LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism'.
Answer: Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC-MS and GC-MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.
Question: Write a study description for the study titled 'Multi-omics toxicity profiling of engineered nanomaterials'.
Answer: This study aims to implement methods for toxicological profiling of engineered nanomaterials using toxicogenomics, proteomics, and metabolomics along with computational analyses. For all three omics layers the human cell lines A549 (lung epithelial cells) and THP1 (monocytes) were separately exposed to the nanomaterials TiO2 NM104, MWNCT NM401, and Ag NM300k. Proteomics and metabolomics samples have been performed as biological triplicates and were taken after 0, 6, 12, 24, and 48 hours. To assess ecotoxic effects C. elegans worms were grown in soil treated with NM300k. Ecotox samples were taken only at 0 and 24 hours. Integrating all three omics layers will enable the identification of (novel) ENM specific modes of action (MoA).Data availability:Proteomic data associated with this study are available in the PRIDE repository: accession number PXD002401.
Question: Write a study description for the study titled 'AMPK activation orchestrated replicative senescence of periodontal ligament stem cells via regulating metabolomics'.
Answer: BACKGROUND: Periodontal ligament mesenchymal stem cells (PDLSCs) are a promising cell resource for cell-based regenerative medicine in dentistry. PDLSCs inevitably acquire a senescent phenotype after prolonged in vitro expansion, and the key regulators of cells during replicative senescence remain unclear.METHODS: We cultured periodontal ligament stem cells to passages 4, 10 and 20 (P4, P10, P20). The senescent phenotypes, proliferation and migration ability of PDLSCs (P4, P10, P20) were detected, and non-targeted metabonomic sequencing was performed. We treated PDLSCs with AICAR and detected the expression of FOXO1, FOXO3a, FOXO6 and AMPK phosphorylation (p-AMPK) levels of replicating senescent PDLSCs to explore the correlation between the metabolic changes and the AMPK pathway.RESULTS: Immunofluorescence staining of γ-H2AX, β-galactosidase staining, cell scratch test and qPCR were performed to confirm the occurrence of replicative senescence in PDLSCs during passaging. Three groups of cells at passage 4 (P4), passage 10 (P10) and passage 20 (P20) were collected for non-targeted metabolomics analysis. Metabonomic sequencing showed that the metabolism of replicative senescence in PDLSCs varied significantly. In particular, the content of fatty acid metabolites decreased with senescence, including capric acid, stearic acid, myristic acid and dodecanoic acid. KEGG pathway analysis showed that the AMPK signaling pathway was closely related to AMP levels. The AMP:ATP ratio increased in senescent PDLSCs; however, the levels of p-AMPK and the profile of FOXO1 and FOXO3a, which are downstream of the AMPK signaling pathway, decreased with senescence. We treated PDLSCs with AICAR, an activator of the AMPK pathway, and the phosphorylated AMPK level at P20 PDLSCs was partially restored. CONCLUSION: In summary, our study suggests that the metabolic process of PDLSCs is active in the early stage of senescence, prefers to consume fatty acids, and is attenuated in the later stages of senescence. AMP accumulates in replicative senescent PDLSCs; however, the sensitivity of AMPK phosphorylation sites is impaired, causing senescent PDLSCs to fail to respond to changes in energy metabolism. Our findings provide a new basis for the clinical application of periodontal ligament stem cells.
Question: Write a study description for the study titled 'The Crosstalk between Microbiota and Metabolites in AP Mice Based on Metagenomics and Untargeted Metabolomics'.
Answer: BACKGROUND AND PURPOSE: The microbiota dysfunction aggravated the severity of acute pancreatitis (AP), but the relationship between microbiota dysfunction and metabolites alteration was not fully explained. This study aimed to explore the crosstalk between microbiota and metabolites in AP mice.METHODS: Experimental AP models were established by caerulein for 7 times plus lipopolysaccharide (LPS) for once in C57/BL mice. To reveal systemic disturbance of AP, metagenomics and untargeted metabolomics were applied to reveal systemic disturbance of microbiota and metabolites in AP progress, respectively.RESULTS: Gut microbiota from AP mice was mainly composed of Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, and presented a 'core microbiota' characterized by an expansion in Proteobacteria as well as a decrease in Actinobacteria. Kyoto encyclopedia of genes and genomes (KEGG) analysis found that the significantly differential microbiota was involved in several signaling networks. Moreover, 872 metabolites were identified from untargeted metabolomics. Among them, lipids and lipid-like molecules were majorly affected. The integrated analysis of metagenomics and metabolomics showed that acetate kinase (Acka) was associated with various gut microbiota, including Alistipes, Butyricimonas and Lactobacillus. Particularly, Acka was tightly correlated with the metabolite daphnoretin. Besides, the functional gene of O-acetyl-L-serine sulfhydrylase (Cysk) was correlated with Alistipes, Jeotgalicoccus and Lactobacillus, and which was associated with metabolites of bufalin and Phlorobenzophenone.CONCLUSION: Our study uncovered the relationship between gut microbiota and metabolites during AP, especially the Lactobacillus, Alistipes and Butyricimonas associated functional genes (Acka and Cysk) was tightly correlated to anti-inflammation and anti-tumor metabolites (daphnoretin and bufalin).
