LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Aberrant L-Fucose accumulation and increased core fucosylation are metabolic liabilities in mesenchymal glioblastoma (Xenograft assays)'.
Answer: Glioblastoma (GBM) is a common and deadly form of brain tumor in adults. Dysregulated metabolism in GBM offers an opportunity to deploy metabolic interventions as precise therapeutic strategies. To identify the molecular drivers and the modalities by which different molecular subgroups of GBM exploit metabolic rewiring to sustain tumor progression, we interrogated the transcriptome, the metabolome, and the glycoproteome of human subgroup-specific GBM sphere-forming cells (GSC). L-fucose abundance and core fucosylation activation were elevated in mesenchymal (MES) compared with proneural GSCs; this pattern was retained in subgroup-specific xenografts and in subgroup-affiliated human patient samples. Genetic and pharmacological inhibition of core fucosylation significantly reduced tumor growth in MES GBM preclinical models. Liquid chromatography-mass spectrometry (LC-MS)-based glycoproteomic screening indicated that most MES-restricted core-fucosylated proteins are involved in therapeutically relevant GBM pathological processes, such as extracellular matrix interaction, cell adhesion, and integrin-mediated signaling. Selective L-fucose accumulation in MES GBMs was observed using preclinical minimally invasive PET, implicating this metabolite as a potential subgroup-restricted biomarker.Overall, these findings indicate that L-fucose pathway activation in MES GBM is a subgroup-specific dependency that could provide diagnostic markers and actionable therapeutic targets.SIGNIFICANCE: Metabolic characterization of subgroup-specific glioblastoma (GBM) sphere-forming cells identifies the L-fucose pathway as a vulnerability restricted to mesenchymal GBM, disclosing a potential precision medicine strategy for targeting cancer metabolism.Xenograft assays are reported in the current study MTBLS730.Stem cell and cell line assays are reported in MTBLS4708.
Question: Write a study description for the study titled 'Absence of MCJ/DnaJC15 promotes brown adipose tissue thermogenesis'.
Answer: Obesity poses a global health challenge, demanding a deeper understanding of adipose tissue (AT) and its mitochondria. This study describes the role of the mitochondrial protein Methylation-controlled J protein (MCJ/DnaJC15) in orchestrating brown adipose tissue (BAT) thermogenesis. Here we show how MCJ expression decreases during obesity, as evident in human and mouse adipose tissue samples. MCJKO mice, even without UCP1, a fundamental thermogenic protein, exhibit elevated BAT thermogenesis. Electron microscopy unveils changes in mitochondrial morphology resembling BAT activation. Proteomic analysis confirms these findings and suggests involvement of the eIF2α mediated stress response. The pivotal role of eIF2α is scrutinized by in vivo CRISPR deletion of eIF2α in MCJKO mice, abrogating thermogenesis. These findings uncover the importance of MCJ as a regulator of BAT thermogenesis, presenting it as a promising target for obesity therapy.
Question: Write a study description for the study titled 'Lipid metabolites as potential diagnostic and prognostic biomarkers for acute community acquired pneumonia'.
Answer: Early diagnosis of acute community-acquired pneumonia (CAP) is important in patient triage and treatment decisions. To identify biomarkers that distinguish patients with CAP from non-CAP controls, we conducted an untargeted global metabolome analysis for plasma samples from142 patients with CAP (CAP cases) and 97 without CAP (non-CAP controls). Thirteen lipid metabolites could discriminate between CAP cases and non-CAP controls with area-under-the-receiver-operating-characteristic curve of > 8 (P ≤ 10-9). The levels of glycosphingolipids, sphingomyelins, lysophosphatidylcholines and L-palmitoylcarnitine were higher, while the levels of lysophosphatidylethanolamines were lower in the CAP cases than those in non-CAP controls. All 13 metabolites could distinguish CAP cases from the non-infection, extrapulmonary infection and non-CAP respiratory tract infection subgroups. The levels of trihexosylceramide (d18:1/16:0) were higher, while the levels of lysophosphatidylethanolamines were lower, in the fatal than those of non-fatal CAP cases. Our ﬁndings suggest that lipid metabolites are potential diagnostic and prognostic biomarkers for CAP.
