Wstępna charakterystyka bakteriofaga Serratia φOS10/Bibliografia

Dodaj linki
Z Wikibooks, biblioteki wolnych podręczników.
  1. Abdollahi, A., Nasirpour, S., Shahmohammad, N., & Zolfaghari, A. (2008). Serratia Marcescens, an Opportunistic Gram Negative Infection in Cardiac Valve Surgery. Iranian Journal of Pathology, 3(1), 40-42.

  2. Abedon, S. T., Herschler, T. D., & Stopar, D. (2001). Bacteriophage latent-period evolution as a response to resource availability. Appl. Environ. Microbiol., 67(9), 4233-4241.

  3. Altschul, S. F., & Gish, W. (1996). [27] local alignment statistics. In Methods in enzymology (Vol. 266, pp. 460-480). Academic Press.

  4. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

  5. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 25(17), 3389-3402.

  6. Ashelford, K. E., Fry, J. C., Bailey, M. J., & Day, M. J. (2002). Characterization of Serratia isolates from soil, ecological implications and transfer of Serratia proteamaculans subsp. quinovora Grimont et al. 1983 to Serratia quinivorans corrig., sp. nov. International journal of systematic and evolutionary microbiology, 52(6), 2281-2289.

  7. Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., ... & Meyer, F. (2008). The RAST Server: rapid annotations using subsystems technology. BMC genomics, 9(1), 75.

  8. Baj, J., Dziewit, Ł., Bartosik, D., Radlińska, M., Drewniak, Ł., Paterczyk, B. (2018). Mikrobiologia. Wydawnictwo naukowe PWN.

  9. Baron, S. (1996). Classification--Medical Microbiology. University of Texas Medical Branch at Galveston.

  10. Barry, M., Van Buuren, N., Burles, K., Mottet, K., Wang, Q., & Teale, A. (2010). Poxvirus exploitation of the ubiquitin-proteasome system. Viruses, 2(10), 2356-2380.

  11. Barylski, J., Enault, F., Dutilh, B. E., Schuller, M. B., Edwards, R. A., Gillis, A., ... & Lavigne, R. (2018). Taxonomy proposal: To create one (1) new family, Herelleviridae, in the order Caudovirales. ICTV Online: International Committee on Taxonomy of Viruses (ICTV).

  12. Bender, K. S., Buckley, D. H., Sattley, W. M., Madigan, M. T., & Stahl, D. A. (2018). Brock Biology of Microorganisms. Pearson.

  13. Benedik, M. J., & Strych, U. (1998). Serratia marcescens and its extracellular nuclease. FEMS microbiology letters, 165(1), 1-13.

  14. Bergan, T., Grimont, P. A., & Grimont, F. (1983). Fatty acids of Serratia determined by gas chromatography. Current Microbiology, 8(1), 7-11.

  15. Bernstein, H., & Bernstein, C. (1973). Circular and branched circular concatenates as possible intermediates in bacteriophage T4 DNA replication. Journal of molecular biology, 77(3), 355-361.

  16. Bhadra, B., Roy, P., & Chakraborty, R. (2005). Serratia ureilytica sp. nov., a novel urea-utilizing species. International journal of systematic and evolutionary microbiology, 55(5), 2155-2158.

  17. Bielmann, R., Habann, M., Eugster, M. R., Lurz, R., Calendar, R., Klumpp, J., & Loessner, M. J. (2015). Receptor binding proteins of Listeria monocytogenes bacteriophages A118 and P35 recognize serovarspecific teichoic acids. Virology, 477, 110-118.

  18. Blum, J. S., Bindi, A. B., Buzzelli, J., Stolz, J. F., & Oremland, R. S. (1998). Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Archives of microbiology, 171(1), 19-30.

  19. Bobay, L. M., Touchon, M., & Rocha, E. P. (2014). Pervasive domestication of defective prophages by bacteria. Proceedings of the National Academy of Sciences, 111(33), 12127-12132.

  20. Bollivar, D. W., Bernardoni, B., Bockman, M. R., Miller, B. M., Russell, D. A., Delesalle, V. A., ... & Eppurath, A. (2016). Complete genome sequences of five bacteriophages that infect Rhodobacter capsulatus. Genome Announc., 4(3), e00051-16.

  21. Breed, R. S., Murray, E. G., & Kitchens, A. P. (1948). Sergey's manual of determinative bacteriology. Sergey's manual of determinative bacteriology. Sixth edition.

  22. Brettin, T., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Olsen, G. J., ... & Shukla, M. (2015). RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific reports, 5, 8365.

  23. Brissette, J. L., Weiner, L., Ripmaster, T. L., & Model, P. (1991). Characterization and sequence of the Escherichia coli stress-induced psp operon. Journal of molecular biology, 220(1), 35-48.

  24. Brüssow, H., Canchaya, C., & Hardt, W. D. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev., 68(3), 560-602.

  25. Bujnicki, J. M., Feder, M., Radlińska, M., & Blumenthal, R. M. (2002). Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA: m6A methyltransferase. Journal of molecular evolution, 55(4), 431-444.

  26. Cases, S., Smith, S. J., Zheng, Y. W., Myers, H. M., Lear, S. R., Sande, E., ... & Erickson, S. K. (1998). Identification of a gene encoding an acyl CoA: diacylglycerol acyltransferase, a key enzyme in triacylglycerol synthesis. Proceedings of the National Academy of Sciences, 95(22), 13018-13023.

