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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.

Calling a Phage a "Phage" by Stephen T. Abedon Assembling the Bacteriophage Ecology Group Bibliography can be challenging, particularly since not all phage-ecology references are obviously phage-ecology references. Generally my strategy has been to do "phage" searches on the various online databases. For example, with Medline I use this search: $phage$ not $phageal not macrophage$ which assures that I catch references by all those individuals who insist on referring to "bacterial viruses" as "phages" or "bacteriophage" or "actinophages," etc., rather than simply as "phage." Typically I customize the output of my search results so that 400 references are displayed per page. Still, even though I often don't need to go more than 1,000 references into these lists before I start seeing references I caught during the last quarter's search, that's a lot of references to consider. Thus, to save time, I've attempted to eliminate a few very common terms that contain "phage", such as "macrophage," but which often have nothing to do with bacterial viruses. Consistently, what I don't do are searches for the terms "virus" or "viral" since the number of phage papers I would find that I wouldn't find using only a "phage" search would be small. Still, it bothers me that clearly I must be missing at least some phage-ecology papers because, as I've found, sometimes authors neglect to call a phage a phage. The purpose of this editorial, therefore, is to suggest that it would be helpful if papers that considered phages actually had the term "phage," or a derivative (e.g., phages or bacteriophage or, indeed, all three), somewhere in their title, or, at the very least, in their abstract. Not only would this be helpful to me, but consider everyone else who might need to wade through endless "virus" searches to find the few papers that refer to "the viruses of bacteria" but not to "phage." Is this really a problem? To attempt to address this question I have employed my handy-dandy BEG bibliography to do a "virus" or "viral" but not "phage" or "bacteriophage" search. Considering only the more modern references (i.e., 1998 through 2001; see below), there are over 40 seemingly phage-ecology (or evolution) references that do not use the word "phage" in their title nor, if I had it to search, in their abstract as well. That's an average, of course, of over 10 "phage"-less phage-ecology papers per year. I observe that avoidance of "phage" is particularly common among ecosystem ecologists. I note that if I am having trouble finding (or noticing) these or, particularly, other "phage"-less references, then clearly at least some of our more "phage"-minded colleagues might as well. What have we missed? Special thanks to Steven McQuinn for the wonderful "phage-virus" gif found at the top of this editorial.

• 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

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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 for inclusion in this section.

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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.

The Contractile-Tail Sheath, In Three Dimensions by Steven McQuinn Phage T4 contractile-tail sheath (with surface texture and fancy lighting). What You Are Seeing... These are synthetic photographs of data. While it is tempting to say, "this is what the extended tail sheath of bacteriophage T4 really looks like," such a statement makes no sense in the nanoscale microcosm where visible light washes over phage the way ocean swells move through plankton. Rather, phage must be probed using the severely short end of the electromagnetic spectrum. Electron microscopists and x-ray crystallographers examining phage details compile data sets of infinitesimal measurements and clever mathematical calculations. Such data sets can be visualized in various ways to illustrate protein morphology, even protein molecular structure. When data is furnished thus to the eye it becomes comprehensible in the most fundamental way, though the caveats of method should never be slighted. We are not looking at a thing, we are looking at the result of a process. Straight-forward, unadorned image of one density surface data set for the T4 tail sheath, extended configuration. Note the fusion between gp18 proteins. Where It Came From... Anyone in middle age can appreciate how reassuring it is to see 20-year-old data looking splendid when dressed up in modern fashion. The images here were created from cryo-electron microscopy density surfaces calculated for a paper published in 1985 in the Journal of Molecular Biology. Kevin Leonard kindly dug up the old mag tapes, converted the files for use with contemporary visualization software (AVS), exported them as VRML files, compressed and sent them to me via email and ftp. All this over his weekend and during his busy workweek. A side view of the sheath, in stereo, with exaggerated depth. See below for how to visualize stereo pairs. How Much Artistic License... The VRML files, imported into my 3D graphics software as a polygon mesh, defined 4 annular rings in a stack, the top and bottom rings clipped somewhat. I trimmed the geometry down to the fully intact middle two rings, assembling duplicates to make a full helical stack 24 rings high. The bump map supplying texture to the gp18 proteins serves purely for displaying the surface curvature and has no structural significance. Ideally, the surface of the protein would show the lumpiness of constituent atoms with van der Waal radii and be colored to indicate surface charge, but I cannot find any such data; apparently the molecular structure of gp18 has not yet been worked out. The 3D synthetic lighting sources consist of a warm-colored tube light extending up the middle of the tail sheath and a cool-colored ring light encircling the sheath. Looking up through the sheath from the baseplate position toward the head. The tail tube fits inside. How To View The Stereo Pairs... Stare through the stereo pairs as if your thoughts were lost in a distant daydream, gazing off into space; suddenly the right/left images will fuse into one. Stereo fusion requires the eyes to drift apart, exactly the opposite of looking cross-eyed. To help you achieve this fusion, the paired images here are set apart the same distance as the separation of your two eyes--if you view the images on my high resolution monitor. However, it may well be that your monitor displays lower resolution than mine, making the paired images more widely separated and thus harder to fuse. In this case, open the link to the PDF version and use the percentage controls in Acrobat Reader to resize the images for best effect. (It is possible to look distantly while focusing closely if you wear strong reading glasses, which you can borrow from someone nearby who is older than 50.) The gp18 proteins in a ring kick up their legs like synchronized swimmers. The "feet" (upper, middle of image) connect with the gp19 proteins of the tail tube inside the sheath (gp19 is not shown). What It All Means... You can see how the gp18 proteins arranged in a helical stack seem to link bulge-to-bulge with their immediate neighbors. Depending how the data is visualized, these bulges can appear as fusions, and likely represent the bonds between the proteins that hold the extended sheath together. However, the extended sheath would not be stable were it not for the tail tube which extends down through the sheath. The tail tube is not included in these visualizations but you can infer it by the arrangement of the inner ends of gp18 positioned like legs with knees and toes pointed upward. Each end "foot" of gp18 is matched by a corresponding gp19 protein in the tail tube. It is thought that the attraction between the tail tube and the inner structure of the tail sheath holds the sheath in extended position. When bacteriophage T4 infects its E. coli host, the baseplate at the bottom of the sheath (not illustrated) springs open, initiating an upward cascade of broken gp18/gp19 connections, allowing the sheath to contract into a different helical arrangement with shorter length and greater radius. It is thought that sheath contraction physically drives the tail tube tip into the host cell wall. Animated comparison of two data sets from Lepault and Leonard. The one without correction (red) shows a slim version of gp18, allowing a view of how distinct units fit together. The version with phase-contrast correction (blue) is thought to be the best representation of shape and size, but the units are hard to distinguish. Shown are three annular rings, essentially, of 6 gp18 subunits each. The red one is a little clipped on top, the blue a little extended on the bottom. Remember Those Caveats... If only I could simply leap to the conclusion that these crisp, clear images of structure represent Truth, my task in animating tail sheath contraction would be a bit easier. The particular data set I used for the above views shows a slim, distinct gp18; however, the data are uncorrected. Lepault and Leonard determined that a different data set, corrected for the phase-contrast transfer function, represents the best display of gp18 size and shape, though the unit proteins in that view are too fused to be distinct. Superposition of the two data sets shows that they are very similar in general structure, with ambiguity about how the gp18 bond together. My challenge as a 3D animator will be to separate artifact from architecture, basing my interpretations on a synthesis of both data sets. It seems that even with data-derived imagery there is no escaping the need for creativity. Credits Lepault J, Leonard K. Three-dimensional structure of unstained, frozen-hydrated extended tails of bacteriophage T4. J Mol Biol 1985 Apr 5;182(3):431-41 [PRESS FOR ABSTRACT] Kevin Leonard (leonard@embl-heidelberg.de), Group Leader (http://mac-leonard4.embl-heidelberg.de/index.html)with the European Molecular Biology Laboratory (http://www.embl-heidelberg.de/) Jean Lepault (LEPAULT@frcgm51.bitnet), Group Leader in the Methods and Electron Microscopy division of Le Laboratoire de Virologie Moleculaire & Structurale (formerly Le Laboratoire de Genetique Des Virus, http://www.gv.cnrs-gif.fr/) of CNRS (http://www.cnrs.fr/index.html)

• 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
• A Few Thoughts on Phage Therapy

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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

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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. Epigenetics as a first exit problem. Aurell, E., Sneppen, K. (2002). Physical Review Letters 88:048101. [PRESS FOR ABSTRACT]

2. Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. Brentlinger, K. L., Hafenstein, S., Novak, C. R., Fane, B. A., Borgon, R., McKenna, R., Agbandje-McKenna, M. (2002). Journal of Bacteriology 184:1089-1094. [PRESS FOR ABSTRACT]

3. On the stability properties of a stochastic model for phage-bacteria interaction in open marine environment. Carletti, M. (2002). Mathematical Biosciences 175:117-131. [PRESS FOR ABSTRACT]

4. [The antiviral activity of chitosan (review)]. Chirkov, S. N. (2002). Prikladnaia Biokhimiia I Mikrobiologiia 38:5-13. [PRESS FOR ABSTRACT]

5. Filamentous phage active on the gram-positive bacterium Propionibacterium freudenreichii. Chopin, M. C., Rouault, A., Ehrlich, S. D., Gautier, M. (2002). Journal of Bacteriology 184:2030-2033. [PRESS FOR ABSTRACT]

6. Snapshot of the genome of the pseudo-T-even bacteriophage RB49. Desplats, C., Dez, C., Tetart, F., Eleaume, H., Krisch, H. M. (2002). Journal of Bacteriology 184:2789-2804. [PRESS FOR ABSTRACT]

