LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Mass Spectrometry Imaging of Lipids in a Gut Epithelial Cell Model'.
Answer: Scope: The Caco2/HT29-MTX co-culture system is widely used as a cell model of the intestinal epithelium. Although the gut epithelium plays an important role in the uptake of free fatty acids and the resynthesis of triglycerides, the lipid distribution profile of the two-dimensional co-culture system is not well understood. Desorption electrospray ionisation (DESI) mass spectrometry (MS) imaging is a mass spectrometry (MS) technique which has been widely used to study the main classes of lipid molecules on different tissue. This has been used to map the lipid distribution in the Caco2- HT29-MTX co-culture system.Methods and results: Caco2 and HT29-MTX cells were seeded on coverslips either singularly or as co-cultures at different ratios. Cells were cultured for 21 days before MS imaging using a DESI source in both positive and negative ionisation modes, the identity of selected lipid being confirmed using tandem MS. Although many lipids were common to both cell lines, there were distinctive patterns in the lipidomes. Thus, the lipidome of Caco2 cells was more heterogeneous and richer in cholesterol esters and certain triglycerides whilst HT29-MTX cells has a distinctive lipidome including phosphatidylethanolamines and odd chain phosphatidylcholines and C17 fatty acids.Conclusion: DESI-MS imaging has shown that Caco2 and HT29-MTX cells have distinctive lipidomes which are still evident when the cells are co-cultured. It has potential to both allow further validation of these widely used cell models and provide insights into how dietary components may modify lipid metabolism in future.
Question: Write a study description for the study titled 'Discovery and validation of potential serum biomarkers for heart failure by untargeted metabolomics'.
Answer: Detection of biomarkers was extremely important for the early diagnosis, prognosis and therapy optimization of diseases. The purpose of this study was to investigate the differences in serum metabolites between patients with heart failure (HF) and healthy controls (HC), and to diagnose HF qualitatively. In this study, serum samples from 83 patients with HF and 35 HC were used as the research subjects for untargeted metabolomic analysis using ultra-performance liquid chromatography combined with quadrupole-time of flight mass spectrometry (UPLC-QTOF/MS) technology. Potential biomarkers were screened and validated using the orthogonal partial least squares-discriminant analysis (OPLS-DA), random forest (RF), binary logistic regression (BLR) and receiver operating characteristic (ROC) analysis. The results indicated that a total of 43 metabolites were considered as differentially expressed metabolites (DEMs). Among these DEMs, glycodeoxycholate was identified as a specific biomarker for differential diagnosis of HF. A ROC curve analysis for HC vs HF discrimination, showed an area under the ROC curve (AUC) of 0.9853 (95% CI: 0.9859-1.0000), a sensitivity of 95% and a specificity of 100%. Hence, glycodeoxycholate might serve as a potential biomarker for HF. Furthermore, the amino acid metabolism was screened as the most significantly altered pathway in patients with HF. By identifying serum biomarkers and analyzing metabolic pathways, our study provided opportunities to enhance the understanding of the pathogenesis and early diagnosis of HF.
Question: Write a study description for the study titled 'Coordinate Regulation of Metabolite Glycosylation and Stress Hormone Biosynthesis by TT8 in Arabidopsis'.
Answer: Secondary metabolites play a key role in coordinating ecology and defense strategies of plants. Diversity of these metabolites arise by conjugation of core structures with diverse chemical moieties, such as sugars in glycosylation. Active pools of phytohormones, including those involved in plant stress response are regulated by glycosylation. While, much is known about glycosylation enzymes, we know little about their regulation or coordination with other biological processes. We characterized the flavonoid pathway transcription factor, TRANSPARENT TESTA 8 (TT8) in Arabidopsis thaliana, using an integrative 'omics strategy to provide a systems level understanding of the cellular machinery used to generate metabolite diversity by glycosylation. Metabolomics analysis of loss-of-function and inducible overexpression lines of TT8 showed that it coordinates glycosylation of not only flavonoids, but also nucleotides, thus, implicating TT8 in regulating pools of activated sugars. Transcriptome and promoter network analyses revealed that TT8 regulome included sugar transporters, sugar binding and sequestration proteins, and carbohydrate active enzymes. Interestingly, TT8 also affects brassinosteroid and jasmonic acid biosynthesis by directly binding to the promoters of key genes of these two pathways. This combined effect on metabolites glycosylation and stress hormones by TT8 overexpression lead to significant increase in tolerance towards multiple abiotic and biotic stresses. Conversely, loss of TT8 leads to increased sensitivity to these stresses. Thus, TT8 is an integrator of secondary metabolism and stress response.
