The level of dysgenic sterility and recessive mutations induced in laboratory strains of Drosophila melanogaster exposed to chronic low-dose gamma irradiation

Recent investigations showed that genetic instability accounts for many radiobiological effects. However, mechanisms underlying this phenomenon are still poorly understood. Assuming that mobile genetic elements may be involved in the induction of genetic instability, we studied parameters that characterize the activity of these elements in Drosophila melanogaster: hybrid dysgenesis and the level of recessive lethal mutations. In our experiments, we used D. melanogaster strains that differed in the type of hybrid dysgenesis (P-M and H-E). It was demonstrated that chronic exposure to radiation leads to substantial changes in the genetic structure of a population and an enhanced level of dysgenic sterility. Our results indicate that genetic instability and adaptation to the effect of chronic gamma-radiation are associated with the radiation-induced mobilization of mobile genetic elements.     

Influence of ionizing radiation of low intensity on the processes of reproduction,aging and dying off of Escherichia coli bacteria

The influence of 60Co gamma-ray irradiation of low intensity (0.1-0.4, 0.76 x 10(3) microGy/h) on the processes of reproduction, aging and dying off of E. coli B/r and E. coli BS-1 bacteria have been investigated. It was shown that the reproduction of this bacteria strains was not dependent on the dose rate in the range 0.1-0.4 microGy/h. It was shown in comparison with the irradiated E. coli B/r cells dynamics of the aging and dying off of the irradiated E. coli BS-1 is decreased in the process of prolonged (about 190 days) irradiation with a dose rate of 0.76 x 10(3) microGy/h. It is proposed the relationship between the revealed phenomenon of the decrease in the intensity of the irradiated E. coli BS-1 cell aging and dying and the Vavilov-Cerenkov emission.     

Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007

Background  

Over the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is pauCity of information concerning the diversity and occurrence of mobile genetic elements in Vibrio cholerae strains implicated in these outbreaks. A total of 65 Vibrio cholerae O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs), conjugative plasmids and for their genotypic relatedness.     

多重耐药肺炎克雷伯菌获得性耐药相关基因和可移动遗传元件检测与指标聚类分析

目的 探讨一组多重耐药肺炎克雷伯菌(MDR-KPN)中获得性耐药相关基因和可移动遗传元件遗传标记的存在状况以及二者的相关性.方法 收集2008年8月至2010年5月浙江省杭州市和湖州市6所医院共47株MDR-KPN,采用聚合酶链反应(PCR)的方法分析74种获得性耐药基因和24种可移动遗传元件遗传标记,并用指标聚类分析(SPSS法)分析获得性耐药相关基因和可移动遗传元件遗传标记的相关性.结果 47株MDR-KPN共检出5种β-内酰胺类获得性耐药基因、6种氨基糖苷类获得性耐药基因、3种喹诺酮类获得性耐药基因、6种其他获得性耐药基因、1种整合子遗传标记、2种转座子遗传标记、4种插入序列遗传标记、2种接合性质粒遗传标记和1种噬菌体原标记;指标聚类分析(SPSS法)将上述阳性检出基因分成A、B两大簇.结论 指标聚类分析提示获得性耐药相关基因和可移动遗传元件密切相关;由Ⅰ类整合子( intI1)、插入序列(IS26、ISEcp1、ISKpn6)、耐药质粒(trbC)介导的TEM-1和KPC是本组菌株的特征.在肺炎克雷伯菌中做指标聚类分析为国内首次报道.     

Variability in the longevity of Drosophila imagoes under chronic irradiation at low doses

The investigation of life span variability induced by a chronic influence of low doses gamma irradiation on the laboratory stocks of D. melanogaster, distinguishing by mobile genetic units, were carried out. Shown was the link of life span alterations in D. melanogaster with features of cytotype and genotype in tested stocks and with induced apoptotic cell death. The life span variation can be determined by a genomic destabilisation with an induction of mobile genetic elements in conditions of chronic gamma irradiation.     

