LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Lipin1 deficiency causes sarcoplasmic reticulum stress and chaperone-responsive myopathy'.
Answer: As a consequence of impaired glucose or fatty acid metabolism, bioenergetic stress in skeletal muscles may trigger myopathy and rhabdomyolysis. Genetic mutations causing loss of function of the LPIN1 gene frequently lead to severe rhabdomyolysis bouts in children, though the metabolic alterations and possible therapeutic interventions remain elusive. Here, we show that lipin1 deficiency in mouse skeletal muscles is sufficient to trigger myopathy. Strikingly, muscle fibers display strong accumulation of both neutral and phospholipids. The metabolic lipid imbalance can be traced to an altered fatty acid synthesis and fatty acid oxidation, accompanied by a defect in acyl chain elongation and desaturation. As an underlying cause, we reveal a severe sarcoplasmic reticulum (SR) stress, leading to the activation of the lipogenic SREBP1c/SREBP2 factors, the accumulation of the Fgf21 cytokine, and alterations of SR-mitochondria morphology. Importantly, pharmacological treatments with the chaperone TUDCA and the fatty acid oxidation activator bezafibrate improve muscle histology and strength of lipin1 mutants. Our data reveal that SR stress and alterations in SR-mitochondria contacts are contributing factors and potential intervention targets of the myopathy associated with lipin1 deficiency.
Question: Write a study description for the study titled 'Absolute quantitative lipidomics reveals lipidome-wide alterations in aging brain (Mouse brain POS UPLC-MS assay)'.
Answer: INTRODUCTION: The absolute quantitation of lipids at the lipidome-wide scale is a challenge but plays an important role in the comprehensive study of lipid metabolism. OBJECTIVES: We aim to develop a high-throughput quantitative lipidomics approach to enable the simultaneous identification and absolute quantification of hundreds of lipids in a single experiment. Then, we will systematically characterize lipidome-wide changes in the aging mouse brain and provide a link between aging and disordered lipid homeostasis. METHODS: We created an in-house lipid spectral library, containing 76,361 lipids and 181,300 MS/MS spectra in total, to support accurate lipid identification. Then, we developed a response factor-based approach for the large-scale absolute quantifications of lipids. RESULTS: Using the lipidomics approach, we absolutely quantified 1212 and 864 lipids in human cells and mouse brains, respectively. The quantification accuracy was validated using the traditional approach with a median relative error of 12.6%. We further characterized the lipidome-wide changes in aging mouse brains, and dramatic changes were observed in both glycerophospholipids and sphingolipids. Sphingolipids with longer acyl chains tend to accumulate in aging brains. Membrane-esterified fatty acids demonstrated diverse changes with aging, while most polyunsaturated fatty acids consistently decreased. CONCLUSION: We developed a high-throughput quantitative lipidomics approach and systematically characterized the lipidome-wide changes in aging mouse brains. The results proved a link between aging and disordered lipid homeostasis. Mouse brain POS UPLC-MS assay data is reported in the current study MTBLS562. Mouse brain NEG UPLC-MS assay data associated to this study is reported in MTBLS495.
Question: Write a study description for the study titled 'Elevated CO2 and virus infection impacts wheat and aphid metabolism'.
Answer: INTRODUCTION: The aphid Rhopalosiphum padi L. is a vector of Barley yellow dwarf virus (BYDV) in wheat and other economically important cereal crops. Increased atmospheric CO2 has been shown to alter plant growth and metabolism, enhancing BYDV disease in wheat. However, the biochemical influences on aphid metabolism are not known.OBJECTIVES: This work aims to determine whether altered host-plant quality, influenced by virus infection and elevated CO2, impacts aphid weight and metabolism.METHODS: Untargeted 1H NMR metabolomics coupled with multivariate statistics were employed to profile the metabolism of R. padi reared on virus-infected and non-infected (sham-inoculated) wheat grown under ambient CO2 (aCO2, 400 µmol mol−1) and future, predicted elevated CO2 (eCO2, 650 µmol mol−1) concentrations. Un-colonised wheat was also profiled to observe changes to host-plant quality (i.e., amino acids and sugars).RESULTS: The direct impacts of virus or eCO2 were compared. Virus presence increased aphid weight under aCO2 but decreased weight under eCO2; whilst eCO2 increased non-viruliferous (sham) aphid weight but decreased viruliferous aphid weight. Discriminatory metabolites due to eCO2 were succinate and sucrose (in sham wheat), glucose, choline and betaine (in infected wheat), and threonine, lactate, alanine, GABA, glutamine, glutamate and asparagine (in aphids), irrespective of virus presence. Discriminatory metabolites due to virus presence were alanine, GABA, succinate and betaine (in wheat) and threonine and lactate (in aphids), irrespective of CO2 treatment.CONCLUSION: This study confirms that virus and eCO2 alter host-plant quality, and these differences are reflected by aphid weight and metabolism.
