LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome'.
Answer: Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides, although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin elevated as complementary foods were introduced to the infants’ diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.
Question: Write a study description for the study titled 'ABHD11/ROLIP maintains the TCA cycle by preserving functional lipoylation of the 2-oxoglutarate dehydrogenase complex'.
Answer: 2-oxoglutarate (2-OG) relates mitochondrial metabolism to cell function: conversion of 2-OG to succinyl-CoA by the 2-OG dehydrogenase complex (OGDHc) is rate-limiting for the Tricarboxylic Acid (TCA) cycle, but 2-OG is also required for oxygen sensitive enzymes (2-OG dependent dioxygenases) that have diverse biological roles ranging from Hypoxia Inducible Factor (HIF) activation to DNA hydroxymethylation. Here, using the 2-OG-mediated stability of HIFs to screen for genes involved in HIF metabolic activation, we identify ABHD11 (termed regulator of lipoylation, ROLIP) as a mitochondrial hydrolase required for OGDHc function. ROLIP loss decreases OGDHc activity, leading to accumulation of 2-OG and formation of L-2-hydroxyglutarate, which drives HIF activation and decreases DNA hydroxymethylation. Rather than altering constituent components of the OGDHc, ROLIP maintains the cyclical reduction and oxidation of the lipoylated OGDHc by preventing the formation of lipoyl adducts, highlighting ROLIP as a fundamental regulator of lipoylation, the TCA cycle, and 2-OG-dependent signalling.
Question: Write a study description for the study titled 'Fatty acid oxidation protects cancer cells from apoptosis through increasing mitochondrial membrane lipids'.
Answer: Overcoming resistance to chemotherapies remains a major unmet need for cancers such as triple negative breast cancer (TNBC). Therefore, mechanistic studies to provide insight for drug development are urgently needed to overcome TNBC therapy resistance. Recently, an important role of fatty acid β-Oxidation (FAO) in chemoresistance has been shown. But how FAO might mitigate tumor cell apoptosis by chemotherapy is unclear. Here, we show that elevated FAO activates STAT3 by acetylation via elevated acetyl-CoA. Acetylated STAT3 upregulates expression of long-chain acyl-CoA synthetase 4 (ACSL4), resulting in increased phospholipid synthesis. Elevating phospholipids in mitochondrial membranes leads to heightened mitochondrial integrity, which in turn overcomes chemotherapy-induced tumor cell apoptosis. Conversely, in both cultured tumor cells and xenograft tumors, enhanced cancer cell apoptosis by inhibiting ASCL4 or specifically targeting acetylated-STAT3 is associated with a reduction in phospholipids within mitochondrial membranes. This study demonstrates a critical mechanism underlying tumor cell chemoresistance.
Question: Write a study description for the study titled '"Metabolic fingerprinting of different populations of Phyllanthus niruri L. from Punjab using electrospray ionization mass spectrometry (ESI–MS)"'.
Answer: "There is growing interest of healthcare and food industry in ingredients of plant origin as they are potent sources of antioxidant, anti-inflammatory, antimicrobial and anticancer agents. In the present work different extracts of Phyllanthus niruri L. from various regions of Punjab were screened for their phenolic profiles and antioxidant properties. Crude extracts obtained by solid–liquid extraction with different solvents were tested for total anthocyanins, flavonoids, phenolic content, and free radical scavenging activity. Out of all the solvents used, methanol was regarded as best to be used for soxhlet extraction of plant metabolites, as it provided highest phenolic, flavonoid, antioxidant, and anthocyanin contents. Similarly, ESI–MS was employed to obtain mass profiles of phenolic and other metabolites present in various P. niruri populations. Out of 72 compounds detected, 51 are reported for the first time in P. niruri L. Similarly, different populations of P. niruri were discriminated through metabolic fingerprinting using ESI–MS."
Question: Write a study description for the study titled 'L-leucine increases the sensitivity of drug-resistant Salmonella to sarafloxacin by stimulating central carbon metabolism and increasing intracellular reactive oxygen species level (LC-MS positive mode)'.
