17 Pools containing 508 characterized Natural Products from different sources_Negative mode
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Environmental Samples <bacillariophyta> (ncbitaxon:33858)
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000092050 | MassIVE | Tue May 30 02:08:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:Analzyed by Giovanni Andrea Vitale and Christian Geibel from Petras Lab.
mode= positive
stepped CE (25, 35, 45)
Res MS1= 30K, MS2=15k
Fragment= Top 5 ions
2023-05-30 | MSV000092049 | MassIVE
Project description:Data dependent analysis of bacterial extract, microflow (0.15 ml/min), mode= positive, stepped CE (25, 35, 45), Res MS1= 45K, MS2=15k, Fragmentation= Top 5 ions
2023-07-07 | MSV000092368 | MassIVE
Project description:Data dependent analysis of bacterial extract, microflow (0.15 ml/min), mode= positive, stepped CE (25, 35, 45), Res MS1= 45K, MS2=15k, Fragmentation= Top 5 ions
2023-07-07 | MSV000092368 | GNPS
Project description:Hydroxyapatite (HA) has significant clinical promise for the repair of bone defects and the modification of implant material interfaces. However, after implantation, there are potential risks of chronic inflammation. Dendritic cells (DCs) are key cells in regulating chronic inflammatory responses, and their phenotype and functions are influenced by the surface structure of materials. Therefore, in order to provide some theoretical guidance for the optimal design of HA surface structures, this study tried to construct stepped structures on HA surfaces and investigate the effects of stepped structures on the cytoskeletal, cellular morphology, and mRNA expression profile of immature dendritic cells (imDCs). HA dishes with stepped structures were prepared utilizing the principle of oriented attachment growth, and subsequently used to construct in vitro cell culture models. The imDCs were observed by immunofluorescence staining to characterize their cytoskeleton structures and cellular morphology. Besides, transcriptome sequencing was used to examine the changes in the mRNA expression profile of imDCs. The results indicated that the stepped structures exposed on HA surfaces would increase the spread area of imDCs and affect the cell adhesion morphology. In addition, the results of the transcriptome sequencing revealed significant alterations in the mRNA expression profile, with differentially expressed genes (DEGs) predominantly enriched in the pathways associated with the focal adhesion signal pathway, the chemokine signal pathway, and the IL-17 signal pathway. Thus, the stepped structures could modulatethe cellular morphology and the immunological functions of imDCs by modulating the aforementioned signal pathways, including the focal adhesion pathway, the chemokine signaling pathway, and the IL-17 signaling pathway, thereby affecting the immune response process.
2024-06-14 | GSE269464 | GEO
Project description:Alkyne-containing natural products are important molecules that are widely distributed in microbes and plants. Inspired by the advantages of acetylenic products used in the fields of medicinal chemistry, organic synthesis and material science, great efforts have focused on discovering the biosynthetic enzymes and pathways for alkyne formation. Here, we summarize the biosyntheses of alkyne-containing natural products and introduce de novo biosynthetic strategies for alkyne-tagged compound production.
| S-EPMC8341276 | biostudies-literature
Project description:Oxidation of three coals with rank from lignite to anthracite in NaOCl aqueous solution was investigated in this study. The oxidation products were characterized by using gas chromatography/mass spectrometry and direct analysis in real-time mass spectrometry. The results showed that most of organic compounds in coals were converted into water-soluble species under mild conditions, even the anthracite. Benzene polycarboxylic acids (BPCAs) and chloro-substituted alkanoic acids (CSAAs) were major products from the reactions. The products from lower rank coals consist of considerable CSAAs and most products from high rank coals are BPCAs. As coal rank increases, the yield of BPCAs with more carboxylic groups increases.
| S-EPMC5925153 | biostudies-literature
Project description:Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
| S-EPMC6429109 | biostudies-literature
Project description:Thiocarboxylic acid-containing natural products are rare and their biosynthesis and biological significance remain unknown. Thioplatensimycin (thioPTM) and thioplatencin (thioPTN), thiocarboxylic acid congeners of the antibacterial natural products platensimycin (PTM) and platencin (PTN), were recently discovered. Here we report the biosynthetic origin of the thiocarboxylic acid moiety in thioPTM and thioPTN. We identify a thioacid cassette encoding two proteins, PtmA3 and PtmU4, responsible for carboxylate activation by coenzyme A and sulfur transfer, respectively. ThioPTM and thioPTN bind tightly to β-ketoacyl-ACP synthase II (FabF) and retain strong antibacterial activities. Density functional theory calculations of binding and solvation free energies suggest thioPTM and thioPTN bind to FabF more favorably than PTM and PTN. Additionally, thioacid cassettes are prevalent in the genomes of bacteria, implicating that thiocarboxylic acid-containing natural products are underappreciated. These results suggest that thiocarboxylic acid, as an alternative pharmacophore, and thiocarboxylic acid-containing natural products may be considered for future drug discovery.
| S-EPMC6006322 | biostudies-literature
Project description:Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
| S-EPMC6146020 | biostudies-literature
Project description:This study was performed to investigate assess the impacts of CO and/or CM containing diets on Atlantic salmon hepatic gene expression in order to identify candidate molecular biomarkers of responses to camelina-containing diets. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial (Control diet: FO; Test diet: 100% FO replacement with CO, with solvent-extracted FM and inclusion of 10% CM (100COSEFM10CM). A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to FO controls at week 16.
2015-05-12 | GSE56784 | GEO