LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabonomics uncovers a reversible proatherogenic lipid profile during infliximab therapy of inflammatory bowel disease'.
Answer: BACKGROUND: One-third of inflammatory bowel disease (IBD) patients show no response to infliximab (IFX) induction therapy, and approximately half of patients responding become unresponsive over time. Thus, identification of potential treatment response biomarkers are of great clinical significance. This study employs spectroscopy-based metabolic profiling of serum from patients with IBD treated with IFX and healthy subjects (1) to substantiate the use of spectroscopy as a semi-invasive diagnostic tool, (2) to identify potential biomarkers of treatment response and (3) to characterise the metabolic changes during management of patients with tumour necrosis factor-α inhibitors.METHODS: Successive serum samples collected during IFX induction treatment (weeks 0, 2, 6 and 14) from 87 IBD patients and 37 controls were analysed by 1H nuclear magnetic resonance (NMR) spectroscopy. Data were analysed with principal components analysis and orthogonal projection to latent structures discriminant analysis using SIMCA-P+ v12 and MATLAB.RESULTS: Metabolic profiles were significantly different between active ulcerative colitis and controls, active Crohn's disease and controls, and quiescent Crohn's disease and controls. Metabolites holding differential power belonged primarily to lipids and phospholipids with proatherogenic characteristics and metabolites in the pyruvate metabolism, suggestive of an intense inflammation-driven energy demand. IBD patients not responding to IFX were identified as a potentially distinct group based on their metabolic profile, although no applicable response biomarkers could be singled out in the current setting.CONCLUSION: 1H NMR spectroscopy of serum samples is a powerful semi-invasive diagnostic tool in flaring IBD. With its use, we provide unique insights into the metabolic changes taking place during induction treatment with IFX. Of distinct clinical relevance is the identification of a reversible proatherogenic lipid profile in IBD patients with active disease, which partially explains the increased risk of cardiovascular disease associated with IBD.
Question: Write a study description for the study titled 'Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata'.
Answer: Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.
Question: Write a study description for the study titled 'Theabrownin from Pu-erh tea attenuates hypercholesterolemia via modulation of gut microbiota and bile acid metabolism'.
Answer: Pu-erh tea displays cholesterol-lowering properties, but the underlying mechanism has not been elucidated. Theabrownin is one of the most active and abundant pigments in Pu-erh tea. Here, we show that theabrownin alters the gut microbiota in mice and humans, predominantly suppressing microbes associated with bile-salt hydrolase (BSH) activity. Theabrownin increases the levels of ileal conjugated bile acids (BAs) which, in turn, inhibit the intestinal FXR-FGF15 signaling pathway, resulting in increased hepatic production and fecal excretion of BAs, reduced hepatic cholesterol, and decreased lipogenesis. The inhibition of intestinal FXR-FGF15 signaling is accompanied by increased gene expression of enzymes in the alternative BA synthetic pathway, production of hepatic chenodeoxycholic acid, activation of hepatic FXR, and hepatic lipolysis. Our results shed light into the mechanisms behind the cholesterol- and lipid-lowering effects of Pu-erh tea, and suggest that decreased intestinal BSH microbes and/or decreased FXR-FGF15 signaling may be potential anti-hypercholesterolemia and anti-hyperlipidemia therapies.
Question: Write a study description for the study titled 'SpaceM reveals metabolic states of single cells'.
Answer: A growing appreciation of the importance of cellular metabolism and revelations concerning the extent of cell-cell heterogeneity demand metabolic characterization of individual cells. We present SpaceM, an open-source method for in situ single-cell metabolomics that detects >100 metabolites from >1,000 individual cells per hour, together with a fluorescence-based readout and retention of morpho-spatial features. We validated SpaceM by predicting the cell types of cocultured human epithelial cells and mouse fibroblasts. We used SpaceM to show that stimulating human hepatocytes with fatty acids leads to the emergence of two coexisting subpopulations outlined by distinct cellular metabolic states. Inducing inflammation with the cytokine interleukin-17A perturbs the balance of these states in a process dependent on NF-κB signaling. The metabolic state markers were reproduced in a murine model of nonalcoholic steatohepatitis. We anticipate SpaceM to be broadly applicable for investigations of diverse cellular models and to democratize single-cell metabolomics.All MALDI-imaging MS data as well as metabolite and lipid annotations and images are publicly available through METASPACE (https://metaspace2020.eu/project/Rappez_2021_SpaceM)
Question: Write a study description for the study titled 'Exercise-driven gut microbiota alterations enhance colonization resistance against methicillin-resistant Staphylococcus aureus'.