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

Background

Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders'' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human microbiomes, we use spacers from CRISPR arrays that we had previously assembled from shotgun metagenomic datasets, and identify contigs that contain these spacers'' targets.

Results

We discover 95,000 contigs that are putative invasive mobile genetic elements, some targeted by hundreds of CRISPR spacers. We find that oral sites in healthy human populations have a much greater variety of mobile genetic elements than stool samples. Mobile genetic elements carry genes encoding diverse functions: only 7% of the mobile genetic elements are similar to known phages or plasmids, although a much greater proportion contain phage- or plasmid-related genes. A small number of contigs share similarity with known integrative and conjugative elements, providing the first examples of CRISPR defenses against this class of element. We provide detailed analyses of a few large mobile genetic elements of various types, and a relative abundance analysis of mobile genetic elements and putative hosts, exploring the dynamic activities of mobile genetic elements in human microbiomes. A joint analysis of mobile genetic elements and CRISPRs shows that protospacer-adjacent motifs drive their interaction network; however, some CRISPR-Cas systems target mobile genetic elements lacking motifs.

Conclusions

We identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and invaders.     

Induction by UV light of the SOS function sfiA in Escherichia coli strains deficient or proficient in excision repair.

The influence of the nucleotide excision repair system on the induction by UV irradiation of the SOS function sfiA has been investigated. The level of sfiA expression was monitored by means of a sfiA::lacZ operon fusion in both the wild-type strain and a uvrA mutant. We found that the initial steady rate of sfiA expression was proportional to the UV dose and was identical in uvr+ and uvrA backgrounds. This suggests that the initial steady rate of sfiA expression is determined by the initial number of lesions and before any effect of excision repair. We confirmed that after 2 h of expression the net synthesis of sfiA product is, for the same UV dose, about five times lower in uvr+ than in uvrA strains. We show that this is due to earlier repression of the SOS system in uvr+ than in uvrA strains and not to different initial rates.     

CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes

Propionibacterium acnes is a skin commensal that occasionally acts as an opportunistic pathogen. The population structure of this species shows three main lineages (I-III). While type I strains are mainly associated with sebaceous follicles of human skin and inflammatory acne, types II and III strains are more often associated with deep tissue infections. We investigated the occurrence and distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) in P. acnes, assessed their immunological memory, and addressed the question if such a system could account for type-specific properties of the species. A collection of 108 clinical isolates covering all known phylotypes of P. acnes was screened for the existence of CRISPR/cas loci. We found that CRISPR loci are restricted to type II P. acnes strains. Sequence analyses of the CRISPR spacers revealed that the system confers immunity to P. acnes-specific phages and to two mobile genetic elements. These elements are found almost exclusively in type I P. acnes strains. Genome sequencing of a type I P. acnes isolate revealed that one element, 54 kb in size, encodes a putative secretion/tight adherence (TAD) system. Thus, CRISPR/cas loci in P. acnes recorded the exposure of type II strains to mobile genetic elements of type I strains. The CRISPR/cas locus is deleted in type I strains, which conceivably accounts for their ability to horizontally acquire fitness or virulence traits and might indicate that type I strains constitute a younger subpopulation of P. acnes.     

含ICE-emm12和ΦHKU.vir化脓链球菌引起的猩红热1例

2011年中国开始出现猩红热疫情,病例以普通型为主,外科型较少报道。ICE-emm12和ΦHKU.vir是中国香港地区猩红热暴发株中首次发现的2个可移动遗传元件,尚不清楚其是否存在于中国内地的猩红热致病株中。本文报道1例猩红热病例,其咽部和皮肤伤口皆分离出同一克隆株的化脓链球菌,该菌株携带ICE-emm12和ΦHKU.vir,从而证实这2个新元件存在于中国内地的化脓链球菌中。因此,国内有必要对猩红热分离株进行ICE-emm12和ΦHKU.vir检测,以监测致病株在基因水平的变化。     

The effect of prolonged gamma irradiation at a decreasing dose rate on survivability and gene mutation induction in cultured Chinese hamster cells

Continuous gamma irradiation at decreasing dose rate was shown to be less effective than acute exposure with regard to the lethal effect and frequency of mutations of resistance to 6-thioguanine in cultured Chinese hamster cells. The cell population subjected to continuous irradiation was more radioresistant than the intact one. Lethal and genetic effects of continuous irradiation at decreasing dose rate were mainly determined by the contribution of the radiation dose received during the first 24 h of exposure.     

