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904 results for “Biosynthesis”
Biosynthesis of Furfurylamines in Batch and Continuous Flow by Immobilized Amine Transaminases
<p>Building blocks with amine functionality are crucial in the chemical industry. Biocatalytic syntheses and chemicals derived from renewable resources are increasingly desired to achieve sustainable production of these amines. As a result, renewable materials such as furfurals, especially furfurylamines like 5-(hydroxymethyl)furfurylamine (HMFA) and 2,5-di(aminomethyl)furan (DAF), are gaining increasing attention. In this study, we identified four different amine transaminases (ATAs) that catalyze the reductive amination of 5-(hydroxymethyl)furfural (HMF) and 2,5-diformylfuran (DFF). We successfully immobilized these ATAs on glutaraldehyde-functionalized amine beads using multiple binding and on amine beads by site-selective binding of the unique Cα-formylglycine within an aldehyde tag. All immobilized ATAs were efficiently reused in five repetitive cycles of reductive amination of HMF with alanine as co-substrate, while the ATA from <em>Silicibacter pomeroyi</em> (ATA-Spo) also exhibited high stability for reuse when isopropylamine was used as an amine donor. Additionally, immobilized ATA-Spo yielded high conversion in the batch syntheses of HMFA and DAF using alanine (87% and 87%, respectively) or isopropylamine (99% and 98%, respectively) as amine donors. We further demonstrated that ATA-Spo was effective for the reductive amination of HMF with alanine or isopropylamine in continuous-flow catalysis with high conversion up to 12 days (48% and 41%, respectively).</p>
Data from: Biosynthesis of long-chain omega-3 fatty acids in a generalist seabird
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Reprogramming feedback strength in gibberellin biosynthesis highlights conditional regulation by the circadian clock and carbon dioxide
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An alternate route for cellulose microfibril biosynthesis in plants
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Supplementary Materials for "The Effects of Chromosome Doubling on Morphology, Salinity Tolerance, Essential Oil Composition, and Gene Expression of Biosynthesis Pathway in Peppermint (Mentha piperita L.)"
<p>Shandong Province Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; zhaozjfrances@163.com (Z.Z.); yanli_wei@163.com (Y.W.); menshenlai@163.com (K.Y.); sdkinghills@sina.com (B.L.); liling33802400@163.com (L.L.); yanght@sdas.org (H.Y)</p>
Data from: Biosynthesis of the redox coenzyme F420 in Thermomicrobia involves reduction by standalone nitroreductase superfamily enzymes.
<p>Coenzyme F<sub>420</sub> is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F<sub>420</sub>-dependent enzymes are attracting increasing interest as tools in biocatalysis, F<sub>420</sub> biosynthesis is being revisited. While it was commonly accepted for long that the 2-phospho-<span>l</span>-lactate (2-PL) moiety of F<sub>420 </sub>is formed from free 2-PL, it was recently shown that PEP is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase superfamily (NTR), converts dehydro-F<sub>420</sub> into saturated F<sub>420</sub>. Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and <i>in-vitro</i> assays that standalone NTR enzymes from Thermomicrobia exhibit dehydro-F<sub>420</sub> reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in <i>Thermomicrobium roseum</i>. These results clarify the biosynthetic route of coenzyme F<sub>420 </sub>in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F<sub>420 </sub>in <i>E. coli</i> in the future.</p>
Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence
<p><i><span>Neosinocalamus affinis</span></i>, a type of cluster bamboo,<i> </i>is a good candidate feedstock for biomass energy. In the study, we found a total of 686 genes were identified as belonging to CAZyme families in the <i><span>N. affinis</span></i> transcriptome, including 222 glycoside hydrolases (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and five polysaccharide lyases (PLs). Expression profiles revealed that several CAZyme genes were up-regulated after insect infestation, particularly the GT, GH, AA and CE family members. Lignocellulose assays showed that the contents of three components, cellulose, hemicellulose and lignin, increased after insect infestation. Our findings showed that CAZyme genes were abundant in the <i><span>N. affinis</span></i> transcriptome and were involved in the response to herbivory. These findings could be applied to protect bamboo against herbivores, such as the bamboo snout beetle <i><span>Cyrtotrachelus buqueti</span></i>, and develop low-cost chemical feedstock from bamboo.</p>
