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904 results for “Biosynthesis”
Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis
<p>A GWAS pipeline for identification of the loci associated with >3000 bacterial species (Selected from over 6000 bacterial species of rice Phyllosphere).</p><p> </p>
Process modeling, environmental and economic sustainability of the valorization of whey and eucalyptus residues for resveratrol biosynthesis
<p>Tables included in the article "Process modeling, environmental and economic sustainability of the valorization of whey and eucalyptus residues for resveratrol biosynthesis"</p>
BIONANO-MSCA4U. Biosynthesis of AgNP from Pseudomonas N5.12 and antimicrobial effect
<p>This dataset presents the collected data corresponding to characterization of the biosynthetized AgNP with <em>Pseudomonas</em> N5.12. Listing of all the different data collected, produced, and published are available open-access for the EU-funded <strong>MSCA4Ukraine project (ID:101101923)</strong> combined in different format (in .cvs, .xlsx, .txt and .pdf versions).</p> <p><em>Abbreviation of sample names: S1-S5 – different ratio of bacterial supernatant and 1 mM AgNO3 solution: <code>S1</code> (5:1), <code>S2</code> (4:2), <code>S3</code> (3:3), <code>S4</code> (2:4), <code>S5</code> (1:5). The next letter indicates the pH of the medium (<code>7</code> or <code>9</code>) at which the samples were synthesized.</em></p>
Interactive map of distribution of gene fragments indicative of cyanotoxin biosynthesis and cyanotoxins in the European Alps
<p><span>Distribution of cyanotoxins and cyanotoxin biosynthesis genes in Alpine region determined by LC-MS/MS and (q)PCR. Cyanotoxins and cyanotoxin genes are mapped on separate layers, and two basemaps are available (simple and relief). Results can be filtered by location, sample type, water body type, cyanotoxins and cyanotoxin genes. Note that cyanotoxin analyses were not performed on all sampling points.</span></p>
Datasets used in: "Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis"
<p>Datasets included in: Bokan Bao+, Benjamin P. Kellman+, Austin W. T. Chiang, Austin K. York, Mahmoud A. Mohammad, Morey W. Haymond, Lars Bode, and Nathan E. Lewis. 2019. “<strong>Correcting for Sparsity and Non-Independence in Glycomic Data through a System Biology Framework.</strong>” bioRxiv. <a href="https://doi.org/10.1101/693507">https://doi.org/10.1101/693507</a></p> <p><strong>Central Datasets</strong><br> - Github_Yang2019_EPO<br> - paper_hmo<br> These are the HMO and EPO datasets used throughout the majority of the manuscript. They are formatted consistent with the github code repository: https://github.com/LewisLabUCSD/GlyCompare</p> <p><strong>Additional Datasets</strong><br> - Webapp_Jin2017_Mucin<br> - Webapp_Riley2019_SiteSpecN<br> - Webapp_Sibile2016_Glycolipid<br> These are additional datasets explored in the final figure and supplement of the manuscript formatted for the webapp: https://glycompare.herokuapp.com/</p> <p>All datasets but Riley2019 have structural data, Riley2019 only contains compositional data</p> <p><strong>Detailed Descriptions</strong></p> <ul> <li>Github_Yang2019_EPO <ul> <li>Sixteen MALDI-TOF glycoprofiles of EPO, where each EPO glycoprofile was produced in a different glycoengineered</li> </ul> </li> <li>CHO cell line- paper_hmo <ul> <li>Forty-eight HPLC glycoprofiles of HMO from six mothers22.</li> </ul> </li> <li>Webapp_Jin2017_Mucin <ul> <li>Mucin-type O-glycans from tumor and normal samples from gastrointestinal cancers</li> </ul> </li> <li>Webapp_Riley2019_SiteSpecN <ul> <li>Site-specific N-glycosylation in mouse brain</li> </ul> </li> <li>Webapp_Sibile2016_Glycolipid <ul> <li>Glycolipid abundance in Rat eye, brain and blood<br> </li> </ul> </li> </ul>
Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato seeds and fruits
