LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolomic characterization of pitaya fruit from three red-skinned cultivars with different pulp colors'.
Answer: Pitaya is a new fruit crop, whose exotically colored fruits have excellent nutritional and antioxidant properties. In this study, the primary metabolite profiles of three pitaya cultivars i.e. 'Guanhuahong' (red peel with red pulp), 'Guanhuabai' (red peel with white pulp) and 'Guanhuahongfen' (red peel with pink pulp) were investigated using GC-MS and Ultraviolet–visible spectroscopy. In the fruit pulp, levels of starch, organic acids, and inositol decreased as the fruit matured. Glucose, fructose, sucrose and sorbitol contents increased gradually during fruit maturation and reached their highest levels in the pulp at the mature stage. Citramalic acid was identified for the first time in the pulp of Hylocereus species. Higher levels of total phenols, flavonoids and antioxidant activities were detected in the peel than in the pulp during fruit maturation of all three cultivars. The finding of higher levels of total phenols and flavonoids in the pitaya peel than in the pulp at the mature stage suggests that pitaya peels are a good source of natural phenols and flavonoids.
Question: Write a study description for the study titled 'Untargeted food contaminant detection using UHPLC-HRMS combined with multivariate analysis: Feasibility study on tea (Dataset 2 - Validation)'.
Answer: Powerful data pretreatment strategies inspired from the field of metabolomics were adapted to chemical food safety context to enable samples discrimination by multivariate methods based on low abundance ions. A highly automated workflow was produced. The open-source XCMS package was used and efficient data filtration strategies were set up. Data were treated using Independent Components Analysis, and data mining strategies developed to automatically detect and annotate ions of low abundance by coupling blind data exploration strategies with a broad scale database approach. Our method was efficient in discriminating tea samples based on their contamination levels (even at 10µg/kg) and detecting unexpected impurities in the spiking mix. Several “tracer” contaminants were considered, covering a broad range of physicochemical properties and structural diversity with overall 66% detected and annotated blindly. The methodology was successfully applied to a data set exhibiting only 3 “tracer” contaminants (at 50µg/kg) and more product diversity.  Dataset 2 with 2 teas spiked with 3 contaminants and referred to as the Validation datase is reported in the current study MTBLS754.  Dataset 1 with 1 tea spiked with 32 contaminants and referred to as the Development dataset is reported in MTBLS752.  Linked Studies: MTBLS752
Question: Write a study description for the study titled 'New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics'.
Answer: Polycyclic aromatic hydrocarbons (PAHs), some of the most widespread organic contaminants, are highly toxic to soil microorganisms. Whether long-term polluted soils can still respond to the fresh input of pollutants is unknown. In this study, the soil enzyme activity, soil microbial community structure and function and microbial metabolism pathways were examined to systematically investigate the responses of soil microorganisms to fresh PAH stress. Microbial activity as determined by soil dehydrogenase and urease activity was inhibited upon microbe exposure to PAH stress. In addition, the soil microbial community and function were obviously shifted under PAH stress. Both microbial diversity and richness were decreased by PAH stress. Rhizobacter, Sphingobium, Mycobacterium, Massilia, Bacillus and Pseudarthrobacter were significantly affected by PAH stress and can be considered important indicators of PAH contamination in agricultural soils. Moreover, the majority of microbial metabolic function predicted to respond to PAH stress were affected adversely. Finally, soil metabolomics further revealed specific inhibition of soil metabolism pathways associated with fatty acids, carbohydrates and amino acids. Therefore, the soil metabolic composition distinctively changed, reflecting a change in the soil metabolism. In summary, fresh contaminant introduction into long-term polluted soils inhibited microbial activity and metabolism, which might profoundly affect the whole soil quality.
Question: Write a study description for the study titled 'Lsr2, a novel cyclic di-GMP receptor, regulate the synthesis of keto-mycolic acid and control biofilm formation in mycobacteria'.
