LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Linking genetic, metabolic and phenotypic diversity 1 among S. cerevisiae strains using multi-omics associations'.
Answer: The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeast’s industrial value is still urgently needed. Here, we analyzed 5400 growth curves obtained from 36 S. cerevisiae strains and comprehensively profiled their resistances against 13 industrially relevant stresses. We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions, however, plant isolates tend to have wider range of resistance, which may be associated with their metabolome and fluxome signatures in TCA cycle and fatty acid metabolism. By deep genomic sequencing we found that industrial strains have more genomic duplications especially affecting transcription factors, presenting disparate evolutionary paths in comparison to the environmental strains which have more InDels, gene deletions and strain-specific genes. Genome-wide association studies coupled with protein-protein interaction networks uncovered novel genetic determinants of stress resistances. These resistance-related engineering targets and strain rankings provide a valuable source for engineering significantly improved industrial platform strains. This metabolomic study of 36 yeast strains measured intra- and extracellular metabolome under standard glucose medium, profiled by GS-MS. This is part of a multi-omic study on yeast strain collection.
Question: Write a study description for the study titled 'A metabolomics exploration of the sexual phase in the marine diatom Pseudo-nitzschia multistriata'.
Answer: Pseudo-nitzschia multistriata is a planktonic diatom species with a diplontic life cycle comprising a short sexual phase during which gametes are produced from the encounter of two diploid cells of opposite mating type (MT). Gene expression studies have highlighted the presence of substantial changes occurring at the onset of sexual reproduction. Collectively, there is clear evidence of a chemical cross talk which mediates the mating step. Herein, we have hypothesized that these major transcriptomic changes are associated to variations in the amount and nature of the metabolites produced by the cells. In order to investigate such chemical diversity in an unbiased manner, we undertook an untargeted metabolomics approach. Liquid chromatography – tandem mass spectrometry was applied to investigate the differences in the metabolic profiles between control cells in the vegetative phase (MT+ and MT-) and mixed strains of opposite MTs (cross) undergoing sexual reproduction. Of the 2408 high-quality features obtained, 70 known metabolites could be identified based on in-house libraries and online databases; molecular networking proved valuable to classify additional 47 non-identified features. The present exploratory study provides an overview of the chemical diversity detectable in P. multistriata, presenting a dynamic picture of the changes occurring during sexual reproduction. In particular, the reduction of phytol detected in the cross can be linked to the general downregulation of photosynthesis during sexual reproduction observed elsewhere. The dysregulation of other metabolites stands as a starting point for the understanding of the mechanisms regulating sexual reproduction: a metabolite that was tentatively identified as 7-dehydrodesmosterol exhibited the highest upregulation in the comparison between the two MTs of opposite sex, as well as between MT+ vs cross. The effects of extraction solvents and harvesting times on the ensemble of endo-metabolites were also analyzed.
Question: Write a study description for the study titled 'A red wine intervention does not modify plasma trimethylamine N-oxide but is associated with broad shifts in the plasma metabolome and gut microbiota composition'.
Answer: BACKGROUND: Gut microbiota profiles are closely related to cardiovascular diseases through mechanisms that include the reported deleterious effects of metabolites, such as trimethylamine N-oxide (TMAO), which have been studied as diagnostic and therapeutic targets. Moderate red wine (RW) consumption is reportedly cardioprotective, possibly by affecting the gut microbiota.OBJECTIVES: To investigate the effects of RW consumption on the gut microbiota, plasma TMAO, and the plasma metabolome in men with documented coronary artery disease (CAD) using a multiomics assessment in a crossover trial.METHODS: We conducted a randomized, crossover, controlled trial involving 42 men (average age, 60 y) with documented CAD comparing 3-wk RW consumption (250 mL/d, 5 d/wk) with an equal period of alcohol abstention, both preceded by a 2-wk washout period. The gut microbiota was analyzed via 16S rRNA high-throughput sequencing. Plasma TMAO was evaluated by LC-MS/MS. The plasma metabolome of 20 randomly selected participants was evaluated by ultra-high-performance LC-MS/MS. The effect of RW consumption was assessed by individual comparisons using paired tests during the abstention and RW periods.RESULTS: Plasma TMAO did not differ between RW intervention and alcohol abstention, and TMAO concentrations showed low intraindividual concordance over time, with an intraclass correlation coefficient of 0.049 during the control period. After RW consumption, there was significant remodeling of the gut microbiota, with a difference in β diversity and predominance of Parasutterella, Ruminococcaceae, several Bacteroides species, and Prevotella. Plasma metabolomic analysis revealed significant changes in metabolites after RW consumption, consistent with improved redox homeostasis.CONCLUSIONS: Modulation of the gut microbiota may contribute to the putative cardiovascular benefits of moderate RW consumption. The low intraindividual concordance of TMAO presents challenges regarding its role as a cardiovascular risk biomarker at the individual level. This study was registered at clinical trials.gov as NCT03232099.
