Deletion-insertion differences between the genomes of Mycobacterium tuberculosis highly virulent strain HN878 and less virulent strain CDC1551

The modfied version of the method of subtracting hybridization for full-genome comparison of M. tuberculosis strain HN878, capable of inducing a nonpulmonary form of tuberculosis, with strain CDC1551 causing tuberculosis--with classical pulmonary symptoms. The clone library of differential fragments, responsible for differences between genome HN878 and genome CDC1551, was created. As the result of the structural analysis carried out in this study, the set of differential fragments was divided into. three main groups: new places of the integration of transposon IS6110; fragments resulting from the transformations of other repeating sequences of the genome; long unique nucleotide sequences, absent in genome CDC1551. Genome transformations may be a highly important factor of the modulation of the phenotypical properties of the pathogen, including those which jointly determined its virulence, and also served as valuable molecular genetic markers for diagnostic purposes.     

Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232

Background

Mycoplasma hyopneumoniae causes respiratory disease in swine and contributes to the porcine respiratory disease complex, a major disease problem in the swine industry. The M. hyopneumoniae strain 232 genome is one of the smallest and best annotated microbial genomes, containing only 728 annotated genes and 691 known proteins. Standard protein databases for mass spectrometry only allow for the identification of known and predicted proteins, which if incorrect can limit our understanding of the biological processes at work. Proteogenomic mapping is a methodology which allows the entire 6-frame genome translation of an organism to be used as a mass spectrometry database to help identify unknown proteins as well as correct and confirm existing annotations. This methodology will be employed to perform an in-depth analysis of the M. hyopneumoniae proteome.

Results

Proteomic analysis indicates 483 of 691 (70%) known M. hyopneumoniae strain 232 proteins are expressed under the culture conditions given in this study. Furthermore, 171 of 328 (52%) hypothetical proteins have been confirmed. Proteogenomic mapping resulted in the identification of previously unannotated genes gatC and rpmF and 5-prime extensions to genes mhp063, mhp073, and mhp451, all conserved and annotated in other M. hyopneumoniae strains and Mycoplasma species. Gene prediction with Prodigal, a prokaryotic gene predicting program, completely supports the new genomic coordinates calculated using proteogenomic mapping.

Conclusions

Proteogenomic mapping showed that the protein coding genes of the M. hyopneumoniae strain 232 identified in this study are well annotated. Only 1.8% of mapped peptides did not correspond to genes defined by the current genome annotation. This study also illustrates how proteogenomic mapping can be an important tool to help confirm, correct and append known gene models when using a genome sequence as search space for peptide mass spectra. Using a gene prediction program which scans for a wide variety of promoters can help ensure genes are accurately predicted or not missed completely. Furthermore, protein extraction using differential detergent fractionation effectively increases the number of membrane and cytoplasmic proteins identifiable my mass spectrometry.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-576) contains supplementary material, which is available to authorized users.     

Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M

The genus Brucella consists of bacterial pathogens that cause brucellosis, a major zoonotic disease characterized by undulant fever and neurological disorders in humans. Among the different Brucella species, Brucella melitensis is considered the most virulent. Despite successful use in animals, the vaccine strains remain infectious for humans. To understand the mechanism of virulence in B. melitensis, the proteome of vaccine strain Rev 1 was analyzed by two-dimensional gel electrophoresis and compared to that of virulent strain 16M. The two strains were grown under identical laboratory conditions. Computer-assisted analysis of the two B. melitensis proteomes revealed proteins expressed in either 16M or Rev 1, as well as up- or down-regulation of proteins specific for each of these strains. These proteins were identified by peptide mass fingerprinting. It was found that certain metabolic pathways may be deregulated in Rev 1. Expression of an immunogenic 31-kDa outer membrane protein, proteins utilized for iron acquisition, and those that play a role in sugar binding, lipid degradation, and amino acid binding was altered in Rev 1.     