Question: Write a study description for the study titled 'Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease'.
Answer: Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune programming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxidative activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (βindirect = -2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.
Question: Write a study description for the study titled 'Ion mobility-based sterolomics reveals spatially and temporally distinctive sterol lipids in the mouse brain'.
Answer: Aberrant sterol lipid metabolism is associated with physiological dysfunctions in the aging brain and aging-dependent disorders such as neurodegenerative diseases. There is an unmet demand to comprehensively profile sterol lipids spatially and temporally in different brain regions during aging. Here, we develop an ion mobility-mass spectrometry based four-dimensional sterolomics technology leveraged by a machine learning-empowered high-coverage library (>2000 sterol lipids) for accurate identification. We apply this four-dimensional technology to profile the spatially resolved landscapes of sterol lipids in ten functional regions of the mouse brain, and quantitatively uncover ~200 sterol lipids uniquely distributed in specific regions with concentrations spanning up to 8 orders of magnitude. Further spatial analysis pinpoints age-associated differences in region-specific sterol lipid metabolism, revealing changes in the numbers of altered sterol lipids, concentration variations, and age-dependent coregulation networks. These findings will contribute to our understanding of abnormal sterol lipid metabolism and its role in brain diseases.
Question: Write a study description for the study titled 'Lipidomics and RNA-Seq Study of Lipid Regulation in Aphis gossypii parasitized by Lysiphlebia japonica'.
Answer: The cotton-melon aphid, Aphis gossypii Glover, is a major insect pest worldwide. Lysiphlebia japonica (Ashmead) is an obligate parasitic wasp of A. gossypii, and has the ability to regulate lipid metabolism of the cotton-melon aphid. Lipids are known to play critical roles in energy homeostasis, membrane structure, and signaling. However, the parasitoid genes that regulate fat metabolism and lipid composition in aphids are not known. 34 glycerolipids and 248 glycerophospholipids were identified in this study. We have shown that a 3-day parasitism of aphids can induce significant changes in the content and acyl chain composition of triacylglycerols (TAGs) and subspecies composition of glycerophospholipids content and acyl chains. It also upregulate the expression of several genes involved in triacylglycerol synthesis and glycerophospholipid metabolism. Pathway analysis showed that a higher expression of genes involved in the tricarboxylic acid cycle and glycolysis pathways may contribute to TAGs synthesis in parasitized aphids. Interestingly, the higher expression of genes in the sphingomyelin pathway and reduced sphingomyelin content may be related to the reproductive ability of A. gossypii. We provide a comprehensive resource describing the molecular signature of parasitized A. gossypii particularly the changes associated with the lipid metabolism and discuss the biological and ecological significance of this change.
Question: Write a study description for the study titled 'Marine metabolomics: measurement of metabolites in seawater by gas chromatography mass spectrometry (Method quantification)'.
Answer: One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats.  Method quantification is reported in the current study MTBLS848. Method development is reported in MTBLS826. The effect of salt and water on metabolite detection is reported in MTBLS839. Cell culture sampling is reported in MTBLS843. Environmental sampling is reported in MTBLS844. Solid phase extraction is reported in MTBLS849.  Linked Studies: MTBLS826 MTBLS839 MTBLS843 MTBLS844 MTBLS849
Question: Write a study description for the study titled 'Deciphering metabolomic alterations in seminal plasma of crossbred (Bos taurus X Bos indicus) bulls through comparative deep metabolomic analysis'.
Answer: The incidence of sub-fertility is higher in crossbred bulls compared to zebu bulls. In the present study, we analysed the metabolomic profile of seminal plasma from crossbred and zebu bulls and uncovered differentially expressed metabolites between these two breeds. Using a high-throughput LC-MS/MS-based approach, we identified 990 and 1,002 metabolites in crossbred and zebu bull seminal plasma respectively. After excluding the exogenous metabolites, we found that 50 and 68 putative metabolites were unique to crossbred and zebu bull seminal plasma, respectively, whilst 87 metabolites were common to both. After data normalisation, 63 metabolites were found to be dysregulated between crossbred and zebu bull seminal plasma. Observed pathways included Linoleic acid metabolism (observed metabolite was phosphatidylcholine) in crossbred bull seminal plasma whereas inositol phosphate metabolism (observed metabolites were phosphatidylinositol-3,4,5-trisphosphate/inositol 1,3,4,5,6-pentakisphosphate/myo-inositol hexakisphosphate) was observed in zebu bull seminal plasma. Abundance of Tetradecanoyl-CoA was significantly higher, whilst abundance of Taurine was significantly lower in crossbred bull seminal plasma. In conclusion, the present study established the seminal plasma metabolomic profile in crossbred and zebu bulls and suggest that increased lipid peroxidation coupled with low concentrations of antioxidants in seminal plasma might be associated with high incidence of sub-fertility in crossbred bulls.
