LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'High-Throughput Detection of an Alkaloidal Plant Metabolome in Plant Extracts Using LC-ESI-QTOF-MS.'.
Answer: Plant alkaloids represent a diverse group of nitrogen-containing natural products. These compounds are considered valuable in drug discovery and development. High-throughput identification of such plant secondary metabolites in complex plant extracts is essential for drug discovery, lead optimization, and understanding the biological pathway. The present study aims to rapidly identify different classes of alkaloids in plant extracts through the liquid chromatography with electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) approach using 161 isolated and purified alkaloids. These are biologically important unique alkaloids belonging to different sub-classes such as isoquinoline, quinoline, indole, tropane, pyridine, piperidine, quinolizidine, aporphine, steroidal, and terpenoid. The majority of these are not available commercially and are known to manifest valuable biological activities. Four pools of a maximum of 50 phytostandards each were prepared, based on their log P value to minimize co-elution for rapid and cost-effective analyses. MS/MS spectra were acquired in the positive ionization mode by using their [M + H]+ and/or [M + Na]+ with both the average collisional energy (25.5-62 eV) and individual collisional energies (10, 20, 30, and 40 eV). Accurate mass, high-resolution mass spectrometry (HR-MS) data, MS/MS data, and retention times were curated for each compound. The developed LC-MS/MS method was successfully used to interrogate and fast dereplicate alkaloids in 13 medicinal plant extracts and a herbal formulation. A total of 56 alkaloids were identified based on the reference standard retention times (RTs), HR-MS spectra, and/or MS/MS spectra. The MS data have been submitted to the MetaboLights online database (MTBLS2914). The mass spectrometric and chromatographic data will be useful for the discovery of new congeners and the study of biological pathways of alkaloids in the plant kingdom.
Question: Write a study description for the study titled 'An Atlas of Inter-Organ Metabolite Trafficking in Health and Atherogenic Conditions'.
Answer: Mammalian organs continuously exchange circulating metabolites for organismal health and survival. However, the landscape of this fundamental process and its perturbation by diet and disease is unknown. Using arteriovenous metabolomics, tissue transcriptomics, hormone arrays and multiple metabolic disease models in pigs, we generated a blueprint of ~1300 circulating metabolites trafficking across 10 organs during fasting/feeding, Western diet and cardiovascular disease progression induced by low-density lipoprotein receptor (LDLR) deficiency. We discovered numerous feeding-dependent and -independent inter-organ metabolite trafficking events and mechanisms by which these are disrupted by Western diet via altered metabolite concentration gradients and hormone imbalances. Surprisingly, both Western diet and LDLR deficiency trigger release of bile acids by multiple extra-hepatic organs. Such abnormality dramatically elevates circulating bile acids, which induce atherogenic inflammation. These findings and resources in highly relevant pig models reveal intricate inter-organ crosstalk across pathophysiological conditions, offering unparalleled insights into diet effects and disease mechanisms.
Question: Write a study description for the study titled 'Metabolic interactions of “catecholamine-cholesterol derivatives” as a potential mechanism for immunomodulation of chicken adipose tissue'.
Answer: In recent years, the immunomodulatory function of adipose tissue has attracted much attention; however, the mechanism of steady-state regulation of the immune microenvironment in adipose tissue remains unclear. Catecholamines (CAs) activate adipocyte surface β3-AR to promote lipid metabolism, and cholesterol metabolism is bi-directionally immunoregulated. However, it remains unknown whether CAs and cholesterol metabolism interactions are a key pathway in the regulation of adipose tissue immune function. In this study, chickens were used as model animals, and dexamethasone and NDV vaccine were used to induce different immune states in chicks. qRT-PCR and metabolomics techniques were used to investigate the dynamic characteristics of lymphocytes, CAs and cholesterol metabolism in adipose tissues of chicks in different immune states, and to further characterize the miRNA regulatory mechanisms of cholesterol metabolism. The results indicate that B cells are present in chicken adipose tissue and respond positively to different immune states through up-regulation.Adipose tissue responds positively to immunosuppression and immune response through alterations in cholesterol and CAs metabolism, and differences in cholesterol and CAs metabolism are a key pathway by which dexamethasone suppresses the immune response in adipose tissue. Adipose tissue synthesizes bile acids and steroid derivatives, and secondary immunization immunity may be the stage of active changes in cholesterol metabolism derivatives in adipose tissue. A “lymphocyte-catecholamine-adipocyte-cholesterol-cholesterol metabolism derivative-lymphocyte” pathway exists in adipose tissue, and this pathway may be a potential mechanism for the homeostatic regulation of the immune microenvironment in chicken adipose tissue. In addition, adipose tissue miR-206 is actively involved in the process of dexamethasone affecting the immune response, and the miR-206/MSMO1 pathway is a potential mechanism for regulating cholesterol metabolism in adipose tissue. This study may provide new insights into the mechanisms of adipose tissue immunomodulation as well as new directions for the development of cholesterol derivatives for immunomodulation.