Answer: Gut microbiota plays a crucial role in resisting the invasion of pathogens, particularly multidrug-resistant (MDR) bacteria, which pose a significant threat to public health. While exercise offers numerous health benefits, its impact on host colonization resistance remains largely unclear. In this study, we demonstrate that moderate exercise significantly reduces gut colonization by methicillin-resistant Staphylococcus aureus (MRSA), a clinically important MDR pathogen. Moreover, we identify an understudied strain of the intestinal probiotic Dubosiella newyorkensis (L8) as a critical factor in mediating exercise-induced colonization resistance against MRSA. Mechanistically, L8 enhances the deprivation of fucose, a crucial carbon source essential for MRSA growth and pathogenicity. This process relies on the high binding affinity of pyruvate to the ILE257 site of the lactate dehydrogenase in L8. Overall, our work highlights the importance of moderate exercise in maintaining host colonization resistance and demonstrates the probiotic of L8 as a probiotic in protecting against MRSA colonization.
Question: Write a study description for the study titled 'Metabolomics Analysis of the Effect of GAT-2 Deficiency on Th1 Cells in Mice'.
Answer: The classic neurotransmitter gamma-aminobutyric acid (GABA) has been shown to shape the activation and function of immune cells. There are four high affinity GABA transporters (GATs, including GAT-1, GAT-2, GAT-3 and GAT-4) responsible for the transmembrane transport of GABA in mice. To explore the effect of GAT-2 on type 1 helper T (Th1) cells, naïve CD4+ T cells were isolated from splenocytes of GAT-2 knockout (KO) and wild-type (WT) mice and cultured for Th1 cell differentiation, and then metabolomics analysis of Th1 cells was performed via gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) added with multivariate analyses. The study will provide insights into T cell response to GAT-2 deficiency in mice.
Question: Write a study description for the study titled 'Extreme genome diversity and cryptic speciation in a harmful algal bloom forming eukaryote'.
Answer: Harmful algal blooms (HABs) of the toxic haptophyte Prymnesium parvum are a recurrent problem in many inland and estuarine waters around the world. Strains of P. parvum vary in the toxins they produce and in other physiological traits associated with HABs, but the genetic basis for this variation is unknown. To investigate genome diversity in this morphospecies, we generated genome assemblies for 15 phylogenetically and geographically diverse strains of P. parvum including Hi-C guided, near-chromosome level assemblies for 2 strains. Comparative analysis revealed considerable DNA content variation between strains, ranging from 115 to 845 Mbp. Strains included haploids, diploids and polyploids, but not all differences in DNA content were due to variation in genome copy number. Haploid genome size between strains of different chemotypes differed by as much as 243 Mbp. Syntenic and phylogenetic analyses indicate that UTEX 2797, a common laboratory strain from Texas, is a hybrid that retains 2 phylogenetically distinct haplotypes. Investigation of gene families variably present across strains identified several functional categories associated with metabolic and genome size variation in P. parvum including genes for the biosynthesis of toxic metabolites and proliferation of transposable elements. Together, our results indicate that P. parvum is comprised of multiple cryptic species. These genomes provide a robust phylogenetic and genomic framework for investigations into the eco-physiological consequences of the intra- and inter-specific genetic variation present in P. parvum and demonstrate the need for similar resources for other HAB-forming morphospecies.
Question: Write a study description for the study titled 'Metabolomics analysis of the effect of GnRH on the pregnancy rate of ewes with estrus synchronization scheme based on progesterone'.
