LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines'.
Answer: Background: Cell line specific, genome-scale metabolic models enable rigorous and systematic in silico investigation of cellular metabolism. Such models have recently become available for Chinese hamster ovary (CHO) too. However, a key ingredient, namely an experimentally validated biomass function that summarizes the cellular composition, was so far missing in all genome-scale metabolic models of CHO cell lines. Here, we close this gap by providing extensive experimental data on the biomass composition of 13 parental and producer CHO cell lines under various conditions.Results: We report protein, lipid, DNA, RNA and carbohydrate content, cell dry mass, and protein and lipid composition. Furthermore, we present meticulous data on exchange rates between cells and environment and provide detailed experimental protocols on how to determine all of the above. The biomass composition is converted into cell line and condition specific biomass functions for usage in cell line specific, genome-scale metabolic models of CHO. Finally, flux-balance analysis (FBA) is used to demonstrate consistency between in silico predictions and experimental analysis.Conclusions: Our study reveals a strong variability of the total protein content and cell dry mass across cell lines. Yet, the relative amino acid composition is independent of the cell lines and conditions and thus needs not be explicitly measured for each new cell line. In contrast, the lipid composition is strongly influenced by the growth media and needs to be determined for each case. These cell line specific variations in the biomass composition have a small impact on growth rate predictions with FBA, as inaccuracies in the predictions are typically dominated by inaccuracies in the exchange rate spectra. Cell specific biomass variations become only important if the experimental errors in the exchange rate spectra drop below twenty percent.Links:All data and code for data processing are available at Data Mendeley.Cell line specific metabolic models were deposited in BioModels, identifiers are listed in the study sample table.
Question: Write a study description for the study titled 'Lipidomic and Metabolomic Changes in Commercial Brewing Strains of Saccharomyces cerevisiae to QSM 2-Phenylethanol'.
Answer: Commercially relevant Saccharomyces cerevisiae strains were cultivated under nitrogen-limiting (SLAD) and nitrogen-sufficient (SHAD) conditions, some supplemented with 200 μM of the aromatic alcohol 2-phenylethanol. After incubation at 24 °C for 72 h, cells were harvested from each condition and analyzed using lipidomic and metabolomic techniques.
Question: Write a study description for the study titled 'Bacillus pacificus inhibits the vitamin absorption of jellyfish Aurelia coerulea polyp to reduce asexual reproduction (Polyps culture media)'.
Answer: Symbiotic microorganisms play an important role in the growth and development of marine invertebrates, such as the sea moon, affecting their metamorphosis process. The outbreak of jellyfish puts pressure on marine ecosystems and affects their stability. However, researches on the development of jellyfish are still fewer, the use of biological control of jellyfish disaster is still in the theoretical stage, and the inhibition mechanism of microorganisms on jellyfish remains to be revealed. We isolated a strain of Bacillus paramycoides SG15 from rhizosphere sediments of seagrass Zostera japonica, and found that this strain could inhibit the asexual reproduction of jellyfish Aurelia coerulea polyp larva. Through co-culture experiments, we used transcriptomics, metabolomics and fluorescence in situ hybridization techniques, combined with the genome and metabolome of SG15, and found that this isolate could inhibit the asexual reproduction rate of the larva polyp by inhibiting the absorption of vitamins, and the endoderm cells were the most important action site of SG15. Although there are relatively high concentrations of vitamins and their derivatives in the surrounding environment, the transport of hydra is reduced, and most vitamins cannot be synthesized in the polys as well, thus affecting the growth and reproduction of polyps. Our study, analyzed the interaction processes between Bacillus and polyps and revealed the inhibiting mechanism of the polyp asexual reproduction by B. paramycoides SG15, which laid a theoretical foundation for the subsequent analysis of interactions between jellyfish and microorganisms, bring materials for the biological control of jellyfish disasters.Polyps culture media is reported in the current study MTBLS9419.Polyps whole organism is reported in MTBLS9409.
Question: Write a study description for the study titled 'Metabolome analysis reveal key regulatory pathways of feed conversion efficiency of oriental river prawn Macrobrachium nipponense'.
Answer: A total of 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle. In addition, 11 KEGG pathways, which mainly include lysine biosynthesis, lysine degradation, aminoacyl-tRNA biosynthesis and purine metabolism, were significantly enriched in hepatopancreas. Also, 14 KEGG pathways, which mainly include pyrimidine metabolism, glutathione metabolism, nitrogen metabolism and mTOR signaling pathway, were significantly enriched in muscle. The metabonomic analysis revealed that the feed conversion efficiency of M. nipponense was affected considerably by amino acid, lipid and nucleotide metabolism. Hence, different RFI groups of M. nipponense have various metabolic capability processes. The differences in response to immunity, digestion and absorption of nutrients may be the critical elements related to the variation of RFI.
