LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Steady state isotope tracing in C. elegans (GC-MS analyses)'.
Answer: The metabolic network, composed of thousands of metabolic reactions, is essential for any organism. Despite its importance, a systems level understanding of how metabolic network is wired by reactions that carry flux in unperturbed condition and rewired by transcriptionally activating or repressing metabolic genes in response to metabolic perturbations are still lacking in any animal. Here, we apply Worm Perturb-Seq (WPS), a high-throughput, whole-animal RNAi and RNA-seq method, to ~900 metabolic genes in the nematode Caenorhabditis elegans. We derive a metabolic gene regulatory network (mGRN) in which 385 perturbations are connected to 9,414 genes by more than 110,000 interactions. The mGRN has a highly modular structure in which 22 perturbation clusters connect to 44 gene expression programs, involving metabolism, stress response and other functions. The mGRN reveals different modes of transcriptional rewiring from simple reaction and pathway compensation to rerouting and more complex network coordination. Using metabolic network modeling, we discover a design principle of transcriptional rewiring we name the ‘compensation/repression’ (CR) model. The CR model explains the majority of the transcriptional responses in metabolic genes and reveals a high-level of compensation and repression in five core metabolic functions related to energy and biomass.Leveraging the comprehensive data from WPS, we find that the transcriptional response to metabolic gene perturbations can be integrated with the genome-scale metabolic network models to infer a highly constrained, semi-quantitative flux distribution of unperturbed animal. We discover several features of adult C. elegans metabolism, including cyclic flux through the pentose phosphate pathway, lack of de novo purine synthesis flux, and the primary use of amino acids and bacterial RNA as a tricarboxylic acid cycle carbon source, all of which we validate by stable isotope tracing. Our strategy for inferring metabolic wiring based on transcriptional phenotypes should be applicable to a variety of systems, including human cells.GC-MS analyses is reported in the current study MTBLS11742.LC-MS analyses is reported in MTBLS11741.
Question: Write a study description for the study titled 'The putative ceramide-conjugation protein Cwh43 regulates G0 quiescence, nutrient metabolism and lipid homeostasis in fission yeast (Metabolome assay)'.
Answer: Cellular nutrient states control whether cells proliferate, or whether they enter or exit quiescence. Here, we report characterizations of fission yeast temperature-sensitive (ts) mutants of the evolutionarily conserved transmembrane protein, Cwh43, and explore its relevance to utilization of glucose, nitrogen-source, and lipids. GFP-tagged Cwh43 localizes at ER associated with the nuclear envelope and the plasma membrane, as in budding yeast. We found that cwh43 mutants failed to divide in low glucose and lost viability during quiescence under nitrogen starvation. In cwh43 mutant, comprehensive metabolome analysis demonstrated dramatic changes in marker metabolites that altered under low glucose and/or nitrogen starvation, although cwh43 apparently consumed glucose in the culture media. Furthermore, we found that cwh43 mutant had elevated levels of triacylglycerols (TGs) and coenzyme A, and that it accumulated lipid droplets. Notably, TG biosynthesis was required to maintain cell division in cwh43 mutant. Thus, Cwh43 affects utilization of glucose and nitrogen-sources, as well as storage lipid metabolism. These results may fit to a notion developed in budding yeast that Cwh43 conjugates ceramide to GPI (glycosylphosphatidylinositol)-anchored proteins and maintains integrity of membrane organization.  Metabolome assay data is reported in the current study MTBLS577.  Lipidome assay data associated to this study is reported in MTBLS578.  Linked Studies: MTBLS578
Question: Write a study description for the study titled 'Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut'.
