21
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

          Related collections

          Most cited references26

          • Record: found
          • Abstract: found
          • Article: not found

          Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power.

          Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (DLR) appeared to be an effective way to predict whether F0 immigrants could be identified for a particular pair of populations using a given set of markers.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Detecting immigration by using multilocus genotypes.

            Immigration is an important force shaping the social structure, evolution, and genetics of populations. A statistical method is presented that uses multilocus genotypes to identify individuals who are immigrants, or have recent immigrant ancestry. The method is appropriate for use with allozymes, microsatellites, or restriction fragment length polymorphisms (RFLPs) and assumes linkage equilibrium among loci. Potential applications include studies of dispersal among natural populations of animals and plants, human evolutionary studies, and typing zoo animals of unknown origin (for use in captive breeding programs). The method is illustrated by analyzing RFLP genotypes in samples of humans from Australian, Japanese, New Guinean, and Senegalese populations. The test has power to detect immigrant ancestors, for these data, up to two generations in the past even though the overall differentiation of allele frequencies among populations is low.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Microsatellites in different eukaryotic genomes: survey and analysis.

              We examined the abundance of microsatellites with repeated unit lengths of 1-6 base pairs in several eukaryotic taxonomic groups: primates, rodents, other mammals, nonmammalian vertebrates, arthropods, Caenorhabditis elegans, plants, yeast, and other fungi. Distribution of simple sequence repeats was compared between exons, introns, and intergenic regions. Tri- and hexanucleotide repeats prevail in protein-coding exons of all taxa, whereas the dependence of repeat abundance on the length of the repeated unit shows a very different pattern as well as taxon-specific variation in intergenic regions and introns. Although it is known that coding and noncoding regions differ significantly in their microsatellite distribution, in addition we could demonstrate characteristic differences between intergenic regions and introns. We observed striking relative abundance of (CCG)(n)*(CGG)(n) trinucleotide repeats in intergenic regions of all vertebrates, in contrast to the almost complete lack of this motif from introns. Taxon-specific variation could also be detected in the frequency distributions of simple sequence motifs. Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are discussed.
                Bookmark

                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                1 April 2016
                2016
                : 11
                : 4
                : e0152434
                Affiliations
                [1 ]Univ Lyon, Université Lyon 1, CNRS UMR 5240 Microbiology Adaptation and Pathogenesis, Villeurbanne, France
                [2 ]Univ Lyon, Université Lyon 1, Villeurbanne, France
                [3 ]Univ Lyon, Université Lyon 1, ISPB EA 4446 Bioactive Molecules and Medicinal Chemistry, Lyon, France
                [4 ]EDF Research and Development, Laboratoire National d’Hydraulique et Environnement, Chatou, France
                National Cheng-Kung University, TAIWAN
                Author notes

                Competing Interests: There are restrictions for the materials i.e., the available strains. The availability of these materials would be possible with the approval of the funder. This did not alter the authors' adherence to PLOS ONE policies on sharing data.

                Conceived and designed the experiments: MP. Performed the experiments: BCG ER AM M. Besseyrias. Analyzed the data: BCG MP. Contributed reagents/materials/analysis tools: MP PH M. Binet. Wrote the paper: MP BCG. Conceived and designed the experiments under supervision of MP: PH BCG M. Binet.

                Article
                PONE-D-15-37302
                10.1371/journal.pone.0152434
                4818093
                27035434
                a74357ae-f2f1-46de-8f44-4a70cadef9c0
                © 2016 Coupat-Goutaland et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 7 September 2015
                : 14 March 2016
                Page count
                Figures: 2, Tables: 5, Pages: 14
                Funding
                The funder EDF played a role in the strains collection, the site access and agreement and decision to publish (insofar the confidentiality of the site is respected). The funder provided support in the form of salaries for authors ER and BCG but did not have any additional role in the study design, data collection and analysis, or preparation of the manuscript. The specific roles of these authors are articulated in the Author Contributions section.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Protozoans
                Parasitic Protozoans
                Naegleria Fowleri
                Biology and Life Sciences
                Genetics
                Gene Types
                Microsatellite Loci
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Artificial gene amplification and extension
                Random amplified polymorphic DNA technique
                Research and analysis methods
                Molecular biology techniques
                Artificial gene amplification and extension
                Random amplified polymorphic DNA technique
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Cloning
                Research and Analysis Methods
                Molecular Biology Techniques
                Cloning
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Heredity
                Heterozygosity
                Biology and Life Sciences
                Genetics
                Heredity
                Inbreeding
                Medicine and Health Sciences
                Parasitic Diseases
                Primary Amoebic Meningoencephalitis
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article