以HIV-1 5＇LTR为靶点的药物筛选细胞模型的构建

构建以人类免疫缺陷病毒（HIV-1）5＇LTR为靶点的药物筛选细胞模型,用于体外筛选潜在的对HIV-1启动子具有抑制作用的药物,或用于筛选与HIV-1复制相关的宿主因子。通过PCR扩增HIV-1 5＇LTR片段和胸苷激酶基因（thymidine kinase gene,TK基因）,以这2片段为模板进行重叠PCR将两者连接起来,连接产物经酶切后与pcDNA3.1载体连接;将连接正确的质粒转染HEK293细胞同时用G418加压筛选获得稳定细胞系;加入药物更昔洛韦（GCV）检测TK基因的表达。成功构建了HIV-1 5＇LTR调控TK基因表达的稳定细胞系,在其培养过程中加入药物更昔洛韦时,细胞逐渐死亡。构建了以HIV-1 5＇LTR为靶点的药物筛选细胞模型,该模型利用TK基因作为报告基因方便灵敏,可用于筛选针对HIV-1 5＇LTR的潜在抗HIV药物。     

PPARδ激动剂高通量筛选模型的建立

为建立基于细胞瞬时转染的过氧化物酶体增殖物激活受体δ(peroxisome proliferator-activated receptor delta PPARδ)激动剂高通量筛选模型,用RT-PCR技术从肝的总RNA中扩增PPARδ基因序列,将其连至T克隆载体进行测序。将序列正确的PPARδ片段连接至pTARGET载体上构建表达载体pTARGET-ppARδ;将合成的3个拷贝的PPRE(peroxisome proliferator receptorresponse element)插入pGL3-promoter构成报告质粒pGl3-PPRE×3-luc。用脂质体转染技术将表达载体与报告质粒共转染细胞系,通过检测荧光素酶基因的表达状况评价化合物对PPARδ的激动活性。通过多种条件的优化,得到了最佳的共转染条件。阳性药苯扎贝特明显提高荧光素酶的表达,最大上调倍增数可达10倍,并且在一定浓度下阳性药与相对荧光酶的活性表达有较好的量效关系。该筛选模型灵敏、稳定,为对PPARδ激动剂进行药物研发和PPARδ机理的研究打下基础。     

Application of MUTIC to the exploration of gene expression data in prostate cancer

We show here an example of the application of a novel method, MUTIC (model utilization-based clustering), used for identifying complex interactions between genes or gene categories based on gene expression data. The method deals with binary categorical data which consist of a set of gene expression profiles divided into two biologically meaningful categories. It does not require data from multiple time points. Gene expression profiles are represented by feature vectors whose component features are either gene expression values, or averaged expression values corresponding to gene ontology or protein information resource categories. A supervised learning algorithm (genetic programming) is used to learn an ensemble of classification models distinguishing the two categories based on the feature vectors corresponding to their members. Each feature is associated with a "model utilization vector", which has an entry for each high-quality classification model found, indicating whether or not the feature was used in that model. These utilization vectors are then clustered using a variant of hierarchical clustering called Omniclust. The result is a set of model utilization-based clusters, in which features are gathered together if they are often considered together by classification models - which may be because they are co-expressed, or may be for subtler reasons involving multi-gene interactions. The MUTIC method is illustrated here by applying it to a dataset regarding gene expression in prostate cancer and control samples. Compared to traditional expression-based clustering, MUTIC yields clusters that have higher mathematical quality (in the sense of homogeneity and separation) and that also yield novel insights into the underlying biological processes.     

