LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'A multi-omics approach to study peroxisome proliferator-activated receptor mediated regulation of lipid metabolism in Atlantic cod (Gadus morhua)'.
Answer: Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, a group of nuclear receptor transcription factors named peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. We have recently cloned the four Ppars in Atlantic cod (Gadus morhua), including Ppara1 and Ppara2, Pparb/d, and Pparg, and studied their tissue specific transcription and ligand activation characteristics. However, the downstream regulative role of Ppars in cod lipid metabolism is not well understood or described. In this study, activation of Atlantic cod Ppar by the fibrate drug WY-14,643 (pirinixic acid) and the performance enhancing drug GW501516 (Cardarine) were first studied using ligand-binding luciferase reporter assays in vitro. Based on the agonist activities found in vitro, juvenile Atlantic cod was injected twice over four days with WY-14,643 and GW501516 in vivo, and sampled seven days after the last injection. Using multiple omics methods, including RNA sequencing, quantitative proteomics, and lipidomics, liver and plasma samples from male cod were analyzed. The resulting multi-omics dataset provides novel insights into the systemic regulation of lipid metabolism in Atlantic cod.
Question: Write a study description for the study titled 'Plasma non-targeted metabolome of high- and low-body-weight broilers'.
Answer: In large-scale poultry farming, broilers of the same breed share a common genetic background and identical management conditions, yet substantial individual variation in body weight persists. In this study, we identified distinct plasma proteomic profiles between high and low weight broilers, with low weight broilers exhibiting a heightened systemic inflammatory response. The gut microbiome differences between groups were minimal, and fecal microbiota transplantation from high or low weight broilers did not significantly affect body weight. However, lung microbiome analysis revealed that high weight broilers had a significantly higher abundance of Lactobacillus, associated with altered plasma tryptophan metabolism. Aerosolized Lactobacillus rhamnosus, Lactobacillus reuteri, and their combination were administered to modulate the lung microbiota. This intervention significantly enhanced production performance and alleviated LPS-induced systemic inflammation. Aerosolization of Lactobacillus strains elevated metabolites such as L-tryptophan (Trp), indoleacrylic acid (IAA), and indole-3-carboxaldehyde (I3C) in plasma and lung tissues. Mechanistic explorations elucidate that IAA and I3C activated the aryl hydrocarbon receptor (AHR) pathway, promoting nuclear translocation and upregulating SOCS3 expression in macrophages. This inhibited the JAK2/STAT3 signaling pathway, mitigating LPS-induced inflammation. Our findings provide insights into the interaction between poultry production and lung microbiota, establishing Lactobacillus aerosolization as a promising strategy to combat systemic inflammation and improve poultry health and performance.
Question: Write a study description for the study titled 'Skeletal muscle metabolomics and blood biochemistry analysis reveal metabolic changes associated with dietary amino acid supplementation in dairy calves'.
Answer: The effects of different amino acid (AA) supplementations of milk protein-based milk replacers in pre-ruminant calves from 3 days to 7 weeks of age were studied. Animals were divided into 4 groups: Ctrl) Control group fed with milk protein-based milk replacer without supplementation; GP) supplementation with 0.1% glycine and 0.3% proline; FY) supplementation with 0.2% phenylalanine and 0.2% tyrosine; MKT) supplementation with 0.62% lysine, 0.22% methionine and 0.61% threonine. For statistical analysis, t-test was used to compare AA-supplemented animals to the Ctrl group. At week 7, body weight and average daily gain (ADG) were measured and blood samples and skeletal muscle biopsies were taken. Blood biochemistry analytes related to energy metabolism were determined and it was shown that MKT group had higher serum creatinine and higher plasma concentration of three supplemented AAs as well as arginine compared with the Ctrl group. GP group had similar glycine/proline plasma concentration compared with the other groups while in FY group only plasma phenylalanine concentration was higher compared with Control. Although the AA supplementations in the GP and FY groups did not affect average daily gain and metabolic health profile from serum, the metabolome analysis from skeletal muscle biopsy revealed several differences between the GP-FY groups and the Ctrl-MKT groups, suggesting a metabolic adaptation especially in GP and FY groups.
Question: Write a study description for the study titled 'Enhanced fatty acid synthesis by Sigma28 in stringent responses contributes to multidrug resistance and biofilm formation in Helicobacter pylori'.
