LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Pathogen-induced phenolic acids biosynthesis is associated with deleterious microbiome changes during Plasmodiophora brassicae-induced clubroot in Pakchoi'.
Answer: Plant diseases have an important impact on the agricultural economy, often causing a decrease in crop yield and quality (Huang et al., 2020). Cruciferous plants can be used as both crops and vegetables, and have important application value. For example edible and oil sources, animal feeds and human biomedicine (Wittkop et al., 2009) (Li et al., 2022). Cruciferous crops are also susceptible to plant diseases, with clubroot being the major disease (Khalid et al., 2022). The pathogen that causes clubroot is Plasmodiophora brassicae, an obligate biotrophic protist and plasmodiophorid (Khalid et al., 2022). After plant infection P. brassicae, the root galls, stunted growth and accelerated flowering (Schuller and Ludwig-Müller, 2016). Meanwhile, P. brassicae can infect almost all cruciferous crops and lead to yields and quality losses of oil crops and vegetables worldwide (Khalid et al., 2022).Here, we hypothesized that Pakchoi disease-resistant plants recruited beneficial microorganisms to reduce clubroot disease infestation. The enhanced recruitment of plant-beneficial microorganisms is hypothesized to occur via changes in Pakchoi root exudates, and some beneficial key microorganisms play a decisive role in the resistance to clubroot disease infection. To test this hypothesis, (1) we evaluated the establishment of soil microbiome in roots and rhizosphere in susceptible and disease-resistant plants; (2) to analyze the changes in the metabolome of rhizosphere soil of susceptible and resistant varieties of Pakchoi, so as to provide clues for the recruitment of beneficial bacteria; (3) the association analysis of metabolome and microbiome was used to determine the control effect of key species on clubroot disease.
Question: Write a study description for the study titled 'Cardiac disruption of SDHAF4-mediated mitochondrial complex II assembly promotes dilated cardiomyopathy'.
Answer: Succinate dehydrogenase, which is known as mitochondrial complex II, has proven to be a fascinating machinery, attracting renewed and increased interest in its involvement in human diseases. Herein, we find that succinate dehydrogenase assembly factor 4 (SDHAF4) is downregulated in cardiac muscle in response to pathological stresses and in diseased hearts from human patients. Cardiac loss of Sdhaf4 suppresses complex II assembly and results in subunit degradation and complex II deficiency in fetal mice. These defects are exacerbated in young adults with globally impaired metabolic capacity and activation of dynamin-related protein 1, which induces excess mitochondrial fission and mitophagy, thereby causing progressive dilated cardiomyopathy and lethal heart failure in animals. Targeting mitochondria via supplementation with fumarate or inhibiting mitochondrial fission improves mitochondrial dynamics, partially restores cardiac function and prolongs the lifespan of mutant mice. Moreover, the addition of fumarate is found to dramatically improve cardiac function in myocardial infarction mice. These findings reveal a vital role for complex II assembly in the development of dilated cardiomyopathy and provide additional insights into therapeutic interventions for heart diseases.
Question: Write a study description for the study titled 'Metabolic and transcriptional response of Arabidopsis thaliana wildtype and mutants to Phytophtora infestans'.
Answer: The oomycete P. infestans is the causal agent of late blight, the most devastating potato disease. In contrast to potato, A. thaliana is able to successfully prevent colonization of the pathogen due to a multi-layered nonhost resistance. Several mutants have been isolated which are impaired in penetration resistance. A mutation in the gene PEN2, which encodes for an enzyme involved in indole glucosinolate metabolism, results in the loss of penetration resistance against P. infestans. Despite its ability to penetrate epidermal cells of pen2 mutant plants, P. infestans is still not able to colonize these plants. Additional mutants were isolated which show enhanced defense responses upon infection with P. infestans: pen2erp1 and pen2erp2, and backcrossed mutants erp140 and erp2D. We used 6 different plant lines, the wildtype-like gl1, and the five different mutants (pen2, pen2erp1, pen2erp2, erp2D, erp140). The plants were either infected with P. infestans spores or treated with water as control, and harvested 6 h and 12 h after treatment. The experiment was repeated 3 times with different P. infestans cultures, resulting in biological triplicates, for an overall of 6 x 2 x 2 x 3 = 72 samples.
