I B Dodd

Summary

Affiliation: University of Adelaide
Country: Australia

Publications

  1. pmc Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny
    I B Dodd
    Department of Molecular Biosciences, University of Adelaide, South Australia 5005, Australia
    Genes Dev 15:3013-22. 2001
  2. pmc Action at a distance in CI repressor regulation of the bacteriophage 186 genetic switch
    Ian B Dodd
    Department of Molecular Biosciences Biochemistry, University of Adelaide, South Australia, Australia
    Mol Microbiol 45:697-710. 2002
  3. pmc Cooperativity in long-range gene regulation by the lambda CI repressor
    Ian B Dodd
    Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
    Genes Dev 18:344-54. 2004
  4. ncbi request reprint Revisited gene regulation in bacteriophage lambda
    Ian B Dodd
    Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
    Curr Opin Genet Dev 15:145-52. 2005
  5. ncbi request reprint Modelling transcriptional interference and DNA looping in gene regulation
    Ian B Dodd
    Centre for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
    J Mol Biol 369:1200-13. 2007
  6. doi request reprint Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states
    Ian B Dodd
    Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
    J Mol Biol 414:624-37. 2011
  7. pmc Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter
    Adam C Palmer
    School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
    Mol Cell 34:545-55. 2009
  8. ncbi request reprint The helix-turn-helix motif of the coliphage 186 immunity repressor binds to two distinct recognition sequences
    Keith E Shearwin
    Department of Molecular Biosciences, University of Adelaide, Adelaide, Australia 5005
    J Biol Chem 277:3186-94. 2002
  9. pmc Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic development
    Rachel A Schubert
    Molecular and Biomedical Sciences Biochemistry, University of Adelaide, Adelaide, SA 5005, Australia
    Genes Dev 21:2461-72. 2007
  10. ncbi request reprint The late-expressed region of the temperate coliphage 186 genome
    R Portelli
    Department of Biochemistry, University of Adelaide, Adelaide, 5005, Australia
    Virology 248:117-30. 1998

Collaborators

Detail Information

Publications18

  1. pmc Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny
    I B Dodd
    Department of Molecular Biosciences, University of Adelaide, South Australia 5005, Australia
    Genes Dev 15:3013-22. 2001
    ..We propose the octameric CI:O(R)-O(L) complex increases the affinity of CI for O(R)3 by allowing a CI tetramer to link O(R)3 and the third operator at O(L), O(L)3...
  2. pmc Action at a distance in CI repressor regulation of the bacteriophage 186 genetic switch
    Ian B Dodd
    Department of Molecular Biosciences Biochemistry, University of Adelaide, South Australia, Australia
    Mol Microbiol 45:697-710. 2002
    ..We propose that the 186 switch is regulated by a novel mechanism in which a CI octamer bound at pR forms alternative DNA loops to pL or to a flanking site, depending on CI concentration...
  3. pmc Cooperativity in long-range gene regulation by the lambda CI repressor
    Ian B Dodd
    Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
    Genes Dev 18:344-54. 2004
    ..The results establish the lambda system as a powerful tool for examining long-range gene regulatory interactions in vivo...
  4. ncbi request reprint Revisited gene regulation in bacteriophage lambda
    Ian B Dodd
    Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
    Curr Opin Genet Dev 15:145-52. 2005
    ..New genetic and quantitative analysis of the lambda gene network is challenging cherished ideas about how complex behaviours emerge from this regulatory system...
  5. ncbi request reprint Modelling transcriptional interference and DNA looping in gene regulation
    Ian B Dodd
    Centre for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
    J Mol Biol 369:1200-13. 2007
    ..Our results demonstrate the power of mathematical modelling for the extraction of detailed biochemical information from in vivo data...
  6. doi request reprint Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states
    Ian B Dodd
    Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
    J Mol Biol 414:624-37. 2011
    ..Thus, a relatively simple set of nucleosome-modifying enzymes and recognition domains is all that is needed to make chromatin-based epigenetics useful and safe...
  7. pmc Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter
    Adam C Palmer
    School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
    Mol Cell 34:545-55. 2009
    ..Gene regulation by pausing-enhanced occlusion provides a general and potentially widespread mechanism by which even weak converging or tandem transcription, either coding or noncoding, can bring about strong in cis repression...
  8. ncbi request reprint The helix-turn-helix motif of the coliphage 186 immunity repressor binds to two distinct recognition sequences
    Keith E Shearwin
    Department of Molecular Biosciences, University of Adelaide, Adelaide, Australia 5005
    J Biol Chem 277:3186-94. 2002
    ..Site-directed mutation of the putative 186 HTH motif eliminates binding to both A and B type sites, supporting the idea that binding to the two distinct DNA sequences is mediated by a variant HTH motif...
  9. pmc Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic development
    Rachel A Schubert
    Molecular and Biomedical Sciences Biochemistry, University of Adelaide, Adelaide, SA 5005, Australia
    Genes Dev 21:2461-72. 2007
    ..Thus a bistable CI-Cro circuit reinforces the commitment to a developmental transition...
  10. ncbi request reprint The late-expressed region of the temperate coliphage 186 genome
    R Portelli
    Department of Biochemistry, University of Adelaide, Adelaide, 5005, Australia
    Virology 248:117-30. 1998
    ..The relative absence of lysogenic conversion genes in 186 suggests that the two phages have evolved to use the lytic and lysogenic reproductive modes to different extents...
  11. ncbi request reprint A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli
    Kim Sneppen
    NORDITA, Nordic Institute for Theoretical Physics, Niels Bohr Institute, Blegdamsvej 17, DK 2100 Copenhagen, Denmark
    J Mol Biol 346:399-409. 2005
    ..The model provides a framework for using transcriptional interference to investigate various dynamic processes on DNA in vivo...
  12. doi request reprint Minimal gene regulatory circuits that can count like bacteriophage lambda
    M Avlund
    Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
    J Mol Biol 394:681-93. 2009
    ..Our study suggests that additional regulatory mechanisms to decouple Cro and CII levels may exist in lambda and that infection counting could be widespread among temperate bacteriophages, many of which contain CI-Cro-like circuits...
  13. pmc Why do phage play dice?
    Mikkel Avlund
    Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
    J Virol 83:11416-20. 2009
    ..Crucial to the argument is the clonal identity of the phage...
  14. doi request reprint Theory for the stability and regulation of epigenetic landscapes
    Mille A Micheelsen
    Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, DK 2100, Copenhagen Ø, Denmark
    Phys Biol 7:026010. 2010
    ..This combined treatment of noisy dynamics both between and during cell division provides an efficient way to calculate the stability of alternative states in a broad range of epigenetic systems...
  15. pmc The generation of promoter-mediated transcriptional noise in bacteria
    Namiko Mitarai
    Department of Physics, Kyushu University, Fukuoka, Japan
    PLoS Comput Biol 4:e1000109. 2008
    ..Both mechanisms are tunable by the alteration of promoter kinetics and therefore allow the optimization of promoter mediated noise...
  16. ncbi request reprint Bacteriophage P4 Vis protein is needed for prophage excision
    Simona Calì
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, 20133 Milan, Italy
    Virology 322:82-92. 2004
    ..Furthermore, we mapped by primer extension the 5' end of the int transcript and found that ectopic expression of Vis reduced its signal intensity, suggesting that Vis is also involved in negative regulation of the int promoter...
  17. ncbi request reprint The structural basis of cooperative regulation at an alternate genetic switch
    Heather W Pinkett
    Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, 19102, USA
    Mol Cell 21:605-15. 2006
    ..Whereas the overall fold of the 186 and lambda repressor monomers is remarkably similar, the way the two repressors cooperatively assemble is quite different and explains in part the differences in their regulatory activity...
  18. pmc Functional alignment of regulatory networks: a study of temperate phages
    Ala Trusina
    Department of Theoretical Physics, Umea University, Umea, Sweden
    PLoS Comput Biol 1:e74. 2005
    ..We finally discuss how network alignment can be used to pinpoint protein similarities viewed from the network perspective...