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47 results for “specialized metabolites”
Raw data: Specialized metabolites accumulation pattern in buckwheat is strongly influenced by accession choice and co-existing weeds
<p>Screening suitable allelopathic crops and crop genotypes that are competitive with weeds can be a sustainable weed control strategy to reduce the massive use of herbicides. In this study, three accessions of common buckwheat <em>Fagopyrum esculentum</em> Moench. (Gema, Kora, and Eva) and one of Tartary buckwheat <em>Fagopyrum tataricum</em> Gaertn. (PI481671) were screened against the germination and growth of the herbicide-resistant weeds <em>Lolium rigidum </em>Gaud. and <em>Portulaca oleracea</em> L. The chemical profile of the four buckwheat accessions was characterised in their shoots, roots, and root exudates in order to know more about their ability to sustainably manage weeds and the relation of this ability with the polyphenol accumulation and exudation from buckwheat plants. Our results show that different buckwheat genotypes may have different capacities to produce and exude several types of specialized metabolites, which lead to a wide range of allelopathic and defence functions in the agroecosystem to sustainably manage the growing weeds in their vicinity. The ability of the different buckwheat accessions to suppress weeds was accession-dependent without differences between species, as the common (Eva, Gema, and Kora) and Tartary (PI481671) accessions did not show any species-dependent pattern in their ability to control the germination and growth of the target weeds. Finally, Gema appeared to be the most promising accession to be evaluated in organic farming due to its capacity to sustainably control target weeds while stimulating the root growth of buckwheat plants.</p>
Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
<p>A better understanding of the relationship between plant specialized metabolism and traditional medicine has the potential to aid in bioprospecting and untangling of cross-cultural use patterns. However, given the limited information available for metabolites in most plant species, understanding medicinal use-metabolite relationships can be difficult. The order Caryophyllales has a unique pattern of lineages of tyrosine- or phenylalanine-dominated specialized metabolism, represented by mutually exclusive anthocyanin and betalain pigments, making Caryophyllales a compelling system to explore the relationship between medicine and metabolites by using pigment as a proxy for tyrosine- vs phenylalanine-dominant metabolism. We compiled a list of medicinal species in select tyrosine- or phenylalanine-dominant families of Caryophyllales (Nepenthaceae, Polygonaceae, Simmondsiaceae, Microteaceae, Caryophyllaceae, Amaranthaceae, Limeaceae, Molluginaceae, Portulacaceae, Cactaceae, and Nyctaginaceae) by searching scientific literature until no new medicinal uses were recovered. We then tested for phylogenetic clustering of uses using a "hot nodes" approach. To test potential non-metabolite drivers of medicinal use, like how often humans encounter a species (apparency), we repeated the analysis using only North American species across the entire order and performed phylogenetic generalized least squares regression (PGLS) with occurrence data from the Global Biodiversity Information Facility (GBIF). We hypothesized families with tyrosine-enriched metabolism would show clustering of different types of medicinal use compared to phenylalanine-enriched metabolism. Instead, wide-ranging, apparent clades in Polygonaceae and Amaranthaceae are overrepresented across nearly all types of medicinal use. Our results suggest that apparency is a better predictor of medicinal use than metabolite profile, although metabolism type may still be a contributing factor.</p>
Fungicides Cuprozin Progress and SWITCH Modulate Primary and Specialized Metabolites of Strawberry Fruits
<p>Numerous pesticides, including fungicides, are applied every year to crop plants. However, such application may affect the plant metabolism and thereby impact crop quality. Strawberry is an economically important crop, but the fruits are highly susceptible, especially to fungal diseases. In the present study, the effects of two fungicides on primary and specialized metabolites determining the fruit aroma were tested in two strawberry cultivars and the wild strawberry. Fruit extracts were analyzed using HPLC (amino acids), GC-MS (organic acids, sugars, flavor metabolites) and photometric quantification (total phenolics). Various metabolites were either significantly higher or lower in fruits of plants exposed to fungicides compared to those of control plants, with differences between strawberry cultivars and species, as well as used fungicides. Given the various changes in metabolites in response to the treatments, the taste and quality of the strawberries may pronouncedly change when plants are treated with fungicides.</p>
Fungicides Cuprozin Progress and SWITCH Modulate Primary and Specialized Metabolites of Strawberry Fruits
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Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
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Data for: Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster
<p>Tremendous plant metabolic diversity arises from phylogenetically-restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acyl sugars were recently discovered in cultivated tomato roots. We demonstrated that acyl sugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acyl sugar pathway genes, and characterized a key paralog required for root acyl sugar biosynthesis, <em>SlASAT1-LIKE</em> (<em>SlASAT1-L</em>), which is nested within a previously-reported trichome acyl sugar BGC. Finally, we provided evidence that <em>ASAT1-L</em> arose through duplication of its paralog, <em>ASAT1</em>, and was trichome-expressed before acquiring root-specific expression in the <em>Solanum</em> genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.</p>
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
<p>Bacterial specialized metabolites are a proven source of antibiotics and cancer therapeutics, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~ 170,000 bacterial genomes and ~ 47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We found that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation of secondary metabolite biosynthetic diversity drops significantly on a genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on Relative Evolutionary Distance revealed that <em>Streptomyces</em> bacteria encode the largest biosynthetic diversity by far, with <em>Amycolatopsis</em>, <em>Kutzneria</em> and <em>Micromonospora</em> also encoding substantial chemical diversity. Finally we find that several less-well-studied taxa such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), <em>Pleurocapsa</em> and Nostocaceae (Cyanobacteria) have potential to produce highly diverse secondary metabolites that warrant further investigation.</p>
Data for: Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster
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Ecophysiology and specialized metabolite trait data for the sunflower association mapping population
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Data from: Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia L.
Coevolutionary theory suggests that an arms race between plants and herbivores yields increased plant specialized metabolite diversity and the geographic mosaic theory of coevolution predicts that coevolutionary interactions vary across geographic scales. Consequently, plant specialized metabolite diversity is expected to be highest in coevolutionary hotspots, geographic regions, which exhibit strong reciprocal selection on the interacting species. Despite being well established theoretical frameworks, technical limitations have precluded rigorous hypothesis testing. Here we aim at understanding how geographic separation over evolutionary time may have impacted chemical differentiation in the cosmopolitan plant genus Euphorbia. We use a combination of state-of-the-art computational mass spectral metabolomics tools together with cell-based high-throughput immunomodulatory testing. Our results show significant differences in specialized metabolite diversity across geographically separated phylogenetic clades. Chemical structural diversity of the highly toxic Euphorbia diterpenoids is significantly reduced in species native to the Americas, compared to Afro-Eurasia. The localization of these compounds to young stems and roots, suggest a possible ecological relevance in herbivory defense. This is further supported by reduced immunomodulatory activity in the American subclade as well as herbivore distribution patterns. We conclude that computational mass spectrometric metabolomics coupled with relevant ecological data provide a strong tool for exploring plant specialized metabolite diversity in a chemo-evolutionary framework.
Code and Data to reproduce figures in -> Relationship of bacterial phylotype with specialized metabolite production in the culturable microbiome of two freshwater sponges
<p>To reproduce the figures/analyses from this work, download the entire Zenodo code/data release (warning- this is a few GB large)</p> <p>Due to a requirement of the mass spectrometry conversion software, data was first converted on a Windows machine to an IDBac database using the script `R/convert_from_bruker.R`. ProteoWizard must be installed before running this script.<br> <br> The resulting SQLite database is available within the Zenodo code/data release</p> <p>To reproduce the figures/analyses you will need to download the Zenodo code/data release and have Docker installed</p> <p>To build the Docker image from scratch open a terminal at `sponge_analysis` and run the following command (warning: this is not fast):<br> </p> <pre><code class="language-bash">docker build -f dockerfile --tag chasemc2/sponge_manuscript .</code></pre> <p>The image has also been archived within the Zenodo code/data release as "docker_image.tar.gz"</p> <p>To build the notebooks/create the figures open a terminal at the top directory of the downloaded Zenodo code/data release and run the following three commands :</p> <p><br> </p> <pre><code class="language-bash"> docker run --user `id -u` --rm -ti -v${PWD}:/top -w/top/analyses chasemc2/sponge_manuscript Rscript -e 'rmarkdown::render("analysis.Rmd", params = list(conditions = "all") , output_file = "all_isolates.html")' docker run --user `id -u` --rm -ti -v${PWD}:/top -w/top/analyses chasemc2/sponge_manuscript Rscript -e 'rmarkdown::render("analysis.Rmd", params = list(conditions = "matched"), output_file = "matched_isolates.html")' docker run --user `id -u` --rm -ti -v${PWD}:/top -w/top/analyses chasemc2/sponge_manuscript Rscript -e 'rmarkdown::render("16s_analysis.Rmd")'</code></pre> <p> </p>
Fig. 11 in Biological activities of organic extracts and specialized metabolites from different parts of Cryptomeria japonica (Cupressaceae) - A critical review
Fig. 11. Lignans (27–33, 35 and 36), norlignans (34, 37 and 38) and anthraquinone (58) from Cryptomeria japonica biomass residues.
