LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolomic and transcriptomic investigations reveal the responses of cucumber leaves exposed to polystyrene nanoplastics (PSNPs)'.
Answer: The uptake and accumulation of nanoplastics by plants have raised particular concerns. However, molecular mechanisms underlying nanoplastic phytotoxicity are still vague and insufficient. Thus, its potential environmental risks and biosafety are receiving increased attention. In this study, cucumber plants were exposed to polystyrene nanoplastics (PSNPs) under different concentration. The results demonstrated that phenotypic parameters (total photosynthetic pigment content, relative membrane permeability, total phenolic content, and lipid peroxidation) were not significantly affected. However, metabolomic and transcriptomic analysis revealed that both doses of PSNPs induced the expression regulation of different key genes, exhibiting considerable distinction on metabolic responses in cucumber. The high dose of PSNPs induced stronger alteration in cucumber leaves than low dose of PSNPs. Low dose exposure significantly affected four metabolic pathways involved in the carbohydrate metabolism. High dose exposure significantly affected five metabolic pathways involved in the carbohydrate metabolism and four metabolic pathways involved in the amino acid metabolism. These findings shed new light on the phytotoxic mechanism and environmental implication behind the interaction of nanoplastics and plants, and advance our understanding of the potential adverse effect induced by the presence of nanoplastics in agricultural systems.
Question: Write a study description for the study titled 'Health outcomes of fruit juice and fruity beverage: a comparative analysis of gut microbiota and metabolomics in rats (Lipidomics assay)'.
Answer: BACKGROUND: Diet is foods and drinks regularly consumed, and its regulation is complicated. It is necessary to obtain a practical understanding of which foods and drinks contribute to health and well-being and which are insalubrious. Clear evidence shows that a high intake of fruity beverage (FB) is associated with a higher risk of metabolic syndromes; unlike FB, the health outcome of fruit juice (FJ) intake is still controversial. Here, we aim to reveal the health outcomes of diet intervention (FJ or FB) with system profiling via the interaction of gut microbiota and metabolomics.RESULTS: Firstly, the glucose, sucrose, fructose and other bioactive metabolites of FJ and FB were analyzed, and FJ possessed higher sucrose and flavonoids, while FB showed higher glucose and fructose. Secondly, C0 was set as the control group on Day 0, and a 4-week diet invention was performed to control, FJ-intake and FB-intake groups with normal saline, FJ and FB, respectively. Then, disparate trends in the metabolic syndrome of FJ-intake and FB-intake groups were revealed through the diet-microbiome-metabolic pathway axis. FJ improved alpha diversity and decreased the F/B ratio of gut microbiota as well as prevented insulin resistance with the reduced food intake in the FJ-intake group. However, FB possessed unchanged microbial diversity and enhanced F/B ratio, causing insulin resistance with renal triglyceride accumulation, increased kidney mass index as well as steadily improved weight change in FB-intake group.CONCLUSIONS: The distinct processing degrees could explain the different FB and FJ intake responses in rats. FB with excess free fructose belongs to ultra-processed foods, while FJ with higher flavonoids belongs to minimally processed foods. We genuinely believe that FJ with a lower processing degree, although naturally contains the similar total amount of 3 main free sugars as FB, could be a healthier drink choice.Lipidomics assay is reported in the current study MTBLS4108.Metabolomics assay is reported in MTBLS3943.
Question: Write a study description for the study titled 'Migratory Zooplankton Excreta and its Influence on Prokaryotic Communities'.
Answer: Particulate organic matter (fecal pellets) from zooplankton has been demonstrated to be important nutrient sources for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12-16 h of incubation. We measured bulk dissolved organic carbon, dissolved free amino acids via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16s rDNA amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.
Question: Write a study description for the study titled 'Metabolite of esculetin plays an important role in cytotoxic effects induced by chloroquine on porcine immature Sertoli cells'.
