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Editorials should be written on subjects relevant to The Bacteriophage Ecology Group as an organization, to BEG News (either the concept or a given issue of BEG News), or the science of Bacteriophage Ecology. While my assumption is that I will be writing the bulk of these editorials, I wish to encourage as many people as possible to seek to relieve me of this duty, as often as possible. Additionally, I welcome suggestions of topics that may be addressed. Please address all correspondences to abedon.1@osu.edu or to "Editorials," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all submissions as Microsoft Word documents, if possible (I'll let you know if I have trouble converting other document formats), and in English.

• BEG: What we are, Where we are, Where we're going by Stephen T. Abedon
• When Grown In Vitro, do Parasites of Multicellular Organisms (MOPs) become Unicellular Organism Parasites (UOPs)? by Stephen T. Abedon
• Bacteriophages as Model Systems by Stephen T. Abedon
• 2000 and Sun: A Phage Odyssey by Stephen T. Abedon
• Lytic, Lysogenic, Temperate, Chronic, Virulent, Quoi? by Stephen T. Abedon
• Which Ecology are You? by Stephen T. Abedon
• Science NetWatch October 13, 2000
• The Best of Times, the Worst of Times by Ry Young
• Naming Bacteriophages by Hans-Wolfgang Ackermann and Stephen T. Abedon
• The Bacteriophage Rise by Stephen T. Abedon
• Mathematics for Microbiologists by Stephen T. Abedon
• Shipping Phages by Hans-Wolfgang Ackermann
• Calling a Phage a "Phage" by Stephen T. Abedon
• Phage or Phages by Hans-Wolfgang Ackermann

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The BEG members page can be found at www.phage.org/beg_members.htm. There are two ways of "joining" BEG. One, the "traditional" way, is to have your name listed on the web page and on the list server. The second, the "non-traditional" way, is to have your name only listed on the list server. The latter I refer to as "non-members" on that list. Members, e.g., individuals listed on the BEG members list page, should be limited to individuals who are actively involved in science (research, instruction, outreach, industry) and who can serve as a phage ecology resource to interested individuals. If you have an interest in phage ecology but no real expertise in the area, then you should join as a non-member. To join as a member, please contact BEG using the following link: abedon.1@osu.edu. Include:

• your name
• your e-mail address
• your snail-mail address
• the URL of your home page (if you have one)
• a statement of whether or not you are the principal investigator
• a statement of your research interests (or phage ecology interests)
• a list of your phage ecology references, if any

Note that it is preferable that you include the full reference, including the abstract, if the reference is not already present in the BEG bibliography. Responsibility of members includes keeping the information listed on the BEG members page up to date including supplying on a reasonably timely basis the full references of your new phage ecology publications. Reprints can also be sent to The Bacteriophage Ecology Group, care of Stephen Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. To join BEG as a non-member, please contact BEG using the following link: abedon.1@osu.edu and minimally include your name and e-mail address.

Please welcome our newest members

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The BEG Meetings link will continue. Reminders of upcoming meetings will be placed in this section of BEG News. If you know of any meetings that might be of interest to BEG members, or would like to recap a meeting that you've attended, then please send this information for posting to abedon.1@osu.edu or to "BEG Meetings," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906.

Please send photos, etc. from meetings, etc. for inclusion in this section.

Three molecular biologists in their native environment. Left to right: Paul Hyman, Steve Abedon, and Danny Munoa = senior scientist at NanoFrames LLC, visiting prof (from Ohio State), and Summer-intern undergrad (from Eddie Goldberg's lab at Tufts), respectively.

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Looking for job? Looking to fill a position? Please send advertisement and information to abedon.1@osu.edu or to "Jobs", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all information as text (e.g., as an e-mail) or as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats), and in English. I will update this section as I receive material, regardless of what date this issue of BEG News goes live.

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Submissions are non-editorial items describing or highlighting some aspect of bacteriophage ecology including news pieces, historical pieces, reviews, and write-ups of research. Peer review of submissions is possible and a desire for peer review should be indicated. Send all submissions to abedon.1@osu.edu or to "Submissions", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all submissions as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats), and in English.

Eye On The Needle: Phage T4 Puncturing Point May Answer Penetrating Questions by Steven McQuinn The elaborate infection mechanics of Bacteriophage T4 are often illustrated as Nature's nanoscale version of a hypodermic syringe. This misleading analogy has flourished in graphics used by introductory textbooks, biology lectures and the popular media, even though phage researchers have long known that "it ain't necessarily so." The real story is infinitesimally more complicated and not fully understood. The recent revelation of structural detail in the cell-puncturing tip of T4 may eventually provide answers to the question, "How does T4 thread its long strand of DNA through the host cell wall into the cytoplasm?" The syringe analogy pictures the phage tip plunging completely through the "skin" of the host, forcibly injecting phage DNA through a penetrating pipe that extends well into the cell interior. Evidence contradicts this model, while suggesting an alternative. The cell envelope of the gram negative bacteria, Escherichia coli, is a laminate similar to a Kevlar flack vest, with an inner and outer membrane and a tough layer of fiber between. The T4 tail tip, pressed into the cell wall by tail sheath contraction, seems to be structured for pushing aside the lipid outer membrane, then cutting through the peptidoglycan fibers using the three lysozyme "scissors" loosely and flexibly deployed around its central barrel. While the literature is not completely clear about the penetration of the inner membrane, the inner and outer membranes apparently fuse across the puncture zone to create a channel through the cell envelope for the hollow tail tube pushing the tail tip. Electron micrographs show that the hollow tail tube usually extends down to, but not into, the cytoplasm. X-ray crystallography to 2.9 Angstrom resolution reveals that the penetrating point itself provides no hollow passageway for DNA. However, the penetrating tip is connected to the tail tube via a hollow ring, allowing a route for DNA, or a leader for the DNA, to reach the backside of the tail tip via the tail tube. Thus poised at the edge of the cytoplasm, what now draws the tail tip and the DNA into the guts of the cell? Again, the structure of the tail tip may provide clues. Researchers have speculated that a voltage difference across the inner membrane (the Proton Motive Force) may act upon both the tail tip and the DNA strand, moving them into the cytoplasm. The distribution of electro-potential on the surface of the tail tip might support that hypothesis. It is clear that the tip, gene product 5 (gp5), is structured to break away from the hollow ring connecting it to the tail tube, gene product 27 (gp27). It is not clear whether the separated tip plays a role in DNA entry or is simply removed to make way for the DNA. In at least one electron micrograph, a string of expelled phage DNA seems to dangle a little bauble that looks suspiciously like a tail tip. One is tempted to make comparisons with a hooked trout spooling the line off a fishing reel, but as can be seen with hypodermic syringes, reasoning by analogy can be dangerous. See Acknowledgements for an alternate version of this animated gif. These images were constructed from data obtained from the web-based Atlas of Macromolecules via Protein Explorer, the web-based interface for the molecular visualization engine, Chime. The Atlas version of 1K28 provides a full model of the gp5/gp27 complex, whereas the Protein Data Bank version, 1K28.pdb, provides only one third of the full structure. After saving the full structure from Chime as a .pdb file, I opened it in the free molecular visualization program, Accelrys ViewerLite, which I used for the electro-potential surface rendering. Exporting the surface and the ribbon as VRML files, I cut the surface mesh using Amapi 6, then assembled and rendered the cutaway view in Carrara Studio 2. Click Here for One More (Spectacular) Image (about 500 kb) Citations: Kanamaru S, Leiman PG, Kostyuchenko VA, Chipman PR, Mesyanzhinov VV, Arisaka F, Rossmann MG. Structure of the cell-puncturing device of bacteriophage T4. Nature. 2002 Jan 31;415(6871):553-7. Abstract Goldberg, E., Grinius, L. & Letellier, L. in Molecular Biology of Bacteriophage T4 (ed. Karam, J. D.) Chapter 34, p. 347-356 (American Society for Microbiology, Washington, DC, 1994). Coombs, D. H. & Arisaka, F. in Molecular Biology of Bacteriophage T4, Chapter 21, p. 259-281. Kutter, E., Guttmann, B., Carlson, K., in Molecular Biology of Bacteriophage T4, Chapter 33, p. 343-356.

• On an Invisible Microbe Antagonistic to the Dysentery Bacillus by Felix d'Herelle
• Obituary: Hansjürgen Raettig - Collector of Bacteriophage References (October 12, 1911 - December 1, 1997)
• Some Quotations
• Bacteriophages: A Model System for Human Viruses
• How Big is 10³⁰?
• Selling Phage Candy
• A List of Phage Names
• An Expanded Overview of Phage Ecology
• Rendering Phage Heads
• The Contractile-Tail Sheath, In Three Dimensions
• Eye On The Needle: Phage T4 Puncturing Point May Answer Penetrating Questions

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Please send any phage images that you would like to present in this section to "Phage Images," The Bacteriophage Ecology Group, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Alternatively, you may scan the images yourself and send them as an attachment to abedon.1@osu.edu. Please save all scans in gif or jpg formats and preferably with an image size (in terms of width, height, and kbytes) that will readily fit on a standard web page. No copyrighted material without permission, please!

