LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Effect of Zanthoxylum bungeanum essential oil on rumen enzyme activity, microbiome, and metabolites in lambs'.
Answer: Antibiotics were once used in animal production to improve productivity and resistance to pathogenic microbiota. However, due to its negative effects, the search for a new class of substances that can replace its efficacy has become one of the urgent problems to be solved. Plant essential oils (EOs) as a natural feed additive can maintain microbiota homeostasis and improve animal performance. However, its specific mechanism of action needs to be further investigated. Therefore, we added different doses of essential oil of Zanthoxylum bungeanum (EOZB) to the diets of Small Tail Han Sheep hybrid male lambs (STH lambs) to evaluate the effect of EOZB on rumen enzyme activity, rumen microbiology and its metabolites in STH lambs. Twenty STH lambs were randomly divided into four groups (n = 5/group) and provided with the same diet. The dietary treatments were as follows: basal diet (BD) group; BD+EOZB 5 mL/kg group; BD+EOZB 10 mL/kg group; BD+EOZB 15 mL/kg group. We found that EOZB 10 ml/kg helped to increase rumen pectinase (P<0.05) and lipase (P<0.05) activities. Microbial 16S rRNA gene analysis showed that EOZB significantly altered the abundance of rumen microbiota (P<0.05). LC/GC-MS metabolomic analysis showed that the addition of EOZB produced a total of 1073 differential metabolites, with 58 differential metabolites remaining after raising the screening criteria. These differential metabolites were mainly enriched in glycerophospholipid metabolism, choline metabolism in cancer, retrograde endocannabinoid signaling, benzoxazinoid biosynthesis, and protein digestion and absorption. Correlation analysis showed that some rumen microbiota were significantly correlated with differential metabolite and enzyme activities.
Question: Write a study description for the study titled 'Lipid-accumulated reactive astrocytes promote disease progression in epilepsy (Mice lipidomics)'.
Answer: Reactive astrocytes play an important role in neurological diseases, but their molecular and functional phenotypes in epilepsy are unclear. Here, we show that in patients with temporal lobe epilepsy (TLE) and mouse models of epilepsy, excessive lipid accumulation in astrocytes leads to the formation of lipid-accumulated reactive astrocytes (LARAs), a new reactive astrocyte subtype characterized by elevated APOE expression. Genetic knockout of APOE inhibited LARA formation and seizure activities in epileptic mice. Single-nucleus RNA sequencing in TLE patients confirmed the existence of a LARA subpopulation with a distinct molecular signature. Functional studies in epilepsy mouse models and human brain slices showed that LARAs promote neuronal hyperactivity and disease progression. Targeting LARAs by intervention with lipid transport and metabolism could thus provide new therapeutic options for drug-resistant TLE.Mice lipidomics is reported in the current study MTBLS8865.Human lipidomics reported in MTBLS8856.
Question: Write a study description for the study titled 'The oncoprotein SET promotes serine-derived one-carbon metabolism by regulating SHMT2 enzymatic activity'.
Answer: Cancer cells frequently reprogram one-carbon metabolic pathways to fulfill their vigorous demands of biosynthesis and antioxidant defense for survival and proliferation. Dysfunction of oncogenes or tumor suppressor genes is critically involved in this process, but the precise mechanisms by which cancer cells actively trigger one-carbon metabolic alterations remain incompletely elucidated. Here, by using nontargeted metabolomic analysis, we identify the oncoprotein SET as a key regulator of one-carbon metabolism in cancer cells. SET physically interacts with mitochondrial SHMT2 and facilitates SHMT2 enzymatic activity. Loss of SET profoundly suppresses serine-derived one-carbon metabolic flux, while reexpression of ectopic SET leads to the opposite effect. Notably, although the presence of SHMT2 is critical for SET-mediated one-carbon metabolic alterations, the depletion of SHMT2 alone is insufficient to antagonize SET-induced tumor growth. Instead, pharmacological targeting of cellular SHMT activity results in dramatic suppression of SET-induced tumor growth. Moreover, by using a Kras/Lkb1 mutation-driven lung tumor mouse model, we demonstrate that loss of SET compromises both tumor formation and intratumoral SHMT2 enzymatic activity. Clinically, overexpression of SET and SHMT2 are observed in lung tumors, both of which correlate with poor prognosis. Our study reveals a SET-SHMT2 axis in regulating serine-derived one-carbon metabolism and uncovers one-carbon metabolic reprogramming as a critical mechanism for aberrant SET-driven tumorigenesis.
Question: Write a study description for the study titled 'Identification of a discriminative metabolomic fingerprint of potential clinical relevance in saliva of patients with periodontitis using 1H nuclear magnetic resonance (NMR) spectroscopy'.
Answer: Periodontitis is characterized by the loss of the supporting tissues of the teeth in an inflammatory-infectious context. The diagnosis relies on clinical and X-ray examination. Unfortunately, clinical signs of tissue destruction occur late in the disease progression. Therefore, it is mandatory to identify reliable biomarkers to facilitate a better and earlier management of this disease. To this end, saliva represents a promising fluid for identification of biomarkers as metabolomic fingerprints. The present study used high-resolution 1H-nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical analysis to identify the metabolic signature of active periodontitis. The metabolome of stimulated saliva of 26 patients with generalized periodontitis (18 chronic and 8 aggressive) was compared to that of 25 healthy controls. Principal Components Analysis (PCA), performed with clinical variables, indicated that the patient population was homogeneous, demonstrating a strong correlation between the clinical and the radiological variables used to assess the loss of periodontal tissues and criteria of active disease. Orthogonal Projection to Latent Structure (OPLS) analysis showed that patients with periodontitis can be discriminated from controls on the basis of metabolite concentrations in saliva with satisfactory explained variance (R2X = 0.81 and R2Y = 0.61) and predictability (Q2Y = 0.49, CV-AUROC = 0.94). Interestingly, this discrimination was irrespective of the type of generalized periodontitis, i.e. chronic or aggressive. Among the main discriminating metabolites were short chain fatty acids as butyrate, observed in higher concentrations, and lactate, gamma-amino-butyrate, methanol, and threonine observed in lower concentrations in periodontitis. The association of lactate, GABA, and butyrate to generate an aggregated variable reached the best positive predictive value for diagnosis of periodontitis. In conclusion, this pilot study showed that 1H-NMR spectroscopy analysis of saliva could differentiate patients with periodontitis from controls. Therefore, this simple, robust, non-invasive method, may offer a significant help for early diagnosis and follow-up of periodontitis.
Question: Write a study description for the study titled 'LC-MS groundwater analysis 'Hainich Critical Zone exploratory', dataset extension (MS1)'.
Answer: Understanding biogeochemical conversions of dissolved organic matter (DOM) in aquifers is paramount for the effective management of groundwater supplies. On its passage through the critical zone, DOM is subject to biogeochemical conversions and therefore carries cross-habitat information useful for monitoring and predicting the stability of groundwater ecosystem services. Groundwater metabolomics assesses this information. However, challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics, and the necessity to maintain analytical conditions for long-term monitoring. We explored fractured sedimentary bedrock by 5-year untargeted metabolomics monitoring for oxic perched and anoxic phreatic sites along a hillslope recharge area, to evaluate DOM as groundwater tracer. Dimension reduction by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels and environmental tracers. The metabolome was highly variable lacking seasonal patterns, and did not segregate by geographic location of sampling wells thus ruling out surface vegetation or (agricultura) land use as driving factor. The metabolome time series provide detailed insights into subsurface responses to recharge dynamics. Metabolomics monitoring provides information on groundwater flows, and allows concluding about below ground ecology and water quality evolution, required to understand the impact of interannual wet-dry cycles.This study is an extension of groundwater monitoring untargeted MS1 data previously published in MTBLS3450 and MTBLS8433
Question: Write a study description for the study titled 'Metabolome analysis via an HPLC-ESI-MS-based experimental and computational pipeline for chronic nephron toxicity profiling'.
Answer: Untargeted metabolomics has the potential to improve the predictivity of in vitro toxicity models and therefore may aid the reduction of expensive and laborious animal models. Here we describe a chronic nephrotoxicity study conducted on a human renal proximal tubular epithelial cell line (RPTEC/TERT1) treated with low (10 µM) and high (35 µM) concentrations of chloroacetaldehyde (CAA) – a known nephrotoxic compound. The presented toxicity study followed two major strategies; the first was to establish an automated and easy to use untargeted metabolomics workflow for HPLC-MS data and second to find time- and dose dependent toxicant-induced cell responses at the metabolite level. The metabolomic changes were integrated with transcriptomics and proteomics data to obtain a more comprehensive picture of the mode of action. Automated data analysis workflows based on open-source software (OpenMS and KNIME) enable a comprehensive and reproducible analysis of the complex and voluminous metabolomics data produced by the profiling approach. For toxicity profiling of CAA, 428 and 317 metabolite features were detectable in positive and negative mode, respectively, after removal of chemical noise and unstable signals. Changes upon treatment were visually explored using principal component analysis and statistically significant differences identified using linear models (LIMMA). The analysis revealed toxic effects only for the high concentration treatment for day 3 and day 14. The most regulated metabolites were glutathione and metabolites related to the oxidative stress response of the cells. These findings are corroborated by proteomics and transcriptomics data, which show, amongst others, an activation of the Nrf2 pathway.
Question: Write a study description for the study titled 'Benchmarking non-targeted metabolomics using yeast extract controls'.
Answer: Non-target analysis based on high resolution mass spectrometry calls for quality controls to validate analytical workflows. So far no community-wide used quality control material has been established in metabolomics. In this work, we propose ethanolic yeast extracts derived from Pichia pastoris in vivo fermentation as stable and cheap controls. The provided open-source database of ca. 200 annotated metabolites enables to benchmark the coverage of non-targeted metabolomics workflows.
Question: Write a study description for the study titled 'Metabolomic profiling of Fraxinus excelsior genotypes tolerant or susceptible to ash dieback disease reveals changes in iridoid glycosides'.
Answer: European common ash, Fraxinus excelsior L., is currently threatened by Ash dieback (ADB) caused by the fungus, Hymenoscyphus fraxineus. To detect and identify metabolites that may be products of pathways important in contributing to resistance against H. fraxineus we performed untargeted metabolomic profiling on leaves from selected F. excelsior individuals showing strong tolerance or susceptibility to H. fraxineus. We identified sets of ""features"" [small molecules] that enabled strong discrimination between tolerant or susceptible genotypes of F. excelsior. Strikingly, tolerant F. excelsior lines exhibited low levels of iridoid glycosides, known anti-feeding deterrents. As Europe is threatened by Emerald Ash Borer (Agrilus planipennis), an invasive wood boring beetle native to East Asia that has devastated North American ash, our study raises the question whether selection for resistance to H. fraxineus leads to ecological trade-offs that result in susceptibility to emerging pests such as emerald ash borer.
Question: Write a study description for the study titled 'The correlation of gut microbiota and serum metabolites with Sasang constitution'.
Answer: In this study, metabolomic analysis with multivariate statistics was performed to examine the serum metabolic changes in human participants, which are divided into three groups (So-Yang, So-Eum and Tae-Eum) according to Sasang Constitution Medicine (SCM), Korean Traditional Oriental Medicine, that has bean an important tool in diagnosis and treatment of patients.
Question: Write a study description for the study titled 'Metabolomic evidence for biogeographic segregation in Espeletiinae (Asteraceae): A new perspective on an Andean adaptive radiation in sky islands (Interspecific chemical variability assay)'.
Answer: The biogeography of tropical Andean plants and the effects of altitudinal barriers as evolutionary constraints have been the focus of great debate. Although genetic markers have provided evidence for the geographic isolation of Andean-endemic groups, even highly variable molecular markers commonly used to assess biogeography do not have the resolving power needed for a fine geographic discrimination in some Andean taxa. We present a metabolomics approach based on ultrahigh-performance liquid chromatography-mass spectrometry combined with multivariate statistical methods and machine learning algorithms of multiple species and populations of Espeletiinae (Asteraceae) to provide metabolomic evidence for biogeographic segregation in this Andean-endemic subtribe. Our approach allows the discrimination of Espeletiinae taxa at different geographic scales with characteristic metabolic fingerprints related to their country of origin on a global scale, to their páramo massifs on a regional scale and to their páramo complexes on a local scale, revealing inter- and intraspecific metabolic variations. Our results, together with previous studies, suggest that Andean geography and Pleistocene glacial cycles not only shaped the evolutionary history of Espeletiinae but also its metabolic fingerprints, demonstrating the potential of metabolomics for understanding biogeographic patterns in recently diversified plant groups where genetic divergence is still at an early stage.Interspecific chemical variability assay protocols and data are reported in the current study MTBLS944.Intraspecific chemical variability assay protocols and data are reported in study MTBLS943.
Question: Write a study description for the study titled '1H NMR Urinary Metabolomic Analysis in Older Adults after Hip Fracture Surgery May Provide Valuable Information for Patient Profiling-A Preliminary Investigation'.
Answer: In these times of precision and personalized medicine, profiling patients to identify their needs is crucial to providing the best and most cost-effective treatment. In this study, we used urine metabolomics to explore the characterization of older adults with hip fractures and to explore the forecasting of patient outcomes. Overnight urine specimens were collected from 33 patients (mean age 80 ± 8 years) after hip fracture surgery during their stay at a rehabilitation hospital. The specimens were analyzed with 1H NMR spectroscopy. We performed a metabolomics study regarding assessments of frailty status, Functional Independence Measure (FIM), and Short Physical Performance Battery (SPPB). The main metabolic variations concerned 10 identified metabolites: paracetamol derivatives (4 peaks: 2.15 ppm; 2.16 ppm; 7.13 ppm and 7.15 ppm); hippuric acid; acetate; acetone; dimethylamine; glycine; alanine; lactate; valine; TMAO. At baseline, the urinary levels of these metabolites were significantly higher (i) in frail compared with non-frail patients, (ii) in persons with poorer FIM scores, and (iii) in persons with poorer compared SPPB scores. Our findings suggested that patients with increased levels of urine metabolites associated with metabolic, inflammatory, and renal disorders presented clear signs of frailty, impaired functional independence, and poor physical performance. Metabolomics could be a valuable tool to further characterize older adults, especially after major medical events.
Question: Write a study description for the study titled 'Anti-cyclooxygenase, antiglycation and anti-skin aging effect of Dendrobium officinale flowers aqueous extract and its phytochemical validation in aging'.
Answer: The information available in the literature concerning the beneficial effects of Dendrobium officinale flowers on the skin is limited. Therefore, the present study aimed to investigate the in vitro biological potency of its aqueous extract and screen its active components. The aqueous extract of D. officinale flowers was found to have potential antioxidant capacity (through 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), the ferric reducing ability of plasma (FRAP) and intracellular reactive oxygen species (ROS) level analyses in primary human epidermal keratinocytes), anti-cyclooxygenase2 (COX-2) effect, anti-glycation potency and anti-aging effects. A total of 34 compounds were identified using ultra-performance liquid chromatography-electrospray ionisation-quadrupole-time-of-flight-mass spectrometry (UPLC-ESI-QTOF-MS/MS). Online ABTS radical UPLC-photodiode array detection (PDA) analysis demonstrated that 1-O-caffeoyl-β-D-glucoside, vicenin-2, luteolin-6-C-β-D-xyloside-8-C-β-D-glucoside, quercetin-3-O-sophoroside, rutin, isoquercitrin and quercetin 3-O-(6''-O-malonyl)-β-D-glucoside are the major potential antioxidants. In addition, 16 components were further analysed using antioxidant assays (DPPH, ABTS and FRAP); COX-2 and advanced glycation end product (AGE) inhibitory activities were assessed. All selected compounds exerted significant ABTS radical scavenging ability and effective AGE suppressive activities. However, only certain compounds, such as rutin and isoquercitrin, displayed selective and significant antioxidant abilities, as shown by DPPH and FRAP, as well as potent COX-2 inhibitory capacity, whereas the remaining compounds displayed relatively weak or no effects. This indicates that specific components contributed to different functionalities. Our finding justified that D. officinale and its active compound targeted related enzymes and highlighted their potential application in anti-aging.
