Bacteriophage Ecology Group
Reference Abstracts (2000)
Dedicated to the ecology and evolutionary biology of the parasites of unicellular organisms (UOPs)
© Stephen T. Abedon
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© Phage et al. last updated on Wednesday, December 26, 2001
  1. The murky origin of Snow White and her T-even dwarfs. Abedon, S.T. (2000). Genetics 155:481-486. The T-even bacteriophages—T2, T4, and T6—represent facile experimental systems that are both relatively complex and meticulously well defined. They played essential roles in the birth and early nurturing of the field of molecular genetics, and could serve similarly as model organisms for ecology. Identification of the source habitat from which these phages were isolated would be satisfying from an ecological as well as historical perspective. Here I infer, mostly from published materials, the habitats from which these three phages were isolated, plus I delve into the history of their host, Eschcerichia coli B. [TOP OF PAGE]

  2. The evolution of pathogen-host interactions mediated by bacteriophages. Ai, Y.-C., Meng, F., Zeng, Y. (2000). Acta Microbiologica Sinica 40:657-661. [TOP OF PAGE]

  3. Phage resistance in Lactococcus lactis subsp. lactis strains isolated from traditional fermented milk products in Turkey. Akcelik, M., Sanlibaba, P., Tükel, C. (2000). International Journal of Food Science & Technology 35:473-481. Lactococcus lactis subsp. lactis strains isolated from traditional fermented milk products in Turkey were used to determine their phage resistance against three different lactic phages. The following modes of action were examined: phage adsorption inhibition in five strains, abortive infection (heat sensitive phage resistance) in three strains, restriction/modification in four strains and blocking of phage DNA injection in one strain. The genetic nature of the phage resistance systems in these strains was determined by comparison of phage proliferation parameters, e.g. adsorption (%), EOP, burst size, latent period and production of major capsid protein, between wild-type strains and their plasmid-cured derivatives. [TOP OF PAGE]

  4. Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri. Allison, G.E., Verma, N.K. (2000). Trends in Microbiology 8:17-23. O-antigen modification (serotype conversion) in Shigella flexneri, which is an important virulence determinant, is conferred by temperate bacteriophages. Several serotype-converting phages have been isolated and preliminary characterization has identified the genes involved in O-antigen modification, and has also provided insight into the molecular biology of these phages. [TOP OF PAGE]

  5. Inactivation of MS-2 phage and poliovirus in groundwater. Alvarez, M.E., Aguilar, M., Fountain, A., Gonzalez, N., Rascon, O., Saenz, D. (2000). Canadian Journal of Microbiology 46:159-165. Since temperature affects the inactivation rate of viruses in natural water systems, the aim of this study was to determine if a temperature shift could influence the structural integrity of model viruses. When crude lysates of MS-2 phage were seeded into groundwater microcosms and incubated at 27 degrees C, complete virus inactivation took place in eight days. The temperature was then shifted to 4 degrees C. Three days after the temperature shift, a two-log increase in virus titer (reactivation) occurred. However, when purified MS-2 lysates were added to groundwater microcosms, no reactivation was obtained. No reactivation of poliovirus took place when similar microcosm experiments were done. The sedimentation coefficients of MS-2 shifted from 80S to 58S, 48S, 37S, 32S, and 18S as inactivation proceeded in groundwater and distilled water controls. Similarly, the sedimentation coefficients of polioviruses changed from 156S to 142S, 135S, 117S, 105S, 95S, and 80 S as inactivation took place. There was no correlation between % virus inactivation and % decrease in virions with intact sedimentation coefficients, as reported earlier for poliovirus inactivated by chlorine. The results presented support our hypothesis that virus inactivation proceeds gradually, involving the rearrangement and (or) loss of capsomere components that may eventually lead to the ejection of nucleic acids. The intermediate particles generated as inactivation proceeds may be in a reversibly inactivated state, and may revert back to a fully infectious state when chemical components stabilize the virus particle. [TOP OF PAGE]

  6. Going through phages. Anonymous (2000). Science 290:227 [TOP OF PAGE]

  7. SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. Arnold, H.P., Ziese, U., Zillig, W. (2000). Virology 272:409-416. We describe a novel virus, SNDV (Sulfolobus neozealandicus droplet-shaped virus), of the crenarchaeotal archaeon Sulfolobus, which was found in a carrier state in a Sulfolobus strain isolated from a field sample from New Zealand. SNDV particles are droplet-shaped and densely covered by thin tail fibers at their pointed ends. The virion consists of a core and a coat. The latter has the appearance of a beehive and has a surface that is either helically ribbed or a stack of hoops. The genome is cccDNA of 20 kb, which is modified by dam-like methylation. It is cleaved by only a few type II restriction enzymes e.g., DpnI but not MboI, demonstrating an N(6)-methylation of the adenine residue in GATC sequences. The DNA-modifying system differentiates between virus and host. We postulate a virus-encoded methylase that is active on hemimethylated DNA. The host range of SNDV is confined to few Sulfolobus strains from New Zealand. The virus persists in an unstable carrier state rather than as a prophage. Due to its uniqueness we propose to assign it to a novel virus family termed Guttaviridae. Copyright 2000 Academic Press. [TOP OF PAGE]

  8. Seasonal population dynamics and interactions of competing bacteriophages and their host in the rhizosphere. Ashelford, K.E., Norris, S.J., Fry, J.C., Bailey, M.J., Day, M.J. (2000). Appl. Environ. Microbiol. 66:4193-4199. We describe two prolonged bacteriophage blooms within sugar beet rhizospheres ensuing from an artificial increase in numbers of an indigenous soil bacterium, Further, we provide evidence of in situ competition between these phages, This is the first in situ demonstration of such microbial interactions in soil, To achieve this, sugar beet seeds were inoculated with Serratia liquefaciens CP6RS or its lysogen, CP6RS-ly-Phi 1. These were sown, along with uninoculated seeds, in 36 field plots arranged in a randomized Latin square. The plots were then sampled regularly over 194 days, and the plants were assayed for the released bacteria and any infectious phages, Both the lysogen and nonlysogen forms of CP6RS survived equally well in situ, contradicting earlier work suggesting lysogens have a competitive disadvantage in nature. A Podoviridae phage, identified as Phi CP6-4, flourished on the nonlysogen-inoculated plants in contrast to those plants inoculated with the lysogen. Conversely, the Siphoviridae phage Phi CP6-1 (used to construct the released lysogen) was isolated abundantly from the lysogen-treated plants but almost never on the nonlysogen-inoculated plants. The uninoculated plants also harbored some Phi CP6-1 phage up to day 137, yet hardly any Phi CP6-4 phages were found, and this was consistent with previous years. We sinew that the different temporal and spatial distributions of these two physiologically distinct phages can be explained by application of optimal foraging theory to phage ecology. This is the first time that such in situ evidence has been provided in support of this theoretical model. [TOP OF PAGE]

  9. Experimental design optimization of filamentous phage transfection into mammalian cells by cationic lipids. Aujame, L., Seguin, D., Droy, C., Hessler, C. (2000). BioTechniques 28:1202-1213. A previous study showed that filamentous phage could be efficiently transfected into mammalian cells in the presence of the cationic lipid Transfectam. In the present study, we used an experimental plan based on a uniform network (Doehlert) matrix to estimate optimal transfection conditions in two different cell lines, CHO and Cos-7. Using the cationic lipid RPR120535b as a model, we show that optimal conditions can be determined much more readily than with standard response curves. Under optimal conditions as analyzed by FACS, up to 60% of Cos-7 and 50% of CHO cells can be transfected. Furthermore, a comparison of different lipids (Transfectam, RPR120535b, TC1-12 and GAP-DLRIE/DOPE) suggests that lipids with multiple amine groups are more efficient for the transfection of filamentous phage. [TOP OF PAGE]

  10. The presence of viruses and bacteria along the Adriatic Coast. Aulicino, F.A., Ammazzalorso, P., Ercolessi, M., Banini, L., Silverii, G., Orsini, P., Mastrantonio, A., Bellucci, C., Carere, M. (2000). Igiene Moderna 113:99-116. A study was carried out on seawater samples, collected from the Adriatic sea near the coast of Pesaro, to determine the presence of enteric viruses and Escherichia coli bacteriophages besides the common indicators of fecal pollution and of trophic conditions of the marine environment (Pseudomonas, Vibrio, algae). During 1994-95, seawater samples were tested in 8 stations located in seaside resorts; in 1994 samples of sediment were also analyzed. Generally the results showed a good situation from the microbiological and eutrophic point of view. Only 2 stations showed fecal pollution. Enteroviruses were not detected while Reovirus was isolated from samples of the two most contaminated stations and from a not polluted area. [TOP OF PAGE]

  11. Microbiological quality of the Catania coastal sea water. Aulicino, F.A., Mauro, L., Marranzano, M., Biondi, M., Ursino, A., Carere, M. (2000). Annali di Igiene 12:533-541. This study was carried out from 1997 to 1998 along a selected coastal area near Catania to ascertain bacteriological and virological quality of marine waters. 44 seawater samples, collected from 4 stations, were assayed for the presence of total and fecal coliforms, fecal streptococci, coliphages, Salmonellae and enteric viruses. Two stations localized at canal outfalls showed high levels of fecal pollution. The other stations were of good microbiological quality and showed a limited number of samples exceeding the standards laid down as guide values for bathing waters by Italian normative during the bathing period. Salmonellae were isolated in 8 out of 44 sea water samples (18%). Their presence was ascertained mainly in samples of the two polluted stations. Enteroviruses were not isolated. Enteric viruses such as Reoviruses were isolated from all stations, in 12 out of 44 samples (27%). The presence of these viruses was ascertained only during autumnal and winter seasons. The results of this study showed that, notwithstanding some stations showed high levels of bacteriological indicators of fecal pollution and presence of Salmonellae, enteroviruses growing on cell cultures were not isolated. Reoviruses confirmed their high diffusion in marine waters. [TOP OF PAGE]

  12. Application of wild starter cultures for flavour development in pilot plant cheese making. Ayad, E.H.E., Verheul, A., Wouters, J.T.M., Smit, G. (2000). International Dairy Journal 10:169-179. A number of wild lactococci of dairy and non-dairy origin which have the ability to produce unusual new flavours in model systems were studied with regard to various characteristics important for cheese making. All strains were found to be non-lysogenic and resistant to phages affecting strains present in commercial starters. Since the overall acidifying activity of many potentially interesting strains is rather low, they were used in combination with commercial starters. Defined-strain starter cultures (DSS) were prepared, composed of a combination of wild strains together with industrial strains, and tested in real cheese making (Gouda-type) experiments. The population dynamics of DSS were studied to understand the behaviour of the selected wild strains in the cheese environment. Wild strains showed various interactions with industrial strains in a defined-strain starter culture. Some wild strains, which were able to grow well together with industrial strains could be used relatively easily for practical applications. Other strains appeared to inhibit the growth of the industrial strains, due to the production of bacteriocins. In many cases the bacteriocin appeared to be nisin. Sensory evaluation revealed that the selected wild strains also produced typical flavours in a real cheese environment which corroborated the results obtained in model systems. GC/MS data confirmed the results of sensory evaluations. [TOP OF PAGE]

  13. A proposal for the reclassification of Bdellovibrio stolpii and Bdellovibrio starrii into a new genus, Bacteriovorax gen. nov. as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively. Baer, M.L., Ravel, J., Chun, J., Hill, R.T., Williams, H.N. (2000). Int J Syst Evol Microbiol 50 Pt 1:219-224. Bdellovibrios are unique bacteria with the ability to prey upon a wide variety of susceptible Gram-negative bacteria. Micro-organisms exhibiting this trait have been included in the genus Bdellovibrio despite their isolation from diverse habitats and relatively unstudied taxonomic relatedness. In this study, 16S rDNA sequences were compared from known terrestrial Bdellovibrio species, Bdellovibrio bacteriovorus 100T, Bdellovibrio stolpii Uki2T and Bdellovibrio starrii A3.12T in order to study their phylogenetic relationship. The two sequences from B. stolpii Uki2T and B. starrii A3.12T were 90.0% similar to each other but exhibited only 81.7% and 81.2% similarity, respectively to B. bacteriovorus 100T. Phylogenetic analysis indicated that B. bacteriovorus 100T clustered in a separate clade from B. starrii A3.12T and B. stolpii Uki2T, demonstrating only a distant relationship between B. bacteriovorus 100T and the other two recognized type species. DNA-DNA hybridization experiments also demonstrated <4% hybridization between these three species. On the basis of the results obtained from the phylogenetic analysis and DNA-DNA hybridization studies, it is proposed that B. stolpii Uki2T and B. starrii A3.12T should be transferred to a new genus, Bacteriovorax gen. nov. as Bacteriovorax stolpii comb. nov. and Bacteriovorax starrii comb. nov., respectively. It is also proposed that the type species for the new genus Bacteriovorax should be Bacteriovorax stolpii comb. nov. [TOP OF PAGE]

