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METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA (

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

Frontiers of Agricultural Science and Engineering   Pages 215-230 doi: 10.15302/J-FASE-2021382

Abstract: Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

Keywords： harvest season     metabolites     tea shoots     transcriptomics     untargeted metabolomics    

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Progress in NMR-based metabolomics of

Qifang PAN,Jingya ZHAO,Yuliang WANG,Kexuan TANG

Frontiers of Agricultural Science and Engineering 2015, Volume 2, Issue 3,   Pages 195-204 doi: 10.15302/J-FASE-2015063

Abstract: Metabolomics has been rapidly developed as an important field in plant sciences and natural productsNMR-based metabolomics has been used in studies of for pathway elucidation, understanding stress responses

Keywords： Catharanthus roseus     monoterpenoid indole alkaloids     NMR     metabolomics    

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Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

Frontiers of Environmental Science & Engineering 2023, Volume 17, Issue 1, doi: 10.1007/s11783-023-1604-5

Abstract:

● Metabolomic temporal profiling of cells exposed to xenobiotics.

Keywords： Metabolomics     BPA     MCF-7     Temporal profiling     Metabolic adaption     Dysregulation correlation    

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Metabolomics in human type 2 diabetes research

Jingyi Lu, Guoxiang Xie, Weiping Jia, Wei Jia

Frontiers of Medicine 2013, Volume 7, Issue 1,   Pages 4-13 doi: 10.1007/s11684-013-0248-4

Abstract: The emergence of metabolomics has allowed researchers to systemically measure the small molecule metabolitesDuring the last decade, the progression made in metabolomics has provided insightful information on diseaseRecent studies using metabolomics approach coupled with statistical tools to predict incident diabetes

Keywords： metabolomics     type 2 diabetes     metabolic pathway     mass spectrometry     nuclear magnetic resonance (NMR)    

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Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Frontiers of Medicine 2014, Volume 8, Issue 1,   Pages 58-67 doi: 10.1007/s11684-014-0318-2

Abstract: available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics

Keywords： sepsis     biomarker     genomics     transcriptomics     proteomics     metabolomics    

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High-throughput metabolomics reveals the perturbed metabolic pathways and biomarkers of Yang Huang syndrome

Heng Fang, Aihua Zhang, Xiaohang Zhou, Jingbo Yu, Qi Song, Xijun Wang

Frontiers of Medicine 2020, Volume 14, Issue 5,   Pages 651-663 doi: 10.1007/s11684-019-0709-5

Abstract: High-throughput metabolomics can clarify the underlying molecular mechanism of diseases via the qualitativeWe used integrated analysis to communicate the multiple results of metabolomics and network pharmacologyOur study indicated that the combination of high-throughput metabolomics and network pharmacology is

Keywords： metabolomics     liquid chromatography-mass spectrometry     metabolites     metabolic pathways    

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Untargeted metabolomic analysis of pregnant women exposure to perfluorooctanoic acid at different degrees

Frontiers of Environmental Science & Engineering 2023, Volume 17, Issue 3, doi: 10.1007/s11783-023-1628-x

Abstract:

● Metabolome can distinguish pregnant women exposure to PFOA at different degrees.

Keywords： Perfluorooctanoic acid     Exposure     Pregnant women     Metabolomic     GSH     Microbiota metabolism    

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Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

Frontiers of Medicine doi: 10.1007/s11684-023-1020-z

Abstract: Retroperitoneal liposarcoma (RLPS) is the main subtype of retroperitoneal soft sarcoma (RSTS) and has a poor prognosis and few treatment options, except for surgery. The proteomic and metabolic profiles of RLPS have remained unclear. The aim of our study was to reveal the metabolic profile of RLPS. Here, we performed proteomic analysis (n = 10), metabolomic analysis (n = 51), and lipidomic analysis (n = 50) of retroperitoneal dedifferentiated liposarcoma (RDDLPS) and retroperitoneal well-differentiated liposarcoma (RWDLPS) tissue and paired adjacent adipose tissue obtained during surgery. Data analysis mainly revealed that glycolysis, purine metabolism, pyrimidine metabolism and phospholipid formation were upregulated in both RDDLPS and RWDLPS tissue compared with the adjacent adipose tissue, whereas the tricarboxylic acid (TCA) cycle, lipid absorption and synthesis, fatty acid degradation and biosynthesis, as well as glycine, serine, and threonine metabolism were downregulated. Of particular importance, the glycolytic inhibitor 2-deoxy-D-glucose and pentose phosphate pathway (PPP) inhibitor RRX-001 significantly promoted the antitumor effects of the MDM2 inhibitor RG7112 and CDK4 inhibitor abemaciclib. Our study not only describes the metabolic profiles of RDDLPS and RWDLPS, but also offers potential therapeutic targets and strategies for RLPS.