Question: Write a study description for the study titled 'Phospholipid acyl chain diversity controls the tissue-specific assembly of mitochondrial cardiolipins'.
Answer: Cardiolipin (CL) is a phospholipid specific for mitochondrial membranes and crucial for many core tasks of this organelle. Its side chain configurations are tissue-specific, functionally important and generated via post-biosynthetic remodeling. However, this process lacks the necessary specificity to explain CL diversity, which is especially evident for highly specific CL compositions in mammalian tissues. To investigate the so far elusive regulatory origin of CL homeostasis in mice we combine lipidomics, integrative transcriptomics and data-driven machine learning. We demonstrate that not transcriptional regulation, but cellular phospholipid compositions are closely linked to the tissue-specificity of CL patterns allowing artificial neural networks to precisely predict cross-tissue CL compositions in a consistent mechanistic specificity rationale. This is especially relevant for the interpretation of disease-related perturbations of CL homeostasis, by allowing to differentiate between specific aberrations in CL metabolism and changes caused by global alterations in cellular (phospho-)lipid metabolism.Links; Analysed data
Question: Write a study description for the study titled 'Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism'.
Answer: We investigated the cumulative contribution of rare, exonic genetic variants on the concentration of 1,487 metabolites and 53,714 metabolite ratios in urine by performing gene-based tests based on 226,233 variants from up to 4,864 participants of the German Chronic Kidney Disease (GCKD) study. There were 128 significant associations (53 metabolite-gene and 75 metabolite ratio-gene pairs) involving 30 unique genes, 16 of which are known to underlie recessively inherited inborn errors of metabolism (IEMs). Across the 30 genes, 47% of individuals carried at least one rare missense, stop or splice variant. The 30 genes were strongly enriched for shared high expression in liver and kidney (OR=65, p-FDR=3e-7), with hepatocytes and proximal tubule cells as driving cell types. Use of whole-exome sequencing data in the UK Biobank allowed for linking genes to diseases that could plausibly be explained by the identified metabolites. In silico constraint-based modeling of knockouts of the implicated genes in a virtual whole-body, organ-resolved metabolic human correctly predicted the observed direction of metabolite changes in urine and blood, highlighting the potential of linking population genetics to modeling to validate associations and to predict metabolic consequences of yet unknown IEMs. Our study extends the map of genes influencing urine metabolite concentrations, reveals metabolic processes and connected health outcomes, and implicates novel candidate variants and genes for IEMs.Further links;German Chronic Kidney Disease (GCKD)
Question: Write a study description for the study titled 'Delineating molecular regulatory network of meat quality of longissimus dorsi indicated by transcriptomic, proteomic, and metabolomics analysis in rabbit (SPME-GC-MS assay)'.
Answer: This study aims to investigate the potential regulatory network responsible for the meat quality using multi-omics to help developing better varieties. Slaughter performance and meat quality of Shuxing No.1 rabbit outperformed Yila rabbit. Differentially expressed genes (DEGs) and differentially abundance proteins (DAPs) were involved in meat quality-related pathways, such as PI3K-Akt and MAPK signaling pathway. Only SMTNL1 and PM20D2 shared between DEGs and DAPs. Olfactory-sensitive undecanal, a differentially abundant metabolite (DAM) in volatilomics (vDAMs), correlated with all of the remaining 11 vDAMs and most of 12 vDAMs were associated with amino acid metabolism. Integration revealed that 829 DEGs/DAPs were associated with 15 DAMs in four KEGG pathways, such as melatonin (a DAM in widely targeted metabolomics) was significantly positively correlated with ALDH and negatively correlated with RAB3D and CAT in tryptophan metabolism pathway. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor.SPME-GC-MS assay is reported in the current study MTBLS8958.UPLC-MS/MS assays are reported in MTBLS8957.
Question: Write a study description for the study titled 'Evidence of a DHA signature in the lipidome and metabolome of human hepatocytes'.
Answer: Cell supplementation with bioactive molecules often causes a perturbation in the whole intracellular environment. Omics techniques can be applied for the assessment of this perturbation. In this study, the overall effect of docosahexaenoic acid (DHA) supplementation on cultured human hepatocyte lipidome and metabolome has been investigated using NMR in combination with traditional techniques. The effect of two additional bioactives sharing with DHA the lipid lowering effect - propionic acid (PRO) and protocatechuic acid (PCA) - has been also evaluated, also considering possible synergism. NMR analysis of the cell lipid extracts showed that DHA supplementation, alone or in combination with PCA or PRO, strongly altered the cell lipid profile. The perfect discrimination between cells receiving DHA (alone or in combination) and the other cells reinforced the idea of a global rearrangement of the lipid environment induced by DHA. Notably, GC and fluorimetric analyses totally confirmed the strong discrimination obtained by NMR. The DHA signature was evidenced not only in the cell lipidome, but also in the metabolome. Results herein reported indicate that NMR, combined with other techniques, represents a fundamental approach while studying the effect of the supplementation of bioactives, particularly in the case of molecules having a broad spectrum of mechanisms of action.
