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Sample records for bacteriophage felix o1

  1. Complete Genomic Sequence of Bacteriophage Felix O1

    Directory of Open Access Journals (Sweden)

    Andrew M. Kropinski

    2010-03-01

    Full Text Available Bacteriophage O1 is a Myoviridae A1 group member used historically for identifying Salmonella. Sequencing revealed a single, linear, 86,155-base-pair genome with 39% average G+C content, 131 open reading frames, and 22 tRNAs. Closest protein homologs occur in Erwinia amylovora phage φEa21-4 and Escherichia coli phage wV8. Proteomic analysis indentified structural proteins: Gp23, Gp36 (major tail protein, Gp49, Gp53, Gp54, Gp55, Gp57, Gp58 (major capsid protein, Gp59, Gp63, Gp64, Gp67, Gp68, Gp69, Gp73, Gp74 and Gp77 (tail fiber. Based on phage-host codon differences, 7 tRNAs could affect translation rate during infection. Introns, holin-lysin cassettes, bacterial toxin homologs and host RNA polymerase-modifying genes were absent.

  2. Detection of Salmonella spp. in milk by using Felix-O1 bacteriophage and high-pressure liquid chromatography.

    OpenAIRE

    Hirsh, D C; Martin, L. D.

    1983-01-01

    A method is described whereby the presence of less than five salmonellae was detected per milliliter of milk within 24 h of sample collection. Salmonellae were removed from milk by means of electropositive large-pore filters. Eluates from the filters were analyzed for the presence of Salmonella spp. by Felix-O1 bacteriophage and high-pressure liquid chromatographic techniques. The method gave only a positive response when salmonellae were present in the milk. Of the serotypes and strains of S...

  3. Bacteriophages

    International Nuclear Information System (INIS)

    Bacteriophages or phages are bacterial viruses and are present in the rumen in large numbers. They are obligate pathogens of bacteria and are ubiquitous to the rumen ecosystem. Bacteriophages are capable of lysing their bacterial hosts within the rumen and are therefore regarded as contributing to protein recycling within the rumen, a process identified as reducing the efficiency of feed utilization. However, their presence may not be entirely detrimental to the ecosystem, and it has been argued that phages may also be involved in the maintenance of a balanced ecosystem and may play a role in recycling limiting nutrients within the rumen. Furthermore, phage therapy is enjoying a renaissance and the use of phages to control or eliminate detrimental or unwanted microbes from the gastro-intestinal tract, such as Shiga-toxin producing E. coli (food-borne disease), Streptococcus bovis (acidosis in grain-fed cattle) and methanogens (produce the greenhouse gas methane), is the focus of current investigation. In order to be able to study the interaction between individual bacteriophages and their bacterial hosts, it is necessary to: (a) isolate the phage of interest from other viruses in the source material; (b) to derive stock cultures of known phage concentration; (c) store the isolated phages; and (d) determine basic physical characteristics, such as morphology. These procedures are achieved using classical microbiological procedures and this will be the methodology described in this chapter. It is also necessary to determine nucleic acid characteristics of the phage genome and to fingerprint the phage population in the rumen using molecular biological techniques. These will be described and discussed in Chapter 4.2

  4. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1.

    Directory of Open Access Journals (Sweden)

    Kimberley D Seed

    2012-09-01

    Full Text Available The Vibrio cholerae lipopolysaccharide O1 antigen is a major target of bacteriophages and the human immune system and is of critical importance for vaccine design. We used an O1-specific lytic bacteriophage as a tool to probe the capacity of V. cholerae to alter its O1 antigen and identified a novel mechanism by which this organism can modulate O antigen expression and exhibit intra-strain heterogeneity. We identified two phase variable genes required for O1 antigen biosynthesis, manA and wbeL. manA resides outside of the previously recognized O1 antigen biosynthetic locus, and encodes for a phosphomannose isomerase critical for the initial step in O1 antigen biosynthesis. We determined that manA and wbeL phase variants are attenuated for virulence, providing functional evidence to further support the critical role of the O1 antigen for infectivity. We provide the first report of phase variation modulating O1 antigen expression in V. cholerae, and show that the maintenance of these phase variable loci is an important means by which this facultative pathogen can generate the diverse subpopulations of cells needed for infecting the host intestinal tract and for escaping predation by an O1-specific phage.

  5. Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella

    Science.gov (United States)

    Bardina, Carlota; Colom, Joan; Spricigo, Denis A.; Otero, Jennifer; Sánchez-Osuna, Miquel; Cortés, Pilar; Llagostera, Montserrat

    2016-01-01

    Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large

  6. Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella.

    Science.gov (United States)

    Bardina, Carlota; Colom, Joan; Spricigo, Denis A; Otero, Jennifer; Sánchez-Osuna, Miquel; Cortés, Pilar; Llagostera, Montserrat

    2016-01-01

    Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large

  7. Genomics of three new bacteriophages useful in the biocontrol of Salmonella

    Directory of Open Access Journals (Sweden)

    Carlota eBardina

    2016-04-01

    Full Text Available Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87 able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs; 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic

  8. A full-acceptance detector at the LHC (FELIX)

    CERN Document Server

    Ageev, A N; Alvero, L; Amelino-Camelia, G; Avati, V; Baier, R; Bartels, Julius; Baur, G; Beneke, Martin; Berera, A; Bjorken, James D; Bondila, M; Britvich, G I; Capella, A; Close, Francis Edwin; Collins, J; Costa, C; Cudell, J R; Derevshchikov, A A; Dick, Louis; Dzhordzhadze, V; Dokshitzer, Y; Dormachie, A; Eggert, Karsten; Engel, R; Frankfurt, L L; Kinder-Geiger, Klaus; Giovannini, Alberto; Goloskokov, S V; Goulianos, K; Gridasov, V I; Gustafson, H R; Halzen, Francis; Hencken, K; Inyakin, A V; Islam, M M; Jones, L; Kaidalov, A B; Karapetian, G V; Karapetian, V V; Karpushov, I D; Kashtanov, E; Kharlov, Yu V; Khoze, V; Klein, S; Klimenko, E Y; Kozlov, O; Kowalski, K L; Kubarovsky, A V; Landshoff, Peter V; Leflat, A; Lippmaa, E; Manankov, V M; Marchesini, G; Medvedkov, A M; Mokhnatuk, V A; Müller, A H; Murzin, V S; Myznikov, K P; Nikitin, V A; Nomokonov, V P; Novikov, S I; Orava, Risto; Ostonen, R; Uvarov, V; Papageorgiou, E; Polyakov, V; Raidal, Martti; Rainwater, D L; Ranft, J; Riege, H; Rufanov, I A; Rubin, N; Sadovsky, S A; Salam, Gavin P; Sauli, Fabio; Schiff, D; Selyugin, O V; Shabalina, E K; Shabratova, G; Shuvalov, R S; Smirnov, V; Strikman, M I; Subbi, J; Sytnik, V V; Taylor, C; Tikhonova, L A; Toukhtarov, A; Treleani, D; Ugoccioni, R; Vasilchenko, V G; Vasilev, A; Vasiliev, L; White, A; Whitmore, J; Wlodarczyk, Z; Yakovlev, V; Yushchenko, O P; Zeppenfeld, Dieter; Zhalov, M B; Zinchenko, S I; Zotov, N P

    2002-01-01

    The FELIX collaboration had proposed the construction of a full- acceptance detector for the LHC. The primary mission of FELIX was the study of QCD: to provide comprehensive and definitive observations of a very broad range of strong-interaction processes. This document contains an extensive discussion of this physics menu. In a further paper the FELIX detector will be reviewed. (172 refs).

  9. FELIX construction status and experimental program

    International Nuclear Information System (INIS)

    FELIX (Fusion Electromagnetic Induction Experiment) is an experimental test facility being constructed at Argonne National Laboratory (ANL) for the study of electromagnetic effects in the first wall/blanket/shield (FWBS) systems of fusion reactors. The facility design, construction status, experimental program, instrumentation, and associated computer-code comparisons are described

  10. The Impact of the Felix Consent Decree.

    Science.gov (United States)

    Wataoka, Phuong

    This paper reviews the literature on the background, legal process, and implications of the Felix consent decree, a legal settlement in which the State of Hawaii agreed to improve its special education program and to develop a self-sustaining system of care for delivering special education services. The paper begins by reviewing federal laws (the…

  11. Tribute to Erwin Felix Lewy-Bertaut

    International Nuclear Information System (INIS)

    Erwin Lewy (alias Felix Bertaut) was born in 1913 in Germany, he emigrated to France where he undertook graduate studies in chemistry. Then, he joined the powder central laboratory where he learnt how to use international tables for structure determination. His thesis work was the X-ray study of the statistical distribution of the size of iron grains. The method Bertaut developed is still a reference in powder granulometry. Bertaut was also interested in the nascent neutron diffraction method and he flew to the United-States to improve his knowledge on this topic. Felix Bertaut created the neutron diffraction laboratory in the atomic research center in Grenoble and later he headed the CNRS' crystallography laboratory till 1982. Felix Bertaut and his laboratories became internationally renowned in crystallography, neutron diffraction and magnetism. He favored the scientific cooperation between France and Germany that led to the creation of the Laue-Langevin Institute (ILL). The ILL became European and was a key partner for building the European Synchrotron Facility (ESRF) in Grenoble. Bertaut was elected as a full member of the French Academy of Sciences in 1979, he died in 2003. (A.C.)

  12. FELIX: the detector readout upgrade of the ATLAS experiment

    CERN Document Server

    Ryu, Soo; The ATLAS collaboration

    2015-01-01

    After the Phase-I upgrade and onward, the Front-End Link eXchange(FELIX) system will be the interface between the readout system and the detector front-end electronics and trigger electronics at the ATLAS experiment. FELIX will function as a gateway to a commodity switched network which will use standard technologies (Ethernet or Infiniband) to communicate with data collecting and processing components. In this talk the system architecture of FELIX will be described and the testing results of the FELIX demonstrator will be presented

  13. New portable FELIX 3D display

    Science.gov (United States)

    Langhans, Knut; Bezecny, Daniel; Homann, Dennis; Bahr, Detlef; Vogt, Carsten; Blohm, Christian; Scharschmidt, Karl-Heinz

    1998-04-01

    An improved generation of our 'FELIX 3D Display' is presented. This system is compact, light, modular and easy to transport. The created volumetric images consist of many voxels, which are generated in a half-sphere display volume. In that way a spatial object can be displayed occupying a physical space with height, width and depth. The new FELIX generation uses a screen rotating with 20 revolutions per second. This target screen is mounted by an easy to change mechanism making it possible to use appropriate screens for the specific purpose of the display. An acousto-optic deflection unit with an integrated small diode pumped laser draws the images on the spinning screen. Images can consist of up to 10,000 voxels at a refresh rate of 20 Hz. Currently two different hardware systems are investigated. The first one is based on a standard PCMCIA digital/analog converter card as an interface and is controlled by a notebook. The developed software is provided with a graphical user interface enabling several animation features. The second, new prototype is designed to display images created by standard CAD applications. It includes the development of a new high speed hardware interface suitable for state-of-the- art fast and high resolution scanning devices, which require high data rates. A true 3D volume display as described will complement the broad range of 3D visualization tools, such as volume rendering packages, stereoscopic and virtual reality techniques, which have become widely available in recent years. Potential applications for the FELIX 3D display include imaging in the field so fair traffic control, medical imaging, computer aided design, science as well as entertainment.

  14. Tribute to Erwin Felix Lewy-Bertaut; Hommage a Erwin Felix Lewy-Bertaut

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2006-07-01

    Erwin Lewy (alias Felix Bertaut) was born in 1913 in Germany, he emigrated to France where he undertook graduate studies in chemistry. Then, he joined the powder central laboratory where he learnt how to use international tables for structure determination. His thesis work was the X-ray study of the statistical distribution of the size of iron grains. The method Bertaut developed is still a reference in powder granulometry. Bertaut was also interested in the nascent neutron diffraction method and he flew to the United-States to improve his knowledge on this topic. Felix Bertaut created the neutron diffraction laboratory in the atomic research center in Grenoble and later he headed the CNRS' crystallography laboratory till 1982. Felix Bertaut and his laboratories became internationally renowned in crystallography, neutron diffraction and magnetism. He favored the scientific cooperation between France and Germany that led to the creation of the Laue-Langevin Institute (ILL). The ILL became European and was a key partner for building the European Synchrotron Facility (ESRF) in Grenoble. Bertaut was elected as a full member of the French Academy of Sciences in 1979, he died in 2003. (A.C.)

  15. Research into communication between L1DDC and FELIX

    CERN Document Server

    Keser, Marceline

    2016-01-01

    This report describes the summer student project of Marceline Keser, performed with the team for the New Small Wheel electronics upgrade of ATLAS. The main goal of the project is to create communication between the FELIX and L1DDC, in order to create a bidirectional data transmission. During this project, research has been done and has resulted in a GBT link between the L1DDC and FELIX.

  16. Chlamydia bacteriophages.

    Science.gov (United States)

    Śliwa-Dominiak, Joanna; Suszyńska, Ewa; Pawlikowska, Małgorzata; Deptuła, Wiesław

    2013-11-01

    Phages are called "good viruses" due to their ability to infect and kill pathogenic bacteria. Chlamydia are small, Gram-negative (G-) microbes that can be dangerous to human and animals. In humans, these bacteria are etiological agents of diseases such as psittacosis or respiratory tract diseases, while in animals, the infection may result in enteritis in cattle and chronic bowel diseases, as well as miscarriages in sheep. The first-known representative of chlamydiaphages was Chp1. It was discovered in Chlamydia psittaci isolates. Since then, four more species of chlamydiaphages have been identified [Chp2, Chp3, φCPG1 φCPAR39 (φCpn1) and Chp4]. All of them were shown to infect Chlamydia species. This paper described all known chlamydiaphages. They were characterised in terms of origin, host range, and their molecular structure. The review concerns the characterisation of bacteriophages that infects pathogenic and dangerous bacteria with unusual, intracellular life cycles that are pathogenic. In the era of antibiotic resistance, it is difficult to cure chlamydophilosis. Those bacteriophages can be an alternative to antibiotics, but before this happens, we need to get to know chlamydiaphages better. PMID:23903989

  17. 21 CFR 866.3410 - Proteus spp. (Weil-Felix) serological reagents.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Proteus spp. (Weil-Felix) serological reagents... Proteus spp. (Weil-Felix) serological reagents. (a) Identification. Proteus spp. (Weil-Felix) serological... fluorescent dye (immunofluorescent reagents), derived from the bacterium Proteus vulgaris used...

  18. 3-dimensional analysis of FELIX brick with hole

    International Nuclear Information System (INIS)

    Electromagnetic induction on FELIX brick with a hole has been analyzed with 3-Dimensional EDDYNET computer code. Incorporating loop currents on hexahedral meshes, the 3-Dimensional EDDYNET program solves eddy current problems by a network approach, and provides good accuracy even for coarse meshes. (author)

  19. FELIX - the new detector readout system for the ATLAS experiment

    CERN Document Server

    AUTHOR|(SzGeCERN)754725; The ATLAS collaboration; Anderson, John Thomas; Borga, Andrea; Boterenbrood, Hendrik; Chen, Hucheng; Chen, Kai; Drake, Gary; Donszelmann, Mark; Francis, David; Gorini, Benedetto; Guest, Daniel; Lanni, Francesco; Lehmann Miotto, Giovanna; Levinson, Lorne; Roich, Alexander; Schreuder, Frans Philip; Schumacher, J\\"orn; Vandelli, Wainer; Vermeulen, Jos; Wu, Weihao; Zhang, Jinlong

    2016-01-01

    From the ATLAS Phase-I upgrade and onward, new or upgraded detectors and trigger systems will be interfaced to the data acquisition, detector control and timing (TTC) systems by the Front-End Link eXchange (FELIX). FELIX is the core of the new ATLAS Trigger/DAQ architecture. Functioning as a router between custom serial links and a commodity network, FELIX is implemented by server PCs with commodity network interfaces and PCIe cards with large FPGAs and many high speed serial fiber transceivers. By separating data transport from data manipulation, the latter can be done by software in commodity servers attached to the network. Replacing traditional point-to-point links between Front-end components and the DAQ system by a switched network, FELIX provides scaling, flexibility uniformity and upgradability. Different Front-end data types or different data sources can be routed to different network endpoints that handle that data type or source: e.g. event data, configuration, calibration, detector control, monito...

  20. BACTERIOPHAGE: BIOLOGY AND GENETICS

    Science.gov (United States)

    Bacteriophage are viruses that infect bacteria. Bacteriophage are very small and made up of a protein coat with an inner core containing their genetic material. They infect bacterium, by attaching to the bacterial cell and injecting their nucleic acids into the bacteria. The phages then use the bac...

  1. Tourist valorization of roman imperial city Felix Romuliana

    OpenAIRE

    Berić Dejan; Ivkov-Džigurski Anđelija; Tomić Nemanja

    2012-01-01

    The tourism industry is a great potential for the development of Serbia. The main characteristics of the existing and potential tourist offer of Serbia are interesting and diverse natural resources and cultural and historical heritage. Felix Romuliana, established palace of the Roman emperor Galerius, is located in the valley of the Black Timok, near Zaječar and the village of Gamzigrad in eastern Serbia. The palace was built in the late third and early fourth century, as a testamentary...

  2. Felix de Roy: a life of variable stars

    CERN Document Server

    Shears, Jeremy

    2010-01-01

    Felix de Roy (1883-1942), an internationality recognised amateur astronomer, made significant contributions to variable star research. As an active observer, he made some 91,000 visual estimates of a number of different variable stars. A Belgian national, he took refuge in England during World War 1. While there, de Roy became well enough known to later serve as Director of the BAA Variable Star Section for seventeen years. Through this office, and his connections with other organisations around the world, he encouraged others to pursue the observation of variable stars. Not merely content to accumulate observational data, de Roy also analysed the data and published numerous papers.

  3. New Cytotoxic 24-Homoscalarane Sesterterpenoids from the Sponge Ircinia felix

    Directory of Open Access Journals (Sweden)

    Ya-Yuan Lai

    2015-09-01

    Full Text Available Two new 24-homoscalarane sesterterpenoids, felixins F (1 and G (2, were isolated from the sponge Ircinia felix. The structures of new homoscalaranes 1 and 2 were elucidated by extensive spectroscopic methods, particularly with one-dimensional (1D and two-dimensional (2D NMR, and, by comparison, the spectral data with those of known analogues. The cytotoxicity of 1 and 2 against the proliferation of a limited panel of tumor cell lines was evaluated and 1 was found to show cytotoxicity toward the leukemia K562, MOLT-4, and SUP-T1 cells (IC50 ≤ 5.0 μM.

  4. Bacteriophage therapy against Enterobacteriaceae

    Institute of Scientific and Technical Information of China (English)

    Youqiang; Xu; Yong; Liu; Yang; Liu; Jiangsen; Pei; Su; Yao; Chi; Cheng

    2015-01-01

    The Enterobacteriaceae are a class of gram-negative facultative anaerobic rods, which can cause a variety of diseases, such as bacteremia, septic arthritis, endocarditis, osteomyelitis, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, intra-abdominal infections and ophthalmic infections, in humans, poultry, animals and fish. Disease caused by Enterobacteriaceae cause the deaths of millions of people every year, resulting in enormous economic loss. Drug treatment is a useful and efficient way to control Enterobacteriaceae infections. However, with the abuse of antibiotics, drug resistance has been found in growing number of Enterobacteriaceae infections and, as such, there is an urgent need to find new methods of control. Bacteriophage therapy is an efficient alternative to antibiotics as it employs a different antibacterial mechanism. This paper summarizes the history of bacteriophage therapy, its bacteriallytic mechanisms, and the studies that have focused on Enterobacteriaceae and bacteriophage therapy.

  5. The FELIX program of experiments and code development

    International Nuclear Information System (INIS)

    An experimental program and test bed called FELIX (Fusion Electromagnetic Induction Experiment) which is under construction at Argonne National Laboratory is described. The facility includes the following facilities; (a) a sizable constant field, analogous to a tokamak toroidal field or the confining field of a mirror reactor, (b) a pulsed field with a sizable rate of change, analogous to a pulsed poloidal field or to the changing field of a plasma disruption, perpendicular to the constant field, and (c) a sufficiently large volume to assure that large, complex test pieces can be tested, and that the forces, torques, currents, and field distortions which are developed are large enough to be measured accurately. The development of the necessary computer codes and the experimental program are examined. (U.K.)

  6. Summary of sensor evaluation for the Fusion ELectromagnetic Induction eXperiment (FELIX)

    International Nuclear Information System (INIS)

    As part of the First Wall/Blanket/Shield Engineering Test Program, a test bed called FELIX (Fusion ELectromagnetic Induction eXperiment) is now under construction at ANL. Its purpose will be to test, evaluate, and develop computer codes for the prediction of electromagnetically induced phenomenon in a magnetic environment modeling that of a fusion reaction. Crucial to this process is the sensing and recording of the various induced effects. Sensor evaluation for FELIX has reached the point where most sensor types have been evaluated and preliminary decisions are being made as to type and quantity for the initial FELIX experiments. These early experiments, the first, flat plate experiment in particular, will be aimed at testing the sensors as well as the pertinent theories involved. The reason for these evaluations, decisions, and proof tests is the harsh electrical and magnetic environment that FELIX presents

  7. Results from the FELIX experiments on electromagnetic effects in hollow cylinders

    International Nuclear Information System (INIS)

    The early experiments with the FELIX (Fusion Electromagnetic Induction eXperiments) facility have been devoted to obtaining data which can be used to validate eddy current computer codes. This paper describes experiments on field variation inside conducting cylinders

  8. FELIX: The New Approach for Interfacing to Front-end Electronics for the ATLAS Experiment

    CERN Document Server

    AUTHOR|(SzGeCERN)754725; The ATLAS collaboration; Anderson, John Thomas; Borga, Andrea; Boterenbrood, Hendrik; Chen, Hucheng; Chen, Kai; Drake, Gary; Donszelmann, Mark; Francis, David; Gorini, Benedetto; Guest, Daniel; Lanni, Francesco; Lehmann Miotto, Giovanna; Levinson, Lorne; Roich, Alexander; Schreuder, Frans Philip; Schumacher, J\\"orn; Vandelli, Wainer; Zhang, Jinlong

    2016-01-01

    From the ATLAS Phase-I upgrade and onward, new or upgraded detectors and trigger systems will be interfaced to the data acquisition, detector control and timing (TTC) systems by the Front-End Link eXchange (FELIX). FELIX is the core of the new ATLAS Trigger/DAQ architecture. Functioning as a router between custom serial links and a commodity network, FELIX is implemented by server PCs with commodity network interfaces and PCIe cards with large FPGAs and many high speed serial fiber transceivers. By separating data transport from data manipulation, the latter can be done by software in commodity servers attached to the network. Replacing traditional point-to-point links between Front-end components and the DAQ system by a switched network, FELIX provides scaling, flexibility uniformity and upgradability and reduces the diversity of custom hardware solutions in favour of software.

  9. Development of hardware configuration and testing tools for the FELIX project.

    CERN Document Server

    Rodriguez, Alberto

    2015-01-01

    This document contains a report about the work I have been doing during my stay as a summer student at CERN. The work described here is part of the FELIX project, a new system that will be progressively integrated in the ATLAS Data Acquisition System during Long Shutdowns 2 and 3. Specifically, my task consisted of the development of testing and configuration software for FELIX.

  10. Prof. dr. Felix Oinase mälestusõhtu külalisesinejad

    Index Scriptorium Estoniae

    2005-01-01

    on Jaan Undusk, kirjandusteadlane, kirjanik, Felix Oinase elutöö tundja Eestis. Tema ettekande teemaks on "Mõnda Felix Oinase teaduslikust mõtteviisist". New Yorki tuleb ka Jaani abikaasa Maarja Undusk, kes on kirjanik, kunstnik ja raamatuillustraator, tema toob külakostiks kaasa näituse oma töödest. Muusikaliseks esinejaks on kandlemängija Tiit Kao Kanadast. Ettekannete õhtu korraldab Eesti Kultuurifond Ameerika Ühendriikides 12. novembril 2005 New Yorgi Eesti Majas

  11. Cytoplasmic bacteriophage display system

    Science.gov (United States)

    Studier, F.W.; Rosenberg, A.H.

    1998-06-16

    Disclosed are display vectors comprising DNA encoding a portion of a structural protein from a cytoplasmic bacteriophage, joined covalently to a protein or peptide of interest. Exemplified are display vectors wherein the structural protein is the T7 bacteriophage capsid protein. More specifically, in the exemplified display vectors the C-terminal amino acid residue of the portion of the capsid protein is joined to the N-terminal residue of the protein or peptide of interest. The portion of the T7 capsid protein exemplified comprises an N-terminal portion corresponding to form 10B of the T7 capsid protein. The display vectors are useful for high copy number display or lower copy number display (with larger fusion). Compositions of the type described herein are useful in connection with methods for producing a virus displaying a protein or peptide of interest. 1 fig.

  12. Bacteriophages and Biofilms

    OpenAIRE

    Harper, David R; Helena M. R. T. Parracho; James Walker; Richard Sharp; Gavin Hughes; Maria Werthén; Susan Lehman; Sandra Morales

    2014-01-01

    Biofilms are an extremely common adaptation, allowing bacteria to colonize hostile environments. They present unique problems for antibiotics and biocides, both due to the nature of the extracellular matrix and to the presence within the biofilm of metabolically inactive persister cells. Such chemicals can be highly effective against planktonic bacterial cells, while being essentially ineffective against biofilms. By contrast, bacteriophages seem to have a greater ability to target this commo...

  13. Told by a myth: Thomas Mann’s Felix Krull

    Directory of Open Access Journals (Sweden)

    Montiel, Luis

    2013-12-01

    Full Text Available This article proposes an approach to the novel Bekenntnisse des Hochstaplers Felix Krull by Thomas Mann from the point of view of the imaginal psychology of James Hillman. From this perspective the novel seems to illustrate the most innovative thesis of that psychology, which is especially relevant for having been written prior to the formulation of Hillman’s theories. The unplanned correspondence between both ways of thinking furnishes a valuable argument that supports the new conception of human psyche introduced by Carl Gustav Jung and developed in this way by James Hillman.El presente artículo propone una lectura de la novela de Thomas Mann desde la óptica de la psicología imaginal de James Hillman. En esta perspectiva la novela parece ofrecer una ilustración de las tesis más innovadoras de dicha psicología, lo que resulta especialmente relevante por haber sido escrita con antelación a la formulación de las teorías del pensador estadounidense. La impremeditada correspondencia entre ambos pensamientos suministra un argumento digno de tenerse en cuenta a favor de la innovadora concepción de la psique humana inaugurada por Carl Gustav Jung y desarrollada en esta línea por James Hillman.

  14. Review of past experiments at the FELIX facility and future plans for ITER applications

    International Nuclear Information System (INIS)

    FELIX is an experimental test facility at Argonne National Laboratory (ANL) for the study of electromagnetic effects in first wall, blanket, shield systems of fusion reactors. From 1983 to 1986 five major test series, including static and dynamic tests, were conducted and are reviewed in this paper. The dynamic tests demonstrated an important coupling effect between eddy currents and motion in a conducting structure. Recently the US has proposed to the ITER Joint Central Team to use FELIX for testing mock-up components to study electromagnetic effects encountered during plasma disruptions and other off-normal events. The near and long term plans for ITER applications are discussed

  15. Review of past experiments at the FELIX facility and future plans for ITER applications

    International Nuclear Information System (INIS)

    FELIX is an experimental test facility at Argonne National Laboratory (ANL) for the study of electromagnetic effects in first wall, blanket, shield systems of fusion reactors. From 1983 to 1986 five major test series, including static and dynamic tests, were conducted and are reviewed in this paper. The dynamic tests demonstrated an important coupling effect between eddy currents and motion in a conducting structure. Recently the U.S. has proposed to the ITER Joint Central Team to use FELIX for testing mock-up components to study electromagnetic effects encountered during plasma disruptions and other off-normal events. The near and long term plans for ITER applications are discussed. (author)

  16. Genetically modified bacteriophages.

    Science.gov (United States)

    Sagona, Antonia P; Grigonyte, Aurelija M; MacDonald, Paul R; Jaramillo, Alfonso

    2016-04-18

    Phages or bacteriophages, viruses that infect and replicate inside bacteria, are the most abundant microorganisms on earth. The realization that antibiotic resistance poses a substantial risk to the world's health and global economy is revitalizing phage therapy as a potential solution. The increasing ease by which phage genomes can be modified, owing to the influx of new technologies, has led to an expansion of their natural capabilities, and a reduced dependence on phage isolation from environmental sources. This review will discuss the way synthetic biology has accelerated the construction of genetically modified phages and will describe the wide range of their applications. It will further provide insight into the societal and economic benefits that derive from the use of recombinant phages in various sectors, from health to biodetection, biocontrol and the food industry. PMID:26906932

  17. Deletion mutations of bacteriophage

    International Nuclear Information System (INIS)

    Resolution of mutation mechanism with structural changes of DNA was discussed through the studies using bacteriophage lambda. One of deletion mutations inductions of phage lambda is the irradiation of ultraviolet ray. It is not clear if the inductions are caused by errors in reparation of ultraviolet-induced damage or by the activation of int gene. Because the effective site of int gene lies within the regions unnecessary for existing, it is considered that int gene is connected to deletion mutations induction. A certain system using prophage complementarity enables to detect deletion mutations at essential hereditary sites and to solve the relations of deletion mutations with other recombination system, DNA reproduction and repairment system. Duplication and multiplication of hereditary elements were discussed. If lambda deletion mutations of the system, which can control recombination, reproduction and repairment of added DNA, are constructed, mutations mechanism with great changes of DNA structure can be solved by phage lambda. (Ichikawa, K.)

  18. Bacteriophages of methanotrophic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Tyutikow, F.M. (All-Union Research Inst. for Genetics and Selection of Industrial Microorganisms, Moscow, USSR); Bespalova, I.A.; Rebentish, B.A.; Aleksandrushkina, N.N.; Krivisky, A.S.

    1980-10-01

    Bacteriophages of methanotrophic bacteria have been found in 16 out of 88 studied samples (underground waters, pond water, soil, gas and oil installation waters, fermentor cultural fluids, bacterial paste, and rumen of cattle) taken in different geographic zones of the Soviet Union. Altogether, 23 phage strains were isolated. By fine structure, the phages were divided into two types (with very short or long noncontractile tails); by host range and serological properties, they fell into three types. All phages had guanine- and cytosine-rich double-stranded deoxyribonucleic acid consisting of common nitrogen bases. By all of the above-mentioned properties, all phages within each of the groups were completely identical to one another, but differed from phages of other groups.

