LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Effect of heat stress on serum enzyme activity, antioxidant capacity and immune parameter metabolomics datasets in Holstein cows at different growth stages'.
Answer: Global climate change has led to an increase in release of atmospheric CO2 and average daily temperatures, making heat stress a major challenge in dairy farming. The present study aimed to investigate metabolite changes of Holstein cows at different stages. In this experiment, 10 growing heifers, 10 heifers and 10 lactating cows were selected for the current study. Blood samples were separately collected from the animals through the caudal root vein in April and August. Samples were transferred to a liquid nitrogen tank for metabolomic analysis.
Question: Write a study description for the study titled 'A Metabolic Profiling Strategy for the Dissection of Plant Defense against Fungal Pathogens (GC-MS assay)'.
Answer: Here we present a metabolic profiling strategy employing direct infusion Orbitrap mass spectrometry (MS) and gas chromatography-mass spectrometry (GC/MS) for the monitoring of soybean's (Glycine max L.) global metabolism regulation in response to Rhizoctonia solani infection in a time-course. Key elements in the approach are the construction of a comprehensive metabolite library for soybean, which accelerates the steps of metabolite identification and biological interpretation of results, and bioinformatics tools for the visualization and analysis of its metabolome. The study of metabolic networks revealed that infection results in the mobilization of carbohydrates, disturbance of the amino acid pool, and activation of isoflavonoid, α-linolenate and phenylpropanoid biosynthetic pathways of the plant. Components of these pathways include phytoalexins, coumarins, flavonoids, signaling molecules, and hormones, many of which exhibit antioxidant properties and bioactivity helping the plant to counterattack the pathogen's invasion. Unraveling the biochemical mechanism operating during soybean-Rhizoctonia interaction in addition to its significance towards the understanding of the plant's metabolism regulation under biotic stress, provides valuable insights with potential for applications in biotechnology, crop breeding, and agrochemical and food industries.
Question: Write a study description for the study titled 'Metabolomic changes in Mycobacterium avium subsp. paratuberculosis (MAP) challenged Holstein-Friesian cattle suggest the role of serum amino acids as indicators of immune system activation'.
Answer: INTRODUCTION: Paratuberculosis, commonly known as Johne’s disease, is a chronic intestinal infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Clinical signs, including reduced milk yields, weight loss and diarrhoea, are typically absent until 2 to 6 years post exposure.OBJECTIVES: To identify metabolomic changes profiles of MAP challenged Holstein-Friesian cattle and correlate identified metabolites to haematological and immunological parameters.METHODS: At approximately 6 weeks of age, calves (n = 9) were challenged with 3.8 x 10^9 cells of MAP (clinical isolate CIT003) on 2 consecutive days. Additional unchallenged calves (n = 9) formed the control group. The study used biobanked serum from cattle sampled periodically from 3- to 33-months post challenge. The assessment of sera using flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) for high throughput, sensitive, non-targeted metabolite fingerprinting highlighted differences in metabolite levels between the two groups.RESULTS: In total, 25 metabolites which were differentially accumulated in MAP challenged cattle were identified, including 20 which could be correlated with certain haematological parameters, particularly monocyte levels.CONCLUSION: The targeted metabolites suggest shifts in amino acid metabolism that could reflect immune system activation linked to MAP and as well as differences in phosphocholine levels which could reflect activation of the Th1 (tending towards pro-inflammatory) immune response. If verified by future work, selected metabolites could be used as biomarkers to diagnose and manage MAP infected cattle.
Question: Write a study description for the study titled 'Metabolomic determinants of carotid atherosclerosis plaque stability'.
