Genome Structure and Evolution of Naegleria and its Relatives

In the 4 yr since the molecular biology of DNA in Naegleria was last reviewed several major advances have been made, and these are reviewed here: isolation and characterization of mitochondrial and ribosomal DNAs; enumeration of chromosomal DNAs by pulsed field gel electrophoresis; sequence analysis of differentially expressed genes; phylogenetic placement of the genus Naegleria among the eukarayotes and Naegleria species within the genus.     

Electrophoretic karyotype and linkage groups of the amoeboflagellate Naegleria gruberi

We have constructed a molecular karyotype for two strains of Naegleria gruberi using pulsed field gel electrophoresis. Each strain has about 23 chromosomes, considerably more than any previous estimate. These chromosomes range in size from 400 kilobasepairs to over 2,000 kilobasepairs. In Naegleria, construction of the DNA karyotype depends on assessment of the anomalous electrophoretic mobility of the circular ribosomal RNA genes. We have determined the chromosomal locations of an identified unique gene (flagellar calmodulin) and four identified multigene families (alpha- and beta-tubulin, actin, ubiquitin), as well as three differentially expressed genes of unknown functions. The ca. 12 actin genes are dispersed over at least seven chromosomes, whereas the majority of the more than eight alpha-tubulin genes are confined to a single chromosome. The ubiquitin genes are found on five chromosomes in one strain and seven in the other and the beta-tubulin genes are on three or four. Our observations provide a foundation for molecular genetic studies in this organism.     

Karyotype polymorphism correlates with intraspecific infertility in the homothallic ascomycete Sordaria macrospora

The homothallic fungus Sordaria macrospora produces perithecia with meiotically derived ascospores. In most cases, intraspecies crosses between strains from different culture collections generate fertile hybrid perithecia in the contact zone of two mycelia. However, in some of these crosses we observed a significant decrease in the fertility of the hybrid perithecia when strains of different origin were used for mating. Since we assumed that chromosome variability between the culture collection strains might contribute to this reduction in fertility, we performed pulsed‐field gel electrophoresis. In the course of our study, we were able to identify two major groups of electrophoretic karyotypes in S. macrospora culture collection strains. A quantitative analysis revealed that polymorphic karyotypes contribute to a reduction of fertility in forced crosses between strains carrying differently sized chromosomes. The observed intraspecific chromosome length polymorphism might have consequences on the speciation process of a homothallic fungus capable of sexual but not of asexual spore formation.     

Characterization of the rrn operons in the channel catfish pathogen Edwardsiella ictaluri

Aims:  To advance diagnostics and phylogenetics of Edwardsiella ictaluri by sequencing and characterizing its rrn operons.
Methods and results:  The Edw. ictaluri rrn operons were identified from a 5–7 kbp insert lambda library and from Edw. ictaluri fosmid clones. We present the complete sequences and analysis of all eight Edw. ictaluri rrn operons and unique regions located upstream and downstream. Two rrn operons were located in tandem with 169 bp separating them, which is apparently a conserved feature between Edw. ictaluri and Edwardsiella tarda. I- Ceu I enzyme digestion of Edw. ictaluri genomic DNA and analysis by pulsed field gel electrophoresis indicated that rrn operon number and chromosomal locations are conserved within the species Edw. ictaluri .
Conclusions:  The rrn operons of Edw. ictaluri have similar structure and flanking regions compared with other members of the family Enterobacteriaceae ; however, the presence of eight copies of the rrn operon makes Edw. ictaluri unique within the family .
Significance and impact of the study:  This research clarifies previous phylogenetic analyses of Edw. ictaluri and provides support for the Edw. ictaluri genome sequencing project. In addition, we identified a unique feature of two rrn operons that shows potential for the development of a diagnostic PCR method.     

