Rapid identification of Aspergillus fumigatus within the section Fumigati

<p>Abstract</p> <p>Background</p> <p>New fungal species that are morphologically similar to <it>Aspergillus fumigatus </it>were recently described and included in section <it>Fumigati</it>. Misidentification of such fungal species, particularly of the human pathogens, <it>Aspergillus lentulus</it>, <it>Neosartorya fischeri</it>, <it>Neosartorya hiratsukae</it>, <it>Neosartorya pseudofischeri </it>and <it>Neosartorya udagawae</it>, has been increasingly reported by numerous clinical labs. Nevertheless, <it>A. fumigatus </it>still accounts for more than 90% of all invasive aspergillosis cases. The purpose of the present study was to develop a rapid method for the molecular identification of <it>A. fumigatus </it>to distinguish it from other species within the section <it>Fumigati</it>.</p> <p>Results</p> <p>A multiplex PCR was developed using prior information based on β-tubulin (βtub) and rodlet A (rodA) partial gene sequences. PCR amplification of βtub and rodA fragments resulted in a distinctive electrophoretic pattern in <it>A. fumigatus </it>and <it>N. udagawae</it>. The polymorphisms found in the smallest amplified sequence of βtub (153 bp) and rodA (103 bp) genes were then compared among and within species of this taxonomic section. βtub was able to differentiate among 13 individual species and two groups of species that included the pathogenic fungus <it>A. lentulus</it>. A more limited number of sequences were available for rodA; nevertheless, we were able to distinguish <it>Aspergillus viridinutans, N. hiratsukae </it>and <it>N. udagawae</it>.</p> <p>Conclusions</p> <p>The assay described in the present study proved to be specific and highly reproducible, representing a fast and economic way of targeting molecular identification of the relevant mould, <it>A. fumigatus</it>, in clinical laboratories.</p

New sequence variants detected at DXS10148, DXS10074 and DXS10134 loci

A great amount of population and forensic genetic data are available for X-STRs supporting the need for having a common and accurate nomenclature among laboratories allowing for better communication, data exchange, and data comparison. DXS10148, DXS10074 and DXS10134 are commonly used X-STRs particularly due to their inclusion in the commercial kit Investigator Argus X-12 (Qiagen). Samples from West Africa and Iraq were sequenced for all three X-STRs allowing the detection of new DNA sequence variants. At DXS10148, variation was detected at four bases downstream from the flanking region from the repeat motif. The sequence AAGG-AAAG has been detected for the first time as a varying (AAGGAAAG)1–3 motif, in the present work. One additional string when compared to the common one (AAGGAAAG)2 adds eight bases to the fragment size of the tetranucleotide STR. This means that 2 repeats are added in these cases to the fragment size of the allele, while the presence of only one copy will reduce the expected allele size by 2 repeats. At DXS10074 two varying stretches consisting of AC and AG dinucleotide repeats were observed in the upstream flanking region, six bases from the main repeat core that also influence the expected allele size. DXS10134 revealed a simpler nomenclature in the Guinea-Bissau sample set when compared to the previously described allele nomenclature. This detected new hidden variation also has impact on the actual allele nomenclature at this locus as it contributes to a new class of short alleles so far undetected in other studies.info:eu-repo/semantics/publishedVersio

Differentiation of candida albicans strains by microsatellite multiplex PCR genotyping

Resumo da comunicação apresentado na conferência Candida and Candidiasis realizada em Março de 2004 em Austin, Texas EUA

Candida albicans microsatellite CAI-21b sequence

Sequência do alelo 21b do microssatélite CAI depositado na base de dados da NCBI em Julho de 2004

Development of a microsatellite multiplex PCR strategy for differentiation of Candida albicans strains

Resumo e poster da comunicação apresentada no Congresso Nacional de Microbiologia, em 2003, Tomar, Portugal.The polymorphism of five new microsatellite loci, located outside and inside known coding regions, in the genome of the pathogenic yeast C. albicans, was investigated in order to evaluate their applicability to accurately differentiate strains. The microsatellites were selected so that each was assigned to a different chromosome in order to evenly span them throughout the genome. A multiplex PCR strategy was developed allowing the simultaneous screening of the five markers, followed by GenScan analysis of the products, providing a rapid and accurate methodology for genotyping large numbers of strains. A total of 122 C. albicans strains, obtained from 80 patients and collected from three health institutions, were analysed using this multiplex system. Seventy-eight different genotypes were observed resulting in a discriminatory power of 0.98. When applying these microsatellites to the identification of strains isolated from recurrent vulvovaginal infections in eight patients, it was found that 13 out of 15 episodes were due to the same strain. When multiple isolates obtained from the same patient were studied the results showed that in different body sites, patients can harbour distinct clones but the infecting population at each body site is monoclonal. These new microsatellites proved to be a valuable tool to differentiate C. albicans strains and when compared to other molecular genotyping techniques, revealed to be simple, efficient and reproducible, being suitable for application in large scale epidemiological studies. Allele nomenclature based on the number of repeat sequences rather than fragment size is proposed for the characterization of each strain and contributes for the construction of a public database in light of what is already in use for other organisms

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European

<p>Abstract</p> <p>Background</p> <p>The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17^th–18^thcentury remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.</p> <p>Results</p> <p>Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17^th–18^thcenturies than today.</p> <p>Conclusion</p> <p>The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.</p

Intercontinental Admixture and Stratification of the European Background

The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time

Candida albicans microsatellite CAI-39 sequence

Sequência do alelo 39 do microssatélite CAI depositado na base de dados da NCBI em Julho de 2004

Candida albicans microsatellite CAI-32a sequence

Sequência do alelo 32a do microssatélite CAI depositado na base de dados da NCBI em Julho de 2004

Candida albicans microsatellite CAI-30 sequence

Sequência do alelo 30 do microssatélite CAI depositado na base de dados da NCBI em Julho de 2004