东南大学目家科技园——用于肿瘤早期诊断的DNA甲基化检测芯片

肿瘤中相关基因的甲基化状态和水平的高通量检测，以及把DNA甲基化检测应用于肿瘤早期诊断，是肿瘤DNA甲基化研究中两个十分重要的问题，目前国际上尚无很好的办法。本成果运用成熟的PCR及基因芯片技术实现对大量重要肿瘤相关基因的甲基化检测。检测内容分为两部分：1、运用基因芯片技术分析肿瘤相关基因的甲基化模式：2、运用基凼芯片技术可同时检测多个与肿瘤相关摹凼的甲基化状态。该研究成果将大大加快与肿瘤发生发展密切相关基因的甲基化研究进程，对于肿瘤的早期分子诊断技术的开发也有重要的临床意义。     

基于基因表达数据的双向聚类算法的综述

随着基因芯片和DNA微阵列等高通量、短读取、低成本检测技术的发展,从而产生了丰富的基因表达数据。对这些数据进行有效的分析已经成为后基因组时代的研究重点。一般的聚类是根据数据的全部属性将数据聚类,这种聚类方式称为传统聚类。传统聚类只能寻找到全局信息,无法找到局部信息,而大量的生物学信息就隐藏在这些局部信息中。为了更好地在数据矩阵中搜索局部信息,人们提出了双聚类概念,这种算法从思想上有别于传统的聚类算法,它主要强调在聚类时基因和条件的同时性。目前比较成熟的双聚类算法大约有十七种左右。基于此本文简要调研了现有的三种具有代表性的双聚类算法,系统的分析了每种算法的设计步骤,算法原理,操作环境以及应用。这对于不同的基因数据如何选择更加合适的双聚类算法和软件提供了一定的指导。     

基因芯片技术在致病微生物研究中的应用

高密度寡核苷酸DNA芯片技术可以通过一次杂交试验获得大量的基因组信息,在基因组结构与基因表达分析中应用最广,在与人类健康有关的遗传病、传染病等诸多疾病中具有广泛的应用前景.本文重点对基因芯片技术在细菌、病毒等致病微生物病原鉴定、分类与致病机制研究中的应用作一简要介绍.     

基因表达谱中特征基因选择的几种方法比较研究

基因表达谱芯片技术的产生,为复杂疾病致病机理的研究提供了一个全方位的视角。从大量的基因表达谱芯片数据中挖掘有用的信息,特征选择技术起到了关键的作用。对当前基因芯片数据的特征选择方法和各种学习器效能进行了综述,并通过说明各种特征选择方法的具体情况来比较它们的优劣性,最终得出从特征自身特点出发的特征选择法可获得较好的分类效能和生物医学的应用。     

2型糖尿病大鼠基因表达变化的研究

研究2型糖尿病大鼠和正常大鼠肾脏组织差异表达基因,筛选与糖尿病相关的基因。应用基因芯片技术对糖尿病和正常大鼠的肾脏组织的mRNA进行检测。在4096条目的基因中共发现差异基因41条（其中5个基因上调,36个基因下调）,全部在GeneBank中登录。2型糖尿病的发生、发展涉及多基因改变,用基因芯片在寻找新的2型糖尿病相关基因方面有极大的应用前景,对于糖尿病的诊断,治疗和预防具有一定的临床应用前景。     

发现判断干细胞多能性的分子标准

动物所周琪研究员和遗传与发育生物学所王秀杰研究组合作,利用长期积累的大量具有不同发育潜能的小鼠ES和iPS细胞系,系统地分析了这些细胞的编码基因、小分子RNA和蛋白质表达谱,发现了一组在胚胎干细胞和具有完全多能性的iPS细胞中高表达,在仅具有部分多能性的iPS细胞中不表达或表达水平极低的一个关键基因组区域。     

检查基因表达分析的生物技术——cDNA阵列开发成功

ｃＤＮＡ阵列是一种对大量基因的功能进行同步分析的技术。它把数千至数万个基因的代表性片断固定在很小面积的基质表面上 ,检测这些基因在不同生物样品中的表达情况 ,从中寻找与特定生命和疾病过程相关的基因。预计人类含有大约 1 0万个基因 ,而人类基因组计划将在 2 0 0 1年前后发现所有这些人类基因。因此 ,人们必须有相应的技术对这些基因的功能进行大规模、高通量的研究。ｃＤＮＡ阵列是目前唯一能够完成这项任务的技术。上海细胞所自1 998年底开始研究ｃＤＮＡ阵列的制备和应用技术 ,通过与陈竺院士领导的国家人类基因组南方中心通力…     

大豆全长cDNA分析

由于大豆种子具有高油高蛋白,且可与土壤微生物共生进行生物固氮的特性,大豆已成为最重要的农作物品种之一。大规模的收集全长c DNA对于基因组序列的准确注释和基因及其产物的功能分析是十分必要的。我们用不同发育阶段和环境条件下的大豆构建了全长c DNA文库,并从中获得了总共39,936个大豆c DNA克隆。分别从每个克隆的5’端和3’端进行测序后,共得到68,661个表达序列标签(Expressed Sequence Tag,EST)。这些EST序列被聚类成包含2580个全长序列的22674个长片段。此外,我们对4712个全长c DNA进行了测序。去除重叠后,我们目前共得到6570条新的大豆c DNA序列。我们的数据表明87.7%的大豆c DNA克隆包含除5’-UTR和3’-UTR的完整编码区序列。已有数据证明我们测得的全长c DNA覆盖了大量不同种类的基因。通过将大豆序列与拟南芥、水稻和其他豆科植物数据进行对比分析后发现,我们的结果中包含一些特异基因,并且其中很大一部分经注释后发现存在未知功能。本研究报道的这组大豆全长c DNA克隆,将为大豆基因发掘提供有用的资源,并有助于大豆基因组的精确注释。     

2006年国内十大科技新闻

1．家蚕基因芯片与表达图谱诞生 1月2日，西南大学蚕桑学重点实验室研制成功家蚕基因芯片与表达图谱。这是我国在家蚕基因研究领域取得的又一项重大进展，将为我国家蚕产业的发展以及人类防病找到有效途径。     

卵细胞重编程机制研究取得重要进展

中科院上海生命科学研究院生物化学与细胞生物学所徐国良、李劲松课题组及其合作单位关于Tet3DNA双加氧酶负责卵细胞重编程的研究取得重要进展。他们研究发现卵细胞来源的母源因子Tet3加氧酶负责父本基因组DNA胞嘧啶甲基的氧化修饰,从而启动DNA的去甲基化．进一步激活Oct4和Nanog等全能性基因的表达。卵细胞内特异性敲除Tet3的母鼠生育力显著下降,其大部分胚胎在着床后发生退化,     

A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis

Boolean logic performs a logical operation on one or more logic input and produces a single logic output. Here, we describe a microfluidic DNA computing processor performing Boolean logic operations for gene expression analysis and gene drug synthesis. Multiple cancer-related genes were used as input molecules. Their expression levels were identified by interacting with the computing related DNA strands, which were designed according to the sequences of cancer-related genes and the suicide gene. When all the expressions of the cancer-related genes fit in with the diagnostic criteria, positive diagnosis would be confirmed and then a complete suicide gene (gene drug) could be synthesized as an output molecule. Microfluidic chip was employed as an effective platform to realize the computing process by integrating multistep biochemical reactions involving hybridization, displacement, denaturalization, and ligation. By combining the specific design of the computing related molecules and the integrated functions of the microfluidics, the microfluidic DNA computing processor is able to analyze the multiple gene expressions simultaneously and realize the corresponding gene drug synthesis with simplicity and fast speed, which demonstrates the potential of this platform for DNA computing in biomedical applications.     

Vif基因体外表达载体构建及其在无细胞系统中的表达

随着-omics（组学）时代的到来,无细胞蛋白质合成系统以具有快速、方便、易于高通量等优点,正在被广泛地研究和应用。本文选取HIV病毒感染因子Vif作为目标蛋白,构建了适宜体外表达的Vif表达载体pIVEX2.4c-Vif,并将其在大肠杆菌无细胞蛋白质合成系统中进行表达,为下一步进行高通量药物筛选奠定了一定的基础。     

DNA序列数形表示的研究

DNA序列的数形表示是用数学方法和计算机处理方法分析生物分子序列首先要解决的问题。序列表示的优劣会对最终分析结果有直接的影响。本文介绍了现有几种DNA序列数形表示方法。     

Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device

Two simple gold nanoparticle (GNP)-based DNA analysis methods using a microfluidic device are presented. In the first method, probe DNA molecules are immobilized on the surface of a self-assembled submonolayer of GNPs. The hybridization efficiency of the target oligonulceotides was improved due to nanoscale spacing between probe molecules. In the second method, target DNA molecules, oligonulceotides or polymerase chain reaction (PCR) amplicons, are first bound to GNPs and then hybridized to the immobilized probe DNA on a glass slide. With the aid of GNPs, we have successfully discriminated, at room temperature, between two PCR amplicons (derived from closely related fungal pathogens, Botrytis cinerea and Botrytis squamosa) with one base-pair difference. DNA analysis on the microfluidic chip avoids the use of large sample volumes, and only a small amount of oligonucelotides (8 fmol) or PCR products (3 ng), was needed in the experiment. The whole procedure was accomplished at room temperature in 1 h, and apparatus for high temperature stringency was not required.     

