LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Post-mortem changes in the metabolomic compositions of rabbit blood, aqueous and vitreous humors'.
Answer: Introduction: The analysis of post-mortem metabolomic changes in biological fluids opens the way to develop new methods for the estimation of post-mortem interval (PMI). It may also help in the analysis of disease-induced metabolomic changes in human tissues when the postoperational samples are compared to the post-mortem samples from healthy donors. Objectives: The goals of this study are to observe and classify the post-mortem changes occurring in the rabbit blood, aqueous and vitreous humors (AH and VH), to identify the potential PMI markers among a wide range of metabolites, and also to determine which biological fluid – blood, AH or VH – is more suitable for the PMI estimation. Methods: The quantitative metabolomic profiling of samples of the rabbit serum, AH and VH taken at different PMIs has been performed with the combined use of high-frequency NMR and high-resolution LC-MS methods. Results: The quantitative levels of 63 metabolites in the rabbit serum, AH and VH at different PMIs have been measured. It has been found that the post-mortem metabolomic changes in AH and VH proceed slower than in blood, and the data scattering is lower. Among the metabolites whose concentrations increase with time, the most significant and linear growth is found for hypoxanthine, choline and glycerol. Conclusion: The obtained results indicate the advantage of ocular fluids, AH and VH, over blood serum for the search of potential biochemical markers for the PMI estimation. Among the compounds studied in the present work, hypoxanthine, choline and glycerol give the biggest promise as the potential PMI biomarkers.
Question: Write a study description for the study titled 'NMR Metabolomics in Frailty disease'.
Answer: Increasing evidence suggests that frailty results from a complex age-associated metabolic decline. Here, we investigated the serum metabolomic profile of a well-characterized cohort of elderly subjects encompassing the whole fit-to-frail continuum. Enrichment analyses revealed a complex dysregulation of amino acids and energy metabolism in both pre-frail and frail participants. Remarkably, upregulated betaine levels emerged as a specific biochemical signature of pre-frailty, holding promise for the development of novel targeted interventions.
Question: Write a study description for the study titled 'Auricularia auricula polysaccharides reduce obesity in mice through gut commensal Papillibacter cinnamivorans'.
Answer: Auricularia auricula is a well-known traditional edible and medicial fungus with high nutritional and pharmacological values, as well as metabolic and immunoregulatory properties. However, the exact mechanisms underlying the effects of Auricularia auricula polysaccharides (AAP) on obesity and related metabolic endpoints, including the role of the gut microbiota, remain insufficiently understood. To determine the mechanistic role of the gut microbiota in observed anti-obesogenic effects AAP, faecal microbiota transplantation (FMT) and pseudo germ-free mice model treated with antibiotics were also applied, together with 16S rRNA genomic-derived taxonomic profiling. HFD murine exposure to AAP thwarted weight-gains, reduced fat depositing, together with upregulating thermogenesis proteomic biomarkers within adipose tissue. These effects were associated with diminished intestine/bloodstream-borne lipid transportation, together with enhanced glucose tolerance. FMT administered in tandem with antibiotic treatment demonstrated the intestinal microbiota was necessary in deploying AAP anti-obesogenic functions. Intestine-dwelling microbial population assessments discovered AAP to enhance (in a selective manner) Papillibacter cinnamivorans, a commensal bacterium having reduced presence within HFD mice. Notably, HFD mice treated with oral formulations of Papillibacter cinnamivorans diminished obesity and was linked to decreased intestinal lipid transportation. Datasets from the present study show that AAP thwarted dietary-driven obesity and metabolism-based disorders through regulating intestinal lipid transportation, a mechanism that is dependent on the gut commensal Papillibacter cinnamivorans. These results indicated AAP and Papillibacter cinnamivorans as newly identified pre- and probiotics that could possibly serve as novel countermeasure against obesity
Question: Write a study description for the study titled 'SIN-3 transcriptional coregulator maintains mitochondrial homeostasis and polyamine flux'.
Answer: Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays an important role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear-encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals identifies a signature of mitochondria stress and deregulation of methionine flux, resulting in decreased S-adenosyl methionine (SAM) and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.
Question: Write a study description for the study titled 'Dissolved organic matter produced by Thalassiosira pseudonana'.
