LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Urinary metabolomic profiling to identify biomarkers of a flavonoid-rich and flavonoid-poor fruits and vegetables diet in adults: the FLAVURS trial'.
Answer: The present study aims to investigate the dose dependent effects of consuming diets enriched in flavonoid-rich and flavonoid-poor fruits and vegetables on the urine metabolome of adults who had a ≥1.5 fold increased risk of cardiovascular diseases. A single-blind, dose-dependent, parallel randomized controlled dietary intervention was conducted where volunteers (n = 126) were randomly assigned to one of three diets: high flavonoid diet, low flavonoid diet or habitual diet as a control for 18 weeks. High resolution LC–MS untargeted metabolomics with minimal sample cleanup was performed using an Orbitrap mass spectrometer. Putative biomarkers which characterize diets with high and low flavonoid content were selected by state-of-the-art data analysis strategies and identified by HR-MS and HR-MS/MS assays. Discrimination between diets was observed by application of two linear mixed models: one including a diet-time interaction effect and the second containing only a time effect. Valerolactones, phenolic acids and their derivatives were among sixteen biomarkers related to the high flavonoid dietary exposure. Four biomarkers related to the low flavonoid diet belonged to the family of phenolic acids. For the first time abscisic acid glucuronide was reported as a biomarker after a dietary intake, however its origins have to be examined by future hypothesis driven experiments using a more targeted approach. This metabolomic analysis has identified a number of dose dependent urinary biomarkers (i.e. proline betaine or iberin-N-acetyl cysteine), which can be used in future observation and intervention studies to assess flavonoids and non-flavonoid phenolic intakes and compliance to fruit and vegetable intervention.
Question: Write a study description for the study titled 'Genetic mapping and molecular mechanism behind color variation in the Asian vine snake'.
Answer: BACKGROUND: Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.RESULTS: We investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77 Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in SMARCE1, which may be involved in the regulation of chromatophore development initiated from neural crest cells. SMARCE1 knockdown in zebrafish and immunofluorescence verify the interactions among SMARCE1, iridophores, and tfec, which may determine color variations in the Asian vine snake.CONCLUSIONS: This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.
Question: Write a study description for the study titled 'Metabolic profiling of maternal serum of women at high-risk of spontaneous preterm birth using NMR and MGWAS approach'.
Answer: Preterm birth (PTB) is a leading global cause of infant mortality. Risk factors include genetics, lifestyle choices and infection. Understanding the mechanism of PTB could aid the development of novel approaches to prevent PTB. This study aimed to investigate the metabolic biomarkers of PTB in early pregnancy and the association of significant metabolites with participant genotypes. Maternal sera collected at 16 and 20 weeks of gestation, from women who previously experienced PTB (high-risk) and women who did not (low-risk controls), were analysed using 1H nuclear magnetic resonance (NMR) metabolomics and genome-wide screening microarray. ANOVA and probabilistic neural network (PNN) modelling were performed on the spectral bins. Metabolomics genome-wide association (MGWAS) of the spectral bins and genotype data from the same participants was applied to determine potential metabolite-gene pathways. Phenylalanine, acetate and lactate metabolite differences between PTB cases and controls were obtained by ANOVA and PNN showed strong prediction at week 20 (AUC = 0.89). MGWAS identified several metabolite bins with strong genetic associations. Cis-eQTL analysis highlighted TRAF1 (involved in the inflammatory pathway) local to a non-coding SNP associated with lactate at week 20 of gestation. MGWAS of a well-defined cohort of participants highlighted a lactate-TRAF1 relationship that could potentially contribute to PTB.
Question: Write a study description for the study titled 'Multi-omics phenotyping of the gut-liver axis reveals metabolic perturbations from a low-dose pesticide mixture in rats'.