Question: Write a study description for the study titled 'Hyperoxia induces glutamine-fuelled anaplerosis in retinal Müller cells'.
Answer: Premature infants require oxygen supplementation to survive, but excess oxygen causes retinovascular growth suppression that underlies the leading cause of infant blindness known as retinopathy of prematurity (ROP). We analyzed changes in intermediary metabolism during hyperoxia in human retinal endothelial cells (RECs) and human retinal Müller glia, which coexist through glutamine consumption and production, respectively. Using a stable isotope labeling technique in human RECs and human Müller cells in culture, here we show that Müller cells in hyperoxia block entry of glycolytic carbon into the tricarboxylic acid (TCA) cycle and instead oxidize glutamine. In hyperoxia, catabolism of glutamine increased ammonium release by 2-fold. Hyperoxia induces glutamine-fueled anaplerosis that reverses basal Müller cell metabolism from production to consumption of glutamine.
Question: Write a study description for the study titled 'Compilation of transcriptomics, non-targeted metabolomics and targeted metabolomics data in bovine mammary epithelial cells stimulated by ten different essential amino acids (Untargeted metabolomics)'.
Answer: Divergence in the non-targeted metabolite profilings of bovine mammary epithelial cells (BMECs) were systematically captured with regard to 10 individual essential amino acid (EAA) availability. BMECs cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6). DMEM-F12 medium is the positive control treatment (POS), while DMEM-F12 medium devoid of all EAA served as the negative control treatment (NEG). A total of 10 treatments were NEG individually supplemented with arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan or valine (Sigma-Aldrich, MO, USA). Individual EAA were supplemented to achieve concentrations equal to those of POS. After 6-h treatment, all cell samples were taken at the same time, frozen in liquid nitrogen and stored at -80 °C until required.Untargeted metabolomics is reported in the current study MTBLS7789.Targeted metabolomics is reported in MTBLS3956.
Question: Write a study description for the study titled 'Industrial by-products as a novel circular source of biocompatible extracellular vesicles'.
Answer: Extracellular vesicles (EVs) constitute an intricate system of molecular exchange that has recently gained tremendous interest. However, sustainable sources of safe biological EVs remain scarce and elusive. In this study we explore and define the use of food industry byproducts (BP) as a circular source of safe biocompatible EVs. Averaged diameter and molecular compositions indicate large yield of exosomes and high abundancy of membrane lipids with signaling capacity in these vesicles. Complex proteomes mimicking those circulating in human blood plasma were also identified. Furthermore, BP-EVs did not show relevant cytotoxicity and displayed excellent oral and intravenous bioavailability together with specific organ targeting capacity. Collectively, we believe that the novel findings reported here will open substantial venues for the use of BP as an optimal source of biocompatible nanovesicles in manifold applications of the bioeconomy and biomedical fields.
Question: Write a study description for the study titled 'A metabolic dependency for host isoprenoids in the obligate intracellular pathogen Rickettsia parkeri underlies a sensitivity for the statin class of host-targeted therapeutics'.
Answer: Gram-negative bacteria in the order Rickettsiales are obligate intracellular parasites that cause human diseases such typhus and spotted fever. They have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome streamlining. However, it remains largely unknown which nutrients they require and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. We further investigated whether the spotted fever group Rickettsia species Rickettsia parkeri scavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry in uninfected and infected cells, we found decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that bacterial growth is prohibited by inhibition of the host isoprenoid pathway with the statins class of drugs. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting statins inhibit cell wall synthesis. Altogether, our results describe an Achilles' heel of obligate intracellular pathogens that can be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth.
Question: Write a study description for the study titled 'Streamlining LC-MS/MS Data Analysis in R with Open-Source *xcms* and *RforMassSpectrometry*: An End-to-End Workflow'.
