSC results showed that blending terpenoids caused a reduction in Tg, which is evident in the DMA results, and a negligible reduction in melting point (Tm).</div> <p> </p> <p><strong>Open access data</strong></p> <p>The datasets for this publication can be accessed using the DOI: 10.5281/zenodo.13829790 or via the zip folder below.</p>
Design of a redox-proficient Escherichia coli for screening terpenoids and modifying cytochrome P450s
<p>20 Terpenoid scaffold.zip: Raw GCMS data for titer comparisons. Required to reproduce Figure 2b.</p> <p>20 Terpenoid scaffold_representative GCMS.zip: Representative GCMS data for 20 terpenoid scaffolds produced by E. coli MEV15 and 20. Required to reproduce Supplementary Figure 3.</p> <p>Characterization of LRD04 derivatives.zip: Raw NMR and GCMS data for 19 ent-kaurenoid derivatives described in this manuscript. Required to reproduce Supplementary Figures 13-33.</p> <p>LRD production optimization.zip: Raw GCMS data for pLRD construct screening with different IPTG concentration. Required to reproduce Supplementary Tables 9-36.</p> <p>LRD scaffolds.zip: Raw GCMS data for LRD production after optimization. Required to reproduce Figure 5 and Supplementary Tables 9-36.</p> <p>Pathway screening.zip: Raw GCMS data for screening biosynthetic pathways of LRD scaffold paired with 64 CYPs. Each GCMS dataset is consisted of 1 pathway producing only LRD scaffold, 64 pathways producing LRD scaffold and different CYPs, and 2 alkane-series standards acquired before and after analyzing the 65 pathways. Required to reproduce Figure 6 and Supplementary Tables 9-36.</p> <p>Redox array characterization 1.zip: Raw GCMS data for comparison of modified terpenoid production in the presence of different redox enzymes. Required to reproduce Figure 3a.</p> <p>Redox array characterization 1_scaffold.zip: Raw GCMS data for comparison of terpenoid scaffold production in the presence of different redox enzymes. Required to reproduce Supplementary Figure 4.</p> <p>Redox array characterization 2.zip: Raw GCMS data for comparison of modified terpenoid production with or without an additional copy of fldA/fpr. Required to reproduce Figure 3b and Supplementary Figure 5.</p> <p>Terpenoid inducer optimization.zip: Raw LCMS and GCMS data for optimizing 01a and 03a production in E. coli MEV20. Required to reproduce Figure 4 and Supplementary Figures 6 and 7.</p> <p>terpenoids_code.zip: Jupyter Notebook used for analyzing GNN results and metabolomic analysis (also available at <a href="https://github.com/gengminlin/terpenoids">https://github.com/gengminlin/</a><a href="https://github.com/gengminlin/GNN-and-Metabolomics-Analysis-for-LRD">GNN-and-Metabolomics-Analysis-for-LRD</a>) </p> <p> </p>
Data from: Geographic distribution of terpenoid chemotypes in Tanacetum vulgare mediates tansy aphid occurrence but not abundance
Open the record for dataset details and reuse information.
Data from: Temperature alters the toxicological impacts of plant terpenoids on the polyphagous model herbivore Vanessa cardui
<p>Terpenes are a major class of secondary metabolites present in all plants, and long hypothesized to have diversified in response to specific plant-herbivore interactions. Herbivory is a major biotic interaction that plays out across broad temporal and spatial scales that vary dramatically in temperature regimes, both due to climatic variation across geographic locations as well as the effect of seasonality. In addition, there is an emerging understanding that global climate change will continue to alter the temperature regimes of nearly every habitat on Earth over the coming centuries. Regardless of source, variation in temperature may influence herbivory, in particular via changes in the efficacy and impacts of plant defensive chemistry. This study aims to characterize temperature-driven variation in toxicological effects across several structural classes of terpenes in the model herbivore Vanessa cardui, the painted lady butterfly. We observed a general increase in monoterpene toxicity to larvae, pupa, and adults at higher temperatures, as well as an increase in development time as terpene concentration increased. Results obtained from this study yield insights into possible drivers of seasonal variation in plant terpene production as well as inform effects of rising global temperatures on plant-insect interactions. In the context of other known effects of climate change on plant-herbivore interactions like carbon fertilization and compensatory feeding, temperature-driven changes in plant chemical defense efficacy may further complicate the prediction of climate change impacts on the fundamental ecological process of herbivory.</p>
The terpenoid emissions of OBEIC from 2016 to 2022
<p>To use this dataset please cite our publications.</p> <p><strong>PUBLICATIONS:</strong></p> <p>Underestimated contribution of open biomass burning to terpenoid emissions revealed by a novel hourly dynamic inventory,<br>Science of The Total Environment,<br>2024,<br>172764,<br>ISSN 0048-9697,<br>https://doi.org/10.1016/j.scitotenv.2024.172764.<br>(https://www.sciencedirect.com/science/article/pii/S0048969724029115)</p> <p><span>More data updates will be posted here in the future.</span><span> For special orders, please contact lijiangyong1105@foxmail.com</span></p> <p><span><strong>Data Update Announcement:</strong> None</span></p>
