LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits'.
Answer: Marine sponges can host abundant and diverse microbiomes, which can largely influence the metabolism and other phenotypic traits of the host. However, information on the potential relationships between sponge microbiomes and metabolic signatures, other than secondary metabolites explored for biotechnological purposes, needs further investigation. Applying an integrated approach, we investigated the microbiomes associated with 4 ubiquitous Mediterranean sponge species (i.e., Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula), correlated with their metabolomic patterns (in terms of lipidomics) and microbial predicted functions. Microscopy observations of sponge tissues revealed differences in microbial abundances, which, however, were only partially linked to their diversity assessed through metabarcoding. The microbiomes of the 4 sponges showed a species-specific composition and a different core size, which was independent from the microbial diversity of the surrounding seawater. Predicted functions of the associated microbiomes allowed identifying 2 functional host clusters: one more related to heterotrophic pathways and the other more linked to phototrophic activities. Differences in the microbiomes were also associated with different metabolic profiles, mostly due to specific compounds characterizing the host and its microbiome. Overall, this study provides new insights on the functionality of sponges and their prokaryotic symbioses’, and in particular, it discloses a descriptive sketch of the diverse compartments forming the sponge holobiont.
Question: Write a study description for the study titled 'Metabolomics-derived insights into the manipulation of terpenoid sysnthesis in Centella asiatica cells by methyl-jasmonate'.
Answer: Centella asiatica is an important medicinal plant with a wide range of bioactivities associated with its secondary metabolites. Using two extraction procedures, metabolomic approaches were used to investigate changes in the metabolome of C. asiatica cells treated with exogenous MeJA. GC–MS and LC–MS platforms were employed for semi-targeted and untargeted analyses, respectively. Multivariate data analyses indicated concentration-dependent changes in the metabolite profiles, indicative of the cellular response to MeJA. Annotation of biomarkers correlated with the treatment indicate differential responses in flavonoid-, phenylpropanoid (cinnamates)- and terpenoid pathways and changes in fatty acid profiles. MeJA treatment triggered the accumulation of bicyclic sesquiterpenoids (aristolochene, deoxy-capsidiol, 15-hydroxysolavetivone, solavetivone, 3-hydroxylubimin) and a tricyclic sesquiterpenoid (phytuberin), indicating the stimulatory effect of MeJA on this branch of the terpenoid pathways. In contrast, flavonoids were mostly negatively correlated with the treatment. The presence of the sesquiterpenoids in MeJA-elicited cells and other tentatively identified metabolites (abscisic acid, fatty acids, phytosterols and metabolites of shikimate–phenylpropanoid pathways) indicates that the changes in the metabolome are associated with a defensive function in response to elicitation by MeJA, rather than just the amplification of existing terpene pathways. These results provide a detailed and comprehensive picture of metabolic changes occurring in C. asiatica cells in response to MeJA elicitation and contribute to the understanding of flexible and controllable aspects of metabolic manipulation.
Question: Write a study description for the study titled 'Deciphering the in vitro interaction dynamics of synthetic mucosal-associated gut bacteria community'.
Answer: Maintaining the integrity of the mucus layer is essential for host health. Studies have implicated that reduced or abnormal mucus production may lead to intestinal inflammation. When dietary nutrients are abundant in the gut, mucin degradation by microbes decreases. However, when nutrient availability declines, microbes increasingly turn to mucin as an energy source. This shift in resource utilization can profoundly alter interaction networks within the gut microbiota. In this study, we aimed to comprehensively investigate the interactions between the community members in different condition. Use non-targeted metabolomics to analyze the relationship between microbial interactions and metabolites.
Question: Write a study description for the study titled 'CXCL12 and MYC control energy metabolism to support adaptive responses after kidney injury'.
Answer: Kidney injury is a common complication of severe disease. Here, we report that injuries of the zebrafish embryonal kidney are rapidly repaired by a migratory response in 2-, but not in 1-day-old embryos. Gene expression profiles between these two developmental stages identify cxcl12a and myca as candidates involved in the repair process. Zebrafish embryos with cxcl12a, cxcr4b, or myca deficiency display repair abnormalities, confirming their role in response to injury. In mice with a kidney-specific knockout, Cxcl12 and Myc gene deletions suppress mitochondrial metabolism and glycolysis, and delay the recovery after ischemia/reperfusion injury. Probing these observations in zebrafish reveal that inhibition of glycolysis slows fast migrating cells and delays the repair after injury, but does not affect the slow cell movements during kidney development. Our findings demonstrate that Cxcl12 and Myc facilitate glycolysis to promote fast migratory responses during development and repair, and potentially also during tumor invasion and metastasis.
Question: Write a study description for the study titled 'A large-scale metabolomics study to harness chemical diversity and explore biochemical mechanisms in ryegrass (HPLC-MS Hypercarb reverse phase NEG assay)'.
