Kinematic Self-Replicating Machines

© 2004 Robert A. Freitas Jr. and Ralph C. Merkle. All Rights Reserved.

Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines, Landes Bioscience, Georgetown, TX, 2004.


 

References 1700-1799

1700. K.P. Williams, D.P. Bartel, “Phylogenetic analysis of tmRNA secondary structure,” RNA 2(1996):1306-1310. See also: “The tmRNA Website”, http://www.indiana.edu/~tmrna/

1701. R.L. Gourse, T. Gaal, M.S. Bartlett, J.A. Appleman, W. Ross, “rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli,” Annu. Rev. Microbiol. 50(1996):645-677.

1702. M.R. Paule, R.J. White, “Survey and summary: transcription by RNA polymerases I and III,” Nucleic Acids Res. 28(15 March 2000):1283-1298.

1703. Y. Huang, R.J. Maraia, “Comparison of the RNA polymerase III transcription machinery in Schizosaccharomyces pombe, Saccharomyces cerevisiae and human,” Nucleic Acids Res. 29(1 July 2001):2675-2690; Nucleic Acids Res. 29(15 August 2001):2 (erratum).

1704. P. Khaitovich, A.S. Mankin, “Effect of antibiotics on large ribosomal subunit assembly reveals possible function of 5 S rRNA,” J. Mol. Biol. 291(3 September 1999):1025-1034.

1705. S.C. Agalarov, J.R. Williamson, “A hierarchy of RNA subdomains in assembly of the central domain of the 30 S ribosomal subunit,” RNA 6(March 2000):402-408.

1706. S.C. Agalarov, G. Sridhar Prasad, P.M. Funke, C.D. Stout, J.R. Williamson, “Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain,” Science 288(7 April 2000):107-113.

1707. Jan Genzer, Kirill Efimenko, “Creating long-lived superhydrophobic polymer surfaces through mechanically assembled monolayers,” Science 290(15 December 2000):2130-2132.

1708. D.E. Cane, C.T. Walsh, “The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases,” Chem. Biol. 6(December 1999):R319-R325.

1709. C. Khosla, R.S. Gokhale, J.R. Jacobsen, D.E. Cane, “Tolerance and specificity of polyketide synthases,” Annu. Rev. Biochem. 68(1999):219-253.

1710. L.E. Quadri, “Assembly of aryl-capped siderophores by modular peptide synthetases and polyketide synthases,” Mol. Microbiol. 37(July 2000):1-12.

1711. H.D. Mootz, M.A. Marahiel, “Design and application of multimodular peptide synthetases,” Curr. Opin. Biotechnol. 10(August 1999):341-348.

1712. D.E. Cane, C.T. Walsh, “The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases,” Chem. Biol. 6(December 1999):R319-R325.

1713. J. Staunton, B. Wilkinson, “Combinatorial biosynthesis of polyketides and nonribosomal peptides,” Curr. Opin. Chem. Biol. 5(April 2001):159-164.

1714. H.D. Mootz, D. Schwarzer, M.A. Marahiel, “Ways of assembling complex natural products on modular nonribosomal peptide synthetases,” Chembiochem 3(3 June 2002):490-504. See also special issue of Chemical Reviews 97(1997) and Jeffrey M. Perkel, “Nonribosomal peptide synthesis,” The Scientist 17(24 March 2003); http://www.the-scientist.com/yr2003/mar/upfront7_030324.html

1715. L. Du, B. Shen, “Biosynthesis of hybrid peptide-polyketide natural products,” Curr. Opin. Drug Discov. Devel. 4(March 2001):215-228; L. Du, C. Sanchez, B. Shen, “Hybrid peptide-polyketide natural products: biosynthesis and prospects toward engineering novel molecules,” Metab. Eng. 3(January 2001):78-95.