Answer: Our objective is to identify the metabolites associated with stability of carotid atheromatous plaques compared to vulnerable plaques, through a metabolomic approach. Eighty consecutive patients with carotid artery stenosis (CAS) who underwent carotid endarterectomy (CEA) according to current guidelines with metabolomic analysis of the removed plaque were included between may 2021 and august 2022, in the vascular surgery department of Marseille University Hospital. Symptomatic patients were qualified by stroke physicians if they experienced an ischemic stroke (IS) or transient ischemic attack (TIA) in the territory of the culprit artery less than a month before the surgery, with an otherwise negative exhaustive etiological assessment. Patients who did not report any medical history of IS/TIA in the last 6 months before surgery were considered asymptomatic. Patients with history of IS/TIA between one and six months before surgery were excluded (n=8). The metabolomes of 72 remaining carotid atherosclerotic plaques were compared according to their symptomatic status. The Institutional Review Board of Assistance Publique-Hôpitaux de Marseille approved this study (No. CSE24-4).
Question: Write a study description for the study titled 'Comparative metabolomic responses to gibberellic acid and 6-benzylaminopurine in Cunila menthoides Benth. (Lamiaceae): a contribution to understand the metabolic pathways'.
Answer: Little is known about the effects of 6-benzylaminopurine (BA) and gibberellic acid (GA3) on the synthesis of secondary metabolites in species of Lamiaceae. In this study, for the first time, the profile of secondary metabolites in plantlets of Cunila menthoides was characterized, using UPLC-ESI-Qq-oaTOF-MS. Ninety metabolites were identified, including polyphenols and terpenes. BA down-regulated most of the identified molecules in relation to GA3 and MS0 (control). The results showed that GA3 elicited synthesis of many phenols from different classes, and seemed to play a major role in the shikimate pathway in relation to BA. GA3 enhanced production of sesquiterpenoids, polyterpenoids, steroids and monoterpenoids compared to MS0 and BA, and also seemed to positively influence the MEP/DOXP and MVA pathways. These data show the most comprehensive metabolomic profile of Cunila menthoides to date, and the effects of BA and GA3 on the synthesis of secondary metabolites, modulating quantitative aspects of metabolism in Lamiaceae.
Question: Write a study description for the study titled 'Integrated transcriptomic and metabolomic analysis reveals the metabolic programming of GM-CSF-and M-CSF-differentiated mouse macrophages'.
Answer: Macrophages play a critical role in the inflammatory response and tumor development. Macrophages are primarily divided into pro-inflammatory M1-like and anti-inflammatory M2-like macrophages based on their activation status and functions. In vitro macrophage models could be derived from mouse bone marrow cells stimulated with two types of differentiation factors: GM-CSF (GM-BMDMs) and M-CSF (M-BMDMs), to represent M1-and M2-like macrophages, respectively. Since macrophage differentiation requires coordinated metabolic reprogramming and transcriptional rewiring in order to fulfill their distinct roles, we combined both transcriptome and metabolome analysis, coupled with experimental validation, to gain insight into the metabolic status of GM-and M-BMDMs. The data revealed higher levels of the tricarboxylic acid cycle (TCA cycle), oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), and urea and ornithine production from arginine in GM-BMDMs, and a preference for glycolysis, fatty acid storage, bile acid metabolism, and citrulline and nitric oxide (NO) production from arginine in M-BMDMs. Correlation analysis with the proteomic data showed high consistency in the mRNA and protein levels of metabolic genes. Similar results were also obtained when compared to RNA-seq data of human monocyte derived macrophages from the GEO database. Furthermore, canonical macrophage functions such as inflammatory response and phagocytosis were tightly associated with the representative metabolic pathways. In the current study, we identified the core metabolites, metabolic genes, and functional terms of the two distinct mouse macrophage populations. We also distinguished the metabolic influences of the differentiation factors GM-CSF and M-CSF, and wish to provide valuable information for in vitro macrophage studies.
Question: Write a study description for the study titled 'Toxicological effects of microplastics and antibiotics on enterohepatic axis of Gymnocypris przewalskii'.
Answer: Metabolites including S-Allylcysteine, trans-Cinnamate,Terephthalate and Misoprostol were significantly altered, along with enrichment in metabolic pathways such as mTOR signaling and oxidative phosphorylation.
Question: Write a study description for the study titled 'A metabolomics approach to unravel the regulating role of phytohormones towards carotenoid metabolism in tomato fruit. (Lycopene metabolism)'.
