LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Characterization of active peptides derived from three leeches and comparison of their anti-thrombotic mechanisms using the tail vein thrombosis model in mice and metabonomics'.
Answer: BACKGROUND AND AIMS: The increasing incidence of cardiovascular diseases has created an urgent need for safe and effective anti-thrombotic agents. Leech, as a traditional Chinese medicine, has the effect of promoting blood circulation and removing blood stasis, but its real material basis and mechanism of action for the treatment of diseases such as blood stasis and thrombosis have not been reported.METHODS: In this study, Whitmania Pigra Whitman (WPW), Hirudo nipponica Whitman (HNW) and Whitmania acranutata Whitman (WAW) were hydrolyzed by biomimetic enzymatic hydrolysis to obtain the active peptides of WPW (APP), the active peptides of HNW (APH) and the active peptides of WAW (APA), respectively. Then their structures were characterized by sykam amino acid analyzer, fourier transform infrared spectrometer (FT-IR), circular dichroism (CD) spectrometer and LC-MS. Next, the anti-thrombotic activities of APP, APH and APA were determined by carrageenan-induced tail vein thrombosis model in mice, and the anti-thrombotic mechanisms of high-dose APP group (HAPP), high-dose APH group (HAPH) and high-dose APA group (HAPA) were explored based on UHPLC-Q-Exactive Orbitrap mass spectrometry.RESULTS: The results showed that the amino acid composition of APP, APH and APA was consistent, and the proportion of each amino acid was few different. The results of FT-IR and CD showed that there were no significant differences in the proportion of secondary structures (such as β-sheet and random coil) and infrared absorption peaks between APP, APH and APA. Mass spectrometry data showed that there were 43 common peptides in APP, APH and APA, indicating that the three have common material basis. APP, APH and APA could significantly inhibit platelet aggregation, reduce black-tail length, whole blood viscosity (WBV), plasma viscosity (PV), and Fibrinogen (FIB), and prolong coagulation time, including activated partial thrombin time (APTT), prothrombin time (PT) and thrombin time (TT). In addition, 24 metabolites were identified as potential biomarkers associated with thrombosis development. Among these, 19, 23, and 20 metabolites were significantly normalized after administration of HAPP, HAPH, and HAPA in the mice, respectively. Furthermore, the intervention mechanism of HAPP, HAPH and HAPA on tail vein thrombosis mainly involved in linoleic acid metabolism, primary bile acid biosynthesis and ether lipid metabolism.CONCLUSION: Our findings suggest that APP, APH and APA can exert their anti-blood stasis and anti-thrombotic activities by interfering with disordered metabolic pathways in vivo, and there is no significant difference in their efficacies.
Question: Write a study description for the study titled 'Absolute quantification of metabolites in tomato fruit extracts by fast 2D NMR (Calibration Standard 700 MHz samples)'.
Answer: Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism.Calibration Standard 700 MHz samples protocols and data are reported in the current study MTBLS134.Tomato 500 MHz samples protocols and data are reported in MTBLS131.Tomato 700 MHz samples protocols and data are reported in MTBLS132.Calibration Standard 500 MHz samples protocols and data are reported in MTBLS133.
Question: Write a study description for the study titled 'Alleviation of high-fat diet-induced lipid metabolism disorders: Role of quinoa peptides in inhibiting high-activity BSH-producing gut microbiota and modulating of BA-FXR/TGR5 signaling'.
Answer: Abstract Background: Lipid metabolism disorders contribute significantly to various metabolic diseases and are closely related to gut microbiota dysbiosis. Our previous study showed that oral gavage of quinoa peptides (QPep) restored gut microbiota composition and alleviated liver lipid metabolism disorders in high-fat diet (HFD)-induced obese mice. Nevertheless, the precise mechanisms are still not fully understood. This study aimed to clarify how QPep improve lipid metabolism disorders in HFD mice. Results: Oral gavage of QPep significantly attenuated HFD-induced metabolic disorders in mice, as evidenced by reduced body weight gain and adipose mass, improved serum lipid profiles, decreased hepatic lipid accumulation, and ameliorated impaired glucose homeostasis. The microbiota clearance and fecal microbiota transplantation experiments demonstrated that the beneficial effect of QPep on lipid metabolism disorders depends on the gut microbiota. QPep selectively suppressed gut bacteria that encode bile salt hydrolase (BSH), with high enzymatic activity, reducing intestinal BSH activity while preserving conjugated bile acids (BAs). These accumulated conjugated BAs served as natural FXR antagonists, inhibiting the ileal FXR-FGF15 signaling pathway and stimulating hepatic BAs synthesis by upregulating CYP7A1/CYP27A1. Concurrently, the altered BAs profile strongly activated TGR5 in epididymal white adipose and ileum tissues, reprogramming systemic lipid metabolism and alleviating metabolic disorders. Conclusions: This study reveals a novel mechanism by which bioactive peptides derived from quinoa protein ameliorate lipid metabolism disorders via gut microbiota-BAs crosstalk. These findings demonstrate the potential of quinoa peptides as functional ingredients for metabolic syndrome management and suggest a strategy for precise gut microbiota regulation through dietary interventions.