7. Biological properties and cell tropism of Chp2, a bacteriophage of the obligate intracellular bacterium Chlamydophila abortus. Everson, J. S., Garner, S. A., Fane, B., Liu, B. L., Lambden, P. R., Clarke, I. N. (2002). Journal of Bacteriology 184:2748-2754. [PRESS FOR ABSTRACT]

8. RS1 element of Vibrio cholerae can propagate horizontally as a filamentous phage exploiting the morphogenesis genes of CTX-Phi. Faruque, S. M., Kamruzzaman, M., Nandi, R. K., Ghosh, A. N., Nair, G. B., Mekalanos, J. J., Sack, D. A. (2002). Infection and Immunity 70:163-170. [PRESS FOR ABSTRACT]

9. Microbiology. A tail of two specifi-cities. Hatfull, G. F. (2002). Science 295:2031-2032. [no abstract]

10. Engineering a reduced Escherichia coli genome. Kolisnychenko, V., Plunkett, G., Herring, C. D., Feher, T., Posfai, J., Blattner, F. R., Posfai, G. (2002). Genome Research 12:640-647. [PRESS FOR ABSTRACT]

11. The activity of chosen bacteriophages on Yersinia enterocolitica strains. Kot, B., Bukowski, K., Jakubczak, A., Kaczorek, I. (2002). Polish Journal of Veterinary Science 5:47-50. [PRESS FOR ABSTRACT]

12. Viruses causing lysis of the toxic bloom-forming alga, Heterosigma akashiwo (Raphidophyceae), are widespread in coastal sediments of British Columbia, Canada. Lawrence, J. E., Chan, A. M., Suttle, C. A. (2002). Limnology and Oceanography 47:545-550. [PRESS FOR ABSTRACT]

13. Efficacy of bacteriophage use in complex treatment of the patients with burn wounds. Lazareva, E. B., Smirnov, S. V., Khvatov, V. B., Spiridonova, T. G., Bitkova, E. E., Darbeeva, O. S., Mayskaya, L. M., Parphenyuk, R. L., Menshikov, D. D. (2002). Antibiotiki i Khimioterapiya 46:10-14. [PRESS FOR ABSTRACT]

14. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Liu, M., Deora, R., Doulatov, S. R., Gingery, M., Eiserling, F. A., Preston, A., Maskell, D. J., Simons, R. W., Cotter, P. A., Parkhill, J., Miller, J. F. (2002). Science 295:2091-2094. [PRESS FOR ABSTRACT]

15. Lysogeny in marine Synechococcus. McDaniel, L., Houchin, L. A., Williamson, S. J., Paul, J. H. (2002). Nature (London) 415:496. [PRESS FOR ABSTRACT]

16. The genome of bacteriophage phiKZ of Pseudomonas aeruginosa. Mesyanzhinov, V. V., Robben, J., Grymonprez, B., Kostyuchenko, V. A., Bourkaltseva, M. V., Sykilinda, N. N., Krylov, V. N., Volckaert, G. (2002). Journal of Molecular Biology 317:1-19. [PRESS FOR ABSTRACT]

17. Uptake and processing of modified bacteriophage M13 in mice: implications for phage display. Molenaar, T. J. M., Michon, I., de Haas, S. A. M., van Berkel, T. J. C., Kuiper, J., Biessen, E. A. L. (2002). Virology 293:182-191. [PRESS FOR ABSTRACT]

18. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. Morgan, G. J., Hatfull, G. F., Casjens, S., Hendrix, R. W. (2002). Journal of Molecular Biology 317:337-359. [PRESS FOR ABSTRACT]

19. Lysogeny and lytic viral production during a bloom of the cyanobacterium Synechococcus spp. Ortmann, A. C., Lawrence, J. E., Suttle, C. A. (2002). Microbial Ecology 43:225-231. [PRESS FOR ABSTRACT]

20. Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Rokyta, D., Badgett, M. R., Molineux, I. J., Bull, J. J. (2002). Molecular Biology and Evolution 19:230-238. [PRESS FOR ABSTRACT]

21. Bacteriophage SP6 is closely related to phages K1-5, K5, and K1E but encodes a tail protein very similar to that of the distantly related P22. Scholl, D., Adhya, S., Merril, C. R. (2002). Journal of Bacteriology 184:2833-2836. [PRESS FOR ABSTRACT]

22. Use of bacteriophage Ba1 to identify properties associated with Bordetella avium virulence. Shelton, C. B., Temple, L. M., Orndorff, P. E. (2002). Infection and Immunity 70:1219-1224. [PRESS FOR ABSTRACT]

23. Sequence analysis of marine virus communities reveals groups of related algal viruses are widely distributed in nature. Short, S. M., Suttle, C. A. (2002). Applied and Environmental Microbiology 68:1290-1296. [PRESS FOR ABSTRACT]

24. Sunlight inactivation of fecal indicator bacteria and bacteriophages from waste stabilization pond effluent in fresh and saline waters. Sinton, L. W., Hall, C. H., Lynch, P. A., Davies-Colley, R. J. (2002). Applied and Environmental Microbiology 68:1122-1131. [PRESS FOR ABSTRACT]

25. Mobile elements as a combination of functional modules. Toussaint, A., Merlin, C. (2002). Plasmid 47:26-35. [PRESS FOR ABSTRACT]

26. Reconsidering transmission electron microscopy based estimates of viral infection of bacterio-plankton using conversion factors derived from natural communities. Weinbauer, M. G., Winter, C., Hofle, M. G. (2002). Aquatic Microbial Ecology 27:103-110. [PRESS FOR ABSTRACT]

27. Direct measurements of viral production in stratified and tidally mixed waters in the Strait of Georgia. Wilhelm, S. W., Brigden, S. M., Suttle, C. A. (2002). Microbial Ecology 43:168-173. [PRESS FOR ABSTRACT]

28. Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico. You, L., Suthers, P. F., Yin, J. (2002). Journal of Bacteriology 184:1888-1894. [PRESS FOR ABSTRACT]

29. Selecting a sensitive bacteriophage assay for evaluation of a prototype water recycling system. Brion, G. M., Silverstein, J. (2001). Life Support Biosph. Sci. 8:9-14. [PRESS FOR ABSTRACT]

30. [Current clinical application of bacteriophages and perspectives for their genetic modifications]. Dabrowska, K., Bus, R., Mazur, A., Weber-Dabrowska, B., Mulczyk, M., Gorski, A. (2001). Polskie Archiwum Medycyny Wewnetrznej 105:85-90. [no abstract]

31. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic streptococci: evolutionary implications for prophage-host interactions. Desiere, F., McShan, W. M., van, Sinderen, Ferretti, J. J., Brussow, H. (2001). Virology 288:325-341. [PRESS FOR ABSTRACT]

32. Identification of a genetic determinant responsible for host specificity in Streptococcus thermophilus bacteriophages. Duplessis, M., Moineau, S. (2001). Molecular Microbiology 41:325-336. [PRESS FOR ABSTRACT]

33. Comparative study of nine Lactobacillus fermentum bacteriophages. Foschino, R., Picozzi, C., Galli, A. (2001). Journal of Applied Microbiology 91:394-403. [PRESS FOR ABSTRACT]

34. Isolation of a lysogenic bacteriophage carrying the stx(1(OX3)) gene, which is closely associated with Shiga toxin-producing Escherichia coli strains from sheep and humans. Koch, C., Hertwig, S., Lurz, R., Appel, B., Beutin, L. (2001). Journal of Clinical Microbiology 39:3992-3998. [PRESS FOR ABSTRACT]

35. [Phagotherapy in terms of bacteriophage genetics: hopes, perspectives, safety, limitations]. Krylov, V. N. (2001). Genetika 37:869-887. [PRESS FOR ABSTRACT]

36. Where are the pseudogenes in bacterial genomes? Lawrence, J. G., Hendrix, R. W., Casjens, S. (2001). Trends in Microbiology 9:535-540. [PRESS FOR ABSTRACT]

37. Presence of bacteriophages in animal feed as indicators of fecal contamination. Maciorowski, K. G., Pillai, S. D., Ricke, S. C. (2001). Journal of Environmental Science and Health Part B Pesticides 36:699-708. [PRESS FOR ABSTRACT]

38. Filamentous bacteriophage stability in non-aqueous media. Olofsson, L., Ankarloo, J., Andersson, P. O., Nicholls, I. A. (2001). Chemistry and Biology 8:661-671. [PRESS FOR ABSTRACT]

39. [Bacteria-killing viruses, Stalinists and "superbugs"]. Olsen, I., Handal, T., Lokken, P. (2001). Tidsskrift for den Norske Laegeforening 121:3197-3200. [PRESS FOR ABSTRACT]

40. Modeling virus inactivation on salad crops using microbial count data. Petterson, S. R., Teunis, P. F., Ashbolt, N. J. (2001). Risk Analysis 21:1097-1108. [PRESS FOR ABSTRACT]

41. [Autoplaque formation in a Pseudomonas fluorescens strain: phage-like particles and transactivation of the defective phage]. Shaburova, O. V., Kurochkina, L. P., Krylov, V. N. (2001). Genetika 37:893-899. [PRESS FOR ABSTRACT]

42. Designing better phages. Skiena, S. S. (2001). Bioinformatics 17 Suppl 1:S253-S261. [PRESS FOR ABSTRACT]

43. Inactivation of bacteriophages in water by means of non-ionizing (UV-253.7 nm) and ionizing (gamma) radiation: a comparative approach. Sommer, R., Pribil, W., Appelt, S., Gehringer, P., Eschweiler, H., Leth, H., Cabaj, A., Haider, T. (2001). Water Research 35:3109-3116. [PRESS FOR ABSTRACT]

