LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Pessary Therapy Restores Vaginal Microbiome Homeostasis in Severe Pelvic Organ Prolapse: A Longitudinal Metagenomic and Metabolic Analysis'.
Answer: Pelvic organ prolapse (POP), affecting up to 50% of elderly women, disrupts vaginal microbial homeostasis, yet the impact of first-line pessary therapy on microbiome dynamics remains poorly characterized. This prospective cohort study employed metagenomic sequencing and clinical metrics to longitudinally analyze vaginal microbiota in 41 postmenopausal POP-III/IV patients undergoing pessary therapy, compared to surgical intervention and healthy controls. Pre-treatment POP patients exhibited dysbiosis marked by elevated aerobic pathogen (e.g., Gardnerella vaginalis, Streptococcus agalactiae) and bacterial vaginosis (BV)-associated taxa, which may correlating with anatomical oxygen exposure. pessary therapy drove time-dependent microbial stabilization: within 3 months, Lactobacillus crispatus and Lactobacillus jensenii reclaimed dominance (∼90% abundance), suppressing BV-associated genera (Corynebacterium spp., Streptococcus spp.), while surgery failed to improve dysbiosis. Patients developing pessary-associated ulcers showed distinct enrichment of G. vaginalis, S. anginosus, and Atopobium vaginae, enabling a predictive model (AUC: 0.848) for complication risk. Metabolomic profiling revealed pessary-induced activation of pentose phosphate and glycerophospholipid pathways, aligning with microbial recovery. These findings establish pessary therapy as a dual restorative intervention—anatomically and microbially—while identifying actionable biomarkers for complication prevention. Our work advocates integrating microbiome-guided strategies into POP management to optimize therapeutic outcomes.
Question: Write a study description for the study titled 'Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts'.
Answer: The composition and changes of the fungal population and of the metabolites present in grapes and in ferments of Vitis vinifera L. cv. Corvina, one of the major components of the Amarone musts, were dissected aiming at the identification of constant characteristics possibly influenced by the productive process. The fungal populations and metabolomic profiles were analyzed in three different vintages. 454-pyrosequencing on the ribosomal ITS1 region has been used to identify the fungal population present in Corvina grapes and fresh must. Samples were also subjected to metabolomics analysis measuring both free volatile compounds and glycosylated aroma precursors through an untargeted approach with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Albeit strongly dependent on the climate, both the mycobiota and metabolome of Corvina grapes and fresh musts show some characteristics recursive in different vintages. Such persistent characteristics are likely determined by the method adopted to produce Amarone or other dry wines made from partially dried grapes. In particular, the harsh conditions imposed by the prolonged withering appear to contribute to the shaping of the fungal populations. The fungal genera and metabolites present in different vintages in V. vinifera L. cv. Corvina grapes and fresh musts represent core components of the peculiar technique of production of Amarone. Their identification allows the in-depth understanding and improved control of the process of production of this economically and culturally relevant wine.Linked cross omic data sets:Meta-taxonomics data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB15229.
Question: Write a study description for the study titled 'Metabolomics analysis identifies metabolites associated with systemic acquired resistance in Arabidopsis'.
Answer: BACKGROUND: Systemic acquired resistance (SAR) is a plant defense response that provides long-lasting, broad-spectrum pathogen resistance to uninfected distal leaves following an initial localized infection. However, little information is available on the molecular biological basis of SAR especially in uninfected distal leaves. METHODS: Here, we used two SAR-inducing pathogen to induce SAR in Arabidopsis, and a metabolomics approach based on ultra-high-performance liquid chromatography (UPLC) and mass spectrometry (MS) technique was used to identify SAR-related metabolites in SAR-inducing pathogen infected local leaves and uninfected distal leaves. RESULTS: Multiple statistical analyses were used to identify differentially expressed metabolites. The result showed that primary metabolism and secondary metabolism were significantly altered in local leaves and distal leaves, including phenolic compounds, amino acids, nucleotides, organic acids and many other metabolites.CONCLUSIONS: The content of amino acids and phenolic compounds increased in distal leaves, suggesting their contribution to the establishment of SAR in distal leaves. In addition, 2’-hydroxy-4, 4’, 6’-trimethoxychalcone, phenylalanine and p-coumaric acid were identified as potential components which may play important roles both in basic resistance and SAR. This study provided a reference for understanding metabolic mechanism associated with SAR in Arabidopsis, which will be useful for further investigation of the molecular basis of SAR.