Question: Write a study description for the study titled 'Faecalibaculum rodentium as a key player in combating maternal obesity-induced labor disorders'.
Answer: The global rise in maternal obesity increases the risk of adverse maternal and neonatal outcomes. This study demonstrates that both long- (12 weeks) and short-term (gestational) exposure to a high-fat diet (HFD) induces uterine labor disorders, elevates stillbirth rates, and alters gut microbiota composition. Fecal microbiota transplantation (FMT) reveals that HFD inhibits uterine AMPK phosphorylation and reduces COX4 expression via gut microbiota modulation, further contributing to labor dysfunction. Faecalibaculum rodentium, a dominant gut bacterium, shows a negative correlation with stillbirth incidence. Transplantation of Faecalibaculum rodentium mitigates HFD-induced labor disorders, restores uterine ATP levels, and reduces stillbirth rates. This intervention increases serum butyric and acetic acid levels, which inhibit ERK phosphorylation via the GPR41 receptor and activate AMPK phosphorylation, promoting Nrf1 and PGC1 expression. These findings highlight the pivotal role of Faecalibaculum rodentium in counteracting HFD-induced uterine mitochondrial dysfunction and stillbirth.
Question: Write a study description for the study titled 'Microbiome and metabolome features in treatment of early weaned piglets via multi-omics integration analyses across cohorts'.
Answer: BACKGROUND: Diarrhea is common in infants, particularly, children less than 2 years old. Intractable or protracted infancy diarrhea is typically associated with feeding intolerance and malabsorption that is lethal for newborns. This study aimed to evaluate the effectiveness of baizhu shaoyao decoction in reducing functional diarrhea induced by weaning stress, while also delving into its potential mechanisms of action.RESULTS: Piglets were allocated into 5 groups, with each group receiving designated medication for a continuous 14-day period: control, zaohu powder, as well as low-, medium- and high-dose baizhu shaoyao decoction groups (n = 6 piglets per group). To identify diarrhea-related biomarkers, microbial communities, functions and metabolites were compared between the early-weaned piglets (control group) and those treated with 1.28 g/kg baizhu shaoyao decoction (medium-dose baizhu shaoyao decoction group). Our findings revealed significant shifts in microbial composition, function and metabolic profiles in piglets from the medium-dose baizhu shaoyao decoction group, intricately associated with the host's diarrhea status. Furthermore, carbohydrate metabolism and biosynthesis, lipid and amino acid metabolism, glycan activity and carbohydrate digestive enzymes exhibited downregulation in piglets of the medium-dose baizhu shaoyao decoction group compared to those in the control group. Transcriptome analysis highlighted the pivotal role of the FoxO1/3 transcription factor in mitigating weaning stress, particularly through the augmentation of CD4+/CD8+ T cell proportions. Our findings underscored that baizhu shaoyao decoction's therapeutic effects on weaning stress involve intestinal barrier restoration, modulation of brain-gut peptide expression and a reduction in mast-cell activity in the ileum.CONCLUSIONS: The key metabolites (chenodeoxycholyglycine, chenodeoxycholyltaurine, dinoprost, chenodeoxyglycocholic acid, glycochenodeoxycholic acid, glycocholic acid, N-choloylglycine, 5-trans-PGE2, Pregnanediol 3-O-glucuronide, spermidine and spermine) exhibited strong correlations with the abundance of Clostridia_bacterium and Lachnospiraceae_bacterium, emphasizing the significance of Clostridia_bacterium and Lachnospiraceae_bacterium in gut metabolism and function. Besides, this study suggests the potential efficacy of baizhu shaoyao decoction in addressing early post-weaning stress-induced diarrhea in infants, showcasing promising prospects for translational and clinical applications.
Question: Write a study description for the study titled 'Impaired Glycolysis-Derived Serine Metabolism as a Key Driver of Podocyte Injury with Senescence'.
