LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Mechanism of interventional effect and targets of Zhuyu Pill in regulating and suppressing colitis and cholestasis'.
Answer: Zhuyu pill (ZYP) is a traditional Chinese medicine prescription composed of two drugs, Coptis chinensis Franch. and Tetradium ruticarpum (A. Jussieu) T. G. Hartley, and is commonly used in the clinical treatment of diseases of the digestive system. However, the mechanism underlying the effect of ZYP on colitis remains unclear. In this study, a colitis rat model was induced with 2,4,6-trinitro-benzenesulfonic acid (TNBS, 100 mg/kg) and treated with ZYP (low dose: 0.6 g/kg, high dose: 1.2 g/kg). Disease activity index, colonic weight index and weight change ratio were used to evaluate the model and efficacy. LC-MS and 16S rRNA gene sequencing were used to measure differences in fecal metabolism and microorganism population among the control, model, low-dose ZYP and high-dose ZYP groups. To elucidate the mechanism of interventional effect of ZYP, Spearman correlation analysis was used to analyze the correlation between fecal metabolism and fecal microbial number. High-dose and low-dose ZYP both exhibited significant interventional effects on colitis rat models, and high-dose ZYP produced a better interventional effect compared with low-dose ZYP. Based on a metabolomics test of fecal samples, significantly altered metabolites in the model and high-dose ZYP treatment groups were identified. In total, 492 metabolites were differentially expressed. Additionally, sequencing of the 16S rRNA gene in fecal samples revealed that the high-dose ZYP could improve TNBS-induced fecal microbiota dysbiosis. Ultimately, changes in tryptophan metabolism and Firmicutes and Gammaproteobacteria populations were detected after ZYP treatment in both colitis and cholestasis. Therefore, we conclude that tryptophan metabolism and Firmicutes and Gammaproteobacteria populations are the core targets of the anti-inflammatory effect of ZYP. These findings provide a scientific basis for further investigation of the anti-inflammatory mechanism of ZYP in the future.
Question: Write a study description for the study titled 'Quantitative Metabolomic Dataset of Avian Eye Lenses'.
Answer: Metabolomics is a powerful set of methods that uses analytical techniques to identify and quantify metabolites in biological samples, providing a snapshot of the metabolic state of a biological system. In medicine, metabolomics can help diagnose diseases, reveal molecular basis of a disease, and monitor treatment responses, while in agriculture, it can improve crop yields and plant breeding. However, animal metabolomics faces several challenges due to the complexity and diversity of animal metabolomes, the lack of standardized protocols, and the difficulty in interpreting metabolomic data. The current dataset includes quantitative metabolomic profiles of eye lens tissues from 26 bird species (111 specimens) that can aid researchers in developing new experiments, mathematical models, and integrations with other omics data. The dataset includes raw 1H NMR spectra, protocols for sample preparation, and data preprocessing with the final table containing information on only 89 reliably identified and quantified metabolites. The dataset is quantitative, making it relevant for supplementing with new specimens or comparison groups, followed by data mining and expected new interpretations. It was obtained from bird specimens collected in compliance with ethical standards and reveals potential differences in metabolic pathways due to phylogenetic difference or environmental exposure.
Question: Write a study description for the study titled 'Metabolic profilings of rat INS-1 β-cells under changing levels of essential amino acids'.
Answer: Application of mass spectrometry enables the detection of metabolic differences between organisms with different nutritional settings. Divergence in the metabolic fingerprints of rat pancreatic INS-1 β-cells were systematically captured with regard to 10 individual essential amino acid (EAA) availability. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a horizontal comparison of metabolic profilings of β-cells with individual EAA elevated to 10 mmol/L by turn or removal individual EAA from the medium one by one. Quality control samples were injected at regular intervals throughout the analytical run to monitor and evaluate the stability of the system. The raw data of samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights to enable efficient reuse of the datasets, such as investigating the difference in metabolic process between diverse EAAs as well as screening and verifying potential metabolites affecting insulin secretion and β-cell function.
Question: Write a study description for the study titled 'DNA nanomachines reveal an adaptive energy mode in confinement-induced amoeboid migration powered by polarized mitochondrial distribution'.
