LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals'.
Answer: Viruses manipulate cellular metabolism and macromolecule recycling processes like autophagy. Dysregulated metabolism might lead to excessive inflammatory and autoimmune responses as observed in severe and long COVID-19 patients. Here we show that SARS-CoV-2 modulates cellular metabolism and reduces autophagy. Accordingly, compound-driven induction of autophagy limits SARS-CoV-2 propagation. In detail, SARS-CoV-2-infected cells show accumulation of key metabolites, activation of autophagy inhibitors (AKT1, SKP2) and reduction of proteins responsible for autophagy initiation (AMPK, TSC2, ULK1), membrane nucleation, and phagophore formation (BECN1, VPS34, ATG14), as well as autophagosome-lysosome fusion (BECN1, ATG14 oligomers). Consequently, phagophore-incorporated autophagy markers LC3B-II and P62 accumulate, which we confirm in a hamster model and lung samples of COVID-19 patients. Single-nucleus and single-cell sequencing of patient-derived lung and mucosal samples show differential transcriptional regulation of autophagy and immune genes depending on cell type, disease duration, and SARS-CoV-2 replication levels. Targeting of autophagic pathways by exogenous administration of the polyamines spermidine and spermine, the selective AKT1 inhibitor MK-2206, and the BECN1-stabilizing anthelmintic drug niclosamide inhibit SARS-CoV-2 propagation in vitro with IC50 values of 136.7, 7.67, 0.11, and 0.13 μM, respectively. Autophagy-inducing compounds reduce SARS-CoV-2 propagation in primary human lung cells and intestinal organoids emphasizing their potential as treatment options against COVID-19.
Question: Write a study description for the study titled 'Drying Enhances Signal Intensities for Global GC–MS Metabolomics'.
Answer: We report here that a straightforward change of the standard derivatization procedure for GC–MS metabolomics is leading to a strong increase in metabolite signal intensity. Drying samples between methoxymation and trimethylsilylation significantly increased signals by two- to tenfold in extracts of yeast cells, plant and animal tissue, and human urine. This easy step reduces the cost of sample material and the need for expensive new hardware.
Question: Write a study description for the study titled 'An LCMS-based untargeted metabolomics protocol for cochlear perilymph: highlighting metabolic effects of hydrogen gas on the inner ear of noise exposed Guinea pigs'.
Answer: INTRODUCTION: Noise-induced hearing loss (NIHL) is an increasing problem in society and accounts for a third of all cases of acquired hearing loss. NIHL is caused by formation of reactive oxygen species (ROS) in the cochlea causing oxidative stress. Hydrogen gas (H2) can alleviate the damage caused by oxidative stress and can be easily administered through inhalation.OBJECTIVES: To present a protocol for untargeted metabolomics of guinea pig perilymph and investigate the effect of H2 administration on the perilymph metabolome of noise exposed guinea pigs.METHODS: The left ear of guinea pigs were exposed to hazardous impulse noise only (Noise, n = 10), noise and H2 (Noise + H2, n = 10), only H2 (H2, n = 4), or untreated (Control, n = 2). Scala tympani perilymph was sampled from the cochlea of both ears. The polar component of the perilymph metabolome was analyzed using a HILIC-UHPLC-Q-TOF-MS-based untargeted metabolomics protocol. Multivariate data analysis (MVDA) was performed separately for the exposed- and unexposed ear.RESULTS: MVDA allowed separation of groups Noise and Noise + H2 in both the exposed and unexposed ear and yielded 15 metabolites with differentiating relative abundances. Seven were found in both exposed and unexposed ear data and included two osmoprotectants. Eight metabolites were unique to the unexposed ear and included a number of short-chain acylcarnitines.CONCLUSIONS: A HILIC-UHPLC-Q-TOF-MS-based protocol for untargeted metabolomics of perilymph is presented and shown to be fit-for-purpose. We found a clear difference in the perilymph metabolome of noise exposed guinea pigs with and without H2 treatment.
Question: Write a study description for the study titled 'Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil’s Hole, Bermuda'.
Answer: Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.