Answer: Cyclic di-GMP (c-di-GMP) is a well-known second messenger that plays a key role in many physiological processes in bacteria. The synthesis of lipids is essential for bacterial biofilm formation. However, whether c-di-GMP signaling modulates the synthesis of lipid and further regulates biofilm formation in mycobacteria is unclear, and the c-di-GMP receptor involved remains unknown. In this study, we characterized the nucleoid-associated protein (NAP) Lsr2 as a novel c-di-GMP receptor in mycobacteria. c-di-GMP specifically binds to Lsr2 at a ratio of 1:1. We showed that c-di-GMP promotes mycobacterial biofilm formation in a manner dependent on Lsr2. Furthermore, Lsr2 mediates the synthesis of keto-mycolic acid, the lipid component of the mycobacterial cell wall, by positively regulating the expression of HadD, a (3R)-hydroxyacyl-ACP dehydratase, thus, Lsr2 ultimately controls biofilm formation. Finally, c-di-GMP promotes the positive regulation of HadD by Lsr2 and mycobacterial biofilm formation. Thus, we report a novel c-di-GMP receptor that links the second messenger’s function to lipid synthesis and biofilm formation in mycobacteria.
Question: Write a study description for the study titled 'Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis'.
Answer: Salidroside is a bioactive tyrosine-derived phenolic natural product found in medicinal plants under the Rhodiola genus. In addition to their roles in traditional medicine as anti-fatigue and anti-anoxia adaptogens, Rhodiola total extract and salidroside have also displayed medicinal properties as anti-cardiovascular diseases and anti-cancer agents. The resulting surge in global demand of Rhodiola plants and salidroside has driven some species close to extinction. Here, we report the full elucidation of Rhodiola salidroside biosynthetic pathway utilizing the first comprehensive transcriptomics and metabolomics datasets for Rhodiola rosea. Unlike the previously proposed pathway involving separate decarboxylation and deamination enzymatic steps from tyrosine to the key intermediate 4-hydroxyphenylacetaldehyde, Rhodiola contains a pyridoxal phosphate (PLP)-dependent 4-hydroxyphenylacetaldehyde synthase (4HPAAS) that directly converts tyrosine to 4-hydroxyphenylacetaldehyde. We further identified genes encoding the subsequent 4-hydroxyphenylacetaldehyde reductase (4HPAR) and tyrosol:UDP-glucose 8-O- glucosyltransferase (T8GT), respectively, to complete salidroside biosynthesis in Rhodiola. We show that heterologous production of salidroside can be achieved in yeast Saccharomyces cerevisiae as well as in plant Nicotiana benthamiana through transgenic expression of Rhodiola salidroside biosynthetic genes. This study provides new tools for engineering sustainable production of salidroside in heterologous hosts.
Question: Write a study description for the study titled 'MAVEN2: An Updated Open-Source Mass Spectrometry Exploration Platform'.
Answer: MAVEN, an open-source software program for analysis of LC-MS metabolomics data, was originally released in 2010. As mass spectrometry has advanced in the intervening years, MAVEN has been periodically updated to reflect this advancement. This manuscript describes a major update to the program, MAVEN2, which supports LC-MS/MS analysis of metabolomics and lipidomics samples. We have developed algorithms to support MS/MS spectral matching and efficient search of large-scale fragmentation libraries. We explore the ability of our approach to separate authentic from spurious metabolite identifications using a set of standards spiked into water and yeast backgrounds. To support our improved lipid identification workflow, we introduce a novel in-silico lipidomics library covering major lipid classes and compare searches using our novel library to searches with existing in-silico lipidomics libraries. MAVEN2 source code and cross-platform application installers are freely available for download from GitHub under a GNU permissive license [ver 3], as are the in silico lipidomics libraries and corresponding code repository.
Question: Write a study description for the study titled 'Metabolic Dynamics of In Vitro CD8+ T Cell Activation'.
