LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolomic Responses of Arabidopsis Suspension Cells to Bicarbonate under Light and Dark Conditions'.
Answer: Global CO2 level presently recorded at 400 ppm is expected to reach 550 ppm in 2050, an increment likely to impact plant growth and productivity. Using targeted LC-MS and GC-MS platforms we quantified 229 and 29 metabolites, respectively in a time-course study to reveal short-term responses to different concentrations (1, 3, and 10 mM) of bicarbonate (HCO3-) under light and dark conditions. Results indicate that HCO3- treatment responsive metabolomic changes depend on the HCO3- concentration, time of treatment, and light/dark. Interestingly, 3 mM HCO3- concentration treatment induced more significantly changed metabolites than either lower or higher concentrations used. Flavonoid biosynthesis and glutathione metabolism were common to both light and dark-mediated responses in addition to showing concentration-dependent changes. Our metabolomics results provide insights into short-term plant cellular responses to elevated HCO3- concentrations as a result of ambient increases in CO2 under light and dark.
Question: Write a study description for the study titled 'Dissolved metabolites from the Bermuda Atlantic Time-series Study: 2016-2019'.
Answer: Organic carbon in seawater plays a significant role in the global carbon cycle. The concentration and composition of dissolved organic carbon, operationally defined in this project as organic carbon that passes through a 0.2 µm filter, reflect the actions of the biological community and chemical reactions that occur in seawater. Here, we repeatedly sampled the oligotrophic northwest Sargasso Sea in the vicinity of the Bermuda Atlantic Time-Series Study site (BATS) to quantitatively follow select known compounds within the pool of dissolved organic matter in the upper 1000 meters of the water column over a four-year period. Metabolite concentrations revealed patterns with depth and time with most metabolites showing surface enrichment and lower concentrations with depth. Select metabolites had a pattern of increased and decreased concentrations throughout the year, which was observed in each of the years sampled. Vitamins, including pantothenic acid, biotin, and riboflavin, presented annual increases in the winter period when mixed layer depths are deepest. Light-sensitive riboflavin also showed significant decreases during daylight hours under diel sampling. The metabolites examined in this study are all components of central carbon metabolism. By examining these metabolites at finer resolution and in a relatively long time series, we have clues on microbial actions in marine systems, data which are fundamental to understanding the chemical response of marine systems to future changes in climate.
Question: Write a study description for the study titled 'Metabolic profiling with UPLC-MS orbitrap of diatoms Coscinodiscus granii infected with parasitic oomycete Lagenisma coscinodisci'.
Answer: The bloom-forming diatoms Coscinodiscus granii were cultivated in a non-contact dual cultivation apparatus. This device allows the exchange of exudates, without transfer of any microorganisms, allowing the investigation of both endo- and exo-metabolome. The treatment consisted in infecting diatom cells with parasitic oomycete Lagenisma coscinodiscii. At late infection stage (5 days of incubation), all cultures were recovered and filtrated and the endometabolome was investigated. The healthy cells which were exposed to the exudates of the infected cells were assigned as exposed cells. Healthy cell populations were taken as the controls. The experiment contained 6 replicates per conditions (control vs control, control/exposed vs treatment). Methanolic extractions of all cells were performed and metabolic profiles of the different conditions was conducted with UPLC-MS orbitrap.
Question: Write a study description for the study titled 'Valine potentiates cefoperazone-sulbactam to kill methicillin resistant Staphylococcus aureus'.
Answer: Metabolic state-reprogramming approach was extended from Gram-negative bacteria to Gram-positive bacterium methicillin-resistant Staphylococcus aureus (MRSA) for identifying desired reprogramming metabolites to synergize existing antibiotic killing to MRSA. Metabolomics comparison between MRSA and methicillinsensitive Staphylococcus aureus showed a depressed metabolic state in MRSA. Valine was identified as the most depressed metabolite/biomarker, and valine, leucine and isoleucine biosynthesis as the most enriched metabolic pathway. Thus, valine was used as a reprogramming metabolite to potentiate existing antibiotic killing to MRSA. Among the tested antibiotics, valine synergized cefoperazone-sulbactam (SCF) to produce the greatest killing effect. The combined effect of SCF and valine was demonstrated in clinical MRSA isolates and in mouse systemic and thigh infection models. Underlying mechanisms were attributed to valine-induced the activation of the pyruvate cycle/the TCA cycle and fatty acid biosynthesis. The activated pyruvate cycle/the TCA cycle elevated proton motive force by NADH and the activated fatty acid biosynthesis promoted membrane permeability by lauric acid. Both together increased cefoperazone uptake, which outpaces efflux action and thereby intracellular drug is elevated to effectively kill MRSA. These results provide the combination of valine and SCF to produce a new drug candidate effective against MRSA.
