LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Sulfadiazine Sodium Improves Dysfunctional Metabolomics in Toxoplasma gondii-infected Mice'.
Answer: Toxoplasma gondii is an obligate intracellular protozoan parasite that poses a severe threat to human health, especially those immune-compromised individuals. Sulfadiazine sodium (SDZ) is widely used for the treatment of human toxoplasmosis. However, systems biology researches on the therapeutic effects and mechanisms are not yet well performed. After T. gondii GT1 (Genotype I) infection, BALB/c mice were treated orally with SDZ (250 µg/mL in water) for consecutive 12 days. Mice showed typical acute toxoplasmosis symptoms on day 20 post infection, and 20 percent survived on day 30 post infection and established a chronic infection. An untargeted metabolomics approach based on an UPLC-MS/MS method was employed to identify the serum metabolic changes during SDZ treatment. Multivariate statistical analyses (PCA and PLS-DA) were employed to profile the serum metabolomes from the control mice, acute infection mice and SDZ treated mice. In total, 16,426 metabolite ions could be detected and 14,039 of them were consistently detected in more than 70% of the runs. Our results identified common and uniquely perturbed metabolites and pathways among acutely infected or SDZ treated groups. Acutely infected mice showed a dramatic global metabolic perturbations, and SDZ had a favorable therapeutic effect on parasite-induced acute toxoplasmosis by adjusting the metabolic disorders. Notably, serum metabolomics is proved to be a powerful and reliable approach into the surveillance of disease progression and treatment. More importantly, findings in this study will help provide useful data support for the development of new and safe pharmaceuticals against human toxoplasmosis.
Question: Write a study description for the study titled 'Lacto-N-tetraose mediates indole-3-lactic acid production by Bifidobacterium longum subsp. infantis to alleviate enterotoxigenic Escherichia coli-induced diarrhea in infants'.
Answer: Enterotoxigenic Escherichia coli (ETEC) is a leading cause of infectious diarrhea and poses a threat to infant health. Current treatments for ETEC infection primarily rely on antibiotics，which face limitations due to resistance and side effect. In this cross-sectional study, we analyzed fecal metabolic profiles in breastfed infants with and without diarrhea. We found a significant decrease in indole-3-lactic acid (ILA) levels in infants with diarrhea.
Question: Write a study description for the study titled 'Metabolome variability for two Mediterranean sponge species of the genus Haliclona: specificity, time, and space'.
Answer: INTRODUCTION: The study of natural variation of metabolites brings valuable information on the physiological state of the organisms as well as their phenotypic traits. In marine organisms, metabolome variability has mostly been addressed through targeted studies on metabolites of ecological or pharmaceutical interest. However, comparative metabolomics has demonstrated its potential to address the overall and complex metabolic variability of organisms.OBJECTIVES: In this study, the intraspecific (temporal and spatial) variability of two Mediterranean Haliclona sponges (H. fulva and H. mucosa) was investigated through an untargeted and then targeted metabolomics approach and further compared to their interspecific variability.METHODS: Samples of both species were collected monthly during 1 year in the coralligenous habitat of the Northwestern Mediterranean sae at Marseille and Nice. Their metabolomic profiles were obtained by UHPLC-QqToF analyses.RESULTS: Marked variations were noticed in April and May for both species including a decrease in Shannon's diversity and concentration in specialized metabolites together with an increase in fatty acids and lyso-PAF like molecules. Spatial variations across different sampling sites could also be observed for both species, however in a lesser extent.CONCLUSIONS: Synchronous metabolic changes possibly triggered by physiological factors like reproduction and/or environmental factors like an increase in the water temperature were highlighted for both Mediterranean Haliclona species inhabiting close habitats but displaying different biosynthetic pathways. Despite significative intraspecific variations, metabolomic variability remains minor when compared to interspecific variations for these congenerous species, therefore suggesting the predominance of genetic information of the holobiont in the observed metabolome.
Question: Write a study description for the study titled 'A profile of the joint Toxoplasma-host infection metabolome finds broad changes to metabolism and discovers a novel parasite metabolic capability'.
