LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS'.
Answer: As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by LC-QTOF-MS facing the challenge of capturing metabolic information from minimal sample amount (120% compared to matrix-derived signals present in blank samples. As a proof-of-concept, the method was applied to examine the early metabolic response of colorectal cancer organoids to 5-fluorouracil treatment. Statistical analysis revealed dose-dependent changes in the metabolic profiles of treated organoids including elevated levels of 2'-deoxyuridine, 2'-O-methylcytidin, inosine and 1-methyladenosine and depletion of 2'-deoxyadenosine and specific phospholipids. In accordance with the mechanism of action of 5-fluorouracil, changed metabolites are mainly involved in purine and pyrimidine metabolism. The novel protocol provides a first basis for the assessment of metabolic drug response phenotypes in 3D organoid models.
Question: Write a study description for the study titled 'Increased fatty acid metabolism and decreased glycolysis are hallmarks of metabolic reprogramming within microglia in degenerating white matter during recovery from experimental stroke'.
Answer: The goal of this study was to evaluate changes in metabolic homeostasis during the first 12 weeks of recovery in a distal middle cerebral artery occlusion mouse model of stroke. To achieve this goal, we compared the brain metabolomes of ipsilateral and contralateral hemispheres from aged male mice up to 12 weeks after stroke to that of age-matched naïve and sham mice. There were 707 biochemicals detected in each sample by liquid chromatography-mass spectroscopy (LC-MS). Mitochondrial fatty acid β-oxidation, indicated by acyl carnitine levels, was increased in stroked tissue at 1 day and 4 weeks following stroke. Glucose and several glycolytic intermediates were elevated in the ipsilateral hemisphere for 12 weeks compared to the aged naïve controls, but pyruvate was decreased. Additionally, itaconate, a glycolysis inhibitor associated with activation of anti-inflammatory mechanisms in myeloid cells, was higher in the same comparisons. Spatial transcriptomics and RNA in situ hybridization localized these alterations to microglia within the area of axonal degeneration. These results indicate that chronic metabolic differences exist between stroked and control brains, including alterations in fatty acid metabolism and glycolysis within microglia in areas of degenerating white matter for at least 12 weeks after stroke.
Question: Write a study description for the study titled 'Multi-hierarchical profiling the structure-activity relationships of engineered nanomaterials at nano-bio interfaces'.
Answer: Increasing concerns over the possible risks of nanotechnology necessitates breakthroughs in structure-activity relationship (SAR) analyses of engineered nanomaterials (ENMs) at nano-bio interfaces. However, current nano-SARs are often based on univariate assessments and fail to provide tiered views on ENM-induced bio-effects. Here we report a multi-hierarchical nano-SAR assessment for a representative ENM, Fe2O3, by metabolomics and proteomics analyses. The established nano-SAR profile allows the visualizing of the contributions of seven basic properties of Fe2O3 to its diverse bio-effects. For instance, although surface reactivity is responsible for Fe2O3-induced cell migration, the inflammatory effects of Fe2O3 are determined by aspect ratio (nanorods) or surface reactivity (nanoplates). These nano-SARs are examined in THP-1 cells and animal lungs, which allow us to decipher the detailed mechanisms including NLRP3 inflammasome pathway and monocyte chemoattractant protein-1-dependent signaling. This study provides more insights for nano-SARs, and may facilitate the tailored design of ENMs to render them desired bio-effects.
Question: Write a study description for the study titled 'Molecular Docking and Dynamic Study of Ethanol Extract of Citrus sinensis as Keap-1 and NMDA inhibitor in Brain Injury'.
Answer: Traumatic brain injury is a significant cause of mortality in young adults and disability in all age groups. Secondary injury involving various processes such as oxidative stress, which induced neuronal apoptosis, ensued afterward. This study aimed to analyze the active compounds of Citrus sinensis and predict its antioxidative activity in traumatic brain injury. Liquid Chromatography High-Resolution Mass Spectrometry (LC-HRMS) was used to identify compounds in ethanol extract of Citrus sinensis peel. We analyzed pharmacokinetics, blood-brain barrier (BBB) permeability and toxicity of active compounds in Citrus sinensis peel using SwissADME and OSIRIS. The compounds have good blood-brain barrier permeability conducted for molecular docking study to identify molecular interaction with Keap1 (Kelch-like ECH Associated Protein 1) and NMDA (N-methyl-D-aspartate) proteins using PyRx, PyMol and Discovery Studio software. Results of the LC-HRMS examination obtained 16 active compounds contained in the ethanol extract of the orange peel. Nootkatone, alminoprofen, linoleic acid, chanoclavine, scoparone and tangeretin are predicted to pass the blood-brain barrier. Active compounds of Citrus sinensis strongly bond against Keap1 and NMDA, especially Scoparone and Nootkatone. The strong binding affinity of scoparone-Keap1 was -5.0, more than the control ligand, and nootkatone-NMDA was -7.8, similar to the control ligand. Active compounds of Citrus sinensis peel showed inhibitory potentials, good pharmacokinetics and toxicity profiles against Keap1 and NMDA. These findings suggested that ethanol extract of Citrus sinensis peels has the potential as an oxidative stress inhibitor for brain injury therapy.
