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1.
Chinese Journal of Biotechnology ; (12): 2211-2222, 2021.
Article in Chinese | WPRIM | ID: wpr-887790

ABSTRACT

Synthetic biology and metabolic engineering have been widely used to construct microbial cell factories for efficient production of bio-based chemicals, which mainly focus on the modification and regulation of metabolic pathways. The characteristics of microorganisms themselves, e.g. morphology, have rarely been taken into consideration in the biotechnological production processes. Morphology engineering aims to control cell shapes and cell division patterns by manipulating the genes related to cell morphology, providing a new strategy for developing efficient microbial cell factories. This review summarized the proteins related to cell morphology, followed by illustrating a few examples of using morphology engineering strategies for improving production of bio-based chemicals. This includes increasing intracellular product accumulation by regulating cell size, enhancing extracellular secretion of target products by improving cell permeability, reducing production cost by achieving high cell density, and improving product performance by controlling the degree of product hydrolysis. Finally, challenges and perspectives for the development of morphology engineering were discussed.


Subject(s)
Biotechnology , Metabolic Engineering , Metabolic Networks and Pathways , Synthetic Biology
2.
Article in Chinese | WPRIM | ID: wpr-921786

ABSTRACT

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry(UPLC-Q-TOF-MS) was used to investigate the metabolites of maackiain in rats based on the prediction function of UNIFI data processing system and liver microsomal incubation in vitro. Ten metabolites of maackiain after oral absorption were reasonably deduced and characterized. It was found that the biotransformation of maackiain mainly included phase Ⅰ oxidation, dehydrogenation, phase Ⅱ sulfate conjugation, glucosylation conjugation, and glucuronic acid conjugation. Among them, the product of glucosylation conjugation, trifolirhizin, was identified by comparison with the reference for the first time. Liver microsomal incubation in vitro further confirmed the metabolites and metabolic pathways of maackiain in rats. The metabolites in the blood, urine, and feces complemented each other, which revealed the migration, metabolism, and excretion modes of maackiain in rats. This study lays a foundation for the further investigation of the metabolic mechanism of maackiain in vivo and the in-depth research on the mechanism of pharmacodynamics and toxicity.


Subject(s)
Animals , Chromatography, High Pressure Liquid , Chromatography, Liquid , Metabolic Networks and Pathways , Pterocarpans , Rats , Rats, Sprague-Dawley
3.
Frontiers of Medicine ; (4): 383-403, 2021.
Article in English | WPRIM | ID: wpr-888735

ABSTRACT

Cancer development is a complicated process controlled by the interplay of multiple signaling pathways and restrained by oxygen and nutrient accessibility in the tumor microenvironment. High plasticity in using diverse nutrients to adapt to metabolic stress is one of the hallmarks of cancer cells. To respond to nutrient stress and to meet the requirements for rapid cell proliferation, cancer cells reprogram metabolic pathways to take up more glucose and coordinate the production of energy and intermediates for biosynthesis. Such actions involve gene expression and activity regulation by the moonlighting function of oncoproteins and metabolic enzymes. The signal - moonlighting protein - metabolism axis facilitates the adaptation of tumor cells under varying environment conditions and can be therapeutically targeted for cancer treatment.


Subject(s)
Energy Metabolism , Epigenesis, Genetic , Humans , Metabolic Networks and Pathways , Neoplasms/genetics , Tumor Microenvironment
4.
Chinese Journal of Biotechnology ; (12): 1564-1577, 2021.
Article in Chinese | WPRIM | ID: wpr-878655

ABSTRACT

As an important model industrial microorganism, Escherichia coli has been widely used in pharmaceutical, chemical industry and agriculture. In the past 30 years, a variety of new strategies and techniques, including artificial intelligence, gene editing, metabolic pathway assembly, and dynamic regulation have been used to design, construct, and optimize E. coli cell factories, which remarkably improved the efficiency for biotechnological production of chemicals. In this review, three key aspects for constructing E. coli cell factories, including pathway design, pathway assembly and regulation, and optimization of global cellular performance, are summarized. The technologies that have played important roles in metabolic engineering of E. coli, as well as their future applications, are discussed.


