LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Organic and Peptidyl Constituents of Snake Venoms: The Picture Is Vastly More Complex Than We Imagined'.
Answer: Small metabolites and peptides in 17 snake venoms (Elapidae, Viperinae, and Crotalinae), were quantified using liquid chromatography-mass spectrometry. Each venom contains >900 metabolites and peptides. Many small organic compounds are present at levels that are probably significant in prey envenomation, given that their known pharmacologies are consistent with snake envenomation strategies. Metabolites included purine nucleosides and their bases, neurotransmitters, neuromodulators, guanidino compounds, carboxylic acids, amines, mono- and disaccharides, and amino acids. Peptides of 2⁻15 amino acids are also present in significant quantities, particularly in crotaline and viperine venoms. Some constituents are specific to individual taxa, while others are broadly distributed. Some of the latter appear to support high anabolic activity in the gland, rather than having toxic functions. Overall, the most abundant organic metabolite was citric acid, owing to its predominance in viperine and crotaline venoms, where it chelates divalent cations to prevent venom degradation by venom metalloproteases and damage to glandular tissue by phospholipases. However, in terms of their concentrations in individual venoms, adenosine, adenine, were most abundant, owing to their high titers in Dendroaspis polylepis venom, although hypoxanthine, guanosine, inosine, and guanine all numbered among the 50 most abundant organic constituents. A purine not previously reported in venoms, ethyl adenosine carboxylate, was discovered in D. polylepis venom, where it probably contributes to the profound hypotension caused by this venom. Acetylcholine was present in significant quantities only in this highly excitotoxic venom, while 4-guanidinobutyric acid and 5-guanidino-2-oxopentanoic acid were present in all venoms.
Question: Write a study description for the study titled 'Identification of BolA protein reveals a novel virulence factor in Klebsiella pneumoniae that contributes to liver abscess in mice'.
Answer: BolA has been characterized as an important transcriptional regulator, which is induced in the stationary phase of growth and is often associated with bacterial virulence. This study was initiated to elucidate the role of the BolA in the virulence of K. pneumoniae. Using a mouse infection model, we revealed bolA mutant strain yielded significantly decreased bacterial loads in liver, spleen, lung and kidney, and failed to form liver abscesses. Gene deletion demonstrated that the bolA is required for siderophore production, biofilm formation and adhesion to human colon cancer epithelial cells HCT116. Quantitative reverse transcriptase PCR (RT-qPCR) indicated that BolA is able to impact the expression of pulK, pulF, pulE, clpV, vgrG, entE, relA and spoT genes on a genome-wide scale, which are related to type II secretion system (T2SS), type VI secretion system (T6SS), guanosine tetraphosphate (ppGpp) and siderophore synthesis and contributes to fitness in the host. Furthermore, the metabolome analysis showed that the deletion of the bolA gene led to decreased pools of 5 metabolites: biotin, spermine, cadaverine, guanosine and flavin adenine dinucleotide, all of which are involved in pathways related to virulence and stress resistance. Taken together, we provided evidence that BolA is a significant virulence factor in the ability of K. pneumoniae to survive and this is an important step in progress to an understanding of the pathways underlying bacterial virulence.
Question: Write a study description for the study titled 'Contributions of the Microbiome-Derived Metabolome for Risk Assessment and Prognostication of Pancreatic Cancer'.
Answer: BACKGROUND Increasing evidence implicates microbiome involvement in the development and progression of pancreatic ductal adenocarcinoma (PDAC). Studies suggest that reflux of gut or oral microbiota can lead to colonization in the pancreas, resulting in dysbiosis that culminates in release of microbial toxins and metabolites that potentiate an inflammatory response and increase susceptibility to PDAC. Moreover, microbe-derived metabolites can exert direct effector functions on precursors and cancer cells, as well as other cell types, to either promote or attenuate tumor development and modulate treatment response.CONTENT The occurrence of microbial metabolites in biofluids thereby enables risk assessment and prognostication of PDAC, as well as having potential for design of interception strategies. In this review, we first highlight the relevance of the microbiome for progression of precancerous lesions in the pancreas and, using liquid chromatography-mass spectrometry, provide supporting evidence that microbe-derived metabolites manifest in pancreatic cystic fluid and are associated with malignant progression of intraductal papillary mucinous neoplasm(s). We secondly summarize the biomarker potential of microbe-derived metabolite signatures for (a) identifying individuals at high risk of developing or harboring PDAC and (b) predicting response to treatment and disease outcomes.SUMMARY The microbiome-derived metabolome holds considerable promise for risk assessment and prognostication of PDAC.
Question: Write a study description for the study titled 'Detection of adulteration in Iranian saffron samples by 1H NMR spectroscopy and multivariate data analysis techniques'.
