LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Intestinal Lachnospiraceae bacterium-derived Propionate Inhibits the Progression of Clear Cell Renal Cell Carcinoma'.
Answer: Gut microbiota has been reported to be associated with the development of various diseases, however, its interaction with clear cell renal cell carcinoma (ccRCC) remains unknown. To investigate the potential relationship between gut microbiota alteration and ccRCC development, we analyze feces from healthy volunteers and ccRCC patients. We realize that ccRCC patients have a lower abundance of Lachnospiraceae bacterium (L. bacterium). Further experiments reveale that L. bacterium and its metabolites propionate exerte the antitumor effects. Mechanistically, L. bacterium-derived propionate inhibit tumor cell proliferation and migration by down-regulating the expression of HOXD10 and its downstream IFITM1 and then activating JAK1-STAT1/2 pathway. Furthermore, we designe a biofilm coated-L. bacterium as a potential probiotic to improve oral delivery and therapeutic efficacy. Finally, the expanded validation cohort confirme that measuring and targeting L. bacterium and its associated pathways will provide valuable insights into clinical management and improve the prognosis of patients with ccRCC.
Question: Write a study description for the study titled 'Chronic inorganic nitrate supplementation does not improve metabolic health and worsens disease progression in mice with diet-induced obesity.'.
Answer: Inorganic nitrate (NO3-) has been proposed to be of therapeutic use as a dietary supplement in obesity and related conditions including the Metabolic Syndrome (MetS), type-II diabetes and metabolic dysfunction associated steatotic liver disease (MASLD). Administration of NO3- to endothelial nitric oxide synthase-deficient mice reversed aspects of MetS, however the impact of NO3- supplementation in diet-induced obesity is not well understood. Here we investigated the whole-body metabolic phenotype and cardiac and hepatic metabolism in mice fed a high-fat high-sucrose (HFHS) diet for up to 12-months of age, supplemented with 1 mM NaNO3 (or NaCl) in their drinking water. HFHS-feeding was associated with a progressive obesogenic and diabetogenic phenotype, which was not ameliorated by NO3-. Furthermore, HFHS-fed mice supplemented with NO3- showed elevated levels of cardiac fibrosis, and accelerated progression of MASLD including development of hepatocellular carcinoma in comparison with NaCl-supplemented mice. NO3- did not enhance mitochondrial B-oxidation capacity in any tissue assayed and did not suppress hepatic lipid accumulation, suggesting it does not prevent lipotoxicity. We conclude that NO3- is ineffective in preventing the metabolic consequences of an obesogenic diet and may instead be detrimental to metabolic health against the background of HFHS-feeding. This is the first report of an unfavorable effect of long-term nitrate supplementation in the context of the metabolic challenges of overfeeding, warranting urgent further investigation into the mechanism of this interaction.
Question: Write a study description for the study titled 'Engineered Oncolytic VSV Enhances Tumor Killing in HBV-Positive HCC'.
Answer: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, with chronic hepatitis B virus (HBV) infection being a major contributor to its development. Despite this, effective treatment for HBV-associated HCC remains a significant challenge. In this study, we combined the strengths of vesicular stomatitis virus (VSV) and therapeutic vaccines to propose a novel strategy for treating HBV-related liver cancer. We engineered an oncolytic virus that delivers hepatitis B surface antigen (HBsAg) and the IL-15 cytokine directly to tumor cells, thereby enhancing immune activation and promoting tumor cell destruction. As the tumor cells die, they release additional virus particles, spreading HBsAg and IL-15 expression to neighboring tumor cells. This approach demonstrated promising efficacy in multiple HBV-positive HCC mouse models.
Question: Write a study description for the study titled 'Rich organic nitrogen impacts clavulanic acid biosynthesis through the arginine metabolic pathway in Streptomyces clavuligerus F613-1'.
Answer: Clavulanic acid (CA) is the preferred clinical drug for the treatment of infections by β-lactam antibiotic-resistant bacteria. CA is produced by Streptomyces clavuligerus, and although there have been many reports on the effects of carbon and nitrogen sources on CA production, the mechanisms involved remain unclear. In this study, we found that CA accumulation in S. clavuligerus F613-1 was increased significantly in MH medium, which is rich in organic nitrogen, compared with that in ML medium, which contains half the amount of organic nitrogen present in MH medium. Transcriptome analysis revealed that genes involved in CA biosynthesis, such as ceas1, ceas2, bls1, bls2, cas2, pah2, gcaS, and cad, and arginine biosynthesis, such as argB, argC, argD, argG, argH, argJ, and argR, were upregulated under rich organic nitrogen. Metabolome data revealed notable differences between cultures of F613-1 grown in MH and ML media with regard to levels of key intracellular metabolites, most of which are involved in arginine metabolic pathways, including arginine, glutamine, and glutamic acid. Additionally, supplementation of ML medium with arginine, glutamine, or glutamic acid resulted in increased CA production by S. clavuligerus F613-1. Our results indicate that rich organic nitrogen mainly affects CA biosynthesis by increasing the levels of amino acids associated with the arginine metabolic pathway and activating the expression of the CA biosynthetic gene cluster. These findings provide important insights for improving medium optimization and engineering of S. clavuligerus F613-1 for high-yield production of CA.