Subject(s)
Artificial Intelligence , Escherichia coli/genetics , Gene Editing , Metabolic Engineering , Metabolic Networks and Pathways/genetics
5.
Chinese Journal of Biotechnology ; (12): 1541-1563, 2021.
Article in Chinese | WPRIM | ID: wpr-878654

ABSTRACT

The regulation of the expression of genes involved in metabolic pathways, termed as metabolic regulation, is vital to construct efficient microbial cell factories. With the continuous breakthroughs in synthetic biology, the mining and artificial design of high-quality regulatory elements have substantially improved our ability to modify and regulate cellular metabolic networks and its activities. The research on metabolic regulation has also evolved from the static regulation of single genes to the intelligent and precise dynamic regulation at the systems level. This review briefly summarizes the advances of metabolic regulation technologies in the past 30 years.


Subject(s)
Metabolic Engineering , Metabolic Networks and Pathways/genetics , Synthetic Biology
6.
Chinese Journal of Biotechnology ; (12): 1526-1540, 2021.
Article in Chinese | WPRIM | ID: wpr-878653

ABSTRACT

Genome-scale metabolic network model (GSMM) is becoming an important tool for studying cellular metabolic characteristics, and remarkable advances in relevant theories and methods have been made. Recently, various constraint-based GSMMs that integrated genomic, transcriptomic, proteomic, and thermodynamic data have been developed. These developments, together with the theoretical breakthroughs, have greatly contributed to identification of target genes, systems metabolic engineering, drug discovery, understanding disease mechanism, and many others. This review summarizes how to incorporate transcriptomic, proteomic, and thermodynamic-constraints into GSMM, and illustrates the shortcomings and challenges of applying each of these methods. Finally, we illustrate how to develop and refine a fully integrated GSMM by incorporating transcriptomic, proteomic, and thermodynamic constraints, and discuss future perspectives of constraint-based GSMM.


Subject(s)
Genome/genetics , Metabolic Engineering , Metabolic Networks and Pathways/genetics , Models, Biological , Proteomics
7.
Chinese Journal of Biotechnology ; (12): 1494-1509, 2021.
Article in Chinese | WPRIM | ID: wpr-878651

ABSTRACT

In 1990s, Bailey and Stephanopoulos put forward the concept of classic metabolic engineering, aiming to use DNA recombination technology to rewire metabolic network to achieve improved cell performance and increased target products. In the last 30 years since the birth of metabolic engineering, life science have flourished, and new disciplines such as genomics, systems biology and synthetic biology have emerged, injecting new connotations and vitality into the development of metabolic engineering. Classic metabolic engineering research has entered into an unprecedented stage of systems metabolic engineering. The application of synthetic biology tools and strategies, such as omics technology, genomic-scale metabolic model, parts assembly, circuits design, dynamic control, genome editing and many others, have greatly improved the design, build, and rewiring capabilities of complex metabolism. The intervention of machine learning and the combination of evolutionary engineering and metabolic engineering will further promote the development of systems metabolic engineering. This paper analyzes the development of metabolic engineering in the past 30 years and summarizes the novel theories, techniques, strategies, and applications of metabolic engineering that have emerged over the past 30 years.


Subject(s)
Gene Editing , Metabolic Engineering , Metabolic Networks and Pathways/genetics , Synthetic Biology , Systems Biology
8.
Chinese Journal of Biotechnology ; (12): 1277-1286, 2021.
Article in Chinese | WPRIM | ID: wpr-878630

ABSTRACT

Microbial cell factories capable of producing valuable chemicals from renewable feedstocks provide a promising alternative towards sustainability. However, environmental stress remarkably affects the performance of microbial cell factories. By extending the chronological lifespan of microbial cells, the performance of microbial cell factories can be greatly improved. Firstly, an evaluation system for chronological lifespan and semi-chronological lifespan was established based on the changes in survival rates. Secondly, the addition of anti-aging drugs such as cysteine, carnosine, aminoguanidine and glucosamine increased the chronological lifespan of E. coli by 80%, 80%, 50% and 120%, respectively. Finally, we demonstrated that extending the chronological lifespan of E. coli increased the yield of metabolites produced by E. coli cell factories with endogenous (lactic acid and pyruvic acid) or exogenous (malic acid) metabolic pathway by 30.0%, 25.0%, and 27.0%, respectively. The strategy of extending chronological lifespan of E. coli provides a potential approach for enhancing the performance of microbial cell factories.


