Long-term clonal lineages within Campylobacter jejuni O:2 strains from different geographical regions and hosts

The genomic diversity of 11 epidemiologically unrelated strains of Campylobacter jejuni (serotype O:2) isolated from different hosts and different geographical regions in Germany over a period of 15 years was studied and results were compared with the reference strain NCTC11168. By flagellin PCR-RFLP typing six fla types were identified, while macrorestriction analysis with three different restriction enzymes revealed almost identical patterns for two human and one bovine strain, even though they were isolated between 1984 and 1996. Interestingly, the PFGE and fla profiles from strain NCTC11168, which was originally isolated in 1977 from an outbreak case in Worcester (UK), were highly similar or even identical to the profiles of these strains. Besides this, mapping of selective genetic markers to the obtained restriction fragments by Southern blot hybridization showed a conserved localization of the investigated sequences in several strains. Our data confirmed considerable degrees of genomic conservation and the occurrence of long-term O:2 serotype-associated clonal lineages in C. jejuni in different geographical regions and hosts.     

Genotypic variation among wild isolates of Heliothis spp nuclear polyhedrosis viruses from different geographical regions

Ten nuclear polyhedrosis viruses infecting insect hosts in the genus Heliothis and isolated in different geographical regions of the world were characterized using restriction endonuclease analysis. Digestion of the dsDNA genomes with BamHI, EcoRI, and HindIII resulted in fragmentation profiles which separated the wild-type isolates into two major genotypes, corresponding with the morphology of the virion (multiply embedded major genotypes, corresponding with the morphology of the virion (multiply embedded vs singly embedded). Isolates within each major genotype have similar fragmentation profiles, showing only slight differences in the number and size of several fragments, and thus represent variants of the major genotype. Submolar fragments present in a number of the digests suggests that these wild-type isolates might themselves consist of two or more genotypic variants. The significance of this genotypic heterogeneity is discussed.     

Nucleotide sequence of the cytochrome B gene and adjacent regions from rat liver mitochondrial DNA

Summary The nucleotide sequence of a 1.76 Kbp segment from rat liver mitochondrial DNA has been determined. It contains the gene for the cytochrome b apoprotein and the tRNA genes for threonine, glutamic acid, and proline. The arrangement of these genes in rat liver mitochondria is the same as in human (Anderson et al. 1981) or mouse (Bibb et al. 1981) mitochondria. The comparison of the cytochrome b sequences so far determined, reveals that several regions in these proteins are highly conserved. Abbreviations: Cyt b, cytochrome b apoprotein; U.R.F., unidentified reading frame (Anderson et al. 1981). Other abbreviations follow IUB-IUPAC conventions     

Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation

The Samaritan community, which numbered more than a million in late Roman times and only 146 in 1917, numbers today about 640 people representing four large families. They are culturally different from both Jewish and non-Jewish populations in the Middle East and their origin remains a question of great interest. Genetic differences between the Samaritans and neighboring Jewish and non-Jewish populations are corroborated in the present study of 7,280 bp of nonrecombining Y-chromosome and 5,622 bp of coding and hypervariable segment I (HVS-I) mitochondrial DNA (mtDNA) sequences. Comparative sequence analysis was carried out on 12 Samaritan Y-chromosome, and mtDNA samples from nine male and seven female Samaritans separated by at least two generations. In addition, 18-20 male individuals were analyzed, each representing Ethiopian, Ashkenazi, Iraqi, Libyan, Moroccan, and Yemenite Jews, as well as Druze and Palestinians, all currently living in Israel. The four Samaritan families clustered to four distinct Y-chromosome haplogroups according to their patrilineal identity. Of the 16 Samaritan mtDNA samples, 14 carry either of two mitochondrial haplotypes that are rare or absent among other worldwide ethnic groups. Principal component analysis suggests a common ancestry of Samaritan and Jewish patrilineages. Most of the former may be traced back to a common ancestor in the paternally-inherited Jewish high priesthood (Cohanim) at the time of the Assyrian conquest of the kingdom of Israel.     

Ribosomal DNA sequence comparison of Babesia and Theileria.

Previous studies on the taxonomy of Babesia spp. (phylum Apicomplexa) using morphological and life cycle characteristics have resulted in their classification into 3 subgenera, with the genus Theileria being most closely related to them. Using a strategy based on the direct sequence analysis of products derived by asymmetric PCR to determine the nucleotide sequences, we have tested the validity of this classification by sequencing the small subunit ribosomal RNA genes amplified from 2 Babesia species, namely Babesia bovis and Babesia rodhaini, and comparing these with previously published sequences of Theileria annulata and Babesia bigemina using Plasmodium falciparum as an outgroup. The results of this phylogenetic analysis support the recognition of at least 2 genera in Babesia--one to include B. bigemina and B. bovis, the other to include B. rodhaini.     

