LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Moxibustion Inhibits Inflammation in Monosodium Urate Crystal-induced Gouty Arthritis Model Rats through Metabolomic Regulation'.
Answer: Background: Moxibustion is a form of therapy that to warm the acupoints located skin by using dried mugwort leaves. It is widely used to treat gouty arthritis (GA). However, the mechanism of moxibustion on improving GA has not been fully revealed. In this study, we explore the mechanism of moxibustion on GA via metabolomics combined with traditional Chinese medicine (TCM) theory.Methods: Three days before model&nbsp;induction, the rats&nbsp;of moxibustion&nbsp;groups were treated with moxibustion in&nbsp;the&nbsp;ST36 and SP6, and then, a GA rat model induced by monosodium urate&nbsp;(MSU) was established. &nbsp;Biological samples, including joint synovial tissue and serum&nbsp;samples,&nbsp;were collected and measured&nbsp;by histopathological staining, molecular biology assays and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics.Results: We found that moxibustion could reduce the ankle edema induced by MSU crystals, decrease the expression of related proinflammatory genes, decrease the levels of serum IL-18 and IL-1β, and restore the metabolism of glycerol phospholipids, niacin and nicotinamide in GA model rats.Conclusion: Moxibustion can regulate the metabolism of GA model rats widely to inhibit inflammation. Our research deepens our understanding of the complex mechanisms of moxibustion and promotes the application of moxibustion in the clinical practice.
Question: Write a study description for the study titled 'Rare and common genetic determinants of metabolic individuality and their effects on human health (INTERVAL study assays)'.
Answer: Garrod’s concept of “chemical individuality” has contributed to comprehension of the molecular origins of human diseases. Untargeted high-throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. We studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals and identified 2,599 variant-metabolite associations (P<1.25x10^-11) within 330 genomic regions, with rare variants (MAF≤1%) explaining 9.4% of associations. Jointly modelling metabolites in each region, we identified 423 regional, co-regulated, variant-metabolite clusters called GIMs (Genetically Influenced Metabotypes). We assigned causal genes for 62.4% of GIMs, providing new insights into fundamental metabolite physiology and their clinical relevance, including metabolite guided discovery of potential adverse drug effects (DPYD, SRD5A2). We show strong enrichment of Inborn Errors of Metabolism (IEM)-causing genes, with examples of metabolite associations and clinical phenotypes of non-pathogenic variant carriers matching characteristics of IEMs. Systematic, phenotypic follow-up of metabolite-specific genetic scores revealed multiple potential aetiological relationships.INTERVAL study assays are reported in the current study MTBLS834EPIC-Norfolk study assays are reported in MTBLS833
Question: Write a study description for the study titled 'Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon'.
Answer: Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.
Question: Write a study description for the study titled 'Dietary carbohydrate and protein levels affect the growth performance of juvenile peanut worm (Sipunculus nudus): an LC–MS-based metabolomics study'.
Answer: The peanut worm (Sipunculus nudus) is an economically important fishery resource in China. To determine how dietary carbohydrate and protein levels affects the growth performance of juvenile S. nudus and identify the mechanisms underlying observedpatterns, five isoenergetic and isolipidic diets with different levels of carbohydrate and protein were formulated and fed to juvenile S. nudus; the experimental groups were referred to as EG1, EG2, EG3, EG4, and EG5, respectively. After 90 days of feeding, S. nudus had significantly lower survival rates when fed D5 compared with other diets (P < 0.05), and the highest survival rate was observed in EG2 individuals. The weight gain rate and specific growth rate were significantly higher in EG2 compared with the other groups (P < 0.05). Metabolomic profiling using LC–MS revealed 83 significantly differential metabolites (POS: 59; NEG: 24), which were identified via an in-house MS2 database. Pathway analysis indicated that the significantly different metabolites were involved in 22 metabolic pathways (POS: 9; NEG: 13), including tyrosine, phenylalanine, and tryptophan biosynthesis; phenylalanine metabolism; D-glutamate and D-glutamine metabolism; proline and arginine metabolism; aspartate, alanine, and glutamate metabolism; and aminoacyl-tRNA biosynthesis. These analyses implied that the biosynthetic capabilities of juvenile S. nudus were greater in the EG2. The results of this research enhance our understanding of the effects of dietary carbohydrate and protein levels on the growth performance of juvenile S. nudus.
Question: Write a study description for the study titled 'Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth'.