Answer: The obligate intracellular parasite Toxoplasma gondii is auxotrophic for several key metabolites and must scavenge these, and carbon sources like glucose. from the host. While the importance of metabolism to Toxoplasma infection it obvious, it is unclear how Toxoplasma infection actually changes metabolism. To address this question, we measured changes in the joint host-parasite metabolome over a time course of infection. Host and parasite transcriptomes were simultaneously generated to measure changes in expression of metabolic enzymes that might correlate with changes in metabolite abundance. Toxoplasma infection changed metabolite abundance in multiple pathways, including the tricarboxylic acid cycle, the pentose phosphate pathway, glycolysis, amino acid synthesis, and nucleotide metabolism. Our analysis indicated that changes in some pathways, such as the tricarboxylic acid cycle, were mirrored by changes in parasite transcription, while changes in others, like the pentose phosphate pathway, were paired with changes in both the host and parasite transcriptomes. Further experiments led to the discovery of a Toxoplasma enzyme, sedoheptulose bisphosphatase, which funnels carbon into the pentose phosphate pathway through an energetically driven dephosphorylation reaction. This second route for ribose synthesis resolves a possible conflict between the Toxoplasma tricarboxylic acid cycle and pentose phosphate pathway, which are both NADP+ dependent. During periods of high energetic and ribose need, the competition for NADP+ could result in lethal redox imbalances. Sedoheptulose bisphosphatase represents a novel step in Toxoplasma central carbon metabolism that allows Toxoplasma to satisfy its ribose demand without using NADP+. Sedoheptulose bisphosphatase is not present in humans, highlighting its potential as a drug target.
Question: Write a study description for the study titled 'LipidIN: a comprehensive repository for flash platform-independent identification and reverse lipidomics'.
Answer: We present expeditious querying, reliable and platform-independent lipid annotation software LipidIN, a comprehensive lipidome atlas with tandem mass spectrometry information, relative retention time and reverse mass spectrometry information. Five-levels spectral fragmentations trees were formulates across 165.6 million lipids with Paternò − Büchi reaction and Electron activated dissociation included. Flash entropy search speeds up 69.65 billion times spectra querying in less than 1 s. Lipid categories intelligence models and reverse mass spectrometry information dramatically reduce false discoveries. Using 1833 clinical cohorts to demonstrate the reliability of lipidIN in clinical lipid investigations.
Question: Write a study description for the study titled 'A data set of 255000 randomly selected and manually classified extracted ion chromatograms for evaluation of peak detection methods'.
Answer: Nontargeted mass spectrometry (MS) has become an important method over the last years in the fields of metabolomics and environmental research. While more and more algorithms and workflows become available to process a large number of data sets nontargeted, there still exist few manually evaluated universal test data sets for refining and evaluating these methods. The first step of nontargeted screening, peak detection (and refinement of it) is arguably the most important step for nontargeted screening. However, the absence of a model data set makes it harder for researchers to evaluate peak detection methods. In this Data Descriptor, we provide a manually checked data set consisting of 255000 EICs (5000 peaks randomly sampled from across 51 samples) for the evaluation on peak detection and gap filling algorithms. The data set was created from a previous real-world study, of which a subset was used to extract and manually classify ion chromatograms by three mass spectrometry experts. The data set consists of 51 converted mass spectral files in mzML format and an MZmine peaklist with annotations.Links:Zenodo complete data set
Question: Write a study description for the study titled 'Multiomics of tomato glandular trichomes reveals distinct features of central carbon metabolism supporting high productivity of specialized metabolites'.
Answer: Glandular trichomes are metabolic cell factories with the capacity to produce large quantities of secondary metabolites. Little is known about the connection between central carbon metabolism and metabolic productivity for secondary metabolites in glandular trichomes. To address this gap in our knowledge, we performed comparative metabolomics, transcriptomics, proteomics and 13C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession. Specific features of glandular trichomes that drive the formation of secondary metabolites could be identified. Tomato type VI trichomes are photosynthetic but acquire their carbon essentially from leaf sucrose. The energy and reducing power from photosynthesis are used to support the biosynthesis of secondary metabolites, while the comparatively reduced Calvin-Benson-Bassham cycle activity may be involved in recycling metabolic CO2. Glandular trichomes cope with oxidative stress by producing high levels of polyunsaturated fatty acids, oxylipins, and glutathione. Finally, distinct mechanisms are present in glandular trichomes to increase the supply of precursors for the isoprenoid pathways. Particularly, the citrate-malate shuttle supplies cytosolic acetyl CoA and plastidic glycolysis and malic enzyme support the formation of plastidic pyruvate. A model is proposed on how glandular trichomes achieve high metabolic productivity.
Question: Write a study description for the study titled 'Small auxin-up RNA promotes GmMYB176 gene transcription to modulate soybean isoflavone content'.