  19. Measurements of reactor-relevant electromagnetic effects with the FELIX facility

    International Nuclear Information System (INIS)

    Recent experiments with the FELIX (Fusion Electromagnetic Induction eXperiment) facility at Argonne National Laboratory (ANL) suggest that the expected electromagnetic forces and torques in a tokamak first wall, blanket, and shield (FWBS) system can be modelled by a single eddy current mode, with a simple characterization

  20. Felix beyond the Closet: Sexuality, Masculinity, and Relations of Power in Arturo Islas's "The Rain God"

    Science.gov (United States)

    Padilla, Yolanda

    2009-01-01

    This essay examines the uneasy relationship that Arturo Islas's "The Rain God" has had with narratives of identity, focusing on how the representation of Felix's sexuality makes him a problematic figure for certain strains of Chicana/o and queer studies. In other writings, Islas criticizes Quinto Sol, the chief publishing house of Chicano…

  1. Lysogenic bacteriophage isolated from acidophilium

    Science.gov (United States)

    Ward, Thomas W.; Bruhn, Debby F.; Bulmer, Deborah K.

    1992-01-01

    A bacteriophage identified as .phi.Ac1 capable of infecting acidophilic heterotropic bacteria (such as Acidiphilium sp.) and processes for genetically engineering acidophilic bacteria for biomining or sulfur removal from coal are disclosed. The bacteriophage is capable of growth in cells existing at pH at or below 3.0. Lytic forms of the phage introduced into areas experiencing acid drainage kill the bacteria causing such drainage. Lysogenic forms of the phase having genes for selective removal of metallic or nonmetallic elements can be introduced into acidophilic bacteria to effect removal of the desired element form ore or coal.

  2. Told by a myth: Thomas Mann’s Felix Krull

    OpenAIRE

    Montiel, Luis

    2013-01-01

    This article proposes an approach to the novel Bekenntnisse des Hochstaplers Felix Krull by Thomas Mann from the point of view of the imaginal psychology of James Hillman. From this perspective the novel seems to illustrate the most innovative thesis of that psychology, which is especially relevant for having been written prior to the formulation of Hillman’s theories. The unplanned correspondence between both ways of thinking furnishes a valuable argument that supports the new conception of ...

  3. FCJ-121 Transversalising the Ecological Turn: Four Components of Felix Guattari’s Ecosophical Perspective

    OpenAIRE

    John Tinnell

    2011-01-01

    Many humanities scholars are working to transform their disciplines in response to new conditions and problems emerging in the twenty-first century. Arguably, two of the most important forces affecting contemporary global culture are the growing awareness of the ecological crisis and the proliferation of digital media. This essay endeavors to develop Felix Guattari’s “unfinished” concept of ecosophy into a theoretical framework for constructing productive syntheses between the ecological an...

  4. FELIX: a High-Throughput Network Approach for Interfacing to Front End Electronics for ATLAS Upgrades

    CERN Document Server

    Anderson, John Thomas; The ATLAS collaboration; Boterenbrood, Hendrik; Chen, Hucheng; Chen, Kai; Drake, Gary; Francis, David; Gorini, Benedetto; Lanni, Francesco; Lehmann Miotto, Giovanna; Levinson, Lorne; Narevicius, Julia; Plessl, Christian; Roich, Alexander; Ryu, Soo; Schreuder, Frans Philip; Schumacher, Jorn; Vandelli, Wainer; Vermeulen, Jos; Zhang, Jinlong

    2015-01-01

    The ATLAS experiment at CERN is planning full deployment of a new unified optical link technology for connecting detector front end electronics on the timescale of the LHC Run 4 (2025). It is estimated that roughly 8000 GBT (GigaBit Transceiver) links, with transfer rates up to 10.24~Gbps, will replace existing links used for readout, detector control and distribution of timing and trigger information. A new class of devices will be needed to interface many GBT links to the rest of the trigger, data-acquisition and detector control systems. In this paper FELIX (Front End LInk eXchange) is presented, a PC-based device to route data from and to multiple GBT links via a high-performance general purpose network capable of a total throughput up to O(20 Tbps). FELIX implies architectural changes to the ATLAS data acquisition system, such as the use of industry standard COTS components early in the DAQ chain. Additionally the design and implementation of a FELIX demonstration platform is presented, and hardware and ...

  5. Replication of bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    In this paper results of studies on the mechanism of bacteriophage lambda replication using molecular biological and biochemical approaches are reported. The purification of the initiator proteins, O and P, and the role of the O and P proteins in the initiation of lambda DNA replication through interactions with specific DNA sequences are described. 47 references, 15 figures

  6. Bacteriophage biocontrol of foodborne pathogens.

    Science.gov (United States)

    Kazi, Mustafa; Annapure, Uday S

    2016-03-01

    Bacteriophages are viruses that only infect bacterial cells. Phages are categorized based on the type of their life cycle, the lytic cycle cause lysis of the bacterium with the release of multiple phage particles where as in lysogenic phase the phage DNA is incorporated into the bacterial genome. Lysogeny does not result in lysis of the host. Lytic phages have several potential applications in the food industry as biocontrol agents, biopreservatives and as tools for detecting pathogens. They have also been proposed as alternatives to antibiotics in animal health. Two unique features of phage relevant for food safety are that they are harmless to mammalian cells and high host specificity, keeping the natural microbiota undisturbed. However, the recent approval of bacteriophages as food additives has opened the discussion about 'edible viruses'. This article reviews in detail the application of phages for the control of foodborne pathogens in a process known as "biocontrol". PMID:27570260

  7. FELIX experiments and computational needs for eddy current analysis of fusion reactors

    International Nuclear Information System (INIS)

    In a fusion reactor, changing magnetic fields are closely coupled to the electrically-conducting metal structure. This coupling is particularly pronounced in a tokamak reactor in which magnetic fields are used to confine, stabilize, drive, and heat the plasma. Electromagnetic effects in future fusion reactors will have far-reaching implications in the configuration, operation, and maintenance of the reactors. This paper describes the impact of eddy-current effects on future reactors, the requirements of computer codes for analyzing those effects, and the FELIX experiments which will provide needed data for code validation

  8. Coupling between angular deflection and eddy currents in the FELIX plate experiment

    International Nuclear Information System (INIS)

    For a conducting body experiencing superimposed changing and steady magnetic field, for example a limiter in a tokamak during plasma quench, the induced eddy currents and the deflections resulting from those eddy currents are coupled. Experimental study of these coupled deflections and currents can be performed with the FELIX (Fusion Electromagnetic Induction Experiment) facility nearing completion at ANL. Predictions of the coupling are described, as computed with the code EDDYNET, which has been modified for this purpose. Effects of the coupling will be readily observable experimentally. In the FELIX plate experiment, the coupling between deflection and eddy currents was readily calculated because the rigid-body rotation of the plate is equivalent to a contrarotation of the applied magnetic fields. For a geometry such as a plasma limiter, in which the eddy currents would cause a deformation of the conducting body, an analysis of the coupling between eddy currents and deformation would require a structural-analysis code and an eddy current code to be simultaneously computing from the same mesh

  9. Review: Felix Heidenreich (2011: Theorien der Gerechtigkeit - Eine Einführung

    Directory of Open Access Journals (Sweden)

    Kramer, Hans-Ulrich

    2012-12-01

    Full Text Available Schon vor der griechischen Antike, nämlich bei den alten Ägyptern und im alten Israel ansetzend, werden unter dem Titel „Antike: Gegebene Gerechtigkeit“(Kapitel 2 anschließend die Theorien der griechischen Klassiker Platon und Aristoteles sowie des Römers Cicero behandelt. Weiter geht es in chronologischer, übersichtlicher Gliederung mit den zwei Gerechtigkeiten des Mittelalters (Kapitel 3, die auf der Zwei-Reiche-Lehre des Augustinus‘ aufbauen. Kapitel 4 steht unter dem Motto: „Neuzeit: Gerechtigkeit wird machbar“ undversammelt die Theorien von Machiavelli über Hobbes, Rousseau und Kant bis hin zu John Stuart Mill. In Kapitel 5 rekapituliertFelix Heidenreich dann Positionen in der aktuellen Debatte. Diese reichen unter anderem von dem sozialliberalen Denker John Rawls über die Kommunitaristen Alasdair MacIntyre und Michael Walzer bis hin zumdeutschen Philosophen und Diskursethiker Jürgen Habermas oder dem indischen Ökonomen Amartya Sen. In Kapitel 6 löst sich Felix Heidenreich schließlich von der personenbezogenen Auflistung und spricht von aktuellen Problemlagen der Gerechtigkeit, etwa der sozialen Gerechtigkeit, der Gerechtigkeit zwischen Frau und Mann oderauch der ökologischen und intergenerationellen Gerechtigkeit. Ein Ausblick zur Gerechtigkeitspolitik rundet den gut strukturierten,rund 250-seitigen Band ab.

  10. Radiation protection Aspects Using the Thermal Waters from the Felix-1 Mai-Oradea Geothermal Deposit

    International Nuclear Information System (INIS)

    Full text: The geothermal 'Felix-1 Mai-Oradea' deposit is situated in the western part of Romania and it is well known long years ago. The waters of this deposit are used in the medical treatments in the two resorts (Felix and 1 Mai) and for heating and swimming pools in Oradea town. The deposit depth (2500-3000 m) determines a high temperature (66-900 deg. C) of these waters also a mineral content of 200-1400 mg/l, the main components being Ca and Mg. First time, during some years, the thermal water was directly used in the central heating radiators from 'Nufarul' residential district. At present a heating switch installation is utilised. The high radium content of these thermal waters comparatively with Italian or Japanese thermal waters suggested us a study of radium deposition on the inner walls of the pipes also in the inner central heating radiators. Analysing these depositions using a high resolution Ge-Li detector, the radium-226 and small quantities of radium-224 and 223 isotopes were registered. Average radium-226 deposition was 1200 Bq/kg. (author)

  11. Two bacteriophages of Clostridium difficile.

    OpenAIRE

    Mahony, D E; Bell, P D; Easterbrook, K. B.

    1985-01-01

    Two temperate bacteriophages of differing morphology and host range were isolated by screening 94 isolates of Clostridium difficile. Phage 41 had a 300-nm flexible tail, whereas phage 56 had a shorter tail with a contractile sheath. Electron microscopy of phage 56 lysates exposed to elevated magnesium concentrations showed small virus-like particles which were 21 nm in diameter. The addition of MgCl2 to semisolid agar overlays enhanced both the titer and plaque size of phage 56. Phage 56 was ...

  12. Propagating the missing bacteriophages: a large bacteriophage in a new class

    Directory of Open Access Journals (Sweden)

    Hardies Stephen C

    2007-02-01

    Full Text Available Abstract The number of successful propagations/isolations of soil-borne bacteriophages is small in comparison to the number of bacteriophages observed by microscopy (great plaque count anomaly. As one resolution of the great plaque count anomaly, we use propagation in ultra-dilute agarose gels to isolate a Bacillus thuringiensis bacteriophage with a large head (95 nm in diameter, tail (486 × 26 nm, corkscrew-like tail fibers (187 × 10 nm and genome (221 Kb that cannot be detected by the usual procedures of microbiology. This new bacteriophage, called 0305φ8-36 (first number is month/year of isolation; remaining two numbers identify the host and bacteriophage, has a high dependence of plaque size on the concentration of a supporting agarose gel. Bacteriophage 0305φ8-36 does not propagate in the traditional gels used for bacteriophage plaque formation and also does not produce visible lysis of liquid cultures. Bacteriophage 0305φ8-36 aggregates and, during de novo isolation from the environment, is likely to be invisible to procedures of physical detection that use either filtration or centrifugal pelleting to remove bacteria. Bacteriophage 0305φ8-36 is in a new genomic class, based on genes for both structural components and DNA packaging ATPase. Thus, knowledge of environmental virus diversity is expanded with prospect of greater future expansion.

  13. Measurements of reactor-relevant electromagnetic effects with the FELIX facility

    International Nuclear Information System (INIS)

    In predicting the electromagnetic consequences of a plasma disruption in a tokamak reactor design, a two-dimensional electromagnetic model of the first wall, blanket, and shield (FWBS) system is typically used. The response to a decaying plasma current is then found to be dominated by a single eddy-current mode, with a single L/R time. Recent experiments with the Fusion ELectromagnetic Induction eXperiment (FELIX) facility at Argonne National Laboratory suggest that such modeling can be used to design against electromagnetic forces and torques, but only if a range of values is used for both tau, the plasma decay time, and tau0, the L/R time of the FWBS system

  14. The science and politics of forest management in Northern Nicaragua after hurricane Felix (2007)

    Science.gov (United States)

    Rossi Idarraga, Esteban

    This dissertation examines the ecological effects of hurricane Felix (2007) in Northern Nicaragua as well as the socio-political factors that influenced forest management efforts in hurricane impacted locations. Specifically, this research focused on the following questions: first, what were the regional damage patterns caused by hurricane Felix on the forests of Northern Nicaragua? Second, what stand and tree attributes explain observed post-hurricane damage patterns? And, third, why were post-hurricane management efforts unsuccessful? The first dissertation article characterizes the intensity and spatial distribution of forest damage after hurricane Felix using satellite imagery from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor and aerial photographs. Results indicated that Broadleaf forests experienced larger damage (>75% trees blown down) than Pine forest, and that Enhanced Vegetation Index data (EVI), obtained from the MODIS sensor, can adequately depict post-hurricane damage in tropical forests. The agreement between the obtained EVI damage map and the reference data set ranged from 91% in high-damage locations to 85% in low-damage locations, with 86% overall agreement. The second dissertation article describes the relationship between hurricane damage patterns and ecological variables at the local level. Specifically, it characterizes the relationship between tree-and-stand attributes (i.e. DBH, height, density, basal area) and wind damage, using field data. Findings indicate that tree attributes such as DBH and height strongly influenced the amount and type of wind damage and that stand attributes such as maximum canopy height and distance to the hurricane path were also predictive of the amount of damage. Observed differences in damage patterns among broadleaf and pine forests were strongly correlated with the height to diameter ratio (H/D). Field observations showed that while post-hurricane regeneration was abundant in broadleaf

  15. Host receptors for bacteriophage adsorption.

    Science.gov (United States)

    Bertozzi Silva, Juliano; Storms, Zachary; Sauvageau, Dominic

    2016-02-01

    The adsorption of bacteriophages (phages) onto host cells is, in all but a few rare cases, a sine qua non condition for the onset of the infection process. Understanding the mechanisms involved and the factors affecting it is, thus, crucial for the investigation of host-phage interactions. This review provides a survey of the phage host receptors involved in recognition and adsorption and their interactions during attachment. Comprehension of the whole infection process, starting with the adsorption step, can enable and accelerate our understanding of phage ecology and the development of phage-based technologies. To assist in this effort, we have established an open-access resource--the Phage Receptor Database (PhReD)--to serve as a repository for information on known and newly identified phage receptors. PMID:26755501

  16. Felix Vodička: Úkoly literární historie a jejich zdroj

    Czech Academy of Sciences Publication Activity Database

    Kubíček, Tomáš

    2010-01-01

    Roč. 92, 1/2 (2010), s. 85-94. ISSN 0862-8459. [100 let generace prvních žáků PLK. Praha, 09.02.2009-09.02.2009] R&D Projects: GA ČR GA405/07/0077 Institutional research plan: CEZ:AV0Z90560517 Keywords : history of literature * Vodička, Felix * structuralism Subject RIV: AJ - Letters, Mass-media, Audiovision

  17. Complete Genome Sequences of Five Bacteriophages That Infect Rhodobacter capsulatus

    Science.gov (United States)

    Bernardoni, Brooke; Bockman, Matthew R.; Miller, Brenda M.; Russell, Daniel A.; Delesalle, Veronique A.; Krukonis, Gregory P.; Hatfull, Graham F.; Cross, Madeline R.; Szewczyk, Marlena M.; Eppurath, Atul

    2016-01-01

    Five bacteriophages that infect the Rhodobacter capsulatus strain YW1 were isolated from stream water near Bloomington, Illinois, USA. Two distinct genome types are represented in the newly isolated bacteriophages. These genomes are different from other bacteriophage genomes previously described. PMID:27231352

  18. Complete Genome Sequence of Bacillus thuringiensis Bacteriophage BMBtp2

    OpenAIRE

    Dong, Zhaoxia; Peng, Donghai; Wang, Yueying; Zhu, Lei; Ruan, Lifang; Sun, Ming

    2013-01-01

    Bacillus thuringiensis is an insect pathogen which has been widely used for biocontrol. During B. thuringiensis fermentation, lysogenic bacteriophages cause severe losses of yield. Here, we announce the complete genome sequence of a bacteriophage, BMBtp2, which is induced from B. thuringiensis strain YBT-1765, which may be helpful to clarify the mechanism involved in bacteriophage contamination.

  19. Neutron irradiation of bacteriophage λ

    International Nuclear Information System (INIS)

    Double strand breaks (DSB) are the most dangerous lesions in DNA caused by irradiation, but many other lesions, usually called mutations, have not been clearly identified. These lesions, like DSB, can be the source of serious chromosomal damages and finally - cell death. Growing interest in heavy particles for radiotherapy and radioprotection encourages the search of the molecular basis of their action. In this respect, we chose bacteriophage λ1390 as the model system for the study of consequences of neutron irradiation. This derivative of λ phage possesses an unique ability to reversibly reorganize their genome in response to various selective pressures. The phages were irradiated with 13 Gy of mixed neutrons (7.5 Gy from fast and 5.6 Gy from thermal neutrons) and phages genomes were tested to DSB and mutations. Additionally, the stability of λ capsid proteins were tested. After all tests, we can conclude that, under our conditions, low flux of neutrons does not induce neither DNA strand break or DNA mutation nor the stability of λ capsid proteins. (author)

  20. Photodynamic Inactivation of Mammalian Viruses and Bacteriophages

    Directory of Open Access Journals (Sweden)

    Liliana Costa

    2012-06-01

    Full Text Available Photodynamic inactivation (PDI has been used to inactivate microorganisms through the use of photosensitizers. The inactivation of mammalian viruses and bacteriophages by photosensitization has been applied with success since the first decades of the last century. Due to the fact that mammalian viruses are known to pose a threat to public health and that bacteriophages are frequently used as models of mammalian viruses, it is important to know and understand the mechanisms and photodynamic procedures involved in their photoinactivation. The aim of this review is to (i summarize the main approaches developed until now for the photodynamic inactivation of bacteriophages and mammalian viruses and, (ii discuss and compare the present state of the art of mammalian viruses PDI with phage photoinactivation, with special focus on the most relevant mechanisms, molecular targets and factors affecting the viral inactivation process.

  1. Rb-Sr geochronology from Sao Felix to Xingu: preliminary results

    International Nuclear Information System (INIS)

    Rb-Sr systematics have been applied on rocks from the Sao Felix do Xingu region, in the southeastern part of the State of Para. An age of 2716 ± 34 Ma with IR of 0.70292 ± 0.00030 (MSWD = 1.54) and an age of 2677 ± 50 Ma with IR of 0.70161 ± 0.00022 (MSWD = 5.21) had been obtained for a granitic body and a tonalitic body respectively, both of them associated to the green stones belts that occur in this area. Gneisses from the Xingu complex gave an age of 2574 ± 57 Ma with an IR of 0.70416 ± 0.00054 (MSWD = 5.06). An age of 1653 ± 14 Ma with IR of 0.70823 ± 0.02361 (MSWD = 1.71) had been obtained for the Velho Guilherme granite that crosscut the granite-green stones terrains. Such geochronological data show the existence of a magmatic event between 2.72 Ga and 2.68 Ga and permit us to conclude on the archaean age of the green stones terrains. (author)

  2. 3-D transient eddy current calculations for the FELIX cylinder experiments

    International Nuclear Information System (INIS)

    The three-dimensional eddy current transient field problem is formulated first using the U-V method. This method breaks the vector Helmholtz equation into two scalar Helmholtz equations. Null field integral equations and the appropriate boundary conditions are used to set up an identification matrix which is independent of null field point locations. Embedded in the identification matrix are the unknown eigenvalues of the problem representing its impulse response in time. These eigenvalues are found by equating the determinant of the identification matrix to zero. When this initial forcing function is Fourier decomposed into its spatial harmonics, each Fourier component can be associated with a unique eigenvalue by this technique. The true transient solution comes through a convolution of the impulse response so obtained with the particular external field decay governing the problem at hand. The technique is applied to the FELIX cylinder experiments; computed results are compared to data. A pseudoanalytic confirmation of the eigenvalues so obtained is formulated to validate the procedure

  3. Felix: A Topology based Framework for Visual Exploration of Cosmic Filaments

    CERN Document Server

    Shivshankar, Nithin; Natarajan, Vijay; van de Weygaert, Rien; Bos, E G Patrick; Rieder, Steven

    2015-01-01

    The large-scale structure of the universe is comprised of virialized blob-like clusters, linear filaments, sheet-like walls and huge near empty three-dimensional voids. Characterizing the large scale universe is essential to our understanding of the formation and evolution of galaxies. The density range of clusters, walls and voids are relatively well separated, when compared to filaments, which span a relatively larger range. The large scale filamentary network thus forms an intricate part of the cosmic web. In this paper, we describe Felix, a topology based framework for visual exploration of filaments in the cosmic web. The filamentary structure is represented by the ascending manifold geometry of the 2-saddles in the Morse-Smale complex of the density field. We generate a hierarchy of Morse-Smale complexes and query for filaments based on the density ranges at the end points of the filaments. The query is processed efficiently over the entire hierarchical Morse-Smale complex, allowing for interactive visu...

  4. FCJ-121 Transversalising the Ecological Turn: Four Components of Felix Guattari’s Ecosophical Perspective

    Directory of Open Access Journals (Sweden)

    John Tinnell

    2011-10-01

    Full Text Available Many humanities scholars are working to transform their disciplines in response to new conditions and problems emerging in the twenty-first century. Arguably, two of the most important forces affecting contemporary global culture are the growing awareness of the ecological crisis and the proliferation of digital media. This essay endeavors to develop Felix Guattari’s “unfinished” concept of ecosophy into a theoretical framework for constructing productive syntheses between the ecological and the digital. In general, the essay first articulates ecosophical models of individual and collective subjectivity, and then argues that the best way to sustain ecosophical identity experience is to invent “post-media” practices, which harness the networked infrastructure of digital media such that specific pedagogical engagements with the technology effectively maximise the user’s capacity to affect and be affected by immanent forces in the world. In addition, this Guattarian rethinking of the ecological turn concurrently challenges the philosophical basis of the pedagogy of Nature appreciation that has characterised the eco-humanities landscape since the 1970s. The essay’s conclusions gesture toward a transversal eco-humanities, which would be rhizomatically rooted in Guattari’s preference for autopoiesis and becoming-other (via new media, rather than a static allegiance to the ideals of “Self-realisation” postulated by the deep ecology movement.

  5. Evidence for a lineage of virulent bacteriophages that target Campylobacter

    Directory of Open Access Journals (Sweden)

    Cummings Nicola

    2010-03-01

    Full Text Available Abstract Background Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in such therapies is a thorough understanding of their genetic complement, genome stability and their ecology to avoid the dissemination or mobilisation of phage or bacterial virulence and toxin genes. Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism. Results Sequencing and genome analysis was performed for two Campylobacter bacteriophages. The genomes were extremely similar at the nucleotide level (≥ 96% with most differences accounted for by novel insertion sequences, DNA methylases and an approximately 10 kb contiguous region of metabolic genes that were dissimilar at the sequence level but similar in gene function between the two phages. Both bacteriophages contained a large number of radical S-adenosylmethionine (SAM genes, presumably involved in boosting host metabolism during infection, as well as evidence that many genes had been acquired from a wide range of bacterial species. Further bacteriophages, from the UK Campylobacter typing set, were screened for the presence of bacteriophage structural genes, DNA methylases, mobile genetic elements and regulatory genes identified from the genome sequences. The results indicate that many of these bacteriophages are related, with 10 out of 15 showing some relationship to the sequenced genomes. Conclusions Two large virulent Campylobacter bacteriophages were found to show very high levels of sequence conservation despite separation in time and place of isolation. The bacteriophages show adaptations to their host and possess genes that may enhance Campylobacter metabolism, potentially advantaging both the bacteriophage and its host

  6. Bacteriophages as Potential Treatment for Urinary Tract Infections

    Science.gov (United States)

    Sybesma, Wilbert; Zbinden, Reinhard; Chanishvili, Nino; Kutateladze, Mzia; Chkhotua, Archil; Ujmajuridze, Aleksandre; Mehnert, Ulrich; Kessler, Thomas M.

    2016-01-01

    Background: Urinary tract infections (UTIs) are among the most prevalent microbial diseases and their financial burden on society is substantial. The continuing increase of antibiotic resistance worldwide is alarming so that well-tolerated, highly effective therapeutic alternatives are urgently needed. Objective: To investigate the effect of bacteriophages on Escherichia coli and Klebsiella pneumoniae strains isolated from the urine of patients suffering from UTIs. Material and methods: Forty-one E. coli and 9 K. pneumoniae strains, isolated from the urine of patients suffering from UTIs, were tested in vitro for their susceptibility toward bacteriophages. The bacteriophages originated from either commercially available bacteriophage cocktails registered in Georgia or from the bacteriophage collection of the George Eliava Institute of Bacteriophage, Microbiology and Virology. In vitro screening of bacterial strains was performed by use of the spot-test method. The experiments were implemented three times by different groups of scientists. Results: The lytic activity of the commercial bacteriophage cocktails on the 41 E. coli strains varied between 66% (Pyo bacteriophage) and 93% (Enko bacteriophage). After bacteriophage adaptation of the Pyo bacteriophage cocktail, its lytic activity was increased from 66 to 93% and only one E. coli strain remained resistant. One bacteriophage of the Eliava collection could lyse all 9 K. pneumoniae strains. Conclusions: Based on the high lytic activity and the potential of resistance optimization by direct adaption of bacteriophages as reported in this study, and in view of the continuing increase of antibiotic resistance worldwide, bacteriophage therapy is a promising treatment option for UTIs highly warranting randomized controlled trials.

  7. Bacteriophages from the forestomachs of Australian marsupials.

    OpenAIRE

    Klieve, A V

    1991-01-01

    Bacteriophages were observed in forestomach contents from three species of Australian macropodoid marsupials possessing a foregut fermentative digestion: the eastern grey kangaroo (Macropus giganteus), the eastern wallaroo (Macropus robustus robustus), and the rufous bettong (Aepyprymnus rufescens). Forty-six morphologically distinct phage types, representing the families Myoviridae, Siphoviridae, and Podoviridae, were identified. The range of forms varied between host species. The greatest d...

  8. An Undergraduate Laboratory Activity Demonstrating Bacteriophage Specificity

    Directory of Open Access Journals (Sweden)

    Mary E. Allen

    2013-02-01

    Full Text Available Bacteriophage are among the most diverse and numerous microbes inhabiting our planet. Yet many laboratory activities fail to engage students in meaningful exploration of their diversity, unique characteristics, and abundance. In this curriculum activity students use a standard plaque assay to enumerate bacteriophage particles from a natural sample and use the scientific method to address questions about host specificity and diversity. A raw primary sewage sample is enriched for bacteriophage using hosts in the family Enterobacteriaceae. Students hypothesize about host specificity and use quantitative data (serial dilution and plaque assay to test their hypotheses. Combined class data also help them answer questions about phage diversity. The exercise was field tested with a class of 47 students using pre- and posttests. For all learning outcomes posttest scores were higher than pretest scores at or below p = 0.01. Average individualized learning gain (G was also calculated for each learning outcome. Students’ use of scientific language in reference to bacteriophage and host interaction significantly improved (p = 0.002; G = 0.50. Improved means of expression helped students construct better hypotheses on phage host specificity (G = 0.31, p = 0.01 and to explain the plaque assay method (G = 0.33, p = 0.002. At the end of the exercise students also demonstrated improved knowledge and understanding of phage specificity as related to phage therapy in humans (p < 0.001; G = 51.

  9. Comparative genomics of Shiga toxin encoding bacteriophages

    Directory of Open Access Journals (Sweden)

    Smith Darren L

    2012-07-01

    Full Text Available Abstract Background Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as Ф24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages. Results The genome of the Stx2 encoding phage, Ф24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC, however Ф24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system. Conclusions The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.

  10. Molecular Biology and Biotechnology of Bacteriophage

    Science.gov (United States)

    Onodera, Kazukiyo

    The development of the molecular biology of bacteriophage such as T4, lambda and filamentous phages was described and the process that the fundamental knowledge obtained in this field has subsequently led us to the technology of phage display was introduced.

  11. FELIX-1.0: A finite element solver for the time dependent generator coordinate method with the Gaussian overlap approximation

    CERN Document Server

    Regnier, D; Dubray, N; Schunck, N

    2015-01-01

    We describe the software package FELIX that solves the equations of the time-dependent generator coordinate method (TDGCM) in N-dimensions (N $\\geq$ 1) under the Gaussian overlap approximation. The numerical resolution is based on the Galerkin finite element discretization of the collective space and the Crank-Nicolson scheme for time integration. The TDGCM solver is implemented entirely in C++. Several additional tools written in C++, Python or bash scripting language are also included for convenience. In this paper, the solver is tested with a series of benchmarks calculations. We also demonstrate the ability of our code to handle a realistic calculation of fission dynamics.

  12. Evolution and the complexity of bacteriophages

    Directory of Open Access Journals (Sweden)

    Serwer Philip

    2007-03-01

    Full Text Available Abstract Background The genomes of both long-genome (> 200 Kb bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions. Hypothesis Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1 Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2 Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection. (3 The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection. (4 The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems. Testing the hypothesis I propose testing this hypothesis by controlled evolution in microbial communities to (1 determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2 find the environmental conditions that

  13. Use of bacteriophages to control biofilms

    OpenAIRE

    Sillankorva, Sanna

    2009-01-01

    Tese de doutoramento em Engenharia Química e Biológica After several years of abandonment, the use of bacteriophages (phages) for killing bacteria has withdrawn recent attention and reappraisal. This has led to a vast phage research, in varied fields, with impressive outcomes and currently several studies are ongoing with animals, horticulture and agriculture products, and even with humans. Despite this enthusiasm, there is a lack of research conserning phage utilization to red...

  14. A new look at bacteriophage phylogenomics

    OpenAIRE

    Nóbrega, Franklin; Pinto, Graça; Azeredo, Joana; Kluskens, Leon

    2012-01-01

    Bacteriophages or phages are viruses that only infect bacteria. The International Committee on Taxonomy of Viruses classified these viruses in accordance with the morphology of their free virion particles and type and size of their genome. This system fails on the classification of several phages, which have their genome already sequenced. It also requires a morphological analysis by transmission electron microscopy, which is very expensive and time consuming [1]. In 2002 Rohwe...

  15. Long-circulating bacteriophage as antibacterial agents.

    OpenAIRE

    Merril, C.R.; B. Biswas; Carlton, R; Jensen, N C; Creed, G J; Zullo, S; Adhya, S

    1996-01-01

    The increased prevalence of multidrug-resistant bacterial pathogens motivated us to attempt to enhance the therapeutic efficacy of bacteriophages. The therapeutic application of phages as antibacterial agents was impeded by several factors: (i) the failure to recognize the relatively narrow host range of phages; (ii) the presence of toxins in crude phage lysates; and (iii) a lack of appreciation for the capacity of mammalian host defense systems, particularly the organs of the reticuloendothe...

  16. Bacteriophage lambda: early pioneer and still relevant

    OpenAIRE

    Casjens, Sherwood R; Hendrix, Roger W.