  14. Light scattering by viral suspensions. Balch, W.M., Vaughn, J., Novotny, J., Drapeau, D.T., Vaillancourt, R., Lapierre, J., Ashe, A. (2000). Limnol. Oceanogr. 45:492-498. Viruses represent one of the most abundant, ocean-borne particle types and have significant potential for affecting optical backscattering. Experiments addressing the light-scattering properties of viruses have heretofore not been conducted. Here we report the results of laboratory experiments in which the volume-scattering functions of several bacterial viruses (bacteriophages) were measured at varying concentrations with a laser light-scattering photometer using a He-Ne and/or Argon ion laser (632.8 and 514.0 nm, respectively). Four bacterial viruses of varying size were examined, including the coliphages MS-2 (capsid size 25-30 nm) and T-4 (capsid size apprx100 nm), and marine phages isolated from Saco Bay, Maine (designation Y-1, capsid size 50-80 nm) and Boothbay Harbor, Maine (designation C-2, capsid size apprx110 nm). Volume-scattering functions (VSFs) were fitted with the Beardsley-Zaneveld function and then integrated in the backward direction to calculate backscattering cross section. This was compared to the virus geometric cross section as determined by transmission electron microscopy and flow-field fractionation. Typical backscattering efficiencies varied from 20 X 10-6 to 1,000 X 10-6. Data on particle size and backscattering efficiencies were incorporated into Mie scattering calculations to estimate refractive index of viruses. The median relative refractive index of the four viruses was apprx1.06. Results presented here suggest that viruses, while highly abundant in the sea, are not a major source of backscattering. [TOP OF PAGE]

  15. Evolution of life's fringes. Balter, M. (2000). Science 289:1866-1867. Fresh evidence that viruses have existed for billions of years has scientists wondering what role these stripped-down microbes played in evolution. [TOP OF PAGE]

  16. A bacteriophage-like particle from Bartonella bacilliformis. Barbian, K.D., Minnick, M.F. (2000). Microbiology 146 ( Pt 3):599-609. Bartonella bacilliformis and Bartonella henselae, the respective agents of Oroya fever and cat-scratch disease in humans, are known to produce bacteriophage-like particles (BLPs) that package 14 kbp segments of the host chromosome. Data from this study suggest that other Bartonella species including Bartonella quintana, Bartonella doshiae and Bartonella grahamii also contain similar BLPs, as evidenced by the presence of a 14 kbp extrachromosomal DNA element in their genomes, whereas Bartonella elizabethae and Bartonella clarridgeiae do not. A purification scheme utilizing chloroform, DNase I and centrifugation was devised to isolate BLPs from B. bacilliformis. Intact BLPs were observed by transmission electron microscopy and were round to icosahedral in shape and approximately 80 nm in diameter. RFLP and Southern blot analysis of BLP DNA from B. bacilliformis suggest that packaging, while non-selective, is less than the near-random packaging previously reported for the B. henselae phage. Data also suggest that the linear, double-stranded BLP DNA molecules have blunt ends with noncovalently closed termini. Packaging of the BLP DNA molecules into a protein coat appears to be closely related to nucleic acid synthesis, as unpackaged phage DNA is not detectable within the host cell. SDS-PAGE analysis of purified BLPs from B. bacilliformis showed three major proteins with apparent molecular masses of 32, 34 and 36 kDa; values that closely correspond to proteins found in B. henselae BLPs. Western blot analysis performed with patient convalescent serum showed that BLP proteins are slightly immunogenic in humans. To determine if BLPs contribute to horizontal gene transfer, mutants of B. bacilliformis were generated by allelic exchange with an internal fragment of the 16S-23S rDNA intergenic spacer region and a suicide vector construct, termed pKB1. BLPs from one of the resultant strains were able to package the mutagenized region containing the kanamycin-resistance cassette; however, numerous approaches and attempts at intraspecies transduction using these BLPs were unsuccessful. [TOP OF PAGE]

  17. A shared strategy for virulence. Barinaga, M. (2000). Science 272:1261-1263. [TOP OF PAGE]

  18. Diversity in the arrangement of the CTX prophages in classical strains of Vibrio cholerae O1. Basu, A., Mukhopadhyay, A.K., Garg, P., Chakraborty, S., Ramamurthy, T., Yamasaki, S., Takeda, Y., Nair, G.B. (2000). FEMS Microbiol. Let. 182:35-40. This study reports the results of a molecular analysis of the CTX prophages in classical biotype strains of Vibrio cholerae O1 of clinical origin isolated between 1970 and 1979 in India. All strains were sensitive to group IV classical phage and polymyxin B but resistant to group 5 El Tor phage. These phenotypic traits are consistent to that exhibited by the classical biotype. PCR studies reconfirmed their biotype assignment and showed the presence of intact CTX prophages and the presence of the recently described toxin linked cryptic plasmid. Restriction fragment length polymorphism of rRNA genes and pulsed-field gel electrophoresis showed clonal diversity among the strains. The most notable observation was the finding that one strain (GP13) has three CTX prophages while another (GP147) has four CTX prophages. This is the first time heterogeneity is reported in the arrangement of the CTX prophages among classical strains of V. cholerae O1. [TOP OF PAGE]

  19. 'Deja vu all over again': the similar structures of bacteriophage PRD1 and adenovirus. Belnap, D.M., Steven, A.C. (2000). Trends in Microbiology 8:91-93. [TOP OF PAGE]

  20. The complete cDNA sequence of a type II Trichomonas vaginalis virus. Bessarab, I.N., Liu, H.W., Ip, C.F., Tai, J.H. (2000). Virology 267:350-359. Trichomonas vaginalis viruses (TVV), which may regulate P270 gene expression in the protozoan pathogen T. vaginalis, are a group of divergent double-stranded (ds) RNA viruses. In the present study, the complete 4674-bp cDNA sequence of a 4.6-kb ds RNA from a newly identified TVV2-1 isolate was determined. The sequence of the plus-strand mRNA contains four open reading frames, which encode overlapping cap and pol genes in the reading frame 2 and reading frame 1, respectively, and two putative serine-threonine-rich basic proteins VP3 and VP4 in the third reading frame. An 85-kDa capsid protein and a 160-kDa CAP-POL fusion protein were identified in crude viruses by Western blotting experiments using antisera raised against gene-specific oligopeptides. In conjunction with the presence of a potential ribosomal slippery heptanucleotide G GGC CCC within the overlap of the cap and pol genes, these observations suggest that the pol gene of TVV2-1 is translated via a -1 ribosomal frameshifting event during translation of the cap gene. Our results also provide insight into the conservation among divergent dsRNA species from TVV and suggest that the genome of TVV2-1 may encode two extra genes in addition to the cap and pol genes. Copyright 2000 Academic Press. [TOP OF PAGE]

  21. A comparison of methods for counting viruses in aquatic systems. Bettarel, Y., Sime-Ngando, T., Amblard, C., Laveran, H. (2000). Appl. Environ. Microbiol. 66:2283-2289. In this study, we compared different methods-including transmission electron microscopy-and various nucleic acid labeling methods in which we used the fluorochromes 4',6'-diamidino-2-phenylindole (DAPI), 4-[3-methyl-2,3-dihydro-(benzo-1, 3-oxazole)-2-methylmethyledene]-1-(3'-trimethyl ammoniumpropyl)-quinilinium diioide (YOPRO-1), and SYBR Green I, which can be detected by epifluorescence microscopy (EM), for counting viruses in samples obtained from freshwater ecosystems whose trophic status varied and from a culture of T7 phages. From a quantitative and qualitative viewpoint, our results showed that the greatest efficiency for all ecosystems was obtained when we used the EM counting protocol in which YOPRO-1 was the label, as this fluorochrome exhibited strong and very stable fluorescence. A modification of the original protocol in which YOPRO-1 was used is recommended, because this modification makes the protocol faster and allows it to be used for routine analysis of fixed samples. Because SYBR Green I fades very quickly, the use of this fluorochrome is not recommended for systems in which the viral content is very high (>108 particles/ml), such as treated domestic sewage effluents. Experiments in which we used DNase and RNase revealed that the number of viruses determined by EM was slightly overestimated (by approximately 15%) because of interference caused by the presence of free nucleic acids. [TOP OF PAGE]

  22. Thermal and chemical inactivation of indigenous Streptococcus thermophilus bacteriophages isolated from Argentinian dairy plants. Binetti, A.G., Reinheimer, J.A. (2000). Journal of Food Protection 63:509-515. Thermal and chemical resistance of five autochthonal bacteriophages of Streptococcus thermophilus, isolated from Cuartirolo cheese wheys and yogurt, was investigated. Times to obtain 99% inactivation of phages (T99) at 63 degrees C and 72 degrees C in three suspension media (enriched tryptic soy broth, reconstituted commercial nonfat skim milk, and tris magnesium gelatin buffer) were determined. The thermal resistance was dependent on the phages studied but not detectable counts (<10 PFU/ml) were only achieved by heating at 90 degrees C during 5 min. The data obtained for the three assayed media did not permit verifying significant differences among them. Sodium hypochlorite (100 ppm) provided a fast inactivation of bacteriophage particles (<10 PFU/ml after 5 min). Ethanol, at concentrations of 75% and 100%, was also effective for phage destruction. Isopropanol was slightly less effective than ethanol at the same concentrations. Peracetic acid (0.15%) was also a very effective agent for phage inactivation. The results showed that these autochthonal bacteriophages were not completely inactivated neither by normal pasteurization treatments nor by some biocides commonly used in disinfection, except sodium hypochlorite and peracetic acid. The practical implications of these findings have pointed out the necessity of recognizing the importance of establishing adequate conditions to assure effective thermal and chemical treatments in dairy plants and laboratory environments. [TOP OF PAGE]

  23. Characterization of mesophilic mixed starter cultures used for the manufacture of aged cheddar cheese. Bissonnette, F., Labrie, S., Deveau, H., Lamoureux, M., Moineau, S. (2000). Journal of Dairy Science 83:620-627. Seventy-one different Lactococcus lactis subsp. cremoris strains were isolated from seven mesophilic mixed starters used in the manufacture of aged Cheddar cheese in Canada. Based on plasmid profiles and growth in milk (with or without glucose, Casamino Acids or both), two mixed starters were highly heterogeneous, containing at least 18 to 24 distinct L. lactis strains. Three mixed starters were comprised of seven to nine strains, whereas two starters were relatively homogeneous, containing two or three strains. Many strains with similar plasmid profiles behaved differently during growth in milk, indicating variability in the phenotypes. Only 20% of the strains could grow in plain milk, whereas 30% could not grow in milk supplemented with glucose and Casamino Acids. Twenty-five lactococcal bacteriophages were also isolated from whey samples with single strains as hosts. Eighteen phages belonged to the 936 species and seven to the c2 species. Thirteen strains were insensitive to all 25 phages. Almost all sensitive strains were phage species-specific. The 936-like phages had a broader host range. [TOP OF PAGE]

  24. Low-frequency transduction of imipenem resistance and high-frequency transduction of ceftazidime and aztreonam resistance by the bacteriophage AP-151 isolated from a Pseudomonas aeruginosa strain. Blahova, J., Kralikova, K., Krcmery, V., Sr., Jezek, P. (2000). JOURNAL OF CHEMOTHERAPY 12:482-486. Bacteriophage AP-151, isolated from a multidrug resistant Pseudomonas aeruginosa strain, was found to transduce antibiotic resistance determinants to recipient strains of P. aeruginosa. Resistance to cefotaxime, ceftazidime, aztreonam, imipenem and meropenem was transduced as a block, at different frequencies, to two P. aeruginosa strains. Resistance was two logarithms higher (in the range 10-5) for cefotaxime, ceftazidime or aztreonam than for imipenem in recipient strain PAO-1670. The frequency of transduced imipenem resistance was also lower in recipient strain ML-1008. This phenomenon reflects the difference in the lytic activity of AP-151 in both strains, as the titer of the AP-151 phage in the PAO strain was found to be restricted to 10-4-10-5 in contrast to the titer of the same phage in the ML strain which was 10-10. The limited lytic activity in the PAO recipient strain was correlated with higher transducing activity. It can be concluded that some wild-type bacteriophages of P. aeruginosa might have highly individual relations between lytic and transducting activity in various potential recipient nosocomial strains of P. aeruginosa. The nature of resistance to ceftazidime and imipenem was studied using clavulanate and EDTA as inhibitors of individual class of beta-lactamases, indicating the presence of extended-spectrum beta-lactamase and a metallo-beta-lactamase in this isolate. [TOP OF PAGE]

