Now showing 1 - 5 of 5
  • Publication
    Role of Genomics and RNA-seq in Studies of Fungal Virulence
    Since its introduction in the last decade, massive parallel sequencing, or "next-generation sequencing", has revolutionized our access to genomic information, providing accurate data with increasingly higher yields and lower costs with respect to first-generation technology. Massive parallel sequencing of cDNA, or RNA-seq, is progressively replacing array-based technology as the method of choice for transcriptomics. This review describes some of the most recent applications of next-generation sequencing technology to the study of pathogenic fungi, including Candida, Aspergillus and Cryptococcusspecies. Several integrated approaches illustrate the power and accuracy of RNA-seq for studying the biology of human fungal pathogens. In addition, the lack of consistency in data analysis is discussed.
      381Scopus© Citations 3
  • Publication
    Characterization of carboxylate nanoparticle adhesion with the fungal pathogen Candida albicans
    Candida albicans is the lead fungal pathogen of nosocomial bloodstream infections worldwide and has mortality rates of 43%. Nanoparticles have been identified as a means to improve medical outcomes for Candida infections, enabling sample concentration, serving as contrast agents for in vivo imaging, and delivering therapeutics. However, little is known about how nanoparticles interact with the fungal cell wall. In this report we used laser scanning confocal microscopy to examine the interaction of fluorescent polystyrene nanoparticles of specific surface chemistry and diameter with C. albicans and mutant strains deficient in various C. albicans surface proteins. Carboxylate-functionalized nanoparticles adsorbed mainly to the hyphae of wild-type C. albicans. The dissociative binding constant of the nanoparticles was ∼150, ∼30 and ∼2.5 pM for 40, 100 nm and 200 nm diameter particles, respectively. A significant reduction in particle binding was observed with a Δals3 strain compared to wild-type strains, identifying the Als3 adhesin as the main mediator of this nanoparticle adhesion. In the absence of Als3, nanoparticles bound to germ tubes and yeast cells in a pattern resembling the localization of Als1, indicating Als1 also plays a role. Nanoparticle surface charge was shown to influence binding – positively charged amine-functionalized nanoparticles failed to bind to the hyphal cell wall. Binding of carboxylate-functionalized nanoparticles was observed in the presence of serum, though interactions were reduced. These observations show that Als3 and Als1 are important targets for nanoparticle-mediated diagnostics and therapeutics, and provide direction for optimal diameter and surface characteristics of nanoparticles that bind to the fungal cell wall.
      367Scopus© Citations 14
  • Publication
    Role of Genomics and RNA-seq in Studies of Fungal Virulence
    Since its introduction in the last decade, massive parallel sequencing, or “next-generation sequencing”, has revolutionized our access to genomic information, providing accurate data with increasingly higher yields and lower costs with respect to first-generation technology. Massive parallel sequencing of cDNA, or RNA-seq, is progressively replacing array-based technology as the method of choice for transcriptomics. This review describes some of the most recent applications of next-generation sequencing technology to the study of pathogenic fungi, including Candida, Aspergillus and Cryptococcus species. Several integrated approaches illustrate the power and accuracy of RNA-seq for studying the biology of human fungal pathogens. In addition, the lack of consistency in data analysis is discussed.
      641Scopus© Citations 3
  • Publication
    Comparative Genome Analysis and Gene Finding in Candida Species Using CGOB
    The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data.
      468Scopus© Citations 90
  • Publication
    The APSES transcription factor Efg1 is a global regulator that controls morphogenesis and biofilm formation in Candida parapsilosis
    Efg1 (a member of the APSES family) is an important regulator of hyphal growth and of the white-to-opaque transition in C. albicans and very closely related species. We show that in Candida parapsilosis Efg1 is a major regulator of a different morphological switch at the colony level, from a concentric to smooth morphology. The rate of switching is at least 20-fold increased in an efg1 knockout relative to wild type. Efg1 deletion strains also have reduced biofilm formation, attenuated virulence in an insect model, and increased sensitivity to SDS and caspofungin. Biofilm reduction is more dramatic in in vitro than in in vivo models. An Efg1 paralog (Efh1) is restricted to Candida species, and does not regulate concentric-smooth phenotype switching, biofilm formation or stress response. We used ChIP-seq to identify the Efg1 regulon. 931 promoter regions bound by Efg1 are highly enriched for transcription factors and regulatory proteins. Efg1 also binds to its own promoter, and negatively regulates its expression. Efg1 targets are enriched in binding sites for 93 additional transcription factors, including Ndt80. Our analysis suggests that Efg1 has an ancient role as regulator of development in fungi, and is central to several regulatory networks.
      481Scopus© Citations 40