44. Characterization of a Shiga toxin-encoding temperate bacteriophage of Shigella sonnei. Strauch, E., Lurz, R., Beutin, L. (2001). Infection and Immunity 69:7588-7595. [PRESS FOR ABSTRACT]

45. Community Structure: Viruses. Suttle, C. A. (2001). pp. 364-370 in Hurst, C. J., Knudson, G. R., McInerney, M. J., Stezenbach, L. D., Walter, M. V. (eds.) Manual of Environmental Microbiology (2nd Edition). ASM Press, Washington, DC. [no abstract]

46. Zoonotic Escherichia coli. Wasteson, Y. (2001). Acta Veterinaria Scandinavica Supplement 95:79-84. [PRESS FOR ABSTRACT]

47. Filamentous phage biology. Occurrence of coliphages in fish and aquaculture farms. Webster, R., Barbas, C. F., III, Burton, D. R., Scott, J. K., Silverman, G. J., Rao, B. M., Surendran, P. K. (2001). Phage display: A laboratory manual. 37:146-149. [PRESS FOR ABSTRACT]

48. A fast method for assessing rapid inactivation and adsorption kinetics of bacteriophages using batch agitation experiments and colloidal clay particles. Rossi, P., Aragno, M. (1999). Canadian Journal of Microbiology 45:9-17. [no abstract]

49. Different trajectories of parallel evolution during viral adaptation. Wichman, H. A., Badgett, M. R., Scott, L. A., Boulianne, C. M., Bull, J. J. (1999). Science 285:422-424. [PRESS FOR ABSTRACT]

50. Bacteriophage tracing techniques. Rossi, P., Käss, W. (1998). pp. 244-270 in Matthes, Käss (eds.) Tracing Techniques in Geohydrology. Balkema, Rotterdam. [no 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. Epigenetics as a first exit problem. Aurell, E., Sneppen, K. (2002). Physical Review Letters 88:048101. We develop a framework to discuss the stability of epigenetic states as first exit problems in dynamical systems with noise. We consider in particular the stability of the lysogenic state of the lambda prophage. The formalism defines a quantitative measure of robustness of inherited states

2. Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. Brentlinger, K. L., Hafenstein, S., Novak, C. R., Fane, B. A., Borgon, R., McKenna, R., Agbandje-McKenna, M. (2002). Journal of Bacteriology 184:1089-1094. A novel single-stranded DNA phage, phiMH2K, of Bdellovibrio bacteriovorus was isolated, characterized, and sequenced. This phage is a member of the Microviridae, a family typified by bacteriophage PhiX174. Although B. bacteriovorus and Escherichia coli are both classified as proteobacteria, phiMH2K is only distantly related to fX174. Instead, phiMH2K exhibits an extremely close relationship to the Microviridae of Chlamydia in both genome organization and encoded proteins. Unlike the double-stranded DNA bacteriophages, for which a wide spectrum of diversity has been observed, the single-stranded icosahedral bacteriophages appear to fall into two distinct subfamilies. These observations suggest that the mechanisms driving single-stranded DNA bacteriophage evolution are inherently different from those driving the evolution of the double-stranded bacteriophages

3. On the stability properties of a stochastic model for phage-bacteria interaction in open marine environment. Carletti, M. (2002). Mathematical Biosciences 175:117-131. In this paper we extend the deterministic model for the epidemics induced by virulent phages on bacteria in marine environment introduced by Beretta and Kuang [Math. Biosci. 149 (1998) 57], allowing random fluctuations around the positive equilibrium. The stochastic stability properties of the model are investigated both analytically and numerically suggesting that the deterministic model is robust with respect to stochastic perturbations

4. [The antiviral activity of chitosan (review)]. Chirkov, S. N. (2002). Prikladnaia Biokhimiia I Mikrobiologiia 38:5-13. Data on the inhibitory effect of chitosan on viral infections in animals, plants, and microorganisms are reviewed. The effects of the physicochemical parameters and structure of chitosan on its antiviral activity are analyzed. Possible mechanisms of the inhibitory effect of chitosan on viral infections are discussed

5. Filamentous phage active on the gram-positive bacterium Propionibacterium freudenreichii. Chopin, M. C., Rouault, A., Ehrlich, S. D., Gautier, M. (2002). Journal of Bacteriology 184:2030-2033. We present the first description of a single-stranded DNA filamentous phage able to replicate in a gram-positive bacterium. Phage B5 infects Propionibacterium freudenreichii and has a genome consisting of 5,806 bases coding for 10 putative open reading frames. The organization of the genome is very similar to the organization of the genomes of filamentous phages active on gram-negative bacteria. The putative coat protein exhibits homology with the coat proteins of phages PH75 and Pf3 active on Thermus thermophilus and Pseudomonas aeruginosa, respectively. B5 is, therefore, evolutionarily related to the filamentous phages active on gram-negative bacteria

6. Snapshot of the genome of the pseudo-T-even bacteriophage RB49. Desplats, C., Dez, C., Tetart, F., Eleaume, H., Krisch, H. M. (2002). Journal of Bacteriology 184:2789-2804. RB49 is a virulent bacteriophage that infects Escherichia coli. Its virion morphology is indistinguishable from the well-known T-even phage T4, but DNA hybridization indicated that it was phylogenetically distant from T4 and thus it was classified as a pseudo-T-even phage. To further characterize RB49, we randomly sequenced small fragments corresponding to about 20% of the approximately 170-kb genome. Most of these nucleotide sequences lacked sufficient homology to T4 to be detected in an NCBI BlastN analysis. However, when translated, about 70% of them encoded proteins with homology to T4 proteins. Among these sequences were the numerous components of the virion and the phage DNA replication apparatus. Mapping the RB49 genes revealed that many of them had the same relative order found in the T4 genome. The complete nucleotide sequence was determined for the two regions of RB49 genome that contain most of the genes involved in DNA replication. This sequencing revealed that RB49 has homologues of all the essential T4 replication genes, but, as expected, their sequences diverged considerably from their T4 homologues. Many of the nonessential T4 genes are absent from RB49 and have been replaced by unknown sequences. The intergenic sequences of RB49 are less conserved than the coding sequences, and in at least some cases, RB49 has evolved alternative regulatory strategies. For example, an analysis of transcription in RB49 revealed a simpler pattern of regulation than in T4, with only two, rather than three, classes of temporally controlled promoters. These results indicate that RB49 and T4 have diverged substantially from their last common ancestor. The different T4-type phages appear to contain a set of common genes that can be exploited differently, by means of plasticity in the regulatory sequences and the precise choice of a large group of facultative genes

7. Biological properties and cell tropism of Chp2, a bacteriophage of the obligate intracellular bacterium Chlamydophila abortus. Everson, J. S., Garner, S. A., Fane, B., Liu, B. L., Lambden, P. R., Clarke, I. N. (2002). Journal of Bacteriology 184:2748-2754. A number of bacteriophages belonging to the Microviridae have been described infecting chlamydiae. Phylogenetic studies divide the Chlamydiaceae into two distinct genera, Chlamydia and Chlamydophila, containing three and six different species, respectively. In this work we investigated the biological properties and host range of the recently described bacteriophage Chp2 that was originally discovered in Chlamydophila abortus. The obligate intracellular development cycle of chlamydiae has precluded the development of quantitative approaches to assay bacteriophage infectivity. Thus, we prepared hybridomas secreting monoclonal antibodies (monoclonal antibodies 40 and 55) that were specific for Chp2. We demonstrated that Chp2 binds both C. abortus elementary bodies and reticulate bodies in an enzyme-linked immunosorbent assay. Monoclonal antibodies 40 and 55 also detected bacteriophage Chp2 antigens in chlamydia-infected eukaryotic cells. We used these monoclonal antibodies to monitor the ability of Chp2 to infect all nine species of chlamydiae. Chp2 does not infect members of the genus Chlamydia (C. trachomatis, C. suis, or C. muridarum). Chp2 can infect C. abortus, C. felis, and C. pecorum but is unable to infect other members of this genus, including C. caviae and C. pneumoniae, despite the fact that these chlamydial species support the replication of very closely related bacteriophages

8. RS1 element of Vibrio cholerae can propagate horizontally as a filamentous phage exploiting the morphogenesis genes of CTX-Phi. Faruque, S. M., Kamruzzaman, M., Nandi, R. K., Ghosh, A. N., Nair, G. B., Mekalanos, J. J., Sack, D. A. (2002). Infection and Immunity 70:163-170. In toxigenic Vibrio cholerae, cholera toxin is encoded by the CTX prophage, which consists of a core region carrying ctxAB genes and genes required for CTX-Phi morphogenesis, and an RS2 region encoding regulation, replication, and integration functions. Integrated CTX-Phi is often flanked by another genetic element known as RS1 which carries all open reading frames (ORFs) found in RS2 and an additional ORF designated rstC. We identified a single-stranded circularized form of the RS1 element, in addition to the CTX-Phi genome, in nucleic acids extracted from phage preparations of 32 out of 83 (38.5%) RS1-positive toxigenic V. cholerae strains analyzed. Subsequently, the corresponding double-stranded replicative form (RF) of the RS1 element was isolated from a representative strain and marked with a kanamycin resistance (Km(r)) marker in an intergenic site to construct pRS1-Km. Restriction and PCR analysis of pRS1-Km and sequencing of a 300-bp region confirmed that this RF DNA was the excised RS1 element which formed a novel junction between ig1 and rstC. Introduction of pRS1-Km into a V. cholerae O1 classical biotype strain, O395, led to the production of extracellular Km(r) transducing particles, which carried a single-stranded form of pRS1-Km, thus resembling the genome of a filamentous phage (RS1-KmF). Analysis of V. cholerae strains for susceptibility to RS1-KmF showed that classical biotype strains were more susceptible to the phage compared to El Tor and O139 strains. Nontoxigenic (CTX(-)) O1 and O139 strains which carried genes encoding the CTX-Phi receptor toxin-coregulated pilus (TCP) were also more susceptible (>1,000-fold) to the phage compared to toxigenic El Tor or O139 strains. Like CTX-Phi, the RS1F genome also integrated into the host chromosomes by using the attRS sequence. However, only transductants of RS1-KmF which also harbored the CTX-Phi genome produced a detectable level of extracellular RS1-KmF. This suggested that the core genes of CTX-Phi are also required for the morphogenesis of RS1F. The results of this study showed for the first time that RS1 element, which encodes a site-specific recombination system in V. cholerae, can propagate horizontally as a filamentous phage, exploiting the morphogenesis genes of CTX-Phi

