Virginia Coryell

Summary

Affiliation: Northern Arizona University
Country: USA

Publications

  1. ncbi request reprint Bacillus anthracis evolution and epidemiology
    P Keim
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Curr Top Microbiol Immunol 271:21-32. 2002
  2. ncbi request reprint Microbial forensics: DNA fingerprinting of Bacillus anthracis (anthrax)
    Paul Keim
    Department of Biological Sciences, Northern Arizona University, USA
    Anal Chem 80:4791-9. 2008
  3. ncbi request reprint Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
    Science 296:2028-33. 2002
  4. pmc Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis
    Stephen M Beckstrom-Sternberg
    Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
    PLoS ONE 2:e947. 2007
  5. pmc Phylogeography of Francisella tularensis: global expansion of a highly fit clone
    Amy J Vogler
    Center for Microbial Genetics and Genomics, Northern Arizona University, P O Box 4073, Flagstaff, AZ 86011, USA
    J Bacteriol 191:2474-84. 2009
  6. pmc Molecular epidemiology of glanders, Pakistan
    Heidie Hornstra
    Northern Arizona University, Flagstaff, Arizona 86011 4073, USA
    Emerg Infect Dis 15:2036-9. 2009
  7. pmc Francisella tularensis in the United States
    Jason Farlow
    Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    Emerg Infect Dis 11:1835-41. 2005
  8. pmc Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America
    Raymond K Auerbach
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
    PLoS ONE 2:e770. 2007
  9. pmc Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue
    Richard T Okinaka
    Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    Emerg Infect Dis 14:653-6. 2008
  10. pmc Pre-Columbian origins for North American anthrax
    Leo J Kenefic
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
    PLoS ONE 4:e4813. 2009

Detail Information

Publications85

  1. ncbi request reprint Bacillus anthracis evolution and epidemiology
    P Keim
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Curr Top Microbiol Immunol 271:21-32. 2002
    ..The A branch is the most common worldwide, though the B branch is locally important in certain areas. The ecology and the evolution of B. anthracis have been greatly influenced by the spore phase of the lifecycle...
  2. ncbi request reprint Microbial forensics: DNA fingerprinting of Bacillus anthracis (anthrax)
    Paul Keim
    Department of Biological Sciences, Northern Arizona University, USA
    Anal Chem 80:4791-9. 2008
  3. ncbi request reprint Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
    Science 296:2028-33. 2002
    ..These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks...
  4. pmc Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis
    Stephen M Beckstrom-Sternberg
    Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
    PLoS ONE 2:e947. 2007
    ..I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis...
  5. pmc Phylogeography of Francisella tularensis: global expansion of a highly fit clone
    Amy J Vogler
    Center for Microbial Genetics and Genomics, Northern Arizona University, P O Box 4073, Flagstaff, AZ 86011, USA
    J Bacteriol 191:2474-84. 2009
    ..Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for F. tularensis subsp. holarctica...
  6. pmc Molecular epidemiology of glanders, Pakistan
    Heidie Hornstra
    Northern Arizona University, Flagstaff, Arizona 86011 4073, USA
    Emerg Infect Dis 15:2036-9. 2009
    ..We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines...
  7. pmc Francisella tularensis in the United States
    Jason Farlow
    Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    Emerg Infect Dis 11:1835-41. 2005
    ..These correlates provide testable hypotheses regarding ecologic factors associated with maintaining tularemia foci...
  8. pmc Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America
    Raymond K Auerbach
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
    PLoS ONE 2:e770. 2007
    ..Recent studies based upon single nucleotide polymorphisms have begun to quantify the genetic diversity of Y. pestis in North America...
  9. pmc Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue
    Richard T Okinaka
    Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    Emerg Infect Dis 14:653-6. 2008
    ..anthracis genotype into 1 of 12 subgroups. Reconstruction of the pagA gene also showed a unique SNP that defines a new lineage for B. anthracis...
  10. pmc Pre-Columbian origins for North American anthrax
    Leo J Kenefic
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
    PLoS ONE 4:e4813. 2009
    ..anthracis isolates. Continent-wide dispersal of WNA B. anthracis likely required movement by later European colonizers, but the continent's first inhabitants may have seeded the initial North American populations...
