LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Toxoplasma gondii infection induces metabolic alterations in the mouse cerebellum'.
Answer: Toxoplasma gondii is a protozoan parasite with a remarkable neurotropic affinity. We recently showed that T. gondii infection can alter the global metabolism of the cerebral cortex of the mice. However, the impact of this infection on the metabolism of the cerebellum remained unclear. In this study, we compared the metabolomic profiles of mouse cerebellum following acute and chronic infection with T. gondii. Three-week-old female BALB/c mice (n = 36) were commercially obtained from Lanzhou University Laboratory Animal Center (Lanzhou, China). Mice were separated into 6 groups (6 mice/group). The mice in the infected groups were challenged with 10 T. gondii cysts of PRU strain suspended in 0.5 ml phosphate-buffered saline (PBS), whereas the mice in the control groups were sham treated with 0.5 ml PBS only. All mice were provided non-medicated feed and water ad libitum during the experiment. The mice were monitored twice daily for signs of illness and mortality. At 7, 14, and 21 days post infection (dpi), mice from infected and control group were humanely sacrificed by CO2 asphyxiation and cerebellum of each mouse was dissected with scissors and forceps. Then, the metabolite profile changes in the cerebellum of mice following infection of T. gondii was analyzed.
Question: Write a study description for the study titled 'On-line untargeted metabolomics monitoring of an Escherichia coli succinate fermentation process'.
Answer: The real-time monitoring of metabolites (RTMet) is instrumental for the industrial production of biobased fermentation products. This study shows the first application of untargeted on-line metabolomics for the monitoring of undiluted fermentation broth samples taken automatically from a 5 L bioreactor every 5 min via flow injection mass spectrometry. The travel time from the bioreactor to the mass spectrometer was 30 s. Using mass spectrometry allows, on the one hand, the direct monitoring of targeted key process compounds of interest and, on the other hand, provides information on hundreds of additional untargeted compounds without requiring previous calibration data. In this study, this technology was applied in an Escherichia coli succinate fermentation process and 886 different m/z signals were monitored, including key process compounds (glucose, succinate, and pyruvate), potential biomarkers of biomass formation such as (R)-2,3-dihydroxy-isovalerate and (R)-2,3-dihydroxy-3-methylpentanoate and compounds from the pentose phosphate pathway and nucleotide metabolism, among others. The main advantage of the RTMet technology is that it allows the monitoring of hundreds of signals without the requirement of developing partial least squares regression models, making it a perfect tool for bioprocess monitoring and for testing many different strains and process conditions for bioprocess development.
Question: Write a study description for the study titled 'Neurotransmitter acetylcholine mediates the mummification of Ophiocordyceps sinensis-infected Thitarodes xiaojinensis larvae (Lipidome data)'.
Answer: Parasites can manipulate host behavior to facilitate parasite transmission. One such host-pathogen interaction occurs between the fungus Ophiocordyceps sinensis (O. sinensis) and the ghost moth Thitarodes xiaojinensis. O. sinensis is involved in the mummification process of infected host larvae. However, the underlying molecular and chemical mechanism for this phenomenon is unknown. We characterized the small molecules regulating host behavior and the altered metabolites in infected and mummified host larvae. Lipid-related metabolites, such as phosphatidylcholine (PC) were identified in infected and mummified larvae. Decreased levels of the neurotransmitter acetylcholine (ACh) and elevated choline levels were observed in the brains of both the infected and mummified larvae. The aberrant activity of acetylcholinesterase (AChE) and relative mRNA expression of ACE2 (acetylcholinesterase) may mediate the altered transformation between ACh and choline, leading to the brain dysfunction of mummified larvae. Caspofungin treatment inhibited the mummification of infected larvae and the activity of AChE. These findings indicate the importance of ACh in the mummification of host larvae after O. sinensis infection.Lipidome data is reported in the current study MTBLS9930.Metabolome data is reported in MTBLS9929.