Question: Write a study description for the study titled 'Research on the quality markers of antioxidant activity of Kai-Xin-San based on spectrum-effect relationship'.
Answer: Kai-Xin-San (KXS) is one of the classic famous traditional Chinese medicine prescriptions for amnesia, which has been applied for thousands of years. Modern pharmacological research has found that KXS has significant therapeutic efficacy on nervous system diseases, which is related to its antioxidant activity. However, the antioxidant material basis and quality markers (Q-makers) of KXS have not been studied. The objective of this study is to explore the Q-makers of antioxidant activity of KXS based on spectrum-effect relationship. Specifically, the metabolites in KXS extracts were identified by UPLC-Q-Exactive Orbitrap MS/MS. The fingerprint profile of KXS extracts were established by high-performance liquid chromatography (HPLC) and seven common peaks were identified. Meanwhile, 2, 2-diphenyl-1-picrylhydrazyl (DPPH) test was used to evaluate the free radical scavenging ability of KXS. The spectrum-effect relationship between its HPLC fingerprint and DPPH free radical scavenging activity was preliminarily examined by the Pearson correlation analysis, grey relation analysis (GRA) and orthogonal partial least squares discrimination analysis (OPLS-DA). Further, the antioxidant effect of KXS and its Q-makers were validated through human neuroblastoma (SH-SY5Y) cells experiment. The results showed that 103 metabolites were identified from KXS, and the similarity values between HPLC fingerprint of twelve batches of KXS were greater than 0.900. At the same time, the results of Pearson correlation analysis showed that the peaks 8, 1, 14, 17, 18, 24, 16, 21, 15, 13, 6, 5 and 3 from KXS were positively correlated with the scavenging activity values of DPPH. Combined with the results of GRA and OPLS-DA, peaks 1, 3, 5 (Sibiricose A6), 6, 13 (Ginsenoside Rg1), 15 and 24 in the fingerprints were screen out as the potential Q-makers of KXS for antioxidant effect. Besides, the results of CCK-8 assay showed that KXS and its Q-makers remarkably reduced the oxidative damage of SH-SY5Y cells caused by H2O2. However, the antioxidant activity of KXS was decreased significantly after Q-makers were knocked out. In conclusion, the metabolites in KXS were successfully identified by UPLC-Q-Exactive Orbitrap MS/MS, and the Q-makers of KXS for antioxidant effect was analyzed based on the spectrum-effect relationship. These results are beneficial to clarify the antioxidant material basis of KXS and provide the quality control standards for new KXS products development.
Question: Write a study description for the study titled 'Bile acid is a significant host factor shaping the gut microbiome of diet induced obese mice (targeted bile acid analysis assay)'.
Answer: BACKGROUND: Intestinal bacteria are known to regulate the bile acid (BA) homeostasis via intestinal biotransformation of BAs and stimulating the expression of fibroblast growth factor 19 through intestinal nuclear farnesoid X receptor (FXR). On the other hand, BAs directly regulate the gut microbiota with their strong antimicrobial activities. It remains unclear, however, how mammalian BAs cross-talk with gut microbiome and shape microbial composition in a dynamic and interactive way.RESULTS: We quantitatively profiled small molecule metabolites derived from host-microbial co-metabolism in mice, demonstrating that Bas were the most significant factor correlated with microbial alterations among all types of endogenous metabolites. HFD intervention resulted in a rapid and significant increase in intestinal BA pool within 12 hrs followed by alteration in microbial composition at 24 hrs, providing supporting evidence that BAs are major dietary factors regulating gut microbiota. Feeding mice with BAs along with normal diet induced obese phenotype and obesity-associated gut microbial composition, similar to HFD fed mice. Finally, inhibition of hepatic BA biosynthesis under HFD conditions attenuated the HFD-induced gut microbiome alterations. Inhibition of BAs and direct suppression of micriobiota improved obese phenotypes.CONCLUSIONS: Our study highlights a liver - BAs - gut microbiome metabolic axis that drives significant modifications of BA and microbiota compositions capable of triggering metabolic disorders, suggesting new therapeutic strategies targeting BA metabolism for metabolic diseases.The untargeted metabolome profile assay for this study can be found in the MetaboLights study MTBLS545.The targeted short chain fatty acid analysis assay for this study can be found in the MetaboLights study MTBLS546.The targeted fatty acid analysis assay for this study can be found in the MetaboLights study MTBLS548.
