PublicationsBooks:Shapiro, J.A. 1967. The structure of the galactose operon in Escherichia coli K-12. Doctoral dissertation, University of Cambridge. Bukhari, A.I., J.A. Shapiro, and S.L. Adhya (eds.) 1977. DNA Insertion Elements, Plasmids and Episomes, Cold Spring Harbor Laboratory. Shapiro, J.A. (ed.) 1983. Mobile Genetic Elements, Academic Press. Shapiro, J.A. and M. Dworkin (eds.). 1997. Bacteria as Multicellular Organisms, Oxford University Press. Complete list of published articles: Shapiro, J.A. 1966. The chromosomal location of the gene determining uridine diphosphoglucose formation in Escherichia coli K-12. J. Bacteriol. 92, 518. Adhya, S. and J.A. Shapiro. 1969. The galactose operon of E. coli K-12. I. Structural and pleiotropic mutants of the operon. Genetics 62, 231-248. (Reprinted in Beckwith J and Silhavy TJ. The Power of Bacterial Genetics: A Literature-Based Course. Cold Spring Harbor Laboratory, 1992) Shapiro, J.A. and S. Adhya. 1969. The galactose operon of E. coli K-12. II. A deletion analysis of operon structure and polarity. Genetics 62, 249. Shapiro, J.A. 1969. Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J. Mol. Biol. 40, 93-105. (Reprinted in Beckwith J and Silhavy TJ. The Power of Bacterial Genetics: A Literature-Based Course. Cold Spring Harbor Laboratory, 1992) Shapiro, J., L. MacHattie, L. Eron, G. Ihler, K. Ippen, J. Beckwith, R. Arditti, W. Reznikoff and R. MacGillivray. 1969. The isolation of pure lac operon DNA. Nature (London) 224, 768. Ippen, K., J.A. Shapiro and J.R. Beckwith. 1971. Transposition of the lac region to the gal region of the Escherichia coli chromosome: Isolation of llac transducing bacteriophages. J. Bacteriol. 108, 5. Shapiro, J., D. Dean and H.O. Halvorson. 1974. Low frequency specialized transduction with Bacillus subtilis bacteriophage F105. Virology62, 393-403. Nieder, M. and J. Shapiro. 1975. Physiological function of the Pseudomonas putida PpG6 (Pseudomonas oleovorans) alkane hydroxylase: monoterminal oxidation of alkanes and fatty acids. J. Bacteriol. 122, 93-98. Grund, A., J. Shapiro, M. Fennewald, P. Bacha, J. Leahy, K. Markbreiter, M.Nieder and M. Toepfer. 1975. Regulation of alkane oxidation in Pseudomonas putida. J. Bacteriol. 123, 546-556. Benson, S. and J. Shapiro. 1975. Induction of alkane hydroxylase protein by unoxidized alkane in Pseudomonas putida. J. Bacteriol. 123, 759-760. Benson, S. and J. Shapiro. 1976. Plasmid-determined alcohol dehydrogenase in alkane-utilizing strains of Pseudomonas putida. J. Bacteriol. 126, 794-798. Shapiro, J.A., S. Benson, M. Fennewald, A. Grund and M. Nieder. 1976. Genetics of alkane utilization. In Microbiology 1976 (D. Schlessinger,ed.), American Society for Microbiology, pp. 568-571. Shapiro, J.A. 1976. Observations on lysogeny in the glutamic acid bacteria. Appl. Environ. Microbiol. 32, 179-182. Benedik, M., M. Fennewald and J. Shapiro. 1977. Transposition of a s -lactamase locus from RP1 in P. putida degradative plasmids. J. Bacteriol. 129, 809-814. Shapiro, J. and P. Sporn. 1977. Tn402: A new transposable element determining trimethoprim resistance that inserts in bacteriophage l. J. Bacteriol. 129, 1632-1635. Shapiro, J.A. 1977. DNA insertion elements and the evolution of chromosome primary structure. Trends in Biochem. Sci. 2, 622-627. Benson, S., M. Fennewald, J. Shapiro and C. Huettner. 1977. Fractionation of inducible alkane hydroxylase activity in P. putida and characterization of hydroxylase- negative plasmid mutations. J. Bacteriol. 132, 614-621. Fennwald, M. and J. Shapiro. 1977. Regulatory mutations of the Pseudomonas plasmid alk regulon. J. Bacteriol. 132, 622-627. Contributions to DNA Insertion Elements, Plasmids and Episomes (1977):