Answer: Chloroquine (CQ) is widely used in the therapy against malarial, tumor and recently the COVID-19 pandemic, as a lysosomotropic agent to inhibit the endolysosomal trafficking in the autophagy pathway. We previously reported that CQ (20 µM, 36 h) could reprogram transcriptome and impair multiple signaling pathways vital to porcine immature Sertoli cells (iSCs). However, whether CQ treatment could affect the metabolomic compositions of porcine iSCs remains unclear. Here, we showed that CQ (20 µM, 36 h) treatment of porcine iSCs induced significant changes of 63 metabolites (11 up and 52 down) by the metabolomics method, which were involved in different metabolic pathways. Caffeic acid and esculetin, the top two up-regulated metabolites, were validated by ELISA. Furthermore, esculetin treatment (53 nM, 36 h) significantly decreased the viability and proliferation, suppressed the mitochondrial function, whereas promoted the apoptosis of porcine iSCs, similar to those by CQ treatment (20 µM, 36 h). Collectively, our results showed that CQ treatment induces metabolic changes, and its effect on porcine iSCs could be partially mediated by esculetin.
Question: Write a study description for the study titled 'Engineered Bacillus subtilis WB600/ZD reduces post-weaning diarrhea in piglets by modulating gut microbiota and aryl hydrocarbon receptor (AHR) signaling'.
Answer: Post-weaning diarrhea (PWD) causes significant economic losses to the pig farming industry. Our previous study demonstrated that the engineered Bacillus subtilis WB600/ZD (an engineered Bacillus subtilis strain expressing the antimicrobial defensin peptide from Zophobas atratus), alleviates intestinal inflammation, modulates gut microbiota, and maintains redox homeostasis in Salmonella-challenged mice, yet the precise mechanisms remain unclear. This study suggests that WB600/ZD has great potential as an antibiotic alternative for improving the intestinal health in newly weaned piglets.Keywords: Engineered Bacillus subtilis WB600/ZD; Post-weaning diarrhea; Salmonella Infantis; Fecal microbiota transplantation; Ileitis; Aryl hydrocarbon receptor
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 673800 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 TEX44 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 'Metabolic Reprogramming and Reliance in Human Skin Wound Healing'.
Answer: Impaired skin wound healing is a significant global health issue, especially among the elderly. Wound healing is a well-orchestrated process involving the sequential phases of inflammation, proliferation, and tissue remodeling. Although wound healing is a highly dynamic and energy-requiring process, the role of metabolism remains largely unexplored. By combining transcriptomics and metabolomics of human skin biopsy samples, we mapped the core bioenergetic and metabolic changes in normal acute as well as chronic wounds in elderly subjects. We found upregulation of glycolysis, the tricarboxylic acid cycle, glutaminolysis, and β-oxidation in the later stages of acute wound healing and in chronic wounds. To ascertain the role of these metabolic pathways on wound healing, we targeted each pathway in a wound healing assay as well as in a human skin explant model using metabolic inhibitors and stimulants. Enhancement or inhibition of glycolysis and, to a lesser extent, glutaminolysis had a far greater impact on wound healing than similar manipulations of oxidative phosphorylation and fatty acid β-oxidation. These findings increase the understanding of wound metabolism and identify glycolysis and glutaminolysis as potential targets for therapeutic intervention.
Question: Write a study description for the study titled 'Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis'.
Answer: Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowing a more unbiased approach, but data interpretation using multivariate analysis is usually not straightforward and requires time and effort. Here we show, for the first time, the application of metabolic pathway enrichment analysis using untargeted and targeted metabolomics data to identify genetic targets for bioprocess improvement in a more streamlined way. The analysis of an Escherichia coli succinate production bioprocess with this methodology revealed three significantly modulated pathways during the product formation phase: the pentose phosphate pathway, pantothenate and CoA biosynthesis and ascorbate and aldarate metabolism. From these, the two former pathways are consistent with previous efforts to improve succinate production in Escherichia coli. Furthermore, to the best of our knowledge, ascorbate and aldarate metabolism is a newly identified target that has so far never been explored for improving succinate production in this microorganism. This methodology therefore represents a powerful tool for the streamlined identification of strain engineering targets that can accelerate bioprocess optimisation.