Question: Write a study description for the study titled 'RANCM: a new ranking scheme for assigning confidence levels to metabolite assignments in NMR-based metabolomics studies'.
Answer: INTRODUCTION: The Metabolomics Standards Initiative has recommended four categories for metabolite assignments in NMR-based metabolic profiling studies. The putatively annotated compound category is most commonly reported by metabolomics investigators. However, there is significant ambiguity in reliability of putatively annotated compound assignments, which can range from low confidence made on minimal corroborating data to high confidence made on substantial corroborating data.OBJECTIVES: To introduce a new ranking system, Rank and AssigN Confidence to Metabolites (RANCM), to assign confidence levels to putatively annotated compound assignments in NMR-based metabolic profiling studies.METHODS: The ranking system was constructed with three confidence levels ranging from Rank 1 for the lowest confidence assignment level to Rank 3 for the highest confidence assignment level. A decision tree was constructed to guide rank selection for each metabolite assignment.RESULTS: Examples are provided from experimental data demonstrating how to use the decision tree to make confidence level assignments to putatively annotated compounds in each of the three rank levels. A standard Excel sheet template is provided to facilitate decision-making, documentation and submission to data repositories.CONCLUSION: RANCM is intended to reduce the ambiguity in putatively annotated compound assignments, to facilitate effective communication of the degree of confidence in putatively annotated compound assignments, and to make it easier for non-experts to evaluate the significance and reliability of NMR-based metabonomics studies. The system is straightforward to implement, based on the most common datasets collected in NMR-based metabolic profiling studies, and can be used with equal rigor and significance with any set of NMR datasets.
Question: Write a study description for the study titled 'Gut microbiota-bile acid crosstalk contributes to the rebound weight gain after calorie restriction in mice'.
Answer: Calorie restriction (CR) and fasting are common approaches to weight reduction, but the maintenance is difficult after resuming food consumption. Meanwhile, the gut microbiome associated with energy harvest alters dramatically in response to nutrient deprivation. Here, we reported that CR and high-fat diet (HFD) both remodeled the gut microbiota with similar microbial composition. Parabacteroides distasonis was most significantly decreased after CR or HFD. CR altered microbiota and reprogramed metabolism, resulting in a distinct serum bile acid profile characterized by depleting the proportion of non-12α-hydroxylated bile acids, ursodeoxycholic acid and lithocholic acid. Downregulation of UCP1 expression in brown adipose tissue and decreased serum GLP-1 were observed in the weight-rebound mice. Moreover, treatment with Parabacteroides distasonis or non-12α-hydroxylated bile acids ameliorated weight regain via increased thermogenesis. Our results highlighted the gut microbiota- bile acid crosstalk in rebound weight gain and Parabacteroides distasonis as a potential probiotic to prevent rapid post-CR weight gain.
Question: Write a study description for the study titled 'Single-cell time-resolved multi-omics reveal apoptotic and ferroptotic heterogeneity during foam cell formation'.
Answer: Macrophage-derived foam cell plays a pivotal role in the plaque formation and rupture during the progression of atherosclerosis. Foam cells are destined to divergent cell fate and functions in response to external stimuli based on their internal states, which however is hidden in the traditional studies based on population of cells. Herein, we used time-resolved and single-cell multi-omics to investigate the macrophage heterogeneity along foam cell formation. Dynamic metabolome and lipidome outlined the dual regulating axis of inflammation and ferroptosis. Single cell metabolomics and lipidomics further demonstrated a macrophage continuum featuring a differed susceptibility to apoptosis and ferroptosis. Using single-cell transcriptomic profiling, we verified the divergent cell fate toward apoptosis or ferroptosis. Therefore, the molecular choreography underlying the divergent cell fate during foam cell formation was revealed, which is of high significance for the understanding of the pathogenesis of atherosclerosis and development of new drug targets.