9. Microbiology. A tail of two specifi-cities. Hatfull, G. F. (2002). Science 295:2031-2032.

10. Engineering a reduced Escherichia coli genome. Kolisnychenko, V., Plunkett, G., Herring, C. D., Feher, T., Posfai, J., Blattner, F. R., Posfai, G. (2002). Genome Research 12:640-647. Our goal is to construct an improved Escherichia coli to serve both as a better model organism and as a more useful technological tool for genome science. We developed techniques for precise genomic surgery and applied them to deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions to the genome. They are loaded with cryptic prophages, transposons, damaged genes, and genes of unknown function. Our method leaves no scars or markers behind and can be applied sequentially. Twelve K-islands were successfully deleted, resulting in an 8.1% reduced genome size, a 9.3% reduction of gene count, and elimination of 24 of the 44 transposable elements of E. coli. These are particularly detrimental because they can mutagenize the genome or transpose into clones being propagated for sequencing, as happened in 18 places of the draft human genome sequence. We found no change in the growth rate on minimal medium, confirming the nonessential nature of these islands. This demonstration of feasibility opens the way for constructing a maximally reduced strain, which will provide a clean background for functional genomics studies, a more efficient background for use in biotechnology applications, and a unique tool for studies of genome stability and evolution

11. The activity of chosen bacteriophages on Yersinia enterocolitica strains. Kot, B., Bukowski, K., Jakubczak, A., Kaczorek, I. (2002). Polish Journal of Veterinary Science 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

12. Viruses causing lysis of the toxic bloom-forming alga, Heterosigma akashiwo (Raphidophyceae), are widespread in coastal sediments of British Columbia, Canada. Lawrence, J. E., Chan, A. M., Suttle, C. A. (2002). Limnology and Oceanography 47:545-550. Viruses that infect and cause lysis of the toxic alga Heterosigma akashiwo are abundant and widespread in the Strait of Georgia, Canada, and adjacent inlets during the summer months when blooms of this alga occur. Because viruses are subjected to many mechanisms of removal and their host is intermittently dormant, the persistence of viruses may be dependent on environmental reservoirs. We extracted pore water from sediments collected in the Strait of Georgia and screened for the presence of infectious agents that cause lysis of H. akashiwo. Lytic agents were widespread throughout the study region, being detected in 17 of 20 sites surveyed. Lytic agents were present in sediments ranging from highly organic to clay-rich and were retrieved from cores taken at water depths of 25-285 m. The highest concentration of lytic agents was found at the sediment-water interface; however, lytic agents were found as deep as 40 cm below the sediment-water interface. Examination of agents isolated from various sites revealed virus-like particles similar to50 nm in diameter. These are similar to other virus-like particles that have been isolated that infect this alga. This suggests that the most abundant lytic agents in the sediments are viruses and that these viruses may be long-lived once buried in the sediments. The widespread presence of viral-size lytic agents that infect H. akashiwo is consistent with viral infection being a mortality agent of this alga in the overlying waters and suggests that they may play in important role in regulating their population dynamics.

13. Efficacy of bacteriophage use in complex treatment of the patients with burn wounds. Lazareva, E. B., Smirnov, S. V., Khvatov, V. B., Spiridonova, T. G., Bitkova, E. E., Darbeeva, O. S., Mayskaya, L. M., Parphenyuk, R. L., Menshikov, D. D. (2002). Antibiotiki i Khimioterapiya 46:10-14. Results of clinical and laboratory evaluation of the treatment with pyobacteriophage in tablets of the patients with burn wounds are presented. It was shown that phagotherapy provided more rapid cure of pyoseptic complications, temperature normalization, wounds purification and lower lethality Bacteriological analysis of wound secretions revealed that after the treatment staphylococci and streptococci were cultured 2 times rarely, Proteus spp. Were isolated 1.5 times rarely, E.coli was not isolated. The amount of positive haemocultures also diminished. Investigation of immunologic status demonstrated statistically significant normalization of immunity on cell level. Phagocytosis level didn't change while in control group (without bacteriophage use) it became lower. Antibody level enhanced but less extensively than in control group. The results of trial demonstrates positive effect of phagotherapy use at the patients with burns

14. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Liu, M., Deora, R., Doulatov, S. R., Gingery, M., Eiserling, F. A., Preston, A., Maskell, D. J., Simons, R. W., Cotter, P. A., Parkhill, J., Miller, J. F. (2002). Science 295:2091-2094. Host-pathogen interactions are often driven by mechanisms that promote genetic variability. We have identified a group of temperate bacteriophages that generate diversity in a gene, designated mtd (major tropism determinant), which specifies tropism for receptor molecules on host Bordetella species. Tropism switching is the result of a template-dependent, reverse transcriptase-mediated process that introduces nucleotide substitutions at defined locations within mtd. This cassette-based mechanism is capable of providing a vast repertoire of potential ligand-receptor interactions

15. Lysogeny in marine Synechococcus. McDaniel, L., Houchin, L. A., Williamson, S. J., Paul, J. H. (2002). Nature (London) 415:496. Viral infection of bacteria can be lytic, causing destruction of the host cell, or lysogenic, in which the viral genome is instead stably maintained as a prophage within its host. Here we show that lysogeny occurs in natural populations of an autotrophic picoplankton (Synechococcus) and that there is a seasonal pattern to this interaction. Because lysogeny confers immunity to infection by related viruses, this process may account for the resistance to viral infection seen in common forms of autotrophic picoplankton

16. The genome of bacteriophage phiKZ of Pseudomonas aeruginosa. Mesyanzhinov, V. V., Robben, J., Grymonprez, B., Kostyuchenko, V. A., Bourkaltseva, M. V., Sykilinda, N. N., Krylov, V. N., Volckaert, G. (2002). Journal of Molecular Biology 317:1-19. Bacteriophage phiKZ is a giant virus that efficiently infects Pseudomonas aeruginosa strains pathogenic to human and, therefore, it is attractive for phage therapy. We present here the complete phiKZ genome sequence and a preliminary analysis of its genome structure. The 280,334 bp genome is a linear, circularly permutated and terminally redundant, A+T-rich double-stranded DNA molecule. The phiKZ DNA has no detectable sequence homology to other viruses and microorganisms, and it does not contain NotI, PstI, SacI, SmaI, XhoI, and XmaIII endonuclease restriction sites. The genome has 306 open reading frames (ORFs) varying in size from 50 to 2237 amino acid residues. According to the orientation of transcription, ORFs are apparently organized into clusters and most have a clockwise direction. The phiKZ genome also encodes six tRNAs specific for Met (AUG), Asn (AAC), Asp (GAC), Leu (TTA), Thr (ACA), and Pro (CCA). A putative promoter sequence containing a TATATTAC block was identified. Most potential stem-loop transcription terminators contain the tetranucleotide UUCG loops. Some genes may be assigned as phage-encoded RNA polymerase subunits. Only 59 phiKZ gene products exhibit similarity to proteins of known function from a diversity of organisms. Most of these conserved gene products, such as dihydrofolate reductase, ribonucleoside diphosphate reductase, thymidylate synthase, thymidylate kinase, and deoxycytidine triphosphate deaminase are involved in nucleotide metabolism. However, no virus-encoded DNA polymerase, DNA replication-associated proteins, or single-stranded DNA-binding protein were found based on amino acid homology, and they may therefore be strongly divergent from known homologous proteins. Fifteen phiKZ gene products show homology to proteins of pathogenic organisms, including Mycobacterium tuberculosis, Haemophilus influenzae, Listeria sp., Rickettsia prowazakeri, and Vibrio cholerae that must be considered before using this phage as a therapeutic agent. The phiKZ coat contains at least 40 polypeptides, and several proteins are cleaved during virus assembly in a way similar to phage T4. Eleven phiKZ-encoded polypeptides are related to proteins of other bacteriphages that infect a variety of hosts. Among these are four gene products that contain a putative intron-encoded endonuclease harboring the H-N-H motif common to many double-stranded DNA phages. These observations provide evidence that phages infecting diverse hosts have had access to a common genetic pool. However, limited homology on the DNA and protein levels indicates that bacteriophage phiKZ represents an evolutionary distinctive branch of the Myoviridae family