Answer: Energy metabolism is highly interdependent with adaptive cell migration in vivo. Mechanical confinement is a critical physical cue that induces switchable migration modes of the mesenchymal-to-amoeboid transition (MAT). However, the energy states in distinct migration modes, especially amoeboid-like stable bleb (A2) movement, remain unclear. In this report, we developed multivalent DNA framework-based nanomachines to explore strategical mitochondrial trafficking and differential ATP levels during cell migration in mechanically heterogeneous microenvironments. Through single-particle tracking and metabolomic analysis, we revealed that fast A2-moving cells driven by biomimetic confinement recruited back-end positioning of mitochondria for powering highly polarized cytoskeletal networks, preferentially adopting an energy-saving mode compared with a mesenchymal mode of cell migration. We present a versatile DNA nanotool for cellular energy exploration and highlight that adaptive energy strategies coordinately support switchable migration modes for facilitating efficient metastatic escape, offering a new perspective for therapeutic interventions in cancer metastasis.
Question: Write a study description for the study titled 'Alterations in gut microbiota and metabolomic profiles in acute stroke: insights into brain–gut axis dysregulation'.
Answer: Acute stroke (AS) is a major public health issue globally, exhibiting high morbidity, disability rate, and mortality. Emerging research has demonstrated the critical roles of gut microbiota and its metabolites in pathogenesis, recovery, and prognosis of AS. In this study, we investigated alterations in gut microbiota composition and metabolomic profiles in AS patients using 16S rRNA sequencing and untargeted liquid chromatography–mass spectrometry (LC-MS) metabolomics technology. The results revealed significant changes in gut microbiota diversity and community structure in AS patients compared with healthy controls. Notably, the abundance of anti-inflammatory microbiota was increased significantly, accompanied by elevated levels of certain metabolites, such as 6,9,12,15,18,21-tetracosahexaenoic acid and bufadienolide, while levels of urobilin and andrenid acid were significantly reduced. Network analysis further uncovered the significant differences in microbiota–metabolite interactions between AS patients and healthy controls, indicating gut ecosystem disruption and functional dysfunction in AS. This study sheds light on the mechanisms of brain-gut axis in AS, suggesting potential microbial and metabolite biomarkers, thus providing valuable insights into AS prediction and treatment.
Question: Write a study description for the study titled 'Co-exposure to Polyethylene Fiber and Salmonella enterica Typhimurium Alters Microbiome and Metabolome of in vitro Chicken Cecal Mesocosms'.
Answer: Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE Fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal model.
Question: Write a study description for the study titled 'Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum'.
Answer: Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity.
Question: Write a study description for the study titled 'In Vitro 1H NMR Metabolic Profiles of Liver, Brain, and Serum in Rats After Chronic Consumption of Alcohol'.
Answer: The impact of alcohol on the body can be investigated with NMR spectroscopy in vitro, which can detect a wide range of metabolites but preparing samples includes tissue biopsy. Blood sampling is less invasive, but blood metabolic content might not reflect the changes occurring in other tissues. Thus, this study aimed to investigate the liver, brain, and serum metabolism and evaluate the link between tissues and serum metabolic content. Two experimental groups with ten outbred rats each were provided intragastrically with water (control group) and 50% ethanol solution (alcohol group) for 28 days. 1H NMR spectroscopy in vitro was performed on the brain cortex, liver, and serum samples. Student’s t test with Holm–Bonferroni correction was used to investigate significant differences between groups. Partial least-squares discriminant analysis (PLS-DA) and two-way ANOVA were performed to compare liver and serum, brain and serum. In all, 38, 37, and 21 metabolites were identified in the liver, brain, and serum samples, respectively. Significant differences for three metabolites were found in the liver (alanine, proline, and glutathione, p < 0.002) and four in serum (lactate, betaine, acetate, and formic acid, p < 0.002) were detected between the control and alcohol groups. The contents of glucose, betaine, and isoleucine were correlated (r > 0.65) between serum and liver samples. PLS-DA determined separation between all tissues (p < 0.001) and between control and alcohol groups only for liver and serum (p < 0.001). Alcohol had a more substantial effect on liver and serum metabolism than on the brain.
Question: Write a study description for the study titled 'Generation and characterization of thiol-deficient Mycobacterium tuberculosis mutants'.
