LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Multiyear dynamics of recent and legacy contaminants in a German hill-slope catchment (MS1 data)'.
Answer: Anthropogenic activities cause the release of vast amounts of contaminants into the environment and thus also into surface- and groundwaters. Regulatory monitoring determines whether critical threshold concentrations are surpassed, by mostly occasional probing. This irregular testing, however, does not capture the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants in response to water flows. We report the detection and tracing of five contaminants in the 'Hainich Critical Zone Exploratory' (CZE) in central Germany, a monitoring site established for regular sampling of groundwater from different depths and locations along a hill-slope recharge area. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids), the latter being volatilised from wood burning in ovens, show phases of seasonal dynamics in line with their release mode. Further, and alongside legacy herbicides (simazine and the triazine transformation product hydroxypropazine) and the concurrent flame retardant and plasticiser TPP (triphenyl phosphate), mobilisation events emerge from periods of high precipitation and water flows. This investigation highlights the persistence and mobilization of anthropogenic contaminants even in pristine environments. It illustrates the importance of long-term research for understanding ecosystem processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time.MS1 data is reported in the current study MTBLS8433.MS2 data is reported in MTBLS3533.
Question: Write a study description for the study titled 'Whole blood metabolomics of dementia patients reveal classes of disease-linked metabolites'.
Answer: Dementia is caused by factors that damage neurons. We quantified small molecular markers in whole blood of dementia patients, using non-targeted liquid chromatography-mass spectroscopy (LC-MS). Thirty-three metabolites, classified into 5 groups (A-E), differed significantly in dementia patients, compared with healthy elderly subjects. Seven Group A metabolites present in plasma, including quinolinic acid, kynurenine, and indoxyl-sulfate, increased. Possibly they act as neurotoxins in the central nervous system (CNS). The remaining 26 compounds (Groups B-E) decreased, possibly causing a loss of support or protection of the brain in dementia. Six Group B metabolites, normally enriched in red blood cells (RBCs) of healthy subjects, all contain trimethylated ammonium moieties. These metabolites include ergothioneine and structurally related compounds have scarcely been investigated as dementia markers, validating the examination of RBC metabolites. Ergothioneine, a potent anti-o xidant, is significantly decreased in various cognition-related disorders, such as mild cognitive impairment and frailty. Group C compounds, also include some oxidoreductants and are normally abundant in RBCs (NADP+, glutathione, ATP, pantothenate, S-adenosyl-methionine, and gluconate). Their decreased levels in dementia patients may also contribute to depressed brain function. Groups D (12) contains plasma compounds, such as amino acids, glycerophosphocholine, dodecanoyl-carnitine, 2-hydroxybutyrate, which normally protect the brain, but their diminution in dementia may reduce that protection. Seven Group D compounds have been identified previously as dementia markers. Group B-E compounds may be critical to maintain the CNS by acting directly or indirectly. How RBC metabolites act in the CNS and why they diminish so significantly in dementia remain to be determined.
Question: Write a study description for the study titled 'Study on the Effect of Bee Venom and Its Main Component melittin In Delaying Skin Aging in Mice'.
Answer: Bee venom (BV) and its main compound melittin (MLT) have antioxidant, anti-inflammatory, and anti-aging activities; however, very little research has been conducted on their effects on skin aging. In this study, a mouse skin aging model induced by D-galactose (D-gal) was constructed via subcutaneous injection into the scruff of the neck, and different doses of BV and MLT were used as interventions. The anti-aging effects and mechanisms of BV and MLT were explored by detecting the skin morphology and structure, anti-aging-related factors and non-targeted metabolomics of mice. BV and MLT improved dermal and epidermal thickness, boosted the collagen fiber content, increased hydroxyproline and hyaluronic acid levels, and enhanced transcript-level expression of IL-10, Col1a1, and Col3a1, while decreasing that of IL-1β. Metabolomic analysis showed that BV and MLT regulated the levels of some metabolites (compared to those in the skin aging control). BV effectively alleviated skin aging by regulating the pentose phosphate pathway, and pathways as-sociated with carbon, galactose, and β-alanine metabolism, whereas MLT regulated the pathways related to lipid metabolism, cholesterol metabolism, and atherosclerosis. This study highlights the potential applicability of BV and MLT in skin aging treatments and cosmetic products.