A rapid reporter system using GFP as a reporter protein for identification and screening of synthetic stationary-phase promoters in Escherichia coli

To develop a rapid reporter system for the screening of stationary-phase promoters in Escherichia coli, the expression pattern of the green fluorescent protein (GFP) during bacterial cultivation was compared with that of the commonly used β-galactosidase. Using GFP with enhanced fluorescence, the expression pattern of both reporter systems GFP and β-galactosidase were similar and showed a typical induction of gene activity of the reporter genes, i.e. increase of expression at the transition from exponential to stationary phase. The expression was affected by the culture medium, i.e. in contrast to the complex medium (LB medium), the stationary-phase specific induction was only observed in synthetic medium (M9) when amino acids were added, whereas there was generally no induction in MOPS medium. To develop a rapid screening method on agar plates for stationary-phase promoters, a photographic approach was used, continued with computational image treatment. A screening method is presented which enables an on-line monitoring of gene activity.     

Embryo sac isolation inArabidopsis thaliana: A simple and efficient technique for structure analysis and mutant selection

Arabidopsis thaliana has been widely used as a model plant in gene function analysis. However, its tiny flower and curved embryo sac make it difficult to study gene expression during megagametogenesis, fertilization, and early embryogenesis, especially in the screening of mutants from those developmental processes. The techniques currently available are sectioning and whole-mount clearing of ovules; however, sectioning is time consuming and laborious for quantitative analysis, and whole-mount clearing, makes clear cytological observation impossible. Reported here is a simple and efficient method based on enzymatic isolation of embryo sacs that enables both quantitative analysis and elaborate cytological observation for gene expression investigation and mutant screening.     

A mathematical programming approach for gene selection and tissue classification

MOTIVATION: Extracting useful information from expression levels of thousands of genes generated with microarray technology needs a variety of analytical techniques. Mathematical programming approaches for classification analysis outperform parametric methods when the data depart from assumptions underlying these methods. Therefore, a mathematical programming approach is developed for gene selection and tissue classification using gene expression profiles. RESULTS: A new mixed integer programming model is formulated for this purpose. The mixed integer programming model simultaneously selects genes and constructs a classification model to classify two groups of tissue samples as accurately as possible. Very encouraging results were obtained with two data sets from the literature as examples. These results show that the mathematical programming approach can rival or outperform traditional classification methods.     

Atelocollagen-based gene transfer in cells allows high-throughput screening of gene functions.

We have previously demonstrated that Atelocollagen, used clinically for wound healing, is a reliable safe carrier for gene delivery. To obtain phenotypic changes by gene expression of cDNA, we developed an efficient technique for high-throughput gene transfer and expression screening in mammalian cells in microarrays by precoating a microplate with an Atelocollagen complexed with cDNA to which cells are then seeded. The complexes with a nanoparticle form were efficiently transduced into cells without use of any additional transfection reagent, and they allowed for long-term gene expression without apparent chromosomal integration. The complex spotted onto the well of a microplate was stable for a long period and allowed the cells to transduce and express reporter genes in a dose-dependent manner. We also showed that the present method using Atelocollagen-based gene transfer is applicable to gene medicines such as antisense ODNs and adenovirus vectors. These results suggest that Atelocollagen may be appropriate for general use in high-throughput screening of large sets of gene medicines for functional analyses in mammalian cells.     

A photoconversion model for full spectral programming and multiplexing of optogenetic systems

Optogenetics combines externally applied light signals and genetically engineered photoreceptors to control cellular processes with unmatched precision. Here, we develop a mathematical model of wavelength‐ and intensity‐dependent photoconversion, signaling, and output gene expression for our two previously engineered light‐sensing Escherichia coli two‐component systems. To parameterize the model, we develop a simple set of spectral and dynamical calibration experiments using our recent open‐source “Light Plate Apparatus” device. In principle, the parameterized model should predict the gene expression response to any time‐varying signal from any mixture of light sources with known spectra. We validate this capability experimentally using a suite of challenging light sources and signals very different from those used during the parameterization process. Furthermore, we use the model to compensate for significant spectral cross‐reactivity inherent to the two sensors in order to develop a new method for programming two simultaneous and independent gene expression signals within the same cell. Our optogenetic multiplexing method will enable powerful new interrogations of how metabolic, signaling, and decision‐making pathways integrate multiple input signals.     