Question: Write a study description for the study titled 'Prophylactic and therapeutic itaconate treatment alleviates COVID-19-associated lung injury'.
Answer: Although itaconate demonstrates anti-inflammatory and antimicrobial properties as an immunomodulatory metabolite, the therapeutic potential and mechanistic basis of vaccine-induced or prophylactic itaconate administration in COVID-19 intervention remains underexplored. Our studies reveal that intranasal delivery of dNS1-RBD significantly upregulates endogenous itaconate production. Subsequent research reals that both systemic (intraperitoneal) and pulmonary-targeted (intranasal) itaconate administration mitigate acute lung injury by augmenting efferocytosis and reprogramming macrophage lipid metabolism. Metabolomic analyses further uncover that exogenous itaconate modulates amino acid flux, with parallel protection observed through ornithine/arginine supplementation, suggesting a universal metabolic preconditioning mechanism. This conserved tolerance pathway, validated in human BALF scRNA-seq datasets, establishes metabolic intervention as a strategic approach to harmonize antiviral responses and inflammation control during viral challenge.
Question: Write a study description for the study titled 'Evaluation of the toxic effects of municipal wastewater effluent on mice using omic approaches'.
Answer: Municipal wastewater effluents (MWWE) contain a lot of trace organic pollutants, which will be a threat to environmental health. However, little information is available for the mixed toxicity of MWWE on mammals. In the present study, male mice were exposed to MWWE for 90 days, and then, histopathology and clinical biochemistry determination and transcriptomic and metabolomic profiling were conducted. The results showed that MWWE exposure resulted in injuries in liver and kidney. Combined transcriptomic and metabolomic data demonstrated that MWWE exposure induced perturbations of metabolism, including lipid, nucleotide, amino acid, and energy metabolism. Furthermore, dysregulation of signal transduction processes were also identified based on differentially expressed genes. These results suggested that chronic exposure to MWWE could induce hepatotoxicity and nephrotoxicity in mice and omic approaches are of practical value to evaluate the complex toxicity of MWWE.
Question: Write a study description for the study titled 'A systems analysis with “simplified source-sink model” reveals metabolic reprogramming in a pair of source-to-sink organs during early fruit development in tomato by LED light treatments'.
Answer: Tomato (Solanum lycopersicum) is a model crop for studying development regulation and ripening in flesh fruits and vegetables. Supplementary light to maintain the optimal light environment can lead to the stable growth of tomatoes in greenhouses and areas without sufficient daily light integral. Technological advances in genome-wide molecular phenotyping have dramatically enhanced our understanding of metabolic shifts in the plant metabolism across tomato fruit development. However, comprehensive metabolic and transcriptional behaviors along the developmental process under supplementary light provided by light-emitting diodes (LED) remain to be fully elucidated. We present integrative omic approaches to identify the impact on the metabolism of a single tomato plant leaf exposed to red LEDs of different intensities during the fruit development stage. Our special light delivery system, the “simplified source-sink model”, involves the exposure of a single leaf below the second truss to red LED light of different intensities. We evaluated fruit-size- and fruit-shape variations elicited by different light intensities. Our findings suggest that more than high-light treatment (500 mmol/m^2/s) with the red LED light is required to accelerate fruit growth for 2 weeks after anthesis. To investigate transcriptomic and metabolomic changes in leaf- and fruit samples we used microarray-, RNA sequencing-, and gas chromatography-mass spectrometry techniques. We found that metabolic shifts in the carbohydrate metabolism and in several key pathways contributed to fruit development, including ripening and cell-wall modification. Our findings suggest that the proposed workflow aids in the identification of key metabolites in the central metabolism that respond to monochromatic red-LED treatment and contribute to increase the fruit size of tomato plants. This study expands our understanding of systems-level responses mediated by low-, appropriate-, and high levels of red light irradiation in the fruit growth of tomato plants.
Question: Write a study description for the study titled 'Determination and comparison of SCFAs in serum and colon content samples: Alzheimer's disease rat as a case study (SCFA serum and colon content determination)'.