• BEG Phage Images Page
• The Face of the Phage
• Bacteriophage T2
• SSV1-Type Phage
• Saline Lake Bacteriophage
• Coliphage LG1
• Bacteriophage HK97
• Phage T4 (art)
• Phage T4 on the pedestal outside of Barker Hall at Berkeley
• Electron micrograph of phage P22
• Thin section of T4 phages hitting a microcolony of E. coli K-12
• T4 phage v1
• T4 Tail Model
• Gingerbread phage
• T4 adsorbing en mass

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New bacteriophage publications are listed below. Each quarter not-yet-listed publications from the previous two years will be presented along with their abstracts. The indicator "???" denotes, of course, that specific information is not yet in the BEG Bibliography. Please help in the compilation of the BEG Bibliography by supplying any updated information, correcting any mistakes, and, of course, sending the references to your bacteriophage ecology publications, as well as the references to any bacteriophage ecology publications that you know of but which are not yet in the bibliography (send to abedon.1@osu.edu or to "BEG Bibliography," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906). Also, be sure to indicate any listed publications that you feel should not be presented in the BEG Bibliography. This list is also present with available abstracts at the end of BEG News.

1. Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri. Allison, G. E., Angeles, D., Tran-Dinh, N., Verma, N. K. (2002). Journal of Bacteriology 184:1974-1987. [PRESS FOR ABSTRACT]

2. The hyaluronan lyase of Streptococcus pyogenes bacteriophage H4489A. Baker, J. R., Dong, S., Pritchard, D. G. (2002). Biochemical Journal 365:317-322. [PRESS FOR ABSTRACT]

3. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Beres, S. B., Sylva, G. L., Barbian, K. D., Lei, B., Hoff, J. S., Mammarella, N. D., Liu, M. Y., Smoot, J. C., Porcella, S. F., Parkins, L. D., Campbell, D. S., Smith, T. M., McCormick, J. K., Leung, D. Y. M., Schlievert, P. M., Musser, J. M. (2002). Proceedings of the National Academy of Sciences, USA 99:10078-10083. [PRESS FOR ABSTRACT]

4. The in vitro interaction of Streptococcus pyogenes with human pharyngeal cells induces a phage-encoded extracellular DNase. Broudy, T. B., Pancholi, V., Fischetti, V. A. (2002). Infection and Immunity 70:2805-2811. [PRESS FOR ABSTRACT]

5. Removal of bacterial and viral faecal indicator organisms in a waste stabilization pond system in Choconta, Cundinamarca (Colombia). Campos, C., Guerrero, A., Cardenas, M. (2002). Water Science and Technology 45:61-66. [PRESS FOR ABSTRACT]

6. Memory in bacteria and phage. Casadesus, J., D'Ari, R. (2002). Bioessays 24:512-518. [PRESS FOR ABSTRACT]

7. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Chen, F., Lu, J. (2002). Applied and Environmental Microbiology 68:2589-2594. [PRESS FOR ABSTRACT]

8. The antibody response to bacteriophage is linked to the lymphopenia gene in congenic BioBreeding rats. Clark, L., Greenbaum, C., Jiang, J., Lernmark, A., Ochs, H. (2002). FEMS Immunology and Medical Microbiology 32:205-209. [PRESS FOR ABSTRACT]

9. Est-ce que les bactériophages pourraient être une thérapie antimicrobienne efficace pour résoudre le problème de la résistance bactérienne aux antibiotiques ? Colbert, M., Guilmette, M. (2002). [NO ABSTRACT]

10. Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Crutz-Le Coq, A.-M., Cesselin, B., Commissaire, J., Anba, J. (2002). Microbiology 148:985-1001. [PRESS FOR ABSTRACT]

11. A satellite phage-encoded antirepressor induces repressor aggregation and cholera toxin gene transfer. Davis, B. M., Kimsey, H. H., Kane, A. V., Waldor, M. K. (2002). EMBO Journal 21:4240-4249. [PRESS FOR ABSTRACT]

12. Bacteriophages: potential treatment for bacterial infections. Duckworth, D. H., Gulig, P. A. (2002). BioDrugs 16:57-62. [PRESS FOR ABSTRACT]

13. Combined antimicrobial effect of nisin and a listeriophage against Listeria monocytogenes in broth but not in buffer or on raw beef. Dykes, G. A., Moorhead, S. M. (2002). International Journal of Food Microbiology 73:71-81. [PRESS FOR ABSTRACT]

14. Giardia and Cryptosporidium removal from waste-water by a duckweed (Lemna gibba L.) covered pond. Falabi, J. A., Gerba, C. P., Karpiscak, M. M. (2002). Letters in Applied Microbiology 34:384-387. [PRESS FOR ABSTRACT]

15. Phages and other mobile virulence elements in gram-positive pathogens. Gentry-Weeks, C., Coburn, P. S., Gilmore, M. S. (2002). Current Topics in Microbiology and Immunology 264:79-94. [NO ABSTRACT]

16. Control of Brochothrix thermosphacta spoilage of pork adipose tissue using bacteriophages. Greer, G. G., Dilts, B. D. (2002). Journal of Food Protection 65:861-863. [PRESS FOR ABSTRACT]

17. Use of signal-mediated amplification of RNA technology (SMART) to detect marine cyanophage DNA. Hall, M. J., Wharam, S. D., Weston, A., Cardy, D. L. N., Wilson, W. H. (2002). BioTechniques 32:604-611. [PRESS FOR ABSTRACT]

18. Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325. Iandolo, J. J., Worrell, V., Groicher, K. H., Qian, Y., Tian, R., Kenton, S., Dorman, A., Ji, H., Lin, S., Loh, P., Qi, S., Zhu, H., Roe, B. A. (2002). Gene 289:109-118. [PRESS FOR ABSTRACT]

19. Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G., Norris, J. S. (2002). Journal of Virology 76:5557-5564. [PRESS FOR ABSTRACT]

20. Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages. Klovins, J., Overbeek, G. P., van, den Worm, Ackermann, H. W., van, Duin (2002). Journal of General Virology 83:1523-1533. [PRESS FOR ABSTRACT]

21. The ability of the plasmid-encoded restriction and modification system LlaBIII to protect Lactococcus lactis against bacteriophages. Kong, J., Josephsen, J. (2002). Letters in Applied Microbiology 34:249-253. [PRESS FOR ABSTRACT]

22. The activity of chosen bacteriophages on Yersinia enterocolitica strains. Kot, B., Bukowski, K., Jakubczak, A., Kaczorek, I. (2002). Pol. J. Vet. Sci. 5:47-50. [PRESS FOR ABSTRACT]

23. A bacteriophage reagent for Salmonella: molecular studies on Felix 01. Kuhn, J., Suissa, M., Chiswell, D., Azriel, A., Berman, B., Shahar, D., Reznick, S., Sharf, R., Wyse, J., Bar-On, T., Cohen, I., Giles, R., Weiser, I., Lubinsky-Mink, S., Ulitzur, S. (2002). International Journal of Food Microbiology 74:217-227. [PRESS FOR ABSTRACT]

24. Detection of bacteria using foreign DNA: the development of a bacteriophage reagent for Salmonella. Kuhn, J., Suissa, M., Wyse, J., Cohen, I., Weiser, I., Reznick, S., Lubinsky-Mink, S., Stewart, G., Ulitzur, S. (2002). International Journal of Food Microbiology 74:229-238. [PRESS FOR ABSTRACT]

25. Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. Labrie, S., Moineau, S. (2002). Virology 296:308-320. [PRESS FOR ABSTRACT]

26. Evolution of bacteriophage in continuous culture: a model system to test antiviral gene therapies for the emergence of phage escape mutants. Lindemann, B. F., Klug, C., Schwienhorst, A. (2002). Journal of Virology 76:5784-5792. [PRESS FOR ABSTRACT]

27. Prevalence of Escherichia coli O157:H7 prophage-like sequences among German Salmonella enterica serotype Typhimurium phage types and their use in detection of phage type DT104 by the polymerase chain reaction. Malorny, B., Schroeter, A., Bunge, C., Helmuth, R. (2002). Veterinary Microbiology 87:253-265. [PRESS FOR ABSTRACT]

28. Use of lacticin 481 to facilitate delivery of the bacteriophage resistance plasmid, pCBG104 to cheese starters. Mills, S., Coffey, A., O'Sullivan, L., Stokes, D., Hill, C., Fitzgerald, G. F., Ross, R. P. (2002). Journal of Applied Microbiology 92:238-246. [PRESS FOR ABSTRACT]

29. Optimisation of ISO 10705-1 on enumeration of F-specific bacteriophages. Mooijman, K. A., Bahar, M., Muniesa, M., Havelaar, A. H. (2002). Journal of Virological Methods 103:129-136. [PRESS FOR ABSTRACT]

30. Microbial quality of wastewater: detection of hepatitis A virus by reverse transcriptase-polymerase chain reaction. Morace, G., Aulicino, F. A., Angelozzi, C., Costanzo, L., Donadio, F., Rapicetta, M. (2002). Journal of Applied Microbiology 92:828-836. [PRESS FOR ABSTRACT]

31. Effect of denture cleaner using ozone against methicillin-resistant Staphylococcus aureus and E. coli T1 phage. Murakami, H., Mizuguchi, M., Hattori, M., Ito, Y., Kawai, T., Hasegawa, J. (2002). Dental Materials Journal 21:53-60. [PRESS FOR ABSTRACT]

32. Evolution and spread of antibiotic resistance. Normark, B. H., Normark, S. (2002). Journal of Internal Medicine 252:91-106. [PRESS FOR ABSTRACT]

33. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. Pajunen, M. I., Elizondo, M. R., Skurnik, M., Kieleczawa, J., Molineux, I. J. (2002). Journal of Molecular Biology 319:1115-1132. [PRESS FOR ABSTRACT]