Answer: Introduction: The high market value of saffron (Crocus sativus L.) has made it an attractive candidate for adulteration. Safflower (Carthamus tinctorius L.) and tartrazine are among the most common herbal and synthetic foreign materials that may be added to pure saffron for the purpose of adulteration. In spite of encouraging advances achieved in the identification of adulteration in saffron samples, the lack of a simple method with sufficient power for discrimination of pure high grade saffron from meticulously adulterated saffron samples persuaded us to perform this study. Objectives: In this work, we show that 1H NMR spectroscopy together with chemometric multivariate data analysis methods can be used for the detection of adulteration in saffron. Methods: Authentic Iranian saffron samples (n?=?20) and adulterated samples that were prepared by adding either different quantities of natural plant materials such as safflower, or synthetic dyes such as tartrazine or naphthol yellow to pure saffron (n?=?22) composed the training set. This training set was used to build multivariate Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) models. The predictive power of the PLS-DA model was validated by testing the model against an external dataset (n?=?13). Results: PCA and PLS-DA models could both discriminate between the authentic and adulterated samples, and the external validation showed 100% sensitivity and specificity for predicting the authenticity of suspicious samples. Peaks specific to authentic and adulterated samples were also characterized. Proximity of samples with unknown adulteration status to the samples adulterated with known compounds in the PCA provided insight regarding the identity of the adulterant in the suspicious samples. Furthermore, the authentic samples could be distinguished based on their cultivation site. Conclusion: The present study demonstrates that the application of 1H NMR spectroscopy coupled with multivariate data analysis is a suitable approach for detection of adulteration in saffron specimens. Outstanding sensitivity and specificity of the PLS-DA model in discriminating the authentic from adulterated samples in external validation confirmed the high predictive power of the model. The advantage of the present method is its power for detecting a wide spectrum of adulterants, ranging from synthetic dyes to herbal materials, in a single assay.
Question: Write a study description for the study titled 'Early postnatal metabolic profile in neonates with different birth weight status: A pilot study'.
Answer: INTRODUCTION: Restricted or enhanced intrauterine growth is associated with elevated risks of early and late metabolic problems in humans. Metabolomics based on amino acid and carnitine/acylcarnitine profile may have a role in fetal and early postnatal energy metabolism. In this study, the relationship between intrauterine growth status and early metabolomics profile was evaluated.MATERIALS AND METHODS: A single center retrospective cohort study was conducted. Newborn infants were enrolled into the study and they were grouped according to their birth weight percentile as small for gestational age (SGA), appropriate for gestational age (AGA) and large for gestational age (LGA) infants. In all infants amino acid and carnitine/acylcarnitine profile with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were recorded and compared between groups.RESULTS: LGA infants had higher levels of glutamic acid and lower levels of ornithine, alanine and glycine (p<0.05) when compared to AGA infants. SGA infants had higher levels of alanine and glycine levels when compared with AGA and LGA infants. Total carnitine, C0, C2, C4, C5, C10:1, C18:1, C18:2, C14-OH and C18:2-OH levels were significantly higher and C3 and C6-DC levels were lower in SGA infants (p<0.05). LGA infants had higher C3 and C5:1 level; and lower C18:2 and C16:1-OH levels (p<0.05). There were positive correlations between free carnitine and phenylalanine, arginine, methionine, alanine and glycine levels (p<0.05). Also a positive correlation between ponderal index and C3, C5-DC, C14, C14:1; and a negative correlation between ponderal index and ornithine, alanine, glycine, C16:1-OH, C18:2 were shown.CONCLUSION: We demonstrated differences in metabolomics possibly reflecting the energy metabolism in newborn infants with intrauterine growth problems in the early postnatal period. These differences might be the footprints of metabolic disturbances in future adulthood.
Question: Write a study description for the study titled 'Dietary iron attenuates Clostridioides difficile infection via modulating intestinal immune response and gut microbiota'.
Answer: Clostridioides difficile (C. difficile) causes antibiotic-associated diarrhea. Susceptibility to C. difficile infection (CDI) is largely affected by the gut microbiota, which in turn is influenced by diet. However, the mechanism underlying the interplay between diet and the gut microbiota that regulates host susceptibility to CDI remains unclear. To investigate the effects of a high-iron diet on the intestinal immune response, microbiota, and metabolism in mice infected with C. difficile, we explored the specific role of the unique gut microbiota and metabolites on CDI. A mouse model of CDI was constructed with or without high dietary iron treatment. High dietary iron (400 mg/kg ferrous sulfate) alleviated CDI by decreasing the pathogenicity of C. difficile and altering host intestinal neutrophil recruitment. The effect of high iron levels on the gut microbiota was analyzed by 16S rRNA gene sequencing, and the role of gut microbiota was confirmed by fecal microbiota transplantation (FMT). Furthermore, E. coli AVS0501, enriched in the gut microbiota of iron-treated CDI mice, was found to have prophylactic and therapeutic effects on CDI. Moreover, the production of L-proline and tauroursodeoxycholic acid (TUDCA) in CDI mice treated with high dietary iron directly determines the colonization and toxin production of C. difficile, and in turn, regulates the intestinal neutrophil response. In summary, high dietary iron alleviates C. difficile induced enteritis by regulating gut microbiota. Overall, the interplay between dietary iron and gut microbiota maintains gut homeostasis in CDI and determines the severity of CDI, suggesting that high dietary iron may be an important determinant of disease control.
