LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Resolvin E1 in follicular fluid acts as a potential biomarker and improves oocyte developmental competence by optimizing cumulus cells'.
Answer: The metabolic profile of follicular fluid (FF) has been investigated to look for biomarkers for oocyte quality. Resolvin E1 (RvE1), a potent pro-resolving mediator, was reported to have protective action in cell function. The study aimed to examine the predictive value of RvE1 for oocyte quality and to explore the cellular mechanism of RvE1 in improving oocyte competence. Metabolic profiles of 80 FF samples showed a higher level of RvE1 in group A (blastocysts scored ≥ B3BC and B3CB according to Gardner's blastocyst scoring system, N=36) than that of group B (blastocysts scored < B3BC and B3CB, N=44, P=.0018). The receiver operating characteristic (ROC) curve analysis showed that RvE1 level in FF below 8.96 pg/ml (AUC:0.75; 95%CI: 0.64 – 0.86; P=.00012) could predict poor oocyte quality with speciﬁcity of 97.22%, suggesting RvE1 as a potential biomarker to exclude inferior oocytes. Besides, the level of RvE1 was found to be significantly lower in FF than in serum (57.49 to 17.62 pg/ml; P=.0037) and was gradually accumulated in the culture medium of cumulus cells (CCs) during cell culture, which indicated that RvE1 came from both blood exudates and local secretion. The in vitro experiment revealed the cellular mechanism of RvE1 in improving oocyte quality by decreasing the cumulus cell apoptotic rate and increasing cell viability and proliferation. It is the first time that the role of RvE1 in reproduction is explored. In conclusion, RvE1 is valuable as a potential exclusive biomarker for oocyte selection and plays a role in improving oocyte quality.
Question: Write a study description for the study titled 'Single-cell metabolic fingerprints discover a cluster of circulating tumor cells with distinct metastatic potential'.
Answer: Circulating tumor cells (CTCs) are recognized as direct seeds of metastasis. However, CTC count may not be the 'best' indicator of metastatic risk because their heterogeneity is generally neglected. In this study, we develop a molecular typing system to predict colorectal cancer metastasis potential based on the metabolic fingerprints of single CTCs. After identification of the metabolites potentially related to metastasis using mass spectrometry-based untargeted metabolomics, setup of a home-built single-cell quantitative mass spectrometric platform for target metabolite analysis in individual CTCs and use of a machine learning method composed of non-negative matrix factorization and logistic regression, CTCs are divided into two subgroups, C1 and C2, based on a 4-metabolite fingerprint. Both in vitro and in vivo experiments demonstrate that CTC count in C2 subgroup is closely associated with metastasis incidence. This is an interesting report on the presence of a specific population of CTCs with distinct metastatic potential at the single-cell metabolite level.
Question: Write a study description for the study titled 'Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease'.
Answer: The gut microbiome is a key factor regulating energy-metabolism, glucose tolerance and the immune system. Akkermansia muciniphila has been identified as being beneficial gut bacterium for metabolic diseases, including obesity and type 2 diabetes (T2D); however, the molecular mechanisms involved in host interactions have yet to be known. Here, we described the effects of A. muciniphila on thermogenesis and GLP-1 secretion through the specific secretory protein produced by A. muciniphila and its mode of action. A. muciniphila significantly elevated thermogenesis with induction of uncoupling protein 1 (UCP1) in brown adipose tissue (BAT) and systemic glucagon-like peptide-1 (GLP-1) secretion. Using fast protein liquid chromatography (FPLC) and liquid chromatography (LC)-mass spectrophotometry (MS)/MS analysis, we discovered that a novel 84-kDa protein, P9 is secreted by A. muciniphila and this protein improves obesity and glucose tolerance by inducing GLP-1 secretion and BAT thermogenesis. P9 induces GLP-1 secretion with direct interaction with the specific host protein, intercellular adhesion molecule-2 (ICAM-2), via IL-6 dependent pathway. This novel host-microbe interaction between P9 and ICAM-2 may become a therapeutic target for metabolic diseases.
Question: Write a study description for the study titled 'Untargeted Lipidomics Profiling Provides Novel Insights into Pediatric Patients with Sepsis: An Exploratory Study'.