Question: Write a study description for the study titled '1H HR-MAS NMR based metabolomics of cancer cells responding to two different doses of the diruthenium trithiolato complex [(p-MeC6H4iPr)2Ru2(SC6H4-p-But)3]+ (DiRu-1)'.
Answer: The trithiolato bridged diruthenium complex DiRu-1 [(p-MeC6H4iPr)2Ru2(SC6H4-p-But)3]+ is highly cytotoxic against various cancer cell lines, but its exact mode of action remained unknown. The present 1H HR-MAS NMR based metabolomic study performed on the ovarian cancer cell lines A2780, its cisPt resistant variant A2780cisR and on the healthy cell line model HEK-293 treated with two doses of DiRu-1 was designed to reveal its mode of action. The resulting changes in the metabolic profile of the cell lines were studied using HR-MAS NMR of cell lysates and subsequent statistical analysis. We show that DiRu-1 in a 0.03 µM dose has significant impact on the levels of a number of metabolites, such as glutamine, glutamate, glutathione, cysteine, lipid, creatine, lactate, and acetate, especially pronounced in the A2780cisR cell line. Overall, the metabolic changes observed suggest that redox homeostasis, the Warburg effect and the lipid metabolism are affected by DiRu-1.
Question: Write a study description for the study titled 'Integrated multi-omics of feces, plasm aand urine can describe and differentiate pediatric active Crohn’s Disease from remission'.
Answer: BackgroundThis study aimed to obtain a holistic view of remission in pediatric Crohn’s Disease (CD) by integrating six omics datasets from three anatomical compartments.MethodsPatients with fecal calprotectin below 250 mg/kg were considered in remission (n = 27), and those above 250 mg/kg as having active disease (n = 31). Proteome and microbiomes (fungi and bacteria) were analyzed in feces. Metabolomes were analyzed in feces, urine, and plasma. Datasets were integrated into a multi-omics model.ResultsThe use of individual datasets shows multiple differences between remission and active disease. Integration yielded a good model (AUC of 0.8) for predicting remission. The most important features in this model are fecal bacteria (40%), fecal metabolites (22%), fecal proteins (16%), plasma metabolites (12%), fecal fungi (6%), and urine metabolites (4%). The interactome reveals Ruminococcaceae and Faecalibacterium as key players, with a correlation between antifungal urine hydroxyphenyllactic acid and fecal fungi. Pathway analysis shows an association of purine metabolism with remission, independent of thiopurine use. Changes in purine metabolism are confirmed in a pediatric CD public dataset.ConclusionThe pathways and correlations identified as playing a role in remission may remain undetectable if individual omics datasets or single anatomical compartments are used, highlighting the need for a holistic approach that integrates multiple datasets from multiple anatomical compartments.
Question: Write a study description for the study titled 'Thioridazine induce phospholipid accumulation and necroptosis in breast cancer cells'.
Answer: An antipsychotic drug, Thioridazine has been shown to inhibit a broad spectrum of cancer cells. However, its molecular mechanism is still not well understood. In the present study, we have shown that thioridazine induces cytostatic effects in both parental and tamoxifen-resistant cancer cells through cell viability, cell count, caspase activation, cell cycle analysis and enhanced p21 levels. Further, using the pharmacometabolomics approach, we identified that thioridazine induces phospholipids accumulation in breast cancer cells. We proved that thioridazine induces only phospholipids accumulation and not neutral lipids in cells by using lipid-specific fluorescent quantification and image analysis. The accumulation of phospholipid induces necroptosis, which was assessed by propidium iodide uptake assay. Thioridazine activates RIP1 and RIP3 signalling and subsequent translocation of pore-forming MLKL to the plasma membrane to initiate necroptosis induction. The MLKL-induced membrane pores were confirmed using a scanning electron microscope cell surface visualization. Further, thioridazine co-treatment enhances the efficacy of tamoxifen in resistant breast cancer cells potentiating its usefulness for combinatorial treatment
Question: Write a study description for the study titled 'Metabolic characterization of the natural progression of chronic hepatitis B (Lipid assays)'.