17. Uptake and processing of modified bacteriophage M13 in mice: implications for phage display. Molenaar, T. J. M., Michon, I., de Haas, S. A. M., van Berkel, T. J. C., Kuiper, J., Biessen, E. A. L. (2002). Virology 293:182-191. Internalization and degradation of filamentous bacteriophage M13 by a specific target cell may have major consequences for the recovery of phage in in vivo biopanning of phage libraries. Therefore, we investigated the pharmacokinetics and processing of native and receptor-targeted phage in mice. ³⁵S-radiolabeled M13 was chemically modified by conjugation of either galactose (lacM13) or succinic acid groups (sucM13) to the coat protein of the phage to stimulate uptake by galactose recognizing hepatic receptors and scavenger receptors, respectively. Receptor-mediated endocytosis of modified phage reduced the plasma half-life of native M13 (t(1/2) = 4.5 h) to 18 min for lactosylated and 1.5 min for succinylated bacterophage. Internalization of sucM13 was complete within 30 min after injection and resulted in up to 5000-fold reduction of bioactive phage within 90 min. In conclusion, these data provide information on the in vivo behavior of wild-type and receptor-targeted M13, which has important implications for future in vivo phage display experiments and for the potential use of M13 as a viral gene delivery vehicle

18. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. Morgan, G. J., Hatfull, G. F., Casjens, S., Hendrix, R. W. (2002). Journal of Molecular Biology 317:337-359. We report the complete 36,717 bp genome sequence of bacteriophage Mu and provide an analysis of the sequence, both with regard to the new genes and other genetic features revealed by the sequence itself and by a comparison to eight complete or nearly complete Mu-like prophage genomes found in the genomes of a diverse group of bacteria. The comparative studies confirm that members of the Mu-related family of phage genomes are genetically mosaic with respect to each other, as seen in other groups of phages such as the phage lambda-related group of phages of enteric hosts and the phage L5-related group of mycobacteriophages. Mu also possesses segments of similarity, typically gene-sized, to genomes of otherwise non-Mu-like phages. The comparisons show that some well-known features of the Mu genome, including the invertible segment encoding tail fiber sequences, are not present in most members of the Mu genome sequence family examined here, suggesting that their presence may be relatively volatile over evolutionary time.The head and tail-encoding structural genes of Mu have only very weak similarity to the corresponding genes of other well-studied phage types. However, these weak similarities, and in some cases biochemical data, can be used to establish tentative functional assignments for 12 of the head and tail genes. These assignments are strongly supported by the fact that the order of gene functions assigned in this way conforms to the strongly conserved order of head and tail genes established in a wide variety of other phages. We show that the Mu head assembly scaffolding protein is encoded by a gene nested in-frame within the C-terminal half of another gene that encodes the putative head maturation protease. This is reminiscent of the arrangement established for phage lambda

19. Lysogeny and lytic viral production during a bloom of the cyanobacterium Synechococcus spp. Ortmann, A. C., Lawrence, J. E., Suttle, C. A. (2002). Microbial Ecology 43:225-231. Lytic viral production and lysogeny were investigated in cyanobacteria and heterotrophic bacteria during a bloom of Synechococcus spp. in a pristine fjord in British Columbia, Canada. Triplicate seawater samples were incubated with and without mitomycin C and the abundances of heterotrophic bacteria, cyanobacteria, total viruses and infectious cyanophage were followed over 24 h. Addition of mitomycin C led to increases in total viral abundance as well as the abundance of cyanophages infecting Synechococcus strain DC2. Given typical estimates of burst size, these increases were consistent with 80% of the heterotrophic bacteria and 0.6% of Synechococcus cells being inducible by the addition of mitomycin C. This is the highest percentage of lysogens reported for a natural microbial community and demonstrates induction in a marine Synechococcus population. It is likely that the cyanophage production following the addition of mitomycin C was much higher than that titered against a single strain of Synechococcus; hence this estimate is a minimum. In untreated seawater samples, lytic viral production was estimated to remove ca. 27% of the gross heterotrophic bacterial production, and a minimum of 1.0% of the gross cyanobacterial production. Our results demonstrate very high levels of lysogeny in the heterotrophic bacterial community, outside of an oligotrophic environment, and the presence of inducible lysogens in Synechococcus spp. during a naturally occurring bloom. These data emphasize the need for further examination of the factors influencing lytic and lysogenic viral infection in natural microbial communities.

20. Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Rokyta, D., Badgett, M. R., Molineux, I. J., Bull, J. J. (2002). Molecular Biology and Evolution 19:230-238. Deletion of the viral ligase gene drastically reduced the fitness of bacteriophage T7 on a ligase-deficient host. Viral evolution recovered much of this fitness during long-term passage, but the final fitness remained below that of the intact virus. Compensatory changes occurred chiefly in genes involved in DNA metabolism: the viral endonuclease, helicase, and DNA polymerase. Two other compensatory changes of unknown function also occurred. Using a method to distinguish compensatory mutations from other beneficial mutations, five additional substitutions from the recovery were shown to enhance adaptation to culture conditions and were not compensatory for the deletion. In contrast to the few previous studies of viral recovery from deletions, the compensatory changes in T7 did not restore the deletion or duplicate major regions of the genome. The ability of this deleted genome to recover much of the lost fitness via mutations in its remaining genes reveals a considerable evolutionary potential to modify the interactions of its elements in maintaining an essential set of functions

21. Bacteriophage SP6 is closely related to phages K1-5, K5, and K1E but encodes a tail protein very similar to that of the distantly related P22. Scholl, D., Adhya, S., Merril, C. R. (2002). Journal of Bacteriology 184:2833-2836. The lytic salmonella phage SP6 encodes a tail protein with a high degree of sequence similarity to the tail protein of the biologically unrelated lysogenic salmonella phage P22. The SP6 tail gene is flanked by an upstream region that contains a promoter and a downstream region that contains a putative Rho-independent transcription terminator, giving it a cassette or modular structure almost identical to the structure of the tail genes of coliphages K1E, K5, and K1-5. It now appears that SP6, K1-5, K5, and K1E are very closely related but have different tail fiber proteins, giving them different host specificities

22. Use of bacteriophage Ba1 to identify properties associated with Bordetella avium virulence. Shelton, C. B., Temple, L. M., Orndorff, P. E. (2002). Infection and Immunity 70:1219-1224. Bordetella avium causes bordetellosis, an upper respiratory disease of birds. Commercially raised turkeys are particularly susceptible. We report here on the use of a recently described B. avium bacteriophage, Ba1, as a tool for investigating the effects of lysogeny and phage resistance on virulence. We found that lysogeny had no effect on any of the in vivo or in vitro measurements of virulence we employed. However, two-thirds (six of nine) spontaneous phage-resistant mutants of our virulent laboratory strain, 197N, were attenuated. Phage resistance was associated, in all cases, with an inability of the mutants to bind phage. Further tests of the mutants revealed that all had increased sensitivities to surfactants, and increased amounts of incomplete (O-antigen-deficient) lipopolysaccharide (LPS) compared to 197N. Hot phenol-water-extracted 197N LPS inactivated phage in a specific and dose-dependent manner. Acid hydrolysis and removal of lipid A had little effect upon the ability of isolated LPS to inactivate Ba1, suggesting that the core region and possibly the O antigen were required for phage binding. All of the mutants, with one exception, were significantly more sensitive to naive turkey serum and, without exception, significantly less able to bind to tracheal rings in vitro than 197N. Interestingly, the three phage-resistant mutants that remained virulent appeared to be O antigen deficient and were among the mutants that were the most serum sensitive and least able to bind turkey tracheal rings in vitro. This observation allowed us to conclude that even severe defects in tracheal ring binding and serum resistance manifested in vitro were not necessarily indicative of attenuation and that complete LPS may not be required for virulence

23. Sequence analysis of marine virus communities reveals groups of related algal viruses are widely distributed in nature. Short, S. M., Suttle, C. A. (2002). Applied and Environmental Microbiology 68:1290-1296. Algal-virus-specific PCR primers were used to amplify DNA polymerase (pol) gene fragments from geographically isolated natural virus communities. Natural algal virus communities were obtained from coastal sites in the Pacific Ocean in British Columbia, Canada, and the Southern Ocean near the Antarctic peninsula. Genetic fingerprints of algal virus communities were generated using denaturing gradient gel electrophoresis (DGGE). Sequencing efforts recovered 33 sequences from the gradient gel. Of the 33 sequences examined, 25 encoded a conserved amino acid motif indicating that the sequences were pol gene fragments. Furthermore, the 25 pol sequences were related to pol gene fragments from known algal viruses. In addition, similar virus sequences (>98% sequence identity) were recovered from British Columbia and Antarctica. Results from this study demonstrate that DGGE with degenerate primers can be used to qualitatively fingerprint and assess genetic diversity in specific subsets of natural virus communities and that closely related viruses occur in distant geographic locations. DGGE is a powerful tool for genetically fingerprinting natural virus communities and may be used to examine how specific components of virus communities respond to experimental manipulations.