  25. The relative importance of competition and predation varies with productivity in a model community. Bohannan, B.J.M., Lenski, R.E. (2000). Am. Nat. 156:329-340. Recent theory predicts that productivity can influence the relative importance of predation and competition in determining patterns in abundance, diversity, and community structure. In low-productivity systems, competition is predicted to be the major influence on community patterns, while at high productivity, the major influence is predicted to be predation. We directly tested this theory using a laboratory model community. Our model community consisted of the bacteriophage T2 (a virus that feeds on Escherichia coli) and two populations of E. coli, in glucose-limited chemostats. One E. coli population consisted of individuals that were sensitive to predation by T2 ("vulnerable" E. coli), and the other population consisted of individuals that were partially resistant to predation by T2 ("less vulnerable" E. coli). We manipulated productivity in this experiment by running replicate chemostats with different input concentrations of glucose. Our observations were consistent with theoretical predictions. We observed the decline of the more vulnerable prey population at higher productivity but not at lower productivity, and the decline of the less vulnerable prey population at lower productivity but not at higher productivity. However, the rate of decline in some replicates was slower than predicted, and extinctions were not observed during the experiments, contrary to theoretical predictions. We present some testable hypotheses that might explain the slow rate of decline observed. [TOP OF PAGE]

  26. Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage. Bohannan, B.J.M., Lenski, R.E. (2000). Ecological Letters 3:362-377. A major goal of community ecology is to link biological processes at lower scales with community patterns. Microbial communities are especially powerful model systems for making these links. In this article, we review recent studies of laboratory communities of bacteria and bacteriophage (viruses that infect bacteria). We focus on the ecology and evolution of bacteriophage-resistance as a case study demonstrating the relationship between specific genes, individual interactions, population dynamics, community structure, and evolutionary change. In laboratory communities of bacteria and bacteriophage, bacteria rapidly evolve resistance to bacteriophage infection. Different resistance mutations produce distinct resistance phenotypes, differing, for example, in whether resistance is partial or complete, in the magnitude of the physiological cost associated with resistance, and in whether the mutation can be countered by a host-range mutation in the bacteriophage. These differences determine whether a mutant can invade, the effect its invasion has on the population dynamics of sensitive bacteria and phage, and the resulting structure of the community. All of these effects, in turn, govern the community's response to environmental change and its subsequent evolution. [TOP OF PAGE]

  27. Integrated management of bacterial leaf spot of mungbean with bacteriophages of Xav and chemicals. Borah, P.K., Jindal, J.K., Verma, J.P. (2000). Journal of Mycology and Plant Pathology 30:19-21. The population of Xanthomonas axonopodis pv vignaeradiatae (Xav) was completely eliminated from mungbean seeds by lytic action of bacteriophage (XMP-1) and streptomycin when the seeds were treated with Xav, phages and streptomycin at a ratio/concentration of 1: 60 + 300 mug ml-1. These results confirmed the synergistic action between phage (XMP-1) and streptomycin, as their combination could eradicate Xav from mungbean seeds at a much lower concentration as compared to when used singly. Moreover, the seed treatment with phage lysate + streptomycin 300 mug ml-1 was also found most effective in checking seedling infection of mungbean by Xav. The seedling infection was 4 per cent as compared to 68 per cent in control. The percentage of seed germination was also increased to 86 per cent in comparison to 75 per cent in control. [TOP OF PAGE]

  28. Pressure cycling technology: a novel approach to virus inactivation in plasma. Bradley, D.W., Hess, R.A., Tao, F., Sciaba-Lentz, L., Remaley, A.T., Laugharn, J.J., Manak, M. (2000). Transfusion 40:193-200. BACKGROUND: Hydrostatic-pressure virus inactivation is a novel approach to the inactivation of pathogens in plasma and blood-derived components, that retains the therapeutic properties of these products. STUDY DESIGN AND METHODS: A custom-built apparatus was used to pressurize human plasma samples spiked with lambda phage. Phage titer and plasma protein activities were monitored after pressure treatment. RESULTS: Pressure-mediated inactivation of lambda phage was found to be an effective means for virus inactivation, particularly when performed at near-zero (0 degrees C) temperatures, rather than at temperatures above 20 degrees C and below -40 degrees C. The efficiency of inactivation was improved by an increase in applied pressure and repeated cycling from atmospheric to high pressure. In contrast, activities of plasma proteins alkaline phosphatase and total amylase did not vary with temperature and remained within 29 percent and 6 percent, respectively, of starting values after the same pressure treatments. By combining cycling, near-zero temperatures, and high pressure, phage titers in serum were reduced approximately 6 log after 10 to 20 minutes of treatment. Activities of plasma proteins IgG, IgM, and factor X were at 104 percent, 89 percent, and 80 percent, respectively, of starting values after 20 minutes of the same temperature and pressure treatment. CONCLUSION: High-pressure procedures may be useful for the inactivation of viruses in blood and other protein-containing components. [TOP OF PAGE]

  29. Viruses of fungi and protozoans: Is everyone sick? Bruenn, J.A. (2000). pp. 297-317. In In Hurst, C.J. (ed.), Viral Ecology. Academic Press, San Diego. [no abstract?[. [TOP OF PAGE]

  30. Flow cytometric detection of viruses. Brussaard, C.P.D., Marie, D., Bratbak, G. (2000). Journal of Virological Methods 85:175-182. Representatives from several different virus families (Baculoviridae, Herpesviridae, Myoviridae, Phycodnaviridae, Picornaviridae, Podoviridae, Retroviridae, and Siphoviridae) were stained using a variety of highly fluorescent nucleic acid specific dyes (SYBR Green I, SYBR Green II, OliGreen, PicoGreen) and examined using a standard flow cytometer equipped with a standard 15 mW argon-ion laser. The highest green fluorescence intensities were obtained using SYBR Green I. DNA viruses with genome sizes between 48.5 and 300 kb could easily be detected. The fluorescence signals of the small genome-sized RNA viruses (7.4–14.5 kb) were found at the limit of detection. No significant linear relationship could be found between genome size and the green fluorescence intensity of the SYBR Green I stained virus preparations. To our knowledge, this is the first report of detecting and discriminating between a wide range of different viruses directly using flow cytometry. This rapid and precise assay represents a new and promising tool in the field of virology. [TOP OF PAGE]

  31. Big-benefit mutations in a bacteriophage inhibited with heat. Bull, J.J., Badgett, M.R., Wichman, H.A. (2000). Molecular Biology and Evolution 17:942-950. High temperature inhibits the growth of the wild-type bacteriophage phiX174. Three different point mutations were identified that each recovered growth at high temperature. Two affected the major capsid protein (residues F188 and F242), and one affected the internal scaffolding protein (B114). One of the major capsid mutations (F242) is located in a beta strand that contacts B114 in the procapsid during viral maturation, whereas the other capsid mutation (F188) is involved in subunit interactions at the threefold axis of symmetry. Selective coefficients of these mutations ranged from 13.9 to 3.8 in the inhibitory, hot environment, but all mutations reduced fitness at normal temperature. The selective effect of one of the mutations (F242) was evaluated at high temperature in four different genetic backgrounds and exhibited epistasis of diminishing returns: as log fitness of the background genotype increased from -0.1 to 4.1, the fitness boost provided by the F242 mutation decreased from 3.9 to 0. 8. These results support a model in which viral fitness is bounded by an upper limit and the benefit of a mutation is scaled according to the remaining opportunity for fitness improvement in the genome. [TOP OF PAGE]

  32. Evolvability of an RNA virus is determined by its mutational neighbourhood. Burch, C.L., Chao, L. (2000). Nature 406:625-628. The ubiquity of mechanisms that generate genetic variation has spurred arguments that evolvability, the ability to generate adaptive variation, has itself evolved in response to natural selection. The high mutation rate of RNA viruses is postulated to be an adaptation for evolvability, but the paradox is that whereas some RNA viruses evolve at high rates, others are highly stable. Here we show that evolvability in the RNA bacteriophage phi6 is also determined by the accessibility of advantageous genotypes within the mutational neighbourhood (the set of mutants one or a few mutational steps away). We found that two phi6 populations that were derived from a single ancestral phage repeatedly evolved at different rates and toward different fitness maxima. Fitness measurements of individual phages showed that the fitness distribution of mutants differed between the two populations. Whereas population A, which evolved toward a higher maximum, had a distribution that contained many advantageous mutants, population B, which evolved toward a lower maximum, had a distribution that contained only deleterious mutants. We interpret these distributions to measure the fitness effects of genotypes that are mutationally available to the two populations. Thus, the evolvability of phi6 is constrained by the distribution of its mutational neighbours, despite the fact that this phage has the characteristic high mutation rate of RNA viruses. [TOP OF PAGE]

  33. Selective accumulation may account for shellfish-associated viral illness. Burkhardt, W., Calci, K.R. (2000). Appl. Environ. Microbiol. 66:1375-1378. From 1991 through 1998, 1,266 cases of shellfish-related illnesses were attributed to Norwalk-like viruses. Seventy-eight percent of these illnesses occurred following consumption of oysters harvested from the Gulf Coast during the months of November through January. This study investigated the ability of eastern oysters (Crassostrea virginica) to accumulate indicator microorganisms (i.e., fecal coliforms, Escherichia coli, Clostridium perfringens, and F(+) coliphage) from estuarine water. One-week trials over a 1-year period were used to determine if these indicator organisms could provide insight into the seasonal occurrence of these gastrointestinal illnesses. The results demonstrate that oysters preferentially accumulated F(+) coliphage, an enteric viral surrogate, to their greatest levels from late November through January, with a concentration factor of up to 99-fold. However, similar increases in accumulation of the other indicator microorganisms were not observed. These findings suggest that the seasonal occurrence of shellfish-related illnesses by enteric viruses is, in part, the result of seasonal physiological changes undergone by the oysters that affect their ability to accumulate viral particles from estuarine waters. [TOP OF PAGE]

  34. Inactivation of indicator microorganisms in estuarine waters. Burkhardt, W., III, Calci, K.R., Watkins, W.D., Rippey, S.R., Chirtel, S.J. (2000). Water Res. 34:2207-2214. In the United States, shellfish growing areas are classified, in part, using standards based on the densities of either the total or fecal coliform groups in surface waters. However, the standards currently employed may not reliably index the presence of certain enteric pathogens, particularly enteric viruses responsible for human illnesses, even though both the pathogens and indicators derive from the same fecal contamination. To some extent, this may be due to differences in the survival of these pathogens in the environment relative to that of the bacterial indicators. This investigation was conducted to assess the effects of temperature, salinity, dissolved oxygen, geographic location, season, and solar radiation on the survival of selected indicator microorganisms in estuarine waters. The indicators examined included fecal coliforms, Escherichia coli, Clostridium perfringens, and male-specific bacteriophage (MSB), a potential indicator of enteric viruses. In situ experiments were performed in estuarine waters of Alabama and Rhode Island. Among the parameters examined, sunlight and/or temperature most significantly affected indicator decay rates. In general, the effects from exposure to sunlight accounted for up to 83, 84, and 99% of the density reductions of MSB, C. perfringens and fecal coliforms, respectively. Thus, the effects from sunlight were greatest on fecal coliforms and much less pronounced on MSB and C. perfringens. For fecal coliforms, the effect of sunlight was more pronounced during the winter than the summer. In the absence of sunlight, the rate of MSB decline was strongly negatively correlated with estuarine water temperatures and dissolved oxygen. Overall, fecal coliform decay rates were dissimilar to those found for MSB. From this, it would appear that fecal coliforms may not be reliable indicators of viruses in estuarine waters. [TOP OF PAGE]

  35. Mathematical analysis of growth and interaction dynamics of streptomycetes and a bacteriophage in soil. Burroughs, N.J., Marsh, P., Wellington, E.M.H. (2000). Appl. Environ. Microbiol. 66:3868-3877. We observed the infection cycle of the temperate actinophage KC301 in relation to the growth of its host Streptomyces lividans TK24 in sterile soil microcosms. Despite a large increase in phage population following germination of host spores, there was no observable impact on host population numbers as measured by direct plate counts. The only change in the host population following infection was the establishment of a small subpopulation of KC301 lysogens. The interaction of S. lividans and KC301 in soil was analyzed with a population-dynamic mathematical model to determine the underlying mechanisms of this low susceptibility to phage attack relative to aquatic environments. This analysis suggests that the soil environment is a highly significant component of the phage-host interaction, an idea consistent with earlier observations on the importance of the environment in determining host growth and phage-host dynamics. Our results demonstrate that the accepted phage-host interaction and host life cycle, as determined from agar plate studies and liquid culture, is sufficient for quantitative agreement with observations in soil, using soil-determined rates. There are four significant effects of the soil environment: (i) newly germinated spores are more susceptible to phage lysis than are hyphae of developed mycelia, (ii) substrate mycelia in mature colonies adsorb about 98% of the total phage protecting susceptible young hyphae from infection, (iii) the burst size of KC301 is large in soil (> 150, 90% confidence) relative to that observed in liquid culture (120, standard error of the mean (SEM), 6), and (iv) there is no measurable impact on the host in terms of reduced growth by the phage. We hypothesize that spatial heterogeneity is the principal cause of these effects and is the primary determinant in bacterial escape of phage lysis in soil. [TOP OF PAGE]