Answer: The metabolism of bacteria is closely associated with antibiotic resistance, yet the role of metabolism in the resistance of Helicobacter pylori remains unclear. In this study, we conducted integrated analysis using transcriptomics and non-targeted metabolomics to investigate the metabolic changes of antibiotic-treated H. pylori. The results revealed an upregulation in the expression of genes related to fatty acid biosynthesis. Inhibiting fatty acid biosynthesis significantly enhanced the sensitivity of H. pylori strains sensitive to antibiotics, artificially selected multidrug-resistant strains, and clinically multidrug-resistant strains, leading to the inability to form intact biofilms. Furthermore, we explored the reasons for the enhanced fatty acid synthesis in H. pylori under antibiotic pressure and found that antibiotic treatment induced a stringent response in H. pylori, activating the regulation of the downstream operon containing hp0560 by σ28, thereby enhancing the fatty acid synthesis pathway and consequently increasing H. pylori's tolerance to various antibiotics. In this study, we identified a novel mechanism by which H. pylori adapts to antibiotic pressure.
Question: Write a study description for the study titled 'Acupuncture Synergized With Bortezomib Improves Survival of Multiple Myeloma Mice via Decreasing Metabolic Ornithine'.
Answer: Multiple myeloma (MM) is a hematological malignancy worldwide in urgent need for novel therapeutic strategies. Since Velcade (bortezomib) was approved for the treatment of relapsed/refractory MM in 2003, we have seen considerable improvement in extending MM patient survival. However, most patients are fraught with high recurrence rate and incurability. Acupuncture is known for alleviating patient symptoms and improving the quality of life, but it is not well investigated in MM, especially in combination with bortezomib. In this study, we employed LC-MS and UHPLC-MS together with bioinformatics methods to test blood samples from 5TMM3VT MM murine model mice with four different treatments (control (C) group, bortezomib (V) treatment group, acupuncture (A) group and combined (VA) group). MM mice in group VA had longer survival time than mice in group A or group V. Joint pathway analysis indicated the underlying arginine and proline metabolism pathway among the 32 significantly decreased metabolites in group VA. CCK-8 assay and in vivo experiments validated that ornithine, the metabolite of arginine, promoted MM cell proliferation. In addition, gene expression omnibus (GEO) database analysis suggested that MM patients with higher ornithine decarboxylase 1 (ODC1) expression were evidently associated with poor overall survival. In summary, this study demonstrates the synergistic effects of acupuncture and bortezomib on extending the survival of MM model mice and provides potential therapeutic targets in the treatment of MM.
Question: Write a study description for the study titled 'Metabolomic evidence for biogeographic segregation in Espeletiinae (Asteraceae): A new perspective on an Andean adaptive radiation in sky islands (Intraspecific chemical variability assay)'.
Answer: The biogeography of tropical Andean plants and the effects of altitudinal barriers as evolutionary constraints have been the focus of great debate. Although genetic markers have provided evidence for the geographic isolation of Andean-endemic groups, even highly variable molecular markers commonly used to assess biogeography do not have the resolving power needed for a fine geographic discrimination in some Andean taxa. We present a metabolomics approach based on ultrahigh-performance liquid chromatography-mass spectrometry combined with multivariate statistical methods and machine learning algorithms of multiple species and populations of Espeletiinae (Asteraceae) to provide metabolomic evidence for biogeographic segregation in this Andean-endemic subtribe. Our approach allows the discrimination of Espeletiinae taxa at different geographic scales with characteristic metabolic fingerprints related to their country of origin on a global scale, to their páramo massifs on a regional scale and to their páramo complexes on a local scale, revealing inter- and intraspecific metabolic variations. Our results, together with previous studies, suggest that Andean geography and Pleistocene glacial cycles not only shaped the evolutionary history of Espeletiinae but also its metabolic fingerprints, demonstrating the potential of metabolomics for understanding biogeographic patterns in recently diversified plant groups where genetic divergence is still at an early stage.Intraspecific chemical variability assay protocols and data are reported in the current study MTBLS943.Interspecific chemical variability assay protocols and data are reported in study MTBLS944.
Question: Write a study description for the study titled 'Persistent Alterations in Plasma Lipid Profiles Before Introduction of Gluten in the Diet Associated With Progression to Celiac Disease'.
Answer: OBJECTIVES: Celiac disease (CD) is a chronic enteropathy characterized by an autoimmune reaction in the small intestine of genetically susceptible individuals. The underlying causes of autoimmune reaction and its effect on host metabolism remain largely unknown. Herein, we apply lipidomics to elucidate the early events preceding clinical CD in a cohort of Finnish children, followed up in the Type 1 Diabetes Prediction and Prevention study.METHODS: Mass spectrometry-based lipidomics profiling was applied to a longitudinal/prospective series of 233 plasma samples obtained from CD progressors (n = 23) and healthy controls (n = 23), matched for human leukocyte antigen (HLA) risk, sex, and age. The children were followed from birth until diagnosis of clinical CD and subsequent introduction of a gluten-free diet.RESULTS: Twenty-three children progressed to CD at a mean age of 4.8 years. They showed increased amounts of triacylglycerols (TGs) of low carbon number and double bond count and a decreased level of phosphatidylcholines by age 3 months as compared to controls. These differences were exacerbated with age but were not observed at birth (cord blood). No significant differences were observed in the essential TGs.DISCUSSION: Our preliminary findings suggest that abnormal lipid metabolism associates with the development of clinical CD and occurs already before the first introduction of gluten to the diet. Moreover, our data suggest that the specific TGs found elevated in CD progressors may be due to a host response to compromised intake of essential lipids in the small intestine, requiring de novo lipogenesis.
