Loading...

Table of Content

    26 November 2015, Volume 31 Issue 11
    Review
    The Next Generation Sequencing Technology and Its Applications
    Tian Li, Zhang Ying, Zhao Yunfeng
    2015, 31(11):  1-8.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.003
    Asbtract ( 569 )   HTML   PDF (1028KB) ( 1994 )  
    References | Related Articles | Metrics
    DNA sequencingtechnology isan important research method inlifescience. Since thebirth of theSanger sequencing technology, DNA sequencingtechnologyhas experienced three generationsof change, resulting the secondgeneration to the fourth generation sequencingtechnology. DNA sequencing not only has been improving its productivity in an exponential growth rate but also been evolving into a new technological territories toward physical disciplines of nanotechnology. Next generation sequencingthat has landmark significance oflife sciences, can improve researches in the genome, transcriptome and epigenome. This review analyzes technical characteristics of the next generation sequencers and provide prospective insights into their future development and applications.
    Progress of Genome-wide Researches on WRKY Transcription Factors
    Yan Jun, Guo Xingqi, Cao Xuecheng
    2015, 31(11):  9-17.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.005
    Asbtract ( 314 )   HTML   PDF (1610KB) ( 987 )  
    References | Related Articles | Metrics
    WRKY transcription factors are one of the largest families of transcriptional regulators found widely in plants. They form integral parts of signaling networks that modulate many plant developmental processes and plant defenses. With the rise of whole-genome sequencing technology in plant, genome-wide identification and analysis of WRKY family became possible. From 2003 to 2006, these studies mainly focused on model organisms Arabidopsis thaliana and Oryza sativa. Then following the accomplishment and publication of other plant genomes, growing research on genome-wide identification and analysis of WRKY family have been published. Especially after 2013, the trend is now turning into a gusher. They not only analyze the phylogenetic evolution on various plant WRKY gene families, but also performed large-scale studies involving in the biological functions by new technologies such as real-time quantitative PCR, microarray, RNA transcriptome sequencing. This paper mainly reviewed the recent researches on genome-wide identification and analysis of WRKY family.
    Application of Proteomics in Cassava Breeding
    Chen Songbi, An Feifei, Zhu Wenli, Li Kaimian, Luiz J.C.B. Carvalho, Li Qingxiao
    2015, 31(11):  18-26.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.011
    Asbtract ( 440 )   HTML   PDF (1071KB) ( 844 )  
    References | Related Articles | Metrics
    Proteomics, studying global proteins relevant to expression, structures, functions and activities in living organisms, is an essential tool to analyze the expression and function of genome. Recently proteomics has provided important means and new clues for cassava breeding. The present study simply introduced the proteomics research platform and summarized the application of proteomics in cassava breeding of varieties with the high photosynthesis efficiency, high starch accumulation, high content of proteins and carotenoids, and high tolerance to extreme environments.
    Research Progress of the Human Long Non-coding RNA Related SNP Identification and Function Prediction
    Gong Jing, Liu Chunjie, Miao Xiaoping, Guo Anyuan
    2015, 31(11):  27-34.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.002
    Asbtract ( 352 )   HTML   PDF (1294KB) ( 1679 )  
    References | Related Articles | Metrics
    Long non-coding RNA(lncRNA)is a class of RNA, whose length is greater than 200 nucleotides and it does not show any protein-coding potential. The latest research shows that lncRNA plays function widely in the development of plants and animals, as well as in various diseases. There have been a series of reports on the discovery, prediction method, function study of lncRNA. Here, we reviewed the study of lncRNA related SNPs, including their identification and functional prediction. A comprehensive review of the bioinformatics methods and databases about the lncRNA related SNP was provided. These reviews may help to provide a new point of view for lncRNA research and a hint for the prediction, diagnosis and treatment of complex diseases based on lncRNA.
    ProgressandProspects in Domestic Animals and Breeding: a Review of Genomic Copy Number Variations
    Cheng Hong,JiangYu
    2015, 31(11):  35-42.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.006
    Asbtract ( 290 )   HTML   PDF (1030KB) ( 1132 )  
    References | Related Articles | Metrics
    The significantprogress of de novo assembly and re-sequencing of agricultural animal genomes, promoted the discovery of abundant genetic variations. Globalvariations mainly include single nucleotide polymorphisms(SNPs)and copy number variations(CNVs). Unlike SNPs, which have been widely studied and applied as molecular marker in breeding, fewer CNVs have been detected and experimental validated. Therefore, CNVs rarely serve as molecular markers in breeding. However, the proportion of genome variation ascribed to CNVs are far larger than to SNPs. So CNVs may have great impacts on agronomic traits. Recently, CNV is on the cutting edge of the research studies as well as applications in livestock and poultry breeding. In this review, we discuss the research progress of CNV, and its prospects for breeding domestic animals.
