基于Bioperl的基因序列获取的程序设计与实现

Bioperl在序列操作和数据库的远程获取方面有独特的优势。为了从Genbank获取大量硫酸盐还原菌的16S rRNA基因序列,进一步研究硫酸盐还原菌的分子进化及系统发育规律,该文基于bioperl设计了远程获取大量基因序列的程序,并成功地实现了硫酸盐还原菌的16S rRNA基因序列的批量获取。该程序小巧灵活方便快捷,perl语言强大的字符串操作和模式匹配功能使程序能实现不同类型基因序列的远程获取,具有很好的通用性和实用性。     

水稻抗逆相关基因的分子进化分析

植物在进化过程中为了适应外界环境,已经具有一套完整的抵抗外界特殊环境的调控系统。但是,关于水稻抗逆相关基因的分子进化方面的研究还未见报道。文章通过Plant Tolerance Gene Database数据库,获得22个水稻抗逆相关基因。利用比较基因组学和生物信息学方法对水稻抗逆相关基因的进化动态进行研究,结果表明水稻抗逆相关基因在低等植物中比较保守;随着植物的不断进化和生存环境的改变,其基因数量也随之增加。具有相似抗性功能的基因往往具有相似的基因结构和基序(motif)结构。文章还发现4个保守motif 的存在：HRDXK、DXXSXG、LLPR和GXGXXG(X代表任意氨基酸)。在GSK1、RAN2抗逆基因中发现了3个特有的motif结构：GSK1特有的P-rich motif,RAN2特有的G-rich motif和E-rich motif。推测这些保守的motif结构与基因的抗逆功能密切相关。进化速率分析结果表明,尽管植物抗逆性相关基因在进化过程中受到较强的纯化选择作用,但是仍然有50%的抗逆性相关基因存在正选择位点。这些正选择位点的存在有可能为基因适应外界环境变化提供了重要的物质基础。     

含几丁质酶基因的双价防卫基因在植物抗逆基因工程中的应用

几丁质酶是一类以几丁质为底物的水解酶,是目前为止研究得最为深入的一类病程相关蛋白(PRP/PRs),在植物抗逆基因工程中有广泛应用。研究表明,将几丁质酶基因与同它起协同作用的其它PRs基因一起转入植物,会获得比转单一几丁质酶基因更为理想的抗逆效果。综述了近年来含几丁质酶的双价防卫基因在植物抗逆基因工程中的应用研究进展。     

棉花抗逆相关基因GhDr1的克隆及生物信息学分析

通过TAIL-PCR的方法从棉花中克隆到未知功能的新基因GhDr1,生物信息学分析结果表明,GhDr1的预测蛋白含有酪氨酸激酶和蛋白酶C磷酸化位点、潜在的锌指类功能模块、MAPK磷酸化位点及MAPK相互作用识别位点;与GhDr1同源基因位于同一基因簇的基因多为参与逆境信号转导的蛋白。推测GhDr1基因可能在逆境信号转导途径的磷酸化级联反应中被调节,参与棉花逆境应答的生理过程。     

基于小麦种子发芽逆境抗逆指数的种子活力评价

以16个小麦品种的种子为材料,通过标准发芽、逆境发芽和田间出苗试验,测定不同基因型小麦品种的种子活力,以不同发芽条件下种子活力指数的抗逆指数和田间出苗率作为衡量抗逆性的指标,利用主成分分析、聚类分析对种子活力进行综合评价.结果表明: 干旱胁迫、人工老化和冷浸胁迫3种逆境对种子活力都有一定的影响.人工老化抗逆指数和冷浸胁迫抗逆指数与田间出苗率呈显著正相关,干旱胁迫抗逆指数与田间出苗率的相关性不显著.通过主成分分析和聚类分析将16个小麦品种划分为3类、豫农949、豫麦49-198、鲁原502、郑育麦9987、石麦21、山农23号、石新828为高活力品种;许农5号、豫农982、唐麦8号、济麦20、济麦22、济南17号、山农20为中活力品种;长4738和轮选061属低活力品种.     