Answer: Carotenoids are important secondary metabolites, which have been recognized as an essential component of the human diet because of their valuable beneficial health effects. With this rationale, there is a continuous aim to define the distribution of these compounds in plants, to better understand their metabolism and to increase their concentration levels in fruits and vegetables. This study aimed at deepening the knowledge on the regulatory role of phytohormones in carotenoid metabolism. More specifically, it was envisaged to reveal the phytohormones involved in the metabolism of alpha-carotene, beta-carotene, lycopene, lutein and zeaxanthin. To this purpose, the phytohormone profiles of 50 tomato fruits were determined by high-resolution Orbitrap mass spectrometry and evaluated towards the associated carotenoid levels. Data mining was performed by differential expression and orthogonal partial least squares analyses. This metabolomics approach revealed 5 phytohormonal metabolites, which significantly influenced (Variable Importance in Projection scores =0.80) carotenoid metabolism. These metabolites were identified as cis-12-oxo-phytodienoic acid, cucurbic acid, 2-oxindole-3-acetic acid, 1-acetylindole-3-carboxaldehyde, and cis-zeatin-O-glucoside. The involvement of the individual phytohormones towards carotenoid metabolism was investigated by regression analysis (P values =0.05, R2 varying between 0.280 and 0.760) and statistical correlation (P values =0.01, correlation varying between 0.403 and 0.846). It was concluded that these phytohormones all have significant contributing value in the regulation of carotenoid metabolism, thereby exhibiting down- and up-regulating influences. As a result, this knowledge encloses the potential for improving tomato fruit nutritional quality by targeted control of agronomic conditions, exogenous use of plant bioregulators, or genetic engineering.
Question: Write a study description for the study titled 'Mechanistic insights into the biological activity of S-Sulfocysteine in CHO cells using a multi-omics approach'.
Answer: S-Sulfocysteine (SSC), a bioavailable L-cysteine derivative (Cys), is known to be taken up and metabolized in Chinese hamster ovary (CHO) cells used to produce novel therapeutic biological entities. To gain a deeper mechanistic insight into the SSC biological activity and metabolization, a multi-omics study was performed on industrially relevant CHO-K1 GS cells throughout a fed-batch process, including metabolomic and proteomic profiling combined with multivariate data and pathway analyses. Multi-layered data and enzymatical assays revealed an intracellular SSC/glutathione mixed disulfide formation and glutaredoxin-mediated reduction, releasing Cys and sulfur species. Increased Cys availability was directed towards glutathione and taurine synthesis, while other Cys catabolic pathways were likewise affected, indicating that cells strive to maintain Cys homeostasis and cellular functions.
Question: Write a study description for the study titled 'Cascading effects of root microbial symbiosis on the development and metabolome of the insect herbivore Manduca sexta L'.
Answer: Root mutualistic microbes can modulate the production of plant secondary metabolites affecting plant–herbivore interactions. Still, the main mechanisms underlying the impact of root mutualists on herbivore performance remain ambiguous. In particular, little is known about how changes in the plant metabolome induced by root mutualists affect the insect metabolome and postlarval development. By using bioassays with tomato plants (Solanum lycopersicum), we analyzed the impact of the arbuscular mycorrhizal fungus Rhizophagus irregularis and the growth-promoting fungus Trichoderma harzianum on the plant interaction with the specialist insect herbivore Manduca sexta. We found that root colonization by the mutualistic microbes impaired insect development, including metamorphosis. By using untargeted metabolomics, we found that root colonization by the mutualistic microbes altered the secondary metabolism of tomato shoots, leading to enhanced levels of steroidal glycoalkaloids. Untargeted metabolomics further revealed that root colonization by the mutualists affected the metabolome of the herbivore, leading to an enhanced accumulation of steroidal glycoalkaloids and altered patterns of fatty acid amides and carnitine-derived metabolites. Our results indicate that the changes in the shoot metabolome triggered by root mutualistic microbes can cascade up altering the metabolome of the insects feeding on the colonized plants, thus affecting the insect development.
Question: Write a study description for the study titled 'Maize Stem Response to Long-Term Attack by Sesamia nonagrioides'.
