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γH2AX， 53BP1 and RAD51 foci analysis for monitoring DNA double-strand breaks WANG Yi-zhao, FAN Li, WANG Hong-xia, YANG Si-lu, CUI Ya-ni, Duan Yi-jun, Duan Jing-jing, REN Lai-feng, SU Wen Journal of Biology    2020, 37 (1): 16-.   DOI: 10.3969/j.issn.2095-1736.2020.01.016 Abstract （6277）      PDF       Knowledge map    γH2AX, 53BP1 and RAD51 foci are the evaluation markers of DNA double strand breaks (DSBs). Above all, γH2AX foci analysis is the most widely used, but recent studies have found that it is not completely consistent with DSBs damage. This study systematically analyzed the dynamic changes of γH2AX, 53BP1 and RAD51 foci during DNA damage and their reasonable application in DSBs damage assessment. According to the results, γH2AX and 53BP1 foci were highly consistent after cells exposed to ionizing radiation treatment, they both could reflect accurately the dynamic changes of DSBs damages and repairs; while RAD51 foci only appeared in part of damaged cells, which was consistent with its role mainly involved in homologous recombination process. Upon treatment with Camptothecin (CPT), γH2AX presented two types of staining (bright and discrete foci and pan-nuclear phosphorylation), while 53BP1 foci only appeared in cells with bright and discrete γH2AX foci and were highly consistent with γH2AX foci. These results revealed that positive staining of γH2AX alone cannot accurately represent DSBs damage, and the extent of DSBs damage should be comprehensively analyzed by combining with staining of 53BP1. The RAD51 foci analysis only reflect the DSBs damage repair of part cells, mainly homologous recombination repair.  Related Articles | Metrics

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Molecular mechanisms of plant in response to abiotic stress CHEN Keqi, DENG Xingguang, LIN Honghui Journal of Biology    2021, 38 (6): 1-.   DOI: 10.3969/j.issn.2095-1736.2021.06.001 Abstract （3922）      PDF       Knowledge map    In this review, the molecular mechanisms by which plants respond to extreme temperature, drought, flooding and salt stress, through an overview of existing studies were summarized. Combining the effects of various stress on plant growth and development, the signal perception mode and signal transduction pathways were introduced. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important secondary metabolites in coordinating stress tolerance were outlined. Finally, an outlook on future research was prospected focusing on the regulatory mechanism of mult-signaling network modules and sustainable development of agriculture. Related Articles | Metrics

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Study on the Cr(VI) reduction properties of Alicycliphilus denitrificans Ylb10 ZUO Qun, LYU Yucai, SONG Tingwei, GUO Jinling, REN Liwei, GONG Dachun Journal of Biology    2021, 38 (6): 36-.   DOI: 10.3969/j.issn.2095-1736.2021.06.036 Abstract （2843）      PDF       Knowledge map    From the bottom mud of Qiusuo Creek, a strain Ylb10 with high efficiency in reducing Cr(VI) was successfully isolated and obtained. The Ylb10 strain was identified by physiological and biochemical methods and 16S rDNA sequencing method, and the Cr(VI) was determined by diphenylcarbazide spectrophotometry to investigate its reduction characteristics. The results showed that Ylb10 was Gram-negative, and the 16S rDNA similarity rate with Alicycliphilus denitrificans was 98.07%. Ylb10 could make good use of α-hydroxy-butyric acid, L-lactic acid, propionic acid, acetic acid, L-aspartic acid, L-glutamic acid, L-alanine, L-erine and other substrates.Compared that with the shaker culture conditions, Cr(VI) could be better reduced during standing culture, and the optimal pH of Cr(VI) reduction was 8-9. When the concentration of Cr(VI) was lower than 200 mg/L, the strain could reduce all Cr(VI), of which, at 50 mg/L Cr(VI) concentration, it had a reduction rate of 96.45% in 18 hours; at 100 mg/L Cr(VI ), it had the reduction rate of 93-83% in 24 hours, and the reduction efficiency at 200 mg/L Cr(VI) concentration in 60 hours was 99.06%. It could be concluded that Alicycliphilus denitrificans Ylb10 was a high-efficiency hexavalent chromium reducing bacteria, and It had high application potential in the treatment of chromium-contaminated water quality and soil. Related Articles | Metrics

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Lysosomes and neurodegenerative diseases QU Lili, CANG Chunlei Journal of Biology    2022, 39 (1): 1-.   DOI: 10. 3969/ j. issn. 2095-1736. 2022. 01. 001 Abstract （2749）      PDF       Knowledge map    Lysosomes are the main degradative organelles in eukaryotic cells, and their dysfunction is closely related to many diseases.The current knowledge on the connection between lysosomal dysfunction and neurodegenerative diseases were reviewed with the focus on lysosomal enzymes, pH regulation, lysosomal membrane proteins, and intracellular localization of lysosomes. It provided a new perspective for understanding the mechanism of neurodegenerative diseases, and also looke Related Articles | Metrics

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Coenzyme specific modification of NADPH-dependent glutamatedehydrogenase LU Libing, ZHOU Haisheng, WU Jianping, YANG Lirong Journal of Biology    2021, 38 (6): 31-.   DOI: 10.3969/j.issn.2095-1736.2021.06.031 Abstract （2664）      PDF       Knowledge map    Based on structural information and conservative sequence alignment, this study modified the NADPH-specific glutamate dehydrogenase, from Pseudomonas putida, to NADH-dependent form in the future through semi-rational design and high-throughput screening. Compared that with the original PpGDH, the preference of the mutant PpGDH-D264V to NADH was increased by 1 607 times（Ratio of kcat/Km）, and it had the catalytic activity of various keto acids, which could be used to prepare various non-protein amino acids. The enzymic properties of PpGDH-D264V were characterized. The optimal temperature was 45 ℃, the optimal pH was 8.0, the temperature of T10 min1/2 reached 58.1 ℃, and the PpGDH-D264V had good stability under neutral and slightly alkaline environment, which laid a foundation for subsequent application. Related Articles | Metrics

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Research progress of UDP-sugar biosynthesis CHEN Guihang, LI Chun, FENG Xudong Journal of Biology    2023, 40 (2): 95-.   DOI: 10.3969/j.issn.2095-1736.2023.02.095 Abstract （2464）      PDF       Knowledge map    Uridine diphosphate(UDP)-sugar is an important type of sugar donors for glycosylation modification. The in vivo synthesis of UDP-sugar was summarized from three aspects: synthase pathway, phosphorylase pathway and kinase pathway. Due to the lack of key enzymes, only UDP-glucose (UDP-Glc) could be quickly obtained from the above three pathways. At the same time, with UDP-glucose as the starting material and UDP-glucuronic acid (UDP GlcA) as the intermediate, the rapid interconversions between UDP-sugars could be realized by specific functional enzymes. The latest progress in UDP-sugar synthesis catalyzed by specific functional enzymes was reviewed, and the important roles of dehydrogenase, decarboxylase, isomerase and reductase in UDP-sugar interconversions were discussed. The existing problems of UDP-sugar synthesis were analyzed and the future research direction of UDP-sugar synthesis was prospected, aiming at providing new ideas for tapping the potential of UDP-sugar donors and realizing glycosylation modification with efficiency and low cost. Related Articles | Metrics

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Rho/ROCK signaling pathway and its active regulation mode CAO Mei-Xia1， 2， QU Chang-Qing1

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Prokaryotic expression and purification of mouse CCL2 protein MA Zhenling, WANG Lei, QIAO Liuhui, LIU Wei Journal of Biology    2021, 38 (6): 20-.   DOI: 10.3969/j.issn.2095-1736.2021.06.020 Abstract （2267）      PDF       Knowledge map    his work aimed to construct a prokaryotic expression for mouse gene CCL2, express and purify recombinant CCL2 protein, and detect the adhesion of leukemia cells. The mouse gene CCL2 was amplified by PCR and cloned into the prokaryotic expression vector pGEX-4T-1 by ligation-independent cloning. The recombinant plasmid pGEX-4T-CCL2 was transformed into Escherichia coli BL21（DE3）and the recombinant protein was purified by affinity chromatography. The purified protein was identified by SDS-PAGE and Western Blot. Finally, the effect of CCL2 on C1498 cell adhesion and migration was detected. Results showed that the recombinant vector pGEX-4T-CCL2 was successfully constructed, and GST-CCL2 was successfully induced by 0.1 mmol/L IPTG at 20 ℃ for 6 h; recombinant protein with biological function was prepared, and CCl2 could promote leukemia cell adhesion and migration. This work would provide a foundation for further study of CCL2 in leukemia. Related Articles | Metrics

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Cloning, bioinformatics analysis, subcellular localization and expressionanalysis of TaZFP33 gene from Triticum aestivum WU Qun, LI Yongliang, ZOU Xiaoxiao, SUN Aolong, LIN Xiaoxia, ZHOU Ping, GUO Xinhong Journal of Biology    2021, 38 (6): 9-.   DOI: 10.3969/j.issn.2095-1736.2021.06.009 Abstract （2194）      PDF       Knowledge map    C2H2 zinc finger protein, as one of the largest transcription factor family in plants, plays an important role in plant growth and stress. In this study, the zinc finger protein TaZFP33 gene in the spring wheat variety Fielder（Triticum aestivum L. cv. Fielder） was cloned. The TaZFP33 gene coding region was 510 bp in length and encoded 169 amino acids. Bioinformatics analysis showed that the molecular weight of TaZFP33 protein was 17.5 ku, and the isoelectric point was 6.43, which belonged to the Q-type zinc finger protein and was an unstable hydrophobic protein. Evolutionary analysis and promoter analysis indicated that the gene may respond to ABA-induced stress regulation. Transient expression analysis of transformed tobacco showed that TaZFP33 was localized on the nucleus. Real-time fluorescence quantitative analysis of tissue-specific expression showed that TaZFP33 gene was expressed in stems, leaves, roots and embryos, and the highest expression level was in embryos. After seedlings were treated with different concentrations of ABA, PEG6000 and NaCl, the results showed that TaZFP33 gene responded to above-mentioned stresses. This research laid a foundation for further exploration on the biological function of the TaZFP33 gene, and also provided candidate genes for the study of stress resistance in Triticum aestivum. Related Articles | Metrics

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Biocontrol effects of Bacillus velezensis on peanut stem rot caused by Sclerotium rolfsii PAN Mengshi, GUO Wenyang, ZHANG Zongyuan, YUE Dandan, QI Landa, WANG Xueyan, ZHANG Yingtao Journal of Biology    2022, 39 (1): 37-.   DOI: 10. 3969/ j. issn. 2095-1736. 2022. 01. 037 Abstract （2150）      PDF       Knowledge map    As the potential biocontrol bacteria, Bacillus velezensis was studied for its biological control of peanut stem rot caused by Sclerotium rolfsii with coculture method, research of antagonistic mechanism and pot experiments. By coculture method on PDA, B.velezensis can inhibit the hyphal growth of S. rolfsii significantly, with an inhibition rate of 81. 93%, destroy the structure of the pathogenic mycelium and prevent the formation of sclerotia. In order to understand antagonistic mechanism of B. velezensis, it was found that B. velezensis can produce protease, cellulase, amylase and siderophore, which aseptic fermentation filtrate also has an antagonistic effect. Under pot experiments the treatments with bacteria liquid can inhibit the occurrence of peanut stem rot caused by S. rolfsii, reduce the peanut disease index, and have a certain promotion effect on the growth of peanuts. Peanuts which colonizated with S. rolfsii for 2 days and then sprayed by the bacteria liquid exhibited greater than other treatments with 66. 15% biocontrol efficacy against S.rolfsii. B. velezensis can be used for the prevention and treatment of peanut stem rot caused by S. rolfsii, and has a good prospect for biocontrol. Related Articles | Metrics

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CRISPR/Cas9-mediated tnaA knockout in Escherichia coli  HE Jing-hua, LE Ke-yi Journal of Biology    2019, 36 (6): 17-.   DOI: 10.3969/j.issn.2095-1736.2019.06.017 Abstract （2027）      PDF       Knowledge map    In Escherichia coli， tnaA gene encodes tryptophanase and it′s inactivation contributes to the L-tryptophan accumulation in E.coli. In the present study, CRISPR/Cas9-mediated gene editing technology was used to knockout the tnaA gene of E.coli. Sequence targeted by CRISPR/Cas9 was designed and gRNA expression plasmid was constructed. Donor DNA for homologous repair was constructed. Donor DNA, gRNA expression plasmid and pCas plasmid co-constituted the CRISPR/Csa9 system. This system was performed on E.coli w3110-Δ. PCR and sequencing results confirmed the successful knockout of tnaA gene with the knockout efficiency of 75%. In conclusion, CRISPR/Cas9-mediated knockout system for E.coli tnaA gene was successfully established, which would provide an effective tool for strain construction for L-tryptophan production. Related Articles | Metrics

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Codon usage bias and evolution analysis of the LaAP2 genein Lepidium apetalum Willd. ZHOU Qian, WANG Yuzhou, CHEN Yun, KAIDIRIYE·Yusupul, LIU Fei, ZHAO Huixin Journal of Biology    2021, 38 (6): 15-.   DOI: 10.3969/j.issn.2095-1736.2021.06.015 Abstract （1968）      PDF       Knowledge map    To understand the codon bias of LaAP2 in Lepidium apetalum, LaAP2 gene codon bias was analyzed by Codon W, and EMBOSS programs was used to analyze the codon usage bias of the Lepidium apetalum LaAP2 gene. Correlation analysis was conducted to compare the bias of the Lepidium apetalum LaAP2 gene in model organisms for which relatively mature genetic transformation systems are available. Neutral drawing, ENc plots and parity rule 2 polt were subsequently used for the exploration of possible factors that affect the formation of the bias. The results showed that the ENc, CAI, and GC content of LaAP2 were respectively 48-65, 0-214, and 42-69%, indicating that the codon bias level of LaAP2 in Lepidium apetalum was low and biased toward the synonymous codons with A or T. According to the RSCU value, 11 codons showed high-frequency. Comparison of the codon usage preference of homolongous genes with other crops suggested that there was a certain difference in codon usage preference among AP2 genes in different species. The RSCU cluster analysis showed that the preference of LaAP2 gene was the closest to that of brassicaceae burnett in dicotyledonous plants. The codon base composition and correlation analysis showed that the codon bias of the Lepidium apetalum LaAP2 gene had many factors such as mutation and selective pressure playing an important role in shaping codon usage bias. Based on the analysis of the frequency of codon usage across species, the prokaryote E. coli expression system was found to be the most suitable for use with the LaAP2 gene, and the model plant Arabidopsis was the most ideal genetic transformation receptor of the LaAP2 gene. This study provided important reference information for further studies on the heterologous sexpression and the function of the LaAP2 gene in Lepidium apetalum. Related Articles | Metrics

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Research progress on key metabolic enzymes in de novo synthesis pathway of ceramide LI Yu-hui, CHEN Cheng Journal of Biology    2020, 37 (4): 90-.   DOI: 10.3969/j.issn.2095-1736.2020.04.090 Abstract （1961）      PDF       Knowledge map    Ceramide is an important active lipid that regulates cell differentiation, proliferation, apoptosis, aging, tumor immunity and other vital life activities, and it is also a universal precursor for a series of important physiological sphingolipids such as glycosphingolipids. As the center of sphingolipid metabolism, the syntheses and degradations of ceramide in the body are strictly regulated. Its syntheses include de novo synthesis pathway, sphingomyelinase pathway and remedy pathway. Although de novo synthesis pathway contributes only 5%-10% to the synthesis of ceramide in the body, recent studies on key metabolic enzymes in this pathway have shown that they are closely related to many diseases, which also illustrates the complexity and importance of this pathway in the life of the organism. The purpose of this article is to systematically review the research progress of key metabolic enzymes in de novo synthesis, in order to provide a theoretical reference for further understanding of this pathway and the functions of key metabolic enzymes, and also lay an foundation for the development of personalized medicine for this pathway in the future. Related Articles | Metrics

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Effects of fusion between breast cancer cells and macrophages on PI3K/AKT and MAPK/ERK signaling pathways ZHANG Lina, ZHANG Didi, ZHAO Lei, GU Yuxuan, SUN Xiaolin Journal of Biology    2021, 38 (6): 25-.   DOI: 10.3969/j.issn.2095-1736.2021.06.025 Abstract （1926）      PDF       Knowledge map    In order to reveal the molecular mechanisms between cell fusion and tumor metastasis, we had successfully conducted a fusion model between breast cancer cells and macrophages. Previous studies found that the fusion hybrids exhibited significantly enhancing proliferation and metastasis abilities.Therefore, we next focused on the effects of cell fusion between breast cancer cells and macrophages on PI3K/AKT and MAPK/ERK signaling pathways closely related to tumor cell proliferation and metastasis. Western Blot results showed that the expression of the key marker proteins of PI3K/AKT and MAPK/ERK signaling pathways including p-PI3K, p-AKT and p-ERK1/2 was significantly up-regulated in the fused cells. After PI3K/AKT and MAPK/ERK signaling pathways being blocked by LY294002 and PD98059 inhibitors, the expression of p-AKT and p-ERK1/2 in the fused cells was obviously reduced, and the proliferation, migration and invasion abilities of the fused cells were inhibited. These results suggested that cell fusion between breast cancer cells and macrophages might promote the proliferation and metastasis of breast cancer by activating PI3K/AKT and MAPK/ERK signaling pathways. Our data also could provide new ideas for further understanding the mechanisms of cell fusion in tumorigenesis and metastasis. Related Articles | Metrics

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Construction and characterization of fliC gene-inactivated mutant of Escherichia coli ZHAO Xingxing, CHENG Yumei, CHEN Xian, CUI Guzhen, QI Xiaolan , HONG Wei Journal of Biology    2022, 39 (1): 27-.   DOI: 10. 3969/ j. issn. 2095-1736. 2022. 01. 027 Abstract （1905）      PDF       Knowledge map    To construct flagellin gene (fliC) inactivation mutant of Escherichia coli (ΔfliC) and explore its biological characteristics under stresses after alteration of biofilm formation. A fliC gene-inactivated mutant strain (ΔfliC420s) was constructed using the Thermotargetron targeted gene inactivation system. The changes of growth rate, motility, biofilm formation ability, autolysis rate, pH sensitivity and antibiotic tolerance of ΔfliC420s and wild-type strain were measured. Compared with wild-type strain, ΔfliC420s mutant had no effect on growth rate, its motility in semi-solid medium was reduced, the biofilm formation ability was significantly reduced, the autolysis rate of bacteria was accelerated, the pH sensitivity was enhanced, Interestingly, the tolerance of ΔfliC420s mutant to D-cycloserine, erythromycin, norfloxacin was reduced. The fliC gene of E. coli plays an important role in the formation of bacterial biofilm and resistance to external stresses. Related Articles | Metrics

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The effect of lentivirus-mediated down-regulation of SHCBP1 on the proliferation of melanoma B16 cells#br# SUN Zhiyang, FENG Guang, LEI Jingjing, TANG Chengcheng, SUN Chenhao, WANG Ling, LU Hongzhao Journal of Biology    2022, 39 (1): 11-.   DOI: 10. 3969/ j. issn. 2095-1736. 2022. 01. 011 Abstract （1863）      PDF       Knowledge map    To construct Shcbp1 lentiviral interference vector to explore the biological function of SHCBP1 in melanoma B16 cells, first,the shRNA-1 and shRNA-2 that target to interfere with the mouse Shcbp1 gene and the control sequence shRNA-NC were designed and connected to the lentiviral backbone vector, HEK293 cells were used to package the lentiviral particles to infect B16 cells, the interference efficiency was tested and CCK-8 and flow cytometry were used to detect cell viability and cell cycle. Western Blot was used to detect the expression of proliferation-related genes. The results showed that knockdown of Shcbp1 significantly inhibited the proliferation of B16 cells; flow cytometry results showed that knockdown of Shcbp1 blocked B16 cells in the G1 phase; the phosphorylation level of ERK1/2 decreased and the expression level of p21 increased. These results indicate that SHCBP1 may inhibit the transcription of P21 through the ERK1/2 signaling pathway and accelerate the progress of B16 cells from G1 to S phase Related Articles | Metrics

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Functional identification and bioinformation analysis of antimicrobial peptide from scorpion venom ZHU Chengang, JIA Ting Journal of Biology    2022, 39 (1): 33-.   DOI: 10. 3969/ j. issn. 2095-1736. 2022. 01. 033 Abstract （1775）      PDF       Knowledge map    A scorpion gland cDNA library was constructed from the scorpion Liocheles australasiae which was collected from Hainan Province of China. And then an antimicrobial peptide gene, named La39, was screened from the cDNA library. Its mature peptide is composed of 18 amino acids, and its secondary structure is α-helix. Hydrophilic and hydrophobic amino acids are located on the opposite side of the molecule, forming a strong amphoteric topological structure. The results of MICs assay, and hemolytic experiments and growth inhibitory assay showed that the minimum inhibition concentration of La39 for Staphylococcus aureus was 50 μg/ mL, which, however, had no inhibitory activity on Escherichia coli, and had hemolytic activity. Related Articles | Metrics

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Machine learning-assisted enzyme directed evolution JIANG Ying-ying, QU Ge, SUN Zhou-tong Journal of Biology    2020, 37 (4): 1-.   DOI: 10.3969/j.issn.2095-1736.2020.04.001 Abstract （1579）      PDF       Knowledge map    Directed evolution plays a central role in the fields of biocatalysis, biomedicine and biotechnology, etc. Taking advantages of increasingly computer performance and numerous datasets, artificial intelligence has rapidly developed. Recently, machine learning algorithms have also been applied to protein engineering, especially in helping prediction of protein structures, improving enzyme stability / selectivity / solubility, and guiding rational protein design as well as other functions. This paper reviews the state of the art in algorithms and descriptors used in enzyme engineering. Related Articles | Metrics

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Functional verification of candidate lipid meTableolism gene Tmem176a based on transcriptome sequencing CUI Maosheng, DUAN Weiwang, LI Xiaoning, TANG Chen, LI Kai, ZHOU Yunxun, XIAO Junhua Journal of Biology    2022, 39 (1): 21-.   DOI: 10. 3969/ j. issn. 2095-1736. 2022. 01. 021 Abstract （1529）      PDF       Knowledge map    The effects of overexpression and knockdown of Tmem176a on lipid metabolic pathways in Hepa1-6 cells were investigated.The constructed Tmem176a overexpression lentivirus vector and siRNA were transfected into Hepa1-6 cells. The overexpressed or knocked down with Tmem176a of Hepa1-6 cells were subjected to RNA-seq, bioinformatics analysis, and Real-Time PCR verification.Compared with the control group, Tmem176a was overexpressed 182 times (P<0. 05) and knocked down 0. 2 times (P<0. 05) in Hepa1-6 cells. There were 424 differentially expressed genes (DEGs) in OE-Tmem176a compared with that in OE-Vector, of which 233genes wereupregulated and 192 genes were downregulated. There were 405 DEGs of KD-Tmem176a compared with that of KD-Scramble,of which 157 genes were upregulated and 248 genes were downregulated. Some of the DEGs were enriched in metabolic pathwayssuch as fat digestion and absorption, cholesterol metabolism, glyceride metabolism, and fatty acid synthesis. The Real-Time PCR wasused to investigate some of the DEGs, and the change trend of the expression level of some investigated DEGs was consistent with that of RNAseq. RNAseq results indicated that Tmem176a affected gene response to lipid metabolism, and the changed expression level of Tmem176a promoted significant changes of gene expression level of lipid metabolism in mouse hepatoma Hepa1-6 cells. Related Articles | Metrics

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Synthetic biology and research progress YAN Wei, XIN Feng-xue, DONG Wei-liang, ZHOU Jie, ZHANG Wen-ming, JIANG Min Journal of Biology    2020, 37 (5): 1-.   DOI: 10.3969/j.issn.2095-1736.2020.05.001 Abstract （1473）      PDF       Knowledge map    Synthetic biology is one of the most potential fields of modern biology, which integrates many disciplines such as life science, engineering and information science. Based on the concept of engineering design, it constructs standardized components and modules, integrates the principles of engineering science, and adopts a bottom-up strategy to synthesize and improve the existing systems or systems, so as to reveal the law of life and build a new generation of bioengineering system. It creates a new research mode of "building knowledge" for life science. After the discovery of DNA double helix and the human genome sequencing project, synthetic biology is starting a new biotechnology revolution. As a new "convergence" discipline, with the progress of DNA synthesis technology and the deepening of the concept of synthetic biology, synthetic biology has made great progress in many research directions. This paper mainly introduces the concept of synthetic biology, summarizes the basic research content of synthetic biology and the research progress in natural products, medicine, energy and industry, and looks forward to the development prospect of synthetic biology. Related Articles | Metrics