Answer: Despite untargeted LC-MS/MS data being a powerful approach for large-scale metabolomics analysis, a significant challenge in the field lies in the reproducible and efficient analysis of such data, in particular. The power of R-based analysis workflows lies in their high customizability and adaptability to specific instrumental and experimental setups, but, while various specialized packages exist for individual analysis steps, their seamless integration and application to large cohort datasets remains elusive. Addressing this gap, we present an comprehensible end-to-end R workflow that leverages xcms and packages of the RforMassSpectrometry environment to encompass all aspects of pre-processing and downstream analyses for LC-MS/MS datasets in a reproducible manner.This workflow delineates a step-by-step analysis of an example untargeted metabolomics dataset tailored to quantify the small polar metabolome in human plasma samples and aimed to identify differences between individuals suffering from a cardiovascular disease and healthy controls. The objective of the workflow is to meticulously detail each step, from the preprocessing of raw mzML files to the annotation of differentially abundant ions between the two groups. Our workflow seamlessly integrates Bioconductor packages, offering adaptability to diverse study designs and analysis requirements.This workflow facilitates preprocessing, feature detection, alignment, normalization, statistical analysis and annotation within a unified framework, thereby enhancing the efficiency of metabolomic investigations. We also discuss alternative approaches to accommodate various dataset and goals, while emphasizing proper quality management for LC-MS data analysis. The source code of the workflow is available at https://github.com/EuracBiomedicalResearch/end-to-end-untargeted-metabolomics.
Question: Write a study description for the study titled 'Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere'.
Answer: Heavy metal contamination poses an escalating global challenge to soil ecosystems. Hyperaccumulators play a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.
Question: Write a study description for the study titled 'CYP51A1-mediated alkaliptosis resistance is a targetable vulnerability in pancreatic cancer'.
Answer: Alkaliptosis, a pH-dependent form of regulated cell death characterized by impaired lysosomal function and lethal alkalinization, holds promise as a target for cancer therapy. Here, we utilize mass spectrometry-based drug target, transcriptomic screens and lipid metabolomics to explore the metabolic mechanisms underlying alkaliptosis. We reveal CYP51A1, a gene involved in cholesterol synthesis, as a key suppressor of alkaliptosis in pancreatic cancer cells. Inducing alkaliptosis leads to a decrease in endoplasmic reticulum cholesterol levels, subsequently activating SREBF2, a transcription factor responsible for controlling the expression of genes involved in cholesterol biosynthesis. Specifically, SREBF2-driven upregulation of CYP51A1 prevents cholesterol accumulation within lysosomes, leading to TMEM175-dependent lysosomal proton efflux, ultimately resulting in the inhibition of alkaliptosis. In animal models, including xenografts, orthotopic and patient-derived models, the genetic or pharmacological inhibition of CYP51A1 enhances the effectiveness of JTC801 in suppressing pancreatic tumors. These findings demonstrate the key role of the CYP51A1-dependent lysosomal pathway in inhibiting alkaliptosis and highlight its potential as a targetable vulnerability in pancreatic cancer.PDAC-PANC1 cell line analysis is reported in the current study MTBLS9283.PDAC-SW1990 cell line analysis is reported in MTBLS9288.
Question: Write a study description for the study titled 'Whole genome CRISPRi screening identifies druggable vulnerabilities in drug-resistant Mycobacterium tuberculosis'.
Answer: Tuberculosis (TB) remains a global health threat, aggravated by the emergence of drug-resistant strains. This study aims to identify genes and metabolic pathways with increased vulnerability in drug-resistant Mycobacterium tuberculosis strains compared to their drug-susceptible counterparts. Using CRISPR interference (CRISPRi), we screened for critical pathways unique or shared across resistant strains. The findings reveal potential therapeutic targets, offering new avenues for anti-TB drug development. This approach addresses the urgent need for effective treatments against drug-resistant TB and advances our understanding of its underlying resistance mechanisms. This work highlights how changes in the physiology of drug-resistant strains generate druggable vulnerabilities that can be exploited to improve clinical outcomes.
Question: Write a study description for the study titled 'A new method for quantitative determination of bitter components of Belgian endive, with a focus on sesquiterpene oxalates'.