Answer: Plants defend themselves against herbivores by activating a plethora of genetic and biochemical mechanisms aimed at reducing plant damage and insect survival. The short-term plant response to insect attack is well understood, but less is known about the maintenance of this response over time. We performed transcriptomic and metabolomics analyses in order to identify genes and metabolites involved in the long-term response of maize to attack by the corn borer Sesamina nonagrioides. To determine the role of elicitors present in caterpillar secretions, we also evaluated the response of maize stem challenged with insect regurgitates. The integrative analysis of the omics results revealed that the long-term response in maize is characterized by repression of the primary metabolism and a strong redox response, mainly mediated by germin-like proteins to produce anti-nutritive and toxic compounds that reduce insect viability, and with the glutathione–ascorbate cycle being crucial to minimize the adverse effects of reactive oxygen species (ROS) on the plant. Our results suggest that different defense mechanisms are involved in the long-term response compared to those reported during the early response. We also observed a marginal effect of the caterpillar regurgitates on the long-term defensive response.
Question: Write a study description for the study titled 'Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis'.
Answer: Cytokinin (CK) in plants regulates both developmental processes and adaptation to environmental stress. Arabidopsis histidine phosphotransfer ahp2,3,5 and type-B response regulator arr1,10,12 triple mutants are almost completely defective in CK signaling, and the ahp2,3,5 mutant was reported to be salt tolerant. Here, we demonstrate that the arr1,10,12 mutant is also more tolerant to salt stress than wild-type plants. A comprehensive metabolite profiling coupled with transcriptome analysis of the ahp2,3,5 and arr1,10,12 mutants was conducted to elucidate the salt tolerance mechanisms mediated by CK signaling. Numerous primary (e.g., sugars, amino acids and lipids) and secondary (e.g., flavonoids and sterols) metabolites accumulated in these mutants under both non-saline and saline conditions, suggesting that both pre- and post-stress accumulation of stress-related metabolites contribute to improved salt tolerance in CK-signaling mutants. Specifically, the level of oligosaccharides, amino acids [e.g., proline and gamma-aminobutyric acid], anthocyanins, sterols, and unsaturated triacyglycerols, were higher in the mutant plants than in wild-type plants. Notably, the reprograming of flavonoid and lipid pools was highly coordinated and concomitant with changes in transcriptional levels, indicating that these metabolic pathways are transcriptionally regulated by CK signaling. The discovery of the regulatory role of CK signaling on membrane lipid remodelling provides a greater understanding of CK-mediated salt tolerance in plants. This knowledge will contribute to the development of salt-tolerant crops with the ability to withstand salinity as a key driver to ensure global food security in the era of climate change.
Question: Write a study description for the study titled 'Integrated transcriptome and metabolome profiling unveils the tolerance network to potassium deficiency in wild soybean ecotypes'.
Answer: Facing the severe challenge of global soil potassium deficiency on crop production, two different ecological row types of wild soybean [ Glycine soja sieb. & Zucc. In order to reveal the physiological and molecular mechanisms of tolerance to low potassium stress in glycine soja, we compared the differences in transcriptional and physiological responses to low potassium stress between the common type (GS1) and the barren tolerant Type (GS2) . Growth parameters and ion content determination found that GS2 exhibited higher root biomass and K+/Na+ ratio. Combined metabolomic and transcriptomic analysis found that sugar metabolism was enhanced in GS2, manifested by the accumulation of soluble sugars such as sucrose and fructose and the maintenance of a stable TCA cycle. The increase of shikimic acid, proline and unsaturated fat constitutes the efficient antioxidant defense system and cell membrane stability maintenance mechanism of GS2. This study not only clarified the key regulatory network of wild soybean tolerance to low potassium stress, but also provided valuable genetic resources and technical support for genetic improvement of crop stress resistance.
Question: Write a study description for the study titled 'Tissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology, and treatment'.