    Genome Assembly Based on Chromatin Interaction
    Tao Jingfen, Xie Ting, Zheng Juefei, Yang Qingyong, Zhang Hongyu
    2015, 31(11):  43-50.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.007
    Asbtract ( 410 )   HTML   PDF (1432KB) ( 2093 )  
    References | Related Articles | Metrics
    With the rapid development of sequencing technology, DNA sequencing is more efficiently and economically and in greater depth than ever before. How to locate the scaffolds into the chromosome becomes the key of getting high-quality genome. High-throughput chromatin conformation capture technique provides a new opportunity for scaffolds anchoring. Compared with traditional method, an assembly method based on chromosome interaction information is simple, low cost experimentation and saving time, and more application is expected in other relative complex polyploidy species. However, because of the limitation of the related technology, the genome assembly based on chromatin interaction still use second-generation technology, there are still many problems to be solved, for example, the resolution and background noise. It is expected to further improvement and enhancement. We still need to make effort to improve and optimize this method.
    Progress in the Study of Environmental Microbes by Metagenomic Methods
    Liu Jiemeng, Qi Ji
    2015, 31(11):  51-59.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.001
    Asbtract ( 299 )   HTML   PDF (1056KB) ( 1061 )  
    References | Related Articles | Metrics
    With the development of Next Generation Sequencing Technology(NGS), metagenomics has become a significant strategy to understand the structures of environmental microbial community and their interactions. Metagenomics analyzes the environmental microbes as a whole rather than extracting the individuals for culture and thus it can avoid the troubles of conventional culturing progress and bypass the accompanying difficulties. Due to this advantage, several sequencing projects of environmental microbes on human, ocean, soil etc. have been launched and largely promoted the progress on metagenomic studies. In this review, we will discuss both the merits and restrictions of current methods and pipelines adopted in the analysis on metagenomic data and introduce the progress brought by their applications in the researches of various environmental samples.
    Research Tool for the Genetic Relationship and Classification System Based on the Whole Genome CVTree3
    Zuo Guanghong, Hao Bailin
    2015, 31(11):  60-67.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.009
    Asbtract ( 312 )   HTML   PDF (3191KB) ( 899 )  
    References | Related Articles | Metrics
    Component vector of Broussonetia papyrifera(cvtree)method is based on whole genome, without sequence alignment and phylogenetic relationships among species research methods. CVTree3 is our latest development of the CVTree network server. It is based on the core program of parallel, in order to adapt to the current increase in the amount of genomic data, it is automatically compared with the species phylogenetic relationship and classification system, and on the web page to interact with the form of display, so that the study is more intuitive. Using the CVTree3 network server, biological workers can quickly analyze the genetic relationship of the whole genome sequence, and the classification status of the preliminary identification. Due to the rational use of the whole genome information, the CVTree method can be used to identify the relationship and classification of the species with high resolution. We hope that with the cvtree method of deepening and improvement, in the future it can set out to become a tool for the definition of prokaryote phylogenetic relationships and classification system.
    Classification, Prediction and Database Construction of Plant Transcription Factors
    Jin Jinpu, Guo Anyuan, He Kun, Zhang He, Zhu Qihui, Chen Xin, Gao Ge, Luo Jingchu
    2015, 31(11):  68-77.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.004
    Asbtract ( 546 )   HTML   PDF (1484KB) ( 990 )  
    References | Related Articles | Metrics
    Transcription factors(TFs)play key regulatory roles in both plant development and stress response. Genome-wide prediction of TFs is essential for functional and evolutionary studies of plant TFs. We made extensive literature review with thousands papers related to plant TFs and summarized a set of classification rules for plant TFs and developed a TF prediction pipeline. Using this pipeline, we predicted 129 288 TFs, classified into 58 families, from 83 plant species covering the main lineages of green plants including many economically important monocot and dicot crops. We made high-quality annotations for these TFs and built a plant TF database PlantTFDB(http: //planttfdb.cbi.pku.edu.cn). A TF prediction server was also developed for users to predict TFs from their own sequences. PlantTFDB has been served as an important portal for the functional and evolutionary studies of plant TF research community.
    An Introduction to Metagenome Databases of Environmental Microbiology
    Wang Huili, Guo Anyuan
    2015, 31(11):  78-88.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.008
    Asbtract ( 385 )   HTML   PDF (1481KB) ( 2027 )  
    References | Related Articles | Metrics
    The huge data produced by metagenome are valuable resources for environmental microbiology research. Until now, there are many big projects such as the Earth Microbiome Project and Census of Marine Life, which generated huge metagenome data and also constructed various databases and platforms to store and analyze these data. In this review, we summarized the current big projects, databases and online analysis platforms for environmental metagenomes. We introduced the project background, the sample information, the data type, the usage mode and the webpage of those databases.