Answer: Health effects of pesticides are not always accurately detected using the current battery of regulatory toxicity tests. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in a subchronic toxicity test of a mixture of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole) in Sprague-Dawley rats. Analysis of water and feed consumption, body weight, histopathology and serum biochemistry showed little effect. Contrastingly, serum and caecum metabolomics revealed that nicotinamide and tryptophan metabolism were affected, which suggested activation of an oxidative stress response. This was not reflected by gut microbial community composition changes evaluated by shotgun metagenomics. Transcriptomics of the liver showed that 257 genes had their expression changed. Gene functions affected included the regulation of response to steroid hormones and the activation of stress response pathways. Genome-wide DNA methylation analysis of the same liver samples showed that 4,255 CpG sites were differentially methylated. Overall, we demonstrated that in-depth molecular profiling in laboratory animals exposed to low concentrations of pesticides allows the detection of metabolic perturbations that would remain undetected by standard regulatory biochemical measures and which could thus improve the predictability of health risks from exposure to chemical pollutants.
Question: Write a study description for the study titled 'The effects of different rootstocks on aroma components, activities and genes expression of aroma-related enzymes in oriental melon fruit'.
Answer: Grafting is widely applied in the cultivation of melon. In this study, 'Qinmi No.1' [Cucumis melo L. (QG)] and 'Ribenxuesong' [Cucurbita maxima Duch. (RG)] were used as rootstocks for 'QingxinYangjiaocui' (Cucumis melo L.). The results showed that grafting with muskmelon rootstocks had no significant effect on fruit aroma, but grafting with pumpkin rootstocks significantly reduced the odor intensity and odor preference scores of melon fruits. Compared with the fruits from self-grafted plants (SG), four new aromatic volatiles with a sweet smell were detected, the alcohol dehydrogenase (ADH) activity was significantly decreased at 30 DAP, but unaffected at 42 DAP in QG fruits. There was no difference for alcohol acetyltransferase (AAT) activity between QG and SG fruits. The expression level of CmADH2 was significantly higher at 30 DAP and 42 DAP, but CmAAT2 was significantly lower at 42 DAP in QG fruits compared with SG fruits. In RG fruits, the main aroma compounds including butanoic acid ethyl ester, 2-methyl-2-butenal and 2-methylheptan-1-al were absent, while the volatile compounds with unpleasant odor characteristics including trans, cis-2,6-nonadien-1-ol, (E,E)-2,4-heptadienal, octanoic acid and styrene were detected. Compared with SG fruits, 1-nonanol and 1-heptanol with green odor characteristics were significantly increased, but eucalyptol and farnesene with fruity aroma characteristics were significantly decreased in RG fruits. The ADH activity of RG fruits was significantly lower than that of SG fruits at 30 DAP and the AAT activity was significantly lower than that of SG fruits at 42 DAP. In addition, the expression levels of CmADH and CmAAT homologs in RG fruits were significantly lower than those in SG or QG fruits. These results show that grafting with pumpkin rootstocks affected the main aroma components, reduced ADH and AAT activities, and down-regulated the expression levels of CmADHs and CmAATs in the melon fruits. This study reveals the mechanism of different rootstocks on melon fruit aroma quality, and lays a theoretical foundation for the selection of rootstocks in melon production. Future studies using overexpression or CRISPR/CAS system to obtain stable transgenic lines of genes encoding key aromatic volatiles, would be promising to effectively improve the flavor quality of melon.
Question: Write a study description for the study titled 'Insights into Metabolic Changes Caused by the Trichoderma virens-Maize Root Interaction'.