Answer: Background: The plasma lipidome has emerged as an important indicator for assessing host metabolic and immune status in sepsis. While previous studies have largely examined specific lipid class changes in adults sepsis, comprehensive investigations into plasma lipidomic alterations in pediatric sepsis are limited. This study aimed to characterize the plasma lipidome in pediatric sepsis using a metabolomics-based exploratory approach, providing insights into pathophysiological mechanisms and potential biomarkers.Methods: A retrospective study was conducted on pediatric patients with sepsis admitted to the pediatric intensive care unit (PICU). Untargeted lipidomics analysis using ultra-performance liquid chromatography coupled with Orbitrap mass spectrometry (UPLC-Orbitrap) was performed to compare metabolomic profiles between non-infected control patients and sepsis patients.Results: Compared to controls, plasma lipid levels in sepsis patients decreased by 33.3%, increased by 20.2%, and remained unchanged in 46.5% of cases. Several lipid molecules were identified to be associated with disease severity and inflammatory markers. In the recovery and deterioration subgroups, 186 differential lipid molecules were identified, with triglycerides (TG) being the most abundant class. Notably, 15 lipid molecules overlapped between those associated with disease severity and those linked to clinical outcomes. Fatty acid (FA) levels were significantly elevated in the sepsis group compared to controls, with arachidonic acid (FA(20:4)) showing the most significant increase (P < 0.001).Conclusion: Alterations in plasma lipid profiles among children with sepsis reflect disease severity, systemic inflammatory responses, and clinical outcomes. These findings underscore the prognostic potential of lipidomics and its value in understanding sepsis pathophysiology.Key words Pediatric sepsis, Plasma lipidome, Untargeted lipidomics, Triglycerides, Fatty acid
Question: Write a study description for the study titled 'Sodium Butyrate mediates Histone Crotonylation and Alleviated Neonatal Rats Hypoxic-Ischemic Brain Injury Through Gut-Brain Axis (untargeted fecal metabolomics)'.
Answer: Neonatal hypoxic-ischemic encephalopathy (HIE) refers to nervous system damage caused by perinatal hypoxia, which is the major cause of long-term neuro-developmental disorders in surviving infants. However, the mechanisms still require further investigation. In this study, we found that the butanoate metabolism pathway exhibited significantly decreased and short chain fatty acid (SCFAs)-producing bacteria, especially butyrate-producing bacteria, were significantly decreased in fecal of neonatal hypoxic-ischemic brain damage (HIBD) rats. Surprisingly, Sodium butyrate (SB) treatment could ameliorate pathological damage both in the cerebral cortex and hippocampus and facilitate recovery of SCFAs-producing bacteria related to metabolic pathways in neonatal HIBD rats. Moreover, we found that in samples from SB treatment neonatal HIBD rats cortex with high levels of butyrate acid along with aberrant key crotonyl-CoA-producing enzymes ACADS levels was observed compared HIBD rats. We also demonstrated that a decrease in histone 3-lysine 9-crotonylation (H3K9cr) downregulated expression of the HIE-related neurotrophic genes Bdnf, Gdnf, Cdnf and Manf in HIBD rats. Furthermore, SB restored H3K9cr binding to HIE-related neurotrophic genes. Collectively, our results indicate that SB contributes to ameliorate pathological of HIBD by altering gut microbiota and brain SCFAs levels subsequently affecting histone crotonylation-mediated neurotrophic-related genes expression. This may be a novel microbiological approach for preventing and treating HIE.Untargeted fecal metabolomics is reported in the current study MTBLS4932.Targeted SCFA brain metabolomics is reported in MTBLS4933.
Question: Write a study description for the study titled 'EFO: In preparation - Early Metabolic Predictors of Type 2 Diabetes Mellitus in Normoglycemic Adults: Insights from Six-Year Prospective Cohort Study'.
Answer: INTRODUCTION: Type 2 Diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by insulin resistance and hyperglycemia, often preceded by latent metabolic disruptions. Early detection of metabolic alterations can facilitate timely intervention to delay or prevent T2DM onset. Metabolic profiling offers a useful tool to identify novel disease biomarkers and metabolic alterations before clinical manifestations. OBJECTIVE: This study aimed to identify early metabolic alterations and potential biomarkers predictive of T2DM in a cohort of healthy normoglycemic participants over a six-year follow-up. METHODS: A cohort of 94 healthy participants, both men and women aged 18-40, was studied at six-year intervals. Clinical and biochemical parameters were measured, and LC/MS/MS-based untargeted metabolomics analysis of plasma was performed at baseline and follow-up. RESULTS: At follow-up, 9 participants developed T2DM, 51 had prediabetes and 34 remained normoglycemic. Increasing insulin resistance and elevated future T2DM risk were observed in both the Prediabetes and Normal groups. Metabolomics analysis identified Phosphatidylethanolamine (PE) (20:3_18:0), 3beta,7alpha-Dihydroxy-5-cholestenoate and Tridecanoic acid – as having good predictive capacity for future T2DM risk at baseline with alterations in Phosphatidylethanolamine (PE) (20:3_18:0), and Tridecanoic acid persisting at follow-up. CONCLUSION: The study highlights the potential of metabolomics in identifying early metabolic predictors of T2DM, emphasizing the need for early interventions in healthy normoglycemic young adults.