    The Cancer-related Bioinformatics Databases
    Yang Jian, Cai Haoyang
    2015, 31(11):  89-101.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.010
    Asbtract ( 918 )   HTML   PDF (1223KB) ( 5216 )  
    References | Related Articles | Metrics
    Malignant tumor has become one of the major diseases that takes seriously risks to human health. In recent years, the rapid development of high-throughput detection technology has become an important means in cancer research. In this way, the cancer genomics data accumulated rapidly. These data is important for the research of mechanisms of tumor initiation and development. Massive biological data management and mining have become the foundation and an important field in cancer research. This article describes the frequently used bioinformatics databases of human tumors, including comprehensive databases, databases of genomics, transcriptomics, proteomics, epigenetics, etc. Here we sum up the status quo of database development in China and abroad, and discuss the existing problems to assist current research.
    Teaching Examples of Applied Bioinformatics Course
    Luo Jingchu
    2015, 31(11):  102-111.  doi:10.13560/j.cnki.biotech.bull.1985.2015.07.001
    Asbtract ( 844 )   HTML   PDF (2527KB) ( 1194 )  
    References | Related Articles | Metrics
    In this article, we introduce the basic bioinformatics analysis methods and tools taking the hemoglobin as an example. The methods include: 1)protein and DNA sequence alignment;2)advanced search for UniProt and RefSeq database;3)Blast database similarity search;4)phylogenetic tree construction under MEGA;5)protein structure comparison using Swiss-PdbViewer.
    Technique
    Application of Mass Spectrometric Technology in DNA Methylation Study
    Huang Xinfeng, Ye Jinbo, Liu Jianjun
    2015, 31(11):  112-120.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.012
    Asbtract ( 344 )   HTML   PDF (1718KB) ( 1624 )  
    References | Related Articles | Metrics
    DNA methylation is one of most important epigenetic modifications, which mainly occurs in carbon-5 position of CpG nucleotide sequence in mammal genomes and relates to organism development, transposable silence, X chromosome inactivation and many diseases. The understanding for molecular mechanism of DNA methylation formation, maintenance and reconstruction remain limited. however, in order to find an optimal method for DNA methylation qualitative and quantitative analysis, mass spectrometric technology with high sensitivity, good performance, high precision, high resolution and good repeatability, has a great value in the study of DNA methylation. In the following, we will make a introduction of mass spectrometric technology application in whole genomic DNA methylation and promoter DNA methylation study.
    Pretreatment and Application of Membrane for Dot Hybridization
    Jiang Chao, Su Xiaoqin, Zhang Xuewen, Pan Yinghong
    2015, 31(11):  121-124.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.013
    Asbtract ( 250 )   HTML   PDF (1705KB) ( 646 )  
    References | Related Articles | Metrics

    In order to solve the problems of the low density, the volume limitation, and the irregular shape of sample point in dot hybridization when samples were manually loaded, the hybridization membrane was pretreated with low melting paraffin waxes to fix sample position, size and shape. Firstly, according to the designed size, arrangement and density of sample location on membrane, different columnar salient moulds could be made. After placed a mould on membrane and tightly closed the columnar salient to the membrane, heated waxes was covering on. When waxes become solidification, the mould was removed and pretreated hybridization membrane was obtained. Using pretreated membrane, fluorescent dye IRDye800 labeled protein sample was directly loaded and detected. And finally, the protein samples of rice, wheat, and soybean were extracted, and detected by dot hybridization assay using this membrane. Results showed that pretreated NC and PVDF membrane with hydrophobic area outside of sample point could be obtained by using this method, and the densities, locations, shapes and sizes of sample points could be designedin advance. All fluorescence images of sample points, onto which different volumes of an antibody tagged with a fluorescent dye were loaded directly, showed similar dimensions. Proteins from leaves of rice, wheat and soybean were also detected with Anti-HSP antibody andstablesignals could be got. Our results show that when samples were manually loaded on the pretreated membrane, the position, size and shape of sample points can be unified, and the volume and density of samples can significantly improved.

    An Optimized Protocol for Crush Cell and Isolation of Protein from Scenedesmus sp. and Ammonia Toxicity Analysis
    Jia Qikun, Liang Qing, Wu Houbo, Wang Guanghua, Wu Hualian, Li Tao, Wang Bing, Xiang Wenzhou
    2015, 31(11):  125-130.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.014
    Asbtract ( 272 )   HTML   PDF (1754KB) ( 706 )  
    References | Related Articles | Metrics
    Propose an optimized protocol for crush cell and isolation of protein from Scenedesmus sp. and study the ammonia toxicity of this algal with this protocol. Liquid nitrogen grinding and ultrasonic crushing method was used to disrupt the algae and acetone precipitation and TCA-acetone precipitation methods to extract and purify protein. Results showed that we found that the combination of liquid nitrogen grinding and TCA-acetone precipitation was effective and efficient as the cell crushed adequately and the protein sample was purified well and the protein amount and abundance was higher. The preliminary inquiry of ammonia toxicity to Scenedesmus sp. with two-dimensional gel electrophoresis(2-DE)technology found that 85 protein spots decreased and 25 protein spots increased as the algae cultured with ammonia compared with nitrate nitrogen. Those proteins have been identified as involved in photosynthesis, carbon dioxide fixation, glycolytic, protein synthesis and degradation of ubiquitinated protein, cell division and material transportation, and radical scavenging pathway.