Answer: The overuse of antibiotics has made public health and safety face a serious crisis. It is urgent to develop new clinical treatment methods to combat drug-resistant bacteria to alleviate the health crisis. The efficiency of antibiotics is closely related to the metabolic state of bacteria. However, studies on fluoroquinolone-resistant Salmonella are relatively rare. In this study, non-targeted metabolomics was used to analyze the metabolic difference between sarafloxacin-susceptible Salmonella Typhimurium (SAR-S) and sarafloxacin-resistant Salmonella Typhimurium (SAR-R), and found that the central carbon metabolism was weakened due to drug resistance. We also confirmed that exogenous L-leucine increased the killing effect of sarafloxacin on SAR-R and other clinically resistant Salmonella serotypes. Exogenous L-leucine stimulated the metabolic state of bacteria, especially the TCA cycle, which increased the working efficiency of the electron transfer chain and increased the intracellular NADH, ATP concentrationa nd reactive oxygen species level. Furthermore, we used real-time quantitative PCR to confirm the changes in various metabolic characteristics. Our results suggest that when the metabolism of drug-resistant bacteria is reprogrammed, the bactericidal effect of antibiotics improves. This study further enhances research in the anti-drug resistance field at the metabolic level and provides theoretical support for solving the current problem of sarafloxacin drug resistance, a unique fluoroquinolone drug for animals. To sum up, our research results showed that exogenous L-leucine promotes the bactericidal effect of antibiotics through metabolic modification of drug-resistant bacteria, which has the potential as a new adjuvant of antibiotics.LC-MS positive mode is reported in the current study MTBLS7711.LC-MS negative mode is reported in MTBLS7713.
Question: Write a study description for the study titled 'Lignocellulose adaptation drives polysaccharide biosynthesis in Tremella fuciformis: Metabolomic and proteomic insights into CAZyme regulation'.
Answer: The polysaccharide content of T. fuciformis grown on a Cyclobalanopsis substrate (TY3) was significantly higher than those grown on a mixed substrate (TF1) made of wheat bran and cottonseed hull. Metabolomics and proteomics were used to assess the effects of the lignocellulose (consists of cellulose, hemicellulose and lignin) in different growth substrates on the polysaccharide content of Tremella fuciformis and its formation mechanism.
Question: Write a study description for the study titled 'Integrated Four Comparative-Omics Reveals the Mechanism of the Terpenoid Biosynthesis in Two Different Overwintering Cryptomeria fortunei Phenotypes'.
Answer: Chinese cedar (Cryptomeria fortunei) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of C. fortunei needles have been considered valuable ingredients in the pharmaceutical and cosmetic industries. However, the possible gene regulation mechanisms that limit terpenoid biosynthesis in this genus are poorly understood. Here, we adopted integrated metabolome analysis, transcriptome, small-RNA (sRNA), and degradome sequencing to analyze the differences in terpenoid regulatory mechanisms in two different overwintering C. fortunei phenotypes (wild-type and an evergreen mutant). A total of 1447/6219 differentially synthesized metabolites (DSMs)/unigenes (DEGs) were detected through metabolome/transcriptome analyses, and these DSMs/DEGs were significantly enriched in flavonoid and diterpenoid biosynthesis pathways. In C. fortunei needles, 587 microRNAs (miRNAs), including 67 differentially expressed miRNAs (DERs), were detected. Among them, 8346 targets of 571 miRNAs were predicted using degradome data, and a 72-miRNA-target regulatory network involved in the metabolism of terpenoids and polyketides was constructed. Forty-one targets were further confirmed to be involved in terpenoid backbone and diterpenoid biosynthesis, and target analyses revealed that two miRNAs (i.e., aly-miR168a-5p and aof-miR396a) may be related to the different phenotypes and to differential regulation of diterpenoid biosynthesis. Overall, these results reveal that C. fortunei plants with the evergreen mutation maintain high terpenoid levels in winter through miRNA-target regulation, which provides a valuable resource for essential oil-related bioengineering research.
Question: Write a study description for the study titled 'ER stress inhibits liver fatty acid oxidation while unmitigated stress leads to anorexia-induced lipolysis and both liver and kidney steatosis'.
Answer: The unfolded protein response (UPR), induced by endoplasmic reticulum (ER) stress, regulates the expression of factors that restore protein folding homeostasis. However, in the liver and kidney, ER stress also leads to lipid accumulation, accompanied at least in the liver by transcriptional suppression of metabolic genes. The mechanisms of this accumulation are unclear, including which pathways contribute to the phenotype in each organ. We combined gene expression profiling, biochemical assays, and untargeted lipidomics to understand the basis of stress-dependent lipid accumulation, taking advantage of enhanced hepatic and renal steatosis in mice lacking the ER stress sensor ATF6α. We found that impaired fatty acid oxidation contributed to the early development of steatosis in the liver, but not the kidney; while anorexia-induced lipolysis promoted late triglyceride and free fatty acid accumulation in both organs. These findings provide evidence for both direct and indirect regulation of peripheral metabolism by ER stress.
Question: Write a study description for the study titled 'The metabolic response of marine copepods to environmental warming and ocean acidification in the absence of food'.