Question: Write a study description for the study titled 'Metabolic characterization of the natural progression of chronic hepatitis B (Biogenic amine and Acyl-carnitine assays)'.
Answer: Background: Worldwide, over 350 million people are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing progressive liver diseases. The confinement of HBV replication to the liver, which also acts as the central hub for metabolic and nutritional regulation, emphasizes the interlinked nature of host metabolism and the disease. Still, the metabolic processes operational during the distinct clinical phases of a chronic HBV infection—immune tolerant, immune active, inactive carrier, and HBeAg-negative hepatitis phases—remains unexplored.  Methods: To investigate this, we conducted a targeted metabolomics approach on serum to determine the metabolic progression over the clinical phases of chronic HBV infection, using patient samples grouped based on their HBV DNA, alanine aminotransferase, and HBeAg serum levels.  Results: Our data illustrate the strength of metabolomics to provide insight into the metabolic dysregulation experienced during chronic HBV. The immune tolerant phase is characterized by the speculated viral hijacking of the glycerol-3-phosphate–NADH shuttle, explaining the reduced glycerophospholipid and increased plasmalogen species, indicating a strong link to HBV replication. The persisting impairment of the choline glycerophospholipids, even during the inactive carrier phase with minimal HBV activity, alludes to possible metabolic imprinting effects. The progression of chronic HBV is associated with increased concentrations of very long chain triglycerides together with citrulline and ornithine, reflective of a dysregulated urea cycle peaking in the HBV envelope antigen-negative phase.  Conclusions: The work presented here will aid in future studies to (i) validate and understand the implication of these metabolic changes using a thorough systems biology approach, (ii) monitor and predict disease severity, as well as (iii) determine the therapeutic value of the glycerol-3-phosphate–NADH shuttle.  The Oxylipin assay and the Lipid assays for this study can be found in the MetaboLights studies MTBLS253 and MTBLS279 respectively.
Question: Write a study description for the study titled 'Metabolic profiling of rheumatoid arthritis neutrophils reveals altered energy metabolism that is not affected by JAK inhibition'.
Answer: Neutrophils play a key role in the pathophysiology of rheumatoid arthritis (RA) where release of ROS and proteases directly causes damage to joints and tissues. Neutrophil function is directly affected by Janus Kinase (JAK) inhibitor drugs, including tofacitinib and baricitinib, which are clinically effective treatments for RA. However clinical trials have reported increased infection rates and transient neutropenia during therapy. The subtle differences in the mode of action, efficacy and safety of JAK inhibitors has been the primary research topic of many clinical trials and systematic reviews, to provide a more precise and targeted treatment to patients. The aim of this study was to determine both the differences in the metabolome of neutrophils from healthy controls and people with RA, and the effect of different JAK inhibitors on the metabolome of healthy and RA neutrophils. Isolated neutrophils from healthy controls (HC) (n=6) and people with RA (n=7) were incubated with baricitinib, tofacitinib or a pan-JAK inhibitor (all 200ng/mL) for 2h. Metabolites were extracted and 1H nuclear magnetic resonance (NMR) was applied to study the metabolic changes. Multivariate analyses and machine learning models show a divergent metabolic pattern in RA neutrophils compared to HC at baseline (F1 score = 86.7%) driven by energy metabolites (ATP, ADP, GTP and glucose). No difference was observed in the neutrophil metabolome when treated with JAK inhibitors. However, JAK inhibitors significantly inhibited ROS production and baricitinib decreased NET production (p-value<0.05). Bacterial killing was not inhibited by JAK inhibitors, indicating their effect on neutrophils is beneficial to inhibit joint damage in RA without impairing host defence. This study highlights altered energy metabolism in RA neutrophils which may explain the cause of their dysregulation in inflammatory disease.