Question: Write a study description for the study titled 'Combined transcriptome and metabolome analysis reveals the regulatory network of histidine kinase QseC in the two-component system of Glaesserella parasuis'.
Answer: Glaesserella parasuis is the causative agent of Glässer's disease in pigs, which can lead to polyserositis, arthritis, and meningitis. This study used transcriptome and metabolomics sequencing techniques to investigate the mechanism of action of qseC gene in Glaesserella parasuis. Transmission electron microscopy revealed that the ΔqseC mutant strain exhibited localized dissolution and rupture of the cell wall and membrane. The cytoplasmic wall separation was obvious, and the cytoplasm appeared sparse. These findings suggest an imbalance in membrane homeostasis。Metabolomics analysis identified 819 metabolites, among which 24 metabolites showed significant differences under positive ion mode, including upregulation of Methionine, Prostaglandin F2 α -1-glyceryl ester, and downregulation of Hypoxantine, UDP, and others. There were significant differences in 36 metabolites under negative ion mode. KEGG enrichment analysis revealed abnormalities in pathways related to amino acid synthesis, lipid metabolism, and quorum sensing. Transcriptomic analysis identified 663 differentially expressed genes, including upregulation of membrane synthesis-related genes (such as plsB and wecA) and downregulation of virulence factors (such as hrpA and pilW). This study systematically analyzed the regulatory networks of differentially expressed genes and metabolites by integrating transcriptome and metabolome data. Key genes such as plsB and wecA form a strong association network with metabolites such as methionine and prostaglandin F2α-1-glyceride. KEGG pathway co-enrichment analysis showed that amino acid synthesis (such as cysteine/methionine metabolism) and purine metabolism pathways were co regulated in positive ion mode, while peptidoglycan synthesis and glycerophospholipid metabolism were significantly enriched in negative ion mode. This study constructed a cross-omics regulatory map of “gene-metabolism” mediated by QseC, revealing the global regulatory role of QseC in Glaesserella parasuis, providing a theoretical basis for the development of new prevention and control strategies against Glaesserella parasuis infection.
Question: Write a study description for the study titled 'Metabolomics of the human aqueous humor'.
Answer: Introduction: The optical elements of the eye – cornea, lens, and vitreous humor – are avascular tissues, and their nutrition and waste removal are provided by aqueous humor (AH). The AH production occurs through the active secretion and the passive diffusion/ultrafiltration of blood plasma. The comparison of the metabolomic profiles of aqueous humor (AH) and plasma is important for understanding of the mechanisms of biochemical processes and metabolite transport taking place in vivo in ocular tissues. Objectives: The work is aimed at the determination of concentrations of a wide range of most abundant metabolites in the human AH, the comparison of the metabolomic profiles of AH and serum, and the analysis of the post-mortem metabolomic changes in these two biological fluids. Methods: The quantitative metabolomic profiling was carried out with the use of two independent methods – high-frequency 1H NMR spectroscopy and HPLC with high-resolution ESI-MS detection (LC-MS). Results: The concentrations of 71 most abundant metabolites in blood serum and AH from living patients and human cadavers have been measured. It has been found that the level of ascorbate in AH is by two orders of magnitude higher than that in serum; the levels of other metabolites are either similar to that in serum, or differ from that by a factor of 2-5. The post-mortem metabolomic composition of both serum and AH undergoes rapid and strong changes. Conclusion: The differences between the metabolomic profiles of AH and serum for majority of metabolites can be attributed to the metabolic activity of the ocular tissues leading to the lack or excess of some metabolites, while the high concentration of ascorbate in AH demonstrates the activity of ascorbate-specific pumps at the blood-aqueous border. The post-mortem metabolomic changes are caused by the disruption of the major biochemical cycles and cell lysis. These changes should be taken into account in the analysis of disease-induced changes in post-mortem samples of the ocular tissues.
Question: Write a study description for the study titled 'Resource Partitioning of Diatom Metabolites that Support Bacterial Heterotrophy in the Ocean (NMR assay)'.