Answer: Introduction: Gonadotropin-releasing hormone (GnRH) is widely used in the timed artificial insemination program of sheep industry, but there is still controversy about the effect of GnRH on pregnancy rate in the process of artificial insemination. Our research shows that the use of GnRH reduces the pregnancy rate. This study aims to analyze the metabolite changes caused by GnRH in Huyang ewes before the implantation period through metabolomics technology, and reveal the mechanism behind the decreased pregnancy rate. Methods: All ewes had a polyurethane sponge containing 45 mg of flurogestone acetate placed in their vagina for 12 days, and were intramuscularly treated with 330 units of equine chorionic gonadotropin (eCG) immediately after sponge removal. The experimental group (n = 69) received an intramuscular treatment of 17 μg GnRH agonist triptorelin (Day 0) 48 h after sponge removal, while the control group (n = 41) was treated with 1 mL of sterile saline. All ewes underwent a single vaginal insemination 58 h after the withdrawal of progesterone sponges. The difference in pregnancy rates between the two groups was then measured. Metabolomic analysis was performed on plasma samples collected on Day 7. Results: Compared with the control group, GnRH treatment significantly reduced the pregnancy rate in the experimental group (72.2% vs 82.9%, P < 0.05). Metabolomic analysis revealed that GnRH treatment influenced metabolites involved in collagen synthesis and metabolites linked to prostaglandin synthesis in the endometrial tissue, which includes a marked decrease in hydroxyproline metabolite content and a substantial increase in corticosterone and prostaglandin D2 metabolite levels. Conclusion: In summary, GnRH agonist Triptorelin injected 48 h after the withdrawal of progesterone sponges can reduce the pregnancy rate of Huyang ewe after artificial insemination and affect the metabolite levels related to endometrial collagen synthesis and prostaglandin synthesis, which are not conducive to embryo implantation.
Question: Write a study description for the study titled 'Compilation of transcriptomics, non-targeted metabolomics and targeted metabolomics data in bovine mammary epithelial cells stimulated by ten different essential amino acids (Targeted metabolomics)'.
Answer: Divergence in the targeted amino acid profilings of bovine mammary epithelial cells (BMECs) were systematically captured with regard to 10 individual essential amino acid (EAA) availability. BMECs cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6). DMEM-F12 medium is the positive control treatment (POS), while DMEM-F12 medium devoid of all EAA served as the negative control treatment (NEG). A total of 10 treatments were NEG individually supplemented with arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan or valine. Individual EAA were supplemented to achieve concentrations equal to those of POS. After 6-h treatment, all cell samples were taken at the same time, frozen in liquid nitrogen and stored at -80 °C until required.Targeted metabolomics is reported in the current study MTBLS3956.Untargeted metabolomics is reported in MTBLS7789.
Question: Write a study description for the study titled 'The Clinical Experiences of Urine Metabolomics of Genitourinary Urothelial Cancer in a Tertiary Hospital in Taiwan'.
Answer: There are few studies which have addressed the impact of diagnostic urine metabolites and clinical outcomes associated with genitourinary urothelial (GU) cancer till this date. Furthermore, the longitudinal analysis of the dynamics of urine metabolites contributing to the detection of GU cancer has not yet been fully investigated; therefore, the discovery of novel diagnostic urine biomarkers is of our enormous interest. We explored the correlation of the urine metabolomics profiles to the GU cancers. The aqueous metabolites of the GU cancer and the control were also identified and analyzed through high-resolution1H nuclear magnetic resonance (NMR) spectroscopy. Compared with the control, the urine metabolites of the tumor were studied in relation to changes over time in a linear mixed model for repeated measures. The urine metabololites of eighty-two (58 males and 24 female) patients with GU cancers were systemically analyzed. The urine metabolite profile in GU cancer was significantly higher than those in the control group (p<0.05). Seven urine metabolites including histidine, propylene glycol, valine, leucine, acetylsalicylate, glycine and isoleucine as well as other pathways were identified statistically significantly associated with GU cancer detection with longitudinal analysis. We discovered that histidine, propylene glycol, valine, leucine, acetylsalicylate, glycine, isoleucine, succinic acid, lysine2-aminobutyric acid and acetic acid are involved significantly in the all types of the male patients in whom the urine metabolites of the upper tract urothelial carcinoma(UTUC) were found statistically significance compared with the control. We did not find any statistically significance in urine biomarkers between female and male patients. However, a statistically insignificant correlation was found among the grade and stage with the metabolites.
Question: Write a study description for the study titled 'Metabolic Profiling of CSF from People Suffering from Sporadic and LRRK2 Parkinson's Disease: A Pilot Study'.