Question: Write a study description for the study titled 'Gut microbiome and metabolome dynamics as predictors of clinical outcomes in hematopoietic stem cell transplantation'.
Answer: Hematopoietic stem cell transplantation (HSCT) induces significant alterations in the gut microbiome and metabolome, which influence transplant-related complications and surviv-al. This study longitudinally analyzed gut microbiota and metabolites at pre- (T1), peri- (T2), and post-transplant (T3) stages to identify key determinants of clinical outcomes. Lower microbiome diversity at T1 and T3 correlated with graft-versus-host disease (GVHD), progressive disease (PD), and reduced overall survival (OS). Short-chain fatty acids (SCFAs), particularly acetate, declined over time, with reductions at T2-T1 linked to GVHD, diarrhea, PD, and lower OS. Specific perspective metabolites (SPMs) such as elevated uric acid at T2 were associated with GVHD, while reduced 1-phenylethylamine correlated with diarrhea. Patients with enriched beneficial taxa (e.g., Lachnospiraceae, Ruminococcaceae) exhibited improved OS. These findings highlight the gut microbiome-metabolome axis as a predictive marker for HSCT outcomes. Identifying microbial and metabolic signatures may provide novel diagnostic and therapeutic targets for mitigating HSCT-related complications, enhancing patient prognosis.
Question: Write a study description for the study titled 'The effects of oligomycin administration and glutamine deprivation on metabolic profile of MCF7 breast cancer cell line measured using [1,2-13C2]-D-glucose and [U-13C5]-L-glutamine as tracers'.
Answer: This study aims to establish a comprehensive, genome-scale metabolic model (GSMM) combining different omics data of different regulatory levels of breast cancer cells in order to elucidate the way that these regulatory levels affect or determine each other. Together with transcriptomics, proteomics and metabolomics data obtained, fluxomics data was also to be integrated. In order to get the fluxomics data, MCF cells were incubated with either the medium containing [1,2-13C2]-D-glucose or [U-13C5]-L-glutamine for 8 or 24 hours. A good GSMM should answer any perturbations applied; therefore, different incubation conditions should be applied to generate different metabolic profiles that will help to test if the model of breast cancer works well. To this end, MCF cells were either administered oligomycine, which is an ATP synthase inhibitor, or were deprived of glutamine. Cells were counted before and after each incubation time so as to get the cell proliferation curve. Later, at the corresponding time points, cells and media were frozen to measure the concentrations of glucose, glutamine and lactate (not shown in the file) and the mass isotopomer distributions of glutamate, ribose, lactate, amino acids and TCA cycle intermediates (shown in the file). Finally, all these data was combined in order to estimate the flux rates of various reactions within the central carbon metabolism (not shown in the file). The fluxomics data obtained in this way is to be introduced in the GSMM designed.
Question: Write a study description for the study titled 'Accumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex'.
Answer: Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that in Arabidopsis thaliana, scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low temperature stress. A genetic screen for altered scopolin levels in Arabidopsis thaliana identified a mutant compromised for scopolin accumulation in response to stress; the lesion was present in a homologue of THO1, the product of which contributes to the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants carrying defective THO and RDR6 genes were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing like the transacting small interfering RNA pathway which requires THO/TREX and RDR6 function.
Question: Write a study description for the study titled '2_Bacillus siamensis to restore the compromised amino acid and energy metabolism of Mesorhizobium metallidurans under saline alkali stress'.
Answer: These findings suggest that B. siamensis BT 9 1 cross-feeds M. metallidurans YC-39 with these metabolites, rescuing the compromised branched-chain amino acid synthesis pathway and the TCA cycle in saline alkaline environments. Eventually, coinoculation with B. siamensis BT 9 1 and M. metallidurans YC 39, along with isopropylmalate and succinic acid supplementation, increased M. metallidurans YC 39 nodule colonization and nitrogenase activity. Our study offers fresh perspectives on how wild S. davidii recruits beneficial Bacillus species to provide key metabolites for M. metallidurans, thereby increasing rhizobial survival under saline alkaline stress.