Answer: Mycothiol (MSH) and ergothioneine (ERG) are thiols able to compensate for each other to protect mycobacteria such as Mycobacterium smegmatis against oxidative stress. Gamma-glutamylcysteine (GGC), another thiol and an intermediate in ERG biosynthesis has detoxification abilities. Five enzymes are involved in ERG biosynthesis, namely EgtA, EgtB, EgtC, EgtD and EgtE. The role of these enzymes in the production of ERG had been unclear. On the other hand, the enzyme MshA is known to be essential for MSH biosynthesis. In this manuscript, we describe the raw data of the generation and characterization of Mycobacterium tuberculosis (M.tb) mutants harbouring a deletion of the gene coding for each of these enzymes, and the raw data of the phenotypic characterization of the obtained thiol-deficient M.tb mutants. Through a high throughput screening approach, compounds not previously used in a tuberculosis (TB) regimen were identified. Raw data depicting the effect of these compounds on the generated thiol-deficient M.tb mutants, on the production of reactive oxygen species (ROS) and thiols in the M.tb wild type strain are described in this study.
Question: Write a study description for the study titled 'Glycerophospholipid remodeling is critical for orthoflavivirus infection'.
Answer: Flavivirus infection is tightly connected to host lipid metabolism. Here, we performed shotgun lipidomics of cells infected with neurotropic Zika, West Nile and tick-borne encephalitis viruses, as well as dengue and yellow fever virus. Early in infection specific lipids accumulated, e.g., neutral lipids in Zika and some lyso-phospholipids in all infections. Ceramide levels increased following infection with viruses that cause a cytopathic effect. In addition, fatty acid desaturation as well as glycerophospholipid metabolism were significantly altered. Importantly, depletion of enzymes involved in phosphatidylserine metabolism as well as phosphatidylinositol biosynthesis reduced orthoflavivirus titers and cytopathic effects while inhibition of fatty acid monounsaturation only rescued from virus-induced cell death. Interestingly, interfering with ceramide synthesis had opposing effects on virus replication and cytotoxicity depending on the targeted enzyme. Thus, lipid remodeling by orthoflaviviruses includes distinct changes but also common patterns shared by several viruses that are needed for efficient infection and replication.
Question: Write a study description for the study titled 'Metabolomics analysis of human acute graft-versus-host disease reveals changes in host and microbiota-derived metabolites (Cohort 2)'.
Answer: Despite improvement in clinical management, allogeneic hematopoietic stem cell transplantation (HSCT) is still hampered by high morbidity and mortality rates, mainly due to Graft versus host disease (GvHD). Recently, it has been demonstrated that the allogeneic immune response might be influenced by external factors such as tissues microenvironment or host microbiota.Here we used high throughput metabolomics (UPLC-MS/MS) in two cohorts of genotypically HLA-identical related recipient and donor pairs. A first monocentric cohort from Saint Louis hospital (Paris, France) was used as an exploratory cohort (n=43) and a second multicentric national cohort from Cryostem biobank was used as a confimatory cohort (n=56).Metabolomic profile markedly differed between recipients and donors. At the onset of acute GvHD, in addition to host-derived metabolites, we identified significant variation in microbiota-derived metabolites, especially in Aryl hydrocarbon Receptor (AhR) ligands, bile acids and plasmalogens. Altogether, our findings support that the allogeneic immune response during acute GvHD might be influenced by bile acids and by the decreased production of AhR ligands by microbiota that could limit indoleamine 2,3-dioxygenase (IDO) induction and influence allogeneic T-cell reactivity.MTBLS204 contains study information relating to cohort 1.MTBLS205 contains study information relating to cohort 2.
Question: Write a study description for the study titled 'Comparative Analysis of Host Metabolic Alterations in Murine Malaria Models with Uncomplicated or Severe Malaria'.
Answer: Malaria varies in severity, with complications ranging from uncomplicated to severe malaria. Severe malaria could be attributed to peripheral hyperparasitemia or cerebral malaria. The metabolic interactions between the host and Plasmodium species are yet to be understood during these infections of varied pathology and severity. An untargeted metabolomics approach utilizing the liquid chromatography-mass spectrometry platform has been used to identify the affected host metabolic pathways and associated metabolites in the serum of murine malaria models with uncomplicated malaria, hyperparasitemia and experimental cerebral malaria. We report that mice with malaria share similar metabolic attributes like higher levels of bile acids, bile pigments, and steroid hormones that have been reported for human malaria infections. Moreover, in severe malaria, upregulated levels of metabolites like phenylalanine, histidine, valine, pipecolate, ornithine and pantothenate, with decreased levels of arginine and hippurate, were observed. Metabolites of sphingolipid metabolism were upregulated in experimental cerebral malaria. Higher levels of 20-hydroxy-leukotriene B4 and epoxyoctadecamonoenoic acids were found in uncomplicated malaria, with lower levels observed for experimental cerebral malaria. Our study provides insights into host biology during different pathological stages of malaria disease and would be useful for the selection of animal models for evaluating diagnostic and therapeutic interventions against malaria.
