基于IBM DB2的中国寄生性膜翅目昆虫资源数据库构建

以IBM DB2数据库作为开发平台,根据寄生性膜翅目昆虫数据的特点组建了分类地位表、寄主表、形态特征图和生物学特性表,将寄生性膜翅目的中文名、拉丁名、定名人、寄主、形态特征、图形、生物学特性等信息分别存储于这4个表中,构建出中国寄生性膜翅目昆虫资源数据库。用Visual Basic 6.0编制了友好的人机对话界面,即信息的录入和修改界面、信息查询界面和用户管理界面,使数据库的应用与维护更加便捷。     

水稻矮缩病毒基因组数据库的构建

二级数据库的构建是生物信息学新的重要领域。目前部分生物的基因组序列测定完成后,正在进行广泛而深入的结构和功能研究,使二级数据库的重要性显得日益突出。水稻矮缩病毒是一种在日本、中国和东南亚感染水稻的病原微生物,给农业生产造成很大损失。根据国际和国内对水稻矮缩病毒基因组的研究,利用已有的基因序列和结构、功能等方面的数据,以计算机网络为载体,参考国际通用数据库的格式,尝试建立一个简洁的、友好的通用性好而且专用性强的二级数据库：水稻矮缩病毒基因组数据库。希望能够为研究普通水稻矮缩病毒的粒子结构、基因表达调控、致病机理和防治方法提供一个良好的工具,为从事水稻矮缩病理论和应用研究的工作者提供方便和帮助,并为探索二级数据库的构建积累经验。     

基于Oracle数据库的水稻病虫综合防治专家系统

应用数据库、计算机网络和空间信息技术,研制出基于Oracle数据库的“水稻病虫综合防治专家系统RIPMES Ⅱ”。系统包括数据采集、数据维护专家决策和GIS应用等子系统,能解决实时数据采集、海量数据存贮与分析、病虫害防治辅助决策、虫害空间分布特征分析等问题,是水稻病虫害综合防治的一个有效工具,同时也可为类似的专家系统的研究提供参考。     

水稻诱导结瘤和根瘤菌导人

一定的水稻品种以无菌水培和砂培,待秧苗长到一定时期,用一定浓度的合成植物生长激素2,4——二氯苯氧乙酸(2,4—D)或二甲四氯钠处理水稻根系,并接种田菁茎瘤根瘤菌(Azorhizobium Caulinodans)处理后10～15天内水稻根系产生瘤状结构(类根瘤),20天后水稻类根瘤经电镜检查,发现根瘤菌已侵入水稻根系,以及根瘤菌在水稻类根瘤内转化形成的类菌体。不同的水稻品种和不同浓度的2,4—D或二甲四氯钠处理,植株的生长状况和根系的结瘤状况各不相同。在参试的11个水稻品种中以湘晚籼4号等四个品种结瘤状况较好。水稻水培2,4—D处理浓度以0.5ppm,水稻砂培2,4—D处理浓度以1ppm、二甲四氯钠以2ppm较为适宜。     

基于MSP430的MIT—BIH心律失常数据库模拟信号源

MIT—BIH心律失常数据库是许多国家的标准测试源。MSP430系列单片机以其低功耗等特点正被广泛应用于医学仪器等设备中。本文的设计实现了用MSP430FG439等器件将MIT—BIH心律失常数据库的48条记录以忠实原记录的模拟信号输出,从而制成信号源,并且包含我国新的国家医药行业标准中关于心电监护仪等仪器测试规定需要的一些信号。     

基于Te-OnAdvanced的肺癌细胞15-脂氧化酶-2基因表达载体的构建与表达

目的：构建肺癌细胞15-脂氧化酶-2（15-Lox-2）的可诱导性真核表达载体pTRE-Tight-15-Lox-2,并在肺癌细胞中检测其是否可受强力霉素（DOX）诱导表达。方法：pcDNA3-15-LOX-2载体经＆0RI和XbaI双酶切线性化,回收15-LOX-2cDNA片段,将其克隆入pTRE-Tight载体的EcoRI和XbaI位点;采用脂质体法将pTet-0n-Ad-vanced与构建的pTRE-Tight-15-Lox-2共转染肺腺癌A549细胞,DOX诱导表达后,Western印迹检测15-Lox-2的表达水平。结果：构建了pTRE-Tight-15-Lox-2诱导表达载体;Western印迹检测表明,该载体能在肺癌细胞内表达,且其表达受DOX调控。结论：Tet-OnAdvanced系统能严密高效地调控15-LOX-2在肺癌细胞中的表达,为进一步研究15-LOX-2在肺癌中的作用奠定了基础。     