Answer: CD8+ T cells detect and kill virally infected or cancerous cells. When activated from their naïve state, T cells undergo a complex transition, including major metabolic reprogramming. Detailed resolution of metabolic dynamics of a wide range of metabolites is needed to advance the field of immunometabolism. Here we outline methodologies that when utilized in parallel achieve broad coverage of the metabolome. Specifically, we used a combination of 2 FIA and 3 LC methods in combination with positive and negative mode high resolution MS to study the transition from naïve to effector T cells with fine-grained time resolution. Depending on the method, between 54% and 98% of cellular metabolites change in a time-dependent manner, with the major changes in both polar metabolites and lipids occurring in the first 48 h. Statistical analysis highlighted remodeling of the polyamine biosynthesis pathway, with marked differences in the dynamics of precursors, intermediates, and cofactors. Moreover, phosphatidylcholines, the major class of membrane lipids, underwent a drastic shift in acyl chain composition with polyunsaturated species decreasing from 60% to 25% and specifically depleting species containing a 20:4 fatty acid. We hope that these MS methodologies and data set of over 11000 features and 9 time points will be a useful resource for future work.
Question: Write a study description for the study titled 'Comparative analysis of the adaptation of Staphylococcus aureus to internalization by different types of human non-professional phagocytic host cells (NMR assay)'.
Answer: Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival and physiological adaptation of S. aureus HG001 after internalization by two human lung epithelial cell lines (S9 and A549), and human embryonic kidney cells (HEK 293). Combining enrichment of bacteria from host-pathogen assays by cell sorting and quantitation of the pathogen's proteome by mass spectrometry we characterized S. aureus adaptation during the initial phase between 2.5 h and 6.5 h post-infection. Starting with about 2 × 10^6 bacteria, roughly 1450 S. aureus proteins, including virulence factors and metabolic enzymes were identified by spectral comparison and classical database searches. Most of the bacterial adaptation reactions, such as decreased levels of ribosomal proteins and metabolic enzymes or increased amounts of proteins involved in arginine and lysine biosynthesis, enzymes coding for terminal oxidases and stress responsive proteins or activation of the sigma factor SigB were observed after internalization into any of the three cell lines studied. However, differences were noted in central carbon metabolism including regulation of fermentation and threonine degradation. Since these differences coincided with different intracellular growth behavior, complementary profiling of the metabolome of the different non-infected host cell types was performed. This revealed similar levels of intracellular glucose but host cell specific differences in the amounts of amino acids such as glycine, threonine or glutamate. With this comparative study we provide an impression of the common and specific features of the adaptation of S. aureus HG001 to specific host cell environments as a starting point for follow-up studies with different strain isolates and regulatory mutants. Metabolome analysis, by nuclear magnetic resonance spectroscopy, was performed for the infection medium (extracellular medium, mock infection of 1 h).
Question: Write a study description for the study titled 'The WEIZMASS spectral library for high-confidence metabolite identification'.
Answer: Annotation of metabolites is an essential, yet problematic, aspect of mass spectrometry (MS)-based metabolomics assays. The current repertoire of definitive annotations of metabolite spectra in public MS databases is limited and suffers from lack of chemical and taxonomic diversity. Furthermore, the heterogeneity of the data prevents the development of universally applicable metabolite annotation tools. Here we present a combined experimental and computational platform to advance this key issue in metabolomics. WEIZMASS is a unique reference metabolite spectral library developed from high-resolution MS data acquired from a structurally diverse set of 3,540 plant metabolites. We also present MatchWeiz, a multi-module strategy using a probabilistic approach to match library and experimental data. This strategy allows efficient and high-confidence identification of dozens of metabolites in model and exotic plants, including metabolites not previously reported in plants or found in few plant species to date.
Question: Write a study description for the study titled 'Production of chain-extended cinnamoyl compounds by overexpressing two adjacent cluster-situated LuxR regulators in Streptomyces globisporus C-1027'.
