LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents'.
Answer: OBJECTIVE: Patients with renal failure suffer from symptoms caused by uraemic toxins, possibly of gut microbial origin, as deduced from studies in animals. The aim of the study is to characterise relationships between the intestinal microbiome composition, uraemic toxins and renal failure symptoms in human end-stage renal disease (ESRD).DESIGN: Characterisation of gut microbiome, serum and faecal metabolome and human phenotypes in a cohort of 223 patients with ESRD and 69 healthy controls. Multidimensional data integration to reveal links between these datasets and the use of chronic kidney disease (CKD) rodent models to test the effects of intestinal microbiome on toxin accumulation and disease severity.RESULTS: A group of microbial species enriched in ESRD correlates tightly to patient clinical variables and encode functions involved in toxin and secondary bile acids synthesis; the relative abundance of the microbial functions correlates with the serum or faecal concentrations of these metabolites. Microbiota from patients transplanted to renal injured germ-free mice or antibiotic-treated rats induce higher production of serum uraemic toxins and aggravated renal fibrosis and oxidative stress more than microbiota from controls. Two of the species, Eggerthella lenta and Fusobacterium nucleatum, increase uraemic toxins production and promote renal disease development in a CKD rat model. A probiotic Bifidobacterium animalis decreases abundance of these species, reduces levels of toxins and the severity of the disease in rats.CONCLUSION: Aberrant gut microbiota in patients with ESRD sculpts a detrimental metabolome aggravating clinical outcomes, suggesting that the gut microbiota will be a promising target for diminishing uraemic toxicity in those patients.
Question: Write a study description for the study titled 'Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative (Streptococcus pneumoniae assays)'.
Answer: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission is specifically for Streptococcus pneumoniae.GC-MS and LC-MS Streptococcus pneumoniae assays are reported in the current study MTBLS2323GC-MS and LC-MS Escherichia coli assays are reported in MTBLS2015GC-MS and LC-MS Staphylococcus aureus assays are reported in MTBLS1898GC-MS and LC-MS Klebsiella pneumoniae assays are reported in MTBLS2322GC-MS and LC-MS Streptococcus pyogenes assays are reported in MTBLS2324
Question: Write a study description for the study titled 'Gluconeogenic enzyme PCK1 supports S-adenosylmethionine biosynthesis and H3K9me3 to suppress HCC progression'.
Answer: Deciphering the crosstalk between metabolic reprogramming and epigenetic regulation is a promising strategy for cancer therapy. In this study, we discovered that the gluconeogenic enzyme PCK1 fuels the generation of S-adenosylmethionine (SAM) through the serine synthesis pathway. The methyltransferase SUV39H1 catalyzes SAM, which serves as a methyl donor to support H3K9me3 modification, leading to the suppression of the oncogene S100A11. Mechanistically, PCK1 deficiency-induced oncogenic activation of S100A11 is due to its interaction with AKT1, which upregulates PI3K/AKT signaling. Intriguingly, the progression of hepatocellular carcinoma (HCC) driven by PCK1 deficiency was suppressed by SAM supplement or S100A11 knockout in vivo and in vitro. These findings reveal the availability of key metabolite SAM as a bridge connecting the gluconeogenic enzyme PCK1 and H3K9 trimethylation in attenuating HCC progression, thus suggesting a potential therapeutic strategy against HCC.
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 (Leaf)'.
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.Leaf analysis is reported in the current study MTBLS10083.Stem analysis is reported in MTBLS10062.Root analysis is reported in MTBLS10051.
Question: Write a study description for the study titled 'Multiplatform serum metabolic phenotyping combined with pathway mapping to identify biochemical differences in smokers (UPLC-MS assay)'.
Answer: A multiplatform comparison of serum of smokers (n=56) and non-smokers (n=57) using NMR spectroscopy and UPLC-MS was carried out to determine perturbed biochemical functions associated with tobacco smoking. This should be helpful for establishing causal relationships between exposure and adverse events. The statistical modelling revealed clustering of the classes, distinguished by metabolic biomarkers. The identified metabolites were subjected to metabolic pathway enrichment, modelling adverse biological events using available databases. Perturbation of metabolites involved in COPD, cardiovascular diseases and cancer were identified. Combining multiplatform metabolic phenotyping with knowledge-based mapping gives mechanistic insights into disease development which can be applied to next-generation tobacco/ nicotine products for risk assessment. UPLC-MS assay is reported in the current study MTBLS364.NMR assay is reported in MTBLS374.
Question: Write a study description for the study titled 'Untargeted LC-MS metabolomics for the analysis of micro-scaled extracellular metabolites from hepatocytes'.
Answer: Metabolome analysis in micro physiological models is a challenge due to the low volume of cell culture medium (CCM). Here, we report a LC-MS-based untargeted metabolomics protocol for the detection of hepatocyte extracellular metabolites from micro-scale samples of CCM. Using a single LC-MS method we have detected 57 metabolites of which 27 showed >2-fold shifts after 72-hours incubation. We demonstrate that micro-scale CCM samples can be used for modelling micro-physiological temporal dynamics in metabolite intensities.