    2015-01-01

    Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid 1950's to mid 1980's was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their ...

  17. Dark repair in bacteriophage systems: overview

    International Nuclear Information System (INIS)

    Studies on dark repair of DNA in bacteriophages T4 and lambda are reviewed. Some topics discussed are: uv sensitivity of phage mutants; effects of endonuclease on uv-irradiated phage DNA; pyrimidine dimers as substrate sites for endonuclease in DNA; electron microscopic studies of enzyme-treated uv-irradiated DNA; role of phage T4 genes in DNA repair; and host-cell reactivation, prophage reactivation, and uv reactivation in phase lambda

  18. Bacteriophage biocontrol in animals and meat products

    OpenAIRE

    Atterbury, R. J.

    2009-01-01

    Summary Since their discovery almost a century ago, bacterial viruses (bacteriophages or ‘phages’) have been used to prevent and treat a multitude of bacterial infections (phage therapy: PT). In addition, they have been the basis for many advances in genetics and biochemistry. Phage therapy was performed on human subjects in the United States, Europe and Asia in the few decades following their discovery. However, Western countries largely abandoned PT in favour of antibiotics in the 1940s. Th...

  19. Bacteriophages for detection of bacterial pathogens

    International Nuclear Information System (INIS)

    The G. Eliava Institute of Bacteriophages, Microbiology and Virology (Tbilisi, Georgia) is one of the most famous institutions focused on bacteriophage research for the elaboration of appropriate phage methodologies for human and animal protection. The main direction of the institute is the study and production of bacteriophages against intestinal disorders (dysentery, typhoid, intesti) and purulent-septic infections (staphylococcus, streptococcus, pyophage, etc.). These preparations were successfully introduced during the Soviet era, and for decades were used throughout the former Soviet Union and in other Socialist countries for the treatment, prophylaxis, and diagnosis of various infectious diseases, including those caused by antibiotic-resistant bacterial strains. Bacteriophages were widely used for identifying and detecting infections caused by the most dangerous pathogens and causative agents of epidemiological outbreaks. The specific topic of this presentation is the phage typing of bacterial species, which can be an important method for epidemiological diagnostics. Together with different genetic methodologies - such as PCR-based methods, PFGE, plasmid fingerprinting, and ribosomal typing - phage typing is one method for identifying bacterial pathogens. The method has a high percentage of determination of phage types, high specificity of reaction, and is easy for interpretation and use by health workers. Phage typing was applied for inter-species differentiation of different species of Salmonella, S. typhi, Brucella spp, Staphylococcus aureus, E. col,i Clostridium deficile, Vibrio cholerae, Yersinia pestis, Yersinia enterocolitica, Lysteria monocytogenes, Clostridium perfringens, Clostridium tetani, plant pathogens, and other bacterial pathogens. In addition to addressing the utility and efficacy of phage typing, the paper will discuss the isolation and selection of diagnostic typing phages for interspecies differentiation of pathogens that is necessary

  20. Genesis of Pre-Hurricane Felix (2007). Part 2; Warm Core Formation, Precipitation Evolution, and Predictability

    Science.gov (United States)

    Wang, zhuo; Montgomery M. T.; Dunkerton, T. J.

    2010-01-01

    This is the second of a two-part study examining the simulated formation of Atlantic Hurricane Felix (2007) in a cloud-representing framework. Here several open issues are addressed concerning the formation of the storm's warm core, the evolution and respective contribution of stratiform versus convective precipitation within the parent wave's pouch, and the sensitivity of the development pathway reported in Part I to different model physics options and initial conditions. All but one of the experiments include ice microphysics as represented by one of several parameterizations, and the partition of convective versus stratiform precipitation is accomplished using a standard numerical technique based on the high-resolution control experiment. The transition to a warm-core tropical cyclone from an initially cold-core, lower tropospheric wave disturbance is analyzed first. As part of this transformation process, it is shown that deep moist convection is sustained near the pouch center. Both convective and stratiform precipitation rates increase with time. While stratiform precipitation occupies a larger area even at the tropical storm stage, deep moist convection makes a comparable contribution to the total rain rate at the pregenesis stage, and a larger contribution than stratiform processes at the storm stage. The convergence profile averaged near the pouch center is found to become dominantly convective with increasing deep moist convective activity there. Low-level convergence forced by interior diabatic heating plays a key role in forming and intensifying the near-surface closed circulation, while the midlevel convergence associated with stratiform precipitation helps to increase the midlevel circulation and thereby contributes to the formation and upward extension of a tropospheric-deep cyclonic vortex. Sensitivity tests with different model physics options and initial conditions demonstrate a similar pregenesis evolution. These tests suggest that the genesis

  1. Bacteriophages and bacteriophage-derived endolysins as potential therapeutics to combat Gram-positive spore forming bacteria.

    Science.gov (United States)

    Nakonieczna, A; Cooper, C J; Gryko, R

    2015-09-01

    Since their discovery in 1915, bacteriophages have been routinely used within Eastern Europe to treat a variety of bacterial infections. Although initially ignored by the West due to the success of antibiotics, increasing levels and diversity of antibiotic resistance is driving a renaissance for bacteriophage-derived therapy, which is in part due to the highly specific nature of bacteriophages as well as their relative abundance. This review focuses on the bacteriophages and derived lysins of relevant Gram-positive spore formers within the Bacillus cereus group and Clostridium genus that could have applications within the medical, food and environmental sectors. PMID:26109320

  2. Genetically modified bacteriophages in applied microbiology.

    Science.gov (United States)

    Bárdy, P; Pantůček, R; Benešík, M; Doškař, J

    2016-09-01

    Bacteriophages represent a simple viral model of basic research with many possibilities for practical application. Due to their ability to infect and kill bacteria, their potential in the treatment of bacterial infection has been examined since their discovery. With advances in molecular biology and gene engineering, the phage application spectrum has been expanded to various medical and biotechnological fields. The construction of bacteriophages with an extended host range or longer viability in the mammalian bloodstream enhances their potential as an alternative to conventional antibiotic treatment. Insertion of active depolymerase genes to their genomes can enforce the biofilm disposal. They can also be engineered to transfer various compounds to the eukaryotic organisms and the bacterial culture, applicable for the vaccine, drug or gene delivery. Phage recombinant lytic enzymes can be applied as enzybiotics in medicine as well as in biotechnology for pathogen detection or programmed cell death in bacterial expression strains. Besides, modified bacteriophages with high specificity can be applied as bioprobes in detection tools to estimate the presence of pathogens in food industry, or utilized in the control of food-borne pathogens as part of the constructed phage-based biosorbents. PMID:27321680

  3. Call for a dedicated European legal framework for bacteriophage therapy.

    Science.gov (United States)

    Verbeken, Gilbert; Pirnay, Jean-Paul; Lavigne, Rob; Jennes, Serge; De Vos, Daniel; Casteels, Minne; Huys, Isabelle

    2014-04-01

    The worldwide emergence of antibiotic resistances and the drying up of the antibiotic pipeline have spurred a search for alternative or complementary antibacterial therapies. Bacteriophages are bacterial viruses that have been used for almost a century to combat bacterial infections, particularly in Poland and the former Soviet Union. The antibiotic crisis has triggered a renewed clinical and agricultural interest in bacteriophages. This, combined with new scientific insights, has pushed bacteriophages to the forefront of the search for new approaches to fighting bacterial infections. But before bacteriophage therapy can be introduced into clinical practice in the European Union, several challenges must be overcome. One of these is the conceptualization and classification of bacteriophage therapy itself and the extent to which it constitutes a human medicinal product regulated under the European Human Code for Medicines (Directive 2001/83/EC). Can therapeutic products containing natural bacteriophages be categorized under the current European regulatory framework, or should this framework be adapted? Various actors in the field have discussed the need for an adapted (or entirely new) regulatory framework for the reintroduction of bacteriophage therapy in Europe. This led to the identification of several characteristics specific to natural bacteriophages that should be taken into consideration by regulators when evaluating bacteriophage therapy. One important consideration is whether bacteriophage therapy development occurs on an industrial scale or a hospital-based, patient-specific scale. More suitable regulatory standards may create opportunities to improve insights into this promising therapeutic approach. In light of this, we argue for the creation of a new, dedicated European regulatory framework for bacteriophage therapy. PMID:24500660

  4. Complete Genome Sequences of Five Paenibacillus larvae Bacteriophages.

    Science.gov (United States)

    Sheflo, Michael A; Gardner, Adam V; Merrill, Bryan D; Fisher, Joshua N B; Lunt, Bryce L; Breakwell, Donald P; Grose, Julianne H; Burnett, Sandra H

    2013-01-01

    Paenibacillus larvae is a pathogen of honeybees that causes American foulbrood (AFB). We isolated bacteriophages from soil containing bee debris collected near beehives in Utah. We announce five high-quality complete genome sequences, which represent the first completed genome sequences submitted to GenBank for any P. larvae bacteriophage. PMID:24233582

  5. The protein interaction map of bacteriophage lambda

    OpenAIRE

    Uetz Peter; Casjens Sherwood; Rajagopala Seesandra V

    2011-01-01

    Abstract Background Bacteriophage lambda is a model phage for most other dsDNA phages and has been studied for over 60 years. Although it is probably the best-characterized phage there are still about 20 poorly understood open reading frames in its 48-kb genome. For a complete understanding we need to know all interactions among its proteins. We have manually curated the lambda literature and compiled a total of 33 interactions that have been found among lambda proteins. We set out to find ou...

  6. Immuno compatibility of Bacteriophages as Nano medicines

    International Nuclear Information System (INIS)

    Bacteriophage-based medical research provides the opportunity to develop targeted nano medicines with heightened efficiency and safety profiles. Filamentous phages also can and have been formulated as targeted drug-delivery nano medicines, and phage may also serve as promising alternatives/complements to antibiotics. Over the past decade the use of phage for both the prophylaxis and the treatment of bacterial infection, has gained special significance in view of a dramatic rise in the prevalence of antibiotic resistance bacterial strains. Two potential medical applications of phages are the treatment of bacterial infections and their use as immunizing agents in diagnosis and monitoring patients with immunodeficiencies. Recently, phages have been employed as gene-delivery vectors (phage nano medicine), for nearly half a century as tools in genetic research, for about two decades as tools for the discovery of specific target-binding proteins and peptides, and for almost a decade as tools for vaccine development. As phage applications to human therapeutic development grow at an exponential rate, it will become essential to evaluate host immune responses to initial and repetitive challenges by therapeutic phage in order to develop phage therapies that offer suitable utility. This paper examines and discusses phage nano medicine applications and the immunomodulatory effects of bacteriophage exposure and treatment modalities.

  7. Bacteriophage recombination systems and biotechnical applications.

    Science.gov (United States)

    Nafissi, Nafiseh; Slavcev, Roderick

    2014-04-01

    Bacteriophage recombination systems have been widely used in biotechnology for modifying prokaryotic species, for creating transgenic animals and plants, and more recently, for human cell gene manipulation. In contrast to homologous recombination, which benefits from the endogenous recombination machinery of the cell, site-specific recombination requires an exogenous source of recombinase in mammalian cells. The mechanism of bacteriophage evolution and their coexistence with bacterial cells has become a point of interest ever since bacterial viruses' life cycles were first explored. Phage recombinases have already been exploited as valuable genetic tools and new phage enzymes, and their potential application to genetic engineering and genome manipulation, vectorology, and generation of new transgene delivery vectors, and cell therapy are attractive areas of research that continue to be investigated. The significance and role of phage recombination systems in biotechnology is reviewed in this paper, with specific focus on homologous and site-specific recombination conferred by the coli phages, λ, and N15, the integrase from the Streptomyces phage, ΦC31, the recombination system of phage P1, and the recently characterized recombination functions of Yersinia phage, PY54. Key steps of the molecular mechanisms involving phage recombination functions and their application to molecular engineering, our novel exploitations of the PY54-derived recombination system, and its application to the development of new DNA vectors are discussed. PMID:24442504

  8. Study of the reactivation of X-ray inactivated lambda bacteriophages by irradiated Escherichia coli bacteria

    International Nuclear Information System (INIS)

    Bacteriophages lambda and E.coli cells were exposed to X-rays in LB medium. Host cells exposed to a dose of 85 to 765 Gy had a reactivation factor 1.3 to 3.0 for bacteriophages inactivated by X-rays. The capacity of the bacteria for bacteriophage mutliplication remained apparently unchanged in this dose range. After UV-irradiation of the host cells, only a reactivation factor of 1.3 was found for bacteriophages exposed to X-radiation. The comparatively low Weigle reactivation of bacteriophages exposed to X-radiation - as compared with bacteriophages exposed to UV radiation was analyzed by counting free, non-adsorbed bacteriophages determined by filtration of radioactively labelled bacteriophage-host complexes, it was found to be due to a reduced adsorptivity. Reactivation experiments with bacteriophages exposed to X-rays and host bacterias with different degrees of radiosensitivity proved this assumption to be correct. (orig.)

  9. Marine organisms as source of extracts to disrupt bacterial communication: bioguided isolation and identification of quorum sensing inhibitors from Ircinia felix

    Directory of Open Access Journals (Sweden)

    Jairo Quintana

    2015-06-01

    Full Text Available AbstractIn this study, 39 extracts from marine organisms were evaluated as quorum sensing inhibitors, collected in the Colombian Caribbean Sea and the Brazilian Coast including 26 sponges, seven soft corals, five algae and one zooanthid. The results showed that crude extracts from the soft coral Eunicea laciniata, and the sponges Svenzea tubulosa, Ircinia felix and Neopetrosia carbonaria were the most promising source of quorum sensing inhibitors compounds without affecting bacterial growth, unlike the raw extracts of Agelas citrina, Agelas tubulata, Iotrochota arenosa, Topsentia ophiraphidites, Niphates caycedoi, Cliona tenuis, Ptilocaulis walpersi, Petrosia pellasarca, and the algae Laurencia catarinensis and Laurencia obtusa, which displayed potent antibacterial activity against the biosensors employed. The crude extract from the sponge I. felix was fractionated, obtaining furanosesterterpenes which were identified and evaluated as quorum sensing inhibitors, showing a moderate activity without affecting the biosensor's growth.

  10. Die Begegnung der Hochstapler oder  : von der Vertracktheit der AggressionRobert Neumanns Olympia als Parodie auf Thomas Manns Bekenntnisse des Hochstaplers Felix Krull1

    OpenAIRE

    Pils, Holger

    2012-01-01

    Cet article met en lumière la richesse des allusions du roman Olympia (1961). Robert Neumann y aborde une problématique-clé de son œuvre : l’imposture. Ce roman, dédié à Thomas Mann et contre lequel ses héritiers ont intenté un procès pour plagiat, est une parodie de l’ouvrage. Felix Krull est un des personnages d’Olympia. Sa sœur, l’héroïne éponyme, est également empruntée au roman de Thomas Mann. Enfin, dans la rencontre de « Felix Krull » avec une autre figure d’imposteur, Neumann transcri...

  11. Felix Mendelssohn-Bartholdy na programech koncertů v Brně v druhé polovině 19. století

    Czech Academy of Sciences Publication Activity Database

    Bartoň, Kamil

    Praha: Agora, 2012 - (Freemanová, M.), s. 124-129 ISBN 978-80-86820-09-5. [Výroční konference České společnosti pro hudební vědu 2009. Praha (CZ), 04.12.2009-05.12.2009] Institutional research plan: CEZ:AV0Z90580513 Keywords : Felix Mendelssohn-Bartholdy * Brno * music life Subject RIV: AL - Art, Architecture, Cultural Heritage

  12. Complete Genome Sequence of Croceibacter Bacteriophage P2559S

    OpenAIRE

    Kang, Ilnam; Kang, Dongmin; Cho, Jang-Cheon

    2012-01-01

    Croceibacter atlanticus HTCC2559T, a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the family Flavobacteriaceae. Strain HTCC2559T possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559T. Many genes predicted in the P2559S geno...

  13. Targeting Antibacterial Agents by Using Drug-Carrying Filamentous Bacteriophages

    OpenAIRE

    Yacoby, Iftach; Shamis, Marina; Bar, Hagit; Shabat, Doron; Benhar, Itai

    2006-01-01

    Bacteriophages have been used for more than a century for (unconventional) therapy of bacterial infections, for half a century as tools in genetic research, for 2 decades as tools for discovery of specific target-binding proteins, and for nearly a decade as tools for vaccination or as gene delivery vehicles. Here we present a novel application of filamentous bacteriophages (phages) as targeted drug carriers for the eradication of (pathogenic) bacteria. The phages are genetically modified to d...

  14. Bacteriophage-based nanoprobes for rapid bacteria separation

    Science.gov (United States)

    Chen, Juhong; Duncan, Bradley; Wang, Ziyuan; Wang, Li-Sheng; Rotello, Vincent M.; Nugen, Sam R.

    2015-10-01

    The lack of practical methods for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. Antibody-tagged magnetic particles are commonly used to pull analytes from a liquid sample. While this method is well-established, improvements in capture efficiencies would result in an increase of the overall detection assay performance. Bacteriophages represent a low-cost and more consistent biorecognition element as compared to antibodies. We have developed nanoscale bacteriophage-tagged magnetic probes, where T7 bacteriophages were bound to magnetic nanoparticles. The nanoprobe allowed the specific recognition and attachment to E. coli cells. The phage magnetic nanprobes were directly compared to antibody-conjugated magnetic nanoprobes. The capture efficiencies of bacteriophages and antibodies on nanoparticles for the separation of E. coli K12 at varying concentrations were determined. The results indicated a similar bacteria capture efficiency between the two nanoprobes.The lack of practical methods for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. Antibody-tagged magnetic particles are commonly used to pull analytes from a liquid sample. While this method is well-established, improvements in capture efficiencies would result in an increase of the overall detection assay performance. Bacteriophages represent a low-cost and more consistent biorecognition element as compared to antibodies. We have developed nanoscale bacteriophage-tagged magnetic probes, where T7 bacteriophages were bound to magnetic nanoparticles. The nanoprobe allowed the specific recognition and attachment to E. coli cells. The phage magnetic nanprobes were directly compared to antibody-conjugated magnetic nanoprobes. The capture efficiencies of bacteriophages and antibodies on nanoparticles for the separation of E. coli K12 at varying

  15. Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni

    OpenAIRE

    Siringan, Patcharin; Connerton, Phillippa L.; Cummmings, Nicola J.; Connerton, Ian F.

    2014-01-01

    Members of the genus Campylobacter are frequently responsible for human enteric disease, often through consumption of contaminated poultry products. Bacteriophages are viruses that have the potential to control pathogenic bacteria, but understanding their complex life cycles is key to their successful exploitation. Treatment of Campylobacter jejuni biofilms with bacteriophages led to the discovery that phages had established a relationship with their hosts typical of the carrier state life cy...

  16. Novel Podoviridae Family Bacteriophage Infecting Weissella cibaria Isolated from Kimchi

    OpenAIRE

    Kleppen, Hans Petter; Holo, Helge; Jeon, Sang-Rok; Nes, Ingolf F.; Yoon, Sung-Sik

    2012-01-01

    The first complete genome sequence of a phage infecting Weissella cibaria (Weissella kimchii) is presented. The bacteriophage ϕYS61 was isolated from kimchi, a Korean fermented vegetable dish. Bacteriophages are recognized as a serious problem in industrial fermentations; however, ϕYS61 differed from many virulent phages associated with food fermentations since it was difficult to propagate and was very susceptible to resistance development. Sequence analysis revealed that ϕYS61 resembles Pod...

  17. Simulated hatchery system to assess bacteriophage efficacy against Vibrio harveyi.

    Science.gov (United States)

    Raghu Patil, J; Desai, Srividya Narayanamurthy; Roy, Panchali; Durgaiah, Murali; Saravanan, R Sanjeev; Vipra, Aradhana

    2014-12-01

    Vibriosis caused by luminous Vibrio harveyi commonly contributes to poor survival in shrimp hatcheries and aquaculture ponds. Lytic bacteriophages pathogenic for V. harveyi are currently being investigated as an alternative to antibiotics to prevent vibriosis. Here, 8 bacteriophages were isolated from oysters and clams using V. harveyi strains as baiting hosts. Among these bacteriophages, 1 strain (VHP6b) identified as broadly pathogenic for 27 V. harveyi strains examined was further characterized by electron microscopy and genome sequence analysis. Phage VHP6b possessed a tail and morphology consistent with it being a member of the family Siphoviridae, and its genome and proteome were most closely related to the Vibrio phages SSP02 and MAR10. An integrase gene essential for lysogeny was not evident. The ability of bacteriophage VHP6b to protect shrimp postlarvae against vibriosis caused by V. harveyi strain VH6 was demonstrated in a model system designed to simulate typical hatchery conditions. Bacteriophage treatment improved survival of postlarvae by 40 to 60% under these conditions, so therapies based on this or other bacteriophages may be useful in shrimp hatcheries. PMID:25449322

  18. Bacteriophage lambda: Early pioneer and still relevant.

    Science.gov (United States)

    Casjens, Sherwood R; Hendrix, Roger W

    2015-05-01

    Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle. PMID:25742714

  19. Why Be Temperate: Lessons from Bacteriophage λ.

    Science.gov (United States)

    Gandon, Sylvain

    2016-05-01

    Many pathogens have evolved the ability to induce latent infections of their hosts. The bacteriophage λ is a classical model for exploring the regulation and the evolution of latency. Here, I review recent experimental studies on phage λ that identify specific conditions promoting the evolution of lysogenic life cycles. In addition, I present specific adaptations of phage λ that allow this virus to react plastically to variations in the environment and to reactivate its lytic life cycle. All of these different examples are discussed in the light of evolutionary epidemiology theory to disentangle the different evolutionary forces acting on temperate phages. Understanding phage λ adaptations yield important insights into the evolution of latency in other microbes, including several life-threatening human pathogens. PMID:26946976

  20. Montmorillonite-induced Bacteriophage φ6 Disassembly

    Science.gov (United States)

    Trusiak, A.; Gottlieb, P.; Katz, A.; Alimova, A.; Steiner, J. C.; Block, K. A.

    2012-12-01

    It is estimated that there are 1031 virus particles on Earth making viruses an order of magnitude more prevalent in number than prokaryotes with the vast majority of viruses being bacteriophages. Clays are a major component of soils and aquatic sediments and can react with RNA, proteins and bacterial biofilms. The clays in soils serve as an important moderator between phage and their host bacteria, helping to preserve the evolutionary balance. Studies on the effects of clays on viral infectivity have given somewhat contradictory results; possibly a consequence of clay-virus interactions being dependent on the unique structure of particular viruses. In this work, the interaction between montmorillonite and the bacteriophage φ6 is investigated. φ6 is a member of the cystovirus family that infects Pseudomonas syringe, a common plant pathogen. As a member of the cystovirus family with an enveloped structure, φ6 serves as a model for reoviruses, a human pathogen. Experiments were conducted with φ6 suspended in dilute, purified homoionic commercial-grade montmorillonite over a range of virus:clay ratios. At a 1:100000 virus:clay ratio, the clay reduced viral infectivity by 99%. The minimum clay to virus ratio which results in a measurable reduction of P. syringae infection is 1:1. Electron microscopy demonstrates that mixed suspensions of smectite and virus co-aggregate to form flocs encompassing virions within the smectite. Both free viral particles as well as those imbedded in the flocs are seen in the micrographs to be missing the envelope- leaving only the nucleocapsid (NC) intact; indicating that smectite inactivates the virus by envelope disassembly. These results have strong implications in the evolution of both the φ6 virus and its P. syringae host cells. TEM of aggregate showing several disassembled NCs.

  1. A Hypothesis for Bacteriophage DNA Packaging Motors

    Directory of Open Access Journals (Sweden)

    Philip Serwer

    2010-08-01

    Full Text Available The hypothesis is presented that bacteriophage DNA packaging motors have a cycle comprised of bind/release thermal ratcheting with release-associated DNA pushing via ATP-dependent protein folding. The proposed protein folding occurs in crystallographically observed peptide segments that project into an axial channel of a protein 12-mer (connector that serves, together with a coaxial ATPase multimer, as the entry portal. The proposed cycle begins when reverse thermal motion causes the connector’s peptide segments to signal the ATPase multimer to bind both ATP and the DNA molecule, thereby producing a dwell phase recently demonstrated by single-molecule procedures. The connector-associated peptide segments activate by transfer of energy from ATP during the dwell. The proposed function of connector/ATPase symmetry mismatches is to reduce thermal noise-induced signaling errors. After a dwell, ATP is cleaved and the DNA molecule released. The activated peptide segments push the released DNA molecule, thereby producing a burst phase recently shown to consist of four mini-bursts. The constraint of four mini-bursts is met by proposing that each mini-burst occurs via pushing by three of the 12 subunits of the connector. If all four mini-bursts occur, the cycle repeats. If the mini-bursts are not completed, a second cycle is superimposed on the first cycle. The existence of the second cycle is based on data recently obtained with bacteriophage T3. When both cycles stall, energy is diverted to expose the DNA molecule to maturation cleavage.

  2. Bacteriophages show promise as antimicrobial agents.

    Science.gov (United States)

    Alisky, J; Iczkowski, K; Rapoport, A; Troitsky, N

    1998-01-01

    The emergence of antibiotic-resistant bacteria has prompted interest in alternatives to conventional drugs. One possible option is to use bacteriophages (phage) as antimicrobial agents. We have conducted a literature review of all Medline citations from 1966-1996 that dealt with the therapeutic use of phage. There were 27 papers from Poland, the Soviet Union, Britain and the U.S.A. The Polish and Soviets administered phage orally, topically or systemically to treat a wide variety of antibiotic-resistant pathogens in both adults and children. Infections included suppurative wound infections, gastroenteritis, sepsis, osteomyelitis, dermatitis, empyemas and pneumonia; pathogens included Staphylococcus, Streptococcus, Klebsiella, Escherichia, Proteus, Pseudomonas, Shigella and Salmonella spp. Overall, the Polish and Soviets reported success rates of 80-95% for phage therapy, with rare, reversible gastrointestinal or allergic side effects. However, efficacy of phage was determined almost exclusively by qualitative clinical assessment of patients, and details of dosages and clinical criteria were very sketchy. There were also six British reports describing controlled trials of phage in animal models (mice, guinea pigs and livestock), measuring survival rates and other objective criteria. All of the British studies raised phage against specific pathogens then used to create experimental infections. Demonstrable efficacy against Escherichia, Acinetobacter, Pseudomonas and Staphylococcus spp. was noted in these model systems. Two U.S. papers dealt with improving the bioavailability of phage. Phage is sequestered in the spleen and removed from circulation. This can be overcome by serial passage of phage through mice to isolate mutants that resist sequestration. In conclusion, bacteriophages may show promise for treating antibiotic resistant pathogens. To facilitate further progress, directions for future research are discussed and a directory of authors from the reviewed

  3. Organic extracts with antimicrobial activity from Penicillium sp (Moniliales) isolated from the sponge ircinia felix (Porifera : Demospongiae)

    International Nuclear Information System (INIS)

    This research expresses the potential of the bacterial activity present in the organic extracts obtained from Penicillium sp., isolated from the e sponge Incr. felix. This activity was evaluated through agar diffusion test and Minimal Inhibitory Concentration (MIC). The susceptibility trials of organic fractions were carried out against Staphylococcus aureus, S. epidermidis. Bacillus cereus and B. subtilis. The use of the chromatographic techniques (CLV and TLC), permitted to obtain bioactive organic extracts of different polarities, of which only the EtOAc and MeOH fractions inhibited the growth of the bacteria used. Of the EtOAc fractionation, only fraction number 3 EtOAc/Hex presented greatest activity against the Gram-positive bacteria. Number 1 EtOAc/Hex fraction increased its activity against S. aureus (24 mm) and S. epidermidis (25 mm), which can be explained by the loss of possible antagonistic effect during the fractionation process. The CMI trials were carried out for the EtOAc number I subtraction against S. aureus, S. epidermidis, B. cereus and B. subtilis, wich was clinical interest, and shows the potential of this organic extract as antimicrobial agent. (Author)

  4. FELIX: construction and testing of a facility to study electromagnetic effects for first wall, blanket, and shield systems

    International Nuclear Information System (INIS)

    An experimental test facility for the study of electromagnetic effects in the FWBS systems of fusion reactors has been constructed over the past 1-1/2 years at Argonne National Laboratory (ANL). In a test volume of 0.76 m3 a vertical pulsed 0.5 T dipole field (B < 50 T/s) is perpendicular to a 1 T solenoid field. Power supplies of 2.75 MW and 5.5 MW and a solid state switch rated 13 kV, 13.1 kA (170 MW) control the pulsed magnetic fields. The total stored energy in the coils is 2.13 MJ. The coils are designed for a future upgrade to 4 T or the solenoid and 1 T for the dipole field (a total of 23.7 MJ). This paper describes the design and construction features of the facility. These include the power supplies, the solid state switches, winding and impregnation of large dipole saddle coils, control of the magnetic forces, computer control of FELIX and of experimental data acquisition and analysis, and an initial experimental test setup to analyze the eddy current distribution in a flat disk

  5. Recombination of bacteriophage phiX174 by the red function of bacteriophage lambda

    International Nuclear Information System (INIS)

    Recombination of bacteriophage phiX174 was effectively promoted when the Red function of lambda was supplied by either co-infection with lambda or induction of lambda lysogens. Mutations in redα and redβ genes of lambda abolished recombination nearly completely, whereas a mutation in gam gene reduced it only slightly. The Red-promoted recombination of phiX174 occurred in recA, recB, and polA mutants as well as in wild-type strains of Escherichia coli. It was further stimulated when phiX174 mutants were irradiated with uv light before infection

  6. 40 CFR 180.1261 - Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages.

    Science.gov (United States)

    2010-07-01

    ... and Pseudomonas syringae pv. tomato specific Bacteriophages. 180.1261 Section 180.1261 Protection of.... vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages. An exemption from the requirement of... syringae pv. tomato specific bacteriophages in or on pepper and tomato....

  7. Bacteriophage Infection of Model Metal Reducing Bacteria

    Science.gov (United States)

    Weber, K. A.; Bender, K. S.; Gandhi, K.; Coates, J. D.

    2008-12-01

    Microbially-mediated metal reduction plays a significant role controlling contaminant mobility in aqueous, soil, and sedimentary environments. From among environmentally relevant microorganisms mediating metal reduction, Geobacter spp. have been identified as predominant metal-reducing bacteria under acetate- oxidizing conditions. Due to the significance of these bacteria in environmental systems, it is necessary to understand factors influencing their metabolic physiology. Examination of the annotated finished genome sequence of G. sulfurreducens PCA, G. uraniumreducens Rf4, G. metallireduceans GS-15 as well as a draft genome sequence of Geobacter sp. FRC-32 have identified gene sequences of putative bacteriophage origin. Presence of these sequences indicates that these bacteria are susceptible to phage infection. Polymerase chain reaction (PCR) primer sets designed tested for the presence of 12 of 25 annotated phage-like sequences in G. sulfurreducens PCA and 9 of 17 phage-like sequences in FRC- 32. The following genes were successfully amplified in G. sulfurreducens PCA: prophage type transcription regulator, phage-induced endonuclease, phage tail sheath, 2 phage tail proteins, phage protein D, phage base plate protein, phage-related DNA polymerase, integrase, phage transcriptional regulator, and Cro-like transcription regulator. Nine of the following sequences were present in FRC-32: 4 separate phage- related proteins, phage-related tail component, viron core protein, phage Mu protein, phage base plate, and phage tail sheath. In addition to the bioinformatics evidence, incubation of G. sulfurreducens PCA with 1 μg mL-1 mytomycin C (mutagen stimulating prophage induction) during mid-log phase resulted in significant cell lysis relative to cultures that remained unamended. Cell lysis was concurrent with an increase in viral like particles enumerated using epifluorescent microscopy. In addition, samples collected following this lytic event (~44hours) were

  8. Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni.

