LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Amomum longiligulare polysaccharide 1 supplementation promotes the proliferation of jejunal epithelial cells in piglets by regulating the cell cycle and intestinal metabolites'.
Answer: Although nonstarch polysaccharides often have growth-promoting effects in animals, little is known about how polysaccharides act when administered as feed additives. Here, we demonstrate that Amomum longiligulare polysaccharide 1 (ALP1) improves the growth performance of piglets by promoting the proliferation of jejunal epithelial cells. ALP1 can be absorbed by jejunal epithelial cells via endocytosis and increases the ratio of cells in the S and G2/M phases by increasing the expression of CDK4 and Cyclin E, which increases the number of proliferating cells. The gut microbiota is an important regulatory target of polysaccharides. ALP1 supplementation can increase the abundance of Lactobacillus in the jejuna of piglets, resulting in a high abundance of 11Z-eicosenoic acid (EA). In addition, EA increases the villus length in the jejunum by promoting cell proliferation. Our findings indicate that oral ALP1 supplementation promotes growth by direct (acting on jejunal epithelial cells) and indirect (acting on jejunal microbiota) mechanisms.
Question: Write a study description for the study titled 'Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach'.
Answer: Deciphering the metabolome is essential for a better understanding of the cellular metabolism as a system. Typical metabolomics data show a few but significant correlations among metabolite levels when data sampling is repeated across individuals grown under strictly controlled conditions. Although several studies have assessed topologies in metabolomic correlation networks, it remains unclear whether highly connected metabolites in these networks have specific functions in known tissue- and/or genotype-dependent biochemical pathways. In our study of metabolite profiles we subjected root tissues to gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) and used published information on the aerial parts of 3 Arabidopsis genotypes, Col-0 wild-type, methionine over-accumulation 1 (mto1), and transparent testa4 (tt4) to compare systematically the metabolomic correlations in samples of roots and aerial parts. We then applied graph clustering to the constructed correlation networks to extract densely connected metabolites and evaluated the clusters by biochemical-pathway enrichment analysis. We found that the number of significant correlations varied by tissue and genotype and that the obtained clusters were significantly enriched for metabolites included in biochemical pathways. We demonstrate that the graph-clustering approach identifies tissue- and/or genotype-dependent metabolomic clusters related to the biochemical pathway. Metabolomic correlations complement information about changes in mean metabolite levels and may help to elucidate the organization of metabolically functional modules.
Question: Write a study description for the study titled 'Bioaccumulation of therapeutic drugs by human gut bacteria (B.animalis assays)'.
Answer: Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. Interactions at this level have only recently started to being systematically mapped and the main underlying mechanism proposed is chemical transformation of drugs by microbes (biotransformation). Here, we investigated the depletion of structurally diverse drugs by 25 representative gut bacterial strains. This revealed 70 bacteria-drug interactions, 29 of which had not been reported before. Over half of the new interactions can be ascribed to bioaccumulation, that is bacteria storing the drug intracellularly without chemically modifying it, and in most cases without their growth being affected. As a case in point, we studied the molecular basis of bioaccumulation of the widely used antidepressant duloxetine by using click-chemistry, thermal proteome profiling and metabolomics. We find that duloxetine binds to several metabolic enzymes and changes metabolite secretion of the respective bacteria. When tested in a defined microbial community of accumulators and non-accumulators, duloxetine markedly altered the community composition through metabolic cross-feeding. We further validated our findings in an animal model, showing that bioaccumulating bacteria attenuate the behavioral response of Caenorhabditis elegans to duloxetine. Taken together, bioaccumulation by gut bacteria may be a common mechanism that alters drug availability and bacterial metabolism, with implications for microbiota composition, pharmacokinetics, side effects and drug responses, likely in an individual manner.Linked studies;UPLC-MS/MS assay of Lacrimispora saccharolytica and Escherichia coli IAI1 is reported in MTBLS1319.UPLC-MS/MS assays of Escherichia coli ED1a, Clostridium saccharolyticum, Escherichia coli IAI1, Streptococcus salivarius, Eubacterium rectale, Lactobacillus plantarum WCFS1 and Lactococcus lactis subsp. lactis Il1403 are reported in MTBLS1627.UPLC-MS/MS assay of Bacteroides uniformis and Clostridium saccharolyticum is reported in MTBLS1757.UPLC-MS/MS assay of Clostridium saccharolyticum, Escherichia coli ED1a, Escherichia coli IAI1, Lactobacillus plantarum WCFS1, Lactococcus lactis subsp. lactis Il1403 and Streptococcus salivarius is reported in MTBLS1791.UPLC-MS/MS assay of Eubacterium rectale and Streptococcus salivarius is reported in MTBLS1792.UPLC-MS/MS assay of Lacrimispora saccharolytica and standards is reported in MTBLS2885.