水稻幼苗特异应答H2O2的miRNA169b启动子表达载体的构建

目的:研究microRNA169b(miRNA169b)启动子不同长度片段的活性及自身调控。方法:用生物信息学方法分析水稻中miRNA169b前体上游1500 bp序列,并从水稻幼苗基因组DNA中扩增miRNA169b前体上游500、1000和1500 bp启动子片段,分别将3个片段克隆至萤光素酶报告基因载体p5XGal4-LUC上。结果:构建了miRNA169b启动子重组载体,序列分析表明与预期结果一致。结论:miRNA169b启动子调控的萤光素酶报告基因表达载体的构建,为研究水稻中miRNA基因自身的转录奠定了基础。     

水稻Rim2/Hipa 超级家族的基因组变异和基于Rim2/Hipa 展示的水稻资源的系统进化和指纹分析

水稻Rim2/Hipa是最近鉴定的一个受逆境诱导的转座因子超级家族.研究表明,Rim2的核心序列在不同来源的水稻材料中存在显著的差异,暗示Rim2家族的长期进化历程.基于Rim2因子间的差异性以及该因子的静止状态,开发出一种利用Rim2因子展示的新的分子指纹技术,可以灵敏地区分不同水稻资源以及它们的遗传关系.仅用5对引物就可以清楚地将53个栽培稻和普通野生稻材料鉴定出来,并可将它们分为不同的系统进化组.研究表明不仅在水稻资源而且在野生稻种质间均存在明显的多样性.野生稻可以被单独分组,或者分散在粳稻中间.这种新的指纹技术还可以将水稻的杂交子代和它们的亲本区分出来,并可用于种子纯度的鉴定,在水稻基因组进化研究、水稻育种和种子生产中有很好的应用前景.     

基于CSSLs群体定位和图位克隆水稻长芒基因GAD1-2

水稻是世界上最早驯化的重要粮食作物之一。水稻芒可以保护水稻种子不被鸟琢食,是水稻重要的驯化性状之一。芒在野生稻中普遍存在,对野生稻的生存和传播至关重要,然而在驯化和人工选择过程中该性状逐渐被淘汰。定位和克隆水稻长芒相关基因是研究水稻芒驯化遗传机制的基础。本研究以籼稻恢复系东南恢810为受体、漳浦野生稻为供体构建的146个染色体片段置换系(chromosome segment substitution lines, CSSLs)为研究材料,调查了146个CSSLs株系和双亲的芒长,结果表明在4个置换系中检测到1个控制水稻芒长主效基因GAD1-2,位于水稻第8号染色体;利用重叠代换作图法,将GAD1-2定位在Ind8-10和RM4936标记之间,遗传距离约为4.75 Mb。选择分离群体中的显性单株,利用开发的标记,最终将GAD1-2 基因定位在两个 Indel 标记之间,两者间的物理距离约为27 kb,该区域内只有两个候选基因Os08g0485500和Os08g0485400。经测序和分析表明,Os08g0485500是GAD1-2的候选基因,GAD1-2在保守的ORF区域存在6个碱基缺失,导致丝氨酸和半胱氨酸这两个氨基酸缺失,从而表现长芒的性状;在Os08g0485500基因位点已克隆了1个控制水稻芒长的GAD1基因,推测GAD1-2与GAD1为等位基因。本研究为进一步理解水稻起源演化和水稻芒长发育基因的遗传机制奠定了基础。     

水稻抗氨基酸类似物突变体的筛选——Ⅰ.抗S-(2-氨乙基)L-半胱氨酸(AEC)突变体的筛选

以赖氨酸类似物S-(2-氨乙基)L-半胱氨酸(AEC)为选择剂,从水稻花药培养中筛选出一个抗性突变体(R_(AEC))。突变体愈伤组织经过6个月继代培养后仍保持抗性稳定。R_(AEC)再生植株根尖诱导的愈伤组织经过3个月继代培养也保持稳定的抗性。R_(AEC)细胞内赖氨酸含量提高了近2倍,苏氨酸提高5倍多。其他氨基酸,如蛋氨酸、酪氨酸、丝氨酸等都有较大量的提高。 R_(AEC)愈伤组织对赖氨酸加苏氨酸混合物也具有抗性。突变体植株较原始类型稍矮小,巳正常结实。     

Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells

Embryonic stem (ES) cell lines represent a population of undifferentiated pluripotent cells capable of multilineage differentiation in vitro. Although very useful for studying developmental processes, human ES cell lines have also been suggested as a potential and unlimited source for cellular transplantation and the treatment of human disease. The proteomic basis of embryonic stemness (pluripotentiality and multilineage differentiation) and the transitions that lead to specific cell lineages however, remain to be defined. As an important first step in defining these processes, we have performed a proteomic analysis of undifferentiated mouse R1 ES cell lines using pH 3-10, 4-7 and 6-11 two-dimensional electrophoresis gels, matrix-assisted laser desorption/ionization and tandem mass spectrometry. Of the 700 gel spots analyzed, 241 distinct protein species were identified corresponding to 218 unique proteins, with a significant proportion functionally related to protein expression.     