Answer: The communities of marine bacteria that assemble around living microphytoplankton are predictably dominated by three taxonomic groups, each of which specializes in the use or transport of different components of the available metabolite pool: Rhodobacterales transport small and polar metabolites, Flavobacteriia use carbohydrate-rich polymers, and Gammaproteobacteria use compounds from both classes. The consistent ecological pattern involving these three taxa is widespread throughout the surface ocean, yet whether it reflects the outcome competition or niche partitioning of the phytoplankton-derived compounds is not clear. Addressing this question requires better knowledge than currently exists of the metabolites that link microbial autotrophs and heterotrophs in the surface ocean. Here we used two untargeted biological screening strategies that leverage bacterial proficiency for scavenging dilute substrates from chemically complex mixtures to characterize metabolite uptake by heterotrophic bacteria. In the first, expression patterns of transporters and diagnostic catabolic genes were analyzed in model marine bacteria grown individually in co-culture with the diatom Thalassiosira pseudonana. In the second, the ability of bacteria to draw down exometabolites from the culture medium was detected by novel approaches in mass spectrometry (MS) and nuclear magnetic resonance (NMR) analysis. These methods identified diverse chemical currencies mediating carbon transfer including low molecular weight metabolites (nucleosides, amino acids, organic acids, monomeric sugars, peptides, and sulfonates) and components of polysaccharides (chrysolaminarin, chitin oligomers, and alginate-like oligosaccharides). Bacterial utilization of bioreactive metabolites in the absence of competition indicated low resource overlap among strains and a dominance of resource partitioning over resource competition among the bacterial groups that process a major fraction of marine net primary production.NMR assay is reported in the current study MTBLS1544UPLC-MS assay is reported in MTBLS1751
Question: Write a study description for the study titled 'Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor‐like kinase'.
Answer: Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defense pathway, consistent with the view that pathogenic defense response is downregulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.
Question: Write a study description for the study titled 'Evidence of altered fatty acid metabolism in dogs with naturally occurring valvular heart disease and congestive heart failure'.
Answer: INTRODUCTION: Myxomatous mitral valve disease (MMVD) is the most common cardiac condition in adult dogs. The disease progresses over several years and affected dogs may develop congestive heart failure (HF). Research has shown that myocardial metabolism is altered in cardiac disease, leading to a reduction in b-oxidation of fatty acids and an increased dependence upon glycolysis.OBJECTIVES: This study aimed to evaluate whether a shift in substrate use occurs in canine patients with MMVD; a naturally occurring model of human disease.METHODS: Client-owned dogs were longitudinally evaluated at a research clinic in London, UK and paired serum samples were selected from visits when patients were in ACVIM stage B1: asymptomatic disease without cardiomegaly and stage C: HF. Samples were processed using ultra-performance liquid chromatography mass spectrometry and lipid profiles were compared using mixed effects models with false discovery rate adjustment. The effect of disease stage was evaluated with patient breed entered as a confounder. Features that significantly differed were screened for selection for annotation efforts using reference databases.RESULTS: Dogs in HF had altered concentrations of lipid species belonging to several classes previously associated with cardiovascular disease. Concentrations of certain acylcarnitines, phospholipids and sphingomyelins were increased after individuals had developed HF, whilst some ceramides and lysophosphatidylcholines decreased.CONCLUSION: The canine metabolome appears to change as MMVD progresses. Findings from this study suggest that in HF myocardial metabolism may be characterised by reduced beta-oxidation. This proposed explanation warrants further research.
Question: Write a study description for the study titled 'Parallel single-cell metabolic analysis and extracellular vesicle profiling reveal vulnerabilities with prognostic significance in acute myeloid leukemia (Lipidomic analysis on extracellular vesicles)'.
Answer: Acute myeloid leukemia (AML) is an aggressive disease with a high relapse rate. In this study, we map the metabolic profile of CD34+(CD38low/-) AML cells and the extracellular vesicle signatures in circulation from AML patients at diagnosis. CD34+ AML cells display high antioxidant glutathione levels and enhanced mitochondrial functionality, both associated with poor clinical outcomes. Although CD34+ AML cells are highly dependent on glucose oxidation and glycolysis for energy, those from intermediate- and adverse-risk patients reveal increased mitochondrial dependence. Extracellular vesicles from AML are mainly enriched in stem cell markers and express antioxidant GPX3, with their profiles showing potential prognostic value. Extracellular vesicles enhance mitochondrial functionality and dependence on CD34+ AML cells via the glutathione/GPX4 axis. Notably, only extracellular vesicles from adverse-risk patients enhance leukemia cell engraftment in vivo. Here, we show a potential noninvasive approach based on liquid ‘cell-extracellular vesicle’ biopsy toward a redefined metabolic stratification in AML.Lipidomic analysis on extracellular vesicles is reported in the current study MTBLS11523.Metabolomic analysis on extracellular vesicles is reported in MTBLS11746.