LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Mining for metabolic responses to long-term salt stress: a case study on Arabidopsis thaliana Col-0 (C)'.
Answer: New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using diverse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and divergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress.
Question: Write a study description for the study titled 'Quantitative trait loci analysis identifies a prominent gene involved in the production of fatty-acid-derived flavor volatiles in tomato'.
Answer: To gain insight into the genetic regulation of lipid metabolism in tomato, we conducted metabolic trait loci (mQTL) analysis following the lipidomic profiling of fruit pericarp and leaf tissue of the Solanum pennellii introgression lines. To enhance mapping resolution for selected fruit-specific mQTL, we profiled the lipids in a subset of independently derived S. pennellii backcross inbred lines, as well as in a near-isogenic (sub-IL) population. We identified a putative lecithin:cholesterol acyltransferase that controls the levels of several lipids, and two members of the class III lipase family, LIP1 and LIP2, that were associated with decreased levels of diacylglycerols (DAGs) and triacylglycerols (TAGs). Lipases of this class cleave fatty acids from the glycerol backbone of acylglycerols. The released fatty acids serve as precursors of flavor volatiles. We show that LIP1 expression correlates with fatty-acid-derived volatile levels. We further confirm the function of LIP1 in TAG and DAG breakdown and volatile synthesis using transgenic plants. In summary, this study provides an extensive characterization of the genetic architecture of lipophilic compounds in tomato in addition to zooming down to the molecular level to demonstrate that release of free fatty acids from the glycerol backbone can have a major impact on downstream volatile synthesis.
Question: Write a study description for the study titled 'Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes'.
Answer: Alteration of various metabolites has been linked to type 2 diabetes (T2D) and insulin resistance. However, identifying significant associations between metabolites and tissue-specific phenotypes requires a multi-omics approach. In a cohort of 42 subjects with different levels of glucose tolerance (normal, prediabetes and T2D) matched for age and body mass index, we calculated associations between parameters of whole-body positron emission tomography (PET)/magnetic resonance imaging (MRI) during hyperinsulinemic euglycemic clamp and non-targeted metabolomics profiling for subcutaneous adipose tissue (SAT) and plasma. Plasma metabolomics profiling revealed that hepatic fat content was positively associated with tyrosine, and negatively associated with lysoPC(P-16:0). Visceral adipose tissue (VAT) and SAT insulin sensitivity (Ki), were positively associated with several lysophospholipids, while the opposite applied to branched-chain amino acids. The adipose tissue metabolomics revealed a positive association between non-esterified fatty acids and, VAT and liver Ki. Bile acids and carnitines in adipose tissue were inversely associated with VAT Ki. Furthermore, we detected several metabolites that were significantly higher in T2D than normal/prediabetes. In this study we present novel associations between several metabolites from SAT and plasma with the fat fraction, volume and insulin sensitivity of various tissues throughout the body, demonstrating the benefit of an integrative multi-omics approach.
Question: Write a study description for the study titled 'Metabolomic analysis of synovial fluid from Thoroughbred racehorses diagnosed with palmar osteochondral disease using magnetic resonance imaging'.
Answer: BACKGROUND: Palmar osteochondral disease (POD) is a common cause of lameness in competition horses. Magnetic resonance imaging (MRI) is the most sensitive diagnostic modality currently available, however it may not be financially or logistically practical for routine screening of POD. There is increasing interest in the use of metabolomics for diagnosis prior to progression to irreversible damage.OBJECTIVES: To determine metabolite levels in synovial fluid (SF) of horses with a clinical diagnosis of POD based on diagnostic analgesia and MRI, with the hypothesis that metabolomic profiles differ between diseased and healthy joints.STUDY DESIGN: Prospective clinical study.METHODS: Synovial fluid was collected from metacarpo/tarsophalangeal joints (MC/TPJ) of 29 horses (n = 51 joints), including 14 controls (n = 26) and 15 cases (n = 25), the latter with lameness localised to the MC/TPJ and MR changes consistent with POD (n = 23). Spectra were produced using 1 H-nuclear magnetic resonance (NMR) spectroscopy and analysed.RESULTS: Twenty-five metabolites were recognised associated with various biosynthetic and degradation pathways. The metabolite abundances within the controls demonstrated increased variability compared with the clinical group. The low level of variance between the spectra of the two groups was explained by five principal components. Cross-validation of the cohort demonstrated modest separation of predictive power (R2 = 0.67; Q2 = 0.34). Although statistical significance was not achieved, the most influential metabolites were glucose and lactate.MAIN LIMITATIONS: The modest sample size and variation in signalment, background and presenting condition of the controls may have impacted the discriminative power of the constructed models. The lack of matched controls, differences in time of fluid collection and freezing times may have also reduced accuracy when representing metabolite profiles.CONCLUSIONS: This study identified and quantified metabolites present in MC/TPJ SF of clinical cases with POD.