    Research report
    Prediction and Analysis of Genes Encoding c-di-GMP-Metabolizing Enzymes in Xanthomonas oryzae pv. oryzae
    Xue Dingrong, Tian Fang, Li Haiyun, Yang Fenghuan, Chen Huamin, He Chenyang
    2015, 31(11):  131-138.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.016
    Asbtract ( 281 )   HTML   PDF (1924KB) ( 749 )  
    References | Related Articles | Metrics
    Cyclic di-GMP, a ubiquitous bacterial second messenger that regulates diverse cellular processes including virulence, is synthesized by diguanylate cyclase(DGC)with the GGDEF domain and degraded by phosphodiesterase(PDE)with the EAL or HD-GYP domain, respectively. To identify genes encoding DGCs and PDEs in Xanthomonas oryzae pv. oryzae, prediction and analysis of the GGDEF, EAL and HD-GYP domain proteins in three genome-sequenced strains PXO99A, MAFF311018 and KACC10331 was comparatively performed in this study. Twenty-five to twenty-six GGDEF, EAL and HD-GYP domain protein genes were identified from each of three strains. Eighteen motif-conserved proteins were predicted to be the active DGCs or PDEs to metabolize c-di-GMP, whereas the remaining with the degenerate motifs might be the c-di-GMP receptors. Moreover, the majority of proteins were demonstrated to contain the input sensor domains to perceive the environmental stimulation and thereby modulate the activity of downstream output domains. The part of proteins was experimentally validated for their functions in the c-di-GMP signaling and regulation of virulence in X. oryzae pv. oryzae.
    Subcellular Localization of Rice Small G Protein OsRab5b in BY-2 Cells
    Shao Junli,Long Yuesheng, Xu Zengfu
    2015, 31(11):  139-145.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.017
    Asbtract ( 316 )   HTML   PDF (2140KB) ( 632 )  
    References | Related Articles | Metrics
    To investigate the subcellular localization of rice OsRab5b and the Gly2 role in the protein subcellular localization. OsRab5b-GFP and OsRab5b(Gly2Ala)-GFP plasmids were transformed into BY-2 cells. The laser confocal microscope was employed to observe the transgenic cells treated with drugs, a marker protein VSRAt-1 or an endocytosis tracer dye FM4-64. Results showed Punctuate and diffuse signals were observed in the OsRab5b-GFP transgenic cells. Wortmannin at a concentration of 16.5 μmol/L led to the change of the OsRab5b-GFP marked organelles into small vacuoles. The signals of OsRab5b-GFP were aggregated after the treatment of Brefeldin A(BFA)at a concentration of 100 μg/mL, but not at 10 μg/mL. Most of the OsRab5b-GFP positive signals colocalized with the VSRAt-1 positive organelles in the cells with and without wortmannin or BFA treatment. Additionally, most of the OsRab5b-GFP marked organelles colocalized with the endosomal marker FM4-64 after 60-min incubation. The diffuse signals of the mutation protein OsRab5b(Gly2Ala)-GFP were observed in the nuclei and cytoplasm of the transgenic cells, which were not affected by the wortmannin or BFA treatment. OsRab5b is localized to the prevacuolar compartment of BY-2 cells and the Gly2 site is essential for the correct subcellular localization of OsRab5b.
    Genome-wide Analysis of the YABBY Gene Family in Cotton
    Xu Zhenzhen, Ni Wanchao, Zhang Xianggui, Guo Qi, Xu Peng, Shen Xinlian
    2015, 31(11):  146-152.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.019
    Asbtract ( 401 )   HTML   PDF (1633KB) ( 1353 )  
    References | Related Articles | Metrics
    The YABBY gene family, as a subfamily of zinc finger super-family, plays a vital role in regulating the development of plant leaf and floral organs. 23 YABBY genes with different subcellular localizations were identified from the genome of upland cotton(Gossypium hirsutum L. acc. TM-1). These 23 YABBY genes distributed on 16 chromosomes and 1 Scaffold, and 9 pairs of them were syntenic genes. The cotton YABBY gene family could be divided into four subfamily groups, and there were homologous genes of Arabidopsis thaliana L. in each group. Furthermore, there were similar motif type and arrangement in each group. The tissue expression analysis showed that the expression pattern of the 23 YABBY genes from TM-1 genome varied among different tissues, and all the YABBY gene family members were expressed in the flower, bud and shoot apical meristem.