An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway
<p>Data underlying the figures/tables of the publication "An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway" <em>Nat. Chem.</em> (2024). https://doi.org/10.1038/s41557-024-01562-5</p>
Data for publication "Selected Simple Natural Antimicrobial Terpenoids as Additives to Control Biodegradation of Polyhydroxy Butyrate"
<p><strong>Abstract</strong></p> <div>In this experimental research, different types of essential oils (EOs) were blended with polyhydroxybutyrate (PHB) to study the influence of these additives on PHB degradation. The blends were developed by incorporating three terpenoids at two concentrations (1 and 3%). The mineralization rate obtained from CO<sub>2</sub> released from each sample was the factor that defined biodegradation. Furthermore, scanning electron microscope (SEM), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA) were used in this research. The biodegradation percentages of PHB blended with 3% of eucalyptol, limonene, and thymol after 226 days were reached 66.4%, 73.3%, and 76.9%, respectively, while the rate for pure PHB was 100% after 198 days, and SEM images proved these results. Mechanical analysis of the samples showed that eucalyptol had the highest resistance level, even before the burial test. The other additives showed excellent mechanical properties although they had less mechanical strength than pure PHB after extrusion. The samples’ mechanical properties improved due to their crystallinity and decreased glass transition temperature (Tg). DSC results showed that blending terpenoids caused a reduction in Tg, which is evident in the DMA results, and a negligible reduction in melting point (Tm).</div> <div> </div> <p>Data for publication contains: Scanning Electron Microscope (SEM), Differential Scanning Calorimetry (DSC), and Dynamic Mechanical Analysis (DMA) figures and images for samples</p> <p>Full publication can be found here: <em>https://zenodo.org/records/13785631</em></p>
Data from: Identification of anti-fungal bioactive terpenoids from the bioenergy crop switchgrass (Panicum virgatum)
<p>Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on functional phytobiomes. Increased knowledge of specialized metabolite bioactivities could inform strategies for sustainable crop production. We hypothesized that – consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly – differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates – <em>Linnemania elongata</em>, <em>Trichoderma</em> sp. and <em>Fusarium</em> sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure – activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties – saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition.</p>
Germplasm diversity of sunflower volatile terpenoid profiles across vegetative and reproductive organs
<p>Cultivated sunflower (<em>Helianthus</em> <em>annuus</em>) is the fourth most important oilseed crop globally and is known to have experienced multiple genetic bottlenecks during domestication and improvement. Homogenization of crop germplasm may limit breeding efforts to improve pest and pathogen resistance or optimize other biotic interactions like pollinator attraction. Such interactions are often strongly influenced by plant phytochemistry, especially volatile compounds like terpenoids. Here we use solid-phase microextraction gas chromatography mass spectrometry (SPME GC-MS) to evaluate volatile phytochemistry across leaves, involucral bracts, disc florets, and ray floret petals in a collection of twelve inbred lines selected to represent a cross-section of sunflower germplasm diversity. Results indicate considerable compositional diversity of volatiles among lines, though substantial reduction in total volatile abundance relative to wild <em>H. annuus</em>. From leaves and bracts to disc florets and petals, we observe a strong increase in the proportion of monoterpenoids relative to sesquiterpenoids accompanying the transition to reproductive structures, with consistently over 85% monoterpenoids in disc florets and petals. This pattern is driven by substantially higher production of monoterpenoids (especially alpha-pinene and sabinene) in reproductive structures. Sesquiterpenoid production is roughly similar across organs, and in leaves varies among lines from 21–55% of volatiles, dominated by cadinene-type sesquiterpenoids. This work suggests that the compositional diversity of volatile terpenoids within cultivated germplasm may be sufficient for many breeding applications, though for breeding increased volatile production the use of wild <em>H. annuus</em> and other wild <em>Helianthus</em> germplasm may be necessary.</p>
Data from: Analgesic effect of the mint terpenoid L-Carvone in sheep
Open the record for dataset details and reuse information.
Germplasm diversity of sunflower volatile terpenoid profiles across vegetative and reproductive organs
Open the record for dataset details and reuse information.
Data from: Identification of anti-fungal bioactive terpenoids from the bioenergy crop switchgrass (Panicum virgatum)
Open the record for dataset details and reuse information.