Answer: Peanut (Arachis hypogaea L.) is considered as a moderately salt-sensitive species and thus soil salinity can be a limiting factor for peanut cultivation. To gain insights into peanut plant physiology in response to salt stress and alleviation, we comprehensively characterized leaf relative electrolyte leakage (REC), photosynthesis, leaf transpiration, and metabolism of plants under salt stress and plants that were subjected to salt stress followed by salt alleviation period. As expected, we found that REC levels were higher when plants were subjected to salt stress compared with the untreated plants. However, in contrast to expectations, REC was even higher compared with salt treated plants when plants were transferred from salt stress to standard conditions. To decipher REC variation in response to salt stress, especial during the recovery, metabolite, and transcript variations were analyzed by GC/MS and RNA-seq method, respectively. Ninety two metabolites, among total 391 metabolites identified, varied in response to salt and 42 metabolites responded to recovery specially. Transcriptomics data showed 1,742 in shoots and 3,281 in roots transcript varied in response to salt stress and 372 in shoots and 1,386 transcripts in roots responded specifically to recovery, but not salt stress. Finally, 95 transcripts and 1 metabolite are indicated as candidates involved in REC, photosynthesis, transpiration, and Na+ accumulation variation were revealed by using the principal component analysis (PCA) and correlation analysis. This study provides valuable information on peanut response to salt stress and recovery and may inspire further study to improve salt tolerance in peanut germplasm innovation.
Question: Write a study description for the study titled 'Clinical Application Value of Ceramide and Sphingomyelin as Biomarkers for the Diagnosis of Drug-Induced Liver Injury'.
Answer: Background : Drug-induced liver injury (DILI) is a serious health concern that presents challenges in early detection and accurate diagnosis, thereby complicating the treatment of this liver disease. Therefore, it is crucial to explore specific biomarkers to improve the accuracy of diagnosing DILI.Methods : A study was conducted involving patients with DILI, non-drug-related benign liver diseases (NDILI), and healthy controls (HCs). Serum metabolomic profiles were analyzed using liquid chromatography-mass spectrometry (LC-MS), and transcriptomic data were retrieved from public datasets for integrated analysis. Biomarkers and cytokines were detected using enzyme-linked immunosorbent assays (ELISA). Differential metabolites were identified through multi-omics joint analysis, large sample validation, and logistic regression models.Results: Transcriptomic analyses highlighted that inflammatory and metabolic pathways are critical to DILI pathogenesis. Integrated transcriptomic-metabolomic analysis revealed significant alterations in sphingolipid metabolism, with ceramide and sphingomyelin emerging as key metabolites for distinguishing DILI, NDILI, and HCs. The multivariable diagnostic model combining ceramide, sphingomyelin, and traditional biomarkers demonstrated superior performance. Notably, levels of IL-6 and IL-8 were significantly elevated in DILI patients compared to HCs.Conclusion: This study preliminarily determined that ceramides and sphingolipids are significantly elevated in DILI compared to NDILI and HCs. Their combination with traditional liver function indicators further improves the diagnostic accuracy of DILI. Therefore, ceramides and sphingolipids may serve as potential biomarkers for the diagnosis and management of DILI.
Question: Write a study description for the study titled 'Gut microbiota ameliorates hepatic fibrosis through modulating intestinal bile acid metabolism and hepatocyte pyroptosis (Hepatic fibrosis serum)'.
Answer: Hepatic fibrosis decreased feces bile acid level. Hepatic fibrosis increased serum bile acid. This result showed that hepatic fibrosis inhibited the excretion of bile acid in clinical patients. This result provided phenotype for hepatic fibrosis patients. Bile acid was important indexes for liver injury. TCDCA was important, and it play toxicity effect through ferroptosis and apoptosis. The research for other bile acid such CA, UDCA, TUDCA, TDCA, LCA, TLCA would be important.Hepatic fibrosis serum (sample 1) analysis is reported in the current study MTBLS6732.Hepatic fibrosis feces (sample 2) analysis is reported in MTBLS6742.Hepatic fibrosis serum+feces (sample 3) analysis is reported in MTBLS6728.
Question: Write a study description for the study titled 'Linking gastrointestinal microbiota and metabolome dynamics to clinical outcomes in pediatric hematopoietic stem cell transplantation'.