Question: Write a study description for the study titled 'Effects of coronatine elicitation on growth and metabolic profiles of Lemna paucicostata culture'.
Answer: In this study, the effects of coronatine treatment on the growth, comprehensive metabolic profiles, and productivity of bioactive compounds, including phenolics and phytosterols, in whole plant cultures of Lemna paucicostata were investigated using gas chromatography-mass spectrometry (GC-MS) coupled with multivariate statistical analysis. To determine the optimal timing of coronatine elicitation, coronatine was added on days 0, 23, and 28 after inoculation. The total growth of L. paucicostata was not significantly different between the coronatine treated groups and the control. The coronatine treatment in L. paucicostata induced increases in the content of hydroxycinnamic acids, such as caffeic acid, isoferulic acid, ρ-coumaric acid, sinapic acid, and phytosterols, such as campesterol and β-sitosterol. The productivity of these useful metabolites was highest when coronatine was added on day 0 and harvested on day 32. These results suggest that coronatine treatment on day 0 activates the phenolic and phytosterol biosynthetic pathways in L. paucicostata to a greater extent than in the control. To the best of our knowledge, this is the first report to investigate the effects of coronatine on the alteration of metabolism in L. paucicostata based on GC-MS profiling. The results of this research provide a foundation for designing strategies for enhanced production of useful metabolites for pharmaceutical and nutraceutical industries by cultivation of L. paucicostata.
Question: Write a study description for the study titled 'Valvular lipidomic changes in progression of human calcific aortic valve stenosis'.
Answer: This study investigates lipid dysregulation in calcific aortic valve stenosis (CAVS) by analyzing lipid profiles in valve tissues from 99 patients across different disease severities (mild, moderate, severe) using liquid chromatography-mass spectrometry (LC-MS). The results reveal distinct lipid alterations that correspond to disease progression, with significant correlations between diacylglycerol (DG) and alkyl lysophosphatidylcholine (LPC(O)) levels and key markers of valve stiffness, such as peak aortic jet velocity and mean pressure gradient. Unique lipid profiles, marked by elevated cholesteryl esters and triacylglycerols, were identified in fast-progressing cases. Additionally, plasma lipids TG 52:4 and TG 54:4 emerged as promising non-invasive diagnostic markers, surpassing traditional markers in diagnostic performance. This study highlights the potential of specific lipidomic pathways as therapeutic targets in CAVS, given the current lack of effective pharmacological treatments.
Question: Write a study description for the study titled 'Untargeted metabolomics reveals species-specific metabolite production and shared nutrient consumption by Pseudomonas aeruginosa and Staphylococcus aureus'.
Answer: While bacterial metabolism is known to impact antibiotic efficacy and virulence, the metabolic capacities of individual microbes in cystic fibrosis lung infections are difficult to disentangle from sputum samples. Here, we show that untargeted metabolomic profiling of supernatants of multiple strains of Pseudomonas aeruginosa and Staphylococcus aureus grown in monoculture in synthetic cystic fibrosis media (SCFM) reveal distinct species-specific metabolic signatures with limited strain-to-strain variability. The majority of metabolites significantly consumed by S. aureus were also consumed by P. aeruginosa, indicating that P. aeruginosa has the flexibility to metabolically outcompete S. aureus in coculture even in the absence of other pathogen-pathogen interactions. Finally, metabolites that were uniquely produced by one species or the other were identified. Specifically, the virulence factor precursor anthranilic acid as well as the quinoline 2,4-Quinolinediol (DHQ) were robustly produced across all tested strains of P. aeruginosa. Through the direct comparison of the extracellular metabolism of P. aeruginosa and S. aureus in a physiologically relevant environment, this work provides insight towards the potential metabolic interactions in vivo and supports the development of species-specific diagnostic markers of infection.
Question: Write a study description for the study titled 'Collected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research'.