Question: Write a study description for the study titled 'Reprogramming yeast metabolism for customized starch-rich micro-grain through low-carbon microbial manufacturing'.
Answer: Starch is a primary food ingredient and bulk industrial feedstock. Producing starch through fermentation-based low-carbon microbial manufacturing serves as an arable land-independent and carbon-neutral/negative approach, while the efficiency of this route is highly dependent on the starch producer. We reconfigure the oleaginous yeast as an efficient cell factory for starch-rich micro-grain production by rewiring the starch biosynthesis and gluconeogenesis pathways and regulating cell morphology. With the CO2 electro-synthesized acetate as the substrate, the strain accumulates starch up to 47.18% of the dry cell weight. Through the cultivation of the micro-grain in fed-batch bioreactors, starch was produced at 19.30 g/L, 29.60% starch content, and spatial-temporal productivity (243.7 g/m2/d), approximately 50-fold higher than that of crop cultivation and an order of magnitude higher rate (160.83 mg/L/h) than the starch production in other microbes. We validated that the starch composition and starch-protein ratio in the micro-grain can be modulated by strain and process engineering. More surprisingly, we found that the engineered artificial strains adopted a cellular resources reallocation strategy to ensure high-level starch production in micro-grain, and could facilitate a highly efficient straw/cellulose-to-starch conversion. Our work lays the foundation for understanding the global cellular machinery for starch biosynthesis and enables a superior-to-nature high-level production of starch with customized composition, aiding the development of efficient and low-carbon production of nutritional resources.
Question: Write a study description for the study titled 'Lipid mediators of inflammation in BALF 3-11 days after infection with influenza'.
Answer: Bioactive lipid mediators play a crucial role in the induction and resolution of inflammation. To elucidate their involvement during influenza infection, liquid chromatography/mass spectrometry lipidomic profiling of 141 lipid species was performed on a mouse influenza model using two viruses of significantly different pathogenicity. Infection by the low-pathogenicity strain X31/H3N2 induced a proinflammatory response followed by a distinct anti-inflammatory response; infection by the high-pathogenicity strain PR8/H1N1 resulted in overlapping pro- and anti-inflammatory states. Integration of the large-scale lipid measurements with targeted gene expression data demonstrated that 5-lipoxygenase metabolites correlated with the pathogenic phase of the infection, whereas 12/15-lipoxygenase metabolites were associated with the resolution phase. Hydroxylated linoleic acid, specifically the ratio of 13- to 9-hydroxyoctadecadienoic acid, was identified as a potential biomarker for immune status during an active infection. Importantly, some of the findings from the animal model were recapitulated in studies of human nasopharyngeal lavages obtained during the 2009-2011 influenza seasons.
Question: Write a study description for the study titled 'High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry (Mixed-mode column chromatography)'.
Answer: Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.Mixed-mode column chromatography is reported in the current study MTBLS2497.Data-independent acquisition is reported in MTBLS2959.
Question: Write a study description for the study titled 'Extracellular-acidosis restricts one-carbon metabolism and preserves T cell stemness'.
Answer: The accumulation of acidic metabolic waste products within the tumor microenvironment profoundly inhibits effector functions of tumor-infiltrating lymphocytes (TILs). However, it is unclear whether extracellular-acidosis impacts T cell metabolic fitness and differentiation status. Here, we surprisingly found that prolonged acid exposure reprogrammed T cell intracellular metabolism and mitochondrial fitness, and preserved T cell stemness. Elevated extracellular-acidosis impaired methionine uptake and metabolism via downregulating SLC7A5, therefore altering H3K27me3 deposition at the promoters of crucial T cell stemness genes. These changes promoted the maintenance of a “stem-like memory” state and improved long-term in vivo persistence and anti-tumor efficacy. Our findings not only reveal the unexpected roles of extracellular-acidosis in the maintenance of stem-like properties of T cells, but also advance our understanding of the direct involvement of methionine metabolism in T cell stemness.
Question: Write a study description for the study titled 'Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development (LC-MS pos assay)'.
