LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Targeting parkin-regulated metabolomic change in cartilage in the treatment of osteoarthritis'.
Answer: Articular cartilage degeneration, which may lead to osteoarthritis (OA), is a normal component of the aging process, but its underlying mechanism remains unknown. We found that chondrocytes exhibited an energy metabolism shift from glycolysis to oxidative phosphorylation (OXPHOS) during aging. Reprogrammed cartilage metabolism by parkin ablation decreased OXPHOS and increased glycolysis, with ameliorated aging-related OA. Metabolomics analysis indicated that lauroyl-L-carnitine (LLC) was decreased in aged cartilage, but increased in parkin-deficient cartilage. In vitro, LLC improved the cartilage matrix synthesis of OA chondrocytes. In vivo, intraarticular injection of LLC in mice with anterior cruciate ligament transaction (ACLT) ameliorated OA. These results suggest that metabolic changes are regulated by parkin-impaired cartilage during aging, and targeting the metabolomic changes by supplementation with LLC is a promising treatment strategy for ameliorating OA.
Question: Write a study description for the study titled 'Chronic sleep loss sensitizes Drosophila melanogaster to nitrogen stress'.
Answer: Chronic sleep loss profoundly impacts metabolic health and shortens lifespan, but studies of the mechanisms involved have focused largely on acute sleep deprivation. To identify metabolic consequences of chronically reduced sleep, we conducted unbiased metabolomics on heads of three adult Drosophila short-sleeping mutants with very different mechanisms of sleep loss: fumin (fmn), redeye (rye), and sleepless (sss). Common features included elevated ornithine and polyamines, with lipid, acyl-carnitine, and TCA cycle changes suggesting mitochondrial dysfunction. Studies of excretion demonstrate inefficient nitrogen elimination in adult sleep mutants, likely contributing to their polyamine accumulation. Increasing levels of polyamines, particularly putrescine, promote sleep in control flies but poison sleep mutants. This parallels the broadly enhanced toxicity of high dietary nitrogen load from protein in chronically sleep-restricted Drosophila, including both sleep mutants and flies with hyper-activated wake-promoting neurons. Together, our results implicate nitrogen stress as a novel mechanism linking chronic sleep loss to adverse health outcomes-and perhaps for linking food and sleep homeostasis at the cellular level in healthy organisms.
Question: Write a study description for the study titled 'Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses'.
Answer: Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.
Question: Write a study description for the study titled 'Metabolomic analysis reveals a differential adaptation process of the larval stages of Anisakis simplex to the host environment'.
Answer: Anisakis simplex are parasitic nematodes that cause anisakiasis. The possibility of infection with this parasite is through consumption of raw or undercooked fish products. A. simplex infections are often misdiagnosed, especially in subclinical cases that do not present with typical symptoms such as urticaria, angioedema and gastrointestinal allergy. The resulting allergic reactions range from rapid-onset and potentially fatal anaphylactic reactions to chronic, debilitating conditions. While there have been numerous published studies on the genomes and proteomes of A. simplex, less attention has been paid to the metabolomes. Metabolomics is concerned with the composition of metabolites in biological systems. Dynamic responses to endogenous and exogenous stimuli are particularly well suited for the study of holistic metabolic responses. In addition, metabolomics can be used to determine metabolic activity at different stages of development or during growth. In this study, we reveal for the first time the metabolomes of infectious stages (L3 and L4) of A. simplex using untargeted metabolomics by ultra-performance liquid chromatography-mass spectrometry. In the negative ionization mode (ESI-), we identified 172 different compounds, whereas in the positive ionization mode (ESI+), 186 metabolites were found. Statistical analysis showed that 60 metabolites were found in the ESI- mode with different concentration in each group, of which 21 were more enriched in the L3 larvae and 39 in the L4 stage of A. simplex. Comparison of the individual developmental stages in the ESI+ mode also revealed a total of 60 differential metabolites, but 32 metabolites were more enriched in the L3 stage larvae, and 28 metabolites were more concentrated in the L4 stage. The metabolomics study revealed that the developmental stages of A. simplex differed in a number of metabolic pathways, including nicotinate and nicotinamide metabolism. In addition, molecules responsible for successful migration within their host, such as pyridoxine and prostaglandins (E1, E2, F1a) were present in the L4 stage. In contrast, metabolic pathways for amino acids, starch and sucrose were mainly activated in the L3 stage. Our results provide new insights into the comparative metabolome profiles of two different developmental stages of A. simplex.