The formulation of the control of an expression pattern in a gene network by propositional calculus

In this study we model a gene network as a continuous-time switching network. In this model, each gene has a binary state which indicates if the gene expresses or not. We propose a method to control a sequence of expression patterns in the gene network model by adding another continuous-time switching network. By using propositional calculus, we will show that the control problem can be formulated as a mixed-integer linear programming problem with linear constraints.     

人FKBP12的基因克隆及其表达产物的生物活性

为获得具有生物学活性的 h FKBP1 2 ,筛选新型的促神经再生药物 .采用 RT- PCR、计算机辅助 p BV2 2 0中外源基因高效表达的数学模型预测方法及超滤截留纯化方法 ,从人 T淋巴白血病细胞系 Jurkat中成功扩增出 h FKBP1 2基因 .按照外源基因高效表达的数学模型 ,将其进行优化改构后 ,在 p BV2 2 0中实现了高效表达 ,表达量约 2 0 % .重组的包涵体蛋白经复性 ,纯化至电泳纯 ,纯化后的 h FKBP1 2显示出肽基脯氨基顺反异构酶活性 .表明原核表达的 h FKBP1 2具有其天然生物学活性     

Development of a highly effective T-DNA inserted mutant screening method in a Chinese cabbage (<Emphasis Type="Italic">Brassica rapa</Emphasis> L. spp. <Emphasis Type="Italic">pekinensis</Emphasis>) reverse genetics system

We present a highly effective T-DNA inserted gene screening method as part of a reverse genetics model system using the Chinese cabbage (Brassica rapa L. spp. pekinensis). Three-step two-dimensional (2D) matrix strategies are potentially accurate and useful for the identification of specific T-DNA inserted mutants from a large population. To construct our Chinese cabbage model, we utilized a forward genetics screening approach for the abnormal phenotypes that were obtained from transgenic plants of Brassica rapa generated with Agrobacteria tumefaciens containing the pRCV2 vector. From one transgenic plant with an abnormal phenotype, we observed that the st1 gene (which is related to senescence-associated process proteins) contained a T-DNA fragment, and that its expression level was decreased. This T-DNA insert was then used as a control to construct an effective screening pool. As a result, the optimum template concentration was found to be 0.1–1 ng in our PCR strategy. For other conditions, positive changes to the Gibbs free energy prevented the formation of oligo dimers and hairpin loop structures, and autosegment extension gave better results for long fragment amplification. Using this effective reverse genetics screening method, only 23 PCR reactions were necessary to select a target gene from a pool of 100 individual DNAs. Finally, we also confirmed that the sequence we obtained from the above method was identical to the flanking sequence isolated by rescue cloning.     

毕赤酵母液滴微流控高通量筛选方法的建立与应用

巴斯德毕赤酵母是当前应用最为方便和广泛的外源蛋白表达系统之一,为了进一步提高其表达外源蛋白的能力,文中建立了基于液滴微流控的毕赤酵母高通量筛选方法,并以木聚糖酶融合荧光蛋白为例,筛选获得木聚糖酶表达和分泌能力提高的突变株。通过PCR扩增得到木聚糖酶xyn5基因和绿色荧光蛋白gfp基因融合片段,并克隆到毕赤酵母表达载体pPIC9K中构建出木聚糖酶融合绿色荧光蛋白的质粒pPIC9K-xyn5-gfp,电转化至毕赤酵母GS115中得到表达木聚糖酶和绿色荧光蛋白的毕赤酵母SG菌株。该菌株经过常压室温等离子体诱变后进行单细胞液滴包埋,液滴培养24h后进行微流控筛选,获得高表达木聚糖酶的突变菌株,进而用于下一轮的诱变突变库构建和筛选。以此类推,经过5轮液滴微流控筛选,获得一株高产菌株SG-m5,其木聚糖酶活为149.17U/mg,较出发菌株提升300%,分泌外源蛋白的能力较出发菌株提高160%。文中建立的毕赤酵母单细胞液滴微流控高通量筛选方法能达到每小时10万菌株的筛选通量,筛选百万级别的菌株库仅需10h,消耗荧光试剂体积100μL,对比传统的微孔板筛选方法降低试剂成本近百万倍,为高效、低成本筛选获得表达和分泌外源蛋白能力提高的毕赤酵母提供了一条新途径。     

