B G Hall

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. ncbi Transposable elements as activators of cryptic genes in E. coli
    B G Hall
    Biology Department, University of Rochester, NY 14627, USA
    Genetica 107:181-7. 1999
  2. ncbi Experimental evolution of Ebg enzyme provides clues about the evolution of catalysis and to evolutionary potential
    B G Hall
    Biology Dept, University of Rochester, NY 14627, USA
    FEMS Microbiol Lett 174:1-8. 1999
  3. ncbi Spectra of spontaneous growth-dependent and adaptive mutations at ebgR
    B G Hall
    University of Rochester, Rochester, New York
    J Bacteriol 181:1149-55. 1999
  4. ncbi Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations
    B G Hall
    Biology Department, University of Rochester, NY 14627, USA
    Genetica 102:109-25. 1998
  5. ncbi Determining the evolutionary potential of a gene
    B G Hall
    Biology Department, University of Rochester, New York 14627
    Mol Biol Evol 15:1055-61. 1998
  6. ncbi Adaptive mutagenesis at ebgR is regulated by PhoPQ
    B G Hall
    Biology Department, University of Rochester, Rochester, New York 14627 0211, USA
    J Bacteriol 180:2862-5. 1998
  7. ncbi Activation of the bgl operon by adaptive mutation
    B G Hall
    Biology Department, University of Rochester, New York 14627, USA
    Mol Biol Evol 15:1-5. 1998
  8. ncbi Physical map location of the asc (formerly sac) operon of Escherichia coli K-12
    B G Hall
    Department of Biology, University of Rochester, New York 14627
    J Bacteriol 173:5250. 1991
  9. ncbi Predicting evolutionary potential. I. Predicting the evolution of a lactose-PTS system in Escherichia coli
    B G Hall
    Department of Biology, University of Rochester, New York 14625 0222, USA
    Mol Biol Evol 18:1389-400. 2001
  10. ncbi On the specificity of adaptive mutations
    B G Hall
    Biology Department, University of Rochester, New York 14627, USA
    Genetics 145:39-44. 1997

Research Grants

  1. A MODEL SYSTEM FOR PREDICTING EVOLUTIONARY POTENTIAL
    Barry Hall; Fiscal Year: 2003

Collaborators

Detail Information

Publications37

  1. ncbi Transposable elements as activators of cryptic genes in E. coli
    B G Hall
    Biology Department, University of Rochester, NY 14627, USA
    Genetica 107:181-7. 1999
    ..In at least one case, IS elements activate an operon during starvation only if the substrate for that operon is present in the environment. It appears that E. coli has managed to take advantage of IS elements for its own benefit...
  2. ncbi Experimental evolution of Ebg enzyme provides clues about the evolution of catalysis and to evolutionary potential
    B G Hall
    Biology Dept, University of Rochester, NY 14627, USA
    FEMS Microbiol Lett 174:1-8. 1999
    ..Studies of the catalytic mechanism of Ebg beta-galactosidase have allowed the widely accepted Albery and Knowles model for the evolution of catalysis to be rejected...
  3. ncbi Spectra of spontaneous growth-dependent and adaptive mutations at ebgR
    B G Hall
    University of Rochester, Rochester, New York
    J Bacteriol 181:1149-55. 1999
    ....
  4. ncbi Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations
    B G Hall
    Biology Department, University of Rochester, NY 14627, USA
    Genetica 102:109-25. 1998
    ..A model to explain that specificity and new evidence in support of that model are considered, as are potential roles of adaptive mutagenesis in evolution and practical aspects of adaptive mutagenesis...
  5. ncbi Determining the evolutionary potential of a gene
    B G Hall
    Biology Department, University of Rochester, New York 14627
    Mol Biol Evol 15:1055-61. 1998
    ..The evolutionary potential of Ebg is thus limited to those two replacements...
  6. ncbi Adaptive mutagenesis at ebgR is regulated by PhoPQ
    B G Hall
    Biology Department, University of Rochester, Rochester, New York 14627 0211, USA
    J Bacteriol 180:2862-5. 1998
    ..The finding that it is regulated implies that adaptive mutagenesis does not simply result from a failure of various error correction mechanisms during prolonged starvation...
  7. ncbi Activation of the bgl operon by adaptive mutation
    B G Hall
    Biology Department, University of Rochester, New York 14627, USA
    Mol Biol Evol 15:1-5. 1998
    ..coli...
  8. ncbi Physical map location of the asc (formerly sac) operon of Escherichia coli K-12
    B G Hall
    Department of Biology, University of Rochester, New York 14627
    J Bacteriol 173:5250. 1991
  9. ncbi Predicting evolutionary potential. I. Predicting the evolution of a lactose-PTS system in Escherichia coli
    B G Hall
    Department of Biology, University of Rochester, New York 14625 0222, USA
    Mol Biol Evol 18:1389-400. 2001
    ..In contrast, biochemical data predict that the cryptic bglB gene, which also currently specifies a phospho-beta-glucosidase, is most likely to evolve into a phospho-beta-galactosidase...
  10. ncbi On the specificity of adaptive mutations
    B G Hall
    Biology Department, University of Rochester, New York 14627, USA
    Genetics 145:39-44. 1997
    ..Here I use the ebg system to provide evidence that when selection is applied to one specific nucleotide site within a gene, mutation occurs at that site but not at an alternative and equally mutable site within the same gene...
  11. ncbi Evolutionary potential of the ebgA gene
    B G Hall
    Biology Department, University of Rochester, New York 14627, USA
    Mol Biol Evol 12:514-7. 1995
  12. ncbi Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coli K12
    B G Hall
    Biology Department, University of Rochester, New York 14627
    Mol Biol Evol 9:688-706. 1992
    ..The duplications that gave rise to these paralogous genes are estimated to have occurred approximately 320 Mya, a time that predates the divergence of E. coli and Salmonella typhimurium...
  13. ncbi The rtn gene of Proteus vulgaris is actually from Escherichia coli
    B G Hall
    University of Rochester, New York 14627, USA
    J Bacteriol 179:2433-4. 1997
    ..It was not possible to verify the presence of rtn in P. vulgaris...
  14. ncbi Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates
    B G Hall
    Department of Biology, University of Rochester, New York 14627
    Mol Biol Evol 9:654-65. 1992
    ..It is surprising that the inducible glucitol-specific enzyme, which is functional, is more variable than the cellobiose-specific enzyme, which is cryptic; the latter might be expected to be under less (if any) purifying selection...
  15. ncbi Predicting the evolution of antibiotic resistance genes
    Barry G Hall
    Biology Department, University of Rochester, USA
    Nat Rev Microbiol 2:430-5. 2004
  16. ncbi Evolution of the serine beta-lactamases: past, present and future
    Barry G Hall
    Department of Biology, University of Rochester, Rochester, NY, USA
    Drug Resist Updat 7:111-23. 2004
    ..We also discuss a method that is being used to predict the future evolution of beta-lactamases in response to selection with new drugs...
  17. ncbi Independent origins of subgroup Bl + B2 and subgroup B3 metallo-beta-lactamases
    Barry G Hall
    Biology Department, University of Rochester, Rochester, NY 14627, USA
    J Mol Evol 59:133-41. 2004
    ..These results lend additional support to the proposal that the metallo-beta-lactamases should be divided into two distinct classes...
  18. ncbi Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences
    Barry G Hall
    Biology Department, University of Rochester, USA
    Mol Biol Evol 22:792-802. 2005
    ....
  19. ncbi Structure-based phylogeny of the metallo-beta-lactamases
    Gianpiero Garau
    , Institut de Biologie Structural Jean-Pierre Ebel, CEA-CNRS-UJF, Grenoble, France
    Antimicrob Agents Chemother 49:2778-84. 2005
    ..The presence of genes from Eubacteria, Archaebacteria, and Eukaryota on that tree is consistent with a very ancient origin of the metallo-beta-lactamase family...
  20. ncbi Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases
    Barry G Hall
    Biology Department, University of Rochester, Rochester, NY, USA
    Ann Epidemiol 16:157-69. 2006
    ..When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates...
  21. ncbi Simple and accurate estimation of ancestral protein sequences
    Barry G Hall
    Bellingham Research Institute, 218 Chuckanut Point Road, Bellingham, WA 98229, USA
    Proc Natl Acad Sci U S A 103:5431-6. 2006
    ..A highly accurate method for correcting the estimated sequences is introduced, and it is shown that the correction permits inferring the sequences of ancient protein sequences with a very high degree of accuracy...
  22. ncbi Measures of clade confidence do not correlate with accuracy of phylogenetic trees
    Barry G Hall
    Bellingham Research Institute, Bellingham, Washington, United States of America
    PLoS Comput Biol 3:e51. 2007
    ....
  23. ncbi Simulating DNA coding sequence evolution with EvolveAGene 3
    Barry G Hall
    Bellingham Research Institute, Bellingham, WA, USA
    Mol Biol Evol 25:688-95. 2008
    ....
  24. ncbi In vitro evolution predicts that the IMP-1 metallo-beta-lactamase does not have the potential to evolve increased activity against imipenem
    Barry G Hall
    Biology Department, University of Rochester, Rochester, New York, USA
    Antimicrob Agents Chemother 48:1032-3. 2004
    ..2 mutations per variant, detected no increased resistance to imipenem. The results predict, with >99.9% confidence, that even under intense selection the IMP-1 beta-lactamase will not evolve to confer increased resistance to imipenem...
  25. ncbi GeneHunter, a transposon tool for identification and isolation of cryptic antibiotic resistance genes
    Stephen J Salipante
    Biology Department, University of Rochester, Rochester, New York, USA
    Antimicrob Agents Chemother 47:3840-5. 2003
    ..It is anticipated that the GeneHunter method will be used to identify potential resistance genes during the development and testing of novel antibiotics, new variants of existing antibiotics, and drug inhibitor combinations...
  26. ncbi Structure-based phylogenies of the serine beta-lactamases
    Barry G Hall
    Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Evol 57:255-60. 2003
    ..From those phylogenies, we show that the Class A and Class D beta-lactamases are sister taxa and that the divergence of the Class C beta-lactamases pre-dated the divergence of the Class A and Class D beta-lactamases...
  27. ncbi Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627-0211, USA
    Genetics 160:823-32. 2002
    ..Additionally, our results predict that a phenotype not yet observed among TEM beta-lactamases in nature-resistance to cefepime-is likely to arise in nature...
  28. ncbi Origin and evolution of the AmpC beta-lactamases of Citrobacter freundii
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627, USA
    Antimicrob Agents Chemother 46:1190-8. 2002
    ..These results suggest that selection for increased resistance to beta-lactam antibiotics has not been a significant force directing the evolution of the C. freundii ampC alleles found in beta-lactam-resistant clinical isolates...
  29. ncbi Predicting evolution by in vitro evolution requires determining evolutionary pathways
    Barry G Hall
    Biology Department, University of Rochester, Rochester, New York 14627 0211, USA
    Antimicrob Agents Chemother 46:3035-8. 2002
    ....
  30. ncbi Phylogenetic analysis shows that the OXA beta-lactamase genes have been on plasmids for millions of years
    Miriam Barlow
    Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627-0211, USA
    J Mol Evol 55:314-21. 2002
    ..That observation contradicts the commonly held impression that mobilization of antibiotic resistance genes is strictly the result of modern use of antibiotics...
  31. ncbi Determining the limits of the evolutionary potential of an antibiotic resistance gene
    Stephen J Salipante
    Biology Department, University of Rochester, USA
    Mol Biol Evol 20:653-9. 2003
    ..typhimurium LT2 has the potential to evolve increased aminoglycoside resistance in nature. The practical implications of being able to determine the evolutionary limits for other antibiotic resistance genes are discussed...
  32. ncbi Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627-0211, USA
    Genetics 164:23-9. 2003
    ..Although we generated CMY-2 evolvants that conferred increased cefepime resistance, we did not recover any CMY-2 evolvants that conferred resistance levels as high as the best cefepime-resistant TEM alleles...
  33. ncbi The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose
    Barry G Hall
    Biology Department, Hutchinson Hall, River Campus, University of Rochester, Rochester, NY 14627 0211, USA
    Genetica 118:143-56. 2003
    ..The analysis of free-energy profiles for the wildtype and all of the various evolved Ebg enzymes has permitted rejection of the Albery-Knowles hypothesis that relates likely changes in free-energy profiles to evolutionary change...
  34. ncbi The metallo-beta-lactamases fall into two distinct phylogenetic groups
    Barry G Hall
    Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Evol 57:249-54. 2003
    ..We present phylogenies of these two groups and suggest a new classification scheme for the beta-lactamases...
  35. ncbi How well does the HoT score reflect sequence alignment accuracy?
    Barry G Hall
    Bellingham Research Institute
    Mol Biol Evol 25:1576-80. 2008
    ..However, HoT scores are overestimates of alignment accuracy in general, with the extent of overestimation depending on the method used for multiple sequence alignment...
  36. ncbi Revised Ambler classification of {beta}-lactamases
    Barry G Hall
    J Antimicrob Chemother 55:1050-1. 2005
  37. ncbi Experimental prediction of the natural evolution of antibiotic resistance
    Miriam Barlow
    Biology Department, University of Rochester, Rochester, New York 14627-0211, USA
    Genetics 163:1237-41. 2003
    ..Sequencing showed that alleles contained from two to six amino acid substitutions, many of which were shared among alleles, and that the best allele contained only three substitutions...

Research Grants4

  1. A MODEL SYSTEM FOR PREDICTING EVOLUTIONARY POTENTIAL
    Barry Hall; Fiscal Year: 2003
    ..The resulting mutants will then be characterized to determine which kind of data most accurately predicted the eventual evolutionary outcome. ..