Question: Write a study description for the study titled 'The stability and functional redundancy of a microbial cheese ecosystem subjected to a biotic perturbation'.
Answer: The cheese microbial community is dense with relatively low complexity and composed of cultivable prokaryotic and eukaryotic microorganisms. The ripening process can thus be reproduced under controlled conditions. A reduced microbial community composed of yeasts and bacteria was assembled to mimic that of smear-ripened cheese. The genomes of the microorganisms have been sequenced and annotated, which allows access to gene expression under various conditions at different ripening times. Through the use of a combined approach using omics (e.g. metatranscriptomics, volatilomics), and biochemical/microbial analyses, we have investigated the effect of a biotic perturbation, omission of some yeast, on the stability and functionality of the microbial cheese community throughout ripening.
Question: Write a study description for the study titled 'Laser-assisted rapid evaporative ionisation mass spectrometry (LA-REIMS) as a metabolomics platform in cervical cancer screening'.
Answer: BACKGROUND: The introduction of high-risk human papillomavirus (hrHPV) testing as part of primary cervical screening is anticipated to improve sensitivity, but also the number of women who will screen positive. Reflex cytology is the preferred triage test in most settings but has limitations including moderate diagnostic accuracy, lack of automation, inter-observer variability and the need for clinician-collected sample. Novel, objective and cost-effective approaches are needed.METHODS: In this study, we assessed the potential use of an automated metabolomic robotic platform, employing the principle of laser-assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) in cervical cancer screening.FINDINGS: In a population of 130 women, LA-REIMS achieved 94% sensitivity and 83% specificity (AUC: 91.6%) in distinguishing women testing positive (n = 65) or negative (n = 65) for hrHPV. We performed further analysis according to disease severity with LA-REIMS achieving sensitivity and specificity of 91% and 73% respectively (AUC: 86.7%) in discriminating normal from high-grade pre-invasive disease.INTERPRETATION: This automated high-throughput technology holds promise as a low-cost and rapid test for cervical cancer screening and triage. The use of platforms like LA-REIMS has the potential to further improve the accuracy and efficiency of the current national screening programme.FUNDING: Work was funded by the MRC Imperial Confidence in Concept Scheme, Imperial College Healthcare Charity, British Society for Colposcopy and Cervical Pathology, National Research Development and Innovation Office of Hungary, Waters corporation and NIHR BRC.
Question: Write a study description for the study titled 'Hierarchical Carbon Metabolism in Iron-Deficient Bacteria Favors Iron-Scavenging Strategy'.
Answer: High-affinity iron (Fe) scavenging compounds, or siderophores, are widely employed by soil bacteria to survive scarcity in bioavailable Fe. Siderophore biosynthesis relies on cellular carbon metabolism, despite reported decrease in both carbon uptake and Fe-containing metabolic proteins in Fe-deficient cells. Given this paradox, the metabolic network required to sustain the Fe-scavenging strategy is poorly understood. Here, through multiple 13C-metabolomics experiments with Fe-replete and Fe-limited cells, we uncover how soil Pseudomonas species reprogram their metabolic pathways to prioritize siderophore biosynthesis. Across the three species investigated (Pseudomonas putida KT2440, Pseudomonas protegens Pf-5, and Pseudomonas putida S12), siderophore secretion is higher during growth on gluconeogenic substrates than during growth on glycolytic substrates. In response to Fe limitation, we capture decreased flux toward the tricarboxylic acid (TCA) cycle during the metabolism of glycolytic substrates but, due to carbon recycling to the TCA cycle via enhanced anaplerosis, the metabolism of gluconeogenic substrates results in an increase in both siderophore secretion (up to threefold) and Fe extraction (up to sixfold) from soil minerals. During simultaneous feeding on the different substrate types, Fe deficiency triggers a hierarchy in substrate utilization, which is facilitated by changes in protein abundances for substrate uptake and initial catabolism. Rerouted metabolism further promotes favorable fluxes in the TCA cycle and the gluconeogenesis-anaplerosis nodes, despite decrease in several proteins in these pathways, to meet carbon and energy demands for siderophore precursors in accordance with increased proteins for siderophore biosynthesis. Hierarchical carbon metabolism thus serves as a critical survival strategy during the metal nutrient deficiency.Data availability:The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD013605.
