Fungal luminescence pathways: research and applications / 生物工程学报

The fungal bioluminescence pathway (FBP) is a metabolic pathway responsible for the generation of bioluminescence derived from fungi. This pathway utilizes caffeic acid as the substrate, generating a high-energy intermediate, and the decomposition of which yields green fluorescence with a wavelength of approximately 520 nm. The FBP is evolutionally conserved in luminescent fungal groups. Unlike other bioluminescent systems, the FBP is particularly suitable for engineering applications in eukaryotic organisms, especially in plants. Currently, metabolically engineered luminescent plants are able to emit visible light to illuminate its surroundings, which can be visualized clearly in the dark. The fungal bioluminescent system could be explored in various applications in molecular biology, biosensors and glowing ornamental plants, and even green lighting along city streets.

Serum metabolomics-based study on the mechanism of action of bergapten in the treatment of liver fibrosis / 中国药房

OBJECTIVE To study the effects of bergapten in the treatment of liver fibrosis and its mechanism based on serum metabolomics. METHODS Forty mice were divided into normal control group （0.5% carboxymethyl cellulose sodium solution）， model group （0.5% carboxymethyl cellulose sodium solution）， and BP low-dose and high-dose groups （50， 100 mg/kg）， with 10 mice in each group. Except for the normal control group， the other three groups were all treated with carbon tetrachloride to induce liver fibrosis model； they were given relevant medicine/solution intragastrically， once a day， for consecutive 8 weeks. After the last medication， the levels of alanine aminotransferase （ALT） and aspartate aminotransferase （AST） in serum were detected， and liver pathological changes were observed； the expressions of α-smooth muscle actin （α-SMA） and Collagen Ⅰ were detected in liver tissue； the serum of the mice was collected for metabolomics analysis. RESULTS Compared with the model group， serum levels of ALT and AST and protein expressions of α-SMA and Collagen Ⅰ in liver tissue were decreased significantly in BP high-dose and low-dose groups （P＜0.05）， while liver fibrosis was improved significantly. Meanwhile， metabolomics analyses showed that there were a total of 175 serum differential metabolites in the BP high-dose group and model group， of which 18 substances were upregulated and 157 substances were downregulated； the main metabolic pathways involved in bergapten intervention were pyrimidine metabolism， butanoate metabolism， fatty acid synthesis， tyrosine metabolism， β-alanine metabolism， nicotinic acid and nicotinamide metabolism， glutathione metabolism， etc. CONCLUSIONS BP is effective in the treatment of liver fibrosis by regulating pyrimidine metabolism， butanoate metabolism， glutathione metabolism and so on in rats with liver fibrosis.

Bioinformatics analysis and validation of differentially expressed genes and small molecule drug prediction in proliferative scar / 中国组织工程研究

BACKGROUND:Hypertrophic scar is a skin fibrosis disease characterized by excessive proliferation of fibroblasts,epidermal thickening,and stratum corneum dysfunction.At present,the pathogenesis of Hypertrophic scar is still unclear. OBJECTIVE:To screen the core(Hub)genes and important signaling pathways in hypertrophic scar-related datasets based on bioinformatics,and then verify them by cell experiments to predict small molecule drugs that may have therapeutic effects on hypertrophic scar. METHODS:Datasets related to hypertrophic scar were searched from Gene Expression Omnibus(GEO)database,and differentially expressed genes were identified by R software analysis.Gene ontology and KEGG enrichment analyses were performed for differentially expressed genes.Protein-protein interaction network of differentially expressed genes was constructed using String online platform.Then,the key genes and core modules in the protein-protein interaction network were screened by Cytohubba and MCODE plugin-in Cytoscape software respectively,and the Hub genes were obtained by the intersection of the above key genes and the genes that formed the core module.Real-time fluorescent quantitative PCR was used to verify the difference in Hub gene mRNA expression between human hypertrophic scar and normal skin epidermal stem cells.The histological data from the Human Protein Atlas were used to verify the differences in the expression and distribution of Hub gene-encoded proteins in the two kinds of human tissues.Finally,the potential drugs for hypertrophic scar were predicted by the connectivity map database. RESULTS AND CONCLUSION:Among the identified differentially expressed genes,102 genes were up-regulated and 702 genes were down-regulated.Gene ontology and KEGG analysis showed that the enriched signaling pathways and biological processes were mainly involved in tight junction,arachidonic acid metabolism,extracellular matrix receptor interaction,epidermal development and keratinization.Eight Hub genes were found to be closely related to the mevalonate pathway that regulates cholesterol metabolism,including HMGCS1,DHCR7,MSMO1,FDPS,MVK,HMGCR,MVD and ACAT2.Compared with the normal skin group,the mRNA expression of HMGCS1,DHCR7,MSMO1,FDPS,HMGCR,MVD and ACAT2 in the hypertrophic scar group decreased significantly(P＜0.05),while MVK mRNA expression had no significant change(P＞0.05).Except for MVK,the expression levels of other Hub gene-encoded proteins in normal skin tissue were higher than those in hypertrophic scar tissue(P＜0.05).The top 10 candidate drugs included protein kinase A inhibitor(H-89),serine protease inhibitor(Dabigatran-Etexilate),FLT3 inhibitor(sunitinib),among which resveratrol and β-sitosterol are plant extracts.To conclude,Hub genes closely related to mevalonate metabolism may affect the structure and function of the epidermis by regulating lipid metabolism,which may an important pathogenesis of hypertrophic scar.The small-molecule compounds identified in this study can be used as candidate drugs for the treatment of hypertrophic scar.