Question: Write a study description for the study titled 'Salmonella Modulates Metabolism during Growth under Conditions that Induce Expression of Virulence Genes'.
Answer: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative pathogen that uses complex mechanisms to invade and proliferate within mammalian host cells. To investigate possible contributions of metabolic processes to virulence in S. Typhimurium grown under conditions known to induce expression of virulence genes, we used a metabolomics-driven systems biology approach coupled with genome scale modeling. First, we identified distinct metabolite profiles associated with bacteria grown in either rich or virulence-inducing media and report the most comprehensive coverage of the S. Typhimurium metabolome to date. Second, we applied an omics-informed genome scale modeling analysis of the functional consequences of adaptive alterations in S. Typhimurium metabolism during growth under our conditions. Modeling efforts highlighted a decreased cellular capability to both produce and utilize intracellular amino acids during stationary phase culture in virulence conditions, despite significant abundance increases for these molecules as observed by our metabolomics measurements. Furthermore, analyses of omics data in the context of the metabolic model indicated rewiring of the metabolic network to support pathways associated with virulence. For example, cellular concentrations of polyamines were perturbed, as well as the predicted capacity for secretion and uptake.
Question: Write a study description for the study titled 'Microbiota-indole-3-propionic acid-heart axis mediates the protection of leflunomide against αPD1-induced cardiotoxicity in mice'.
Answer: Anti-programmed death 1 (αPD1) immune checkpoint blockade is used in combination for cancer treatment but associated with cardiovascular toxicity. Finding drugs that suppress cardiovascular toxicity but not compromise the efficacy of αPD1-mediated immunotherapy is of great importance. Leflunomide (Lef) can suppress the growth of several tumor and mitigate cardiac remodeling in mice. However, the specific role of Lef in αPD1-induced cardiotoxicity remains unclear.
Question: Write a study description for the study titled 'Transcriptomic and metabolomic comparison of two Kandelia obovata cultivas in response to cold wave'.
Answer: Temperature is the primary environmental factor that restricts the growth and distribution of mangrove plants. With the escalating severity of global climate change, Kandelia obovata has gained widespread recognition as an ideal species for investigating the response mechanisms of mangroves to cold stress. Although previous studies have explored the genetic and molecular aspects of cold response in K. obovata, there is a paucity of reports focusing on its response to freezing stress and its adaptive mechanisms during recovery periods. In this study, we subjected two cultivars of K. obovata, namely southern F-J (Fu-Jian) and northern Z-J (Zhe-Jiang), located in the southeast coastal area of China, to controlled temperature drops below freezing point followed by recovery periods simulating typical cold waves. We conducted phenotype analyses along with comparative transcriptomics and metabolomics investigations on these two cultivars, which exhibited differential tolerance towards lethal freezing challenges. Our findings revealed stronger transcriptional and metabolic induction in both cultivars during recovery stages compared to freezing processes, highlighting candidate genes and metabolites that may enhance adaptability and survival capacity of K. obovata when exposed to cold waves. Furthermore, significant differences were observed between these two cultivars in various pathways related to cold responses such as photosynthesis and jasmonic acid synthesis/transduction; while F-J cultivar failed to resume growth due to irreversibly damaged photosystems/cell structures after exposure to extreme low temperatures, Z-J cultivar demonstrated resistance by adjusting JA synthesis as well as accumulating soluble amino acids during their respective recovery periods. This study provides novel insights into understanding the survival mechanisms employed by K. obovata against cold waves, which are crucial for introducing mangroves into more northern coastal areas.
Question: Write a study description for the study titled 'Nitisinone’s mosquitocidal properties hold promise for malaria control'.
Answer: Nitisinone’s mosquitocidal properties hold promise for malaria control