Answer: The interactions of crops with root-colonizing endophytic microorganisms are highly relevant to agriculture, because endophytes can modify plant resistance to pests and increase crop yields. We investigated the interactions between the host plant Zea mays and the endophytic fungus Trichoderma virens at 5 days postinoculation grown in a hydroponic system. Wild-type T. virens and two knockout mutants, with deletion of the genes tv2og1 or vir4 involved in specialized metabolism, were analyzed. Root colonization by the fungal mutants was lower than that by the wild type. All fungal genotypes suppressed root biomass. Metabolic fingerprinting of roots, mycelia, and fungal culture supernatants was performed using ultrahigh performance liquid chromatography coupled to diode array detection and quadrupole time-of-flight tandem mass spectrometry. The metabolic composition of T. virens-colonized roots differed profoundly from that of noncolonized roots, with the effects depending on the fungal genotype. In particular, the concentrations of several metabolites derived from the shikimate pathway, including an amino acid and several flavonoids, were modulated. The expression levels of some genes coding for enzymes involved in these pathways were affected if roots were colonized by the ∆vir4 genotype of T. virens. Furthermore, mycelia and fungal culture supernatants of the different T. virens genotypes showed distinct metabolomes. Our study highlights the fact that colonization by endophytic T. virens leads to far-reaching metabolic changes, partly related to two fungal genes. Both metabolites produced by the fungus and plant metabolites modulated by the interaction probably contribute to these metabolic patterns. The metabolic changes in plant tissues may be interlinked with systemic endophyte effects often observed in later plant developmental stages.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Question: Write a study description for the study titled 'Effects of altering serine metabolic pathways and ROS levels on macrolide resistant strains of Streptococcus suis'.
Answer: In this study, we proposed to obtain the differential metabolic pathways before and after the development of macrolide resistance in Streptococcus suis strain ATCC700494 and the macrolide resistant strain obtained by pre-laboratory induction of strain ATCC700794 as the test strains by non-targeted metabolomics techniques.
Question: Write a study description for the study titled 'Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory'.
Answer: While cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene regulatory processes, these have rarely been explored by non-targeted metabolomics. Here we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism by combining tissue-wide non-targeted mass spectral data acquisition, information theory analysis, and MS/MS molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 non-redundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome and, through MS/MS molecular networks, most unique metabolites of anthers and other tissues were annotated. Finally, tissue-metabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene-silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation for their quest to understand gene function.
Question: Write a study description for the study titled 'Divergent metabolism between Trypanosoma congolense and Trypanosoma brucei results in differential sensitivity to metabolic inhibition'.
Answer: Animal African Trypanosomiasis (AAT) is a debilitating livestock disease prevalent across sub-Saharan Africa, a main cause of which is the protozoan parasite Trypanosoma congolense. In comparison to the well-studied T. brucei, there is a major paucity of knowledge regarding the biology of T. congolense. Here, we use a combination of omics technologies and novel genetic tools to characterise core metabolism in T. congolense mammalian-infective bloodstream-form parasites, and test whether metabolic differences compared to T. brucei impact upon sensitivity to metabolic inhibition. Like the bloodstream stage of T. brucei, glycolysis plays a major part in T. congolense energy metabolism. However, the rate of glucose uptake is significantly lower in bloodstream stage T. congolense, with cells remaining viable when cultured in concentrations as low as 2 mM. Instead of pyruvate, the primary glycolytic endpoints are succinate, malate and acetate. Transcriptomics analysis showed higher levels of transcripts associated with the mitochondrial pyruvate dehydrogenase complex, acetate generation, and the glycosomal succinate shunt in T. congolense, compared to T. brucei. Stable-isotope labelling of glucose enabled the comparison of carbon usage between T. brucei and T. congolense, highlighting differences in nucleotide and saturated fatty acid metabolism. To validate the metabolic similarities and differences, both species were treated with metabolic inhibitors, confirming that electron transport chain activity is not essential in T. congolense. However, the parasite exhibits increased sensitivity to inhibition of mitochondrial pyruvate import, compared to T. brucei. Strikingly, T. congolense exhibited significant resistance to inhibitors of fatty acid synthesis, including a 780-fold higher EC50 for the lipase and fatty acid synthase inhibitor Orlistat, compared to T. brucei. These data highlight that bloodstream form T. congolense diverges from T. brucei in key areas of metabolism, with several features that are intermediate between bloodstream- and insect-stage T. brucei. These results have implications for drug development, mechanisms of drug resistance and host-pathogen interactions.