Question: Write a study description for the study titled 'Community-integrated multi-omics facilitates screening and isolation of the organohalide dehalogenation microorganism'.
Answer: A variety of anthropogenic organohalide contaminants generated from industry are released into the environment, and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by whole-metagenome sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavobạcteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes (MAGs) were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 MAGs were identified, suggesting that the potential for hydrolytic organohalide dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.
Question: Write a study description for the study titled 'NAD+ augmentation restores mitophagy and limits accelerated aging in Werner syndrome (Extracellular UPLC-MS assay)'.
Answer: Metabolic dysfunction is a primary feature of Werner syndrome (WS), a human premature aging disease caused by mutations in the gene encoding the Werner (WRN) DNA helicase. WS patients exhibit severe metabolic phenotypes, but the underlying mechanisms are not understood, and whether the metabolic deficit can be targeted for therapeutic intervention has not been determined. Here we report impaired mitophagy and depletion of NAD+, a fundamental ubiquitous molecule, in WS patient samples and WS invertebrate models. WRN regulates transcription of a key NAD+ biosynthetic enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1). NAD+ repletion restores NAD+ metabolic profiles and improves mitochondrial quality through DCT-1 and ULK-1-dependent mitophagy. At the organismal level, NAD+ repletion remarkably extends lifespan and delays accelerated aging, including stem cell dysfunction, in C. elegans and Drosophila melanogaster models of WS. Our findings suggest that accelerated aging in WRN syndrome is mediated by impaired mitochondrial function and mitophagy, and that bolstering cellular NAD+ levels counteracts WS phenotypes.Extracellular UPLC-MS assay protocols and data are reported in the current study MTBLS1221.Intracellular UPLC-MS assay protocols and data are reported in MTBLS1223.
Question: Write a study description for the study titled 'Hemolymph metabolome of Plagiodera versicolora'.
Answer: Analyze the differences in hemolymph metabolites between Rosenbergiella nectarea-monocolonized third-instar larvae of Plagiodera versicolora and germ-free larvae.
Question: Write a study description for the study titled 'Analysis of the Effects of Bacillus velezensis HJ-16 Inoculation on Tobacco Leaves Based on Multi-omics Methods'.
Answer: In this study, a strain isolated from the surface of flue-cured tobacco leaves, identified as Bacillus velezensis HJ-16, was applied in the solid-state fermentation of tobacco leaves. This strain, known for producing thermally stable enzymes, including amylase, cellulase, and protease, significantly improved the sensory qualities of tobacco, enhancing aromatic intensity, density, and softness, while reducing irritation. Whole-genome sequencing and functional annotation revealed that B. velezensis HJ-16 possesses a single circular chromosome containing genes associated with enzyme production and metabolic activities, particularly in carbohydrate metabolism and amino acid metabolism. Untargeted metabolomics analysis identified significant changes in non-volatile metabolites induced by fermentation. These metabolites were enriched in pathways related to flavonoid biosynthesis, alkaloid biosynthesis, aromatic amino acid metabolism, lipid metabolism, and carbon metabolism. Metagenomic analysis showed that Bacillus became the dominant genus on the tobacco leaf surface following inoculation with B. velezensis HJ-16, altering the microbial community composition, reducing diversity and evenness, and enhancing microbial metabolic activity. These findings underscore the potential of B. velezensis HJ-16 as a biotechnological tool to improve tobacco leaf quality.
Question: Write a study description for the study titled 'Multi-omics resources for targeted agronomic improvement of pigmented rice'.
Answer: Pigmented rice (Oryza sativa L.) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.
Question: Write a study description for the study titled 'Gut Microbiota and Urine Metabolomics Signature in Autism Spectrum Disorder children from Southern China'.