<p>Steryl esters (SE) are a storage pool of sterols that accumulates in cytoplasmic lipid droplets and helps to maintaining plasma membrane sterol homeostasis throughout plant growth and development. Ester formation of plant SE is catalyzed by phospholipid:sterol acyltransferase (PSAT) and acyl-CoA:sterol acyltransferase (ASAT), which transfer long-chain fatty acid groups to free sterols from phospholipids and acyl-CoA, respectively. Comparative mass spectrometry-based metabolomic analysis between ripe fruits and seeds of a tomato (Solanum lycopersicum cv Micro-Tom) mutant lacking functional PSAT and ASAT enzymes (slasat1xslpsat1) shows that disruption of SE biosynthesis has a differential impact on the metabolome of these organs, including changes in the relative proportions of free and glycosylated sterols. Significant perturbations were observed in the fruit lipidome in contrast to the mild effect detected in the lipidome of seeds. A contrasting response was also observed in phenylpropanoid metabolism, which is down-regulated in fruits and appears to be stimulated in seeds. Comparison of global metabolic changes using volcano plot analysis suggests that disruption of SE biosynthesis favors a general state of metabolic activation that is more evident in seeds than fruits. Interestingly, there is an induction of autophagy in both tissues, which may contribute along with other metabolic changes to the phenotypes of early seed germination and enhanced fruit resistance to Botrytis cinerea displayed by the slasat1xslpsat1 mutant. The results of this study reveal unreported connections between SE metabolism and the metabolic status of plant cells, and lay the basis for further studies aimed at elucidating the mechanisms underlying the observed effects.</p> <p> </p> <p>Data: </p> <p>W1-54; AxP LC polar.zip: raw files LC-polar</p> <p>W1-1 (1)-(54); AxP LC lipid.zip: raw files lipid LC</p> <p>GCtomato.zip: raw files GC polar</p> <p>spreadsheet (.csv) with sample IDs</p>
Gene-guided discovery and ribosomal biosynthesis of anticancer moroidin peptides
<p>Moroidin is a bicyclic plant octapeptide with tryptophan side-chain crosslinks, originally isolated as a pain-causing agent from Australian stinging tree <em>Dendrocnide moroides</em>. Moroidin and its analog celogentin C, derived from <em>Celosia argentea</em>, are inhibitors of tubulin polymerization and, thus, lead structures for cancer therapy. However, low isolation yields from source plants and challenging organic synthesis hinder moroidin-based drug development. Here, we present biosynthesis as an alternative route to moroidin-type bicyclic peptides and report that they are ribosomally synthesized and posttranslationally modified peptides (RiPPs) derived from BURP-domain peptide cyclases in plants.</p> <p>This submission includes the 793 plant transcriptomes from the 1kp databases [1] of Table S2 which were assembled de novo by rnaSPAdes [2,3] and searched for moroidin peptide cyclases.</p> <ol> <li>Yan, Z., Carpenter, E.J., Wickett, N.J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M. and Burleigh, J.G., 2014. Data access for the 1,000 Plants (1KP) project. <em>Gigascience</em>, <em>3</em>(1), pp.2047-217X.</li> <li>Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D. and Pyshkin, A.V., 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. <em>Journal of computational biology</em>, <em>19</em>(5), pp.455-477.</li> <li>Bushmanova, E., Antipov, D., Lapidus, A. and Prjibelski, A.D., 2019. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. <em>GigaScience</em>, <em>8</em>(9), p.giz100.</li> </ol> <p> </p>
Figure 2 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 2 Comparisons and annotations of the official gene set (OGS) of Archegozetes longisetosus.a – Number of gene models of the mites compared to other mites, chelicerates and the fruit fly (Grbić et al., 2011; Cao et al., 2013; dos Santos et al., 2015; Gulia-Nuss et al., 2016; Schwager et al., 2017). b – Non-linear multidimensional scaling plot (NMDS) of clustered orthogroups based on the OGS or predicted proteins
Figure 3 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 3 Orthology comparison and phylogenetic placement of Archegozetes longisetosusamong other chelicerates. a – Maximum likelihood phylogeny based on concatenation of 1,121 orthologs showing the mites phylogenetic position within the Oribatida (all nodes have 100%
Figure 7 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 7 Horizontal gene transfer (HGT) and implications for the feeding biology of Archegozetes longisetosus. a – Blob-plot of the long- read genome assembly contigs plotting the read coverage against GC proportion [%]. Contigs are colored according to the taxonomic order
