LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Plasma metabolic profile in COPD patients: effects of exercise and endurance training'.
Answer: The study examines plasma metabolic profiles of patients with chronic obstructive pulmonary disease (COPD) to prove whether the disease influences metabolism at rest and after endurance training. This is based on the hypothesis that metabolome levels should reflect impaired skeletal muscle bioenergetics in COPD. The study aims to test this hypothesis by evaluating plasma metabolic profiles in COPD patients before and after 8 weeks of endurance exercise training. We studied blood samples from 18 COPD patients and 12 healthy subjects. Pre- and post-training blood plasma samples at rest and after constant-work rate exercise (CWRE) at 70% of pretraining Watts peak were analyzed by 1H-nuclear magnetic resonance spectroscopy to assess metabolite profiles. The two groups presented training-induced physiological changes in the VO2 peak and in blood lactate levels (P0.01 each). Before training, the two groups also showed differences in metabolic profiles at rest (P0.05). Levels of valine (r = 0.51, P0.01), alanine (r = 0.45, P0.05) and isoleucine (r = 0.51, P0.01) were positively associated with body composition (Fat Free Mass Index). While training showed a significant impact on the metabolic profile in healthy subjects (P0.001), with changes in levels of amino acids, creatine, succinate, pyruvate, glucose and lactate (P0.05 each), no equivalent training-induced effects were seen in COPD patients in whom only lactate decreased (P0.05). This study shows that plasma metabolic profiling contributes to the phenotypic characterization of COPD patients.
Question: Write a study description for the study titled 'Metabolome patterns identify active dechlorination in bioaugmentation consortium SDC-9'.
Answer: Ultra-high performance liquid chromatography-high resolution mass spectrometry (UPHLC-HRMS) is used to discover and monitor single or sets of biomarkers informing about metabolic processes of interest. The technique can detect thousands of molecules (i.e., metabolites) in a single instrument run and provide a measurement of the global metabolome, which could be a fingerprint of activity. Despite the power of this approach, technical challenges have hindered the effective use of metabolomics to interrogate microbial communities implicated in the removal of priority contaminants. Herein, our efforts to circumvent these challenges and apply this emerging systems biology technique to synthetic microbiomes relevant for contaminant biodegradation will be discussed. Chlorinated ethenes impact many contaminated sites, and detoxification can be achieved by organohalide-respiring bacteria, a process currently assessed by quantitative gene-centric tools (e.g., quantitative PCR). This laboratory study monitored the metabolome of the SDC-9 bioaugmentation consortium during cis-1,2-dichloroethene conversion to vinyl chloride and nontoxic ethene. Untargeted metabolomics using an UPLC-Orbitrap mass spectrometer and performed on SDC-9 cultures at different stages of the reductive dechlorination process detected ~10,000 spectral features per sample arising from water-soluble molecules with both known and unknown structures. Multivariate statistical techniques including partial least squares-discriminate analysis (PLS-DA) identified patterns of measurable spectral features (peak patterns) that correlated with dechlorination (in)activity. ANOVA analyses identified 18 potential biomarkers of reductive dechlorination activity. Statistical clustering of samples with these 18 features predicted dechlorination activity more reliably than clustering of samples based only on chlorinated ethene concentration and Dhc 16S rRNA gene abundance data, highlighting the value of metabolomic workflows as an innovative site assessment and bioremediation monitoring tool.
Question: Write a study description for the study titled 'Evaluation of sample preparation protocols for quantitative NMR-based metabolomics'.