Answer: "Perennial ryegrass (Lolium perenne) is integral to temperate pastoral agriculture, which contributes most of the milk and meat production worldwide. Chemical profiles and diversity of ryegrass offer several opportunities to harness specific traits and elucidate underlying biological mechanisms for forage improvement. We conducted a large-scale metabolomics study of perennial ryegrass comprising 715 genotypes, representing 118 populations from 21 countries. Liquid/gas chromatography-mass spectrometry based targeted and non-targeted techniques were used to analyse fructan oligosaccharides, lipids, fatty acid methyl esters, polar and semi-polar compounds. Fructan diversity across all genotypes was evaluated, high- and low-sugar groups identified, and fructan accumulation mechanisms explored. Metabolites differentiating the two groups were characterised, modules and pathways they represent deduced, and finally, visualisation and interpretation provided in a biological context. We also demonstrate a workflow for large-scale metabolomics studies from raw data through to statistical and pathway analysis.  HPLC-MS Hypercarb reverse phase NEG assay is reported in the current study MTBLS529. UPLC-MS HILIC POS assay is reported in MTBLS62. UPLC-MS HILIC NEG assay is reported in MTBLS63. UPLC-MS C18 reverse phase POS assay is reported in MTBLS64. UPLC-MS C18 reverse phase NEG assay is reported in MTBLS65. UPLC-MS C1 reverse phase POS and GC-MS FAME assays are reported in MTBLS66. UPLC-MS C1 reverse phase NEG assay is reported in MTBLS68."
Question: Write a study description for the study titled 'PTER is an N-acetyltaurine hydrolase that regulates feeding and obesity'.
Answer: Taurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans1-3. In endogenous taurine metabolism, dedicated enzymes are involved in biosynthesis of taurine from cysteine as well as the downstream metabolism of secondary taurine metabolites4,5. One such taurine metabolite is N-acetyltaurine6. Levels of N-acetyltaurine are dynamically regulated by stimuli that alter taurine or acetate flux, including endurance exercise7, dietary taurine supplementation8, and alcohol consumption6,9. To date, the identity of enzymes involved in N-acetyltaurine metabolism, and the potential functions of N-acetyltaurine itself, have remained unknown. Here we show that the body mass index-associated orphan enzyme PTER (phosphotriesterase-related)10 is a physiologic N-acetyltaurine hydrolase. In vitro, PTER catalyzes degradation of N-acetyltaurine to taurine and acetate. In mice, PTER is expressed in the kidney, liver, and brainstem. Genetic ablation of PTER in mice results in complete loss of tissue N-acetyltaurine hydrolysis activity and systemic elevation of N-acetyltaurine levels. Upon stimuli that increase taurine levels, PTER-KO mice exhibit reduced food intake, resistance to diet-induced obesity, and improved glucose homeostasis. Administration of N-acetyltaurine to obese wild-type mice also reduces food intake and body weight in a GFRAL-dependent manner. These data place PTER into a central enzymatic node of secondary taurine metabolism and uncover a role for PTER and N-acetyltaurine in body weight control and energy balance.
Question: Write a study description for the study titled 'Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness'.
Answer: Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to influence the frequencies of mtDNA types in nature and human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four Drosophila mitotypes and assayed their frequency in population cages. The nuclear genome was standardised. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result was repeated when the laboratory diet was replaced by natural fruits having high and low P:C ratios and when the nuclear genome was permuted. Quaternary structural modelling, in vitro assays of electron transport chain protein complexes, and protein gels suggested a V161L mutation in the ND4 subunit of Complex I of Dahomey mtDNA was functionally deleterious and resulted in an increase in larval development time on the 1:2 P:C diet. Conversely, the 1:16 P:C diet resulted in an elegant remodelling of energy metabolism and relative reduction in development time of larvae harbouring Dahomey mtDNA. These data question the use of mtDNA as an assumed neutral maker. We posit that humans with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of first-world diseases including cardiovascular disease, diabetes, obesity and perhaps Parkinson’s Disease.
Question: Write a study description for the study titled 'Local and systemic metabolic alterations in brain, plasma, and liver of rats in response to aging and ischemic stroke, as detected by nuclear magnetic resonance (NMR) spectroscopy'.
Answer: Cerebral ischemia and aging induce local and systemic effects, and impact severity of stroke outcome. We performed comprehensive metabolic profiling to detect metabolites in brain, plasma, and liver as a function of aging and ischemia/reperfusion (IR). Ischemic stroke was induced by middle cerebral artery occlusion. Abundant metabolites were identified and quantified by 1H-NMR. Older rats aged 12 months showed significant changes in metabolic profiles in the brain, but only a few metabolites were changed in the liver and plasma as compared to younger rats aged 3 months. However, I/R injury at day 2 resulted in major changes in metabolites in liver and plasma of older rats. In younger rats, focal cerebral ischemia induced reperfusion-time dependent changes in metabolites in brain, plasma, and liver. Metabolic changes were seen in brain as early as day 2 of I/R, plasma showed significant changes at day 3 of reperfusion, and liver exhibited delayed response after day 3 that continued to remain at week 2 of reperfusion-time. Pathways involved in energy and amino acid metabolism, inflammation, and oxidative stress were altered as a result of aging and I/R. Thus, age, tissue, and I/R time affect changes in metabolites and may have implications in stroke outcome.
