Archive

  • Select all
    |
    Reviews
  • ZHOU Ting-Ting, FENG Jian-Nan
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 750-755. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.01
    Abstract ( ) Download PDF ( )   Knowledge map   Save
    The antibody is an important type of immunoglobulin that mediates humoral immunity. In recent years antibody drugs have emerged in the worldwide pharmaceutical market. With more therapeutic antibody entering the market and with their widening clinical applications, they have become the pillar of biopharmaceutical industry. The antibody information database is an important tool to manage, search and use antibodies. With the deepening of antibody research and the emergence of antibody sequences, structures, functional epitopes and other related data, antibody information databases are successively developed and implemented, and continuously playing an important role in the antibody research, development, production and sale. Here we introduce several antibody information databases, such as Kabat, IMGT, abYsis and hope to promote innovation and development for antibody resources.
  • XIAO Hai-Nan, DING Yong
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 756-759. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.02
    Abstract ( ) Download PDF ( )   Knowledge map   Save
    Extracellular vesicles (EVs) are membranous vesicles released by a variety of cells into their microenvironment. EVs carry the mother cellderived molecules and participate in almost all physiological and pathological processes of the organism. It has become a research focus to identify the components and functions of EVs. At present, a lot of protein, nucleic acid, lipid, and other molecular data of EVs from different species, tissues and cells have been obtained. In order to use these data, some EV databases have been established by different communities to serve as a useful resource to stimulate EV research. This review introduces the characteristics and applications of the three influential databases in the field: the ExoCarta, Vesiclepedia and Evpedia databases. We hope to provide a reference for researchers to use the EV databases.
  • Jian Wang
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 760-767. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.03
    Abstract ( ) Download PDF ( )   Knowledge map   Save
    With the rapid development of proteomics and the accumulation of knowledge about the mechanism of biological macromolecules, a large amount of protein-protein interaction data have emerged. The researchers have developed more than 300 protein-protein interaction databases for storage, display and re-use of these data. These protein-protein interactions are valuable resources for system biology, molecular biology and clinical drug development. In this review, these databases are divided into three categories: (1) General protein-protein interaction databases; (2) Specific protein-protein interaction databases; (3) Pathway and reactions databases. The protein interaction databases including BioGRID, STRING, IntAct, MINT, DIP, IMEx, HPRD, Reactome, KEGG, etc. were introduced in detail.
  • SHI Kai-Wen, LI Wu-Ju, LIU Tao
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 768-773. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.04
    Abstract ( ) Download PDF ( )   Knowledge map   Save
    The RNA world has enormous members with complicated structures and important functions, which have made it one of the important hot research areas. RNA functions are closely related to their structures. With the discovery of new RNA molecules and their functions, several RNA secondary structure databases have emerged, which will benefit not only to the understanding of the structural basis of RNA functions, but also to the development of prediction models for RNA structure. Here we present an overview of those databases, to facilitate the researchers to understand and use them.
  • WANG Zheng, LIU Tao*, LI Wu-Ju*
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 774-780. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.05
    Abstract ( ) Download PDF ( )   Knowledge map   Save
    Bacterial sRNAs are a class of small regulatory RNAs with their lengths varying from 50 nt to 500 nt. These sRNAs play a variety of biological roles through binding to target mRNAs or target proteins. Currently, with the application of bioinformatics prediction tools and highthrought sequencing, more and more sRNAs have been found, and a lot of databases associated with sRNAs have been developed. To help sRNA biologists understand those datasets systematically and apply them, we intend to present an overview of comprehensive and special sRNA databases, and give our suggestions in developing new sRNA databases in future.
  • Research Papers
  • LI Zhen, SITU Fang-Min, FENG Qi, ZHENG Wu-Jian, LIU Jiao, SHENG Hao, WANG Ju, SHAN Chang-Liang, ZHANG Shuai
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 781-788. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.06
    Abstract ( ) Download PDF ( )   Knowledge map   Save