Answer: BACKGROUND: Hematopoietic stem cell transplantation is a curative procedure for a variety of conditions. Despite major advances, a plethora of adverse clinical outcomes can develop post-transplantation including graft-versus-host disease and infections, which remain the major causes of morbidity and mortality. There is increasing evidence that the gastrointestinal microbiota is associated with clinical outcomes post-hematopoietic stem cell transplantation. Herein, we investigated the longitudinal dynamics of the gut microbiota and metabolome and potential associations to clinical outcomes in pediatric hematopoietic stem cell transplantation at a single centre.RESULTS: On admission (baseline), the majority of patients presented with a different gut microbial composition in comparison to healthy control children with a significantly lower alpha diversity. A further, marked decrease in alpha diversity was observed immediately post-transplantation and in most microbial diversity, and composition did not return to baseline status while hospitalized. Longitudinal trajectories identified continuous fluctuations in microbial composition, with the dominance of a single taxon in a significant proportion of patients. Using pam clustering, three clusters were observed in the dataset. Cluster 1 was common pre-transplantation, characterized by a higher abundance of Clostridium XIVa, Bacteroides and Lachnospiraceae; cluster 2 and cluster 3 were more common post-transplantation with higher abundance of Streptococcus and Staphylococcus in the former whilst Enterococcus, Enterobacteriaceae and Escherichia predominated in the latter. Cluster 3 was also associated with a higher risk of viraemia. Likewise, further multivariate analysis reveals Enterobacteriaceae, viraemia, use of total parenteral nutrition and various antimicrobials contributing towards cluster 3, Streptococcaceae, Staphylococcaceae, Neisseriaceae, vancomycin and metronidazole contributing towards cluster 2. Lachnospiraceae, Ruminococcaceae, Bifidobacteriaceae and not being on total parenteral nutrition contributed to cluster 1. Untargeted metabolomic analyses revealed changes that paralleled fluctuations in microbiota composition; importantly, low fecal butyrate was associated with higher risk of viraemia.CONCLUSIONS: These findings highlight the frequent shifts and dominations in the gut microbiota of pediatric patients undergoing hematopoietic stem cell transplantation. The study reveals associations between the fecal microbiota, metabolome and viraemia. To identify and explore the potential of microbial biomarkers that may predict risk of complications post-HSCT, larger multi-centre studies investigating longitudinal microbial profiling in pediatric hematopoietic stem cell transplantation are warranted.
Question: Write a study description for the study titled 'Combined metabolomics with transcriptomics reveals important serum biomarkers correlated with lung cancer proliferation through calcium signaling pathway'.
Answer: Lung cancer (LC) is still one of the most deadly cancers in the world, but there is a lack of non-invasive biomarkers to assist diagnosis and guide treatment. Herein, untargeted serum metabolomics of 57 LC patients and 59 HC people was performed based on gas chromatography-mass spectrography (GC-MS). Differential metabolites were identified by NIST14 database and human metabolome database (HMDB). The random forest (RF) classification algorithm was then carried out for selecting the optimal panel of biomarkers among differential metabolites. The biomarker panel was finally validated by support vector machine (SVM) and partial least squares-discriminant analysis (PLS-DA) classification algorithm. After that, each biomarker was targeted quantitated using GC-MS/SIM in a test set consisted of 50 LC patients and 41 HC people. Subsequently, the Network analysis of Ingenuity Pathway Analysis (IPA) was applied to browse the biomarker panel-related genes, and the transcriptome data from GEO database were used to verify the gene expression. In the results, five metabolites including cholesterol, oleic acid, myo-inositol, 2-hydroxybutyric acid and 4-hydroxybutyric acid were combined to be biomarker panel from totally 15 differential metabolites. The genes of INPP5A, MAP2K2, CAMK1D, GABARAPL1, NDUFS4/8 were involved in biomarker panel-related biological pathway, and calcium signaling pathways might mediate their role in the proliferation of LC. Our study provided effective candidate biomarkers for the diagnosis of LC, and elucidated part of the underlying pathological mechanism of LC from the perspective of metabolites.
Question: Write a study description for the study titled 'Bile acid is a significant host factor shaping the gut microbiome of diet induced obese mice (targeted free fatty acid analysis assay)'.