Answer: Drought represents a major threat to food security. Mechanistic data describing plant responses to drought have been studied extensively and genes conferring drought resistance have been introduced into crop plants. However, plants with enhanced drought resistance usually display lower growth, highlighting the need for strategies to uncouple drought resistance from growth. Here, we show that overexpression of BRL3, a vascular-enriched member of the brassinosteroid receptor family, can confer drought stress tolerance in Arabidopsis. Whereas loss-of-function mutations in the ubiquitously expressed BRI1 receptor leads to drought resistance at the expense of growth, overexpression of BRL3 receptor confers drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress, increased BRL3 triggers the accumulation of osmoprotectant metabolites including proline and sugars. Transcriptomic analysis suggests that this results from differential expression of genes in the vascular tissues. Altogether, this data suggests that manipulating BRL3 expression could be used to engineer drought tolerant crops.
Question: Write a study description for the study titled 'LC-MS/MS metabolomics unravels the resistant phenotype of carbapenemase-producing Enterobacteriaceae'.
Answer: Introduction: The degree of antimicrobial resistance demonstrated by carbapenemase-producing Enterobacteriaceae (CPE) represents a growing public health challenge. Conventional methods for detecting CPE involve culture-based techniques with lengthy incubation steps. There is a need to develop rapid and accurate methods for the detection of resistance, for implementation into clinical diagnostics.Objectives: With cellular phenotype closely linked to the metabolome, the acquisition of resistance should result in detectable differences in microbial metabolism. Accordingly, we sought to profile the metabolome of Enterobacteriaceae isolates belonging to both CPE and non-CPE groups to identify metabolites linked to CPE.Methods: We used liquid chromatography-mass spectrometry to profile the endo- and exometabolome of 32 Klebsiella pneumoniae and Escherichia coli isolates to identify metabolites which could predict CPE in antibiotic-free conditions after 6 h of growth.Results: Using supervised machine learning and multivariate analysis algorithms (partial least squares-discriminant analysis, k-nearest neighbour and random forest), we identified 21 metabolite biomarkers which displayed high performance metrics for the prediction of CPE (AUROCs ≥ 0.845). Results revealed a range of alterations between the metabolomes of CPE and non-CPE isolates. Pathway analysis revealed enrichment of microbial pathways including arginine metabolism, ATP-binding cassette transporters, purine metabolism, biotin metabolism, nucleotide metabolism, and biofilm formation, providing mechanistic insight into the resistance phenotype of CPE.Conclusion: Our models demonstrates the ability to distinguish CPE from non-CPE in under 7 h using metabolite biomarkers, showing potential for the development of a targeted diagnostic assay.
Question: Write a study description for the study titled 'Plasma metabolome reveals altered oxidative stress, inflammation, and amino acid metabolism in dogs with idiopathic epilepsy.'.
Answer: OBJECTIVE: Idiopathic epilepsy (IE) is the most common chronic neurological disease in dogs, and an established natural animal model for human epilepsy types with genetic and unknown etiology. However, the metabolic pathways underlying IE remain largely unknown. METHODS: Plasma samples of healthy dogs (n = 39) and dogs with IE (n = 49) were metabolically profiled (n = 121 known target metabolites) and fingerprinted (n = 1825 untargeted features) using liquid chromatography coupled to mass spectrometry. Dogs with IE were classified as drug-sensitive (DS) (n = 22) or drug-resistant (DR) (n = 27). All dogs received the same standard adult maintenance diet for minimum 20 days (35 ± 11 days) before sampling. Data were analysed using a combination of univariate (one-way ANOVA or Kruskal-Wallis rank sum test), multivariate (limma, OPLS-DA) and pathway enrichment statistical analysis. RESULTS: In dogs with both DR and DS IE, a distinct plasma metabolic profile and fingerprint compared to healthy dogs was observed. Metabolic pathways involved in these alterations included oxidative stress, inflammation and amino acid metabolism. Vitamin B6 was found to play a key role, with significantly lower plasma concentrations found in DS (P = 0.001) and DR (P = 0.005) compared to healthy dogs. SIGNIFICANCE: Our data provide new insights in the metabolic pathways underlying IE in dogs, further substantiating its potential as a sentinel for humans with epilepsy, reflected by related metabolic changes in oxidative stress metabolites and vitamin B6. Even more, several metabolites within the uncovered pathways offer promising therapeutic targets for the management of IE, primarily for dogs, and ultimately for humans.
Question: Write a study description for the study titled 'COSY catalyzes trans-cis isomerization and lactonization in the biosynthesis of coumarins'.