Question: Write a study description for the study titled 'Lipid Data Analyzer: Discrimination of isobaric pairs of lipid standards from different lipid subclasses (Control experiment 2)'.
Answer: Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectrometry instruments with several collision energies, the method's platform independence is proved. The software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete.  In lipidomics, overlaps of species from isobars from other subclasses/adducts frequently occur. In this experiment, isobars from PC and PE, and from LPC and LPE are mixed in one sample. The LC-method was made worse, so that these species generated overlapping peaks. In this experiment, the LDA's propensity to detect and seperate such species was tested.  Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398. Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396. LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397. HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462. Linked Studies: MTBLS394 MTBLS396 MTBLS397 MTBLS398 MTBLS462
Question: Write a study description for the study titled 'Metabolite profiling of tubers of an early- and a late-maturing potato line and their grafts'.
Answer: INTRODUCTION: Earliness of tuberisation and the quality of potato tubers are important traits in potato breeding. The qualitative traits rely on the metabolite profile of tubers, which are storage organs and net importers of assimilates. Thus, the quality of tubers largely depends on the metabolites transported from leaves to developing tubers.OBJECTIVES: To test the influence of canopy on the quality of tubers by metabolite profiling of tubers of an early- and a late-maturing potato line and their grafts.METHODS: Potatoes were grown under greenhouse conditions, grafted and the tubers harvested at the end of the scions' vegetation period. Metabolite profiling of freshly harvested tubers was performed using gas chromatography coupled with mass spectrometry. Statistical analyses were applied to determine the significant differences between the different tubers.RESULTS: 99 metabolites were identified and an additional 181 peaks detected in chromatograms, out of which 186 were polar and 94 non-polar compounds. The concentrations of 113 metabolites were significantly different in the tubers from the early-maturing CE3130 and the late-maturing CE3027 line. Hetero-grafting resulted in considerable changes in the metabolite content of tubers. Especially, the effect of CE3027 on the metabolite composition of tubers formed on CE3130 rootstocks was readily apparent. Nevertheless, many compounds were present at similar levels in the tubers of hetero-grafted plants as was found in the tubers of their scion counterparts.CONCLUSION: Hetero-grafting resulted in many compounds at similar concentrations in rootstock tubers as in scion tubers suggesting that these are transported from the source leaves to tubers.
Question: Write a study description for the study titled 'High-level de novo synthesis of medical plant derived flavonoid glycosides'.
Answer: Pichia pastoris is a widely used eukaryotic host for recombinant protein expression in biopharmaceutical and biomanufacturing, offering advantages such as broad carbon source utilization, high cell density, a mature fermentation process, and genomic stability. Recent advances in genetic editing and regulatory tools have also enabled P. pastoris to synthesize various natural products. This study uses P. pastoris as a chassis cell to engineer biosynthetic pathways for specific flavonoid glycosides derived from Trollius chinensis Bunge. Through systematic metabolic engineering, we improved synthesis efficiency and validated production potential at a 3-L bioreactor scale.
Question: Write a study description for the study titled 'Simultaneously discovering the fate and biochemical effects of pharmaceuticals through untargeted metabolomics'.
Answer: Untargeted metabolomics is an established approach in toxicology for characterising endogenous metabolic responses to xenobiotic exposure. Detecting the xenobiotic and its biotransformation products as part of the metabolomics analysis provides an opportunity to simultaneously gain deep insights into its fate and metabolism, and to associate the xenobiotic’s internal relative dose directly with endogenous metabolic responses. This integration of untargeted exposure and response measurements into a single assay has yet to be fully demonstrated. Here we assembled a workflow to discover and analyse xenobiotic-related measurements from routine untargeted UHPLC-MS metabolomics datasets, derived from in vivo (rat plasma and cardiac tissue, and human plasma) and in vitro (human cardiomyocytes) studies that were principally designed to investigate endogenous metabolic responses to drug exposure. Our findings clearly demonstrate how untargeted metabolomics can discover extensive xenobiotic biotransformation maps, temporally-changing relative systemic exposure, and direct associations of endogenous biochemical responses to the internal dose.