植物抗逆诱变育种技术研究进展

随着分子生物学技术的飞速发展,通过基因工程方法可以更快更好地获得农作物抗逆新品种,其首要任务是通过分离相应的表型改变的突变体来鉴定、克隆在胁迫条件下表达模式发生改变的基因。主要介绍几种常用的及最新的突变体诱变和筛选技术,并分析每种技术的优缺点。     

基于省级平台的远程医疗系统设计

提出了一种基于省级平台的远程医疗系统的设计方案,主要从系统整体架构设计、网络结构设计、功能规划以及系统的业务流程设计几个方面进行了详细分析。通过建立省级远程医疗服务平台,可完成省内各医院之间远程医疗服务的统一调度和费用结算,各医院所建立的远程医疗业务平台完成医院间的各种远程医疗服务,系统可实现省内其他医院和省外医院的无缝接入。     

植物果聚糖的代谢途径及其在植物抗逆中的功能研究进展

植物果聚糖是一类重要的碳水化合物和渗透调节物质,可以提高植物的抗逆性。目前对植物果聚糖代谢酶基因的研究较多,主要包括相关基因的克隆、表达和利用基因工程技术将果聚糖相关代谢基因转入植物中。该文主要介绍了果聚糖的分布、种类、代谢途径及相关基因的克隆和表达,重点阐述了果聚糖在植物抗逆中的作用及其分子生物学研究进展。     

抗逆蛋白查询系统的初步建立

运用生物信息学的手段从NCBI获得不同的植物抗逆基因,对基因的名称,功能,该基因的数据来源,及相关文献作整理,初步建立了抗逆蛋白查询系统。此系统与很多生物软件兼容,利用这些软件可方便的在该数据库中进行序列比对、抗逆蛋白同源性的比较、未知蛋白功能预测、绘制分子树等多项功能。     

Two haplotypes of resistance gene analogs have been conserved during evolution at the leaf rust resistance locus Lr10in wild and cultivated wheat

The isolation of genes of agronomic interest such as disease resistance genes is a central issue in wheat research. A good knowledge of the organization and evolution of the genome can greatly help in defining the best strategies for efficient gene isolation. So far, very few wheat disease resistance loci have been studied at the molecular level and little is known about their evolution during polyploidization and domestication. In this study, we have analyzed the haplotype structure at loci orthologous to the leaf rust resistance locus Lr10 in hexaploid wheat which spans 350 kb in diploid wheat. Two haplotypes (H1, H2) were defined by the presence (H1) or the absence (H2) of two different resistance gene analogs (rga1, rga2) at this locus on chromosome 1AS. Both haplotypes were found in a collection of 113 wild and cultivated diploid and polyploid wheat lines and they do not reflect phylogenetic relationships. This indicates an ancient origin for this disease resistance locus and the independent conservation of the two haplotypes throughout the evolution of the wheat genome. Finally, the coding regions of the H1 haplotype RGAs are extremely conserved in all the species. This suggests a selective pressure for maintaining the structural and functional configuration of this haplotype in wheat. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0051-9. Electronic Publication     

A potato hypersensitive resistance gene against potato virus X maps to a resistance gene cluster on chromosome 5

 The dominant Nb gene of potato confers strain-specific hypersensitive resistance against potato virus X (PVX). A population segregating for Nb was screened for resistance by inoculating with PVX strain CP2, which is sensitive to Nb. Through a combination of bulked segregant analysis and selective restriction fragment amplification, several amplified fragment length polymorphism (AFLP) markers linked to Nb were identified. These were cloned and converted into dominant cleaved amplified polymorphic sequence (CAPS) markers. The segregation of these markers in a Lycopersicon esculentum×L. pennellii mapping population suggested that Nb is located on chromosome 5. This was confirmed by examining resistant and susceptible potato individuals with several tomato and potato chromosome-5-specific markers. Nb maps to a region of chromosome 5 where several other resistance genes– including R1, a resistance gene against Phytophthora infestans, Gpa, a locus that confers resistance against Globodera pallida, and Rx2, a gene that confers extreme resistance against PVX–have previously been identified. Received: 2 January 1997/Accepted: 7 February 1997     

粪肠球菌对泰利霉素药物敏感性与耐药基因erm的分布

目的 了解粪肠球菌对泰利霉素和其他常用抗菌药物的耐药性,以及泰利霉素耐药与红霉素耐药相关基因ermA、ermB、ermC之间的关系。方法 对本院2010‒2016年从各种临床标本收集鉴定的320株粪肠球菌,用微量肉汤稀释法测定这些菌株对泰利霉素及8种临床常用抗菌药物的最小抑菌浓度,并用PCR法检测耐药基因ermA、ermB、ermC的分布。结果 320株粪肠球菌对泰利霉素中介耐药26株,耐药138株,耐药率达51.3%;对红霉素耐药率达95.6%,泰利霉素抗粪肠球菌效果优于红霉素。对利奈唑胺、万古霉素、呋喃妥因和氨苄西林耐药率分别为15.6%、0.6%、2.2%和0.6%。共10株（3.1%）携带ermA基因,207株（64.7%）携带ermB基因,对泰利霉素中介组中有23株ermB基因阳性,耐药组有131株ermB基因阳性,仅1株（0.3%）ermC基因阳性,该菌同时携带ermB基因。结论 粪肠球菌对泰利霉素已有较高耐药率。粪肠球菌对泰利霉素MIC值改变与ermB基因密切相关,与ermA、ermC基因无明显相关性。     

A molecular phylogeny of bryophytes based on nucleotide sequences of the mitochondrialnad5 gene

In contrast to animals, the slowly evolving mitochondrial nucleotide sequences of plants appear well suited to investigate phylogenetic relations between old taxonomic groups. Analysis ofnad5 gene sequences in 47 bryophytes, the living representatives of very early land plants, confirm this assessment. Statistically reliable phylogenetic trees are obtained with different mathematical approaches. A group I intron sequence conserved in thenad5 gene of all 30 mosses and 15 liverworts investigated supports a sister group relationship of the two classes. The intron sequence adds phylogenetic information for fine resolution on top of the conserved exon sequences down to the level of classically defined orders or families, respectively. This intron is not present in the hornwortsAnthoceros husnotii andA. punctatus. The results allow statements on diverging taxonomic interpretations and support the monophyly of the liverworts, mosses, Jungermanniidae, Marchantiidae and Bryidae, and allow recognition of subclasses like Hypnanae and Dicrananae. Among the mosses, the derived orders (subclass Bryidae) are confidently set apart from the Sphagnales, Andreaeales, Polytrichales and Tetraphidales with Buxbaumiales occupying a mediating position. Among the liverworts, full support is found for the classic separation of simple (jungermanniid) and complex thalloid (marchantiid) species with a strikingly low mitochondrial sequence divergence among the latter.     

Isolation of a full-length CC–NBS–LRR resistance gene analog candidate from sugar pine showing low nucleotide diversity

The nucleotide-binding-site and leucine-rich-repeat (NBS–LRR) class of R proteins is abundant and widely distributed in plants. By using degenerate primers designed on the NBS domain in lettuce, we amplified sequences in sugar pine that shared sequence identity with many of the NBS–LRR class resistance genes catalogued in GenBank. The polymerase chain reaction products were used to probe a cDNA library constructed from needle tissue of sugar pine seedlings. A full-length cDNA was obtained that demonstrated high predicted amino acid sequence similarity to the coiled coil (CC)–NBS–LRR subclass of NBS–LRR resistance proteins in GenBank. Sequence analyses of this gene in megagametophytes from two sugar pine trees segregating for the hypersensitive response to white pine blister rust revealed zero nucleotide variation. Moreover, there was no variation found in 24 unrelated sugar pine trees except for three single-nucleotide polymorphisms located in the 3′ untranslated region. Compared to other genes sequenced in Pinaceae, such a low level of sequence variation in unrelated individuals is unusual. Although, numerous studies have reported that plant R genes are under diversifying selection for specificity to evolving pathogens, the resistance gene analog discussed here appears to be under intense purifying selection.An erratum to this article can be found at     

基于线粒体基因cyt b的鹟亚科部分鸟类系统发育

采用分子系统学方法对鹟亚科(Muscicapinae)6属31种鸟类的cytb基因序列992bp进行系统发生分析。以荒漠伯劳(Lanius isabellinus)和发冠卷尾(Dicrurus hottentottus)为外群,采用贝叶斯法(Bayesian,BI)、最大似然法(Maximum-likelihood,ML)和最大简约法(Maximumparsimony,MP)分别构建鹟亚科的系统发育树。结果支持:寿带属(Terpsiphone)、扇尾鹟属(Rhipidura)与方尾鹟属(Culicicapa)可从鹟亚科中移出,其中寿带属归入王鹟科(Monarchidae),扇尾鹟属与方尾属归入扇尾鹟科(Rhipiduridae);鹟属(Muscicapa)、仙鹟属(Niltava)为单系发生,并聚为姐妹群,亲缘关系较近;姬鹟属(Ficedula)并非单系发生,白眉姬鹟(Ficedulazanthopygia)在3种系统发生树中的位置差别较大,研究结果未能确定其分类地位;铜蓝(Muscicapa thalassina)与白腹蓝(Cyanoptila cyanomelana)亲缘关系较近,前者应从属中移出,后者应从姬属移出,共同归入仙属或列为仙属的姐妹属。上述结论解决了亚科部分有争议属、种间的进化关系,为亚科分类系统提供了DNA水平证据。     