Human mitochondrial DNA variation in Southern Italy

Background: Since prehistoric times Southern Italy has been a cultural crossroads of the Mediterranean basin. Genetic data on the peoples of Basilicata and Calabria are scarce and, particularly, no records on mtDNA variability have been published.

Aim: In this study mtDNA haplotypes of populations from Basilicata, Calabria and Sicily are compared with those of other Italian and Mediterranean populations, so as to investigate their genetic relationships.

Subjects and methods: A total of 341 individuals was analysed for mtDNA in order to provide their classification into haplogroups. Multivariate analysis was used to compare the studied populations with other Mediterranean samples; median-joining network analysis was applied to observe the relationship between the major lineages of the Southern Italians.

Results: The haplogroup distribution in the Southern Italian samples falls within the typical pattern of mtDNA variability of Western Eurasia. The comparison with other Mediterranean countries showed a substantial homogeneity of the area, which is probably related to the historic contact through the Mediterranean Sea.

Conclusion: The mtDNA analysis demonstrated that Southern Italy displays a typical pattern of Mediterranean basin variability, even though it appears plausible that Southern Italy was less affected by the effects of the Late Glacial Maximum, which reduced genetic diversity in Europe.     

Several different mitochondrial DNA regions are involved in intergenomic recombination in Brassica napus cybrid plants

Summary An important mitochondrial (mt) DNA polymorphism was detected by SalI restriction enzyme analysis in five Brassica napus cybrids plants which combine B. napus chloroplasts and a cytoplasmic male sterility (cms) trait from Raphanus sativus. Novel restriction fragments observed in these cybrids were analysed. One of them was found to be constituted by fragments of both parent mt genomes. Sites involved in rut recombination in cybrids were compared by molecular hybridization to sites supposedly implicated in intragenomic mt recombination in B. oleracea The results indicate that mt recombination events arising through protoplast fusion involve several different rut DNA regions. Some of these regions appeared homologous to regions presumably involved in intragenomic mt recombination in B. oleracea.     

The regions of sequence variation in caulimovirus gene VI

The sequence of gene VI from figwort mosaic virus (FMV) clone x4 was determined and compared with that previously published for FMV clone DxS. Both clones originated from the same virus isolation, but the virus used to clone DxS was propagated extensively in a host of a different family prior to cloning whereas that used to clone x4 was not. Differences in the amino acid sequence inferred from the DNA sequences occurred in two clusters. An N-terminal conserved region preceded two regions of variation separated by a central conserved region. Variation in cauliflower mosaic virus (CaMV) gene VI sequences, all of which were derived from virus isolates from hosts from one host family, was similar to that seen in the FMV comparison, though the extent of variation was less. Alignment of gene VI domains from FMV and CaMV revealed regions of amino acid sequence identical in both viruses within the conserved regions. The similarity in the pattern of conserved and variable domains of these two viruses suggests common host-interactive functions in caulimovirus gene VI homologues, and possibly an analogy between caulimoviruses and certain animal viruses in the influence of the host on sequence variability of viral genes.     

Ribosomal and mitochondrial DNA target for real-time PCR diagnosis of invasive aspergillosis

The aim of the present study was to assess the diagnostic efficacy of a combination of two quantitative Aspergillus PCR assays, targeting a mitochondrial and a ribosomal target, in patients with risk factors for invasive aspergillosis (IA) and positive galactomannan (GM) antigen. Forty-four patients with hematological malignancies and risk factors for IA according to revised European Organization for Research on Treatment of Cancer and the Mycoses Study Group criteria (EORTC/MSG) criteria and presenting at least two sequential GM-positive sera were included in the study. Mitochondrial PCR was carried out prospectively on all GM-positive serum samples. Ribosomal PCR was carried out retrospectively on frozen stored sera. The sensitivities of mitochondrial and ribosomal PCRs were 58% and 50%, respectively. The diagnostic test performance was improved by using a combination of both PCR assays and by considering a patient PCR positive when at least two positive results were obtained. The sensitivity, specificity, and positive and negative likelihood ratios were 65%, 94%, and 11.8 and 0.37, respectively. A significant association between fatal outcome at 90 days and positive results of ribosomal PCR assays was observed (adjusted hazard ratio = 8.2; 95% confidence interval [CI] = 1.0 to 65.8; P = 0.048). Our results showed that the combination of two PCR assays targeting mitochondrial and ribosomal Aspergillus DNA improves the sensitivity of PCR in the diagnosis of IA in hematological patients with risk factors and positive GM results. This study also confirms that a positive PCR result is associated with a poor prognosis in these patients and should lead to specific antifungal therapy being introduced immediately.     

Characterization and sequence of lupin mitochondrial plasmid-like DNA

Summary Two minicircular DNAs of 1.2 kb (K1) and 1.4 kb (K2) were found in mitochondria of fertile lupin (Lupinus albus). The plasmid-like DNA, K1, was cloned, labelled and hybridized with mitochondrial DNA from three different species of lupin. We have found no evidence for integrated copies of K1 in any of the mitochondrial genomes probed in this study. No sequence homology between plasmid K1 and K2, and no homology of either with chloroplast DNA, has been detected. The K1 DNA is two-fold more abundant than the K2 DNA and about seven-fold more abundant than a unique segment of the mtDNA. The entire nucleotide sequence of the K1 DNA has been determined. This sequence exibits a 340 base pair region with highly organized repeats. The sequence of K1 shows no substantial homology with sequence of other mitochondrial plasmids of higher plants.     

Skin-scale genetic structure of <Emphasis Type="Italic">Sarcoptes scabiei</Emphasis> populations from individual hosts: empirical evidence from Iberian ibex-derived mites

The objective of the present study was to examine the extent of genetic diversity among Sarcoptes scabiei individuals belonging to different skin subunits of the body from individual mangy hosts. Ten microsatellite primers were applied on 44 individual S. scabiei mites from three mangy Iberian ibexes from Sierra Nevada Mountain in Spain. Dendrograms of the mites from the individual Iberian ibexes, showing the proportion of shared alleles between pairs of individual mites representing three skin subpopulations (head, back, and abdomen subunits), allowed the clustering of some mite samples up to their skin subunits. This genetic diversity of S. scabiei at skin-scale did not have the same pattern in all considered hosts: for the first Iberian ibex (Cp1), only mites from the head subunit were grouped together; in the second individual (Cp2), the clustering was detected only for mites from the abdomen subunit; and for the third one (Cp3), only mites from the back subunit were clustered together. Our results suggest that the local colonization dynamics of S. scabiei would have influenced the nonrandom distribution of this ectoparasite, after a single infestation. Another presumable explanation to this skin-scale genetic structure could be the repeated infestations. To our knowledge, this is the first documentation of genetic structuring among S. scabiei at individual host skin-scale. Further studies are warranted to highlight determining factors of such trend, but the pattern underlined in the present study should be taken into account in diagnosis and monitoring protocols for studying the population genetic structure and life cycle of this neglected but important ectoparasite.     

Extensive mitochondrial DNA variation in somatic tissue cultures initiated from wheat immature embryos

Summary Wheat mitochondria) DNA has been isolated from callus cultures initiated from both immature embryos and the corresponding parental cultivar. A Sall restriction pattern study has shown that the organization of callus culture mitochondria) DNA underwent extensive change, characterized by either the disappearance or the decrease in the relative stoichiometry of several restriction bands. Hybridization of labelled mitochondrial fragments obtained from a recombinant cosmid library to Southern blots of callus and parental line restricted mitochondria) DNAs has shown that a fraction of the mitochondria) genome was lost in callus cultures. Data from a Sall + HindIII restriction map of a defined part of the wheat mitochondria) genome concerned with some of these variations strongly suggest that the observed variations correspond to the disappearance of at least one mitochondria) DNA subgenomic molecule in callus cultures.Abbreviations mtDNA mitochondrial DNA - cpDNA chloroplast DNA - rRNA ribosomal RNA - mRNA messenger RNA - kb kilobase - cv cultivar     

Human mitochondrial DNA variation and the origin of Basques

The hypervariable segment I of the control region of the mtDNA (positions 16024–16383) was PCR-amplified from mouth scrape and hairs and sequenced in 45 unrelated individuals of pure matrilineal Basque descent. Twenty-seven different sequences were found, of which 21 are unique to the Basques. The allelic partition observed, together with resampling experiments, suggested that much more variation remained to be discovered. The mean pairwise difference in number of nucleotides between individuals was 3·15, a very low value. Moreover, the number of steps for the most parsimonious tree is very low compared to the number of different sequences. Both findings suggest that the Basque population was founded by a few lineages that diverged in a short time span. The number of nucleotide differences between individuals was shown not to be influenced by the distance between their birthplaces, thus validating the sampling strategy used a posteriori. The pairwise difference distribution agreed well with the three-parameter model proposed by Rogers & Harpending (1992). The parameter estimates found for the Basques implied that a demographic expansion (or perhaps two, given the bimodal shape of the distribution) took place sometime between 14500 and 42000 BP which is in agreement with archaeological data. Our sample was compared to other populations for which D-loop sequences were available through the Nei & Miller (1990) distance. In a neighbour-joining tree, all the Caucasoid samples, including the Basques, appeared tightly clustered, whereas African samples were the most distant to the Caucasoids and also the most heterogeneous. Although classical markers, such as blood groups and protein polymorphisms, clearly separate the Basques (and the Sardinians) from other European populations, this distinctiveness was not found using D-loop sequences.     

Morphological, biometrical, and molecular characterization of Ctenocephalides felis and Ctenocephalides canis isolated from dogs from different geographical regions

In the present work, a comparative morphological, biometrical and molecular study of Ctenocephalides spp. isolated from dogs (Canis lupus familiaris) from different geographical regions (Spain, Iran, and South Africa) has been carried out. The internal transcribed spacer 1 (ITS1) sequences of Ctenocephalides felis and Ctenocephalides canis collected from dogs from different geographical regions have been determined to clarify the taxonomic status of these species and to assess intraspecific variation and interspecific sequence differences. In addition, a phylogenetic analysis based on ITS1 sequences has been performed. Four different morphological populations were observed in the individuals of C. felis collected from dogs from different geographical locations. Nevertheless, the comparative study of the ITS1 sequences of the different morphological populations observed in C. felis did not show molecular differences. The results showed clear molecular differences between C. felis and C. canis and some specific recognition sites for endonucleases were detected between both species. Thus, BfrBI and DraI sites have diagnostic value for specific determination in C. felis. The phylogenetic tree based on the ITS1 sequences of C. felis and C. canis revealed that all the populations of C. felis from different geographical regions clustered together and separated, with high bootstrap values, from C. canis. We conclude that ITS1 region is a useful tool to approach different taxonomic and phylogenetic questions in Ctenocephalides species.     

Genetic characterization of German Mycobacterium avium strains isolated from different hosts and specimens by multilocus sequence typing

Infections caused by Mycobacterium avium and its subspecies are reported as emerging disease in many countries worldwide. In our study we applied the multilocus sequence typing technology to 98 German M. avium strains originating from different hosts and specimens to examine the degree of the genetic diversity. By MLST, 80% of strains were identified as subspecies ‘M. avium hominissuis’, and 20% as subspecies M. avium avium/M. avium silvaticum. Distinctly different MLST profiles were identified for both subspecies. Based on the analysis of 4 and 5 loci, 87 and 106 SNPs and 1 codon deletion could be detected, respectively, resulting in 40 different strain profiles. Twelve out of these have recently been described for strains coming from different countries, yet in our study, additional new strain profiles (n = 28) were found. The high degree of diversity within ‘M. avium subsp. hominissuis’ as well as the relatedness of human, porcine and environmental strains could be confirmed by IS1245 RFLP fingerprinting. The detection of ISMav6 and hsp65 code 15 in one adult patient strain being positive for IS901, but displaying ‘M. avium subsp. hominissuis’ MLST profile revealed that PCR for detection of IS901 is not a definitive proof of M. avium subsp. avium/M. avium subsp. silvaticum.     

Seroprevalence of human herpesvirus-8 in blood donors from different geographical regions of Argentina, Brazil, and Chile

Human herpesvirus-8 (HHV-8) causes Kaposi's sarcoma (KS) and lymphoproliferative disorders in both HIV-infected and uninfected patients. HHV-8 has a worldwide occurrence but infection rates vary according to a combination of geographic and behavioral risks. The main transmission route seems to be sexual, nevertheless, nasal secretions, saliva, blood, and organ graft have been proposed. HHV-8 was postulated as a new infectious agent for screening in blood donors. The aim of this study was to evaluate the prevalence of antibodies against HHV-8 antigens in blood donors of South America. Serum samples from 2,470 blood donors from Argentina, Brazil, and Chile corresponding to five geographic regions were studied by indirect immunofluorescence assay (IFA). Seroprevalence rate was 3.7% (92/2,470; 95% CI 2.9-4.5) in the entire blood donor population distributed as follows: Argentina, 4.0% (Buenos Aires city, 4.3%; Bahia Blanca, 2.4%; and Córdoba, 4.0%), Campinas (Brazil), 2.8%; and Santiago de Chile, 3.0%. There was no difference (P>0.05) between men and women or age related, except in Brazil where positive cases were 30-49-year-old males. The present study, which includes different geographical areas of multiple countries from South America, has not been done before. The results show similar prevalence rates among the studied zones corresponding to low-prevalence regions. South America is a large sub-continent with a wide spectrum of population and geographical characteristics, thus, more HHV-8 prevalence studies should be necessary to establish possible regional differences.