Answer: BACKGROUND: Intestinal bacteria are known to regulate the bile acid (BA) homeostasis via intestinal biotransformation of BAs and stimulating the expression of fibroblast growth factor 19 through intestinal nuclear farnesoid X receptor (FXR). On the other hand, BAs directly regulate the gut microbiota with their strong antimicrobial activities. It remains unclear, however, how mammalian BAs cross-talk with gut microbiome and shape microbial composition in a dynamic and interactive way.RESULTS: We quantitatively profiled small molecule metabolites derived from host-microbial co-metabolism in mice, demonstrating that Bas were the most significant factor correlated with microbial alterations among all types of endogenous metabolites. HFD intervention resulted in a rapid and significant increase in intestinal BA pool within 12 hrs followed by alteration in microbial composition at 24 hrs, providing supporting evidence that BAs are major dietary factors regulating gut microbiota. Feeding mice with BAs along with normal diet induced obese phenotype and obesity-associated gut microbial composition, similar to HFD fed mice. Finally, inhibition of hepatic BA biosynthesis under HFD conditions attenuated the HFD-induced gut microbiome alterations. Inhibition of BAs and direct suppression of micriobiota improved obese phenotypes.CONCLUSIONS: Our study highlights a liver - BAs - gut microbiome metabolic axis that drives significant modifications of BA and microbiota compositions capable of triggering metabolic disorders, suggesting new therapeutic strategies targeting BA metabolism for metabolic diseases.The untargeted metabolome profile assay for this study can be found in the MetaboLights study MTBLS545.The targeted short chain fatty acid analysis assay for this study can be found in the MetaboLights study MTBLS546.The targeted bile acid analysis assay for this study can be found in the MetaboLights study MTBLS547.
Question: Write a study description for the study titled 'Bioaccumulation and degradation of common pollutants by human gut bacteria'.
Answer: The environmental contamination by manufactured chemicals has by some estimates exceeded the safe planetary boundary. Due to the widespread contamination of water and agricultural systems, a vast number of chemical pollutants make it into the food and hence into the human body. The gut microbiota is particularly susceptible to exposure and adverse interactions therein could cause systemic effects on the host due to the critical role of the microbiota in host physiology. Here we investigate the potential of human gut bacteria to bioaccumulate or degrade common environmental pollutants.
Question: Write a study description for the study titled 'Elucidation of the epitranscriptomic RNA modification landscape of chikungunya virus'.
Answer: The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analyzed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyze the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNAmodifications in viral RNA genomes.
Question: Write a study description for the study titled 'Gain-of-function genetic screens in human cells identify SLC transporters overcoming environmental nutrient restrictions'.
Answer: Solute carrier (SLC) transporters control fluxes of nutrients and metabolites across membranes and thereby represent a critical interface between the microenvironment and cellular and subcellular metabolism. Because of substantial functional overlap, the interplay and relative contributions of SLCs in response to environmental stresses remain poorly elucidated. To infer functional relationships between SLCs and metabolites, we developed a strategy to identify SLCs able to sustain cell viability and proliferation under growth-limiting concentrations of essential nutrients. One-by-one depletion of 13 amino acids required for cell proliferation enabled gain-of-function genetic screens using a SLC-focused CRISPR/Cas9–based transcriptional activation approach to uncover transporters relieving cells from growth-limiting metabolic bottlenecks. Among the transporters identified, we characterized the cationic amino acid transporter SLC7A3 as a gene that, when up-regulated, overcame low availability of arginine and lysine by increasing their uptake, whereas SLC7A5 was able to sustain cellular fitness upon deprivation of several neutral amino acids. Moreover, we identified metabolic compensation mediated by the glutamate/aspartate transporters SLC1A2 and SLC1A3 under glutamine-limiting conditions. Overall, this gain-of-function approach using human cells uncovered functional transporter-nutrient relationships and revealed that transport activity up-regulation may be sufficient to overcome environmental metabolic restrictions.
Question: Write a study description for the study titled 'Untargeted metabolomics analysis of dissolved organic matter in the western Atlantic Ocean'.