毕赤酵母组成型表达脂肪酶及其高通量筛选方法

【目的】获得组成型表达脂肪酶毕赤酵母,建立利用橄榄油罗丹明B平板高通量筛选组成型表达华根霉脂肪酶基因的有效方法。【方法】运用PCR技术从pGAPZαA表达载体上扩增得到GAP启动子片段,插入到表达载体pPIC9K-proRCL中,构建组成型表达载体pGAPK-proRCL。在保留含有同源双交换重组序列的诱导型启动子AOX1序列的基础上,电转化后华根霉Rhizopus chinensis CCTCC M201021脂肪酶基因proRCL表达盒在毕赤酵母基因组上发生双交换整合事件,从而组成型表达单拷贝的华根霉脂肪酶基因。【结果】重组菌发酵144 h后,脂肪酶最高酶活为130 U/mL。利用橄榄油罗丹明B平板高通量筛选组成型表达华根霉脂肪酶基因。【结论】该方法将初筛时间从12 d缩短为3 d,排除了多拷贝突变株的干扰,为后续脂肪酶的定向进化及筛选奠定了基础。     

快速筛选高效表达重组蛋白毕赤酵母菌株新方法的建立及评价

毕赤酵母是当前应用最为广泛的重组蛋白表达系统之一,文中建立了一种快速筛选高效表达重组蛋白的毕赤酵母菌株的新方法。首先,对内质网转膜蛋白Sec63融合表达增强型绿色荧光蛋白EGFP的改造菌株GS115-E表达重组蛋白的能力进行检测;之后将携带不同拷贝数的植酸酶phy基因或木聚糖酶xyn基因的质粒转化进入GS115-E中,得到具有不同植酸酶或木聚糖酶表达水平的重组菌株,分别检测不同菌株的EGFP与重组蛋白的表达水平;最后,利用分选型流式细胞仪,根据绿色荧光值的高低对包含不同植酸酶表达水平的重组菌株的菌群进行分选。结果显示重组菌株中EGFP的荧光值与重组蛋白的活性表达水平之间具有良好的线性相关性(0.8|R|1),且利用流式细胞仪可高效地从混合菌群中筛选得到高产菌株,所分选得到的高荧光菌株在摇瓶发酵120 h时植酸酶表达水平是低荧光菌株的4.09倍。本方法通过检测菌株的EGFP荧光值代替检测重组蛋白的表达水平和活性,从而实现高表达菌株的筛选,大大提高了其应用的便捷性及通用性。与流式细胞仪、液滴微流控等高通量筛选仪器或技术结合将进一步提高筛选的速度与通量,为筛选获得高效表达重组蛋白的毕赤酵母菌株提供了简便、快速的新途径。     

利用基于CRISPR-Cas9 的基因编辑技术对miR-29a在GT1-7 细胞中进 行基因敲除

目的:本文利用CRISPR-Cas9技术在GT1-7细胞中对miR-29a基因进行基因编辑,用于构建miR-29a基因敲除GT1-7细胞模型。方法:通过构建Cas9稳转的GT1-7细胞株并转染sgRNA质粒用于在靶向miR-29a基因区域引发突变。然后构建EGFP与sgRNA共表达质粒并转染Cas9稳转GT1-7细胞,利用流式细胞仪富集表达绿色荧光蛋白的阳性细胞和分选阳性单克隆细胞。最后利用实时荧光定量PCR(realtimefluorescencequantitativePCR)对富集细胞和单克隆细胞进行miR-29a表达量检测。结果:T7E1检测结果显示CRISPR-Cas9系统有效地在miR-29a基因区域引发了突变。荧光定量PCR结果显示,与对照组相比,富集后阳性细胞miR-29a的表达量整体下降了50%左右(P0.05)。此外,通过流式筛选获得了一个纯合miR-29a基因敲除细胞克隆,与对照组相比,其miR-29a的表达量下降了75%左右(P0.05)。结论:本文建立了一种有效编辑GT1-7细胞基因的方法,并采用该方法构建了miR-29a稳定敲除细胞模型。     