Cloning and characterization of receptor kinase class disease resistance gene candidates in Citrus

The rice gene Xa21 represents a unique class of plant disease resistance (R) genes with distinct protein structure and broad-spectrum specificity; few sequences or genes of this class have been cloned and characterized in other plant species. Degenerate primers were designed from the conserved motifs in the kinase domains of Xa21 and tomato Pto, and used in PCR amplification to identify this class of resistance gene candidate (RGC) sequences from citrus for future evaluation of possible association with citrus canker resistance. Twenty-nine RGC sequences highly similar to the kinase domain of Xa21 (55%–60% amino-acid identity) were cloned and characterized. To facilitate recovery of full-length gene structures and to overcome RGC mapping limitations, large-insert genomic clones (BACs) were identified, fingerprinted and assembled into contigs. Southern hybridization revealed the presence of 1–3 copies of receptor-like kinase sequences (i.e., clustering) in each BAC. Some of these sequences were sampled by PCR amplification and direct sequencing. Twenty-three sequences were thus obtained and classified into five groups and eight subgroups, which indicates the possibility of enhancing RGC sequence diversity from BACs. A primer-walking strategy was employed to derive full-length gene structures from two BAC clones; both sequences 17o6RLK and 26m19RLK contained all the features of the rice Xa21 protein, including a signal peptide, the same number of leucine-rich-repeats, and transmembrane and kinase domains. These results demonstrate that PCR amplification with appropriately designed degenerate primers is an efficient approach for cloning receptor-like kinase class RGCs. Utilization of BAC clones can facilitate this approach in multiple ways by improving sequence diversity, providing full-length genes, and assisting in understanding gene structures and distribution.Communicated by P. Langridge     

Characterization of an NBS-LRR resistance gene homologue from soybean

Conserved motifs such as the nucleotide-binding site (NBS) were found in many characterized plant disease resistance genes. Based on the NBS domain, resistance gene analogs have been isolated in our previous study and were used as probes to screen a soybean (Glycine max) cDNA library. A full-length cDNA, KR4, was isolated by screening the library and rapid amplification of cDNA ends method. Sequence analysis revealed that the cDNA was 3818 bp in length and the open reading frame coded for a polypeptide of 1211 amino acids with an NBS and five leucine-rich repeats domains, which were identified by Pfam protein analysis. Sequence alignment showed that KR4 was similar to 12 protein of tomato. Southern analysis indicated that the KR4 gene had low copies in soybean genome and it was mapped on the molecular linkage group E. Its expression was also investigated and it was found that KR4 was induced by exogenous salicylic acid and responded upon infection of soybean mosaic virus strain N3.     

Isolation and linkage mapping of NBS-LRR resistance gene analogs in red raspberry (<Emphasis Type="Italic">Rubus idaeus</Emphasis> L.) and classification among 270 Rosaceae NBS-LRR genes

Plant R genes confer resistance to pathogens in a gene-for-gene mode. Seventy-five putative resistance gene analogs (RGAs) containing conserved domains were cloned from Rubus idaeus L. cv. ‘Latham’ using degenerate primers based on RGAs identified in Rosaceae species. The sequences were compared to 195 RGA sequences identified from five Rosaceae family genera. Multiple sequence alignments showed high similarity at multiple nucleotide-binding site (NBS) motifs with homology to Drosophila Toll and mammalian interleukin-1 receptor (TIR) and non-TIR RNBSA-A motifs. The TIR sequences clustered separately from the non-TIR sequences with a bootstrap value of 76%. There were 11 clusters each of TIR and non-TIR type sequences of multiple genera with bootstrap values of more than 50%, including nine with values of more than 75% and seven of more than 90%. Polymorphic sequence characterized amplified region and cleaved amplified polymorphic sequence markers were developed for nine Rubus RGA sequences with eight placed on a red raspberry genetic linkage map. Phylogenetic analysis indicated four of the mapped sequences share sequence similarity to groupTIR I, while three others were spread in non-TIR groups. Of the 75 Rubus RGA sequences analyzed, members were placed in five TIR groups and six non-TIR groups. These group classifications closely matched those in 12 of 13 studies from which these sequences were derived. The analysis of related DNA sequences within plant families elucidates the evolutionary relationship and process involved in pest resistance development in plants. This information will aid in the understanding of R genes and their proliferation within plant genomes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.