Answer: INTRODUCTION: Quantification of metabolites in biological fluids and tissues by NMR spectroscopy is challenged by the presence of abundant macromolecules and lipoproteins in samples, which give broad signals in the NMR spectra. To improve the quality of NMR spectra the different protocols for protein and lipid removal from the sample are used.OBJECTIVES: This work is aimed at the evaluation of the effectiveness of various methods of purification of blood serum from proteins and lipids for 1H NMR metabolomic profiling.METHODS: The advantages and limitations of different methods of the sample preparation for NMR-based quantitative metabolomics have been compared, including ultrafiltration, methanol and ethanol extractions with and without additional lipid removal, and methanol-chloroform extraction.RESULTS: The concentrations of 30 abundant metabolites extracted from human blood serum have been measured. It is found that ultrafiltration provides the best lipid removal, but causes significant and inhomogeneous metabolite losses. Ethanol and methanol extractions demonstrate similar performance with the minimal metabolite losses, and are ideal for fluids and tissues with low lipid content. The additional purification of alcohol extracts from lipids allows for the significant improving of NMR spectra, but causes additional metabolite losses.CONCLUSIONS: The methanol-chloroform extraction seems to be an optimal method for tissues with the high lipid content, providing a satisfactory lipid removal and low metabolite losses. The ultrafiltration leads to large losses of metabolites (up to 60 %) and for this reason is not suitable for quantitative analysis.
Question: Write a study description for the study titled 'Saliva metabolome and microbiome in permanent teeth caries'.
Answer: Metabolites are important determinants of disease progression. In this study, we conducted a case-control study to explore permanent teeth caries-related differences in salivary metabolite profiles and related changes in the composition of the oral microbiota in 200 subjects including 100 caries-free individuals and 100 with moderate-to-severe caries with good homogeneity through widely targeted metabolomics and 16S rRNA deep sequencing technologies. We found that: 1) 822 metabolites were detectable in salivary samples from these participants, of which 4-acetamidobutyric acid and adipic acid were respectively enriched in healthy individuals and individuals with caries, exhibited the greatest area under the curve (AUC) values of > 0.970; 2) less diversity was observed in individuals with dental caries relative to caries-free individuals, and significant differences in the dominant taxa were evident between the two groups. For example, the healthy oral microbiome is enriched for Rothia aeria and Neisseria perflava, whereas Prevotella melaninogenica, Streptococcus salivarius, Streptococcus parasanguinis and Prevotella histicola, and Streptococcus mutans were enriched in individuals with caries; 3) Prevotella histicola, Oribacterium asaccharolyticum and Rothia aeria were the top 3 species being required to differentiate caries from caries free population; 4) adipic acid and 4-acetamidobutyric acid derived from microbiota and host-microbiota co-metabolism, respectively. A negative correlation was observed between the microbes enriched in caries individuals (such as Prevotella histicola) and 4-acetamidobutyric acid. Moreover, the upstream regulatory factor ALDH of 4-acetamidobutyric acid is expressed throughout the entire process of tooth development including the differentiation of tooth bud, ameloblasts and odontoblasts. Together, these results suggest that 4-acetamidobutyric acid and adipic acid are important targets for future caries-focused research, offering insight into cariogenic activity or risk assessment in moderate or severe cases.
Question: Write a study description for the study titled 'Maslinic acid-enriched diet decreases intestinal tumorigenesis in Apc(Min/+) mice through transcriptomic and metabolomic reprogramming'.
Answer: Chemoprevention is a pragmatic approach to reduce the risk of colorectal cancer, one of the leading causes of cancer-related death in western countries. In this regard, maslinic acid (MA), a pentacyclic triterpene extracted from wax-like coatings of olives, is known to inhibit proliferation and induce apoptosis in colon cancer cell lines without affecting normal intestinal cells. The present study evaluated the chemopreventive efficacy and associated mechanisms of maslinic acid treatment on spontaneous intestinal tumorigenesis in Apc(Min/+) mice. Twenty-two mice were randomized into 2 groups: control group and MA group, fed with a maslinic acid-supplemented diet for six weeks. MA treatment reduced total intestinal polyp formation by 45% (P<0.01). Putative molecular mechanisms associated with suppressing intestinal polyposis in Apc(Min/+) mice were investigated by comparing microarray expression profiles of MA-treated and control mice and by analyzing the serum metabolic profile using NMR techniques. The different expression phenotype induced by MA suggested that it exerts its chemopreventive action mainly by inhibiting cell-survival signaling and inflammation. These changes eventually induce G1-phase cell cycle arrest and apoptosis. Moreover, the metabolic changes induced by MA treatment were associated with a protective profile against intestinal tumorigenesis. These results show the efficacy and underlying mechanisms of MA against intestinal tumor development in the Apc(Min/+) mice model, suggesting its chemopreventive potential against colorectal cancer.