Question: Write a study description for the study titled 'Metabolomics reveals impaired maturation of HDL particles in adolescents with hyperinsulinaemic androgen excess'.
Answer: Hyperinsulinaemic androgen excess (HIAE) in prepubertal and pubertal girls usually precedes a broader pathological phenotype in adulthood that is associated with anovulatory infertility, metabolic syndrome and type 2 diabetes. The metabolic derangements that determine these long-term health risks remain to be clarified. Here we use NMR and MS-based metabolomics to show that serum levels of methionine sulfoxide in HIAE girls are an indicator of the degree of oxidation of methionine-148 residue in apolipoprotein-A1. Oxidation of apo-A1 in methionine-148, in turn, leads to an impaired maturation of high-density lipoproteins (HDL) that is reflected in a decline of large HDL particles. Notably, such metabolic alterations occur in the absence of impaired glucose tolerance, hyperglycemia and hypertriglyceridemia, and were partially restored after 18 months of treatment with a low-dose combination of pioglitazone, metformin and flutamide.
Question: Write a study description for the study titled 'Metabolomic Responses of Guard Cells and Mesophyll Cells to Bicarbonate'.
Answer: Anthropogenic CO2 presently at 400 ppm is expected to reach 550 ppm in 2050, an increment expected to affect plant growth and productivity. Paired stomatal guard cells (GCs) are the gate-way for water, CO2, and pathogen, while mesophyll cells (MCs) represent the bulk cell-type of green leaves mainly for photosynthesis. We used the two different cell types, i.e., GCs and MCs from canola (Brassica napus) to profile metabolomic changes upon increased CO2 through supplementation with bicarbonate (HCO3-). Two metabolomics platforms enabled quantification of 268 metabolites in a time-course study to reveal short-term responses. The HCO3- responsive metabolomes of the cell types differed in their responsiveness. The MCs demonstrated increased amino acids, phenylpropanoids, redox metabolites, auxins and cytokinins, all of which were decreased in GCs in response to HCO3-. In addition, the GCs showed differential increases of primary C-metabolites, N-metabolites (e.g., purines and amino acids), and defense-responsive pathways (e.g., alkaloids, phenolics, and flavonoids) as compared to the MCs, indicating differential C/N homeostasis in the cell-types. The metabolomics results provide insights into plant responses and crop productivity under future climatic changes where elevated CO2 conditions are to take center-stage.
Question: Write a study description for the study titled 'Exploring the Glucose Fluxotype of the E. coli y-ome Using High-Resolution Fluxomics'.
Answer: We have developed a robust workflow to measure high-resolution fluxotypes (metabolic flux phenotypes) for large strain libraries under fully controlled growth conditions. This was achieved by optimizing and automating the whole high-throughput fluxomics process and integrating all relevant software tools. This workflow allowed us to obtain highly detailed maps of carbon fluxes in the central carbon metabolism in a fully automated manner. It was applied to investigate the glucose fluxotypes of 180 Escherichia coli strains deleted for y-genes. Since the products of these y-genes potentially play a role in a variety of metabolic processes, the experiments were designed to be agnostic as to their potential metabolic impact. The obtained data highlight the robustness of E. coli's central metabolism to y-gene deletion. For two y-genes, deletion resulted in significant changes in carbon and energy fluxes, demonstrating the involvement of the corresponding y-gene products in metabolic function or regulation. This work also introduces novel metrics to measure the actual scope and quality of high-throughput fluxomics investigations.
Question: Write a study description for the study titled 'LipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation, Targeted Phospho and Glycerolipid Profiling'.
Answer: Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.In MTBLS1369, to validate the performance and accuracy of the transition lists provided by LipidCreator and their applicabability on other MS platforms, we used the transition lists for targeted profiling of phospho- and glycerolipids in human platelet material. Platelets were stimulated with 0.01 U/ml thrombin, 1 U/ml thrombin, 1 µg/ml CRP or 5 µg/ml CRP for 5 min. The MS profiling of unstimulated and stimulated platelet material was performed after HPLC separation on a Q-Exactive HF (Thermo Scientific, Bremen, Germany) in positive and negative mode, based on scheduled PRM. Samples were measured in triplicates, interspersed with blank / buffer and standard runs.Studies linked to this manuscript include;MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HFMTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTofMTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid ProfilingMTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standardMTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identificationMTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator ProfilingMTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation
Question: Write a study description for the study titled 'Blocking Toxin function and Modulating Gut Microbiota: Caffeic Acid and its Derivatives as Potential Treatments for Clostridioides difficile Infections'.