Question: Write a study description for the study titled 'N6-methyladenosine modification is not a general trait of positive-sense RNA viral genomes'.
Answer: Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with a high rate of false positives. Here, we addressed the presence of m6A in CHIKV and DENV RNAs. For this, we combined m6A-seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we found no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery did not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection had no effect on the m6A machinery’s localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.
Question: Write a study description for the study titled 'A non-­invasive method for sampling the body odour of mammals'.
Answer: Olfaction is a central aspect of mammalian communication, providing information about individual attributes such as identity, sex, group membership or genetic quality. Yet, the chemical underpinnings of olfactory cues remain little understood, one of the reasons being the difficulty in obtaining high quality samples for chemical analysis. In this study, we adjusted and evaluated the use of thermal desorption (TD) tubes, commonly used in plant metabolomic and environmental studies, for non-invasive sampling of mammalian body odour. We obtained chemical profiles of meerkat (Suricata suricatta) body odour samples, using TD tubes analysed with gas chromatography–mass spectrometry. TD tubes captured a wide range of volatile and semi-volatile organic compounds, including compounds likely originating from the target animals. Adjustment of sampling parameters (distance, volume, flow rate, interruption of sampling) to increase the feasibility for a non-invasive application yielded samples of adequate quality. However, to minimize the variability between samples, sampling parameters should be kept constant and samples should be collected when no conspecifics are close-by. The method was sensitive enough to pick up population differences in the chemical profiles of two captive groups of meerkats, demonstrating its applicability to biological questions. With sufficiently habituated animals, the method is applicable non-invasively, allowing short- and long-term studies on a wide range of questions, including e.g. chemical signatures of kinship, diet, individual health or reproductive state.
Question: Write a study description for the study titled 'Dissection of two routes to naïve pluripotency using different kinase inhibitors'.
Answer: Embryonic stem cells (ESCs) can be maintained in the naïve state through inhibition of Mek1/2 and Gsk3 (2i). A relevant effect of 2i is the inhibition of Cdk8/19, which are negative regulators of the Mediator complex, responsible for the activity of enhancers. Inhibition of Cdk8/19 (Cdk8/19i) stimulates enhancers and, similar to 2i, stabilizes ESCs in the naïve state. Here, we use mass spectrometry to describe the molecular events (phosphoproteome, proteome, and metabolome) triggered by 2i and Cdk8/19i on ESCs. Our data reveal widespread commonalities between these two treatments, suggesting overlapping processes. We find that post-transcriptional de-repression by both 2i and Cdk8/19i might support the mitochondrial capacity of naive cells. However, proteome reprogramming in each treatment is achieved by different mechanisms. Cdk8/19i acts directly on the transcriptional machinery, activating key identity genes to promote the naïve program. In contrast, 2i stabilizes the naïve circuitry through, in part, de-phosphorylation of downstream transcriptional effectors.
Question: Write a study description for the study titled 'HERPES SIMPLEX VIRUS TYPE 1 IMPAIRS DENDRITIC CELL FUNCTION BY REMODELLING NEUTRAL LIPID METABOLISM AND INDUCING LIPID DROPLET ACCUMULATION'.
Answer: Herpes simplex virus type 1 (HSV-1) infects dendritic cells (DCs), professional antigen-presenting cells that initiate and regulate host antiviral responses. HSV-1 infects DCs limiting their maturation, migration to draining lymph nodes and T cell activation capacity, ultimately promotes their apoptosis. Here, we investigated the impact of HSV-1 infection over neutral lipid metabolism in DCs and their function. We found that HSV-1 significantly alters neutral lipid metabolism in infected DCs and promotes LD accumulation. Pharmacological inhibition of cholesterol ester synthesis, or fatty acid transporter proteins in infected DCs reduced LD accumulation and viral replication, enhanced DC viability and DC migration to draining lymph nodes and promoted DC priming of virus-specific CD8+ T cells. These findings highlight the role of neutral lipid metabolism in HSV-1-infected DCs and its impact over host immunity against this virus, underscoring lipid metabolism in DCs as a potential therapeutical target for triggering antiviral immunity against HSV-1.