Question: Write a study description for the study titled 'A longitudinal ¹H NMR-based urinary metabolomics dataset in a birth cohort for childhood atopic diseases'.
Answer: This dataset presents longitudinal urinary metabolomic profiles from 198 children at 1 month, 6 months, 1 year, 3 years and 5 years. It includes demographic data, feeding practices, parental atopy, household income and atopic disease status over time. Total and allergen-specific IgE (mite, egg, cow's milk) were measured to track allergic sensitization. Metabolomic data, obtained via ¹H-NMR spectroscopy and normalized for analysis, support investigations into the links between early development, metabolism and atopic disease progression.
Question: Write a study description for the study titled 'A metabolomics approach to unravel the regulating role of phytohormones towards carotenoid metabolism in tomato fruit. (Zeaxanthin metabolism)'.
Answer: Carotenoids are important secondary metabolites, which have been recognized as an essential component of the human diet because of their valuable beneficial health effects. With this rationale, there is a continuous aim to define the distribution of these compounds in plants, to better understand their metabolism and to increase their concentration levels in fruits and vegetables. This study aimed at deepening the knowledge on the regulatory role of phytohormones in carotenoid metabolism. More specifically, it was envisaged to reveal the phytohormones involved in the metabolism of alpha-carotene, beta-carotene, lycopene, lutein and zeaxanthin. To this purpose, the phytohormone profiles of 50 tomato fruits were determined by high-resolution Orbitrap mass spectrometry and evaluated towards the associated carotenoid levels. Data mining was performed by differential expression and orthogonal partial least squares analyses. This metabolomics approach revealed 5 phytohormonal metabolites, which significantly influenced (Variable Importance in Projection scores =0.80) carotenoid metabolism. These metabolites were identified as cis-12-oxo-phytodienoic acid, cucurbic acid, 2-oxindole-3-acetic acid, 1-acetylindole-3-carboxaldehyde, and cis-zeatin-O-glucoside. The involvement of the individual phytohormones towards carotenoid metabolism was investigated by regression analysis (P values =0.05, R2 varying between 0.280 and 0.760) and statistical correlation (P values =0.01, correlation varying between 0.403 and 0.846). It was concluded that these phytohormones all have significant contributing value in the regulation of carotenoid metabolism, thereby exhibiting down- and up-regulating influences. As a result, this knowledge encloses the potential for improving tomato fruit nutritional quality by targeted control of agronomic conditions, exogenous use of plant bioregulators, or genetic engineering.
Question: Write a study description for the study titled 'NMR-based metabolic profiling provides diagnostic and prognostic information in critically ill children with suspected infection'.
Answer: Sepsis, defined as life-threatening organ dysfunction caused by infection is difficult to distinguish clinically from infection or post-operative inflammation. We hypothesized that in a heterogeneous group of critically ill children, there would be different metabolic profiles between post-operative inflammation, bacterial and viral infection and infection with or without organ dysfunction. 1D 1H nuclear magnetic resonance spectra were acquired in plasma samples from critically ill children. We included children with bacterial (n = 25) and viral infection (n = 30) and controls (n = 58) (elective cardiac surgery without infection). Principal component analysis was used for data exploration and partial least squares discriminant analysis models for the differences between groups. Area under receiver operating characteristic curve (AUC) values were used to evaluate the models. Univariate analysis demonstrated differences between controls and bacterial and viral infection. There was excellent discrimination between bacterial and control (AUC = 0.94), and viral and control (AUC = 0.83), with slightly more modest discrimination between bacterial and viral (AUC = 0.78). There was modest discrimination (AUC = 0.73) between sepsis with organ dysfunction and infection with no organ dysfunction. In critically ill children, NMR metabolomics differentiates well between those with a post-operative inflammation but no infection, and those with infection (bacterial and viral), and between sepsis and infection.