Question: Write a study description for the study titled '1H HR-MAS NMR Based Metabolic Profiling of Cells in Response to Treatment with a Hexacationic Ruthenium Metallaprism as Potential Anticancer Drug'.
Answer: 1H high resolution magic angle spinning (HR-MAS) NMR spectroscopy was applied in combination with multivariate statistical analyses to study the metabolic response of whole cells to the treatment with a hexacationic ruthenium metallaprism [1]6+ as potential anticancer drug. Human ovarian cancer cells (A2780), the corresponding cisplatin resistant cells (A2780cisR), and human embryonic kidney cells (HEK-293) were each incubated for 24 h and 72 h with [1]6+ and compared to untreated cells. Different responses were obtained depending on the cell type and incubation time. Most pronounced changes were found for lipids, choline containing compounds, glutamate and glutathione, nucleotide sugars, lactate, and some amino acids. Possible contributions of these metabolites to physiologic processes are discussed. The time-dependent metabolic response patterns suggest that A2780 cells on one hand and HEK-293 cells and A2780cisR cells on the other hand may follow different cell death pathways and exist in different temporal stages thereof.
Question: Write a study description for the study titled 'Ultraperformance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry-Based Metabolomics and Lipidomics Identify Biomarkers for Efficacy Evaluation of Mesalazine in a Dextran Sulfate Sodium-Induced Ulcerative Colitis Mouse Model'.
Answer: This study aims to identify biomarkers for evaluating the therapeutic efficacy of mesalazine on ulcerative colitis by metabolomics and lipidomics. A dextran sulfate sodium-induced mouse model was used. The disease status was assessed by a disease activity index, the TNF-α level of colon was measured by an enzyme-linked immunosorbent assay, and the pathological changes of colon tissue was examined by hematoxylin-eosin staining. Serum metabolomics and lipidomics analysis based on ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry were applied to decipher the metabolic profile changes. Multivariate analysis was applied to differentiate the metabolites of controls, models, and mesalazine-treated mice. By the receiver operating characteristic (ROC) analysis, 40 differential metabolites with an area under curve (AUC) >0.80 were screened out between control and model groups. Among them, four potential biomarkers (palmitoyl glucuronide, isobutyrylglycine, PC (20:3 (5Z, 8Z, 11Z)/15:0) and L-arginine) had a signficantly reversed level of peak areas in the mesalazine group, and three of them were closely correlated with mesalazine efficacy by linear regression analysis. Furthermore, metabolic pathway analysis revealed several dysregulated pathways in colitis mice, including glycerophospholipid metabolism, pyrimidine metabolism, linoleic acid metabolism, arginine biosynthesis, etc. This study indicates that serum metabolomics is a useful approach that can noninvasively evaluate the therapeutic effect and provide unique insights into the underlying mechanism of mesalazine.
Question: Write a study description for the study titled 'Metabonomic analysis of human and 12 kinds of livestock mature milk'.
Answer: Mature milk, as a nutrient-rich endogenous metabolite, has various beneficial effects on the human body. In order to investigate the specific nutrients provided by different dairy products to humans, we used UHPLC-Q-TOF MS to analyze the highly significantly differentially expressed metabolites in 13 species of mammalian mature milk, which were grouped into 17 major metabolite classes with 1992 metabolites based on chemical classification. KEGG shows that 5 pathways in which differentially significant metabolites are actively involved are ABC transporters, Purine metabolism, Pyrimidine metabolism, Phosphotransferase system, Galactose metabolism. The study found that pig milk and goat milk are closer to human milk and contain more nutrients that are beneficial to human health, followed by camel milk and cow milk. In the context of dairy production, the development of goat milk is more likely to meet human needs and health.
Question: Write a study description for the study titled 'Metabolic mapping of the entire human solute carrier superfamily'.
Answer: Solute carrier (SLC) transporters govern most of the chemical exchange across cellular membranes and are integral to metabolic regulation, which in turn is linked to cellular function and identity. Despite their key role, individual functions of the SLC superfamily members were not evaluated systematically. We determined the metabolic and transcriptional profiles upon SLC overexpression in knock-out or wild-type isogenic cell backgrounds for 378 SLCs and 441 SLCs, respectively. Targeted metabolomics provided a fingerprint of 189 intracellular metabolites, while transcriptomics offered insights into cellular programs modulated by SLC expression. Beyond the metabolic profiles of 102 SLCs directly related to their known substrates, we identified putative substrates or metabolic pathway connections for 71 SLCs without previously annotated bona fide substrates, including SLC45A4 as a new polyamine transporter. By comparing the molecular profiles, we identified functionally related SLC groups, including some with distinct impacts on osmolyte balancing and glycosylation. The assessment of functionally related human genes presented here may serve as a blueprint for other systematic studies and supports future investigations into the functional roles of SLCs.