Question: Write a study description for the study titled 'Tubular insulin-induced gene 1 deficiency promotes NAD+ consumption and exacerbates kidney fibrosis'.
Answer: Profibrotic proximal tubular (PT) were identified as a unique phenotype of PTCs in renal fibrosis by single-cell RNA sequencing (scRNA-seq). Controlling the process of renal fibrosis requires understanding how to manage the S1 subset's branch to the S3 subset rather than to the profibrotic PT subset. Insulin-induced gene 1 (Insig1) is one of the branch-dependent genes involved in controlling this process, although its role in renal fibrosis is unknown. Here, we discovered that tubular Insig1 deficiency, rather than fibroblast Insig1 deficiency, play a detrimental role in the pathogenesis of renal fibrosis in vivo and in vitro. Overexpression of Insig1 profoundly inhibited renal fibrosis. Mechanistically, Insig1 deletion in PTCs boosted SREBP1 nuclear localization, increasing Aldh1a1 transcriptional activity, causing excessive NAD+ consumption and ER enlargement, as well as accelerating renal fibrosis. We also identified nicardipine as a selective inhibitor of Aldh1a1, which could restore NAD+ and maintain ER homeostasis, as well as improve renal fibrosis. Together, our findings support tubular Insig1 as a new therapeutic target for chronic kidney disease (CKD).
Question: Write a study description for the study titled 'Metabolomics profiling of pre-and post-anesthesia plasma samples obtained via Ficoll separation'.
Answer: 1H Nuclear Magnetic Resonance (NMR) spectroscopy was used to investigate the metabolic consequences of general anesthesia in the plasma of two groups of patients with diagnosis for non-metastatic colorectal cancer and metastatic colorectal cancer with liver-metastasis, respectively. Patients were treated with Etomidate or Propofol, two frequently used sedation agents. Plasma samples were obtained via Ficoll separation. Here, we demonstrated that this procedure introduces a number of limitations for NMR-based metabolomics studies, due to the appearance of spurious signals. Nevertheless, the comparison of the 1H NMR metabolomic profiles of patients treated with Etomidate or Propofol at equipotent dose ranges was still feasible and proved that both agents significantly decrease the plasma levels of several NMR-detectable metabolites. Consequently, samples collected during anesthesia are not suitable for metabolic profiling studies aimed at patient stratification, because interpersonal variability are reduced by the overall depression of metabolites levels. On the other hand, this study showed that plasma metabolomics could represent a valuable tool to monitor the effect of different sedation agents and/or the individual metabolic response to anesthesia, providing hints for an appropriate tuning of personalized sedation procedures. In our reference groups, the metabolomic signatures were slightly different in patients anesthetized with Etomidate versus Propofol. The importance of standardized collection procedures and availability of exhaustive metadata of the experimental design for the accurate evaluation of the significance of the observed changes in metabolites levels are critically discussed.
Question: Write a study description for the study titled 'NMR-based metabonomics and correlative analysis reveals potential bomarkers associated with chronic atrophic gastritis'.
Answer: Chronic atrophic gastritis (CAG) is one of the most important pre-cancerous states with a high prevalence. Exploring of the underlying mechanism and potential biomarkers is of significant importance for CAG. In the present work, 1H NMR-based metabonomics with correlative analysis was performed to analyze the metabolic features of CAG. 19 plasma metabolites and 18 urine metabolites were enrolled to construct the circulatory and excretory metabolome of CAG, which was in response to alterations of energy metabolism, inflammation, immune dysfunction, as well as oxidative stress. 7 plasma biomarkers and 7 urine biomarkers were screened to elucidate the pathogenesis of CAG based on the further correlation analysis with biochemical indexes. Finally, 3 plasma biomarkers (arginine, succinate and 3-hydroxybutyrate) and 2 urine biomarkers (a-ketoglutarate and valine) highlighted the potential to indicate risks of CAG in virtue of correlation with pepsin activity and ROC analysis. Here, our results paved a way for elucidating the underlying mechanisms in the development of CAG, and provided new avenues for the diagnosis of CAG and presented potential drug targets for treatment of CAG.
Question: Write a study description for the study titled 'Immunoglobulin expression in the endoplasmic reticulum shapes the metabolic fitness of B lymphocytes'.