Question: Write a study description for the study titled 'High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry (Data-independent acquisition)'.
Answer: Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.Data-independent acquisition is reported in the current study MTBLS2959.Mixed-mode column chromatography is reported in MTBLS2497.
Question: Write a study description for the study titled 'Pantothenate biosynthesis is critical for chronic infection by the neurotropic parasite Toxoplasma gondii'.
Answer: Coenzyme A (CoA) is an essential molecule acting in metabolism, post-translational modification, and regulation of gene expression. While all organisms synthesize CoA, many, including humans, are unable to produce its precursor, pantothenate. Intriguingly, like most plants, fungi and bacteria, parasites of the coccidian subgroup of Apicomplexa, including the human pathogen Toxoplasma gondii, possess all the enzymes required for de novo synthesis of pantothenate. Here, the importance of CoA and pantothenate biosynthesis for the acute and chronic stages of T. gondii infection is dissected through genetic, biochemical and metabolomic approaches, revealing that CoA synthesis is essential for T. gondii tachyzoites, due to the parasite's inability to salvage CoA or intermediates of the pathway. In contrast, pantothenate synthesis is only partially active in T. gondii tachyzoites, making the parasite reliant on its uptake. However, pantothenate synthesis is crucial for the establishment of chronic infection, offering a promising target for intervention against the persistent stage of T. gondii.
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 short chain 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 bile acid analysis assay for this study can be found in the MetaboLights study MTBLS547.The targeted fatty acid analysis assay for this study can be found in the MetaboLights study MTBLS548.
Question: Write a study description for the study titled 'Imidazole ketone erastin induces ferroptosis and slows tumor growth in a mouse lymphoma model'.
Answer: Ferroptosis is a form of regulated cell death that can be induced by inhibition of the cystine-glutamate antiporter, system xc-. Among the existing system xc- inhibitors, imidazole ketone erastin (IKE) is a potent, metabolically stable inhibitor of system xc- and inducer of ferroptosis potentially suitable for in vivo applications. We investigated the pharmacokinetic and pharmacodynamic features of IKE in a diffuse large B cell lymphoma (DLBCL) xenograft model and demonstrated that IKE exerted an antitumor effect by inhibiting system xc-, leading to glutathione depletion, lipid peroxidation, and the induction of ferroptosis biomarkers both in vitro and in vivo. Using untargeted lipidomics and qPCR, we identified distinct features of lipid metabolism in IKE-induced ferroptosis. In addition, biodegradable polyethylene glycol-poly(lactic-co-glycolic acid) nanoparticles were employed to aid in IKE delivery and exhibited reduced toxicity compared with free IKE in a DLBCL xenograft model.
Question: Write a study description for the study titled 'Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling.'.
Answer: Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. However, their involvement in the gut-brain axis has been poorly investigated. In this study, we aimed to investigate the cargo capacity of MEVs for bioactive metabolites and their interactions with the host. Metabolomics analysis identified various neuro-related compounds encapsulated within the MEVs, such as arachidonyl-dopamine, gabapentin, glutamate and N-acylethanolamines. Metaproteomics unveiled an enrichment of enzymes involved in neuronal metabolism, primarily in the glutamine/glutamate/GABA pathway. The detected neuro-related proteins and metabolites were correlated with Bacteroides spp. A GABA-producing Bacteroides isolate, B. finegoldii, released EVs with a high GABA content (4 µM) as opposed to a low GABA-producing isolate, Phocaeicola massiliensis. MEVs exhibited a dose-dependent paracellular transport and were endocytosed by Caco-2 and hCMEC/D3 cells. RNA-Seq analyses showed that MEVs stimulate several immune pathways while suppressing cell apoptosis process. The in vivo biodistribution confirmed the presence of MEVs in the brain, liver, stomach and spleen. Overall, our results highlight the ability of MEVs to cross the intestinal and blood-brain barriers to deliver their cargoes to distant organs, including the brain, where it may modulate the organ functionalities. MEVs could be an integral part of microbiome-host communications, with potential implication for the gut-brain axis.