Answer: Isoflavones have been widely studied because of their potential health benefits, including antioxidant, anti-inflammatory, and anticancer properties. Soybeans (Glycine max (L.) Merr) are an effective source of natural isoflavones in humans. Therefore, it is important to cultivate varieties showing increased isoflavone contents and elucidate the secondary metabolic pathways of soybean isoflavones. The small auxin-up RNA (SAUR) gene family is the largest family in the auxin response. However, few reports have described their roles in soybean flavonoid metabolism. In this study, the contents of 200 flavonoid target metabolites in GmSAUR:GmSAUR transgenic soybeans were determined. The results showed that the transgenic soybeans had higher daidzein and genistin contents. Chromatin immunoprecipitation sequencing identified potential targets, including GmMYB176. GmSAUR bound to the promoter of GmMYB176; activated the expression of cinnamate 4-hydroxylase, isoflavone-7-O-beta-glucoside 6′′-O-malonyltransferase, cytochrome P450 84A1-like, and cytochrome P450 84A1; and promoted the accumulation of soybean isoflavones. These results suggested that the GmSAUR gene promoted the accumulation of soybean isoflavones by regulating the expression of GmMYB176.
Question: Write a study description for the study titled 'Mining for metabolic responses to long-term salt stress: a case study on Arabidopsis thaliana Col-0 (A)'.
Answer: New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using diverse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and divergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress.
Question: Write a study description for the study titled 'Hypusination Orchestrates the Antimicrobial Response of Macrophages'.
Answer: Innate responses of myeloid cells defend against pathogenic bacteria via inducible effectors. Deoxyhypusine synthase (DHPS) catalyzes the transfer of the N-moiety of spermidine to the lysine-50 residue of eukaryotic translation initiation factor 5A (EIF5A) to form the amino acid hypusine. Hypusinated EIF5A (EIF5AHyp) transports specific mRNAs to ribosomes for translation. We show that DHPS is induced in macrophages by two gastrointestinal pathogens, Helicobacter pylori and Citrobacter rodentium, resulting in enhanced hypusination of EIF5A. EIF5AHyp was also increased in gastric macrophages from patients with H. pylori gastritis. Furthermore, we identify the bacteria-induced immune effectors regulated by hypusination. This set of proteins includes essential constituents of antimicrobial response and autophagy. Mice with myeloid cell-specific deletion of Dhps exhibit reduced EIF5AHyp in macrophages and increased bacterial burden and inflammation. Thus, regulation of translation through hypusination is a critical hallmark of the defense of eukaryotic hosts against pathogenic bacteria.
Question: Write a study description for the study titled 'Short-term changes in the serum metabolome after laparoscopic sleeve gastrectomy and Roux-en-Y gastric bypass'.
Answer: INTRODUCTION: Bariatric surgery is known to be the most effective treatment for weight loss in obese patients and for the rapid remission of obesity-related comorbidities. These short-term improvements result from not only limited digestion or absorption but also dynamic changes in metabolism throughout the whole body. However, short-term metabolism studies associated with bariatric surgery in Asian individuals have not been reported.OBJECTIVES: The aim of this study was to investigate the short-term metabolome changes in the serum promoted by laparoscopic sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) and to determine the underlying mechanisms that affect obesity-related comorbidities.METHODS: Serum samples were collected from Korean patients who underwent RYGB or SG before and 4 weeks after the surgery. Metabolomic and lipidomic profiling was performed using UPLC-Orbitrap-MS, and data were analyzed using statistical analysis.RESULTS: Metabolites mainly related to amino acids, lipids (fatty acids, glycerophospholipids, sphingolipids, glycerolipids) and bile acids changed after surgery, and these changes were associated with the lowering of risk factors for obesity-related diseases such as nonalcoholic fatty liver disease (NAFLD), type 2 diabetes (T2D) and atherosclerosis. Interestingly, the number of significantly altered metabolites related to the lipid metabolism were greater in SG than in RYGB. Furthermore, the metabolites related to amino acid metabolism were significantly changed only after SG, whereas bile acid changed significantly only following RYGB.CONCLUSION: These differences could result from anatomical differences between the two surgeries and could be related to the gut microbiota. This study provides crucial information to expand the knowledge of the common but different molecular mechanisms involved in obesity and obesity-related comorbidities affected by each bariatric procedure.
Question: Write a study description for the study titled 'Volatilomic and sensorial profiles of Cabernet Sauvignon wines fermented with different commercial yeasts'.
Answer: Cabernet Sauvignon wines from San Vicente, B.C., México, vintage 2021 fermented with three different commercial yeasts (WLP740, ICVD80 and ICVD254) were analyzed by HS-SPME-GC-qTOF/MS.
Question: Write a study description for the study titled 'An interoperability framework for multicentric breath metabolomic studies'.
Answer: Exhaled breath contains valuable information at the molecular level and offers promising potential for precision medicine. However, few breath tests transition to routine clinical practice, partly because of the missing validation in multicenter trials. Therefore, we developed and applied an interoperability framework for standardized multicenter data acquisition and processing for breath analysis with secondary electrospray ionization-high resolution mass spectrometry. We aimed to determine the technical variability and metabolic coverage. Comparison of multicenter data revealed a technical variability of ∼20% and a core signature of the human exhaled metabolome consisting of ∼850 features, corresponding mainly to amino acid, xenobiotic, and carbohydrate metabolic pathways. In addition, we found high inter-subject variability for certain metabolic classes (e.g., amino acids and fatty acids), whereas other regions such as the TCA cycle were relatively stable across subjects. The interoperability framework and overview of metabolic coverage presented here will pave the way for future large-scale multicenter trials.
Question: Write a study description for the study titled 'The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism'.
Answer: The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids (BIAs) such as sanguinarine (SAN) and chelerythrine (CHE), but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding 13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.
Question: Write a study description for the study titled 'Comparison of lipidome profiles of Caenorhabditis elegans—results from an inter-laboratory ring trial'.
Answer: IntroductionLipidomic profiling allows 100s if not 1000s of lipids in a sample to be detected and quantified. Modern lipidomics techniques are ultra-sensitive assays that enable the discovery of novel biomarkers in a variety of fields and provide new insight in mechanistic investigations. Despite much progress in lipidomics, there remains, as for all high throughput 'omics' strategies, the need to develop strategies to standardize and integrate quality control into studies in order to enhance robustness, reproducibility, and usability of studies within specific fields and beyond.ObjectivesWe aimed to understand how much results from lipid profiling in the model organism Caenorhabditis elegans are influenced by different culture conditions in different laboratories.MethodsIn this work we have undertaken an inter-laboratory study, comparing the lipid profiles of N2 wild type C. elegans and daf-2(e1370) mutants lacking a functional insulin receptor. Sample were collected from worms grown in four separate laboratories under standardized growth conditions. We used an UPLC-UHR-ToF-MS system allowing chromatographic separation before MS analysis.ResultsWe found common qualitative changes in several marker lipids in samples from the individual laboratories. On the other hand, even in this controlled experimental system, the exact fold-changes for each marker varied between laboratories.ConclusionOur results thus reveal a serious limitation to the reproducibility of current lipid profiling experiments and reveal challenges to the integration of such data from different laboratories.
Question: Write a study description for the study titled 'Exposomic Biomonitoring of Polyphenols by Non-Targeted Analysis and Suspect Screening'.
Answer: Polyphenols, prevalent in plants and fungi, are investigated intensively in nutritional and clinical settings because of their beneficial bioactive properties. Due to their complexity, analysis with untargeted approaches is favorable, which typically use high-resolution mass spectrometry (HRMS) rather than low-resolution mass spectrometry (LRMS). Here, the advantages of HRMS were evaluated by thoroughly testing untargeted techniques and available online resources. By applying data-dependent acquisition on real-life urine samples, 27 features were annotated with spectral libraries, 88 with in silico fragmentation and 113 by MS1 matching with PhytoHub, an online database containing >2000 polyphenols. Moreover, other exogenous and endogenous molecules were screened to measure chemical exposure and potential metabolic effects using the Exposome-Explorer database, further annotating 144 features. Additional polyphenol-related features were explored using various non-targeted analysis techniques including MassQL for glucuronide and sulfate neutral losses, and MetaboAnalyst for statistical analysis. As HRMS typically suffers a sensitivity loss compared to state-of-the-art LRMS used in targeted workflows, the gap between the two instrumental approaches was quantified in three spiked human matrices (urine, serum, plasma) as well as real-life urine samples. Both instruments showed feasible sensitivity, with median limits of detection in the spiked samples being 10-18 ng/mL for HRMS and 4.8-5.8 ng/mL for LRMS. The results demonstrate that, despite its intrinsic limitations, HRMS can readily be used for comprehensively investigating human polyphenol exposure. In the future, this work is expected to allow for linking human health effects with exposure patterns and toxicological mixture effects with other xenobiotics.