  36. Large-plaque mutants of Sindbis virus show reduced binding to heparan sulfate, heightened viremia, and slower clearance from the circulation. Byrnes, A.P., Griess, G.A. (2000). J. Virol. 74:644-651. Laboratory strains of Sindbis virus must bind to the negatively charged glycosaminoglycan heparan sulfate in order to efficiently infect cultured cells. During infection of mice, however, we have frequently observed the development of large-plaque viral mutants with a reduced ability to bind to heparan sulfate. Sequencing of these mutants revealed changes of positively charged amino acids in putative heparin-binding domains of the E2 glycoprotein. Recombinant viruses were constructed with these changes as single amino acid substitutions in a strain Toto 1101 background. All exhibited decreased binding to heparan sulfate and had larger plaques than Toto 1101. When injected subcutaneously into neonatal mice, large-plaque viruses produced higher-titer viremia and often caused higher mortality. Because circulating heparin-binding proteins are known to be rapidly sequestered by tissue heparan sulfate, we measured the kinetics of viral clearance following intravenous injection. Much of the parental small-plaque Toto 1101 strain of Sindbis virus was cleared from the circulation by the liver within minutes, in contrast to recombinant large-plaque viruses, which had longer circulating half-lives. These findings indicate that a decreased ability to bind to heparan sulfate allows more efficient viral production in vivo, which may in turn lead to increased mortality. Because Sindbis virus is only one of a growing number of viruses from many families which have been shown to bind to heparan sulfate, these results may be generally applicable to the pathogenesis of such viruses. [TOP OF PAGE]

  37. Effect of five dietary antimutagens on the genotoxicity of six mutagens in the microscreen prophage-induction assay. Cabrera, G. (2000). Environmental and Molecular Mutagenesis 36:206-220. Dietary antimutagens have been studied extensively in the last two decades, using mainly bacterial and mammalian cells. These studies have shown that certain dietary antimutagens, acting individually or as mixtures, are useful in counteracting the effects of certain mutagens and/or carcinogens to which humans are commonly exposed. However, there are some inconsistencies among publications using different bioassays. The general purpose of the research presented here was to conduct a comparative study of the antigenotoxic activity of five dietary antimutagens against six mutagens, using three rather different short-term tests: the Microscreen prophage-induction assay, the Tradescantia micronucleus test, and the Salmonella/mammalian microsome test. In this study I report the results with the Microscreen prophage-induction assay. The antimutagens selected were chlorophyllin, beta-carotene, and vitamins A, C, and E. The mutagens selected were 2-aminoanthracene, benzo[a]pyrene, 2-nitrofluorene, toxaphene, dichlorvos, and nitrofen. The results show that chlorophyllin and beta-carotene inhibited the genotoxicity of all six mutagens; vitamin E inhibited all except dichlorvos; and vitamins C and A inhibited 2-aminoanthracene, benzo[a]pyrene, 2-nitrofluorene, and nitrofen. [TOP OF PAGE]

  38. Lateral gene transfer in prokaryotes. Campbell, A.M. (2000). Theor. Pop. Biol. 57:71-77. Evolutionists have traditionally depicted organismal descent on a tree, where all lineages branch from a com- mon ancestor. Such a tree phylogeny implies that all genetic traits within a lineage are derived from its founder. Lateral (horizontal) gene transfer negates this exclusive relationship between ancestor and descendants by the introduction into a lineage of genes originating elsewhere. [TOP OF PAGE]

  39. Helicobacter pylori-antigen-binding fragments expressed on the filamentous M13 phage prevent bacterial growth. Cao, J., Sun, Y., Berglindh, T., Mellgard, B., Li, Z., Mardh, B., Mardh, S. (2000). Biochim. Biophys. Acta 1474:107-113. Colonization of the human stomach by Helicobacter pylori is associated with the development of gastritis, duodenal ulcer, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric cancer. H. pylori-antigen-binding single-chain variable fragments (ScFv) were derived from murine hybridomas producing monoclonal antibodies and expressed as a g3p-fusion protein on a filamentous M13 phage. The recombinant ScFv-phage reacted specifically with a 30-kDa monomeric protein of a H. pylori surface antigen preparation and by means of immunofluorescence microscopy the phage was shown to bind to both the spiral and coccoid forms of the bacterium. In vitro, the recombinant phage exhibited a bacteriocidal effect and inhibited specifically the growth of all the six strains of H. pylori tested. When H. pylori was pretreated with the phage 10 min before oral inoculation of mice, the colonization of the mouse stomachs by the bacterium was significantly reduced (P<0.01). The results suggest that genetic engineering may be used to generate therapy-effective phages. [TOP OF PAGE]

  40. Transport and retention of bacteriophages in two types of willow-cropped lysimeters. Carlander, A., Aronsson, P., Allestam, G., Stenstrom, T.A., Perttu, K. (2000). Journal of Environmental Science and Health Part A Toxic-Hazardous Substances & Environmental Engineering A35:1477-1492. Irrigation and fertilization of short-rotation willow coppice with wastewater is a new way of reusing wastewater in Sweden. To evaluate the possible impact of viruses on groundwater quality, the transport and retention of the bacteriophage Salmonella Typhimurium type 28B were studied in two types of willow-cropped field lysimeters containing clay or sand soil. Phages were applied to the soil surface and moderate irrigation was done daily under field-like conditions. In the clay, soil rapid transport of bacteriophages was recorded with breakthrough at 1.2-m depth after 2-24 hours indicating macropore flow through the soil. Phage transport through the sand oil varied considerably, but was in general much slower and the phage retention much higher compared with the clay soil. The willow plants were not found to facilitate phage leaching. Instead, the results indicate the presence of phage retaining processes in the rhizosphere. [TOP OF PAGE]

  41. Development and evaluation of a phage typing scheme for Vibrio cholerae O139. Chakrabarti, A.K., Ghosh, A.N., Nair, G.B., Niyogi, S.K., Bhattacharya, S.K., Sarkar, B.L. (2000). Journal of Clinical Microbiology 38:44-49. The scenario of cholera that existed previously changed in 1992 and 1993 with the emergence of toxigenic Vibrio cholerae O139 in India. The genesis of the new serogroup formed the impetus to search for O139 phages in and around the country. A total of five newly isolated phages lytic to V. cholerae O139 strains were used for the development of this phage typing scheme. These phages differed from each other and also differed from the existing O1 phages in their lytic patterns, morphologies, restriction endonuclease digestion profiles, and immunological criteria. With this scheme, 500 V. cholerae O139 strains were evaluated for their phage types, and almost all strains were found to be typeable. The strains clustered into 10 different phage types, of which type 1 (38.2%) was the dominant type, followed by type 2 (22.4%) and type 3 (18%). Additionally, a comparative study of phage types in 1993 and 1994 versus those from 1996 to 1998 for O139 strains showed a higher percentage of phage type 1 (40.5%), followed by type 3 (18.8%) during the period between 1993 and 1994, whereas phage type 2 (32. 1%) was the next major type during the period from 1996 to 1998. This scheme comprising five newly isolated phages would be another useful tool in the study of the epidemiology of cholera caused by V. cholerae O139. [TOP OF PAGE]

  42. Genome organization and the evolution of the virulence gene locus in Listeria species. Chakraborty, T., Hain, T., Domann, E. (2000). IJMM International Journal of Medical Microbiology 290:167-174. The chromosomal region of Listeria monocytogenes harboring the gene cluster prfA-plcA-hly-mpl-actA-plcB (virulence gene cluster; vgc) harbors virulence genes critical for the survival of the bacteria following infection. Previous studies have implicated it as an ancestral pathogenicity island, derivatives of which are present in the species L. ivanovii and L. seeligeri, but absent in non-pathogenic species such as L. innocua. We cloned the corresponding region from L. innocua and L. welshimeri and compared its sequences to those from L. monocytogenes, L. ivanovii and L. seeligeri. The analysis allowed exact determination of delineation and size of the vgc and suggests that these genes may have been acquired by bacteriophage transduction. Thus, here we present an alternative view of the evolution of Listeria spp. and suggest that L. monocytogenes may be the primordial species of this genus. [TOP OF PAGE]

  43. Emmental cheese: A complex microbial ecosystem. Consequences on selection and use of starters. Chamba, J.F. (2000). Sciences des Aliments 20:37-54. Two fermentations usually take place in emmental cheese, lactic acid fermentation, followed by propionic acid fermentation. Unfortunately, an undesirable fermentation sometimes occurs during cheese ripening: the butyric acid fermentation. Numerous microorganisms cooperate and interact in these fermentations: lactococci, thermophilic streptococci and lactobacilli, heterofermentative lactobacilli and pediococci, propionic acid bacteria. Thus, the cheese is a microbial ecosystem which, in addition to bacteriophages, has other parasites. The properties and the role of each species, the effects of various strains (and the interactions between them) on curd acidification, proteolysis during ripening, eye formation and sensorial characteristics of emmental cheese is demonstrated using examples. Such properties should be taken into account during the selection of lactic and propionic acid bacteria for use as starters. [TOP OF PAGE]

  44. Evolution of virulence in parasites: making hard and soft choices. Chao, L., Hanley, K.A., Burch, C.L., Dahlberg, C., Turner, P.E. (2000). Q. Rev. Biol. 75:261-275. [TOP OF PAGE]

  45. A high yielding mutant of mycobacteriophage L1 and its application as a diagnostic tool. Chatterjee, S., Mitra, M., Das, G.S. (2000). FEMS Microbiol. Let. 188:47-53. L1 is a lysogenic phage of mycobacteria, which along with L5 and D29 constitute a closely linked family of homoimmune mycobacteriophages. These phages can be potentially used for genetic engineering of mycobacteria and diagnosis of mycobacterial infection. The effectiveness of such phage based systems depends on the efficiency with which they infect and grow within target cells. While working with phage L1c1ts which is a temperature sensitive mutant of phage L1, we observed that high yielding phage stocks were generated by repeated passage through the host, Mycobacterium smegmatis. A plaque purified mutant L1-P2, obtained from one such high yielding stock, when analyzed further was found to infect host cells with increased efficiency. The DNA obtained from L1-P2 was examined by restriction digestion, and it was observed that spontaneous loss of DNA fragment from the right arm, which encodes early regulatory factors, had occurred. It has been further demonstrated that the high yielding property of the mutant phage could be utilized to increase the sensitivity of mycobacteriophage-based detection systems. [TOP OF PAGE]

  46. Forces dictating colloidal interactions between viruses and soil. Chattopadhyay, D., Puls, R.W. (2000). Chemosphere 41:1279-1286. The fate and transport of viruses in soil and aquatic environments were studied with respect to the different forces involved in the process of sorption of these viruses on soil particles. In accordance with the classical DLVO theory, we have calculated the repulsive electrostatic forces and the attractive van der Waals forces. Bacteriophages have been used as model sorbates, while different clays have been used as model sorbents. The equations used for the determination of the change in free energy for the process (?G) takes into consideration the roughness of the sorbent surfaces. Results indicate that attractive van der Waals forces predominate the process of sorption of the selected bacteriophages on clays. [TOP OF PAGE]

  47. Isolation of a virulent bacteriophage from a Propionibacterium species in the sheep rumen. Cheong, J.P.E., Brooker, J.D. (2000). Australian Journal of Agricultural Research 51:119-123. Propionibacterium is a facultative anaerobe associated with the rumen epithelium, the presence of which may influence the anaerobic environment through oxygen scavenging, as well as providing a source of propionate. Factors such as bacteriophages that influence Propionibacterium populations may therefore be important regulators of rumen function. This study describes the isolation and identification of a ruminal Propionibacterium bacteriophage. Sheep rumen fluid was screened for Propionibacterium species and 3 isolates were identified and characterised. One isolate, PA1, was used as an indicator strain to screen for the presence of Propionibacterium-specific virulent bacteriophages. A virulent bacteriophage, PB2, was isolated from clear plaques on a lawn of PA1 cells and was shown by transmission electron microscopy to be a siphovirus-like particle comprising an icosahedral head 50 nm in diameter and a tail 140 nm in length. The bacteriophage was visibly attached to and within PA1 cells, and was shown to infect all 3 ruminal isolates of Propionibacterium and 4 of 6 clinical isolates of P. acnes. Restriction mapping of bacteriophage PB2 demonstrated a 30.8 kb genome. [TOP OF PAGE]

  48. Transfer of conjugative plasmids and bacteriophage lambda occurs in the presence of antibiotics that prevent de novo gene expression. Cooper, T.F., Heinemann, J.A. (2000). Plasmid ???:???-??? [TOP OF PAGE]