24. Sunlight inactivation of fecal indicator bacteria and bacteriophages from waste stabilization pond effluent in fresh and saline waters. Sinton, L. W., Hall, C. H., Lynch, P. A., Davies-Colley, R. J. (2002). Applied and Environmental Microbiology 68:1122-1131. Sunlight inactivation in fresh (river) water of fecal coliforms, enterococci, Escherichia coli, somatic coliphages, and F-RNA phages from waste stabilization pond (WSP) effluent was compared. Ten experiments were conducted outdoors in 300-liter chambers, held at 14C (mean river water temperature). Sunlight inactivation (k(S)) rates, as a function of cumulative global solar radiation (insolation), were all more than 10 times higher than the corresponding dark inactivation (k(D)) rates in enclosed (control) chambers. The overall k(S) ranking (from greatest to least inactivation) was as follows: enterococci > fecal coliforms greater-than-or-equal E. coli > somatic coliphages > F-RNA phages. In winter, fecal coliform and enterococci inactivation rates were similar but, in summer, enterococci were inactivated far more rapidly. In four experiments that included freshwater-raw sewage mixtures, enterococci survived longer than fecal coliforms (a pattern opposite to that observed with the WSP effluent), but there was little difference in phage inactivation between effluents. In two experiments which included simulated estuarine water and seawater, sunlight inactivation of all of the indicators increased with increasing salinity. Inactivation rates in freshwater, as seen under different optical filters, decreased with the increase in the spectral cutoff (50% light transmission) wavelength. The enterococci and F-RNA phages were inactivated by a wide range of wavelengths, suggesting photooxidative damage. Inactivation of fecal coliforms and somatic coliphages was mainly by shorter (UV-B) wavelengths, a result consistent with photobiological damage. Fecal coliform repair mechanisms appear to be activated in WSPs, and the surviving cells exhibit greater sunlight resistance in natural waters than those from raw sewage. In contrast, enterococci appear to suffer photooxidative damage in WSPs, rendering them susceptible to further photooxidative damage after discharge. This suggests that they are unsuitable as indicators of WSP effluent discharges to natural waters. Although somatic coliphages are more sunlight resistant than the other indicators in seawater, F-RNA phages are the most resistant in freshwater, where they may thus better represent enteric virus survival

25. Mobile elements as a combination of functional modules. Toussaint, A., Merlin, C. (2002). Plasmid 47:26-35. Prokaryotic mobile elements have traditionally been classified as bacteriophages, plasmids, and transposons. We propose here a global classification of these and other bacterial and archaeal mobile elements based on their modular structure. This would allow for setting up interconnected databases where mobile elements could be stored as combinations of functional modules. Such a database would be very helpful. It would, for instance, allow for analyzing the phylogeny of individual blocks within an element, to understand how modules get associated and properly express the functions they carry in various bacterial hosts. Modules of practical importance, as for instance those that encode toxins or other virulence factors, could be identified and compared, and probes devised to test bacterial populations for the presence of such modules

26. Reconsidering transmission electron microscopy based estimates of viral infection of bacterio-plankton using conversion factors derived from natural communities. Weinbauer, M. G., Winter, C., Hofle, M. G. (2002). Aquatic Microbial Ecology 27:103-110. The frequency of virus infected bacterial cells (FIC) was estimated in surface waters of the Mediterranean Sea, the Baltic Sea and the North Sea using the frequency of visibly infected cells (FVIC) as determined by transmission electron microscopy (TEM) and published average conversion factors (average 5.42, range 3.7 to 7.14) to relate FVIC to FIC. A virus dilution approach was used to obtain an independent estimation of FIC in bacterioplankton, and we provide evidence for the reliability of this approach. Across all investigated environments, FIC ranged from 2.4 to 43.4 %. FIC data using both approaches were well correlated; however, the values were higher using the virus dilution approach, This indicates that the TEM approach has the potential to reveal spatiotemporal trends of viral infection; however, it may underestimate the significance of viral infection of bacteria when average conversion factors are used. Using data from the virus dilution approach and the TEM approach, we calculated new conversion factors for relating FVIC to FIC (average 7.11, range 4.34 to 10.78). Virally caused mortality of bacteria estimated from published FVIC data of marine and freshwater systems and using the new conversion factors ranged from not detectable to 129 %, thus confirming that viral infection is a significant and spatiotemporally variable cause of bacterial cell death.

27. Direct measurements of viral production in stratified and tidally mixed waters in the Strait of Georgia. Wilhelm, S. W., Brigden, S. M., Suttle, C. A. (2002). Microbial Ecology 43:168-173. The abundance of heterotrophic bacteria and viruses, as well as rates of viral production and virus-mediated mortality, were measured in Discovery Passage and the Strait of Georgia (British Columbia, Canada) along a gradient of tidal mixing ranging from well mixed to stratified. The abundances of bacteria and viruses were approximately 10⁶ and 10⁷ mL^-1, respectively, independent of mixing regime. Viral production estimates, monitored by a dilution technique, demonstrated that new viruses were produced at rates of 10⁶ to 10⁷ mL^-1 h^-1 across the different mixing regimes. Using an estimated burst size of 50 viruses per lytic event, ca. 19 to 27% of the standing stock of bacteria at the stratified stations and 46 to 137% at the deep-mixed stations were removed by viruses. The results suggest that mixing of stratified waters during tidal exchange enhances virus-mediated bacterial lysis. Consequently, viral lysis recycled a greater proportion of the organic carbon required for bacterial growth under non-steady-state compared to steady-state conditions.

28. Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico. You, L., Suthers, P. F., Yin, J. (2002). Journal of Bacteriology 184:1888-1894. Phage development depends not only upon phage functions but also on the physiological state of the host, characterized by levels and activities of host cellular functions. We established Escherichia coli at different physiological states by continuous culture under different dilution rates and then measured its production of phage T7 during a single cycle of infection. We found that the intracellular eclipse time decreased and the rise rate increased as the growth rate of the host increased. To develop mechanistic insight, we extended a computer simulation for the growth of phage T7 to account for the physiology of its host. Literature data were used to establish mathematical correlations between host resources and the host growth rate; host resources included the amount of genomic DNA, pool sizes and elongation rates of RNA polymerases and ribosomes, pool sizes of amino acids and nucleoside triphosphates, and the cell volume. The in silico (simulated) dependence of the phage intracellular rise rate on the host growth rate gave quantitatively good agreement with our in vivo results, increasing fivefold for a 2.4-fold increase in host doublings per hour, and the simulated dependence of eclipse time on growth rate agreed qualitatively, deviating by a fixed delay. When the simulation was used to numerically uncouple host resources from the host growth rate, phage growth was found to be most sensitive to the host translation machinery, specifically, the level and elongation rate of the ribosomes. Finally, the simulation was used to follow how bottlenecks to phage growth shift in response to variations in host or phage functions

29. Selecting a sensitive bacteriophage assay for evaluation of a prototype water recycling system. Brion, G. M., Silverstein, J. (2001). Life Support Biosph. Sci. 8:9-14. A rapid, simple, and direct (RSD) assay of eluate from filter concentration was developed to enumerate low numbers of MS2 bacteriophage, used as a surrogate for enteric viruses, from samples collected from a prototype-sized water recycling system. The RSD assay utilized a 50-ml eluate volume in a modified single-layer assay, neutralizing eluate pH by buffered, double-strength agar. The RSD assay developed was simpler and minimized sample-handling steps compared with another published method. The RSD assay method showed greater sensitivity than the other published method for recovering phage from filter eluate while avoiding pH shifts, which can inactivate phage. Grant numbers: NAGW 2356

30. [Current clinical application of bacteriophages and perspectives for their genetic modifications]. Dabrowska, K., Bus, R., Mazur, A., Weber-Dabrowska, B., Mulczyk, M., Gorski, A. (2001). Polskie Archiwum Medycyny Wewnetrznej 105:85-90.

31. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic streptococci: evolutionary implications for prophage-host interactions. Desiere, F., McShan, W. M., van, Sinderen, Ferretti, J. J., Brussow, H. (2001). Virology 288:325-341. The genome of the highly pathogenic M1 serotype Streptococcus pyogenes isolate SF370 contains eight prophage elements. Only prophage SF370.1 could be induced by mitomycin C treatment. Prophage SF370.3 showed a 33.5-kb-long genome that closely resembled the genome organization of the cos-site temperate Siphovirus r1t infecting the dairy bacterium Lactococcus lactis. The two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA packaging, head and tail genes. Analysis of the SF370.3 genome revealed mutations in the replisome organizer gene that may prevent the induction of the prophage. The mutated phage replication gene was closely related to a virulence marker identified in recently emerged M3 serotype S. pyogenes strains in Japan. This observation suggests that prophage genes confer selective advantage to the lysogenic host. SF370.3 encodes a hyaluronidase and a DNase that may facilitate the spreading of S. pyogenes through tissue planes of its human host. Prophage SF370.2 showed a 43-kb-long genome that closely resembled the genome organization of pac-site temperate Siphoviridae infecting the dairy bacteria S. thermophilus and L. lactis. Over part of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205 extended to the nucleotide sequence level. SF370.2 showed two probable inactivating mutations: one in the replisome organizer gene and another in the gene encoding the portal protein. Prophage SF370.2 also encodes a hyaluronidase and in addition two very likely virulence factors: prophage-encoded toxins acting as superantigens that may contribute to the immune deregulation observed during invasive streptococcal infections. The superantigens are encoded between the phage lysin and the right attachment site of the prophage genome. The genes were nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer. The trend for prophage genome inactivation was even more evident for the remaining five prophage sequences that showed massive losses of prophage DNA. In these prophage remnants only 13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes strain SF370 within the framework of Darwinian coevolution of prophages and lysogenic bacteria and suggest elements of genetic cooperation and elements of an arms race in this host-parasite relationship