Question: Write a study description for the study titled 'A high-resolution Orbitrap mass spectral library for trace volatile compounds in fruit wines'.
Answer: The overall aroma is an important factor of the sensory quality of fruit wines, which attributed to hundreds of volatile compounds. However, the qualitative determination of trace volatile compounds is considered to be very challenging work. GC-Orbitrap-MS with high resolution and high sensitivity provided more possibilities for the determination of volatile compounds, but without the high-resolution mass spectral library. For accuracy of qualitative determination in fruit wines by GC-Orbitrap-MS, a high-resolution mass spectral library, including 22 esters, 11 carbonyl compounds, 10 high alcohols, 7 lactones, 6 acids, 6 furans, 5 pyrazines, 5 terpenes, 4 benzenes, 4 volatile phenols and 1 sulfide, was developed in this study. Not only the HRMS spectrum but also the exact ion fragment, relative abundance, retention indices (RI), CAS number, chemical structure diagram, aroma description and aroma threshold were provided and were shown in a database website (Food Flavor Laboratory, http://foodflavorlab.cn/). HRMS library was used to successfully identify the volatile compounds mentioned above in 16 fruit wines (5 blueberry wines, 6 goji berry wines and 5 hawthorn wines). The library was developed as an important basis for further understanding of trace volatile compounds in fruit wines.
Question: Write a study description for the study titled 'Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory'.
Answer: UV-B radiation regulates numerous morphogenic, biochemical and physiological responses in plants, and can stimulate some responses typically associated with other abiotic and biotic stimuli, including invertebrate herbivory. Removal of UV-B from the growing environment of various plant species has been found to increase their susceptibility to consumption by invertebrate pests, however, to date, little research has been conducted to investigate the effects of UV-B on crop susceptibility to field pests. Here, we report findings from a multi-omic and genetic-based study investigating the mechanisms of UV-B-stimulated resistance of the crop, Brassica napus (oilseed rape), to herbivory from an economically important lepidopteran specialist of the Brassicaceae, Plutella xylostella (diamondback moth). The UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8), was not found to mediate resistance to this pest. RNA-Seq and untargeted metabolomics identified components of the sinapate/lignin biosynthetic pathway that were similarly regulated by UV-B and herbivory. Arabidopsis mutants in genes encoding two enzymes in the sinapate/lignin biosynthetic pathway, CAFFEATE O-METHYLTRANSFERASE 1 (COMT1) and ELICITOR-ACTIVATED GENE 3-2 (ELI3-2), retained UV-B-mediated resistance to P. xylostella herbivory. However, the overexpression of B. napus COMT1 in Arabidopsis further reduced plant susceptibility to P. xylostella herbivory in a UV-B-dependent manner. These findings demonstrate that overexpression of a component of the sinapate/lignin biosynthetic pathway in a member of the Brassicaceae can enhance UV-B-stimulated resistance to herbivory from P. xylostella.
Question: Write a study description for the study titled 'Diagnostic metabolite biomarkers of chronic typhoid carriage'.
Answer: Background: Salmonella Typhi and Salmonella Paratyphi A are the agents of enteric (typhoid) fever; both can establish chronic carriage in the gallbladder. Chronic Salmonella carriers are typically asymptomatic, intermittently shedding bacteria in the feces, and contributing to disease transmission. Detecting chronic carriers is of public health relevance in areas where enteric fever is endemic, but there are no routinely used methods for prospectively identifying those carrying Salmonella in their gallbladder. Methodology/Principal Findings: Here we aimed to identify biomarkers of Salmonella carriage using metabolite profiling. We performed metabolite profiling on plasma from Nepali patients undergoing cholecystectomy with confirmed S. Typhi or S. Paratyphi A gallbladder carriage (and non-carriage controls) using two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GCxGC-TOFMS) and supervised pattern recognition modeling. We were able to significantly discriminate Salmonella carriage samples from non-carriage control samples. We were also able to detect differential signatures between S. Typhi and S. Paratyphi A carriers. We additionally compared carriage metabolite profiles with profiles generated during acute infection; these data revealed substantial heterogeneity between metabolites associated with acute enteric fever and chronic carriage. Lastly, we found that Salmonella carriers could be significantly distinguished from non-carriage controls using only five metabolites, indicating the potential of these metabolites as diagnostic markers for detecting chronic Salmonella carriers. Conclusions/Significance: Our novel approach has highlighted the potential of using metabolomics to search for diagnostic markers of chronic Salmonella carriage. We suggest further epidemiological investigations of these potential biomarkers in alternative endemic enteric fever settings.