  49. Evolutionary Reversals During Viral Adaptation to Alternating Hosts. Crill, W.D., Wichman, H.A., Bull, J.J. (2000). Genetics 154:27-37. Experimental adaptation of the bacteriophage fX174 to a Salmonella host depressed its ability to grow on the traditional Escherichia host, whereas adaptation to Escherichia did not appreciably affect growth on Salmonella. Continued host switching consistently exhibited this pattern. Growth inhibition on Escherichia resulted from two to three substitutions in the major capsid gene. When these phages were forced to grow again on Escherichia, fitness recovery occurred predominantly by reversions at these same sites, rather than by second-site compensatory changes, the more frequently observed mechanism in most microbial systems. The affected residues lie on the virion surface and they alter attachment efficiency, yet they occur in a region distinct from a putative binding region previously identified from X-ray crystallography. These residues not only experienced high rates of evolution in our experiments, but also exhibited high levels of radical amino acid variation among fX174 and its known relatives, consistent with a history of adaptation involving these sites. [TOP OF PAGE]

  50. Determination of enteroviruses, hepatitis A virus, bacteriophages and Escherichia coli in Adriatic Sea mussels. Croci, L., De, M.D., Scalfaro, C., Fiore, A., Divizia, M., Donia, D., Cosentino, A.M., Moretti, P., Costantini, G. (2000). Journal of Applied Microbiology 88:293-298. The aim of the present study was to evaluate the incidence of enteric viruses in mussels and to verify the possibility of using phages as indirect indicators of mussel viral contamination. Mussels (36 samples) collected from three different areas of the Adriatic Sea were analysed to determine the following parameters: Escherichia coli, somatic coliphage (T6 phage), F-Plus (MS2 phage), B40-8 (phage of Bacteroides fragilis), enteroviruses and hepatitis A virus. Most of the results of the bacteriological analysis (most probable number (MPN) ml-1) were in accordance with the bacteriological limits established by European law, with the exception of seven samples. The bacteriophage analyses were always negative for F-Plus and B40-8, with the exception of a few samples, whereas the somatic coliphages were generally between 0 and 20 MPN g-1, with the exception of two samples (110 MPN g-1). The virological analysis showed five samples positive for the presence of enteroviruses and 13 for the presence of hepatitis A virus (in three samples both viruses were present). Most of these samples presented acceptable bacteriological parameters and the bacteriophages were absent or their value was generally very low. The results show that the detection of E. coli and phages does not seem to be a good indicator of viral contamination. [TOP OF PAGE]

  51. Development of a genetically modified bacteriophage for use in tracing sources of pollution. Daniell, T.J., Davy, M.L., Smith, R.J. (2000). Journal of Applied Microbiology 88:860-869. Bacteriophage are frequently used as biotracers to identify the source of water pollutants. Genetic manipulation of bacteriophage M13mp18 has been used to enhance this technique by creating a library in which each recombinant bacteriophage genome contains a unique identification sequence. Techniques that identify a recombinant bacteriophage by the presence of the identification sequence, including polymerase chain reaction, restriction site polymorphism and plaque hybridization, have been developed. Recombinant bacteriophage can be used to test a large number of suspected sources simultaneously. The identification sequence also eliminates confusion with natural bacteriophage present in water samples. The performance of the modified bacteriophage and the techniques were assessed in simulated field trials on a restricted site carried out under a consent for environmental release of a genetically modified organism. The techniques were also field tested at sites in northwest England using wild-type M13 bacteriophage. [TOP OF PAGE]

  52. CTX prophages in classical biotype Vibrio cholerae: functional phage genes but dysfunctional phage genomes. Davis, B.M., Moyer, K.E., Boyd, E.F., Waldor, M.K. (2000). J. Bacteriol. 182:6992-6998. CTXphi is a filamentous, lysogenic bacteriophage whose genome encodes cholera toxin, the primary virulence factor produced by Vibrio cholerae. CTX prophages in O1 El Tor and O139 strains of V. cholerae are found within arrays of genetically related elements integrated at a single locus within the V. cholerae large chromosome. The prophages of O1 El Tor and O139 strains generally yield infectious CTXphi. In contrast, O1 classical strains of V. cholerae do not produce CTXphi, although they produce cholera toxin and they contain CTX prophages integrated at two sites. We have identified the second site of CTX prophage integration in O1 classical strains and characterized the classical prophage arrays genetically and functionally. The genes of classical prophages encode functional forms of all of the proteins needed for production of CTXphi. Classical CTX prophages are present either as solitary prophages or as arrays of two truncated, fused prophages. RS1, a genetic element that is closely related to CTXphi and is often interspersed with CTX prophages in El Tor strains, was not detected in classical V. cholerae. Our model for CTXphi production predicts that the CTX prophage arrangements in classical strains will not yield extrachromosomal CTX DNA and thus will not yield virions, and our experimental results confirm this prediction. Thus, failure of O1 classical strains of V. cholerae to produce CTXphi is due to overall deficiencies in the structures of the arrays of classical prophages, rather than to mutations affecting individual CTX prophage genes. [TOP OF PAGE]

  53. Convergence of the secretory pathways for cholera toxin and the filamentous phage, CTXphi. Davis, B.M., Lawson, E.H., Sandkvist, M., Ali, A., Sozhamannan, S., Waldor, M.K. (2000). Science 288:333-335. Virulence of Vibrio cholerae depends on secretion of cholera toxin (CT), which is encoded within the genome of a filamentous phage, CTXphi. Release of CT is mediated by the extracellular protein secretion (eps) type II secretion system. Here, the outer membrane component of this system, EpsD, was shown to be required for secretion of the phage as well. Thus, EpsD plays a role both in pathogenicity and in horizontal transfer of a key virulence gene. Genomic analysis suggests that additional filamentous phages also exploit chromosome-encoded outer membrane channels. [TOP OF PAGE]

  54. Effect of deleterious mutation-accumulation on the fitness of RNA bacteriophage MS2. de la Pena, M., Elena, S.F., Moya, A. (2000). Evolution 54:686-691. RNA viruses show the highest mutation rate in nautre. It has been extensively demonstrated that, in the absence of purifying selection, RNA viruses accumulate deleterious mutations at a high rate. However, the parameters describing this accumulation are, in general, poorly understood. The present study reports evidences for fitness declines by the accumulation of deleterious mutations in the bacteriophage MS2. We estimated the rate of fitness decline to be as high as 16% per bottleneck transfer. In addition, our results agree with an additive model of fitness effects. [TOP OF PAGE]

  55. An introduction to the evolutionary ecology of viruses. DeFilippis, V.R., Villarreal, L.P. (2000). pp. 125-208. In In Hurst, C.J. (ed.), Viral Ecology. Academic Press, San Diego. [no abstract?]. [TOP OF PAGE]

  56. Comparative genomics of the late gene cluster from Lactobacillus phages. Desiere, F., Pridmore, R.D., Brossow, H. (2000). Virology 275:294-305. Three prophage sequences were identified in the Lactobacillus johnsoni strain NCC533. Prophage Lj965 predicted a gene map very similar to those of pac-site Streptococcus thermophilus phages over its DNA packaging and head and tail morphogenesis modules. Sequence similarity linked the putative DNA packaging and head morphogenesis genes at the protein level. Prophage Lj965/S. thermophilus phage Sfi 11/Lactococcus lactis phage TP901-1 on one band and Lactobacillus delbrueckii phage LL-H/Lactbacillus plantarum phage phig 1e/Listeria monocytogenes phage A118 on the other hand defined two sublines of structural gene clusters in pac-site Siphoviridae from low-GC Gram-positive bacteria. Bacillus subtilis phage SPP1 linked both sublines. The putative major head and tail proteins from Lj965 shared weak sequence similarity with phages from Gram-negative bacteria. A clearly independent line of structural genes in Siphoviridae from low-GC Grampositive bacteria is defined by temperate cos-site phages including Lactobacillus gasserl phage adh, which also shared sequence similarity with phage D3 infecting a Gram-negative bacterium. A phylogenetic tree analysis demonstrated that the ClpP-like protein identified in four cos-site Siphoviridae from Lactobacillus, Lactococcus, Streptococcus, and Pseudomonas showed graded sequence relationships The tree suggested that the ClpP-like proteins from the phages were not acquired by horizontal gene transfer from their corresponding bacterial hosts. [TOP OF PAGE]

  57. Present and potential applications of genetic engineering in agronomy and agro-food. Desmazeaud, M. (2000). Comptes Rendus de l'Academie d'Agriculture de France 86:97-102. In agronomy, genetically engineered Rhizobium can improve plant growth. In the case of food productions, a bakery yeast was modified for increasing maltose utilization. Brewery and wine yeasts were modified for better properties than wild strains about alcohol or pH or sulfite resistance. New flavor profiles are obtained also: Kluyveromyces lactis can produce chymosin A used in cheese-making; lactic acid bacteria (mainly Lactococcus lactis) are modified for a controlled action during cheese ripening; genetic engineering can produce bacteriophage resistant strains. [TOP OF PAGE]

  58. Pathogenicity islands and phage conversion: Evolutionary aspects of bacterial pathogenesis. Dobrindt, U., Reidl, J. (2000). IJMM International Journal of Medical Microbiology 290:519-527. Horizontal gene transfer plays a key role in the generation of novel bacterial pathogens. Besides plasmids and bacteriophages, large genomic regions termed pathogenicity islands (PAIs) can be transferred horizontally. All three mechanisms for DNA exchange or transfer may be important for the evolution of bacterial pathogens. [TOP OF PAGE]

  59. [Water quality control of 2 swimming pools in Rome. Evaluation of the bacteriophage parameter]. Donia, D., Divizia, M., della, S.M., Pana, A. (2000). Annali di Igiene 12:35-39. [TOP OF PAGE]

  60. Evaluation of F-specific RNA bacteriophage as a candidate human enteric virus indicator for bivalve molluscan shellfish. Dore, W.J., Henshilwood, K., Lees, D.N. (2000). Appl. Environ. Microbiol. 66:1280-1285. Escherichia coli is a widely utilized indicator of the sanitary quality of bivalve molluscan shellfish sold for human consumption. However, it is now well documented that shellfish that meet the E. coli standards for human consumption may contain human enteric viruses that cause gastroenteritis and hepatitis. In this study we investigated using F-specific RNA bacteriophage (FRNA bacteriophage) to indicate the likely presence of such viruses in shellfish sold for consumption. FRNA bacteriophage and E. coli levels were determined over a 2-year period for oysters (Crassostrea gigas) harvested from four commercial sites chosen to represent various degrees of sewage pollution. Three sites were classified as category B sites under the relevant European Community (EC) Directive (91/492), which required purification (depuration) of oysters from these sites before sale. One site was classified as a category A site, and oysters from this site could be sold directly without further processing. Samples were tested at the point of sale following commercial processing and packaging. All of the shellfish complied with the mandatory EC E. coli standard (less than 230 per 100 g of shellfish flesh), and the levels of contamination for more than 90% of the shellfish were at or below the level of sensitivity of the assay (20 E. coli MPN per 100 g), which indicated good quality based on this criterion. In contrast, FRNA bacteriophage were frequently detected at levels that exceeded 1,000 PFU per 100 g. High levels of FRNA bacteriophage contamination were strongly associated with harvest area fecal pollution and with shellfish-associated disease outbreaks. Interestingly, FRNA bacteriophage contamination exhibited a marked seasonal trend that was consistent with the trend of oyster-associated gastroenteritis in the United Kingdom. The correlation between FRNA bacteriophage contamination and health risk was investigated further by using a reverse transcription-PCR assay for Norwalk-like virus (NLV). NLV contamination of oysters was detected only at the most polluted site and also exhibited a seasonal trend that was consistent with the trend of FRNA bacteriophage contamination and with the incidence of disease. The results of this study suggest that FRNA bacteriophage could be used as viral indicators for market-ready oysters. [TOP OF PAGE]

  61. Genomic relatedness of Staphylococcus aureus phages of the International Typing Set and detection of serogroup A, B, and F prophages in lysogenic strains. Doskar, J., Pallova, P., Pant, c., Rosypal, S., R, z., Pant, c., Kailerova, J., Kleparnik, K., Mala, Z., Bocek, P. (2000). Canadian Journal of Microbiology 46:1066-1076. On the basis of HindIII-restriction digest analysis of genomic DNAs, the S. aureus bacteriophages of the International Typing Set were divided into five clusters designated as A, F, Ba, Bb, and Bc. The clusters A and F include all the phages of serogroups A and F and correspond to species 3A and 77 proposed by Ackermann and DuBow (1987). On the other hand, the phages of serogroup B were divided into three clusters designated as Ba, Bb, and Bc that differ significantly each from the other in their restriction patterns. The clusters Ba and Bb may represent two separate species, while the cluster Bc may include more than one phage species. For each of the phage serogroups A, B, and F, common HindIII-restriction fragments of phage 3A (1700 bp), of 53 (4060 bp), and of 77 (8300 bp) were used for the preparation of probes specific to the phages of serogroups A, B, and F. These probes were very effective, making it possible to detect up to three different prophages in a given lysogenic strain at the same time. Restriction enzyme maps of phages 3A, 53, and 77, each representing a different serogroup, were constructed. The restriction maps of phage 3A and that of phage 77 are linear, whereas that of phage 53 is circular and exhibits a circular permutation. DNAs of the phages of serogroups A and F have cohesive ends. On each restriction map, the sites corresponding to specific probes are indicated. The size of intact genomic DNA of all phages estimated by PFGE varies within the range of 41.5-46.2 kb. [TOP OF PAGE]