1716. R. Lal, R. Kumari, H. Kaur, R. Khanna, N. Dhingra, D. Tuteja, “Regulation and manipulation of the gene clusters encoding type-I PKSs,” Trends Biotechnol. 18(June 2000):264-274.

1717. C.R. Hutchinson, R. McDaniel, “Combinatorial biosynthesis in microorganisms as a route to new antimicrobial, antitumor and neuroregenerative drugs,” Curr. Opin. Investig. Drugs 2(December 2001):1681-1690; C.R. Hutchinson, “Combinatorial biosynthesis for new drug discovery,” Curr. Opin. Microbiol. 1(June 1998):319-329; C.R. Hutchinson, “Drug synthesis by genetically engineered microorganisms,” Biotechnology (NY) 12(April 1994):375-380.

1718. J.A. Robinson, “Polyketide synthase complexes: their structure and function in antibiotic biosynthesis,” Philos. Trans. R. Soc. Lond. B Biol. Sci. 332(29 May 1991):107-114.

1719. C.R. Hutchinson, I. Fujii, “Polyketide synthase gene manipulation: a structure-function approach in engineering novel antibiotics,” Annu. Rev. Microbiol. 49(1995):201-238.

1720. E. Dittmann, B.A. Neilan, T. Borner, “Molecular biology of peptide and polyketide biosynthesis in cyanobacteria,” Appl. Microbiol. Biotechnol. 57(November 2001):467-473.

1721. B.S. Moore, C. Hertweck, “Biosynthesis and attachment of novel bacterial polyketide synthase starter units,” Nat. Prod. Rep. 19(February 2002):70-99.

1722. J.G. Wallis, J.L. Watts, J. Browse, “Polyunsaturated fatty acid synthesis: what will they think of next?” Trends Biochem. Sci. 27(September 2002):467.

1723. S.J. Sowerby, N.G. Holm, G.B. Petersen, “Origins of life: a route to nanotechnology,” Biosystems 61(June 2001):69-78.

1724. J. Otsuka, Y. Nozawa, “Self-reproducing system can behave as Maxwell’s demon: theoretical illustration under prebiotic conditions,” J. Theor. Biol. 194(1998):205-221.

1725. K. Matsuno, “Compartmentalization of self-reproducing machineries: Multiplication of micro-systems with self-instructing polymerization of amino acids,” Origins of Life 10(December 1980):361-370.

1726. C.R. Woese, “On the evolution of cells,” Proc. Natl. Acad. Sci. (USA) 99(25 June 2002):8742-8747; http://www.pnas.org/cgi/content/full/99/13/8742

1727. J.B. Whitfield, “Estimating the age of the polydnavirus/braconid wasp symbiosis,” Proc. Natl. Acad. Sci. (USA) 99(28 May 2002):7508-7513.

1728. V. Ahmadjian, “Lichens,” Annu. Rev. Microbiol. 19(1965):1-20.

1729. D.C. Smith, “Symbiosis and the biology of lichenised fungi,” Symp. Soc. Exp. Biol. 29(1975):373-405.

1730. W.D. Stewart, P. Rowell, A.N. Rai, “Cyanobacteria-eukaryotic plant symbioses,” Ann. Microbiol. (Paris) 134B(July-August 1983):205-228.

1731. Thomas H. Nash III, ed., Lichen Biology, Cambridge University Press, New York, 1995.

1732. M.W. Karakashian, “Symbiosis in Paramecium bursaria,” Symp. Soc. Exp. Biol. 29(1975):145-173.

1733. Stanley B. Prusiner, “Shattuck lecture – neurodegenerative diseases and prions,” New England J. Med. 344(17 May 2001):1516-1526.