Question: Write a study description for the study titled 'Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan'.
Answer: Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis.
Question: Write a study description for the study titled 'NMR- and LC–MS/MS-based urine metabolomic investigation of the subacute effects of hexabromocyclododecane in mice (NMR assay)'.
Answer: In the present study, both untargeted and targeted metabolomics approaches were used to evaluate the subacute effects of hexabromocyclododecane (HBCD) on mice urine metabolome. Untargeted metabolomics based on 1H NMR showed that HBCD exposure disturbed mice metabolism in both dosed groups, especially in high dosed group. The low-dose HBCD led to a decrease in alanine, malonic acid, and trimethylamine (TMA). High-dose HBCD-treated mice developed high levels of citric acid and 2-ketoglutarate, together with decreased alanine, acetate, formate, TMA, 3-hydroxybutyrate, and malonic acid. Targeted metabolomics for metabolic profiling of 20 amino acids identified alanine, lysine, and phenylalanine as significantly disturbed metabolites. These results indicated that subchronic exposure to HBCD caused a disturbance of mice metabolism, especially in TCA cycle, lipid metabolism, gut microbial metabolism, and homeostasis of amino acids, and the application of untargeted and targeted metabolomics combined with conventional toxicology approaches to evaluate the subacute effects of pollutants will provide more comprehensive information and aid in predicting health risk of these pollutants.
Question: Write a study description for the study titled 'Ornithine Decarboxylase in Gastric Epithelial Cells Promotes the Immunopathogenesis of Helicobacter pylori Infection'.
Answer: Colonization by H. pylori is associated with a wide range of gastric diseases, ranging from superficial gastritis to more severe pathologies, including intestinal metaplasia and adenocarcinoma. The interplay of the host response and the pathogen affect the outcome of disease. One major component of the mucosal response to H. pylori is the activation of a strong, but inefficient immune response that fails to control the infection and frequently causes tissue damage. We have shown that polyamines can regulate H. pylori-induced inflammation. Chemical inhibition of ornithine decarboxylase (ODC), which generates putrescine from L-ornithine, reduces gastritis in mice and adenocarcinoma incidence in gerbils infected with H. pylori. However, we have also demonstrated that Odc deletion in myeloid cells enhances M1 macrophage activation and gastritis. Here we used a genetic approach to assess the specific role of gastric epithelial ODC during H. pylori infection. Deletion of Odc in gastric epithelial cells reduces gastritis, attenuates epithelial proliferaton, alters the metabolome, and dowregulates the expression of immune mediators induced by H. pylori. Inhibition of ODC activity in gastric epithelial cells reduces H. pylori-induced NF-kB activation and CXCL8 mRNA expression. Chronic inflammation is a major risk factor for the progression to more severe pathologies associated with H. pylori infection and we now show that epithelial ODC plays an important role in mediating this inflammatory response.
Question: Write a study description for the study titled 'Prokaryotic viperins produce diverse antiviral molecules'.
Answer: Viperin is an interferon-induced cellular protein conserved in animals. It was shown to inhibit the replication of multiple viruses by producing a ribonucleotide called 3’-deoxy-3’4’-didehydro-CTP (ddhCTP), which acts as a chain terminator for the viral RNA polymerase. Here we show that the eukaryotic viperin has originated from a clade of bacterial and archaeal proteins that protect against phage infection. Prokaryotic viperins (pVips) produce a set of modified ribonucleotides that include, in addition to ddhCTP, also ddhGTP and ddhUTP. We further provide evidence that pVips protect against T7 phage infection by inhibiting viral polymerase-dependent transcription, suggesting a conserved mechanism of action shared between pVips and the animal viperin. Our results unveil a potential repository of natural antiviral compounds produced by bacterial immune systems.