  11. pmc Global genetic population structure of Bacillus anthracis
    Matthew N Van Ert
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
    PLoS ONE 2:e461. 2007
    ..Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated...
  12. pmc Within-host evolution of Burkholderia pseudomallei in four cases of acute melioidosis
    Erin P Price
    Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, Arizona, United States of America
    PLoS Pathog 6:e1000725. 2010
    ....
  13. pmc A decade of plague in Mahajanga, Madagascar: insights into the global maritime spread of pandemic plague
    Amy J Vogler
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA
    MBio 4:e00623-12. 2013
    ..However, the temporary large pathogen population expansion provides the means for plague pathogens to disperse and become ecologically established in more suitable nonurban environments...
  14. pmc Castor bean organelle genome sequencing and worldwide genetic diversity analysis
    Maximo Rivarola
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e21743. 2011
    ....
  15. pmc Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar
    Amy J Vogler
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA
    PLoS Negl Trop Dis 5:e1319. 2011
    ..pestis in Madagascar...
  16. pmc Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe
    Erin P Price
    Northern Arizona University, Flagstaff, Arizona, USA
    Emerg Infect Dis 18:1307-13. 2012
    ..Our results suggest accidental contamination along the drug trafficking route through a cutting agent or animal hides used to smuggle heroin into Europe...
  17. pmc Melt analysis of mismatch amplification mutation assays (Melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models
    Dawn N Birdsell
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
    PLoS ONE 7:e32866. 2012
    ..We detail the parameters most important for the successful application of Melt-MAMA, which should prove useful to the wider scientific community...
  18. pmc Within-host evolution of Brucella canis during a canine brucellosis outbreak in a kennel
    Miklós Gyuranecz
    Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest 1143, Hungária körút 21, Hungary
    BMC Vet Res 9:76. 2013
    ....
  19. pmc Genotyping of Brucella species using clade specific SNPs
    Jeffrey T Foster
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    BMC Microbiol 12:110. 2012
    ....
  20. pmc FungiQuant: a broad-coverage fungal quantitative real-time PCR assay
    Cindy M Liu
    Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ 86011, USA
    BMC Microbiol 12:255. 2012
    ..Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques...
  21. pmc Detection of Burkholderia pseudomallei O-antigen serotypes in near-neighbor species
    Joshua K Stone
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
    BMC Microbiol 12:250. 2012
    ..Sero-crossreactivity is common among O-antigens of Burkholderia species. Here, we identified the presence of multiple B. pseudomallei O-antigen types and sero-crossreactivity in its near-neighbor species...
  22. pmc BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay
    Cindy M Liu
    Division of Pathogen Genomics, Translational Genomics Research Institute, 3051 W, Shamrell Blvd, Suite 106, Flagstaff, AZ 86001, USA
    BMC Microbiol 12:56. 2012
    ..We further utilized in silico evaluation to complement laboratory-based qPCR characterization to validate BactQuant...
  23. pmc Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries
    David M Engelthaler
    Translational Genomics Research Institute, Flagstaff, AZ, USA
    BMC Infect Dis 13:339. 2013
    ..New molecular tools need to be employed to improve subtyping of dominant local MRSA strains (e.g., spa type t003)...
  24. pmc Dominance of multidrug resistant CC271 clones in macrolide-resistant streptococcus pneumoniae in Arizona
    Jolene R Bowers
    Translational Genomics Research Institute, Flagstaff, AZ, USA
    BMC Microbiol 12:12. 2012
    ....
  25. pmc Identifying experimental surrogates for Bacillus anthracis spores: a review
    David L Greenberg
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    Investig Genet 1:4. 2010
    ..thuringiensis provided the best overall fit as a non-pathogenic surrogate for B. anthracis. Thus, we suggest focusing on this surrogate in future experiments of spore fate and transport modelling...
  26. pmc Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)
    Jeffrey T Foster
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    BMC Plant Biol 10:13. 2010
    ..We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci...
  27. pmc Phylogeography of Francisella tularensis subspecies holarctica from the country of Georgia
    Gvantsa Chanturia
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    BMC Microbiol 11:139. 2011
    ..In this study, we address this knowledge gap by describing the phylogenetic structure of F. tularensis subsp. holarctica isolates from the country of Georgia, and by placing these isolates into a global phylogeographic context...