Question: Write a study description for the study titled 'Metabolomics and Proteomics Reveal the Inhibitory Effect of Lactobacillus crispatus on Cervical Cancer Cells'.
Answer: Cervical cancer remains a significant global health issue due to its high morbidity and mortality rates. Recently, Lactobacillus crispatus has been recognized for its crucial role in maintaining cervical health. While some studies have explored the use of L. crispatus to mitigate cervical cancer, the underlying mechanisms remain largely unknown. In this study, we employed non-targeted proteomics and metabolomics techniques to investigate how L. crispatus affects the growth of cervical cancer cells (SiHa) and normal cervical cells (Ect1/E6E7). Our findings indicated that the inhibitory effect of L. crispatus on SiHa cells was associated with various biological processes, notably the ferroptosis pathway. Specifically, L. crispatus was found to regulate the expression of proteins such as HMOX1, SLC39A14, VDAC2, ACSL4, and LPCAT3 by SiHa cells, which are closely related to ferroptosis. Additionally, it activated the TCA cycle in SiHa cells, leading to increased levels of reactive oxygen species (ROS) and lipid peroxides (LPO). These results reveal the therapeutic potential of L. crispatus in targeting the ferroptosis pathway for cervical cancer treatment, opening new avenues for research and therapy in cervical cancer.
Question: Write a study description for the study titled 'Intracellular iron overload rewires HSC metabolism by impairing mitochondrial fitness'.
Answer: Iron is an essential element for several cellular processes and recent evidence highlighted its role in regulating the function of hematopoietic stem cells (HSCs). When in excess it reduces quiescence and self-renewal, however, whether and how iron influences HSC metabolism is still unknown. Here, we show that intracellular iron overload (IO) impairs mitochondrial fitness and bioenergetics, inducing metabolic rewiring in HSCs. In three models of IO, HSCs accumulate mitochondria with elevated reactive oxygen species (ROS), low membrane potential and reduced oxidative phosphorylation (OXPHOS). IO HSCs proliferate despite low mitochondrial activity and OXPHOS and rely on glycolysis for energy production. Notably, restoration of mitochondrial function by targeting in vivo iron and mitochondrial ROS improved the quiescence and self-renewal of IO HSCs. Our results unravel the critical interplay between iron, ROS and mitochondria in HSCs, disclosing that iron acts as an extrinsic regulator of HSC metabolic programs.
Question: Write a study description for the study titled 'Hidden molecular clues in marine sediments revealed by untargeted mass spectrometry imaging'.
Answer: Mass spectrometry imaging (MSI) in sedimentary archives can produce records of molecular proxies at μm-scale resolution. For example, in annually varved sediments of the Santa Barbara Basin, such a fine resolution allows deciphering sub-annual distributions of archaeal tetraether lipids, haptophyte-derived alkenones and sterols. Herein, we reported the establishment of an untargeted data processing workflow aimed at dissecting the MSI datasets and extracting information beyond that obtained by targeted analysis of known molecular proxies. The combination of MSI and the untargeted workflow not only increases the spatial resolution for molecular stratigraphy but also dramatically broadens the number and diversity of molecular signals evaluated, enabling us to discover unique molecular signatures imprinted by various biogeochemical processes. We applied the proposed workflow to two MSI datasets that were both measured on the uppermost ∼10 cm of the Santa Barbara Basin sediments while covering different mass ranges. Two matrices of 18625 x 293 and 18963 x 323 (number of spectra x number of peaks) were, respectively, extracted after peak alignment using bin-wise kernel density estimation and subsequent peak picking by peak prominence filtering combined with geochemical context-based filtering. Feature extraction by non-negative matrix factorization revealed in total 15 stable molecular clusters with distinct spatial distributions in the sediments. Each cluster typically comprised several to dozens of compounds, with the majority of compounds in each cluster likely belonging to similar chemical taxonomies. Some of these clusters can be linked to specific biogeochemical processes. For example, chlorin-like compounds are possibly related to diatom production, alkenones are related to coccolithophorid production, and steranes and long-chain fatty acids likely represent terrigenous input. Supervised learning from these data mining results further extracted molecular signatures with proxy potential that appear to be linked to specific environmental conditions inferred from historical oceanographic data. However, generalizability to other sedimentary settings will require further investigation.
Question: Write a study description for the study titled 'Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit (Volatile organic compounds; SPME-GC-MS assay)'.
Answer: Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.SPME-GC-MS assay of Volatile organic compounds is reported in the current study MTBLS982UPLC-DAD assay of Carotenoids is reported in MTBLS984UPLC-MS/MS assay of Phenolics is reported in MTBLS898
Question: Write a study description for the study titled 'FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry imaging MS (LC-MS assay)'.