Answer: Chronic kidney disease (CKD) is a major health issue, with podocyte injury with senescence playing a central role in glomerulosclerosis. This study investigates the link between glycolysis-derived serine metabolism and podocyte injury with senescence, focusing on the role of phosphoglycerate kinase 1 (PGK1) in the regulation of L-serine synthesis and podocyte homeostasis. Using in vivo and in vitro models, we examined the effects of angiotensin II (Ang II)-induced metabolic dysregulation on serine metabolism and its impact on podocyte function. The results demonstrate that Ang II downregulates PGK1 expression through the transcription factor FOXA1, leading to reduced L-serine biosynthesis, mitochondrial dysfunction, and increased cellular senescence in podocytes. Supplementing with L-serine or enhancing PGK1 expression in podocytes alleviated these pathological changes, restored mitochondrial function, and reduced senescence-associated phenotypes in CKD mouse models. Moreover, PGK1 was found to interact with keratin, type II cytoskeletal 1 (KRT1), stabilizing the cytoskeletal integrity of podocytes. These findings identify a novel metabolic pathway linking glycolysis, serine metabolism, and podocyte injury with senescence, suggesting that targeting the PGK1-serine axis may offer therapeutic potential for slowing podocyte senescence and CKD progression.
Question: Write a study description for the study titled 'Metabolomics reveals an involvement of pantothenate for male production responding to the short-day stimulus in the water flea, Daphnia pulex'.
Answer: Under favorable conditions, the micro-crustacean Daphnia pulex produces female offspring by parthenogenesis, whereas in response to various unfavorable external cues, they produce male offspring to induce sexual reproduction (environmental sex determination: ESD). We recently established a suitable experimental system for ESD studies using D. pulex WTN6 strain, in which the sex of the offspring can be regulated simply by alterations in day-length; long-day and short-day conditions can induce female and male offspring respectively. Taking advantage of this system, we have already demonstrated that methyl farnesoate (MF) synthesis is necessary for male offspring production. Further, we identified ionotropic glutamate receptors as an upstream regulator of MF signaling by transcriptome analysis. Despite these findings, the molecular mechanisms associated with MF signaling have not yet been well elucidated in D. pulex. To more comprehensively understand the molecular mechanisms of ESD, we analyzed the whole metabolic profiles of mother daphniids reared under long-day (female-producing) and short-day (male-producing) conditions using mass spectrometry based metabolomics. We discovered that pantothenate (vitamin B5), a known precursor to coenzyme A, was significantly accumulated in response to the short-day condition. To confirm the role of pantothenate in D. pulex ESD, this metabolite was administered to mother daphniids (under long-day conditions) resulting in a significantly increased proportion of male offspring producing mothers. This study not only provides several candidates for further investigations into the molecular changes involved in male offspring production, but also novel insights into the metabolic mechanisms of the ESD system in D. pulex.
Question: Write a study description for the study titled 'hRUV: Hierarchical approach to removal of unwanted variation for large-scale metabolomics data'.
Answer: Liquid chromatography-mass spectrometry-based metabolomics studies are increasingly applied to large population cohorts, which run for several weeks or even years in data acquisition. This inevitably introduces unwanted intra- and inter-batch variations over time that can overshadow true biological signals and thus hinder potential biological discoveries. To date, normalisation approaches have struggled to mitigate the variability introduced by technical factors whilst preserving biological variance, especially for protracted acquisitions. Here, we propose a study design framework with an arrangement for embedding biological sample replicates to quantify variance within and between batches and a novel workflow that uses these replicates to remove unwanted variation in a hierarchical (hRUV) manner. We use this design to produce a dataset of more than 1,000 human plasma samples run over an extended period of time. We demonstrate significant improvement of hRUV over existing methods in preserving biological signals whilst removing unwanted variation for large scale metabolomics studies. Our novel tools not only provide a strategy for large scale data normalization, but also provides guidance on the design strategy for large omics studies.
Question: Write a study description for the study titled 'A Metabolomic Approach for Predicting Diurnal Changes in Cortisol'.