    Science.gov (United States)

    Siringan, Patcharin; Connerton, Phillippa L; Cummings, Nicola J; Connerton, Ian F

    2014-01-01

    Members of the genus Campylobacter are frequently responsible for human enteric disease, often through consumption of contaminated poultry products. Bacteriophages are viruses that have the potential to control pathogenic bacteria, but understanding their complex life cycles is key to their successful exploitation. Treatment of Campylobacter jejuni biofilms with bacteriophages led to the discovery that phages had established a relationship with their hosts typical of the carrier state life cycle (CSLC), where bacteria and bacteriophages remain associated in equilibrium. Significant phenotypic changes include improved aerotolerance under nutrient-limited conditions that would confer an advantage to survive in extra-intestinal environments, but a lack in motility eliminated their ability to colonize chickens. Under these circumstances, phages can remain associated with a compatible host and continue to produce free virions to prospect for new hosts. Moreover, we demonstrate that CSLC host bacteria can act as expendable vehicles for the delivery of bacteriophages to new host bacteria within pre-colonized chickens. The CSLC represents an important phase in the ecology of Campylobacter bacteriophage. PMID:24671947

  9. The DNA ejection process in bacteriophage lambda

    Science.gov (United States)

    Grayson, Paul

    Bacteriophages have long served as model systems through which the nature of life may be explored. From a physical or mechanical point of view, phages are excellent examples of natural nanotechnology: they are nanometer-scale systems which depend critically on forces, pressures, velocities, and other fundamentally physical quantities for their biological functions. The study of the physical properties of phages has therefore provided an arena for application of physics to biology. In particular, recent studies of the motor responsible for packaging a phage gnome into a capsid showed a buildup of pressure within the capsid of tens of atmospheres. This thesis reports a combined theoretical and experimental study on various aspects of the genome ejection process, so that a comparison may be drawn with the packaging experiments. In particular, we examine various theoretical models of the forces within a phage capsid, deriving formulas both for the force driving genome ejection and for the velocity at which the genome is translocated into a host cell. We describe an experiment in which the force was measured as a function of the amount of genome within the phage capsid, and another where the genome ejection velocity was measured for single phages under the microscope. We make direct quantitative comparisons between the theory and experiments, stringently testing the extent to which we are able to model the genome ejection process.

  10. Genesis of Pre-Hurricane Felix (2007). Part 1; The Role of the Easterly Wave Critical Layer

    Science.gov (United States)

    Wang, Zhuo; Montgomery, M. T.; Dunkerton, T. J.

    2010-01-01

    The formation of pre Hurricane Felix (2007) in a tropical easterly wave is examined in a two-part study using the Weather Research and Forecasting (WRF) model with a high-resolution nested grid configuration that permits the representation of cloud system processes. The simulation commences during the wave stage of the precursor African easterly-wave disturbance. Here the simulated and observed developments are compared, while in Part II of the study various large-scale analyses, physical parameterizations, and initialization times are explored to document model sensitivities. In this first part the authors focus on the wave/vortex morphology, its interaction with the adjacent intertropical convergence zone complex, and the vorticity balance in the neighborhood of the developing storm. Analysis of the model simulation points to a bottom-up development process within the wave critical layer and supports the three new hypotheses of tropical cyclone formation proposed recently by Dunkerton, Montgomery, and Wang. It is shown also that low-level convergence associated with the ITCZ helps to enhance the wave signal and extend the "wave pouch" from the jet level to the top of the atmospheric boundary layer. The region of a quasi-closed Lagrangian circulation within the wave pouch provides a focal point for diabatic merger of convective vortices and their vortical remnants. The wave pouch serves also to protect the moist air inside from dry air intrusion, providing a favorable environment for sustained deep convection. Consistent with the authors' earlier findings, the tropical storm forms near the center of the wave pouch via system-scale convergence in the lower troposphere and vorticity aggregation. Components of the vorticity balance are shown to be scale dependent, with the immediate effects of cloud processes confined more closely to the storm center than the overturning Eliassen circulation induced by diabatic heating, the influence of which extends to larger radii.

  11. Bacteriophages as potential treatment option for antibiotic resistant bacteria.

    Science.gov (United States)

    Bragg, Robert; van der Westhuizen, Wouter; Lee, Ji-Yun; Coetsee, Elke; Boucher, Charlotte

    2014-01-01

    The world is facing an ever-increasing problem with antibiotic resistant bacteria and we are rapidly heading for a post-antibiotic era. There is an urgent need to investigate alterative treatment options while there are still a few antibiotics left. Bacteriophages are viruses that specifically target bacteria. Before the development of antibiotics, some efforts were made to use bacteriophages as a treatment option, but most of this research stopped soon after the discovery of antibiotics. There are two different replication options which bacteriophages employ. These are the lytic and lysogenic life cycles. Both these life cycles have potential as treatment options. There are various advantages and disadvantages to the use of bacteriophages as treatment options. The main advantage is the specificity of bacteriophages and treatments can be designed to specifically target pathogenic bacteria while not negatively affecting the normal microbiota. There are various advantages to this. However, the high level of specificity also creates potential problems, the main being the requirement of highly specific diagnostic procedures. Another potential problem with phage therapy includes the development of immunity and limitations with the registration of phage therapy options. The latter is driving research toward the expression of phage genes which break the bacterial cell wall, which could then be used as a treatment option. Various aspects of phage therapy have been investigated in studies undertaken by our research group. We have investigated specificity of phages to various avian pathogenic E. coli isolates. Furthermore, the exciting NanoSAM technology has been employed to investigate bacteriophage replication and aspects of this will be discussed. PMID:24619620

  12. Bacteriophages of Soft Rot Enterobacteriaceae-a minireview.

    Science.gov (United States)

    Czajkowski, Robert

    2016-01-01

    Soft rot Enterobacteriaceae (Pectobacterium spp. and Dickeya spp., formerly pectinolytic Erwinia spp.) are ubiquitous necrotrophic bacterial pathogens that infect a large number of different plant species worldwide, including economically important crops. Despite the fact that these bacteria have been studied for more than 50 years, little is known of their corresponding predators: bacteriophages, both lytic and lysogenic. The aim of this minireview is to critically summarize recent ecological, biological and molecular research on bacteriophages infecting Pectobacterium spp. and Dickeya spp. with the main focus on current and future perspectives in that field. PMID:26626879

  13. Complete genome sequence of Croceibacter bacteriophage P2559S.

    Science.gov (United States)

    Kang, Ilnam; Kang, Dongmin; Cho, Jang-Cheon

    2012-08-01

    Croceibacter atlanticus HTCC2559(T), a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the family Flavobacteriaceae. Strain HTCC2559(T) possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559(T). Many genes predicted in the P2559S genome had their homologs in Bacteroides phages. PMID:22843867

  14. Genetically engineered acidophilic heterotrophic bacteria by bacteriophage transduction

    Energy Technology Data Exchange (ETDEWEB)

    Ward, T.E.; Bruhn, D.F.; Bulmer, D.F.

    1989-05-10

    A bacteriophage capable of infecting acidophilic heterotrophic bacteria and processes for genetically engineering acidophilic bacteria for biomining or sulfur removal from coal are disclosed. The bacteriophage is capable of growth in cells existing at pH at or below 3.0. Lytic forms of the phage introduced into areas experiencing acid drainage kill the bacteria causing such drainage. Lysogenic forms of the phage having genes for selective removal of metallic or nonmetallic elements can be introduced into acidophilic bacteria to effect removal of the desired element from ore or coal. 1 fig., 1 tab.

  15. Mechanism of bacteriophage conversion of lipase activity in Staphylococcus aureus.

    OpenAIRE

    Lee, C Y; Iandolo, J J

    1985-01-01

    Staphylococcus aureus PS54 harbors two temperate bacteriophages and manifests no lipase activity on egg yolk agar. Curing of one of the resident prophages (L54a) restores lipase activity. To study the mechanism of bacteriophage conversion, the prophage was cured, and the gene encoding lipase activity was cloned into pBR322 in Escherichia coli on a 2.9-kilobase DNA fragment of the chromosome. The fragment was subcloned into a shuttle vector and subsequently transformed into S. aureus and Bacil...

  16. Novel bacteriophages containing a genome of another bacteriophage within their genomes.

    Directory of Open Access Journals (Sweden)

    Maud M Swanson

    Full Text Available A novel bacteriophage infecting Staphylococus pasteuri was isolated during a screen for phages in Antarctic soils. The phage named SpaA1 is morphologically similar to phages of the family Siphoviridae. The 42,784 bp genome of SpaA1 is a linear, double-stranded DNA molecule with 3' protruding cohesive ends. The SpaA1 genome encompasses 63 predicted protein-coding genes which cluster within three regions of the genome, each of apparently different origin, in a mosaic pattern. In two of these regions, the gene sets resemble those in prophages of Bacillus thuringiensis kurstaki str. T03a001 (genes involved in DNA replication/transcription, cell entry and exit and B. cereus AH676 (additional regulatory and recombination genes, respectively. The third region represents an almost complete genome (except for the short terminal segments of a distinct bacteriophage, MZTP02. Nearly the same gene module was identified in prophages of B. thuringiensis serovar monterrey BGSC 4AJ1 and B. cereus Rock4-2. These findings suggest that MZTP02 can be shuttled between genomes of other bacteriophages and prophages, leading to the formation of chimeric genomes. The presence of a complete phage genome in the genome of other phages apparently has not been described previously and might represent a 'fast track' route of virus evolution and horizontal gene transfer. Another phage (BceA1 nearly identical in sequence to SpaA1, and also including the almost complete MZTP02 genome within its own genome, was isolated from a bacterium of the B. cereus/B. thuringiensis group. Remarkably, both SpaA1 and BceA1 phages can infect B. cereus and B. thuringiensis, but only one of them, SpaA1, can infect S. pasteuri. This finding is best compatible with a scenario in which MZTP02 was originally contained in BceA1 infecting Bacillus spp, the common hosts for these two phages, followed by emergence of SpaA1 infecting S. pasteuri.

  17. The protein interaction map of bacteriophage lambda

    Directory of Open Access Journals (Sweden)

    Uetz Peter

    2011-09-01

    Full Text Available Abstract Background Bacteriophage lambda is a model phage for most other dsDNA phages and has been studied for over 60 years. Although it is probably the best-characterized phage there are still about 20 poorly understood open reading frames in its 48-kb genome. For a complete understanding we need to know all interactions among its proteins. We have manually curated the lambda literature and compiled a total of 33 interactions that have been found among lambda proteins. We set out to find out how many protein-protein interactions remain to be found in this phage. Results In order to map lambda's interactions, we have cloned 68 out of 73 lambda open reading frames (the "ORFeome" into Gateway vectors and systematically tested all proteins for interactions using exhaustive array-based yeast two-hybrid screens. These screens identified 97 interactions. We found 16 out of 30 previously published interactions (53%. We have also found at least 18 new plausible interactions among functionally related proteins. All previously found and new interactions are combined into structural and network models of phage lambda. Conclusions Phage lambda serves as a benchmark for future studies of protein interactions among phage, viruses in general, or large protein assemblies. We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins.

  18. Combined use of Bacteriophage K and a novel Bacteriophage to reduce Staphylococcus aureus biofilm formation

    DEFF Research Database (Denmark)

    Alves, DR; Gaudion, A.; Bean, JE;

    2014-01-01

    Biofilms are major causes of impairment of wound healing and patient morbidity. One of the most common and aggressive wound pathogens is Staphylococcus aureus, displaying a large repertoire of virulence factors and commonly reduced susceptibility to antibiotics, such as the spread of methicillin-......-resistant S. aureus (MRSA). Bacteriophages are obligate parasites of bacteria. They multiply intracellularly and lyse their bacterial host, releasing their progeny. We isolated a novel phage, DRA88, which has a ......Biofilms are major causes of impairment of wound healing and patient morbidity. One of the most common and aggressive wound pathogens is Staphylococcus aureus, displaying a large repertoire of virulence factors and commonly reduced susceptibility to antibiotics, such as the spread of methicillin...

  19. Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge

    Science.gov (United States)

    Cornell, Jessica L.; Breslin, Eileen; Schuhmacher, Zachary; Himelright, Madison; Berluti, Cassandra; Boyd, Charles; Carson, Rachel; Del Gallo, Elle; Giessler, Caris; Gilliam, Benjamin; Heatherly, Catherine; Nevin, Julius; Nguyen, Bryan; Nguyen, Justin; Parada, Jocelyn; Sutterfield, Blake; Tukruni, Muruj

    2016-01-01

    Smudge, a bacteriophage enriched from soil using Bacillus thuringiensis DSM-350 as the host, had its complete genome sequenced. Smudge is a myovirus with a genome consisting of 292 genes and was identified as belonging to the C1 cluster of Bacillus phages. PMID:27540049

  20. Multiple roles of genome-attached bacteriophage terminal proteins

    International Nuclear Information System (INIS)

    Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer. - Highlights: • Protein-primed genome replication constitutes a strategy to initiate DNA or RNA synthesis in linear genomes. • Bacteriophage terminal proteins (TPs) are covalently attached to viral genomes by their primary function priming DNA replication. • TPs are also DNA-binding proteins and target phage genomes to the host nucleoid. • TPs can also localize in the eukaryotic nucleus and may have a role in phage-mediated interkingdom gene transfer

  1. Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge.

    Science.gov (United States)

    Cornell, Jessica L; Breslin, Eileen; Schuhmacher, Zachary; Himelright, Madison; Berluti, Cassandra; Boyd, Charles; Carson, Rachel; Del Gallo, Elle; Giessler, Caris; Gilliam, Benjamin; Heatherly, Catherine; Nevin, Julius; Nguyen, Bryan; Nguyen, Justin; Parada, Jocelyn; Sutterfield, Blake; Tukruni, Muruj; Temple, Louise

    2016-01-01

    Smudge, a bacteriophage enriched from soil using Bacillus thuringiensis DSM-350 as the host, had its complete genome sequenced. Smudge is a myovirus with a genome consisting of 292 genes and was identified as belonging to the C1 cluster of Bacillus phages. PMID:27540049

  2. Bacteriophage for prophylaxis and therapy in cattle, poultry, and pigs.

    Science.gov (United States)

    The successful use of virulent (lytic) bacteriophages (phages) in preventing and treating neonatal enterotoxigenic Escherichia coli infections in calves, lambs and pigs has prompted investigation of other applications phage therapy in food animals. While results have been very variable, some indica...

  3. Multiple roles of genome-attached bacteriophage terminal proteins

    Energy Technology Data Exchange (ETDEWEB)

    Redrejo-Rodríguez, Modesto; Salas, Margarita, E-mail: msalas@cbm.csic.es

    2014-11-15

    Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer. - Highlights: • Protein-primed genome replication constitutes a strategy to initiate DNA or RNA synthesis in linear genomes. • Bacteriophage terminal proteins (TPs) are covalently attached to viral genomes by their primary function priming DNA replication. • TPs are also DNA-binding proteins and target phage genomes to the host nucleoid. • TPs can also localize in the eukaryotic nucleus and may have a role in phage-mediated interkingdom gene transfer.

  4. Vibrio cholerae O1 isolated in Kenya.

    OpenAIRE

    Iwanaga, M; Mori, K.; Kaviti, J N

    1982-01-01

    Biological and serological analyses of 272 isolates of Vibrio cholerae O1 from six epidemics and from a few sporadic cases in Kenya were carried out. All of the isolates were identified as V. cholerae biotype E1 Tor, and 210 out of 272 isolates were hemolytic as examined by Feeley's method.

  5. Prevalence of Broad-Host-Range Lytic Bacteriophages of Sphaerotilus natans, Escherichia coli, and Pseudomonas aeruginosa

    OpenAIRE

    Jensen, Ellen C.; Schrader, Holly S.; Rieland, Brenda; Thompson, Thomas L.; Lee, Kit W.; Nickerson, Kenneth W.; Kokjohn, Tyler A.

    1998-01-01

    Two bacteriophage collections were examined with regard to their ability to form plaques on multiple bacterial host species. Nine of 10 phages studied were found to be broad-host-range bacteriophages. These phages fell into two groups. Group 1, the SN series, was isolated from sewage treatment plant samples with Sphaerotilus natans ATCC 13338 as a host. The DNAs of these bacteriophages contained modified bases and were insensitive to cleavage by type I and II restriction endonucleases. The ef...

  6. The gene for type A streptococcal exotoxin (erythrogenic toxin) is located in bacteriophage T12.

    OpenAIRE

    Weeks, C R; Ferretti, J J

    1984-01-01

    The infection of Streptococcus pyogenes T25(3) with the temperate bacteriophage T12 results in the conversion of the nontoxigenic strain to type A streptococcal exotoxin (erythrogenic toxin) production. Although previous research has established that integration of the bacteriophage genome into the host chromosome is not essential for exotoxin production, the location of the gene on the bacteriophage or bacterial chromosome had not been determined. In the present investigation, recombinant DN...

  7. Simultaneous loss of bacteriophage receptor and coaggregation mediator activities in Actinomyces viscosus MG-1.

    OpenAIRE

    Tylenda, C A; Enriquez, E.; Kolenbrander, P. E.; Delisle, A L

    1985-01-01

    Actinomyces bacteriophages were used as tools to study coaggregation between actinomyces and streptococci. Four bacteriophage isolates, phages AV-1, AV-2, AV-3, and 1281, bound to coaggregation group A Actinomyces viscosus and to group E A. naeslundii. No binding to groups B, C, D, or F was observed. Only A. viscosus MG-1 was capable of supporting a productive infection by these phages. Spontaneously occurring bacteriophage-resistant mutants of A. viscosus MG-1 were isolated and were shown to...

  8. Template reporter bacteriophage platform and multiple bacterial detection assays based thereon

    Science.gov (United States)

    Goodridge, Lawrence (Inventor)

    2007-01-01

    The invention is a method for the development of assays for the simultaneous detection of multiple bacteria. A bacteria of interest is selected. A host bacteria containing plasmid DNA from a T even bacteriophage that infects the bacteria of interest is infected with T4 reporter bacteriophage. After infection, the progeny bacteriophage are plating onto the bacteria of interest. The invention also includes single-tube, fast and sensitive assays which utilize the novel method.

  9. Pegasus ja puuhobune. James Joyce’i „Kunstniku noorpõlveportree” ja Friedebert Tuglase „Felix Ormusson”. Pegasus and the Wooden Horse: James Joyce’s Portrait of the Artist as a Young Man and Friedebert Tuglas’ Felix Ormusson

    Directory of Open Access Journals (Sweden)

    Tiina Ann Kirss

    2012-04-01

    Full Text Available Friedebert Tuglas’ Felix Ormusson and James Joyce’s Portrait of the Artist as a Young Man were finished in the same year – 1914, but the writing of both novels took the writers almost a decade, a time of searching and exile for both of them. Joyce completely rewrote the initial draft of his novel, entitled Stephen Hero, experimenting with basic forms, such as the short prose piece he called the ”epiphany”. Tuglas’ Felix Ormusson was initially conceived as a three-volume picaresque novel, which was distilled into a single volume of prose fragments arranged as a diary novel: the rest was left unfinished, and exists only in the form of two novella-length fragments. A comparative juxtaposition of the two novels is suggestive, not just because of parallels between the authors’ life trajectories and creative biographies, nor because of similarities between the protagonists, not even by the somewhat deceptive placement in the rubric of the 'Künstlerroman'. Both novels partake of ironic autobiography, and both resonate with the subgenre of the ”diary novel”, increasingly in vogue in European literature of the fin-de-siècle, modelled in turn on the published journal intime. Felix Ormusson and Stephen Dedalus were their authors’ long-time fictional fellow travellers, alter ego’s, in whose confessions one can read the pressing desire to emerge from the provinces and peripheries of Europe toward broader, metropolitan cultural horizons. The protagonists’ quests open onto the problematics of modernism – the split between life and literature, and the burden of ”overreflexivity” which obstructed literary creation and sentimental education. Behind the aesthetic polemics of both novels are shadows of the politics of the era: for Felix Ormusson, the aftermath of the 1905 revolution and political exile, and in the milieu of young Stephen Dedalus, the entanglement of national politics and the Catholic church. In the first part of the

  10. Methods for generation of reporter phages and immobilization of active bacteriophages on a polymer surface

    Science.gov (United States)

    Applegate, Bruce Michael (Inventor); Perry, Lynda Louise (Inventor); Morgan, Mark Thomas (Inventor); Kothapalli, Aparna (Inventor)

    2012-01-01

    Novel reporter bacteriophages are provided. Provided are compositions and methods that allow bacteriophages that are used for specific detection or killing of E. coli 0157:H7 to be propagated in nonpathogenic E. coli, thereby eliminating the safety and security risks of propagation in E. coli 0157:H7. Provided are compositions and methods for attaching active bacteriophages to the surface of a polymer in order to kill target bacteria with which the phage comes into contact. Provided are modified bacteriophages immobilized to a surface, which capture E. coli 0157:H7 and cause the captured cells to emit light or fluorescence, allowing detection of the bacteria in a sample.

  11. Insights into Bacteriophage Application in Controlling Vibrio Species

    Science.gov (United States)

    Letchumanan, Vengadesh; Chan, Kok-Gan; Pusparajah, Priyia; Saokaew, Surasak; Duangjai, Acharaporn; Goh, Bey-Hing; Ab Mutalib, Nurul-Syakima; Lee, Learn-Han

    2016-01-01

    Bacterial infections from various organisms including Vibrio sp. pose a serious hazard to humans in many forms from clinical infection to affecting the yield of agriculture and aquaculture via infection of livestock. Vibrio sp. is one of the main foodborne pathogens causing human infection and is also a common cause of losses in the aquaculture industry. Prophylactic and therapeutic usage of antibiotics has become the mainstay of managing this problem, however, this in turn led to the emergence of multidrug resistant strains of bacteria in the environment; which has raised awareness of the critical need for alternative non-antibiotic based methods of preventing and treating bacterial infections. Bacteriophages – viruses that infect and result in the death of bacteria – are currently of great interest as a highly viable alternative to antibiotics. This article provides an insight into bacteriophage application in controlling Vibrio species as well underlining the advantages and drawbacks of phage therapy. PMID:27486446

  12. A method for the detection of bacteriophages from ocean water

    Science.gov (United States)

    Moebus, K.

    1980-03-01

    A method for the isolation of bacteriophages from ocean water is described. It precludes sample storage before starting phage-enrichment cultures and provides for the use of 3 sub-samples enriched with organic nutrients after 1, 2 and 3 days of incubation. The method was used with samples collected from 6 m below the surface at 48 stations between the European continental shelf and the Sargasso Sea. With 213 among 931 bacterial isolates about 250 strains of bacteriophages were detected by two methods of different sensitivity. From 14 samples taken east of the Azores 115 host bacteria have been found versus only 98 from 34 samples collected at westerly stations. The employment of more than one sub-sample per station as well as the use of more sensitive phage-detection procedures was found to be more advantageous the lower the concentration of cultivatable bacteria in a sample.

  13. Biocontrol of Pectobacterium carotovorum subsp. carotovorum using bacteriophage PP1.

    Science.gov (United States)

    Lim, Jeong-A; Jee, Samnyu; Lee, Dong Hwan; Roh, Eunjung; Jung, Kyusuk; Oh, Changsik; Heu, Sunggi

    2013-08-01

    Pectobacterium carotovorum subsp. carotovorum (formerly Erwinia carotovora subsp. carotovora) is a plant pathogen that causes soft rot and stem rot diseases in several crops, including Chinese cabbage, potato, and tomato. To control this bacterium, we isolated a bacteriophage, PP1, with lytic activity against P. carotovorum subsp. carotovorum. Transmission electron microscopy revealed that the PP1 phage belongs to the Podoviridae family of the order Caudovirales, which exhibit icosahedral heads and short non-contractile tails. PP1 phage showed high specificity for P. carotovorum subsp. carotovorum, and several bacteria belonging to different species and phyla were resistant to PP1. This phage showed rapid and strong lytic activity against its host bacteria in liquid medium and was stable over a broad range of pH values. Disease caused by P. carotovorum subsp. carotovorum was significantly reduced by PP1 treatment. Overall, PP1 bacteriophage effectively controls P. carotovorum subsp. carotovorum. PMID:23727798

  14. The nucleotide sequence of the bacteriophage T5 ltf gene.

    Science.gov (United States)

    Kaliman, A V; Kulshin, V E; Shlyapnikov, M G; Ksenzenko, V N; Kryukov, V M

    1995-06-01

    The nucleotide sequence of the bacteriophage T5 Bg/II-BamHI fragment (4,835 bp in length) known to carry a gene encoding the LTF protein which forms the phage L-shaped tail fibers was determined. It was shown to contain an open reading frame for 1,396 amino acid residues that corresponds to a protein of 147.8 kDa. The coding region of ltf gene is preceded by a typical Shine-Dalgarno sequence. Downstream from the ltf gene there is a strong transcription terminator. Data bank analysis of the LTF protein sequence reveals 55.1% identity to the hypothetical protein ORF 401 of bacteriophage lambda in a segment of 118 amino acids overlap. PMID:7789514

  15. Bacteriophage application to control the contaminated water with Shigella.

    Science.gov (United States)

    Jun, Jin Woo; Giri, Sib Sankar; Kim, Hyoun Joong; Yun, Sae Kil; Chi, Cheng; Chai, Ji Young; Lee, Byeong Chun; Park, Se Chang

    2016-01-01

    Shigella is one of the most important waterborne and foodborne pathogens around the world. Emergence of antibiotic-resistant Shigella has made the development of alternatives to conventional antibiotics necessary. In this study, a virulent Myoviridae bacteriophage, pSs-1 was isolated from environmental water in South Korea and showed infectivity to S. flexneri as well as S. sonnei strains. One-step growth analysis showed that pSs-1 has a short latent period (25 min) and a large burst size (97 PFU/cell). According to the genomic analysis, pSs-1 contains 164,999 bp of genome with a G + C content of 35.54% and it is considered as a member of the T4-like bacteriophage group. These results showed that pSs-1 may have potential as a biocontrol agent instead of conventional antibiotics for shigellosis. PMID:26971572

  16. FoxO1 in embryonic development

    OpenAIRE

    Ferdous, Anwarul; Hill, Joseph A.

    2012-01-01

    Establishment of the maternal-fetal circulation during embryonic development is a fundamental process required for effective exchange of nutrients, waste products and signaling factors critical to all subsequent stages of fetal growth and development. Recent work has uncovered a previously unrecognized role of the transcription factor FoxO1 in the orchestration of molecular events underlying establishment of maternal-fetal circulatory interaction. These new data contribute to a larger body of...

  17. Bacteriophage-encoded depolymerases: their diversity and biotechnological applications

    OpenAIRE

    Pires, Diana Priscila Penso; Oliveira, Hugo Alexandre Mendes; Melo, Luís D. R.; Sillankorva, Sanna; Azeredo, Joana

    2016-01-01

    Bacteriophages (phages), natural enemies of bacteria, can encode enzymes able to degrade polymeric substances. These substances can be found in the bacterial cell surface, such as polysaccharides, or are produced by bacteria when they are living in biofilm communities, the most common bacterial lifestyle. Consequently, phages with depolymerase activity have a facilitated access to the host receptors, by degrading the capsular polysaccharides, and are believed to have a better performance agai...

  18. P. fluorescens biofilm control using bacteriophage ΦS1

    OpenAIRE

    Sillankorva, Sanna; Oliveira, Rosário; Vieira, M. J.; Sutherland, Ian W.; Azeredo, Joana

    2004-01-01

    Pseudomonas fluorescens biofilms contribute to the spoilage of dairy industry products due to the proteolytic activity of some Pseudomonas fluorescens strains. The eradication of these biofilms is difficult using the traditional chemical biocides due to the low removal action of these agents. Additionally chemical control leaves inactivated cells attached to the surface that tends to provide an ideal environment for further bacterial adhesion and growth. Bacteriophages can be seen as good alt...

  19. Choline-containing bacteriophage receptors in Streptococcus pneumoniae.

    OpenAIRE

    Lopez, R. (Rafael); Garcia, E.; Garcia, P.; Ronda, C; Tomasz, A.

    1982-01-01

    Choline-containing teichoic acid seems to be essential for the adsorption of bacteriophage Dp-1 to pneumococci. This conclusion is based on the following observations: In contrast to pneumococci grown in choline-containing medium, cells grown in medium containing ethanolamine or other submethylated aminoalcohols instead of choline were found to be resistant to infection by Dp-1. Live choline-grown bacteria and heat- or UV-inactivated cells and purified cell walls prepared from these cells wer...

  20. Bacteriophages : an underestimated role in human and animal health ?

    OpenAIRE

    Marianne eDe Paepe; Marion eLeclerc; Tinsley, Colin R.; Marie-Agnès ePetit

    2014-01-01

    Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e. the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associa...

  1. Genetic analysis of bacteriophages from clinical and environmental samples

    OpenAIRE

    Knapik, Kamila Z.

    2013-01-01

    Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populat...

  2. Molecular and Chemical Engineering of Bacteriophages for Potential Medical Applications

    OpenAIRE

    Hodyra, Katarzyna; Dąbrowska, Krystyna

    2014-01-01

    Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug d...

  3. Salmonella bacteriophage diversity reflects host diversity on dairy farms

    OpenAIRE

    Switt, Andrea I. Moreno; den Bakker, Henk C.; Vongkamjan, Kitiya; Hoelzer, Karin; Warnick, Lorin D.; Cummings, Kevin J.; Wiedmann, Martin

    2013-01-01

    Salmonella is an animal and human pathogen of worldwide concern. Surveillance programs indicate that the incidence of Salmonella serovars fluctuates over time. While bacteriophages are likely to play a role in driving microbial diversity, our understanding of the ecology and diversity of Salmonella phages is limited. Here we report the isolation of Salmonella phages from manure samples from 13 dairy farms with a history of Salmonella presence. Salmonella phages were isolated from 10 of the 13...

  4. Identification of mutations conferring 5-azacytidine resistance in bacteriophage

    OpenAIRE

    Arribas, María; Cabanillas, Laura; Lázaro, Ester

    2011-01-01

    RNA virus replication takes place at a very high error rate, and additional increases in this parameter can produce the extinction of virus infectivity. Nevertheless, RNA viruses can adapt to conditions of increased mutagenesis, which demonstrates that selection of beneficial mutations is also possible at higher-than-standard error rates. In this study we have analysed the evolutionary behaviour of bacteriophage Qβ populations when replication proceeds in the presence of the mutagenic nucleos...