Answer: High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites directly from tissues, cell cultures, and agar plates with cellular resolution, but is hampered by the lack of bioinformatics for automated metabolite identification. We developed the first bioinformatics framework for False Discovery Rate (FDR)-controlled metabolite annotation for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM) introducing a Metabolite-Signal Match (MSM) score and a target-decoy FDR-estimate for spatial metabolomics. LC-MS(/MS) datasets acquired from wild type adult mouse brain were used for the development of spatial metabolomics annotation bioinformatics. This study together with MTBLS317 and MTBLS378 provide the accompanying data for FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.
Question: Write a study description for the study titled 'Androgens drive SLC1A5-dependent metabolic reprogramming in polycystic ovary syndrome-LC-MS analysis of granulosa cells'.
Answer: Polycystic ovary syndrome (PCOS) is the primary cause of female infertility. Growing evidence suggests that dysregulation of amino acid metabolism plays a significant role in the onset and progression of PCOS. However, the underlying mechanism remains unclear. In this study, we conducted targeted metabolite profiling of human follicular fluid (FF) and granulosa cells (GCs). A significant increase in glutamine (Gln) uptake was observed in patients with hyperandrogenic-PCOS (HA-PCOS), mediated by the upregulation of SLC1A5, a specific Gln transporter. We subsequently confirmed that androgen excess primarily activates SLC1A5 expression. Furthermore, Slc1a5 overexpression in female mice induced PCOS-like phenotypes, including hyperandrogenism and abnormal follicle development. Additionally, the pharmacological blockade of SLC1A5 provided reproductive benefits to mice exhibiting PCOS-like symptoms. Mechanistically, we found that elevated flux of Gln-derived α-ketoglutarate (α-KG) enhanced HDAC5 expression and suppressed acetylation on histone 3 lysine residue 14 and lysine residue 56. The reduction in acetylation level correlated with the downregulation of several genes related to folliculogenesis, including CYP19A1, thereby exacerbating androgenic homeostasis imbalance. These findings indicate that androgen-induced aberrant Gln uptake via SLC1A5 is crucial for the development and progression of PCOS, suggesting pharmacological blockade of SLC1A5 as a potential therapeutic strategy for PCOS patients.
Question: Write a study description for the study titled 'Variable Secondary Metabolite Profiles across Cultivars of Curcuma longa L. and C. aromatica Salisb'.
Answer: BACKGROUND: Curcuma spp. (Zingiberaceae), are used as a spice and coloring agent. Their rhizomes and essential oils are known for medicinal properties, besides their use in the flavoring and cosmetic industry. Most of these biological activities were attributed to volatile and non-volatile secondary metabolites present in the rhizomes of Curcuma spp. The metabolite variations among the species and even cultivars need to be established for optimized use of Curcuma spp.OBJECTIVES: We compared the phytochemical profiles of rhizomes and their essential oils to establish the variability among seven cultivars: five of Curcuma longa L. (Alleppey Supreme, Duggirala Red, Prathibha, Salem, Suguna/PCT-13), and two of C. aromatica Salisb. (Kasturi Araku, Kasturi Avidi). The GC-MS and LC-MS-based analyses were employed to profile secondary metabolites of these selected cultivars.METHODS: Rhizomes of Curcuma spp. were subjected to hydro-distillation to collect essential oil and analyzed by GC-MS. The methanol extracts of fresh rhizomes were subjected to LC-MS analyses. The compounds were identified by using the relevant MS library databases as many compounds as possible.RESULTS: The essential oil content of the cultivars was in the range of 0.74% to 1.62%. Several compounds were detected from the essential oils and rhizome extracts by GC-MS and LC-MS, respectively. Of these, 28 compounds (13 from GCMS and 15 from LCMS) were common in all seven cultivars, e.g. α–thujene, and diarylheptanoids like curcumin. Further, a total of 39 new compounds were identified from C. longa L. and/or C. aromatica Salisb., most of them being cultivar-specific. Of these compounds, 35 were detected by GC-MS analyses of essential oils: phenol, 2-methoxy-3-(2-propenyl); santolina alcohol; to name a few. The other four compounds were detected by LC-MS of the methanolic extracts of the rhizomes, e.g., kaempferol 3,7-dimethyl ether and 5,7,8-trihydroxy-2′,5′-dimethoxy-3′,4′-methylene dioxyisoflavanone.CONCLUSIONS: We identified and recorded the variability in the metabolite profiles of essential oils and whole rhizome extracts from seven cultivars of Curcuma longa L. and C. aromatica Salisb. In. As many as 39 new metabolites were detected in these seven Indian cultivars of Curcuma spp. Many of these compounds have health benefits.