Answer: MIADB: a cumulative collection of 172 tandem mass spectrometry (MS/MS) of a vast array of monoterpene indole alkaloids. Samples were analyzed using an Agilent LC-MS system composed of an Agilent 1260 Infinity HPLC coupled to an Agilent 6530 ESI-Q-TOF-MS operating in positive mode. A Sunfire analytical C18 column (150 × 2.1 mm; i.d. 3.5 μm, Waters) was used, with a flow rate of 250 μL/min and a linear gradient from 5% B (A: H2O + 0.1% formic acid, B: MeOH) to 100% B over 30 min. ESI conditions were set with the capillary temperature at 320 °C, source voltage at 3.5 kV, and a sheath gas flow rate of 10 L/min. The divert valve was set to waste for the first 3 min. There were four scan events: positive MS, window from m/z 100−1200, then three data-dependent MS/MS scans of the first, second, and third most intense ions from the first scan event. MS/MS settings were three fixed collision energies (30, 50, and 70 eV), default charge of 1, minimum intensity of 5000 counts, and isolation width of m/z 2. In the positive-ion mode, purine C5H4N4 [M + H]+ ion (m/z 121.050873) and the hexakis(1H,1H,3H-tetrafluoropropoxy)-phosphazene C18H18F24N3O6P3 [M + H]+ ion (m/z 922.009 798) were used as internal lock masses. Full scans were acquired at a resolution of 11 000 (at m/z 922). A permanent MS/MS exclusion list criterion was set to prevent oversampling of the internal calibrant.
Question: Write a study description for the study titled 'Redox proteomics reveal a role for peroxiredoxinylation in stress protection.'.
Answer: The redox state of proteins is essential for their function and guarantees cell fitness. Peroxiredoxins protect cells against oxidative stress, maintain redox homeostasis, act as chaperones, and transmit hydrogen peroxide signals to redox regulators. Despite the profound structural and functional knowledge of peroxiredoxins action, information on how the different functions are concerted is still scarce. Using global proteomic analyses, we show here that the yeast peroxiredoxin Tsa1 interacts with many proteins of essential biological processes, including protein turnover and carbohydrate metabolism. Several of these interactions are of a covalent nature, and we show that failure of peroxiredoxinylation of Gnd1 affects its phosphogluconate dehydrogenase activity and impairs recovery upon stress. Thioredoxins directly remove TSA1-formed mixed disulfide intermediates, thus expanding the role of the thioredoxin-peroxiredoxin redox cycle pair to buffer the redox state of proteins.
Question: Write a study description for the study titled 'A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms'.
Answer: INTRODUCTION: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus - hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence.OBJECTIVES: To explore the interaction, we used a novel GC-Orbitrap – based mass spectrometer, the QExactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards.METHODS: Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed in addition to the fresh and spent bacterial growth media.RESULTS: The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. We detected an additional 22 highly scoring compounds from untargeted analysis.CONCLUSION: Many of the results were as expected – rapid consumption of glucose and fructose from the medium regardless of the cell type. We also detected trehalose from the untargeted data, only in medium that contained C. albicans, commensurate with it being a predominantly fungal sugar. Notable from the results is that the pentose phosphate pathway appears to be enhanced in the cells from co-cultured biofilms.
Question: Write a study description for the study titled 'Altered fecal metabolomics and potential biomarkers of psoriatic arthritis differing from rheumatoid arthritis'.
Answer: Psoriatic arthritis (PsA) is a chronic inflammatory joint disease, and the diagnosis is quite difficult due to the unavailability of reliable clinical markers. This study aimed to investigate the fecal metabolites in PsA by comparison with rheumatoid arthritis (RA), and to identify potential diagnostic biomarkers for PsA. The metabolic profiles of the fecal samples from 27 PsA and 29 RA patients as well as 36 healthy controls (HCs) were performed on ultra-high-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). And differentially altered metabolites were screened and assessed using multivariate analysis for exploring the potential biomarkers of PsA. The results showed that 154 fecal metabolites were significantly altered in PsA patients when compared with HCs, and 45 metabolites were different when compared with RA patients. A total of 14 common differential metabolites could be defined as candidate biomarkers. Furthermore, a support vector machines (SVM) model was performed to distinguish PsA from RA patients and HCs, and 5 fecal metabolites, including α/β-turmerone, glycerol 1-hexadecanoate, dihydrosphingosine, pantothenic acid and glutamine, were determined as biomarkers for PsA. Through the metabolic pathways analysis, we found that the abnormality of amino acid metabolism, bile acid metabolism and lipid metabolism might contribute to the occurrence and development of PsA. In summary, our research provided ideas for the early diagnosis and treatment of PsA by identifying fecal biomarkers and analyzing metabolic pathways.
Question: Write a study description for the study titled 'Serum-based metabolomics characterization of pigs treated with ractopamine'.