Answer: INTRODUCTION: The dysregulation of cortisol secretion has been associated with a number of mental health and mood disorders. However, diagnostics for mental health and mood disorders are behavioral and lack biological contexts.OBJECTIVES: The goal of this work is to identify volatile metabolites capable of predicting changes in total urinary cortisol across the diurnal cycle for long-term stress monitoring in psychological disorders.METHODS: We applied comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry to sample the urinary volatile metabolome using an untargeted approach across three time points in a single day for 60 subjects.RESULTS: The finalized multiple regression model includes 14 volatile metabolites and 7 interaction terms. A review of the selected metabolites suggests pyrrole, 6-methyl-5-hepten-2-one and 1-iodo-2-methylundecane may originate from endogenous metabolic mechanisms influenced by glucocorticoid signaling mechanisms.CONCLUSION: This analysis demonstrated the feasibility of using specific volatile metabolites for the prediction of secreted cortisol across time.
Question: Write a study description for the study titled 'Fatty acid synthesis in colorectal cancer: characterization of lipid metabolism in serum, tumour, and normal host tissues'.
Answer: The objective of the experiment was to compare serum fatty acid metabolite abundance between individuals with varying clinical stages of colorectal cancer (stage I-IV) and age-and-gender matched disease-free controls. Fatty acid metabolite abundance was compared between locoregional (stage I-III) and liver metastatic (stage IV) cancer, as well as between all stages of colorectal cancer (stage I-IV) and disease-free controls. Reprogrammed energy metabolism is now listed as one of the central hallmarks of cancer cells. Aberrant fatty acid metabolism contributes to tumourigenesis through provision of substrates for membrane synthesis, signalling molecules, and synthesis of complex lipids. In this thesis, the role of fatty acid metabolism is explored in the context of colorectal cancer. Metabolomics techniques were employed to characterize fatty acid metabolites in serum, and lipogenic gene expression was quantified in tumour and normal tissues to investigate host response to cancer. Fatty acid metabolite abundance was increased in the serum of individuals with colorectal cancer, and a growth factor signalling axis and lipogenic transcription factor upstream of the endogenous fatty acid synthesis pathway were increased in colorectal liver metastases. It was concluded that liver metastases have an effect on growth factor production in the hepatic microenvironment, leading to increased signalling through a pathway that activates the lipogenic transcription factor that regulates fatty acid synthesis.
Question: Write a study description for the study titled 'Clock regulation of metabolites reveals coupling between transcription and metabolism'.
Answer: The circadian clock is intricately connected with metabolism, however the precise details of these connections are incomplete. Here we used high temporal resolution metabolite profiling to determine circadian regulation of mouse liver and cell autonomous metabolism. In mouse liver, we found ~50% of metabolites were circadian, with strong enrichment of the nucleotide, amino acid, and methylation pathways. In U2OS cells, 27% of metabolites were circadian, including amino acids and NAD biosynthesis, also clock controlled in liver. To assess whether cell autonomous metabolite rhythms were clock-dependent, we used RNAi to perturb Bmal1, Cry1, and Cry2. Bmal1 knockdown eliminated most metabolite rhythms, while Cry1 generally shortened and Cry2 lengthened rhythms. Surprisingly, we found Cry1 knockdown induced 8 hr rhythms in amino acid, methylation, and vitamin metabolites, decoupling metabolite and transcriptional rhythms. These results provide the first comprehensive views of circadian liver and cell autonomous metabolism.
Question: Write a study description for the study titled 'Individual variability in human blood metabolites identifies age-related differences (30 persons, plasma data)'.