Question: Write a study description for the study titled 'Study on the mechanism of p-hydroxybenzyl alcohol against OGD/R damage based on metabonomic analysis'.
Answer: Gastrodia elata Blume (GE) has been widely used to treat various central and peripheral nerve diseases, and P-Hydroxybenzaldehyde (PHBA) is one of the indicative components of GE brain protection. Since the previous study of our group found that PHBA has a good effect on protecting mitochondria against cerebral ischemia-reperfusion injury in rats (I/R). We will further explore how PHBA regulates the metabolic mechanism in blood after cerebral I/R to find an effective therapeutic target to prevent and treat IS. Firstly, using the rat model of cerebral ischemia-reperfusion injury induced by middle cerebral artery occlusion/Reperfusion (MCAO/R). The therapeutic effect of PHBA on brain I/R was evaluated by neurological function score, triphenyl tetrazolium chloride (TTC), Hematoxylin and eosin (HE), and Nissl staining. Secondly, a non-targeted metabonomic based on HPLC-QTOF-MS/MS was established to identify differential metabolites. Finally, we analyzed a targeted metabolic spectrum and verified the potential therapeutic targets. The results showed that the neurological function score, cerebral infarction area, hippocampal morphology, and the number of neurons in the PHBA group were significantly improved compared with the model group. Metabonomic analysis showed that 13 different metabolites were identified between the model and PHBA group, which may be involved in the 'tricarboxylic acid cycle', 'glutathione metabolism', 'mutual transformation of pentose and glucuronates', and so on. Among them, the most significant differential metabolite, dGMP, decreased significantly after PHBA treatment. We used WB to verify the expression of membrane-associated guanosine kinase PSD-95 and The subunit of glutamate AMPA receptor GluA1, which significantly increased after PHBA treatment. In addition, we also found that PHBA increased the expression of the light chain-3 protein (LC3) and autophagy effector protein 1 (Beline1) in WB while decreasing the expression of sequestosome-1 (p62), indicating that autophagy activity was promoted. Similarly, in TUNEL staining and detection of apoptosis-related proteins, it was found that MCAO/R up-regulated the expression of Bax and Cleaved-caspase-3 while down-regulated the expression of Bcl-2, and increased the apoptosis of hippocampal neurons, but PHBA could improve this situation. In summary, these results suggest that cerebral I/R causes postsynaptic dysfunction by disrupting the interaction between PSD-95 and AMPARs, and the inhibition of the autophagy system eventually leads to the apoptosis of hippocampal neurons.
Question: Write a study description for the study titled 'DNA-PKcs drives CKD progression by activating TAF7/RAPTOR/mTORC1 signaling-mediated metabolic reprogramming'.
Answer: Kidney injury initiates epithelial dedifferentiation and myofibroblast activation during the progression of chronic kidney disease (CKD). Herein, we found that the expression of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) was significantly increased in the kidney tissues of both CKD patients and CKD mice induced by unilateral ureteral obstruction (UUO) and unilateral ischemia-reperfusion (UIR) injury. In vivo, knockout of DNA-PKcs or treatment with its specific inhibitor NU7441 hampered the development of CKD in mice. In vitro, DNA-PKcs deficiency preserved epithelial cell phenotype and inhibited fibroblast activation induced by transforming growth factor-beta 1 (TGF-beta-1). Additionally, our results showed that TBP-associated factor 7 (TAF7), as a possible substrate of DNA-PKcs, enhanced mTORC1 activation by upregulating RAPTOR expression, which subsequently promoted metabolic reprogramming in injured epithelial cells and myofibroblasts. Taken together, DNA-PKcs can be inhibited to correct metabolic reprogramming via the TAF7/mTORC1 signaling in CKD, and serve as a new target for treating CKD.