Electrophoretic karyotype polymorphism of sibling species of the Paramecium aurelia complex

Variability of karyotypes is one of the main mechanisms of speciation in organisms. Electrophoretic karyotypes of the macronucleus (MAC) obtained by pulsed-field gel electrophoresis were compared for 86 strains of all 15 sibling species of the Paramecium aurelia complex in order to determine if karyotype differences corresponded to biological species boundaries. Because the electrophoretic karyotype of the MAC reflects indirectly the frequency and distribution of fragmentation sites in the micronuclear (MIC) chromosomes, any change in MAC electrophoretic karyotype may be a marker of certain chromosomal mutations in the MIC. Thirteen main variants of electrophoretic MAC karyotypes were observed in this species complex. Ten of them appeared to correspond to biological species, while the three other variants characterized several species each. Intraspecific polymorphism was observed for several species: in some cases a certain variant of MAC karyotype was specific for all strains from the same part of the world. Distribution of the MAC karyotype variants along molecular phylogenetic trees of the P. aurelia complex shows that isolation of each species or group of species of this complex was accompanied by divergence in the molecular organization of the genome.     

The Size of DNA Molecules and Chromatin Organization in the Macronucleus of the Ciliate Didinium nasutum (Ciliophora)

Pulsed‐field gel electrophoresis (PFGE) was applied to analyze the molecular karyotype of the ciliate Didinium nasutum. The data obtained indicate that D. nasutum belongs to the ciliate species with subchromosomal macronuclear genome organization. No short “gene‐sized” DNA molecules were detected. Macronuclear DNAs formed a continuous spectrum from 50 kbp to approximately 1,000 kbp in size with a peak plateau between 250 and 400 kbp. The macronuclear DNA molecules were packed into chromatin bodies of 80–265 nm in size. Comparison of the PFGE and electron microscopic data shows that most if not all chromatin bodies contain more than one DNA molecule.     

Amoeboid Locomotion of Naegleria gruberi: the Effects of Cytochalasin B on Cell-Substratum Interactions and Motile Behaviour

The major manifestations of amoeboid locomotion in Naegleria—cytoplasmic streaming, pseudopod production, cell polarity and focal contact production—require that the actin-based cytoskeleton be extremely dynamic. Whether these features are causally linked is unclear. In an attempt to answer this question we have used the fungal product cytochalasin B (cyt B) to dissect the motility process. This drug can perturb the organisation of actin filaments both in vivo and in vitro. Essentially cyt B acts as a molecule which can cap the barbed ends of actin filaments. Not surprisingly therefore cyt B has an effect on rates of actin polymerization and the dynamic state of actin in the cytoplasm. We have found that cyt B has a profound effect on focal contact production and breakdown. Within minutes of addition of cyt B focal contact production ceases, existing focal contacts are stabilised but cytoplasmic streaming and pseudopod production are not blocked. In conclusion it is now clear that the state of actin required for focal contact production is different from that required for pseudopod extension and cytoplasmic streaming.     

水稻核基因组DNA的YAC克隆和鉴定

将EcoRI部分消化的水稻(Oryza sativa L.)细胞核高分子量DNA电泳分部,回收大于200kb的片段,与内切酶消化过的酵母人工染色体(YAC)双质粒载体pJs97。pJS98DNA连接,转化酵母YPH252感受态原生质球,用ura^-,TrP^-双选择培养基直接筛选转化子,已获得2 000多个克隆。转化子DNA的southern杂交显示插入片段在200～820kb范围。     

Molecular typing of Pasteurella pneumotropica isolated from rodents by amplified 16S ribosomal DNA restriction analysis and pulsed-field gel electrophoresis

A total of 52 isolates of Pasteurella pneumotropica obtained from rodents were examined for their genetic heterogeneity. On the basis of DNA restriction analysis, including amplified 16S ribosomal DNA restriction analysis (ARDRA) and pulsed-field gel electrophoresis (PFGE), differences were identified among the isolates. ARDRA typing with Hae III revealed 4 different banding patterns of the P. pneumotropica isolates. Eighty-two percent of the 23 isolates identified as a-1 were derived from mice, whereas all the isolates identified as a-3 were derived from rats. Most of the isolates, which showed hemolytic activity on blood agar, obtained from mice and rats, were identified as a-2 and a-4, respectively. By restriction analysis of genomic DNA, Apa I and Not I digestion differentiated 9 variants and an undiscriminating group. However, no close relation with regard to the phenotypic characteristics was observed among the variants. The isolates identified as a-2 and a-4 could not be distinguished by PFGE analysis. DNA restriction analysis revealed that the genetic diversity of the P. pneumotropica isolates was more complex than the phenotypic characteristics among the species, and that at least the P. pneumotropica isolates were clearly differentiated into 4 groups by ARDRA typing with Hae III.     

Assignment of Alu-repetitive sequences to large restriction fragments from human chromosomes 6 and 22

We have employed a pulsed field gel electrophoresis and Alu hybridization approach for identification of large restriction fragments on chromosome 6 and 22. This technique allows large portions of selected human chromosomes to be visualized as discrete hybridization signals. Somatic cell hybrid DNA which contains chromosome 6 or chromosome 22 was restricted with either Notl or Mlul. The restriction fragments were separated by pulsed field gel electrophoresis (PFGE) and hybridized against an Alu repetitive sequence (Blur 8). The hybridization signals result in a fingerprint-like pattern which is unique for each chromosome and each restriction enzyme. In addition, a continuous pattern of restriction fragments was demonstrated by gradually increasing puls times. This approach will also be suitable to analyze aberrant human chromosomes retained in somatic cell hybrids and can be used to analyze flow sorted human chromosomes. To this end, our method provides a valuable alternative to standard cytogenetic analysis.     

Molecular identification and differentiation of Staphylococcus species and strains of cheese origin

Amplified Ribosomal-DNA Restriction Analysis (ARDRA) was used to differentiate among 12 species and 4 subspecies of the genus Staphylococcus. With a universal primer pair a 2.4 kbp PCR-product was amplified, including the 16S rDNA, the 16S-23S rDNA interspacer region, and about 500 bp of the 23S rDNA. Species-specific restriction patterns were found using the restriction enzymes HindIII and XmnI separately. Cheese related staphylococci were clearly differentiated. ARDRA results were in good agreement with results of partial sequencing of the 16S rDNA. ARDRA could fully replace the biochemical identification with ID32 Staph (BioMerieux) which was less reliable when staphylococci of cheese origin were analysed. Genomic restriction digests of cheese-related S. equorum strains by SmaI and SacI gave unique strain-specific restriction patterns which can be used to identify starter staphylococci in a complex microbial environment such as the surface of Red-Smear cheeses.     

Preparation of HMW DNA from Plant Nuclei and Chromosomes Isolated from Root Tips

Simple, fast and cost-effective method for preparation of DNA with high molecular weight (HMW DNA) from plant nuclei and mitotic chromosomes has been developed. The technique involves mechanical homogenization of formaldehyde-fixed root tips, purification of nuclei and/or chromosomes on sucrose gradient, embedding in low-melting-point agarose, and DNA isolation in agarose plugs. Alternatively, nuclei and chromosomes may be purified using flow cytometry. Majority of DNA obtained is megabase-sized and well digestible by restriction endonucleases. The method is highly efficient as microgram amounts of DNA can be obtained from only several milligrams of plant tissue. Handling negligible amounts of plant material reduces the consumption of chemicals. Furthermore, the use of root tips makes it possible to obtain high-quality DNA even from plant species with leaves that are rigid or rich in secondary metabolites such as polyphenols. It is expected that preparation of HMW DNA from root tip nuclei will facilitate long-range mapping and construction of large-insert DNA libraries also in these species. Successful isolation of HMW DNA from flow-sorted chromosomes opens a way for construction of chromosome-specific large-insert libraries in plants. This revised version was published online in July 2006 with corrections to the Cover Date.     

The use of (GTG)5 oligonucleotide as an RAPD primer to type Campylobacter concisus

AIM: DNA fingerprinting using (GTG)(5) oligonucleotide as a primer in a random amplified polymorphic DNA (RAPD) assay was assessed by typing isolates of Campylobacter concisus strains, collected over a period of 8 years. METHODS AND RESULTS: RAPD analysis using the (GTG)(5) oligonucleotide as a primer was used to type 100 isolates of C. concisus comprising mostly isolates from children with diarrhoea. Using this method, 86% of the isolates were found to be genotypically diverse. Of these heterogeneous isolates, 25 of the strains were also shown to be genetically distinct in a previous study using pulsed field gel electrophoresis. The remaining isolates (14) could be classified into five profile groups based on the DNA fingerprinting patterns. The assay successfully identified epidemiologically linked strains from the unrelated genetically diverse pool of strains. CONCLUSIONS: Laboratory RADP typing using the (GTG)(5) primer proved to be useful in distinguishing related strains of C. concisus from a large pool of unrelated strains of this organism. SIGNIFICANCE AND IMPACT OF THE STUDY: RAPD typing using (GTG)(5) is a simple method that could be used to investigate the epidemiology of C. concisus. The results suggest that homologous lineages of C. concisus may exist within an otherwise heterogeneous species complex. However, these data need to be confirmed using a more robust typing method.     