Question: Write a study description for the study titled 'Induction of resistance against Sclerotinia sclerotiorum in rapeseed by β-ocimene through enhanced production of coniferyl aldehyde'.
Answer: Rapeseed (Brassica napus) is an important oil resource, but its yield can be significantly compro-mised by Sclerotinia sclerotiorum (S. sclerotiorum) infection. Due to the lack of rapeseed strains that are highly or completely immune to S. sclerotiorum, enhancing rapeseed resistance through genetic approaches is challenging. Here, we developed a novel method to enhance rapeseed resistance to S. sclerotiorum using β-ocimene. The results showed that β-ocimene treatment significantly strength-ened defense capabilities of rapeseed. β-ocimene treatment can activate various defense-related signaling pathways, including jasmonic acid signaling, salicylic acid signaling, and MAPK sig-naling, in rapeseed and induce the accumulation of secondary metabolites coniferyl aldehyde, a core component of the phenylpropanoid pathway in plant defense response. Applying coniferyl al-dehyde to the leaves of rapeseed can remarkably enhance its resistance to sclerotinia disease. Col-lectively, these findings further clarify that β-ocimene activates the defense system of rapeseed, el-evates the content of coniferyl aldehyde, and thereby enables rapeseed to effectively resist sclero-tinia disease. In conclusion, we have not only uncovered the mechanism by which β-ocimene in-duces rapeseed resistance to sclerotinia disease but also provided a novel approach for the preven-tion and control of the harm caused by sclerotinia disease to rapeseed.
Question: Write a study description for the study titled 'Untargeted metabolomics analyses and contaminant chemistry of Dreissenid mussels at the Maumee River Area of Concern in the Great Lakes'.
Answer: Bivalves serve as an ideal ecological indicator; hence, their use by the NOAA Mussel Watch Program to monitor environmental health. This study aimed to expand the baseline knowledge of using metabolic end points in environmental monitoring by investigating the dreissenid mussel metabolome in the field. Dreissenids were caged at four locations along the Maumee River for 30 days. The mussel metabolome was measured using nuclear magnetic resonance spectroscopy, and mussel tissue chemical contaminants were analyzed using gas or liquid chromatography coupled with mass spectrometry. All Maumee River sites had a distinct mussel metabolome compared to the reference site and revealed changes in the energy metabolism and amino acids. Data also highlighted the importance of considering seasonality or handling effects on the metabolome at the time of sampling. The furthest upstream site presented a specific mussel tissue chemical signature of pesticides (atrazine and metolachlor), while a downstream site, located at Toledo's wastewater treatment plant, was characterized by polycyclic aromatic hydrocarbons and other organic contaminants. Further research into the dreissenid mussel's natural metabolic cycle and metabolic response to specific anthropogenic stressors is necessary before successful implementation of metabolomics in a biomonitoring program.
Question: Write a study description for the study titled 'Neuronal Hyperactivity due to Loss of Inhibitory Tone in APOE4 Mice Lacking Alzheimer’s Disease-like Pathology'.
Answer: Metabolite profiling was performed on metabolites extracted from the entorhinal cortex and primary visual cortex of 14-15 month old APOE3/3, APOE3/4 and APOE4/4 mice. Metabolites were run on a TOF Mass Spectrometer using an ANP column. Initial analysis was done in an untargeted manner, and processing was done to determine the differentially expressed metabolites based on their mass and retention times. Further analysis was then performed to assign identities to the differentially expressed metabolites using a database of biologically-relevant metabolites whose standards had been run under identical conditions as the samples in the study.
Question: Write a study description for the study titled 'Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase'.
Answer: Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
Question: Write a study description for the study titled 'Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome'.