Answer: Coumarins or 1,2-benzopyrones comprise a large class of secondary metabolites ubiquitously found in the plant kingdom. In many plant species, coumarins are particularly important for iron acquisition and plant defense. Here we show that COUMARIN SYNTHASE (COSY) is a key enzyme in the biosynthesis of coumarins. Arabidopsis thaliana cosy mutants are strongly reduced in coumarin levels and accumulate o-hydroxyphenylpropanoids instead. Accordingly, cosy mutants have reduced iron content and show growth defects when grown under conditions where iron availability is limited. Recombinant COSY is able to produce umbelliferone, esculetin and scopoletin from their respective o-hydroxycinnamoyl-CoA thioesters via two reaction steps: a trans-cis isomerization followed by a lactonization. This conversion happens partially spontaneously and is catalyzed by light, which explains why the need for an enzyme for this conversion has been overlooked. The combined results show that COSY has an essential role in the biosynthesis of coumarins in organs that are shielded from light, such as roots. These findings provide routes to improving coumarin production in crops or via microbial fermentation.
Question: Write a study description for the study titled 'SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia'.
Answer: Acute myeloid leukemia (AML) cells rely on phospho-signaling pathways to gain unlimited proliferation potential. Here, we used domain-focused CRISPR screening to identify the nuclear phosphatase SCP4 as a dependency in AML, yet this enzyme is dispensable in normal hematopoietic progenitor cells. Using CRISPR exon scanning and gene complementation assays, we show that the catalytic function of SCP4 is essential in AML. Through mass spectrometry analysis of affinity-purified complexes, we identify the kinase paralogs STK35 and PDIK1L as binding partners and substrates of the SCP4 phosphatase domain. We show that STK35 and PDIK1L function catalytically and redundantly in the same pathway as SCP4 to maintain AML proliferation and to support amino acid biosynthesis and transport. We provide evidence that SCP4 regulates STK35/PDIK1L through two distinct mechanisms: catalytic removal of inhibitory phosphorylation and by promoting kinase stability. Our findings reveal a phosphatase-kinase signaling complex that supports the pathogenesis of AML.
Question: Write a study description for the study titled 'To explore the role of circulating oxidized lipids in the progression and prognosis of SA-AKI by means of histochemistry'.
Answer: Background: Plasma oxidized lipids are intimately linked to immune regulation as bioactive mediators. However, it is not clear whether they are related to the progression of sepsis-associated acute kidney injury (SA-AKI) and the effect of continuous renal replacement therapy (CRRT). This study intends to explore the changes in certain oxidized lipid during CRRT treatment and their correlation with the immune microenvironment and prognosis by analyzing plasma oxidative lipidomics.Methods: A total of 48 SA-AKI patients undergoing CRRT for more than 72 hours were enrolled in this prospective cohort study. Oxidative lipidomics was analyzed by ultra performance liquid chromatography coupled with tandem mass spectrometric (UPLC-MS/MS) detection at the beginning of CRRT (T0) and 72 hours later (T72), respectively.Results: Compared with survivors, plasma EETs, EpOMEs and EpDPEs in non-survivors were significantly down-regulated at T0, while PGFs, TXB and HEPEs were up-regulated. After 72 hours of CRRT, DiHETEs were significantly up-regulated and PGFs were down-regulated in non-survivors, while HEPEs and EpOMEs were up-regulated and 6keto-PGF1α was down-regulated in survivors. KEGG annotation showed that the differential lipids of survivors before and after CRRT were mainly enriched and up-regulated in metabolic pathway.Conclusion: This study provided a comprehensive overview of plasma oxidized lipids in SA-AKI patients undergoing CRRT and further elucidated the lipids and pathways linked to patient severity and prognosis. Additionally, we unveiled the potential mechanisms by which CRRT improves the prognosis of SA-AKI patients by removing PGFs and TXs while simultaneously upregulating HEPE to ameliorate the immune microenvironment, as well as the potential significance of adjusting CRRT prescriptions based on plasma oxidized lipidomics.
Question: Write a study description for the study titled 'Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (A)'.