Answer: Background: Worldwide, over 350 million people are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing progressive liver diseases. The confinement of HBV replication to the liver, which also acts as the central hub for metabolic and nutritional regulation, emphasizes the interlinked nature of host metabolism and the disease. Still, the metabolic processes operational during the distinct clinical phases of a chronic HBV infection—immune tolerant, immune active, inactive carrier, and HBeAg-negative hepatitis phases—remains unexplored.  Methods: To investigate this, we conducted a targeted metabolomics approach on serum to determine the metabolic progression over the clinical phases of chronic HBV infection, using patient samples grouped based on their HBV DNA, alanine aminotransferase, and HBeAg serum levels.  Results: Our data illustrate the strength of metabolomics to provide insight into the metabolic dysregulation experienced during chronic HBV. The immune tolerant phase is characterized by the speculated viral hijacking of the glycerol-3-phosphate–NADH shuttle, explaining the reduced glycerophospholipid and increased plasmalogen species, indicating a strong link to HBV replication. The persisting impairment of the choline glycerophospholipids, even during the inactive carrier phase with minimal HBV activity, alludes to possible metabolic imprinting effects. The progression of chronic HBV is associated with increased concentrations of very long chain triglycerides together with citrulline and ornithine, reflective of a dysregulated urea cycle peaking in the HBV envelope antigen-negative phase.  Conclusions: The work presented here will aid in future studies to (i) validate and understand the implication of these metabolic changes using a thorough systems biology approach, (ii) monitor and predict disease severity, as well as (iii) determine the therapeutic value of the glycerol-3-phosphate–NADH shuttle.  The Oxylipin assay and the Biogenic amine and Acyl-carnitine assays for this study can be found in the MetaboLights studies MTBLS253 and MTBLS280 respectively.
Question: Write a study description for the study titled 'Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle.'.
Answer: Marine picocyanobacteria Prochlorococcus and Synechococcus, the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within Prochlorococcus. Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.
Question: Write a study description for the study titled 'A next-generation yeast chassis: comprehensive characterization of a robust fast-growing Saccharomyces cerevisiae'.
Answer: Robust and efficient hosts are necessary to facilitate advances in biotechnology. We unveil Saccharomyces cerevisiae strain XP as a promising new microbial chassis owing to its high growth rate and robustness. This strain has a doubling time of 48.2 min, which is 12.8 min faster than the model yeast S. cerevisiae S288C. Strain XP can grow well at low pH (≤ 3.0) and 30% (w/v) glucose under oligotrophic conditions. We establish a genetic manipulation toolbox using URA3 auxotroph and haploid strains, a Cre/loxP-based knocking-out method, and CRISPR/Cas9 genome editing tools. Genomic, transcriptomic and metabolomic data were analyzed in an integrated manner to characterize the strain. The multi-omics analysis reveals that changes in energy and essential nutrient metabolism are linked to rapid growth and robustness. A high-producing strain, XH352-D, was successfully constructed, which produced L-lactic acid with a titer of 52.6 g/L. Here, we comprehensively characterized a robust fast-growing yeast, laying foundation for its potential in industrial production of bulk chemicals.
Question: Write a study description for the study titled 'Impact of the used solvent on the reconstitution efficiency of evaporated biosamples for untargeted metabolomics studies'.
Answer: IntroductionUntargeted metabolomics intends to objectively analyze a wide variety of compounds. Their diverse physicochemical properties make it difficult to choose an appropriate reconstitution solvent after sample evaporation without influencing the chromatography or hamper column sorbent integrity.ObjectivesThe study aimed to identify the most appropriate reconstitution solvent for blood plasma samples in terms of feature recovery, four endogenous compounds, and one selected internal standard.MethodsWe investigated several reconstitution solvent mixtures containing acetonitrile and methanol to resolve human plasma extract and evaluated them concerning the peak areas of tryptophan-d5, glucose, creatinine, palmitic acid, and the phophatidylcholine PC(P-16:0/P-16:0), as well as the total feature count RESULTS: Results indicated that acetonitrile containing 30% methanol was best suited to match all tested criteria at least for human blood plasma samples.ConclusionDespite identifying the mixture of acetonitrile and methanol being suitable as solvent for human blood plasma extracts, we recommend to systematically test for an appropriate reconstitution solvent for each analyzed biomatrix.
Question: Write a study description for the study titled 'Metabolite Standards for the development and validation of MassCascade'.
Answer: A collection of biologically-relevant plant metabolite standards. The standards are fully semantically annotated with peak information, ChEBI identifiers, and chemical ontology. The standards were acquired on on a high-resolution LC-MS/MS Orbitrap instrument.