  5. In vivo gene delivery and expression by bacteriophage lambda vectors

    OpenAIRE

    Lankes, HA; Zanghi, CN; Santos, K; Capella, C.; Duke, CMP; Dewhurst, S

    2007-01-01

    Aims Bacteriophage vectors have potential as gene transfer and vaccine delivery vectors because of their low cost, safety and physical stability. However, little is known concerning phage-mediated gene transfer in mammalian hosts. We therefore performed experiments to examine phage-mediated gene transfer in vivo. Methods and Results Mice were inoculated with recombinant lambda phage containing a mammalian expression cassette encoding firefly luciferase (luc). Efficient, dose-dependent in vivo...

  6. A second function of the S gene of bacteriophage lambda.

    OpenAIRE

    Wilson, D.B.; Okabe, A

    1982-01-01

    Infection of Escherichia coli by bacteriophage lambda caused an immediate inhibition of uptake by members of all three classes of E. coli active transport systems and made the inner membrane permeable to sucrose and glycine; however, infection stimulated alpha-methyl glucoside uptake. Phage infection caused a dramatic drop in the ATP pool of the cell, but the membrane did not become permeable to nucleotides. Infection by only one phage per cell was sufficient to cause transport inhibition. Ho...

  7. Isolation of Actinomyces bacteriophage from human dental plaque.

    OpenAIRE

    Tylenda, C A; Calvert, C.; Kolenbrander, P. E.; Tylenda, A

    1985-01-01

    Human dental plaque samples were screened for the presence of bacteriophage for Actinomyces viscosus and Streptococcus sanguis. None of the 336 samples yielded phage for S. sanguis, but 10 contained virulent actinomyces phage. A high host cell specificity was observed in that one phage isolate infected only A. viscosus T14V, eight phage isolates infected only A. viscosus MG-1, and one infected both strains. None was capable of productively infecting various other actinomyces strains that repr...

  8. Effects of sunlight on bacteriophage viability and structure

    International Nuclear Information System (INIS)

    Viruses are now widely recognized as the most abundant member of aquatic planktonic communities. Questions concerning the ecological role of viruses in such communities have lead to resurgent interest in the persistence of free fivuses in marine waters. This study seeks to evaluate the effects of solar radiation on the survival of viruses in surface waters. In situ effects of natural sunlight on infectivity and destruction of viral capsids of two estuarine bacteriophages were examined

  9. Characterization of bacteriophage communities and CRISPR profiles from dental plaque

    OpenAIRE

    Naidu, Mayuri; Robles-Sikisaka, Refugio; Abeles, Shira R.; Boehm, Tobias K; Pride, David T

    2014-01-01

    Background Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type. Results We found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-...

  10. Bacteriophages and medical oncology: targeted gene therapy of cancer.

    Science.gov (United States)

    Bakhshinejad, Babak; Karimi, Marzieh; Sadeghizadeh, Majid

    2014-08-01

    Targeted gene therapy of cancer is of paramount importance in medical oncology. Bacteriophages, viruses that specifically infect bacterial cells, offer a variety of potential applications in biomedicine. Their genetic flexibility to go under a variety of surface modifications serves as a basis for phage display methodology. These surface manipulations allow bacteriophages to be exploited for targeted delivery of therapeutic genes. Moreover, the excellent safety profile of these viruses paves the way for their potential use as cancer gene therapy platforms. The merge of phage display and combinatorial technology has led to the emergence of phage libraries turning phage display into a high throughput technology. Random peptide libraries, as one of the most frequently used phage libraries, provide a rich source of clinically useful peptide ligands. Peptides are known as a promising category of pharmaceutical agents in medical oncology that present advantages such as inexpensive synthesis, efficient tissue penetration and the lack of immunogenicity. Phage peptide libraries can be screened, through biopanning, against various targets including cancer cells and tissues that results in obtaining cancer-homing ligands. Cancer-specific peptides isolated from phage libraries show huge promise to be utilized for targeting of various gene therapy vectors towards malignant cells. Beyond doubt, bacteriophages will play a more impressive role in the future of medical oncology. PMID:25012686

  11. Bacteriophage P22 in vitro DNA packaging monitored by agarose gel electrophoresis: rate of DNA entry into capsids.

    OpenAIRE

    Gope, R.; Serwer, P

    1983-01-01

    Bacteriophage P22, like other double-stranded DNA bacteriophages, packages DNA in a preassembled, DNA-free procapsid. The P22 procapsid and P22 bacteriophage have been electrophoretically characterized; the procapsid has a negative average electrical surface charge density (sigma) higher in magnitude than the negative sigma of the mature bacteriophage. Dextrans, sucrose, and maltose were shown to have a dramatic stimulatory effect on the in vitro packaging of DNA by the P22 procapsid. However...

  12. Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: Evolution, structure, and genome organization of lactococcal bacteriophages

    DEFF Research Database (Denmark)

    Brøndsted, Lone; Østergaard, Solvej; Pedersen, Margit; Hammer, Karin; Vogensen, F.K.

    2001-01-01

    -1 may have evolved by homologous recombination between the host chromosome and a mother phage and support the observation that phage remnants as well as prophages located in the Lactococcus chromosome contribute significantly to bacteriophage evolution. Some proteins encoded in the early transcribed...... bacteriophage TP901-1 proliferation. Short regions of microhomology in intergenic regions present in several lactococcal bacteriophages and chromosomal fragments of Lactococcus lactis are suggested to be points of exchange of genetic material through homologous recombination. Our results indicate that TP901...

  13. Biocontrol of Escherichia coli O157:H7 using a bacteriophage cocktail in laboratory media

    Science.gov (United States)

    Bacteriophages are natural enemies of bacteria, and therefore, logical candidates to evaluate as antibacterial agents for the control of foodborne pathogens. The effect of a bacteriophage treatment on the prevention of E. coli O157:H7 growth was investigated in Tryptic Soy Broth (TSB) laboratory med...

  14. Isolation and characterization of a lytic bacteriophage φKp-lyy15 of Klebsiella pneumoniae

    Institute of Scientific and Technical Information of China (English)

    Yinyin; Lu; Hongyan; Shi; Zhe; Zhang; Fang; Han; Jinghua; Li; Yanbo; Sun

    2015-01-01

    <正>Dear Editor,Bacteriophages(phages)are viruses that specifically infect and kill bacteria.They are ubiquitous throughout all environments that bacteria inhabit.Following their discovery by F.W.Twort in 1915 and F.d’Herele in 1917,bacteriophages were recognized as potential agents to treat bacterial diseases and phage therapy has been used

  15. UV ability to destroy poliovirus end FRNA specific bacteriophages

    Energy Technology Data Exchange (ETDEWEB)

    Baron, J.; Joret, J.C.; Lesavre, J.; Perrot, J.Y.

    1996-01-01

    In France, the use of ultraviolet radiation to disinfect secondary effluents is only in its initial stage. The aim of this study was to examine the ability of UV to destroy Poliovirus Type 1 and FRNA specific bacteriophages (laboratory MS2 phages and indigenous phages). Concentrated viral solutions were mixed with secondary effluents artificially enriched with suspended solids and then irradiated at various UV dose in a collimated beam. Bacteriological analysis of Escherichia coli and enterococci were performed at the same time. UV were very efficient to kill Poliovirus : Inactivation of 3 and 5 log units were observed respectively at UV doses of 20 and 40 mW/cm{sup 2}. The Poliovirus disinfection rate was almost the same than Escherichia coli. Enterococci were more resistant than E. coli. Inactivation of MS2 bacteriophages was significantly correlated to UV dose following the relationship MS2 Inactivation = 0.047{sup *} Dose + 0,396. At UV dose of 20 mWs/cm{sup 2}, MS2 phages were 2.3 times more resistant to UV than Poliovirus, i.e. they need UV dose 2,3 times greater to be disinfected at the same level. A review of the literature has also shown that viruses more resistant to UV treatment have never been reported. All this would tend to confirm the interest of this group of virus as indicators of the disinfection efficiency of UV, which could indicate, on site, the inactivation of pathogenic viruses. Inactivation rates obtained for FRNA phages proved the good virucidal activity of UV. The inactivation of indigenous FRNA bacteriophages was not correlated with E. coli inactivation. On the other hand, it was correlated with enterococci inactivation. (Author). 23 refs., 7 figs., 4 tabs.

  16. Molecular Characterization of a Bacteriophage (Chp2) from Chlamydia psittaci

    OpenAIRE

    Liu, B. L.; Everson, J. S.; Fane, B.; Giannikopoulou, P.; Vretou, E.; Lambden, P R; Clarke, I N

    2000-01-01

    Comparisons of the proteome of abortifacient Chlamydia psittaci isolates from sheep by two-dimensional gel electrophoresis identified a novel abundant protein with a molecular mass of 61.4 kDa and an isoelectric point of 6.41. C-terminal sequence analysis of this protein yielded a short peptide sequence that had an identical match to the viral coat protein (VP1) of the avian chlamydiaphage Chp1. Electron microscope studies revealed the presence of a 25-nm-diameter bacteriophage (Chp2) with no...

  17. [Bacteriophage therapy of septic complications of orthopaedic surgery (author's transl].

    Science.gov (United States)

    Lang, G; Kehr, P; Mathevon, H; Clavert, J M; Séjourne, P; Pointu, J

    1979-01-01

    Seven septic cases have been treated by bacteriophage; two infections after insertion of a hip prosthesis, two septic arthritis of the knee, one osteomyelitis of the tibia, one septic non-union of the femur and one septic complication following Harrington rodding. Only specific phages were used in association with several types of surgical procedure. The technique of treatment is described. All cases were long-term infections with resistant organisms. Results were good in five, fair in one and one case was a failure. It is concluded that phage therapy may be helpful in the treatment of long-term infections. PMID:156386

  18. Bacteriophage-Derived Vectors for Targeted Cancer Gene Therapy

    Directory of Open Access Journals (Sweden)

    Md Zahidul Islam Pranjol

    2015-01-01

    Full Text Available Cancer gene therapy expanded and reached its pinnacle in research in the last decade. Both viral and non-viral vectors have entered clinical trials, and significant successes have been achieved. However, a systemic administration of a vector, illustrating safe, efficient, and targeted gene delivery to solid tumors has proven to be a major challenge. In this review, we summarize the current progress and challenges in the targeted gene therapy of cancer. Moreover, we highlight the recent developments of bacteriophage-derived vectors and their contributions in targeting cancer with therapeutic genes following systemic administration.

  19. Re-initiation repair in bacteriophage T4

    International Nuclear Information System (INIS)

    Irradiation of bacteriophage T4 with ultraviolet light induces the formation of pyrimidine dimers in its DNA. These dimers hamper replication of DNA and, to a lesser extent, transcription of DNA after its infection of bacteria. A number of pathways enable phage T4 to multiply dimer-containing DNA. One of these pathways has been named replication repair and is described in this thesis. The properties of two phage strains, unable to perform replication repair, have been studied to obtain a picture of the repair process. The mutations in these strains that affect replication repair have been located on the genomic map of T4. (Auth.)

  20. 26 CFR 31.3121(o)-1 - Crew leader.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 15 2010-04-01 2010-04-01 false Crew leader. 31.3121(o)-1 Section 31.3121(o)-1... Contributions Act (Chapter 21, Internal Revenue Code of 1954) General Provisions § 31.3121(o)-1 Crew leader. The term “crew leader” means an individual who furnishes individuals to perform agricultural labor...

  1. Application of bacteriophages in post-harvest control of human pathogenic and food spoiling bacteria.

    Science.gov (United States)

    Pérez Pulido, Rubén; Grande Burgos, Maria José; Gálvez, Antonio; Lucas López, Rosario

    2016-10-01

    Bacteriophages have attracted great attention for application in food biopreservation. Lytic bacteriophages specific for human pathogenic bacteria can be isolated from natural sources such as animal feces or industrial wastes where the target bacteria inhabit. Lytic bacteriophages have been tested in different food systems for inactivation of main food-borne pathogens including Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, Salmonella enterica, Shigella spp., Campylobacter jejuni and Cronobacter sakazkii, and also for control of spoilage bacteria. Application of lytic bacteriophages could selectively control host populations of concern without interfering with the remaining food microbiota. Bacteriophages could also be applied for inactivation of bacteria attached to food contact surfaces or grown as biofilms. Bacteriophages may receive a generally recognized as safe status based on their lack of toxicity and other detrimental effects to human health. Phage preparations specific for L. monocytogenes, E. coli O157:H7 and S. enterica serotypes have been commercialized and approved for application in foods or as part of surface decontamination protocols. Phage endolysins have a broader host specificity compared to lytic bacteriophages. Cloned endolysins could be used as natural preservatives, singly or in combination with other antimicrobials such as bacteriocins. PMID:26042353

  2. Pulmonary bacteriophage therapy on Pseudomonas aeruginosa cystic fibrosis strains: first steps towards treatment and prevention.

    Directory of Open Access Journals (Sweden)

    Eric Morello

    Full Text Available Multidrug-resistant bacteria are the cause of an increasing number of deadly pulmonary infections. Because there is currently a paucity of novel antibiotics, phage therapy--the use of specific viruses that infect bacteria--is now more frequently being considered as a potential treatment for bacterial infections. Using a mouse lung-infection model caused by a multidrug resistant Pseudomonas aeruginosa mucoid strain isolated from a cystic fibrosis patient, we evaluated bacteriophage treatments. New bacteriophages were isolated from environmental samples and characterized. Bacteria and bacteriophages were applied intranasally to the immunocompetent mice. Survival was monitored and bronchoalveolar fluids were analysed. Quantification of bacteria, bacteriophages, pro-inflammatory and cytotoxicity markers, as well as histology and immunohistochemistry analyses were performed. A curative treatment (one single dose administrated 2 h after the onset of the infection allowed over 95% survival. A four-day preventive treatment (one single dose resulted in a 100% survival. All of the parameters measured correlated with the efficacy of both curative and preventive bacteriophage treatments. We also showed that in vitro optimization of a bacteriophage towards a clinical strain improved both its efficacy on in vivo treatments and its host range on a panel of 20 P. aeruginosa cystic fibrosis strains. This work provides an incentive to develop clinical studies on pulmonary bacteriophage therapy to combat multidrug-resistant lung infections.

  3. Isolation and Characterization of Bacteriophages Against Pseudomonas syringae pv. actinidiae Causing Bacterial Canker Disease in Kiwifruit.

    Science.gov (United States)

    Yu, Ji-Gang; Lim, Jeong-A; Song, Yu-Rim; Heu, Sunggi; Kim, Gyoung Hee; Koh, Young Jin; Oh, Chang-Sik

    2016-02-01

    Pseudomonas syringae pv. actinidiae causes bacterial canker disease in kiwifruit. Owing to the prohibition of agricultural antibiotic use in major kiwifruit-cultivating countries, alternative methods need to be developed to manage this disease. Bacteriophages are viruses that specifically infect target bacteria and have recently been reconsidered as potential biological control agents for bacterial pathogens owing to their specificity in terms of host range. In this study, we isolated bacteriophages against P. syringae pv. actinidiae from soils collected from kiwifruit orchards in Korea and selected seven bacteriophages for further characterization based on restriction enzyme digestion patterns of genomic DNA. Among the studied bacteriophages, two belong to the Myoviridae family and three belong to the Podoviridae family, based on morphology observed by transmission electron microscopy. The host range of the selected bacteriophages was confirmed using 18 strains of P. syringae pv. actinidiae, including the Psa2 and Psa3 groups, and some were also effective against other P. syringae pathovars. Lytic activity of the selected bacteriophages was sustained in vitro until 80 h, and their activity remained stable up to 50°C, at pH 11, and under UV-B light. These results indicate that the isolated bacteriophages are specific to P. syringae species and are resistant to various environmental factors, implying their potential use in control of bacterial canker disease in kiwifruits. PMID:26628254

  4. Ecology of Anti-Biofilm Agents I: Antibiotics versus Bacteriophages

    Directory of Open Access Journals (Sweden)

    Stephen T. Abedon

    2015-09-01

    Full Text Available Bacteriophages, the viruses that infect bacteria, have for decades been successfully used to combat antibiotic-resistant, chronic bacterial infections, many of which are likely biofilm associated. Antibiotics as anti-biofilm agents can, by contrast, be inefficacious against even genetically sensitive targets. Such deficiencies in usefulness may result from antibiotics, as naturally occurring compounds, not serving their producers, in nature, as stand-alone disruptors of mature biofilms. Anti-biofilm effectiveness by phages, by contrast, may result from a combination of inherent abilities to concentrate lytic antibacterial activity intracellularly via bacterial infection and extracellularly via localized population growth. Considered here is the anti-biofilm activity of microorganisms, with a case presented for why, ecologically, bacteriophages can be more efficacious than traditional antibiotics as medically or environmentally applied biofilm-disrupting agents. Four criteria, it can be argued, generally must be met, in combination, for microorganisms to eradicate biofilms: (1 Furnishing of sufficiently effective antibacterial factors, (2 intimate interaction with biofilm bacteria over extended periods, (3 associated ability to concentrate antibacterial factors in or around targets, and, ultimately, (4 a means of physically disrupting or displacing target bacteria. In nature, lytic predators of bacteria likely can meet these criteria whereas antibiotic production, in and of itself, largely may not.

  5. Minimal gene regulatory circuits that can count like bacteriophage lambda.

    Science.gov (United States)

    Avlund, M; Dodd, Ian B; Sneppen, K; Krishna, S

    2009-12-11

    The behavior of living systems is dependent on large dynamical gene regulatory networks (GRNs). However, the functioning of even the smallest GRNs is difficult to predict. The bistable GRN of bacteriophage lambda is able to count to make a decision between lysis and lysogeny on the basis of the number of phages infecting the cell, even though replication of the phage genome eliminates this initial difference. By simulating the behavior of a large number of random transcriptional GRNs, we show that a surprising variety of GRNs can carry out this complex task, including simple CI-Cro-like mutual repression networks. Thus, our study extends the repertoire of simple GRNs. Counterintuitively, the major effect of the addition of CII-like regulation, generally thought to be needed for counting by lambda, was to improve the ability of the networks to complete a simulated prophage induction. Our study suggests that additional regulatory mechanisms to decouple Cro and CII levels may exist in lambda and that infection counting could be widespread among temperate bacteriophages, many of which contain CI-Cro-like circuits. PMID:19796646

  6. PET Imaging and biodistribution of chemically modified bacteriophage MS2.

    Science.gov (United States)

    Farkas, Michelle E; Aanei, Ioana L; Behrens, Christopher R; Tong, Gary J; Murphy, Stephanie T; O'Neil, James P; Francis, Matthew B

    2013-01-01

    The fields of nanotechnology and medicine have merged in the development of new imaging and drug delivery agents based on nanoparticle platforms. As one example, a mutant of bacteriophage MS2 can be differentially modified on the exterior and interior surfaces for the concurrent display of targeting functionalities and payloads, respectively. In order to realize their potential for use in in vivo applications, the biodistribution and circulation properties of this class of agents must first be investigated. A means of modulating and potentially improving the characteristics of nanoparticle agents is the appendage of PEG chains. Both MS2 and MS2-PEG capsids possessing interior DOTA chelators were labeled with (64)Cu and injected intravenously into mice possessing tumor xenografts. Dynamic imaging of the agents was performed using PET-CT on a single animal per sample, and the biodistribution at the terminal time point (24 h) was assessed by gamma counting of the organs ex vivo for 3 animals per agent. Compared to other viral capsids of similar size, the MS2 agents showed longer circulation times. Both MS2 and MS2-PEG bacteriophage behaved similarly, although the latter agent showed significantly less uptake in the spleen. This effect may be attributed to the ability of the PEG chains to mask the capsid charge. Although the tumor uptake of the agents may result from the enhanced permeation and retention (EPR) effect, selective tumor imaging may be achieved in the future by using exterior targeting groups. PMID:23214968

  7. Phenotypic and genotypic variations within a single bacteriophage species

    Directory of Open Access Journals (Sweden)

    Kulakov Leonid

    2011-03-01

    Full Text Available Abstract Background Although horizontal gene transfer plays a pivotal role in bacteriophage evolution, many lytic phage genomes are clearly shaped by vertical evolution. We investigated the influence of minor genomic deletions and insertions on various phage-related phenotypic and serological properties. Findings We collected ten different isolates of Pseudomonas aeruginosa bacteriophage ϕKMV. All sequenced genomes (42-43 kb, long direct terminal repeats are nearly identical, which intuitively implied strongly similar infections cycles. However, their latent periods vary between 21 and 28 minutes and they are able to lyse between 5 and 58% of a collection of 107 clinical P. aeruginosa strains. We also noted that phages with identical tail structures displayed profound differences in host spectra. Moreover, point mutations in tail and spike proteins were sufficient to evade neutralization by two phage-specific antisera, isolated from rabbits. Conclusion Although all analyzed phages are 83-97% identical at the genome level, they display a surprisingly large variation in various phenotypic properties. The small overlap in host spectrum and their ability to readily escape immune defences against a nearly identical phage are promising elements for the application of these phages in phage therapy.

  8. Comparative analysis of two bacteriophages of Xanthomonas arboricola pv. juglandis.

    Science.gov (United States)

    Dömötör, Dóra; Frank, Tamara; Rákhely, Gábor; Doffkay, Zsolt; Schneider, György; Kovács, Tamás

    2016-09-01

    Walnut blight caused by Xanthomonas arboricola pv. juglandis (Xaj) is one of the most frequent infective diseases of walnut, resulting in serious economic losses. One potential solution to control this disease could be the application of bacteriophages. In this study, 24 phages were isolated from soil and walnut aerial tissues infected with Xaj. Two polyvalent bacteriophages, Xaj2 and Xaj24 were chosen for further characterization including their morphological, physiological and genomic analyses. Xaj2 was classified as Siphoviridae whereas Xaj24 belonged to the Podoviridae family. Both phages demonstrated lytic effect on Xaj in laboratory trials. Complete genomes of Xaj2 and Xaj24 were determined. Genomes of Xaj2 and Xaj24 consisted of 49.241 and 44.861 nucleotides encoding 80 and 53 genes, respectively. Comparative genome analyses have revealed that Xaj2 had a unique genome sequence, while Xaj24 was a phiKMV-like phage and it was most similar to the Prado phage which is virulent for Xylella fastidiosa and Xanthomonas spp. In this study, we present the first two complete Xaj phage sequences enabling an insight into the genomics of Xaj phages. PMID:27275846

  9. [Reconstruction of possible paths of the origin and morphological evolution of bacteriophages].

    Science.gov (United States)

    Letarov, A V

    1998-11-01

    The problem of the origin and evolution of viruses and, in particular, the origin and evolution of bacteriophages is of considerable interest. However, so far, this problem has not been solved with quantitative methods of molecular systematics. In the present study, an attempt to reconstruct the possible paths of appearance and evolution of bacteriophages based on their structural features and morphogenesis, as well as general characteristics of their life cycles and genome organization, was carried out. A scheme describing phylogeny of the main bacteriophage groups and evolution of their life cycles is suggested. Existence of two independently evaluating types of morphogenesis ("budding outward" and "budding inward") is postulated. PMID:10096023

  10. Complete Genome Sequences of Lytic Bacteriophages of Xanthomonas arboricola pv. Juglandis

    Science.gov (United States)

    Vasquez, Ignacio; Santos, Leonardo; Segovia, Cristopher; Ayala, Manuel; Alvarado, Romina; Nuñez, Pablo

    2016-01-01

    Three bacteriophages, f20-Xaj, f29-Xaj, and f30-Xaj, with lytic activity against Xanthomonas arboricola pv. juglandis were isolated from walnut trees (VIII Bío Bío Region, Chile). These lytic bacteriophages have double-stranded DNA (dsDNA) genomes of 43,851 bp, 41,865 bp, and 44,262 bp, respectively. These are the first described bacteriophages with lytic activity against X. arboricola pv. juglandis that can be utilized as biocontrol agents. PMID:27257210

  11. Natural products from the ascidian Botrylloides giganteum, from the sponges Verongula gigantea, Ircinia felix, Cliona delitrix and from the nudibranch Tambja eliora, from the Brazilian coastline

    International Nuclear Information System (INIS)

    Two new marine metabolites, 3Z, 6Z, 9Z-dodecatrien-1-ol (1) from the ascidian Botrylloides giganteum and 4H-pyran-2ol acetate from the sponge Ircinia felix (4) are herein reported. The known bromotyrosine compounds, 2-(3,5-dibromo-4-methoxyphenyl)-N,N,Ndimethylethanammonium (2) and 2,6-dibromo-4-(2-(trimethylammonium)ethyl)phenol (3), have been isolated from the sponge Verongula gigantea. Serotonin (5) is reported for the first time from the sponge Cliona delitrix, and tambjamines A (15) and D (16) isolated as their respective salts from the nudibranch Tambja eliora. Only tambjamine D presented cytotoxicity against CEM (IC5)0 12.2 μg/mL) and HL60 (IC50 13.2 μg/mL) human leukemia cells, MCF-7 breast cancer cells (IC50 13.2 μg/mL), colon HCT-8 cancer cells (IC50 10.1 μg/mL) and murine melanoma B16 cancer cells (IC50 6.7 μg/mL). (author)

  12. Albany/FELIX: a parallel, scalable and robust, finite element, first-order Stokes approximation ice sheet solver built for advanced analysis

    Directory of Open Access Journals (Sweden)

    I. Kalashnikova

    2014-11-01

    Full Text Available This paper describes a new parallel, scalable and robust finite-element based solver for the first-order Stokes momentum balance equations for ice flow. The solver, known as Albany/FELIX, is constructed using the component-based approach to building application codes, in which mature, modular libraries developed as a part of the Trilinos project are combined using abstract interfaces and Template-Based Generic Programming, resulting in a final code with access to dozens of algorithmic and advanced analysis capabilities. Following an overview of the relevant partial differential equations and boundary conditions, the numerical methods chosen to discretize the ice flow equations are described, along with their implementation. The results of several verification studies of the model accuracy are presented using: (1 new test cases derived using the method of manufactured solutions, and (2 canonical ice sheet modeling benchmarks. Model accuracy and convergence with respect to mesh resolution is then studied on problems involving a realistic Greenland ice sheet geometry discretized using structured and unstructured meshes. Also explored as a part of this study is the effect of vertical mesh resolution on the solution accuracy and solver performance. The robustness and scalability of our solver on these problems is demonstrated. Lastly, we show that good scalability can be achieved by preconditioning the iterative linear solver using a new algebraic multilevel preconditioner, constructed based on the idea of semi-coarsening.

  13. BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes.

    Directory of Open Access Journals (Sweden)

    Laura J Marinelli

    Full Text Available Advances in DNA sequencing technology have facilitated the determination of hundreds of complete genome sequences both for bacteria and their bacteriophages. Some of these bacteria have well-developed and facile genetic systems for constructing mutants to determine gene function, and recombineering is a particularly effective tool. However, generally applicable methods for constructing defined mutants of bacteriophages are poorly developed, in part because of the inability to use selectable markers such as drug resistance genes during viral lytic growth. Here we describe a method for simple and effective directed mutagenesis of bacteriophage genomes using Bacteriophage Recombineering of Electroporated DNA (BRED, in which a highly efficient recombineering system is utilized directly on electroporated phage DNA; no selection is required and mutants can be readily detected by PCR. We describe the use of BRED to construct unmarked gene deletions, in-frame internal deletions, base substitutions, precise gene replacements, and the addition of gene tags.

  14. [The challenge of controlling foodborne diseases: bacteriophages as a new biotechnological tool].

    Science.gov (United States)

    Jorquera, Denisse; Galarce, Nicolás; Borie, Consuelo

    2015-12-01

    Foodborne diseases are an increasing public health issue, in which bacterial pathogens have a transcendental role. To face this situation, the food industry has implemented several control strategies, using in the last decade some biotechnological tools, such as direct application of bacteriophages on food, to effectively control bacterial pathogens. Their bactericidal and safe properties to humans and animals have been widely described in the literature, being nowadays some bacteriophage-based products commercially available. Despite this, there are so many factors that can interfere in their biocontrol effectiveness on food, therefore is essential to consider these factors before their application. Thus, the optimal bacterial reduction will be achieved, which would produce a safer food. This review discusses some factors to consider in the use of bacteriophages as biocontrol agents of foodborne pathogens, including historical background, taxonomy and biological description of bacteriophages, and also advantages, disadvantages, and considerations of food applications. PMID:26928505

  15. Pecularities of mutagenesis of T4Br bacteriophage under the direct and indirect radiation effects

    International Nuclear Information System (INIS)

    Different lethal and mutagenic effects were shown when bacteriophage T4Br+ (470 r/min) was irradiated in broth (direct effect) and a buffer solution (direct and indirect action). The survival rate of the bacteriophage in the buffer solution was 0.1 percent for a dose rate of 60 kr; in the broth it was 10 percent. The frequency of mutation of the bacteriophage also showed the greater effect of the irradiation in the buffer solution than in the broth (25 and 5 r-mutants respectively at a dose rate of 10 kr). An analysis of the ratio of the r-groups when the bacteriophage was treated in various ways revealed differences between mutagenesis produced in the broth and the buffer, and spontaneous mutagenesis. (V.A.P.)

  16. Genetic diversity among five T4-like bacteriophages

    Directory of Open Access Journals (Sweden)

    Bertrand Claire

    2006-05-01

    Full Text Available Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4

  17. BRED: A Simple and Powerful Tool for Constructing Mutant and Recombinant Bacteriophage Genomes

    OpenAIRE

    Marinelli, Laura J.; Mariana Piuri; Zuzana Swigonová; Amrita Balachandran; Oldfield, Lauren M.; van Kessel, Julia C.; Hatfull, Graham F.

    2008-01-01

    Advances in DNA sequencing technology have facilitated the determination of hundreds of complete genome sequences both for bacteria and their bacteriophages. Some of these bacteria have well-developed and facile genetic systems for constructing mutants to determine gene function, and recombineering is a particularly effective tool. However, generally applicable methods for constructing defined mutants of bacteriophages are poorly developed, in part because of the inability to use selectable m...

  18. Isolation of Dickeya dadantii strains from potato disease and biocontrol by their bacteriophages

    OpenAIRE

    Soleimani-Delfan, Abbas; Etemadifar, Zahra; Emtiazi, Giti; Bouzari, Majid

    2015-01-01

    One of the most economically important bacterial pathogens of plants and plant products is Dickeya dadantii. This bacterium causes soft rot disease in tubers and other parts of the potato and other plants of the Solanaceae family. The application of restricted host range bacteriophages as biocontrol agents has recently gained widespread interest. This study purposed to isolate the infectious agent of the potato and evaluate its biocontrol by bacteriophages. Two phytopathogenic strains were is...

  19. Hexagonally packed DNA within bacteriophage T7 stabilized by curvature stress.

    OpenAIRE

    Odijk, T

    1998-01-01

    A continuum computation is proposed for the bending stress stabilizing DNA that is hexagonally packed within bacteriophage T7. Because the inner radius of the DNA spool is rather small, the stress of the curved DNA genome is strong enough to balance its electrostatic self-repulsion so as to form a stable hexagonal phase. The theory is in accord with the microscopically determined structure of bacteriophage T7 filled with DNA within the experimental margin of error.