Causal relationship between blood metabolites and sarcopenia-related traits:a Mendelian randomization study / 中国组织工程研究

BACKGROUND:Clinical evidences have suggested a correlation between metabolic factors and sarcopenia.Blood metabolites have been found as biological factors underlying the mechanisms of musculoskeletal disorders.However,the causal relationship between blood metabolites and sarcopenia is unclear. OBJECTIVE:To explore the causal relationship between blood metabolites and sarcopenia-related traits through a two-sample Mendelian randomization analysis and to analyze their metabolic pathways. METHODS:A dataset of 486 blood metabolites and sarcopenia-related traits was obtained from public databases.The inverse variance weighting,MR-Egger and weighted median methods were used to assess the causal relationship of blood metabolites with muscle mass and strength across genders.Sensitivity analyses,including heterogeneity and gene pleiotropy,were performed to explore the robustness of the results.Metabolic pathway analysis of potential causal relationships was performed using the Metaboanayst 5.0 tool. RESULTS AND CONCLUSION:A total of 124 metabolites and sarcopenia-related traits were observed to have potential causal relationships(P<0.05).Mannose and 1-arachidonoylglycerophosphocholine were significantly causally associated with an increased muscle mass in males(P<1.03×10-4).Pentadecanoate and glycine were significantly causally associated with decreased muscle mass and muscle strength in females,respectively(P<1.03×10-4).Metabolic pathway analysis identified eight metabolic pathways associated with altered levels of muscle mass and muscle strength in sarcopenia,including the"glyoxylate and dicarboxylate metabolism"and"Glycine,serine and threonine metabolism."The identified metabolites are considered as useful circulating metabolic biomarkers for screening and prevention of sarcopenia in clinical practice,serving as candidate molecules for future mechanistic exploration and drug target selection.

Lipid metabolomic changes in liver injury in BTBR ob/ob mice with type 2 diabetes mellitus / 安徽医科大学学报

Objective @#To investigate the changes of lipid biomarkers and lipid metabolic pathways related to liver injury in BTBR ob/ob mice with type 2 diabetes mellitus by biochemical and metabolomics methods．@*Methods @# 16 BTBR wild-type (WT) mice (WT group) and 14 BTBR ob/ob obese mice (ob / ob group) at 7 weeks of age were selected and fed in SPF environment until 20 weeks of age．Liver injury was compared between the two groups : The activities of mitochondrial respiratory enzyme complex in liver tissue were detected by high-resolution respirators，and the lipid metabolomic analysis of liver tissue samples in the two groups of mice was performed by ultra-perform- ance liquid chromatography-quadrupole time-of-flight mass spectrometry，mainly detecting endogenous metabolites. Principal component analysis (PCA) ，orthogonal partial least squares discriminant analysis ( OPLS-DA) and other models were used to screen potential biomarkers，and the metabolic pathway analysis of the identified metabolites was performed by MetaboAnalyst 5. 0 . @*Results @#Compared with the WT group，the ob / ob group had significantly increased body weight，fasting blood glucose ，serum levels of aspartate aminotransferase ( AST) ，alanine amin- otransferase (ALT) ，low-density lipoprotein (LDL-C) and cholesterol ( CHO) (P＜0. 01) ．Liver hematoxylin-eo- sin staining (HE) staining showed that the mice in ob / ob group had structural disorder of liver lobules，swelling of liver cells ，a large number of fat vacuoles in cells ，diffuse distribution and loose cytoplasm． Oil red O staining showed that there was a large amount of lipid deposition in the hepatocytes ofob/ob mice．The high resolution spi- rometer showed that the ob/ob mice had mitochondrial oxidative phosphorylation disorder and the activity of complex Ⅳ decreased．Lipid metabolomic analysis showed that the lipid metabolic profile of ob/ob mice changed，and the metabolic pathways involved mainly included glycerophospholipid metabolism，glycosylphosphatidylinositol ( GPI) anchor biosynthesis，triglyceride metabolism，linoleic acid metabolism，α-linolenic acid metabolism and arachidon- ic acid metabolism．@*Conclusion @#The liver injury of ob / ob group mice may be related to the disorder of lipid me- tabolism，in which the disorder of glycerophospholipid metabolism is the most critical metabolic pathway.

Evaluation of A Liver Yin Deficiency Mouse Model Based on Untargeted Metabolomics / 中国实验方剂学杂志

ObjectiveBased on ultra performance liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry（UPLC-Q-TOF-MS）， to evaluate the establishment of a mouse model of liver Yin deficiency by thyroid tablet suspension combined with 10% carbon tetrachloride（CCl4） from the perspective of non-targeted metabolomics， in order to lay the foundation for the establishment of a traditional Chinese medicine（TCM） syndrome model. MethodA total of 24 mice were randomly divided into blank group and model group. The model group was given thyroid tablet suspension（0.003 2 g·kg-1） by gavage for 14 consecutive days， and 10% CCl4（5 mL·kg-1） was intraperitoneally injected once a week to establish a liver Yin deficiency model， while the blank group was injected with an equal amount of olive oil intraperitoneally and gavaged with an equal amount of distilled water， and was fed with normal feed. After the modeling was completed， 6 mice in each group were randomly selected， the levels of alanine aminotransferase（ALT）， aspartate aminotransferase（AST）， cyclic adenosine monophosphate（cAMP）， cyclic guanosine monophosphate（cGMP）， interleukin（IL）-6， IL-10， tumor necrosis factor-α（TNF-α）were measured in the mice serum， and malondialdehyde（MDA）， superoxide dismutase（SOD）， total protein（TP）， hydroxyproline（HYP） and other indicators were measured in the mice liver. Liver tissue sections were taken for hematoxylin-eosin（HE） staining and observing pathological changes. The remaining 6 mice in each group were subjected to UPLC-Q-TOF-MS combined with principal component analysis（PCA） and orthogonal partial least squares-discriminant analysis（OPLS-DA） were used to screen differential metabolites in the liver Yin deficiency mouse model， Kyoto Encyclopedia of Genes and Genomes（KEGG） database was used to analyze the corresponding metabolic pathways of differential metabolites. ResultCompared with the blank group， mice in the model group showed liver Yin deficiency manifestations such as reduced body weight， fatigue and sleepiness， disheveled and lusterless hair， irritability. The levels of ALT， cAMP/cGMP， IL-6， AST， MDA， cAMP， TNF-α significantly increased（P<0.05， P<0.01）， while the levels of SOD， IL-10 and cGMP significantly decreased（P<0.05， P<0.01）， and the changes of HYP and TP were not statistically significant. Hepatic steatosis and distortion of the radial arrangement of the liver plate cells were seen in the section images of the model group， endogenous substances were clearly separated， and 252 differential metabolites were identified in the serum samples， which were mainly involved in the metabolic pathways of purine metabolism， steroid hormone biosynthesis and pyrimidine metabolism. A total of 229 differential metabolites were identified in the liver samples， mainly involving nucleotide metabolism， purine metabolism， steroid hormone biosynthesis， pyrimidine metabolism， antifolate resistance， insulin resistance， primary bile acid biosynthesis， prostate cancer， sulfur relay system， arachidonic acid metabolism and other metabolic pathways. ConclusionThe successful establishment of liver Yin deficiency model in mice by CCl4 combined with thyroid hormone is evaluated through the investigation of serum and liver metabolomics， combined with biochemical indicators， which provides a biological basis and experimental foundation for the Yin deficiency syndrome model of TCM.

Investigation on the mechanism of Compound zaoren granules in improving insomnia based on serum meta-bonomics / 中国药房

OBJECTIVE To study the mechanism of Compound zaoren granule in improving insomnia. METHODS Forty-nine mice were divided into blank group， model group， positive control group 1 （Estazolam tablets 0.5 mg/kg），control group 2 （Shumian capsule 0.6 g/kg）， Compound zaoren granule low-dose， medium-dose and high-dose groups （2.5， 5， 10 g/kg）， with 7 mice in each group. The insomnia model was established by chronic unpredictable mild stress combined with 4-chloro-DL- phenylacetic acid. The behavioral changes of mice were investigated through open field test and pentobarbital sodium synergistic hypnosis experiment， as well as the pathomorphology of mice hypothalamus tissue was observed by HE staining. The metabonomics analysis and multivariate statistical analysis of serum in mice were performed by UHPLC-Q-TOF-MS/MS， and the differential metabolites were screened out； the metabolic pathway analysis was conducted based on MetaboAnalyst 5.0 database. RESULTS Compared with blank group， the total travelling distance， the number of entering the central region and the moving distance in the central region of the model group were significantly reduced （P＜0.05）， the proportion of total rest time was significantly increased （P＜0.05）， the sleep duration of mice was significantly shortened （P＜0.05）， and hypothalamic nerve cells damaged and severely vacuolated. Compared with model group， the total travelling distance of Compound zaoren granule low-dose and medium-dose groups were increased significantly and the proportions of total rest time of those groups were decreased significantly （P＜0.05）， and the sleep duration of mice in Compound zaoren granule high-dose group was prolonged significantly （P＜0.05）； the hypothalamic nerve cells of mice in each administration group recovered to varying degrees， and the hypothalamus histiocytes of mice in the Compound zaoren granules high-dose group were closer to those in the blank group. A total of 18 differential metabolites （such as phenylalanine， taurine， norvaline， methionine） and 4 important amino acid metabolic pathways （L-phenylalanine， tyrosine and tryptophan biosynthesis； taurine and hypotaurine metabolism； L-phenylalanine metabolism； cysteine and methionine metabolism） were identified through metabolomics analysis. CONCLUSIONS Compound zaoren granules can normalize the disordered metabolism in vivo by regulating differential metabolites such as phenylalanine， taurine， and four amino acid metabolic pathways， so as to improve insomnia.

Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice / 神经科学通报·英文版

Gene transcription and new protein synthesis regulated by epigenetics play integral roles in the formation of new memories. However, as an important part of epigenetics, the function of chromatin remodeling in learning and memory has been less studied. Here, we showed that SMARCA5 (SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 5), a critical chromatin remodeler, was responsible for hippocampus-dependent memory maintenance and neurogenesis. Using proteomics analysis, we found protein expression changes in the hippocampal dentate gyrus (DG) after the knockdown of SMARCA5 during contextual fear conditioning (CFC) memory maintenance in mice. Moreover, SMARCA5 was revealed to participate in CFC memory maintenance via modulating the proteins of metabolic pathways such as nucleoside diphosphate kinase-3 (NME3) and aminoacylase 1 (ACY1). This work is the first to describe the role of SMARCA5 in memory maintenance and to demonstrate the involvement of metabolic pathways regulated by SMARCA5 in learning and memory.

Combined analysis of transcriptomics and metabolomics revealed complex metabolic genes for diterpenoids biosynthesis in different organs of Anoectochilus roxburghii / 中草药·英文版

OBJECTIVE@#Diterpenoids with a wide variety of biological activities from Anoectochilus roxburghii, a precious medicinal plant, are important active components. However, due to the lack of genetic information on the metabolic process of diterpenoids in A. roxburghii, the genes involved in the molecular regulation mechanism of diterpenoid metabolism are still unclear. This study revealed the complex metabolic genes for diterpenoids biosynthesis in different organs of A. roxburghii by combining analysis of transcriptomics and metabolomics.@*METHODS@#The differences in diterpenoid accumulation in roots, stems and leaves of A. roxburghii were analyzed by metabonomic analysis, and its metabolic gene information was obtained by transcriptome sequencing. Then, the molecular mechanism of differential diterpenoid accumulation in different organs of A. roxburghii was analyzed from the perspective of gene expression patterns.@*RESULTS@#A total of 296 terpenoid metabolites were identified in the five terpenoid metabolic pathways in A. roxburghii. There were 38, 34, and 18 diterpenoids with different contents between roots and leaves, between leaves and stems, and between roots and stems, respectively. Twenty-nine metabolic enzyme genes with 883 unigenes in the diterpenoid synthesis process were identified, and the DXS and FDPS in the terpenoid backbone biosynthesis stage and CPA, GA20ox, GA3ox, GA2ox, and MAS in the diterpenoid biosynthesis stage were predicted to be the key metabolic enzymes for the accumulation of diterpenoids. In addition, 14 key transcription factor coding genes were predicted to be involved in the regulation of the diterpenoid biosynthesis. The expression of genes such as GA2ox, MAS, CPA, GA20ox and GA3ox might be activated by some of the 14 transcription factors. The transcription factor NTF-Y and PRE6 were predicted to be the most important transcription factors.@*CONCLUSION@#This study determined 29 metabolic enzyme genes and predicted 14 transcription factors involved in the molecular regulation mechanism of diterpenoid metabolism in A. roxburghii, which provided a reference for the further study of the molecular regulation mechanism of the accumulation of diterpenoids in different organs of A. roxburghii.

Mechanism of famous classical formula Huaihua Powder in treatment of ulcerative colitis based on metabonomics / 中国中药杂志

Ultra-high performance liquid chromatography-quadrupole-time of flight tandem mass spectrometry(UHPLC-Q-TOF-MS) was employed in this study to observe the effect of Huaihua Powder on the serum metabolites of mice with ulcerative colitis and reveal the mechanism of Huaihua Powder in the treatment of ulcerative colitis. The mouse model of ulcerative colitis was established by dextran sodium sulfate salt(DSS). The therapeutic effect of Huaihua Powder on ulcerative colitis was preliminarily evaluated based on the disease activity index(DAI), colon appearance, colon tissue morphology, and the content of inflammatory cytokines such as tumor necrosis factor-α(TNF-α), interleukin-6(IL-6), and interleukin-1β(IL-1β). UHPLC-Q-TOF-MS was employed to profile the endogenous metabolites of serum samples in blank control group, model group, and low-, medium-, and high-dose Huaihua Powder groups. Multivariate analyses such as principal component analysis(PCA), partial least squares discriminant analysis(PLS-DA), and orthogonal partial least squares discriminant analysis(OPLS-DA) were performed for pattern recognition. Potential biomarkers were screened by Mass Profiler Professional(MPP) B.14.00 with the thresholds of fold change≥2 and P<0.05. The metabolic pathways were enriched by MetaboAnalyst 5.0. The results showed that Huaihua Powder significantly improved the general state and colon tissue morphology of mice with ulcerative colitis, reduced DAI, and lowered the levels of TNF-α, IL-6, and IL-1β in serum. A total of 38 potential biomarkers were predicted to be related to the regulatory effect of Huaihua Powder, which were mainly involved in glycerophospholipid metabolism, glycine, serine, and threonine metabolism, mutual transformation of glucuronic acid, and glutathione metabolism. This study employed metabolomics to analyze the mechanism of Huaihua Powder in the treatment of ulcerative colitis, laying a foundation for the further research.

Metabolomic study on urine of chronic inflammation rats treated with Buyang Huanwu Decoction based on UPLC-Q-TOF-MS / 中国中药杂志

The study investigated the effect of Buyang Huanwu Decoction(BYHWD) on endogenous biomarkers in the urine of rats with chronic inflammation induced by lipopolysaccharide(LPS) using ultra-high performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry(UPLC-Q-TOF-MS), aiming to elucidate the molecular mechanism underlying the therapeutic effect of BYHWD on chronic inflammation from a metabolomics perspective. Male SD rats were randomly divided into a normal group, a model group, and low-, medium-, and high-dose BYHWD groups(7.5, 15, and 30 g·kg~(-1)). The model group and BYHWD groups received tail intravenous injection of LPS(200 μg·kg~(-1)) on the first day of each week, followed by oral administration of BYHWD once a day for four consecutive weeks. Urine samples were collected at the end of the administration period, and UPLC-Q-TOF-MS was used to analyze the metabolic profiles of the rat urine in each group. Multivariate statistical analysis methods such as principal component analysis(PCA), partial least squares-discriminant analysis(PLS-DA), and orthogonal partial least squares-discriminant analysis(OPLS-DA) were used to analyze the effect of BYHWD on endogenous metabolites. One-way ANOVA and variable importance for the projection(VIP) were used to screen for potential biomarkers related to chronic inflammation. The identified biomarkers were subjected to pathway and enrichment analysis using MetaboAnalyst 5.0. A total of 25 potential biomarkers were screened and identified in the rat urine in this experiment. Compared with the normal group, the model group showed significant increases in the levels of 14 substances(P<0.05) and significant decreases in the levels of 11 substances(P<0.05). BYHWD was able to effectively reverse the trend of most endogenous biomarkers. Compared with the model group, BYHWD significantly down-regulated 13 biomarkers(P<0.05) and up-regulated 10 biomarkers(P<0.05). The metabolic products were mainly related to the biosynthesis of pantothenic acid and coenzyme A, tryptophan metabolism, retinol metabolism, and propionate metabolism. BYHWD has therapeutic effect on chronic inflammation induced by LPS, which may be related to its ability to improve the levels of endogenous metabolites, enhance the body's anti-inflammatory and antioxidant capabilities, and restore normal metabolic activity.

Transcriptional regulation mechanism of differential accumulation of flavonoids in leaves and roots of Sarcandra glabra based on metabonomics and transcriptomics / 中国中药杂志

This study aims to explore the molecular regulation mechanism of the differential accumulation of flavonoids in the leaves and roots of Sarcandra glabra. Liquid chromatography-mass spectrometry(LC-MS) and high-throughput transcriptome sequencing(RNA-seq) were employed to screen out the flavonoid-related differential metabolites and differentially expressed genes(DEGs) encoding key metabolic enzymes. Eight DEGs were randomly selected for qRT-PCR verification. The results showed that a total of 37 flavonoid-related differential metabolites between the leaves and roots of S. glabra were obtained, including pinocembrin, phlorizin, na-ringenin, kaempferol, leucocyanidin, and 5-O-caffeoylshikimic acid. The transcriptome analysis predicted 36 DEGs associated with flavonoids in the leaves and roots of S. glabra, including 2 genes in the PAL pathway, 3 genes in the 4CL pathway, 2 genes in the CHS pathway, 4 genes in the CHI pathway, 2 genes in the FLS pathway, 1 gene in the DFR pathway, 1 gene in the CYP73A pathway, 1 gene in the CYP75B1 pathway, 3 genes in the PGT1 pathway, 6 genes in the HCT pathway, 2 genes in the C3'H pathway, 1 gene in the CCOAOMT pathway, 1 gene in the ANR pathway, 1 gene in the LAR pathway, 2 genes in the 3AT pathway, 1 gene in the BZ1 pathway, 2 genes in the IFTM7 pathway, and 1 gene in the CYP81E9 pathway. Six transcription factors, including C2H2, bHLH, and bZIP, were involved in regulating the differential accumulation of flavonoids in the leaves and roots of S. glabra. The qRT-PCR results showed that the up-or down-regulated expression of the 8 randomly selected enzyme genes involved in flavonoid synthesis in the leaves and roots of S. glabra was consistent with the transcriptome sequencing results. This study preliminarily analyzed the transcriptional regulation mechanism of differential accumulation of flavonoids in the leaves and roots of S. glabra, laying a foundation for further elucidating the regulatory effects of key enzyme genes and corresponding transcription factors on the accumulation of flavonoids in S. glabra.

Phenylpropanoid pathway in plants and its role in response to heavy metal stress: a review / 生物工程学报

Phenylpropanoid metabolic pathway is one of the most important secondary metabolic pathways in plants. It directly or indirectly plays an antioxidant role in plant resistance to heavy metal stress, and can improve the absorption and stress tolerance of plants to heavy metal ions. In this paper, the core reactions and key enzymes of the phenylpropanoid metabolic pathway were summarized, and the biosynthetic processes of key metabolites such as lignin, flavonoids and proanthocyanidins and relevant mechanisms were analyzed. Based on this, the mechanisms of key products of phenylpropanoid metabolic pathway in response to heavy metal stress were discussed. The perspectives on the involvement of phenylpropanoid metabolism in plant defense against heavy metal stress provides a theoretical basis for improving the phytoremediation efficiency of heavy metal polluted environment.

Metabolomics study on occupational acute methyl acetate poisoning using patient plasma / 中国职业医学

Objective: To investigate the specificity of endogenous metabolic profile in plasma of patients with occupational acute methyl acetate poisoning using non-targeted metabolomics. Methods: A total of six patients with occupational acute methyl acetate poisoning were selected as the poisoning group, while 10 healthy workers without occupational exposure history of chemical hazards in the same industry were selected as the control group using the judgment sampling method. Metabolites in patient plasma of the two groups were detected using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, and non-targeted metabolomics analysis was performed. Principal component analysis and partial least squares discriminant analysis were used to identify differential metabolites and analyze their metabolic pathways. Results: There were significant differences in metabolite profiles in patient plasma between poisoning group and control group. A total of 195 differentially expressed metabolites were screened in plasma of patients in poisoning group, including 119 upregulated and 76 downregulated metabolites. Lipid substances (lipids and lipid-like molecules) accounted for the highest proportion (21.5%). The differential metabolites of poisoning group were related to folate biosynthesis, amino acid metabolism, pyrimidine metabolism, sphingolipid biosynthesis and other metabolic pathways in plasma compared with the control group (all P<0.05). Conclusion: Occupational acute methyl acetate poisoning affects metabolism of the body. The folic acid biosynthesis, amino acid and lipid metabolism and other pathways may be involved in the occurrence and development of poisoning.

Main ways and target prediction of detoxification mechanism of Euphorbia kansui after stir-frying with vinegar / 中国药房

OBJECTIVE To study main way and target of Euphorbia kansui after stir-frying with vinegar. METHODS Twenty-four SPF grade SD rats were randomly divided into blank group， E. kansui group （850 mg/kg） and vinegar stir-fried E. kansui group （850 mg/kg）， with 8 rats in each group. Blank group was given 0.5% sodium carboxymethyl cellulose solution intragastrically， and E. kansui group and vinegar stir-fried E. kansui group were given relevant test sample for consecutive 20 d. The rats’ urine of 12 hours was collected on the 20th day. The urine samples of rats in each group were determined by UPLC-Q- Exactive-MS. The data was pre-processed by Compound Discoverer 3.0 software， and the metabolite structure was identified by BioCyc， HMDB and other databases. Whether different groups presented their own clustering phenomenon was observed by principal component analysis （PCA） and orthogonal partial least squares-discriminant analysis （OPLS-DA）， etc. Based on the pathway analysis of MetaboAnalyst， the potential targets of detoxification mechanism of E. kansui after stir-frying with vinegar were predicted. RESULTS Twenty significantly differential endogenous metabolites were identified， of which 10 target metabolites， such as N-acetyl-L-aspartate and 3-phosphonooxypyruvic acid， were targets of detoxification mechanism of E. kansui after stir- frying with vinegar. The main metabolic pathways included arginine biosynthesis， alanine， aspartic acid and glutamic acid metabolism， cysteine and methionine metabolism， and arginine and D-ornithine metabolism. The biological significance of all related metabolites in the pathways was analyzed and speculated； after stir-frying with vinegar， E. kansui may alleviate neurotoxicity by reducing the level of N-acetyl-L-aspartic acid； E. kansui had a protective effect on cardio-cerebrovascular system by increasing the level of L-high arginine. CONCLUSIONS After stir-frying with vinegar， E. kansui can significantly improve the adverse factors in terms of nervous system， cardio-cerebrovascular system， immune system and energy metabolism. The most concentrated metabolic pathway related to its detoxification mechanism is arginine biosynthesis.

Research progress on metabonomics of traditional Chinese medicine in the treatment of ulcerative colitis / 中国药房

OBJECTIVE Ulcerative colitis （UC）， as a common and refractory disease of the digestive system， has always been a hot and difficult point in medical research. Traditional Chinese medicine has the advantages of good efficacy， high safety and not easy to relapse after drug withdrawal in the treatment of UC， but the mechanism has not been fully elucidated. Metabonomics looks for potential biomarkers and metabolic pathways from the point of view of the endogenous dynamic metabolism of the whole body， which is helpful to evaluate the efficacy of drugs and explore related mechanisms. Metabolomics studies on the treatment of UC with traditional Chinese medicine have shown that traditional Chinese medicine formulas， single herbs and herbs monomers act on various related pathways such as amino acid metabolism， lipid metabolism and energy metabolism by regulating endogenous metabolites in the body， thereby inhibiting immune inflammatory reactions， improving oxidative stress， reducing intestinal sensitivity， regulating intestinal microbiota， repairing intestinal mucosal damage， and restoring normal metabolic activity in the body. However， further screening and validation of relevant metabolic markers are needed.

Preparation of Fe3O4@SW-MIL-101-NH2 for selective pre-concentration of chlorogenic acid metabolites in rat plasma,urine,and feces samples / 药物分析学报

An innovative sandwich-structural Fe-based metal-organic framework magnetic material(Fe3O4@SW-MIL-101-NH2)was fabricated using a facile solvothermal method.The characteristic properties of the material were investigated by field emission scanning electron microscopy,transmission electron mi-croscopy(TEM),energy-dispersive X-ray spectroscopy,Fourier transform infrared spectroscopy,X-ray powder diffraction,vibrating sample magnetometry,and Brunauer-Emmett-Teller measurements.Fe3O4@SW-MIL-101-NH2 is associated with advantages,such as robust magnetic properties,high specific surface area,and satisfactory storage stability,as well as good selective recognition ability for chlorogenic acid(CA)and its metabolites via chelation,hydrogen bonding,and π-interaction.The results of the static adsorption experiment indicated that Fe3O4@SW-MIL-101-NH2 possessed a high adsorption capacity toward CA and its isomers,cryptochlorogenic acid(CCA)and neochlorogenic acid(NCA),and the adsorption behaviors were fitted using the Langmuir adsorption isotherm model.Then,a strategy using magnetic solid-phase extraction(MSPE)and ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry(UPLC-Q-TOF MS/MS)was developed and suc-cessfully employed for the selective pre-concentration and rapid identification of CA metabolites in rat plasma,urine,and feces samples.This work presents a prospective strategy for the synthesis of magnetic adsorbents and the high-efficiency pretreatment of CA metabolites.

Microorganisms capable of degrading neonicotinoids and their metabolic pathways: a review / 生物工程学报

Neonicotinoid compounds are usually considered harmless and eco-friendly in terms of their targeted toxicity compared to that of pyrethroids and phosphorus-containing pesticides. However, overuse of neonicotinoid insecticides resulted in the accumulation of its residuals or intermediates in soil and water, which consequently affected beneficial insects as well as mammals, yielding pollution and secondary risks. This review summarized the recent advances in neonicotinoid degrading microorganisms and their metabolic diversity, with the aim to address the urgent need for degrading these insecticides. These advances may facilitate the development of controllable and reliable technologies for efficiently transforming neonicotinoid insecticides into value-added products by synthetic biology and metagenomics.

Anaerobic digestion pathways in biochemistry: a teaching practice / 生物工程学报

Anaerobic digestion is another important anaerobic catabolism pathway besides lactic acid and ethanol fermentation, which is of great significance for recycling resources, maintaining the ecological balance, optimizing the energy structure, alleviating the energy crisis, and promoting the implementation of the "Carbon Peaking and Carbon Neutrality" strategy. However, such an important metabolic process has not been involved in the current textbooks and teaching of biochemistry courses, making the teaching system incomplete. The anaerobic digestion process involves many reactions and complex metabolic pathways. In order to improve the students' understanding to this process, we created a full chart of the whole anaerobic digestion process based on systemic literature review and integrated it into the classroom teaching through the BOPPPS teaching mode. It was found that the classroom teaching assisted by this metabolic chart could help students establish the structural framework of the anaerobic digestion process and enrich the knowledge system of metabolism, achieving a good teaching effect. This paper introduces the content of the metabolic pathways of anaerobic digestion and the design of the teaching process, which would facilitate the teaching reforms and perfection of textbooks for related courses, such as Biochemistry, Environmental Engineering Microbiology and New Energy Engineering.

Microbial synthesis of monoterpenoids: a review / 生物工程学报

Monoterpenoids that belong to the terpenoids family are usually volatile and have strong aroma. Some monoterpenoids also have antioxidant, antibacterial and anti-inflammatory activities, which make them important raw materials for medicine, food and cosmetics industry. In recent years, the heterologous synthesis of monoterpenoids by microorganisms has attracted extensive attention. However, its large-scale application is greatly hampered by the low yield and high production cost. Nowadays, the rapid development of synthetic biology provides new approaches for enhancing the production of monoterpenoids by microorganisms. Different kinds of recombinant strains can be obtained via engineering of microbial cells to produce a variety of monoterpenoids with different properties. This paper summarized the latest strategies and progress in the application of synthetic biology to produce monoterpenoids by microorganisms, including the design and modification of biosynthetic pathway, as well as the design and optimization of high-yield monoterpenoids producing chassis cells.