    Cloning and Expression Analysis of the Ethylene-responsive Transcription Factor III-1 Gene cDNA from Melon(Cucumis melo)
    Guo Chengyu, Sun Xiaolei, Shao Qi, Bai Lihua, Niu Yiding, Hasi Agula
    2015, 31(11):  153-158.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.020
    Asbtract ( 222 )   HTML   PDF (2038KB) ( 619 )  
    References | Related Articles | Metrics
    According to the clustering results of the ERF subfamily in melon, CmERFIII-1(accession ID: MELO3C005465)was chosen to be studied. A pair of specific primers was designed based on the cDNA of CmERFIII-1. The full-length cDNA of CmERFIII-1 was cloned by RT-PCR from the fruit of melon(Cucumis melo L.cv. Hetao).The length of cDNA was 711 bp, encoding 236 amino acids. Sequences analysis and the phylogenetic trees showed that the protein amino acid sequence of CmERFIII-1 was closely related to two ERF subfamily member of Cucumis sativus(GeneBank ID: XP_004143677.1、XP_004158119.1). The Real-time quantitative RT-PCR assay showed CmERFIII-1 gene was expressed and its expression levels were different in tissues of the plant and fruits of different developmental stages . The expression level of this gene was highest in leaf.
    Clone and Expression Analysis of The High-affinity K+ Transporter Gene SeHKT1 from the Halophyte Salicornia europaea
    Ma Jinbiao, Zhang Dayong, Zhang Meiru, Xiao Xinlong , Zhang Xuan, Li Li
    2015, 31(11):  159-165.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.021
    Asbtract ( 314 )   HTML   PDF (1938KB) ( 571 )  
    References | Related Articles | Metrics
    A putative high-affinity potassium transporter gene named SeHKT1 was cloned from halophyte Salicornia europaea using RACE techniques with GenBank number of KP739261. The characteristics of sequence was analyzed by bioinformatics and the expression patterns were verified by Real-time PCR in different tissues and under different salt stresses. The results showed that the SeHKT1 was highly closely related to SbHKT1 of Sorghum bicolor and with a 1 761 bp open reading frame(ORF)and encoding a polypeptide of 550 amino acids. Real-time PCR results showed that the SeHKT1 was expressed both in shoot and root by NaCl stimulus, but the transcription level were higher in root than shoot. The expression level reached highest level at 6 h and decreased after this time point in root under 200 mmol/L NaCl solution treatment. Under potassium starvation condition, the SeHKT1 was also induced in both of roots and shoots with high level. All of these results demonstrate SeHKT1 not only response NaCl stresses, but also regulate potassium absorption under potassium starvation environment.
    Cloning and Expression Analysis of PtLIR1 Gene from Puccinellia tenuiflora Under NaCl Stress
    Zhou Qi, Luo Chun, Guo Min, Fu Chang
    2015, 31(11):  166-172.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.022
    Asbtract ( 242 )   HTML   PDF (2557KB) ( 504 )  
    References | Related Articles | Metrics
    Light regulated protein 1-like gene is closely associated with plant stress resistance and may mediated sucrose level. In this study, the open reading frame of PtLIR1 gene was cloned from Puccinellia tenuiflora, and its expression characteristics under NaCl stress were analyzed. The full length open reading frame of PtLIR1 was 408 bp, which encoded 135 amino acids. The deduced amino acid sequence of PtLIR1 gene shared high identity with its homologs from Oryza sativa, Zea mays, Brassica rapa, Thellungiella halophila, Arabidopsis thalian, Oryza brachyantha, Setaria italica, Solanum tuberosum, Vitis vinifera, Brachypodium distachyon, Glycine max, respectively, and showed the highest identity of 80% with Lolium perenne. At the early stage of salt stress, the expression of PtLIR1 was negatively correlated with the accumulation of soluble sugar, and the other sucrose metabolism related genes may play more important roles in the regulation of sucrose level. However, during the late stage of salt stress, PtLIR1 gene was up-regulated in Puccinellia tenuiflora roots and may play a vital role in regulating sucrose level. PtLIR1 gene was involved in response to NaCl stress, and maybe contribute to the salt tolerance of Puccinellia tenuiflora.
    The Differential Expression Characteristics of miR319 and Four Targets Response to Low Temperature Treatments in Two Cassava Varieties
    Zeng Changying, Zhou Yufei, Peng Ming
    2015, 31(11):  173-178.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.015
    Asbtract ( 243 )   HTML   PDF (1637KB) ( 678 )  
    References | Related Articles | Metrics
    To study the regulation roles of microRNAs in cassava low temperature adaption, our early small RNA transcriptome profile identified miR319 response to low temperature in cassava. This study, we assayed the expression patterns of miR319 and its 4 different target genes between two cassava varieties under 4 low temperature treatments based on real-time quantitative polymerase chain reaction(PCR)technique. The results showed that the expression patterns of miR319a and its target genes differed in two different cassava varieties, differed among the four cryogenic treatments, and same to the correlation coefficients between microRNAs and four different target genes. After the comparison study, we found that the negative correlations between miR319 with three targets(MYB33, TCP4 and Unknown)are larger in C4 than those in SC124, and the NAH treatment has most typical negative correlation, and the order of negative correlation coefficients between miR319 and its target gene from large to small are: MYB33>Unknown>TCP4>GSTU8. All those data reveal that MYB33 and Unknown target(021030m)are priority target genes miR319 might execute its negative regulation under NAH treatment in C4, and thus the regulation of miR319 on MYB33 and unknown target in cassava low temperature adoption is worth in-depth study in the future.