Answer:  To determine the gut microbiota and urine metabolomics signature and identify the regional characteristics in Autism spectrum disorder (ASD), we conducted a cohort study of 88 well-characterized participants from Guangxi Zhuang Autonomous Region in Southern China. Gut microbiota and urine metabolomics signature was explored by 16S rRNA sequences and untargeted metabolomic profiles respectively. We found that the gut microbial α-diversity of ASD were signiﬁcantly lower than healthy controls. The β-diversity analysis indicated that the community structure in ASD group was obviously distinctive. Significant microbiota enriched in 5 sensitive species, Faecalibacterium prausnitzii, Bifidobacterium catenulatum, Blautia obeum, Lachnoclostridium sp., and Blautia sp. in ASD children. In addition, functional analysis of the gut microbiota revealed that the ATP-binding cassette and ABC-2 type transport system ATP-binding protein were closely associated with ASD. Notably, microbiota showing a positive correlation with Androstenedione, Stearamide, Oleamide, Cadaverine, Hexadecanamide, Orotic acid, Linoleic acid, Palmitoleic acid, Lauric acid, suggesting a potential association with the Arginine and proline metabolism pathway. These findings demonstrated that there was typical signature of microbiota and metabolites discriminated Zhuang ethnic group ASD children of regional characteristics.
Question: Write a study description for the study titled 'Characterization of Constituents with Potential Anti-Inflammatory Activity in Chinese Lonicera Species by UHPLC-HRMS Based Metabolite Profiling'.
Answer: This study centered on detecting potentially anti-inflammatory active constituents in ethanolic extracts of Chinese Lonicera species by taking an UHPLC-HRMS-based metabolite profiling approach. Extracts from eight different Lonicera species were subjected to both UHPLC-HRMS analysis and to pharmacological testing in three different cellular inflammation-related assays. Compounds exhibiting high correlations in orthogonal projections to latent structures discriminant analysis (OPLS-DA) of pharmacological and MS data served as potentially activity-related candidates. Of these candidates, 65 were tentatively or unambiguously annotated. 7-Hydroxy-5,3',4',5'-tetramethoxyflavone and three bioflavonoids, as well as three C32- and one C34-acetylated polyhydroxy fatty acid, were isolated from Lonicera hypoglauca leaves for the first time, and their structures were fully or partially elucidated. Of the potentially active candidate compounds, 15 were subsequently subjected to pharmacological testing. Their activities could be experimentally verified in part, emphasizing the relevance of Lonicera species as a source of anti-inflammatory active constituents. However, some compounds also impaired the cell viability. Overall, the approach was found useful to narrow down the number of potentially bioactive constituents in the complex extracts investigated. In the future, the application of more refined concepts, such as extract prefractionation combined with bio-chemometrics, may help to further enhance the reliability of candidate selection.
Question: Write a study description for the study titled 'Controlling mitochondrial membrane architecture via MIC60 determines viral replication to promote anti-viral immunity'.
Answer: Virus-infected cells often exhibit dramatic cellular changes accompanied by altered mitochondrial function. The contribution of factors shaping the inner mitochondrial membrane (IMM) and cristae architecture on viral replication is insufficiently understood. Single cell transcriptomics applying vesicular stomatitis virus (VSV) infection suggests involvement of factors determining IMM architecture following infection. Consistently, inhibition of the F1Fo ATP synthase reduces viral replication which is associated with oligomerization of the complex and altered IMM structure. Moreover, deletion of mitochondrial contact site and cristae organizing system (MICOS) complex by targeting MIC60 results in reduced viral replication. Generation of Mic60inv/inv CD11c-Cre+ mice uncovers reduced crista junctions and viral replication in bone marrow-derived dendritic cells. Consequently, reduced viral replication in CD11c-expressing cells limits prolonged immune activation. Altogether, by linking the F1Fo ATP synthase and the MICOS complex to viral replication and immune activation, we describe links between the mitochondrial structure-metabolism and the immune response against viral infection.
Question: Write a study description for the study titled 'Isotopomer analysis of MCF-7 breast cancer cell line incubated with 13C labelled glucose (NMR assay)'.