Genetic aspects of the irradiation in small doses of laboratory lines and experimental populations Drosophila melanogaster

One of explanations of revealed effects of small doses of an irradiation is induced genetic instability on which background there is a realization of the various radiobiological reactions resulting as to stimulation, and significant oppression of the vital functions of a cell or an organism. In work the given estimations of consequences of an irradiation in small doses of mutant lines of the drosophila are submitted. Paramount value in definition of their size and an orientation of reaction of a genotype is supposed, that, have processes leaders to change of activity of mobile genetic elements and programmed destruction of a cell.     

Peculiarities of the effect of low-dose-rate radiation simulating high-altitude flight conditions on mice in vivo

In the present work, the effect of a low-dose rate of high-LET radiation in polychromatic erythrocytes of mice bone marrow was investigated in vivo. The spectral and component composition of the radiation field used was similar to that present in the atmosphere at an altitude of about 10 km. The dose dependence, adaptive response, and genetic instability in the F₁ generation born from males irradiated under these conditions were examined using the micronucleus test. Irradiation of the mice was performed for 24 h per day in the radiation field behind the concrete shield of the Serpukhov accelerator. Protons of 70 GeV were used over a period of 15–31 days, to accumulate doses of 11.5–31.5 cGy. The experiment demonstrated that irradiation of mice in vivo in this dose range leads to an increase in cytogenetic damage to bone marrow cells, but does not induce any adaptive response. In mice pre-irradiated with a dose of 11.5 cGy, an increase in sensitivity was observed after an additional irradiation with a dose of 1.5 Gy. The absence of an adaptive response suggests existence of genetic instability.     

Qualitative and quantitative analyses of the transpositions of P element--based genetic construction into the region of Drosophila melanogaster hsp70 genes

The hsp70 genes is among the main systems underlying the adaptation of organisms to adverse environmental factors. The ever increasing amount of data in literature demonstrates an important adaptive role of mobile genetic elements in microevolution. Drosophila hsp70 genes are potential target for transpositions of various mobile elements in natural populations. We have analyzed the frequency and localization of a P element-based genetic construction, EPgy2, in the region of Drosophila melanogaster hsp70 genes. A hot spot for the transposition was discovered in the promoter regions of genes hsp70Aa and hsp70Ab. No insertions of this construction in the coding or 3'-flanking regions of hsp70 genes have been recorded. It was demonstrated that the region of 161 to 7800 bp adjacent to the original construction is in certain cases also involved in the transposition. No transpositions of any other mobile elements have been observed. The inserts were shown to change the activity of hsp70 genes and the thermotolerance of transgenic strains.     

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications

Background

Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30.

Results

Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34.

Conclusions

Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others.     

蜡状芽孢杆菌群中规律成簇间隔短回文重复序列的生物信息学分析

规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)是最近发现针对噬菌体等外源遗传物质的获得性和可遗传性的新型原核生物防御系统。通过BLAST、多序列比对、RNA二级结构预测等生物信息学方法对已经完成全基因组测序的蜡状芽孢杆菌群24个菌株进行CRISPR的系统分析,结果表明:42%的菌株含有该结构;8个CRISPR座位的正向重复序列可以形成RNA二级结构,提示正向重复序列可能介导外源DNA或RNA与CAS编码蛋白的相互作用;31%的间区序列与噬菌体、质粒、蜡状芽孢杆菌群基因组序列具有同源性,进一步验证间区序列很可能来源于外源可移动遗传因子。由于大部分蜡状芽孢杆菌群菌株含有多个前噬菌体和质粒,通过对蜡状芽孢杆菌群CRISPR的分析,为揭示其对宿主菌与噬菌体,以及宿主菌与质粒间的关系奠定基础。     