    Cloning,Expression and Characterization of Enzyme for Mpr1 from P. pastoris GS115 in RecombinantE.coli
    Zhu Haifeng, Wu Dan, Wu Jing
    2015, 31(11):  179-185.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.023
    Asbtract ( 353 )   HTML   PDF (2370KB) ( 468 )  
    References | Related Articles | Metrics
    Due to the nature in P. pastoris methanol metabolism, it suffers much more ROS oxidative stress. There is one Mpr1 enzyme in P. pastoris. It plays significant physiological roles in ROS oxidative stress resistance ability and related research is still blank. For a detailed study about the physiological characteristics of P. pastoris Mpr1, Mpr1 from P. pastoris GS115 had been successfully expressed in E.coli JM109.Fermentation optimization of recombinant cell was studied from induction temperature, IPTG induction concentration, Initial induction OD by using Response Surface Analysis, activity reached(610.3±9.5)mU/mL. Enzymatic properties showed that the optimal pH of Mpr1 was about 7.0 to 7.5, the optimum temperature of Mpr1 was 30℃. In order to explore the nature of Mpr1, PQE30-E.coli JM109 strain and PQE30-Mpr1-E.coli JM109 strain were cultured under the same fermentation conditions in this experiment. The results showed that the growth capacity of the recombinant strain was stronger. The reason is that Mpr1 reduces levels of intracellular ROS.
    Cloning and Expression of Sulfur Oxygenase Reductase Gene from Acidithiobacillus caldus and the Study of the Recombinant Enzyme Activity
    Li Lingling, Lü Zaosheng, Zuo Zhenyu, Li Yaoyi
    2015, 31(11):  186-194.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.024
    Asbtract ( 226 )   HTML   PDF (2867KB) ( 673 )  
    References | Related Articles | Metrics
    In order to investigate biochemical properties of sulfur oxygenase reductase from Acidithiobacillus caldus(AcSOR), the sor gene was amplified by PCR with the extracted A. caldus TST3 genomic DNA as template, which was inserted into vector pET-28a to construct recombinant plasmid pET-sor. And the plasmid was then transformed into Escherichia coli BL21(DE3)to obtain recombinant strain E.coli BL21(pET-sor2). SDS-PAGE showed that the target enzyme SOR could be expressed in this recombinant strain after induction by IPTG. Induction conditions were optimized. The recombinant AcSOR was purified with Ni+-NTA column from the supernatant of the sonicated E.coli BL21(pET-sor2)induced under the optimal conditions. For the oxidation reaction, specific activity, Km and Vmax of the purified AcSOR were 0.70 units of oxidase/mg of protein, 15.672×10-2 g/mL and 12.755×10-5 mol/(L·min), respectively. Furthermore, specific activity, Km and Vmax of AcSOR for the reduction reaction were 2.21 units of reductase/mg of protein, 0.507×10-2 g/mL and 4.876×10-5 mol/(L·min), respectively.
    Screening of High-yield Rhamnolipid Producing Strain by ARTP and the Effect of Rhamnolipid on the Cellulase and Xylanase
    Chen Lijuan, Wu Bin, He Bingfang
    2015, 31(11):  195-201.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.025
    Asbtract ( 237 )   HTML   PDF (2026KB) ( 787 )  
    References | Related Articles | Metrics
    In order to obtain an industrial strain with higher rhamnolipid production, the original strain of Pseudomonas aeruginosa C3 was mutated by atmospheric and room temperature plasmas. A good genetic stability strain SC-11 was screened from the mutants, which produced rhamnolipid 74.1% higher than that by the original strain. Through single factor experiments, the culture medium for rhamnolipid production was opttimized. The yield of rhamnolipid could reach 42 g/L and the substrate conversion rate is 0.7 g/g substrates. 0.01% rhamnolipid could enhance CMCase by 12.9% and xylanase by 18.3%. The results show that rhamnolipid increased the production of cellulase by increasing cell permeability.
    Expression, Self-assembly and Antioxidation of Escherichia coli DPS
    Liu Wen, Jia Yihua, Fang Li, Liu Changai, Chen Hao, Lu Kaimin, Hu Wei
    2015, 31(11):  202-206.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.026
    Asbtract ( 300 )   HTML   PDF (1996KB) ( 559 )  
    References | Related Articles | Metrics
    DNA-binding protein from starved cells(DPS)is a key protective proteins in bacterial growth under stress environment. DPS was expressed in prokaryotic cells and purified so as to study its self-assembly activity in vitro. The dps gene was amplified by polymerase chain reaction with specific primers that was inserted by his tag at 3' end and the template was genome from Escherichia coli strain 0111. After digested together with EcoR I and BamH I restrict enzymes, the dps and pBV220 were linked in order to construct pBVDPSHis expression vector. DPS expressed in E. coli by temperature induction was purified with affinity chromatography column and its self-assembly in vitro was tested with natural PAGE on the basis of protein molecular weight. DPS protection for DNA from oxidation was detected with 1.2% agarose electrophoresis. The results showed that a specific fragment with 522 bp length was acquired and pBVDPSHis vector was constructed correctly using enzyme digestion and sequencing tests. The DPS with 19.5 kD relative molecular weight on SDS-PAGE was identified with Western blotting, the purified DPS could self-assembly in vitro into polymers with much larger molecular weight than 19.5 kD in pH7.5 PBS solution and DPS protection DNA resistance to hydroxyl radicals oxidation could be demonstrated in Fenton reaction system. It was concluded that E.coli DPS expressed genetically in prokaryotic cells could correctly self-assembly to functional multi-polymers and had a ability of protection DNA from ROS oxidant damage in vitro.