Tables S1 and S2. Structural Diversity, Biosynthesis, and Function of Plant Falcarin-type Polyactylenic Lipids
<p>Table S1. Compounds and structures used to generate structural similarity network in Figure 2.</p> <p>Table S2. List of functional FAD2s used to generate Figures 4 and 5.</p>
Characterization of a Clematis terniflora DC. coumarin synthase involved in coumarin biosynthesis
<p><em>Clematis terniflora</em> DC. has been used for anti-inflammatory, antihypertensive and other diseases in some Asian countries, and has high medicinal value. Coumarins are the major secondary metabolites produced by<em> C. terniflora</em> leaves under ultraviolet B (UV-B) radiation followed by dark treatment, but the synthesis of coumarin in <em>C. terniflora</em> has not been fully elucidated. Coumarin synthase is a key enzyme to produce coumarin core structure, which is the first step to form coumarins. Based on previous transcriptome data, we identified a BADH acyltransferase CtCOSY highly expressed in leaves after stresses and characterized it functionally. Experiments have proved that CtCOSY could couple with 4-coumarinyl CoA-ligase in vitro to produce umbelliferone. By analyzing the proteomics and metabolomics of control plants and CtCOSY-silenced plants before and after UV-B followed by dark treatment, we found that double stresses disturbed the energy metabolism pathway and phenylpropanoids synthesis pathway. CtCOSY silencing affected plant’s regulation of primary metabolism to a certain extent, and it also affected the accumulation of compounds in shikimic acid pathway and coumarin synthesis. This study provides evidence that CtCOSY is involved in the synthesis of coumarin in <em>C. terniflora.</em></p>
Insights into Heterocycle Biosynthesis in the Cytotoxic Polyketide Alkaloid Janustatin A from a Plant-Associated Bacterium
<p>Data underlying the manuscript 'Insights into Heterocycle Biosynthesis in the Cytotoxic Polyketide Alkaloid Janustatin A from a Plant-Associated Bacterium' by Leopold-Messer, Chawengrum and Piel.</p> <p>The repository contains:</p> <p>Sequencing data - Genbanks files of construct designs and ab1 files from Sanger sequencing. Contains both plasmids used to construct mutants, as well as sequencing data from final mutants.</p> <p>NMR data - MestReNova files of compounds 2-4.</p> <p>HPLC-MS data - Raw data collected on Thermo-Fisher instruments for the purified compounds (1-4) and the extract of all mutants. </p> <p>EICs - extracted ion chromatograms used to analyse the metabolic differences between mutants. These data are based on the raw files.</p> <p>Bioactivity data - cytotoxicity data of compounds 1-4. </p>
Inferred ancestry of scytonemin biosynthesis proteins in cyanobacteria indicates a response to Paleoproterozoic oxygenation
<p>Protection from radiation damage is an important adaptation for phototrophic microbes. In the case of cyanobacteria, surface, shallow water, and peritidal environments are especially exposed to long- wavelength ultraviolet (UVA) radiation. Several groups of cyanobacteria within these environments are protected from UVA damage by the production of the pigment scytonemin. Paleontological evidence of cyanobacteria in UVA-exposed environments from the Proterozoic, and possibly as early as the Archaean, suggests a long evolutionary history of radiation protection within this group. We show that phylogenetic analyses of enzymes in the scytonemin biosynthesis pathway support this hypothesis, and reveal a deep history of vertical inheritance of this pathway within extant cyanobacterial diversity. Referencing this phylogeny to cyanobacterial molecular clocks suggests that scytonemin production likely appeared during the early Proterozoic, soon after the Great Oxygenation Event. This timing is consistent with an adaptive scenario for the evolution of scytonemin production, wherein the threat of UVA-generated reactive oxygen species becomes significantly greater once molecular oxygen was more pervasive across photosynthetic environments.</p>
The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis
<p>Electronic energies, entropies, enthalpies, Gibbs free energies, and lowest frequencies of the QM-calculated structures (<em>QM_Energies.xlsx</em>).</p> <p>Gaussian 16 input and output files, and optimized geometries in MOL2 format, for all QM-calculated structures <em>(QM_calculations.zip</em>).</p> <p>Input coordinates, topology file (in Amber and PDB formats) and output geometries (in PDB format) for the Molecular Dynamics equilibration of the GST-GSH-flav-3-on-4-ol (<strong>7</strong>) ternary complex (<em>MD_equilibration.zip</em>).</p> <p>Optimized geometries for the PtGSTF8-catalyzed deprotonation-protonation reaction: flavan-3-on-4-ol (<strong>7</strong>), transition state for deprotonation (<strong>7-TS</strong>), deprotonation product (<strong>8-enolate</strong>) and cyanidin (<strong>8-B4</strong>) bound to the wildtype enzyme and the C13S variant (<em>QMMM_optimized_structures.zip</em>).</p> <p> </p> <p> </p>
The weaken-fill-repair model for cell budding: Linking cell wall biosynthesis with mechanics
<p>The interplay between cellular mechanics and other biochemical processes leading to the cell cycle is poorly understood. Here, we propose a quantitative model of the mechanism of cell budding, particularly for Saccharomyces cerevisiae, as a ''weaken-fill-repair'' process. This model links Newtonian mechanics over the cell wall with biochemical processes that change the mechanical properties of the wall. Our model shows that: (1) The oscillatory behavior in the size of the mother compartment during cell division, as observed experimentally, is an inevitable consequence of the budding mechanism; (2) The asymmetry of cell division is necessary for the daughter cell to maintain mechanical stiffness; (3) Although different aspects of a cell are strictly constrained and intricately interconnected, the budding process is governed by a single reduced parameter that, when at an appropriate value, can automatically achieve homeostasis. Our quantitative model of the evolution of cell walls and their impact on cell division could provide valuable insights into cell morphology from a system perspective. This knowledge could be instrumental in developing effective antimicrobial treatments against microorganisms with cell walls and even in building synthetic cells.</p>
Comprehensive Re-annotation and Transcriptome Analysis Provide Insights into Pepper Development and Ascorbic Acid Biosynthesis
<p>This archive contains high-quality gene annotation file termed v2a of the pepper reference genome CA59 and gene expression file in pepper development in the pepper "Comprehensive Re-annotation and Transcriptome Analysis Provide Insights into Pepper Development and Ascorbic Acid Biosynthesis"</p>
Ether lipid biosynthesis promotes lifespan extension and enables diverse prolongevity paradigms in Caenorhabditis elegans
<p class="MsoNormal">Biguanides, including the world's most prescribed drug for type 2 diabetes, metformin, not only lower blood sugar but also promote longevity in preclinical models. Epidemiologic studies in humans parallel these findings, indicating favorable effects of metformin on longevity and on reducing the incidence and morbidity associated with aging-related diseases. Despite this promise, the full spectrum of molecular effectors responsible for these health benefits remains elusive. Through unbiased screening in <em>C. elegans</em>, we uncovered a role for genes necessary for ether lipid biosynthesis in the favorable effects of biguanides. We demonstrate that biguanides prompt lifespan extension by stimulating ether lipid biogenesis. Loss of the ether lipid biosynthetic machinery also mitigates lifespan extension attributable to dietary restriction, target of rapamycin (TOR) inhibition, and mitochondrial electron transport chain inhibition. A possible mechanistic explanation for this finding is that ether lipids are required for activation of longevity-promoting, metabolic stress defenses downstream of the conserved transcription factor <em>skn-1/</em>Nrf. In alignment with these findings, overexpression of a single, key, ether lipid biosynthetic enzyme, <em>fard-1</em>/FAR1, is sufficient to promote lifespan extension. These findings illuminate the ether lipid biosynthetic machinery as a novel therapeutic target to promote healthy aging.</p>
Biosynthesis of PGD2 in Vivo
ClinicalTrials.gov study NCT01275300. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Elucidating the origins of phycocyanobilin biosynthesis and phycobiliproteins
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Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence
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Data from: Molecular regulation of oil gland development and biosynthesis of essential oils in Citrus spp.
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Underlying data for characterization of phycocyanobilin (PCB) biosynthesis in Galdieria sulphuraria
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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.