Question: Write a study description for the study titled 'Ceramide Promotes Lytic Reactivation of Epstein-Barr Virus in Gastric Carcinoma'.
Answer: Epstein-Barr virus (EBV) has a lifelong latency period after initial infection. Rarely, however, when the EBV immediate early gene BZLF1 is expressed by a specific stimulus, the virus switches to the lytic cycle to produce progeny viruses. We found that EBV infection reduced levels of various ceramide species in gastric cancer cells. As ceramide is a bioactive lipid implicated in the infection of various viruses, we assessed the effect of ceramide on the EBV lytic cycle. Treatment with C6-ceramide (C6-Cer) induced an increase in the endogenous ceramide pool and increased production of the viral product as well as BZLF1 expression. Treatment with the ceramidase inhibitor ceranib-2 induced EBV lytic replication with an increase in the endogenous ceramide pool. The glucosylceramide synthase inhibitor Genz-123346 inhibited C6-Cer-induced lytic replication. C6-Cer induced ERK1/2 and CREB phosphorylation, c-JUN expression, and accumulation of the autophagosome marker LC3B. Treatment with MEK1/2 inhibitor U0126 or autophagy initiation inhibitor 3-MA suppressed C6-Cer-induced EBV lytic replication. In contrast, the autophagosome-lysosome fusion inhibitor chloroquine induced BZLF1 expression. Transfection with siCREB reduced ERK1/2 phosphorylation and C6-Cer-induced BZLF1 expression. On the other hand, siJUN transfection did not affect BZLF1 expression. Our results show that increased endogenous ceramide and glycosyl ceramide (GlyCer) following C6-Cer treatment induce EBV lytic replication in gastric cancer cells via ERK1/2 and CREB phosphorylation and autophagosome accumulation.
Question: Write a study description for the study titled 'Antiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19'.
Answer: BACKGROUND: There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing.METHODS: Using untargeted high-resolution liquid chromatography coupled with mass spectrometry, we compared the admission serum metabolome of emergency department patients with acute viral infections, including COVID-19, bacterial infections, inflammatory conditions and healthy controls. Sera from an independent cohort of emergency department patients admitted with viral or bacterial infections underwent profiling to validate findings. Associations between whole-blood gene expression and the identified metabolite of interest were examined.FINDINGS: 3'-Deoxy-3',4'-didehydro-cytidine (ddhC), a free base of the only known human antiviral small molecule ddhC-triphosphate (ddhCTP), was detected for the first time in serum. When comparing 60 viral with 101 non-viral cases in the discovery cohort, ddhC was the most differentially abundant metabolite, generating an area under the receiver operating characteristic curve (AUC) of 0.954 (95% CI: 0.923-0.986). In the validation cohort, ddhC was again the most significantly differentially abundant metabolite when comparing 40 viral with 40 bacterial cases, generating an AUC of 0.81 (95% CI: 0.708-0.915). Transcripts of viperin and CMPK2, enzymes responsible for ddhCTP synthesis, were amongst the 5 genes most highly correlated with ddhC abundance.CONCLUSIONS: The antiviral precursor molecule ddhC is detectable in serum and an accurate marker for acute viral infection. Interferon-inducible genes, viperin and CMPK2 are implicated in ddhC production in vivo. These findings highlight a future diagnostic role for ddhC in viral diagnosis, pandemic preparedness and acute infection management.FUNDING: National Institute for Health Research Imperial Biomedical Research Centre; Medical Research Council.
Question: Write a study description for the study titled 'Photosynthetic Carbon Partitioning and Metabolic Regulation in Response to Very-Low and High CO2 in Microchloropsis gaditana NIES 2587'.