Question: Write a study description for the study titled 'Absolute quantification of metabolites in tomato fruit extracts by fast 2D NMR (Calibration Standard 500 MHz samples)'.
Answer: Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism.Calibration Standard 500 MHz samples protocols and data are reported in the current study MTBLS133.Tomato 500 MHz samples protocols and data are reported in MTBLS131.Tomato 700 MHz samples protocols and data are reported in MTBLS132.Calibration Standard 700 MHz samples protocols and data are reported in MTBLS134.
Question: Write a study description for the study titled 'Exploring the gut microbiome and serum metabolome interplay in non-functioning pituitary neuroendocrine tumors.'.
Answer: The gut microbiome has emerged as a potential factor in cancer pathogenesis, but its role in non-functioning pituitary neuroendocrine tumors (NF-PitNETs) remains unclear. This study aimed to elucidate gut microbiome and metabolomic alterations in NF-PitNETs by comparing microbial diversity, pathogenic bacteria and serum metabolomic profiles between NF-PitNET patients and healthy controls. The gut microbiome was assessed through 16S rRNA sequencing, while serum metabolomics was analyzed using mass spectrometry. Correlation analyses identified potential links between microbial characteristics and metabolic markers. The results revealed that specific pathogenic bacteria, such as Bacteroides, were significantly enriched in NF-PitNET patients. Multi-omics correlations suggested that altered microbiota might contribute to NF-PitNET pathogenesis by modulating host metabolic pathways. These findings highlight the potential role of gut microbiome dysbiosis and its metabolic effects in NF-PitNET development, offering insights into possible therapeutic and diagnostic targets.
Question: Write a study description for the study titled 'A Novel Metabolic Signature To Predict the Requirement of Dialysis or Renal Transplantation in Patients with Chronic Kidney Disease'.
Answer: Identification of chronic kidney disease patients at risk of progressing to end-stage renal disease (ESRD) is essential for treatment decision-making and clinical trial design. Here, we explored whether proton nuclear magnetic resonance (NMR) spectroscopy of blood plasma improves the currently best performing kidney failure risk equation, the so-called Tangri score. Our study cohort comprised 4640 participants from the German Chronic Kidney Disease (GCKD) study, of whom 185 (3.99%) progressed over a mean observation time of 3.70 ± 0.88 years to ESRD requiring either dialysis or transplantation. The original four-variable Tangri risk equation yielded a C statistic of 0.863 (95% CI, 0.831-0.900). Upon inclusion of NMR features by state-of-the-art machine learning methods, the C statistic improved to 0.875 (95% CI, 0.850-0.911), thereby outperforming the Tangri score in 94 out of 100 subsampling rounds. Of the 24 NMR features included in the model, creatinine, high-density lipoprotein, valine, acetyl groups of glycoproteins, and Ca2+-EDTA carried the highest weights. In conclusion, proton NMR-based plasma fingerprinting improved markedly the detection of patients at risk of developing ESRD, thus enabling enhanced patient treatment.
Question: Write a study description for the study titled 'System Xc- exacerbates metabolic stress under glucose depletion in oral squamous cell carcinoma'.
Answer: OBJECTIVE: Emerging evidence suggests that glucose depletion (GD)-induced cell death depends on system Xc-, a glutamate/cystine antiporter extensively studied in ferroptosis. However, the underlying mechanism remains debated. Our study confirmed the correlation between system Xc- and GD-induced cell death and provided a strategic treatment for oral squamous cell carcinoma (OSCC).METHODS: qPCR and Western blotting were performed to detect changes in xCT and CD98 expression after glucose withdrawal. Then, the cell viability of OSCCs under the indicated conditions was measured. To identify the GD-responsible transcriptional factors of SLC7A11, we performed a luciferase reporter assay and a ChIP assay. Further, metabolomics was conducted to identify changes in metabolites. Finally, mitochondrial function and ATP production were evaluated using the seahorse assay, and NADP+/NADPH dynamics were measured using a NADP+/NADPH kit.RESULTS: In OSCCs, system Xc- promoted GD-induced cell death by increasing glutamate consumption, which promoted NADPH exhaustion and TCA blockade. Moreover, GD-induced xCT upregulation was governed by the p-eIF2α/ATF4 axis.CONCLUSIONS: System Xc- overexpression compromised the metabolic flexibility of OSCC under GD conditions, and thus, glucose starvation therapy is effective for killing OSCC cells.
Question: Write a study description for the study titled 'Monitoring of system conditioning after blank injections in untargeted UPLC-MS metabolomic analysis'.
Answer: Ultra-performance liquid chromatography - mass spectrometry (UPLC-MS) is widely used for untargeted metabolomics in biomedical research. To optimize the quality and precision of UPLC-MS metabolomic analysis, evaluation of blank samples for the elimination of background features is required. Although blanks are usually run either at the beginning or at the end of a sequence of samples, a systematic analysis of their effect of the instrument performance has not been properly documented. Using the analysis of two common bio-fluids (plasma and urine), we describe how the injection of blank samples within a sequence of samples may affect both the chromatographic and MS detection performance depending on several factors, including the sample matrix and the physicochemical properties of the metabolites of interest. The analysis of blanks and post-blank conditioning samples using t-tests, PCA and guided-PCA provides useful information for the elimination of background UPLC-MS features, the identification of column carry over and the selection of the number of samples required to achieve a stable performance.
Question: Write a study description for the study titled 'Pseudomonas sp. Strain 273 Incorporates Organofluorine into the Lipid Bilayer during Growth with Fluorinated Alkanes'.
Answer: Anthropogenic organofluorine compounds are recalcitrant, globally distributed, and a human health concern. Although rare, natural processes synthesize fluorinated compounds, and some bacteria have evolved mechanisms to metabolize organofluorine compounds. Pseudomonas sp. strain 273 grows with 1-fluorodecane (FD) and 1,10-difluorodecane (DFD) as carbon sources, but inorganic fluoride release was not stoichiometric. Metabolome studies revealed that this bacterium produces fluorinated anabolites and phospholipids. Mass spectrometric fatty acid profiling detected fluorinated long-chain (i.e., C12-C19) fatty acids in strain 273 cells grown with FD or DFD, and lipidomic profiling determined that 7.5 ± 0.2 and 82.0 ± 1.0% of the total phospholipids in strain 273 grown with FD or DFD, respectively, were fluorinated. The detection of the fluorinated metabolites and macromolecules represents a heretofore unrecognized sink for organofluorine, an observation with consequences for the environmental fate and transport of fluorinated aliphatic compounds.
Question: Write a study description for the study titled 'Four Weeks of Probiotic Supplementation Alters the Metabolic Perturbations Induced by Marathon Running: Insight from Metabolomics'.
Answer: Few data are available that describe how probiotics influence systemic metabolism during endurance exercise. Metabolomic profiling of endurance athletes will elucidate mechanisms by which probiotics may confer benefits to the athlete. In this study, twenty-four runners (20 male, 4 female) were block randomised into two groups using a double-blind matched-pairs design according to their most recent Marathon performance. Runners were assigned to 28-days of supplementation with a multi-strain probiotic (PRO) or a placebo (PLB). Following 28-days of supplementation, runners performed a competitive track Marathon race. Venous blood samples and muscle biopsies (vastus lateralis) were collected on the morning of the race and immediately post-race. Samples were subsequently analysed by untargeted 1H-NMR metabolomics. Principal component analysis (PCA) identified a greater difference in the post-Marathon serum metabolome in the PLB group vs. PRO. Univariate tests identified 17 non-overlapped metabolites in PLB, whereas only seven were identified in PRO. By building a PLS-DA model of two components, we revealed combinations of metabolites able to discriminate between PLB and PRO post-Marathon. PCA of muscle biopsies demonstrated no discernible difference post-Marathon between treatment groups. In conclusion, 28-days of probiotic supplementation alters the metabolic perturbations induced by a Marathon. Such findings may be related to maintaining the integrity of the gut during endurance exercise.