Question: Write a study description for the study titled 'Lactate controls cancer stemness and plasticity through epigenetic regulation.'.
Answer: Tumours arise from uncontrolled cell proliferation driven by mutations in genes that regulate stem cell renewal and differentiation. Intestinal tumours, however, retain some hierarchical organization, maintaining both cancer stem cells (CSCs) and cancer differentiated cells (CDCs). This heterogeneity, coupled with cellular plasticity enabling CDCs to revert to CSCs, contributes to therapy resistance and relapse. Using fluorescent metabolic and signalling reporters in human tumour organoids, combined with our machine learning-based cell tracker, CellPhenTracker, we simultaneously traced cell type specification, metabolic changes, and reconstructed cell lineage trajectories during tumour organoid development. Our findings reveal distinctive metabolic phenotypes in CSCs and CDCs. We find that lactate regulates tumour dynamics, suppressing CSC differentiation and inducing dedifferentiation into a proliferative CSC state. Mechanistically, lactate increases histone acetylation, epigenetically activating MYC. Given that lactate’s regulation of MYC depends on BRD4, targeting cancer metabolism combined with BET inhibitors emerges as a promising strategy to prevent tumour relapse.
Question: Write a study description for the study titled 'Improving Metabolite Identification with DecoID for Database-Assisted Deconvolution of Metabolomic MS/MS Spectra'.
Answer: Chimeric MS/MS spectra contain fragments from multiple precursor ions and therefore hinder compound identification in metabolomics. Historically, deconvolution of these chimeric spectra has been challenging and relied upon specific experimental methods that introduce variation in the ratios of precursor ions between multiple MS/MS scans. DecoID introduces a complementary, method-independent approach where database spectra are computationally mixed to match an experimentally acquired spectrum using LASSO regression. When applied to human plasma, DecoID increased the number of identified metabolites by over 30%.
Question: Write a study description for the study titled 'Mapping the metabolism of five amino acids in bloodstream form Trypanosoma brucei using U-13C-labelled substrates and LC–MS'.
Answer: The metabolism of the parasite Trypanosoma brucei has been the focus of numerous studies since the 1940s. Recently it was shown, using metabolomics coupled with heavy-atom isotope labelled glucose, that the metabolism of the bloodstream form parasite is more complex than previously thought. The present study also raised a number of questions regarding the origin of several metabolites, for example succinate, only a proportion of which derives from glucose. In order to answer some of these questions and explore the metabolism of bloodstream form T. brucei in more depth we followed the fate of five heavy labelled amino acids – glutamine, proline, methionine, cysteine and arginine – using an LC–MS based metabolomics approach. We found that some of these amino acids have roles beyond those previously thought and we have tentatively identified some unexpected metabolites which need to be confirmed and their function determined.
Question: Write a study description for the study titled 'Delineating molecular regulatory network of meat quality of longissimus dorsi indicated by transcriptomic, proteomic, and metabolomics analysis in rabbit (UPLC-MS/MS assays)'.