Genetic effects of low-dose chronic irradiation of developing seeds of Arabidopsis thaliana Heynh

A six-year study, starting in 1987, focused on the frequency of embryonic lethals and chlorophyll mutations that arose in developing seeds of Arabidopsis thaliana growing at sites varying in the level of radioactive contamination in the 30-km control region of the Chernobyl Atomic Power Plant. The dose rate of chronic irradiation varied from 200 microR/h to 2.4 R/h. To study the genetic effects of various levels of radioactive contamination, the frequency of mutations arising in a particular generation was determined and the irradiation dose was estimated for the given generation. The dose dependence of the mutation frequency proved to follow a power function with a power less than unity, suggesting a relatively high effect for low-dose irradiation. Possible explanations of this phenomenon are discussed.     

Non-typeable pneumococci circulating in Portugal are of cps type NCC2 and have genomic features typical of encapsulated isolates

Background

Pneumococcus is a major human pathogen and the polysaccharide capsule is considered its main virulence factor. Nevertheless, strains lacking a capsule, named non-typeable pneumococcus (NT), are maintained in nature and frequently colonise the human nasopharynx. Interest in these strains, not targeted by any of the currently available pneumococcal vaccines, has been rising as they seem to play an important role in the evolution of the species. Currently, there is a paucity of data regarding this group of pneumococci. Also, questions have been raised on whether they are true pneumococci. We aimed to obtain insights in the genetic content of NT and the mechanisms leading to non-typeability and to genetic diversity.

Results

A collection of 52 NT isolates representative of the lineages circulating in Portugal between 1997 and 2007, as determined by pulsed-field gel electrophoresis and multilocus sequence typing, was analysed. The capsular region was sequenced and comparative genomic hybridisation (CGH) using a microarray covering the genome of 10 pneumococcal strains was carried out. The presence of mobile elements was investigated as source of intraclonal variation. NT circulating in Portugal were found to have similar capsular regions, of cps type NCC2, i.e., having aliB-like ORF1 and aliB-like ORF2 genes. The core genome of NT was essentially similar to that of encapsulated strains. Also, competence genes and most virulence genes were present. The few virulence genes absent in all NT were the capsular genes, type-I and type-II pili, choline-binding protein A (cbpA/pspC), and pneumococcal surface protein A (pspA). Intraclonal variation could not be entirely explained by the presence of prophages and other mobile elements.

Conclusions

NT circulating in Portugal are a homogeneous group belonging to cps type NCC2. Our observations support the theory that they are bona-fide pneumococcal isolates that do not express the capsule but are otherwise essentially similar to encapsulated pneumococci. Thus we propose that NT should be routinely identified and reported in surveillance studies.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-863) contains supplementary material, which is available to authorized users.     

Effect of heparin on the antiradiation activity of cystamine, decreasing with a reduction in radiation intensity

It was shown that a single injection of heparin (250 units/kg) 15 min and 24 h before irradiation potentiated a slight radioprotective effect of cystamine (dichlorohydrate, 170 mg/kg) which was registered after the administration thereof to mice 30 min before irradiation with an absolutely lethal dose at a dose rate of 0.0025 Gy/c.     

Genetic Effects of Low-Dose Chronic Irradiation of Developing Seeds of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> (L.) Heynh.

A six-year study, starting in 1987, was focused on the frequency of embryonic lethals and chlorophyll mutations that arose in developing seeds of Arabidopsis thaliana growing at sites varying in the level of radioactive contamination in the 30-km control region of the Chernobyl Atomic Power Plant. The dose rate of chronic irradiation varied from 200 μR/h to 2.4 R/h. To study the genetic effects of various levels of radioactive contamination, the frequency of mutations arising in a particular generation was determined and the irradiation dose was estimated for the given generation. The dose dependence of the mutation frequency proved to follow a power function with a power less than unity, suggesting a relatively high effect for low-dose irradiation. Possible explanations of this phenomenon are discussed.