Answer: Photosynthetic organisms fix inorganic carbon through carbon capture machinery (CCM) that regulates the assimilation and accumulation of carbon around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). However, few constraints that govern the central carbon metabolism are regulated by the carbon capture and partitioning machinery. In order to divert the cellular metabolism toward lipids and/or biorenewables it is important to investigate and understand the molecular mechanisms of the CO2-driven carbon partitioning. In this context, strategies for enhancement of CO2 fixation which will increase the overall biomass and lipid yields, can provide clues on understanding the carbon assimilation pathway, and may lead to new targets for genetic engineering in microalgae. In the present study, we have focused on the physiological and metabolomic response occurring within marine oleaginous microalgae Microchloropsis gaditana NIES 2587, under the influence of very-low CO2 (VLC; 300 ppm, or 0.03%) and high CO2 (HC; 30,000 ppm, or 3% v/v). Our results demonstrate that HC supplementation in M. gaditana channelizes the carbon flux toward the production of long chain polyunsaturated fatty acids (LC-PUFAs) and also increases the overall biomass productivities (up to 2.0 fold). Also, the qualitative metabolomics has identified nearly 31 essential metabolites, among which there is a significant fold change observed in accumulation of sugars and alcohols such as galactose and phytol in VLC as compared to HC. In conclusion, our focus is to understand the entire carbon partitioning and metabolic regulation within these photosynthetic cell factories, which will be further evaluated through multiomics approach for enhanced productivities of biomass, biofuels, and bioproducts (B3).
Question: Write a study description for the study titled 'α-ketoglutarate maintains AMPK translation for energy sensing in human cancer cells_untargeted metabolites_flux_FAO'.
Answer: The energy sensor AMPK promotes tumor cell survival under stress, but how to prevent AMPK activation to blunt tumor progression remains unclear. Here we show that the metabolite α-ketoglutarate (α-KG) controls AMPK translation through a TET-YBX1 axis, which can be exploited to sensitize human cancer cells to energy stress. α-KG-deficient cells fail to activate AMPK under glucose starvation, which elicits cytosolic NADPH depletion and cell death . Mechanistically, α-KG insufficiency inhibits TET-dependent transcription of YBX1, an RNA-binding protein required for human-specific AMPK translation. Similarly, α-KG competitors including succinate and itaconate inhibit the YBX1-AMPK axis and sensitize cancer cells to glucose starvation. Finally, co-targeting oncogenic YBX1 and GLUT1 creates a synthetic lethality and therapeutically blunts tumor growth in vivo. Together, our findings link α-KG to energy sensing through AMPK translation, and propose that targeting α-KG-YBX1-dependent AMPK translation can sensitize human cancer cells to energy stress for treatment.
Question: Write a study description for the study titled 'Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism and mTORC1 signaling'.
Answer: Cells use glycolytic intermediates for anabolism e.g., via the serine synthesis and pentose phosphate pathways. However, we still understand poorly how these metabolic pathways contribute to skeletal muscle cell biomass generation. The first aim of this study was therefore to identify enzymes that limit protein synthesis, myotube size and proliferation in skeletal muscle cells. We inhibited key enzymes of glycolysis, the pentose phosphate pathway and serine synthesis pathway to evaluate their importance in C2C12 myotube protein synthesis. Based on the results of this first screen, we then focused on the serine synthesis pathway enzyme phosphoglycerate dehydrogenase (PHGDH). We used two different PHGDH inhibitors and mouse C2C12 and human primary muscle cells to study the importance and function of the PHGDH. Both myoblasts and myotubes incorporated glucose-derived carbon into proteins, RNA and lipids and we showed that PHGDH is essential in these processes. PHGDH inhibition decreased protein synthesis, myotube size and myoblast proliferation without cytotoxic effects. The decreased protein synthesis in response to PHGDH inhibition appears to occur mainly mTORC1 dependently as was evident from experiments with insulin-like growth factor 1 and rapamycin. Further metabolomics analyses revealed that PHGDH inhibition accelerated glycolysis and altered amino acid, nucleotide and lipid metabolism. Lastly, we found that supplementing an antioxidant and redox modulator N-acetylcysteine partially rescued the decreased protein synthesis and mTORC1 signaling during PHGDH inhibition. The data suggest that PHGDH activity is critical for skeletal muscle cell biomass generation from glucose, and that it regulates protein synthesis and mTORC1 signaling.
Question: Write a study description for the study titled 'TEX44 CPT1B Axis Regulates Mitochondrial Sheath Assembly and Fatty Acid Oxidation in Sperm'.
