Nucleotide sequences of 72 species of Drosophilidae were determined for divergent D1 and D2 domains (representing 200 and 341 nucleotides respectively in D. melanogaster) of large ribosomal RNA, using the rRNA direct sequencing method. Molecular phylogenetic trees were reconstructed using both distance and parsimony methods and the robustness of the nodes was evaluated by the bootstrap procedure. The trees obtained by these methods revealed four main lineages or clades which do not correspond to the taxonomical hierarchy. In our results, the genus Chymomyza is associated with the subgenus Scaptodrosophila of the genus Drosophila and their cluster constitutes the most ancient clade. The two other clades are constituted of groups belonging to the subgenus Sophophora of the genus Drosophila: the so-called Neotropical clade including the willistoni and saltans groups and the obscura-melanogaster clade itself split into three lineages: (1) obscura group + ananassae subgroup, (2) montium subgroup, and (3) melanogaster + Oriental subgroups. The fourth clade, the Drosophila one, contains three lineages. D. polychaeta, D. iri, and D. fraburu are branched together and constitute the most ancient lineage; the second lineage includes the annulimana, bromeliae, dreyfusi, melanica, mesophragmatica, repleta, robusta, and virilis groups. The third lineage is composed of the immigrans and the cardini, funebris, guaramunu, guarani, histrio, pallidipennis, quinaria, and tripunctata groups. The genera Samoaia, Scaptomyza, and Zaprionus are branched within the Drosophila clade. Although these four clades appear regularly in almost all tree calculations, additional sequencing will be necessary to determine their precise relationships.
Internal transcribed spacers (ITS) and the 5.8S ribosomal gene of 21 Naegleria fowleri strains and eight other species including Naegleria gruberi were sequenced. The results showed that this region can help differentiate between and within species. The phylogeny of Naegleria spp. deduced from the ITS and the 5.8S gene produced four major lineages, fowleri-lovaniensis, galeacystis-italica-clarki-gruberi-australiensis, andersoni-jamiesoni, and pussardi, that fit perfectly with those inferred from the 18S rRNA gene analysis. The N. gruberi isolate, NG260, was closely related to Naegleria pussardi. The other N. gruberi isolates branched together with Naegleria australiensis in another lineage. The ITS and 5.8S results for N. fowleri were congruent with those previously deduced by RAPD analysis. The phylogenetic analysis inferred from ITS and RAPD data revealed two major groups. The French Cattenom and Chooz and South Pacific strains constituted the first group. The second group encompassed the strains corresponding to the Euro-American and Widespread RAPD variants and shared the same substitution in the 5.8S gene. In addition, it was possible to define species specific primers in ITS regions to rapidly identify N. fowleri.
It has often been suggested that the frequently observed Watson-Crick base-pair compensatory substitutions in RNA helical structures occur mainly through a slightly deleterious G'U intermediate state. We have scored base substitutions in a set of 82 related Drosophila species for the D1 and D2 variable domains of the large rRNA subunit. In all locations where a G-C +-A-U compensatory base change occurred, a G-U pair has been observed in one or several species. As this dominant process implies two transitions, their rate was far higher in paired regions (92%) than in unpaired regions (47%). The other types of compensation were rarer and no intermediate states were observed. Most of the GNU base pairs observed in a species are not slightly deleterious. The rate of evolution of compensatory substitution is close to that predicted by a simple model of compensatory substitution through slightly deleterious or slightly advantageous GNU pairs, although some exceptions are presented.The secondary structure of rRNAs is remarkably uniform across taxa (1-3). This conservation is ensured by a special pattern of base change known as compensatory mutation (although what is observed is a compensatory substitution): when a substitution has occurred at a given site, the corresponding site, located vis-A-vis in the helical structure formed by the folding of the single RNA strand, also exhibits a change that restores the Watson-Crick base complementarity.This observation is so general for the "stable" RNAs that the most efficient method used to confirm a secondary structure inferred from a sequence is based on the observation in various species of compensatory substitutions in the putative helices. Biochemical studies (4) or functional studies of double mutants (5, 6) have confirmed results obtained with the comparative method.A simple model assumes that A-U* and G-C are optimal and stable states and that A-U * G-C compensatory substitutions occur mainly through a slightly deleterious intermediate GNU state that is somewhat less stable but retains the helical structure. This slightly deleterious intermediate would be short-lived and, therefore, rarely observed. The low frequency of G-U in RNA sequences is generally explained in this way (7,8). However, when only distantly related species are compared, as usual, there is no evidence that the G-U pairs effectively observed are deleterious or fugacious (9). In fact, some of these pairs may be deleterious states whereas others may be conserved over more or less prolonged times. The terms fugacious and stable states have a temporal significance and the time reference will be the average life span of a neutral pair (see Results).The recognition of intermediate states per se must be achieved through comparison of numerous and related sequences that have evolved during a short time. This requires the study in related species of a region of the molecule variable enough to allow the observation of a sufficient number of substitutions. For this purpose, we have focused our study on t...
A multiplex PCR was developed to simultaneously detect Naegleria fowleri and other Naegleria species in the environment. Multiplex PCR was also capable of identifying N. fowleri isolates with internal transcribed spacers of different sizes. In addition, restriction fragment length polymorphism analysis of the PCR product distinguished the main thermophilic Naegleria species from the sampling sites.The free-living amoebae belonging to the genus Naegleria occur worldwide and inhabit soil and aquatic environments. One member of this genus, Naegleria fowleri, causes primary amoebic meningoencephalitis (PAM) in humans. Although PAM is rare (more than 190 cases reported worldwide [15]), this central nervous system disease is lethal within 1 week in most cases (3). The majority of the fatal infections due to N. fowleri occur in young people exposed to warm water in ponds, swimming pools, and lakes. N. fowleri is thermophilic and generally found in natural and artificially heated water, in particular in the cooling ponds of power plants, in which this species can proliferate intensively (4,11,12,27,28). Two other thermophilic Naegleria species are currently found in these sites: Naegleria lovaniensis, which is harmless, and Naegleria australiensis, which is pathogenic in mice. The thermophilic species Naegleria italica was also reported to be pathogenic in mice but is rarely encountered (7). These two species could be potentially dangerous for humans.In a preventive measure, water monitoring was performed regularly in the nuclear power plants of France in order to check for the proliferation of N. fowleri. The identification of Naegleria species has been carried out by an isoenzymatic procedure which allowed simultaneous detection of the three main thermophilic Naegleria species. Other immunological and molecular techniques are now available to specifically detect N. fowleri in environmental sites (14,25,26). Recently, ribosomal internal transcribed spacers (ITS) were reported to be useful markers for Naegleria (10,20), and species-specific primers were defined for N. fowleri (20). In addition, variations in the sequence and size of the ITS were found within this humanpathogenic species, with five different variants which were mostly detected in France. However, the geographic dispersal and the prevalence of these variants were not well established, since too few samples were examined at different sites.In this study, we applied a simplified ITS PCR procedure to the environmental Naegleria isolates for several reasons: (i) to rapidly and easily analyze a large number of isolates, (ii) to detect the presence of N. fowleri in the potential sites and to further explore the genetic diversity of this species, and (iii) to identify the other thermophilic Naegleria isolates at the sites by using PCR restriction fragment length polymorphism (RFLP) analysis.Amoeba isolation from the environment. Five hundred environmental strains were isolated from water of the cooling ponds and downstream of five different nuclear power plants ...
We examined a partial SSU-rDNA sequence from 20 Acanthamoeba isolates associated with keratitis infections. The phylogenetic tree inferred from this partial sequence allowed to assign isolates to genotypes. Among the 20 isolates examined, 16 were found to be of the T4 genotype, 2 were T3, 1 was a T5, and 1 was a T2, confirming the predominance of T4 in infections. However, the study highlighted other genotypes more rarely associated with infections, particularly the T2 genotype. Our study is the second one to detect that this genotype is associated with keratitis. Additionally, the phylogenetic analyses showed five main emerging clusters, T4/T3/T11, T2/T6, T10/T12/T14, T13/T16, and T7/T8/T9/T17, regularly obtained whichever method was used. A similar branching pattern was found when the full rDNA sequence was investigated.
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