Answer: Phytoplankton are significant producers of dissolved organic matter (DOM) in marine ecosystems but the identity and dynamics of this DOM remain poorly constrained. Knowledge on the identity and dynamics of DOM are crucial for understanding the molecular-level reactions at the base of the global carbon cycle. Here we apply emerging analytical and computational tools from metabolomics to investigate the composition of DOM produced by the centric diatom Thalassiosira pseudonana. We assessed both intracellular metabolites within T. pseudonana (the endo-metabolome) and extracellular metabolites released by T. pseudonana (the exo-metabolome). The intracellular metabolites had a more variable composition than the extracellular metabolites. We putatively identified novel compounds not previously associated with T. pseudonana as well as compounds that have previously been identified within T. pseudonana’s metabolic capacity (e.g. dimethylsulfoniopropionate and degradation products of chitin). The resulting information will provide the basis for future experiments to assess the impact of T. pseudonana on the composition of dissolved organic matter in marine environments.
Question: Write a study description for the study titled 'Appropriate taxonomic classification of intestinal microbiome by 16S rRNA gene targeting metagenomic approach'.
Answer: 16S metagenomic analysis has provided much information about the intestinal microbiome. However, there are no reports that describe their appropriate taxonomic classification rank. Moreover, studies differ on the taxonomic ranking of the same microorganism. Intestinal microbiome exerts a significant degree of influence on the host via the metabolome. In the present study, we searched for their appropriate classification ranks based on the correlation between the metabolome and microbiome. Over 200 metabolites were identified by capillary electrophoresis and time-of-flight mass spectrometry (CE-TOFMS) based metabolomics of faeces from antibiotics-treated and untreated mice. Nine phyla, 15 orders, 22 classes, 40 families, and 59 genera were identified by 16S metagenomic analysis. Principle component analysis (PCA) of the intestinal microbiome at each taxonomic rank revealed differences between the antibiotic-treated and untreated groups on the first principle component in the family and genus-level analyses. These differences were similar to those found in the metabolome PCA. In addition, a strong correlation between principle component score of the metabolome and that of the microbiome was observed in the case of family and genus-level analyses. From these results, we hypothesize that lower taxonomic ranks such as family or genus are preferable while using 16S metagenome analysis for investigating the crosstalk, via metabolites, between intestinal microbiome and the host.
Question: Write a study description for the study titled 'Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans'.
Answer: Plant fibers in byproduct streams produced by non-harsh food processing methods represent biorepositories of diverse, naturally occurring, and physiologically active biomolecules. To demonstrate one approach for their characterization, mass spectrometry of intestinal contents from gnotobiotic mice, plus in vitro studies, revealed liberation of N-methylserotonin from orange fibers by human gut microbiota members including Bacteroides ovatus. Functional genomic analyses of B. ovatus strains grown under permissive and non-permissive N-methylserotonin 'mining' conditions revealed polysaccharide utilization loci that target pectins whose expression correlate with strain-specific liberation of this compound. N-methylserotonin, orally administered to germ-free mice, reduced adiposity, altered liver glycogenesis, shortened gut transit time, and changed expression of genes that regulate circadian rhythm in the liver and colon. In human studies, dose-dependent, orange-fiber-specific fecal accumulation of N-methylserotonin positively correlated with levels of microbiome genes encoding enzymes that digest pectic glycans. Identifying this type of microbial mining activity has potential therapeutic implications.
Question: Write a study description for the study titled 'Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes'.
Answer: In Eco-Metabolomics, non-model organisms are typically studied in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such data involve, among others, complex ecological experiment designs, peak detection parameter settings and high variation of metabolite profiles of different species. Here, we present a representative dataset generated from 108 samples of 9 bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry (LC/MS) acquisition method. With this dataset, we address the challenges in data processing focusing on data import, analytical quality control and peak detection. We expect that this representative dataset will encourage researchers to conduct subsequent Eco-Metabolomics studies.
Question: Write a study description for the study titled 'Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype (UPLC-MS HILIC NEG assay)'.