Answer: Seed development dedicates to reserve synthesis and accumulation and uncovering its genetic and biochemical mechanisms has been a major research focus. Although proteomic and transcriptomic analyses revealed dynamic changes of genes and enzymes involved, the information regarding concomitant metabolic changes is missing. Here we investigated the dynamic metabolic changes along the rice grain development of two japonica and two indica cultivars using non-targeted metabolomics approach, in which we successfully identified 214 metabolites. Statistical analyses revealed both cultivar and developmental stage dependent metabolic changes in rice grains. Generally, the stage specific metabolic kinetics corresponded well to the physiological status of the developing grains, and metabolic changes in developing rice grain are similar to those of dicot Arabidopsis and tomato at reserve accumulation stage but are different from those of dicots at seed desiccation stage. The remarkable difference in metabolite abundances between japonica and indica rice grain was observed at the reserve accumulation stage. Metabolite-metabolite correlation analysis uncovered potential new pathways for several metabolites. Taken together, this study uncovered both conserved and diverse development associated metabolic kinetics of rice grains, which facilitates further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in crop improvement.LC-MS pos assay is reported in MTBLS286.LC-MS neg assay is reported in MTBLS287.GC-MS assay is reported in MTBLS288.
Question: Write a study description for the study titled 'Model-guided development of evolutionarily stable yeast chassis for dicarboxylic acids production'.
Answer: Chassis strain suitable for producing multiple compounds is a central concept in synthetic biology. Design of a chassis using computational, first-principle, models is particularly attractive due to the predictability and control it offers, including against phenotype reversal due to adaptive mutations. Yet, the theory of model-based chassis design has rarely been put to rigorous experimental test and assessed at multiomics level. Here, we report two Saccharomyces cerevisiae chassis strains for dicarboxylic acid production based on genome-scale metabolic modelling. The chassis strain, harbouring gene knockouts in serine biosynthesis and in pentose-phosphate pathway, is geared for higher flux towards three target products - succinate, fumarate and malate - but does not appreciably secrete any. Introducing modular product-specific mutations resulted in improved secretion of the corresponding acid as predicted by the model. Adaptive laboratory evolution of the chassis-derived producer cells further improved production for succinate and fumarate attesting to the evolutionary robustness of the underlying growth-product coupling. In the case of malate, which exhibited decreased production during evolution, the multiomics analysis revealed flux bypass at peroxisomal malate dehydrogenase that was not accounted in the model. Integration of transcriptomics, proteomics and metabolomics data showed overall concordance with the flux re-routing predicted by the model. Together, our results provide experimental evidence for model-based design of microbial chassis and have implications for computer-aided design of microbial cell factories.
Question: Write a study description for the study titled 'Operation of a TCA cycle subnetwork in the mammalian nucleus'.
Answer: Nucleic acid and histone modifications critically depend on tricarboxylic acid (TCA) cycle for substrates and co-factors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the TCA cycle is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Nuclear localization of the latter enzyme, which produces succinyl-CoA, changed from pluripotency to differentiated state with accompanying changes in the nuclear protein succinylation. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization.
Question: Write a study description for the study titled 'The Lipopolysaccharide-Induced Metabolome Signature in Arabidopsis thaliana Reveals Dynamic Reprogramming of Phytoalexin and Phytoanticipin Pathways'.
Answer: Lipopolysaccharides (LPSs), as MAMP molecules, trigger the activation of signal transduction pathways involved in defence. Currently, plant metabolomics is providing new dimensions into understanding the intracellular adaptive responses to external stimuli. The effect of LPS on the metabolomes of Arabidopsis thaliana cells and leaf tissue was investigated over a 24 h period. Cellular metabolites and those secreted into the medium were extracted with methanol and liquid chromatography coupled to mass spectrometry was used for quantitative and qualitative analyses. Multivariate statistical data analyses were used to extract interpretable information from the generated multidimensional LC-MS data. The results show that LPS perception triggered differential changes in the metabolomes of cells and leaves, leading to variation in the biosynthesis of specialised secondary metabolites. Time-dependent changes in metabolite profiles were observed and biomarkers associated with the LPS-induced response were tentatively identified. These include the phytohormones salicylic acid and jasmonic acid, and also the associated methyl esters and sugar conjugates. The induced defensive state resulted in increases in indole-and other glucosinolates, indole derivatives, camalexin as well as cinnamic acid derivatives and other phenylpropanoids. These annotated metabolites indicate dynamic reprogramming of metabolic pathways that are functionally related towards creating an enhanced defensive capacity. The results reveal new insights into the mode of action of LPS as an activator of plant innate immunity, broadens knowledge about the defence metabolite pathways involved in Arabidopsis responses to LPS, and identifies specialised metabolites of functional importance that can be employed to enhance immunity against pathogen infection.