Fennwald, M., W. Prevatt, R. Meyer and J. Shapiro. 1978. Isolation of IncP-2 plasmid DNA from Pseudomonas aeruginosa. Plasmid 1, 164-173. MacHattie, L. and J. Shapiro. 1978. Chromosomal integration of bacteriophage lmeans of a DNA insertion element. Proc. Nat. Acad. Sci. U.S.A. 75, 1490-1494. Benson, S. and J. Shapiro. 1978. TOL is a broad host-range plasmid. J. Bacteriol. 135, 278-280. Shapiro, J. and L. MacHattie. 1979. Integration and excision of l prophage mediated by the IS1 element. Cold Spr. Harb. Symp. Quant. Biol. 43, 1135-1142. Meyer, R., G. Boch, and J. Shapiro. 1979. Transposition of DNA inserted into deletions of the Tn5 kanamycin resistance element. Molec. Gen. Genet. 171, 7-13. Shapiro, J. 1979. A molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc. Nat. Acad. Sci. U.S.A. 76, 1933-1937. (Reprinted in Beckwith J and Silhavy TJ., 1992, The Power of Bacterial Genetics: A Literature-Based Course, Cold Spring Harbor Laboratory, and in Miller, JH, 1996, Discovering Molecular Genetics: A case study course wiuth problems and scenarios, Cold Spring Harbor Laboratory) Shapiro, J., M. Fennewald and S. Benson. 1979. Plasmid-determined alkane oxidation in Pseudomonas. In Genetics of Industrial Microorganisms (O. Sebek, ed.), American Society for Microbiology, pp. 147-153. Fennewald, M. and J. Shapiro. 1979. Transposition of Tn7 in P. aeruginosa and isolation of alk::Tn7 mutations. J. Bacteriol. 136, 264-269. Fennewald, M., S. Benson, M. Oppici and J. Shapiro. 1979. Insertion element analysis and mapping of the Pseudomonas plasmid alk regulon. J. Bacteriol. 139, 940-952. Benson, S., M. Oppici, J. Shapiro and M. Fennewald. 1979. Regulation of membrane peptides by the Pseudomonas plasmid alk regulon. J. Bacteriol. 140, 754-762. Shapiro, J., S. Benson and M. Fennewald. 1980. Genetics of plasmid-determined hydrocarbon oxidation. In Plasmids and Transposons: Environmental Effects and Maintenance Mechanisms (C. Stuttard and K. Rozee, eds.), Academic Press, New York, pp. 1-19. Shapiro, J. 1980. A model for the genetic activity of transposable elements involving DNA replication. In Plasmids and Transposons: Environmental Effects and Maintenance Mechanisms (C. Stuttard and K. Rozee, eds.), Academic Press, New York, pp. 229-247. Meyer, R. and J. Shapiro. 1980. Genetic organization of the broad host-range IncP-1 plasmid R751. J. Bacteriol. 143, 1362-1373. Cohen, S.N. and J.A. Shapiro. 1980. Transposable genetic elements. Sci. American 242 (2), 40-49. Krylov, V.N., V.G. Bogush and J.A. Shapiro. 1980. Pseudomonas aeruginosa phages whose DNA structure is similar to Mu1 phage DNA. I. General description, localization of endonuclease-sensitive sites in DNA, and the structure of D3112 phage homoduplexes. Genetika 16, 824-832 (in Russian). Muster, C.J. and J.A. Shapiro. 1981. Recombination involving transposable elements: On replicon fusion. Cold. Spr. Harb. Symp. Quant. Biol. 45, 239-242. Shapiro, J.A., A. Charbit, S. Benson, M. Caruso, R. Laux, R. Meyer and F. Banuett. 1981. Perspectives for genetic engineering of hydrocarbon oxidizing bacteria. In Trends in the Biology of Fermentations for Fuels and Chemicals (A. Hollaender et al, eds.), Plenum Press, New York, pp. 243-272. Muster, C.J., L.A. MacHattie and J.A. Shapiro. 