Answer: Women have a lower incidence of colorectal cancer (CRC) than men, however, they have a higher incidence of right-sided colon cancer (RCC). This is of concern as patients with RCC have the poorest clinical outcomes among all CRC patients. Aberrant metabolism is a known hallmark and therapeutic target for cancer. We propose that metabolic subphenotypes exist between CRCs due to intertumoral molecular and genomic variation, and differences in environmental milieu of the colon which vary between the sexes. Metabolomics analysis of patient colon tumors (n = 197) and normal tissues (n = 39) revealed sex-specific metabolic subphenotypes dependent on anatomic location. Tumors from women with RCC were nutrient-deplete, showing enhanced energy production to fuel asparagine synthesis and amino acid uptake. The clinical importance of our findings were further investigated in an independent data set from The Cancer Genomic Atlas, and demonstrated that high asparagine synthetase (ASNS) expression correlated with poorer survival for women. This is the first study to show a unique, nutrient-deplete metabolic subphenotype in women with RCC, with implications for tumor progression and outcomes in CRC patients.UPLC-MS HILIC POS assay is reported in MTBLS1122.UPLC-MS HILIC NEG assay is reported in MTBLS1124.UPLC-MS RP POS assay is reported in MTBLS1129.UPLC-MS RP NEG assay is reported in MTBLS1130.
Question: Write a study description for the study titled 'Plasma Metabolome Analysis for Predicting Antiviral Treatment Efficacy in Chronic Hepatitis B: Diagnostic Biomarkers and Therapeutic Insights'.
Answer: The early and accurate identification of predictive biomarkers for antiviral treatment efficacy remains a significant clinical challenge, particularly in the management of chronic hepatitis B (CHB). This study aimed to assess whether the plasma metabolome could reliably predict the success of antiviral therapy in CHB patients. We conducted a retrospective analysis on 56 treatment-naive CHB patients at the First Affiliated Hospital of Zhejiang University from December 2013 to March 2016. Patients were randomly assigned to either a discovery cohort (n=29) or a validation cohort (n=27) and underwent a 48-week treatment regimen of entecavir (ETV) and interferon-alpha (IFN-α). Based on the outcome of the treatment, patients were classified as HBeAg seroconversion either (High responders, Hrp) or the non-remission group (Low responder, Lrp). Our methodology involved an untargeted analysis of the amine/phenol and carboxylic acid submetabolomes in the CHB patients under treatment, utilizing chemical isotope labeling (CIL) techniques with liquid chromatography-mass spectrometry (LC-MS).Several metabolites were identified as having significant diagnostic potential for distinguishing Hrp from Lrp, with areas under the receiver operating characteristic curve (AUC) exceeding those typically clinical indicators. Notably, four metabolites, namely 2-methyl-3-ketovaleric acid, 2-ketohexanoic acid, 6-oxo-1,4,5,6-tetrahydronicotinic acid, and α-ketoisovaleric acid, demonstrated exceptionally high sensitivity and specificity in both cohorts, nearing 100%. In contrast, the clinical indicators, including HBcAb, log(HBsAg), and HBeAb, demonstrated lower and inconsistent sensitivity and specificity between the discovery and validation cohorts. Using HBcAb as a marker, the sensitivity was 87.5% with 76.9% specificity in the discovery cohort; however, the sensitivity dropped to 46.7% with 91.7% specificity in the validation cohort. Using log(HBsAg), the sensitivity was 84.6% with 69.2% specificity in the discovery cohort, compared to 85.7% sensitivity and 83.3% specificity in the validation cohort. For HBeAb, the separation of Hrp and Lrp had a sensitivity of 87.5% with 69.2% specificity in the discovery cohort, while the validation cohort showed 86.7% sensitivity and 91.7% specificity.
Question: Write a study description for the study titled 'Alterations in the gut microbiota and metabolic profiles coincide with intestinal damage in mice with a bloodborne Candida albicans infection'.
Answer: Candida albicans is an opportunistic fungus that can threaten life especially in patients with candidemia. The morbidity and mortality of candidemia originating from a central venous catheter (CVC) and illicit intravenous drug use (IVDU) are increasing. However, the mechanism underlying the bloodborne C. albicans infection remains unclear. Herein, we evaluated the gut microbiome, metabolites and intestinal mucosa by constructing the mouse models with candidemia. Model mice were injected with C. albicans via tail vein. Control mice underwent sham procedures. We observed basic life characteristics, intestinal damage-related alterations using hematoxylin and eosin (H&E) staining, intestinal tight junction protein levels, and intestinal permeability in these mice. Fecal samples were analyzed by performing 16S rRNA gene sequencing of the microbiota and LC-MS metabolomics to reveal the perturbations in intestinal flora and metabolism exacerbating intestinal damage. Weight loss, a decreased survival rate, C. albicans infection spread, and colonic epithelial damage occurred in the model group. Furthermore, the intestinal flora abundance was reduced. Several probiotics, such as Lactobacillus, and butyrate-producing bacteria, including Roseburia, Lachnospiraceae, and Clostridia, were depleted, and some pathogenic bacteria, such as Escherichia-Shigella and Proteus, belonging to the Proteobacteria phylum, and the inflammation mediators Ruminococcus and Parabacteroides were enriched in model mice. Multiple differentially altered metabolic pathways were observed and mainly related to bile acid, arachidonic acid, bile secretion, and arachidonic acid metabolism. This study illustrated the effects of a bloodborne C. albicans on the intestinal microbiota, metabolites, and intestinal barrier, which may provide new insights into tests or treatments for candidemia originating from CVC or IVDU.