Question: Write a study description for the study titled 'Targeted degradation of the α-ketoglutarate dehydrogenase mediated by a mitochondrial DNAJC protein regulates metabolism'.
Answer: Mitochondrial heat shock proteins and co-chaperones play essential roles in maintaining proteostasis. They are renowned for regulating unfolded proteins, usually without specific target preferences. In this study, we identified T cell activation inhibitor, mitochondria (TCAIM), as a novel DNAJC-type co-chaperone and demonstrated its specific binding to α-ketoglutarate dehydrogenase (OGDH), a key rate-limiting enzyme of mitochondrial metabolism. Unexpectedly, this interaction leads to the suppression of OGDH function and subsequent carbohydrate catabolism in both cultured cells and murine models. We further revealed that TCAIM binds to OGDH without inducing changes in its apo structure through cryo-EM resolution of the human TCAIM-OGDH complex. Most significantly, we discovered that TCAIM facilitates the degradation of functional OGDH through this binding, in a manner dependent on mitochondrial heat shock proteins and proteases. Hence, our study unveils an unprecedented role of the mitochondrial proteostasis system in the targeted degradation of a crucial metabolic enzyme. It also introduces a novel post-translational regulatory mechanism.
Question: Write a study description for the study titled 'Therapeutic effects of traditional Chinese medicine compound Hua-Feng-Dan in a rat model of ischemic stroke involve renormalization of gut microbiota'.
Answer: Hua-Feng-Dan is a traditional Chinese medicine compound used to treat ischemic stroke, but little is known about its therapeutic mechanism. This study explored whether and how the mechanism involves readjustment of gut microbiota. Rats were subjected to middle cerebral artery occlusion as a model of ischemic stroke or to sham surgery, then treated or not with Hua-Feng-Dan. The different groups of animals were compared in terms of neurological score, cerebral infarct volume and brain histopathology to assess stroke severity. They were also compared in terms of indices of intestinal barrier permeability, inflammation and oxidative stress as well as composition of the gut microbiota and their metabolites. Hua-Feng-Dan significantly reduced cerebral infarct volume and improved neurological score and brain histopathology on the ischemic side of the brain. It partially reversed stroke-induced intestinal leakiness, inflammation, dyslipidemia and oxidative stress, as well as the stroke-induced increase in pathogenic gut microbiota (e.g. Escherichia-Shigella, Enterococcus, Clostridium_innocuum_group) and decrease in beneficial microbiota (e.g. Lachnospiraceae, unclassified__f__Lachnospiracea and Ruminococcus_torques_group). The treatment altered levels of 39 metabolites produced during metabolism mainly of amino acids, short-chain fatty acids and essential fatty acids. Levels of factors related to inflammation and intestinal barrier permeability correlated positively with relative abundance of Escherichia-Shigella and Clostridium_innocuum_group, and negatively with 4-(glutamylamino)butanoate, 2-hydroxy-3-methylbutyric acid, dihomo-alpha-linolenic acid, dihomolinoleic acid and 10-nitrolinoleic acid. Conversely, levels of 4-(glutamylamino)butanoate, 2-hydroxy-3-methylbutyric acid and 10-nitrolinoleic acid correlated positively with relative abundance of unclassified__f__Lachnospiracea. Our results suggest that Hua-Feng-Dan may mitigate ischemic stroke injury by renormalizing gut microbiota and restoring gut barrier function and gut metabolism, thereby helping to alleviate inflammatory and neurological damage.