地花菌属的研究概况和进展

地花菌属（Albatrellus Gray）是多孔菌类中具有突出特征和特殊地位的一个属,有极高的系统学和分类学研究价值,但专门的针对性研究很少。综述了地花菌属在分类学、系统学、牛态习性、经济价值、保护生物学等方面的研究概况和进展,并对该属的深入研究提出了针对性的建议。     

地花菌属的研究概况和进展*

地花菌属(AlbatrellusGray)是多孔菌类中具有突出特征和特殊地位的一个属,有极高的系统学和分类学研究价值,但专门的针对性研究很少。综述了地花菌属在分类学、系统学、生态习性、经济价值、保护生物学等方面的研究概况和进展,并对该属的深入研究提出了针对性的建议。     

植物内生菌的功能研究进展

植物内生菌是一类种类丰富、生物学功能多样的微生物。由于它们与宿主植物长期进化,有了一些特殊的生物学功能。综述了内生菌的系列生物学功能,包括产生活性物质、固氮功能、促进植物生长、增强宿主植物抗性、他感作用、作为外源基因载体等,并总结了内生菌研究中要注意的方面。     

耐辐射球菌辐射耐受机制的研究进展

耐辐射球菌(Deinococcus radiodurans,Dr)是迄今为止地球上发现的最具辐射抗性的生物之一,对紫外线、干旱和诱变剂等损伤因子均表现出极强的抗性,备受世界各国科学家的广泛关注。目前关于其抗辐射机理已有大量的文献报道。根据国内外最新的研究成果,从DNA损伤修复机制、抗氧化防御系统、特殊的生存方式及细胞净化系统等方面,对耐辐射球菌辐射抗性机理的研究进行了简单的概述,并对未来Dr耐辐射机制的研究趋势进行了展望,以期为进一步研究该菌的辐射耐受机制奠定基础。     

戈登链球菌的生物学特性及在黏膜疫苗的应用

戈登氏链球菌是一种非致病性革兰氏阳性黏膜共生菌, 参与组成人类口腔正常菌群。它具有特殊的生物学特性, 非常适合作为黏膜疫苗的载体。了解戈登氏链球菌的生物学特性, 常用表达体系及该菌在黏膜疫苗的应用情况, 将为其黏膜疫苗的进一步研制提供重要参考。     

戈登链球菌的生物学特性及在黏膜疫苗的应用

戈登氏链球菌是一种非致病性革兰氏阳性黏膜共生菌,参与组成人类口腔正常菌群.它具有特殊的生物学特性,非常适合作为黏膜疫苗的载体.了解戈登氏链球菌的生物学特性,常用表达体系及该菌在黏膜疫苗的应用情况,将为其黏膜疫苗的进一步研制提供重要参考.     

海洋交替假单胞菌活性物质的研究

海洋交替假单胞菌是一个新鉴定的海洋细菌,其次生代谢产物具有特殊的化学结构和广泛的生物活性而受到研究者的广泛关注.本文以海洋交替假单胞菌为探讨对象,综述海洋交替假单胞菌的生物学特性及其产生的生物活性代谢产物的研究进展,最后对该菌的发展前景进行展望.     

一种新型相干辐射--THz辐射在生物学中的应用

脉冲THz辐射是一种新型的远红外相干辐射源,近年来在不同的研究领域得到了广泛的应用。本文简要介绍THz辐射产生、探测的基本原理和方法;THz辐射的基本性质和它在生物学研究中应用的物理基础;对生物体系进行时域光谱分析和成像研究所取得的成果和最新进展,以及对该领域研究前景的展望。     

微波介导的载体快速转化及克隆筛选方法

应用微波辐射进行载体快速转化及重组体鉴定。经选择辐射转化条件,表明在低渗钙离子(0.05mol/L或0.1mol/L)条件下,150W、45s的辐射可得到理想的转化率。采用微波碎菌抽提质粒方法对重组体进行快速鉴定,不需特殊设备,省时、可靠。用该方法对肾综合征出血热病原汉坦病毒76-118株S片段基因进行克隆、转化和重组体鉴定试验,证实其具有简易、快速、高效等优点。     

γ射线对副溶血性弧菌辐射效应的PCR检测

目的:研究γ射线对副溶血性弧菌(Vibrio parahaemolyticus)的辐射效应。方法:采用0kGy~7.0kGy内不同剂量的60Co-γ对浓度为2.0×108CFU/mL的副溶血性弧菌进行辐射,通过菌落计数计算该菌的致死率与存活率,并采用菌液PCR和常规PCR间接检测DNA浓度研究其致死效应。结果:菌落计数表明,在0kGy~3.0kGy内,该菌致死率随辐射剂量增加而呈线性增长;3.0kGy以上可全部杀灭试验浓度的副溶血性弧菌。常规PCR和菌液PCR结果表明,PCR扩增条带亮度都随着辐射剂量的增大而增强。常规PCR中,辐射剂量3.0kGy以上,电泳条带的亮度明显增加。结论:γ射线辐射剂量与存活副溶血性弧菌数、DNA的释放量都有明显的剂量-反应关系,辐射致死的主要原因是由射线对菌体细胞膜造成损伤、DNA外流造成的。     

Mutation in recR gene of Deinococcus radiodurans and possible involvement of its product in the repair of DNA interstrand cross-links

We previously reported that some Deinococcus radiodurans mutants are sensitive to DNA interstrand cross-linking agents but resistant to UV and gamma-rays. We isolated DNA fragments from a D. radiodurans genomic library which complemented the mitomycin C sensitivity of one of these mutants. One 3.2kb-long fragment contains an open reading frame of approximately 700bp and the deduced amino acid sequence is very homologous to other prokaryotic RecR proteins. This open reading frame in the mitomycin C-sensitive mutant strain contains a frame shift mutation at its carboxyl terminal region. These data suggest that RecR protein plays an important role in the resistance to interstrand cross-links in this bacterium.     

PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation

The extraordinary radiation resistance of Deinococcus radiodurans results from the efficient capacity of the bacterium to repair DNA double-strand breaks. By analysing the DNA damage repair-deficient mutant, KH311, a unique radiation-inducible gene (designated pprA) responsible for loss of radiation resistance was identified. Investigations in vitro showed that the gene product of pprA (PprA) preferentially bound to double-stranded DNA carrying strand breaks, inhibited Escherichia coli exonuclease III activity, and stimulated the DNA end-joining reaction catalysed by ATP-dependent and NAD-dependent DNA ligases. These results suggest that D. radiodurans has a radiation-induced non-homologous end-joining repair mechanism in which PprA plays a critical role.     

耐辐射球菌转录因子DdrO 的基因克隆与生物信息学分析

目的:克隆耐辐射球菌ddrO基因,并对其进行生物信息学分析,预测其功能。方法:根据耐辐射球菌ddrO基因序列,由Primer Premier 5设计一对引物,以提取的耐辐射球菌基因组为模板,PCR扩增获得耐辐射球菌ddrO基因,序列测定并利用生物信息学软件对ddrO基因的理化性质、高级结构及生物学功能等进行分析与预测。结果:成功获得了ddrO基因。生物信息学分析发现,ddrO基因核苷酸序列长度为396bp,编码一个131aa组成的相对分子质量为14.993kD的预测的DdrO转录因子。核酸同源性搜索及比较分析仅在与耐辐射球菌同属的Deinococcus geothermalis和Deinococcus deserti中发现高度相似的序列;蛋白同源性搜索发现一些与DdrO显著同源的蛋白,如Deide₂0570（95%）,Dgeo₀336（90%）,Deide₃p02170（82%）等;结构域分析发现DdrO含有HTH（helix-turn-helix）DNA结合结构域。结论:根据生物信息学结果预测DdrO蛋白可能具有转录调控作用,参与DNA修复和复制,在耐辐射球菌的DNA损伤修复过程中发挥一定作用。     

Radiation resistance: the fragments that remain

The complete genome sequence of the bacterium, Deinococcus radiodurans R1 has been released. This achievement will greatly aid efforts to study this organism, but analysis of the sequence reveals little that helps explain the extreme ionizing radiation resistance of this species.     