Question: Write a study description for the study titled 'RP-based analysis of human faecal samples using the ZenoTOF 7600'.
Answer: This study contains replicated measurements of a reference human fecal sample from BioIVT. It serves as test and training data for metabolite annotation.
Question: Write a study description for the study titled 'SNAP25 inhibits glioma progression by regulating synapse plasticity via GLS-mediated glutaminolysis'.
Answer: INTRODUCTION: Neuronal activity regulated by synaptic communication exerts an important role in tumorigenesis and progression in brain tumors. Genes for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) annotated with the function ‘vesicle’ about synaptic connectivity were identified and one of these proteins, synaptosomal-associated protein 25 (SNAP25), was found to have discrepant expression levels in neuropathies. However, the specific mechanism and prognostic value of SNAP25 during glioma progression remain unclear. METHODS: Using RNA sequencing data from The Cancer Genome Atlas (TCGA) database, the differential synaptosis-related genes between LGG and GBM were identified as highly correlated. Cox proportional hazards regression analysis and survival analysis indicated that the candidate gene SNAP25 could differentiate the outcome of low- and high-risk patients, and the Chinese Glioma Genome Atlas (CGGA) cohort was used for validation of the data set. RT-qPCR, western blot, and immunohistochemistry assays were performed to examine the expression level of SNAP25 in glioma cells and samples. Functional assays were performed to identify the effects of SNAP25 knockdown and overexpression on cell viability, migration, and invasion. Then, an immunofluorescence assay of the xenograft tissue was applied to evaluate the expression of the neuronal dendron formation marker-MAP2. Liquid chromatography-high re solution mass spectrometry (LC-MS)-based metabolomics approach was presented for identifying crucial metabolic disturbances in glioma cells. In situ mouse xenograft model was used to investigate the role of SNAP25 in vivo.RESULTS: SNAP25 was down expressed in glioma tissues and cell lines and low-level SNAP25 indicated an unfavorable prognosis of glioma patients. SNAP25 inhibited cell proliferation, migration, invasion and fostered glutamate metabolism of glioma cells, exerting a tumor suppressor role. SNAP25 overexpression expressed lower expression of MAP2, indicating poor neuronal plasticity and connectivity. SNAP25 could interact with glutaminase（GLS）and GLS knockdown could rescue the anti-tumor effect of SNAP25 in glioma cells. Moreover, upregulation of SNAP25 also decreased tumor volume and prolonged the overall survival (OS) of the xenograft mouse.CONCLUSION: SNAP25 inhibited carcinogenesis of glioma via sponging glutamate metabolism by regulating GLS expression, as well as inhibiting dendritic formation, which could be considered as a molecular target for glioma diagnosis and therapy.
Question: Write a study description for the study titled 'Characterization of Yak Common Biofluids Metabolome by Means of Proton Nuclear Magnetic Resonance Spectroscopy'.
Answer: The aim of this study was to evaluate the metabolic profiles of yak (Bos grunniens) serum, feces, and urine by using proton nuclear magnetic resonance (1H-NMR), to serve as a reference guide for the healthy yak milieu. A total of 108 metabolites, giving information about diet, protein digestion, and energy generation or gut-microbial co-metabolism, were assigned across the three biological matrices. A core metabolome of 15 metabolites was ubiquitous across all biofluids. Lactate, acetate, and creatinine could be regarded as the most abundant metabolites in the metabolome of serum, feces, and urine, respectively. Metabolic pathway analysis showed that the molecules identified could be able to give thorough information about four main metabolic pathways, namely valine, leucine, and isoleucine biosynthesis; phenylalanine, tyrosine, and tryptophan biosynthesis; glutamine and glutamate metabolism; and taurine and hypotaurine metabolism.
Question: Write a study description for the study titled 'Isotope tracing-based metabolite identification for mass spectrometry metabolomics'.