Question: Write a study description for the study titled 'Comparative metabolomics and transcriptomics revealed multiple pathways associated with polymyxin killing in Pseudomonas aeruginosa'.
Answer: Polymyxins are the last-line antibiotics against multidrug-resistant Pseudomonas aeruginosa however, resistance to polymyxins has been increasingly reported. Therefore, understanding the mechanisms of polymyxin activity and resistance is crucial for preserving their clinical usefulness. This study employed comparative metabolomics and transcriptomics to investigate the responses of polymyxin-susceptible PAK (polymyxin B MIC 1 mg/l) and its polymyxin-resistant pmrB mutant PAKpmrB6 (MIC 16 mg/l) to polymyxin B (4, 8, and 128 mg/l) at 1, 4, and 24h. Our results revealed that polymyxin B at 4 mg/l induced different metabolic and transcriptomic responses between polymyxin-susceptible and -resistant P. aeruginosa. In PAK, polymyxin B significantly activated PmrAB and the mediated arn operon, leading to increased 4-amino-4-deoxy-L-arabinose (L-Ara4N) synthesis and the addition to lipid A. On the contrary, polymyxin B did not increase lipid A modification in PAKpmrB6. Moreover, the syntheses of lipopolysaccharide and peptidoglycan were significantly decreased in PAK, but increased in PAKpmrB6 due to polymyxin B treatment. In addition, 4 mg/l polymyxin B significantly perturbed phospholipid and fatty acid levels and induced oxidative stress in PAK, but not in PAKpmrB6. Notably, the increased trehalose-6-phosphate levels indicate that polymyxin B potentially caused osmotic imbalance in both strains. Furthermore, 8 and 128 mg/l polymyxin B significantly elevated lipoamino acid levels and decreased phospholipid levels, but without dramatic changes in lipid A modification in both wildtype and mutant strains. Overall, this systems study is the first to elucidate the complex and dynamic interactions of multiple cellular pathways associated with polymyxin mode of action against P. aeruginosa.
Question: Write a study description for the study titled 'Elucidation of xenoestrogen metabolism by non-targeted, stable isotope-assisted mass spectrometry in breast cancer cells'.
Answer: Environmental exposure to xenoestrogens, i.e., chemicals that imitate the hormone 17β-estradiol, has the potential to influence hormone homeostasis and action. Detailed knowledge of xenobiotic biotransformation processes in cell models is key when transferring knowledge learned from in vitro models to in vivo relevance. This study elucidated the metabolism of two naturally-occurring phyto- and myco-estrogens; namely genistein and zearalenone, in an estrogen receptor positive breast cancer cell line (MCF-7) with the aid of stable isotope-assisted metabolomics and the bioinformatic tool MetExtract II. Metabolism was studied in a time course experiment after 2, 6 and 24 h incubation. Twelve and six biotransformation products of zearalenone and genistein were detected, respectively, clearly demonstrating the abundant xenobiotic biotransformation capability of the cells. Zearalenone underwent extensive phase-I metabolism resulting in α-zearalenol (α-ZEL), a molecule known to possess a significantly higher estrogenicity, and several phase-II metabolites (sulfo- and glyco-conjugates) of the native compound and the major phase I metabolite α-ZEL. Moreover, potential adducts of zearalenone with a vitamin and several hydroxylated metabolites were annotated. Genistein metabolism resulted in sulfation, combined sulfation and hydroxylation, acetylation, glucuronidation and unexpectedly adduct formation with pentose- and hexose-sugars. Kinetics of metabolite formation and subsequent excretion into the extracellular medium revealed a time-dependent increase in most biotransformation products. The untargeted elucidation of biotransformation products formed during cell culture experiments enables an improved and more meaningful interpretation of toxicological assays and has the potential to identify unexpected or unknown metabolites.