    Cisplatin (also known as diaminedichloroplatinum, DDP) is currently one of the most effective chemotherapeutics for treatment of ovarian cancer. However, the resistance to DDP is a common obstacle. The mechanisms of DDP resistance are unclear. Copper chaperone for superoxide dismutase1 (CCS) mediates the transfer of Cu2+ to superoxide dismutase 1 (SOD1), thereby maintains cell proliferation and survival. Contrarily, inhibition of CCS can retard tumor cell proliferation. This study aims to demonstrate that AMPKdependent CCS expression is involved in ovarian cancer DDP resistance. Realtime quantitative PCR (RT-qPCR) and Western blotting results showed that the levels of CCS mRNA and protein in DDP-resistant ovarian cancer C13* cells were markedly up-regulated when compared to that of DDP-sensitive OV2008 cells. Silencing CCS by shRNA or inhibiting CCS by the inhibitor DC_AC50 could significantly enhance DDP-inhibited proliferation of C13* cells, indicating that high expression of CCS is associated with DDP resistance, and suppression of CCS can reverse DDP resistance. Similarly, Western blotting results revealed that the levels of CCS in six lung cancer cells including A549 and H1944 were closely correlated to the sensitivities of cancer cells to DDP. Silencing CCS expression markedly increased DDP sensitivity of A549, while overexpression of CCS decreased DDP sensitivity of H1944, which further demonstrated the correlation of CCS with DDP resistance. In addition, blocking the phosphorylation/activation of AMPKα at Thr172 by Compound C, an inhibitor of AMPK, could down-regulate CCS expression in C13* and enhance its sensitivity to DDP. These data suggest that AMPK signal-dependent CCS expression is involved in the mechanism of DDP resistance in cancers, and suppressing CCS reverses DDP resistance. These data also indicate that the CCS is hopeful to be a potential target for overcoming DDP resistance.

  • JIANG Yun-Lu, WANG Zheng-Wen, CHENG Bao-Hua, BAI Bo, CHEN Jing
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 789-798. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.07
    Abstract ( ) Download PDF ( )   Knowledge map   Save

    The orexin 1 receptor (OX1R) and cholecystokinin 2 receptor (CCK2R), which are closely correlated to cellular proliferation, are highly expressed in colon cancer cells. Its mechanism, however, is unclear. Based on the previous finding that OX1R and CCK1R can form dimer in HT-29 cells, in this study we investigate whether OX1R and CCK2R may heterodimerize to function in living cells by using a variety of resonance energy transfer techniques and coimmunoprecipitation (Co-IP). The bioluminescence resonance energy transfer (BRET) signals (BRET ratios) of OX1R and CCK2R in HEK293T cells were analyzed after the cells were exposed to orexin or gastrin for 5 minutes. Results showed that compared with non-exposed (control) cells, BRET signals were increased and reached a maximum when increased the acceptor (CCK2R-eYFP) expression without changes in donor (OX1R-Rluc) expression. The resonance energy transfer signals between OX1R-eYFP and CCK2R-eCFP over-expressed in HEK293T cells were detected by fluorescence resonance energy transfer (FRET) method. Moreover, receptor photobleaching FRET (apFRET) revealed that the FRET efficiency (FRETe) of the donor protein (CCK2ReCFP) in the OX1R-eYFP and CCK2R-eCFP co-transfected living cells was significantly increased to 3.7 folds of that in transfected control cells (P<0.05) after complete photobleaching which disrupted the receptor protein (OX1R-eYFP) and receptor-donor interaction. In addition, the combination of gene transfection and co-immunoprecipitation (Co-IP) indicated that the HA-OX1R and Myc-CCK2R fusion proteins were detectable only in the immunoprecipitates from HAOX1R and Myc-CCK2R co-transfected cells but not in that from transfected control and/or Myc-CCK2R- transfected cells. These dates suggest that OX1R can interact with CCK2R in living cells, which may provide new clues for further investigating the role of OX1R-CCK1R interaction in colon cancer cell proliferation and the relative signaling pathways.

  • LI Na, DU Qing-Lin,ZHANG Wei, MA Xiao-Jing
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 799-809. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.08
    Abstract ( ) Download PDF ( )   Knowledge map   Save