Two-dimensional gel electrophoresis as tool for proteomics studies in combination with protein identification by mass spectrometry

The proteome analysis by 2-DE is one of the most potent methods of analyzing the complete proteome of cells, cell lines, organs and tissues in proteomics studies. It allows a fast overview of changes in cell processes by analysis of the entire protein extracts in any biological and medical research projects. New instrumentation and advanced technologies provide proteomics studies in a wide variety of biological and biomedical questions. Proteomics work is being applied to study antibiotics-resistant strains and human tissues of various brain, lung, and heart diseases. It cumulated in the identification of antigens for the design of new vaccines. These advances in proteomics have been possible through the development of advanced high-resolution 2-DE systems allowing resolution of up to 10 000 protein spots of entire cell lysates in combination with protein identification by new highly sensitive mass spectrometric techniques. The present technological achievements are suited for a high throughput screening of different cell situations. Proteomics may be used to investigate the health effects of radiation and electromagnetic field to clarify possible dangerous alterations in human beings.     

Comparative proteomics using 2-D gel electrophoresis and mass spectrometry as tools to dissect stimulons and regulons in bacteria with sequenced or partially sequenced genomes

We propose two-dimensional gel electrophoresis (2-DE) and mass spectrometry to define the protein components of regulons and stimulons in bacteria, including those organisms where genome sequencing is still in progress. The basic 2-DE protocol allows high resolution and reproducibility and enables the direct comparison of hundreds or even thousands of proteins simultaneously. To identify proteins that comprise stimulons and regulons, peptide mass fingerprint (PMF) with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF-MS) analysis is the first option and, if results from this tool are insufficient, complementary data obtained with electrospray ionization tandem-MS (ESI-MS/MS) may permit successful protein identification. ESI-MS/MS and MALDI-TOF-MS provide complementary data sets, and so a more comprehensive coverage of a proteome can be obtained using both techniques with the same sample, especially when few sequenced proteins of a particular organism exist or genome sequencing is still in progress.     

Proteomic analysis of melanoma-derived exosomes by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry

Exosomes are 40-100 nm vesicles released by numerous cell types and are thought to have a variety of roles depending on their origin. Exosomes derived from antigen presenting cells have been shown to be capable of initiating immune responses in vivo and eradicating established tumours in murine models. Tumour-derived exosomes can be utilised as a source of tumour antigen for cross-priming to T-cells and are thus of interest for use in anti-tumour immunotherapy. Further exploration into the protein composition of exosomes may increase our understanding of their potential roles in vivo and this study has examined the proteome of exosomes purified from cell supernatants of the melanoma cell lines MeWo and SK-MEL-28. The vesicular nature and size (30-100 nm) of the purified exosomes was confirmed by electron microscopy and sucrose density gradient centrifugation. Western blotting demonstrated the absence of calnexin and cytochrome c, verifying the purity of the exosome preparations, as well as enrichment of MHC class I and the tumour-associated antigens Mart-1 and Mel-CAM. The two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) protein profiles of exosomes from the two cell lines were highly comparable and strikingly different from the profiles of the total cell lysates. Mass spectrometric sequencing identified proteins present in 49 protein spots in the exosome lysates. Several of these have been identified previously in exosomes but some are novel, including p120 catenin, radixin, and immunoglobulin superfamily member 8 (PGRL). Proteins present in whole-cell lysates that were significantly reduced or excluded from exosomes were also identified and included several mitochondrial and lysosomal proteins, again confirming the proposed endosomal origin of exosomes. This study presents a starting point for future more in-depth protein studies of tumour-derived exosomes which will aid the understanding of their biogenesis and targeting for use in anti-tumour immunotherapy protocols.     

Extensive analysis of the human platelet proteome by two-dimensional gel electrophoresis and mass spectrometry

Platelets play a key role in the control of bleeding and wound healing, contributing to the formation of vascular plugs. Under pathologic circumstances, they are involved in thrombotic disorders, including heart disease. Since platelets do not have a nucleus, proteomics offers a powerful alternative approach to provide data on protein expression in these cells, helping to address their biology. In this publication we extend the previously reported analysis of the pI 4-5 region of the human platelet proteome to the pI 5-11 region. By using narrow pI range two-dimensional electrophoresis (2-DE) for protein separation followed by high-throughput tandem mass spectrometry (MS/MS) for protein identification, we were able to identify 760 protein features, corresponding to 311 different genes, resulting in the annotation of 54% of the pI 5-11 range 2-DE proteome map. We evaluated the physicochemical properties and functions of the identified platelet proteome. Importantly, the main group of proteins identified is involved in intracellular signalling and regulation of the cytoskeleton. In addition, 11 hypothetical proteins are reported. In conclusion, this study provides a unique inventory of the platelet proteome, contributing to our understanding of platelet function and building the basis for the identification of new drug targets.     

Two-dimensional gel electrophoresis image registration using block-matching techniques and deformation models

Block-matching techniques have been widely used in the task of estimating displacement in medical images, and they represent the best approach in scenes with deformable structures such as tissues, fluids, and gels. In this article, a new iterative block-matching technique—based on successive deformation, search, fitting, filtering, and interpolation stages—is proposed to measure elastic displacements in two-dimensional polyacrylamide gel electrophoresis (2D–PAGE) images. The proposed technique uses different deformation models in the task of correlating proteins in real 2D electrophoresis gel images, obtaining an accuracy of 96.6% and improving the results obtained with other techniques. This technique represents a general solution, being easy to adapt to different 2D deformable cases and providing an experimental reference for block-matching algorithms.     

Identification of specific proteins from seed embryos by two-dimensional gel electrophoresis for the discrimination between indica and japonica rice

Summary Proteins extracted from seed embryos of 29 different cultivated rice (Oryza sativa L.) and one wild rice (O. rufipogon Griff.) were compared by two-dimensional gel electrophoresis analysis. Among more than 300 protein spots on the gel we found some interesting variations in ten spots which were individually designated as proteins A-J. Protein E was observed in all indica cultivars but was not found in those of the subspecies japonica. In contrast, protein F was only detected in japonica cultivars. Protein A existed in all japonica cultivars but, with the exception of IR-36, could not be found in other indica cultivars. Therefore, proteins A, E and F can be used as markers for the identification of indica and japonica. Some so-called Javanica cultivars showed the characteristics of japonica subspecies with regard to proteins A and F, while one other cultivar of Javanica expressed a type intermediate between indica and japonica interms of proteins A and E. One feature discriminating between Javanica and japonica cultivars was found in the D, G, and J proteins which were expressed strongly in Javanica cultivars but were scarcely expressed in those of japonica. Expression of subspecies-specific proteins E and F in f₁ hybrids was also investigated.     

Sub-proteome differential display: single gel comparison by 2D electrophoresis and mass spectrometry

Two-dimensional (2D) gel electrophoresis and mass spectrometry (MS) have been used in comparative proteomics but inherent problems of the 2D electrophoresis technique lead to difficulties when comparing two samples. We describe a method (sub-proteome differential display) for comparing the proteins from two sources simultaneously. Proteins from one source are mixed with radiolabelled proteins from a second source in a ratio of 100:1. These combined proteomes are fractionated simultaneously using column chromatographic methods, followed by analysis of the pre-fractionated proteomes (designated sub-proteomes) using 2D gel electrophoresis. Silver staining and (35)S autoradiography of a single gel allows precise discrimination between members of each sub-proteome, using commonly available computer software. This is followed by MS identification of individual proteins. We have demonstrated the utility of the technology by identifying the product of a transfected gene and several proteins expressed differentially between two renal carcinoma proteomes. The procedure has the capacity to enrich proteins prior to 2D electrophoresis and provides a simple, inexpensive approach to compare proteomes. The single gel approach eliminates differences that might arise if separate proteome fractionations or 2D gels are employed.     

Separation and identification of soybean leaf proteins by two-dimensional gel electrophoresis and mass spectrometry

To establish a proteomic reference map for soybean leaves, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 260 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS. Fifty-three of these protein spots were identified by searching NCBInr and SwissProt databases using the Mascot search engine. Sixty-seven spots that were not identified by MALDI-TOF-MS analysis were analyzed with liquid chromatography tandem mass spectrometry (LC-MS/MS), and 66 of these spots were identified by searching against the NCBInr, SwissProt and expressed sequence tag (EST) databases. We have identified a total of 71 unique proteins. The majority of the identified leaf proteins are involved in energy metabolism. The results indicate that 2D-PAGE, combined with MALDI-TOF-MS and LC-MS/MS, is a sensitive and powerful technique for separation and identification of soybean leaf proteins. A summary of the identified proteins and their putative functions is discussed.