Question: Write a study description for the study titled 'Frailty markers comprise blood metabolites involved in antioxidation, cognition, and mobility'.
Answer: As human society ages globally, age-related disorders are becoming increasingly common. Due to decreasing physiological reserves and increasing organ system dysfunction associated with age, frailty affects many elderly people, compromising their ability to cope with acute stressors. Frail elderly people commonly manifest complex clinical symptoms, including cognitive dysfunction, hypomobility, and impaired daily activity, the metabolic basis of which has been little understood. We applied untargeted, comprehensive, LC-MS metabolomic analysis to human blood from 19 frail and non-frail elderly patients, who were clinically evaluated using the Edmonton Frail Scale, the MoCA-J for cognition, and the TUG for mobility. Among 131 metabolites assayed, we identified 22 markers for frailty, cognition, and hypomobility, most of which were abundant in blood. Frailty markers included 5 of 6 markers specifically related to cognition and 6 of 12 associated with hypomobility. These overlapping sets of markers include metabolites related to antioxidation, muscle or nitrogen metabolism, and amino acids, most of which decrease in frail elderly people. Five frailty-related metabolites that decreased (1,5-anhydroglucitol, acetyl-carnosine, ophthalmic acid, leucine, and isoleucine) have been previously reported as markers of aging, providing a metabolic link between human aging and frailty. Our findings clearly indicate that metabolite profiles efficiently distinguish frailty from non-frailty. Importantly, the antioxidant, ergothioneine, which decreases in frailty, is neuroprotective. Oxidative stress resulting from diminished antioxidant levels, could be a key vulnerability for pathogenesis of frailty, exacerbating illnesses related to human aging.
Question: Write a study description for the study titled 'A metabolomic study of adipose tissue in mice with a disruption of the circadian system'.
Answer: Adipose tissue functions in terms of energy homeostasis as a rheostat for blood triglyceride, regulating its concentration, in response to external stimuli. In addition it acts as a barometer to inform the central nervous system of energy levels which can vary dramatically between meals and according to energy demand. Here a metabolomic approach, combining both Mass Spectrometry and Nuclear Magnetic Resonance spectroscopy, was used to analyse both white and brown adipose tissue in mice with adipocyte-specific deletion of Arntl (also known as Bmal1), a gene encoding a core molecular clock component. The results are consistent with a peripheral circadian clock playing a central role in metabolic regulation of both brown and white adipose tissue in rodents and show that Arntl induced global changes in both tissues which were distinct for the two types. In particular, anterior subcutaneous white adipose tissue (ASWAT) tissue was effected by a reduction in the degree of unsaturation of fatty acids, while brown adipose tissue (BAT) changes were associated with a reduction in chain length. In addition the aqueous fraction of metabolites in BAT were profoundly affected by Arntl disruption, consistent with the dynamic role of this tissue in maintaining body temperature across the day/night cycle and an upregulation in fatty acid oxidation and citric acid cycle activity to generate heat during the day when rats are inactive (increases in 3-hydroxybutyrate and glutamate), and increased synthesis and storage of lipids during the night when rats feed more (increased concentrations of glycerol, choline and glycerophosphocholine).The data and protocols for NMR assay are reported in current study MTBLS382. The data and protocols for UPLC-QTOF-MS are reported in study MTBLS380.The data and protocols for GC-FID are reproted in study MTBLS390.
Question: Write a study description for the study titled 'Metabolomics reveals changes in soil metabolic profiles during vegetation succession in karst area'.
Answer: The metabolite characteristics of karst soils with different vegetation stages (grassland, brushwood, secondary forest and primary forest) based on untargeted metabolomics were investigated.
Question: Write a study description for the study titled 'Supplemental data for CAMERA, an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets'.
Answer: Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis.