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127 results for “plant metabolism”
Data in support of 'Mechanistic insights into plant community responses to environmental variables: genome size, cellular nutrient investments, and metabolic trade-offs.'
Data was collected to examine whether and how the plant genome size (GS) influences traits (stomata size, stomata density, cellular and tissue level carbon (C), nitrogen (N), and phosphorus (P) contents) and metabolic-tradeoffs (of photosynthesis, evapotranspiration, water-use, efficiency) of plants in treatment plots in which nothing, N, P, or NP had been annually added. Data was collected from ~500 plants from seven grassland sites that are all part of the Nutrient Network (https://nutnet.org), a globally distributed experiment in which plots have different nutrient amendment treatments that are administered identically to allow cross-site comparisons of the effects of nutrients on biodiversity patterning. The sites chosen varied along a North-South latitude, longitude, mean annual precipitation (MAP) and mean annual temperature (MAT) gradient.
Data from: What goes in must come out? The metabolic profile of plants and caterpillars, frass, and adults of Asota (Erebidae: Aganainae) feeding on Ficus (Moraceae) in New Guinea
<p>Insect herbivores have evolved a broad spectrum of adaptations in response to the diversity of chemical defences employed by plants. Here we focus on two species of New Guinean Asota and determine how these specialist moths deal with the leaf alkaloids of their fig (Ficus) hosts. As each focal Asota species is restricted to one of three chemically distinct species of Ficus, we also test whether these specialized interactions lead to similar alkaloid profiles in both Asota species. We reared Asota caterpillars on their respective Ficus hosts in natural conditions and analyzed the alkaloid profiles of leaf, frass, caterpillar, and adult moth samples using UHPLC–MS/MS analyses. We identified 43 alkaloids in our samples. Leaf alkaloids showed various fates. Some were excreted in frass or found in caterpillars and adult moths. We also found two apparently novel indole alkaloids likely synthesized de novo by the moths or their microbiota—in both caterpillar and adult tissue but not in leaves or frass. Overall, alkaloids unique or largely restricted to insect tissue were shared across moth species despite feeding on different hosts. This indicates that a limited number of plant compounds have a direct ecological function that is conserved among the studied species. Our results provide evidence for the importance of phytochemistry and metabolic strategies in the formation of plant–insect interactions and food webs in general. Furthermore, we provide a new potential example of insects acquiring chemicals for their benefit in an ecologically relevant insect genus.</p>
Supplementary dataset for "Phenylacetic acid metabolism in land plants: novel pathways and metabolites"
<p>Supplementary dataset with measured data for publication "Phenylacetic acid metabolism in land plants: novel pathways and metabolites"</p>
Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
<p>This dataset supports the article "Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth", which is under minor revision in Journal of Experimental Botany. The study addresses the combined effects of and plant population origin, drought and heat stress on plant growth, plant morphology and the leaf metabolome. The data were assessed in Northern and Southern European individuals of <em>Cakile maritma</em> (See Rocket). An R-script containing all statistical analyses that have been implemented with these data is also provided.</p>
Data from: Leaf metabolic traits reveal hidden dimensions of plant form and function
<p>In this study, we interpreted leaf metabolome variation among 457 tropical and 339 temperate plant species to understand how the metabolome contributes to macroecological variation in plant functioning. Metabolome data were generated using liquid chromatography mass spectrometry, annotated with compound names (where possible), and cross-referenced against chemoinformatics databases to derive metabolite chemical properties. We then compared variation in leaf metabolite chemical properties among species with variation in classical plant functional traits.</p>
Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
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Data from: What goes in must come out? The metabolic profile of plants and caterpillars, frass, and adults of Asota (Erebidae: Aganainae) feeding on Ficus (Moraceae) in New Guinea
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Data from: Leaf metabolic traits reveal hidden dimensions of plant form and function
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Within and cross species predictions of plant specialized metabolism genes using transfer learning
<p>Datasets for <em>Within and cross species predictions of plant specialized metabolism genes using transfer learning.</em> </p> <ol> <li>Dataset 1: All gene features used in the full feature machine learning models including expression, co-expression, evolutionary, duplication, and protein domain features.</li> <li>Dataset 2: All gene features used in shared feature machine learning models including expression, evolutionary, duplication, and protein domain features.</li> <li>Table S1: All gene annotations from TomatoCyc or manual annotation.</li> <li>Table S2: All model scores.</li> <li>Table S3: All gene scores and predictions from each model.</li> <li>Table S4: Feature importance for 5 models.</li> <li>Table S5: Statistical analysis between classes for binary and continuous feature data.</li> <li>Table S6: RNAseq datasets used in analysis.</li> </ol>
Soil inoculation alters leaf metabolic profiles in genetically identical plants
<p> Abiotic and biotic properties of soil can influence growth and chemical composition of plants. Although it is well-known that soil microbial composition can vary greatly spatially, how this variation affects plant chemical composition is poorly understood. We grew genetically identical <em>Jacobaea vulgaris</em> in sterilized soil inoculated with live soil collected from four natural grasslands and in 100% sterilized soil. Within each grassland we sampled eight plots, totalling 32 different inocula. Two samples per plot were collected, leading to three levels of spatial variation: within plot, between and within grasslands. The leaf metabolome was analysed with <sup>1</sup>H Nuclear magnetic resonance spectroscopy (NMR) to investigate if inoculation altered the metabolome of plants and how this varied between and within grasslands. Inoculation led to changes in metabolomics profiles of J. vulgaris in two out of four sites. Plants grown in sterilized and inoculated soils differed in concentrations of malic acid, tyrosine, trehalose and two pyrrolizidine alkaloids (PA). Metabolomes of plants grown in inoculated soils from different sites varied in glucose, malic acid, trehalose, tyrosine and in one PA. The metabolome of plants grown in soils with inocula from the same site was more similar than with inocula from distant sites. We show that soil influences leaf metabolomes. Performance of aboveground insects often depends on chemical composition of plants. Hence our results imply that soil microbial communities, via affecting aboveground plant metabolomes, can impact aboveground plant-insect food chains but that it is difficult to make general predictions due to spatial variation in soil microbiomes.</p> <div> <div> <div class="msocomtxt"> </div> </div> </div>
Fifteen physiological traits related to osmoregulation and reactive oxygen species metabolism in two life form aquatic plants under a natural water salinity gradient on the Tibetan Plateau and Northwest China
<p><span>Aquatic plants, as the primary producers, determine the community structure and ecological function of freshwater ecosystems. However, salinization threatens inland freshwater wetlands and thus the survival of aquatic plants. Exploring the plant physiological responses to increasing water salinity could enhance our understandings of plant adaptive strategies under future climate change regimes in wetlands. We measured 15 physiological traits of 49 aquatic plant species along a large environmental gradient in alpine and arid regions of western China, to explore the physiological adaptions and compare the similarities and differences in adaptive strategies between the two life forms to natural water salinity. We found that both water salinity and low temperature were key factors affecting aquatic plants in alpine and arid regions. Aquatic plants adapt to saline habitats by accumulating proline and sulfur (S) concentrations, and to cold habitats by increasing ascorbate peroxidase activity. Plant trait network analysis showed that the hub trait in emergent plants was S, but in submerged plants was proline, suggesting that emergent plants balanced osmoregulation and reactive oxygen metabolism via S-containing compounds, while submerged plants prioritizing the regulation of osmotic balance via proline.</span></p>
Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants
<p><span>Plant secondary metabolites (SMs) play crucial roles in plant-environment interactions and contribute greatly to human health. Global climate changes are expected to dramatically affect plant secondary metabolism, yet a systematic understanding of such influences is still lacking. Here, we employed medicinal and aromatic plants (MAAPs) as model plant taxa and performed a meta-analysis from 360 publications using 1828 paired observations to assess the responses of different SMs levels and the accompanying plant traits to elevated carbon dioxide (eCO<sub>2</sub>), elevated temperature (eT), elevated nitrogen deposition (eN), and decreased precipitation (dP). The overall results showed that phenolic and terpenoid levels generally respond positively to eCO<sub>2</sub> but negatively to eN, while the total alkaloid concentration was increased remarkably by eN. By contrast, dP promotes the levels of all SMs, while eT exclusively exerts a positive influence on the levels of phenolic compounds. Further analysis highlighted the dependence of SM responses on different moderators such as plant functional types, climate change levels or exposure durations, mean annual temperature and mean annual precipitation. Moreover, plant phenolic and terpenoid responses to climate changes could be attributed to the variations in C/N ratio and total soluble sugar levels, while the <em>trade-off</em> supposition contributed to SM responses to climate changes other than eCO<sub>2</sub>. Taken together, our results predicted the distinctive SM responses to diverse climate changes in MAAPs, and allowed us to define potential moderators responsible for these variations. Further, linking SM responses to C-N metabolism and growth-defence balance provided biological understandings in terms of plant secondary metabolic regulation.</span></p>
Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage
<p>The dataset contains all the original raw files for the following study:</p> <p><strong>Metabolic enzymes moonlight as selective autophagy receptors </strong><strong>to protect plants against viral-induced cellular damage</strong></p> <p>Marion Clavel<sup>1,2,*</sup>, Anita Bianchi<sup>1</sup>, Roksolana Kobylinska<sup>1</sup>, Roan Groh<sup>1,3</sup>, Juncai Ma<sup>4</sup>, Ranjith K. Papareddy<sup>1</sup>, Nenad Grujic<sup>1</sup>, Lorenzo Picchianti<sup>1,3</sup>, Ethan Stewart<sup>5</sup>, Michael Schutzbier<sup>1</sup>, Karel Stejskal<sup>1</sup>, Juan Carlos de la Concepcion<sup>1</sup>, Victor Sanchez de Medina Hernandez<sup>1,3</sup>, Yoav Voichek<sup>1</sup>, Pieter Clauw<sup>1</sup><strong>, </strong>Joanna Gunis<sup>1</sup>, Gerhard Durnberger<sup>1</sup>, Jens Christian Muelders<sup>2</sup>, Annett Grimm<sup>2</sup>, Arthur Sedivy<sup>5</sup>, Mathieu Erhardt<sup>6</sup>, Victoria Vyboishchikov<sup>1</sup>, Peng Gao<sup>1</sup>, Esther Lechner<sup>6</sup>, Emilie Vantard<sup>6</sup>, Jakub Jez<sup>5</sup>, Elisabeth Roitinger<sup>1</sup>, Pascal Genschik<sup>6</sup>, Byung-Ho Kang<sup>4</sup>, Yasin Dagdas<sup>1,*</sup></p> <p><strong> </strong></p> <p><strong>Affiliations</strong></p> <p><sup>1</sup>Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.</p> <p><sup>2</sup>Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany</p> <p><sup>3</sup>Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna, Austria</p> <p><sup>4</sup>School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China</p> <p><sup>5</sup>Vienna Biocenter Core Facilities (VBCF), Vienna, Austria</p> <p><sup>6</sup>Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12, rue du Général Zimmer, 67084 Strasbourg, France</p> <p> </p> <p>*Correspondence: Marion Clavel (marion.clavel@mpimp-golm.mpg.de),</p> <p> Yasin Dagdas (yasin.dagdas@gmi.oeaw.ac.at)</p> <p><strong> </strong></p> <p><strong>Abstract</strong></p> <p>RNA viruses co-opt the host endomembrane system and organelles to build replication complexes for infection. How the host responds to these membrane perturbations is poorly understood. Here, we explore the autophagic response of <em>Arabidopsis thaliana</em> to three viruses that hijack different cellular compartments. Autophagy is significantly induced within systemically infected tissues, its disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense mechanism as previously suggested, quantitative analyses of the viral loads established autophagy as a tolerance pathway. Further analysis of one of these viruses, the Turnip Crinkle Virus (TCV) that hijack mitochondria, showed that despite perturbing mitochondrial integrity, TCV does not trigger a typical mitophagy response. Instead, TCV and Turnip yellow mosaic virus (TYMV) infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death such as EDS1. Altogether, our study reveals an autophagy-regulated metabolic rheostat that gauges cellular integrity during viral infection and degrades cell death executors to avoid catastrophic amplification of immune signaling.</p> <p> </p> <p>One archive corresponds to one main or supplemental figure.</p>
Designing a Synthetic Microbial Community through Genome Metabolic Modeling to enhance Plant-Microbe Interaction
<p>Supplementary data 1 - <strong>Reconstructed genome-scale metabolic networks from MAGs and Hosts</strong></p> <p>Supplementary data 2 - P<strong>lant growth-promoting traits among members of the minimal community</strong></p> <p> </p> <p>Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynCom, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and a careful selection of compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed an <em>in-silico</em> approach using genome metabolic modeling to design a synthetic microbial community aimed at improving the yield of important crop plants. We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, EPS production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our selection process for the SymCom, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. Our study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.</p>
Prandial Metabolic Phenotyping in Sarcopenic Older Adults Comparing Plant Based and Whey Based Protein
ClinicalTrials.gov study NCT06628349. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants
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Fifteen physiological traits related to osmoregulation and reactive oxygen species metabolism in two life form aquatic plants under a natural water salinity gradient on the Tibetan Plateau and Northwest China
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Data from: Enhanced competitive advantage of invasive plants by growth-defense trade-off: Evidence from phytohormone metabolism and transcriptomic analysis
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Soil inoculation alters leaf metabolic profiles in genetically identical plants
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Fig. 1 in Reactive oxygen species in cell wall metabolism and development in plants
Fig. 1. Schematic representation of the enzymes at the plasma membrane and in the cell wall that are able to form reactive oxygen species (ROS: superoxide anion radical · — hydrogen peroxide hydroxyl radical. into the apoplast. · — is dismutated either enzymatically catalyzed by superoxide dismutase, (O 2 ), (H2O2), ( OH)) O 2 to H2O2 or nonenzymatically in the acidic pH that is typical in the cell wall. ROS play important roles both in cell wall loosening during cell elongation and cross-link formation involved in cell growth restriction..OH is considered as a cell wall-loosening agent formed from H O either non-enzymatically by Fenton reaction involving a transition metal such as 2 2 Fe2+ or Cu +, or enzymatically by peroxidases (not depicted). Di- and oligoferulate bridges, bonds between tyrosine residues abundant in cell wall structural proteins, lignin formation, or cross-linkages between ferulates and lignin are possible cross-links involved in cell growth restriction. For the cross-link formation, oxidative enzymes (peroxidase in a peroxidative cycle using H2O2 as an oxidant, or laccase using O2 as an oxidant) catalyze the oxidation of the phenolic residues after which they make a crosslink. In addition to cell wall modifications, ROS are important signalling components in various biological processes. The left cell shows the enzymes producing ROS, and the right cell shows the enzymes consuming ROS during cell wall cross-linking. Note that all enzymes and the cross-link types mentioned may not be present in the same cell, or in all species. In case of quinone reductases, further studies are needed to find out whether enough quinones are present in the plasma membranes to be able to mediate electron transport from the cytoplasmic reductant to apoplastic molecular oxygen.
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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)
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.