34. Bacteriophage resistance of a deltathyA mutant of Lactococcus lactis blocked in DNA replication. Pedersen, M. B., Jensen, P. R., Janzen, T., Nilsson, D. (2002). Applied and Environmental Microbiology 68:3010-3023. [PRESS FOR ABSTRACT]

35. Les bactériophages, nouvelle perspective dans le traitement des maladies infectieuses? Resch, G., Meyer, J. (2002). Rev. Mens. Suisse Odontostomatol. 112:643-645. [PRESS FOR ABSTRACT]

36. The Phage Proteomic Tree: a genome-based taxonomy for phage. Rohwer, F., Edwards, R. (2002). Journal of Bacteriology 184:4529-4535. [PRESS FOR ABSTRACT]

37. Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain. Schaper, M., Jofre, J., Uys, M., Grabow, W. O. K. (2002). Journal of Applied Microbiology 92:657-667. [PRESS FOR ABSTRACT]

38. Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2). Sumby, P., Smith, M. C. M. (2002). Molecular Microbiology 44:489-500. [PRESS FOR ABSTRACT]

39. 50 million years of genomic stasis in endosymbiotic bacteria. Tamas, I., Klasson, L., Canback, B., Naslund, A. K., Eriksson, A. S., Wernegreen, J. J., Sandstrom, J. P., Moran, N. A., Andersson, S. G. E. (2002). Science 296:2376-2379. [PRESS FOR ABSTRACT]

40. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. Tangney, M., Fitzgerald, G. F. (2002). FEMS Microbiology Letters 210:67-72. [PRESS FOR ABSTRACT]

41. One of two copies of the gene for the activatable shiga toxin type 2d in Escherichia coli O91:H21 strain B2F1 is associated with an inducible bacteriophage. Teel, Louise D., Melton-Celsa, Angela R., Schmitt, Clare K., O'Brien, Alison D. (2002). Infection and Immunity 70:4282-4291. [PRESS FOR ABSTRACT]

42. [Study of Erwinia carotovora phage resistance with the use of temperate bacteriophage ZF40]. Tovkach, F. I. (2002). Mikrobiologija (Microbiologiia) 71:82-88. [PRESS FOR ABSTRACT]

43. [Temperate bacteriophage ZF40 of Erwinia carotovora: phage particle structure and DNA restriction analysis]. Tovkach, F. I. (2002). Mikrobiologija (Microbiologiia) 71:75-81. [PRESS FOR ABSTRACT]

44. [Comparative study of properties of temperate erwiniophages 49 and 59]. Tovkach, F. I., Shevchenko, T. V., Gorb, T. E., Mukvich, N. S., Romaniuk, L. V. (2002). Mikrobiolohichnyi Zhurnal 64:65-81. [PRESS FOR ABSTRACT]

45. Role of bacteriophage MAV1 as a mycoplasmal virulence factor for the development of arthritis in mice and rats. Tu, A. H., Lindsey, J. R., Schoeb, T. R., Elgavish, A., Yu, H., Dybvig, K. (2002). Journal of Infectious Diseases 186:432-435. [PRESS FOR ABSTRACT]

46. Bacteriophage control of bacterial virulence. Wagner, P. L., Waldor, M. K. (2002). Infection and Immunity 70:3985-3993. [NO ABSTRACT]

47. Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei. Woods, D. E., Jeddeloh, J. A., Fritz, D. L., DeShazer, D. (2002). Journal of Bacteriology 184:4003-4017. [PRESS FOR ABSTRACT]

48. Genomic analysis of Clostridium perfringens bacteriophage phi3626, which integrates into guaA and possibly affects sporulation. Zimmer, M., Scherer, S., Loessner, M. J. (2002). Journal of Bacteriology 184:4359-4368. [PRESS FOR ABSTRACT]

49. Microbial indicator removal in onsite constructed wetlands for wastewater treatment in the southeastern U.S. Barrett, E. C., Sobsey, M. D., House, C. H., White, K. D. (2001). Water Science and Technology 44:177-182. [PRESS FOR ABSTRACT]

50. First evidence for a restriction-modification system in Leptospira sp. Brenot, A., Werts, C., Ottone, C., Sertour, N., Charon, N. W., Postic, D., Baranton, G., Saint Girons, I (2001). FEMS Microbiology Letters 201:139-143. [PRESS FOR ABSTRACT]

51. Isolation and characterization of two types of actinophage infecting Streptomyces scabies. el Sayed, S. A., el Didamony, G., Mansour, K. (2001). Folia Microbiologica 46:519-526. [PRESS FOR ABSTRACT]

52. Removal of Salmonella and microbial indicators in constructed wetlands treating swine wastewater. Hill, V. R., Sobsey, M. D. (2001). Water Science and Technology 44:215-222. [PRESS FOR ABSTRACT]

53. Removal of bacterial indicators and pathogens from dairy wastewater by a multi-component treatment system. Karpiscak, M. M., Sanchez, L. R., Freitas, R. J., Gerba, C. P. (2001). Water Science and Technology 44:183-190. [PRESS FOR ABSTRACT]

54. Viral and chemical tracer movement through contrasting soils. McLeod, M., Aislabie, J., Smith, J., Fraser, R., Roberts, A., Taylor, M. (2001). J. Environ. Qual. 30:2134-2140. [PRESS FOR ABSTRACT]

55. A field study of virus removal in septic tank drainfields. Nicosia, L. A., Rose, J. B., Stark, L., Stewart, M. T. (2001). J. Environ. Qual. 30:1933-1939. [PRESS FOR ABSTRACT]

56. Detection of homologous recombination among bacteriophage P2 relatives. Nilsson, A. S., Haggard-Ljungquist, E. (2001). Molecular Phylogenetics and Evolution 21:259-269. [PRESS FOR ABSTRACT]

57. Reduction of enteric microorganisms at the Upper Occoquan Sewage Authority Water Reclamation Plant. Rose, J. B., Huffman, D. E., Riley, K., Farrah, S. R., Lukasik, J. O., Hamann, C. L. (2001). Water Environment Research 73:711-720. [PRESS FOR ABSTRACT]

58. [Characterization of Vibrio cholerae eltor isolates according to their epidemic potential using new diagnostic cholera bacteriophages eltor ctx+ and ctx- and by the polymerase chain reaction]. Smirnova, N. I., Cheldyshova, N. B., Kostromitina, E. A., Kulichenko, A. N., Kutyrev, V. V. (2001). Zhurnal Mikrobiologii, Epidemiologii i Immunobiologii 11-16. [PRESS FOR ABSTRACT]

59. Occurrence and die-off of indicator organisms in the sediment in two constructed wetlands. Stenstrom, T. A., Carlander, A. (2001). Water Science and Technology 44:223-230. [PRESS FOR ABSTRACT]

60. Bacteriophage therapy. Summers, W. C. (2001). Annual Review of Microbiology 55:437-451. [PRESS FOR ABSTRACT]

61. Susceptibility of Staphylococcus epidermidis biofilm in CSF shunts to bacteriophage attack. Wood, H. L., Holden, S. R., Bayston, R. (2001). European Journal of Pediatric Surgery 11 Suppl 1:S56-S57. [NO ABSTRACT]

62. Quantifying viral propagation in vitro: toward a method for characterization of complex phenotypes. Yin, J., Duca, K., Lam, V., Keren, I., Endler, E. E., Letchworth, G. J., Novella, I. S. (2001). Biotechnology Progress 17:1156-1165. [PRESS FOR ABSTRACT]

63. Horizontal gene transfer and the origin of species: lessons from bacteria. de la Cruz, F., Davies, J. (2000). Trends in Microbiology 8:128-133. [PRESS FOR ABSTRACT]

64. Biological control of Sclerotinia minor using chitinolytic bacterium and actinomycetes. El-Tarabily, K. A., Soliman, M. H., Nassar, A. H., Al-Hassani, H. A., Sivasithamparam, K., McKenna, F., Hardy, G. E. StJ. (2000). Plant Pathology (Oxford) 49:573-583. [NO ABSTRACT]

65. Temporal variability of viruses, bacteria, phytoplankton and zooplankton in the western English Channel off Plymouth. Rodriguez, F., Frenandez, E., Head, R. N., Harbour, D. S., Bratbak, G., Heldal, M., Harris, R. P. (2000). Journal of the Marine Biological Association of the United Kingdom 80:575-586. [PRESS FOR ABSTRACT]

66. Monitoring of environmental UV radiation by biological dosimeters. Ronto, G., Berces, A., Grof, P., Fekete, A., Kerekgyarto, T., Gaspar, S., Stick, C. (2000). Advances in Space Research 26:2021-2028. [PRESS FOR ABSTRACT]

67. A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. Villarreal, L. P., DeFillips, V. R. (2000). Journal of Virology 74:7079-7084. [PRESS FOR ABSTRACT]

68. Diffusion of bacteriophage through alginate gels. Ibrahim, L. J., Denyer, S. P., Hanlon, G. W. (1999). Journal of Pharmacy and Pharmacology 51:38. [NO ABSTRACT]

69. Identification of two types of actionophage parasitic to potato common scab pathogens in Hokkaido, Japan. Ogiso, H., Akino, S., Ogoshi, A. (1999). Soil Microorganisms 53:37-43. [NO ABSTRACT]

70. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. Plunkett III, G., Rose, D. J., Durfee, T. J., Blattner, F. R. (1999). Journal of Bacteriology 181:1767-1778. [PRESS FOR ABSTRACT]

71. Bacteriophages as surface and ground water tracers. Rossi, P., Doerfliger, N., Kennedy, K., Müller, I., Aragno, M. (1998). Hydrology and Earth System Science 2:101-110. [PRESS FOR ABSTRACT]

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For your convenience, a list of new publications without associated abstracts (but with links to abstracts) is found above. The list presented below is identical to the above list except that abstracts are included.

1. Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri. Allison, G. E., Angeles, D., Tran-Dinh, N., Verma, N. K. (2002). Journal of Bacteriology 184:1974-1987. Bacteriophage SfV is a temperate serotype-converting phage of Shigella flexneri. SfV encodes the factors involved in type V O-antigen modification, and the serotype conversion and integration-excision modules of the phage have been isolated and characterized. We now report on the complete sequence of the SfV genome (37,074 bp). A total of 53 open reading frames were predicted from the nucleotide sequence, and analysis of the corresponding proteins was used to construct a functional map. The general organization of the genes in the SfV genome is similar to that of bacteriophage lambda, and numerous features of the sequence are described. The superinfection immunity system of SfV includes a lambda-like repression system and a P4-like transcription termination mechanism. Sequence analysis also suggests that SfV encodes multiple DNA methylases, and experiments confirmed that orf-41 encodes a Dam methylase. Studies conducted to determine if the phage-encoded methylase confers host DNA methylation showed that the two S. flexneri strains analyzed encode their own Dam methylase. Restriction mapping and sequence analysis revealed that the phage genome has cos sites at the termini. The tail assembly and structural genes of SfV show homology to those of phage Mu and Mu-like prophages in the genome of Escherichia coli O157:H7 and Haemophilus influenzae. Significant homology (30% of the genome in total) between sections of the early, regulatory, and structural regions of the SfV genome and the e14 and KpLE1 prophages in the E. coli K-12 genome were noted, suggesting that these three phages have common evolutionary origins

2. The hyaluronan lyase of Streptococcus pyogenes bacteriophage H4489A. Baker, J. R., Dong, S., Pritchard, D. G. (2002). Biochemical Journal 365:317-322. Many pathogenic streptococci produce extracellular hyaluronan lyases which are thought to aid the spread of the organism in host tissues. In addition, several phages of group A streptococci are known to synthesize a bound form of hyaluronidase. It has been suggested that the function of this hyaluronidase is to facilitate penetration of the hyaluronan capsule by phage and thus to gain access for the phage to the cell surface of the host streptococcus [Hynes, Hancock and Ferretti (1995) Infect. Immun. 63, 3015-3020]. In the present work, the hyaluronidase of Streptococcus pyogenes bacteriophage H4489A, expressed in E. coli, has been purified and characterized. The enzyme was shown to be a lyase with a distributive action pathway. Unlike most bacterial hyaluronidases that have been characterized, the phage enzyme was found to specifically cleave hyaluronan, which adds credence to the view that its function is to digest the hyaluronan capsule of the host organism. This bacteriophage lyase may provide a practical alternative to the lyase from Streptomyces hyalurolyticus as a reagent for the specific cleavage of hyaluronan

3. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Beres, S. B., Sylva, G. L., Barbian, K. D., Lei, B., Hoff, J. S., Mammarella, N. D., Liu, M. Y., Smoot, J. C., Porcella, S. F., Parkins, L. D., Campbell, D. S., Smith, T. M., McCormick, J. K., Leung, D. Y. M., Schlievert, P. M., Musser, J. M. (2002). Proceedings of the National Academy of Sciences, USA 99:10078-10083. Genome sequences are available for many bacterial strains, but there has been little progress in using these data to understand the molecular basis of pathogen emergence and differences in strain virulence. Serotype M3 strains of group A Streptococcus (GAS) are a common cause of severe invasive infections with unusually high rates of morbidity and mortality. To gain insight into the molecular basis of this high-virulence phenotype, we sequenced the genome of strain MGAS315, an organism isolated from a patient with streptococcal toxic shock syndrome. The genome is composed of 1,900,521 bp, and it shares approximately 1.7 Mb of related genetic material with genomes of serotype M1 and M18 strains. Phage-like elements account for the great majority of variation in gene content relative to the sequenced M1 and M18 strains. Recombination produces chimeric phages and strains with previously uncharacterized arrays of virulence factor genes. Strain MGAS315 has phage genes that encode proteins likely to contribute to pathogenesis, such as streptococcal pyrogenic exotoxin A (SpeA) and SpeK, streptococcal superantigen (SSA), and a previously uncharacterized phospholipase A(2) (designated Sla). Infected humans had anti-SpeK, -SSA, and -Sla antibodies, indicating that these GAS proteins are made in vivo. SpeK and SSA were pyrogenic and toxic for rabbits. Serotype M3 strains with the phage-encoded speK and sla genes increased dramatically in frequency late in the 20th century, commensurate with the rise in invasive disease caused by M3 organisms. Taken together, the results show that phage-mediated recombination has played a critical role in the emergence of a new, unusually virulent clone of serotype M3 GAS

4. The in vitro interaction of Streptococcus pyogenes with human pharyngeal cells induces a phage-encoded extracellular DNase. Broudy, T. B., Pancholi, V., Fischetti, V. A. (2002). Infection and Immunity 70:2805-2811. The role lysogenic bacteriophage play in the pathogenesis of the host bacterium is poorly understood. In a previous study, we found that streptococcal coculture with human pharyngeal cells resulted in the induction of lysogenic bacteriophage as well as the phage-associated streptococcal pyrogenic exotoxin C (SpeC). In this study, we have determined that in addition to SpeC induction, a number of other streptococcal proteins are also released by the bacteria during coculture with pharyngeal cells. Among these, we identified and characterized a novel 27-kDa secreted protein. Sequence analysis of this novel protein demonstrated it to be encoded by the same lysogenic bacteriophage which harbors speC. Protein sequence analysis revealed varied homologies with several streptococcal DNases. Further biochemical characterization of the recombinantly expressed protein verified it to be a divalent cation-dependent streptococcal phage-encoded DNase (Spd1). Although functionally distinct, SpeC and Spd1 are associated by a number of parameters, including genetic proximity and transcriptional regulation. Finally, we speculate on the induction of phage-encoded DNase (Spd1) enhancing the fitness of both bacteria and phage

5. Removal of bacterial and viral faecal indicator organisms in a waste stabilization pond system in Choconta, Cundinamarca (Colombia). Campos, C., Guerrero, A., Cardenas, M. (2002). Water Science and Technology 45:61-66. A major objective for domestic wastewater treatment using waste stabilization pond systems is the removal of pathogenic microorganisms. Traditional evaluation parameters for faecal contamination are the total and faecal coliforms. However, epidemiological studies, environmental resistance and the behaviour in the treatment systems, show that viruses are an important disease agent and even more resistant to disinfection than bacteria. Therefore, it is important to introduce viruses as a faecal indicator and to compare them with the traditional bacterial indicators. A waste stabilization pond system was evaluated in the municipality of Choconta, Cundinamarca (Colombia), for the removal of faecal indicators (such as Escherichia coli, Streptococcus faecalis, Clostridium perfringens) and viruses like F+, somatic and Bacteroides fragilis phages. The system includes two facultative ponds in series with a flow of 1555 m3/day. Samples were collected at the entrance of the system, in the two ponds and from the final effluent. Results show a decrease between 0.3 and 4.7 logarithmic units in the bacterial indicators and between 1 and 4.6 logarithmic units with viral indicators

6. Memory in bacteria and phage. Casadesus, J., D'Ari, R. (2002). Bioessays 24:512-518. Whenever the state of a biological system is not determined solely by present conditions but depends on its past history, we can say that the system has memory. Bacteria and bacteriophage use a variety of memory mechanisms, some of which seem to convey adaptive value. A genetic type of heritable memory is the programmed inversion of specific DNA sequences, which causes switching between alternative patterns of gene expression. Heritable memory can also be based on epigenetic circuits, in which a system with two possible steady states is locked in one or the other state by a positive feedback loop. Epigenetic states have been observed in a variety of cellular processes, and are maintained by diverse mechanisms. Some of these involve alternative DNA methylation patterns that are stably transmitted to daughter molecules and can affect DNA-protein interactions (e.g., gene transcription). Other mechanisms exploit autocatalytic loops whereby proteins establish the proper conditions for their continued synthesis. Template polymers other than nucleic acids (e.g., components of the cell wall) may also propagate epigenetic states. Non-heritable memory is exemplified by parasitic organisms that bear a signature of their previous host, such as host-controlled modification of phage DNA or porin hitchhiking in predatory bacteria. The heterogeneous nature of the examples known may be indicative of widespread occurrence of memory mechanisms in bacteria and phage. However, the actual extent, variety and potential selective value of prokaryotic memory devices remain open questions, still to be addressed experimentally

7. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Chen, F., Lu, J. (2002). Applied and Environmental Microbiology 68:2589-2594. The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, fYeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for nucleotide metabolism were found between cyanophage P60 and marine unicellular cyanobacteria

8. The antibody response to bacteriophage is linked to the lymphopenia gene in congenic BioBreeding rats. Clark, L., Greenbaum, C., Jiang, J., Lernmark, A., Ochs, H. (2002). FEMS Immunology and Medical Microbiology 32:205-209. Congenic BioBreeding (BB) rats, homozygous for the autosomal lymphopenia (Lyp) gene (Lyp/Lyp), heterozygous (Lyp/+), or wild-type (+/+), were immunized with the T cell-dependent bacteriophage fX174 to determine effects of Lyp on primary and secondary antibody responses. The primary fX174 antibody response did not differ between the three different genotypes. In contrast, the secondary immune response, expressed as the peak neutralizing titer, was markedly reduced in Lyp/Lyp (9.9+/-3.2; mean value+/-S.E.M. for seven rats) compared to both Lyp/+ (51+/-12; n=13; P=0.006) and +/+ (100+/-20; n=7; P=0.004) BB rats. We suggest that the secondary antibody response to the T cell-dependent neoantigen fX174 is linked in a recessive manner to genetic factor(s) in the Lyp gene region

9. Est-ce que les bactériophages pourraient être une thérapie antimicrobienne efficace pour résoudre le problème de la résistance bactérienne aux antibiotiques ? Colbert, M., Guilmette, M. (2002).

10. Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Crutz-Le Coq, A.-M., Cesselin, B., Commissaire, J., Anba, J. (2002). Microbiology 148:985-1001. The complete 31754 bp genome of bIL170, a virulent bacteriophage of Lactococcus lactis belonging to the 936 group, was analysed. Sixty-four ORFs were predicted and the function of 16 of them was assigned by significant homology to proteins in databases. Three putative homing endonucleases of the HNH family were found in the early region. An HNH endonuclease with zinc-binding motif was identified in the late cluster, potentially being part of the same functional module as terminase. Three putative structural proteins were analysed in detail and show interesting features among dairy phages. Notably, gpl12 (putative fibre) and gpl20 (putative baseplate protein) of bIL170 are related by at least one of their domains to a number of multi-domain proteins encoded by lactococcal or streptococcal phages. A 110- to 150-aa-long hypervariable domain flanked by two conserved motifs of about 20 aa was identified. The analysis presented here supports the participation of some of these proteins in host-range determination and suggests that specific adsorption to the host may involve a complex multi-component system. Divergences in the genome of phages of the 936 group, that may have important biological properties, were noted. Insertions/deletions of units of one or two ORFs were the main source of divergence in the early clusters of the two entirely sequenced phages, bIL170 and sk1. An exchange of fragments probably affected the regions containing the putative origin of replication. It led to the absence in bIL170 of the direct repeats recognized in sk1 and to the presence of different ORFs in the ori region. Shuffling of protein domains affected the endolysin (putative cell-wall binding part), as well as gpl12 and gpl20

11. A satellite phage-encoded antirepressor induces repressor aggregation and cholera toxin gene transfer. Davis, B. M., Kimsey, H. H., Kane, A. V., Waldor, M. K. (2002). EMBO Journal 21:4240-4249. CTXphi is a filamentous bacteriophage whose genome encodes cholera toxin, the principal virulence factor of Vibrio cholerae. We have found that the CTXphi-related element RS1 is a satellite phage whose transmission depends upon proteins produced from a CTX prophage (its helper phage). However, unlike other satellite phages and satellite animal viruses, RS1 can aid the CTX prophage as well as exploit it, due to the RS1-encoded protein RstC. RstC, whose function previously was unknown, is an antirepressor that counteracts the activity of the phage repressor RstR. RstC promotes transcription of genes required for phage production and thereby promotes transmission of both RS1 and CTXphi. Antirepression by RstC also induces expression of the cholera toxin genes, ctxAB, and thus may contribute to the virulence of V.cholerae. In vitro, RstC binds directly to RstR, producing unusual, insoluble aggregates containing both proteins. In vivo, RstC and RstR are both found at the cell pole, where they again appear to form stable complexes. The sequestration/inactivation process induced by RstC resembles those induced by mutant polyglutamine-containing proteins implicated in human neurodegenerative disorders

12. Bacteriophages: potential treatment for bacterial infections. Duckworth, D. H., Gulig, P. A. (2002). BioDrugs 16:57-62. Bacteriophages (phages) are viruses of bacteria that can kill and lyse the bacteria they infect. After their discovery early in the 20th century, phages were widely used to treat various bacterial diseases in people and animals. After this enthusiastic beginning to phage therapy, problems with inappropriate use and uncontrolled studies and ultimately the development of antibacterials caused a cessation of phage therapy research in the West. However, a few institutions in Eastern Europe continued to study and use phages as therapeutic agents for human infections. The alarming rise in antibacterial resistance among bacteria has led to a review of the Eastern European studies and to the initiation of controlled experiments in animal models. These recent studies have confirmed that phages can be highly effective in treating many different types of bacterial infections. The lethality and specificity of phages for particular bacteria, the ability of phages to replicate within infected animal hosts, and the safety of phages make them efficacious antibacterial agents. Although there are still several hurdles to be overcome, it appears likely that phage therapy will regain a role in both medical and veterinary treatment of infectious diseases, especially in the scenario of emerging antibacterial resistance

13. Combined antimicrobial effect of nisin and a listeriophage against Listeria monocytogenes in broth but not in buffer or on raw beef. Dykes, G. A., Moorhead, S. M. (2002). International Journal of Food Microbiology 73:71-81. The effect of nisin and listeriophage LH7, alone and in combination, on the growth and survival of two strains of Listeria monocytogenes in broth and two model food systems, with appropriate controls, was determined. Growth curves for both bacterial strains in tryptic soy broth incubated at 7 or 30 degrees C, and with the addition of nisin and/or listeriophage at lag, mid-exponential or early stationary phase, were obtained by measuring absorbance at 550 nm. Numbers of mixed populations of both L. monocytogenes strains in phosphate buffered saline (pH 5.5) and on vacuum-packaged fresh beef, both stored for 4 weeks at 4 degrees C, and with the addition of nisin and/or listeriophage, were determined. This was achieved by plating appropriately diluted samples on both Tryptic Soy Agar and Modified Oxford Agar to determine both L. monocytogenes numbers and the presence of sub-lethal injury. In broth nisin alone, reduced levels or prevented growth of the two strains under the conditions studied, but regrowth to levels equivalent to those of untreated cells, occurred. Listeriophage LH7 alone, on the other hand, had no effect in broth under the conditions studied. Notably, however, a mixture of nisin and listeriophage displayed a combined effect in broth and reduced levels of cells substantially without regrowth under the conditions studied. In both model food systems only nisin appeared to be active, in a manner consistent with existing literature, and no combined action was apparent. The use of nisin and listeriophage has potential to control L. monocytogenes in foods but a further understanding of the interactions in this complex system needs to be achieved before it could be applied practically

14. Giardia and Cryptosporidium removal from waste-water by a duckweed (Lemna gibba L.) covered pond. Falabi, J. A., Gerba, C. P., Karpiscak, M. M. (2002). Letters in Applied Microbiology 34:384-387. AIMS: To determine the ability of duckweed ponds used to treat domestic waste-water to remove Giardia and Cryptosporidium. METHODS AND RESULTS: The influent and effluent of a pond covered with duckweed with a 6 day retention time was tested for Giardia cysts, Cryptosporidium oocysts, faecal coliforms and coliphage. Giardia cysts and Cryptosporidium oocysts were reduced by 98 and 89%, respectively, total coliforms by 61%, faecal coliforms by 62% and coliphage by 40%. There was a significant correlation between the removal of Giardia cysts and Cryptospordium oocysts by the pond (P < 0.001). Influent turbidity and parasite removal were also significantly correlated (Cryptosporidium and turbidity, P=0.05; Giardia and turbidity, P=0.01). CONCLUSIONS: The larger organisms (parasites) probably settled to the bottom of the pond, while removal of smaller bacteria and coliphages in the pond was not as effective. SIGNIFICANCE AND IMPACT OF THE STUDY: Duckweed ponds may play an important role in wetland systems for reduction of Giardia and Cryptosporidium

15. Phages and other mobile virulence elements in gram-positive pathogens. Gentry-Weeks, C., Coburn, P. S., Gilmore, M. S. (2002). Current Topics in Microbiology and Immunology 264:79-94.

16. Control of Brochothrix thermosphacta spoilage of pork adipose tissue using bacteriophages. Greer, G. G., Dilts, B. D. (2002). Journal of Food Protection 65:861-863. Adipose tissue discs were coinoculated with Brochothrix thermosphacta and homologous bacteriophages (phages) to determine the effects these had on phage multiplication, bacterial growth, and off-odor development during storage at 2 degrees C or under simulated retail display at 6 degrees C. In the presence of about 10(5) bacteria/cm2 and an equivalent number of phages, there was a 3-log increase in phage numbers and a 2-log decrease in bacterial numbers, and objectionable off-odors were suppressed during refrigerated storage. Up to 68% of the surviving bacterial population were resistant to phages. The storage life of adipose tissue could be increased from 4 days in controls to 8 days in phage-treated samples by preventing the development of off-odors associated with the growth of B. thermosphacta. Phages may provide a novel approach to extending the storage quality of chilled meats

17. Use of signal-mediated amplification of RNA technology (SMART) to detect marine cyanophage DNA. Hall, M. J., Wharam, S. D., Weston, A., Cardy, D. L. N., Wilson, W. H. (2002). BioTechniques 32:604-611. Here, we describe the application of an isothermal nucleic acid amplification assay, signal-mediated amplification of RNA technology (SMART), to detect DNA extracted from marine cyanophages known to infect unicellular cyanobacteria from the genus Synechococcus. The SMART assay is based on the target-dependent production of multiple copies of an RNA signal, which is measured by an enzyme-linked oligosorbent assay. SMART was able to detect both synthetic oligonucleotide targets and genomic cyanophage DNA using probes designed against the portal vertex gene (g20). Specific signals were obtained for each cyanophage strain (S-PM2 and S-BnMI). Nonspecific genomic DNA did not produce false signals or inhibit the detection of a specific target. In addition, we found that extensive purification of target DNA may not be required since signals were obtained from crude cyanophage lysates. This is the first report of the SMART assay being used to discriminate between two similar target sequences

18. Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325. Iandolo, J. J., Worrell, V., Groicher, K. H., Qian, Y., Tian, R., Kenton, S., Dorman, A., Ji, H., Lin, S., Loh, P., Qi, S., Zhu, H., Roe, B. A. (2002). Gene 289:109-118. The genomes of the three temperate bacteriophages contained in the chromosome of Staphylococcus aureus 8325 have been extracted from the sequence database and analyzed. phi 11, phi 12 and phi 13 are members of the same lytic group but different serogroups and consequently co-habitate the same host cell. Their genomes are approximately 42 kb to 45 kb and contain about 90 ORFs of at least 50 codons. Of these, about 50 have similarities to known genes or to genes of other staphylococcal phages. Each of the phages clusters within a homology group that share large regions of sequence identity while intergroup homology is comparatively low. The arrangement of genes on the chromosomes of the three phages is similar and consistent with current modular theory of phage gene organization. The replicated genomes appear to be packaged by different mechanisms. Phage phi 11 and phi 12 have been found to contain sequences consistent with pac-site phages while phi 13 has sequences consistent with cos-site phages. The attBsite for phi 11 is located in an intergenic region of the S. aureus chromosome while phi 12 and phi 13 integrate into specific genes. The phi 12 att-site is within an unknown gene, but the phi 13 att-site is within the beta-toxin gene. In contrast to the other two phages, phi 13 also introduces the staphylokinase gene (sak) and a second gene related to expression of fib

19. Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G., Norris, J. S. (2002). Journal of Virology 76:5557-5564. Prior observations of phage-host systems in vitro have led to the conclusion that susceptible host cell populations must reach a critical density before phage replication can occur. Such a replication threshold density would have broad implications for the therapeutic use of phage. In this report, we demonstrate experimentally that no such replication threshold exists and explain the previous data used to support the existence of the threshold in terms of a classical model of the kinetics of colloidal particle interactions in solution. This result leads us to conclude that the frequently used measure of multiplicity of infection (MOI), computed as the ratio of the number of phage to the number of cells, is generally inappropriate for situations in which cell concentrations are less than 10(7)/ml. In its place, we propose an alternative measure, MOI(actual), that takes into account the cell concentration and adsorption time. Properties of this function are elucidated that explain the demonstrated usefulness of MOI at high cell densities, as well as some unexpected consequences at low concentrations. In addition, the concept of MOI(actual) allows us to write simple formulas for computing practical quantities, such as the number of phage sufficient to infect 99.99% of host cells at arbitrary concentrations

20. Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages. Klovins, J., Overbeek, G. P., van, den Worm, Ackermann, H. W., van, Duin (2002). Journal of General Virology 83:1523-1533. The complete nucleotide sequence of ssRNA phage AP205 propagating in Acinetobacter species is reported. The RNA has three large ORFs, which code for the following homologues of the RNA coliphage proteins: the maturation, coat and replicase proteins. Their gene order is the same as that in coliphages. RNA coliphages or Leviviridae fall into two genera: the alloleviviruses, like Qb, which have a coat read-through protein, and the leviviruses, like MS2, which do not have this coat protein extension. AP205 has no read-through protein and may therefore be classified as a levivirus. A major digression from the known leviviruses is the apparent absence of a lysis gene in AP205 at the usual position, overlapping the coat and replicase proteins. Instead, two small ORFs are present at the 5' terminus, preceding the maturation gene. One of these might encode a lysis protein. The other is of unknown function. Other new features concern the 3'-terminal sequence. In all ssRNA coliphages, there are always three cytosine residues at the 3' end, but in AP205, there is only a single terminal cytosine. Distantly related viruses, like AP205 and the coliphages, do not have significant sequence identity; yet, important secondary structural features of the RNA are conserved. This is shown here for the 3' UTR and the replicase-operator hairpin. Interestingly, although AP205 has the genetic map of a levivirus, its 3' UTR has the length and RNA secondary structure of an allolevivirus. Sharing features with both MS2 and Q(beta) suggests that, in an evolutionary sense, AP205 should be placed between Q(beta) and MS2. A phylogenetic tree for the ssRNA phages is presented

21. The ability of the plasmid-encoded restriction and modification system LlaBIII to protect Lactococcus lactis against bacteriophages. Kong, J., Josephsen, J. (2002). Letters in Applied Microbiology 34:249-253. AIMS: To investigate the potential of the plasmid-encoded restriction and modification (R/M) system LlaBIII to protect Lactococcua lactis against bacteriophages during milk fermentations. METHODS AND RESULTS: The R/M system LlaBIII on plasmid pJW566 was cloned with a chloramphenicol cassette, resulting in plasmid pJK1. When introduced into L. lactis strains, pJK1 conferred increased phage resistance against the three most common lactococcal phage species 936, c2, and P335 and three unclassified industrial phages. The growth of the strains in RSM was not affected by the presence of plasmid pJK1. CONCLUSIONS: The plasmid-encoded R/M system LlaBIII has great ability to protect L. lactis strains against bacteriophages in milk fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: This study evaluates the ability of the LlaBIII R/M system to function as a phage defence mechanism which is an essential step prior to considering utilizing it for improving starter cultures

22. The activity of chosen bacteriophages on Yersinia enterocolitica strains. Kot, B., Bukowski, K., Jakubczak, A., Kaczorek, I. (2002). Pol. J. Vet. Sci. 5:47-50. The aim of the present study was to evaluate the lytic activity of three bacteriophages on Yersinia enterocolitica strains isolated from humans and pigs. The Y. enterocolitica strains tested belonged to 0:3, 0:9 and 0:2 serogroups. The ZD5 phage was obtained from a water sample, but remaining phages were obtained from the lysogenic Y. frederiksenii 7291 and Y. enterocolitica 8684 strains. All the Y. enterocolitica strains tested which belonged to 0:9 serogroup did not show any susceptibility to the bacteriophages used. The bacteriophages tested showed different lytic activity on the Y. enterocolitica 0:3 strains investigated. The phage susceptibility of Y. enterocolitica 0:3 strains revealed 9 different phage patterns. ZD5 phage showed the highest lytic activity, because it produced confluent lysis of the most Y. enterocolitica 0:3 strains tested. The Y. enterocolitica 0:2 strains isolated from pigs showed the similar phage susceptibility. The Y. kristensenii and Y. pseudotuberculosis strains tested were not sensitive to the bacteriophages used

23. A bacteriophage reagent for Salmonella: molecular studies on Felix 01. Kuhn, J., Suissa, M., Chiswell, D., Azriel, A., Berman, B., Shahar, D., Reznick, S., Sharf, R., Wyse, J., Bar-On, T., Cohen, I., Giles, R., Weiser, I., Lubinsky-Mink, S., Ulitzur, S. (2002). International Journal of Food Microbiology 74:217-227. Felix 01 (F01) is a bacteriophage originally isolated by Felix and Callow which lyses almost all Salmonella strains and has been widely used as a diagnostic test for this genus. Molecular information about this phage is entirely lacking. In the present study, the DNA of the phage was found to be a double-stranded linear molecule of about 80 kb. 11.5 kb has been sequenced and in this region A + T content is 60%. There are relatively few restriction endonuclease cleavage sites in the native genome and clones show this is due to their absence rather than modification. A restriction map of the genome has been constructed. The ends of the molecule cannot be ligated although they contain 5' phosphates. At least 60% of the genome must encode proteins. In the sequenced portion, many open reading frames exist and these are tightly packed together. These have been examined for homology to published proteins but only 1 to 17 shows similarity to known proteins. F01 is therefore the prototype of a new phage family. On the basis of restriction sites, codon usage and the distribution of nonsense codons in the unused reading frames, a strong case can be made for natural selection that reacts to mRNA structure and function

24. Detection of bacteria using foreign DNA: the development of a bacteriophage reagent for Salmonella. Kuhn, J., Suissa, M., Wyse, J., Cohen, I., Weiser, I., Reznick, S., Lubinsky-Mink, S., Stewart, G., Ulitzur, S. (2002). International Journal of Food Microbiology 74:229-238. A phage-based reagent was developed for the detection of Salmonella in food samples. The parental phage was Felix 01, which lyses practically all Salmonella. Using data obtained about the molecular biology of the phage, a recombinant phage that carried the bacterial genes specifying luciferase was produced. The method involved the isolation of amber nonsense mutations and subsequent crosses to render doubly mutant phage with a very low reversion rate on strains lacking an amber suppressor. A plasmid was constructed that contained a segment of Felix 01 DNA with two adjacent genes, one dispensable and the other essential, and their flanking sequences. Recombinant DNA technology was used to remove the two genes and the luxA and luxB genes for luciferase, and a gene specifying a tRNA that recognizes amber codons (supF=tyrT) was put in their stead. This region could be transferred into the genome of the phage by homologous recombination. The recombinant phage cannot grow because it lacks an essential gene. However, it can grow in a host that synthesizes the missing protein. This technique allows the construction of "locked" recombinant phages that carry foreign DNA but which cannot propagate themselves in nature

25. Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. Labrie, S., Moineau, S. (2002). Virology 296:308-320. The complete genomic sequence of the Lactococcus lactis virulent phage ul36 belonging to P335 lactococcal phage species was determined and analyzed. The genomic sequence of this lactococcal phage contained 36,798 bp with an overall G+C content of 35.8 mol %. Fifty-nine open reading frames (ORFs) of more than 40 codons were found. N-terminal sequencing of phage structural proteins as well as bioinformatic analysis led to the attribution of a function to 24 ORFs (41%). A lysogeny module was found within the genome of this virulent phage. The putative integrase gene seems to be the product of a horizontal transfer because it is more closely related to Streptococcus pyogenes phages than it is to L. lactis phages. Comparative genome analysis with six complete genomes of temperate P335-like phages confirmed the heterogeneity among phages of P335 species. A dUTPase gene is the only conserved gene among all P335 phages analyzed as well as the phage BK5-T. A genetic relationship between P335 phages and the phage-type of the BK5-T species was established. Thus, we proposed that phage BK5-T be included within the P335 species and thereby reducing the number of lactococcal phage species to 11

26. Evolution of bacteriophage in continuous culture: a model system to test antiviral gene therapies for the emergence of phage escape mutants. Lindemann, B. F., Klug, C., Schwienhorst, A. (2002). Journal of Virology 76:5784-5792. The emergence of viral escape mutants is usually a highly undesirable phenomenon. This phenomenon is frequently observed in antiviral drug applications for the treatment of viral infections and can undermine long-term therapeutic success. Here, we propose a strategy for evaluating a given antiviral approach in terms of its potential to provoke the appearance of resistant virus mutants. By use of Q beta RNA phage as a model system, the effect of an antiviral gene therapy, i.e., a virus-specific repressor protein expressed by a recombinant Escherichia coli host, was studied over the course of more than 100 generations. In 13 experiments carried out in parallel, 12 phage populations became resistant and 1 became extinct. Sequence analysis revealed that only two distinct phage mutants emerged in the 12 surviving phage populations. For both escape mutants, sequence variations located in the repressor binding site of the viral genomic RNA, which decrease affinity for the repressor protein, conferred resistance to translational repression. The results clearly suggest the feasibility of the proposed strategy for the evaluation of antiviral approaches in terms of their potential to allow resistant mutants to appear. In addition, the strategy proved to be a valuable tool for observing virus-specific molecular targets under the impact of antiviral drugs

27. Prevalence of Escherichia coli O157:H7 prophage-like sequences among German Salmonella enterica serotype Typhimurium phage types and their use in detection of phage type DT104 by the polymerase chain reaction. Malorny, B., Schroeter, A., Bunge, C., Helmuth, R. (2002). Veterinary Microbiology 87:253-265. A 1.6kb DNA fragment identified by random amplifiable polymorphic DNA differentiation (RAPD) from a Salmonella enterica serotype Typhimurium phage type DT104 isolate was used to investigate the prevalence of the region in 160 DT104 isolates, 83 other epidemiological important S. Typhimurium phage types and 20 strains selected from 17 other Salmonella serotypes. PCR screening tests using two different primer-sets derived from the RAPD fragment's nucleotide sequence showed that 76% of the 160 DT104 isolates investigated, including subtypes DT104A, DT104B, DT104B low, DT104H and DT104L, reacted positively. High sensitivity was shown for DT104 strains expressing at least the penta-resistance pattern ACSSuT (97% of 104 strains tested). DT104 susceptible strains showed only a sensitivity of 35% (17 strains tested). In contrast, 83% of the 83 strains from the other S. Typhimurium phage types reacted negatively. Strains from five out of the 17 other serotypes showed a positive signal with one primer-set. The other primer-set exhibited only a positive reaction with one S. Dublin isolate. The analysis of a 2415bp extended sequence revealed homologies to genes encoded by Escherichia coli O157:H7 prophages, suggesting that the described region contains genes of a prophage specific for DT104 and related phage types

28. Use of lacticin 481 to facilitate delivery of the bacteriophage resistance plasmid, pCBG104 to cheese starters. Mills, S., Coffey, A., O'Sullivan, L., Stokes, D., Hill, C., Fitzgerald, G. F., Ross, R. P. (2002). Journal of Applied Microbiology 92:238-246. AIMS: Use of lacticin 481 to facilitate the conjugal transfer of the bacteriophage resistance plasmid pCBG104 to various starter cultures. METHODS AND RESULTS: A raw milk isolate of Lactococcus was found to harbour determinants for lacticin 481 production and immunity and phage resistance on a plasmid designated pCBG104. The lacticin 481 was successfully used to mobilize the phage resistance determinant to a variety of cheese starters enabling the formation of highly phage resistant starters. In addition, it facilitated the stacking of a number of phage resistance genes, namely a type I restriction modification system, a phage abortive infection system and a phage adsorption blocking system in a single Lactococcus strain without the use of recombinant techniques. The transconjugants were all shown to produce lacticin 481 and to contain the entire 481 operon. Subsequently one transconjugant was selected and successfully used for large-scale cheddar cheese manufacture. CONCLUSIONS: Lacticin 481 could be used as a food-grade selectable marker to facilitate the introduction of advantageous traits to starter cultures for industrial food fermentations. SIGNIFICANCE AND IMAPCT OF THE STUDY: Food-grade selectable markers greatly facilitate the introduction of various advantageous traits to starter cultures for industrial food fermentation. Indeed self-cloning which is becoming increasingly important for strain improvement has a requirement for the identification and demonstration of the utility of tools such as lacticin 481

29. Optimisation of ISO 10705-1 on enumeration of F-specific bacteriophages. Mooijman, K. A., Bahar, M., Muniesa, M., Havelaar, A. H. (2002). Journal of Virological Methods 103:129-136. During the European project 'Bacteriophages in bathing waters' (January 1996-June 1999), research was carried out to optimise the method for detection and enumeration of F-specific (RNA) phages in water. It was evaluated whether further optimisation would be possible/needed for the procedure as described in the standard method of the International Organisation for Standardisation (ISO) 10705-1. The research focused mainly on optimisation of the different steps for culturing the host strain WG49 Salmonella Typhimurium. It was concluded that all steps described in ISO 10705-1 are necessary and, if followed carefully, using a culture of host strain WG49 Salmonella Typhimurium of good quality, reliable results could be obtained for the enumeration of F-specific RNA phages

30. Microbial quality of wastewater: detection of hepatitis A virus by reverse transcriptase-polymerase chain reaction. Morace, G., Aulicino, F. A., Angelozzi, C., Costanzo, L., Donadio, F., Rapicetta, M. (2002). Journal of Applied Microbiology 92:828-836. AIMS: The persistent circulation of hepatitis A virus (HAV) in the Mediterranean area suggests the need for monitoring its presence in the environment. A reverse transcriptase-polymerase chain reaction (RT-PCR) was used to detect the presence of HAV in several consecutive raw sewage and final effluent samples, collected over an 8-month period from an activated sludge treatment plant in southern Italy. METHODS AND RESULTS: Two distinct purification protocols, either based on antigen-capture with monoclonal antibody (AC) or RNA extraction, were compared. The possible influence of the antibody used in the AC phase was evaluated in preliminary experiments on HAV-spiked samples, using two different monoclonal antibodies. Hepatitis A virus RNA was detected in all but one sewage environmental sample examined. The contemporary presence of enteroviruses, reoviruses and phages was observed, while HAV growth in cell culture was hampered. CONCLUSIONS: The RT-PCR technique was confirmed to be a valuable tool for the rapid monitoring of HAV in sewage samples. In addition, this study demonstrated that application of different sample purification methods can result in different levels of sensitivity of the assay and that, in the antigen-capture method, the choice of antibody can have a crucial role. SIGNIFICANCE AND IMPACT OF THE STUDY: This work underlines the need for technical uniformity in environmental studies from different laboratories for a correct and useful comparison of the results

31. Effect of denture cleaner using ozone against methicillin-resistant Staphylococcus aureus and E. coli T1 phage. Murakami, H., Mizuguchi, M., Hattori, M., Ito, Y., Kawai, T., Hasegawa, J. (2002). Dental Materials Journal 21:53-60. We examined the bactericidal and virucidal effectiveness of a denture cleaner that uses ozone (ozone concentration, 10 ppm) against methicillin-resistant Staphylococcus aureus (MRSA) and T1 phage, respectively. In the bactericidal activity test, with the ozone supply turned on, the number of bacteria was 3.1 x 10(3) CFU/mL at the beginning of the experiment, fell to 1.0 x 10(0) CFU/mL 10 min later, and was 1.0 x 10(0) CFU/mL or less afterwards. In contrast, when the ozone supply was cut off (air bubble only), the number of bacteria was 3.4 x 10(3) CFU/mL at the beginning of the experiment, and had fallen to 3.0 x 10(3) CFU/mL 60 min later (no statistically significant difference). In the virucidal activity test, the number of phages was 1.2 x 10(6) PFU/mL before ozone treatment, fell to about 1/10 of that number 10 min later, and was 6.1 x 10(0) PFU/mL 40 min later. These results indicate that the use of ozone in this denture cleaner is effective against MRSA and viruses