    Comparative Study of Chitosan Degradation Enzymes from Aspergillus sp. in Solid-State and Liquid-State Fermentation
    Yan Hejing, Shi Yue, Liu Chang
    2015, 31(11):  207-213.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.027
    Asbtract ( 279 )   HTML   PDF (2000KB) ( 528 )  
    References | Related Articles | Metrics
    Aspergillus sp. was cultured in solid and liquid fermentation condition respectively, enzyme production from which was studied. The results showed that solid-state fermentation produced more enzyme components than liquid state fermentation did. Enzyme preparation from solid state fermentation showed many kinds of hydrolytic enzyme activity like that of protease, cellulase, pectinase, amylase, lipase and hemcellulase beside to chitosan degradation activity, and enzyme preparation from liquid fermentation showed weak protease and cellulase activity beside to chitosan degradation activity. The optimal temperature for chitosan degradation of these two enzyme preparation was 45℃ and 40℃, and they showed high chitosan degradation activity at 40-55℃ and 35-40℃, respectively. Furthermore, the optimal pH of them was pH5.8 and pH5.2, and they showed high chitosan degradation activity at pH4.6-6.4 and pH4.6-5.8, respectively. These results indicated that Aspergillus sp. could produce different enzymes with different characteristics in solid and liquid state fermentation conditions. Thus solid state fermentation can be used to produce enzymes with chitosan degradation activities.
    Analysis of Digestive Stability in Simulative Digestive Tract Fluid and Heat Stability of Cry1Ie Protein
    Li Xinzhu, Geng Lili, Gao Jiguo, Zhang Jie
    2015, 31(11):  214-221.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.028
    Asbtract ( 313 )   HTML   PDF (2152KB) ( 572 )  
    References | Related Articles | Metrics
    Due to the high virulence to Asian corn borer(Ostrinia furnacalis)of Cry1Ie, this protein had applied into the germplasm creating of transgenic insect-resistant maize. To evaluate the food safety of Cry1Ie protein, this study carried out the digestion and heat stability assays. Using the expressing vector which the laboratory has constructed, the Cry1Ie protein(81 kD)was expressed in Escherichia coli, and the high purity protein was obtained using Ni-NTA chromatography and Superdex-75 size-exclusion chromatography. The results of artificial digestion assay showed that Cry1Ie was degraded rapidly within 15 s in simulated gastric fluid and intestinal fluid, without any peptide left in SDS-PAGE. In the heat stability assay, Cry1Ie was not stable in the extracting solution of maize meal, and most was degraded within 30 min under 100℃. In the bioassay of the Asian corn borer(Ostrinia furnacalis), it suggested that Cry1Ie lost the bio-activity after the treatment of digestion and heat. In conclusion, Cry1Ie was not stable in the gastrointestinal fliud and the heat treatment, which had lost the bio-activity to the Asian corn borer(Ostrinia furnacalis).
    Examination and Analysis on Pathogenic Vibrio anguillarum from Turbot Scophthalmus maximus
    Guo Yangliu, Wu Nan, Fang Hai, Chen Cuizhen, Li Yanyun, Wang Xiaoshan, Lu Huipeng, Zhang Donglin
    2015, 31(11):  222-227.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.029
    Asbtract ( 370 )   HTML   PDF (2112KB) ( 413 )  
    References | Related Articles | Metrics
    Ten strains isolated from died larve of cultured turbot were examined and analyzed. 10 strains were detected by phenotypic information, detection and phylogenetic analysis of the 16S rRNA gene sequence, serological, as well as pathogenic role of artificial model infection. It was found that Vibrio anguillarum showed strong pathogenicity on turbot, which was tested with various sources Vibrio anguillarum antiserum and occurred strong serological agglutination on immunity.