Answer: A study was performed to determine if serum-metabolomics could be used to establish a predictive tool for identifying ractopamine misuse in pigs. Ractopamine, a beta-agonist used as growth promoter in livestock, is with great controversy, and it has been forbidden in most countries worldwide. However, due to economic benefits, the possibility of widespread abuse of ractopamine still exists. “Omics” strategies, based on the observation of physiological perturbations, are promising approaches to tackle drug misuse in breeding animals. In this context, our aim was to set up a high performance liquid chromatography - high resolution mass spectrometry (HPLC-HRMS) based metabolomics workflow for screening pig serum for ractopamine administration. Therefore, an untargeted metabolomics approach was developed to characterize and compare serum metabolic profiles from control and treated pigs. Two different extraction strategies were investigated, and the results showed that the combination of methanol extraction and methanol-water extraction protocols significantly improve the metabolites coverage. A two-level data analysis using univariate and multivariate statistical analyses was carried out to establish descriptive and predictive models, which enabled the discrimination of treated animals from control animals and highlighted a number of candidate biomarkers that contributed the most in the observed discrimination. This research indicates that metabolomics approach can be considered as a powerful strategy to highlight biomarkers related to ractopamine treatment in pig which may subsequently be implemented as screening strategy to predict for such illicit practices.
Question: Write a study description for the study titled 'Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype (UPLC-MS HILIC POS 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 'Transcriptional differentiation of Trypanosoma brucei during in vitro acquisition of resistance to acoziborole'.
Answer: Subspecies of the protozoan parasite Trypanosoma brucei are the causative agents of Human African Trypanosomiasis (HAT), a debilitating neglected tropical disease prevalent across sub-Saharan Africa. HAT case numbers have steadily decreased since the start of the century, and sustainable elimination of one form of the disease is in sight. However, key to this is the development of novel drugs to combat the disease. Acoziborole is a recently developed benzoxaborole, currently in advanced clinical trials, for treatment of stage 1 and stage 2 HAT. Importantly, acoziborole is orally bioavailable, and curative with one dose. Recent studies have made significant progress in determining the molecular mode of action of acoziborole. However, less is known about the potential mechanisms leading to acoziborole resistance in trypanosomes. In this study, an in vitro derived acoziborole-resistant (AcoR) cell line was generated and characterised. The AcoR line exhibited significant cross-resistance with the methyltransferase inhibitor sinefungin as well as hypersensitisation to known trypanocides. Interestingly, transcriptomics analysis of AcoR cells indicated the parasites had obtained a procyclic- or stumpy-like transcriptome profile, with upregulation of procyclin surface proteins as well as differential regulation of key metabolic genes known to be expressed in a life cycle-specific manner, even in the absence of major morphological changes. However, no changes were observed in transcripts encoding CPSF3, the recently identified protein target of acoziborole. The results suggest that generation of resistance to this novel compound in vitro can be accompanied by transcriptomic switches resembling a procyclic- or stumpy-type phenotype.
Question: Write a study description for the study titled 'Urinary metabolomics reveals kynurenine pathway perturbation in newborns with transposition of great arteries after surgical repair'.
Answer: INTRODUCTION: Transposition of the great arteries (TGA) is a cyanotic congenital heart defect that requires surgical correction, with the use of cardiopulmonary-bypass (CPB), usually within 3 weeks of life. The use of CPB in open heart surgery results in brain hypoperfusion and in a powerful systemic inflammatory response and oxidative stress.OBJECTIVE: We aimed to develop a novel untargeted metabolomics approach to detect early postoperative changes in metabolic profile following neonatal cardiac surgery.METHODS: We studied 14 TGA newborns with intact ventricular septum undergoing arterial switch operation with the use of CPB. Urine samples were collected preoperatively and at the end of the surgery and were analyzed using an untargeted metabolomics approach based on UHPLC-high resolution mass spectrometry.RESULTS: Since post surgery metabolic spectra were heavily contaminated by metabolites derived from administered drugs, we constructed a list of drugs used during surgery and their related metabolites retrieved from urine samples. This library was applied to our samples and 1255 drugs and drug metabolites were excluded from the analysis. Afterward, we detected over 39,000 unique compounds and 371 putatively annotated metabolites were different between pre and post-surgery samples. Among these metabolites, 13 were correctly annotated or identified. Metabolites linked to kynurenine pathway of tryptophan degradation displayed the highest fold change.CONCLUSIONS: This is the first report on metabolic response to cardiac surgery in TGA newborns. We developed an experimental design that allowed the identification of perturbed metabolic pathways and potential biomarkers of brain damage, limiting drugs interference in the analysis.