Harley McAdams

Honors and Awards

• Fellow, American Academy of Microbiologists (2006)

Professional Education

• PhD, Rice University Physics (1967)
• MA, Rice University Physics (1965)
• MS, U. Illinois (Urbana) Physics (1962)
• BS, Texas A&M Physics (1960)

Web Site Links

• Personal Web site

Research Interests

We are focused on understanding the nature of bacterial genetic regulation. We use a variety of tools: gene expression microarrays, advanced techniques of fluorescence and electron microscopy, and a broad range of computational tools for bioinformatics and modeling.

The marine bacterium, Caulobacter crescentus, is our primary model organism. The graduate students in the McAdams group include Electrical Engineering, Physics, and Physical Chemistry students who are interested in biologically focused research. We work closely with geneticists and biochemists who are graduate students and postdoctoral fellows in Lucy Shapiro's group to bring a multi-disciplinary approach to the analysis of bacterial regulation and control.

Our interests range far beyond "conventional" approaches to genetic regulation to include the effects of dynamic spatial and temporal positioning of regulatory proteins and the regulatory effects working through the dynamic three-dimensional organization of the chromosome in the dividing cell. We are exploring how regulatory molecules are dynamically localized to particular cell positions and how this localization is integrated into the control mechanisms of the cell.

Publications

• System-level design of bacterial cell cycle control. McAdams HH,  Shapiro L.  FEBS Lett.  2009;
• Caulobacter requires a dedicated mechanism to initiate chromosome segregation. Toro E,  Hong SH, McAdams HH, Shapiro L.  Proc Natl Acad Sci U S A.  2008; 105 (40): 15435-40
• Architecture and inherent robustness of a bacterial cell-cycle control system. Shen X,  Collier J, Dill D, Shapiro L, Horowitz M, McAdams HH.  Proc Natl Acad Sci U S A.  2008; 105 (32): 11340-5
• Small non-coding RNAs in Caulobacter crescentus. Landt SG,  Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L.  Mol Microbiol.  2008; 68 (3): 600-14
• A DNA methylation ratchet governs progression through a bacterial cell cycle. Collier J,  McAdams HH, Shapiro L.  Proc Natl Acad Sci U S A.  2007; 104 (43): 17111-6
• A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator. McGrath PT,  Iniesta AA, Ryan KR, Shapiro L, McAdams HH.  Cell.  2006; 124 (3): 535-47
• Dynamic Chromosome Organization and Protein Localization Coordinate the Regulatory Circuitry that Drives the Bacterial Cell Cycle. Goley ED,  Toro E, McAdams HH, Shapiro L.  Cold Spring Harb Symp Quant Biol.  2009;
• Systems biology of Caulobacter. Laub MT,  Shapiro L, McAdams HH.  Annu Rev Genet.  2007; 41 429-41
• High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. McGrath PT,  Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, Hillson NJ, Hu P, Shapiro L, McAdams HH.  Nat Biotechnol.  2007; 25 (5): 584-92
• A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression. Iniesta AA,  McGrath PT, Reisenauer A, McAdams HH, Shapiro L.  Proc Natl Acad Sci U S A.  2006; 103 (29): 10935-40
• Integrated Protein Interaction Networks for 11 Microbes Srinivasan, B.,  Novak A, Flannick J, Batzoglou S, McAdams H..  Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB 2006).  2006; 1-14
• Graemlin: general and robust alignment of multiple large interaction networks. Flannick J,  Novak A, Srinivasan BS, McAdams HH, Batzoglou S.  Genome Res.  2006; 16 (9): 1169-81
• Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease. Chen JC,  Hottes AK, McAdams HH, McGrath PT, Viollier PH, Shapiro L.  EMBO J.  2006; 25 (2): 377-86
• Bacterial stalks are nutrient-scavenging antennas. McAdams HH,  Proc Natl Acad Sci U S A.  2006; 103 (31): 11435-6
• Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes. Judd EM,  Comolli LR, Chen JC, Downing KH, Moerner WE, McAdams HH.  J Bacteriol.  2005; 187 (20): 6874-82
• Global approaches to the bacterial cell as an integrated system M. T. Laub,  Lucy Shapiro, Harley McAdams.  in The Bacterial Chrosome, edited by N. Patrick Higgins, ASM Press.  2005;
• Integrated Protein Interaction Networks for 230 Microbes Srinivasan, B.,  A. F. Novak, J. A. Flannick, S. Batzoglou, H. H. McAdams.  BCATS.  2005;
• DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus. Hottes AK,  Shapiro L, McAdams HH.  Mol Microbiol.  2005; 58 (5): 1340-53
• Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. Hu P,  Brodie EL, Suzuki Y, McAdams HH, Andersen GL.  J Bacteriol.  2005; 187 (24): 8437-49
• Conserved modular design of an oxygen sensory/signaling network with species-specific output. Crosson S,  McGrath PT, Stephens C, McAdams HH, Shapiro L.  Proc Natl Acad Sci U S A.  2005; 102 (22): 8018-23
• Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Viollier PH,  Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L.  Proc Natl Acad Sci U S A.  2004; 101 (25): 9257-62
• Visualization of the movement of single histidine kinase molecules in live Caulobacter cells. Deich J,  Judd EM, McAdams HH, Moerner WE.  Proc Natl Acad Sci U S A.  2004; 101 (45): 15921-6
• Codon usage between genomes is constrained by genome-wide mutational processes. Chen SL,  Lee W, Hottes AK, Shapiro L, McAdams HH.  Proc Natl Acad Sci U S A.  2004; 101 (10): 3480-5
• Setting the pace: mechanisms tying Caulobacter cell-cycle progression to macroscopic cellular events. McGrath PT,  Viollier P, McAdams HH.  Curr Opin Microbiol.  2004; 7 (2): 192-7
• A genetic oscillator and the regulation of cell cycle progression in Caulobacter crescentus. Crosson S,  McAdams H, Shapiro L.  Cell Cycle.  2004; 3 (10): 1252-4
• Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. Hottes AK,  Meewan M, Yang D, Arana N, Romero P, McAdams HH, Stephens C.  J Bacteriol.  2004; 186 (5): 1448-61
• The evolution of genetic regulatory systems in bacteria. McAdams HH,  Srinivasan B, Arkin AP.  Nat Rev Genet.  2004; 5 (3): 169-78
• Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Holtzendorff J,  Hung D, Brende P, Reisenauer A, Viollier PH, McAdams HH, Shapiro L.  Science.  2004; 304 (5673): 983-7
• Fluorescence bleaching reveals asymmetric compartment formation prior to cell division in Caulobacter. Judd EM,  Ryan KR, Moerner WE, Shapiro L, McAdams HH.  Proc Natl Acad Sci U S A.  2003; 100 (14): 8235-40
• A bacterial cell-cycle regulatory network operating in time and space. McAdams HH,  Shapiro L.  Science.  2003; 301 (5641): 1874-7
• Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Laub MT,  Chen SL, Shapiro L, McAdams HH.  Proc Natl Acad Sci U S A.  2002; 99 (7): 4632-7
• Generating and exploiting polarity in bacteria. Shapiro L,  McAdams HH, Losick R.  Science.  2002; 298 (5600): 1942-6
• Global analysis of the genetic network controlling a bacterial cell cycle. Laub MT,  McAdams HH, Feldblyum T, Fraser CM, Shapiro L.  Science.  2000; 290 (5499): 2144-8
• Towards a circuit engineering discipline. McAdams HH,  Arkin A.  Curr Biol.  2000; 10 (8): R318-20
• Toggles and oscillators: new genetic circuit designs. Judd EM,  Laub MT, McAdams HH.  Bioessays.  2000; 22 (6): 507-9
• It's a noisy business! Genetic regulation at the nanomolar scale. McAdams HH,  Arkin A.  Trends Genet.  1999; 15 (2): 65-9
• Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Arkin A,  Ross J, McAdams HH.  Genetics.  1998; 149 (4): 1633-48
• Simulation of prokaryotic genetic circuits. McAdams HH,  Arkin A.  Annu Rev Biophys Biomol Struct.  1998; 27 199-224
• Stochastic mechanisms in gene expression. McAdams HH,  Arkin A.  Proc Natl Acad Sci U S A.  1997; 94 (3): 814-9
• Circuit simulation of genetic networks. McAdams HH,  Shapiro L.  Science.  1995; 269 (5224): 650-6
• New Liquid 4HE Experimental cryostat McAdams, H. H.,  Rev. Sci. Instr..  1968; 39 (1)
• Dynamic nuclear polarization of liquid helium-three by optical pumping McAdams, H. H.,  Walters, G. K..  Phys. Rev..  1968; 170 (1): 276
• Dynamic polarization of liquid helium three McAdams, H. H.,  Walters, G. K..  Physical Review Letters.  1967; 18 (12): 436