Fig. 7 in Biological activities of organic extracts and specialized metabolites from different parts of Cryptomeria japonica (Cupressaceae) - A critical review
Fig. 7. Sesquiterpenes from Cryptomeria japonica biomass residues, including eudesmanes (17 and 48), bisabolanes (18, 47, 49, 50, 56 and 59) and cadinanes (39, 43–46, 52, 57 and 60) types.
Fig. 4 in Biological activities of organic extracts and specialized metabolites from different parts of Cryptomeria japonica (Cupressaceae) - A critical review
Fig. 4. Pimarane (10, 14 and 61) and isopimarane-type diterpenes from Cryptomeria japonica biomass residues.
Fig. 4 in The complexity of sound quantification of specialized metabolite biosynthesis: The stress related impact on the alkaloid content of Catharanthus roseus
Fig. 4. The stress-related increase of the concentration of natural products. In principle, two major effects are responsible for the stress-related increase, i. e., the decrease of the reference value (e.g. dry weight), and an enhancement of biosynthetic activity. The latter one is due either to stress-related up-regulation ("active increase" of enzymatic activity) or a "passive shift" cause by the stress-related overreduction due to stomatal closure. Decreases of factors are displayed in red, the related enhancements in blue. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in The complexity of sound quantification of specialized metabolite biosynthesis: The stress related impact on the alkaloid content of Catharanthus roseus
Fig. 3. Dry weight, alkaloid concentration, and alkaloid content in leaves of Catharanthus roseus plants under salt stress. (a): Dry weight of the entire leaves; (b): Concentration of alkaloids in old leaves; (c): Concentration of alkaloids in young leaves; (d): Total alkaloids content in all aerial plant parts. Differentiation between young and old leaves is mentioned in the Materials and methods section. Different lower-case letters on top of the columns for each period of time (10 and 20 days) indicate significant differences (P ≤ 0.05) as calculated using the least significant difference (LSD) test; n = 8. Every period has 5 bars, and these bars from left to right are control, 100 mM, 200 mM, 300 mM, 400 mM NaCl solution, respectively. The bars display the standard deviation.
Fig. 1 in The complexity of sound quantification of specialized metabolite biosynthesis: The stress related impact on the alkaloid content of Catharanthus roseus
Fig. 1. Evapotranspiration rate of drought-stressed Catharanthus roseus plants. The evapotranspiration rates for mild (20% watering) and severe drought stress (40% watering) were obtained by calculating the amount of water lost. Control plant results were used as a reference to normalize the rate. Arrows indicate the days of sampling.
Fig. 4 in Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers
Fig. 4. Epigenetic alterations include DNA methyl transferase (DNMT) mediated methylation of DNA (A) and Histone acetyl transferase (HAT) mediated acetylation or Histone deaetylase (HDAC) mediated deacetylation of Histones (B). These tags are associated with chromatin modulation required for expression of cryptic genes.
Fig. 3 in Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers
Fig. 3. Small molecular weight compounds with potential to induce specialized metabolites production in fungi.
Fig. 2 in Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers
Fig. 2. Attenuation of Camptothecin and Paclitaxel production on subculture over five generations of endophytic fungi Fusarium solani and Periconia sp. respectively. Notice the 12-fold decrease of camptothecin production with F. solani in going from the first to the fifth generation (Kusari et al., 2009). Similarly,,b) reported a reduction of 2.96-fold in the yield of Paclitaxel produced by Periconia sp. in going from generation one to generation five.
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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)
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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.
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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
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