  28. pmc Bacillus anthracis in China and its relationship to worldwide lineages
    Tatum S Simonson
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    BMC Microbiol 9:71. 2009
    ..Canonical single nucleotide polymorphism (canSNP) and multiple locus VNTR analysis (MLVA) typing has been used to examine this archival collection of isolates...
  29. pmc Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping
    Jana M U'ren
    Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, Arizona 86011, USA
    BMC Microbiol 7:23. 2007
    ..pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations...
  30. pmc An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics
    Richard T Okinaka
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011, USA
    BMC Genomics 12:477. 2011
    ..These phenotypes prompted Ezzell et al., (J. Clin. Microbiol. 28:223) to reclassify this isolate to Bacillus anthracis in 1990...
  31. pmc Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant
    Lila O Vodkin
    Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
    BMC Genomics 5:73. 2004
    ..In addition, discovery of the molecular basis of traits through examination of naturally occurring variation in hundreds of mutant lines could be enhanced by the construction and use of soybean cDNA microarrays...
  32. pmc Genomic islands from five strains of Burkholderia pseudomallei
    Apichai Tuanyok
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    BMC Genomics 9:566. 2008
    ..The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species...
  33. pmc Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
    Talima Pearson
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA
    BMC Biol 7:78. 2009
    ..We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction...
  34. pmc Tularemia in Alaska, 1938 - 2010
    Cristina M Hansen
    Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, 902 N, Koyukuk Dr, Fairbanks, AK 99775, USA
    Acta Vet Scand 53:61. 2011
    ..The results show that both F. t. tularensis and F. t. holarctica are present in Alaska and that subtype A.I, the most virulent type, is responsible for most recently reported human clinical cases in the state...
  35. pmc The genome and variation of Bacillus anthracis
    Paul Keim
    The Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff AZ 86011 4073, USA
    Mol Aspects Med 30:397-405. 2009
    ..A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria...
  36. pmc Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases
    PAUL S KEIM
    The Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    Nat Rev Microbiol 7:813-21. 2009
    ..This Review describes the distributions of the bacteria that cause anthrax, plague and tularaemia and investigates the forces that created clonal structures in these species...
  37. pmc Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing
    Craig A Cummings
    Northern Arizona University, Flagstaff, Arizona, USA
    Investig Genet 1:5. 2010
    ....
  38. ncbi request reprint Molecular diversity in Bacillus anthracis
    P Keim
    Department of Biological Sciences, Northern Arizona University, Flagstaff 86011 5640, USA
    J Appl Microbiol 87:215-7. 1999
    ..anthracis clones. The lineages reconstructed using these data may reflect the dispersal and evolution of this pathogen...
  39. pmc Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers
    P Keim
    Environmental Molecular Biology, Los Alamos National Laboratory, New Mexico 87545, USA
    J Bacteriol 179:818-24. 1997
    ..Based on AFLP marker similarity, the ongoing anthrax epidemic in Canada and the northern United States is due to a single strain introduction that has remained stable over at least 30 years and a 1,000-mile distribution...
  40. ncbi request reprint Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales
    Paul Keim
    Keim Genetics Laboratory, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Infect Genet Evol 4:205-13. 2004
    ..This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates...
  41. ncbi request reprint Molecular epidemiology, evolution, and ecology of Francisella
    Paul Keim
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Ann N Y Acad Sci 1105:30-66. 2007
    ..tularensis subsp. holarctica from tularemia outbreaks in Europe and the United States proves regional identity among isolates and also demonstrates that this subspecies successfully disseminated worldwide in recent evolutionary time...
  42. pmc Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis
    P Keim
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    J Bacteriol 182:2928-36. 2000
    ..Some of these clones show worldwide distribution, while others are restricted to particular geographic regions. Human commerce doubtlessly has contributed to the dispersal of particular clones in ancient and modern times...
  43. pmc Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan
    P Keim
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    J Clin Microbiol 39:4566-7. 2001
    ..Spore samples were obtained from the release site, cultured, and characterized by molecular genetic typing. The isolates were consistent with strain Sterne 34F2, which is used in Japan for animal prophylaxis against anthrax...
  44. pmc A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions
    Apichai Tuanyok
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Bacteriol 189:9044-9. 2007
    ..In addition, clinical isolates are more likely to belong to group YLF, whereas environmental isolates are more likely to belong to group BTFC. These groups should be further characterized in an animal model...
  45. pmc BurkDiff: a real-time PCR allelic discrimination assay for Burkholderia pseudomallei and B. mallei
    Jolene R Bowers
    Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
    PLoS ONE 5:e15413. 2010
    ..Concordance of results with traditional speciation methods and no cross-reactivity to non-target species show BurkDiff is a robust, highly validated assay for the detection and differentiation of B. pseudomallei and B. mallei...
  46. pmc Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry
    Andrew E Waters
    Division of Pathogen Genomics, Translational Genomics Research Institute, Northern Arizona University, Flagstaff, USA
    Clin Infect Dis 52:1227-30. 2011
    ..S. aureus contaminated 47% of samples, and multidrug resistance was common among isolates (52%). S. aureus genotypes and resistance profiles differed significantly among sample types, suggesting food animal-specific contamination...
  47. pmc Macroscale spatial variation in chronic wound microbiota: a cross-sectional study
    Lance B Price
    Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona 86001, USA
    Wound Repair Regen 19:80-8. 2011
    ..A composite sample from multiple sites across the surface of individual wounds may provide the most robust characterization of wound microbiota...
  48. ncbi request reprint Phylogenetic understanding of clonal populations in an era of whole genome sequencing
    Talima Pearson
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
    Infect Genet Evol 9:1010-9. 2009
    ..Understanding the ways in which current and emerging technologies can be used to maximize phylogenetic knowledge is advantageous only with a complete understanding of the strengths and weaknesses of these methods...
  49. ncbi request reprint Development of a rapid, cost-effective TaqMan Real-Time PCR Assay for identification and differentiation of Coccidioides immitis and Coccidioides posadasii
    Kelly W Sheff
    Translational Genomics Research Institute, Pathogen Genomics Division TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona, USA
    Med Mycol 48:466-9. 2010
    ..This assay can be used as a tool to improve disease surveillance, increase understanding of the natural history of the infection, and assist in clinical differentiation studies...
  50. pmc Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain
    Matthew N Van Ert
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Clin Microbiol 45:47-53. 2007
    ..This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis...
  51. pmc Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing
    Talima Pearson
    Department of Biology, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Proc Natl Acad Sci U S A 101:13536-41. 2004
    ..Our use of nonhomoplastic whole-genome SNP characters allows branch points and clade membership to be estimated with great precision, providing greater insight into epidemiological, ecological, and forensic questions...
  52. pmc Use of single nucleotide polymorphisms in the plcR gene for specific identification of Bacillus anthracis
    W Ryan Easterday
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Clin Microbiol 43:1995-7. 2005
    ..cereus, and B. thuringiensis isolates. The assay differentiated B. anthracis from these genetic near-neighbors and determined that the nonsense mutation is ubiquitous across 89 globally and genetically diverse B. anthracis strains...
  53. pmc Fine-scale genetic diversity among Burkholderia pseudomallei soil isolates in northeast Thailand
    Heidie Hornstra
    Northern Arizona University, Department of Biological Sciences, Box 5640, Flagstaff, AZ 86011 5640, USA
    Appl Environ Microbiol 73:6678-81. 2007
    ..MLVA identified 19 genotypes within three clades, while MLST revealed two genotypes. These close genetic relationships imply a recent colonization followed by localized expansion, similar to what occurs in an outbreak situation...
  54. doi request reprint The otologic microbiome: a study of the bacterial microbiota in a pediatric patient with chronic serous otitis media using 16SrRNA gene-based pyrosequencing
    Cindy M Liu
    Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, USA
    Arch Otolaryngol Head Neck Surg 137:664-8. 2011
    ..To characterize bacterial microbiota in middle ear, adenoid, and tonsil specimens using 16SrRNA gene-based pyrosequencing analysis...
  55. ncbi request reprint Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis
    Matthew N Van Ert
    Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Biotechniques 37:642-4, 646, 648 passim. 2004
    ..This technology represents a significant advance in our ability to rapidly characterize B. anthracis isolates using VNTR and SNP loci...
  56. ncbi request reprint Plant genes link forests and streams
    Carri J LeRoy
    Department of Biological Sciences, Northern Arizona University, Flagstaff 86011, USA
    Ecology 87:255-61. 2006
    ..Importantly, these findings argue that genetic interactions link terrestrial and aquatic communities and may have significant evolutionary and conservation implications...
  57. pmc Detection of diverse new Francisella-like bacteria in environmental samples
    Susan M Barns
    Los Alamos National Laboratory, Bioscience Division, Mail Stop M888, Los Alamos, NM 87545, USA
    Appl Environ Microbiol 71:5494-500. 2005
    ..The results of this study revise our understanding of the diversity and distribution of Francisella and have implications for tularemia epidemiology and our ability to detect bioterrorist activities...
  58. doi request reprint Interactions between the yeast Ogataea pini and filamentous fungi associated with the western pine beetle
    Thomas S Davis
    School of Forestry, Southwest Forest Science Complex 82, Northern Arizona University, Flagstaff, AZ 86001, USA
    Microb Ecol 61:626-34. 2011
    ..pini as an important component in D. brevicomis community ecology, and we introduce multiple hypotheses for future tests of the effects of yeasts in the symbiont assemblages associated with Dendroctonus bark beetles...
  59. ncbi request reprint Do muscles function as adaptable locomotor springs?
    Stan L Lindstedt
    Physiology and Functional Morphology Group, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Exp Biol 205:2211-6. 2002
    ..Further, we speculate that a crucial element in that muscle spring may be the protein titin. It too seems to adapt to muscle use, and its stiffness seems to be 'tuned' to the frequency of normal muscle use...
  60. ncbi request reprint Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis
    Amy J Vogler
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Mutat Res 616:145-58. 2007
    ....
  61. pmc Whole-genome-based phylogeny and divergence of the genus Brucella
    Jeffrey T Foster
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 4073, USA
    J Bacteriol 191:2864-70. 2009
    ....
  62. pmc Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92
    Amy J Vogler
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Biotechniques 44:201, 203-4, 207. 2008
    ..We present TaqMan-minor groove binding (MGB) assays for an SNP that separates the Yersinia pestis strain CO92 from all other strains and for another SNP that separates North American strains from all other global strains...
  63. pmc Real-time PCR assays of single-nucleotide polymorphisms defining the major Brucella clades
    Jeffrey T Foster
    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Clin Microbiol 46:296-301. 2008
    ..These PCR assays provide a rapid and highly sensitive method of differentiating the major Brucella groups that will be valuable for clinical and forensic applications...
  64. pmc Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis
    Cliff S Han
    Department of Energy Joint Genome Institute, Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    J Bacteriol 188:3382-90. 2006
    ..cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms...
  65. ncbi request reprint VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia
    Talima Pearson
    Northern Arizona University, Center for Microbial Genetics and Genomics, Box 5640, Flagstaff, AZ 86011, USA
    Infect Genet Evol 7:416-23. 2007
    ..These methods provide the ability to generate robust evolutionary hypotheses that enable tracking of B. pseudomallei in forensic and epidemiological outbreaks at fine phylogenetic scales...
  66. pmc Use of a real-time PCR TaqMan assay for rapid identification and differentiation of Burkholderia pseudomallei and Burkholderia mallei
    Jana M U'ren
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Clin Microbiol 43:5771-4. 2005
    ..The assay rapidly identifies and discriminates between these two highly pathogenic bacteria and does not cross-react with genetic near neighbors, such as Burkholderia thailandensis and Burkholderia cepacia...
  67. pmc Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates
    Karen K Hill
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Appl Environ Microbiol 70:1068-80. 2004
    ..B. thuringiensis isolates of a particular subspecies tended to cluster together...
  68. pmc The effects of circumcision on the penis microbiome
    Lance B Price
    Translational Genomics Research Institute TGen, Flagstaff, Arizona, United States of America
    PLoS ONE 5:e8422. 2010
    ..Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female partners...
  69. pmc Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales
    Jessica M Girard
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Proc Natl Acad Sci U S A 101:8408-13. 2004
    ..This pattern seems consistent across local, regional, and even global scales...
  70. pmc Molecular typing of Mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates
    R Scott Spurgiesz
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    J Clin Microbiol 41:4224-30. 2003
    ..These nine loci provide a useful, discriminatory extension of VNTR typing methods for application to molecular epidemiologic studies of M. tuberculosis...
  71. ncbi request reprint Specific detection of bacillus anthracis using a TaqMan mismatch amplification mutation assay
    William R Easterday
    Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Biotechniques 38:731-5. 2005
    ..We anticipate that the ability to selectively amplify and detect low copy number DNAs with single nucleotide specificity will represent a valuable tool in the arena of biodefense and microbial forensics...
  72. pmc Fine-scale identification of the most likely source of a human plague infection
    Rebecca E Colman
    Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    Emerg Infect Dis 15:1623-5. 2009
    ..We illustrate the utility of this approach using data from a North American human plague investigation...
  73. doi request reprint Rapid quantification of single-nucleotide mutations in mixed influenza A viral populations using allele-specific mixture analysis
    Cindy M Liu
    Division of Pathogen Genomics, Translational Genomics Research Institute TGen, Flagstaff, AZ 86001, USA
    J Virol Methods 163:109-15. 2010
    ..Results from the current study demonstrate that FluASMA is a highly sensitive and quantitative SNP analysis method, even for minor mutant components (<1%)...
  74. pmc The complete genome sequence of Bacillus thuringiensis Al Hakam
    Jean F Challacombe
    Department of Energy Joint Genome Institute, Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Bacteriol 189:3680-1. 2007
    ..thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003)...
  75. pmc Strain typing of Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii by using multiple-locus variable-number tandem repeat analysis
    Jason Farlow
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    J Clin Microbiol 40:4612-8. 2002
    ..This new level of strain identification and discrimination will allow more detailed epidemiological and phylogenetic analysis in future studies...
  76. pmc Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota
    Lance B Price
    Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
    PLoS ONE 4:e6462. 2009
    ..We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota...
  77. pmc Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7
    Amy J Vogler
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    J Bacteriol 188:4253-63. 2006
    ..Finally, we describe a general model for VNTR mutations that encompasses insertions and deletions, single- and multiple-repeat mutations, and their relative frequencies based upon our empirical mutation rate data...
  78. pmc Molecular analysis of rifampin resistance in Bacillus anthracis and Bacillus cereus
    Amy J Vogler
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    Antimicrob Agents Chemother 46:511-3. 2002
    ..The spontaneous rate of resistance was estimated at 1.57 x 10(-9) mutations/generation by a Luria-Delbrück fluctuation test...
  79. ncbi request reprint Lack of genetic differentiation in aggressive and secondary bark beetles (Coleoptera: Curculionidae, Scolytinae) from Arizona
    Christopher J Allender
    Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011 5640, USA
    Environ Entomol 37:817-24. 2008
    ..We conclude that our results are consistent with strong dispersal patterns and large population sizes of all three species...
  80. pmc In vitro selection and characterization of Bacillus anthracis mutants with high-level resistance to ciprofloxacin
    Lance B Price
    Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 5640, USA
    Antimicrob Agents Chemother 47:2362-5. 2003
    ..Mutants for which MICs were 32 microg/ml had no additional target modifications but showed evidence of enhanced ciprofloxacin efflux...
  81. ncbi request reprint Phenotypic and functional characterization of Bacillus anthracis biofilms
    Keehoon Lee
    Northern Arizona University, Flagstaff, AZ 86001, USA
    Microbiology 153:1693-701. 2007
    ..anthracis. The results demonstrate that B. anthracis readily forms biofilms which are inherently resistant to commonly prescribed antibiotics, and that antibiotic resistance is not solely the function of sporulation...
  82. ncbi request reprint Flea abundance, diversity, and plague in Gunnison's prairie dogs (Cynomys gunnisoni) and their burrows in montane grasslands in northern New Mexico
    Megan M Friggens
    School of Forestry, 200 Pine Knoll Drive, Northern Arizona University, Flagstaff, Arizona 86011 5018, USA
    J Wildl Dis 46:356-67. 2010
    ..hirsuta populations for determining plague outbreaks...

Research Grants4

  1. Real-Time PCR Assays for Direct Detection of Sepsis and CAP Pathogens
    Paul Keim; Fiscal Year: 2007
    ..Quantitative data will be generated with every real-time PCR assay and will analyzed together, to better understand bacterial loads in contrast to pathogens. ..
  2. Burkholderia: International Collaborative Development of Novel Diagnostics
    Paul Keim; Fiscal Year: 2007
    ....