Answer: Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea that seriously threaten public health. Disruption of normal gut microbiota by the use of broad-spectrum antimicrobial agents enables C. difficile to proliferate in the colon. The emergence and prevalence of hypervirulent C. difficile strains result in increased morbidity, mortality and recurrence rates of CDI, thus creating a pressing need for novel therapeutics. The multi-domain toxins TcdA and TcdB are the primary determinant of CDI pathogenesis, renders them ideal drug targets in the anti-virulence paradigm. In this study, we identified caffeic acid and its derivatives as active inhibitors of TcdB via a cell-based high-throughput phenotypic screening. Further mechanistic investigations revealed that caffeic acid phenethyl ester (CAPE) could directly bind to TcdB, thus suppressing InsP6-induced autoproteolysis and inhibiting the glucosyltransferase activity. CAPE-treatment remarkably reduces the pathology of CDI in a murine infection model in terms of alleviated diarrhea symptom, decreased bacterial colonization and relieved histopathological lesions. Moreover, CAPE-treatment of C. difficile-challenged mice induces remarkable increase in the diversity and composition of the gut microbiota (e.g. Bacteroides) and alterations of gut metabolites (e.g. adenosine, D-proline and melatonin), which might partially contribute to the therapeutic outcomes of CAPE against CDI. Our results reveal the potential of CAPE as a therapeutic for the management of CDI, or CAPE might be served as a lead compound for the development of anti-virulence drug targeting TcdB.
Question: Write a study description for the study titled 'Biological Potential of Lophosoria quadripinnata Fern Extract: Integration of UHPLC/ESI/QToF/MS Analysis, Antioxidant Activity, Molecular Docking and Molecular Dynamics Simulation'.
Answer: Lophosoria quadripinnata (J.F.Gmel.) C.Chr., a fern species from the Dicksoniaceae family, is widely distributed in Central and South America. This study aimed to identify the bioactive compounds in the aqueous extract of L. quadripinnata, evaluate its antioxidant potential through in vitro analysis, and assess its neuroprotective effects via molecular docking and dynamics studies. Fourteen compounds were identified using ultra-high-performance liquid chromatography coupled with quadrupole-timeof-flight mass spectrometry (UHPLC-ESI-QToF-MS). In vitro assays revealed high concentrations of phenolic and flavonoid compounds, alongside significant antioxidant activity. Molecular docking studies, involving acetylcholinesterase (AChE), butyrylcholinesterase (BChE), tyrosinase, and the Nrf2-Keap1 protein complex, identified three compounds-5C3M (5-O-caffeoyl-3-O-malonylquinic acid), 5GDC (5-O-glucoside-6,7-dimethoxycoumarin), and irifloside-as promising inhibitors. These compounds exhibited favorable binding affinities, minimal toxicity, and strong interactions with key residues involved in the inhibition of the enzymes and protein complex. Additionally, molecular dynamics simulations revealed stable binding with AChE, BChE, and tyrosinase, with irifloside showing the highest binding affinity. The compounds also demonstrated the ability to modulate the Nrf2-Keap1 pathway, potentially enhancing the cellular antioxidant response. These findings suggest that L. quadripinnata contains bioactive compounds with significant potential for the development of neuroprotective agents, especially in oxidative stress-related diseases such as Alzheimer's and Parkinson's.
Question: Write a study description for the study titled 'Integrated proteome and lipidome analyses place OCIAD1 at mitochondria-peroxisome intersection balancing lipid metabolism'.
Answer: OCIAD1 (Ovarian Cancer Immunoreactive Antigen Domain Containing 1) is a membrane protein largely localized to mitochondria, however, its function in health or disease is not well understood. To comprehensively characterize the molecular changes upon lack of OCIAD1, we used mass spectrometry to study the mitochondrial and cellular proteome and lipidome. We find extensive lipidome rearrangement in OCIAD1 KO cells, characterized by two main phenotypes of decreased ether phospholipids and decreased phospholipids with an odd number of carbons. The lipidomic changes suggest alterations in peroxisomal lipid metabolism. At the same time, proteins responsible for mitochondrial fatty acid β oxidation are significantly increased. Together with a global loss in peroxisomal proteins, aberrant peroxisomal morphology and a meta-analysis of proximity labeling data, this gives a function to the previously observed partial localization of OCIAD1 to peroxisomes. We suggest a role for OCIAD1 in balancing mitochondrial and peroxisomal lipid metabolism, and a direct impact on the key enzymes FAR1 and ABCD3.