Answer: Marine copepods are central to the productivity and biogeochemistry of marine ecosystems. Nevertheless, the direct and indirect effects of climate change on their metabolic functioning remain poorly understood. Here, we use metabolomics, the unbiased study of multiple low molecular weight organic metabolites, to examine how the physiology of Calanus spp. is affected by end-of-century global warming and ocean acidification scenarios. We report that the physiological stresses associated with incubation without food over a 5-day period greatly exceed those caused directly by seawater temperature or pH perturbations. This highlights the need to contextualise the results of climate change experiments by comparison to other, naturally occurring stressors such as food deprivation, which is being exacerbated by global warming. Protein and lipid metabolism were up-regulated in the food-deprived animals, with a novel class of taurine-containing lipids and the essential polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid and docosahexaenoic acid, changing significantly over the duration of our experiment. Copepods derive these PUFAs by ingesting diatoms and flagellated microplankton respectively. Climate-driven changes in the productivity, phenology and composition of microplankton communities, and hence the availability of these fatty acids, therefore have the potential to influence the ability of copepods to survive starvation and other environmental stressors.
Question: Write a study description for the study titled 'Non-canonical Metabolic and Molecular Effects of Calorie Restriction Are Revealed by Varying Temporal Conditions'.
Answer: Calorie restriction (CR) extends lifespan and healthspan in diverse species. However, comparing ad libitum (AL) and CR-fed mice is challenging due to their significantly different feeding patterns. CR-fed mice consume their daily meal in approximately 2 hours, subjecting themselves to a prolonged self-imposed fast each day. To gain deeper insights into the effects of CR, we conducted a comprehensive examination of how AL and CR-fed mice respond to tests performed at various times relative to the completion of their once-daily CR meal. Our findings reveal that many well-known effects of CR, including its impact on insulin sensitivity, result from the specific temporal conditions. CR animals exhibit a divergent response to insulin, and this response varies based on the time elapsed since the CR-fed mice consumed their food. Utilizing an unbiased metabolomics approach, we discovered that the effects of CR on circulating metabolites are heavily dependent upon the time-of-day and feeding regimen. Finally, while it is widely believed that CR functions in part by reducing activity of the kinase mTORC1, our study suggests that the observed differences in mTORC1 activity between AL and CR-fed mice are dependent upon both fasting duration and the specific tissue examined. Furthermore, we find that the metabolic effects of CR are independent of hepatic mTORC1. Our results shed new light on the physiological, metabolic and molecular effects of a CR diet, and highlight that much of our understanding of the effects of CR are related to when, relative to feeding, we choose to examine the mice.
Question: Write a study description for the study titled 'Biochemical Profiling of the Brain and Blood Metabolome in a Mouse Model of Prodromal Parkinson’s Disease Reveals Distinct Metabolic Profiles (NMR assay)'.
Answer: Parkinson’s disease is the second most common neurodegenerative disease. In the vast majority of cases the origin is not genetic and the cause is not well understood, although progressive accumulation of α-synuclein aggregates appears central to the pathogenesis. Currently, treatments that slow disease progression are lacking, and there are no robust biomarkers that can facilitate the development of such treatments or act as aids in early diagnosis. Therefore, we have defined metabolomic changes in the brain and serum in an animal model of prodromal Parkinson’s disease. We biochemically profiled the brain tissue and serum in a mouse model with progressive synucleinopathy propagation in the brain triggered by unilateral injection of preformed α-synuclein fibrils in the olfactory bulb. In total, we accurately identified and quantified 71 metabolites in the brain and 182 in serum using 1H NMR and targeted mass spectrometry, respectively. Using multivariate analysis, we accurately identified which metabolites explain the most variation between cases and controls. Using pathway enrichment analysis, we highlight significantly perturbed biochemical pathways in the brain and correlate these with the progression of the disease. Furthermore, we identified the top six discriminatory metabolites and were able to develop a model capable of identifying animals with the pathology from healthy controls with high accuracy (AUC (95% CI) = 0.861 (0.755–0.968)). Our study highlights the utility of metabolomics in identifying elements of Parkinson’s disease pathogenesis and for the development of early diagnostic biomarkers of the disease.  NMR assay is reported in the current study MTBLS640.  MS assays are reported in MTBLS674.  Linked Studies: MTBLS674
Question: Write a study description for the study titled 'Sarcosine decreases in sarcopenia and enhances muscle regeneration and adipose thermogenesis by activating ant-inflammatory macrophages (cohort2)'.