琉璃苣BoD6D载体的构建及转化

运用植物基因工程手段构建琉璃苣BoD6D转化载体,为提高油料作物油份中γ-亚麻酸含量奠定基础.以琉璃苣基因组DNA为模板克隆BoD6D,构建酵母表达载体并转化酿酒酵母,对酵母进行诱导表达,提取脂肪酸后进行甲酯化反应,利用气相色谱分析脂肪酸含量;同时构建植物双元表达载体,经农杆菌介导通过蘸花法转化拟南芥,最后对转基因拟南...     

Screening of multi-copy mannanase recombinants of Pichia pastoris based on colony size

Pichia pastoris pGAP (glyceraldehyde dehydrogenase promoter) expression system was widely used for the expression and production of heterologous proteins. Screening multi-copy recombinants was an effective strategy to improve the heterologous protein production in P. pastoris. Because multiple gene insertion events occurred with a low frequency, hundreds to thousands of antibiotic-resistance recombinants need to be screened. The common way of improving screening efficiency was to increase antibiotic concentration in screening plates. Here we developed a screening method by selecting small colonies from low-concentration antibiotic screening plates. This strategy greatly improved the probability of obtaining multi-copy mannanase gene (man) recombinants and it could replace the common strategy by increasing antibiotic concentration in screening plates. The further study in liquid shake flask cultures revealed that cell concentrations, growth rates and substrate consumption rates of recombinants gradually decreased with the increase in man copy number. This indicated that such a screening strategy was effective to screen multi-copy recombinants based on colony size.     

Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models

MOTIVATION: The development of gene expression microarray technology has allowed the identification of differentially expressed genes between different clinical phenotypic classes of cancer from a large pool of candidate genes. Although many class comparisons concerned only a single phenotype, simultaneous assessment of the relationship between gene expression and multiple phenotypes would be warranted to better understand the underlying biological structure. RESULTS: We develop a method to select genes related to multiple clinical phenotypes based on a set of multivariate linear regression models. For each gene, we perform model selection based on the doubly-adjusted R-square statistic and use the maximum of this statistic for gene selection. The method can substantially improve the power in gene selection, compared with a conventional method that uses a single model exclusively for gene selection. Application to a bladder cancer study to correlate pre-treatment gene expressions with pathological stage and grade is given. The methods would be useful for screening for genes related to multiple clinical phenotypes. AVAILABILITY: SAS and MATLAB codes are available from author upon request.     

人胰腺α-淀粉酶抑制剂高通量筛选模型的建立及其应用

【目的】针对人胰腺α-淀粉酶这个糖代谢途径中重要的靶蛋白,建立α-淀粉酶抑制剂高通量筛选模型。【方法】采用毕赤酵母表达系统克隆和表达人胰腺α-淀粉酶;利用酶的催化特性建立α-淀粉酶抑制剂筛选模型;应用该模型对放线菌发酵液冻干物进行高通量筛选;通过构建16S rRNA系统发育树分析阳性菌株的分类地位。【结果】成功克隆、表达了具催化活性的人胰腺α-淀粉酶;建立了α-淀粉酶抑制剂的筛选模型;对近2000株放线菌的发酵液冻干物进行高通量筛选,最终得到14株α-淀粉酶抑制剂产生菌株,且在分类学上具有丰富的菌种多样性。【结论】本研究建立的α-淀粉酶抑制剂高通量筛选模型具有很强的实用价值,可用于新型淀粉酶抑制剂类降糖药物的开发。