  62. Genetic analysis of chromosomal regions of Lactococcus lactis acquired by recombinant lytic phages. Durmaz, E., Klaenhammer, T.R. (2000). Appl. Environ. Microbiol. 66:895-903. Recombinant phages are generated when Lactococcus lactis subsp. lactis harboring plasmids encoding the abortive type (Abi) of phage resistance mechanisms is infected with small isometric phages belonging to the P335 species. These phage variants are likely to be an important source of virulent new phages that appear in dairy fermentations. They are distinguished from their progenitors by resistance to Abi defenses and by altered genome organization, including regions of L. lactis chromosomal DNA. The objective of this study was to characterize four recombinant variants that arose from infection of L. lactis NCK203 (Abi(+)) with phage phi31. HindIII restriction maps of the variants (phi31.1, phi31.2, phi31.7, and phi31.8) were generated, and these maps revealed the regions containing recombinant DNA. The recombinant region of phage phi31.1, the variant that occurred most frequently, was sequenced and revealed 7.8 kb of new DNA compared with the parent phage, phi31. This region contained numerous instances of homology with various lactococcal temperate phages, as well as homologues of the lambda recombination protein BET and Escherichia coli Holliday junction resolvase Rus, factors which may contribute to efficient recombination processes. A sequence analysis and phenotypic tests revealed a new origin of replication in the phi31.1 DNA, which replaced the phi31 origin. Three separate HindIII fragments, accounting for most of the recombinant region of phi31.1, were separately cloned into gram-positive suicide vector pTRK333 and transformed into NCK203. Chromosomal insertions of each plasmid prevented the appearance of different combinations of recombinant phages. The chromosomal insertions did not affect an inducible prophage present in NCK203. Our results demonstrated that recombinant phages can acquire DNA cassettes from different regions of the chromosome in order to overcome Abi defenses. Disruption of these regions by insertion can alter the types and diversity of new phages that appear during phage-host interactions. [TOP OF PAGE]

  63. Bacteriophages of spirochetes. Eggers, C.H., Casjens, S., Hayes, S.F., Garon, C.F., Damman, C.J., Oliver, D.B., Samuels, D.S. (2000). J Mol Microbiol Biotechnol 2:365-373. Historically, a number of bacteriophage-like particles have been observed in association with members of the bacterial order Spirochetales, the spirochetes. In the last decade, several spirochete bacteriophages have been isolated and characterized at the molecular level. We have recently characterized a bacteriophage of the Lyme disease agent, Borrelia burgdorferi, which we have designated phiBB-1. Here we review the history of the association between the spirochetes and their bacteriophages, with a particular emphasis on phiBB-1 and its prophage, the 32-kb circular plasmid family of B. burgdorferi. [TOP OF PAGE]

  64. Characterization of a Phage Resistance Plasmid, pLKS, of Silage-Making Lactobacillus plantarum NGRI0101. Eguchi, T., Doi, K., Nishiyama, K., Ohmomo, S., Ogata, S. (2000). Biosci. Biotech. Biochem. 64:751-756. [TOP OF PAGE]

  65. The two faces of mutation: Extinction and adaptation in RNA viruses. Elena, S.F., Miralles, R., Cuevas, J.M., Turner, P.E., Moya, A. (2000). IUBMB Life 49:5-9. From a population standpoint, two main features characterize the replication of RNA viruses and viruses that use RNA as a replicative intermediate: high genetic variability, and enormous fluctuations in population size. Their genetic variability mainly reflects a lack of the proof-reading and post-replicative error correction mechanisms that operate during cellular DNA replication, but recombination and segment exchange can also play an important role, Viral population size can change tremendously as a consequence of transmission between hosts or between different tissues within an infected host. A new infection can be initiated with very few particles that subsequently expand many trillion-fold. Repeated bottleneck events can lead to drastic fitness losses or even to viral extinction, whereas continuously large population sizes result in fitness gains and adaptation. Here we review experimental evidence for the effects of mutation, selection, and genetic drift on the adaptation and extinction of RNA viruses. [TOP OF PAGE]

  66. Toward antiviral strategies that resist viral escape. Endy, D., Yin, J. (2000). Antimicrobial Agents and Chemotherapy 44:1097-1099. We studied the effect on viral growth of drugs targeting different virus functions using a computer simulation for the intracellular growth of bacteriophage T7. We found that drugs targeting components of negative-feedback loops gain effectiveness against mutant viruses that attenuate the drug-target interaction. The greater inhibition of such mutants than of the wild type suggests a drug design strategy that would hinder the development of drug resistance. [TOP OF PAGE]

  67. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Endy, D., You, L., Yin, J., Molineux, I.J. (2000). Proc. Natl. Acad. Sci. USA 97:5375-5380. We created a simulation based on experimental data from bacteriophage T7 that computes the developmental cycle of the wild-type phage and also of mutants that have an altered genome order. We used the simulation to compute the fitness of more than 105 mutants. We tested these computations by constructing and experimentally characterizing T7 mutants in which we repositioned gene 1, coding for T7 RNA polymerase. Computed protein synthesis rates for ectopic gene 1 strains were in moderate agreement with observed rates. Computed phage-doubling rates were close to observations for two of four strains, but significantly overestimated those of the other two. Computations indicate that the genome organization of wild-type T7 is nearly optimal for growth: only 2.8% of random genome permutations were computed to grow faster, the highest 31% faster, than wild type. Specific discrepancies between computations and observations suggest that a better understanding of the translation efficiency of individual mRNAs and the functions of qualitatively "nonessential" genes will be needed to improve the T7 simulation. In silico representations of biological systems can serve to assess and advance our understanding of the underlying biology. Iteration between computation, prediction, and observation should increase the rate at which biological hypotheses are formulated and tested. [TOP OF PAGE]

  68. Sunlight-Induced Propagation of the Lysogenic Phage Encoding Cholera Toxin. Faruque, S.M., Rahman, A.M.M., Waldor, M.K., Sack, D.A. (2000). Infect. Immun. 68:4795-4801. [TOP OF PAGE]

  69. Control of bacterial spot on tomato in the greenhouse and field with h-mutant bacteriophages. Flaherty, J.E., Jones, J.B., Harbaugh, B.K., Somodi, G.C., Jackson, L.E. (2000). Hortscience 35:882-884. A mixture of host-range mutant (h-mutant) bacteriophages specific for tomato race 1 (T1) and race 3 (T3) of the bacterial spot pathogen, Xanthomonas campestris pv. vesicatoria (Doidge) Dye was evaluated for biological control of bacterial spot on 'Sunbeam' tomato (Lycopersicon esculentum Mill.) transplants and field-grown plants for two seasons (Fall 1997 and Fall 1998). Foliar applications of bacteriophages were compared with similar applications of water (control) and of copper/mancozeb bactericides, the commonly used chemical control strategy for tomato seedling and field production. In 1997, the incidence of bacterial spot on greenhouse-grown seedlings was reduced from 40.5% (control) to 5.5% or 0.9% for bactericide- or bacteriophage-treated plants, respectively. In 1998, the incidence of bacterial spot was 17.4% on control plants vs. 5.5% and 2.7% for bactericide- and bacteriophage-treated plants, respectively, although these differences were not statistically significant at P ltoreq 0.05. Applications of bacteriophages to field-grown tomatoes decreased disease severity as measured by the area under the disease progress curve (AUDPC) by 17.5% (1997) and 16.8% (1998) compared with untreated control plants. Preharvest plant vigor ratings, taken twice during each field season, were higher in the bacteriophage-treated plants than in either bactericide-treated plants or nontreated controls except for the early vigor rating in 1998. Use of bacteriophages increased total weight of extra-large fruit 14.9% (1997) and 24.2% (1998) relative to that of nontreated control plants, and 37.8% (1997) and 23.9% (1998) relative to that of plants treated with the chemical bactericides. Chemical names used: manganese, zinc, carboxy-ethylene his dithiocarbamate (mancozeb). [TOP OF PAGE]

  70. Elimination of enteroviruses, other enteric viruses, F-specific coliphages, somatic coliphages and E. coli in four sewage treatment plants of southern Germany. Fleischer, J., Schlafmann, K., Otchwemah, R., Botzenhart, K. (2000). Journal of Water Supply Research and Technology - AQUA 49:127-138. The reduction processes at four advanced sewage treatment plants in Baden-Wuerttemberg were evaluated with regard to virus elimination and the elimination of indicator organisms from wastewater. The results of virus elimination were compared with the reduction of somatic and male specific bacteriophages and of E. coli. In total, 222 water samples were examined. The results obtained for the different treatment plants show reduction rates from 80.0% to 99.9% for enteroviruses, enumerated as PFU l-1 on BGM cell line, and reduction rates from 59.4% to 99.9% for other enteric viruses, enumerated as MPN l-1 on MA-104 cell line. Identification of the isolated enteroviruses yielded 88.3% for Coxsackie virus B (1-5), 18.3% were positive for Polio (1-3) and 8.3% for Echo virus (1+11). The reduction rates of somatic bacteriophages ranged from 76.4% to 99.90%, for male specific bacteriophages from 87.5% to 99.9% and for E. coli from 75.0% to 99.9% respectively. Two of the plants use standard chemical precipitation and the other two employ combinations of chemical and biological elimination techniques to reduce the concentrations of phosphorus and nitrogen. A correlation between the amount of precipitators and the elimination rates of the tested microorganisms could not be demonstrated, perhaps due to the fact that the treatment conditions could not be modified by the investigators. It is concluded that the tested treatment plants using combinations of chemical and biological techniques for P and N removal show equal or higher elimination rates than conventional treatment processes using chemical elimination techniques. [TOP OF PAGE]

  71. Evaluation of CD4+ T cell function In vivo in HIV-infected patients as measured by bacteriophage phiX174 immunization. Fogelman, I., Davey, V., Ochs, H.D., Elashoff, M., Feinberg, M.B., Mican, J., Siegel, J.P., Sneller, M., Lane (2000). J. Infect. Dis. 182:435-441. Bacteriophage phiX174 immunization was used to measure CD4(+) T cell function in vivo in human immunodeficiency virus (HIV)-infected patients across all disease stages. Function was evaluated by measuring the ability of T cells to provide help to B cells in antibody production, amplification, and isotype switching. A total of 33 patients and 10 controls received 3 bacteriophage phiX174 immunizations 6 weeks apart. The patients' responses regarding bacteriophage-specific total antibody titers and IgG titers were quantitatively and qualitatively inferior to the controls' responses. Overall, 7 of 33 patients had normal T cell function. Baseline CD4 counts provided the strongest correlation with total antibody and IgG titers. HIV RNA had a weaker association with responses but had some predictive power among patients with a CD4 count >200 cells/microL. Bacteriophage phiX174 immunization seems to be a useful tool for measuring immune function in vivo, which suggests that most HIV-infected patients may have abnormal CD4(+) T cell function despite adequate antiretroviral treatment. [TOP OF PAGE]

  72. Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages. Foley, S., Bruttin, A., Brussow, H. (2000). J. Virol. 74:611-618. Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilus bacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns from Lactococcus, Lactobacillus, and Bacillus phages. [TOP OF PAGE]

  73. Occurrence and distribution of microbiological indicators in groundwater and stream water. Francy, D.S., Helsel, D.R., Nally, R.A. (2000). Water Environment Research 72:152-161. A total of 136 stream water and 143 groundwater samples collected in five important hydrologic systems of the United States were analyzed for microbiological indicators to test monitoring concepts in a nationally consistent program. Total coliforms were found in 99%, Escherichia coli in 97%, and Clostridium perfringens in 73% of stream water samples analyzed for each bacterium. Total coliforms were found in 20%, E. coli in less than 1%, and C. perfringens in none of the groundwater samples analyzed for each bacterium. Although coliphage analyses were performed on many of the samples, contamination in the laboratory and problems discerning discrete plaques precluded quantification. Land use was found to have the most significant effect on concentrations of bacterial indicators in stream water. Presence of septic systems on the property near the sampling site and well depth were found to be related to detection of coliforms in groundwater, although these relationships were not statistically significant. A greater diversity of sites, more detailed information about some factors, and a larger dataset may provide further insight to factors that affect microbiological indicators. [TOP OF PAGE]