Answer: Mitochondrial fatty acid β-oxidation (FAO) is essential for energy production and cellular homeostasis, yet its specific role in sperm function has remained unclear. Through whole-exome sequencing of 673 patients with asthenozoospermia, we identified biallelic TEX44 variants in six individuals, all of whom exhibited defective mitochondrial sheath assembly and impaired sperm motility. Using Tex44 knockout mice, we demonstrated that TEX44 interacts with carnitine palmitoyltransferase 1B (CPT1B) to form a mitochondrial glue, anchoring adjacent mitochondria and facilitating the assembly of the sperm-specific mitochondrial sheath. In vitro, we show that purified TEX44 protein can modulates CPT1B enzymatic activity, limiting the conversion of long-chain fatty acids such as palmitic acid and myristic acid into acyl-carnitines, thereby reducing reactive oxygen species (ROS) production. Loss of TEX44 disrupts this regulatory mechanism, leading to unregulated FAO, excessive ROS generation, and severe oxidative damage to sperm DNA and flagellar structure. Additionally, germ cell-specific Cpt1b knockout mice exhibited phenotypes similar to TEX44 deficiency, including mitochondrial sheath defects and reduced sperm motility. These findings reveal a sperm-specific mechanism by which TEX44 regulates CPT1B activity to balance FAO and ROS generation, providing critical insights into energy metabolism, mitochondrial integrity, and male infertility.
Question: Write a study description for the study titled 'Rabbit plasma metabolomic analysis of Nitroproston: a multi target natural prostaglandin based-drug (Untargeted study)'.
Answer: INTRODUCTION: Nitroproston® is a novel multi-target drug bearing natural prostaglandin E2 (PGE2) and nitric oxide (NO)-donating fragments for treatment of inflammatory and obstructive diseases (i.e. asthma and obstructive bronchitis).  OBJECTIVES: To investigate the effects of Nitroproston® administration on plasma metabolomics in vivo.  METHODS: Experimental in vivo study randomly assigning the target drug (treatment group) or a saline solution without the drug (vehicle control group) to 12 rabbits (n=6 in each group). Untargeted (5880 initial features; 1869 negative-4011 positive ion peaks; UPLC-IT-TOF/MS) and 84 targeted moieties (Nitroproston® related metabolites, prostaglandins, steroids, purines, pyrimidines and amino acids; HPLC-QQQ-MS/MS) were measured from plasma at 0, 2, 4, 6, 8, 12, 18, 24, 32 and 60 minutes after administration.  RESULTS: PGE2, 13,14-dihydro-15-keto-PGE2, PGB2, 1,3-GDN and 15-keto-PGE2 increased in the treatment group. Steroids (i.e. cortisone, progesterone), organic acids, 3-oxododecanoic acid, nicotinate D-ribonucleoside, thymidine, the amino acids serine and aspartate, and derivatives pyridinoline, aminoadypic acid and uric acid increased (p0.75) after treatment. Purines (i.e. xanthine, guanine, guanosine), bile acids, acylcarnitines and the amino acids L-tryptophan and L-phenylalanine were decreased. Nitroproston® impacted steroidogenesis, purine metabolism and ammonia recycling pathways, among others.  CONCLUSION: Nitroproston®, a multi action novel drug based on natural prostaglandins, altered metabolites previously implicated as having anti inflammatory or anti-asthma properties (i.e. guanine, adenine, cortisol, cortisone and aspartate). Steroids, purine, urea and ammonia biological cycles were impacted. Mechanisms of action, metabolic pathway interconnections and useful information to further understand the metabolic effects of prostaglandin administration are presented.  The untargeted study data is reported in the current study MTBLS727.  The targeted study data associated with this study is reported in MTBLS728.  Linked Studies: MTBLS728
Question: Write a study description for the study titled 'Branched-chain ketoacids derived from cancer cells modulate macrophage polarization and metabolic reprogramming'.