Question: Write a study description for the study titled 'LipidCreator workbench to probe the lipidomic landscape - Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators, Agilent QTof'.
Answer: Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.In MTBLS1334, 55 lipid mediator standards were used to study the lipid fragmentation on the Agilent QTof 6545 MS platform (Agilent Technologies, Waldbronn, Germany), build optimal collision energy models and create an in-silico spectral library for use with LipidCreator. Lipid fragment masses of mediators were validated with the Metlin database (https://metlin.scripps.edu/).Studies linked to this manuscript include;MTBLS1333; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Thermo QExactive HFMTBLS1334; LipidCreator: Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators - Agilent QTofMTBLS1369; LipidCreator: Platelet isolation and stimulation - Targeted Phospho- and Glycerolipid ProfilingMTBLS1375; LipidCreator: Targeted lipidomics analysis of Human Plasma samples and comparison with NIST SRM 1950 standardMTBLS1376; LipidCreator: Targeted lipidomics analysis of S. cerevisiae to determine true and false identificationMTBLS1381; LipidCreator: Platelet isolation and stimulation - Targeted Lipid Mediator ProfilingMTBLS1382; LipidCreator: Platelet isolation and stimulation - DIA Lipid Mediator Validation
Question: Write a study description for the study titled 'Transcriptomic and metabolomic changes in postharvest sugarbeet roots reveal widespread metabolic changes in storage and identify genes potentially responsible for respiratory sucrose loss'.
Answer: Endogenous metabolism is primarily responsible for losses in sucrose content and processing quality in postharvest sugarbeet roots. The genes responsible for this metabolism and the transcriptional changes that regulate it, however, are largely unknown. To identify genes and metabolic pathways that participate in postharvest sugarbeet root metabolism and the transcriptional changes that contribute to their regulation, transcriptomic and metabolomic profiles were generated for sugarbeet roots at harvest and after 12, 40 and 120 d storage at 5 and 12°C and gene expression and metabolite concentration changes related to storage duration or temperature were identified. During storage, 8656 genes, or 34% of all expressed genes, and 225 metabolites, equivalent to 59% of detected metabolites, were altered in expression or concentration, indicating extensive transcriptional and metabolic changes in stored roots. These genes and metabolites contributed to a wide range of cellular and molecular functions, with carbohydrate metabolism being the function to which the greatest number of genes and metabolites classified. Because respiration has a central role in postharvest metabolism and is largely responsible for sucrose loss in sugarbeet roots, genes and metabolites involved in and correlated to respiration were identified. Seventy-five genes participating in respiration were differentially expressed during storage, including two bidirectional sugar transporter SWEET17 genes that highly correlated with respiration rate. Weighted gene co-expression network analysis identified 1896 additional genes that positively correlated with respiration rate and predicted a pyruvate kinase gene to be a central regulator or biomarker for respiration rate. Overall, these results reveal the extensive and diverse physiological and metabolic changes that occur in stored sugarbeet roots and identify genes with potential roles as regulators or biomarkers for respiratory sucrose loss.
Question: Write a study description for the study titled 'Endophytic mycobiont provides growth benefits via a Phenylpropanoid-Auxin axis in host plants'.
Answer: Beneficial association with symbiotic fungi helps improve the growth and fitness in most land plants, and shows great potential as biofertilizers in precision agriculture. Here, we demonstrated that a root fungal endophyte, Tinctoporellus species isolate AR8, enabled yield improvement in Brassicaceae leafy green Choy Sum (Brassica rapa var. parachinensis). Mechanistically, AR8 colonized the root endosphere during plant interaction and channeled the metabolic flux to phenylpropanoids and requisite secondary metabolites to promote plant growth. AR8 enabled biosynthesis of auxin improved root growth and provided an intrinsic source for long-distance signal that enhanced shoot biomass. Chemical complementation with p-coumaric acid restored the auxin signaling and enhanced growth in AR8-inoculated pal1 mutant plants, thus implicating such phenylpropanoid-auxin nexus as a pivotal regulator of symbiotic plant growth. Comparative metabolomics established hydroxycinnamic acid and p-coumaric acid as major plant growth-promoting hubs that bridge phenylpropanoid pathway and auxin signaling in the AR8 symbiosis model.