Figure 6 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 6 The sensory systems of Archegozetes longisetosusand phylogenetic analysis of selected photoreceptor and chemosensory genes. a – Scanning electron micrograph (SEM) showing the end of tarsus on Archegozetes′ first leg. Images shows normal setae, but also modified chemosensory setae, namely eupathidia, both paired (p) and single (s), as well as an omega-3 solenidium. SEM picture courtesy of Michael Heethoff. b – Phylogeny and classification of opsin genes across the Metazoa, including those of several Chelicerata. The tree was constructed using a maximum likelihood approach (LG+F+R4 model) and rooted with a jelly fish opsin. Archegozetes sequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. c – Maximum likelihood phylogeny of ionotropic receptors and ionotropic glutamate receptors (LG+F+R6 model) of Archegozetes (Along), Dinothrombium (Dt), Leptothrombidium (Ld), Tetranychus (Tu) and Drosophila (Dmel). IR25a/IR8a and antenna/1 st leg IRs contain genes with known chemosensory function in Drosophila. The tree was rooted to the middle point; Archegozetes sequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. Bootstrap values can be found in the supplementary Figure S13. d – Maximum likelihood phylogenetic tree of gustatory receptors (JTT+F+R6 model) of Archegozetes(Along), Ixodes (Is), Tropilaelaps (Tm), Metaseiulus (Mocc) and Drosophila (Dmel). The tree was rooted to the middle point; Archegozetessequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. Bootstrap values can be found in the supplementary Figure S14. e – Combined image of volume rendering (grey) and reconstructed nervous system of Archegozetesin dorsal view. Color-code corresponds to different parts of the nervous system, as depicted in the legend. The blue structure in the middle of the synganglion is the part of the esophagus which penetrates the synganglion. Scale bar: 200 µm. Image courtesy of Sebastian Schmelzle based
Figure 1 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 1 The mite, Archegozetes longisetosus, in its phylogenetic and natural environment. a – Species tree of selected oribatid mites of the family Trhypochthoniidae based on phylogenetic analyses and divergence time estimates (Heethoff et al., 2011b). b – Two adults and one tritonymph of Archegozeteson a piece of leaf litter. The algae growing on the leaf serves as a food source for the mites. c – Habitus of an adult mite based on a surface rendering of a µCT-scan reconstruction. Image courtesy of Sebastian Schmelzle. d – Hi-C interaction matrix maps of the nine Archegozeteschromosomes. The corrected contacts are indicated by the color scale on the right from red (high density) to blue (low density)
Figure 8 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 8 Reconstruction of the biosynthetic pathway leading to monoterpenes in Archegozetes longisetosus. a – Representative gas chro- matogram of the mite′ gland content; in order of retention time: 2-hydroxy-6-methyl-benzaldehyde (2,6-HMBD), neral (( Z)-3,7-dimethylocta- 2,6-dienal) neryl formate (( Z)-3,7-dimethyl-2,6-octadienyl formate), tridecane, 3-hydroxybenzene-1,2-dicarbaldehyde (γ-acaridial). Further alkanes/alkenes (pentadec-7-ene, pentadecane, heptadeca-6,9-diene, heptadec-8-ene, heptadecane) are not shown. Monoterpenes are marked
Figure 5 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 5 The genomic organization of the Hox genes and life-stage specific expression patters of developmental genes in Archegozetes longisetosus. a – Schematic of the genomic region enclosing the ArchegozetesHox cluster. The genomic organization of the Hox cluster is collinear,
Figure 4 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 4 Comparison of repeat content estimations and transposable element (TE) landscape of Archegozetes longisetosus. a – Repetitive element categories of Archegozetes based on the results from RepeatModeler and MITETracker. LINE= long interspersed nuclear element, LTR= long terminal repeat. b – Comparison of total repetitive content among Archegozetes, other model chelicerates and the fly. All values are from the respective genome paper of the species, except for the fly. c – Repeat divergence plot showing TE activity through time for the major TE superfamilies of Archegozetes.Transposable elements with a low divergence from the consensus were recently active, while TEs diverging
Figure 3 in Amino acids L-phenylalanine and L-lysine involvement in trans and cis piperamides biosynthesis in two Piper species
Figure 3. The incorporation of the amino acid L-lysine in C –C5 piperidine amide (4,5-dihydropiperine, 2) and two C -C 6 6 3 dihydropyridinone amides (trans-piplartine, 7 and cis-piplartine, 8).