Question: Write a study description for the study titled 'Combined analysis of cecal microbiota and metabolomics reveals the intervention mechanism of Dayuan Yin in acute lung injury'.
Answer: The ancient Chinese medicinal formula, Dayuan Yin (DYY), has a long history of use in treating respiratory ailments and shown to be effective in treating acute infectious diseases. This study aims to explore how DYY may impact intestinal flora and metabolites induced by acute lung injury (ALI). ALI rats were induced with lipopolysaccharide (LPS) to serve as models for assessing the anti-ALI efficacy of DYY through multiple lung injury indices. Changes in intestinal microflora were assessed via 16SrRNA gene sequencing, while cecum contents were analyzed using non-targeted metabonomics. Differential metabolites were identified through data analysis, and correlations between metabolites, microbiota and in flammatory markers were examined using Pearson correlation analysis. DYY demonstrated a significant improvement in LPS-induced lung injury and altered the composition of intestinal microorganisms, especially reduced the potential harmful bacteria and enriched the beneficial bacteria. At the gate level, DYY exhibited a significant impact on the abundance of Bacteroidota and Firmicutes in ALI rats, as well as on the regulation of genera such as Ruminococcus, Lactobacillus and Romboutsia. Additionally, cecal metabonomics analysis revealed that DYY effectively modulated the abnormal expression of 12 key metabolic biomarkers in ALI rats, thereby promoting intestinal homeostasis through pathways such as Purine metabolism. Furthermore, Pearson analysis indicated a strong correlation between the dysregulation of intestinal microbiota, differential metabolites and inflammation. These findings preliminarily confirm that ALI is closely related to the disorder of cecal microbial and metabolic, and DYY can play a protective role by regulating this imbalance, which provides a new understanding of the multi-system linkage mechanism of DYY improving ALI.
Question: Write a study description for the study titled 'Circulatory metabolomics reveals the association of the metabolites with clinical features in the patients with intrahepatic cholestasis of pregnancy'.
Answer: OBJECTIVE: Intrahepatic cholestasis of pregnancy (ICP) is associated with an increased risk of adverse pregnancy outcomes to the mother and fetus. As yet, the metabolic profiles and the association of the clinical features remain obscure.METHODS: Fifty seven healthy pregnant women and 52 patients with ICP were recruited in this study. Plasma samples were obtained from pregnancies who received prenatal care between the 30-36 weeks. Untargeted metabolomics to portray metabolic profiles were performed by LC/MS. Mul- combined with univariate data analysis and statistical analysis were performed to select differential metabolites between ICP and control group. Debiased sparse partial correlation (DSPC) network analysis of differential metabolites was performed to explore the potential mutual regulation among metabolites on the basis of de-sparsified graphical lasso modeling procedure. Pathway analysis was performed using MetaboAnalyst. Linear regression and Pearson correlation analysis were applied to analyze correlations associated with bile acid levels, metabolites, newborn weight and pregnancy outcome in ICP patients.RESULTS: Conspicuous metabolic changes and choreographed metabolic profiles were disclosed: 125 annotated metabolites and eighteen metabolic pathways were disturbed in ICP patients. DSPC networks indicated dense interactions among amino acids and their derivatives, bile acids, carbohydrates and organic acids. The levels of total bile acid were increased in ICP patients with meconium-stained amniotic fluid compared with those without MSAF. Abnormal tryptophan metabolism, elevated long chain saturated fatty acid and estrone sulfate levels, and low antioxidant capacity were relevant to increasing bile acid levels. Correlation analysis showed that newborn body weights were significant correlated with the levels of several bile acids and some metabolites of amino acids.CONCLUSION: The ICP patient showed metabolic disorder, and the levels of a number of metabolites were correlated with TBA levels and neonatal body weights. These results provide us important information to further understand the metabolic characteristics of patients with ICP and adverse pregnancy outcomes.