Question: Write a study description for the study titled 'Metabolomic Profile of Diet-Induced Obesity Mice in Response to Human and Small Humanin-like Peptide 2 Treatment'.
Answer: INTRODUCTION: The mitochondrial-derived peptides (MDPs) are a novel group of natural occurring peptides that have important signaling functions and biological activity. Both humanin and small-humanin-like peptide 2 (SHLP2) have been reported to act as insulin sensitizers and modulate metabolism.OBJECTIVES: By using a metabolomic approach, this study explores how the plasma metabolite profile is regulated in response to humanin and SHLP2 treatment in a diet-induced obesity (DIO) mouse model. The results also shed light on the potential mechanism underlying MDPs insulin sensitization effects.METHODS Plasma samples were obtained from DIO mice subjected to vehicle (water) treatment, or peptide treatment with either humanin analog S14G (HNG) or SHLP2 (n = 6 per group). Vehicle or peptides were given as intraperitoneal (IP) injections twice a day at dose of 2.5mg/kg/injection for 3 days. Metabolites in plasma samples were comprehensively identified and quantified using UPLC-MS/MS.RESULTS: HNG and SHLP2 administration significantly altered the concentrations of amino acid and lipid metabolites in plasma. Among all the metabolic pathways, the glutathione and sphingolipid metabolism responded most strongly to the peptide treatment.CONCLUSIONS: The present study indicates that humanin and SHLP2 can lower several markers associated with age-related metabolic disorders. With the previous understanding of the effects of humanin and SHLP2 on cardiovascular function, insulin sensitization, and anti-inflammation, this metabolomic discovery provides a more comprehensive molecular explanation of the mechanism of action for humanin and SHLP2 treatment.
Question: Write a study description for the study titled 'Hemocyanin-modulated niacinamide shapes the hemolymph microbiota of penaeid shrimp'.
Answer: In aquatic invertebrates, the hemolymph functions as a conduit between the host and its environment, hence, maintaining hemolymph microbial homeostasis significantly influences disease pathogenesis. This study examined the critical role of the respiratory glycoprotein hemocyanin as a host factor in modulating hemolymph microbial composition in penaeid shrimp. Shrimp depleted of hemocyanin followed by Vibrio parahaemolyticus infection had a disruption in the niacinamide salvage pathway, which consequently increased total bacteria and relative abundance of the conditional pathogens Vibrio and Shewanella in the hemolymph. Moreover, in vivo knockdown of hemocyanin followed by niacinamide supplementation restored hemolymph microbial homeostasis, mitigating the competitive advantage of Vibrio. Overall, our data present novel insights into the pivotal role of niacinamide metabolism in modulating shrimp hemolymph microbial composition through hemocyanin.
Question: Write a study description for the study titled 'Gut microbiota regulates the brain metabolism of sexually mature drones'.