Answer: Translational genomics, the use of model species to generate knowledge about biological processes and the functions of genes, offers great promise to biotechnologists. Few studies have sought robust responses of model plants to environmental stresses, such as salinity, by altering the stress dosage or by repeating experiments in consecutive years and/or different seasons.We mined our published and unpublished data on legume salt acclimation for robust system features at the ionomic, transcriptomic and metabolomic levels. We analysed data from the model legume Lotus japonicus, obtained through six independent, longterm, non-lethal salt stress experiments which were carried out over two consecutive years. Best possible controlled greenhouse conditions were applied and two main questions asked: how reproducible are results obtained from physiologically meaningful salinity experiments, and what degree of bias may be expected if conclusions are drawn from less well-repeated sampling. A surprisingly large fraction of the transcriptional and metabolic responses to salt stress were not reproducible between experiments. A core set of robust changes was found that was shared between experiments. Many of these robust responses were qualitatively and quantitatively conserved between different accessions of the same species, indicating that the robust responses may be a sound starting point for translational genomics.
Question: Write a study description for the study titled 'The lipid-metabolism enzyme ECI2 reduces neutrophil extracellular traps formation for colorectal cancer suppression'.
Answer: Abnormalities in ether lipid metabolism as well as the formation of neutrophil extracellular traps have recently been recognized as detrimental factors affecting tumorigenesis and progression. However, the role of abnormal ether lipid metabolism in colorectal cancer (CRC) evolution has not been reported. Here we show that the lipid metabolism-related gene enoyl-CoA δ-isomerase 2 (ECI2) plays a tumor-suppressor role in CRC and is negatively associated with poor prognosis in CRC patients. We mechanistically demonstrate that ECI2 reduces ether lipid-mediated Interleukin 8 (IL-8) expression leading to decreased neutrophil recruitment and neutrophil extracellular traps formation for colorectal cancer suppression. In particular, ECI2 inhibits ether lipid production in CRC cells by inhibiting the peroxisomal localization of alkylglycerone phosphate synthase (AGPS), the rate-limiting enzyme for ether lipid synthesis. These findings not only deepen our understanding of the role of metabolic reprogramming and neutrophil interactions in the progression of CRC, but also provide ideas for identifying potential diagnostic markers and therapeutic targets for CRC.
Question: Write a study description for the study titled 'Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent'.
Answer: Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the most recent outbreak of VL in the ISC. We show that the ISC1 population is very different from the CG, both at genome and metabolome levels. The genomic differences include SNPs, CNV and small indels in genes coding for known virulence factors, immunogens and surface proteins. Both genomic and metabolic approaches highlighted dissimilarities related to membrane lipids, the nucleotide salvage pathway and the urea cycle in ISC1 versus CG. Many of these pathways and molecules are important for the interaction with the host/extracellular environment. Altogether, our data predict major functional differences in ISC1 versus CG parasites, including virulence. Therefore, particular attention is required to monitor the fate of this emerging ISC1 population in the ISC, especially in a post-VL elimination context.Linked cross omic data sets:Raw sequencing data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJNA419531.
Question: Write a study description for the study titled '12,13-diHOME protects against the age-related decline in cardiovascular function via attenuation of CaMKII.'.
Answer: Liquid chromatography mass spectrometry (LC-MS/MS) on plasma of young (aged 24-40) and aged (aged 65-90) human subjects.
Question: Write a study description for the study titled '"Exploring the mode of action of dithranol therapy for psoriasis: a metabolomic analysis using HaCaT cells."'.
Answer: "Psoriasis is a common, immune-mediated inflammatory skin disease characterized by red, heavily scaled plaques. The disease affects over one million people in the UK and causes significant physical, psychological and societal impact. There is limited understanding regarding the exact pathogenesis of the disease although it is believed to be a consequence of genetic predisposition and environmental triggers. Treatments vary from topical therapies, such as dithranol, for disease of limited extent (< 5% body surface area) to the new immune-targeted biologic therapies for severe psoriasis. Dithranol (also known as anthralin) is a topical therapy for psoriasis believed to work by inhibiting keratinocyte proliferation. To date there have been no metabolomics-based investigations into psoriasis. The HaCaT cell line is a model system for the epidermal keratinocyte proliferation characteristic of psoriasis and was thus chosen for study. Dithranol was applied at therapeutically relevant doses to HaCaT cells. Following the optimisation of enzyme inactivation and metabolite extraction, gas chromatography-mass spectrometry was employed for metabolomics as this addresses central metabolism. Cells were challenged with 0-0.5 μg/mL in 0.1 μg/mL steps and this quantitative perturbation generated data that were highly amenable to correlation analysis. Thus, we used a combination of traditional principal components analysis, hierarchical cluster analysis, along with correlation networks. All methods highlighted distinct metabolite groups, which had different metabolite trajectories with respect to drug concentration and the interpretation of these data established that cellular metabolism had been altered significantly and provided further clarification of the proposed mechanism of action of the drug."