Answer: The discovery of the oncometabolite 2-hydroxyglutarate in isocitrate dehydrogenase 1-mutated (IDH1-mutated) tumor entities affirmed the role of metabolism in cancer. However, large databases with tissue metabolites that are modulated by IDH1 mutation remain an area of development. Here, we present an unprecedented and valuable resource for tissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology, and tumor treatments in 101 tissue samples from 73 diffuse glioma patients (24 astrocytoma, 17 oligodendroglioma, 32 glioblastoma), investigated by NMR-based metabolomics and supported by RNA-Seq. We discovered comparison-specific metabolites and pathways modulated by IDH1 (IDH1 mutation status cohort) and tumor entity. The Longitudinal investigation cohort provides metabolic profiles of untreated and corresponding treated glioma samples at first progression. Most interestingly, univariate and multivariate cox regressions and Kaplan-Meier analyses revealed that tissue metabolites correlate with progression-free and overall survival. Thus, this study introduces potentially novel candidate prognostic and surrogate metabolite biomarkers for future prospective clinical studies, aiming at further refining patient stratification in diffuse glioma. Furthermore, our data will facilitate the generation of so-far-unanticipated hypotheses for experimental studies to advance our molecular understanding of glioma biology.
Question: Write a study description for the study titled 'Oxygen-induced pathological angiogenesis promotes intense lipid synthesis and remodeling in the retina'.
Answer: The retina is a notable tissue with high metabolic needs which relies on specialized vascular networks to protect the neural retina while maintaining constant supplies of oxygen, nutrients and dietary essential fatty acids. Here we analyzed the lipidome of the mouse retina under healthy and pathological angiogenesis using the oxygen-induced retinopathy model. By matching lipid profiles to changes in mRNA transcriptome, we identified a lipid signature showing that pathological angiogenesis leads to intense lipid remodeling favoring pathways for neutral lipid synthesis, cholesterol import/export and lipid droplet formation. Noteworthy, it also shows profound changes in pathways for long-chain fatty acid production, vital for retina homeostasis. The net result is accumulation of large quantities of mead acid, a marker of essential fatty acid deficiency, and a potential marker for retinopathy severity. Thus, our lipid signature might contribute to better understand diseases of the retina that lead to vision impairment or blindness.
Question: Write a study description for the study titled 'Comprehensive lipid analysis of green Arabica coffee beans by LC-HRMS/MS'.
Answer: Lipids play an important role in coffee bean development, coffee brew and in the effects of coffee on human health. They account for around 17% of the dry bean weight and encompass different classes and subclasses, mostly triacylglycerols (TAG) and a minor quantity of phospholipids (PL) and βN-alkanoyl-5-hydroxytryptamides (C-5HT). To comprehensive profile these different lipids, it is important to evaluate extraction methods that provide high lipid coverage and to analyze the lipids in high-resolution techniques. In this work, liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) was employed to comprehensive profile lipids from green Arabica coffee beans and to evaluate the extraction efficiency and lipid coverage of three methods: Bligh-Dyer (BD), Folch (FO), and Matyash (MA). The MA method yielded the greatest number of annotated compounds (131 lipids) compared to the other methods. In the positive electrospray ionization (ESI) mode, the main difference among extraction methods was observed for TAG and diacylglycerols, whereas for the negative ESI it was observed differences for phosphatidylinositol (PI), lysophosphatidylinositol and phosphatidic acid (p < 0.05). The analysis of coffees from different maturation stages and/or post-harvest processes were also performed using the MA method. Immature beans were discriminated from mature and overripe beans by its lower levels of C-5HT, PI, phosphatidylcholine, lysophosphatidylcholine, phosphatidyletanolamine, and lysophosphatidylethanolamine. These results can help to better understand the coffee lipid composition and its association with coffee quality.
Question: Write a study description for the study titled 'Targeted metabolomics data from two freshwater strains of SAR11'.
Answer: In an abundant aquatic groups of microorganisms, SAR11, the transition between salt- and freshwater environments has happened only once: all freshwater SAR11 belong to subclade IIIb/LD12, which has also been found to inhabit coastal environments where salinity varies widely. The first reported isolates of the SAR11 freshwater clade LD12 and a member of the sister clade IIIa from the same region are now available. This project quantifed concentrations of select, known intracellular metabolites within two strains of SAR11: LSUCC0261 and LSUCC0530.