Question: Write a study description for the study titled 'A robust intracellular metabolite extraction protocol for human neutrophil metabolic profiling'.
Answer: BACKGROUND: Neutrophils are phagocytic innate immune cells that play essential roles in host defence, but are also implicated in inflammatory diseases such as rheumatoid arthritis (RA) where they contribute to systemic inflammation and joint damage. Transcriptomic analysis of neutrophils has revealed significant changes in gene expression in neutrophils activated in vitro by cytokines and in vivo during inflammation in RA. However, there are no reports on the global metabolomic changes that occur during neutrophil activation. The aim of this study was to establish protocols for the study changes in the metabolome of human neutrophils using 1H NMR spectroscopy.
Question: Write a study description for the study titled 'Integrated metabolomics and network pharmacology investigation of cardioprotective effects of myricetin after 1-week high-intensity exercise'.
Answer: Cardiovascular adverse effects caused by high-intensity exercise (HIE) have become a public health problem of widespread concern. As a phytochemical with potential therapeutic effects, the therapeutic effect and metabolic regulation mechanism of myricetin have rarely been studied. In this study, we established different doses of myricetin intervention with 1 week of HIE after intervention. Cardiac function tests, serology and pathological examinations were used to evaluate the protective effect of myricetin on the myocardium. The possible therapeutic targets of myricetin were obtained using integrated analysis of metabolomics and network pharmacology and verified using molecular docking and RT-qPCR experiments. Different concentrations of myricetin improved cardiac function, significantly reduced the levels of myocardial injury markers, alleviated myocardial ultrastructural damage, reduced the area of ischemia/hypoxia, and increased the content of CX43. Through combined analysis with metabolomics and network pharmacology and then verification with molecular docking and RT-qPCR, we found that PTGS2, MAOB, EGFR, MAP2K1 were the key targets for injury protection. Arachidonic acid metabolism, glycine-serine-threonine acid metabolism and FoxO metabolism may be the key metabolic pathways affected by myricetin intervention. In summary, our findings suggest that myricetin exert cardiac protective effects of HIE by regulating myocardial metabolic network.
Question: Write a study description for the study titled 'The HuMet Repository: Watching human metabolism at work'.
Answer: Metabolism oscillates between catabolic and anabolic states depending on food intake, exercise, or stresses that change a multitude of metabolic pathways simultaneously. We present the HuMet Repository for exploring dynamic metabolic responses to oral glucose/lipid loads, mixed meals, 36-h fasting, exercise, and cold stress in healthy subjects. Metabolomics data from blood, urine, and breath of 15 young, healthy men at up to 56 time points are integrated and embedded within an interactive web application, enabling researchers with and without computational expertise to search, visualize, analyze, and contextualize the dynamic metabolite profiles of 2,656 metabolites acquired on multiple platforms. With examples, we demonstrate the utility of the resource for research into the dynamics of human metabolism, highlighting differences and similarities in systemic metabolic responses across challenges and the complementarity of metabolomics platforms. The repository, providing a reference for healthy metabolite changes to six standardized physiological challenges, is freely accessible through a web portal.
Question: Write a study description for the study titled 'Metabolic effects of dietary glycerol supplementation in muscle and liver of European seabass and rainbow trout by 1H NMR metabolomics'.
Answer: The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such as growth. In the present study, the effects of dietary glycerol supplementation on the muscle and liver metabolomes of rainbow trout (Oncorhynchus mykiss) and European seabass (Dicentrarchus labrax) were evaluated. Fish juveniles were fed diets with 0%, 2.5%, and 5% glycerol. Muscle and liver aqueous fractions were extracted and 1H NMR spectra were acquired. Metabolite profiles derived from the 1H NMR signals were assessed using univariate and multivariate statistical analyses. The adenylate energy charge was determined in the muscle. For both species, the muscle metabolite profile showed more variability compared to that of the liver and was most perturbed by the 5.0% glycerol diet. For the liver metabolite profile, rainbow trout showed fewer differences compared to European seabass. No differences were observed in energy charge between experimental groups for either species. Thus, rainbow trout appeared to be less susceptible to tissue metabolite perturbations, compared to seabass, when the diet was supplemented with up to 5% glycerol.
Question: Write a study description for the study titled 'Biomarker Discovery in Oral Cancer (OSMF & OSCC) and its severity'.
Answer: Oral squamous cell carcinoma (OSCC) is frequently the outcome of oral submucous fibrosis (OSMF), a common possibly premalignant disease. In our study, a cohort of 50 patients with OSCC and OSMF, along with 50 healthy controls, was analyzed to identify significant metabolic differences between the patient and control groups through multivariate statistical analysis using NMR-based metabolomics in saliva samples. The 2D scatter plot of PC1 versus PC2 scores clearly shows a distinction between the groups, with the principal component analysis (PCA) explaining 24.6% of the variance. Partial least-squares discriminant analysis (PLS-DA) demonstrated R2 and Q2 values of 0.94 and 0.90, respectively, indicating a robust model fit. A total of 20 distinct metabolites were identified, including 5 that were up-regulated and 5 down-regulated. Univariate ROC curve analysis identified 9 salivary metabolites with AUC values exceeding 0.70, including acetone, tryptophan, 5-aminopentanoic acid, betaine, aspartic acid, ethanol, acetoacetate, adipic acid and citrate. Notably, the distinct presence of three metabolites - acetone, tryptophan and 5-aminopentanoic acid - yielded AUC values of 0.98123, 0.95358 and 0.91506, respectively. The refined statistical model was subjected to metabolic pathway analysis, revealing interconnected pathways. We could also predict the disease's severity, specifically distinguishing between Stage I and Stage II OSCC. This differentiation was highlighted by the PCA score plot, which explained 28.6% of the variance. PLS-DA further confirmed these results. These insights pave the way for early diagnosis and predicting severity in oral cancer patients, enabling better management of the disease.
Question: Write a study description for the study titled 'Inositol polyphosphates regulate resilient mechanisms in the green alga Chlamydomonas reinhardtii to adapt to extreme nutrient conditions'.
Answer: In the actual context of climate changing environments, photosynthetic organisms need to adapt to more extreme conditions. Microalgae can be excellent organisms to understand molecular mechanisms that activate survival mechanisms under stress. Chlamydomonas reinhardtii signaling mutants are extremely useful to decipher which strategies they use to cope with changeable environments. In this study, we conducted prolonged starvation in wild type and vip1-1 Chlamydomonas cells. The mutant vip1-1 has an altered profile of pyroinositol polyphosphates (PP-InsPs) which are signaling molecules present in all eukaryotes. These molecules have been connected to P signaling in other organisms including plants but their implications in other nutrient signaling is still under evaluation. After prolonged starvation, WT and vip1-1 showed important differences in the levels of chlorophyll and PSII activity. We also performed a metabolomic analysis under these conditions and found an overall decrease in different organic compounds such as amino acids including arginine and its precursors and tryptophan which is considered as a signaling molecule itself in plants. In addition, we observed significant differences in RNA levels of genes related to nitrogen assimilation that are under the control of NIT2 transcription factor. Overall our data indicate an important role of PP-InsPs in the regulation of nutrient starvation especially regarding N assimilation and C distribution. These data are of great importance for the generation of resilient strains to be used in open ponds and high capacity bioreactors.
Question: Write a study description for the study titled 'NQO1 protects obese mice through improvements in glucose and lipid metabolism.'.
Answer: Chronic nutrient excess leads to metabolic disorders and insulin resistance. Activation of stress-responsive pathways via Nrf2 activation contributes to energy metabolism regulation. Here, inducible activation of Nrf2 in mice and transgenesis of the Nrf2 target, NQO1, conferred protection from diet-induced metabolic defects through preservation of glucose homeostasis, insulin sensitivity, and lipid handling with improved physiological outcomes. NQO1-RNA interaction mediated the association with and inhibition of the translational machinery in skeletal muscle of NQO1 transgenic mice. NQO1-Tg mice on high-fat diet had lower adipose tissue macrophages and enhanced expression of lipogenic enzymes coincident with reduction in circulating and hepatic lipids. Metabolomics data revealed a systemic metabolic signature of improved glucose handling, cellular redox, and NAD+ metabolism while label-free quantitative mass spectrometry in skeletal muscle uncovered a distinct diet- and genotype-dependent acetylation pattern of SIRT3 targets across the core of intermediary metabolism. Thus, under nutritional excess, NQO1 transgenesis preserves healthful benefits.
Question: Write a study description for the study titled 'Production of new microbially conjugated bile acids by human gut microbiota'.
Answer: Gut microbes have been recognized to convert the human bile acids by deconjugation, dehydroxylation, dehydrogenation and epimerization of the cholesterol core, but the ability to re-conjugate them with amino acids as an additional conversion has only been recently described. These new bile acids are known as microbially conjugated bile acids (MCBAs). The aim of this study was evaluating the MCBAs diversity produced by the gut microbiota through a metabolomics approach. In this study, fresh fecal samples from healthy donors were evaluated to explore the re-conjugation of chenodeoxycholic and 3-oxo-chenodeoxycholic acids by the human gut microbiota. No significant differences were found between the conversion trend of both BAs incubations. The in vitro results showed a clear trend to first accumulate the epimer isoursochenodeoxycholic acid, and the dehydroxylated lithocholic acid derivatives in samples incubated with chenodeoxycholic and 3-oxo-chenodeoxycholic acid. Also showed a strong trend for the production of microbially conjugated dehydroxylated bile acids, instead of chenodeoxycholic backbone conjugates. Different molecules and isomers of microbial conjugates with valine and leucine were also identified and confirmed by MS/MS. These results document the gut microbiota capability to produce esters of MCBAs on hydroxyls of the sterol backbone in addition to amides at the C24 acyl site. This study opens a new perspective to study the BAs diversity produced by the human gut microbiota.
