Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1

A stoichiometric model describing the central metabolism of Shewanella oneidensis MR-1 wild-type and derivative strains was developed and used in elementary mode analysis (EMA). Shewanella oneidensis MR-1 can anaerobically respire a diverse pool of electron acceptors, and may be applied in several biotechnology settings, including bioremediation of toxic metals, electricity generation in microbial fuel cells, and whole-cell biocatalysis. The metabolic model presented here was adapted and verified by comparing the growth phenotypes of 13 single- and 1 double-knockout strains, while considering respiration via aerobic, anaerobic fumarate, and anaerobic metal reduction (Mtr) pathways, and utilizing acetate, n-acetylglucosamine (NAG), or lactate as carbon sources. The gene ppc, which encodes phosphoenolpyruvate carboxylase (Ppc), was determined to be necessary for aerobic growth on NAG and lactate, while not essential for growth on acetate. This suggests that Ppc is the only active anaplerotic enzyme when cultivated on lactate and NAG. The application of regulatory and substrate limitations to EMA has enabled creation of metabolic models that better reflect biological conditions, and significantly reduce the solution space for each condition, facilitating rapid strain optimization. This wild-type model can be easily adapted to include utilization of different carbon sources or secretion of different metabolic products, and allows the prediction of single- and multiple-knockout strains that are expected to operate under defined conditions with increased efficiency when compared to wild type cells.     

Identification of differentially expressed microRNAs and their PKC-isoform specific gene network prediction during hypoxic pre-conditioning and focal cerebral ischemia of mice

We previously reported the involvement of conventional protein kinase C (cPKC) βII, γ, novel PKC (nPKC) ε and their interacting proteins in hypoxic pre-conditioning (HPC)-induced neuroprotection. In this study, the large-scale miRNA microarrays and bioinformatics analysis were used to determine the differentially expressed miRNAs and their PKC-isoform specific gene network in mouse brain after HPC and 6?h middle cerebral artery occlusion (MCAO). We found 4 up-regulated and 13 down-regulated miRNAs in the cortex of HPC mice, 26 increased and 39 decreased gene expressions of miRNAs in the peri-infarct region of 6?h MCAO mice, and 11 up-regulated and 22 down-regulated miRNAs in the peri-infarct region of HPC and 6?h MCAO mice. Based on Diff Score, 19 differentially expressed miRNAs were identified in HPC and 6?h MCAO mouse brain. Then the miRNA-gene-network of 19 specified miRNAs target genes of cPKCβII, γ and nPKCε-interacting protein was predicted by using bioinformatics analysis of genome databases. Furthermore, the down-regulated miR-615-3p during HPC had a detrimental effect on the oxygen-glucose deprivation (OGD)-induced N2A cell injury. These results suggested that the identified 19 miRNAs, notably miR-615-3p, might target these genes of cPKCβII, γ and nPKCε-interacting proteins involved in HPC-induced neuroprotection.     

干旱胁迫条件下发菜Ferritin差异表达与基因克隆

发菜(Nostoc flagelliforme)是一种陆生固氮蓝藻,具有强烈的旱生生态适应性.运用双向电泳技术、凝胶图像分析、MALDI-TOF-TOF/MS质谱鉴定和数据库检索,发现发菜Ferritin在干旱胁迫条件下表达量逐渐降低.根据鉴定的Ferritin已知氨基酸序列设计简并性引物克隆该基因,获得了长度为540 bp的DNA,GenBank登陆号为HM854287.序列比较显示该基因具有较高的保守性,蛋白质二级结构主要由α螺旋和随机卷曲构成.RT-PCR分析表明,Ferritin mRNA在干旱胁迫条件下表达量逐渐降低,与Ferritin的表达趋势一致.将Ferritin基因在大肠杆菌中表达,获得符合预期的外源重组蛋白(22.4 kD).实验结果可为进一步研究发菜耐旱的分子机理及探讨发菜对极端干旱环境的适应和保护机制奠定基础.     

Simplifier: a web tool to eliminate redundant NGS contigs

Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions. Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms.

Availability

Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher.     