32. Evolution and spread of antibiotic resistance. Normark, B. H., Normark, S. (2002). Journal of Internal Medicine 252:91-106. Antibiotic resistance is a clinical and socioeconomical problem that is here to stay. Resistance can be natural or acquired. Some bacterial species, such as Pseudomonas aeruginosa, show a high intrinsic resistance to a number of antibiotics whereas others are normally highly antibiotic susceptible such as group A streptococci. Acquired resistance evolve via genetic alterations in the microbes own genome or by horizontal transfer of resistance genes located on various types of mobile DNA elements. Mutation frequencies to resistance can vary dramatically depending on the mechanism of resistance and whether or not the organism exhibits a mutator phenotype. Resistance usually has a biological cost for the microorganism, but compensatory mutations accumulate rapidly that abolish this fitness cost, explaining why many types of resistances may never disappear in a bacterial population. Resistance frequently occurs stepwise making it important to identify organisms with low level resistance that otherwise may constitute the genetic platform for development of higher resistance levels. Self-replicating plasmids, prophages, transposons, integrons and resistance islands all represent DNA elements that frequently carry resistance genes into sensitive organisms. These elements add DNA to the microbe and utilize site-specific recombinases/integrases for their integration into the genome. However, resistance may also be created by homologous recombination events creating mosaic genes where each piece of the gene may come from a different microbe. The selection with antibiotics have informed us much about the various genetic mechanisms that are responsible for microbial evolution

33. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. Pajunen, M. I., Elizondo, M. R., Skurnik, M., Kieleczawa, J., Molineux, I. J. (2002). Journal of Molecular Biology 319:1115-1132. We report the complete genome sequence (38,208 bp) of bacteriophage T3 and provide a bioinformatic comparative analysis with other completely sequenced members of the T7 group of phages. This comparison suggests that T3 has evolved from a recombinant between a T7-like coliphage and a yersiniophage. To assess this, recombination between T7 and the Yersinia enterocolitica serotype O:3 phage phiYeO3-12 was accomplished in vivo; coliphage progeny from this cross were selected that had many biological properties of T3. This represents the first experimentally observed recombination between lytic phages whose normal hosts are different bacterial genera

34. Bacteriophage resistance of a deltathyA mutant of Lactococcus lactis blocked in DNA replication. Pedersen, M. B., Jensen, P. R., Janzen, T., Nilsson, D. (2002). Applied and Environmental Microbiology 68:3010-3023. The thyA gene, which encodes thymidylate synthase (TS), of Lactococcus lactis CHCC373 was sequenced, including the upstream and downstream regions. We then deleted part of thyA by gene replacement. The resulting strain, MBP71 deltathyA, was devoid of TS activity, and in media without thymidine, such as milk, there was no detectable dTTP pool in the cells. Hence, DNA replication was abolished, and acidification by MBP71 was completely unaffected by the presence of nine different phages tested at a multiplicity of infection (MOI) of 0.1. Nonreplicating MBP71 must be inoculated at a higher level than CHCC373 to achieve a certain pH within a specified time. For a pH of 5.2 to be reached in 6 h, the inoculation level of MBP71 must be 17-fold higher than for CHCC373. However, by adding a limiting amount of thymidine this could be lowered to just 5-fold the normal amount, while acidification was unaffected with MBP71 up to an MOI of 0.01. It was found that nonreplicating MBP71 produced largely the same products as CHCC373, though the acetaldehyde production of the former was higher

35. Les bactériophages, nouvelle perspective dans le traitement des maladies infectieuses? Resch, G., Meyer, J. (2002). Rev. Mens. Suisse Odontostomatol. 112:643-645. De nombreuses bactéries ont été identifiées, et cela depuis des décennies, comme étant des agents responsables de nombreuses maladies infectieuses de l'homme. Ainsi, il a été mis en évidence que certaines bactéries buccales jouent un rôle primordial dans l'étiologie de la carie et des pathologies du parodontium. Ces bactéries peuvent être, à leur tour, infectées par des virus appelés bactériophages. Ces bactériophages, qui sont des parasites obligatoires, sont capables d'altérer profondément les caractéristiques de leur hôte. Nous verrons, dans la suite, quelques aspects de la biologie de ces virus et de leur importance.

36. The Phage Proteomic Tree: a genome-based taxonomy for phage. Rohwer, F., Edwards, R. (2002). Journal of Bacteriology 184:4529-4535. There are approximately 10³¹ phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the "Phage Proteomic Tree," which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage

37. Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain. Schaper, M., Jofre, J., Uys, M., Grabow, W. O. K. (2002). Journal of Applied Microbiology 92:657-667. AIMS: To assess whether the distribution of genotypes of F-specific RNA bacteriophages reflects faecal pollution of human and animal origin in water environments. METHODS AND RESULTS: Stool samples, animal feedlot waste slurries and a wide variety of faecally polluted waters were studied in South Africa and Spain. Genotyping was performed by plaque and spot hybridization with genotype-specific probes. Only genotypes II and III were detected in human stool. Animal faeces contained predominantly, but not exclusively, genotypes I and IV. Raw hospital and municipal sewage contained mostly genotypes II and III, whereas genotypes I and II prevailed in settled sewage, secondary treated sewage and non-point diffuse effluents from developing communities. Abattoir wastewaters contained mostly genotypes I and IV. No differences were observed between the distribution of genotypes in Spain and South Africa. CONCLUSIONS: Although the association of genotypes II and III with human excreta and I and IV with animal excreta was statistically significant, the results suggest that the association cannot be used for absolute distinction between faecal pollution of human and animal origin. SIGNIFICANCE AND IMPACT OF THE STUDY: This study contributes greatly to understanding the usefulness of genotypes of F-specific RNA bacteriophages in source tracking of faecal wastes

38. Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2). Sumby, P., Smith, M. C. M. (2002). Molecular Microbiology 44:489-500. The phage growth limitation (Pgl) system, encoded by Streptomyces coelicolor A3(2), confers protection against the temperate bacteriophage phiC31 and its homoimmune relatives. The Pgl phenotype is characterized by the ability of Pgl+ hosts to support a phage burst on initial infection but subsequent cycles are severely attenuated. Previously, two adjacent genes pglY and pglZ were shown to be required for Pgl. It had been shown by Southern blotting that Streptomyces lividans, a close relative of S. coelicolor and naturally Pgl-, does not contain homologues of pglYZ and that introduction of pglYZ into S. lividans is not sufficient to confer a Pgl+ phenotype. Moreover, the mechanism of the Pgl+<--> Pgl- phase variation associated with this phenotype is also not understood. Here we describe two novel genes, pglW and pglX, that were shown to be part of this system by complementation of Pgl- mutants and by insertional mutagenesis. pglW encodes a 169 kDa protein that includes putative motifs for both serine/threonine protein kinase activity and DNA binding. pglX encodes a 136 kDa protein with putative adenine-specific DNA methyltransferase activity. pglW and pglX have overlapping stop-start codons suggesting transcriptional and translational coupling. S1 mapping of transcripts initiating up-stream of pglW indicated that, like pglYZ, pglWX is expressed in uninfected cultures. A homologue of pglX with 76% amino acid identity was identified in S. coelicolor, and insertional mutagenesis indicated that this gene was not required for the Pgl+ phenotype. Southern blots indicated that S. lividans does not contain homologues of pglW or pglX. A plasmid encoding pglWXYZ was able to confer the Pgl+ phenotype to S. lividans implying that these four genes constitute the whole system

39. 50 million years of genomic stasis in endosymbiotic bacteria. Tamas, I., Klasson, L., Canback, B., Naslund, A. K., Eriksson, A. S., Wernegreen, J. J., Sandstrom, J. P., Moran, N. A., Andersson, S. G. E. (2002). Science 296:2376-2379. Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts

40. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. Tangney, M., Fitzgerald, G. F. (2002). FEMS Microbiology Letters 210:67-72. Four lactococcal abortive infection mechanisms were introduced into strains which were sensitive hosts for P335 type phages and plaque assay experiments performed to assess their effect on five lactococcal bacteriophages from this family. Results indicate that AbiA inhibits all five P335 phages tested, while AbiG affects phiP335 itself and phiQ30 but not the other P335 species phages. AbiA was shown to retard phage Q30 DNA replication as previously reported for other phages. It was also demonstrated that AbiG, previously shown to act at a point after DNA replication in the cases of c2 type and 936 type phages, acts at the level of, or prior to phage Q30 DNA replication. AbiE and AbiF had no effect on the P335 type phages examined

41. One of two copies of the gene for the activatable shiga toxin type 2d in Escherichia coli O91:H21 strain B2F1 is associated with an inducible bacteriophage. Teel, Louise D., Melton-Celsa, Angela R., Schmitt, Clare K., O'Brien, Alison D. (2002). Infection and Immunity 70:4282-4291. Shiga toxin (Stx) types 1 and 2 are encoded within intact or defective temperate bacteriophages in Stx-producing Escherichia coli (STEC), and expression of these toxins is linked to bacteriophage induction. Among Stx2 variants, only stx(2e) from one human STEC isolate has been reported to be carried within a toxin-converting phage. In this study, we examined the O91:H21 STEC isolate B2F1, which carries two functional alleles for the potent activatable Stx2 variant toxin, Stx2d, for the presence of Stx2d-converting bacteriophages. We first constructed mutants of B2F1 that produced one or the other Stx2d toxin and found that the mutant that produced only Stx2d1 made less toxin than the Stx2d2-producing mutant. Consistent with that result, the Stx2d1-producing mutant was attenuated in a streptomycin-treated mouse model of STEC infection. When the mutants were treated with mitomycin C to promote bacteriophage induction, Vero cell cytotoxicity was elevated only in extracts of the Stx2d1-producing mutant. Additionally, when mice were treated with ciprofloxacin, an antibiotic that induces the O157:H7 Stx2-converting phage, the animals were more susceptible to the Stx2d1-producing mutant. Moreover, an stx(2d1)-containing lysogen was isolated from p