Answer: The sesquiterpene lactones typical of the genera Cichorium and Lactuca were historically thought to be present in the free and glycosylated form, but recent developments have highlighted the presence of highly unusual oxalyl esters. In this work, first a liquid chromatography method that requires minimal sample preparation and can measure both free and conjugated sesquiterpene lactones was developed. Then the most common sample preparation techniques used in the past studies (e.g., solid-phase extraction, liquid/liquid extraction) were evaluated and shown to introduce significant bias against the polar oxalyl-terpenes. Finally the method was applied to a case study, highlighting the effect of variety, duration and temperature of forcing on the sesquiterpene lactone content of Belgian endive.
Question: Write a study description for the study titled 'A lipidomic human population and translational feeding study of hepatic steatosis and de novo lipogenesis (Murine liver assay)'.
Answer: Background: Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Our aims were to investigate whether a sub-set of TAGs were associated with hepatic steatosis and whether they arise from de novo lipogenesis (DNL) from the consumption of carbohydrates.  Results: We conducted direct infusion mass spectrometry of lipids in plasma to study the association between specific triacylglycerols (TAGs) and hepatic steatosis assessed by ultrasound and fatty liver index in volunteers from the UK-based Fenland Study (n=1507), and evaluated clustering of TAGs in the National Survey of Health and Development UK cohort (n=1701). TAGs formed 3 clusters, with those TAGs containing saturated and monounsaturated fatty acids with 16-18 carbons being specifically associated with hepatic steatosis. These TAGs were associated with higher consumption of carbohydrate and saturated fat, hepatic steatosis, and variations in the gene for protein phosphatase 1, regulatory subunit 3b (PPP1R3B), which in part regulates glycogen synthesis. DNL was measured in hyperphagic ob/ob mice, mice on a Western diet (high in fat and free sugar) and in healthy humans using stable isotope techniques following high carbohydrate meals, demonstrating the rate of DNL correlates with increased synthesis of this cluster of TAGs. Furthermore, these TAGs were increased in plasma from patients with biopsy-confirmed steatosis.  Conclusion: A sub-set of TAGs are associated with hepatic steatosis, even when correcting for common confounding factors. We suggest that hepatic steatosis risk in Western populations is in part driven by increased DNL following carbohydrate rich meals.  The protocols and data of the human carbohydrate feeding study in healthy volunteers are reported in the study MTBLS616.  Linked Studies: MTBLS616
Question: Write a study description for the study titled 'Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction'.
Answer: Poor maternal nutrition causes intrauterine growth restriction (IUGR); however, its effects on fetal cardiac development are unclear. We have developed a baboon model of moderate maternal undernutrition, leading to IUGR. We hypothesized that the IUGR affects fetal cardiac structure and metabolism. Six control pregnant baboons ate ad-libitum (CTRL)) or 70% CTRL from 0.16 of gestation (G). Fetuses were euthanized at C-section at 0.9G under general anesthesia. Male but not female IUGR fetuses showed left ventricular fibrosis inversely correlated with birth weight. Expression of extracellular matrix protein TSP-1 was increased (p<0.05) in male IUGR. Expression of cardiac fibrotic markers TGFß, SMAD3 and ALK-1 were downregulated in male IUGRs with no difference in females. Autophagy was present in male IUGR evidenced by upregulation of ATG7 expression and lipidation LC3B. Global miRNA expression profiling revealed 56 annotated and novel cardiac miRNAs exclusively dysregulated in female IUGR, and 38 cardiac miRNAs were exclusively dysregulated in males (p<0.05). Fifteen (CTRL) and 23 (IUGR) miRNAs, were differentially expressed between males and females (p<0.05) suggesting sexual dimorphism, which can be at least partially explained by differential expression of upstream transcription factors (e.g. HNF4a, and NF?B p50). Lipidomics analysis of fetal cardiac tissue exhibited a net increase in diacylglycerol and plasmalogens and a decrease in triglycerides and phosphatidylcholines. In summary, IUGR resulting from decreased maternal nutrition is associated with sex-dependent dysregulations in cardiac structure, miRNA expression, and lipid metabolism. If these changes persist postnatally, they may program offspring for higher later life cardiac risk.
Question: Write a study description for the study titled 'Lipid mediators of inflammation in BALF 3-19 days after infection with influenza'.
Answer: In this study broncho-alveolar lavage fluid (BALF) from mice infected with influenza A virus, PR8 (200 PFU and 200,000 PFU), X31 (2000,000 PFU) was analyzed for lipidomic host response in comparison with the mock infected animals. Time Points: 3, 5, 7, 9, 11, 13, 19 days post infection, done in 8-10 replicates.)