Answer: Spontaneous preterm birth (sPTB) is a leading cause of maternal and neonatal morbidity and mortality, yet its prevention and early risk stratification are limited. Previous investigations have suggested that vaginal microbes and metabolites may be implicated in sPTB. Here we performed untargeted metabolomics on 232 second-trimester vaginal samples, 80 from pregnancies ending preterm. We find multiple associations between vaginal metabolites and subsequent preterm birth, and propose that several of these metabolites, including diethanolamine and ethyl glucoside, are exogenous. We observe associations between the metabolome and microbiome profiles previously obtained using 16S ribosomal RNA amplicon sequencing, including correlations between bacteria considered suboptimal, such as Gardnerella vaginalis, and metabolites enriched in term pregnancies, such as tyramine. We investigate these associations using metabolic models. We use machine learning models to predict sPTB risk from metabolite levels, weeks to months before birth, with good accuracy (area under receiver operating characteristic curve of 0.78). These models, which we validate using two external cohorts, are more accurate than microbiome-based and maternal covariates-based models (area under receiver operating characteristic curve of 0.55-0.59). Our results demonstrate the potential of vaginal metabolites as early biomarkers of sPTB and highlight exogenous exposures as potential risk factors for prematurity.
Question: Write a study description for the study titled 'Using network analysis to discern compositional patterns in ultrahigh resolution mass spectrometry data of dissolved organic matter'.
Answer: RATIONALE: Marine dissolved organic matter (DOM) has long been recognized as a large and dynamic component of the global carbon cycle. Yet, DOM is chemically varied and complex and these attributes present challenges to researchers interested in addressing questions about the role of DOM in global biogeochemical cycles.METHODS: Organic matter extracts from seawater were analyzed by direct infusion with electrospray ionization into a Fourier transform ion cyclotron resonance mass spectrometer. Network analysis was used to quantify the number of chemical transformations between mass-to-charge values in each sample. The network of chemical transformations was calculated using the MetaNetter plug-in within Cytoscape. The chemical transformations serve as markers for the shared structural characteristics of compounds within complex DOM.RESULTS: Network analysis revealed that transformations involving selected sulfur-containing moieties and isomers of amino acids were more prevalent in the deep sea than in the surface ocean. Common chemical transformations were not significantly different between the deep sea and surface ocean. Network analysis complements existing computational tools used to analyze ultrahigh-resolution mass spectrometry data.CONCLUSIONS: This combination of ultrahigh-resolution mass spectrometry with novel computational tools has identified new potential building blocks of organic compounds in the deep sea, including the unexpected importance of dissolved organic sulfur components. The method described here can be readily applied by researchers to analyze heterogeneous and complex DOM.
Question: Write a study description for the study titled 'Phosphorus availability regulates intracellular nucleotides in marine eukaryotic phytoplankton'.
Answer: Phosphorus limitation is pervasive in the oligotrophic surface ocean and marine microorganisms use different strategies to survive, and thrive, at these low nutrient levels. Eukaryotic algae such as diatoms are extremely sensitive to phosphorus limitation and recent transcriptomics work has suggested that multiple cellular processes are affected under these growth conditions. Metabolomics is the systematic study of intra- and extracellular metabolites, i.e. the end products of microbial metabolism. As such, metabolomics complements genomics and transcriptomics through the identification and quantification of metabolic intermediates that reflect cellular physiology. Here, we applied intracellular metabolomics to examine the differential response of the model diatom Thalassiosira pseudonana to phosphate-replete and phosphate-limited growth conditions. We focused on metabolites from the purine and pyrimidine biochemical pathways, due to their role in phosphorus cycling associated with nucleic acid synthesis. Under phosphate-replete conditions, T. pseudonana stored nucleotides with phosphate moieties such as adenosine 5'-monophosphate (AMP) and, to a lesser extent, inosine 5'-monophosphate (IMP). In contrast, under phosphate-limited conditions, T. pseudonana had higher concentrations of adenine, inosine, and adenosine all of which lack phosphate moieties. Furthermore, based on previously published transcriptomics data, T. pseudonana differentially regulates select genes that can alter these nucleic acid precursors through the gain or loss of the phosphate moiety. Thus, our analysis of the metabolomics and transcriptomics data converged upon the sensitivity of the purine biochemical pathway to phosphorus availability.
Question: Write a study description for the study titled 'A metabolite roadmap of the wood-forming tissue in Populus tremula (GC-MS assay; Wood ring and extraxylary tissue)'.