  27. Casey, E., Fitzgerald, B., Mahony, J., Lugli, G. A., Ventura, M., & van Sinderen, D. (2017). Genome sequence of Serratia marcescens phage BF. Genome Announc., 5(23), e00211-17.

  28. Casjens, S. (2003). Prophages and bacterial genomics: what have we learned so far?. Molecular microbiology, 49(2), 277-300.

  29. Casjens, S. R., Gilcrease, E. B., Winn-Stapley, D. A., Schicklmaier, P., Schmieger, H., Pedulla, M. L., ... & Hendrix, R. W. (2005). The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. Journal of bacteriology, 187(3), 1091-1104.

  30. Casjens, S., & Hayden, M. (1988). Analysis in vivo of the bacteriophage P22 headful nuclease. Journal of molecular biology, 199(3), 467-474.

  31. Cenens, W., Makumi, A., Mebrhatu, M. T., Lavigne, R., & Aertsen, A. (2013). Phage–host interactions during pseudolysogeny: Lessons from the Pid/dgo interaction. Bacteriophage, 3(1), e1003269.

  32. Cerritelli, M. E., Conway, J. F., Cheng, N., Trus, B. L., & Steven, A. C. (2003). Molecular mechanisms in bacteriophage T7 procapsid assembly, maturation, and DNA containment. Advances in protein chemistry, 64, 301-324.

  33. Chandrakanth, K., Virupakshaiah, D. B. M., Gavimath, C. C., Udaykumar, M., & Kangralkar, V. A. (2010). Comparative genomics of Staphylococcus aureus Coagulase gene. Journal of Advanced Bioinformatics Applications and Research, 1(1), 31-36.

  34. Chang, C. Y., Kemp, P., & Molineux, I. J. (2010). Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell. Virology, 398(2), 176-186.

  35. Charbit, A., Clement, J. M., & Hofnung, M. (1984). Further sequence analysis of the phage lambda receptor site: possible implications for the organization of the LamB protein in Escherichia coli K12. Journal of molecular biology, 175(3), 395-401.

  36. Blum, J. S., Bindi, A. B., Buzzelli, J., Stolz, J. F., & Oremland, R. S. (1998). Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Archives of microbiology, 171(1), 19-30.

  37. Bobay, L. M., Touchon, M., & Rocha, E. P. (2014). Pervasive domestication of defective prophages by bacteria. Proceedings of the National Academy of Sciences, 111(33), 12127-12132.

  38. Bollivar, D. W., Bernardoni, B., Bockman, M. R., Miller, B. M., Russell, D. A., Delesalle, V. A., ... & Eppurath, A. (2016). Complete genome sequences of five bacteriophages that infect Rhodobacter capsulatus. Genome Announc., 4(3), e00051-16.

  39. Breed, R. S., Murray, E. G., & Kitchens, A. P. (1948). Sergey's manual of determinative bacteriology. Sergey's manual of determinative bacteriology. Sixth edition.

  40. Brettin, T., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Olsen, G. J., ... & Shukla, M. (2015). RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific reports, 5, 8365.

  41. Brissette, J. L., Weiner, L., Ripmaster, T. L., & Model, P. (1991). Characterization and sequence of the Escherichia coli stress-induced psp operon. Journal of molecular biology, 220(1), 35-48.

  42. Brüssow, H., Canchaya, C., & Hardt, W. D. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev., 68(3), 560-602.

  43. Bujnicki, J. M., Feder, M., Radlińska, M., & Blumenthal, R. M. (2002). Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA: m6A methyltransferase. Journal of molecular evolution, 55(4), 431-444.

  44. Cases, S., Smith, S. J., Zheng, Y. W., Myers, H. M., Lear, S. R., Sande, E., ... & Erickson, S. K. (1998). Identification of a gene encoding an acyl CoA: diacylglycerol acyltransferase, a key enzyme in triacylglycerol synthesis. Proceedings of the National Academy of Sciences, 95(22), 13018-13023.

  45. Casey, E., Fitzgerald, B., Mahony, J., Lugli, G. A., Ventura, M., & van Sinderen, D. (2017). Genome sequence of Serratia marcescens phage BF. Genome Announc., 5(23), e00211-17.

  46. Casjens, S. (2003). Prophages and bacterial genomics: what have we learned so far?. Molecular microbiology, 49(2), 277-300.

  47. Casjens, S. R., Gilcrease, E. B., Winn-Stapley, D. A., Schicklmaier, P., Schmieger, H., Pedulla, M. L., ... & Hendrix, R. W. (2005). The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. Journal of bacteriology, 187(3), 1091-1104.

  48. Casjens, S., & Hayden, M. (1988). Analysis in vivo of the bacteriophage P22 headful nuclease. Journal of molecular biology, 199(3), 467-474.

  49. Cenens, W., Makumi, A., Mebrhatu, M. T., Lavigne, R., & Aertsen, A. (2013). Phage–host interactions during pseudolysogeny: Lessons from the Pid/dgo interaction. Bacteriophage, 3(1), e1003269.

  50. Cerritelli, M. E., Conway, J. F., Cheng, N., Trus, B. L., & Steven, A. C. (2003). Molecular mechanisms in bacteriophage T7 procapsid assembly, maturation, and DNA containment. Advances in protein chemistry, 64, 301-324.

  51. Chandrakanth, K., Virupakshaiah, D. B. M., Gavimath, C. C., Udaykumar, M., & Kangralkar, V. A. (2010). Comparative genomics of Staphylococcus aureus Coagulase gene. Journal of Advanced Bioinformatics Applications and Research, 1(1), 31-36.

  52. Chang, C. Y., Kemp, P., & Molineux, I. J. (2010). Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell. Virology, 398(2), 176-186.

  53. Charbit, A., Clement, J. M., & Hofnung, M. (1984). Further sequence analysis of the phage lambda receptor site: possible implications for the organization of the LamB protein in Escherichia coli K12. Journal of molecular biology, 175(3), 395-401.

  54. CŁAPA, T., NAROŻNA, D., SIUDA, R., Borkowski, A., Selwet, M., MĄDRZAK, C. J., & KOŹLECKA, E. (2017). Bacterial communities from the arsenic mine in Złoty Stok, Sudety mountains, Poland. Polish journal of microbiology, 66(3), 375-381.

  55. Colier L, Oxford J. Wirusologia. Wydawnictwo lekarskie PZWL. 2001.

  56. Comeau, A. M., Arbiol, C., & Krisch, H. M. (2010). Gene network visualization and quantitative synteny analysis of more than 300 marine T4-like phage scaffolds from the GOS metagenome. Molecular biology and evolution, 27(8), 1935-1944.

  57. Coordinators, N. R. (2017). Database resources of the national center for biotechnology information. Nucleic acids research, 45(Database issue), D12.

  58. Creager, A. N., Scholthof, K. B. G., Citovsky, V., & Scholthof, H. B. (1999). Tobacco mosaic virus: pioneering research for a century.

  59. Cumby, N., Edwards, A. M., Davidson, A. R., & Maxwell, K. L. (2012). The bacteriophage HK97 gp15 moron element encodes a novel superinfection exclusion protein. Journal of bacteriology, 194(18), 5012-5019.

  60. Cyr, D. M., Langer, T., & Douglas, M. G. (1994). DnaJ-like proteins: molecular chaperones and specific regulators of Hsp70. Trends in biochemical sciences, 19(4), 176-181.

  61. d’Herelle, F. (1917). Sur un microbe invisible antagoniste des bacilles dysentériques. CR Acad. Sci. Paris, 165, 373-375.

  62. Daugelavičius, R., Gaidelytė, A., Cvirkaitė-Krupovič, V., & Bamford, D. H. (2007). On-line monitoring of changes in host cell physiology during the one-step growth cycle of Bacillus phage Bam35. Journal of microbiological methods, 69(1), 174-179.

  63. Davidson, A. R. (2018). A common trick for transferring bacterial DNA. Science, 362(6411), 152-153.

  64. Denyes, J. M., Krell, P. J., Manderville, R. A., Ackermann, H. W., She, Y. M., & Kropinski, A. M. (2014). The genome and proteome of Serratia bacteriophage η which forms unstable lysogens. Virology journal, 11(1), 6.

  65. Drewniak, L., Matlakowska, R., & Sklodowska, A. (2008). Arsenite and arsenate metabolism of Sinorhizobium sp. M14 living in the extreme environment of the Zloty Stok gold mine. Geomicrobiology Journal, 25(7-8), 363-370.

  66. Drewniak, L., Matlakowska, R., Rewerski, B., & Sklodowska, A. (2010). Arsenic release from gold mine rocks mediated by the activity of indigenous bacteria. Hydrometallurgy, 104(3-4), 437-442.

  67. Dziewit, L., Oscik, K., Bartosik, D., & Radlinska, M. (2014). Molecular characterization of a novel temperate Sinorhizobium bacteriophage, ФLM21, encoding DNA methyltransferase with CcrM-like specificity. Journal of virology, 88(22), 13111-13124.

  68. Echols, H., Green, L., Oppenheim, A. B., Oppenheim, A., & Honigman, A. (1973). Role of the cro gene in bacteriophage λ development. Journal of molecular biology, 80(2), 203-216.

  69. Edwards, R. A., & Rohwer, F. (2005). Viral metagenomics. Nature Reviews Microbiology, 3(6), 504.

  70. Eisenstein, E., Gilliland, G. L., Herzberg, O., Moult, J., Orban, J., Poljak, R. J., ... & Howard, A. J. (2000). Biological function made crystal clear—annotation of hypothetical proteins via structural genomics. Current Opinion in Biotechnology, 11(1), 25-30.

  71. Ellis, E. L., & Delbrück, M. (1939). The growth of bacteriophage. The Journal of general physiology, 22(3), 365-384.

  72. Erez, Z., Steinberger-Levy, I., Shamir, M., Doron, S., Stokar-Avihail, A., Peleg, Y., ... & Amitai, G. (2017). Communication between viruses guides lysis–lysogeny decisions. Nature, 541(7638), 488.

  73. Esposito, D., Fitzmaurice, W. P., Benjamin, R. C., Goodman, S. D., Waldman, A. S., & Scocca, J. J. (1996). The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic acids research, 24(12), 2360-2368.

  74. EWING, W. H., DAVIS, B. R., FIFE, M. A., & LESSEL, E. F. (1973). Biochemical characterization of Serratia liquefaciens (Grimes and Hennerty) Bascomb et al.(formerly Enterobacter liquefaciens) and Serratia rubidaea (Stapp) comb. nov. and designation of type and neotype strains. International Journal of Systematic and Evolutionary Microbiology, 23(3), 217-225.

  75. Fan, L., Arvai, A. S., Cooper, P. K., Iwai, S., Hanaoka, F., & Tainer, J. A. (2006). Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Molecular cell, 22(1), 27-37.

  76. Fenner, F., Henderson, D. A., Arita, I., Jezek, Z., & Ladnyi, I. D. (1988). Smallpox and its eradication (Vol. 6). Geneva: World Health Organization.

  77. Fitzmaurice, W. P., Waldman, A. S., Benjamin, R. C., Huang, P. C., & Scocca, J. J. (1984). Nucleotide sequence and properties of the cohesive DNA termini from bacteriophage HP1c1 of Haemophilus influenzae Rd. Gene, 31(1-3), 197-203.

  78. Fokine, A., & Rossmann, M. G. (2014). Molecular architecture of tailed double-stranded DNA phages. Bacteriophage, 4(2), e28281.

  79. Fortier, L. C., & Sekulovic, O. (2013). Importance of prophages to evolution and virulence of bacterial pathogens. Virulence, 4(5), 354-365.

  80. Fortuna, M. A., Barbour, M. A., Zaman, L., Hall, A. R., Buckling, A., & Bascompte, J. (2019). Coevolutionary dynamics shape the structure of bacteria‐phage infection networks. Evolution, 73(5), 1001-1011.

  81. Frederik A. Murphy, Claude M. Fauquet, David H.L. Bishop, Said A. Ghabrial, Audrey W. Jarvis, Giovanni P. Martelli, Mike A. Mayo, Max D. (2012) Summers Springer Science & Business Media.

  82. Fujisawa, H., & Morita, M. (1997). Phage DNA packaging. Genes to Cells, 2(9), 537-545.

  83. Gavini, F., Ferragut, C., Izard, D., Trinel, P. A., Leclerc, H., Lefebvre, B., & Mossel, D. A. A. (1979). Serratia fonticola, a new species from water. International Journal of Systematic and Evolutionary Microbiology, 29(2), 92-101.

  84. Geiger, A., Fardeau, M. L., Falsen, E., Ollivier, B., & Cuny, G. (2010). Serratia glossinae sp. nov., isolated from the midgut of the tsetse fly Glossina palpalis gambiensis. International journal of systematic and evolutionary microbiology, 60(6), 1261-1265.

  85. Gill, V. J., Farmer, J. J., Grimont, P. A., Asbury, M. A., & McIntosh, C. L. (1981). Serratia ficaria isolated from a human clinical specimen. Journal of clinical microbiology, 14(2), 234-236.

  86. Graham, K., Freeman, M., Newkirk, H., Liu, M., Cahill, J., & Ramsey, J. (2019). Complete Genome Sequence of Serratia marcescens Phage MTx. Microbiology Resource Announcements, 8(25), e0057319.

  87. Grimes, M., & Hennerty, A. J. (1931). A study of bacteria belonging to the sub-genus Aerobacter. Royal Dublin Society.

  88. Grimont, F., & Grimont, P. A. D. (2005). Genus XXXIV. Serratia Bizio 1823, 288AL. Bergey’s Manual of Systematic Bacteriology, 2nd Ed. Volume two: the Proteobacteria, Part B: the Gammaproteobacteria. Springer, New York, 799-811.

  89. Grimont, P. A. D., Farmer III, J. J., Grimont, F., Asbury, M. A., Brenner, D. J., & Deval, C. (1983, January). Ewingella americana gen. nov., sp. nov., a new Enterobacteriaceae isolated from clinical specimens. In Annales De l'Institut Pasteur/Microbiologie (Vol. 134, No. 1, pp. 39-52). Elsevier Masson.

  90. Grimont, P. A. D., GRIMONT, F., Richard, C., Davis, B. R., Steigerwalt, A. G., & BRENNER, D. J. (1978b). Deoxyribonucleic acid relatedness between Serratia plymuthica and other Serratia species, with a description of Serratia odorifera sp. nov.(type strain: ICPB 3995). International Journal of Systematic and Evolutionary Microbiology, 28(4), 453-463.

  91. Grimont, P. A., & Grimont, F. (1978a). Biotyping of Serratia marcescens and its use in epidemiological studies. Journal of Clinical Microbiology, 8(1), 73-83.

  92. GRIMONT, P. A., JACKSON, T. A., AGERON, E., & NOONAN, M. J. (1988). Serratia entomophila sp. nov. associated with amber disease in the New Zealand grass grub Costelytra zealandica. International Journal of Systematic and Evolutionary Microbiology, 38(1), 1-6.

  93. Grkovic, S., Glare, T. R., Jackson, T. A., & Corbett, G. E. (1995). Genes Essential for Amber Disease in Grass Grubs Are Located on the Large Plasmid Found in Serratia entomophila and Serratia proteamaculans. Appl. Environ. Microbiol., 61(6), 2218-2223.

  94. Groth, A. C., & Calos, M. P. (2004). Phage integrases: biology and applications. Journal of molecular biology, 335(3), 667-678.

  95. Guttman, B. S. (2001). Virus. Encyclopedia of Genetics, 2108–2114.

  96. Hatfull, G. F., & Hendrix, R. W. (2011). Bacteriophages and their genomes. Current opinion in virology, 1(4), 298-303.

  97. Hendrix, R. W. (2002). Bacteriophages: evolution of the majority. Theoretical population biology, 61(4), 471-480.

  98. Henikoff, S., & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences, 89(22), 10915-10919.

  99. Heo, Y. J., Chung, I. Y., Choi, K. B., Lau, G. W., & Cho, Y. H. (2007). Genome sequence comparison and superinfection between two related Pseudomonas aeruginosa phages, D3112 and MP22. Microbiology, 153(9), 2885-2895.

  100. Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., & Hauer, C. R. (1986). Protein sequencing by tandem mass spectrometry. Proceedings of the National Academy of Sciences, 83(17), 6233-6237.

  101. ICTV (2018a). EC 50, Washington, DC, July 2018; Email ratification October 2018 (MSL #33)

  102. ICTV (2018b). EC 50, Washington, DC, July 2018; Email ratification February 2019 (MSL #34)

  103. Iguchi, A., Nagaya, Y., Pradel, E., Ooka, T., Ogura, Y., Katsura, K., ... & Sebaihia, M. (2014). Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen. Genome biology and evolution, 6(8), 2096-2110.

  104. Iyer, L. M., Burroughs, A. M., & Aravind, L. (2005). The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism. Bioinformatics, 22(3), 257263.

  105. Janion, C. (2008). Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli. International journal of biological sciences, 4(6), 338.

  106. Johnson, J. E. (2010). Virus particle maturation: insights into elegantly programmed nanomachines. Current opinion in structural biology, 20(2), 210-216.

  107. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: a better web interface. Nucleic acids research, 36(suppl_2), W5-W9.

  108. Juhala, R. J., Ford, M. E., Duda, R. L., Youlton, A., Hatfull, G. F., & Hendrix, R. W. (2000). Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. Journal of molecular biology, 299(1), 27-51.

  109. Kemp, P., Garcia, L. R., & Molineux, I. J. (2005). Changes in bacteriophage T7 virion structure at the initiation of infection. Virology, 340(2), 307-317.

  110. King, G., & Murray, N. E. (1995). Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K‐12. Molecular microbiology, 16(4), 769-777.

  111. Kostyuchenko, V. A., Leiman, P. G., Chipman, P. R., Kanamaru, S., Van Raaij, M. J., Arisaka, F., ... & Rossmann, M. G. (2003). Three-dimensional structure of bacteriophage T4 baseplate. Nature Structural & Molecular Biology, 10(9), 688.

  112. Krafft, T., & Macy, J. M. (1998). Purification and characterization of the respiratory arsenate reductase of Chrysiogenes arsenatis. European Journal of Biochemistry, 255(3), 647-653.

  113. Krasnykh, V., Belousova, N., Korokhov, N., Mikheeva, G., & Curiel, D. T. (2001). Genetic targeting of an adenovirus vector via replacement of the fiber protein with the phage T4 fibritin. Journal of virology, 75(9), 4176-4183.

  114. Kropinski, A., Turner, D., Nash, J., Ackermann, H. W., Lingohr, E., Warren, R., ... & Ehrlich, M. (2018). The sequence of two bacteriophages with hypermodified bases reveals novel phage-host interactions. Viruses, 10(5), 217.

  115. Kropiński, A. M. (2018). Practical advice on the one-step growth curve. In Bacteriophages (pp. 41-47). Humana Press, New York, NY.

  116. Krupovic, M., Prangishvili, D., Hendrix, R. W., & Bamford, D. H. (2011). Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol. Mol. Biol. Rev., 75(4), 610635.

  117. Labonté, J. M., Pachiadaki, M., Fergusson, E., McNichol, J., Grosche, A., Gulmann, L. K., ... & Stepanauskas, R. (2019). Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system. Frontiers in Microbiology, 10.

  118. Labrie, S. J., Samson, J. E., & Moineau, S. (2010). Bacteriophage resistance mechanisms. Nature Reviews Microbiology, 8(5), 317.

  119. Laslett, D., & Canback, B. (2004). ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic acids research, 32(1), 11-16.

  120. Laverman, A. M., Blum, J. S., Schaefer, J. K., Phillips, E., Lovley, D. R., & Oremland, R. S. (1995). Growth of strain SES-3 with arsenate and other diverse electron acceptors. Appl. Environ. Microbiol., 61(10), 3556-3561.

  121. Lawrence, J. G., Hatfull, G. F., & Hendrix, R. W. (2002). Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. Journal of bacteriology, 184(17), 4891-4905.

  122. Lebedev, A. A., Krause, M. H., Isidro, A. L., Vagin, A. A., Orlova, E. V., Turner, J., ... & Antson, A. A. (2007). Structural framework for DNA translocation via the viral portal protein. The EMBO journal, 26(7), 1984-1994.

  123. Lee, P. Y., Costumbrado, J., Hsu, C. Y., & Kim, Y. H. (2012). Agarose gel electrophoresis for the separation of DNA fragments. JoVE (Journal of Visualized Experiments), (62), e3923.

  124. Leplae, R., Lima-Mendez, G., & Toussaint, A. (2009). ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic acids research, 38(suppl_1), D57-D61.

  125. Lepore, B. W., Ruzicka, F. J., Frey, P. A., & Ringe, D. (2005). The x-ray crystal structure of lysine-2, 3-aminomutase from Clostridium subterminale. Proceedings of the National Academy of Sciences, 102(39), 13819-13824.

  126. Lin, H., & Black, L. W. (1998). DNA requirements in vivo for phage T4 packaging. Virology, 242(1), 118-127.

  127. Lin, N. T., Chiou, P. Y., Chang, K. C., Chen, L. K., & Lai, M. J. (2010). Isolation and characterization of ϕAB2: a novel bacteriophage of Acinetobacter baumannii. Research in microbiology, 161(4), 308314.

  128. Loeffler, F., & Frosch, P. (1898). Report of the commission for research on foot-and-mouth disease. Zentrabl. Bacteriol. Parasitenkunde Infektionkrankh., 23, 371-391.

  129. Loessner, M. J. (2005). Bacteriophage endolysins—current state of research and applications. Current opinion in microbiology, 8(4), 480-487.

  130. Lopes, A., Tavares, P., Petit, M. A., Guérois, R., & Zinn-Justin, S. (2014). Automated classification of tailed bacteriophages according to their neck organization. BMC genomics, 15(1), 1027.

  131. Lu, M. J., & Henning, U. (1994). Superinfection exclusion by T-even-type coliphages. Trends in microbiology, 2(4), 137-139.

  132. Łoś, M., & Węgrzyn, G. (2012). Pseudolysogeny. In Advances in virus research (Vol. 82, pp. 339-349). Academic Press.

  133. Mahony, J., Alqarni, M., Stockdale, S., Spinelli, S., Feyereisen, M., Cambillau, C., & Van Sinderen, D. (2016). Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1. Scientific reports, 6, 36667.

  134. Marsh, P., & Wellington, E. M. H. (1994). Phage-host interactions in soil. FEMS Microbiology Ecology, 15(1-2), 99-107.

  135. Marsin, S., McGovern, S., Ehrlich, S. D., Bruand, C., & Polard, P. (2001). Early steps of Bacillus subtilis primosome assembly. Journal of Biological Chemistry, 276(49), 45818-45825

  136. Matilla, M. A., & Salmond, G. P. (2012). Complete genome sequence of Serratia plymuthica bacteriophage ϕMAM1. J Virol. 86(24):13872-3. doi: 10.1128/JVI.02702-12

  137. Matsushita, N., Sogawa, K., Ema, M., Yoshida, A., & Fujii-Kuriyama, Y. (1993). A factor binding to the xenobiotic responsive element (XRE) of P-4501A1 gene consists of at least two helix-loop-helix proteins, Ah receptor and Arnt. Journal of Biological Chemistry, 268(28), 21002-21006.

  138. Mc Grath, S., & van Sinderen, D. (Eds.). (2007). Bacteriophage: genetics and molecular biology. Horizon Scientific Press.

  139. Mohl, D. A., Easter Jr, J., & Gober, J. W. (2001). The chromosome partitioning protein, ParB, is required for cytokinesis in Caulobacter crescentus. Molecular microbiology, 42(3), 741-755

  140. Mohr, I. J., Pe’ery, T., & Mathews, M. B. (2007). 20 Protein Synthesis and Translational Control during Viral Infection. Cold Spring Harbor Monograph Archive, 48, 545-599.

  141. Molineux, I. J. (2001). No syringes please, ejection of phage T7 DNA from the virion is enzyme driven. Molecular microbiology, 40(1), 1-8.

  142. Moore, S. D., & Prevelige Jr, P. E. (2002). Bacteriophage p22 portal vertex formation in vivo. Journal of molecular biology, 315(5), 975-994.

  143. Murray, C. L., & Rabinowitz, J. C. (1982). Nucleotide sequences of transcription and translation initiation regions in Bacillus phage phi 29 early genes. Journal of Biological Chemistry, 257(2), 10531062.

  144. Nicholson, W. L., Leonard, M. T., Fajardo-Cavazos, P., Panayotova, N., Farmerie, W. G., Triplett, E. W., & Schuerger, A. C. (2013). Complete genome sequence of Serratia liquefaciens strain ATCC 27592. Genome Announc., 1(4), e00548-13.

  145. Novick, R. P., Christie, G. E., & Penadés, J. R. (2010). The phage-related chromosomal islands of Gram-positive bacteria. Nature Reviews Microbiology, 8(8), 541.

  146. Onesti, S., Miller, A. D., & Brick, P. (1995). The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure, 3(2), 163-176.

  147. Ostendorf, T., Cherepanov, P., de Vries, J., & Wackernagel, W. (1999). Characterization of a dam Mutant ofSerratia marcescens and Nucleotide Sequence of thedam Region. Journal of bacteriology, 181(13), 3880-3885.

  148. Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., ... & Vonstein, V. (2013). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic acids research, 42(D1), D206-D214.

  149. PAINE, S. G., & Stansfield, H. (1919). STUDIES IN BACTERIOSIS. III.: A BACTERIAL LEAF‐SPOT DISEASE OF PEOTEA CYNAROIDES, EXHIBITING A HOST REACTION OF POSSIBLY BACTERIOLYTIC NATURE. Annals of Applied Biology, 6(1), 27-39.

  150. Parker, A. P., & Dean, D. H. (1986). Temperate Bacillus bacteriophage SP16 genome is circularly permuted and terminally redundant. Journal of bacteriology, 167(2), 719-721.

  151. Paschen, E. (1906). Was wissen wir über den Vakzineerreger. Münchner medizinische Wochenschrift, 53, 2391-2393.

  152. Pawluk, A., Staals, R. H., Taylor, C., Watson, B. N., Saha, S., Fineran, P. C., ... & Davidson, A. R. (2016). Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nature microbiology, 1(8), 16085.

  153. Pennisi, E. (2011). Will computers crash genomics? doi:10.1126/science.331.6018.666

  154. Perez, F. (2004). Serial Cloner v. 2.6. 0. Software SerialBasics.

  155. Rafferty, J. B., Bolt, E. L., Muranova, T. A., Sedelnikova, S. E., Leonard, P., Pasquo, A., ... & Lloyd, R. G. (2003). The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold. Structure, 11(12), 1557-1567.

  156. Rakhuba, D. V., Kolomiets, E. I., Dey, E. S., & Novik, G. I. (2010). Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol. J. Microbiol, 59(3), 145-155.

  157. Raya, R. R., Fremaux, C., De Antoni, G. L., & Klaenhammer, T. R. (1992). Site-specific integration of the temperate bacteriophage phi adh into the Lactobacillus gasseri chromosome and molecular characterization of the phage (attP) and bacterial (attB) attachment sites. Journal of bacteriology, 174(17), 5584-5592.

  158. Reed, W., Carroll, J. A. S., & Agramonte, A. (1901). THE ETIOLOGY OF YELLOW FEVER.: AN ADDITIONAL NOTE. Journal of the American Medical Association, 36(7), 431-440.

  159. Rekapalli, B., Halloy, C., & Zhulin, I. B. (2009, March). HSP-HMMER: a tool for protein domain identification on a large scale. In Proceedings of the 2009 ACM symposium on Applied Computing (pp. 766-770). ACM.

  160. Roberts, J. W., Yarnell, W., Bartlett, E., Guo, J., Marr, M., Ko, D. C., ... & Roberts, C. W. (1998, January). Antitermination by bacteriophage λ Q protein. In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 63, pp. 319-326). Cold Spring Harbor Laboratory Press.

  161. Rohozková, J., Šebela, M., & Navrátil, M. (2014). P1 peptidase of Pea seed-borne mosaic virus contains non-canonical C2H2 zinc finger and may act in a truncated form. journal of Plant Science and Molecular Breeding, 3(1), 1.

  162. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M. A., & Barrell, B. (2000). Artemis: sequence visualization and annotation. Bioinformatics, 16(10), 944-945.

  163. Sabri, A., Leroy, P., Haubruge, E., Hance, T., Frere, I., Destain, J., & Thonart, P. (2011). Isolation, pure culture and characterization of Serratia symbiotica sp. nov., the R-type of secondary endosymbiont of the black bean aphid Aphis fabae. International journal of systematic and evolutionary microbiology, 61(9), 2081-2088.

  164. Santiago, A. E., Ruiz-Perez, F., Jo, N. Y., Vijayakumar, V., Gong, M. Q., & Nataro, J. P. (2014). A large family of antivirulence regulators modulates the effects of transcriptional activators in Gramnegative pathogenic bacteria. PLoS pathogens, 10(5), e1004153.

  165. Santos, S. B., Kropinski, A. M., Ceyssens, P. J., Ackermann, H. W., Villegas, A., Lavigne, R., ... & Azeredo, J. (2011). Genomic and proteomic characterization of the broad-host-range Salmonella phage PVP-SE1: creation of a new phage genus. Journal of Virology, 85(21), 11265-11273.

  166. Schuch, R., & Fischetti, V. A. (2009). The secret life of the anthrax agent Bacillus anthracis: bacteriophage-mediated ecological adaptations. PloS one, 4(8), e6532.

  167. Schwartz, M. (1976). The adsorption of coliphage lambda to its host: effect of variations in the surface density of receptor and in phage-receptor affinity. Journal of molecular biology, 103(3), 521-536.

  168. Sebaihia, M., Wren, B. W., Mullany, P., Fairweather, N. F., Minton, N., Stabler, R., ... & Holden, M. T. (2006). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nature genetics, 38(7), 779.

  169. Seki, M., Enomoto, T., Yanagisawa, J., Hanaoka, F., & Ui, M. (1988). Further characterization of DNA helicase activity of mouse DNA-dependent adenosine triphosphatase B (DNA helicase B). Biochemistry, 27(5), 1766-1771.

  170. Shen, M., Yang, Y., Shen, W., Cen, L., McLean, J. S., Shi, W., ... & He, X. (2018). A linear plasmidlike prophage of Actinomyces odontolyticus Promotes Biofilm Assembly. Applied and environmental microbiology, 84(17), e01263-18.

  171. Shin, J., Jardine, P., & Noireaux, V. (2012). Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS synthetic biology, 1(9), 408-413.

  172. Shinder, G. A. Y. L. E., & Gold, M. A. R. V. I. N. (1988). The Nul subunit of bacteriophage lambda terminase binds to specific sites in cos DNA. Journal of virology, 62(2), 387-392.

  173. Sillankorva, S., Neubauer, P., & Azeredo, J. (2008). Isolation and characterization of a T7-like lytic phage for Pseudomonas fluorescens. BMC biotechnology, 8(1), 80.

  174. Slater, S. C., Lifsics, M. R., O'Donnell, M., & Maurer, R. (1994). holE, the gene coding for the theta subunit of DNA polymerase III of Escherichia coli: characterization of a holE mutant and comparison with a dnaQ (epsilon-subunit) mutant. Journal of Bacteriology, 176(3), 815-821.

  175. Söding, J. (2004). Protein homology detection by HMM–HMM comparison. Bioinformatics, 21(7), 951-960.

  176. Srinivasiah, S., Bhavsar, J., Thapar, K., Liles, M., Schoenfeld, T., & Wommack, K. E. (2008). Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Research in Microbiology, 159(5), 349-357.

  177. Stapp, C. (1940). Bacterium rubidaeum nov. spec. Zentratbl Bakteriol Abt, 102, 251-261.

  178. Stern, A., & Sorek, R. (2011). The phage‐host arms race: shaping the evolution of microbes. Bioessays, 33(1), 43-51.

  179. Sullivan, M. B., Lindell, D., Lee, J. A., Thompson, L. R., Bielawski, J. P., & Chisholm, S. W. (2006). Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS biology, 4(8), e234.

  180. Sun, S., Rao, V. B., & Rossmann, M. G. (2010). Genome packaging in viruses. Current opinion in structural biology, 20(1), 114-120.

  181. Sun, X., Göhler, A., Heller, K. J., & Neve, H. (2006). The ltp gene of temperate Streptococcus thermophilus phage TP-J34 confers superinfection exclusion to Streptococcus thermophilus and Lactococcus lactis. Virology, 350(1), 146-157.

  182. Susskind, M. M., Botstein, D., & Wright, A. (1974). Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium: III. Failure of superinfecting phage DNA to enter sieA+ lysogens. Virology, 62(2), 350-366.

  183. Suttle, C. A. (2005). Viruses in the sea. Nature, 437(7057), 356.

  184. Tang, J., Lander, G. C., Olia, A., Li, R., Casjens, S., Prevelige Jr, P., ... & Johnson, J. E. (2011). Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22. Structure, 19(4), 496-502.

  185. Taylor, K., & Węgrzyn, G. (1995). Replication of coliphage lambda DNA. FEMS microbiology reviews, 17(1-2), 109-119.

  186. Touchon, M., Bernheim, A., & Rocha, E. P. (2016). Genetic and life-history traits associated with the distribution of prophages in bacteria. The ISME journal, 10(11), 2744.

  187. Twort, F. W. (1915). An investigation on the nature of ultra-microscopic viruses. The Lancet, 186(4814), 1241-1243

  188. Vandamme, E. J., & Mortelmans, K. (2019). A century of bacteriophage research and applications: impacts on biotechnology, health, ecology and the economy!. Journal of Chemical Technology & Biotechnology, 94(2), 323-342.

  189. Vogel, W., & Schmieger, H. (1986). Selection of bacterial pac sites recognized by Salmonella phage P22. Molecular and General Genetics MGG, 205(3), 563-567.

  190. Walker, D. H., & Anderson, T. F. (1970). Morphological variants of coliphage P1. Journal of virology, 5(6), 765-782.

  191. Walters, J. P., Meng, X., Chaudhary, V., Oliver, T., Yeow, L. Y., Schmidt, B., ... & Landman, J. (2007). MPI-HMMER-boost: distributed FPGA acceleration. The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, 48(3), 223-238.

  192. Wang, X., Kim, Y., Ma, Q., Hong, S. H., Pokusaeva, K., Sturino, J. M., & Wood, T. K. (2010). Cryptic prophages help bacteria cope with adverse environments. Nature communications, 1, 147.

  193. Wei, Y., Vollmer, A. C., & LaRossa, R. A. (2001). In vivo titration of mitomycin C action by four Escherichia coli genomic regions on multicopy plasmids. Journal of bacteriology, 183(7), 2259-2264.

  194. Weinbauer, M. G. (2004). Ecology of prokaryotic viruses. FEMS microbiology reviews, 28(2), 127-181.

  195. Wilson, C. R. (2014). Applied plant virology. CABI.

  196. Wilson, G. G., & Murray, N. E. (1991). Restriction and modification systems. Annual review of genetics, 25(1), 585-627.

  197. Wommack, K. E., & Colwell, R. R. (2000). Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev., 64(1), 69-114

  198. Xu, J., & Xiang, Y. (2017). Membrane penetration by bacterial viruses. Journal of virology, 91(13), e00162-17.

  199. Yu, L., Wen, Z., Yang, W., Li, N., Wang, J., Lu, J., & Li, J. (2008). Isolation and characterization of Serratia marcescens phage. Wei sheng wu xue bao= Acta microbiologica Sinica, 48(4), 498-502.

  200. Zhang, C. X., Yang, S. Y., Xu, M. X., Sun, J., Liu, H., Liu, J. R., ... & Zhang, K. Y. (2009). Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae). International journal of systematic and evolutionary microbiology, 59(7), 1603-1608.

  201. Zhang, J., Yoon, K. J., & Zimmerman, J. J. (2019). Overview of Viruses. Diseases of Swine, 425-437.

  202. Zięcina M., 2014. Analiza genomiczna bakteriofagów łagodnych z psychrofilnych szczepów Pseudomonas spp. Praca dyplomowa realizowana na Wydziale Biologii Uniwersytetu Warszawskiego.



Strony:


Tekst udostępniony jest na licencji Creative Commons Uznanie autorstwa-Na tych samych warunkach 3.0.
Dodatkowe informacje o autorach i źródle znajdują się na stronie dyskusji.
Źródło: „https://pl.wikibooks.org/w/index.php?title=Wstępna_charakterystyka_bakteriofaga_Serratia_φOS10/Bibliografia&oldid=476334”