Question: Write a study description for the study titled 'Isotope Labeled Reactivity-Based Metabolomics Reveal Cysteine as a Potent In Vivo Scavenger of Lactoylglutathione'.
Answer: Metabolite adducts are increasingly being recognized as important intermediates in cellular metabolism and as circulating messengers. Methylglyoxal (MG) is a highly reactive metabolite involved in diabetes and aging, via formation of a wide variety of protein adducts. Though new types of protein adducts with biological function continuously appear, little is known regarding the potentially more diverse MG-metabolite adductome. To address this, we here devise a “symmetric” isotopic labeling and reactivity-based metabolomics approach. We find more than 100 direct MG- as well as lactoylglutathione (LGSH)-derived adducts and among them characterize 10 as D- and L-lactoylated amino acids. We find cysteine to generate mainly L-Lac-Cys from MG, whereas the diasteromer , D-lactoyl-cysteine, mainly originate via a rapid reaction with LGSH with rates on par with click-reactions. The reaction salvages glutathione and also scavenges/regulate prote in cysteine lactoylation, in aggregate assigning cysteine with both glyoxalase 1 and 2 like function.  Several of the adducts are circulating human metabolites, as well as D-Lac-Cys, L-Lac-Cys and D-Lac-Phe are increased in the urine of diabetic mice and may serve as a novel type of biomarker for metabolic diseases.
Question: Write a study description for the study titled 'Host-parasite co-metabolic activation of antitrypanosomal aminomethyl-benzoxaboroles'.
Answer: Recent development of benzoxaborole-based chemistry gave rise to a collection of compounds with great potential in targeting diverse infectious diseases, including human African Trypanosomiasis (HAT), a devastating neglected tropical disease. However, further medicinal development is largely restricted by a lack of insight into mechanism of action (MoA) in pathogenic kinetoplastids. We adopted a multidisciplinary approach, combining a high-throughput forward genetic screen with functional group focused chemical biological, structural biology and biochemical analyses, to tackle the complex MoAs of benzoxaboroles in Trypanosoma brucei. We describe an oxidative enzymatic pathway composed of host semicarbazide-sensitive amine oxidase and a trypanosomal aldehyde dehydrogenase TbALDH3. Two sequential reactions through this pathway serve as the key underlying mechanism for activating a series of 4-aminomethylphenoxy-benzoxaboroles as potent trypanocides; the methylamine parental compounds as pro-drugs are transformed first into intermediate aldehyde metabolites, and further into the carboxylate metabolites as effective forms. Moreover, comparative biochemical and crystallographic analyses elucidated the catalytic specificity of TbALDH3 towards the benzaldehyde benzoxaborole metabolites as xenogeneic substrates. Overall, this work proposes a novel drug activation mechanism dependent on both host and parasite metabolism of primary amine containing molecules, which contributes a new perspective to our understanding of the benzoxaborole MoA, and could be further exploited to improve the therapeutic index of antimicrobial compounds.
Question: Write a study description for the study titled 'Sterol-O acyltransferase inhibition ameliorates high-fat diet-induced renal fibrosis and tertiary lymphoid tissue maturation after ischemic reperfusion injury (Mice+injury analysis)'.