Keywords： RLPS     proteomics     metabolomics     lipidomics     metabolism    

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Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

Frontiers of Medicine doi: 10.1007/s11684-023-1022-x

Abstract: The treatment of PML/RARA+ acute promyelocytic leukemia (APL) with all-trans-retinoic acid and arsenic trioxide (ATRA/ATO) has been recognized as a model for translational medicine research. Though an altered microenvironment is a general cancer hallmark, how APL blasts shape their plasma composition is poorly understood. Here, we reported a cross-sectional correlation network to interpret multilayered datasets on clinical parameters, proteomes, and metabolomes of paired plasma samples from patients with APL before or after ATRA/ATO induction therapy. Our study revealed the two prominent features of the APL plasma, suggesting a possible involvement of APL blasts in modulating plasma composition. One was characterized by altered secretory protein and metabolite profiles correlating with heightened proliferation and energy consumption in APL blasts, and the other featured APL plasma-enriched proteins or enzymes catalyzing plasma-altered metabolites that were potential trans-regulatory targets of PML/RARA. Furthermore, results indicated heightened interferon-gamma signaling characterizing a tumor-suppressing function of the immune system at the first hematological complete remission stage, which likely resulted from therapy-induced cell death or senescence and ensuing supraphysiological levels of intracellular proteins. Overall, our work sheds new light on the pathophysiology and treatment of APL and provides an information-rich reference data cohort for the exploratory and translational study of leukemia microenvironment.

Keywords： acute promyelocytic leukemia     plasma proteomics     plasma metabolomics     cross-sectional correlation network    

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Genomic and metabolomic analysis of with enhanced poly--glutamic acid production through atmospheric and room temperature plasma mutagenesis

Frontiers of Chemical Science and Engineering 2022, Volume 16, Issue 12,   Pages 1751-1760 doi: 10.1007/s11705-022-2211-x

Abstract: Poly-γ-glutamic acid is an extracellular polymeric substance with various applications owing to its valuable properties of biodegradability, flocculating activity, water solubility, and nontoxicity. However, the ability of natural strains to produce poly-γ-glutamic acid is low. Atmospheric and room temperature plasma was applied in this study to conduct mutation breeding of Bacillus licheniformis CGMCC 2876, and a mutant strain M32 with an 11% increase in poly-γ-glutamic acid was obtained. Genome resequencing analysis identified 7 nonsynonymous mutations of ppsC encoding lipopeptide synthetase associated with poly-γ-glutamic acid metabolic pathways. From molecular docking, more binding sites and higher binding energy were speculated between the mutated plipastatin synthase subunit C and glutamate, which might contribute to the higher poly-γ-glutamic acid production. Moreover, the metabolic mechanism analysis revealed that the upregulated amino acids of M32 provided substrates for glutamate and promoted the conversion between L- and D-glutamate acids. In addition, the glycolytic pathway is enhanced, leading to a better capacity for using glucose. The maximum poly-γ-glutamic acid yield of 14.08 g·L–1 was finally reached with 30 g·L–1 glutamate.

Keywords： ARTP mutagenesis     Bacillus licheniformis     poly-γ-glutamic acid     metabolomics    

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Chinmedomics: A Powerful Approach Integrating Metabolomics with Serum Pharmacochemistry to Evaluate the Review

Ai-Hua Zhang, Hui Sun, Guang-Li Yan, Ying Han, Qi-Qi Zhao, Xi-Jun Wang

Engineering 2019, Volume 5, Issue 1,   Pages 60-68 doi: 10.1016/j.eng.2018.11.008

Abstract: The serum pharmacochemistry of the TCM approach with metabolomics were integrated to establish an innovative

Keywords： Chinmedomics     Serum pharmacochemistry of TCM     Efficacy     Metabolomics     Syndrome     Biomarkers     Quality markers    

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Functional Metabolomics Reveals that Astragalus Polysaccharides Improve Lipids Metabolism through Article