  20. A Fluoroquinolone Induces a Novel Mitogen-Encoding Bacteriophage in Streptococcus canis

    OpenAIRE

    Ingrey, Keely T.; Ren, Jun; Prescott, John F.

    2003-01-01

    This study investigated whether the recently recognized emergence of canine streptococcal toxic shock syndrome (STSS) and necrotizing fasciitis (NF) might be partly attributed to the use of fluoroquinolones to treat Streptococcus canis infections in dogs. Both mitomycin and the fluoroquinolone enrofloxacin caused bacteriophage-induced lysis of S. canis strain 34, an isolate from a case of canine STSS and NF. Fluoroquinolone-evoked, bacteriophage-induced lysis occurred over a range of concentr...

  1. Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans belonging to the 'phiKMV-like viruses'

    OpenAIRE

    Adriaenssens, Evelien; Ceyssens, Pieter-Jan; Dunon, Vincent; Ackermann, Hans-Wolfgang; Van Vaerenbergh, Johan; Maes, Martine; De Proft, Maurice; Lavigne, Rob

    2011-01-01

    Pantoea agglomerans is a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight of P. agglomerans are lytic phages, isolated from soil samples, belonging to the Podoviridae and are the first Pantoea phages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,03...

  2. Excision repair and patch size in UV-irradiated bacteriophage T4.

    OpenAIRE

    Yarosh, D B; Rosenstein, B S; Setlow, R B

    1981-01-01

    We determined the average size of excision repair patches in repair of UV lesions in bacteriophage T4 by measuring the photolysis of bromodeoxyuridine incorporated during repair. The average patch was small, approximately four nucleotides long. In control experiments with the denV1 excision-deficient mutant, we encountered an artifact, a protein(s) which remained bound to phenol-extracted DNA and prevented nicking by the UV-specific endonucleases of Micrococcus luteus and bacteriophage T4.

  3. Access to bacteriophage therapy: discouraging experiences from the human cell and tissue legal framework.

    Science.gov (United States)

    Verbeken, G; Huys, I; De Vos, D; De Coninck, A; Roseeuw, D; Kets, E; Vanderkelen, A; Draye, J P; Rose, T; Jennes, S; Ceulemans, C; Pirnay, J P

    2016-02-01

    Cultures of human epithelial cells (keratinocytes) are used as an additional surgical tool to treat critically burnt patients. Initially, the production environment of keratinocyte grafts was regulated exclusively by national regulations. In 2004, the European Tissues and Cells Directive 2004/23/EC (transposed into Belgian Law) imposed requirements that resulted in increased production costs and no significant increase in quality and/or safety. In 2007, Europe published Regulation (EC) No. 1394/2007 on Advanced Therapy Medicinal Products. Overnight, cultured keratinocytes became (arguably) 'Advanced' Therapy Medicinal Products to be produced as human medicinal products. The practical impact of these amendments was (and still is) considerable. A similar development appears imminent in bacteriophage therapy. Bacteriophages are bacterial viruses that can be used for tackling the problem of bacterial resistance development to antibiotics. Therapeutic natural bacteriophages have been in clinical use for almost 100 years. Regulators today are framing the (re-)introduction of (natural) bacteriophage therapy into 'modern western' medicine as biological medicinal products, also subject to stringent regulatory medicinal products requirements. In this paper, we look back on a century of bacteriophage therapy to make the case that therapeutic natural bacteriophages should not be classified under the medicinal product regulatory frames as they exist today. It is our call to authorities to not repeat the mistake of the past. PMID:26678555

  4. Isolation of Dickeya dadantii strains from potato disease and biocontrol by their bacteriophages

    Directory of Open Access Journals (Sweden)

    Abbas Soleimani-Delfan

    2015-09-01

    Full Text Available One of the most economically important bacterial pathogens of plants and plant products is Dickeya dadantii. This bacterium causes soft rot disease in tubers and other parts of the potato and other plants of the Solanaceae family. The application of restricted host range bacteriophages as biocontrol agents has recently gained widespread interest. This study purposed to isolate the infectious agent of the potato and evaluate its biocontrol by bacteriophages. Two phytopathogenic strains were isolated from infected potatoes, identified based on biochemical and 16S rRNA gene sequencing, and submitted to GenBank as D. dadantii strain pis3 (accession no. HQ423668 and D. dadantii strain sip4 (accession no. HQ423669. Their bacteriophages were isolated from Caspian Sea water by enriching the water filtrate with D. dadantii strains as hosts using spot or overlay methods. On the basis of morphotypes, the isolated bacteriophages were identified as members of the Myoviridae and Siphoviridae families and could inhibit the growth of antibiotic resistant D. dadantii strains in culture medium. Moreover, in Dickeya infected plants treated with bacteriophage, no disease progression was detected. No significant difference was seen between phage-treated and control plants. Thus, isolated bacteriophages can be suggested for the biocontrol of plant disease caused by Dickeya strains.

  5. Isolation of Dickeya dadantii strains from potato disease and biocontrol by their bacteriophages.

    Science.gov (United States)

    Soleimani-Delfan, Abbas; Etemadifar, Zahra; Emtiazi, Giti; Bouzari, Majid

    2015-01-01

    One of the most economically important bacterial pathogens of plants and plant products is Dickeya dadantii. This bacterium causes soft rot disease in tubers and other parts of the potato and other plants of the Solanaceae family. The application of restricted host range bacteriophages as biocontrol agents has recently gained widespread interest. This study purposed to isolate the infectious agent of the potato and evaluate its biocontrol by bacteriophages. Two phytopathogenic strains were isolated from infected potatoes, identified based on biochemical and 16S rRNA gene sequencing, and submitted to GenBank as D. dadantii strain pis3 (accession no. HQ423668) and D. dadantii strain sip4 (accession no. HQ423669). Their bacteriophages were isolated from Caspian Sea water by enriching the water filtrate with D. dadantii strains as hosts using spot or overlay methods. On the basis of morphotypes, the isolated bacteriophages were identified as members of the Myoviridae and Siphoviridae families and could inhibit the growth of antibiotic resistant D. dadantii strains in culture medium. Moreover, in Dickeya infected plants treated with bacteriophage, no disease progression was detected. No significant difference was seen between phage-treated and control plants. Thus, isolated bacteriophages can be suggested for the biocontrol of plant disease caused by Dickeya strains. PMID:26413062

  6. A simple and novel modification of comet assay for determination of bacteriophage mediated bacterial cell lysis.

    Science.gov (United States)

    Khairnar, Krishna; Sanmukh, Swapnil; Chandekar, Rajshree; Paunikar, Waman

    2014-07-01

    The comet assay is the widely used method for in vitro toxicity testing which is also an alternative to the use of animal models for in vivo testing. Since, its inception in 1984 by Ostling and Johansson, it is being modified frequently for a wide range of application. In spite of its wide applicability, unfortunately there is no report of its application in bacteriophages research. In this study, a novel application of comet assay for the detection of bacteriophage mediated bacterial cell lysis was described. The conventional methods in bacteriophage research for studying bacterial lysis by bacteriophages are plaque assay method. It is time consuming, laborious and costly. The lytic activity of bacteriophage devours the bacterial cell which results in the release of bacterial genomic material that gets detected by ethidium bromide staining method by the comet assay protocol. The objective of this study was to compare efficacy of comet assay with different assay used to study phage mediated bacterial lysis. The assay was performed on culture isolates (N=80 studies), modified comet assay appear to have relatively higher sensitivity and specificity than other assay. The results of the study showed that the application of comet assay can be an economical, time saving and less laborious alternative to conventional plaque assay for the detection of bacteriophage mediated bacterial cell lysis. PMID:24681053

  7. [Determination of Azospirillum Brasilense Cells With Bacteriophages via Electrooptical Analysis of Microbial Suspensions].

    Science.gov (United States)

    Gulii, O I; Karavayeva, O A; Pavlii, S A; Sokolov, O I; Bunin, V D; Ignatov, O V

    2015-01-01

    The dependence-of changes in the electrooptical properties of Azospirillum brasilense cell suspension Sp7 during interaction with bacteriophage ΦAb-Sp7 on the number and time of interactions was studied. Incubation of cells with bacteriophage significantly changed the electrooptical signal within one minute. The selective effect of bacteriophage ΦAb on 18 strains of bacteria of the genus Azospirillum was studied: A. amazonense Ami4, A. brasilense Sp7, Cd, Sp107, Sp245, Jm6B2, Brl4, KR77, S17, S27, SR55, SR75, A. halopraeferans Au4, A. irakense KBC1, K A3, A. lipoferum Sp59b, SR65 and RG20a. We determined the limit of reliable determination of microbial cells infected with bacteriophage: - 10(4) cells/mL. The presence of foreign cell cultures of E. coli B-878 and E. coli XL-1 did not complicate the detection of A brasilense Sp7 cells with the use of bacteriophage ΦAb-Sp7. The results demonstrated that bacteriophage (ΦAb-Sp7 can be used for the detection of Azospirillum microbial cells via t electrooptical analysis of cell suspensions. PMID:26204775

  8. Bacteriophages in clinical samples can interfere with microbiological diagnostic tools

    Science.gov (United States)

    Brown-Jaque, Maryury; Muniesa, Maite; Navarro, Ferran

    2016-01-01

    Bacteriophages are viruses that infect bacteria, and they are found everywhere their bacterial hosts are present, including the human body. To explore the presence of phages in clinical samples, we assessed 65 clinical samples (blood, ascitic fluid, urine, cerebrospinal fluid, and serum). Infectious tailed phages were detected in >45% of ascitic fluid and urine samples. Three examples of phage interference with bacterial isolation were observed. Phages prevented the confluent bacterial growth required for an antibiogram assay when the inoculum was taken from an agar plate containing lysis plaques, but not when taken from a single colony in a phage-free area. In addition, bacteria were isolated directly from ascitic fluid, but not after liquid enrichment culture of the same samples, since phage propagation lysed the bacteria. Lastly, Gram-negative bacilli observed in a urine sample did not grow on agar plates due to the high densities of infectious phages in the sample. PMID:27609086

  9. The role of temperate bacteriophages in bacterial infection.

    Science.gov (United States)

    Davies, Emily V; Winstanley, Craig; Fothergill, Joanne L; James, Chloe E

    2016-03-01

    Bacteriophages are viruses that infect bacteria. There are an estimated 10(31) phage on the planet, making them the most abundant form of life. We are rapidly approaching the centenary of their identification, and yet still have only a limited understanding of their role in the ecology and evolution of bacterial populations. Temperate prophage carriage is often associated with increased bacterial virulence. The rise in use of technologies, such as genome sequencing and transcriptomics, has highlighted more subtle ways in which prophages contribute to pathogenicity. This review discusses the current knowledge of the multifaceted effects that phage can exert on their hosts and how this may contribute to bacterial adaptation during infection. PMID:26825679

  10. Capstan friction model for DNA ejection from bacteriophages

    CERN Document Server

    Ghosal, Sandip

    2013-01-01

    Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell.The phage DNA is then transcribed by the cell's transcription machinery.A number of physical mechanisms by which DNA can be translocated from the phage capsid into the cell have been identified. A fast ejection driven by the elastic and electrostatic potential energy of the compacted DNA within the viral capsid appears to be used by most phages, at least to initiate infection.In recent in vitro experiments, the speed of DNA translocation from a lambda phage capsid has been measured as a function of ejected length over the entire duration of the event.Here a mechanical model is proposed that is able to explain the observed dependence of exit velocity on ejected length, and that is also consistent with the accepted picture of the geometric arrangement of DNA within the viral capsid.

  11. Role of osmotic and hydrostatic pressures in bacteriophage genome ejection

    Science.gov (United States)

    Lemay, Serge G.; Panja, Debabrata; Molineux, Ian J.

    2013-02-01

    A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly in vitro, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution or culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection in vivo; the mechanism is perfectly consistent with phage genome ejection in vitro.

  12. Role of osmotic and hydrostatic pressures in bacteriophage genome ejection

    CERN Document Server

    Lemay, Serge G; Molineux, Ian J

    2012-01-01

    A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly \\textit{in vitro}, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution/culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection \\textit{in vivo}; the mechanism is perfectly consistent with phage genome ejection \\textit{in vitro}.

  13. Modelling the interaction between bacteriophages and their bacterial hosts.

    Science.gov (United States)

    Beke, Gabor; Stano, Matej; Klucar, Lubos

    2016-09-01

    A mathematical model simulating the interaction between bacteriophages and their bacterial hosts has been developed. It is based on other known models describing this type of interaction, enhanced with an ability to model the system influenced by other environmental factor such as pH and temperature. This could be used for numerous estimations of growth rate, when the pH and/or the temperature of the environment are not constant. The change of pH or the temperature greatly affects the specific growth rate which has an effect on the final results of the simulation. Since the model aims on practical application and easy accessibility, an interactive website has been developed where users can run simulations with their own parameters and easily calculate and visualise the result of simulation. The web simulation is accessible at the URL http://www.phisite.org/model. PMID:27393678

  14. A quorum-sensing-induced bacteriophage defense mechanism

    DEFF Research Database (Denmark)

    Høyland-Kroghsbo, Nina Molin; Mærkedahl, Rasmus Baadsgaard; Svenningsen, Sine

    2013-01-01

    . Specifically, E. coli reduces the numbers of ¿ receptors on the cell surface in response to N-acyl-l-homoserine lactone (AHL) quorum-sensing signals, causing a 2-fold reduction in the phage adsorption rate. The modest reduction in phage adsorption rate leads to a dramatic increase in the frequency of...... sensing plays an important role in determining the susceptibility of E. coli to infection by bacteriophages ¿ and ¿. On the basis of our findings in the classical Escherichia coli-¿ model system, we suggest that quorum sensing may serve as a general strategy to protect bacteria specifically under...... uninfected survivor cells after a potent attack by virulent phages. Notably, this mechanism may apply to a broader range of phages, as AHLs also reduce the risk of ¿ phage infection through a different receptor. IMPORTANCE To enable the successful manipulation of bacterial populations, a comprehensive...

  15. The Allosteric Switching Mechanism in Bacteriophage MS2

    CERN Document Server

    Perkett, Matthew R

    2015-01-01

    In this article we use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopt different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We disc...

  16. Detection and characterization of agarose-binding, capsid-like particles produced during assembly of a bacteriophage T7 procapsid.

    OpenAIRE

    Serwer, P; Watson, R H; Hayes, S J

    1982-01-01

    It has previously been shown that: (i) during infection of its host, the DNA bacteriophage T7 assembles a DNA-free procapsid (capsid I), a capsid with an envelope differing physically and chemically from the capsid of the mature bacteriophage, and (ii) capsid I converts to a capsid (capsid II) with a bacteriophage-like envelope as it packages DNA. Lysates of phage T7-infected Escherichia coli contained a particle (AG particle) which copurified with capsid II during buoyant density sedimentati...

  17. Sewage bacteriophage inactivation by cationic porphyrins: influence of light parameters.

    Science.gov (United States)

    Costa, Liliana; Carvalho, Carla M B; Faustino, Maria A F; Neves, Maria G P M S; Tomé, João P C; Tomé, Augusto C; Cavaleiro, José A S; Cunha, Angela; Almeida, Adelaide

    2010-08-01

    Photodynamic therapy has been used to inactivate microorganisms through the use of targeted photosensitizers. Although the photoinactivation of microorganisms has already been studied under different conditions, a systematic evaluation of irradiation characteristics is still limited. The goal of this study was to test how the light dose, fluence rate and irradiation source affect the viral photoinactivation of a T4-like sewage bacteriophage. The experiments were carried out using white PAR light delivered by fluorescent PAR lamps (40 W m(-2)), sun light (600 W m(-2)) and an halogen lamp (40-1690 W m(-2)). Phage suspensions and two cationic photosensitizers (Tetra-Py(+)-Me, Tri-Py(+)-Me-PF) at concentrations of 0.5, 1.0 and 5.0 microM were used. The results showed that the efficacy of the bacteriophage photoinactivation is correlated not only with the sensitizer and its concentration but also with the light source, energy dose and fluence rate applied. Both photosensitizers at 5.0 microM were able to inactivate the T4-like phage to the limit of detection for each light source and fluence rate. However, depending of the light parameters, different irradiation times are required. The efficiency of photoinactivation is dependent on the spectral emission distribution of the light sources used. Considering the same light source and a fixed light dose applied at different fluence rates, phage inactivation was significantly higher when low fluence rates were used. In this way, the light source, fluence rate and total light dose play an important role in the effectiveness of the antimicrobial photodynamic therapy and should always be considered when establishing an optimal antimicrobial protocol. PMID:20563346

  18. Bacteriophage-encoded shiga toxin gene in atypical bacterial host

    Directory of Open Access Journals (Sweden)

    Casas Veronica

    2011-07-01

    Full Text Available Abstract Background Contamination from fecal bacteria in recreational waters is a major health concern since bacteria capable of causing human disease can be found in animal feces. The Dog Beach area of Ocean Beach in San Diego, California is a beach prone to closures due to high levels of fecal indicator bacteria (FIB. A potential source of these FIB could be the canine feces left behind by owners who do not clean up after their pets. We tested this hypothesis by screening the DNA isolated from canine feces for the bacteriophage-encoded stx gene normally found in the virulent strains of the fecal bacterium Escherichia coli. Results Twenty canine fecal samples were collected, processed for total and bacterial fraction DNA, and screened by PCR for the stx gene. The stx gene was detected in the total and bacterial fraction DNA of one fecal sample. Bacterial isolates were then cultivated from the stx-positive fecal sample. Eighty nine of these canine fecal bacterial isolates were screened by PCR for the stx gene. The stx gene was detected in five of these isolates. Sequencing and phylogenetic analyses of 16S rRNA gene PCR products from the canine fecal bacterial isolates indicated that they were Enterococcus and not E. coli. Conclusions The bacteriophage-encoded stx gene was found in multiple species of bacteria cultivated from canine fecal samples gathered at the shoreline of the Dog Beach area of Ocean Beach in San Diego, California. The canine fecal bacteria carrying the stx gene were not the typical E. coli host and were instead identified through phylogenetic analyses as Enterococcus. This suggests a large degree of horizontal gene transfer of exotoxin genes in recreational waters.

  19. Bacteriophage and their potential roles in the human oral cavity

    Science.gov (United States)

    Edlund, Anna; Santiago-Rodriguez, Tasha M.; Boehm, Tobias K.; Pride, David T.

    2015-01-01

    The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts. PMID:25861745

  20. Bacteriophage and their potential roles in the human oral cavity.

    Science.gov (United States)

    Edlund, Anna; Santiago-Rodriguez, Tasha M; Boehm, Tobias K; Pride, David T

    2015-01-01

    The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts. PMID:25861745

  1. Bacteriophage and their potential roles in the human oral cavity

    Directory of Open Access Journals (Sweden)

    Anna Edlund

    2015-04-01

    Full Text Available The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts.

  2. Review: elimination of bacteriophages in whey and whey products

    Directory of Open Access Journals (Sweden)

    Zeynep eAtamer

    2013-07-01

    Full Text Available As the cheese market faces strong international competition, the optimization of production processes becomes more important for the economic success of dairy companies. In dairy productions, whey from former cheese batches is frequently re-used to increase the yield, to improve the texture and to increase the nutrient value of the final product. Recycling of whey cream and particulated whey proteins is also routinely performed. Most bacteriophages, however, survive pasteurization and may re-enter the cheese manufacturing process. There is a risk that phages multiply to high numbers during the production. Contamination of whey samples with bacteriophages may cause problems in cheese factories because whey separation often leads to aerosol-borne phages and thus contamination of the factory environment. Furthermore, whey cream or whey proteins used for recycling into cheese matrices may contain thermo-resistant phages. Drained cheese whey can be contaminated with phages as high as 109 phages per mL. When whey batches are concentrated, phage titers can increase significantly by a factor of 10 hindering a complete elimination of phages. To eliminate the risk of fermentation failure during recycling of whey, whey treatments assuring an efficient reduction of phages are indispensable. This review focuses on inactivation of phages in whey by thermal treatment, ultraviolet (UV light irradiation and membrane filtration. Inactivation by heat is the most common procedure. However, application of heat for inactivation of thermo-resistant phages in whey is restricted due to negative effects on the functional properties of native whey proteins. Therefore an alternative strategy applying combined treatments should be favoured - rather than heating the dairy product at extreme temperature/time combinations. By using membrane filtration or UV treatment in combination with thermal treatment, phage numbers in whey can be reduced sufficiently to prevent subsequent

  3. The Effectiveness of Bacteriophages against Methicillin-Resistant Staphylococcus aureus ST398 Nasal Colonization in Pigs

    Science.gov (United States)

    Duim, Birgitta; Fluit, Ad C; Carney, Jennifer; van Nes, Arie; Wagenaar, Jaap A

    2016-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is an important colonizer in animals and an opportunistic pathogen in humans. In humans, MRSA can cause infections that might be difficult to treat because of antimicrobial resistance. The use of bacteriophages has been suggested as a potential approach for the control of MRSA colonization to minimize the—often occupational—exposure of humans. The aim of this study was to assess the efficacy of bacteriophage treatment on porcine nasal colonization with MRSA in vitro, in vivo, and ex vivo. The effectiveness of a bacteriophage combination of phage K*710 and P68 was assessed in vitro by incubating them with MRSA V0608892/1 (ST398) measuring the OD600 hourly. To study the in vivo effect, bacteriophages were administered in a gel developed for human application, which contain 109 plaque-forming units (pfu)/mL (K and P68 in a 19.25:1 ratio) for 5 days to piglets (N = 8) that were experimentally colonized with the MRSA strain. Eight piglets experimentally colonized were used as a negative control. The MRSA strain was also used to colonize porcine nasal mucosa explants and bacteriophages were applied to assess the ex vivo efficacy of treatment. Bacteriophages were effective in vitro. In vivo, sixteen piglets were colonized with MRSA but the number of CFU recovered after the application of the bacteriophages in 8 piglets was not reduced compared to the control animals (approx. 105 CFU/swab). In the ex vivo model, 108 CFU were used to establish colonization with MRSA; a reduction of colonization was not observed after application of bacteriophages. However, application of mupirocin both in vivo and ex vivo resulted in a near eradication of MRSA. In conclusion: i) The MRSA strain was killed in the presence of the bacteriophages phage K*710 and P68 in vitro. ii) Bacteriophages did not reduce porcine nasal colonization in vivo or ex vivo. Physiological in vivo and ex vivo conditions may explain these observations. Efficacy

  4. Diagnostic Immunization with Bacteriophage ΦX 174 in Patients with Common Variable Immunodeficiency/Hypogammaglobulinemia

    Directory of Open Access Journals (Sweden)

    Lauren L Smith

    2014-08-01

    Full Text Available Purpose: Use of the T cell-dependent neoantigen bacteriophage ΦX 174 has been described since the 1960s as a method to assess specific antibody response in patients with primary immunodeficiencies. We reviewed a cohort of patients at Duke University Medical Center (DUMC who received immunization with bacteriophage and report the clinical utility and safety of the immunization, as well as patient characteristics. Methods: A retrospective chart review was performed of all Duke Immunology Clinic patients (pediatric and adult who received immunizations with bacteriophage, from 1976-2012. Subjects were selected for inclusion if their diagnosis at the time of bacteriophage was either presumed or confirmed common variable immunodeficiency (CVID, hypogammaglobulinemia, transient hypogammaglobulinemia, or antibody deficiency unspecified. Follow up post-immunization was also recorded.Results: One hundred twenty-six patients were identified, 36 adult and 90 pediatric patients. Diagnoses prior to bacteriophage were CVID (n=100, hypogammaglobulinemia (n=23, and antibody deficiency (n=3. Post-immunization diagnoses were CVID (n=65, hypogammaglobulinemia (n=19, unknown (n=23, no primary immune deficiency (n=10, and other primary immunodeficiency (n=9. Seventy-five patients had abnormal bacteriophage results, 37 were normal, and 14 were borderline. There were 257 recorded administrations of the immunization. Information was available on adverse reactions for 171 administrations. Fourteen immunizations were associated with minor adverse events. Nineteen patients stopped their immunoglobulin replacement therapy based on reported normal responses to immunization. Conclusions: Bacteriophage ΦX 174 immunization is a safe, well-tolerated, and clinically useful method to assess antibody response in patients with suspected antibody-mediated immunodeficiencies, particularly those who are on immunoglobulin replacement therapy at the time of immunization

  5. Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages

    Science.gov (United States)

    Djordjevic, Marko

    2005-11-01

    Due to rapid accumulation of biological data, bioinformatics has become a very important branch of biological research. In this thesis, we develop novel bioinformatic approaches and aid design of biological experiments by using ideas and methods from statistical physics. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of the regulatory circuits that control expression of genes. We propose a novel, biophysics based algorithm, for the supervised detection of transcription factor (TF) binding sites. The method classifies potential binding sites by explicitly estimating the sequence-specific binding energy and the chemical potential of a given TF. In contrast with the widely used information theory based weight matrix method, our approach correctly incorporates saturation in the transcription factor/DNA binding probability. This results in a significant reduction in the number of expected false positives, and in the explicit appearance---and determination---of a binding threshold. The new method was used to identify likely genomic binding sites for the Escherichia coli TFs, and to examine the relationship between TF binding specificity and degree of pleiotropy (number of regulatory targets). We next address how parameters of protein-DNA interactions can be obtained from data on protein binding to random oligos under controlled conditions (SELEX experiment data). We show that 'robust' generation of an appropriate data set is achieved by a suitable modification of the standard SELEX procedure, and propose a novel bioinformatic algorithm for analysis of such data. Finally, we use quantitative data analysis, bioinformatic methods and kinetic modeling to analyze gene expression strategies of bacterial viruses. We study bacteriophage Xp10 that infects rice pathogen Xanthomonas oryzae. Xp10 is an unusual bacteriophage, which has morphology and genome organization that most closely

  6. Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio harveyi myovirus like.

    Science.gov (United States)

    Bochow, S; Elliman, J; Owens, L

    2012-11-01

    The adenine methyltransferase (DAM) gene methylates GATC sequences that have been demonstrated in various bacteria to be a powerful gene regulator functioning as an epigenetic switch, particularly with virulence gene regulation. However, overproduction of DAM can lead to mutations, giving rise to variability that may be important for adaptation to environmental change. While most bacterial hosts carry a DAM gene, not all bacteriophage carry this gene. Currently, there is no literature regarding the role DAM plays in life cycle regulation of bacteriophage. Vibrio campbellii strain 642 carries the bacteriophage Vibrio harveyi myovirus like (VHML) that has been proven to increase virulence. The complete genome sequence of VHML bacteriophage revealed a putative adenine methyltransferase gene. Using VHML, a new model of phage life cycle regulation, where DAM plays a central role between the lysogenic and lytic states, will be hypothesized. In short, DAM methylates the rha antirepressor gene and once methylation is removed, homologous CI repressor protein becomes repressed and non-functional leading to the switching to the lytic cycle. Greater understanding of life cycle regulation at the genetic level can, in the future, lead to the genesis of chimeric bacteriophage with greater control over their life cycle for their safe use as probiotics within the aquaculture industry. PMID:22681538

  7. Control of Listeria monocytogenes growth in soft cheeses by bacteriophage P100.

    Science.gov (United States)

    Silva, Elaine Nóbrega Gibson; Figueiredo, Ana Cláudia Leite; Miranda, Fernanda Araújo; de Castro Almeida, Rogeria Comastri

    2014-01-01

    The purpose of this study was to determine the effect of bacteriophage P100 on strains of Listeria monocytogenes in artificially inoculated soft cheeses. A mix of L. monocytogenes 1/2a and Scott A was inoculated in Minas Frescal and Coalho cheeses (approximately 10(5) cfu/g) with the bacteriophage added thereafter (8.3 × 10(7) PFU/g). Samples were analyzed immediately, and then stored at 10 °C for seven days. At time zero, 30 min post-infection, the bacteriophage P100 reduced L. monocytogenes counts by 2.3 log units in Minas Frescal cheese and by 2.1 log units in Coalho cheese, compared to controls without bacteriophage. However, in samples stored under refrigeration for seven days, the bacteriophage P100 was only weakly antilisterial, with the lowest decimal reduction (DR) for the cheeses: 1.0 log unit for Minas Frescal and 0.8 log units for Coalho cheese. The treatment produced a statistically significant decrease in the counts of viable cells (p cycle in the number of viable cells of L. monocytogenes in the samples under refrigeration for seven days. Moreover, a smaller effect of phages was observed. These results, along with other published data, indicate that the effectiveness of the phage treatment depends on the initial concentration of L. monocytogenes, and that a high concentration of phages per unit area is required to ensure sustained inactivation of target pathogens on food surfaces. PMID:24948908

  8. Genetically engineered bacteriophage delivers a tumor necrosis factor alpha antagonist coating on neural electrodes

    International Nuclear Information System (INIS)

    This paper reports a novel approach for the formation of anti-inflammatory surface coating on a neural electrode. The surface coating is realized using a recombinant f88 filamentous bacteriophage, which displays a short platinum binding motif and a tumor necrosis factor alpha antagonist (TNF-α antagonist) on p3 and p8 proteins, respectively. The recombinant bacteriophages are immobilized on the platinum surface by a simple dip coating process. The selective and stable immobilization of bacteriophages on a platinum electrode is confirmed by quartz crystal microbalance with dissipation monitoring, atomic force microscope and fluorescence microscope. From the in vitro cell viability test, the inflammatory cytokine (TNF-α) induced cell death was prevented by presenting recombinant bacteriophage coating, albeit with no significant cytotoxic effect. It is also observed that the bacteriophage coating does not have critical effects on the electrochemical properties such as impedance and charge storage capacities. Thus, this approach demonstrates a promising anti-apoptotic as well as anti-inflammatory surface coating for neural implant applications. (paper)

  9. Proteins responsible for lysogeny of deep-sea thermophilic bacteriophage GVE2 at high temperature.

    Science.gov (United States)

    Song, Qing; Ye, Ting; Zhang, Xiaobo

    2011-06-15

    The lytic and lysogenic life cycle switch of bacteriophages plays very important roles in virus-host interactions. However, the lysogeny of thermophilic bacteriophage infecting thermophile at high temperatures has not been addressed. In this study, two lysogeny-related genes encoding the CI protein and recombinase of GVE2, a thermophilic bacteriophage obtained from a deep-sea hydrothermal vent, were characterized. Temporal analyses showed that the two genes were expressed at early stages of GVE2 infection. Based on chromatin immunoprecipitation (ChIP) assay and electrophoretic mobility shift assay (EMSA), the GVE2 CI protein was bound with only one DNA fragment located at 24264-24036 bp in the GVE2 genome. This location might be the original transcription site and the lysis-lysogeny switch site, which was very different from mesophilic bacteriophages. The GVE2 CI and recombinase proteins could function only at high temperatures. Therefore our study improved our understanding of the lysogeny process of bacteriophages at high temperatures. PMID:21303688

  10. Biocontrol of Escherichia coli O157:H7 on fresh-cut lettuce and cantaloupe by treatment with bacteriophage

    Science.gov (United States)

    Introduction: Outbreaks of foodborne illness have been associated with the consumption of cantaloupes and fresh-cut lettuce. Bacteriophage mixtures may be effective biocontrol agents to reduce E. coli O157:H7 on produce. Purpose: The effectiveness of a mixture of bacteriophages (ECP-100) in reducin...