The histone H3K27 demethylase REF6/JMJ12 promotes thermomorphogenesis in ArabidopsisOA

Dynamic trimethylation of histone H3 at Lys27(H3 K27 me3) affects gene expression and controls plant development and environmental responses.In Arabidopsis thaliana,RELATIVE OF EARLY FLOWERING 6(REF6)/JUMONJI DOMAIN-CONTAINING PROTEIN 12 demethylates H3 K27 me3 by recognizing a specific DNA motif.However,little is known about how REF6 activates target gene expression after recognition,especially in environmental responses.In response to warm ambient temperature, plants undergo thermomorphogenesi...     

A lossless DNA data hiding approach for data authenticity in mobile cloud based healthcare systems

We present a lossless Deoxyribonucleic Acid (DNA) sequence hiding method that can be used for ensuring authenticity of DNA sequence in the context of Mobile Cloud based healthcare systems. Hiding data within DNA sequence results in permanent information loss in DNA sequence. Therefore, providing DNA sequence authenticity using data hiding is challenging. Moreover, existing works on DNA data hiding require a reference DNA sequence data to retrieve hidden data. Hence, current methods are not blind approaches and inappropriate for ensuring authenticity of DNA sequence in the Mobile Cloud. The proposed method hides authentication data within DNA sequence, extracts authentication data, and reconstructs the DNA sequence without any loss of information. From there, our proposed approach guarantees DNA sequence authenticity and integrity in Mobile Cloud based healthcare systems. We present a security analysis of our method to show that the method is secured. We conduct several experiments to demonstrate the performance of our proposed method.     

拟南芥GH3基因家族启动子序列分析

GH3 基因家族是植物生长素早期响应基因家族之一.拟南芥 10个GH3 基因启动子序列分析表明:GH3 基因的转录起始位点一般在起始密码子上游65~145bp之内,TATA box大多分布在(-24)~(-40)bp区域.MDB和MatInspector分析显示,AtGH3 s基因的上游调控区域普遍存在组织和器官特异性表达元件、激素响应元件以及环境响应元件,表明GH3 基因的表达受到多因素调控;同时,基因芯片数据显示AuxREs对生长素的响应非常重要,但也可能存在其他的生长素响应元件.     

Production of recombinant enveloped structural proteins from the Chinese WSSV isolate

The white spot syndrome virus (WSSV) is one of the deadly pathogens of penaeid shrimps and other crustaceans. The WSSV virion consists of an enveloped rod-shaped nucleocapsid enclosing a large circular double stranded DNA genome of 305 Kb with 181 open reading frames. The two major structural genes, VP19 and VP28 were amplified from the genomic DNA of Chinese isolate of WSSV and cloned in pUCm-T vector and sub cloned in pET-30a (+) vector. The expressions of genes inE. coli (BL21) were confirmed by SDS-PAGE analysis. The clones were sequenced, submitted to the gene bank and the Xiang Shan strain of WSSV were compared with the previous reported sequence of WSSV of various regions which revealed that VP19 and VP28 gene sequences had certain differences from the sequences of similar genes of the isolate already reported. The recombinant proteins expressed, purified and characterized.     

SSTS: A syntactic tool for pattern search on time series

Nowadays, data scientists are capable of manipulating and extracting complex information from time series data, given the current diversity of tools at their disposal. However, the plethora of tools that target data exploration and pattern search may require an extensive amount of time to develop methods that correspond to the data scientist's reasoning, in order to solve their queries. The development of new methods, tightly related with the reasoning and visual analysis of time series data, is of great relevance to improving complexity and productivity of pattern and query search tasks. In this work, we propose a novel tool, capable of exploring time series data for pattern and query search tasks in a set of 3 symbolic steps: Pre-Processing, Symbolic Connotation and Search. The framework is called SSTS (Symbolic Search in Time Series) and uses regular expression queries to search the desired patterns in a symbolic representation of the signal. By adopting a set of symbolic methods, this approach has the purpose of increasing the expressiveness in solving standard pattern and query tasks, enabling the creation of queries more closely related to the reasoning and visual analysis of the signal. We demonstrate the tool's effectiveness by presenting 9 examples with several types of queries on time series. The SSTS queries were compared with standard code developed in Python, in terms of cognitive effort, vocabulary required, code length, volume, interpretation and difficulty metrics based on the Halstead complexity measures. The results demonstrate that this methodology is a valid approach and delivers a new abstraction layer on data analysis of time series.