    Progranulin (PGRN) is overexpressed in a variety of tumors. However, little is known presently about the function of PGRN in the progression of melanoma. To fill this gap of knowledge, we established a mouse melanoma B16 cell line named B16-PGRNlow with PGRN expression stably knocked down by the CRISPR-Cas9 gene editing technique. MTS and BrdU assays showed that knock-down of PGRN had little effect on B16 cell proliferation or cell cycle status in vitro. We subsequently established the B16 tumor model by subcutaneously injecting B16-ctrl or B16-PGRNlow cells into wild type (WT) and PGRN knockout (KO) mice, respectively. B16-PGRNlow cells displayed significant growth deficiency in both WT and PGRN KO mice (in WT mice, P<0.05; in KO mice, P<0.01) compared with B16-ctrl cells, whereas little difference was observed in tumor growth of WT and KO mice implanted with B16-ctrl cells or with B16 PGRNlow cells. These results indicated that tumor-originated, not host-derived PGRN, is dominate in promoting B16 tumor growth. Last but not least, flow cytometric analysis revealed increased percentage of CD4+and CD8+ T cells in the spleen and tumor-draining lymph nodes in WT mice carrying B16PGRNlow tumor compared with WT mice bearing B16-ctrl tumor, while little difference was found in KO mice carrying either type of tumors. Our study demonstrates for the first time in a definitive manner in vivo that tumor-, not host-derived PGRN promotes B16 melanoma growth. Furthermore, knockdown of PGRN in the tumor results in increased recruitment of CD4+ T and CD8+ T cells in spleen and tumor draining lymph node suggesting the involvement of enhanced cellular immunity of the host. This original study provides insights into the role of PGRN in tumorigenesis and highlights the potential of tumorderived PGRN as a therapeutic target in melanoma.

  • XIE Li-Ling, ZHU Lin, WANG Ai-Xia, ZHU Yan-Kun, LI Jia-Jie, ZHOU Liang, BI Xiao
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 810-817. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.09
    Abstract ( ) Download PDF ( )   Knowledge map   Save

     

    Vibrio harveyi is one of common pathogenic bacteria, which is seriously imperilling human health and aquatic industry. Because of antibiotics abuse, drug residues and drug-resistance are becoming more serious. It is urgent to look for new alternatives with low toxicity and susceptiblilty to drug-resistance.In this study, we reveal the antibacterial effects of the ethanol extracts from Scutellaria on V. harveyi. The results showed that the ethanol extracts of Scutellaria had a strong inhibitory effect on V. harvey, the diameter of inhibition zone was 18.33±0.58 mm. The minimum inhibitory concentrations (MIC) and minimal bactericidal concentration (MBC) were 7.92 mg/mL and 15.84 mg/mL, respectively. By observation with scanning electron microscope (SEM) and concentration determination of intracellular and extracellular proteins, we found that although there were many little pores on the surface of V. harveyi, it remained smooth and integrated. After treated with ethanol extracts of Scutellaria, a band of protein disappeared in SDS-PAGE which was identified as NAD-specific glutamate dehydrogenase (NAD-GDH) by MALDITOF-TOF-MS. Furthermore, the real-time PCR results showed that the mRNA levels of this gene were affected by ethanol extracts of Scutellaria. These results are in good agreement with Scutellaria application in aqueous infection, and indicate that ethanol extracts of Scutellaria inhibit V. harveyi growth effectively through downregulating the expression of NAD-dependent glutamate dehydrogenase, which provides new evidence for the application of traditional Chinese medicine in the fields of aquaculture.
     
  • LI Wei-Bin, WANG Kai-Yu, ZHAO Meng, YAN Hui-Hui, LAN Xiao-Peng
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 818-825. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.10
    Abstract ( ) Download PDF ( )   Knowledge map   Save
    Human neutrophil FcγRI (i.e., CD64), one of the high affinity Fc receptors for IgG, is a new specific and sensitive biomarker for early diagnosis of sepsis and systematic bacterial infection. Expression of FcγRI is presently determined by flow cytometry analysis, which is not available for most laboratories. This study aims to select aptamers against human FcγRI with high affinity and specificity from a synthesized random oligonucleotide library by a novel in vitro selection technique, termed systematic evolution of ligands by exponential enrichment (SELEX) protocol. Human FcγRI immobilized on carboxytic acid magnetic beads was used as the target for eight rounds of selection of aptamers by SELEX, and three key monoclonal aptamers against FcγRI were obtained. Bioinformatics analysis showed that stem-loop and G-quartet are the main predicted secondary structures of aptamers to human FcγRI, suggesting the potential binding sites between FcγRI and aptamers, and G-T mismatch is also common. Flow cytometry and fluorescence microscopy assays respectively demonstrated that equilibrium dissociation constant (Kd) for the selected key monoclonal aptamers are in the nanomolar range, and aptamers only recognize neutrophils from the patient with sepsis, indicating their good affinity and specificity. Our results suggest that specific aptamers against human FcγRI have been successfully screened by SELEX. This study provides valuable information for further development of new detection methods based on aptamer molecular probes for early laboratory diagnosis of sepsis.
  • AN Ran, ZHANG Jing-Jing, GUO Hai-Xia, SHI Wen-Hui, QIAO Yan, WANG Zhi-Wei, SHI Jing, ZHANG Jin-Wen
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 826-834. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.11
    Abstract ( ) Download PDF ( )   Knowledge map   Save