  11. "China is Playing More and More Important Role in the World" Felix SELINGER-Global CEO of Putzmeister%"中国正在世界上扮演越来越重要的角色"——专访普茨迈斯特全球CEO Felix SELINGER先生

    Institute of Scientific and Technical Information of China (English)

    王刚

    2008-01-01

    @@ 作为一家年产值超过10亿欧元(15亿美元)的全球化公司,普茨迈斯特(Putzmeister)在稠性流体输送机械领域,无论在技术上,还是在生产规模上,始终保持着绝对领先. 面对愈演愈烈的金融危机和逐渐趋向下滑的实体经济增长,普茨迈斯特的一举一动始终是全球用户与同行关注的焦点,记者有幸专访了普茨迈斯特全球CEO Felix SELINGER先生,与他面对面探讨了普茨迈斯特将如何面对这场全世界需要共同应对的危机.

  12. Produtos naturais da ascídia Botrylloides giganteum, das esponjas Verongula gigantea, Ircinia felix, Cliona delitrix e do nudibrânquio Tambja eliora, da costa do Brasil Natural products from the ascidian Botrylloides giganteum, from the sponges Verongula gigantea, Ircinia felix, Cliona delitrix and from the nudibranch Tambja eliora, from the Brazilian coastline

    Directory of Open Access Journals (Sweden)

    Ana Claudia Granato

    2005-03-01

    Full Text Available Two new marine metabolites, 3Z, 6Z, 9Z-dodecatrien-1-ol (1 from the ascidian Botrylloides giganteum and 4H-pyran-2ol acetate from the sponge Ircinia felix (4 are herein reported. The known bromotyrosine compounds, 2-(3,5-dibromo-4-methoxyphenyl-N,N,N-dimethylethanammonium (2 and 2,6-dibromo-4-(2-(trimethylammoniumethylphenol (3, have been isolated from the sponge Verongula gigantea. Serotonin (5 is reported for the first time from the sponge Cliona delitrix, and tambjamines A (15 and D (16 isolated as their respective salts from the nudibranch Tambja eliora. Only tambjamine D presented cytotoxicity against CEM (IC50 12.2 µg/mL and HL60 (IC50 13.2 µg/mL human leukemya cells, MCF-7 breast cancer cells (IC50 13.2 µg/mL, colon HCT-8 cancer cells (IC50 10.1 µg/mL and murine melanoma B16 cancer cells (IC50 6.7 µg/mL.

  13. DNA damage under simulated extraterrestrial conditions in bacteriophage T7

    Science.gov (United States)

    Fekete, A.; Módos, K.; Hegedüs, M.; Kovács, G.; Rontó, Gy.; Péter, Á.; Lammer, H.; Panitz, C.

    The experiment "Phage and Uracil response" will be accommodated in the EXPOSE facility of the International Space Station. Its objective is to examine and quantify the effect of specific space conditions on nucleic acid models, especially on bacteriophage T7 and isolated T7 DNA thin films. In order to define the environmental and technical requirements of the EXPOSE, the samples were subjected to the experiment verification test (EVT). During EVT, the samples were exposed to vacuum (10 -4-10 -6 Pa) and polychromatic UV-radiation (200-400 nm) in air, in inert atmosphere, as well as in simulated space vacuum. The effect of extreme temperature in vacuum and the influence of temperature fluctuations around 0 °C were also studied. The total intraphage/isolated DNA damage was determined by quantitative PCR using 555 and 3826 bp fragments of T7 DNA. The type of the damage was resolved using a combination of enzymatic probes and neutral and alkaline agarose gel electrophoresis; the structural/chemical effects were analyzed by spectroscopic and microscopical methods. We obtained substantial evidence that DNA lesions accumulate throughout exposure, but the amount of damage depends on the thickness of the layers. According to our preliminary results, the damages by exposure to conditions of dehydration and UV-irradiation are larger than the sum of vacuum alone, or radiation alone case, suggesting a synergistic action of space vacuum and UV radiation with DNA being the critical target.

  14. Disposable amperometric biosensor based on nanostructured bacteriophages for glucose detection

    Science.gov (United States)

    Kang, Yu Ri; Hwang, Kyung Hoon; Kim, Ju Hwan; Nam, Chang Hoon; Kim, Soo Won

    2010-10-01

    The selection of electrode material profoundly influences biosensor science and engineering, as it heavily influences biosensor sensitivity. Here we propose a novel electrochemical detection method using a working electrode consisting of bio-nanowires from genetically modified filamentous phages and nanoparticles. fd-tet p8MMM filamentous phages displaying a three-methionine (MMM) peptide on the major coat protein pVIII (designated p8MMM phages) were immobilized on the active area of an electrochemical sensor through physical adsorption and chemical bonding. Bio-nanowires composed of p8MMM phages and silver nanoparticles facilitated sensitive, rapid and selective detection of particular molecules. We explored whether the composite electrode with bio-nanowires was an effective platform to detect the glucose oxidase. The current response of the bio-nanowire sensor was high at various glucose concentrations (0.1 µm-0.1 mM). This method provides a considerable advantage to demonstrate analyte detection over low concentration ranges. Especially, phage-enabled bio-nanowires can serve as receptors with high affinity and specificity for the detection of particular biomolecules and provide a convenient platform for designing site-directed multifunctional scaffolds based on bacteriophages and may serve as a simple method for label-free detection.

  15. Dual Functionalized Bacteriophage Qβ as a Photocaged Drug Carrier.

    Science.gov (United States)

    Chen, Zhuo; Li, Na; Chen, Luxi; Lee, Jiyong; Gassensmith, Jeremiah J

    2016-09-01

    Proteinatious nanoparticles are emerging as promising materials in biomedical research owing to their many unique properties and our interest focuses on integrating environmental responsivity into these systems. In this work, the use of a virus-like particle (VLP) derived from bacteriophage Qβ as a photocaged drug delivery system is investigated. Ideally, a photocaged nanoparticle platform should be harmless and inert without activation by light yet, upon photoirradiation, should cause cell death. Approximately 530 photocleavable doxorubicin complexes are installed initially onto the surface of Qβ by CuAAC reaction for photocaging therapy; however, aggregation and precipitation are found to cause cell death at higher concentrations. In order to improve solution stability, thiol-dibromomaleimide chemistry has been developed to orthogonally modify the VLP. This chemistry provides a robust method of incorporating additional functionality at the disulfides on Qβ, which was used to increase the stability and solubility of the drug-loaded VLPs. As a result, the dual functionalied VLPs with polyethylene glycol and photocaged doxorubicin show not only negligible cytotoxicity before photoactivation but also highly controllable photorelease and cell killing power. PMID:27351167

  16. BENEFICIAL FACE OF BACTERIOPHAGES: APPLICATIONS IN FOOD PROCESSING

    Directory of Open Access Journals (Sweden)

    H. V. Raghu

    2012-06-01

    Full Text Available Foods are processed to make them available at all places; consequently, our awareness regarding hygiene measures in food production has also increased dramatically over the last decades. In many countries cases associated with foodborne infectious are increased. However, available techniques are unable to effectively control the problem. Further, exploring novel methods and technologies for ensuring the safety of food with effective quality control approaches are under research. Phages are the natural enemies of bacteria, and are more specific to host renders them ideal candidates for applications designed to increase food safety during the production process. Scientific findings are available showing the possibility to use as biocontrol agents against various pathogens with out interfering with the natural microflora or the cultures in fermented products. Furthermore, phages or phage derived proteins can also be used to detect the presence of unwanted pathogens in food or the production environments, which allows quick and sp ecific identification of viable cells. Bacteriophages are natural, found in various environments including water; foods etc. and are not found significantly influence the human cells.

  17. The allosteric switching mechanism in bacteriophage MS2

    Science.gov (United States)

    Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F.

    2016-07-01

    We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

  18. Bacteriophage-encoded depolymerases: their diversity and biotechnological applications.

    Science.gov (United States)

    Pires, Diana P; Oliveira, Hugo; Melo, Luís D R; Sillankorva, Sanna; Azeredo, Joana

    2016-03-01

    Bacteriophages (phages), natural enemies of bacteria, can encode enzymes able to degrade polymeric substances. These substances can be found in the bacterial cell surface, such as polysaccharides, or are produced by bacteria when they are living in biofilm communities, the most common bacterial lifestyle. Consequently, phages with depolymerase activity have a facilitated access to the host receptors, by degrading the capsular polysaccharides, and are believed to have a better performance against bacterial biofilms, since the degradation of extracellular polymeric substances by depolymerases might facilitate the access of phages to the cells within different biofilm layers. Since the diversity of phage depolymerases is not yet fully explored, this is the first review gathering information about all the depolymerases encoded by fully sequenced phages. Overall, in this study, 160 putative depolymerases, including sialidases, levanases, xylosidases, dextranases, hyaluronidases, peptidases as well as pectate/pectin lyases, were found in 143 phages (43 Myoviridae, 47 Siphoviridae, 37 Podoviridae, and 16 unclassified) infecting 24 genera of bacteria. We further provide information about the main applications of phage depolymerases, which can comprise areas as diverse as medical, chemical, or food-processing industry. PMID:26767986

  19. Disposable amperometric biosensor based on nanostructured bacteriophages for glucose detection

    International Nuclear Information System (INIS)

    The selection of electrode material profoundly influences biosensor science and engineering, as it heavily influences biosensor sensitivity. Here we propose a novel electrochemical detection method using a working electrode consisting of bio-nanowires from genetically modified filamentous phages and nanoparticles. fd-tet p8MMM filamentous phages displaying a three-methionine (MMM) peptide on the major coat protein pVIII (designated p8MMM phages) were immobilized on the active area of an electrochemical sensor through physical adsorption and chemical bonding. Bio-nanowires composed of p8MMM phages and silver nanoparticles facilitated sensitive, rapid and selective detection of particular molecules. We explored whether the composite electrode with bio-nanowires was an effective platform to detect the glucose oxidase. The current response of the bio-nanowire sensor was high at various glucose concentrations (0.1 µm–0.1 mM). This method provides a considerable advantage to demonstrate analyte detection over low concentration ranges. Especially, phage-enabled bio-nanowires can serve as receptors with high affinity and specificity for the detection of particular biomolecules and provide a convenient platform for designing site-directed multifunctional scaffolds based on bacteriophages and may serve as a simple method for label-free detection

  20. Salmonella bacteriophage diversity reflects host diversity on dairy farms.

    Science.gov (United States)

    Switt, Andrea I Moreno; den Bakker, Henk C; Vongkamjan, Kitiya; Hoelzer, Karin; Warnick, Lorin D; Cummings, Kevin J; Wiedmann, Martin

    2013-12-01

    Salmonella is an animal and human pathogen of worldwide concern. Surveillance programs indicate that the incidence of Salmonella serovars fluctuates over time. While bacteriophages are likely to play a role in driving microbial diversity, our understanding of the ecology and diversity of Salmonella phages is limited. Here we report the isolation of Salmonella phages from manure samples from 13 dairy farms with a history of Salmonella presence. Salmonella phages were isolated from 10 of the 13 farms; overall 108 phage isolates were obtained on serovar Newport, Typhimurium, Dublin, Kentucky, Anatum, Mbandaka, and Cerro hosts. Host range characterization found that 51% of phage isolates had a narrow host range, while 49% showed a broad host range. The phage isolates represented 65 lysis profiles; genome size profiling of 94 phage isolates allowed for classification of phage isolates into 11 groups with subsequent restriction fragment length polymorphism analysis showing considerable variation within a given group. Our data not only show an abundance of diverse Salmonella phage isolates in dairy farms, but also show that phage isolates that lyse the most common serovars causing salmonellosis in cattle are frequently obtained, suggesting that phages may play an important role in the ecology of Salmonella on dairy farms. PMID:24010608

  1. Computational approaches to predict bacteriophage-host relationships.

    Science.gov (United States)

    Edwards, Robert A; McNair, Katelyn; Faust, Karoline; Raes, Jeroen; Dutilh, Bas E

    2016-03-01

    Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus-host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage-host signals. Sequence homology approaches are the most effective at identifying known phage-host pairs. Compositional and abundance-based methods contain significant signal for phage-host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage-host relationships, with potential relevance for medical and industrial applications. PMID:26657537

  2. Effect of ultrashort laser irradiation on bacteriophage lambda

    International Nuclear Information System (INIS)

    Bacteriophage lambda was irradiated by picosecond and nanosecond laser UV pulses with high intensity (105 - 109 W/cm2) at a wavelength of 266 nm. It was found that the photoreactivation in the phages decreased from 85% (continuous irradiation with low intensity 10-5 W/cm2) to 27% (laser nanosecond irradiation with intensity 3 x 105 W/cm2) and to 20% (laser picosecond irradiation with intensity 109 W/cm2), resp. Furthermore the ratio of D37 for phage lambda upon the infection of wild type (AB 1157) and uvrA-mutant E. coli K12 (AB 1886) is diminished from 6.2 (continuous irradiation with intensity 10-5 W/cm2) to 2.0 (pico- and nanosecond irradiation with intensity 7 x 107 W/cm2 and 3 x 105 W/cm2, resp.). It is supposed that high intensity DNA irradiation by UV laser pulses leads mainly to the formation of photoproducts, which do not correspond to cyclobutane-type pyrimidine dimers. (author)

  3. Factors influencing lysis time stochasticity in bacteriophage λ

    Directory of Open Access Journals (Sweden)

    Dennehy John J

    2011-08-01

    Full Text Available Abstract Background Despite identical genotypes and seemingly uniform environments, stochastic gene expression and other dynamic intracellular processes can produce considerable phenotypic diversity within clonal microbes. One trait that provides a good model to explore the molecular basis of stochastic variation is the timing of host lysis by bacteriophage (phage. Results Individual lysis events of thermally-inducible λ lysogens were observed using a temperature-controlled perfusion chamber mounted on an inverted microscope. Both mean lysis time (MLT and its associated standard deviation (SD were estimated. Using the SD as a measure of lysis time stochasticity, we showed that lysogenic cells in controlled environments varied widely in lysis times, and that the level of lysis time stochasticity depended on allelic variation in the holin sequence, late promoter (pR' activity, and host growth rate. In general, the MLT was positively correlated with the SD. Both lower pR' activities and lower host growth rates resulted in larger SDs. Results from premature lysis, induced by adding KCN at different time points after lysogen induction, showed a negative correlation between the timing of KCN addition and lysis time stochasticity. Conclusions Taken together with results published by others, we conclude that a large fraction of λ lysis time stochasticity is the result of random events following the expression and diffusion of the holin protein. Consequently, factors influencing the timing of reaching critical holin concentrations in the cell membrane, such as holin production rate, strongly influence the mean lysis time and the lysis time stochasticity.

  4. Modeling the interactions between pathogenic bacteria, bacteriophage and immune response

    Science.gov (United States)

    Leung, Chung Yin (Joey); Weitz, Joshua S.

    The prevalence of antibiotic-resistant strains of pathogenic bacteria has led to renewed interest in the use of bacteriophage (phage), or virus that infects bacteria, as a therapeutic agent against bacterial infections. However, little is known about the theoretical mechanism by which phage therapy may work. In particular, interactions between the bacteria, the phage and the host immune response crucially influences the outcome of the therapy. Few models of phage therapy have incorporated all these three components, and existing models suffer from unrealistic assumptions such as unbounded growth of the immune response. We propose a model of phage therapy with an emphasis on nonlinear feedback arising from interactions with bacteria and the immune response. Our model shows a synergistic effect between the phage and the immune response which underlies a possible mechanism for phage to catalyze the elimination of bacteria even when neither the immune response nor phage could do so alone. We study the significance of this effect for different parameters of infection and immune response, and discuss its implications for phage therapy.

  5. Novel lytic bacteriophages from soil that lyse Burkholderia pseudomallei.

    Science.gov (United States)

    Yordpratum, Umaporn; Tattawasart, Unchalee; Wongratanacheewin, Surasakdi; Sermswan, Rasana W

    2011-01-01

    Burkholderia pseudomallei is a Gram-negative saprophytic bacterium that causes severe sepsis with a high mortality rate in humans and a vaccine is not available. Bacteriophages are viruses of bacteria that are ubiquitous in nature. Several lysogenic phages of Burkholderia spp. have been found but information is scarce for lytic phages. Six phages, ST2, ST7, ST70, ST79, ST88 and ST96, which lyse B. pseudomallei, were isolated from soil in an endemic area. The phages belong to the Myoviridae family. The range of estimated genome sizes is 24.0-54.6 kb. Phages ST79 and ST96 lysed 71% and 67% of tested B. pseudomallei isolates and formed plaques on Burkholderia mallei but not other tested bacteria, with the exception of closely related Burkholderia thailandensis which was lysed by ST2 and ST96 only. ST79 and ST96 were observed to clear a mid-log culture by lysis within 6 h when infected at a multiplicity of infection of 0.1. As ST79 and ST96 phages effectively lysed B. pseudomallei, their potential use as a biocontrol of B. pseudomallei in the environment or alternative treatment in infected hosts could lead to benefits from phages that are available in nature. PMID:21091532

  6. Comparative genomics and evolution of the tailed-bacteriophages.

    Science.gov (United States)

    Casjens, Sherwood R

    2005-08-01

    The number of completely sequenced tailed-bacteriophage genomes that have been published increased to more than 125 last year. The comparison of these genomes has brought their highly mosaic nature into much sharper focus. Furthermore, reports of the complete sequences of about 150 bacterial genomes have shown that the many prophage and parts thereof that reside in these bacterial genomes must comprise a significant fraction of Earth's phage gene pool. These phage and prophage genomes are fertile ground for attempts to deduce the nature of viral evolutionary processes, and such analyses have made it clear that these phage have enjoyed a significant level of horizontal exchange of genetic information throughout their long histories. The strength of these evolutionary deductions rests largely on the extensive knowledge that has accumulated during intensive study into the molecular nature of the life cycles of a few 'model system' phages over the past half century. Recent molecular studies of phages other than these model system phages have made it clear that much remains to be learnt about the variety of lifestyle strategies utilized by the tailed-phage. PMID:16019256

  7. A promiscuous DNA packaging machine from bacteriophage T4.

    Science.gov (United States)

    Zhang, Zhihong; Kottadiel, Vishal I; Vafabakhsh, Reza; Dai, Li; Chemla, Yann R; Ha, Taekjip; Rao, Venigalla B

    2011-01-01

    Complex viruses are assembled from simple protein subunits by sequential and irreversible assembly. During genome packaging in bacteriophages, a powerful molecular motor assembles at the special portal vertex of an empty prohead to initiate packaging. The capsid expands after about 10%-25% of the genome is packaged. When the head is full, the motor cuts the concatemeric DNA and dissociates from the head. Conformational changes, particularly in the portal, are thought to drive these sequential transitions. We found that the phage T4 packaging machine is highly promiscuous, translocating DNA into finished phage heads as well as into proheads. Optical tweezers experiments show that single motors can force exogenous DNA into phage heads at the same rate as into proheads. Single molecule fluorescence measurements demonstrate that phage heads undergo repeated initiations, packaging multiple DNA molecules into the same head. These results suggest that the phage DNA packaging machine has unusual conformational plasticity, powering DNA into an apparently passive capsid receptacle, including the highly stable virus shell, until it is full. These features probably led to the evolution of viral genomes that fit capsid volume, a strikingly common phenomenon in double-stranded DNA viruses, and will potentially allow design of a novel class of nanocapsid delivery vehicles. PMID:21358801

  8. A promiscuous DNA packaging machine from bacteriophage T4.

    Directory of Open Access Journals (Sweden)

    Zhihong Zhang

    Full Text Available Complex viruses are assembled from simple protein subunits by sequential and irreversible assembly. During genome packaging in bacteriophages, a powerful molecular motor assembles at the special portal vertex of an empty prohead to initiate packaging. The capsid expands after about 10%-25% of the genome is packaged. When the head is full, the motor cuts the concatemeric DNA and dissociates from the head. Conformational changes, particularly in the portal, are thought to drive these sequential transitions. We found that the phage T4 packaging machine is highly promiscuous, translocating DNA into finished phage heads as well as into proheads. Optical tweezers experiments show that single motors can force exogenous DNA into phage heads at the same rate as into proheads. Single molecule fluorescence measurements demonstrate that phage heads undergo repeated initiations, packaging multiple DNA molecules into the same head. These results suggest that the phage DNA packaging machine has unusual conformational plasticity, powering DNA into an apparently passive capsid receptacle, including the highly stable virus shell, until it is full. These features probably led to the evolution of viral genomes that fit capsid volume, a strikingly common phenomenon in double-stranded DNA viruses, and will potentially allow design of a novel class of nanocapsid delivery vehicles.

  9. Decreased survival of the λ15 bacteriophage induced by UV-365 nanometers in Escherichia coli

    International Nuclear Information System (INIS)

    The results of our investigation showed a new effect (not yet described in the current literature) of the UV-365 nm, verified when the bacteria E. coli was irradiated with this wavelenght and then infected with bacteriophage irradiated with short UV (254 nm). In these conditions we observed a decrease in the phage survival. This phenomenon was called Decreased Survival of the Bacteriophage (DSB). We were able to show that DSB was only induced in bacteria irradiated with UV-365 nm, proficient in recombination repair and owning 4-thiouridine in their tRNA. For the induction of DSB it is necessary to promote damage in the bacteriophage through UVA and UVB. It seems that DSB and SOS are antagonistic since DSB is able to suppress the mutation induced by SOS. (author)

  10. Research of pathogenic bacteria and bacteriophages in the residuals of wastewater treatment plants

    International Nuclear Information System (INIS)

    The aim of this study is to find the pathogenic bacteria Listeria and Salmonella and to detect of bacterial (fecal coliforms) and viral indicators (bacteriophage) of fecal contamination in the residues of three sewage treatment plants in Greater Tunis: Charguia, Jdaida and Wardia. Three types of samples were analyzed: raw sewage, treated wastewater and sludge. The study showed the presence of pathogenic bacteria in some samples with a frequency of 7 pour cent for Listeria and 21 pour cent for Salmonella. However, none of these organisms has been detected in treated water of Jdaida and Chargia reflecting the efficiency of the purification process in these stations. Furthermore, all samples were positive for the presence of fecal coliforms and bacteriophages with important titles: up to 8.23 log10 (CFU/L) for coliforms and 8.36 log10 (pfu/L) for bacteriophages.

  11. Magic-angle spinning NMR of intact bacteriophages: Insights into the capsid, DNA and their interface

    Science.gov (United States)

    Abramov, Gili; Morag, Omry; Goldbourt, Amir

    2015-04-01

    Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.

  12. Antibacterial Efficacy of Lytic Bacteriophages against Antibiotic-Resistant Klebsiella Species

    Directory of Open Access Journals (Sweden)

    M. Khajeh Karamoddini

    2011-01-01

    Full Text Available Bacterial resistance to antibiotics is a leading and highly prevalent problem in the treatment of infectious diseases. Bacteriophages (phages appear to be effective and safe alternatives for the treatment of resistant infections because of their specificity for bacterial species and lack of infectivity in eukaryotic cells. The present study aimed to isolate bacteriophages against Klebsiella spp. and evaluate their efficacy against antibiotic-resistant species. Seventy-two antibiotic-resistant Klebsiella spp. were isolated from samples of patients who referred to the Ghaem Hospital (Mashhad, Iran. Lytic bacteriophages against Klebsiella spp. were isolated from wastewater of the septic tank of the same hospital. Bactericidal activity of phages against resistant Klebsiella spp. was tested in both liquid (tube method; after 1 and 24 h of incubation and solid (double-layer agar plate method; after 24 h of incubation phases. In each method, three different concentrations of bacteriophages (low: 107 PFU/mL were used. Bacteriophages showed promising bactericidal activity at all assessed concentrations, regardless of the test method and duration of incubation. Overall, bactericidal effects were augmented at higher concentrations. In the tube method, higher activity was observed after 24 h of incubation compared to the 1-h incubation. The bactericidal effects were also higher in the tube method compared to the double-layer agar plate method after 24 h of incubation. The findings of the present study suggest that bacteriophages possess effective bactericidal activity against resistant Klebsiella spp. These bactericidal activities are influenced by phage concentration, duration of incubation, and test method.

  13. Genetic analysis of the bacteriophage T4-encoded cochaperonin Gp31.

    OpenAIRE

    Richardson, A.; Georgopoulos, C

    1999-01-01

    Previous genetic and biochemical analyses have established that the bacteriophage T4-encoded Gp31 is a cochaperonin that interacts with Escherichia coli's GroEL to ensure the timely and accurate folding of Gp23, the bacteriophage-encoded major capsid protein. The heptameric Gp31 cochaperonin, like the E. coli GroES cochaperonin, interacts with GroEL primarily through its unstructured mobile loop segment. Upon binding to GroEL, the mobile loop adopts a structured, beta-hairpin turn. In this ar...

  14. Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry▿

    Science.gov (United States)

    Colomer-Lluch, Marta; Imamovic, Lejla; Jofre, Juan; Muniesa, Maite

    2011-01-01

    This study evaluates the occurrence of bacteriophages carrying antibiotic resistance genes in animal environments. blaTEM, blaCTX-M (clusters 1 and 9), and mecA were quantified by quantitative PCR in 71 phage DNA samples from pigs, poultry, and cattle fecal wastes. Densities of 3 to 4 log10 gene copies (GC) of blaTEM, 2 to 3 log10 GC of blaCTX-M, and 1 to 3 log10 GC of mecA per milliliter or gram of sample were detected, suggesting that bacteriophages can be environmental vectors for the horizontal transfer of antibiotic resistance genes. PMID:21807968

  15. Identification of the bacteriophage T5 dUTPase by protein sequence comparisons.

    Science.gov (United States)

    Kaliman, A V

    1996-01-01

    It is shown by protein sequence comparisons that a 148 amino acid open reading frame (ORF 148) located at 67% of the bacteriophage T5 genome encodes a protein with strong similarity to known dUTPases. This protein contains five characteristic amino acid sequence motifs that are common to the dUTPase gene family. A similarity in size and high degree of sequence identity strongly suggest that the protein encoded by the ORF 148 of bacteriophage T5 is dUTPase. PMID:8988373

  16. The Viral DNA Packaging Motor of Bacteriophage Lambda

    Science.gov (United States)

    Catalano, Carlos E.

    2007-03-01

    Terminase enzymes are common to both eukaryotic and prokaryotic double-stranded DNA viruses. These enzymes, which serve as molecular motors that selectively ``package'' viral DNA into a pre-formed procapsid structure, are among the most powerful biological motors characterized to date. Bacteriophage lambda terminase is a heteroligomer composed of gpA and gpNu1 subunits. The smaller gpNu1 subunit is required for specific recognition of viral DNA, a process that is modulated by ATP. The gpA subunit possesses site-specific nuclease and helicase activities that ``mature'' the viral genome prior to packaging. The subunit further possesses a DNA translocase activity that is central to the packaging motor complex. Discrete ATPase sites in gpA modulate the DNA maturation reactions and fuel the DNA packaging reaction. Kinetic characterization of lambda terminase indicates significant interaction between the multiple catalytic sites of the enzyme and has led to a minimal kinetic model describing the assembly of a catalytically-competent packaging motor complex. Biophysical studies demonstrate that purified lambda terminase forms a homogenous, heterotrimeric structure consisting of one gpA subunit in association with two gpNu1 proteins. Four heterotrimers further assemble into a ring-like structure of sufficient size to encircle duplex DNA. The ensemble of data suggests that the ring tetramer represents the biologically relevant, catalytically-competent motor complex responsible for genome processing and packaging reactions. We present a model for the functional DNA packaging motor complex that finds general utility in our global understanding of the enzymology of virus assembly.

  17. Novel DNA packaging recognition in the unusual bacteriophage N15

    International Nuclear Information System (INIS)

    Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cosN15) is closely related to cosλ, but whereas the cosBN15 subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosBλ. A bioinformatic study of N15-like phages indicates that cosBN15 also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15

  18. Novel DNA packaging recognition in the unusual bacteriophage N15

    Energy Technology Data Exchange (ETDEWEB)

    Feiss, Michael [Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242 (United States); Geyer, Henriette, E-mail: henriettegeyer@gmail.com [Division of Viral Infections, Robert Koch Institute, Berlin (Germany); Division of Viral Infections, Robert Koch Institute, Berlin (Germany); Klingberg, Franco, E-mail: franco.klingberg@thermofisher.com [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Moreno, Norma, E-mail: nmoreno@islander.tamucc.edu [Texas A& M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, United States. (United States); Texas A& M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, United States. (United States); Forystek, Amanda, E-mail: eamanda-forystek@uiowa.edu [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Room # 2911 JPP, Dept. of Psychiatry, The University of Iowa, 200 Hawkins Drive, Iowa City, Iowa, 52242 (United States); Maluf, Nasib Karl, E-mail: fKarl.Maluf@ap-lab.com [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Alliance Protein Laboratories, Inc. 6042 Cornerstone Court West, Suite ASan Diego, CA 92121, USA. (United States); Sippy, Jean [Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242 (United States)

    2015-08-15

    Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.

  19. Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

    Science.gov (United States)

    Cox, Christopher R.; Voorhees, Kent J.

    Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

  20. Identification of the N gene protein of bacteriophage lambda

    International Nuclear Information System (INIS)

    The N gene protein, pN, of bacteriophage lambda stimulates early gene transcription by allowing mRNA chain elongation to proceed into genes distal to transcription termination sites normally recognized by the Escherichia coli transcription termination protein rho. pN has previously eluded detection on sodium dodecyl sulfate/polyacrylamide gels because of its small size, its instability, and the difficulty of distinguising pN itself both from host proteins and from other early lambda proteins whose synthesis depends on pN action. These problems have now been overcome and we find that the major form of pN present in crude cell extracts of infected cells has an apparent molecular weight of 13,500. Lambda bio256, a deletion-substitution mutant terminating in N, codes for a shorter pN of molecular weight 12,500. A nonsense fragment of 10,500 molecular weight coded by lambda N/sub am7/ has also been identified. These conclusions are based on examination of the electrophoretic profiles of the proteins synthesized after infection of UV-irradiated E. coli by various lambda N- temperature-sensitive, nonsense, and deletion-substitution mutants. It has also been possible to distinguish pN itself from other early lambda polypeptides by infecting ron- cells with either lambda N/sub mar/ phage allowing pN synthesis but not pN action or lambda N/sub am/ phage defective in pN synthesis and pN action. Our results together with previous data are discussed with respect to the possible existence of multiple molecular weight forms of pN and the location of the coding sequences in the N gene region

  1. Dynamics of bacteriophage genome ejection in vitro and in vivo

    International Nuclear Information System (INIS)

    Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ∼500 mg ml−1. This high density requires substantial compression of the normal B-form helix, leading to the conjecture that DNA in mature phage virions is under significant pressure, and that pressure is used to eject the DNA during infection. A large number of theoretical, computer simulation and in vitro experimental studies surrounding this conjecture have revealed many—though often isolated and/or contradictory—aspects of packaged DNA. This prompts us to present a unified view of the statistical physics and thermodynamics of DNA packaged in phage capsids. We argue that the DNA in a mature phage is in a (meta)stable state, wherein electrostatic self-repulsion is balanced by curvature stress due to confinement in the capsid. We show that in addition to the osmotic pressure associated with the packaged DNA and its counterions, there are four different pressures within the capsid: pressure on the DNA, hydrostatic pressure, the pressure experienced by the capsid and the pressure associated with the chemical potential of DNA ejection. Significantly, we analyze the mechanism of force transmission in the packaged DNA and demonstrate that the pressure on DNA is not important for ejection. We derive equations showing a strong hydrostatic pressure difference across the capsid shell. We propose that when a phage is triggered to eject by interaction with its receptor in vitro, the (thermodynamic) incentive of water molecules to enter the phage capsid flushes the DNA out of the capsid. In vivo, the difference between the osmotic pressures in the bacterial cell cytoplasm and the culture medium similarly results in a water flow that drags the DNA out of the capsid and into the bacterial cell

  2. Mobile CRISPR/Cas-mediated bacteriophage resistance in Lactococcus lactis.

    Directory of Open Access Journals (Sweden)

    Anne M Millen

    Full Text Available Lactococcus lactis is a biotechnological workhorse for food fermentations and potentially therapeutic products and is therefore widely consumed by humans. It is predominantly used as a starter microbe for fermented dairy products, and specialized strains have adapted from a plant environment through reductive evolution and horizontal gene transfer as evidenced by the association of adventitious traits with mobile elements. Specifically, L. lactis has armed itself with a myriad of plasmid-encoded bacteriophage defensive systems to protect against viral predation. This known arsenal had not included CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins, which forms a remarkable microbial immunity system against invading DNA. Although CRISPR/Cas systems are common in the genomes of closely related lactic acid bacteria (LAB, none was identified within the eight published lactococcal genomes. Furthermore, a PCR-based search of the common LAB CRISPR/Cas systems (Types I and II in 383 industrial L. lactis strains proved unsuccessful. Here we describe a novel, Type III, self-transmissible, plasmid-encoded, phage-interfering CRISPR/Cas discovered in L. lactis. The native CRISPR spacers confer resistance based on sequence identity to corresponding lactococcal phage. The interference is directed at phages problematic to the dairy industry, indicative of a responsive system. Moreover, targeting could be modified by engineering the spacer content. The 62.8-kb plasmid was shown to be conjugally transferrable to various strains. Its mobility should facilitate dissemination within microbial communities and provide a readily applicable system to naturally introduce CRISPR/Cas to industrially relevant strains for enhanced phage resistance and prevention against acquisition of undesirable genes.

  3. Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials.

    Directory of Open Access Journals (Sweden)

    Maya Merabishvili

    Full Text Available We describe the small-scale, laboratory-based, production and quality control of a cocktail, consisting of exclusively lytic bacteriophages, designed for the treatment of Pseudomonas aeruginosa and Staphylococcus aureus infections in burn wound patients. Based on successive selection rounds three bacteriophages were retained from an initial pool of 82 P. aeruginosa and 8 S. aureus bacteriophages, specific for prevalent P. aeruginosa and S. aureus strains in the Burn Centre of the Queen Astrid Military Hospital in Brussels, Belgium. This cocktail, consisting of P. aeruginosa phages 14/1 (Myoviridae and PNM (Podoviridae and S. aureus phage ISP (Myoviridae was produced and purified of endotoxin. Quality control included Stability (shelf life, determination of pyrogenicity, sterility and cytotoxicity, confirmation of the absence of temperate bacteriophages and transmission electron microscopy-based confirmation of the presence of the expected virion morphologic particles as well as of their specific interaction with the target bacteria. Bacteriophage genome and proteome analysis confirmed the lytic nature of the bacteriophages, the absence of toxin-coding genes and showed that the selected phages 14/1, PNM and ISP are close relatives of respectively F8, phiKMV and phage G1. The bacteriophage cocktail is currently being evaluated in a pilot clinical study cleared by a leading Medical Ethical Committee.

  4. Isolation and characterization of glacier VMY22, a novel lytic cold-active bacteriophage of Bacillus cereus

    Institute of Scientific and Technical Information of China (English)

    Xiuling; Ji; Chunjing; Zhang; Yuan; Fang; Qi; Zhang; Lianbing; Lin; Bing; Tang; Yunlin; Wei

    2015-01-01

    As a unique ecological system with low temperature and low nutrient levels, glaciers are considered a "living fossil" for the research of evolution. In this work, a lytic cold-active bacteriophage designated VMY22 against Bacillus cereus MYB41-22 was isolated from Mingyong Glacier in China, and its characteristics were studied. Electron microscopy revealed that VMY22 has an icosahedral head(59.2 nm in length, 31.9 nm in width) and a tail(43.2 nm in length). Bacteriophage VMY22 was classified as a Podoviridae with an approximate genome size of 18 to 20 kb. A one-step growth curve revealed that the latent and the burst periods were 70 and 70 min, respectively, with an average burst size of 78 bacteriophage particles per infected cell. The pH and thermal stability of bacteriophage VMY22 were also investigated. The maximum stability of the bacteriophage was observed to be at pH 8.0 and it was comparatively stable at p H 5.0–9.0. As VMY22 is a cold-active bacteriophage with low production temperature, its characterization and the relationship between MYB41-22 and Bacillus cereus bacteriophage deserve further study.

  5. An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics

    Directory of Open Access Journals (Sweden)

    Lina Zhang

    2015-09-01

    Full Text Available Bacteriophage virion proteins and non-virion proteins have distinct functions in biological processes, such as specificity determination for host bacteria, bacteriophage replication and transcription. Accurate identification of bacteriophage virion proteins from bacteriophage protein sequences is significant to understand the complex virulence mechanism in host bacteria and the influence of bacteriophages on the development of antibacterial drugs. In this study, an ensemble method for bacteriophage virion protein prediction from bacteriophage protein sequences is put forward with hybrid feature spaces incorporating CTD (composition, transition and distribution, bi-profile Bayes, PseAAC (pseudo-amino acid composition and PSSM (position-specific scoring matrix. When performing on the training dataset 10-fold cross-validation, the presented method achieves a satisfactory prediction result with a sensitivity of 0.870, a specificity of 0.830, an accuracy of 0.850 and Matthew’s correlation coefficient (MCC of 0.701, respectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous studies with a sensitivity of 0.853, a specificity of 0.815, an accuracy of 0.831 and MCC of 0.662 on the independent testing dataset. These results suggest that the proposed method can be a potential candidate for bacteriophage virion protein prediction, which may provide a useful tool to find novel antibacterial drugs and to understand the relationship between bacteriophage and host bacteria. For the convenience of the vast majority of experimental Int. J. Mol. Sci. 2015, 16 21735 scientists, a user-friendly and publicly-accessible web-server for the proposed ensemble method is established.

  6. Isolation and Genetic Analysis of an Environmental Bacteriophage: A 10-Session Laboratory Series in Molecular Virology

    Science.gov (United States)

    Williamson, Ryan P.; Barker, Brent T.; Drammeh, Hamidou; Scott, Jefferson; Lin, Joseph

    2014-01-01

    Bacterial viruses, otherwise known as bacteriophage (or phage), are some of the most abundant viruses found in the environment. They can be easily isolated from water or soil and are ideal for use in laboratory classrooms due to their ease of culture and inherent safety. Here, we describe a series of 10 laboratory exercises where students collect,…

  7. Occurrence of Salmonella-specific bacteriophages in swine feces collected from commercial farms

    Science.gov (United States)

    Salmonella is one of the primary foodborne pathogens associated with swine production and represents a significant threat to human health. Bacteriophage are naturally-occurring viruses that prey on bacteria and have been suggested as a potential intervention strategy to reduce Salmonella in food an...

  8. Fusions of bacteriophage P22 late genes to the Escherichia coli lacZ gene.

    OpenAIRE

    Riggs, P D; Botstein, D

    1987-01-01

    The late genes of bacteriophage P22 were fused to lacZ to study their differential expression from the late operon transcript. No instances of posttranscriptional regulation were uncovered, thus supporting the model that the late genes are expressed, by and large, in fixed ratios based on their translational efficiency and message stability.

  9. Isolation of Salmonella spp. and bacteriophage active against Salmonella spp. from commercial swine

    Science.gov (United States)

    Bacteriophage are viruses that prey on bacteria and may be a potential strategy to reduce foodborne pathogenic bacteria in the gastrointestinal tract of food animals. Phages are fairly common in the gastrointestinal microbial ecosystem of mammals, but the incidence is unknown. If phage are to be e...

  10. Induction of genetic recombination in the lambda bacteriophage by ultraviolet radiation of the Escherichia Coli cells

    International Nuclear Information System (INIS)

    In this work there are reported the results that show that although the stimulation of the recombination of the Lambda bacteriophage, by UV irradiation of the cells of Escherichia Coli, it looks to be the result of the high expression of the functions of the SOS system, doesn't keep some relationship with the high concentration of protein reached RecA. (Author)

  11. A century of phage research: bacteriophages and the shaping of modern biology.

    Science.gov (United States)

    Keen, Eric C

    2015-01-01

    2015 marks the centennial of the discovery of bacteriophages, viruses that infect bacteria. Phages have been central to some of biology's most meaningful advances over the past hundred years (shown here); they greatly influence the workings of the biosphere, and are poised to play expanded roles in biomedicine, biotechnology, and ecology. PMID:25521633

  12. Interaction of Pseudomonas putida ATCC 12633 and Bacteriophage gh-1 in Berea Sandstone Rock

    OpenAIRE

    Chang, Philip Lee; Yen, Teh Fu

    1985-01-01

    Measurements of the passage of Pseudomonas putida ATCC 12633 and a phage-resistant mutant through Berea sandstone rock were made. When bacteriophage gh-1 was adsorbed within the rock matrix, a reduction in the passage of the susceptible but not the resistant cells through the rock was observed.

  13. Interaction of Pseudomonas putida ATCC 12633 and Bacteriophage gh-1 in Berea Sandstone Rock.

    Science.gov (United States)

    Chang, P L; Yen, T F

    1985-12-01

    Measurements of the passage of Pseudomonas putida ATCC 12633 and a phage-resistant mutant through Berea sandstone rock were made. When bacteriophage gh-1 was adsorbed within the rock matrix, a reduction in the passage of the susceptible but not the resistant cells through the rock was observed. PMID:16346956

  14. The membrane-bound form of gene 9 minor coat protein of bacteriophage M13

    NARCIS (Netherlands)

    Houbiers, M.C.

    2002-01-01

    Bacteriophage M13 is a virus that infects the bacteria Escherichia coli ( E. coli ), a single cell organism that resides in our intestines. It consists of the cytoplasm (contents) and a double membrane that keeps the contents together (the barrier to the outside world). The membra

  15. 76 FR 16285 - Food Additives Permitted for Direct Addition to Food for Human Consumption; Bacteriophage...

    Science.gov (United States)

    2011-03-23

    ... Additives Permitted for Direct Addition to Food for Human Consumption; Bacteriophage Preparation AGENCY... own guidelines for assessing the safety of food additives. Specifically, FWW states that FDA did not... the NAS/NRC as a guide that the Agency uses in its safety evaluations of food additives....

  16. Bacteriophage remediation of bacterial pathogens in aquaculture: a review of the technology

    Science.gov (United States)

    Bacteriophages have been proposed as an alternative to antibiotic usage and several studies on their application in aquaculture have been reported. This review highlights progress to date on phage therapies for the following fish and shellfish diseases and associated pathogens: hemorrhagic septicem...

  17. Optimal foraging predicts the ecology but not the evolution of host specialization in bacteriophages.

    Directory of Open Access Journals (Sweden)

    Sébastien Guyader

    Full Text Available We explore the ability of optimal foraging theory to explain the observation among marine bacteriophages that host range appears to be negatively correlated with host abundance in the local marine environment. We modified Charnov's classic diet composition model to describe the ecological dynamics of the related generalist and specialist bacteriophages phiX174 and G4, and confirmed that specialist phages are ecologically favored only at high host densities. Our modified model accurately predicted the ecological dynamics of phage populations in laboratory microcosms, but had only limited success predicting evolutionary dynamics. We monitored evolution of attachment rate, the phenotype that governs diet breadth, in phage populations adapting to both low and high host density microcosms. Although generalist phiX174 populations evolved even broader diets at low host density, they did not show a tendency to evolve the predicted specialist foraging strategy at high host density. Similarly, specialist G4 populations were unable to evolve the predicted generalist foraging strategy at low host density. These results demonstrate that optimal foraging models developed to explain the behaviorally determined diets of predators may have only limited success predicting the genetically determined diets of bacteriophage, and that optimal foraging probably plays a smaller role than genetic constraints in the evolution of host specialization in bacteriophages.

  18. Virulence Changes to Harveyi Clade Bacteria Infected with Bacteriophage from Vibrio owensii.

    Science.gov (United States)

    Busico-Salcedo, Nancy; Owens, Leigh

    2013-09-01

    Vibrio owensii is one of the most virulent vibrios known being able to kill crustacean larvae at 10(2) CFU ml(-1). This study describes virulence changes to naïve strains of Vibrio harveyi and Vibrio campbellii when infected with the bacteriophage VOB from a closely related species V. owensii 47666-1. The bacteriophage from V. owensii was induced into lytic phase by using mitomycin C at 100 ng ml(-1). One strain of V. harveyi and two strains of V. campbellii from 29 tested containing no prophage were susceptible to lysogenic conversion with VOB. Virulence changes induced in Harveyi clade bacteria included the up-regulation of protein secretion, statistically significant increased haemolysin and chitinase production and increased mortality to nauplii of Penaeus monodon. No change in siderophore production was observed. Bacteriophage VOB is likely to be responsible for some of the virulence factors expressed by V. owensii. As this bacteriophage is able to infect strains of V. harveyi and V. campbellii this phage may contribute to increased virulence of other vibrios in aquaculture and in the natural environment. PMID:24426274

  19. Detection and characterization of a lytic Pediococcus bacteriophage from the fermenting cucumber brine

    Science.gov (United States)

    Of the twelve lytic bacteriophages recovered from five different fermenting cucumber tanks that were inoculated with Pediococcus sp. LA0281, a lytic phage, 'ps05, was characterized in the present study. The plaques were mostly clear and round-shaped on the lawn of starter strain, indicating lytic ph...

  20. Primary Isolation Strain Determines Both Phage Type and Receptors Recognised by Campylobacter jejuni Bacteriophages

    DEFF Research Database (Denmark)

    Sørensen, Martine C. Holst; Gencay, Yilmaz Emre; Birk, Tina; Baldvinsson, Signe Berg; Jaeckel, Claudia; Hammerl, Jens A.; Vegge, Christina S.; Neve, Horst; Brøndsted, Lone

    2015-01-01

    In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated...

  1. Quantification and Evaluation of Infectivity of Shiga Toxin-Encoding Bacteriophages in Beef and Salad ▿

    OpenAIRE

    Imamovic, Lejla; Muniesa, Maite

    2011-01-01

    Stx bacteriophages in 68 samples of beef and salad were quantified by real-time quantitative PCR (qPCR). Stx phages from the samples were propagated in Escherichia coli C600, E. coli O157:H7, and Shigella strains and further quantified. Fifty percent of the samples carried infectious Stx phages that were isolated from plaques generated by lysis.

  2. Problem-Solving Test: RNA and Protein Synthesis in Bacteriophage-Infected "E. coli" Cells

    Science.gov (United States)

    Szeberenyi, Jozsef

    2008-01-01

    The classic experiment presented in this problem-solving test was designed to identify the template molecules of translation by analyzing the synthesis of phage proteins in "Escherichia coli" cells infected with bacteriophage T4. The work described in this test led to one of the most seminal discoveries of early molecular biology: it dealt a…

  3. Bacteriophage T4 genes sp and 40 apparently are the same.

    OpenAIRE

    Obringer, J; McCreary, P.; Bernstein, H

    1988-01-01

    The bacteriophage T4 spackle gene, which maintains host membrane integrity, mapped at the same position as gene 40 (head morphogenesis). The cloned spackle gene complemented and cross-reactivated a gene 40 mutant. Like the spackle mutant, gene 40 mutants were defective in genetic exclusion. Apparently, genes spackle and 40 are the same gene.

  4. Transfection of Bacillus subtilis protoplasts by bacteriophage phi do7 DNA.

    OpenAIRE

    Perkins, J B; Dean, D H

    1983-01-01

    DNA from the Bacillus subtilis temperate bacteriophage phi do7 was found to efficiently transfect B. subtilis protoplasts; protoplast transfection was more efficient than competent cell transfection by a magnitude of 10(3). Unlike competent cell transfection, protoplast transfection did not require primary recombination, suggesting that phi do7 DNA enters the protoplast as double-stranded molecules.

  5. Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection

    Science.gov (United States)

    Staphylococcus aureus is a Gram-positive pathogen relevant for both human and animal health. With multi-drug resistant S. aureus strains becoming increasingly prevalent, alternative therapeutics are urgently needed. Bacteriophage endolysins (peptidoglycan hydrolases, PGH) are capable of killing Gra...

  6. In vitro evaluation of a novel bacteriophage cocktail as a preventative for bovine coliform mastitis.

    Science.gov (United States)

    Porter, J; Anderson, J; Carter, L; Donjacour, E; Paros, M

    2016-03-01

    The objective of this study was to investigate the potential use of bacteriophage in preventing Escherichia coli mastitis on dairies. A cocktail consisting of 4 distinct bacteriophages was generated by screening against 36 E. coli isolates from dairy cows in Washington State with clinical mastitis. The bacteriophage significantly inhibited growth of 58% of the Washington State isolates and 54% of E. coli mastitis isolates from New York State, suggesting that the cocktail of phages had a relatively broad spectrum of action against relevant strains from 2 distinct geographies. The ability to suppress bacterial growth of these isolates in a liquid growth medium was not affected by the ratio of bacteriophage particles to bacterial cells (multiplicity of infection, MOI). For those E. coli that were completely inhibited by the phage cocktail, an MOI as low as 10had the same effect as 10µg/mL of ceftiofur on the growth rate of E. coli over a 12-h period using optical density measurements. A 3.3- to 5.6-log reduction of growth was achieved when E. coli was co-incubated with our phage cocktail in raw milk over a 12-h period at physiologic temperature. A modified gentamicin protection assay using bovine mammary epithelial cells provided a model to test whether bacteriophage could prevent cell attachment and invasion by chronic coliform mastitis strains. Pretreatment of cell cultures with the phage cocktail significantly reduced adhesion and intracellular survival of E. coli compared with controls. When combined with a bismuth-based teat sealant, the phage cocktail was able to inhibit bacterial growth when challenged with 1.6×10(3) cfu/mL of a clinical mastitis E. coli strain. In vitro results show bactericidal activity by our phage in raw milk and mammary tissue culture systems. Before a bacteriophage-based dry-cow treatment becomes a potential option for dairies, in vivo studies must be able to demonstrate that a specific dose of bacteriophage can protect cows from

  7. Pb-Pb age and Rb-Sr and Sm-Nd isotope signature of paleoproterozoic syenitic plutonism in the south of Salvador-Curaca mobile belt: Sao Felix Syenitic Massif, Bahia-Brazil

    International Nuclear Information System (INIS)

    The Sao Felix Syenitic Massif (MSSF) has a tabular shape with about 32 km2 that represents the south expression of the aligned syenitic plutonism, which occur in the middle part of Salvador-Curaca mobile belt (CMSC). Single zircon dating by stepwise Pb evaporation methodology yields an age of 2098 ± 1 Ma to SFSM. This data correlate the emplacement of the SFSM with the late stages of SCMB stabilization. This massif is isotopically characterized by negative epsilon neodymium values (-1.45 to -2.89) and low initial strontium ratio (0.701 to 0.704). SFSM isotopic signature is similar to the ones displayed by the others syenites from the belt and reflects an enriched source which should be related to a metasomatic enriched mantle. (author)

  8. The bacteriophage ϕ29 tail possesses a pore-forming loop for cell membrane penetration.

    Science.gov (United States)

    Xu, Jingwei; Gui, Miao; Wang, Dianhong; Xiang, Ye

    2016-06-23

    Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine that plays a central role in host cell recognition and attachment, cell wall and membrane penetration, and viral genome ejection. The mechanisms involved in the penetration of the inner host cell membrane by bacteriophage tails are not well understood. Here we describe structural and functional studies of the bacteriophage ϕ29 tail knob protein gene product 9 (gp9). The 2.0 Å crystal structure of gp9 shows that six gp9 molecules form a hexameric tube structure with six flexible hydrophobic loops blocking one end of the tube before DNA ejection. Sequence and structural analyses suggest that the loops in the tube could be membrane active. Further biochemical assays and electron microscopy structural analyses show that the six hydrophobic loops in the tube exit upon DNA ejection and form a channel that spans the lipid bilayer of the membrane and allows the release of the bacteriophage genomic DNA, suggesting that cell membrane penetration involves a pore-forming mechanism similar to that of certain non-enveloped eukaryotic viruses. A search of other phage tail proteins identified similar hydrophobic loops, which indicates that a common mechanism might be used for membrane penetration by prokaryotic viruses. These findings suggest that although prokaryotic and eukaryotic viruses use apparently very different mechanisms for infection, they have evolved similar mechanisms for breaching the cell membrane. PMID:27309813

  9. Control of Listeria monocytogenes growth in soft cheeses by bacteriophage P100

    Directory of Open Access Journals (Sweden)

    Elaine Nóbrega Gibson Silva

    2014-01-01

    Full Text Available The purpose of this study was to determine the effect of bacteriophage P100 on strains of Listeria monocytogenes in artificially inoculated soft cheeses. A mix of L. monocytogenes 1/2a and Scott A was inoculated in Minas Frescal and Coalho cheeses (approximately 10(5 cfu/g with the bacteriophage added thereafter (8.3 x 10(7 PFU/g. Samples were analyzed immediately, and then stored at 10 ºC for seven days. At time zero, 30 min post-infection, the bacteriophage P100 reduced L. monocytogenes counts by 2.3 log units in Minas Frescal cheese and by 2.1 log units in Coalho cheese, compared to controls without bacteriophage. However, in samples stored under refrigeration for seven days, the bacteriophage P100 was only weakly antilisterial, with the lowest decimal reduction (DR for the cheeses: 1.0 log unit for Minas Frescal and 0.8 log units for Coalho cheese. The treatment produced a statistically significant decrease in the counts of viable cells (p < 0.05 and in all assays performed, we observed an increase of approximately one log cycle in the number of viable cells of L. monocytogenes in the samples under refrigeration for seven days. Moreover, a smaller effect of phages was observed. These results, along with other published data, indicate that the effectiveness of the phage treatment depends on the initial concentration of L. monocytogenes, and that a high concentration of phages per unit area is required to ensure sustained inactivation of target pathogens on food surfaces.

  10. Single molecule studies of DNA packaging by bacteriophages

    Science.gov (United States)

    Fuller, Derek Nathan

    The DNA packaging dynamics of bacteriophages φ29, gamma, and T4 were studied at the single molecule level using a dual trap optical tweezers. Also, a method for producing long DNA molecules by PCR for optical tweezers studies of protein DNA interactions is presented and thoroughly characterized. This DNA preparation technique provided DNA samples for the φ29 and T4 studies. In the studies of φ29, the role of charge was investigated by varying the ionic conditions of the packaging buffer. Ionic conditions in which the DNA charge was highly screened due to divalent and trivalent cations showed the lowest resistance to packaging of the DNA to high density. This confirmed the importance of counterions in shielding the DNA interstrand repulsion when packaged to high density. While the ionic nature of the packaging buffer had a strong effect on packaging velocities, there was no clear trend between the counterion-screened charge of the DNA and the maximum packaging velocity. The packaging studies of lambda and T4 served as systems for comparative studies with φ29. Each system showed similarities to the φ29 system and unique differences. Both the lambda and T4 packaging motors were capable of generating forces in excess of 50 pN and showed remarkably high processivity, similar to φ29. However, dynamic structural transitions were observed with lambda that are not observed with φ29. The packaging of the lambda genome showed capsid expansion at approximately 30 percent of the genome packaged and capsid rupture at 90 percent of the genome packaged in the absence of capsid stabilizing protein gpD. Unique to the T4 packaging motor, packaging dynamics showed a remarkable amount of variability in velocities. This variability was seen both within individual packaging phages and from one phage to the next. This is possibly due to different conformational states of the packaging machinery. Additionally, lambda and T4 had average packaging velocities under minimal load of 600

  11. Vibrio cholerae non-serogroup O1 cystitis.

    OpenAIRE

    Dumler, J.S.; Osterhout, G J; Spangler, J G; Dick, J D

    1989-01-01

    We report a case of a patient who developed cystitis caused by non-serogroup O1 Vibrio cholerae after swimming in the Chesapeake Bay. Treatment was empirical, with complete symptomatic resolution. Genitourinary tract infections by Vibrio spp. are uncommon but should be considered when cystitis occurs after saltwater exposure in appropriate geographic regions.

  12. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable rates of evolution within a core genome

    Science.gov (United States)

    Background: Biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context. We sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricu...

  13. Ability of Bacillus subtilis protoplasts to repair irradiated bacteriophage deoxyribonucleic acid via acquired and natural enzymatic systems

    International Nuclear Information System (INIS)

    A novel form of enzyme therapy was achieved by utilizing protoplasts of Bacillus subtilis. Photoreactivating enzyme of Escherichia coli was successfully inserted into the protoplasts of B. subtilis treated with polyethylene glycol. This enzyme was used to photoreactivate ultraviolet-damaged bacteriophage deoxyribonucleic acid (DNA). Furthermore, in polyethylene glycol-treated protoplasts, ultraviolet-irradiated transfecting bacteriophage DNA was shown to be a functional substrate for the host DNA excision repair system. Previous results (R.E. Yasbin, J.D. Fernwalt, and P.I. Fields, J. Bacteriol.; 137: 391-396) showed that ultraviolet-irradiated bacteriophage DNA could not be repaired via the excision repair system of competent cells. Therefore, the processing of bacteriophage DNA by protoplasts and by competent cells must be different. This sensitive protoplast assay can be used to identify and to isolate various types of DNA repair enzymes

  14. T4-Related Bacteriophage LIMEstone Isolates for the Control of Soft Rot on Potato Caused by 'Dickeya solani'

    OpenAIRE

    Adriaenssens, Evelien; Van Vaerenbergh, Johan; Vandenheuvel, Dieter; Dunon, Vincent; Ceyssens, Pieter-Jan; De Proft, Maurice; Kropinski, Andrew M; Noben, Jean-Paul; Maes, Martine; Lavigne, Rob

    2012-01-01

    The bacterium ‘Dickeya solani’, an aggressive biovar 3 variant of Dickeya dianthicola, causes rotting and blackleg in potato. To control this pathogen using bacteriophage therapy, we isolated and characterized two closely related and specific bacteriophages, vB_DsoM_LIMEstone1 and vB_DsoM_LIMEstone2. The LIMEstone phages have a T4-related genome organization and share DNA similarity with Salmonella phage ViI. Microbiological and molecular characterization of the phages deemed them suitable an...

  15. Comparative (Meta)genomic Analysis and Ecological Profiling of Human Gut-Specific Bacteriophage φB124-14

    OpenAIRE

    Ogilvie, Lesley A.; Caplin, Jonathan; Dedi, Cinzia; Diston, David; Cheek, Elizabeth; Bowler, Lucas; Taylor, Huw; Ebdon, James; Jones, Brian V.

    2012-01-01

    Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-s...

  16. Biological Properties and Cell Tropism of Chp2, a Bacteriophage of the Obligate Intracellular Bacterium Chlamydophila abortus

    OpenAIRE

    Everson, J. S.; Garner, S. A.; Fane, B.; Liu, B.-L.; Lambden, P R; Clarke, I N

    2002-01-01

    A number of bacteriophages belonging to the Microviridae have been described infecting chlamydiae. Phylogenetic studies divide the Chlamydiaceae into two distinct genera, Chlamydia and Chlamydophila, containing three and six different species, respectively. In this work we investigated the biological properties and host range of the recently described bacteriophage Chp2 that was originally discovered in Chlamydophila abortus. The obligate intracellular development cycle of chlamydiae has prec...

  17. Fc receptor-mediated, antibody-dependent enhancement of bacteriophage lambda-mediated gene transfer in mammalian cells

    OpenAIRE

    Sapinoro, Ramil; Volcy, Ketna; Shanaka, W.W.; Rodrigo, I.; Schlesinger, Jacob J.; Dewhurst, Stephen

    2008-01-01

    Lambda phage vectors mediate gene transfer in cultured mammalian cells and in live mice, and in vivo phage-mediated gene expression is increased when mice are pre-immunized with bacteriophage lambda. We now show that, like eukaryotic viruses, bacteriophage vectors are subject to Fc receptor-mediated, antibody-dependent enhancement of infection in mammalian cells. Antibody-dependent enhancement of phage gene transfer required FcγRI, but not its associated γ chain, and was not supported by othe...

  18. Inactivation of F-specific bacteriophages during flocculation with polyaluminum chloride - a mechanistic study.

    Science.gov (United States)

    Kreißel, Katja; Bösl, Monika; Hügler, Michael; Lipp, Pia; Franzreb, Matthias; Hambsch, Beate

    2014-03-15

    Bacteriophages are often used as surrogates for enteric viruses in spiking experiments to determine the efficiencies of virus removal of certain water treatment measures, like e.g. flocculation or filtration steps. Such spiking experiments with bacteriophages are indispensable if the natural virus concentrations in the raw water of water treatment plants are too low to allow the determination of elimination levels over several orders of magnitude. In order to obtain reliable results from such spiking tests, it is essential that bacteriophages behave comparable to viruses and remain stable during the experiments. To test this, the influence of flocculation parameters on the bacteriophages MS2, Qβ and phiX174 was examined. Notably, the F-specific phages MS2 and Qβ were found to be inactivated in flocculation processes with polyaluminum chloride (PACl). In contrast, other aluminum coagulants like AlCl3 or Al2(SO4)3 did not show a comparable effect on MS2 in this study. In experiments testing the influence of different PACl species on MS2 and Qβ inactivation during flocculation, it could be shown that cationic dissolved PACl species (Al13) interacted with the MS2 surface and hereby reduced the surviving phage fraction to c/c0 values below 1*10(-4) even at very low PACl concentrations of 7 μmol Al/L. Other inactivation mechanisms like the irreversible adsorption of phages to the floc structure or the damage of phage surfaces due to entrapment into the floc during coagulation and floc formation do not seem to contribute to the low surviving fraction found for both F-specific bacteriophages. Furthermore, no influence of phage agglomeration or pH drops during the flocculation process on phage inactivation could be observed. The somatic coliphage phiX174 in contrast did not show sensitivity to chemical stress and in accordance only slight interaction between Al13 and the phage surface was observed. Consequently, F-specific phages like MS2 should not be used as

  19. O1s photoionization dynamics in oriented NO2

    Science.gov (United States)

    Stener, Mauro; Decleva, Piero; Yamazaki, Masakazu; Adachi, Jun-ichi; Yagishita, