The association of phospholipase C and virulence of C. albicans

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Low linkage disequilibrium in wild Anopheles gambiae s.l. populations

<p>Abstract</p> <p>Background</p> <p>In the malaria vector <it>Anopheles gambiae</it>, understanding diversity in natural populations and genetic components of important phenotypes such as resistance to malaria infection is crucial for developing new malaria transmission blocking strategies. The design and interpretation of many studies here depends critically on Linkage disequilibrium (LD). For example in association studies, LD determines the density of Single Nucleotide Polymorphisms (SNPs) to be genotyped to represent the majority of the genomic information. Here, we aim to determine LD in wild <it>An. gambiae s.l</it>. populations in 4 genes potentially involved in mosquito immune responses against pathogens (<it>Gambicin</it>, <it>NOS</it>, <it>REL2 </it>and <it>FBN9</it>) using previously published and newly generated sequences.</p> <p>Results</p> <p>The level of LD between SNP pairs in cloned sequences of each gene was determined for 7 species (or incipient species) of the <it>An. gambiae </it>complex. In all tested genes and species, LD between SNPs was low: even at short distances (< 200 bp), most SNP pairs gave an r²< 0.3. Mean r²ranged from 0.073 to 0.766. In most genes and species LD decayed very rapidly with increasing inter-marker distance.</p> <p>Conclusions</p> <p>These results are of great interest for the development of large scale polymorphism studies, as LD generally falls below any useful limit. It indicates that very fine scale SNP detection will be required to give an overall view of genome-wide polymorphism. Perhaps a more feasible approach to genome wide association studies is to use targeted approaches using candidate gene selection to detect association to phenotypes of interest.</p

Characterization of the genetic diversity in superficial and systemic human isolates of Candida parapsilosis by randomly amplified polymorphic DNA (RAPD)

The application of randomly amplified polymorphic DNA (RAPD) technology for strain delineation of medically important yeasts has proved to be a valuable tool in clinico-epidemiological studies of Candida species. Candida parapsilosis, a form species of the fungi imperfecti, is an emerging pathogen gaining recognition as an opportunistic agent, especially in the immunocompromised. Therefore, 15 clinical isolates of C. parapsilosis obtained from oral, cutaneous and systemic Candida infections were typed by RAPD analysis using four different primers. The primers RSD6 and RSD9 elicited 7 genotypes each, whereas primers RSD7 and RSD12 revealed 6 and 10 genotypes, respectively. When the data were correlated, a higher degree of genomic heterogeneity in systemic isolates was noted compared with the oral and cutaneous isolates, which shared somewhat similar RAPD profiles. However, a single oral isolate (P5) and two systemic isolates (P13 and P15) elicited radically divergent profiles, dissimilar to their counterparts. RAPD study of the latter two isolates with three additional primers (RSD8, RSD10 and RSD11) confirmed the observed genomic disparity. These data substantiate the previous observations on the genomic heterogeneity in C. parapsilosis and point to genetic shifts which may be associated with ecodiversity, as well as the possible existence of distinct genetic groups within this form species.link_to_subscribed_fulltex

The genetic diversity in superficial and systemic isolates of Candida parapsilosis

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Randomly amplified polymorphic DNA fingerprinting: the basics.

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Amplification-based nucleic acid scanning techniques to assess genetic polymorphism in Candida

Opportunistic pathogen Candida causes common fungal infections that manifest both superficially and systemically, especially in compromised patients. Although C. albicans is by far the main etiological agent of candidosis, the frequency of isolation of other non-albicans species such as C. glabrata and C. krusei is increasing at an alarming rate. Therefore, the epidemiology, pathogenicity, and diagnosis of infections due to these organisms are of great importance. Of a variety of genotyping methods utilized for strain delineation of these Candida species, amplification-based techniques such as randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), restriction digestion-mediated PCR (RFLP-PCR), and single-stranded conformational polymorphism (SSCP) and microsatellite PCR (interrepeat PCR, IR-PCR) are the most popular and widely used. In the last decade or so these techniques have helped unravel the clinical epidemiological features of pathogenicity, diversity, microevolution, and natural heterozygosity in Candida species. Here we review in detail the basic principles of RAPD, the nature of the primer and factors influencing its selection, and the limitations of RAPD assays as well as analysis and interpretation of banding profiles generated using the software programs. In addition, the principles of other RAPD-based amplification techniques (AFLP, RFLP-PCR, SSCP, and IR-PCR) and their application in molecular epidemiologic studies of Candida species in particular and other fungi in general are also reviewed. It is concluded that these methods have wide applicability in genotyping fungi, although they differ greatly in their resolution and have advantages and drawbacks depending on the task in question.link_to_subscribed_fulltex

Genomic diversity of oral Candida krusei isolates as revealed by DNA fingerprinting and electrophoretic karyotyping

Candida krusei is receiving increasing attention as an important human pathogen, especially in compromised patients, who frequently manifest with multiepisodes of candidosis. As there is scant information on the genetic diversity of this pathogen the present study was undertaken to establish its genetic profiles using three different typing methods: PFGE (pulsed-field gel electrophoresis), RFLP (restriction fragment length polymorphism), RAPD (randomly amplified polymorphic DNA). When 11 oral isolates of C. krusei were molecular typed by PFGE, 3 to 5 chromosomes with sizes ranging from 1000 kb to 3000 kb per isolate were revealed. All isolates produced a single bright band at approximately 1,100 kb and two to three bands between 2,500 kb and 3,000 kb, demonstrating 5 different karyotypes. RFLP with HinfI yielded 9 different genotypes, while DNA fingerprinting by RAPD with 3 primers (RSD6 (5′GCGATCCCCA3′), RSD7 (5′AGTGAATTCG CGGTGAGATGCC3′) and RSD12 (5′GCATATCAATAAGC GCAGGAAAAG 3′)), resulted in 8, 3 and 11 different genotypes, respectively. This study provides evidence hitherto unavailable on the genetic polymorphism of C. krusei isolates colonizing the oral niche under different clinical conditions. Such genotypic polymorphism should help strain delineation in epidemiologic surveillance of either nosocomial or community outbreaks of C. krusei infections.link_to_subscribed_fulltex