Question: Write a study description for the study titled 'Human age-declined saliva metabolic markers determined by LC-MS'.
Answer: Metabolites in human biofluids reflect individual physiological body states influenced by various factors. Using liquid chromatography-mass spectrometry (LC-MS), we conducted non-targeted, non-invasive, comprehensive metabolomics using saliva of 27 healthy volunteers in Okinawa, consisting of 13 young (30 ± 3 yr) and 14 elderly (76 ± 4 yr) people. Quantitative analysis of whole 99 saliva metabolites has been scarce. Twenty-one of 99 salivary metabolites quantified appear to be statistically age-linked. Their abundances decline with advancing age, except for ATP, which increased 1.96-fold in the elderly, possibly due to reduced ATP consumption. Fourteen age-linked and highly correlated compounds function in a metabolic network of amino acids, purines/pyrimidines, the pentose-phosphate pathway and glycolysis/gluconeogenesis. The remaining seven metabolites, while age-linked, but less strongly correlated, include ATP, muscle-related acetyl-carnosine, carnitine, N-methyl-histidine and creatinine, RNA-related dimethyl-xanthine, N-methyl-adenosine, anti-oxidation related glutathione disulfide, and N-methyl-adenosine. These metabolites together may provide detailed information on the metabolic network of oral aging, which is required to understand the functional decline of oral activity during human aging.
Question: Write a study description for the study titled 'PREDICT: untargeted metabolomic profiling in a Brassica napus (canola) breeding population by GC-MS'.
Answer: Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalize on a diverse canola population with spring-type 477 lines which was previously analysed by high-throughput phenotyping (Knoch et al., 2020), and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction (Knoch et al., 2021). We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and re-analysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly (Rousseau-Gueutin et al., 2020). Genome-wide association testing revealed 61,298 robust quantitative trait loci (QTL) including 187 metabolite-QTL, 56,814 expression-QTL, and 4,297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritized candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1), and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.
Question: Write a study description for the study titled 'Metabolic phenotyping of urine from a dementia research cohort'.
Answer: To better understand the molecular mechanisms underpinning physiological variation in human populations, metabolic phenotyping approaches are increasingly being applied to studies involving hundreds and thousands of biofluid samples. Hyphenated ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) has become a fundamental tool for this purpose. However, the seemingly inevitable need to analyze large studies in multiple analytical batches for UPLC-MS analysis poses a challenge to data quality which has been recognized in the field. Herein, we describe in detail a fit-for-purpose UPLC-MS platform, method set, and sample analysis workflow, capable of sustained analysis on an industrial scale and allowing batch-free operation for large studies. Using complementary reversed-phase chromatography (RPC) and hydrophilic interaction liquid chromatography (HILIC) together with high resolution orthogonal acceleration time-of-flight mass spectrometry (oaTOF-MS), exceptional measurement precision is exemplified with independent epidemiological sample sets of approximately 650 and 1000 participant samples. Evaluation of molecular reference targets in repeated injections of pooled quality control (QC) samples distributed throughout each experiment demonstrates a mean retention time relative standard deviation (RSD) of <0.3% across all assays in both studies and a mean peak area RSD of <15% in the raw data. To more globally assess the quality of the profiling data, untargeted feature extraction was performed followed by data filtration according to feature intensity response to QC sample dilution. Analysis of the remaining features within the repeated QC sample measurements demonstrated median peak area RSD values of <20% for the RPC assays and <25% for the HILIC assays. These values represent the quality of the raw data, as no normalization or feature-specific intensity correction was applied. While the data in each experiment was acquired in a single continuous batch, instances of minor time-dependent intensity drift were observed, highlighting the utility of data correction techniques despite reducing the dependency on them for generating high quality data. These results demonstrate that the platform and methodology presented herein is fit-for-use in large scale metabolic phenotyping studies, challenging the assertion that such screening is inherently limited by batch effects. Details of the pipeline used to generate high quality raw data and mitigate the need for batch correction are provided.
Question: Write a study description for the study titled 'Seagrasses excrete sugars to their rhizosphere making them the sweet spots in the sea (Plant roots; MALDI-MSI assay)'.