Answer: Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.GC-MS assay of Wood ring and extraxylary tissue is reported in the current study MTBLS1796.UPLC-MS assay of Wood ring and extraxylary tissue is reported in MTBLS1797.UPLC-MS assay of Wood fibre and ray cell tissue is reported in MTBLS1831.
Question: Write a study description for the study titled 'The accumulation profiles of terpene metabolites in three Muscat table grape cultivars through HS-SPME-GCMS'.
Answer: Aroma is an important parameter for table grapes and wines; terpenes are typical compounds in Muscat-type grape cultivars and can be easily perceived by humans because of their low olfactory threshold. Volatile terpenes contribute directly to the aroma character, while glycoside-bound terpenes are potential aromatic compounds and can be changed to their volatile forms via hydrolysis. With gas chromatography-mass spectrometry and a solid-phase microextraction method, an automatic data analysis platform was constructed; terpene compounds were identified and quantified from three table grape cultivars at three stages during berry development, and the raw data were deposited in MetaboLights. Terpene metabolite accumulation profiles are presented in this article for integrative analysis with the transcriptome data and phenotypic data to elucidate the important candidate genes and mechanism for terpene biosynthesis. Our method has applications in the identification and quantification of terpene compounds with very low or trace concentrations.
Question: Write a study description for the study titled 'Large neutral amino acid levels tune perinatal neuronal excitability and survival'.
Answer: Surprisingly little is known about the critical metabolic changes that neural cells have to undergo during development and how even mild, temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically-essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes. But what are the consequences of interfering with this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons perturbs specifically the postnatal metabolic state leading to a shift in lipid metabolism and a stage- and cell- type-specific alteration in neuronal activity patterns, resulting in a long-term circuit dysfunction.
Question: Write a study description for the study titled 'Monitoring recombinant protein expression in bacteria by rapid evaporative ionisation mass spectrometry'.
Answer: RATIONALE: There is increasing interest in methods of direct analysis mass spectrometry that bypass complex sample preparation steps.METHODS: One of the most interesting new ionisation methods is rapid evaporative ionisation mass spectrometry (REIMS) in which samples are vapourised and the combustion products are subsequently ionised and analysed by mass spectrometry (Synpat G2-si). The only sample preparation required was the recovery of a cell pellet from a culture that could immediately be analysed.RESULTS: In this paper, we demonstrate that REIMS can be used to monitor the expression of heterologous recombinant proteins in Escherichia coli. Clear segregation was achievable between bacteria harvesting plasmids that were strongly expressed when compared to other cultures in which the plasmid did not result in the expression of large amounts of recombinant product.CONCLUSION: REIMS has considerable potential as a near-instantaneous monitoring tool for protein production in a biotechnology environment.
Question: Write a study description for the study titled 'Metabolomic analysis of the mechanism of action of yerba mate extract on Salmonella Typhimurium'.
Answer: Background: Salmonella Typhimurium is a gram-negative enteropathogen that infects millions worldwide; the rapid emergence of antibiotic resistant strains has heightened the urgency of developing effective treatment for this pathogen. Previous studies have demonstrated that the aqueous extract of yerba mate (Ilex paraguariensis) provides effective therapy, in vitro, for the drug-resistant S. Typhimurium DT104. Unfortunately, while some of the chemical constituents that contribute to the extract’s antibacterial activity have been identified, the mechanism of action of the extract is still unknown and of crucial importance to its future potential in combating antibiotic resistant bacteria. Results: Yerba mate extract altered central carbon metabolism in S. Typhimurium, reduced catalase activity by means other than direct inhibition, and did not change membrane integrity (except at the initial 0 time point, where differences were not resolved) despite a significant increase in the production of a cell wall precursor. Additional significant differences were observed in the global metabolic regulators alpha-ketoglutarate and acetylphosphate, the energy-related molecule NAD+, and in an unexpected match to the antibacterial compound yohimbine. Conclusions: This work provides the first insight into the mechanism of action of yerba mate extract on S. Typhimurium by revealing a major impact on central carbon metabolism, catalase activity, and possible metabolic links to interference in energy production and membrane integrity. The putative identification of the antibacterial compound yohimbine and the many unidentified compounds provides additional avenues for future investigations of novel yerba mate compounds capable of traversing or binding to S. Typhimurium’s membrane.