Answer: Metabolites present in human blood document individual physiological states influenced by genetic, epigenetic, and life-style factors. Using high-resolution liquid chromatography-mass spectrometry (LC-MS), we performed non-targeted, quantitative metabolomics analysis in blood of 15 young (29±4 yr) and 15 elderly (81±7 yr) individuals. Coefficients of variation (CV=standard deviation/mean) were obtained for 126 blood metabolites of all 30 donors. Fifty-five RBC-enriched metabolites, for which metabolomics studies have been scarce, are highlighted here. We found fourteen blood compounds that show remarkable age-related increases or decreases; they include 1,5-anhydroglucitol, dimethyl-guanosine, acetyl-carnosine, carnosine, ophthalmic acid, UDP-acetyl-glucosamine, N-acetyl-arginine, N6-acetyl-lysine, pantothenate, citrulline, leucine, isoleucine, NAD+, NADP+. Six of them are RBC-enriched, suggesting that RBC metabolomics is highly valuable for human aging research. Age differences are partly explained by a decrease in anti-oxidant production or increasing inefficiency of urea metabolism among the elderly. Pearson’s coefficients demonstrated that some age-related compounds are correlated, suggesting that aging affects them concomitantly. While our CV values are mostly consistent with those previously published, we here report novel CVs of 51 blood compounds. Compounds having moderate to high CV values (0.4-2.5) are often modified. Compounds having low CV values such as ATP and glutathione may be related to various diseases as their concentrations are strictly controlled, and changes in them would compromise health. Thus human blood is a rich source of information about individual metabolic differences.  Data from three injections of the same sample and three samples prepared from the same donated blood are available under accession number MTBLS263. Blood samples drawn from four volunteers four times within 24 h are available under accession number MTBLS264. Whole blood metabolomic data from all 30 subjects are available under accession number MTBLS265. RBC data from all 30 subjects can be found under MTBLS267.
Question: Write a study description for the study titled 'Untargeted plasma metabolome identifies biomarkers in patients with extracranial arteriovenous malformations'.
Answer: OBJECTIVE: This study aimed to investigate the plasma metabolic profile of patients with extracranial arteriovenous malformations (AVM).METHOD: Plasma samples were collected from 32 AVM patients and 30 healthy controls (HC). Ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) was employed to analyze the metabolic profiles of both groups. Metabolic pathway enrichment analysis was performed through Kyoto Encyclopedia of Genes and Genomes (KEGG) database and MetaboAnalyst. Additionally, machine learning algorithms such as Least Absolute Shrinkage and Selection Operator (LASSO) and random forest (RF) were conducted to screen characteristic metabolites. The effectiveness of the serum biomarkers for AVM was evaluated using a receiver-operating characteristics (ROC) curve.RESULT: In total, 184 differential metabolites were screened in this study, with 110 metabolites in positive ion mode and 74 metabolites in negative mode. Lipids and lipid-like molecules were the predominant metabolites detected in both positive and negative ion modes. Several significant metabolic pathways were enriched in AVMs, including lipid metabolism, amino acid metabolism, carbohydrate metabolism and protein translation. Through machine learning algorithms, 9 metabolites were identify as characteristic metabolites, including hydroxy-proline, L-2-Amino-4-methylenepentanedioic acid, piperettine, 20-hydroxy-PGF2a, 2,2,4,4-tetramethyl-6-(1-oxobutyl)-1,3,5-cyclohexanetrione, DL-tryptophan, 9-oxoODE, alpha-Linolenic acid and dihydrojasmonic acid.CONCLUSION: Patients with extracranial AVMs exhibited significantly altered metabolic patterns compared to healthy controls, which could be identified using plasma metabolomics. These findings suggest that metabolomic profiling can aid in the understanding of AVM pathophysiology and potentially inform clinical diagnosis and treatment.
Question: Write a study description for the study titled 'Mining for natural product antileishmanials in a fungal extract library'.
Answer: Leishmaniasis is a Neglected Tropical Disease caused by the insect-vector borne protozoan parasite, Leishmania species. Infection affects millions of the World’s poorest, however vaccines are absent and drug therapy limited. Recently, public-private partnerships have developed to identify new modes of controlling leishmaniasis. Most of these collaborative efforts have relied upon the small molecule synthetic compound libraries held by industry, but the number of New Chemical Entities (NCE) identified and entering development as antileishmanials has been very low. In light of this, here we describe a public-private effort to identify natural products with activity against Leishmania mexicana, a causative agent of cutaneous leishmanaisis (CL). Utilising Hypha Discovery’s fungal extract library which is rich in small molecule (<500 molecular weight) secondary metabolites, we undertook an iterative phenotypic screening and fractionation approach to identify potent and selective antileishmanial hits. This led to the identification of a novel oxidised bisabolane sequiterpene which demonstrated activity in an infected cell model and was shown to disrupt multiple processes using a metabolomic approach. In addition, and importantly, this study also sets a precedent for new approaches for CL drug discovery.