Answer: CSF from unique groups of Parkinson's disease (PD) patients was biochemically profiled to identify previously unreported metabolic pathways linked to PD pathogenesis, and novel biochemical biomarkers of the disease were characterized. Utilizing both 1H NMR and DI-LC-MS/MS we quantitatively profiled CSF from patients with sporadic PD (n = 20) and those who are genetically predisposed (LRRK2) to the disease (n = 20), and compared those results with age and gender-matched controls (n = 20). Further, we systematically evaluated the utility of several machine learning techniques for the diagnosis of PD. 1H NMR and mass spectrometry-based metabolomics, in combination with bioinformatic analyses, provided useful information highlighting previously unreported biochemical pathways and CSF-based biomarkers associated with both sporadic PD (sPD) and LRRK2 PD. Results of this metabolomics study further support our group's previous findings identifying bile acid metabolism as one of the major aberrant biochemical pathways in PD patients. This study demonstrates that a combination of two complimentary techniques can provide a much more holistic view of the CSF metabolome, and by association, the brain metabolome. Future studies for the prediction of those at risk of developing PD should investigate the clinical utility of these CSF-based biomarkers in more accessible biomatrices. Further, it is essential that we determine whether the biochemical pathways highlighted here are recapitulated in the brains of PD patients with the aim of identifying potential therapeutic targets.
Question: Write a study description for the study titled 'Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics'.
Answer: Sweet cherry (Prunus avium L.) is a stone fruit widely consumed and appreciated for its organoleptic properties, as well as its nutraceutical potential. We here investigated the characteristics of six non-commercial Tuscan varieties of sweet cherry maintained at the Regional Germplasm Bank of the CNR-IBE in Follonica (Italy) and sampled ca. 60 days post-anthesis over three consecutive years (2016-2017-2018). We adopted an approach merging genotyping and targeted gene expression profiling with metabolomics. To complement the data, a study of the soluble proteomes was also performed on two varieties showing the highest content of flavonoids. Metabolomics identified the presence of flavanols and proanthocyanidins in highest abundance in the varieties Morellona and Crognola, while gene expression revealed that some differences were present in genes involved in the phenylpropanoid pathway during the 3 years and among the varieties. Finally, proteomics on Morellona and Crognola showed variations in proteins involved in stress response, primary metabolism and cell wall expansion. To the best of our knowledge, this is the first multi-pronged study focused on Tuscan sweet cherry varieties providing insights into the differential abundance of genes, proteins and metabolites.
Question: Write a study description for the study titled 'Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.) (Phenolics; UPLC-MS/MS assay)'.
Answer: BACKGROUND: Secondary metabolism contributes to the adaptation of a plant to its environment. In wine grapes, fruit secondary metabolism largely determines wine quality. Climate change is predicted to exacerbate drought events in several viticultural areas, potentially affecting the wine quality. In red grapes, water deficit modulates flavonoid accumulation, leading to major quantitative and compositional changes in the profile of the anthocyanin pigments; in white grapes, the effect of water deficit on secondary metabolism is still largely unknown.RESULTS: In this study we investigated the impact of water deficit on the secondary metabolism of white grapes using a large scale metabolite and transcript profiling approach in a season characterized by prolonged drought. Irrigated grapevines were compared to non-irrigated grapevines that suffered from water deficit from early stages of berry development to harvest. A large effect of water deficit on fruit secondary metabolism was observed. Increased concentrations of phenylpropanoids, monoterpenes, and tocopherols were detected, while carotenoid and flavonoid accumulations were differentially modulated by water deficit according to the berry developmental stage. The RNA-sequencing analysis carried out on berries collected at three developmental stages-before, at the onset, and at late ripening-indicated that water deficit affected the expression of 4,889 genes. The Gene Ontology category secondary metabolic process was overrepresented within up-regulated genes at all the stages of fruit development considered, and within down-regulated genes before ripening. 18 phenylpropanoid, 16 flavonoid, 9 carotenoid, and 16 terpenoid structural genes were modulated by water deficit, indicating the transcriptional regulation of these metabolic pathways in fruit exposed to water deficit. An integrated network and promoter analyses identified a transcriptional regulatory module that encompasses terpenoid genes, transcription factors, and enriched drought-responsive elements in the promoter regions of those genes as part of the grapes response to drought.CONCLUSION: Our study reveals that grapevine berries respond to drought by modulating several secondary metabolic pathways, and particularly, by stimulating the production of phenylpropanoids, the carotenoid zeaxanthin, and of volatile organic compounds such as monoterpenes, with potential effects on grape and wine antioxidant potential, composition, and sensory features.UPLC-MS/MS assay of Phenolics is reported in the current study MTBLS897.SPME-GC-MS assay of Volatile organic compounds is reported in MTBLS892.UPLC-DAD assay of Carotenoids is reported in MTBLS889.