LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'A Generalized Strategy to Kill Leukemic Cells by Targeting the Regulatory Systems Governing Mitochondrial Membrane Potential'.
Answer: Targeting mitochondria emerges as a promising anti-leukemia strategy, yet selective mitochondrial disruption remains challenging. Here, we identified elevated mitochondrial membrane potential (MMP) as a hallmark of leukemic transformation and chemotherapy-resistant cells, prompting screening for MMP-targeting agents. Alexidine, an MMP-depleting compound, demonstrated potent anti-leukemic activity with low toxicity. Mechanistically, Alexidine binds unsaturated cardiolipin to destabilize the inner membrane localization of mitochondrial ribosome, suppressing cardiolipin-dependent mitochondrial translation, a process validated as an independent prognostic marker in leukemia. Unlike chemotherapy, Alexidine eradicates baseline MMP and MMP heterogeneity within leukemic populations, a functional signature linked to stemness and chemoresistance. Intriguingly, this heterogeneity originates not from cardiolipin-mediated translation but from asparagine-driven mitochondrial protein synthesis, which leukemia cells selectively activate to bypass chemotherapy. Critically, pharmacological asparagine depletion synergistically enhances chemosensitivity by disrupting this resistance pathway. Our findings establish that MMP regulation through cardiolipin-maintained homeostasis and asparagine-fueled adaptation represents therapeutic vulnerabilities, advocating co-targeting strategies to overcome resistance.
Question: Write a study description for the study titled 'Absorption efficiency of RESV through mouse skin using 3 bases in different tissues'.
Answer: Resveratrol (RESV) is a plant polyphenol, which is thought to have beneficial metabolic effects in laboratory animals as well as in humans. Following oral administration, RESV is immediately catabolized, resulting in low bioavailability. This study compared RESV metabolites and their tissue distribution after oral uptake and skin absorption. Metabolomic analysis of various mouse tissues revealed that RESV can be absorbed and metabolized through skin. We detected sulfated and glucuronidated RESV metabolites, as well as dihydroresveratrol. These metabolites are thought to have lower pharmacological activity than RESV. Similar quantities of most RESV metabolites were observed 4 h after oral or skin administration, except that glucuronidated RESV metabolites were more abundant in skin after topical RESV application than after oral administration. This result is consistent with our finding of glucuronidated RESV metabolites in cultured skin cells. RESV applied to mouse ears significantly suppressed inflammation in the TPA inflammation model. The skin absorption route could be a complementary, potent way to achieve therapeutic effects with RESV.  One mg of RESV dissolved in ethanol was applied directly (Et) or mixed with hydrophilic ointment (HO), macrogol (Ma) or CMC gel (CMC), and swabbed on mouse dorsal skin. After 4 h mice were sacrificed, metabolites were extracted from tissues and analyzed by LC-MS. Peak areas of metabolites were normalized using peak areas of spiked internal standards (10 nmol 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and piperazine-N,N’-bis(2-ethanesulfonic acid) (PIPES).
Question: Write a study description for the study titled 'Lactobacillus plantarum MR1 alleviates high-carbohydrate diet-induced oxidative stress and liver lipid deposition via upregulating uridine synthesis'.
Answer: The overconsumption of carbohydrates induces oxidative stress and lipid accumulation in the liver, which can be alleviated by modulation of intestinal microbiota; however, the underlying mechanism remains unclear. Here, we demonstrated that a strain affiliated with Lactobacillus plantarum (designed as MR1) efficiently attenuated lipid deposition, oxidative stress, as well as inflammatory response, which are caused by high-carbohydrate diet (HC) in fish with poor utilization ability of carbohydrates. Serum untargeted metabolome analysis indicated that pyrimidine metabolism was the significantly changed pathway among the groups. In addition, the content of serum uridine was significantly decreased in the HC group compared with the control group, while it increased by supplementation with L. plantarum MR1. Further analysis showed that addition of L. plantarum MR1 reshaped the composition of gut microbiota and increased the content of intestinal acetate. In vitro experiment showed that sodium acetate could induce the synthesis of uridine in hepatocytes. Furthermore, we proved that uridine could directly ameliorate oxidative stress and decrease liver lipid accumulation in the hepatocytes. In conclusion, this study indicated that probiotic L. plantarum MR1 ameliorated high-carbohydrate diet-induced hepatic lipid accumulation and oxidative stress by increasing the circulating uridine, suggesting that intestinal microbiota can regulate the metabolism of nucleotides to maintain host physiological homeostasis.