1981. Transposition and rearrangements in plasmid evolution. In Molecular Biology, Pathogenicity and Ecology of Bacterial Plasmids (S.B. Levy, R.C. Clowes and E.L. Koenig, eds.), Plenum Press, New York, pp. 349-358. Meyer, R., R. Laux, G. Boch, M. Hinds, R. Bayly and J.A. Shapiro. 1982. Broad host-range IncP-4 plasmid R1162: Effects of deletions and insertions on plasmid maintenance and host range. J. Bacteriol. 152, 140-150. Caruso, M. and J.A. Shapiro. 1982. Interactions of Tn7 and temperate phage F116L of Pseudomonas aeruginosa. Mol. Gen. Genet. 188, 292-298. Shapiro, J.A. 1982. Changes in gene order and gene expression. Natl. Cancer Inst. Monograph 60, 87-110. Shapiro, J.A. and B. Cordell. 1982. Eukaryotic mobile and repeated genetic elements. Biol. Cell. 43, 31-54. Shapiro, J.A. 1982. Mobile genetic elements and reorganization of prokaryotic genomes. In Genetics of Industrial Microorganisms, 1982 (Y. Ikeda and T. Beppu, eds.), Kodansha, Tokyo, pp. 9-32 Shapiro, J.A. 1983. Variation as a genetic engineering process. In Evolution from Molecules to Men (D.S. Bendall, ed.), Cambridge University Press, Cambridge, pp. 253-270. Muster, C.J., L.A. MacHattie and J.A. Shapiro. 1983. The plCM system: Observations on the roles of transposable elements in the formation and breakdown of plasmids derived from bacteriophage l replicons. J. Bacteriol. 153, 976-990. Muster, C.J., J.A. Shapiro and L.A. MacHattie. 1983. Recombination involving transposable elements: The role of target molecule replication in Tn1DAp-mediated replicon fusion. Proc. Nat. Acad. Sci. U.S.A. 80, 2314-2317. Shapiro, J.A., D.J. Owen, M. Kok, and G. Eggink. 1983. Pseudomonas hydrocarbon oxidation. In Genetic Control of Environmental Pollutants (G. Omenn and A. Hollaender, eds.), Plenum Press, New York. Rehmat, S. and J.A. Shapiro. 1983. Insertion and replication of the Pseudomonas aeruginosa mutator phage D3112. Molec. Gen. Genet. 192, 416-423. Hauer, B., and J.A. Shapiro. 1984. Control of Tn7 transposition. Molec. Gen. Genet. 194, 149-158. Burck, C.J., J.A. Shapiro and B. Hauer. 1984. The plCM system: Phage immunity-specific incompatibility with IncP-1 plasmids. Mol. Gen.Genet. 194, 340-342. Shapiro, J.A.1984a. Observations on the formation of clones containing araB-lacZ cistron fusions. Molec. Gen. Genet. 194, 79-90. Shapiro, J.A. 1984b. Transposable elements, genome reorganization and cellular differentiation in Gram-negative bacteria. Symp. Soc. Gen. Microbiol. 36 (Part 2), 169-193. Shapiro, J.A. 1984c. The use of Mudlac transposons as tools for vital staining to visualize clonal and non-clonal patterns of organization in bacterial growth on agar surfaces. J. Gen. Microbiol. 130, 1169-1181. Shapiro, J.A. and P. Brinkley. 1984. Programming of DNA rearrangements involving Mu prophages. Cold Spr. Harb. Symp. Quant. Biol. 49, 313-320. Owen, D.J., G. Eggink, B. Hauer, M. Kok, D.L. McBeth, Y.L. Yang and J.A. Shapiro. 1984.Physical structure, genetic content and expression of the alkBAC operon. Molec. Gen. Genet. 197, 373-383. McBeth, D.L. and J.A. Shapiro. 1984. Reversal by DNA amplifications of an unusual mutation blocking alkane and alcohol utilization in Pseudomonas putida. Molec. Gen. Genet. 197, 384-391. Shapiro, J.A. 1985a. Photographing bacterial colonies. A.S.M. News 51, 62-69. (Reprinted in Miller JH. A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory, 1992). Shapiro, J.A. 1985b. Mechanisms of DNA reorganization in bacteria. Int. Rev. Cytol. 93, 25-56. Shapiro, J.A. 1985c. Intercellular communication and genetic change in bacteria. In Halvorson, H.O., D. Pramer & M. Rogul (eds.), Engineered Organisms in the Environment: Scientific Issues, American Society for Microbiology, pp. 63-69. Shapiro, J.A. 1985d. Scanning electron microscope study of Pseudomonas putida colonies. J. Bacteriol. 164, 1171-1181. Shapiro, J.A. 1986. Control of Pseudomonas putida growth on agar surfaces. In The Bacteria, vol. X (J.R. Sokatch, ed.), Academic Press, New York, pp. 27-69. Shapiro, J.A. 1987a. Organization of Developing E. coli colonies viewed by scanning electron microscopy. J. Bacteriol. 197, 142-156. Shapiro, J.A. 1987b. Some lessons of phage Mu. In The Bacteriophage Mu (N. Symonds, A. Toussaint, P van de Putte and M. Howe, eds.), Cold Spring Harbor Laboratory, pp. 251-258. Shapiro, J.A. 1987c. Eukaryotic transposable elements as mutagenic agents: a meeting review. Genes and Development 1, 747-749. Shapiro, J.A. 1988a. What transposable elements do in bacteria. In Eukaryotic Transposable Elements as Mutagenic Agents, Banbury Report 30, 3-16. Shapiro, J.A. and N.P. Higgins. 1988. Variation of Shapiro, J.A. 1988b. Bacteria as multicellular organisms. Scientific American 256 (6), 82-89. Shapiro, J.A. and N.P. Higgins. 1989. Differential activity of a transposable element in E. coli colonies. J. Bacteriol. 171, 5975-5986. Shapiro, J.A. and C. Hsu. 1989. E. coli K-12 cell-cell interactions seen by time-lapse video. J. Bacteriol. 171, 5963-5974. Shapiro, J.A. and D. Leach. 1990. Action of a transposable element in coding sequence fusions. Genetics 126, 293-299. Shapiro, J.A. and D. Trubatch. 1991. Sequential events in bacterial colony morphogenesis. Physica D 49, 214-223. Shapiro, J.A. 1991a. Multicellular behavior of bacteria. ASM News57, 247-253 (meeting report). Shapiro, J.A. 1991b. Genomes as smart systems. Genetica 84, 3-4. Shapiro, J.A. 1992a. Concentric rings in Escherichia coli colonies. In Oscillations and Morphogenesis, L. Rensing (ed.), Marcell Dekker, pp 297 - 310. Shapiro, J.A. 1992b. Natural genetic engineering in evolution. Genetica86, 99-111(reprinted in J.F. McDonald (ed.), 1993, Transposable Elements and Evolution, Kluwer, Dordrecht). Shapiro, J.A. 1992c. Kernels and colonies: The challenge of pattern. In The Dynamic Genome, N. Federoff and D. Botstein (eds), Cold Spring Harbor Press, pp. 213-221. Shapiro, J.A. 1992d. Differential action and differential expression of E. coli DNA polymerase I during colony development. J. Bacteriol. 174, 7262-7272. Shapiro, J.A. 1992e. Barbara McClintock, 1902-1992. BioEssays14, 791-792. Shapiro, J.A. 1993a. A role for the Clp protease in activating Mu-mediated DNA rearrangements. J. Bacteriol. 175, 2625-2631. Shapiro, J.A. 1993b. Natural genetic engineering of the bacterial genome. Curr. Opin. Genet. Devel. 3, 845-848. Shapiro, J.A. 1994a. Pattern and control in bacterial colonies. Science Progress 76, 399-424. Shapiro, J.A. 1994b. The smallest cells have important lessons to teach. In Cosmic Beginnings and Human Ends, C. Matthews, R. Varghese and D. Steele (eds), Open Court Publishing, pp. 205-224. Maenhaut-Michel, G. & Shapiro, J.A. 1994c. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J. 13, 5229-5239. Shapiro, J.A. 1994d. Adaptive mutation. Science 265, 94 (letter). Shapiro, J.A. 1995a. The discovery and significance of mobile genetic elements. In Mobile Genetic Elements - Frontiers in Molecular Biology, D.J. Sherratt (ed.), IRL Press, Oxford, pp. 1-17. Shapiro, J.A. 1995b. Adaptive mutation: Who's really in the garden? Science268, 373-4. Shapiro, J.A. 1995c. The significances of bacterial colony patterns. Bioessays17, 597-607. Shapiro, J.A. 1995d. Adaptive mutation: The debate goes on. Science269, 286-288 (letter). Rauprich,O., M. Matsushita, K. Weijer, F. Siegert, S. Esipov, and J.A. Shapiro. 1996. Periodic phenomena in Proteus mirabilis swarm colony development. J. Bacteriol. 178, 6525-6538. James A. Shapiro. 1996. "Darwin's Black Box: The Biochemical
Challenge
to Evolution." Shapiro, J.A. 1997a. Multicellularity is the rule, not the exception: Lessons from E. coli colonies. In Shapiro, J.A. and Dworkin, M. (eds.). Bacteria as Multicellular Organisms, Oxford University Press, pp. 14-49. Shapiro, J.A. 1997. A third way [alternative to Darwinism
& Creationism]. Boston
Review 22 (1), 32-33. Shapiro, J.A. 1997b. Genome organization, natural genetic engineering, and adaptive mutation. Trends in Genetics 13, 98-104. Maenhaut-Michel, G., C.E. Blake, D.R.F. Leach and J.A. Shapiro. 1997. Different structures of selected and unselected araB-lacZ fusions. Molec. Micro. 23, 1133-1146. Esipov, S. and J.A.Shapiro. 1998. Kinetic model of Proteus
mirabilis
swarm colony development. J. Math. Biol. 36,
249-268. Shapiro, J.A. 1998. Thinking about bacterial populations as
multicellular
organisms. Ann. Rev. Microbiol. 52, 81-104. Shapiro, J.A. 1999. Natural genetic engineering, adaptive mutation & bacterial evolution, in Microbial Ecology and Infectious Disease, E. Rosenberg (ed.), ASM Press, Washington, pp. 259-275. Shapiro, J.A. 1999. Genome system architecture and natural genetic engineering in evolution. In Molecular Strategies for Biological Evolution, L. Caporale, ed., Annal. NY Acad. Sci. 870, 23-35. Shapiro, J.A. 1999. Views about evolution are evolving. ASM News 65 (4), in press (meeting report) Lamrani. S., C. Ranquet, M.-J. Gama, H. Nakai, J.A. Shapiro, A. Toussaint and G. Maenhaut-Michel. 1999. Starvation-induced Mucts62-mediated Coding Sequence Fusion: Roles for ClpXP, Lon, RpoS and Crp. Molec. Microbiol. 32, 327-343. Newman, D.L. and J.A. Shapiro. 1999. Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development. Molec. Microbiol. 33, 18-32. Shapiro, J.A. 1999. Transposable elements as the key to a 21st Century view of evolution. Genetica 107 (1/3):171-179. (reprinted in Georgia Genetics Review I: Transposable Elements & Genome Evolution, edited by John F. McDonald, Kluwer, 2000) Shapiro, J.A. 2002. "Genome system architecture and natural genetic engineering." In Evolution as Computation, L.F. Landweber and E. Winfree (eds.), Springer, Berlin, pp 1-14. Shapiro, J.A. 2002. A 21st Century View of Evolution. J. Biol. Phys. 28: 1-20. (PROCEEDINGS of the 4th International Conference on Biological Physics, Kyoto, Japan, July 30 - August 3, 2001) Shapiro, J.A. 2002. Genome
Organization
and Reorganization in Evolution: Formatting for Computation and
Function.
In From Epigenesis to Epigenetics: The Genome in Context, L.Van
Speybroack,
G. Van de Vijver, and D. de Waele (eds.), Ann. NY Acad Sci 981, 111-134. Sternberg, R.v. and Shapiro, J.A. 2005. How repeated retroelements format genome function. Cytogenet. Genome Res., 110:108-116. Shapiro, JA. 2005. A 21st
Century View Of Evolution: Genome
System Architecture, Repetitive DNA, And Natural Genetic Engineering.
Gene 345: 91-100 (special
issue on "Structural approaches to sequence
evolution:
Molecules, networks, populations"). Shapiro JA. 2005. Retrotransposons and regulatory suites.
BioEssays 27, 122-125. Shapiro JA. 2005. Thinking about evolution in terms of
cellular computing. Natural Computing,
4, 297-324. |
-galactosidase expression from Mudlac elements during the
development
of E. coli colonies. Annales de l'Institut Pasteur 139,
79-103.