Answer: This study aims to investigate the potential regulatory network responsible for the meat quality using multi-omics to help developing better varieties. Slaughter performance and meat quality of Shuxing No.1 rabbit outperformed Yila rabbit. Differentially expressed genes (DEGs) and differentially abundance proteins (DAPs) were involved in meat quality-related pathways, such as PI3K−Akt and MAPK signaling pathway. Only SMTNL1 and PM20D2 shared between DEGs and DAPs. Olfactory-sensitive undecanal, a differentially abundant metabolite (DAM) in volatilomics (vDAMs), correlated with all of the remaining 11 vDAMs, and most of 12 vDAMs were associated with amino acid metabolism. Integration revealed that 829 DEGs/DAPs were associated with 15 DAMs in four KEGG pathways, such as melatonin (a DAM in widely targeted metabolomics) was significantly positively correlated with ALDH and negatively correlated with RAB3D and CAT in tryptophan metabolism pathway. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor.UPLC-MS/MS assays are reported in the current study MTBLS8957.SPME-GC-MS assay is reported in MTBLS8958.
Question: Write a study description for the study titled 'Caffeine Enhances Antitumor T-cell Activity via COL12A1/IDO1/Kyn axis and Sensitivity to Anti-PD-1 Immunotherapy in Colorectal Cancer'.
Answer: Metabolomic sequencing on supernatants from caffeine-treated and untreated tumor cells to identify which metabolites are involved in activating CD8+ T cells
Question: Write a study description for the study titled 'Unveiling molecular changes in guabiju during Aspergillus brasiliensis cultivation: insights from untargeted metabolomics'.
Answer: Black aspergilli exhibit remarkable bioconversion potential by transforming plant matrices into bioactive compounds, although their metabolic processes remain underexplored. This study investigated the biotransformation of metabolites during the solid-state cultivation of guabiju (Myrcianthes pungens) by Aspergillus brasiliensis using an LC-MS-based untargeted metabolomics approach, aiming to elucidate dynamic changes in metabolite profiles over 0, 3, 7, 10 and 15 days of cultivation. Key metabolites, such as gallic acid, epigallocatechin, mono- and di- O-galloylquinic acids, quercetin and citric acid, increased during cultivation, with a significant rise in gallic acid release and citric acid production observed after seven days. Fungal metabolites including hexylitaconic acid also increased, indicating potential to produce itaconic acid-derived compounds. Data analysis indicated that most significant metabolic changes occurred within the first seven days, especially for tannin hydrolysis and organic acid production. These findings highlighted the potential of A. brasiliensis to enhance fermented foods through targeted biotransformation.
Question: Write a study description for the study titled 'Metabolomic and Lipidomic Characterization of Meningioma Grades Using LC-HRMS and Machine Learning'.
Answer: Meningiomas are among the most common brain tumors that arise from the leptomeningeal cover of the brain and spinal cord and account for around 37% of all central nervous system tumors. According to the World Health Organization, meningiomas are classified into three histological subtypes: benign, atypical, and anaplastic. Sometimes, meningiomas with a histological diagnosis of benign tumors show clinical characteristics and behavior of aggressive tumors. In this study, we examined the metabolomic and lipidomic profiles of meningioma tumors, focusing on comparing low-grade and high-grade tumors and identifying potential markers that can discriminate between benign and malignant tumors. High-resolution mass spectrometry coupled to liquid chromatography was used for untargeted metabolomics and lipidomics analyses of 85 tumor biopsy samples with different meningioma grades. We then applied feature selection and machine learning techniques to find the features with the highest information to aid in the diagnosis of meningioma grades. Three biomarkers were identified to differentiate low- and high-grade meningioma brain tumors. The use of mass-spectrometry-based metabolomics and lipidomics combined with machine learning analyses to prospect and characterize biomarkers associated with meningioma grades may pave the way for elucidating potential therapeutic and prognostic targets.
Question: Write a study description for the study titled 'The correlation between leaf-surface and leaf-tissue secondary metabolites: a case study with pyrrolizidine alkaloids in Jacobaea hybrid plants'.
Answer: Introduction: Usually whole plant or whole leaf extracts are analyzed to study the chemical ecology of insect-plant interactions. For herbivore species the contact with the leaf surface enables them to estimate the quality of the plant. The relationship between the leaf-surface and leaf-tissue secondary metabolites (SMs) could offer important new insights in insect-plant interactions mediated by SMs. Pyrrolizidine alkaloids (PAs), typical defense chemicals in Jacobaea species, are repellent for generalist herbivores but are attractive to specialists. Objectives: Explore whether the PAs on the leaf surface are a reliable representation of the PAs in the leaf tissue in PA-containing plants. Method: The concentration of individual PAs present on the leaf surface and in the corresponding leaf tissue from 37 genotypes (one plant from each genotype) of an F2 generation of a cross between Jacobaea vulgaris and Jacobaea aquatica was measured by high performance liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). PAs were removed from the leaf surface by extraction with a slightly acidic aqueous solution. Results: The total amount of PAs present on the surface of the leaves was only 0.015% (range: 0.001-0.163%) of the total amount present in the leaf tissue. Most PAs present in the leaf tissue were also found on the surface, except for jaconine, dehydrojaconine, dehydrojacoline and usaramine N-oxide. Positive correlations between leaf-surface and leaf-tissue concentrations were found for most of the jacobine-like and otosenine-like PAs, but correlations for total PA, senecionine- and erucifoline-like PAs were not significant. Conclusion: These results indicate that PA variation on the leaf surface only partially reflects the PA variation in the leaf tissue. Because most herbivores are affected in a different manner by individual PAs, this result means that the leaf surface does not give a reliable estimate of plant quality to herbivores.
Question: Write a study description for the study titled 'Sertraline Hydrochloride Exposure Leads to Reactive Oxygen Species Burst in Model Microalgae Species (Raphidocelis subcapitata)'.
Answer: Microalgae play important ecological roles and serve as useful models for assessing impacts of environmental contaminants on lower trophic aquatic organisms. Sertraline, a commonly prescribed selective serotonin reuptake inhibitor (SSRI) found in urban waters, has been observed to induce chlorosis in Raphidocelis subcapitata close to environmentally relevant concentrations. This study estimated potentially hazardous concentrations of sertraline hydrochloride by deriving transcriptomic and metabolomic points of departure (tPODs and mPODs) below which chronic adverse effects would not be expected. Additionally, an Adverse Outcome Pathway describing the mechanism by which sertraline hydrochloride impacted R. subcapitata was proposed using a multi-omics approach. This data contains the raw and processed files of nontargeted metabolomics for extracted R. subcapitata metabolites after exposure to sertraline hydrochloride.
Question: Write a study description for the study titled 'Metabolic alterations in immune cells associate with progression to type 1 diabetes'.
Answer: AIMS: Previous metabolomics studies suggest that type 1 diabetes is preceded by specific metabolic disturbances. The aim of this study was to investigate whether distinct metabolic patterns occur in peripheral blood mononuclear cells (PBMCs) of children who later develop pancreatic beta cell autoimmunity or overt type 1 diabetes.METHODS: In a longitudinal cohort setting, PBMC metabolomic analysis was applied in children who (1) progressed to type 1 diabetes (PT1D, n = 34), (2) seroconverted to ≥1 islet autoantibody without progressing to type 1 diabetes (P1Ab, n = 27) or (3) remained autoantibody negative during follow-up (CTRL, n = 10).RESULTS: During the first year of life, levels of most lipids and polar metabolites were lower in the PT1D and P1Ab groups compared with the CTRL group. Pathway over-representation analysis suggested alanine, aspartate, glutamate, glycerophospholipid and sphingolipid metabolism were over-represented in PT1D. Genome-scale metabolic models of PBMCs during type 1 diabetes progression were developed by using publicly available transcriptomics data and constrained with metabolomics data from our study. Metabolic modelling confirmed altered ceramide pathways, known to play an important role in immune regulation, as specifically associated with type 1 diabetes progression.CONCLUSIONS: Our data suggest that systemic dysregulation of lipid metabolism, as observed in plasma, may impact the metabolism and function of immune cells during progression to overt type 1 diabetes.Links: The GEMs for PBMCs have been submitted to BioModels, under accession number MODEL1905270001.