Answer: The data are dissolved organic compounds from three stations sampled in the western Atlantic Ocean in 2013. Seawater samples spanning from the surface ocean to the seafloor were collected, filtered, acidified, and extracted using solid phase extraction with Bond Elut PPL cartridges. The extracts were separated using reversed phase chromatography and analyzed with ultrahigh resolution mass spectrometry in negative ion mode. The resulting data are features, or a unique combination of mass-to -charge values and retention time.
Question: Write a study description for the study titled 'AspSnFR: A Genetically-Encoded Biosensor for Real-Time Monitoring of Aspartate in Live Cells'.
Answer: Aspartate is crucial for nucleotide synthesis, ammonia detoxification and maintaining redox balance via the malate-aspartate-shuttle (MAS). To disentangle these multiple roles of aspartate metabolism, tools are required that measure aspartate concentrations in real time and in live cells. We introduce AspSnFR, a genetically encoded green fluorescent biosensor for intracellular aspartate, engineered through displaying and screening biosensor libraries on mammalian cells. In live cells, AspSnFR is able to precisely and quantitatively measure cytosolic aspartate concentrations and dissect its production from glutamine. Combining high-content imaging of AspSnFR with pharmacological perturbations exposes differences in metabolic vulnerabilities of aspartate levels based on nutrient availability. Further, AspSnFR facilitates tracking of aspartate export from mitochondria through SLC25A12, the MAS’ key transporter. We show that SLC25A12 is a rapidly responding and direct route to couple Ca2+ signaling with mitochondrial aspartate export. This establishes SLC25A12 as a crucial link between cellular signaling, mitochondrial respiration and metabolism.
Question: Write a study description for the study titled 'A Comprehensive and Ultrasensitive Isotope Calibration Method for Soil Amino Compounds Using Orbitrap Mass Spectrometry'.
Answer: Bound amino compounds (amino acid and amino sugar polymers) comprise a significant proportion (~40%) of soil organic nitrogen and therefore represent an essential source of nitrogen for plant and microbial nutrition. The analysis of their content and isotope enrichment still represents a significant challenge due to the low isotope enrichment levels reached under near-native soil conditions and the lack of isotopically labeled standards for some key amino compounds. In this study, we used both a 13C-labeled and an unlabeled amino acid mixture to establish isotope calibration curves for 16 amino compounds, using the 6-Aminoquinolyl-N-hydroxysccinimidyl carbamate (AQC) derivatization method and ultra-high-performance liquid chromatography with high-resolution Orbitrap mass spectrometry (UPLC-Orbitrap MS). Molecular ions of AQC-derivatives for all standard amino compounds were identified at the expected m/z values of the respective isotopologues. The isotope calibration curves exhibited excellent linear fits across the whole 13C enrichment range and polynomial fits in the low 13C enrichment range (R2 > 0.990). However, the polynomial fitting terms differed between individual amino acids. Subsequently, we developed equations to relate the calibrated regression terms to the physicochemical properties of the respective amino acids, here mainly the ratio of amino compound-C atoms to total C atoms in AQC-amino compound derivatives. Based on these regressions, we could ultimately predict isotope calibration curves for those amino compounds unavailable as 13C labeled standards, for example muramic acid, hydroxyproline and diaminopimelic acid. To test the model accuracy, we compared the outcomes of measured calibrations with predicted calibrations for amino acids where we had isotopically enriched standards. The results of linear regression between measured and predicted data were excellent, where R2 was >0.97, and mean absolute (percentage) deviation, MAD and MAPD, were 0.334 and 15.8%. Finally, we applied both standard and predicted calibration curves to low 13C amended soil samples and unlabeled controls to test the applicability of our model. The limit of detection (LOD) as the minimum detectable atom % 13C incorporation of amino compounds ranged from 0.0003 to 0.14 atom % among different amino compounds. This general predictive model can be used to comprehensively quantify isotope enrichments across the entire soil amino compound profile, including amino sugars and proteinogenic and non-proteinogenic amino acids, providing valuable insights for a better understanding of the overall fate of different amino compounds in soils or broader environmental samples.