Subject(s)
Escherichia coli/genetics , Lactic Acid , Longevity , Metabolic Engineering , Metabolic Networks and Pathways
9.
Chinese Journal of Biotechnology ; (12): 860-873, 2021.
Article in Chinese | WPRIM | ID: wpr-878601

ABSTRACT

Genome-scale metabolic network model (GSMM) is an extremely important guiding tool in the targeted modification of industrial microbial strains, which helps researchers to quickly obtain industrial microbes with specific traits and has attracted increasing attention. Here we reviewe the development history of GSMM and summarized the construction method of GSMM. Furthermore, the development and application of GSMM in industrial microorganisms are elaborated by using four typical industrial microorganisms (Bacillus subtilis, Escherichia coli, Corynebacterium glutamicum, and Saccharomyces cerevisiae) as examples. In addition, prospects in the development trend of GSMM are proposed.


Subject(s)
Corynebacterium glutamicum/genetics , Escherichia coli/genetics , Metabolic Engineering , Metabolic Networks and Pathways/genetics
10.
Chinese Journal of Biotechnology ; (12): 253-265, 2021.
Article in Chinese | WPRIM | ID: wpr-878559

ABSTRACT

Based on observing the cytological characteristics of the flower buds of the functional male sterile line (S13) and the fertile line (F142) in eggplant, it was found that the disintegration period of the annular cell clusters in S13 anther was 2 days later than that of F142, and the cells of stomiun tissue and tapetum in F142 disintegrated on the blooming day, while it did not happen in S13. The comparative transcriptomic analysis showed that there were 1 436 differential expression genes (DEGs) (651 up-regulated and 785 down-regulated) in anthers of F142 and S13 at 8, 5 days before flowering and flowering day. The significance analysis of GO enrichment indicated that there were more unigene clusters involved in single cell biological process, metabolism process and cell process, and more catalytic activity and binding function were involved in molecular functions. Through KEGG annotation we found that the common DEGs were mainly enriched in the biosynthesis of secondary metabolites, metabolic pathway, protein processing in endoplasmic reticulum, biosynthesis of amino acids, carbon metabolism and plant hormone signal transduction. The fifteen genes co-expression modules were identified from 16 465 selected genes by weighted gene co-expression network analysis (WGCNA), three of which (Plum2, Royalblue and Bisque4 modules) were highly related to S13 during flower development. KEGG enrichment showed that the specific modules could be enriched in phenylpropanoid biosynthesis, photosynthesis, porphyrin and chlorophyll metabolism, α-linolenic acid metabolism, polysaccharide biosynthesis and metabolism, fatty acid degradation and the mutual transformation of pentose and glucuronic acid. These genes might play important roles during flower development of S13. It provided a reference for further study on the mechanism of anther dehiscence in eggplant.


Subject(s)
Flowers/genetics , Gene Expression Profiling , Gene Expression Regulation, Plant , Humans , Infertility, Male , Male , Metabolic Networks and Pathways/genetics , Solanum melongena/genetics , Transcriptome/genetics
11.
Braz. arch. biol. technol ; 64: e21190480, 2021. tab, graf
Article in English | LILACS | ID: biblio-1278442

ABSTRACT

Abstract The evolution of species is inevitably accompanied by the evolution of metabolic networks to adapt to different environments. The metabolic networks of different species were collected from the Kyoto Encyclopedia of Genes and Genomes (KEGG) website, and some enzyme reactions with the highest occurrence frequency in all species were found and are reported in this paper. The correlation coefficients of whether the enzyme reactions appear in all species were calculated, and the corresponding evolutionary correlation connection networks were calculated according to different correlation coefficient thresholds. These studies show that, as the evolutionary correlation of enzyme reactions increases, the weighted average of the mean functional concentration ratios of the enzyme reactions also increases, indicating that the functional concentration ratio of enzyme reactions has a certain correlation with the evolutionary correlation. The work presented in this paper enhances our understanding of the characteristics and general rules of metabolic network evolution.