Bingbing Li, Ying Hong, Yu Gu, Shengjie Ye, Kaili Hu, Jian Yao, Kan Ding, Aihua Zhao, Wei Jia, Houkai Li

Engineering 2022, Volume 9, Issue 2,   Pages 111-122 doi: 10.1016/j.eng.2020.05.023

Abstract: Functional metabolomics is increasingly used to investigate systemic effects on the host by identifyingunderlying the metabolic benefits of Astragalus polysaccharides (APS) by adopting a functional metabolomicsThen, gas chromatography–time-of-flight mass spectrometry (GC–TOFMS)-based untargeted metabolomicsThen, metabolomics analysis revealed that APS supplementation reversed the HFD-induced metabolic changesOur results also highlight that functional metabolomics is practical for investigating the mechanism

Keywords： Astragalus     polysaccharides (APS)     Functional metabolomics     2-Hydroxybutyric acid     Obesity    

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Deeper Chemical Perceptions for Better Traditional Chinese Medicine Standards Review

Jin-Jun Hou,Jian-Qing Zhang,Chang-Liang Yao,Rudolf Bauer,Ikhlas A. Khan,Wan-Ying Wu,De-an Guo

Engineering 2019, Volume 5, Issue 1,   Pages 83-97 doi: 10.1016/j.eng.2018.12.005

Abstract:

Traditional Chinese medicines (TCMs), a complex system of natural resources with many diverse components, are widely used as approved medicinal agents in China. Quality control of TCMs is a huge challenge for the government and for testing institutes and is associated with numerous scientific issues. Among these considerations include the following questions: How many components are in TCMs? How can the multiple components in TCMs be comprehensively delineated and subsequently characterized? What is the level and range of these (active) metabolites within these multiple-component TCMs, in order to recommend standards? and What are the qualities required for a marker constituent to be selected, and from a practical perspective, how can these components be assessed with low cost and in a short time? All of these factors require significant and deep thinking in order to understand the individualistic chemistry of TCM in order to develop enhanced TCM quality standards for improved and consistent patient care. In this review, the latest exploratory research in TCM chemistry analytical techniques and methods is summarized in order to begin to develop responses to these scientific issues. Advances in these methods have included multidimensional separation for liquid chromatography–high-resolution mass spectrometry (LC–HRMS), smart triggering data-dependent acquisition of LC–HRMS, target analysis with liquid chromatography–mass spectrometry (LC–MS), supercritical fluid chromatography, and data mining of large mass spectrometry (MS) datasets. In addition, two quality strategies have been introduced in order to save reference standards and the analysis time for a TCM quality standard, including the application of the single standard to determine multi-components (SSDMC) and monomethodheterotrait matrix methods. Finally, a series of future improvements for analytical methods for TCMs are proposed.

Keywords： Traditional Chinese medicine     Liquid chromatography     Mass spectrometry     Data-dependent acquisition     Chemometrics     Untargeted    

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Photosynthesis and related metabolic mechanism of promoted rice (Oryza sativa L.) growth by TiO2 nanoparticles

Yingdan Zhang, Na Liu, Wei Wang, Jianteng Sun, Lizhong Zhu

Frontiers of Environmental Science & Engineering 2020, Volume 14, Issue 6, doi: 10.1007/s11783-020-1282-5

Abstract: Abstract • The rice growth was promoted by nano-TiO2 of 0.1–100 mg/L. • Nano-TiO2 enhanced the energy storage in photosynthesis. • Nano-TiO2 reduced energy consumption in carbohydrate metabolism and TCA cycle. Titanium dioxide nanoparticle (nano-TiO2), as an excellent UV absorbent and photo-catalyst, has been widely applied in modern industry, thus inevitably discharged into environment. We proposed that nano-TiO2 in soil can promote crop yield through photosynthetic and metabolic disturbance, therefore, we investigated the effects of nano-TiO2 exposure on related physiologic-biochemical properties of rice (Oryza sativa L.). Results showed that rice biomass was increased >30% at every applied dosage (0.1–100 mg/L) of nano-TiO2. The actual photosynthetic rate (Y(II)) significantly increased by 10.0% and 17.2% in the treatments of 10 and 100 mg/L respectively, indicating an increased energy production from photosynthesis. Besides, non-photochemical quenching (Y(NPQ)) significantly decreased by 19.8%–26.0% of the control in all treatments respectively, representing a decline in heat dissipation. Detailed metabolism fingerprinting further revealed that a fortified transformation of monosaccharides (D-fructose, D-galactose, and D-talose) to disaccharides (D-cellobiose, and D-lactose) was accompanied with a weakened citric acid cycle, confirming the decrease of energy consumption in metabolism. All these results elucidated that nano-TiO2 promoted rice growth through the upregulation of energy storage in photosynthesis and the downregulation of energy consumption in metabolism. This study provides a mechanistic understanding of the stress-response hormesis of rice after exposure to nano-TiO2, and provides worthy information on the potential application and risk of nanomaterials in agricultural production.