Answer: Age-related changes in circulating metabolites significantly influence systemic physiology and may contribute to diseases like sarcopenia. Although metabolic dysregulation is closely linked to sarcopenia, the roles of specific metabolites remain unclear. Here we performed comprehensive plasma metabolomic and lipidomic analyses across two cohorts comprising 1,013 individuals. Our findings revealed the metabolic characteristics of sarcopenia, including a notable decline in plasma sarcosine levels in both aging and sarcopenic individuals. Functional studies showed that sarcosine helps maintain muscle mass homeostasis during aging, promotes adipose thermogenesis and enhances muscle regeneration. These effects may increase energy expenditure and restore metabolic balance to reduce chronic inflammation and improve insulin sensitivity, which are crucial for managing sarcopenia. We demonstrate that sarcosine activated the GCN2 signaling pathway to enhance anti-inflammatory macrophage polarization, promoting adipose thermogenesis and muscle regeneration. This study underscores the potential of sarcosine supplementation as an adjunctive strategy for preventing sarcopenia in older adults.cohort2 is reported in the current study MTBLS12036.cohort1 is reported in MTBLS12015.
Question: Write a study description for the study titled 'A large-scale metabolomics study to harness chemical diversity and explore biochemical mechanisms in ryegrass (UPLC-MS C18 reverse phase NEG assay)'.
Answer: "Perennial ryegrass (Lolium perenne) is integral to temperate pastoral agriculture, which contributes most of the milk and meat production worldwide. Chemical profiles and diversity of ryegrass offer several opportunities to harness specific traits and elucidate underlying biological mechanisms for forage improvement. We conducted a large-scale metabolomics study of perennial ryegrass comprising 715 genotypes, representing 118 populations from 21 countries. Liquid/gas chromatography-mass spectrometry based targeted and non-targeted techniques were used to analyse fructan oligosaccharides, lipids, fatty acid methyl esters, polar and semi-polar compounds. Fructan diversity across all genotypes was evaluated, high- and low-sugar groups identified, and fructan accumulation mechanisms explored. Metabolites differentiating the two groups were characterised, modules and pathways they represent deduced, and finally, visualisation and interpretation provided in a biological context. We also demonstrate a workflow for large-scale metabolomics studies from raw data through to statistical and pathway analysis.  UPLC-MS C18 reverse phase NEG assay is reported in the current study MTBLS65. UPLC-MS HILIC POS assay is reported in MTBLS62. UPLC-MS HILIC NEG assay is reported in MTBLS63. UPLC-MS C18 reverse phase POS assay is reported in MTBLS64. UPLC-MS C1 reverse phase POS and GC-MS FAME assays are reported in MTBLS66. UPLC-MS C1 reverse phase NEG assay is reported in MTBLS68. HPLC-MS Hypercarb reverse phase NEG assay is reported in MTBLS529."
Question: Write a study description for the study titled 'Emerging mechanisms and promising approaches in pancreatic cancer metabolism.'.
Answer: Pancreatic cancer is an aggressive cancer with a poor prognosis. Metabolic abnormalities are one of the hallmarks of pancreatic cancer, and pancreatic cancer cells can adapt to biosynthesis, energy intake and redox needs through metabolic reprogramming to tolerate nutrient deficiency and hypoxic microenvironments. Pancreatic cancer cells can use glucose, amino acids and lipids as energy to maintain malignant growth. Moreover, they also metabolically interact with cells in the tumour microenvironment to change cell fate, promote tumour progression and even affect immune responses. Importantly, metabolic changes at the body level deserve more attention. Basic research and clinical trials based on targeted metabolic therapy or in combination with other treatments are in full swing. A more comprehensive and in-depth understanding of the metabolic regulation of pancreatic cancer cells will not only enrich the understanding of the mechanisms of disease progression but also provide inspiration for new diagnostic and therapeutic approaches.
Question: Write a study description for the study titled 'Effect of Genetically Reduced Maternal Myostatin on Late Gestation Maternal, Fetal, and Placental Metabolomes in Mice.'.
Answer: Myostatin (gene symbol: Mstn) is an autocrine and paracrine inhibitor of muscle growth. Pregnant mice with genetically reduced levels of myostatin give birth to offspring with greater adult muscle mass and bone biomechanical strength. However, maternal myostatin is not detectable in fetal circulations. Fetal growth is dependent on the maternal environment, and the provisioning of nutrients and growth factors by the placenta. Thus, this study examined the effect of reduced maternal myostatin on maternal and fetal serum metabolomes, as well as the placental metabolome. Fetal and maternal serum metabolomes were highly distinct, which is consistent with the role of the placenta in creating a specific fetal nutrient environment. There was no effect from myostatin on maternal glucose tolerance or fasting insulin. In comparisons between pregnant control and Mstn+/- mice, there were more significantly different metabolite concentrations in fetal serum, at 50, than in the mother's serum at 33, confirming the effect of maternal myostatin reduction on the fetal metabolic milieu. Polyamines, lysophospholipids, fatty acid oxidation, and vitamin C, in fetal serum, were all affected by maternal myostatin reduction.