Subject(s)
Enzyme Activation , Metabolic Networks and Pathways , Adaptation, Biological , Metabolism
12.
Chinese Journal of Biotechnology ; (12): 1101-1112, 2020.
Article in Chinese | WPRIM | ID: wpr-826867

ABSTRACT

As an important platform compound, 3-hydroxypropionic acid (3-HP) can be used as a substrate to synthesize a variety of biological products with commercial potential. The titer of 3-HP by wild-type bacteria is low, which severely limits the large-scale application and production of 3-HP. By modifying the genes related to the metabolic pathway, engineered bacteria using cheap substrates as carbon sources are constructed, the aim of reducing production cost and increasing output is realized. In this paper, the recent progress in the synthesis of 3-HP by metabolic engineering at home and abroad is reviewed. The advantages and disadvantages of glycerol pathway, malonyl-CoA pathway and beta-alanine pathway for synthesis of 3-HP are also summarized and analyzed, and the future development of 3-HP is prospected.


Subject(s)
Glycerol , Metabolism , Industrial Microbiology , Lactic Acid , Metabolic Engineering , Metabolic Networks and Pathways , Genetics
13.
Chinese Journal of Biotechnology ; (12): 2113-2125, 2020.
Article in Chinese | WPRIM | ID: wpr-878471

ABSTRACT

Glutamic acid is an important amino acid with wide range of applications and huge market demand. Therefore, by performing transcriptome sequencing and re-sequencing analysis on Corynebacterium glutamicum E01 and high glutamate-producing strain C. glutamicum G01, we identified and selected genes with significant differences in transcription and gene levels in the central metabolic pathway that may have greatly influenced glutamate synthesis and further increased glutamic acid yield. The oxaloacetate node and α-ketoglutarate node play an important role in glutamate synthesis. The oxaloacetate node and α-ketoglutarate node were studied to explore effect on glutamate production. Based on the integrated strain constructed from the above experimental results, the growth rate in a 5-L fermenter was slightly lower than that of the original strain, but the glutamic acid yield after 48 h reached (136.1±5.53) g/L, higher than the original strain (93.53±4.52) g/L, an increase by 45.5%; sugar-acid conversion rate reached 58.9%, an increase of 13.7% compared to 45.2% of the original strain. The application of the above experimental strategy improved the glutamic acid yield and the sugar-acid conversion rate, and provided a theoretical basis for the metabolic engineering of Corynebacterium glutamicum.


Subject(s)
Citric Acid Cycle , Corynebacterium glutamicum/metabolism , Glutamic Acid/metabolism , Metabolic Engineering , Metabolic Networks and Pathways/genetics
14.
Article in English | WPRIM | ID: wpr-878293

ABSTRACT

Objective@#To explore potential serum biomarkers of children with Kashin-Beck Disease (KBD) and the metabolic pathways to which the biomarkers belong.@*Methods@#A two-stage metabolomic study was employed. The discovery cohort included 56 patients, 51 internal controls, and 50 external controls. The metabolites were determined by HPLC-(Q-TOF)-MS and confirmed by Human Metabolome Databases (HMDB) and Metlin databases. MetaboAnalyst 3.0 and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to analyze the metabolic pathways of the candidate metabolites. The use of HPLC-(Q-TRAP)-MS enabled quantitative detection of the target metabolites which were chosen using the discovery study and verified in another independent verification cohort of 31 patients, 41 internal controls, and 50 external controls.@*Results@#Eight candidate metabolites were identified out in the discovery study, namely kynurenic acid, N-α-acetylarginine, 6-hydroxymelatonin, sphinganine, ceramide, sphingosine-1P, spermidine, and glycine. These metabolites exist in sphingolipid, glutathione, and tryptophan metabolic pathways. In the second-stage study, five candidate metabolites were validated, including kynurenic acid, N-α-acetylarginine, sphinganine, spermidine, and sphingosine-1P. Except for spermidine, all substances exhibited low expression in the case group compared with the external control group, and the difference in levels of sphinganine, spermidine, and sphingosine-1P was statistically significant.@*Conclusion@#The direction of change of levels of sphinganine, spermidine, and sphingosine-1P in the two-stage study cohorts was completely consistent, and the differences were statistically significant. Therefore, these substances can be used as potential biomarkers of KBD. Furthermore, these results raise the possibility that sphingolipid metabolic pathways may be closely related to KBD.