1734. Stanley B. Prusiner, “Prions,” Proc. Natl. Acad. Sci. (USA) 95(10 November 1998):13363-13383.

1735. R. Riek, S. Hornemann, G. Wider, M. Billeter, R. Glockshuber, K. Wuthrich, “NMR structure of the mouse prion protein domain PrP(121-321),” Nature 382(11 July 1996):180-182. Online prion image source: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/gallery.html

1736. A. Slepoy, R.R. Singh, F. Pazmandi, R.V. Kulkarni, D.L. Cox, “Statistical mechanics of prion diseases,” Phys. Rev. Lett. 87(30 July 2001):58-101.

1737. S. Liemann, R. Glockshuber, “Transmissible spongiform encephalopathies,” Biochem. Biophys. Res. Commun. 250(18 September 1998):187-193.

1738. A. Ogayar, M. Sanchez-Perez, “Prions: an evolutionary perspective,” Int. Microbiol. 1(September 1998):183-190.

1739. Gudrun Wildegger1, Susanne Liemann, Rudi Glockshuber, “Extremely rapid folding of the C-terminal domain of the prion protein without kinetic intermediates,” Nature Struct. Biol. 6(June 1999):550-553; http://www.nature.com/cgi-taf/DynaPage.taf?file=/nsb/journal/v6/n6/full/nsb0699_550.html

1740. S. Supattapone, H.O. Nguyen, F.E. Cohen, S.B. Prusiner, M.R. Scott, “Elimination of prions by branched polyamines and implications for therapeutics,” Proc. Natl. Acad. Sci. (USA) 96(7 December 1999):14529-14534.

1741. B.D. Stollar, T.O. Diener, “Potato spindle tuber viroid. V. Failure of immunological tests to disclose double-stranded RNA or RNA-DNA hybrids,” Virology 46(October 1971):168-170; T.O. Diener, “Viroids,” Sci. Am. 244(January 1981):66-73; T.O. Diener, “Viroids,” Adv. Virus Res. 17(1972):295-313.

1742. D.A. Lafontaine, P. Deschenes, F. Bussiere, V. Poisson, J.P. Perreault, “The viroid and viroid-like RNA database,” Nucleic Acids Res. 27(1 January 1999):186-187; http://www.callisto.si.usherb.ca/jpperra

1743. Ricardo Flores, “A naked plant-specific RNA ten-fold smaller than the smallest known viral RNA: the viroid,” C. R. Acad. Sci. III 324(October 2001):943-952.

1744. T.O. Diener, “Viroids and the nature of viroid diseases,” Arch. Virol. Suppl. 15(1999):203-220.

1745. Image derived from: Y. Hu, P.A. Feldstein, J. Hammond, R.W. Hammond, P.J. Bottino, R.A. Owens, “Destabilization of potato spindle tuber viroid by mutations in the left terminal loop,” J. Gen. Virol. 78(June 1997):1199-1206; online text and image from: Robert A. Owens, “Molecular biology of viroid-host interaction,” http://www.barc.usda.gov/psi/mppl/owens/owens2.htm. See also: R.A. Owens, “Viroids,” in A. Granoff, R.G. Webster, eds., Encyclopedia of Virology, Second Edition, Academic Press, London, 1999, pp. 1928-1937.

1746. Demin Zhou, “In vitro and in vivo evolution of a synthetic viroid,” Schultz Lab Research Projects, Molecular Diversity and Catalytic Antibodies, 14 August 2000; http://schultz.scripps.edu/projects/moleculardiversity/

1747. T.O. Diener, “Subviral pathogens of plants: viroids and viroidlike satellite RNAs,” FASEB J. 5(October 1991):2808-2813.

1748. R.Flores, J.W. Randles, M. Bar-Joseph, T.O. Diener, in M.H.V. van Regenmortel, C. Fauquet, D.H.L. Bishop, E.B. Carstens, M.K. Estes, S.M. Lemon, J. Maniloff, M.A. Mayo, D.J. McGeoch, C.R. Pringle, R.B. Wickner, eds., Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses, Academic Press, San Diego, CA, 2000, pp. 1009-1024.

1749. Marcos De la Pena, Ricardo Flores, “An extra nucleotide in the consensus catalytic core of a viroid hammerhead ribozyme: implications for the design of more efficient ribozymes,” J. Biol. Chem. 276(14 September 2001):34586-34593; http://www.jbc.org/cgi/content/full/276/37/34586

1750. M. Schmitz, G. Steger, “Description of RNA folding by ‘simulated annealing’,” J. Mol. Biol. 255(12 January 1996):254-266; A.P. Gultyaev, F.H. van Batenburg, C.W. Pleij, “Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm,” J. Mol. Biol. 276(13 February 1998):43-55; B.A. Shapiro, D. Bengali, W. Kasprzak, J.C. Wu, “RNA folding pathway functional intermediates: their prediction and analysis,” J. Mol. Biol. 312(7 September 2001):27-44.

1751. W.M. Stanley, E.G. Valens, Viruses and the Nature of Life, Dutton, New York, 1961.

1752. Benjamin Harrow, Abraham Mazur, Textbook of Biochemistry, 7th Edition, W.B. Saunders Company, Philadelphia PA, 1958.

1753. Peixuan Guo, C. Zhang, C. Chen, K. Garver, M. Trottier, “Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation,” Mol. Cell 2(July 1998):149-155. See also: F. Zhang, S. Lemieux, X. Wu, D. St.-Arnaud, C.T. McMurray, F. Major, D. Anderson, “Function of hexameric RNA in packaging of bacteriophage phi29 DNA in vitro,” Mol. Cell 2(July 1998):141-147, 405.

1754. D. Shu, Peixuan Guo, “A viral RNA that binds ATP and contains a motif similar to an ATP-binding aptamer from SELEX,” J. Biol. Chem. 278(28 February 2003):7119-7125.

1755. D. Shu, L.P. Huang, S. Hoeprich, P. Guo, “Construction of phi29 DNA-packaging RNA monomers, dimers, and trimers with variable sizes and shapes as potential parts for nanodevices,” J. Nanosci. Nanotechnol. 3(August 2003):295-302.

1756. F. d’Herelle, The Bacteriophage: Its Role in Immunity, Williams & Wilkins, Baltimore MD, 1922. Translated by G.H. Smith. See also: F. d’Herelle, The Bacteriophage and Its Clinical Applications, Thomas, Baltimore MD, 1930; A. Raiga-Clemenceau, “d’Herelle’s bacteriophage and its therapeutic property,” Sem. Hop. Ther. 50(March 1974):229-231. In French.

1757. R.J. Payne, D. Phil, V.A. Jansen, “Phage therapy: the peculiar kinetics of self-replicating pharmaceuticals,” Clin. Pharmacol. Ther. 68(September 2000):225-230.

1758. William B. Wood, R.S. Edgar, “Building a bacterial virus,” Sci. Amer. 217(July 1967):61-66.

1759. R.S. Edgar, I. Lielausis, “Some steps in the morphogenesis of bacteriophage T4,” J. Mol. Biol. 32(March 1968):263-276.

1760. B.F. Poglazov, Morphogenesis of T-Even Bacteriophages, S. Karger, New York, 1973.

1761. Christopher K. Mathews, Elizabeth M. Kutter, Gisela Mosig, Peter B. Berget, Bacteriophage T4, American Society for Microbiology, Washington DC, 1983.

1762. Jim D. Karam, John W. Drake, Kenneth N. Kreuzer, Molecular Biology of Bacteriophage T4, American Society for Microbiology, Washington, DC, 1994.

1763. D.L.D. Caspar, “Movement and self-control in protein assemblies. Quasi-equivalence revisited,” Biophys. J. 32(1980):103-135.

1764. V. Zarybnicky, “Mechanism of T-even DNA ejection,” J. Theor. Biol. 22(January 1969):33-42.

1765. R. Kilkson, M.F. Maestre, “Structure of T-2 bacteriophage,” Nature 195(1962):494-495.

1766. Charles E. Jones, Timothy C. Mueser, Kathleen C. Dudas, Kenneth N. Kreuzer, Nancy G. Nossal, “Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: A versatile couple with roles in replication and recombination,” Proc. Natl. Acad. Sci. (USA) 98(17 July 2001):8312-8318; http://www.pnas.org/cgi/content/full/98/15/8312

1767. W.B. Wood, “Bacteriophage T4 morphogenesis as a model for assembly of subcellular structure,” Q. Rev. Biol. 55(December 1980):353-367.

1768. A.D. Doerman, “Lysis and lysis inhibition with Escherichia coli bacteriophage,” J. Bacteriol. 55(1948):257-275.

1769. R.S. Edgar, R.H. Epstein, “The genetics of a bacterial virus,” Sci. Amer. (February 1965).

1770. Alan J. Cann, “Chapter 4: Virus Replication,” Principles of Molecular Virology, Third Edition, Academic Press, New York, 2001; http://www.tulane.edu/~dmsander/WWW/224/Replication.html

1771. Michael T. Madigan, John M. Martinko, Jack Parker, eds., Brock’s Biology of Microorganisms, 9th Edition, Prentice-Hall, NJ, 1999; Kenneth J. Ryan, ed., Sherris Medical Microbiology: An Introduction to Infectious Diseases, 3rd Edition, McGraw-Hill, New York, 1994.

1772. H.N. Schulz, T. Brinkhoff, T.G. Ferdelman, M. Hernandez Marine, A. Teske, B.B. Jorgensen, “Dense populations of a giant sulfur bacterium in Namibian shelf sediments,” Science 284(16 April 1999):493-495.

1773. E. Olavi Kajander, Neva Ciftcioglu, “Nanobacteria: An alternative mechanism for pathogenic intra- and extracellular calcification and stone formation,” Proc. Natl. Acad. Sci. 95(7 July 1998):8274-8279. See also: John Travis, “Nanobacteria strike the kidney again,” Science News 155(19 June 1999):395.

1774. H.J. Morowitz, M.E. Tourtellotte, “The smallest living cells,” Sci. Amer. 206(March 1962):117-126. See also: Harold J. Morowitz, Mark E. Tourtellotte, “The smallest living cells,” in Donald Kennedy, ed., The Living Cell, W.H. Freeman and Co., San Francisco, 1965, pp. 31-39.

1775. F. Mayer, “Principles of functional and structural organization in the bacterial cell: ‘Compartments’ and their enzymes,” FEMA Microbiol. Rev. 10(April 1993):327-345.

1776. Colin R. Bell, Alanna MacGregor, “Chapter 1: The Basics. Microbial Replication,” Microbial Ecology Lab, Acadia University, Wolfville, Nova Scotia, August 1996; http://plato.acadiau.ca/courses/biol/Microbiology/Replication.htm

1777. V. Norris, “Hypothesis: chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation,” Mol. Microbiol. 16(June 1995):1051-1057.

1778. S.J. Dewar, R. Dorazi, “Control of division gene expression in Escherichia coli,” FEMS Microbiol. Lett. 187(1 June 2000):1-7.

1779. Jonathan King, “Chapter 9. The biotechnology revolution: self-replicating factories and the ownership of life forms,” in Jim Davis, Thomas A. Hirschl, Michael Stack, eds., Cutting Edge: Technology, Information Capitalism and Social Revolution, Verso Books, 1997.

1780. M. Kleerebezemab, P. Hols, J. Hugenholtz, “Lactic acid bacteria as a cell factory: rerouting of carbon metabolism in Lactococcus lactis by metabolic engineering,” Enzyme Microb. Technol. 26(1 June 2000):840-848; J. Hugenholtz, M. Kleerebezem, M. Starrenburg, J. Delcour, W. de Vos, P. Hols, “Lactococcus lactis as a cell factory for high-level diacetyl production,” Appl. Environ. Microbiol. 66(September 2000):4112-4114; http://aem.asm.org/cgi/content/full/66/9/4112

1781. Bernard R. Glick, Jack J. Pasternak, Molecular Biotechnology: Principles and Applications of Recombinant DNA, American Society for Microbiology, Washington, DC, 2003.

1782. E. Gerhart, H. Wagner, “Replication control in bacterial plasmids,” 19 March 1999; http://www.mikrob.slu.se/genexp/general/plasmid.htm. See also: E. Gerhart, H. Wagner, S. Brantl, “Kissing and RNA stability in antisense control of plasmid replication,” Trends Biochem. Sci. 23(December 1998):451-454.

1783. C.M. Thomas, “Paradigms of plasmid organization,” Mol. Microbiol. 37(August 2000):485-491.

1784. J. Burian, L. Guller, M. Macor, W.W. Kay, “Small cryptic plasmids of multiplasmid, clinical Escherichia coli,” Plasmid 37(1997):2-14.

1785. B. Futcher, E. Reid, D.A. Hickey, “Maintenance of the 2 micron circle plasmid of Saccharomyces cerevisiae by sexual transmission: an example of a selfish DNA,” Genetics 118(March 1988):411-415.

1786. D.M. Gordon, “Rate of plasmid transfer among Escherichia coli strains isolated from natural populations,” J. Gen. Microbiol. 138(January 1992):17-21.

1787. S.G. Sedgwick, S.M. Thomas, V.M. Hughes, D. Lodwick, P. Strike, “Mutagenic DNA repair genes on plasmids from the ‘pre-antibiotic era’,” Mol. Gen. Genet. 218(August 1989):323-329.

1788. D. Summers, “Timing, self-control and a sense of direction are the secrets of multicopy plasmid stability,” Mol. Microbiol. 29(September 1998):1137-1145.

1789. P. Stougaard, S. Molin, K. Nordstrom, “RNAs involved in copy-number control and incompatibility of plasmid R1,” Proc. Natl. Acad. Sci (USA) 78(October 1981):6008-6012.

1790. A. Rasooly, R.S. Rasooly, “How rolling circle plasmids control their copy number,” Trends Microbiol. 5(November 1997):440-446.

1791. G. del Solar, M. Espinosa, “Plasmid copy number control: an ever-growing story,” Mol. Microbiol. 37(August 2000):492-500.

1792. J. Paulsson, M. Ehrenberg, “Noise in a minimal regulatory network: plasmid copy number control,” Q. Rev. Biophys. 34(February 2001):1-59.

1793. Gloria del Solar, Rafael Giraldo, Maria Jesus Ruiz-Echevarria, Manuel Espinosa, Ramon Diaz-Orejas, “Replication and control of circular bacterial plasmids,” Microbiol. Mol. Biol. Rev. 62(June 1998):434-464; http://mmbr.asm.org/cgi/content/full/62/2/434?view=full&pmid=9618448

1794. K. Nordstrom, E.G. Wagner, “Kinetic aspects of control of plasmid replication by antisense RNA,” Trends Biochem. Sci. 19(July 1994):294-300.

1795. L.E. Bingle, C.M. Thomas, “Regulatory circuits for plasmid survival,” Curr. Opin. Microbiol. 4(April 2001):194-200.

1796. D.K. Chattoraj, “Control of plasmid DNA replication by iterons: no longer paradoxical,” Mol. Microbiol. 37(August 2000):467-476.

1797. Peter Fantes, Robert Brooks, eds., The Cell Cycle: A Practical Approach, Oxford University Press, New York, 1994.

1798. Christopher Hutchison, David M. Glover, eds., Cell Cycle Control, Oxford University Press, New York, 1995.

1799. B. Stillman, “Cell cycle control of DNA replication,” Science 274(6 December 1996):1659-1664.

 


Last updated on 1 August 2005