Question: Write a study description for the study titled 'Serum metabolomics analysis of patients with chronic obstructive pulmonary disease and 'frequent exacerbator' phenotype'.
Answer: BACKGROUND: Chronic obstructive pulmonary disease (COPD) exacerbations significantly contribute to morbidity and mortality. The complex nature of COPD presents challenges in accurately predicting and understanding frequent exacerbations.OBJECTIVE: This study aimed to investigate the metabolic characteristics of frequent exacerbation of COPD (COPD-FE) phenotype, identify potential metabolic biomarkers associated with COPD-FE risk and explore underlying pathogenic mechanisms.METHODS: An internal cohort of 30 stable COPD patients was recruited. A widely targeted metabolomics approach was employed to detect and compare serum metabolite expressions between patients with COPD-FE and non-frequent exacerbations (COPD-NE). Subsequently, bioinformatics analysis was utilized for pathway enrichment of the identified metabolites; Spearman correlation analysis explored associations between metabolites and clinical indicators, and receiver operating characteristic (ROC) analysis assessed the predictive performance of identified metabolites. An external cohort of 20 patients with COPD validated findings from the internal cohort.RESULTS: Out of 484 detected metabolites, 25 exhibited significant differences between COPD-FE and COPD-NE. Metabolomic analysis revealed differences in lipid, energy, amino acid and immunity pathways. Spearman correlation analysis showed associations between metabolites and clinical indicators of acute exacerbation risk. ROC analysis revealed that D-fructose 1,6-bisphosphate (AUC=0.871), arginine (AUC=0.836), L-2-Hydroxyglutarate (L-2HG, AUC=0.849), Diacylglycerol (DG)(16:0/20:5) (AUC=0.827), DG(16:0/20:4) (AUC=0.818) and carnitine-C18:2 (AUC=0.804) had area under the curve (AUC) values above 0.8, highlighting their superior discriminative capacity between the two groups. External validation results showed that DG(16:0/20:5), DG(16:0/20:4), carnitine-C18:2 and L-2HG were significantly different between COPD-FE patients and COPD-NE patients (p-value<0.05).CONCLUSION: This study offers insights into early identification, mechanistic understanding and personalized management of COPD-FE phenotype.
Question: Write a study description for the study titled 'LC-MS untargeted approach showed that methyl jasmonate application on Vitis labrusca L. grapes increases phenolics at subtropical Brazilian regions'.
Answer: Vitis labrusca L. grapes are largely cultivated in Brazil, but the tropical climate affect negatively the phenols content, especially anthocyanin. Therefore, researches are focusing on increase grape phenols content; with methyl jasmonate application (MeJa) considered a good alternative. The aim was to investigate with an untargeted approach the metabolic changes caused by the MeJa pre-harvest application on two Vitis labrusca L. cultivars grape, both grown in two Brazilian regions. Isabel Precoce and Concord grapes cultivated under subtropical climate, on south and southeast of Brazil, received MeJa pre-harvest treatment. Grape metabolome was extracted and analyzed with a MS based metabolomics protocol by UPLC-HRMS-QTOF. Unsupervised data analysis reveal clear separation between the two regions and the two cultivars, while supervised data analysis revealed biomarkers between MeJa and control group. Between the biomarkers, stilbenes, hydrocinnamates, flavonols and anthocyanins were identified. These results suggest that MeJa can be used as elicitor to secondary metabolism in grapes grown even under subtropical climate, affecting phenolic biosynthesis.
Question: Write a study description for the study titled 'Effect of NAC154 transcription factor overexpression on the field grown poplar stem wood metabolome'.