Subject(s)
Adolescent , Biomarkers/blood , Child , China , Cohort Studies , Female , Humans , Kashin-Beck Disease/blood , Male , Metabolic Networks and Pathways , Metabolome
15.
Acta Physiologica Sinica ; (6): 566-574, 2020.
Article in Chinese | WPRIM | ID: wpr-878202

ABSTRACT

Ferroptosis is a newly discovered non-apoptotic form of regulated cell death driven by iron-dependent lipid peroxidation. The present studies have shown that many metabolic processes and homeostasis are affected by ferroptosis. It is related to many lung diseases, including acute lung injury, chronic obstructive pulmonary disease and pulmonary fibrosis, etc. Currently, the research on ferroptosis is still in its infancy. Previous studies have confirmed that ferroptosis is regulated by a variety of genes, and the mechanism is complex, mainly involving iron homeostasis and lipid peroxidation metabolism. This review summarizes some regulation networks of metabolic processes associated with ferroptosis and discusses the roles of ferroptosis in the pathophysiological progression of many lung diseases. We expected to provide new ideas and references for the treatment of these diseases.


Subject(s)
Ferroptosis , Humans , Iron , Lipid Peroxidation , Metabolic Networks and Pathways , Pulmonary Disease, Chronic Obstructive
16.
Article in Chinese | WPRIM | ID: wpr-827987

ABSTRACT

Numerous studies showed that the growth of medicinal plants in their native areas was simultaneously affected by abiotic stress combinations. Compared with single stress, plants have unique responses to a combination of different abiotic stresses and cannot be inferred directly from plants' responses to each individual stress. The effect of combined stresses on plants usually has three types of synergistic antagonism or independence. The secondary metabolism in the process of medicinal plant stress combination response also played a vital role, and environmental stresses can spur the accumulation of secondary metabolites, but under the stress combination, plants induce specific gene expression of key enzymes on secondary metabolic pathways, in turn, the accumulation of secondary metabolites against stress is formed. When plants are subjected to stress combination, the interaction of multiple signaling pathways makes it highly complex for plants to respond to stress combination. This paper summarized the effects of stress combination on physiological and secondary metabolism of medicinal plants, and discussed the related physiological, biochemical and molecular mechanisms. It provides theoretical basis for improving the adaptability of medicinal plants to adversity, improving the quality of Chinese medicinal materials, and further optimizing the cultivation of medicinal plants.


Subject(s)
Gene Expression Regulation, Plant , Metabolic Networks and Pathways , Plants, Medicinal , Secondary Metabolism , Stress, Physiological
17.
Arch. endocrinol. metab. (Online) ; 63(6): 549-556, Nov.-Dec. 2019. graf
Article in English | LILACS | ID: biblio-1055020

ABSTRACT

ABSTRACT Growth hormone (GH) is best known for its effect stimulating tissue and somatic growth through the regulation of cell division, regeneration and proliferation. However, GH-responsive neurons are spread over the entire central nervous system, suggesting that they have important roles in the brain. The objective of the present review is to summarize and discuss the potential physiological importance of GH action in the central nervous system. We provide evidence that GH signaling in the brain regulates the physiology of numerous functions such as cognition, behavior, neuroendocrine changes and metabolism. Data obtained from experimental animal models have shown that disruptions in GH signaling in specific neuronal populations can affect the reproductive axis and impair food intake during glucoprivic conditions, neuroendocrine adaptions during food restriction, and counter-regulatory responses to hypoglycemia, and they can modify gestational metabolic adaptions. Therefore, the brain is an important target tissue of GH, and changes in GH action in the central nervous system can explain some dysfunctions presented by individuals with excessive or deficient GH secretion. Furthermore, GH acts in specific neuronal populations during situations of metabolic stress to promote appropriate physiological adjustments that restore homeostasis. Arch Endocrinol Metab. 2019;63(6):549-56


Subject(s)
Humans , Brain/metabolism , Neuroprotective Agents/metabolism , Human Growth Hormone/metabolism , Metabolic Networks and Pathways/physiology , Signal Transduction , Nerve Regeneration/physiology
18.
Article in Chinese | WPRIM | ID: wpr-775077

ABSTRACT

Metabolomics is an emerging and popular subject in the post-genome era, and a large number of studies have been noted on the application of metabolomics in health evaluation, growth and development evaluation, disease diagnosis, and therapeutic efficacy evaluation. As a special period of life, the neonatal period is characterized by rapid cell renewing, consumption of a lot of energy and materials, and changes in metabolic pathways, all of which affect the level of metabolites. However, there is still no reference standard for metabolic level and profile in neonates. This article reviews the current status of metabolic research on neonatal growth and development and common diseases and related clinical application of metabolomics, so as to provide new ideas for nutrition guidance and evaluation, selection of therapeutic regimens, and new drug research in neonates.