Answer: MS and NMR are two of the most powerful spectroscopic techniques used in the field of fluxomics, to analyze the flux distributions in cellular metabolomic pathways. Both of them possess pros and cons, such as, MS being the most sensitive and low-cost technique, while needs extensive sample processing and providing incomplete labeling data, whereas NMR needs lesser sample preparation and provides more detailed labeling data, while being less sensitive and expensive. Since both techniques could be viewed as complementary to each other, combining their data could yield a detailed and complete information about a system under study. In this case, samples were generated from a single experiment and the same set of samples was used both in MS and 1D NMR to analyze the 13C label distributions in TCA cycle intermediates. The data generated from both methods were used with a simulation script that was developed to integrate the MS and NMR data. MCF-7 breast cancer cell line was used as an experimental model and it was incubated with 100% [1,2-13C]-glucose and 100% [U-13C]-glucose for 8 hours. The cells, before and after incubation with tracers, were frozen in liquid nitrogen and then later processed for extracting the TCA cycle intermediates. Same set of samples were separated for GC-MS and NMR based analysis and processed for the respective techniques. The isotopologue analysis was performed by GC-MS and the isotopomer analysis was performed by NMR and both sets of data were integrated with the simulation software. In this study there is the data for NMR analysis. This study contains the data for NMR analysis.  The GC-MS assay for this study can be found in the MetaboLights study MTBLS182. Linked Studies: MTBLS182
Question: Write a study description for the study titled 'Salmonella enterica and Pseudomonas syringe uniquely alter the exometabolomic profile of the Arabidopsis leaf surface'.
Answer: To successfully colonize healthy plants, bacterial pathogens must overcome stressful conditions on the leaf surface before entering the leaf tissues through natural openings. In this study, we developed an approach to examine the exometabolomic profiles of the leaf surface when exposing plants with the plant pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) and the human pathogen Salmonella enterica ser. Typhimurium 14028s (STm 14028s). Our data indicate clear differences in metabolic dynamics in the phyllosphere as Pst DC3000 and STm 14028s colonize this niche, where STm 14028s induced the largest changes in the metabolite accumulation. Specifically, we detected a reduction of several monosaccharides and organic acids that STm 14028s may consume as sources of energy. Furthermore, STm 14028s alters several amino acids and nucleic acids that promote growth and survival by providing essential substrates and serving as signaling molecules under stressful conditions. In addition, we identified differential accumulation of amino acids and other metabolites, such as phytohormones, which could potentially contribute to plant defense against biotic stresses. Overall, we gained valuable insights into the metabolites secreted onto the leaf surface, which might facilitate bacterial transitioning to an endophytic lifestyle and the unique response of Arabidopsis towards these bacteria.
Question: Write a study description for the study titled 'Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow'.
Answer: Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis.  Serum metabolome of 40 age-related macular degeneration patients and 20 control samples was analyzed using untargeted mass spectrometry. We used data dependent acquisition data to build a MS/MS spectral assay library for more than 1,000 compounds and performed targeted extraction of MS2 ion chromatograms from data independent acquisition analysis.
Question: Write a study description for the study titled 'Evaluation of extraction solvents for untargeted metabolomics analysis of enrichment reactor cultures performing enhanced biological phosphorus removal (EBPR)'.
Answer: INTRODUCTION: The extraction solvent mixtures were optimized for untargeted metabolomics analysis of microbial communities from two laboratory scale activated sludge reactors performing enhanced biological phosphorus removal (EBPR).OBJECTIVE: To develop a robust and simple analytical protocol to analyse microbial metabolomics from EBPR bioreactors.METHODS: Extra- and intra-cellular metabolites were extracted using five methods and analysed by ultraperformance liquid chromatography mass spectrometry (UPLC-MS).RESULTS: The optimal extraction method was biomass specific and methanol:water (1:1 v/v) and methanol:chloroform:water (2:2:1 v/v) were chosen, respectively, for each of the two different bioreactors.CONCLUSION: Our approach provides direct surveys of the metabolic state of PAO-enriched EBPR communities, showing that extraction methods should be carefully tailored to the microbial community under study