Figure 2 in Amino acids L-phenylalanine and L-lysine involvement in trans and cis piperamides biosynthesis in two Piper species
Figure 2. HPLC analysis of the enzymatic reactions (L-phenylalanine + enzymatic extract of P. tuberculatum leaves). Chromatogram A shows the formation of the cinnamic acid product after incubation of the amino acid L-phenylalanine with the enzymatic extract. Chromatogram B show the the blank for comparison (L-phenylalanine + enzymatic extract of P. tuberculatum leaves, previously treated with 6M hydrochloric acid for enzyme inactivation). Chromatogram C shows the retention time of the phenylpropanoid cinnamic acid (standard). In addition to the amino acidL-phenylalanine, L-tyrosine was also used as a possible precursor to phenylpropanoids, but no conversion to p-coumaric acid was observed.The same results were observed for P. arboreum.
Figure 1 in Amino acids L-phenylalanine and L-lysine involvement in trans and cis piperamides biosynthesis in two Piper species
Figure 1. Piperine (1), 4,5-dihydropiperine (2), fagaramide (4), piperlonguminine (5), 4,5-dihydropiperlonguminine (6), trans-piplartine (7), cis-piplartine (8), and dihydropiplartine (9) are piperamides biosynthesized by P. tuberculatum; 4,5-dihydropiperiline (3) is biosynthesized by P. arboreum.
Pyruvate transamination and NAD biosynthesis enable proliferation of succinate dehydrogenase-deficient cells by supporting aerobic glycolysis
<p>Data supporting results published by Ricci et al. Pyruvate transamination and NAD biosynthesis enable proliferation of succinate dehydrogenase-deficient cells by supporting aerobic glycolysis. Cell Death and Disease (2023) 14:403 (https://doi.org/10.1038/s41419-023-05927-5).</p>
Supplementary Data: Evolution of the cholesterol biosynthesis pathway in animals
<p>Cholesterol plays essential roles in animal development and disease progression. Here, we characterize the evolutionary pattern of the canonical cholesterol biosynthesis pathway (CBP) in the animal kingdom using both genome-wide analyses and functional experiments. CBP genes in the basal metazoans were inherited from their last common eukaryotic ancestor and evolutionarily conserved for cholesterol biosynthesis. The genomes of both the basal metazoans and deuterostomes retain almost the full set of CBP genes, while Cnidaria and many protostomes have independently experienced multiple massive losses of CBP genes that might be due to the geologic events during the Ediacaran period, such as the appearance of an exogenous sterol supply and the frequent perturbation of ocean oxygenation. Meanwhile, the indispensable utilization processes of cholesterol potentially strengthened the maintenance of the complete set of CBP genes in vertebrates. These results strengthen both biotic and abiotic roles in the macroevolution of a biosynthesis pathway in animals.</p>
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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.