    The solanidine glycosyltransferase (Sgt) family, comprising Sgt1, Sgt2 and Sgt3, participates in the biosynthesis of glycoalkaloids (GAs) in potatoes. It has been shown that inhibition of any one of the Sgt family members influences GA biosynthesis. However, blocking the expression of a single gene of the family does not effectively eliminate the accumulation of total GAs in the tuber. In this study, we employed a strategy to inhibit the expression of Sgt1, Sgt2 and Sgt3 genes simultaneously by RNA interference (RNAi) to reduce the accumulation of GAs in the potato tuber. First, we constructed the RNAi vector pCEI-PFR, in which the expression of siRNAs targeting Sgt1, Sgt2 and Sgt3 genes were driven by the tuber-specific Patatin promoter, and transformed the vector into potato internodal explants by Agrobacterium-mediated transformation. As a result, we obtained ten transgenic plants that contain the Patatin-RNAi fusion gene. Real-time Quantitative PCR (RT-qPCR) showed that the relative expression levels of the three Sgt transcripts decreased by approximately 32%~60% (Sgt1), 29%~55% (Sgt2) and 25%~66% (Sgt3), respectively, while the relative expression levels of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, one of the glyphosate tolerance genes, increased by about 48%~135%. High performance liquid chromatography (HPLC) revealed that the GA content of green tissues did not show a significant difference between transgenic lines and the wild type. Importantly, the GA content in the tuber of transgenic lines decreased by 46%~59% (Zhuangshu No.3) and 42%~62% (Favorita), respectively. We propose that silencing multiple genes of the Sgt gene family reduces the accumulation of GAs in potato tubers. Hence we provide a basis to deeply understand the distribution and accumulation of GAs in different potato tissues, and may promote innovation and development for potato germplasm resources.

  • Techniques and Methods
  • SHI Jing-Ming, LIU Hang, MA Hui, WU Mei-Na, WU Tao, SUN Zheng-Qi
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 835-844. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.12
    Abstract ( ) Download PDF ( )   Knowledge map   Save

    The formation of β-amyloid peptide (Aβ) oligomers is an important event in the pathogenesis of Alzheimer’s disease (AD). However, identification of the aggregation state of Aβ42 is essential for studies of cytotoxicity and inhibition of aggregation. A series of reasonable and simple methods were evaluated to distinguish Aβ42 monomers and oligomers based on previous studies, such as optimization of the Aβ42 amount, increase of the crosslinker, size exclusion chromatography (SEC) and thioflavin T (ThT) fluorescence analysis, etc. The following modification and optimization results are obtained: (1) Optimization of electrophoresis and electron microscopy, which are commonly used for detection of Aβ42 monomers and oligomers, has strict requirements for the amount of Aβ42. A concentration of 16.5% tris-tricine gel is best suited for electrophoretic analysis of Aβ42. For silver staining, the Aβ42 quantity in each lane is 0.5 μg. Aβ42 monomer at a concentration of 50 μg/mL is most suitable for electron microscope observation. (2) Addition of crosslinker BS3 at the final concentration of 0.3 mmol/L was found to be more effective for differentiation of Aβ42 aggregation forms. (3) Size exclusion chromatography (SEC) can be used to separate Aβ42 monomers and oligomers depending on pore size under non-denaturing conditions, but previous reports did not show the amount of Aβ42. Our methods provided detailed information for the amounts of Aβ42. The amount of Aβ42 sample added must be higher than 6.75 μg per time in SEC analysis when compared with Aβ40. (4) Cytotoxicity test and ThT analysis can be used to reveal whether a method is suitable for identifying the Aβ42 oligomerization state. Refinement and improvement of these methods will provide a reference for the study of Aβ42 in patients with Alzheimer’s disease. Some methods for the identification of specific Aβ42 oligomers have not been mentioned in this paper, and further studies are needed.

  • Short Communication
  • ZHAO Bing-Ling, YANG Yu-Jing, CHEN Tian-Zhi, YU Xiu-Ju,YANG Lin-Pei, DONG Chang-Sheng, YANG Shan-Shan
    Chinese Journal of Biochemistry and Molecular Biol. 2017, 33(8): 845-852. https://doi.org/10.13865/j.cnki.cjbmb.2017.08.13
    Abstract ( ) Download PDF ( )   Knowledge map   Save