Question: Write a study description for the study titled 'Changes in lipid profiles of epileptic mouse model'.
Answer: INTRODUCTION: Approximately 1% of the world's population is impacted by epilepsy, a chronic neurological disorder characterized by seizures. One-third of epileptic patients are resistant to AEDs, or have medically refractory epilepsy (MRE). One non-invasive treatment that exists for MRE includes the ketogenic diet, a high-fat, low-carbohydrate diet. Despite the KD's success in seizure attenuation, it has a few risks and its mechanisms remain poorly understood. The KD has been shown to improve metabolism and mitochondrial function in epileptic phenotypes. Potassium channels have implications in epileptic conditions as they have dual roles as metabolic sensors and control neuronal excitation.OBJECTIVES: The goal of this study was to explore changes in the lipidome in hippocampal and cortical tissue from Kv1.1-KO model of epilepsy.METHODS: FT-ICR/MS analysis was utilized to examine nonpolar metabolome of cortical and hippocampal tissue isolated from a Kv1.1 channel knockout mouse model of epilepsy (n = 5) and wild-type mice (n = 5).RESULTS: Distinct metabolic profiles were observed, significant (p < 0.05) features in hippocampus often being upregulated (FC ≥ 2) and the cortex being downregulated (FC ≤ 0.5). Pathway enrichment analysis shows lipid biosynthesis was affected. Partition ratio analysis revealed that the ratio of most metabolites tended to be increased in Kv1.1-/-. Metabolites in hippocampal tissue were commonly upregulated, suggesting seizure initiation in the hippocampus. Aberrant mitochondrial function is implicated by the upregulation of cardiolipin, a common component in the mitochondrial membrane.CONCLUSION: Generally, our study finds that the lipidome is changed in the hippocampus and cortex in response to Kv1.1-KO indicating changes in membrane structural integrity and synaptic transmission.
Question: Write a study description for the study titled 'Following a 5-day pretreatment with Lactobacillus reuteri, HDCA, or DMSO, piglets were challenged with PEDV, and subsequent jejunal content samples were subjected to targeted bile acid metabolic profiling.'.
Answer: Twenty 3-day-old piglets that tested negative for both PEDV and PRRS antigens/antibodies were randomly divided into four groups: mock, DMSO, LR, and HDCA groups. The treatment groups received oral administration for five consecutive days prior to PEDV challenge. Intestinal contents were collected from piglets showing severe clinical symptoms for metabolomic sequencing. For piglets that either remained asymptomatic or displayed mild symptoms, jejunal contents were collected following euthanasia on day 7 post-challenge for subsequent metabolomic analysis.
Question: Write a study description for the study titled 'Investigation of cross-platform analytical precision in NMR and UPLC-MS based metabolic-phenotyping'.
Answer: Dataset of six samples of pooled human urine, aliquoted, and independently prepared and aquired by NMR spectroscopy, and UPLC-MS. Each source sample is seperatly prepared and assayed thirteen times. A pooled QC sample and independent external reference of a compariable matrix is also aquired to assist in assesing analytical precision.
Question: Write a study description for the study titled 'Multiyear dynamics of recent and legacy contaminants in a German hill-slope catchment (MS2 data)'.
Answer: Anthropogenic activities cause the release of vast amounts of contaminants into the environment and thus also into surface- and groundwaters. Regulatory monitoring determines whether critical threshold concentrations are surpassed, by mostly occasional probing. This irregular testing, however, does not capture the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants in response to water flows. We report the detection and tracing of five contaminants in the 'Hainich Critical Zone Exploratory' (CZE) in central Germany, a monitoring site established for regular sampling of groundwater from different depths and locations along a hill-slope recharge area. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids), the latter being volatilised from wood burning in ovens, show phases of seasonal dynamics in line with their release mode. Further, and alongside legacy herbicides (simazine and the triazine transformation product hydroxypropazine) and the concurrent flame retardant and plasticiser TPP (triphenyl phosphate), mobilisation events emerge from periods of high precipitation and water flows. This investigation highlights the persistence and mobilization of anthropogenic contaminants even in pristine environments. It illustrates the importance of long-term research for understanding ecosystem processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time.MS2 data is reported in the current study MTBLS3533.MS1 data is reported in MTBLS8433.