Question: Write a study description for the study titled 'Metabolomic Profiling of Submaximal Exercise at a Standardised Relative Intensity in Healthy Adults'.
Answer: Ten physically active subjects underwent two cycling exercise trials. In the first, aerobic capacity (VO2max) was determined and the second was a 45 min submaximal exercise test. Urine samples were collected separately the day before (day 1), the day of (day 2), and the day after (day 3) the submaximal exercise test (12 samples per subject). Metabolomic profiling of the samples was carried out using hydrophilic interaction chromatography (HILIC) coupled to an Orbitrap Exactive mass spectrometer. Data were extracted, database searched and then subjected to principle components (PCA) and orthogonal partial least squares (OPLSDA) modelling. The best results were obtained from pre-treating the data by normalising the metabolites to their mean output on days 1 and 2 of the trial. This allowed PCA to separate the day 2 first void samples (D2S1) from the day 2 post-exercise samples (D2S3) PCA also separated the equivalent samples obtained on day 1 (D1S1 and D1S3). OPLSDA modelling separated both the D2S1 and D2S3 samples and D1S1 and D1S3 samples. The metabolites affected by the exercise samples included a range of purine metabolites and several acyl carnitines. Some metabolites were subject to diurnal variation these included bile acids and several amino acids, the variation of these metabolites was similar on day 1 and day 2 despite the exercise intervention on day 2. Using OPLS modelling it proved possible to identify a single abundant urinary metabolite provisionally identified as oxo-aminohexanoic acid (OHA) as being strongly correlated with VO2max when the levels in the D2S3 samples were considered.
Question: Write a study description for the study titled 'BMAL1-depletion remodels ceramide metabolism to regulate ferroptosis and sorafenib chemosensitivity in acute myeloid leukemia'.
Answer: Acute myeloid leukemia (AML) is a hematologic malignancy with a poor prognosis. We discovered that BMAL1 is a ferroptosis suppressor. Furthermore, it was also found to be overexpressed in AML patients, affecting the cell cycle and promoting tumor cell growth and progression. In this study, we further validated the association of BMAL1 with the progression and survival outcomes of AML. Lipidomic revealed that the levels of ceramide increased in AML cells following the depletion of BMAL1. Ceramide facilitated ferroptosis in AML cells. ASAH2 played a key role in this process. BMAL1 could not directly regulate ASAH2 but instead through IKZF2. Elevated levels of ceramide promoted the degradation of the ferroptosis protection molecule GPX4, ultimately promoting ferroptosis. Furthermore, ceramide treatment has been demonstrated to enhance the responsiveness of AML cells to sorafenib. In summary, this study elucidates that BMAL1 depletion remodels ceramide metabolism to regulate the sensitivity of AML cells to ferroptosis and targeted drug sorafenib.
Question: Write a study description for the study titled 'Targeting the SREBP-dependent lipidomic reprogramming by virus infection for broad-spectrum therapeutic intervention'.
Answer: Viruses are obligate intracellular parasites that exploit the host metabolic machineries to meet their extraordinary biosynthetic demands. Integrative transcriptomic and lipidomic profiling confirmed that Middle East respiratory syndrome coronavirus (MERS-CoV) infection reprograms the host lipid metabolism. By exploring a bioactive lipid library, we identified a tool compound, AM580 which is highly potent in interrupting the life cycle of diverse viruses including MERS-CoV and influenza A virus. Using click chemistry, the sterol regulatory element binding protein (SREBP) was identified as the primary cellular target of AM580 which accounts for its broad-spectrum antiviral activity. Mechanistic studies pinpoint multiple SREBP proteolytic processes and SREBP-regulated lipid biosynthesis pathways, including the downstream viral protein palmitoylation and double-membrane vesicles formation, that are indispensable for virus replication. Collectively, our study identifies a basic lipogenic transactivation event with broad relevance to human viral infections and represents SREBP as an ideal target for the development of broad-spectrum intervention strategies.
Question: Write a study description for the study titled 'Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics'.