Question: Write a study description for the study titled 'Identification of chemotypes in bitter melon by metabolomics: a plant with potential benefit for management of diabetes in traditional Chinese medicine'.
Answer: INTRODUCTION: Bitter melon (Momordica charantia, Cucurbitaceae) is a popular edible medicinal plant, which has been used as a botanical dietary supplement for the treatment of diabetes and obesity in Chinese folk medicine. Previously, our team has proved that cucurbitanes triterpenoid were involved in bitter melon's anti-diabetic effects as well as on increasing energy expenditure. The triterpenoids composition can however be influenced by changes of varieties or habitats.OBJECTIVES: To clarify the significance of bioactive metabolites diversity among different bitter melons and to provide a guideline for selection of bitter melon varieties, an exploratory study was carried out using a UHPLC-HRMS based metabolomic study to identify chemotypes.METHODS: Metabolites of 55 seed samples of bitter melon collected in different parts of China were profiled by UHPLC-HRMS. The profiling data were analysed with multivariate (MVA) statistical methods. Principle component analysis (PCA) and hierarchical cluster analysis (HCA) were applied for sample differentiation. Marker compounds were identified by comparing spectroscopic data with isolated compounds, and additional triterpenes were putatively identified by propagating annotations through a molecular network (MN) generated from UHPLC-HRMS & MS/MS metabolite profiling.RESULTS: PCA and HCA provided a good discrimination between bitter melon samples from various origins in China. This study revealed for the first time the existence of two chemotypes of bitter melon. Marker compounds of those two chemotypes were identified at different MSI levels. The combined results of MN and MVA demonstrated that the two chemotypes mainly differ in their richness in cucurbitane versus oleanane triterpenoid glycosides (CTGs vs. OTGs).CONCLUSION: Our finding revealed a clear chemotype distribution of bioactive components across bitter melon varieties. While bioactivities of individual CTGs and OTGs still need to be investigated in more depth, our results could help in future the selection of bitter melon varieties with optimised metabolites profile for an improved management of diabetes with this popular edible Chinese folk medicine.
Question: Write a study description for the study titled 'PKM2 methylation by CARM1 activates aerobic glycolysis to promote tumorigenesis'.
Answer: Metabolic reprogramming is a hallmark of cancer. Herein we discover that the key glycolytic enzyme pyruvate kinase M2 isoform (PKM2), but not the related isoform PKM1, is methylated by co-activator-associated arginine methyltransferase 1 (CARM1). PKM2 methylation reversibly shifts the balance of metabolism from oxidative phosphorylation to aerobic glycolysis in breast cancer cells. Oxidative phosphorylation depends on mitochondrial calcium concentration, which becomes critical for cancer cell survival when PKM2 methylation is blocked. By interacting with and suppressing the expression of inositol-1,4,5-trisphosphate receptors (InsP3Rs), methylated PKM2 inhibits the influx of calcium from the endoplasmic reticulum to mitochondria. Inhibiting PKM2 methylation with a competitive peptide delivered by nanoparticles perturbs the metabolic energy balance in cancer cells, leading to a decrease in cell proliferation, migration and metastasis. Collectively, the CARM1-PKM2 axis serves as a metabolic reprogramming mechanism in tumorigenesis, and inhibiting PKM2 methylation generates metabolic vulnerability to InsP3R-dependent mitochondrial functions.
Question: Write a study description for the study titled 'The Toxoplasma micropore mediates endocytosis for selective nutrient salvage from host cell compartments'.
Answer: Apicomplexan parasite growth and replication relies on nutrient acquisition from host cells, in which intracellular multiplication occurs, yet the mechanisms that underlie the nutrient salvage remain elusive. Numerous ultrastructural studies have documented a plasma membrane invagination with a dense neck, termed the micropore, on the surface of intracellular parasites. However, the function of this structure remains unknown. Here we validate the micropore as an essential organelle for endocytosis of nutrients from the host cell cytosol and Golgi in the model apicomplexan Toxoplasma gondii. Detailed analyses demonstrated that Kelch13 is localized at the dense neck of the organelle and functions as a protein hub at the micropore for endocytic uptake. Intriguingly, maximal activity of the micropore requires the ceramide de novo synthesis pathway in the parasite. Thus, this study provides insights into the machinery underlying acquisition of host cell-derived nutrients by apicomplexan parasites that are otherwise sequestered from host cell compartments.
Question: Write a study description for the study titled 'Evidence for quorum sensing and differential metabolite production by Ruegeria pomeroyi in response to DMSP'.