Answer: Seagrasses are one of the most efficient natural sinks of carbon dioxide (CO2) on Earth. Despite covering less than 0.1% of coastal regions, they have the capacity to bury up to 10% of marine organic matter and can bury the same amount of carbon 35 times faster than tropical rainforests. On land, the soil’s ability to sequestrate carbon is intimately linked to microbial metabolism. Despite the growing attention to the link between plant production, microbial communities, and the carbon cycle in terrestrial ecosystems, these processes remain enigmatic in the sea. Here, we show that seagrasses excrete organic sugars, namely in the form of sucrose, into their rhizospheres. Surprisingly, the microbial communities living underneath meadows do not fully use this sugar stock in their metabolism. Instead, sucrose piles up in the sediments to mM concentrations underneath multiple types of seagrass meadows. Sediment incubation experiments show that microbial communities living underneath a meadow use sucrose at low metabolic rates. Our metagenomic analyses revealed that the distinct community of microorganisms occurring underneath meadows is limited in their ability to degrade simple sugars, which allows these compounds to persist in the environment over relatively long periods of time. Our findings reveal how seagrasses form blue carbon stocks despite the relatively small area they occupy. Unfortunately, anthropogenic disturbances are threatening the long-term persistence of seagrass meadows. Given that these sediments contain a large stock of sugars that heterotopic bacteria can degrade, it is even more important to protect these ecosystems from degradation.MALDI-MSI assay of Plant roots is reported in the current study MTBLS1746GC-MS assay of Seawater sediment is reported in MTBLS1570GC-MS assay of Plant tissues is reported in MTBLS1579GC-MS assay of Sediment porewater is reported in MTBLS1610
Question: Write a study description for the study titled 'Multiple omics reveal link between the microbiota-gut-brain axis and intracranial aneurysm rupture'.
Answer: Intracranial aneurysms (IAs) are benign cerebrovascular maladies characterized by pathological dilatation in the walls of intracranial arteries. However, spontaneous subarachnoid hemorrhage (SAH) resulting from aneurysm rupture poses a grave threat to the patient's life. Accumulating evidence implicates gut ecological dysregulation in the pathogenesis of IAs. Nevertheless, the relevance of gut dysbiosis to the rupture of IAs remains unknown. In this study, altogether 124 fecal samples were employed for microbiome sequencing by third-generation 16s rRNA sequencing, while 160 fecal samples were sequenced for metabolomics sequencing by liquid chromatography-mass spectroscopy techniques. Furthermore, the stool samples from IAs and healthy family controls were partitioned into two cohorts: the discovery set and the validation set for mutual cross-validation. Differential gut microbiota and metabolites associated with ruptured intracranial aneurysms (RIAs) were identified. Additionally, a superior risk assessment model for RIAs was constructed utilizing these differential species and metabolites. Subsequent integrated metabolomics and microbiomics analyses have uncovered a profound link between the dysregulation of unsaturated fatty acid and essential amino acid metabolic pathways and the rupture of IAs. This metabolic imbalance is attributed to alternations in the gut microbiota composition. Furthermore, we further revealed alterations in the gut flora of patients with IAs at high-risk rupture locations, incorporating the clinical characteristics. Finally, 30 peripheral blood and paired cerebrospinal fluid samples were tested to confirm variations in α-linolenic acid, linoleic acid and butyric acid concentrations among IA patients. This study underscores the crucial role of gut microbiota and metabolisms dysbiosis in IAs formation, while also highlighting a novel risk factor for aneurysm rupture. The identification and validation of differential species and metabolites provide new assessment biomarkers against IAs rupture.
Question: Write a study description for the study titled 'Metabolomics study of different tissues of mume 'Longyan' plant grafted on mume rootstock and peach rootstock (Root)'.
Answer: Background: Grafting with the dwarf rootstock is an efficient method to control the plant height in fruit production. However, the molecular mechanism is still unclear. Our previous study showed that the plants with Prunus mume rootstock exhibit a considerable reduction in plant height, internode length and number of nodes compared with Prunus persica rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by ‘P. mume’ rootstocks through transcriptome and metabolomic analysis with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’. Results: The findings of the study indicate a significant decrease in brassinolide levels in plants that were grafted onto ‘P. mume’ rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased in the research. The present work observed a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto ‘P. mume’ rootstocks. Auxin signaling cues promote PmARF3 transcription, which directly controls this upregulation. Through its binding to PmBAS1 and PmSAUR36 gene promoters, PmLBD3 promotes endogenous brassinolide inactivation and inhibits cell proliferation. Conclusions: Auxin signaling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and caused dwarf plants in stone fruits.Root analysis is reported in the current study MTBLS10051.Leaf analysis is reported in MTBLS10083.Stem analysis is reported in MTBLS10062.