家兔支气管败血波氏杆菌重组百日咳杆菌粘附素（PRN）蛋白的原核表达及其间接ELISA方法的建立

目的表达支气管败血波氏杆菌（Bordetella bronchiseptica,Bb）PRN蛋白,并以此建立检测Bb抗体的间接ELISA方法。方法参照GenBank公布的猪源支气管败血波氏杆菌prn基因序列（AY376325）设计了一对特异性引物,PCR扩增出相应的核苷酸片段。将PCR扩增产物连接至原核表达载体pGEX-4T-1中,以E.coli BL21（DE3）为表达菌株进行诱导表达,以纯化重组蛋白PRN作为诊断抗原,通过探索最佳抗原包被量和抗体血清稀释倍数等,建立检测支气管败血波氏杆菌抗体的间接ELISA方法。结果成功克隆了prn全基因序列,并在E.coliBL21（DE3）中获得高效表达,经SDS-PAGE、Western blot分析显示重组蛋白PRN具有良好的抗原性。应用重组蛋白PRN为抗原建立了检测Bb血清抗体的间接ELISA诊断方法。试验确定重组蛋白PRN抗原的包被浓度为500ng/mL,最适血清稀释度为1∶40。结论建立的ELISA检测方法,不仅为Bb抗体检测提供了实用的血清学检测手段,也为进一步开发Bb检测试剂盒奠定了基础。     

拟南芥转录因子NF-YC的原核表达及多克隆抗体制备

采用PCR方法扩增NF-YC基因得到其全长cDNA序列,并将其克隆至原核表达载体pET-48b中,在大肠杆菌BL21中用IPTG诱导出分子量约为45 kD的融合蛋白,SDS-PAGE和Western blotting检测鉴定表达产物。利用亲和层析技术对融合蛋白进行纯化,纯化后的目的蛋白免疫新西兰兔制备多克隆抗体。间接ELISA检测抗体效价大于1 62 500,Western blotting结果显示,该抗体可特异性识别NF-YC蛋白。     

拟南芥生长素结合蛋白ABP1 的原核表达及蛋白纯化

目的:鉴于生长素结合蛋白(Auxin Binding Protein,ABP)能与生长素特异性结合,因而探讨研究其直接用于生长素信号转导机理和生物传感器的可能性与可行性。方法:通过RT-PCR获得拟南芥生长素结合蛋白1(Auxin bing protein 1,ABP1)的全长CDS,将其克隆到原核表达载体pGEX4T-1中,成功构建pGEX4T-1-ABP1重组表达载体。经酶切、PCR及DNA测序鉴定后,将阳性质粒转化表达受体菌BL21(DE3)。加入异丙基-β-D-硫代半乳糖苷(IPTG)进行诱导后,取样进行SDS-PAGE分析。结果:成功表达出一个分子量约为43 kD的可溶性融合蛋白,并利用GST亲和柱纯化方式得到了ABPl。结论:通过原核表达并经GST柱纯化后获得ABP1,为生长素生物传感器的研制开辟新的途径。同时为进一步研究ABP1与生长素的信号转导机制和生长素在生物传感测定技术中的研究和应用奠定基础。     

淋巴囊肿病毒中国株TNFR类似物的原核表达与结构分析

肿瘤坏死因子受体(TNFR)是细胞因子受体家族中的一员,在大DNA病毒的免疫逃避中起着重要的作用。 淋巴囊肿病毒中国株(LCDV-C)是一种大DNA病毒,属于虹彩病毒科。参照已知虹彩病毒TNFR基因设计引物: P1,5′GGATCCAAAACTATGATTAAAATAAAGA 3′;P2:5′ATTACTCGAGAATGTTAAAAATTAAGCTT 3′。以LCDV-C基因组DNA为模板,PCR扩增得到一个834bp的DNA片段,并对该片段进行测序。构建原核表 达重组质粒后,在大肠杆菌DE3中诱导表达,其产物经SDS-PAGE电泳后,显示为45kDa的融合蛋白带。对测序 结果进行计算机辅助分析的结果显示,LCDV-C TNFR类似物是一个含278个氨基酸的多肽,具有典型的半胱氨 酸富集区功能结构域,与宿主牙鲆TNFRII氨基酸同源性为34％。     

鳜传染性脾肾坏死病毒主要衣壳蛋白基因的原核表达

根据鳜鱼传染性脾肾坏死病毒(Infectious spleen and kidney necrosis virus,ISKNV)丰要衣壳蚩白(Major Capsid protein,MCP)基因(mcp)序列设计引物,PCR扩增得到一长约1400bp的DNA片段,将其克隆到pGEM-T Easy Vector。氨基酸亲水性分析表明,在150—250位氨基酸之间亲水性很高,可构成主要抗原决定簇及形成跨膜区。mcp基因经PCR改造后克隆至原核表达裁体pBV220,构建表达MCP的大肠杆菌基因工程菌,该工程菌经42℃诱导,SDS—PAGE检测,在约50kDa处有一特异蛋白带,含量约为菌体总蛋白的23％。用纯化和复性后的蛋白免疫新西兰大白兔制备抗血清,Western—blotting分忻显示,重组MCP制备的抗血清能与ISKNV MCP特异结合,说明表达产物具有与ISKNV MCP相似的抗原特性。