Answer: Natural products from microorganisms are important sources for drug discovery. With the development of high-throughput sequencing technology and bioinformatics, a large amount of uncharacterized biosynthetic gene clusters (BGCs) in microorganisms have been found, which show the potential for novel natural product production. 9 BGCs containing PKS and/or NRPS in Streptomyces globisporus C-1027 were transcriptionally low/silent under the experimental fermentation conditions, and the products of these clusters are unknown. Thus, we tried to activate these BGCs to explore cryptic products of this strain. We constructed the cluster-situated regulator overexpressing strains which contained regulator gene(s) under the control of the constitutive promoter ermE*p in S. globisporus C-1027. Overexpression of regulators in cluster 26 resulted in significant transcriptional upregulation of biosynthetic genes. With the separation and identification of products from the overexpressing strain OELuxR1R2, 3 ortho-methyl phenyl alkenoic acids (compounds 1-3) were obtained. Gene disruption showed that compounds 1 and 2 were completely abolished in the mutant GlaEKO, but were hardly affected by deletion of the genes orf3 or echA in cluster 26. The type II PKS biosynthetic pathway of chain-extended cinnamoyl compounds was deduced by bioinformatics analysis. This study showed that overexpression of the 2 adjacent cluster-situated LuxR regulator(s) is an effective strategy to connect the orphan BGC to its products.
Question: Write a study description for the study titled 'Integrated transcriptomics and metabolomics analysis of gasa1 and gasa4 mutants in response to P.syringae infection in Arabidopsis'.
Answer: The Gibberellic acid-stimulated Arabidopsis (GASA) gene family encodes a class of cysteine-rich proteins characterized by an N-terminal signal peptide and a conserved C-terminal GASA domain containing 12 cysteine (Cys) residues. These plant-specific small proteins have been identified across various species, where they primarily regulate plant growth and abiotic stress responses. However, the molecular mechanisms by which AtGASA1 and AtGASA4 contribute to Arabidopsis immunity against P.syringae remain unclear. In this study, we found that the gasa1 and gasa4 mutants exhibited increased susceptibility to P. syringae infection compared to Col-0. To elucidate these roles in plant immunity, we performed transcriptomic and metabolomic analyses. Transcriptomic profiling identified 957 differentially expressed genes (DEGs) in the gasa1 and gasa4 mutants upon pathogen infection, with significant enrichment in plant-pathogen interaction, glycerolipid metabolism, and MAPK signaling pathways. Metabolomic analysis revealed 900 differentially accumulated metabolites (DAMs), enriched in pathways including ascorbate and aldarate metabolism, pentose and glucuronate interconversions, and biosynthesis of cofactors. Integrated transcriptomic and metabolomic analyses further demonstrated that DEGs and DAMs were co-enriched in key pathways, including plant hormone signal transduction, biosynthesis of various plant secondary metabolites, and cysteine and methionine metabolism. Notably, within the plant hormone signal transduction pathway, we found that AtGASA1 and AtGASA4 regulate the expression of multiple genes involved in the salicylic acid (SA) signaling pathway, such as ICS1, EDS1, PAD4, PR1, and PR5. Consistently, SA levels in the gasa1 and gasa4 mutants were significantly lower than in Col-0. Our findings provide new insights into the immune functions of AtGASA1 and AtGASA4 in plant immunity against P. syringae infection.
Question: Write a study description for the study titled 'Golgi-IP, a tool for multimodal analysis of Golgi molecular content'.
Answer: The Golgi is a membrane-bound organelle that is essential for protein and lipid biosynthesis. It represents a central trafficking hub that sorts proteins and lipids to various destinations or for secretion from the cell. The Golgi has emerged as a docking platform for cellular signaling pathways including LRRK2 kinase whose deregulation leads to Parkinson disease. Golgi dysfunction is associated with a broad spectrum of diseases including cancer, neurodegeneration, and cardiovascular diseases. To allow the study of the Golgi at high resolution, we report a rapid Golgi immunoprecipitation technique (Golgi-IP) to isolate intact Golgi mini-stacks for subsequent analysis of their content. By fusing the Golgi-resident protein TMEM115 to three tandem HA epitopes (GolgiTAG), we purified the Golgi using Golgi-IP with minimal contamination from other compartments. We then established an analysis pipeline using liquid chromatography coupled with mass spectrometry to characterize the human Golgi proteome, metabolome, and lipidome. Subcellular proteomics confirmed known Golgi proteins and identified proteins not previously associated with the Golgi. Metabolite profiling established the human Golgi metabolome and revealed the enrichment of uridine-diphosphate (UDP) sugars and their derivatives, which is consistent with their roles in protein and lipid glycosylation. Furthermore, targeted metabolomics validated SLC35A2 as the subcellular transporter for UDP-hexose. Finally, lipidomics analysis showed that phospholipids including phosphatidylcholine, phosphatidylinositol, and phosphatidylserine are the most abundant Golgi lipids and that glycosphingolipids are enriched in this compartment. Altogether, our work establishes a comprehensive molecular map of the human Golgi and provides a powerful method to study the Golgi with high precision in health and disease.