Question: Write a study description for the study titled 'Global transcription and metabolic profiles of five tissues in pepper fruits'.
Answer: The sample to be tested was fully ground into powder in the grinder, 50 mg of the sample was freeze-dried, 1000 μL of the extraction solution containing the inner target was added (methanol:acetonitrile:water, 2:2:1, v/v/v, internal standard concentration 20 mg/L) and vortex mixed for 30 s; then add the steel ball to the 45 Hz grinder for 10 min, ultrasonic 10 min; the sample to be tested is obtained after filtration. When detecting metabolites, metabolite determination was performed based on the LC-MS system, which mainly consists of Waters Acquity I-Class PLUS ultra-high performance liquid tandem and Waters Xevo G2-XS QTof high-resolution mass spectrometer. Meanwhile, the Waters Acquity UPLC HSS T3 column (1.8 um 2.1 x 100 mm) was used as the chromatographic column. Positive and negative ion modes were used to determine the metabolites. Mobile phase A: 0.1% formic acid aqueous solution; Mobile phase B: 0.1% acetonitrile formate. The mobile phase conditions of liquid chromatography were as follows: the flow rate was 400 μL/min, 0.0 min: 98% flow A, 2% flow B; 0.25 min: 98% flow A, 2% flow B, 10.0 min: 2% flow A, 98% flow B; 13.0 min: 2% flow A, 98% flow B; 13.1 min: 98% flow A, 2% flow B; 15.0 min: 98% flow A, 2% flow B. MSe mode controlled by acquisition software (MassLynx v4.2, Waters) was used for primary and secondary mass spectrum data acquisition. ESI ion source parameters are as follows: Capillary voltage, 2500 V (positive ion mode) or -2000 V (negative ion mode); Cone hole voltage, 30 V; Ion source temperature, 100 °C; Desolvent temperature, 500 °C; Air flow rate, 50 L/h; Desolvent gas flow rate, 800 L/h; Plastic-nucleus ratio (m/z) collection range 50-1200 m/z. In the qualitative and quantitative analysis of metabolites, the original data collected by MassLynx v4.2 were processed by the Progenesis QI software for peak extraction, peak alignment, and other data, and the metabolites were identified based on the Progenesis QI software online METLIN database. Then, based on the results of the total score, MS2 score, and mass error (ppm), the metabolites were qualitatively determined.
Question: Write a study description for the study titled 'Characterization of Blood Metabolites and the Uterine Microbiota in Estrus Simmental Cattle'.
Answer: Accurate oestrus detection is critical for optimizing reproductive efficiency in beef cattle, yet the underlying metabolic and microbial mechanisms remain poorly understood, particularly in Simmental cattle. To address this gap, we employed an integrated metabolomics and microbiome approach to systematically characterize blood metabolic profiles and uterine microbiota dynamics during oestrus. The results revealed significantly elevated serum levels of total protein, albumin, glucose and insulin-like growth factor-1 (IGF-1) (P<0.01) during oestrus, and metabolomics revealed 258 differentially abundant metabolites enriched primarily in amino acid and lipid metabolism pathways. Cervical microbiome analysis revealed Firmicutes and Bacteroidetes as the dominant bacterial phyla, whereas fungal Ascomycota presented significantly increased relative abundance (78.38% vs 67.20%) with reduced α diversity (P<0.05) during estrus. Functional prediction analysis further revealed significant enrichment of bacterial energy metabolism pathways (TCA cycle; q<0.01), strong positive correlations between Bacteroides and bile acids (r>0.6, P<0.01), and significant associations between Candida and lipid metabolites. These findings establish a 'microbiota‒metabolite‒host' interaction network specific to oestrus in Simmental cattle, providing novel theoretical foundations and potential biomarkers for optimizing reproductive management in cattle herds.