  74. Titration of infective and noninfective Ff filamentous bacteriophages using a monoclonal antibody against g3p. Frisch, C., Knappik, A., Choidas, M., Tesar, M. (2000). BioTechniques 29:26-8, 30. [TOP OF PAGE]

  75. Effect of host bacteria genotype on spontaneous reversions of Bacillus subtilis bacteriophage PHI29 sus17 nonsense codon. Fucik, V., Beran, J., Krasny, L., Jonak, J. (2000). FEMS Microbiol. Let. 183:143-146. Gene 17 of Bacillus subtilis bacteriophage PHI29 is an early gene playing a role in DNA replication. Its mutant sus17(112) carries the TAA nonsense triplet at the fifth codon of the gene. We isolated and sequenced 73 spontaneous revertants producing normal-size plaques on bacteria without an informational suppressor gene. In all revertants, the TAA triplet was changed by a one-base substitution and the sequences CAA, AAA, TTA, TAC and TAT were recovered at its place. The spectrum of these mutations was markedly influenced by the genotype of the bacteria in which the revertants arose. In agreement with the results described in Escherichia coli, the ratio of transversions to transitions (CAA being the only transition acceptable) was higher in strains harboring the functional allele recA+ than in those with recA4. Our results support the idea that also in the Gram-positive B. subtilis, the spectra of spontaneous mutations are specifically modified by an SOS function. It is assumed that the single-stranded DNA chains generated in the course of phage DNA replication might act as an inducing factor. [TOP OF PAGE]

  76. Horizontal gene transfer in bacterial and archaeal complete genomes. Garcia-Vallve, S., Romeu, A., Palau, J. (2000). Genome Research 10:1719-1725. There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied from 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation. [TOP OF PAGE]

  77. Sensitivity of microorganisms to different wavelengths of UV light: Implications on modeling of medium pressure UV systems. Giese, N., Darby, J. (2000). Water Res. 34:4007-4013. The responses of three species of coliform bacteria (Citrobacter diversus, Citrobacter freundii and Klebsiella pneumoniae) and the bacteriophage (virus) variant phiX-174 to three wavelengths of UV light (254, 280 and 301 nm) were measured. The values of germicidal efficiency at 280 nm determined for each of the microorganisms were not significantly different. At 301 nm, the values of germicidal efficiency were significantly different, but all values were too small (< 0.06) to warrant consideration in the modeling of the germicidal intensity delivered by a medium pressure UV system. The data from this study provide some evidence that the values of germicidal efficiency determined for one species of bacteria or virus may be used to represent the relative responses of all bacteria and viruses to medium pressure UV irradiation. [TOP OF PAGE]

  78. Phage-displayed peptides as biosensor reagents. Goldman, E.R., Pazirandeh, M.P., Mauro, J.M., King, K.D., Frey, J.C., Anderson, G.P. (2000). Journal of Molecular Recognition 13:382-387. This study investigated the potential to utilize phage-displayed peptides as reagents in sensor applications. A library of random 12-mers displayed on phage was panned against staphylococcal enterotoxin B (SEB), a causative agent of food poisoning. Nine SEB binding phage clones were isolated, all of which share the consensus sequence Trp His Lys at their amino terminus. Binding of several of these phage was shown to be inhibited when they were assayed in a competitive enzyme-linked immunosorbent assay (ELISA) format with synthesized peptide corresponding to the peptide-encoding region of one of the clones. Whole phage were labeled with the dye Cy5, and incorporated into fluoroimmunoassays. Labeled phage were able to detect SEB down to a concentration of 1.4 ng/well in a fluorescence-based immunoassay. When incorporated into an automated fluorescence-based sensing assay, Cy5-labeled phage bound to probes coated with SEB generated a robust signal of about 10,000 pA, vs a signal of 1000 pA using a control fiber coated with streptavidin. These results demonstrate the potential for development of phage-based sensor reagents. [TOP OF PAGE]

  79. Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida. Griffin, D.W., Stokes, R., Rose, J.B., Paul, J.H., III (2000). Microb. Ecol. 39:56-64. A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study. [TOP OF PAGE]

  80. Characterization of natural isolates of Lactobacillus strains to be used as starter cultures in dairy fermentation. Hebert, E.M., Raya, R.R., Tailliez, P., de, G.G. (2000). Int. J. Food Microbiol. 59:19-27. The technological relevant characteristics of five homofermentative lactobacilli strains, isolated from natural fermented hard cheeses, were studied. Isolates CRL 581 and CRL 654, from Argentinian artesanal hard cheeses, and isolates CRL 1177, CRL 1178, and CRL 1179, from Italian Grana cheeses, were identified as Lactobacillus delbrueckii subsp. lactis and Lactobacillus helveticus, respectively, by physiological and biochemical tests, SDS-PAGE of whole-cell proteins and sequencing of the variable (V1) region of the 16S ribosomal DNA. All strains showed high levels of beta-galactosidase activity. However, proteolytic activity varied widely among isolates. Strains CRL 581, CRL 654, and CRL 1177 hydrolyzed alpha- and beta-caseins and were able to coagulate reconstituted skim milk in less than 16 h at 42 degrees C. According to the substrate specificity, these proteinases have a caseinolytic activity comparable to that of the P(III)-type of lactococcal proteinases. No strains produced inhibitor substances (bacteriocin) and all were insensitive to attack by 14 L. helveticus- and L. delbrueckii subsp. lactis-specific bacteriophages. [TOP OF PAGE]

  81. The origins and ongoing evolution of viruses. Hendrix, R.W., Lawrence, J.G., Hatfull, G.F., Casjens, S. (2000). Trends in Microbiology 8:504-508. Genome analyses of double strand DNA tailed bacteriophages argue that they evolve by recombinational reassortment of genes and by the acquisition of novel genes as simple genetic elements termed morons. These processes suggest a model for early virus evolution, wherein viruses can be regarded less as having derived from cells and more as being partners in their mutual co-evolution. [TOP OF PAGE]

  82. Intramuscular immunization with genetically inactivated (ghosts) Actinobacillus pleuropneumoniae serotype 9 protects pigs against homologous aerosol challenge and prevents carrier state. Hensel, A., Huter, V., Katinger, A., Raza, P., Strnistschie, C., Roesler, U., Brand, E., Lubitz, W. (2000). Vaccine 18:2945-2955. Bacterial ghosts are empty cell envelopes achieved by the expression of a cloned bacteriophage lysis gene and, unlike classical bacterins, suffer no denaturing steps during their production. These properties may lead to a superior presentation of surface antigens to the immune system. Currently available porcine Actinobacillus pleuropneumoniae vaccines afford only minimal protection by decreasing mortality but not morbidity. Pigs which survive infection can still be carriers of the pathogen, so a herd once infected remains infected. Carrier pigs harbour A. pleuropneumoniae in their nasal cavities, in their tonsils, or within lung lesions. A dose-defined nose-only aerosol infection model for pigs was used to study the immunogenic and protective potential of systemic immunization with ghosts made from A. pleuropneumoniae serotype 9 reference strain CVI 13261 against an homologous aerogenous challenge. Pigs were vaccinated twice intramuscularly with a dose of 5x10(9) CFU ghosts (GVPs) or formalin-inactivated A. pleuropneumoniae bacterins (BVPs). After 2 weeks vaccinated pigs and non-vaccinated placebo controls (PCs) were challenged with a dose of 10(9) CFU by aerosol. The protective efficacy of immunization was evaluated by clinical, bacteriological, serological and post-mortem examinations. Bronchoalveolar lavage in pigs was performed during the experiment to obtain lavage samples (BALF) for assessment of local antibodies. Isotype-specific antibody responses in serum and BALF were determined by ELISAs based on whole-cell antigen. Immunization with ghosts did not cause clinical side-effects. After aerosol challenge PCs developed fever and pleuropneumonia. GVPs or BVPs were found to be fully protected against clinical disease or lung lesions in both vaccination groups, whereas colonization of the respiratory tract with A. pleuropneumoniae was only prevented in GVPs. Specific immunoglobins against A. pleuropneumoniae were not detectable in BALF after immunization. A significant systemic increase of IgM, IgA, IgG(Fc'), or IgG(H+L) antibodies reactive with A. pleuropneumoniae was measured in GVPs and BVPs when compared to the non-exposed controls. BVPs reached higher titers of IgG(Fc') and IgG(H+L) than GVPs. However, prevention of carrier state in GVPs coincided with a significant increase of serum IgA when compared to BVPs. These results suggest that immunization with ghosts, that bias antibody populations specific to non-denaturated surface antigens, may be more efficacious in protecting pigs against colonization and infection than bacterins. [TOP OF PAGE]

  83. Characterization of PHI8, a bacteriophage containing three double-stranded RNA genomic segments and distantly related to PHI6. Hoogstraten, D., Qiao, X., Sun, Y., Hu, A., Onodera, S., Mindich, L. (2000). Virology 272:218-224. The three double-stranded RNA genomic segments of bacteriophage PHI8 were copied as cDNA, and their nucleotide sequences were determined. Although the organization of the genome is similar to that of PHI6, there is no similarity in either the nucleotide sequences or the amino acid sequences, with the exception of the motifs characteristic of viral RNA polymerases that are found in the presumptive polymerase sequence. Several features of the viral proteins differ markedly from those of PHI6. Although both phages are covered by a lipid-containing membrane, the protein compositions are very different. The most striking difference is that protein P8, which constitutes a shell around the procapsid in PHI6, is part of the membrane in PHI8. The host attachment protein consists of two peptides rather than one and the phage attaches directly to the lipopolysaccharide of the host rather than to a type IV pilus. The host range of PHI8 includes rough strains of Salmonella typhimurium and of pseudomonads. [TOP OF PAGE]

  84. Phage infection of the obligate intracellular bacterium, Chlamydia psittaci strain Guinea Pig Inclusion Conjunctivitis. Hsia, R.C., Ohayon, H., Gounon, P., Dautry-Varsat, A., Bavoil, P.M. (2000). Microbes and Infection 2:761-772. The infectious cycle of phiCPG1, a bacteriophage that infects the obligate intracellular pathogen, Chlamydia psittaci strain Guinea Pig Inclusion Conjunctivitis, was observed using transmission electron microscopy of phage-hyperinfected, Chlamydia-infected HeLa cells. Phage attachment to extracellular, metabolically dormant, infectious elementary bodies and cointernalisation are demonstrated. Following entry, phage infection takes place as soon as elementary bodies differentiate into metabolically active reticulate bodies. Phage-infected bacteria follow an altered developmental path whereby cell division is inhibited, producing abnormally large reticulate bodies, termed maxi-reticulate bodies, which do not mature to elementary bodies. These forms eventually lyse late in the chlamydial developmental cycle, releasing abundant phage progeny in the inclusion and, upon lysis of the inclusion membrane, into the cytosol of the host cell. Structural integrity of the hyperinfected HeLa cell is markedly compromised at late stages. Released phage particles attach avidly to the outer leaflet of the outer membranes of lysed and unlysed Chlamydiae at different stages of development, suggesting the presence of specific phage receptors in the outer membrane uniformly during the chlamydial developmental cycle. A mechanism for phage infection is proposed, whereby phage gains access to replicating chlamydiae by attaching to the infectious elementary body, subsequently subverting the chlamydial developmental cycle to its own replicative needs. The implications of phage infection in the context of chlamydial infection and disease are discussed. [TOP OF PAGE]

  85. Microvirus of Chlamydia psittaci strain Guinea pig inclusion conjunctivitis: Isolation and molecular characterization. Hsia, R.C., Ting, L.M., Bavoil, P.M. (2000). Microbiology (Reading) 146:1651-1660. The authors report the isolation and molecular characterization of a bacteriophage, phiCPG1, which infects Chlamydia psittaci strain Guinea pig Inclusion Conjunctivitis. Purified virion preparations contained isometric particles of 25 nm diameter, superficially similar to spike-less members of the phiX174 family of bacteriophages. The single-stranded circular DNA genome of phiCPG1 included five large ORFs, which were similar to ORFs in the genome of a previously described Chlamydia bacteriophage (Chp1) that infects avian C. psittaci. Three of the ORFs encoded polypeptides that were similar to those in a phage infecting the mollicute Spiroplasma melliferum, a pathogen of honeybees. Lesser sequence similarities were seen between two ORF products and the major capsid protein of the phiX174 coliphage family and proteins mediating rolling circle replication initiation in phages, phagemids and plasmids. Phage phiCPG1 is the second member of the genus Chlamydiamicrovirus, the first to infect a member of a Chlamydia species infecting mammals. Similarity searches of the nucleotide sequence further revealed a highly conserved (75% identity) 375 base sequence integrated into the genome of the human pathogen Chlamydia pneumoniae. This genomic segment encodes a truncated 113 residue polypeptide, the sequence of which is 72% identical to the amino-terminal end of the putative replication initiation protein of phiCPG1. This finding suggests that C. pneumoniae has been infected by a phage related to phiCPG1 and that infection resulted in integration of some of the phage genome into the C. pneumoniae genome. [TOP OF PAGE]