Question: Write a study description for the study titled 'Lactobacillus reuteri bile acid metabolism in vitro'.
Answer: Upon reaching an OD600 of 0.3, L.reuteri cultures were treated with 100 µM TCA, HCA, orTCDCA. For BSHs inhibition assays, additional wells were treated with 100 µMHCA + GR7. Both negative control and MRS medium control groups were included.Cultures were terminated at 72 h by flash-freezing in liquid nitrogen.
Question: Write a study description for the study titled 'Advancing Reef Monitoring Techniques through Exometabolomics: Quantification of Labile Dissolved Organic Metabolites on Coral Reefs'.
Answer: Extracellular chemical cues constitute much of the language of life among marine organisms from microbes to mammals. These chemical cues shape foraging and feeding strategies, symbiotic interactions, selection of mates and habitats, and the transfer of energy and nutrients within and among ecosystems. Changes in the chemical pool flux within these ecosystems serve as invisible signals of overall ecosystem health and, conversely, disruption to this finely tuned equilibrium. In coral reef systems, the full scope and magnitude of the chemicals involved in maintaining reef equilibria [m1] are largely unknown, and in particular, processes involving small, polar molecules, which form the majority components of labile dissolved organic carbon (DOC), are often poorly captured using traditional techniques and therefore remain unconstrained. [m2] In this study, we employed a recently developed chemical derivatization method and mass spectrometry-based targeted exometabolomics to capture and quantify polar dissolved phase metabolites on five coral reefs in the U.S. Virgin Islands. We detected and quantified 45 exometabolites, and further demonstrate their variability across the investigated geographic landscape and contextualize these findings in terms of geographic and benthic cover differences.  By comparing our results to previously published coral reef exometabolomes that did not employ chemical derivatization, we show the novel quantification of 23 metabolites which were previously undetected in the coral reef exometabolome, including compounds involved in central carbon metabolism (e.g., glutamate) and novel metabolites such as homoserine betaine. We highlight the immense potential of chemical derivatization-based exometabolomics for quantifying labile chemical cues on coral reefs and measuring molecular level responses to environmental stressors. Overall, improving our understanding of the composition and dynamics of reef exometabolites is vital for effective ecosystem monitoring and management strategies.
Question: Write a study description for the study titled 'Dubosiella sp. alleviates hypertension with improving arachidonic acid metabolism'.
Answer: We identify a novel microbiota-driven anti-hypertensive mechanism mediated by Achyranthes bidentata (Ab) extract and gut microbe Dubosiella sp.. Using a hypertensive mouse model induced by L-NAME and a high-salt diet, we show that Ab extract significantly ameliorates hypertension and renal damage by selectively enriching Dubosiella in the gut microbiota. Metabolomics suggested that Ab significantly changed the metabolic profiles and enriched the lipid metabolism including arachidonic acid metabolism. In vitro, Ab significantly promote the biofilm formation of Dubosiella DSM103457. Further gavage experiments with Dubosiella DSM103457 confirmed its effects of alleviating hypertension and heart injury. Microbial and metabolic profiling via 16S rRNA sequencing, metagenomics and metabolomics revealed that Dubosiella DSM103457 modulates arachidonic acid metabolism, restoring critical prostaglandins and leukotrienes associated with cardiovascular homeostasis.
Question: Write a study description for the study titled 'Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (B)'.
Answer: Translational genomics, the use of model species to generate knowledge about biological processes and the functions of genes, offers great promise to biotechnologists. Few studies have sought robust responses of model plants to environmental stresses, such as salinity, by altering the stress dosage or by repeating experiments in consecutive years and/or different seasons.We mined our published and unpublished data on legume salt acclimation for robust system features at the ionomic, transcriptomic and metabolomic levels. We analysed data from the model legume Lotus japonicus, obtained through six independent, longterm, non-lethal salt stress experiments which were carried out over two consecutive years. Best possible controlled greenhouse conditions were applied and two main questions asked: how reproducible are results obtained from physiologically meaningful salinity experiments, and what degree of bias may be expected if conclusions are drawn from less well-repeated sampling. A surprisingly large fraction of the transcriptional and metabolic responses to salt stress were not reproducible between experiments. A core set of robust changes was found that was shared between experiments. Many of these robust responses were qualitatively and quantitatively conserved between different accessions of the same species, indicating that the robust responses may be a sound starting point for translational genomics.