Answer: The major function of B lymphocytes is to sense antigens and to produce protective antibodies after activation. This function requires the expression of a B-cell antigen receptor (BCR), and evolutionary conserved mechanisms seem to exist that ensure that B cells without a BCR do not develop nor survive in the periphery. Here, we show that the loss of BCR expression on Burkitt lymphoma cells leads to decreased mitochondrial function and impaired metabolic flexibility. Strikingly, this phenotype does not result from the absence of a classical Syk-dependent BCR signal but rather from compromised ER expansion. We show that the reexpression of immunoglobulins (Ig) in the absence of the BCR signaling subunits Igα and Igβ rescues the observed metabolic defects. We demonstrate that immunoglobulin expression is needed to maintain ER homeostasis not only in lymphoma cells but also in resting B cells. Our study provides evidence that the expression of BCR components, which is sensed in the ER and shapes mitochondrial function, represents a novel mechanism of metabolic control in B cells.
Question: Write a study description for the study titled 'Exploring Salivary Metabolites as Biomarkers in Chronic Craniofacial and Orofacial Pain: A Metabolomic Analysis.'.
Answer: Chronic facial pain (CFP) includes a range of conditions such as musculoskeletal, neurovascular, and neuropathic disorders affecting the facial and jaw regions, often causing significant distress to patients. This study aims to investigate the metabolomic profile of patients with CFP, focusing on salivary metabolites as potential biomarkers for pain diagnosis and management. Metabolomics investigation was performed using combined liquid chromatography with mass spectrometry (UPLC-MS) for metabolic profiling. A comprehensive analysis was conducted, utilizing both untargeted and targeted metabolomics to examine 28 metabolites previously associated with pain conditions. The results revealed significant differences in 18 metabolites between the CFP group and a control group, with seven metabolites consistently showing elevated levels regardless of gender: DL-Isoleucine, DL-Glutamine, DL-Citrulline, D-(+)-Pyroglutamic acid, DL-Tryptophan, DL-Phenylalanine, and Spermidine. The findings suggest a potential link between specific salivary metabolites and CFP, highlighting the complexity of pain mechanisms. Further research is needed to understand the causality and implications of these metabolic changes, which could lead to more targeted and personalized approaches in managing pain.
Question: Write a study description for the study titled 'GABA regulates IL-1β production in macrophages'.
Answer: Neurotransmitters have been well-documented to determine immune cell fates; however, whether and how γ-amino butyric acid (GABA) shapes the function of innate immune cells is still obscure. Here, we demonstrated that GABA orchestrates macrophage maturation and inflammation. GABA treatment during macrophage maturation inhibits interleukin (IL)-1β production from inflammatory macrophages. Mechanistically, GABA enhances succinate-FAD-lysine demethylase1 (LSD1) signaling to regulate the histone demethylation of Bcl2l11 and Dusp2, lowering the formation of NLRP3-ASC-Caspase-1 complex. Meanwhile, GABA-succinate axis lowers succinylation of mitochondrial proteins to promote mitochondrial oxidative phosphorylation (OXPHOS). We also found that GABA alleviates the LPS-induced sepsis as well as high-fat diet-induced obesity in mice. Our study proves that GABA is potential in lessening the pro-inflammatory macrophage responses associating with metabolic reprogramming and protein succinylation, thus providing a strategy for treating macrophage-related inflammatory diseases.
Question: Write a study description for the study titled 'A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)'.
Answer: Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.
Question: Write a study description for the study titled 'Untargeted metabolites of supernatant of wild-type and Nlrp3-/- bone marrow-derived macrophages with or without LPS and ATP costimulation'.
Answer: Untargeted metabolites of supernatant of wild-type and Nlrp3-/- bone marrow-derived macrophages without stimulation or with 4 hours of LPS preconditioning and subsequently 30 min of ATP stimulation.
Question: Write a study description for the study titled 'Mitochondrial NAD+ Deficiency in Vascular Smooth Muscle Impairs Collagen III Turnover to Trigger Aortic Disease'.
Answer: Aortic disease poses a significant mortality risk in adults, yet many of its underlying factors remain undiscovered. In this study, we identify mitochondrial NAD⁺ deficiency as a causal factor. Metabolomics analysis of 73 surgical aortic specimens revealed impaired NAD⁺ salvage and mitochondrial transport in diseased aortas. Precursor metabolites NMN and NAM were significantly elevated, while NAD⁺ levels were decreased, indicating a disrupted salvage biosynthesis pathway. Using mouse models, we provided mechanistic insights into the pathogenic process. The production of type III procollagen during aortic medial matrix turnover imposes a high demand for proline, an essential amino acid in collagen. A deficiency in the mitochondrial NAD⁺ pool, regulated by NAD⁺ salvage and transport, impairs proline biosynthesis in mitochondria, potentially contributing to the progression of aortic disease.