从琼脂糖电泳凝胶中回收DNA的几种简便方法

介绍两类从普通琼脂糖电泳凝胶中回收ＤＮＡ的简便、快捷、高效且廉价的方法．第一类为电泳洗脱法．方法ａ：利用１．５ｍＬ微量离心管、ｌｍＬ吸头、尼龙网膜和透析膜做成的一个小装置,快速有效回ＤＮＡ,最终回收率为７０％左右．方法ｂ：不用ＤＥＡＥ－纤维素膜,而用透析膜在凝胶中作出横隔挡在ＤＮＡ条带前,最终回收率为５０％左右;第二类为冰冻融解法,最终回收率也在５０％左右．如果联合使用冰冻融解法和电泳洗脱法,回收率可进一步提高至９０％．     

Genetic Diversity of Pneumocystis carinii Derived from Infected Rats, Mice, Ferrets, and Cell Cultures

ABSTRACT. The degree of strain and/or species diversity among Pneumocystis carinii isolates is unknown. As a first approach to the study of P. carinii genetic relatedness, we compared the pulsed field gel electrophoretic karyotypes of P. carinii derived from lung homogenates of three immunosuppressed host animals: rats transtracheally inoculated with P. carinii -infected rat lung; mice transtracheally inoculated with P. carinii -infected mouse lung; and ferrets which developed reactivated latent P. carinii pneumonia. Rat P. carinii propagated on HEL299 cells was also examined. Karyotypes of P. carinii DNA from both rat lung homogenate and cell culture were identical (14 bands, 315–680 kb). In contrast, mouse and ferret P. carinii DNA karyotypes were each distinctly different from the rat P. carinii samples (mouse P. carinii 15 bands, 315–610 kb; ferret P. carinii nine bands, 410–760 kb). Three distinct rat P. carinii gene probes reacted with both Southern-transferred rat and mouse P. carinii DNA but not with ferret P. carinii DNA. Thus, P. carinii from rat, mouse, and ferret are genetically diverse. The results are consistent with recently reported antigenic and nucleic acid sequence differences among P. carinii isolates recovered from different hosts.     

Characterization of the Legionella anisa population structure by pulsed-field gel electrophoresis

We analysed 38 French isolates of Legionella anisa by means of pulsed-field gel electrophoresis (PFGE) with single or double digestion. Double digestion was more discriminatory than single digestion, and can thus be useful for epidemiological studies of L. anisa. Several isolates from different parts of France clustered together on the basis of their PFGE patterns (similarity cutoff of 80%), suggesting that the L. anisa population structure is homogenous or that a few clones of L. anisa strains have spread widely in France.     

H2O2－Fe3+所致人淋巴细胞DNA双链断裂损伤

采用脉冲电场凝胶电泳法检测H₂O₂－Fe³⁺体系产生的OH^·对人淋巴细胞DNA的双链断裂损伤．H₂O₂－Fe³⁺浓度与DNA双链断裂呈明显量效关系;随OH^·作用时间延长,细胞DNA双链断裂加重;过氧化氢酶对OH^·损伤有明显抑制作用．脉冲电场凝胶电泳法可检测到的H₂O₂和FeCl₃引起细胞DNA双链断裂的最低浓度为0.3 mmol/L和6 μmol/L．     

H_2O_2－Fe~（3＋）所致人淋巴细胞DNA双链断裂损伤

采用脉冲电场凝胶电泳法检测Ｈ２Ｏ２－Ｆｅ（３＋）体系产生的ＯＨ对人淋巴细胞ＤＮＡ的双链断裂损伤．Ｈ２Ｏ２－Ｆｅ（３＋）浓度与ＤＮＡ双链断裂呈明显量效关系;随ＯＨ作用时间延长,细胞ＤＮＡ双链断裂加重;过氧化氢酶对ＯＨ损伤有明显抑制作用．脉冲电场凝胶电泳法可检测到的Ｈ２Ｏ２和ＦｅＣｌ３引起细胞ＤＮＡ双链断裂的最低浓度为０．３ｍｍｏｌ／Ｌ和６μｍｏｌ／Ｌ．