Question: Write a study description for the study titled 'Metabolomic analysis of gut microbiota metabolites'.
Answer: In mice induced by DSS, oral administration of silibinin was used for intervention, and then the colonic contents were removed for LC-MS non-targeted metabolomics analysis. In mice induced by DSS, colonic contents were taken, fecal bacteria were extracted, and co-cultured with silibinin ex vivo. Subsequently, metabolomics analysis was performed using the same method.
Question: Write a study description for the study titled 'Transcriptional memory of dFOXO activation in youth curtails later-life mortality'.
Answer: Identifying processes occurring in early life affect subsequent life and health span is an urgent aim to improve human health. In this study, we identified a novel mechanism of dFOXO in longevity determination in Drosophila. We found that early adulthood induction of dFOXO is sufficient to reduce mortality in old age through different pathways than chronic dFOXO. We showed that dFOXO requires specific ATP-dependent chromatin modifiers to extend lifespan, and we could mimic this lifespan extension by modulating dFOXO’s targets in later life. Furthermore, dFOXO in early life induces a specific transcriptional programme that counteracts the natural transcriptomic changes occurring with age. Our findings provide a better understanding of transcriptional mechanisms related to longevity and opens new avenues for possible time-restricted interventions to improve human health in the future.
Question: Write a study description for the study titled 'Microbiomics combined metabolomics reveals Akkermansia modulating chicken gut microenvironment to protect from gamma coronavirus infection'.
Answer: In this study, we comprehensively investigated the influence of gut microbiota on gamma coronavirus replication in chickens. Using multi-omics approaches, we systematically examined microbial, viral and metabolic differences among adult chickens, young chickens and young chickens subjected to fecal microbiota transplantation from adults, establishing a mechanistic basis for the observed enhanced resistance to infectious bronchitis virus (IBV) in adult chickens
Question: Write a study description for the study titled 'Metabolomics reveals increased toxicity in earthworms (Eisenia fetida) of the transformation product methyl-triclosan'.
Answer: The effects of the antimicrobial triclosan (TCS) and its transformation product methyl-triclosan (MTCS) on the earthworm Eisenia fetida were investigated using GC-MS metabolomics. TCS is ubiquitous in sewage sludge, but a large proportion is transformed into MTCS during wastewater treatment and in soil when sewage sludge is applied to land. Our objective was to determine if earthworms exposed to ng/g to μg/g concentrations of TCS or MTCS exhibit toxic effects, and to identify the toxic mode of action of each compound. Ten individual earthworm replicates in 10 g worm bedding were exposed to 0, 0.25, 1, 4, 16, or 64 μg/g of either TCS or MTCS (120 experimental units) for 14 days. No mortalities were observed. All MTCS exposed worms had an instantaneous growth rate (IGR) over two times higher than the control during the study, but there was no effect of increasing concentration. Succinic acid was elevated relative to the control at concentrations ≥ 0.25 μg/g and glucose was elevated at 1 μg/g. There was separation from the control at all concentrations except 4 μg/g using Principal Components Analysis. Glucose, palmitic acid, and IGR contributed most strongly to the separation. Discriminant analysis with succinic acid, glucose, and IGR as variables showed a clear separation at all concentrations from the control along Canonical 1. Disruption of energy metabolism was hypothesized as a possible mode of action for MTCS.