Answer: SCFAs are the main microbial fermentation products from dietary fibers in colon and play a key role in keeping healthy in the whole-body. However, differences of SCFAs concentration in the serum and colon samples collected from rats had attracted few attentions. Here, we optimized the extract and analysis methods for quantification of ten SCFAs in both serum and colon content samples. Methanol and acetonitrile were chosen for extraction of SCFAs from serum and colon content samples, respectively. Biological samples collected from Alzheimer's disease rats treated by extract of Schisandra chinensis (Turcz.) Baill (SC-extract) were taken as research objects. The results showed that, the relative peak intensities of SCFAs in colon content from all groups were quite similar, and the trend was identical in serum samples. Compared with the values in human, the ratio of ten SCFAs in rat's colon was similar, while the percent of acetate in rat's serum was significantly higher. For therapy of AD, SC-extract decreased the concentration of butyrate, 3-Methyvalerate and caproate in serum samples towards the trend of normal rats. The present study may help to understand the transport of SCFAs across colonic epithelium in healthy and diseased organisms.SCFA serum and colon content determination is reported in the current study MTBLS2088Method validation is reported in MTBLS2146
Question: Write a study description for the study titled 'Analysis of 3274 bacterial isolates by rapid evaporative ionisation mass spectrometry (REIMS)'.
Answer: Analysis of bacterial composition using rapid evaporative ionisation mass spectrometry (REIMS) allows for the detection of metabolites that may be considered specific to particular taxons. This database of 3274 isolates covering gram positive and negative bacteria across 5 phyla, 12 classes, 24 orders, 49 families, 85 genera and 239 different species was used to determine m/z features with a high degree of specificity and sensitivity to particular taxonomic levels. To do so, a subset of 597 isolates was identified, from which ~5000 m/z variables were derived, of which 359 were identified as taxon specific markers (TSMs) using this code [1]. Validation was performed using the remaining observations from this dataset. Human colorectal cancer samples analysed by mass spectrometry imaging were also analysed as part of the study to determine if the TSMs could be detected from clinical samples. These files can be found in MTBLS289 [2].[1] https://github.com/jsmckenzie/bacterialTSM[2] https://www.ebi.ac.uk/metabolights/MTBLS289
Question: Write a study description for the study titled 'An LC–MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology'.
Answer: INTRODUCTION: Given a raw LC–MS dataset, it is often required to rapidly generate initial hypotheses, in conjunction with other ‘omics’ datasets, without time-consuming lipid verifications. Furthermore, for meta-analysis of many datasets, it may be impractical to conduct exhaustive confirmatory analyses. In other cases, samples for validation may be difficult to obtain, replicate or maintain. Thus, it is critical that the computational identification of lipids is of appropriate accuracy, coverage, and unbiased by a researcher’s experience and prior knowledge. OBJECTIVES: We aim to prescribe a systematic framework for lipid identifications, without usage of their characteristic retention-time by fully exploiting their underlying mass features. RESULTS: Initially, a hybrid technique, for deducing both common and distinctive daughter ions, is used to infer parent lipids from deconvoluted spectra. This is followed by parent confirmation using basic knowledge of their preferred product ions. Using the framework, we could achieve an accuracy of ~ 80% by correctly identified 101 species from 18 classes in Chinese hamster ovary (CHO) cells. The resulting inferences could explain the recombinant-producing capability of CHO-SH87 cells, compared to non-producing CHO-K1 cells. For comparison, a XCMS-based study of the same dataset, guided by a user’s ad-hoc knowledge, identified less than 60 species of 12 classes from thousands of possibilities. CONCLUSION: We describe a systematic LC–MS-based framework that identifies lipids for rapid hypothesis generation.
Question: Write a study description for the study titled 'Comparative analysis of whole plant, flower and root extracts of Chamomilla recutita L. and characteristic pure compounds reveals differential anti-inflammatory effects on human T cells'.