O-antigen structure in a virulent strain of Aeromonas hydrophila

Abstract Lipopolysaccharide (LPS) was isolated from a strain of Aeromonas hydrophila which had displayed serological, bacteriophage attachment and virulence properties similar to those found in strains of Aeromonas salmonicida . The structure of the O-antigen was determined and had many points of similarity with that previously elucidated for the O-antigen of A. salmonicida . Methylation analysis, chromium trioxide oxidation and ¹H-n.m.r. were used to confirm that the repeating unit of the O-chain had the following structure:
     

Characterization with crossed immunoelectrophoresis of some antigens differentiating a virulent Candida albicans from its derived, avirulent strain

Antigenic differences between a wild-type virulent Candida albicans 4918 (wt) and its spontaneous avirulent mutant (m-10) were found with crossed immunoelectrophoresis. Yeast cell extracts as well as soluble protein and mannoprotein fractions obtained by affinity chromatography on concanavalin A (Con A) were analyzed. Sera from patients with candidiasis and antisera from rabbits infected with live wt cells and boosted with wt extracts or rabbits immunized with purified wt cell wall preparation were used as counter reactants. Qualitative differences in serum precipitins formed by patients with suspected or culture-proven candidiasis to polysaccharide antigens of wt and m-10 origin were observed. In comparison, except for a spike-formed precipitate detected only with the wt extract, the serum from infected rabbits precipitated the wt and m-10 cell wall polysaccharide antigens about equally. The same type of precipitate was also found with the Con A wt mannoprotein fractions but was again lacking with the m-10 mannoproteins. This precipitate, with extremely slow electromobility in the first dimension, may be related to some special immunodeterminant of the wt mannan molecule. No substantial differences in the precipitation patterns of the Con A wt and m-10 proteins were found when analyzed with patients' sera or rabbit anti-cell sera. However, using these protein fractions with anti-cell wall sera revealed a larger number of precipitates for the wt as opposed to the m-10 strain. The observed antigenic differences between the virulent- and the avirulent-derived strains seem to be mainly associated with cell wall determinants (components) and might be related to the greater adherence and infectivity of the wild strain.     

Evidence for recombination of live, attenuated immunodeficiency virus vaccine with challenge virus to a more virulent strain

Live, attenuated immunodeficiency virus vaccines, such as nef deletion mutants, are the most effective vaccines tested in the simian immunodeficiency virus (SIV) macaque model. In two independent studies designed to determine the breadth of protection induced by live, attenuated SIV vaccines, we noticed that three of the vaccinated macaques developed higher set point viral load levels than unvaccinated control monkeys. Two of these vaccinated monkeys developed AIDS, while the control monkeys infected in parallel remained asymptomatic. Concomitant with an increase in viral load, a recombinant of the vaccine virus and the challenge virus could be detected. Therefore, the emergence of more-virulent recombinants of live, attenuated immunodeficiency viruses and less-aggressive wild-type viruses seems to be an additional risk of live, attenuated immunodeficiency virus vaccines.     

Identification of a flavobacterium strain virulent against Giardia lamblia cysts

We have isolated from a Kentucky stream a bacterial strain capable of killing the cyst form of Giardia lamblia. This bacterium, designated Sun4, is a Gram-negative, aerobic rod which produces a yellow pigment, but not of the flexirubin-type. Although true gliding motility has not been observed in Sun4, this strain does exhibit a spreading colony morphology when grown on R2A agar. Strain Sun4 has been identified by 16S rRNA sequencing and phylogenetic analysis as belonging to the genus Flavobacterium, and is most closely related to Cytophaga sp. strain Type 0092 and associated Flavobacterium columnare strains. Lipid analysis also identified fatty acids characteristic of the Cytophaga–Flavobacterium group of bacteria. In culture, Sun4 is able to degrade casein and cellulose, but not chitin, gelatin, starch, or agar. Degradation of Giardia cysts by Sun4 appears to require direct cellular contact as neither cell-free extracts nor cells separated from the cysts by dialysis membranes showed any activity against cysts. Activity against Giardia cysts is rapid, with Sun4 killing over 90% of cysts within 48 h. Strain Sun4 requires elevated levels of Ca²⁺ for optimal growth and degradative activity against Giardia cysts. We propose that bacterial strains such as Sun4 could be used as biological control agents against Giardia cysts in drinking water treatment systems.     