Question: Write a study description for the study titled 'In Vitro and In Vivo Metabolomic Profiling after Infection with Virulent Newcastle Disease Virus'.
Answer: Newcastle disease (ND) is an acute, febrile, and highly contagious disease caused by the virulent Newcastle disease virus (vNDV) worldwide. The disease causes serious economic losses to the poultry industry. However, the metabolic changes caused by vNDV infection remain unclear. The objective of this study was to determine whether small molecule metabolites contribute to the pathogenesis of vNDV. DF-1 cells and the lungs of specific pathogen free (SPF) chickens infected with the vNDV strain Herts/33 were analyzed via ultra high-performance liquid tandem chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) in combination with multivariate statistical analysis. A total of 304 metabolites were significantly changed post vNDV infection, and most belong to the amino acid and nucleotide metabolic pathway. It is suggested that the increased pools of amino acids and nucleotides may be used for viral protein synthesis and genome amplification. Similar results were also confirmed in vivo; this is consistent with the characteristic of acute vNDV infection. The identification of these different metabolites will provide a great deal of important information to further understand the mechanism of vNDV replication and pathogenesis.
Question: Write a study description for the study titled 'How Does the Seed Pre-germinative Metabolism Fight against Imbibition Damage? Emerging Roles of Fatty Acid Cohort and Antioxidant Defence'.
Answer: During seed imbibition, lipids are engaged in membrane reorganization while facing free radical-mediated oxidative injury. In the present work, we explored changes in lipid components at different timepoints of imbibition (0.5, 2, 4, 6, and 8 h) in the legume Medicago truncatula, by combining biochemical approaches with targeted lipidomics and untargeted metabolomics. ROS and RNS (reactive oxygen and nitrogen species) accumulation was observed throughout the tested timepoints whereas lipid peroxidation increased at 4 h of imbibition. The seed response to oxidative damage was evidenced by a significant increase in tocopherols starting from 0.5 h of imbibition as well as by the reduction in total thiol content occurring at 2 h of imbibition. Since under physiological conditions, the proper functions of the cell membranes are strongly dependent on the qualitative and quantitative balance of fatty acid residues in phospholipids, the investigation was expanded to the fatty acid cohort of Medicago truncatula seeds. Total saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), omega-3 and omega-6 fatty acids showed fluctuations during seed imbibition. The most remarkable finding was the profile of the omega-3 PUFA docosopentaenoic acid (DPA, 7 cis, 10 cis, 13 cis, 16 cis, 19 cis-22:5) that showed a peak (up to 1.0% of the total fatty acid content) at 0.5 and 8 h of imbibition, respectively, concomitant with the peaks observed in tocopherol levels. It is possible that the observed changes in DPA alter the physical properties of membranes, as reported in animal cells, triggering signaling pathways relevant for the cell defence against oxidative injury. Furthermore, the content and balance between tocopherols and PUFAs is regarded as a determinant of storage stability. No enhancement in trans-fatty acids occurred throughout imbibition, suggesting for a proper antioxidant response carried by the seed. Fatty acids profiles were integrated with data from untargeted metabolomics showing changes in lipid sub-pathways, among which fatty acid amide, lyso-phospholipids and phospholipid metabolism. The emerging lipid profiles and dynamics are discussed in view of the overall imbibition damage generated during M. truncatula seed imbibition.
Question: Write a study description for the study titled 'Leptin increases hepatic triglyceride export via a vagal mechanism in humans'.
Answer: Recombinant human leptin (metreleptin) reduces hepatic lipid content in patients with lipodystrophy and overweight patients with non-alcoholic fatty liver disease and relative hypoleptinemia independent of its anorexic action. In rodents, leptin signaling in the brain increases very-low-density lipoprotein triglyceride (VLDL-TG) secretion and reduces hepatic lipid content via the vagus nerve. In this randomized, placebo-controlled crossover trial (EudraCT Nr. 2017-003014-22), we tested whether a comparable mechanism regulates hepatic lipid metabolism in humans. A single metreleptin injection stimulated hepatic VLDL-TG secretion (primary outcome) and reduced hepatic lipid content in fasted, lean men (n = 13, age range 20-38 years) but failed to do so in metabolically healthy liver transplant recipients (n = 9, age range 26-62 years) who represent a model for hepatic denervation. In an independent cohort of lean men (n = 10, age range 23-31 years), vagal stimulation by modified sham feeding replicated the effects of metreleptin on VLDL-TG secretion. Therefore, we propose that leptin has anti-steatotic properties that are independent of food intake by stimulating hepatic VLDL-TG export via a brain-vagus-liver axis.