  86. Control of the eel (Anguilla japonica) pathogens, Aeromonas hydrophila and Edwardsiella tarda, by bacteriophages. Hsu, C.H., Lo, C.Y., Liu, J.K., Lin, C.S. (2000). Journal of the Fisheries Society of Taiwan 27:21-31. Aeromonas hydrophila and Edwardsiella tarda are the two major pathogens of the eel, Anguilla japonica. The prevalent method to control the diseases is antibiotics. Long term and large scale application of the drugs results in resistance which makes disease control difficult. In the nature, bacteriophages are an important factor in controling bacterial population. The purpose of this research is to study the capability of the phages to control the pathogens in pond water. Several bacteriophages of A. hydrophila and E. tarda were isolated from the water samples of southern Taiwan. In pure culture, the phages could reduce the host 3 orders of magnitude in 2 hr when the multiplicity of infection (moi) was above 11.5 at 25ºC. In the pond water with added A. hydrophila to 6 X 105 / ml, the number dropped 250 folds at phage moi of 0.23 in 8 hr with accompanying phage multiplication to the level of 106 PFU/ml in the water. Most (85%) of the surviving hosts were still vulnerable to the phage. The resistant strains (15%) appeared to be lysogens since the culture broth of the strains could form phage plaques on A. hydrophila. In the case of E. tarda, the bacteria subsided rapidly even in the absence of phage in 48 hr in the pond water. [TOP OF PAGE]

  87. Characterization of Streptococcus thermophilus strains that undergo lysis under unfavourable environmental conditions. Husson-Kao, C., Mengaud, J., Gripon, J.C., Benbadis, L., Chapot-Chartier, M.P. (2000). Int. J. Food Microbiol. 55:209-213. The autolysis of starter lactic acid bacteria appears as a promising way to enhance the flavour of fermented dairy products. The present work was aimed at investigating the autolysis phenomenon in Streptococcus thermophilus, a thermophilic lactic acid bacteria involved in the starters used for the production of yoghurts, Italian and Swiss-type cheeses. Out of 146 strains screened for their aptitude to spontaneously lyse at the end of growth in M17 medium containing lactose in limited concentration, six strains, among which is the type strain CNRZ 1358, were found to be highly autolytic. These autolytic strains are characterized by a typical bell-shaped growth curve. Lysis of the type strain, which was studied as the model, was triggered under unfavourable environmental conditions, such as lactose depletion and NaCl or organic solvents addition. The lysogenic character of this strain was evidenced. Taken together, our results indicate that the autolytic phenotype in S. thermophilus is linked to the lysogenic character but does not result from the massive prophage induction under stressing conditions. [TOP OF PAGE]

  88. The Streptococcus thermophilus autolytic phenotype results from a leaky prophage. Husson-Kao, C., Mengaud, J., Cesselin, B., van, S.D., Benbadis, L., Chapot-Chartier, M.P. (2000). Appl. Environ. Microbiol. 66:558-565. Streptococcus thermophilus autolytic strains are characterized by a typical bell-shaped growth curve when grown under appropriate conditions. The cellular mechanisms involved in the triggering of lysis and the bacteriolytic activities of these strains were investigated in this study. Lactose depletion and organic solvents (ethanol, methanol, and chloroform) were shown to trigger a premature and immediate lysis of M17 exponentially growing cells. These factors and compounds are suspected to act by altering the cell envelope properties, causing either the permeabilization (organic solvents) or the depolarization (lactose depletion) of the cytoplasmic membrane. The autolytic character was shown to be associated with lysogeny. Phage particles, most of which were defective, were observed in the culture supernatants after both mitomycin C-induced and spontaneous lysis. By renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a bacteriolytic activity was detected at 31 kDa exclusively in the autolytic strains. This enzyme was detected during both growth and spontaneous lysis with the same intensity. We have shown that it was prophage encoded and homologous to the endolysin Lyt51 of the streptococcal temperate bacteriophage phi01205 (M. Sheehan, E. Stanley, G. F. Fitzgerald, and D. van Sinderen, Appl. Environ. Microbiol. 65:569-577, 1999). It appears from our results that the autolytic properties are conferred to the S. thermophilus strains by a leaky prophage but do not result from massive prophage induction. More specifically, we propose that phagic genes are constitutively expressed in almost all the cells at a low and nonlethal level and that lysis is controlled and achieved by the prophage-encoded lysis proteins. [TOP OF PAGE]

  89. Protocol for the manufacture of miniature washed-curd cheeses under controlled microbiological conditions. Hynes, E., Ogier, J.C., Delacroix-Buchet, A. (2000). International Dairy Journal 10:733-737. A protocol for the preparation of miniature washed-curd cheeses under controlled bacteriological conditions was designed and tested for reproducibility. The process was adapted from "Saint-Paulin" technology, and involves inoculation and renneting in autoclaved bottles, and cutting, stirring, curd washing and removal of whey by centrifugation. Pressing was simulated by low-speed centrifugation. All operations were performed using sterile techniques and autoclaved equipment. Forty miniature cheeses (approximately 40 g) were produced over 10 working days, and ripened for 28 days. Gross composition (dry matter, salt-in-moisture and pH) of the one-day-old cheeses did not differ significantly between cheesemaking days, and average values were 45.16, 2.46 and 5.15%, respectively. Adventitious Lactobacillus population remained less than 200 CFU g-1 all during ripening, and phages were absent. Nitrogen soluble at pH 4.4 and in phosphotungstic acid attained 21 and 3% of total nitrogen, respectively, in 28-day-old cheeses. The proposed model was shown to be suitable for the preparation of miniature cheese specimens for use in microbiological studies of cheese manufacture and ripening. [TOP OF PAGE]

  90. Inducible stx2 phages are lysogenized in the enteroaggregative and other phenotypic Escherichia coli O86:HNM isolated from patients. Iyoda, S., Tamura, K., Itoh, K., Izumiya, H., Ueno, N., Nagata, K., Togo, M., Terajima, J., Watanabe, H. (2000). FEMS Microbiol. Let. 191:7-10. We characterized two Shiga toxin-producing Escherichia coli (STEC) O86:HNM isolates from a patient with hemolytic uremic syndrome (HUS) or bloody diarrhea. Both of them did not possess the eaeA gene. However, the isolate from a HUS patient carried genetic markers of enteroaggregative E. coli (EAEC) and showed aggregative adherence pattern to HEp-2 cells. The other isolate from bloody diarrhea, which was negative with EAEC markers, was diffusely adhered to HEp-2 cells. The stx2 gene in both E. coli O86:HNM strains was encoded in each infectious phage, which was partially homologous to that of strain EDL933, a STEC O157:H7. These results will help to explain the genotypic divergences of STEC. [TOP OF PAGE]

  91. Ultraviolet radiation effects on bacterioplankton and viruses in marine ecosystems. Jeffrey, W.H., Kase, J.P., Wilhelm, S.W. (2000). pp. 206-236. In In De Mora, S.J. and et al. (eds.), Effects Of UV Radiation On Marine Ecosystems. Cambridge University Press, Cambridge. [TOP OF PAGE]

  92. Virus removal and transport in saturated and unsaturated sand columns. Jin, Y., Chu, Y., Li, Y. (2000). Journal of Contaminant Hydrology 43:111-128. The purpose of this research was to determine the role that unsaturated flow conditions play in virus sorption and inactivation during transport through sand columns. Column flow experiments were conducted in Ottawa sand under both saturated and unsaturated flow conditions using two bacteriophages, MS2 and phiX174. Input solution containing bromide (Br-) tracer and the viruses was applied to the column as a step function and samples were collected at the effluent end using a fraction collector. The convection-dispersion equation, partially calibrated with the transport parameters measured from the Br- signal, was used to evaluate the sorption and inactivation characteristics of the viruses. We found that, while removal of both MS2 and phiX174 increased significantly under unsaturated flow conditions, the mechanisms responsible for removing the two viruses seemed to be different. The results from elution experiments using beef extract solution revealed that the increased removal of phiX174 in the Ottawa sand under unsaturated conditions appeared to be caused by increased sorption whereas the increased removal of MS2 was due to inactivation. The difference in virus removal and transport behavior between saturated and unsaturated conditions was likely caused by additional sorption at the solid surfaces and the presence of the air-water interface (AWI) in the unsaturated system. [TOP OF PAGE]

  93. The microbial genetics of antibiotic cycling. John, J.F.J., Rice, L.B. (2000). INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY 21:S22-S31 Cycling of currently available antibiotics to reduce resistance is an attractive concept. For cycling strategies to be successful, their implementation must have a demonstrable impact on the prevalence of resistance determinants already dispersed throughout the hospital and associated healthcare facilities. While antibiotic use in hospitals clearly constitutes a stimulus for the emergence of resistance, it is by no means the only important factor. The incorporation of resistance determinants into potentially stable genetic structures, including bacteriophages, plasmids, transposons, and the more newly discovered movable elements termed integrons and gene cassettes, forces some degree of skepticism about the potential for such strategies in institutions where resistance determinants are already prevalent. In particular, the expanding role of integrons may pose an ultimate threat to formulary manipulations such as cycling. Despite these concerns, the crisis posed by antimicrobial resistance warrants investigation of any strategy with the potential for reducing the prevalence of resistance. Over the next decade, new studies with carefully designed outcomes should determine the utility of antibiotic cycling as one control measure for nosocomial resistance. [TOP OF PAGE]

  94. Structures of virus and virus-like particles. Johnson, J.E., Chiu, W. (2000). Current Opinion in Structural Biology 10:229-235. Virus structures continue to be the basis for mechanistic virology and serve as a paradigm for solutions to problems concerning macromolecular assembly and function in general. The use of X-ray crystallography, electron cryomicroscopy and computational and biochemical methods has provided not only details of the structural folds of individual viral components, but also insights into the structural basis of assembly, nucleic acid packaging, particle dynamics and interactions with cellular molecules. [TOP OF PAGE]

  95. Bacteriophage infections in the industrial acetone butanol (AB) fermentation process. Jones, D.T., Shirley, M., Wu, X., Keis, S. (2000). J Mol Microbiol Biotechnol 2:21-26. The reported incidence and effects of bacteriophage infections occurring in the industrial acetone butanol (AB) fermentation processes operated in the USA, Japan, and Puerto Rico during the earlier part of the twentieth century is reviewed. The growth characteristics and solvent-producing ability of a lysogenic strain of Clostridium madisonii isolated from a phage infection in Puerto Rico was determined in molasses fermentation medium. The host strain harbours a large lysogenic phage belonging to the Siphoviridae and the growth rate of the lysogenic strain was found to be slower than the non-lysogenic parent strain and exhibited reduced solvent production. The history of phage infections that occurred in the South African AB process is documented along with the various remedial actions that were taken to restore production. A more detailed account of the last phage infection that occurred in 1980 involving a small pseudo-lysogenic phage belonging to the Podoviridae is given. This phage infected Clostridium beijerinckii P260 and a number of closely related industrial strains. Factory-scale fermentations contaminated by this phage were compared with equivalent laboratory-scale control fermentations. The effect of the phage infection in the full-scale and laboratory-scale fermentations were monitored. Results obtained in laboratory-based studies included an assessment of the effect of the multiplicity of infection and the timing of phage infection. The general effects and symptoms of phage infections in the industrial AB fermentation are reviewed including gross changes in the fermentation and changes in cell morphology. Common techniques used for the diagnosis of phage infections and approaches for controlling phage contamination in the AB fermentation are discussed. Prevention strategies included good factory hygiene, sterilisation, decontamination and disinfection, and the use of resistant strains immunised against specific phages. [TOP OF PAGE]

  96. Isolation of coliphages specific to enterotoxigenic E. coli (ETEC). Jothikumar, N., Reddy, C.G., Sundari, R.B., Saigopal, D.V. (2000). Journal of Environmental Monitoring 2:372-374. Bacteriophages specific to Enterotoxigenic E. coli (ETEC) are reported for the first time. Out of 15 isolated phages only 10 were specific to strains of ETEC. All ten phages of dsDNA could be grouped into three different genotypes based on their RAPD patterns observed and it is likellly that they belong to only 3 different strains. The three phages yielded clear plaques on 10 strains of ETEC within 4-6 h at 37 degrees C. [TOP OF PAGE]

  97. Genomic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages. Juhala, R.J., Ford, M.E., Duda, R.L., Youlton, A., Hatfull, G.F., Hendrix, R.W. (2000). J. Mol. Biol. 299:27-51. We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022 (40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and members of the lambdoid or lambda-like group of phages. We provide a comparative analysis of these sequences with each other and with two previously determined lambdoid family genome sequences, those of E. coli phage lambda and Salmonella typhimurium phage P22. The comparisons confirm that these phages are genetic mosaics, with mosaic segments separated by sharp transitions in the sequence. The mosaici