Answer: The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomics provides novel perspectives to study microbial processes and facilitates a more profound understanding at the metabolic level. The advanced statistical framework enables deciphering the complexity of large metabolomics data sets. More specifically, a series of lab-scale batch reactors were set up with different ammonia sources added. Samples of 9 time points over the degradation were analyzed with liquid chromatography-mass spectrometry. A filtering procedure was applied to select the promising metabolomic peaks from 1262 peaks, followed by modeling their intensities across time. The metabolomic peaks with similar time profiles were clustered, evidencing the correlation of different biological processes. Differential analysis was performed to seek the differences in metabolite dynamics caused by different anions. Finally, tandem mass spectrometry and metabolite annotation provided further information on the molecular structure and possible metabolic pathways. For example, the consumption of 5-aminovaleric acid, a short-chain fatty acid obtained from l-lysine degradation, was slowed down by phosphates. Overall, by investigating the effect of anions on anaerobic digestion, our study demonstrated the effectiveness of metabolomics in providing detailed information in a set of samples from different experimental conditions. With the statistical framework, the approach enables capturing subtle differences in metabolite dynamics between samples while accounting for the differences caused by time variations.
Question: Write a study description for the study titled 'Gut Microbiome and Serum Metabolic Alterations in Recurrent Gestational Diabetes Mellitus'.
Answer: Gestational diabetes mellitus (GDM) is a common complication of pregnancy, particularly affecting multiparous women with a history of GDM, who face a recurrence risk approaching 50%. This study investigates the association between gut microbiota modifications and metabolic profiles from early to mid-pregnancy and the recurrence of GDM in a cohort of 70 multiparous women with prior GDM. Conducted as a prospective cohort study at Beijing Obstetrics and Gynecology Hospital from July 2018 to December 2020, participants underwent assessments including oral glucose tolerance tests (OGTT) and collection of fecal and serum samples. Microbial DNA was extracted, with the V3-V4 region of the 16S rRNA gene sequenced, while serum metabolites were analyzed through non-targeted metabolomics using mass spectrometry. Results indicated significant alterations in gut microbiota composition, with specific genera associated with increased GDM risk. Notably, the study identified distinct metabolic patterns, revealing downregulation of several key metabolites in recurrent GDM cases compared to controls. Pathway enrichment analysis highlighted dysregulation in metabolic functions pertinent to serotonergic synapses, arachidonic acid metabolism, unsaturated fatty acid biosynthesis, and caffeine metabolism. Overall, this research underscores the critical role of gut microbiota and metabolic changes in understanding GDM recurrence, providing insights that may inform targeted preventive strategies.
Question: Write a study description for the study titled 'Plot diversity differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species'.
Answer: Plants produce thousands of compounds, collectively called the metabolome, which mediate interactions with other organisms. The metabolome of an individual plant may change according to the number and nature of these interactions. We tested the hypothesis that tree diversity level affects the metabolome of four subtropical tree species in a biodiversity ecosystem-functioning experiment, BEF-China. We postulated that the chemical diversity of leaves, roots and root exudates increases with tree diversity. We expected the strength of this diversity effect to differ among leaf, root and root exudates samples. Considering their role in plant competition, we expected to find the strongest effects in root exudates. In an ecometabolomics approach, roots, root exudates and leaves of four tree species (Cinnamomum camphora, Cyclobalanopsis glauca, Daphniphyllum oldhamii, Schima superba) were sampled from selected plots in BEF-China. Samples were extracted and analysed using Liquid Chromatography-Time of Flight-Mass Spectrometry. The exudate metabolomes were normalized over their non-purgeable organic carbon level. Multivariate analyses were applied to identify the effect of both neighbouring (local) trees and plot diversity on tree metabolomes. The species and sample specific metabolites were assigned to major compound classes using the ClassyFire tool, whereas m/z features related to diversity effects were annotated manually. Individual tree species showed distinct leaf, root and root exudate metabolomes. The main compound class in leaves were the flavonoids, whereas carboxylic acids, prenol lipids and specific alkaloids were most prominent in root exudates and roots. Overall plot diversity had a stronger effect on metabolome profiles than the diversity of local, directly neighbouring trees. Leaf metabolomes responded more often to tree diversity level than exudates, whereas root metabolomes varied the least. We found not overall correlation between metabolite richness or diversity and tree diversity. Synthesis: Classification of metabolites supported initial ecological interpretation of differences among species and organs. Particularly the metabolomes of leaves and root exudates respond to differences in tree diversity. These responses were neither linear nor uniform and individual metabolites showed different dynamics. More controlled interaction experiments are needed to dissect the causes and consequences of the observed shifts in plant metabolomes.
Question: Write a study description for the study titled 'Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health'.
Answer: In order to explore opportunities for personalized and predictive health care, we collected serial clinical measurements, health surveys and multiomics profiles (genomics, proteomics, autoantibodies, metabolomics and gut microbiome) from 96 individuals. The participants underwent data-driven health coaching over a 16-month period with continuous digital monitoring of activity and sleep. Multiomics factor analysis resulted in an unsupervised, data-driven and integrated view of human health, revealing distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet and hormonal effects. The data revealed novel and previously uncovered associations between risk factors, molecular pathways, and quantitative lifestyle parameters. For example, ethinyl estradiol use had a distinct impact on metabolites, proteins and physiology. Multidimensional molecular and digital health signatures uncovered biological variability between people and quantitative effects of lifestyle changes, hence illustrating the value of the combined use of molecular and digital monitoring of human health.
Question: Write a study description for the study titled 'Transcriptomics and Metabolomics Reveal Alterations in Xenobiotic Metabolism and Appearance of Steroidal Alkaloid Metabolites in Mouse Livers after Tomato Consumption'.
Answer: SCOPE: Tomato consumption is associated with many health benefits including lowered risk for developing certain cancers. It is hypothesized that tomato phytochemicals are transported to the liver and other tissues where they alter gene expression in ways that lead to favorable health outcomes. However, the effects of tomato consumption on mammalian liver gene expression and chemical profile are not well defined.METHODS AND RESULTS: We hypothesized that tomato consumption would alter mouse liver transcriptomes and metabolomes compared to a control diet. C57BL/6 mice (n=11-12/group) were fed a macronutrient matched diet containing either 10% red tomato, 10% tangerine tomato, or no tomato powder for 6 weeks after weaning. RNA-Seq followed by gene set enrichment analyses indicated that tomato type and consumption, in general, altered expression of phase I and II xenobiotic metabolism genes. Untargeted metabolomics experiments revealed distinct clustering between control and tomato fed animals. Nineteen molecular formulas (representing 75 chemical features) were identified or tentatively identified as steroidal alkaloids and isomers of their phase I and II metabolites; many of which are reported for the first time in mammals.CONCLUSION: These data together suggest tomato consumption may impart benefits partly through enhancing detoxification potential.
Question: Write a study description for the study titled 'Multi-Omic Insights into the Cellular Response of Phaeodactylum Tricornutum (Bacillariophyta) Strains under Grazing Pressure'.
Answer: BACKGROUND/AIMS: Phaeodactylum tricornutum, a model organism of diatoms, plays a crucial role in Earth's primary productivity. Investigating its cellular response to grazing pressure is highly significant for the marine ecological environment. Furthermore, the integration of multi-omics approaches has enhanced the understanding of its response mechanism. METHODS: To assess the molecular and cellular responses of P. tricornutum to grazer presence, we conducted transcriptomic, proteomic and metabolomic analyses, combined with phenotypic data from previous studies. Sequencing data were obtained by Illumina RNA sequencing, TMT Labeled Quantitative Proteomics and Non-targeted Metabolomics, and WGCNA analysis and statistical analysis were performed.RESULTS: Among the differentially expressed genes, we observed complex expression patterns of the core genes involved in the phenotypic changes of P. tricornutum under grazing pressure across different strains and multi-omics datasets. These core genes primarily regulate the levels of various proteins and fatty acids, as well as the cellular response to diverse signals. CONCLUSION: Our research reveals the association of multi-omics in four strains responses to grazing effects in P. tricornutum. Grazing pressure significantly impacted cell growth, fatty acid composition, stress response, and the core genes involved in phenotype transformation.
Question: Write a study description for the study titled 'Seawater Analysis by Ambient Mass Spectrometry-Based Seaomics'.
Answer: A transmission mode-direct analysis in real time-quadrupole time of flight-mass spectrometry (TM-DART-QTOF-MS)-based analytical method coupled to multivariate statistical analysis was developed to interrogate lipophilic compounds in seawater samples without the need of desalinization. An untargeted metabolomics approach addressed here as seaomics was successfully implemented to discriminate sea surface microlayer (SML) from underlying water (ULW) samples (n=22, 10 paired samples) collected during a field campaign at the Cape Verde islands in September-October 2017. A panel of 11 ionic species detected in all samples allowed sample class discrimination by means of supervised multivariate statistical models. Tentative identification of species enriched at SML samples suggests that fatty alcohols, halogenated compounds, and oxygenated boron-containing organic compounds are available at the surface for water-air transfer processes. A subset of SML samples (n=5) were subject to on-site experiments during the campaign using a lab-to-the-field approach to test their secondary organic aerosol (SOA) formation potency. Results from these experiments and the analytical seaomics strategy provide a proof of concept for an approach to identifying organic molecules involved in aerosol formation processes at the water/air interface.