Answer: Modern mass spectrometry-based metabolomics is a key technology for biomedicine, enabling discovery and quantification of a wide array of biomolecules critical for human physiology. Yet, only a fraction of human metabolites have been structurally determined, and the majority of features in typical metabolomics data remain unknown. To date, metabolite identification relies largely on comparing MS2 fragmentation patterns against known standards, related compounds or predicted spectra. Here, we propose an orthogonal approach to identification of endogenous metabolites, based on mass isotopomer distributions (MIDs) measured in an isotope-labeled reference material. We introduce a computational measure of pairwise distance between metabolite MIDs that allows identifying metabolites by their similarity to previously known peaks. Using human epithelial cells labeled with 20 individual 13C tracers, this method identified 273 out of 620 peaks representing likely metabolites (62%). Importantly, MID-based identification is highly complementary to MS2-based methods in that MIDs reflect the biochemical origin of metabolites, and therefore also yields insight into their synthesis pathways, while MS2 spectra mainly reflect structural features. Accordingly, our method performed best for small molecules, while MS2-based identification was stronger on lipids and complex natural products. We also report the discovery of trimethylglycyl-lysine, a novel amino acid derivative that is altered in human muscle tissue after exercise and dietary restriction. MID-based annotation using isotope-labeled reference materials enables identification of novel endogenous metabolites, extending the reach of mass spectrometry-based metabolomics.
Question: Write a study description for the study titled 'Wheat growth, applied water use efficiency and flag leaf metabolome under continuous and pulsed deficit irrigation'.
Answer: The intensity and frequency of precipitation events are predicted to change over the coming decades. For many areas, longer periods without rainfall are expected. We investigated the importance of irrigation frequency under water deficit conditions for growth, physiology and chemistry of wheat (Triticum aestivum). Drought-stressed plants received 40% of the water provided for control plants and were either watered every other day (continuous drought, cd) or every eight days (pulsed drought, pd). Maximum quantum yield of photosystem II (Fv/Fm), aboveground biomass, applied water use efficiency (WUEapl) and the flag leaf metabolome were assessed twice during development. Fv/Fm was not affected by irrigation. Drought-exposed plants produced less biomass, but had higher WUEapl than control plants. More metabolic features responded to the pd compared to the cd treatment and more features were increased than decreased in pool size in flag leaves. Salicylic acid glucoside was generally decreased under drought. In pd plants, two benzoxazinoid glucosides were enhanced at the first time point and concentrations of several flavonoid glycosides were modulated. This study extends our knowledge about drought effects on wheat; it highlights that the frequency of watering determines how plant growth, physiology and metabolism are affected by drought.
Question: Write a study description for the study titled 'Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing (Seed assays)'.
Answer: BACKGROUND: Amaranth (Amaranthus spp.) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabolomic and genome sequence data for many cultivars. To support the improvement of this versatile, sustainable crop, a detailed metabolome profiling of the edible grains and leaves and genome sequencing resources is required for the widely cultivated grain amaranth cultivars such as Coral Fountain (CF), Emerald Tassels (ET), Golden Giant (GG), Hopi Red Dye (HR), and New Mexico (NM).RESULTS: Through a non-targeted high-throughput metabolic profiling using ultra-performance liquid chromatography-tandem mass spectrometry, we precisely determined the whole-grain and leaf metabolites of these five cultivars. This analysis identified 426 and 420 metabolites with known chemical structures in the grain and leaf, respectively. The five amaranth cultivars differed significantly in the levels of several nutritionally valuable compounds in grains and leaves, including sulfur amino acids, vitamins, and chlorogenic acids, as well as potentially anti-nutritive compounds, such as oxalate and raffinose family oligosaccharides. On average, the cultivars CF and ET had more favorable levels of most identified health-promoting compounds compared to GG, HR, and NM. In addition, we provide high-quality reference genome sequences for the five cultivars using the PacBio Sequel II sequencing platform with an estimated genome size of 465-483 Mb comprising 46.9-48.7% repetitive elements. We generated an iso-seq library from different amaranth plant parts and utilized it to predict the amaranth genes and annotate their function into their respective gene ontology terms.CONCLUSIONS: These resources will assist in breeding improved amaranth varieties and identifying targeted genes for trait modification and advancement through genome editing and engineering technologies.Seed assays are reported in the current study MTBLS815.Leaf assays are reported in MTBLS3498.
Question: Write a study description for the study titled 'Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons'.
Answer: Tet3 is the main α-ketoglutarate (αKG)-dependent dioxygenase in neurons that converts 5-methyl-dC into 5-hydroxymethyl-dC and further on to 5-formyl- and 5-carboxy-dC. Neurons possess high levels of 5-hydroxymethyl-dC that further increase during neural activity to establish transcriptional plasticity required for learning and memory functions. How αKG, which is mainly generated in mitochondria as an intermediate of the tricarboxylic acid cycle, is made available in the nucleus has remained an unresolved question in the connection between metabolism and epigenetics. We show that in neurons the mitochondrial enzyme glutamate dehydrogenase, which converts glutamate into αKG in an NAD+-dependent manner, is redirected to the nucleus by the αKG-consumer protein Tet3, suggesting on-site production of αKG. Further, glutamate dehydrogenase has a stimulatory effect on Tet3 demethylation activity in neurons, and neuronal activation increases the levels of αKG. Overall, the glutamate dehydrogenase-Tet3 interaction might have a role in epigenetic changes during neural plasticity.