32. Identification of a genetic determinant responsible for host specificity in Streptococcus thermophilus bacteriophages. Duplessis, M., Moineau, S. (2001). Molecular Microbiology 41:325-336. Phage-host interactions remain poorly understood in lactic acid bacteria and essentially in all Gram-positive bacteria. The aim of this study was to identify the phage genetic determinant (anti-receptor) involved in the recognition of Streptococcus thermophilus hosts. The complete genomic sequence of the lytic S. thermophilus phage DT1 was determined previously, and bioinformatic analysis indicated that orf18 might be the anti-receptor gene. The orf18 of six additional S. thermophilus phages was determined (DT2, DT4, MD1, MD2, MD4 and Q5) and compared with the orf18 of DT1. The deduced ORF18 was divided into three domains. The first domain, which contains the N-terminal part of the protein, was conserved in all seven phages. The second domain was detected in only two phages and flanked by a motif called collagen-like repeats. The second domain also contained a variable region (VR1). All seven phages had a third domain that consisted of the C-terminal section of the protein as well as another variable region (VR2). Chimeric DT1 phages were constructed by recombination; a portion of its orf18 was replaced by the corresponding section in orf18 of the phage MD4. All DT1 chimeric phages acquired the host range of phage MD4. Analysis of the orf18 in the chimeric phages revealed that host specificity in phages DT1 and MD4 resulted from VR2. This is the first report on the identification and characterization of a phage gene involved in the host recognition process of Gram-positive bacteria

33. Comparative study of nine Lactobacillus fermentum bacteriophages. Foschino, R., Picozzi, C., Galli, A. (2001). Journal of Applied Microbiology 91:394-403. AIMS: To investigate the basic properties of six temperate and three virulent phages, active on Lactobacillus fermentum, on the basis of morphology, host ranges, protein composition and genome characterization. METHODS AND RESULTS: All phages belonged to the Siphoviridae family; two of them showed prolate heads. The host ranges of seven phages contained a common group of strains. SDS-PAGE protein profiles, restriction analysis of DNA and Southern blot hybridization revealed a high degree of homology between four temperate phages; partial homologies were also detected among virulent and temperate phages. Clustering derived from host range analysis was not related to the results of the DNA hybridizations. CONCLUSION: The phages investigated have common characteristics with other known phages active on the genus Lactobacillus. Sensitivity to viral infection is apparently enhanced by the presence of a resident prophage. SIGNIFICANCE AND IMPACT OF THE STUDY: These relationships contribute to the explanation for the origin of phage infection in food processes where Lact. fermentum is involved, such as sourdough fermentation

34. Isolation of a lysogenic bacteriophage carrying the stx(1(OX3)) gene, which is closely associated with Shiga toxin-producing Escherichia coli strains from sheep and humans. Koch, C., Hertwig, S., Lurz, R., Appel, B., Beutin, L. (2001). Journal of Clinical Microbiology 39:3992-3998. A specific PCR for the detection of a variant of the gene encoding Shiga toxin 1 (stx(1)) called stx(1(OX3)) (GenBank accession no. Z36901) was developed. The PCR was used to investigate 148 Stx(1)-producing Escherichia coli strains from human patients (n = 72), cattle (n = 27), sheep (n = 48), and a goat (n = 1) for the presence of the stx(1(OX3)) gene. The stx(1(OX3)) gene was present in 38 Shiga toxin-producing E. coli (STEC) strains from sheep belonging to serogroups O5, O125, O128, O146, and OX3 but was absent from Stx(1)-positive ovine STEC O91 strains. The stx(1(OX3)) gene was also detected in 22 STEC strains from humans with nonbloody diarrhea and from asymptomatic excreters. Serotypes O146:H21 and O128:H2 were most frequently associated with stx(1(OX3))-carrying STEC from sheep and humans. In contrast, Stx(1)-producing STEC strains from cattle and goats and 50 STEC strains from humans were all negative for the stx(1(OX3)) gene. The stx(1(OX3))-negative strains belonged to 13 serotypes which were different from those of the stx(1(OX3))-positive STEC strains. Moreover, the stx(1(OX3)) gene was not associated with STEC belonging to enterohemorrhagic E. coli (EHEC) serogroups O26, O103, O111, O118, O145, and O157. A bacteriophage carrying the stx(1(OX3)) gene (phage 6220) was isolated from a human STEC O146:H21 strain. The phage was able to lysogenize laboratory E. coli K-12 strain C600. Phage 6220 shared a similar morphology and a high degree of DNA homology with Stx(2)-encoding phage 933W, which originates from EHEC O157. In contrast, few similarities were found between phage 6220 and Stx(1)-encoding bacteriophage H-19B from EHEC O26

35. [Phagotherapy in terms of bacteriophage genetics: hopes, perspectives, safety, limitations]. Krylov, V. N. (2001). Genetika 37:869-887. The appearance and spreading of multidrug-resistant bacterial pathogens is a consequence of the large-scale use of antibiotics in medicine. In view of this, claims for the phage therapy were renewed: in recent studies, the natural phages and their products neutralizing various proteins, as well as the bacterial products often controlled by defective prophages (bacteriocins) were applied for treatment of bacterial infections. Constructs obtained by gene engineering are increasingly used to change some bacteriophage: properties to expand the spectrum of their lytic activity and to eliminate therapeutic drawbacks of some natural phages. In this review, the problem of phage therapy is discussed in general with respect to bacteriophage properties, their genetics, structure, evolution, taking into account long-term experience of the author in the field of bacteriophage genetics. Note that the general concept of phage therapy should be developed to ensure long-term, efficient and harmless phage therapy

36. Where are the pseudogenes in bacterial genomes? Lawrence, J. G., Hendrix, R. W., Casjens, S. (2001). Trends in Microbiology 9:535-540. Most bacterial genomes have very few pseudogenes; notable exceptions include the genomes of the intracellular parasites Rickettsia prowazekii and Mycobacterium leprae. As DNA can be introduced into microbial genomes in many ways, the compact nature of these genomes suggests that the rate of DNA influx is balanced by the rate of DNA deletion. We propose that the influx of dangerous genetic elements such as transposons and bacteriophages selects for the maintenance of relatively high deletion rates in most bacteria; the sheltered lifestyle of intracellular parasites removes this threat, leading to reduced deletion rates and larger pseudogene loads

37. Presence of bacteriophages in animal feed as indicators of fecal contamination. Maciorowski, K. G., Pillai, S. D., Ricke, S. C. (2001). Journal of Environmental Science and Health Part B Pesticides 36:699-708. The objectives of this study were to determine if indigenous male specific and somatic bacteriophages could be detected in animal feeds and if isolated phages contained RNA or DNA. Seven fresh feeds, 2 fresh feed ingredients, 7 stored feeds, 2 stored feed ingredients, and 8 samples of poultry diets suspected to contain Salmonella spp. were enriched and spot plated for indigenous phages using Escherichia coli Famp and CN-13 as hosts. Bacteriophage numbers were below detection without enrichment, but both male specific and somatic coliphages were detected in all animal feeds, feed ingredients, and poultry diets after 16 h of enrichment, even after the samples had been stored for 14 months of storage at -20 C. Five out of 9 fresh feeds and 7 out of 8 stored feeds contained RNA somatic phages

38. Filamentous bacteriophage stability in non-aqueous media. Olofsson, L., Ankarloo, J., Andersson, P. O., Nicholls, I. A. (2001). Chemistry and Biology 8:661-671. BACKGROUND: Filamentous bacteriophage are used as general cloning vectors as well as phage display vectors in order to study ligand-receptor interactions. Exposure to biphasic chloroform-water interface leads to specific contraction of phage, to non-infective I- or S-forms. RESULTS: Upon exposure, phage were inactivated (non-infective) at methanol, ethanol and 1-propanol concentrations inversely dependent upon alcohol hydrophobicity. Infectivity loss of phage at certain concentrations of 1-propanol or ethanol coincided with changes in the spectral properties of the f1 virion in ultraviolet fluorescence and circular dichroism studies. CONCLUSIONS: The alcohols inactivate filamentous phage by a general mechanism--solvation of coat protein--thereby disrupting the capsid in a manner quite different from the previously reported I- and S-forms. The infectivity retention of phagemid pG8H6 in 99% acetonitrile and the relatively high general solvent resistance of the phage strains studied here open up the possibility of employing phage display in non-aqueous media

39. [Bacteria-killing viruses, Stalinists and "superbugs"]. Olsen, I., Handal, T., Lokken, P. (2001). Tidsskrift for den Norske Laegeforening 121:3197-3200. In June 2000, the WHO warned that the level of resistance to drugs used to treat common infectious diseases is now reaching a crisis point. If world governments do not control infections better in order to slow down the development of drug resistance, entire populations could be wiped out by superbugs against which there is no efficient treatment. Development of resistance is due to both underuse and overuse of drugs, and strategies have been worked out, to slow down the development of resistance for instance by the Norwegian Ministry of Health and Social Affairs. The present article deals with an old principle, mainly developed behind the Iron Curtain, which is now attracting renewed attention in the west: the application of bacterial viruses (bacteriophages) in the fight against bacteria. According to clinical trials in Eastern Europe, mostly uncontrolled, phages have been used successfully in treatments against antibiotic-resistant bacteria, for instance in suppurative wound infections, gastroenteritis, sepsis, osteomyelitis and pneumonia. These encouraging data are supported by recent findings in well-controlled animal models demonstrating that phages can rescue animals from a variety of fatal infections. The present review discusses possible advantages and limitations of phage treatment in humans