Answer: Microbial alteration and remineralization of organic matter in the ocean play essential roles in the carbon cycle. The impact of individual compounds as either growth substrates or infochemicals is still poorly constrained in models, particularly for organisms with relatively versatile genomes. Here, we use metabolomics techniques to characterize the response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on the abundant algal metabolite dimethylsulfoniopropionate (DMSP). DMSP is a valuable source of reduced carbon and sulfur as well as a chemo-attractant. It is present at higher concentrations during phytoplankton blooms. When cultivated on DMSP, R. pomeroyi synthesized a quorum sensing molecule, N-(3-oxotetradecanoyl)-L-homoserine lactone, which was not synthesized at the same levels during growth on propionate, another carbon substrate. More broadly, we observed differential production of intra- and extracellular metabolites with implications for nitrogen assimilation and microbial cross-feeding. This multi-faceted response suggests that R. pomeroyi uses a two-component regulatory system dependent on the presence of DMSP and high cell densities to activate a suite of metabolic changes that may shape how it accesses nutrients and impacts the surrounding microbial consortium.
Question: Write a study description for the study titled 'Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage'.
Answer: Maintaining the health of seafarers is a difficult task during long-term voyages. Little is known about the corresponding changes in the gut microbiome-host interaction. This study recruited 30 seafarers undertaking a 6-month voyage and analyzed their gut microbiota using 16S rRNA gene sequencing. Fecal untargeted metabolomics analysis was performed using liquid chromatography-mass spectrometry. Significant changes in the composition of the gut microbiota and an increased ratio of Firmicutes/Bacteroidetes at the end (day 180) of the 6-month voyage, relative to the start (day 0), were observed. At the genus level, the abundances of Holdemanella and Plesiomonas were significantly increased, while the abundance of Bacteroides was decreased. Predicted microbial functional analysis revealed significant decreases in folate biosynthesis and biotin metabolism. Furthermore, 20 differential metabolites within six differentially enriched human metabolic pathways (including arginine biosynthesis, lysine degradation, phenylalanine metabolism, sphingolipid metabolism, pentose and glucuronate interconversions, and glycine, serine, and threonine metabolism) were identified by comparing the fecal metabolites at day 0 and day 180. Spearman correlation analysis revealed close relationships between the 14 differential microbiota members and the six differential fecal metabolites that might affect specific human metabolic pathways. This study adopted a multi-omics approach and provides potential targets for maintaining the health of seafarers during long-term voyages. These findings are worthy of more in-depth exploration in future studies.IMPORTANCE: Maintaining the health of seafarers undertaking long-term voyages is a difficult task. Apart from the alterations in the gut microbiome and fecal metabolites after a long-term voyage, our study also revealed that 20 differential metabolites within six differentially enriched human metabolic pathways are worthy of attention. Moreover, we found close relationships between the 14 differential microbiota members and the six differential fecal metabolites that might impact specific human metabolic pathways. Accordingly, preventative measures, such as adjusting the gut microbiota by decreasing potential pathobionts or increasing potential probiotics as well as offsetting the decrease in B vitamins and beneficial metabolites (e.g., d-glucuronic acid and citrulline) via dietary adjustment or nutritional supplements, might improve the health of seafarers during long-term sea voyages. These findings provide valuable clues about gut microbiome-host interactions and propose potential targets for maintaining the health of seafarers engaged in long-term sea voyages.
Question: Write a study description for the study titled 'Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative (Klebsiella pneumoniae assays)'.
Answer: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission is specifically for Klebsiella pneumoniae complex.GC-MS and LC-MS Klebsiella pneumoniae assays are reported in the current study MTBLS2322GC-MS and LC-MS Escherichia coli assays are reported in MTBLS2015GC-MS and LC-MS Staphylococcus aureus assays are reported in MTBLS1898GC-MS and LC-MS Streptococcus pneumoniae assays are reported in MTBLS2323GC-MS and LC-MS Streptococcus pyogenes assays are reported in MTBLS2324
Question: Write a study description for the study titled 'DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics'.
Answer: The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges of data-independent acquisition results and their filtering. Another factor is that the creation of assay libraries for data-independent acquisition analysis and the processing of extracted ion chromatograms have not been automated in metabolomics. Here we present a fully automated open-source workflow for high-throughput metabolomics that combines data-dependent and data-independent acquisition for library generation, analysis, and statistical validation, with rigorous control of the false-discovery rate while matching manual analysis regarding quantification accuracy. Using an experimentally specific data-dependent acquisition library based on reference substances allows for accurate identification of compounds and markers from data-independent acquisition data in low concentrations, facilitating biomarker quantification.