Genomic analysis of a virulent and a less virulent strain of the entomopathogenic fungus Beauveria bassiana, using restriction fragment length polymorphisms.

The genomic DNA of two strains of the entomopathogenic fungus Beauveria bassiana, strain GK2016, a "wild type" (virulent), and strain GK2051, a less virulent mutant to grasshoppers, was digested with 12 restriction endonucleases. Gel electrophoresis conditions were established to show restriction fragment length patterns visually in the digested DNA stained with ethidium bromide. The less virulent mutant was generated by ultraviolet illumination of conidiospores at a 95% lethal dose. Both strains of the fungi were identical in morphology as well as in 16 of 22 API-ZYM kit enzyme assays. Differences in levels of total enzyme activity were observed for esterase, esterase-lipase, beta-galactosidase, chitinase, and protease. A Neurospora crassa beta-tubulin gene (heterologous gene) and two homologous DNA probes (pJK16 and pJK18) hybridized to several specific DNA bands in B. bassiana strain GK2016 but not in strain GK2051. Strain GK2051 gave different restriction fragment length pattern when compared with its parent strain. Taken together, the data show restriction fragment length differences between the genomic DNA of the two strains, including the loss of some DNA sequences from the mutant strain, which may be involved in pathogenicity. Finally, B. bassiana GK2016 contains a beta-tubulin gene with at least partial homology to that of N. crassa.     

Association of a new Wolbachia strain with, and its effects on, Leptopilina victoriae, a virulent wasp parasitic to Drosophila spp

Wolbachia bacteria are ubiquitous intracellular bacteria of arthropods. Often considered reproductive parasites, they can benefit certain host species. We describe a new Wolbachia strain from Leptopilina victoriae, a Drosophila wasp. The strain is closely related to Wolbachia from Culex sp. Located to the posterior poles of oocytes, it manipulates its host's reproduction by inducing a male development type of cytoplasmic incompatibility. We also report its diverse effects on the wasp's life history traits.     

Characterization of Bacillus anthracis typical virulent test strain 81/1

The results of the prolonged and many-sided study of B. anthracis strain 81/1 by different authors are presented. The cultural and morphological, biochemical, antigenic, molecular-genetic characteristics of this strain give grounds for regarding it as a typical test strain to be used for the determination of the vaccines immunogenicity, the effectiveness of antibiotics and immunomodulators.     

褐飞虱高毒力绿僵菌菌株的筛选

从田间褐飞虱Nilaparvata lugens (St?l)罹病虫体上新分离鉴定一株黄绿绿僵菌Mf82,将其与实验室保存的8株绿僵菌Metarhizium spp.一起,分别测定其对褐飞虱成虫毒力和几丁质酶活力,并用扫描电镜观察侵入昆虫表皮的过程和体表的形态变化,进而分析侵入能力与几丁质酶的相关性。结果表明：菌株Mf82累计校正死亡率和几丁质酶活力均最高,为82.1%和9.78U/mg,与其他菌株差异显著。同时,扫描电镜照片显示Mf82分生孢子既可以由褐飞虱体壁节间膜和凹陷处侵入,还可以从含几丁质较多的胸部背板侵入。比较9株绿僵菌菌株菌落生长速度、产孢初始时间、产孢量和萌发率显示,Mf82菌株具有生长速度快、产孢初始时间短、萌发率高和产孢量大等优点,可见筛选的Mf82菌株致病力强,在褐飞虱的微生物防治方面将有良好的应用前景。     