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 of GC-FID assay are reported in current study MTBLS390. The data and protocols for UPLC-QTOF-MS assay are reported in study MTBLS380. The data and protocols for NMR assay are reported in study MTBLS382.
Question: Write a study description for the study titled 'Cell-intrinsic metabolic phenotypes identified in glioblastoma patients using mass spectrometry imaging of 13C-labeled glucose metabolism'.
Answer: Transcriptomic studies attempted to classify glioblastoma (GB) into subtypes that predict survival and that have different therapeutic vulnerabilities1-3. Here we identified three metabolic subtypes: glycolytic, oxidative and a mixed glycolytic/oxidative by mass spectrometry imaging of rapidly excised tumour sections from two GB patients infused with [U-13C]glucose and from spatial transcriptomic analysis of contiguous sections. The phenotypes are not correlated with microenvironmental features, including proliferation rate, immune cell infiltration and vascularisation, are retained when patient-derived cells are grown in vitro, or as orthotopically implanted xenografts, and are robust to changes in oxygen concentration, demonstrating their cell intrinsic nature. The spatial extent of the regions occupied by cells displaying these distinct metabolic phenotypes are large enough to be detected using clinically applicable metabolic imaging techniques. A limitation of the study is that it is based on only two patient tumours, albeit on multiple sections, and therefore represents a proof-of-concept study.
Question: Write a study description for the study titled 'Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis'.
Answer: The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.
Question: Write a study description for the study titled 'Metabolite Profiling of wildtype and overexpression Arabidopsis thaliana'.
Answer: We use metabolite profiles of the model plant Arabidopsis thaliana measured on an UPLC-ESI/QqTOF-MS to evaluate uni- and multivariate statistical analysis of redundant features in compound spectra. Comparison was performed between the wild-type Col-0 and the 90.32 mutant. The mutant is a transposon based activation tagged A. th. line from the TAMARA population Schneider et al. [2005]. This particular mutant has an over-expression of the AT5G55880 - AT5G55890 genetic region with unknown function.
Question: Write a study description for the study titled 'Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing (Leaf assays)'.
Answer: BACKGROUND: Amaranth (Amaranthus spp.) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabolomic and genome sequence data for many cultivars. To support the improvement of this versatile, sustainable crop, a detailed metabolome profiling of the edible grains and leaves and genome sequencing resources is required for the widely cultivated grain amaranth cultivars such as Coral Fountain (CF), Emerald Tassels (ET), Golden Giant (GG), Hopi Red Dye (HR), and New Mexico (NM).RESULTS: Through a non-targeted high-throughput metabolic profiling using ultra-performance liquid chromatography-tandem mass spectrometry, we precisely determined the whole-grain and leaf metabolites of these five cultivars. This analysis identified 426 and 420 metabolites with known chemical structures in the grain and leaf, respectively. The five amaranth cultivars differed significantly in the levels of several nutritionally valuable compounds in grains and leaves, including sulfur amino acids, vitamins, and chlorogenic acids, as well as potentially anti-nutritive compounds, such as oxalate and raffinose family oligosaccharides. On average, the cultivars CF and ET had more favorable levels of most identified health-promoting compounds compared to GG, HR, and NM. In addition, we provide high-quality reference genome sequences for the five cultivars using the PacBio Sequel II sequencing platform with an estimated genome size of 465-483 Mb comprising 46.9-48.7% repetitive elements. We generated an iso-seq library from different amaranth plant parts and utilized it to predict the amaranth genes and annotate their function into their respective gene ontology terms.CONCLUSIONS: These resources will assist in breeding improved amaranth varieties and identifying targeted genes for trait modification and advancement through genome editing and engineering technologies.Leaf assays are reported in the current study MTBLS3498.Seed assays are reported in MTBLS815.
Question: Write a study description for the study titled 'Differential expression of Transcriptomics and Metabolomics in different developmental periods of poria cocos'.
Answer: Poria cocos, a traditional medicinal fungus, exhibits a wide array of biological activities. Through the integration of metabolomic and transcriptomic analyses, we have determined that the development of Poria cocos mycelia is predominantly propelled by biochemical reactions triggered by oxidative stress. Within this process, the mitogenactivated protein kinase (MAPK) signaling pathway assumes a pivotal regulatory function. As Poria cocos reaches its maturation stage, we have identified several functional substances, such as oleanolic acid, 18β-glycyrrhetinic acid, hawthorn acid, ergosterol and dehydroergosterol, among others. Our findings have unveiled the molecular mechanism underlying the formation of sclerotia in Poria cocos, providing crucial insights into its biological traits and its response to environmental stressors. These functional substances underscore the potential of Poria cocos in the development and application of nutraceuticals.