Answer: Metabolic syndrome is a growing global health problem and is strongly associated with the development of chronic kidney disease (CKD). Recently, the prevalence of CKD has been increasing worldwide, particularly among the older adults. We previously demonstrated that aged kidneys are prone to developing tertiary lymphoid tissues (TLTs) and sustain chronic inflammation after injury; however, the relationship between renal TLT formation and metabolic syndrome is unknown. In the present study, we demonstrated that high-fat diet (HFD) feeding partly promoted TLT formation and chronic inflammation in the kidneys via sterol-O acyltransferase (SOAT) 1-dependent lipid deposition. Wild-type mice fed a HFD prior to ischemic reperfusion injury (IRI) exhibited pronounced TLT formation with respect to size, number and maturity in the kidneys, and sustained chronic inflammation compared to the controls. Untargeted lipidomics revealed that the levels of a selective group of lipids, including cholesteryl esters (CEs), were significantly increased in aged kidneys associated with TLT formation after renal IRI. Consistently, the gene expression level of Soat1 was significantly increased in aged kidneys associated with TLT formation after renal IRI. Notably, treatment with avasimibe, a SOAT inhibitor, significantly attenuated TLT maturation and improved renal inflammation and fibrosis in HFD-fed mice subjected to IRI. Together, our findings suggest the importance of dysregulated lipid metabolism, particularly SOAT1-dependent CE accumulation, in the pathophysiology of CKDs associated with TLT formation.Mice+injury analysis (dataset 1) is reported in the current study MTBLS4988.Mice+diet analysis (dataset 2) is reported in MTBLS4994.
Question: Write a study description for the study titled 'Metabolomics analysis of human acute graft-versus-host disease reveals changes in host and microbiota-derived metabolites (Cohort 1)'.
Answer: Despite improvement in clinical management, allogeneic hematopoietic stem cell transplantation (HSCT) is still hampered by high morbidity and mortality rates, mainly due to Graft versus host disease (GvHD). Recently, it has been demonstrated that the allogeneic immune response might be influenced by external factors such as tissues microenvironment or host microbiota.Here we used high throughput metabolomics (UPLC-MS/MS) in two cohorts of genotypically HLA-identical related recipient and donor pairs. A first monocentric cohort from Saint Louis hospital (Paris, France) was used as an exploratory cohort (n=43) and a second multicentric national cohort from Cryostem biobank was used as a confimatory cohort (n=56).Metabolomic profile markedly differed between recipients and donors. At the onset of acute GvHD, in addition to host-derived metabolites, we identified significant variation in microbiota-derived metabolites, especially in Aryl hydrocarbon Receptor (AhR) ligands, bile acids and plasmalogens. Altogether, our findings support that the allogeneic immune response during acute GvHD might be influenced by bile acids and by the decreased production of AhR ligands by microbiota that could limit indoleamine 2,3-dioxygenase (IDO) induction and influence allogeneic T-cell reactivity.MTBLS204 contains study information relating to cohort 1.MTBLS205 contains study information relating to cohort 2.
Question: Write a study description for the study titled 'A metabolic dependency of EBV can be targeted to hinder B cell transformation'.
Answer: Following infection of B cells, Epstein Barr virus (EBV) engages host pathways that mediate cell proliferation and transformation, contributing to the propensity of the virus to drive immune dysregulation and lymphomagenesis. We found that the EBV protein EBNA2 initiates NAD de novo biosynthesis by driving expression of the host metabolic enzyme IDO1. Virus-enforced NAD production sustained mitochondrial complex I activity, to match ATP-production with bioenergetic requirements of proliferation and transformation. In transplant patients, IDO1 expression in EBV-infected B cells, and a serum signature of increased IDO1 activity, preceded development of lymphoma. In humanized mice infected with EBV, IDO1 inhibition reduced both viremia and lymphomagenesis. Virus-orchestrated NAD biosynthesis is thus a druggable metabolic vulnerability of EBV-driven B cell transformation – opening therapeutic possibilities for EBV-related diseases.
Question: Write a study description for the study titled 'MTCH2 modulates CPT1 activity to regulate lipid metabolism of adipocytes'.
Answer: To understand the molecular changes that underwrite enhanced mitochondrial respiration upon MTCH2 knockdown, we performed lipidomics profiling in hMADs adipocytes.
Question: Write a study description for the study titled 'The Role of Annexin A1 in Candida albicans and Candida auris infections in murine neutrophils'.