40. Modeling virus inactivation on salad crops using microbial count data. Petterson, S. R., Teunis, P. F., Ashbolt, N. J. (2001). Risk Analysis 21:1097-1108. Microbial counts of the persistent Bacteroides fragilis bacteriophage B40-8 from a virus decay experiment conducted under glasshouse conditions were used to model the decay of viruses on wastewater-irrigated lettuce and carrot crops. The modeling approach applied gave specific consideration to the discrete nature of microbial count data. The experimental counts were best fit by a negative binomial distribution indicating highly dispersed distribution of viruses on lettuce and carrot crops following irrigation with wastewater. In addition, there was evidence for biphasic inactivation of viruses, signifying the presence of a persistent subpopulation of viruses that decayed slowly, resulting in virus accumulation on the crop surface over subsequent irrigations. Maximum likelihood estimates of initial and persistent subpopulation inactivation rates were 2.48 day(-1) and 0.51 day(-1) for lettuces and 0.84 day(-1) and 0.046 day(-1) for carrots. Maximum likelihood estimates of the persistent virus subpopulation size were 0.12% and 2% for lettuce and carrots, respectively

41. [Autoplaque formation in a Pseudomonas fluorescens strain: phage-like particles and transactivation of the defective phage]. Shaburova, O. V., Kurochkina, L. P., Krylov, V. N. (2001). Genetika 37:893-899. Natural bacteriophages of Pseudomonas fluorescens are rare and its temperate phages have not been described so far. In search for these phages, we have found that one of the P. fluorescens strains forms numerous small transparent autoplaques of different size and shape, which contained material reproducible on the same strains. When centrifuged in a cesium chloride gradient, this material yielded a band in the density zone of about 1.3 g/cm3, where protein components or bacteriophages with a relatively low content of nucleic acid are usually located. In the band material, electron microscopy revealed phagelike particles with empty and mostly undamaged heads and tails carrying in their distal region a formation resembling contracted sheath. DNA isolated from the preparation consisted of two components: a distinct 54-kb fragment, and a diffuse fragment ranging in size from 20 to 9.5 kb. Treatment of the large DNA fragment with various endonucleases yielded 42.2- and 29.5-kb fragments (on average for different endonucleases); whereas the same treatment of the diffuse fragment yielded two- to three distinct fragments with the overall molecular sizes of 8.9 and 6.2 kb (for different nucleases). We have suggested that cells harbor two different genetic elements whose interaction results in the autoplaque appearance and in the formation of negative colonies after infection with the autoplaque material. One of the two elements displays properties of a defective prophage with disturbed DNA synthesis and assembly, whereas the other exhibits the properties of a transposable phage. After complementation or some other interaction between these elements (transactivation, prophage induction caused by repressor inactivation), a bulk of defective phage particles devoid of DNA and a few DNA-containing particles were produced. It remains unclear whether both DNA types are contained in the same or different particles. The phage (or a system of elements) referred to as PT3 is noninducible. The phage mutants forming larger negative colonies (NCs) were also revealed. Some of bacterial mutants resistant to PT3 infection produce the mutant phage with small and turbid NCs. PT3 produces no NCs on the lawns of other strains of the same or other pseudomonade species. This is the first case of describing a natural temperate bacteriophage in P. fluorescens. The two different elements of this phage may represent the same genome of the defective prophage divided into two portions within a bacterial chromosome, each of which is capable of packaging into the phage head

42. Designing better phages. Skiena, S. S. (2001). Bioinformatics 17 Suppl 1:S253-S261. We propose a method to engineer the genome of bacteriophages to increase their effectiveness as antibacterial agents. Specifically, we exploit the redundancy of the triplet code to design genomes that avoid restriction sites while producing the same proteins as wild-type phages. We give an efficient algorithm to minimize the number of restriction sites against sets of cutter sequences, and demonstrate that that phage genomes can be significantly protected against surprisingly large sets of enzymes with no loss of function. Finally, we develop a model to explain why evolution has failed to eliminate many possible restriction sites despite selective pressure, thus motivating the need for genome-level sequence engineering

43. Inactivation of bacteriophages in water by means of non-ionizing (UV-253.7 nm) and ionizing (gamma) radiation: a comparative approach. Sommer, R., Pribil, W., Appelt, S., Gehringer, P., Eschweiler, H., Leth, H., Cabaj, A., Haider, T. (2001). Water Research 35:3109-3116. Thc inactivation behaviour of the bacteriophages PHI X 174 (ssDNA virus). MS2 (ssRNA virus) and B40-8 (dsDNA) toward non-ionizing (UV-253.7 nm) as well as to ionizing radiation (gamma radiation) was studied in order to evaluate their potential as viral indicators for water disinfection by irradiation. Previous findings of the high UV-253.7 nm resistance of MS2 were confirmed whereas an unexpected high sensitivity to gamma radiation compared to the two other phages was found. On the other hand, PHI X 174 revealed an enhanced UV sensitivity but a high resistance to ionizing radiation. B40-8 had an intermediate position between the other two bacteriophages relative to both types of radiation. As expected, the data of E. coli reconfirmed the unreliability of fecal indicator bacteria for the purpose of predicting responses of viruses to water treatment. In UV disinfection the influence of water matrix may be adequately controlled by considering the UV (253.7 nm) absorption of the water whereas so far no such parameter has existed for the influence of the water quality on ionizing irradiation with respect to the scavenger concentration

44. Characterization of a Shiga toxin-encoding temperate bacteriophage of Shigella sonnei. Strauch, E., Lurz, R., Beutin, L. (2001). Infection and Immunity 69:7588-7595. A Shiga toxin (Stx)-encoding temperate bacteriophage of Shigella sonnei strain CB7888 was investigated for its morphology, DNA similarity, host range, and lysogenization in Shigella and Escherichia coli strains. Phage 7888 formed plaques on a broad spectrum of Shigella strains belonging to different species and serotypes, including Stx-producing Shigella dysenteriae type 1. With E. coli, only strains with rough lipopolysaccharide were sensitive to this phage. The phage integrated into the genome of nontoxigenic S. sonnei and laboratory E. coli K-12 strains, which became Stx positive upon lysogenization. Moreover, phage 7888 is capable of transducing chromosomal genes in E. coli K-12. The relationships of phage 7888 with the E. coli Stx1-producing phage H-19B and the E. coli Stx2-producing phage 933W were investigated by DNA cross-hybridization of phage genomes and by nucleotide sequencing of an 8,053-bp DNA region of the phage 7888 genome flanking the stx genes. By these methods, a high similarity was found between phages 7888 and 933W. Much less similarity was found between phages H-19B and 7888. As in the other Stx phages, a regulatory region involved in Q-dependent expression is found upstream of stxA and stxB (stx gene) in phage 7888. The morphology of phage 7888 was similar to that of phage 933W, which shows a hexagonal head and a short tail. Our findings demonstrate that stx genes are naturally transferable and are expressed in strains of S. sonnei, which points to the continuous evolution of human-pathogenic Shigella by horizontal gene transfer

45. Community Structure: Viruses. Suttle, C. A. (2001). pp. 364-370 in Hurst, C. J., Knudson, G. R., McInerney, M. J., Stezenbach, L. D., Walter, M. V. (eds.) Manual of Environmental Microbiology (2nd Edition). ASM Press, Washington, DC.

46. Zoonotic Escherichia coli. Wasteson, Y. (2001). Acta Veterinaria Scandinavica Supplement 95:79-84. Escherichia coli is a normal inhabitant of the gastrointestinal tract of all warm-blooded animals, but variants of this species is also among the important etiological agents of enteritis and several extraintestinal diseases. The E. coli strains that cause diarrhoeal illness are categorised into pathogenicity groups based on virulence properties, mechanisms of pathogenicity, clinical symptoms and serology. The five main categories include enterotoxinogenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAggEC), enteroinvasive E. coli (EIEC) and Shiga (Vero) toxin-producing E. coli (STEC/VTEC). From a zoonotic point of view, STEC is the only E. coli pathogenicity group of major interest, as the shiga toxin-producing strains are able to cause severe disease in humans when being transmitted through the food chain from their animal reservoirs. The focus of this manuscript is therefore on STEC; pathogenicity factors, disease, the reservoirs and on-farm ecology, transmission into the food chain, growth and survival in food and in the environment, and the shiga toxin-encoding bacteriophages

47. Filamentous phage biology. Occurrence of coliphages in fish and aquaculture farms. Webster, R., Barbas, C. F., III, Burton, D. R., Scott, J. K., Silverman, G. J., Rao, B. M., Surendran, P. K. (2001). Phage display: A laboratory manual. 37:146-149. Coliphages were detected in water samples collected from brackish water and fresh water fish farms. Coliphages were also detected in the farmed fresh water fish, common carp and marine fish, oil sardine, from local market. Coliphage levels obtained were as follows:- water from brackish water fish farm 3 pfu.ml-1, water from fresh water fish farm 23 pfu.ml-1, fresh water fish 240 pfu.g-1 and marine fish 3500 pfu.g-1

48. A fast method for assessing rapid inactivation and adsorption kinetics of bacteriophages using batch agitation experiments and colloidal clay particles. Rossi, P., Aragno, M. (1999). Canadian Journal of Microbiology 45:9-17.

49. Different trajectories of parallel evolution during viral adaptation. Wichman, H. A., Badgett, M. R., Scott, L. A., Boulianne, C. M., Bull, J. J. (1999). Science 285:422-424. The molecular basis of adaptation is a major focus of evolutionary biology, yet the dynamic process of adaptation has been explored only piecemeal. Experimental evolution of two bacteriophage lines under strong selection led to over a dozen nucleotide changes genomewide in each replicate. At Least 96 percent of the amino acid substitutions appeared to be adaptive, and half the changes in one line also occurred in the other. However, the order of these changes differed between replicates, and parallel substitutions did not reflect the changes with the largest beneficial effects or indicate a common trajectory of adaptation.

50. Bacteriophage tracing techniques. Rossi, P., Käss, W. (1998). pp. 244-270 in Matthes, Käss (eds.) Tracing Techniques in Geohydrology. Balkema, Rotterdam.

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