马立克氏病病毒超强毒感染鸡羽髓蛋白质组分析

【目的】羽毛是细胞游离马立克氏病病毒(Marek’s disease virus,MDV)释放的部位,为了解感染MDV后鸡羽中宿主基因表达的变化及对病毒感染的应答,进行了MDV感染鸡的羽髓蛋白质组学分析。【方法】1日龄无特定病原体(specific pathogen free,SPF)鸡人工感染MDV超强毒RB1B株(1000PFU),感染后21d采集鸡羽毛,提取羽髓蛋白,以17cm,pH5-8的IPG胶条进行二维电泳,以未感染病毒的SPF鸡羽髓蛋白为对照,使用PDQuest软件对二维电泳图谱进行差异蛋白分析,并选取部分差异斑点进行质谱鉴定。【结果】PDQuest软件分析发现攻毒组和对照组表达差异大于两倍的蛋白点有41个,其中攻毒组表达上调的蛋白点25个,下调的蛋白点7个,新出现的蛋白点有9个。质谱分析共成功鉴定了21个斑点,对应于20个蛋白。如载脂蛋白AI(apolipoprotein AI)、14-3-3 sigma(两个斑点均为该蛋白)、癌蛋白18(stathmin)等。【结论】功能预测表明这些蛋白涉及到宿主的抗病毒应答、物质代谢、细胞骨架成分、细胞增殖相关等方面。     

Cytokine expression in the liver of mice infected with a highly virulent strain of Francisella tularensis

Abstract Cytokine mRNA expression was determined in the liver of mice subcutaneously inoculated with a lethal dose of the highly virulent strain FSC 041 of Francisella tularensis subvar. tularensis or a sublethal dose of the live vaccine strain of F. tularensis subvar. palaearctica . Expression of mRNA for TNF-α, IL-12, IFN-γ, and IL-10 was demonstrated within 48 h of inoculation, the kinetics being similar irrespective of bacterial strain used. Thus, the expression of a cytokine response believed to be important in the early host defence against live vaccine strain seemed insufficient to prevent the lethality of a more virulent strain.     

Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain

Coxsackievirus B3 (CV-B3) is a cardiovirulent enterovirus that utilizes a 5′ untranslated region (5′UTR) to complete critical viral processes. Here, we directly compared the structure of a 5′UTR from a virulent strain with that of a naturally occurring avirulent strain. Using chemical probing analysis, we identified a structural difference between the two 5′UTRs in the highly substituted stem-loop II region (SLII). For the remainder of the 5′UTR, we observed conserved structure. Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation. To investigate independent folding and function, two chimeric CV-B3 strains were created by exchanging nucleotides 104–184 and repeating the 5′UTR structural analysis. Neither the parent SLII nor the remaining domains of the background 5′UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function. We show that the attenuated 5′UTR lacks structure in the SLII cardiovirulence determinant.     

带有REV-LTR片段的马立克氏病病毒重组野毒株与超强毒株致病性和横向传播性比较

[目的]GX0101是一株插入了禽网状内皮组织增生症病病毒(REV)-LTR片段的马立克氏病病毒(MDV)重组野毒株,本文将其致病性、致肿瘤性和横向传播能力与超强毒参考株(vvd5)进行比较.[方法]利用MDV特异性核酸探针对同罩饲养的对照鸡的羽毛囊DNA进行检测.[结果]在经抗MDV疫苗免疫的SPF鸡攻毒试验中表明,GX0101株的致死率28.6%和致肿瘤率7.1%均低于超强毒参考株Md5的致死率63.1%和致肿瘤率19.0%.但是,利用MDV特异性核酸探针对同罩饲养的对照鸡的羽毛囊DNA检测表明,GXO101从攻毒后第28天就有6/15的比例从羽毛囊中检出MDV,而与vvMd5接种鸡同一隔离罩的对照鸡,在35 d时才在2/14的个体中检出MDV,即GX0101的横向传播能力大于超强毒株.这一结果表明,MDV的致病性不一定与横向传播力相平行.[结论]由此推测,显著增高的横向传播能力可能就是这一整合进REV-LTR的重组病毒株能在鸡群中逐渐流行开来的选择性竞争优势之一.