    Cloning and Characterization of mpd and ophc2 from an Organophosphorus Pesticide-degrading Bacteria YC-YH1
    Jia Yang, Shi Yanhua, Ren Lei, Qiao Cheng, Wang Junhuan, Yan Yanchun
    2015, 31(11):  228-235.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.030
    Asbtract ( 275 )   HTML   PDF (2413KB) ( 493 )  
    References | Related Articles | Metrics
    We cloned two organophosphorus hydrolase genes mpd and ophc2 from an organophosphorus pesticide-degrading bacteria Pseudomonas stutzeri YC-YH1. The two genes were inserted into the expression vector pET-32a and transformed into E. coli BL21(DE3)respectively. We used Ni-affinity column to purify enzymes and then study the nature of the two enzymes. It was suggested that the optimal temperature of MPH is 40℃, and the MPH displays high activity in the pH range of 8 to 12. The optimal temperature of OPHC2 is 30℃. In the pH ranging of 8 to12, OPHC2 has higher activity. The mixture of MPH and OPHC2 in theproportion of1:1 showsed higher activity in the range of 30℃ to 40℃, the enzyme showsed more than 95% activity in the range of pH8-12. A variety of metalions affect the activity of the enzymes and the enzymes are sensitive to SDS and EDTA, but the compound could reduce the sensitivity to the metalions.
    Monocrystal Culture and Crystallization Conditions Optimization of HspB from Pseudomonas putida
    Wu Zhijie, Wu Geng, Tang Hongzhi, Xu Ping
    2015, 31(11):  236-242.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.031
    Asbtract ( 267 )   HTML   PDF (2338KB) ( 632 )  
    References | Related Articles | Metrics

    It was to obtain the monocrystal of HspB, the key monooxygenase in the nicotine degradation pathway from Pseudomonas putida, for X-ray diffraction. The expression plasmid was constructed by site-directed mutagenesis PCR and was expressed in Escherichia coli. Target protein was purified with immobilized metal-chelating affinity chromatography, TEV protease digestion and gel filtration chromatography. Crystal culture though hanging-drop vapor-diffusion method. The recombinant plasmid was successfully constructed and expressed high. Compared to digestion on the column, digestion in the solution during dialysis is more efficient, and the purification strategy was determined to obtain HspB with high purity. The optimal crystallization condition was identified as 22% PEG3350, 0.1 mol/L Bis-Tris pH6.5, 0.21 mol/L MgCl2, 18℃, seeding after orthogonal experiments. HspB with His-tag cleavaged can obtain a monocrystal which resolution reaches 1.8Å.

    Effects of TOI on H1N1 Virus Propagation in MDCK Cell Culture
    Huang Ding, Liu Xuping, Fan Li, Zhao Liang, Tan Wensong, Chen Ze
    2015, 31(11):  243-250.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.032
    Asbtract ( 342 )   HTML   PDF (2055KB) ( 944 )  
    References | Related Articles | Metrics
    In order to improve the production efficiency of influenza vaccine in processes based on MDCK cell culture, the effects of TOI on influenza A(H1N1)virus propagation in MDCK cells were investigated. By infecting MDCK cells with H1N1 influenza virus at different TOI, the characteristics of MDCK growth and metabolism and influenza A(H1N1)virus were studied. The results showed that maximum influenza A(H1N1)virus yield reached when TOI was 72 h. However, the cell specific virus yield was reduced as TOI increased. To find out the reason behind this phenomenon, further analysis of TOI and CCI effects on cell specific virus yield were studied. Results showed that, the phenomenon was caused by cell status rather than high cell density. The study reveals the importance of cell status difference due to TOI, showed that influenza A(H1N1)virus production efficiency in MDCK cells could be improved by cell state adjusting.
    Constructing a Human Oocyte Reporter System
    Luo Mengyuan, Kee Kehkooi
    2015, 31(11):  251-256.  doi:10.13560/j.cnki.biotech.bull.1985.2015.11.033
    Asbtract ( 232 )   HTML   PDF (1870KB) ( 570 )  
    References | Related Articles | Metrics
    In vitro differentiation of stem cells into mature germ cells has important significance both in scientific research and in clinical treatment. An oocyte reporter system will become a useful tool for this goal. ZP2 is a component of the zona pellucida in mammalian oocytes and its expression is known to be restricted in oocyte. In this experiment we cloned 300 bp and 2 500 bp fragment of human ZP2 promoter and fused them to eGFP aiming to build an oocyte reporter sysem. We tested the specificity of the reporter in WI38, undifferentiated human embryonic stem cell(hESC)line H9 and mouse oocyte. Results show that ZP2-2500-eGFP can specifically drive eGFP expression in mouse oocyte but no eGFP was detected in WI38 and undifferentiated hESCs.
    Others
    Cover
    2015, 31(11):  777. 
    Asbtract ( 158 )   HTML   PDF (4651KB) ( 254 )  
    Related Articles | Metrics
    Table of content
    2015, 31(11):  888. 
    Asbtract ( 169 )   HTML   PDF (263KB) ( 344 )  
    Related Articles | Metrics
    Copyright
    2015, 31(11):  999. 
    Asbtract ( 155 )   HTML   PDF (252KB) ( 313 )  
    Related Articles | Metrics
Copyright © Biotechnology Bulletin, All Rights Reserved.
Tel: 86-010-82109925, 82109903 E-mail: biotech@mail.caas.net.cn
Powered by Beijing Magtech Co., Ltd.