Answer: Macrophages are prominent immune cells in the tumor microenvironment that can be educated into pro-tumoral phenotype by tumor cells to favor tumor growth and metastasis. The mechanisms that mediate a mutualistic relationship between tumor cells and macrophages remain poorly characterized. Here, we have shown in vitro that different human and murine cancer cell lines release branched‐chain α‐ketoacids (BCKAs) into the extracellular milieu, which influence macrophage polarization in an monocarboxylate transporter 1 (MCT1)‐dependent manner. We found that α‐ketoisocaproate (KIC) and α‐keto‐β‐methylvalerate (KMV) induced a pro‐tumoral macrophage state, whereas α‐ketoisovalerate (KIV) exerted a pro‐inflammatory effect on macrophages. This process was further investigated by a combined metabolomics/proteomics platform. KMV and KIC altered macrophage tricarboxylic acid (TCA) cycle intermediates and increased polyamine metabolism. Proteomic and pathway analyses revealed that the three BCKAs, especially KMV, exhibited divergent effects on the inflammatory signal pathways, phagocytosis, apoptosis and redox balance. These findings uncover cancer‐derived BCKAs as novel determinants for macrophage polarization with potential to be selectively exploited for optimizing antitumor immune responses.
Question: Write a study description for the study titled 'The timing of bacterial mesophyll infection shapes the leaf chemical landscape during the interaction'.
Answer: Chemistry in eukaryotic intercellular spaces is shaped by both hosts and symbiotic microorganisms such as bacteria. Pathogenic microorganisms like barley associated Xanthomonas translucens (Xt) swiftly overtake the inner leaf tissue becoming the dominant microbial community member during disease development. The dynamic metabolic changes due to Xt pathogenesis in the mesophyll spaces remain unknown. Genomic group I of Xt consists of 2 barley-infecting lineages: pathovar translucens (Xtt) and pathovar undulosa (Xtu). Xtu and Xtt, although genomically distinct, cause similar water-soaked lesions. To define the metabolic signals associated with inner leaf colonization, we used untargeted metabolomics to characterize Xtu and Xtt metabolism signatures associated with mesophyll growth. We found that mesophyll apoplast fluid from infected tissue yielded a distinct metabolic profile and shift from catabolic to anabolic processes over time compared to water-infiltrated control. The pathways with the most differentially expressed metabolites by time were glycolysis, tricarboxylic acid cycle, sucrose metabolism, pentoses interconversion, amino acids, galactose, and purine metabolism. Hierarchical clustering and principal components analysis showed that metabolic changes were more affected by the time point rather than by the individual colonization of the inner leaves by Xtt compared to Xtu. Overall, in this study, we identified metabolic pathways that explain carbon and nitrogen usage during host-bacterial interactions over time for mesophyll tissue colonization. This foundational research provides initial insights into shared metabolic strategies of inner leaf colonization niche occupation by related but phylogenetically distinct phyllosphere bacteria.
Question: Write a study description for the study titled 'Untargeted metabolomics approach using UPLC-ESI-QTOF-MS to explore the metabolome of fresh-cut iceberg lettuce'.
Answer: An untargeted metabolomics approach using UPLC-ESI-QTOF-MS was performed to explore the metabolome of iceberg lettuce and the changes related to storage time and genetics. Two cultivars with different browning susceptibility, fast- browning (FB) and slow-browning (SB) were studied juts after cutting (d0) and after 5 days of storage (d5). Extraction, metabolic profiling, and data-pretreatment procedures were optimized to obtain a robust and reliable data set. Preliminary principal component analysis (PCA) and hierarchical cluster analysis (HCA) of the full dataset (around 8551 extracted, aligned and filtered metabolites) showed a clear separation between the different samples (FB-d0, FB-d5, SB-d0, and SB-d5), highlighting a clear storage time-dependent effect. After statistical analysis applying Student´s t-test, 536 metabolites were detected as significantly different between d0 and d5 of storage in FB and 633 in SB. Some metabolites (221) were common to both cultivars. Out of these significant compounds, 22 were tentatively identified by matching their molecular formulae with those previously reported in the literature. Five families of metabolites were identified, some of them closely related to quality loss: amino acids, phenolic compounds, sesquiterpene lactones, fatty acids, and lysophospholipids. All compounds showed a clear trend to decrease at d5 except phenolic compounds that increased after storage. Overall, cutting and storage were shown to have a significant impact on the changes of lettuce metabolomics, with different trends depending on the browning susceptibility.