Question: Write a study description for the study titled 'Effects of MeJA on Arabidopsis metabolome under endogenous JA deficiency'.
Answer: Jasmonates (JAs) play important roles in plant growth, development and defense. Comprehensive metabolomics profiling of plants under JA treatment provides insights into the interaction and regulation network of plant hormones. Here we applied high resolution mass spectrometry based metabolomics approach on Arabidopsis wild type and JA synthesis deficiency mutant opr3. The effects of exogenous MeJA treatment on the metabolites of opr3 were investigated. More than 10000 ion signals were detected and more than 2000 signals showed significant variation in different genotypes and treatment groups. Multivariate statistic analyses (PCA and PLS-DA) were performed and a differential compound library containing 174 metabolites with high resolution precursor ion-product ions pairs was obtained. Classification and pathway analysis of 109 identified compounds in this library showed that glucosinolates and tryptophan metabolism, amino acids and small peptides metabolism, lipid metabolism, especially fatty acyls metabolism, were impacted by endogenous JA deficiency and exogenous MeJA treatment. These results were further verified by quantitative reverse transcription PCR (RT-qPCR) analysis of 21 related genes involved in the metabolism of glucosinolates, tryptophan and a-linolenic acid pathways. The results would greatly enhance our understanding of the biological functions of JA.
Question: Write a study description for the study titled 'Probabilistic networks of blood metabolites in healthy subjects as indicators of latent cardiovascular risk'.
Answer: The complex nature of the mechanisms behind cardiovascular diseases prevents the detection of latent early risk conditions. Network representations are ideally suited to investigate the complex interconnections between the individual components of a biological system underlying complex diseases. Here we investigate the patterns of correlations of an array of 29 metabolites identified and quantified in the plasma of 864 healthy blood donors and use a systems biology approach to define metabolite probabilistic networks specific for low and high latent cardiovascular risk. We adapted methods based on the likelihood of correlation and methods from information theory and combined them with resampling techniques. Our results show that plasma metabolite networks can be defined that associate with latent cardiovascular disease risk. The analysis of the networks supports our previous finding of a possible association between cardiovascular risk and impaired mitochondrial activity and highlights post-translational modifications (glycosilation and oxidation) of lipoproteins as a possible target-mechanism for early detection of latent cardiovascular risk.
Question: Write a study description for the study titled 'Optimizing peak picking and development of a suspect screening tool for rapid annotation of the human chemical exposome from LC- HRMS datasets'.
Answer: The technological advances of cutting-edge high-resolution mass spectrometry (HRMS) has set the stage for a new paradigm for exposure assessment. However, it is critical to ensure that bioinformatics software developed to process raw HRMS data can disentangle low-abundant xenobiotics from the noise. It is also essential to provide tools to speed up the annotation process. In this study, we optimized and compared the efficiency of open source (e.g. XCMS and MzMine2) and vendor software (e.g. MarkerViewTM and Progenesis QI) to detect low-abundant xenobiotics in human plasma and serum. We show that the rates of false negative can be decreased to below 5% when critical parameters are identified and tuned. Even though similar performances can be achieved using the best tuning for all software, the best detection rate was observed for MzMine2 (ADAP pipeline). We then developed an automatized suspect screening workflow (XenoScreener) based on the mass, three Rt prediction models and isotopic pattern. Indicators were developed to provide intermediate annotation scores for each predictor as well as a global score. With XenoScreener, we show that it is possible to efficiently pre-annotate with a high level of confidence a mix of xenobiotics spiked at real-life concentrations in human plasma and serum samples in a very short time (i.e. less than 3 hours after acquisition). We also demonstrate XenoScreener’s high efficiency for the rapid annotation of various xenobiotics (pharmaceuticals, lifestyle markers, plasticizers, flame-retardant, antifungals) in human plasma and serum using a library of about 2200 xenobiotics (annotation confirmed with MS/MS data).