Data from: Temperature alters the toxicological impacts of plant terpenoids on the polyphagous model herbivore Vanessa cardui
Open the record for dataset details and reuse information.
Data from: Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids
<p>Chiococca alba (L.) Hitchc. (snowberry), a member of the Rubiaceae, has been used as a folk remedy for a range of health issues including inflammation and rheumatism and produces a wealth of specialized metabolites including terpenes, alkaloids, and flavonoids. We generated a 558 Mb draft genome assembly for snowberry which encodes 28,707 high confidence genes. Comparative analyses with other angiosperm genomes revealed enrichment in snowberry of lineage-specific genes involved in specialized metabolism. Synteny between snowberry and Coffea canepehora Pierre ex A. Froehner (coffee) was evident, including the chromosomal region encoding caffeine biosynthesis in coffee, albeit syntelogs of N-methyltransferase were absent in snowberry. A total of 27 putative terpene synthase genes were identified, including 10 that encode diterpene synthases. Functional validation of a subset of putative terpene synthases revealed that combinations of diterpene synthases yielded access to products of both general and specialized metabolism. Specifically, we identified plausible intermediates in the biosynthesis of merilactone and ribenone, structurally unique antimicrobial diterpene natural products. Access to the C. alba genome will enable additional characterization of biosynthetic pathways responsible for health-promoting compounds in this medicinal species.</p>
Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>Background: Plants exhibit wide chemical diversity due to production of specialized metabolites which function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs and as sources of insect repellents, health-promoting compounds, and fragrance. Findings: We report the chromosome-scale genome assembly of <em>Callicarpa americana</em> L. (American beautyberry), a species within the early diverging Callicarpoideae clade of the Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long reads and Hi-C scaffolding, we generated a 506.1 Mb assembly spanning 17 pseudomolecules with an N50 contig and N50 scaffold size of 7.5 Mb and 29.0 Mb, respectively. A total of 32,164 genes was annotated including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Whole genome duplication analyses revealed three putative events, which together with local tandem duplication events, contributed to gene family expa, American beautyberransion of terpene synthases. Kolavenyl diphosphate is a gateway to many of <em>C. americana</em>'s bioactive terpenoids; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with <em>Tectona grandis</em> L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 <em>C. americana</em> syntelogs. Conclusions: Access to the <em>C. americana</em> genome provides a roadmap for rapid discovery of genes encoding plant-derived agrichemicals and a key resource to understand the evolution of chemical diversity in Lamiaceae. </p> <p> </p>
Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae
<p>Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (<i>Ocimum basilicum </i>L<i>.</i>), sweet marjoram (<i>Origanum majorana </i>L.), oregano (<i>Origanum vulgare </i>L<i>.</i>), and rosemary (<i>Rosmarinus officinalis </i>L<i>.</i>), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the four species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all four species, a total of 235 terpene synthases were identified, ranging from 27 in <i>O. majorana</i> to 137 in the tetraploid <i>O. basilicum</i>. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.</p>
Fig. 2 in Botryane, noreudesmane and abietane terpenoids from the ascomycete Hypoxylon rickii
Fig. 2. Selected COSY and HMBC correlations determining the carbon backbones of (A) 1, (B) 7 and (C) 10.
Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations
<p>Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: tar -zcvf terpenoidpermeability.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf" --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" Terpenoid-Permeability, which intentionally excludes large files. The full dataset that includes trajectories is available upon request.</p> <p>The data is split into two directories initially "<strong>build</strong>" and "<strong>Simulations</strong>"</p> <ul> <li>"<strong>build</strong>" directory is the part where initial system for unbiased and biased simulation were build using "<strong>resolvate.tcl</strong>" and "<strong>smd-single-build-system.tcl</strong>" respectively.</li> <li>"<strong>Simulations</strong>" directory has the different namd files for running unbiased simulation, steered molecular dynamics and replica exchange umbrella sampling.</li> </ul> <p>The folder structure was generated using "<strong>gendirs*.py</strong>".<br> The unbiased simulations were run using "<strong>run.namd</strong>".<br> Steered molecular dynamics namd files were with name "<strong>step*.namd</strong>" and colvars configuration file are named "<strong>step*.conf</strong>".<br> <br> Replica exchange moleuclar dynamics (REUS) system was generated using "<strong>buildreplicas.tcl</strong>".<br> Replica windows size and force constant were written into a namd configuration file using "<strong>reus-genscript.py</strong>".<br> REUS general configuration file containing the parameters and forcefield is named as "<strong>base.namd</strong>".<br> Colvars for REUS are in "<strong>replicadistZcolvars.conf</strong>".<br> Umbrella sampling is performed with "<strong>umbrella.namd</strong>".</p>
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