Natalie Fedorova Abrams

Publications (32) View all

• Source

  Available from: Muhammad Saqib

  Article: Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements.

  Liliana Losada, Catherine M Ronning, David DeShazer, Donald Woods, Natalie Fedorova, H Stanley Kim, Svetlana A Shabalina, Talima R Pearson, Lauren Brinkac, Patrick Tan, Tannistha Nandi, Jonathan Crabtree, Jonathan Badger, Steve Beckstrom-Sternberg, Muhammad Saqib, Steven E Schutzer, Paul Keim, William C Nierman
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  ABSTRACT: Burkholderia mallei (Bm), the causative agent of the predominately equine disease glanders, is a genetically uniform species that is very closely related to the much more diverse species Burkholderia pseudomallei (Bp), an opportunistic human pathogen and the primary cause of melioidosis. To gain insight into the relative lack of genetic diversity within Bm, we performed whole-genome comparative analysis of seven Bm strains and contrasted these with eight Bp strains. The Bm core genome (shared by all seven strains) is smaller in size than that of Bp, but the inverse is true for the variable gene sets that are distributed across strains. Interestingly, the biological roles of the Bm variable gene sets are much more homogeneous than those of Bp. The Bm variable genes are found mostly in contiguous regions flanked by insertion sequence (IS) elements, which appear to mediate excision and subsequent elimination of groups of genes that are under reduced selection in the mammalian host. The analysis suggests that the Bm genome continues to evolve through random IS-mediated recombination events, and differences in gene content may contribute to differences in virulence observed among Bm strains. The results are consistent with the view that Bm recently evolved from a single strain of Bp upon introduction into an animal host followed by expansion of IS elements, prophage elimination, and genome rearrangements and reduction mediated by homologous recombination across IS elements.
  Genome Biology and Evolution 01/2010; 2:102-16. · 4.62 Impact Factor
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  Available from: Natalie Fedorova Abrams

  Article: Using aCGH to study intraspecific genetic variability in two pathogenic molds, Aspergillus fumigatus and Aspergillus flavus.

  Natalie D Fedorova, Stephanie Harris, Dan Chen, David W Denning, Jiujiang Yu, Peter J Cotty, William C Nierman
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  ABSTRACT: We have examined the feasibility of using array comparative genomic hybridization (aCGH) to explore intraspecific genetic variability at the genomic level in two pathogenic molds, Aspergillus fumigatus and Aspergillus flavus. Our analysis showed that strain-specific genes may comprise up to 2% of their genomes in comparison to isolates from different vegetative (heterokaryon) compatibility groups (VCGs). In contrast, isolates with the same VCG affiliations have almost identical gene content. Most isolate-specific genes are annotated as 'hypothetical' and located in a few large subtelomeric indels. The list includes highly polymorphic loci that contain putative het (heterokaryon compatibility) loci, which determine the individual's VCG during parasexual crossing. Incidentally, VCGs in both species seem to be significantly associated with either alpha or HMG mating type (Chi-square test, P=0.05). In conclusion CGH can be used to effectively to identify isolate-specific genes in Aspergillus species. Preliminary evidence suggests that gene flow in both species is largely constrained by VCG boundaries, although further VCG sampling is required to confirm this observation.
  Medical mycology: official publication of the International Society for Human and Animal Mycology 04/2009; 47 Suppl 1:S34-41. · 2.13 Impact Factor
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  Available from: Natalie Fedorova Abrams

  Article: Potential of Aspergillus flavus genomics for applications in biotechnology.

  Thomas E Cleveland, Jiujiang Yu, Natalie Fedorova, Deepak Bhatnagar, Gary A Payne, William C Nierman, Joan W Bennett
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  ABSTRACT: Aspergillus flavus is a common saprophyte and opportunistic pathogen that produces numerous secondary metabolites. The primary objectives of the A. flavus genomics program are to reduce and eliminate aflatoxin contamination in food and feed and to discover genetic factors that contribute to plant and animal pathogenicity. A. flavus expressed sequence tags (ESTs) and whole-genome sequencing have been completed. Annotation of the A. flavus genome has revealed numerous genes and gene clusters that are potentially involved in the formation of aflatoxin and other secondary metabolites, as well as in the degradation of complex carbohydrate polymers. Analysis of putative secondary metabolism pathways might facilitate the discovery of new compounds with pharmaceutical properties, as well as new enzymes for biomass degradation.
  Trends in Biotechnology 03/2009; 27(3):151-7. · 9.15 Impact Factor
• Article: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

  William C. Nierman, Arnab Pain, Michael J. Anderson, Jennifer R. Wortman, H. Stanley Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B. Archer, Clara Bermejo, [......], Owen White, John Woodward, Jae-Hyuk Yu, Claire Fraser, James E. Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall, Bart Barrell, David W. Denning
  Nature 01/2006; 439(7075):502-502. · 36.28 Impact Factor
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  Available from: Natalie Fedorova Abrams

  Article: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.

  William C Nierman, Arnab Pain, Michael J Anderson, Jennifer R Wortman, H Stanley Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B Archer, Clara Bermejo, [......], Owen White, John Woodward, Jae-Hyuk Yu, Claire Fraser, James E Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall, Bart Barrell, David W Denning
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  ABSTRACT: Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.
  Nature 01/2006; 438(7071):1151-6. · 36.28 Impact Factor