Answer: Previous studies have found that gut microbiota and metabolites may be crucial in insect sexual maturation. For example, during sexual maturity, the increased dopamine in the drone's brain can affect its reproductive behavior, such as flight, mating, etc. In addition, gut microbiota can affect brain functions such as learning and memory through metabolites. However, it is currently unclear about the changes in gut microbiota during drone sexual maturation and whether they can affect brain function through their metabolites. Thus, we analyzed gut microbiota and brain metabolome in drones during sexual maturation based on multi-omics and identified markers associated with sexual maturation. In addition, we also explored the potential correlation between differentially expressed microorganisms and metabolites before and after sexual maturation. The results showed significant changes in microbes (Lactobacillus, Chaetothyriales, Mortierella, Entrophospora), and metabolite pathways (glycerophospholipids), with substantial changes. Lactobacillus and Chaetothyriales showed the most significant changes and therefore can be used as marker bacteria in the sexual maturation of drones. In addition, PS (16:0/20:1(11Z)), PE (P-18:0/20:4) and LysoPC (P-18:0/0:0) showed significant differences in the variation of substances, which can be used as markers related to memory in sexually mature drones. This suggests that the intestinal flora of sexually mature drones undergoes substantial changes and has a stronger glycerophospholipid metabolism. Furthermore, microbial-metabolite correlation analysis revealed that Lactobacillus, Aspergillus, Mortierella and Pleosporales were strongly correlated with PC and PE in the glycerophospholipid metabolic pathway. Therefore, we hypothesize that these four species may affect the brain function of drones by influencing glycerophospholipid metabolism, thereby affecting their learning and memory behavior. These findings provide new insights into the interactions between sexual maturation, gut microbes and brain metabolism in drones.
Question: Write a study description for the study titled 'High complexity and diel dynamics of planktonic microbiome revealed by multi-omics in Taihu, China'.
Answer: Cyanobacterial blooms result from continued short-term succession of planktonic microbiomes, but these short-term variations are little known. Here we address this question with a field diel study in Lake Tai. By integrating untargeted metabolomics—verified by targeted metabolomics—and metagenomics, we reveal the diel cycle of planktonic microbiome in Lake Tai are highly dynamic and complex. First, metabolite abundance and their molecular mass display clear diel changes along with shift in the taxon abundance and biological functions, following the same environmental factors. Some taxa and biological functions (reactions) are highly correlated with the metabolite abundance, and large compounds appear to be more taxon specific. Second, phytoplanktonic and overall planktonic microbiome showed different temporal variation of abundance, opposite levels of abundance and different molecular sizes, and different inter- and intra-specific diversity dynamics. Last, planktonic microbiomes are highly dynamic and complex in inter- and intraspecific diversity in merely one diel cycle, which point to different temperature preference between species, Microcystis aeruginosa and Anabaena sp. This difference was experimentally confirmed in laboratory. Using a multi-omics approach, our study underscores the importance of diel interaction triad between population abundance, biological functions, and environmental factors in leading to microbiome structural change and blooms.
Question: Write a study description for the study titled 'Salivary MUC5B Modulation of Glucose Metabolism in Early Oral Biofilms'.
Answer: To investigate how early mono- and dual species biofilms of oral Actinomyces naeslundii and Streptococcus gordonii clinical isolates metabolized glucose in the presence of the complex salivary mucin MUC5B, this study employed NMR-based metabolomics with interpretation of network integration. Untargeted NMR data analysis for metabolite detection and annotation and in silico studies of biochemical relationships between metabolites and cellular processes was performed to study functional differences in the early biofilm metabolomes. Significant differences in metabolite abundance elicited by the presence of MUC5B were detected. The main metabolites that distinguished the biofilms grown with 25% MUC5B with 20 mM glucose (MUC5B+G) from those grown with physiologic buffer with 20 mM glucose (PBS+G) were the unannotated metabolites 68 and 73. In the conditions were they were each present, pyruvate, ethanol and metabolite 134 were significantly more abundant in the presence of MUC5B, while metabolites 84, 97 and sarcosine were significantly less abundant. The pathway enrichment analysis of the metabolites that were differently expressed in early A. naeslundii, S. gordonii and dual species biofilms grown with PBS+G or MUC5B+G showed that pyruvate metabolism was significantly over-represented. Studying the metabolic interactions between commensal members of oral biofilms and modulatory effects of host factors such as glycoproteins in saliva during metabolism of substrates that are potential drivers of dysbiosis, such as glucose, is essential to understand the roles of oral microbial ecosystems in oral health and disease.