Answer: Annexin A1 (AnxA1) is an anti-inflammatory protein present in different cells in biological systems, especially expressed in macrophages and neutrophils. Since neutrophils play an important role in infections and inflammatory processes and the AnxA1 and its relation in Candida spp. infections is not well understood, our study highlights a perspective in AnxA1 as a target protein in control the immune response during fungi infection. C57BL/6 wild-type (WT) and AnxA1 knockout (AnxA1-/-) peritoneal neutrophils were coinfected with Candida albicans or Candida auris for 4 hours. High levels of COX-2 were observed in WT and AnxA1-/- neutrophils infected with C. albicans and C. auris coinfection. In addition, AnxA1-/- neutrophils exhibited a marked increase of phosphorylated ERK, p-38 and JNK levels after coinfection with both Candida spp. Lipidomics approach shows that lack of AnxA1 produced a marked difference in lipid profile of control or coinfected neutrophil supernatants compared to WT, especially glycerophospholipids and glycerolipids. In summary, our results showed that endogenous AnxA1 regulates neutrophil response under fungal infection and its lipid membrane organization and metabolism.
Question: Write a study description for the study titled 'Metabolomics reveals plasma profiles of Mycoplasma synovise infection with different virulence'.
Answer: Mycoplasma synovise (MS) is a prominent pathogen of poultry, causing considerable economic pressure to the poultry industry. Although we have a basic understanding of MS infection, the research on the pathogenicity and interactions between host and MS especially the metabolic bases of MS infection are still unclear. In this study, untargeted metabolomics analyses were conducted on plasma of SPF chickens infected with different virulence MS strains ZX313 and SD2. A total of 801 and 834 significant different metabolites (SDMs) were observed in ZX313 and SD2 infected samples respectively, among which 195 and 228 metabolites were group specific. Metabolic pathway enrichment analysis showed that MS infection disrupted amino acid metabolism, nucleotide metabolism and lipid metabolism of host. Moreover, tryptophan metabolites and fatty acid metabolites, differentially expressed in different virulence group, may related to the severity of the disease and the pathogenicity of MS. These findings may offer new insights into pathogenesis of MS and host-MS interaction.
Question: Write a study description for the study titled 'Apoptosis-inducing effects of aqueous extract of Eleutherococcus senticosus on non-small cell lung cancer cell proliferation'.
Answer: Non-small cell lung cancer is a malignant tumor with high morbidity and mortality worldwide. Eleutherococcus senticosus can induce apoptosis in non-small cell lung cancer cells, but the mechanism remains unclear. This study aimed to elucidate the role of Eleutherococcus senticosus in inducing apoptosis in non-small cell lung cancer cells and analyze its potential active constituents, targets and molecular mechanisms. The results of network pharmacology analysis showed that Eleutherococcus senticosus contained 49 active ingredients that induced apoptosis in non-small cell lung cancer cells, and these components could act on 66 apoptosis-related targets. Compared to the control group, Eleutherococcus senticosus significantly increased apoptosis in A549 cells with increasing concentration (p < 0.05). The results of transcriptome and metabolomic analyses showed that Eleutherococcus senticosus significantly changed 5836 genes and 418 metabolites in A549 cells (p < 0.05), with the most significant changes in 18 genes and 34 metabolites related to apoptosis. qRT-PCR and Western blot results showed that, after Eleutherococcus senticosus treatment, the mRNA and protein expression of EGFR, MAPK3, and ICAM1 significantly increased, while CTSK decreased (p < 0.01 or p < 0.001). Correlation analysis and molecular docking results indicated that calycanthoside and oleanolic acid can directly modify the expression levels of the transcription factors POU2F3, FOXS1 and TGIF2LY or indirectly influence the binding affinity of these transcription factors to the promoters of key target genes, ultimately leading to the activation of EGFR, MAPK3, ICAM1 and CTSK, which triggers apoptosis in non-small cell lung cancer cells.
Question: Write a study description for the study titled 'Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants (alternative assay to MTBLS36)'.
Answer: The purpose of this study was to highlight metabolic differences between different cultivars of tomato through development and ripening. Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. For original information, see MTBLS36