Answer: IntroductionChronic inflammation is a hallmark of chronic wounds and inflammatory skin diseases. Due to a hyperactive and prolonged inflammation triggered by proinflammatory immune cells, transitioning to the repair and healing phase is halted. T cells may exacerbate the proinflammatory milieu by secreting proinflammatory cytokines. Chamomilla recutita L. (chamomile) has been suggested for use in several inflammatory diseases, implying a capability to modulate T cells. Here, we have characterized and compared the effects of differently prepared chamomile extracts and characteristic pure compounds on the T cell redox milieu as well as on the migration, activation, proliferation, and cytokine production of primary human T cells.MethodsPhytochemical analysis of the extracts was carried out by LC-MS/MS. Primary human T cells from peripheral blood (PBTs) were pretreated with aqueous or hydroethanolic chamomile extracts or pure compounds. Subsequently, the effects on intracellular ROS levels, SDF-1α induced T cell migration, T cell activation, proliferation, and cytokine production after TCR/CD3 and CD28 costimulation were determined. Gene expression profiling was performed using nCounter analysis, followed by ingenuity pathway analysis, and validation at protein levels.ResultsThe tested chamomile extracts and pure compounds differentially affected intracellular ROS levels, migration, and activation of T cells. Three out of five differently prepared extracts and two out of three pure compounds diminished T cell proliferation. In line with these findings, LC-MS/MS analysis revealed high heterogeneity of phytochemicals among the different extracts. nCounter based gene expression profiling identified several genes related to T cell functions associated with activation and differentiation to be downregulated. Most prominently, apigenin significantly reduced granzyme B induction and cytotoxic T cell activity.ConclusionOur results demonstrate an anti-inflammatory effect of chamomile- derived products on primary human T cells. These findings provide molecular explanations for the observed anti-inflammatory action of chamomile and imply a broader use of chamomile extracts in T cell driven chronic inflammatory diseases such as chronic wounds and inflammatory skin diseases. Importantly, the mode of extract preparation needs to be considered as the resulting different phytochemicals can result in differential effects on T cells.
Question: Write a study description for the study titled 'Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis'.
Answer: Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of Yersinia pestis (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (n = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences.
Question: Write a study description for the study titled 'Exploring plant stress mechanism based on metabolomics'.
Answer: This study investigates lipid dysregulation in calcific aortic valve stenosis (CAVS) by analyzing lipid profiles in valve tissues from 99 patients across different disease severities (mild, moderate, severe) using liquid chromatography-mass spectrometry (LC-MS). The results reveal distinct lipid alterations that correspond to disease progression, with significant correlations between diacylglycerol (DG) and alkyl lysophosphatidylcholine (LPC(O)) levels and key markers of valve stiffness, such as peak aortic jet velocity and mean pressure gradient. Unique lipid profiles, marked by elevated cholesteryl esters and triacylglycerols, were identified in fast-progressing cases. Additionally, plasma lipids TG 52:4 and TG 54:4 emerged as promising non-invasive diagnostic markers, surpassing traditional markers in diagnostic performance. This study highlights the potential of specific lipidomic pathways as therapeutic targets in CAVS, given the current lack of effective pharmacological treatments.
Question: Write a study description for the study titled 'Aging markers in human urine: A comprehensive, non-targeted LC-MS study'.
Answer: Summary Metabolites in human biofluids document individual physiological status. We conducted comprehensive, non-targeted, non-invasive metabolomic analysis of urine from 27 healthy human subjects, comprising 13 youths (30±3 yr) and 14 seniors (76±4 yr). Quantitative analysis of 99 metabolites revealed 55 that were linked to aging, displaying significant differences in abundance between the two groups. These include 13 standard amino acids, 5 methylated, 4 acetylated, and 9 other amino acids, 6 nucleosides, nucleobases, and derivatives, 4 sugar derivatives, 5 sugar phosphates, 4 carnitines, 2 hydroxybutyrates, 1 choline, and 1 ethanolamine derivative, and glutathione disulfide. Abundances of 53 compounds decreased, while 2 increased in elderly people. Many age-linked markers were highly correlated; 42 of 55 compounds, showed Pearson’s correlation coefficients larger than 0.70. As metabolite profiles of urine and blood are quite different, age-related information in urine components offer yet more valuable insights into aging mechanisms of endocrine system and related organ systems.