Protein recycling is a major component of post-irradiation recovery in Deinococcus radiodurans strain R1

Exposure to 6kGy dose of (60)Co gamma-rays resulted in immediate growth arrest, followed by complete recovery of Deinococcus radiodurans strain R1 cells. Selective degradation and resynthesis of several predicted highly expressed proteins (including major chaperones, key TCA cycle enzymes, and few stress proteins) and several hypothetical proteins marked the lag period, preceding resumption of growth. A major exercise in protein recycling appears to be an integral component of post-irradiation recovery in D. radiodurans and complements the extensive DNA repair, characteristic of this extremely radioresistant bacterium.     

Analysis of interaction between DNA and Deinococcus radiodurans PprA protein by atomic force microscopy

A DNA repair-promoting protein, PprA, was isolated from a radiation resistant bacterium, Deinococcus radiodurans [I. Narumi, K. Sato, S. Cui, T. Funayama, S. Kitayama, H. Watanabe, PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation, Mol. Microbiol. 54 (2004) 278-285]. Despite several studies, however, the function of PprA is not still clear. We used atomic force microscopy (AFM) to elucidate the role of this protein in the DNA repair pathway. In the present study, interaction between the linear DNA and PprA protein was imaged and analyzed by AFM without any fixation or staining. Though both end-bound and internally bound PprA was observed, the affinity of the end-bound protein was greater considering the proportion of features of binding analyzed by AFM. In some conditions, looping forms of the DNA-PprA complex were observed. Gel filtration high performance liquid chromatography (HPLC) was also conducted to estimate the molecular weight of this protein. The result of the HPLC analysis suggested that PprA formed multimers in buffer solution without DNA.     

耐辐射球菌转录因子DdrO的基因克隆与生物信息学分析

目的：克隆耐辐射球菌ddrO基因,并对其进行生物信息学分析,预测其功能。方法：根据耐辐射球菌ddrO基因序列,由Primer Premier 5设计一对引物,以提取的耐辐射球菌基因组为模板,PCR扩增获得耐辐射球菌ddrO基因,序列测定并利用生物信息学软件对ddrO基因的理化性质、高级结构及生物学功能等进行分析与预测。结果：成功获得了ddrO基因。生物信息学分析发现,ddrO基因核苷酸序列长度为396bp,编码一个131aa组成的相对分子质量为14.993kD的预测的DdrO转录因子。核酸同源性搜索及比较分析仅在与耐辐射球菌同属的Deinococcus geothermalis和Deinococcus deserti中发现高度相似的序列;蛋白同源性搜索发现一些与DdrO显著同源的蛋白,如Deide_20570（95%）,Dgeo_0336（90%）,Deide_3p02170（82%）等;结构域分析发现DdrO含有HTH（helix-turn-helix）DNA结合结构域。结论：根据生物信息学结果预测DdrO蛋白可能具有转录调控作用,参与DNA修复和复制,在耐辐射球菌的DNA损伤修复过程中发挥一定作用。     

A comparative proteomic approach to better define Deinococcus nucleoid specificities

Compared to radiation-sensitive bacteria, the nucleoids of radiation-resistant Deinococcus species show a higher degree of compaction. Such a condensed nucleoid may contribute to the extreme radiation resistance of Deinococcus by limiting dispersion of radiation-induced DNA fragments. Architectural proteins may play a role in this high degree of nucleoid compaction, but comparative genomics revealed only a limited number of Deinococcus homologs of known nucleoid-associated proteins (NAPs) from other species such as Escherichia coli. A comparative proteomic approach was used to identify potentially novel proteins from isolated nucleoids of Deinococcus radiodurans and Deinococcus deserti. Proteins in nucleoid enriched fractions were identified and semi-quantified by shotgun proteomics. Based on normalized spectral counts, the histone-like DNA-binding protein HU appeared to be the most abundant among candidate NAPs from both micro-organisms. By immunofluorescence microscopy, D. radiodurans HU and both DNA gyrase subunits were shown to be distributed throughout the nucleoid structure and absent from the cytoplasm. Taken together, our results suggest that D. radiodurans and D. deserti bacteria contain a very low diversity of NAPs, with HU and DNA gyrase being the main proteins involved in the organization of the Deinococcus nucleoids.     

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.