Answer: Several xylem-associated regulatory genes have been identified that control processes associated with wood formation in poplar. Prominent among these are the NAC domain transcription factors (NACs). We evaluated the putative involvement of Populus NAC154, a co-ortholog of the Arabidopsis gene SND2, as a regulator of secondary biosynthetic processes in stem internode tissues by interrogating methanol:water extracts from control and transgenic trees. Comprehensive untargeted metabolite profiling was accomplished with a liquid chromatography-mass spectrometry platform that utilized two different chromatographic supports (HILIC and reversed phase) and both positive and negative ionization modes. Evaluation of current and previous year tissues provided datasets for assessing the effects of NAC154 overexpression in wood maturation processes. Phenolic glycoside levels as well as those of oligolignols, sucrose and arginine were modulated with phenotypic and chemotypic traits exhibiting similar trends. Specifically, increased levels of arginine in the NAC154 overexpressing tissues supports a role for the transcription factor in senescence/dormancy-associated processes.
Question: Write a study description for the study titled 'Plant species richness promotes the decoupling of leaf and root defence traits while species-specific responses in physical and chemical defences are rare'.
Answer: The increased positive impact of plant diversity on ecosystem functioning over time is often attributed to the gradual accumulation of mutualists and dilution of antagonists in diverse plant communities. While increased plant diversity alters traits related to resource acquisition, it remains unclear whether it reduces defence allocation, whether this reduction differs between roots and leaves, or varies among species.To answer these questions, we assessed the effect of plant species richness, plant species identity and their interaction on the expression of twenty-three physical and chemical leaf and fine root defence traits of sixteen plant species in a nineteen-year-old biodiversity experiment.Only leaf mass per area, leaf and root dry matter content, and root nitrogen, traits related to both, resource acquisition and physical defence, responded consistently to species richness. However, species richness promoted a decoupling of these physical defences in leaves and fine roots, possibly in response to resource limitations in diverse communities. Changes in traits related to chemical defence and mutualist collaboration, however, varied among species, possibly in response to species-specific antagonists’ dilution.Overall, our study suggests that resource limitation in diverse communities mediates the relationship between plant defence traits and antagonist dilution.
Question: Write a study description for the study titled 'Characterizing COPD phenotypes with a targeted signaling lipids metabolomics approach'.
Answer: A targeted metabolomics approach reveals distinct metabolic patterns associated with different GOLD stages, KNGF profiles and SYS subtypes in COPD patients, highlighting unique mechanisms and pathways underlying various COPD classification systems.
Question: Write a study description for the study titled 'Assessing the potentiality of sputtered gold nanolayers in mass spectrometry imaging for metabolomics applications (Liver MALDI-MSI assay)'.
Answer: Mass spectrometry imaging (MSI) is a molecular imaging technique that maps the distribution of molecules in biological tissues with high spatial resolution. The most widely used MSI modality is matrix-assisted laser desorption/ionization (MALDI), but some organic matrices used in classical MALDI may impact the quality of the molecular images due to limited lateral resolution and strong background noise in the low mass range, hindering its use in metabolomics. Here we present a matrix-free LDI technique based on the deposition by sputtering of gold nanolayers on tissue sections. This gold coating method is quick, fully automated and repetitive and allows growing highly controlled nanolayers, necessary for high quality and high resolution MS image acquisition. The performance of the developed method has been tested on the acquisition of MS images of brain. The obtained spectra showed a high number of MS peaks on the low mass region (m/z below 1000 Da) with few background peaks, demonstrating the viability of the sputtered gold nanolayers of promoting the desorption/ionization of a wide range of metabolites. These results, together with the reliable MS spectrum calibration using gold peaks, make the developed method a valuable alternative for MSI applications.Liver MALDI MS imaging assay is reported in the current study MTBLS589.Brain MALDI MS imaging assay is reported in MTBLS588.
Question: Write a study description for the study titled 'Rapid biotransformation of STW 5 constituents by human gut microbiome from IBS- and non-IBS donors'.
Answer: STW 5, a blend of 9 medicinal plant extracts, exhibits promising efficacy in treating functional gastrointestinal disorders, notably irritable bowel syndrome (IBS). Nonetheless, its effects on the gastrointestinal microbiome and the role of microbiota on the conversion of its constituents are still largely unexplored. This study employed an experimental ex vivo model to investigate STW 5's differential effects on fecal microbial communities and metabolite production in samples from individuals with and without IBS. Using 560 fecal microcosms (IBS patients, n=6; healthy controls, n=10), we evaluated the influence of pre-digested STW 5 and controls on microbial and metabolite composition at time points 0, 0.5, 4 and 24 h. Our findings demonstrate the potential of this ex vivo platform to analyze herbal medicine turnover within 4 h with minimal microbiome shifts due to abiotic factors. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products, such as 18β-glycyrrhetinic acid, davidigenin, herniarin, 3-(3-hydroxyphenyl)propanoic acid and 3-(2-hydroxy-4-methoxyphenyl)propanoic acid occurred. For davidigenin, 3-(3-hydroxyphenyl)propanoic acid and 18β-glycyrrhetinic acid, anti-inflammatory, cytoprotective or spasmolytic activities have been previously described. Notably, the microbiome-driven metabolic transformation did not induce a global microbiome shift, and the detected metabolites were minimally linked to specific taxa. Observed biotransformations were independent of IBS diagnosis, suggesting potential benefits for IBS patients from biotransformation products of STW 5.
Question: Write a study description for the study titled 'Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer'.
Answer: BACKGROUND: Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota and metabolites to explain the site-specific difference.METHODS: Here, 494 participants from a 16S rRNA gene sequencing cohort (50 RCC, 114 LCC and 100 healthy controls) and a multi-omics cohort (63 RCC, 79 LCC and 88 healthy controls) were analyzed. 16S rRNA gene, metagenomic sequencing and metabolomics analyses of fecal samples were evaluated to identify tumor location-related bacteria and metabolites. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-seq) were conducted to obtain the mutation burden and genomic expression pattern.RESULTS: We found unique profiles of the intestinal microbiome, metabolome, and host genome between RCC and LCC. The bacteria Flavonifractor plautii (Fp) and Fusobacterium nucleatum, the metabolites L-phenylalanine, and the host genes PHLDA1 and WBP1 were the key omics features of RCC; whereas the bacteria Bacteroides sp. A1C1 (B.A1C1) and Parvimonas micra, the metabolites L-citrulline and D-ornithine, and the host genes TCF25 and HLA-DRB5 were considered the dominant omics features in LCC. Multi-omics correlation analysis indicated that RCC-enriched Fp was related to the accumulation of the metabolite L-phenylalanine and the suppressed WBP1 signal in RCC patients. In addition, LCC-enriched B.A1C1 was associated with accumulation of the metabolites D-ornithine and L-citrulline as well as activation of the genes TCF25, HLA-DRB5 and AC079354.1.CONCLUSION: Our findings identify previously unknown links between intestinal microbiota alterations, metabolites and host genomics in RCC vs. LCC, suggesting that it may be possible to treat colorectal cancer (CRC) by targeting the gut microbiota-host interaction.
Question: Write a study description for the study titled 'Non-targeted multimodal metabolomics and lipidomics data from ovine rumen fluid fractions'.
Answer: From an animal production and health perspective, our understanding of the metabolites in ruminant biofluids, particularly rumen fluid across different host species is poorly understood. Metabolomics is a powerful and sensitive approach for investigating low molecular weight metabolite profiles present in rumen biofluids. It can be used to identify potential roles of metabolites in the rumen microbiome and provide and understanding of host-level regulatory mechanisms associated with animal production. The rumen is a strictly anaerobic environment enriched with a complex community of bacteria, protozoa, fungi, archaea and bacteriophages. Here, we present a metabolomic dataset generated using hydrophilic interaction liquid chromatography (HILIC) and semi-polar (C18) chromatography methods coupled to high resolution mass spectrometry (MS), collected in both positive and negative ionization modes, of ovine rumen samples that were fractionated based on molecular weight (20 kDa, 8-10 kDa and 100 Da). This study highlights the potential of HILIC and C18 chromatography combined with non-targeted mass spectrometric methods to detect the polar and semi-polar metabolite species of the ruminal fluid metabolome.
Question: Write a study description for the study titled 'Metabolomics reveals molecular signatures for psoriasis biomarkers and drug targets discovery'.
Answer: Psoriasis is a chronic skin disease that affects multiple systems and can be influenced by immunological, environmental, and genetic factors. The discovery of plasma biomarkers of psoriasis and the regulation of metabolic pathways helps us understand psoriasis and may assist clinicians in the diagnosis and treatment of psoriasis. Here, we used untargeted metabolomics based on high-resolution liquid chromatography-mass spectrometry to study the changes of metabolites and metabolic pathways in plasma samples of psoriasis. A total of 301 differential metabolites were detected, of which 10 metabolites were possible potential biomarkers, including vitamins, amino acids and lipids. At the same time, KEGG pathway enrichment analysis was performed on all the detected differential metabolites, and it was found that protein digestion and absorption, amino acid metabolism and lipid metabolism may jointly participate in the regulation of pathogenesis of psoriasis. In addition, three proteins ESR1, OPRM1 and HSD11B1 were identified as possible potential topical therapeutic targets for psoriasis by metabolite-protein interaction network analysis. In this study, plasma metabolites were characterized in patients with psoriasis which provided a new understanding of the role of metabolites in psoriasis. It also deepened the understanding of the pathogenesis of psoriasis and proposed new ideas and methods for the auxiliary diagnosis and treatment of the disease.
Question: Write a study description for the study titled 'Molecular mechanisms of growth differences in large yellow croaker: Metabolomic and metagenomic analyses'.
Answer: Gut microbiota can modulate nutrient metabolism, considerably affecting host growth and development. However, mechanisms by which gut microbiota regulate large yellow croaker (LYC; Larimichthys crocea) growth remain unclear. We assessed gut contents of fast-growing male (IWHM) and female (IWHF) LYCs and slow-growing male (IWLM) and female (IWLF) LYCs and subjected the data to metagenomic and metabolomic analyses. Gut microbiota composition significantly differed among LYCs with different growth rates: Vibrio abundance was considerably lower in IWHM LYCs (2.53%) than in IWLM LYCs (41.47%); Arthrobacter D abundance was the highest in IWHF LYCs (8.19%) but the lowest in IWLF LYCs (1.52%). Moreover, 124 and 483 differential metabolites were noted in IWHM-IWLM and IWHF-IWLF LYC pairs, respectively. Finally, we established a model for gut microbiota-metabolite relationship in LYCs to understand molecular mechanisms by which gut microbiota regulates nutrient metabolism. Our results highlight differences in gut microbiota between LYCs with high and low growth rates and provide comprehensive insights into molecular mechanisms underlying LYC growth regulation by gut microbiota.
Question: Write a study description for the study titled 'Repurposing the orphan drug nitisinone to control the transmission of African trypanosomiasis'.
Answer: Tsetse transmit African trypanosomiasis, which is a disease fatal to both humans and animals. A vaccine to protect against this disease does not exist so transmission control relies on eliminating tsetse populations. Although neurotoxic insecticides are the gold standard for insect control, they negatively impact the environment and reduce populations of insect pollinator species. Here we present a promising, environment-friendly alternative to current insecticides that targets the insect tyrosine metabolism pathway. A bloodmeal contains high levels of tyrosine, which is toxic to haematophagous insects if it is not degraded and eliminated. RNA interference (RNAi) of either the first two enzymes in the tyrosine degradation pathway (tyrosine aminotransferase (TAT) and 4-hydroxyphenylpyruvate dioxygenase (HPPD)) was lethal to tsetse. Furthermore, nitisinone (NTBC), an FDA-approved tyrosine catabolism inhibitor, killed tsetse regardless if the drug was orally or topically applied. However, oral administration of NTBC to bumblebees did not affect their survival. Using a novel mathematical model, we show that NTBC could reduce the transmission of African trypanosomiasis in sub-Saharan Africa, thus accelerating current disease elimination programmes.