Subject(s)
Humans , Infant, Newborn , Metabolic Networks and Pathways , Metabolomics
19.
Article in Chinese | WPRIM | ID: wpr-774534

ABSTRACT

To predict the targets of active ingredients of Kuihua Hugan Tablets by network pharmacology, and explore the "multi-component-multi-target-multi-pathway" hepatoprotective mechanism of action. First, through traditional Chinese medicine systems pharmacology(TCMSP) and TCM Database@Taiwan Database, main active ingredients of Kuihua Hugan Tablets were screened out based on oral bioavailability(OB), drug-likeness(DL) and effective half-lives(HL). The targets of active ingredients of Kuihua Hugan Tablets were predicted based on the PharmMapper method. Then, the prediction was conducted by screening the target genes associated with chronic hepatitis and early cirrhosis through CooLGeN and GeneCards databases. Target gene functions and signal pathways were analyzed by bioinformatics annotation database Metascape. Cytoscape software was used to construct the Kuihua Hugan Tablets ingredient-target and ingredient-target-pathway network. String database combined with Cytoscape software was used to construct the networks of component-target and component-target-pathway. STRING database was combined with Cytoscape software to draw protein-protein interaction(PPI) network and conduct network topology analysis. Finally, Systems Dock Web Site software was applied in verifying the molecular docking between active ingredients and potential protein targets. A total of 26 compounds and 509 potential targets were screened out from Kuihua Hugan Tablets in the experiment. The results of PPI network analysis indicated that albumin(ALB), insulin-like growth factor 1(IGF1), matrix metalloproteinase-9(MMP9), matrix metalloproteinase-2(MMP2), non-receptor tyrosine kinase proto-oncogene(SRC), estrogen receptor 1(ESR1) and cancer-signal transduction-inflammation-drugs metabolism-related biological processes and metabolic pathways were closely associated with the active ingredients in Kuihua Hugan Tablets. The effects of Kuihua Hugan Tablets in alleviating chronic hepatitis and early cirrhosis indicated the multi-component, multi-target, and multi-pathway characteristics of traditional Chinese medicines, providing new ideas for further research and development of Kuihua Hugan Tablets.


Subject(s)
Drugs, Chinese Herbal , Pharmacology , Medicine, Chinese Traditional , Metabolic Networks and Pathways , Molecular Docking Simulation , Protein Interaction Mapping , Tablets
20.
Article in Chinese | WPRIM | ID: wpr-774089

ABSTRACT

OBJECTIVE@#To study the features of serum metabolites in preterm infants based on gas chromatography-mass spectrometry (GC-MS), and to find differentially expressed metabolites in the serum of preterm infants.@*METHODS@#Serum samples were collected from 19 preterm infants and 20 full-term infants before feeding. GC-MS was used to measure metabolic profiles, and the metabolic features of 397 serum metabolites in preterm infants were analyzed.@*RESULTS@#There was a significant difference in serum metabolic features between the preterm and full-term infants before feeding. There were significant differences between the full-term and preterm infants in the levels of metabolites such as O-phosphonothreonine, digicitrin, tannic acid, and fructose-1,6-diphosphate (P<0.01), suggesting that the above differentially expressed metabolites were highly differentiated between the preterm and full-term infants. Most differentially expressed metabolites were involved in the metabolic pathways such as ABC transporters, β-alanine and pyrimidines and were correlated with some clinical parameters (albumin and total bilirubin) (P<0.05).@*CONCLUSIONS@#There is a significant difference in serum metabolites between preterm and full-term infants before feeding. Metabolomics plays an important role in improving metabolic disorders and exploring metabolism-related diseases in preterm infants.


Subject(s)
Gas Chromatography-Mass Spectrometry , Humans , Infant, Newborn , Infant, Premature , Metabolic Networks and Pathways , Metabolome , Metabolomics
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