Keywords： Nano-TiO2     Rice     Photosynthesis     Metabolomics     Energy storage    

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Screening for main components associated with the idiosyncratic hepatotoxicity of a tonic herb, Polygonum multiflorum

Chunyu Li, Ming Niu, Zhaofang Bai, Congen Zhang, Yanling Zhao, Ruiyu Li, Can Tu, Huifang Li, Jing Jing, Yakun Meng, Zhijie Ma, Wuwen Feng, Jinfa Tang, Yun Zhu, Jinjie Li, Xiaoya Shang, Zhengsheng Zou, Xiaohe Xiao, Jiabo Wang

Frontiers of Medicine 2017, Volume 11, Issue 2,   Pages 253-265 doi: 10.1007/s11684-017-0508-9

Abstract: In addition, plasma metabolomics analysis showed that cis-SG-disturbing enriched pathways

Keywords： Polygonum multiflorum     idiosyncratic hepatotoxicity     metabolomics     stilbene     cis-transisomerization    

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Title Author Date Type Operation

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA (

Chen-Kai JIANG, De-Jiang NI, Ming-Zhe YAO, Jian-Qiang MA, Liang CHEN

Journal Article

Progress in NMR-based metabolomics of

Qifang PAN,Jingya ZHAO,Yuliang WANG,Kexuan TANG

Journal Article

Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

Journal Article

Metabolomics in human type 2 diabetes research

Jingyi Lu, Guoxiang Xie, Weiping Jia, Wei Jia

Journal Article

Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Journal Article

High-throughput metabolomics reveals the perturbed metabolic pathways and biomarkers of Yang Huang syndrome

Heng Fang, Aihua Zhang, Xiaohang Zhou, Jingbo Yu, Qi Song, Xijun Wang

Journal Article

Untargeted metabolomic analysis of pregnant women exposure to perfluorooctanoic acid at different degrees

Journal Article

Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

Journal Article

Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

Journal Article

Genomic and metabolomic analysis of with enhanced poly--glutamic acid production through atmospheric and room temperature plasma mutagenesis

Journal Article

Chinmedomics: A Powerful Approach Integrating Metabolomics with Serum Pharmacochemistry to Evaluate the

Ai-Hua Zhang, Hui Sun, Guang-Li Yan, Ying Han, Qi-Qi Zhao, Xi-Jun Wang

Journal Article

Functional Metabolomics Reveals that Astragalus Polysaccharides Improve Lipids Metabolism through

Bingbing Li, Ying Hong, Yu Gu, Shengjie Ye, Kaili Hu, Jian Yao, Kan Ding, Aihua Zhao, Wei Jia, Houkai Li

Journal Article

Deeper Chemical Perceptions for Better Traditional Chinese Medicine Standards

Jin-Jun Hou,Jian-Qing Zhang,Chang-Liang Yao,Rudolf Bauer,Ikhlas A. Khan,Wan-Ying Wu,De-an Guo

Journal Article

Photosynthesis and related metabolic mechanism of promoted rice (Oryza sativa L.) growth by TiO2 nanoparticles

Yingdan Zhang, Na Liu, Wei Wang, Jianteng Sun, Lizhong Zhu

Journal Article

Screening for main components associated with the idiosyncratic hepatotoxicity of a tonic herb, Polygonum multiflorum

Chunyu Li, Ming Niu, Zhaofang Bai, Congen Zhang, Yanling Zhao, Ruiyu Li, Can Tu, Huifang Li, Jing Jing, Yakun Meng, Zhijie Ma, Wuwen Feng, Jinfa Tang, Yun Zhu, Jinjie Li, Xiaoya Shang, Zhengsheng Zou, Xiaohe Xiao, Jiabo Wang

Journal Article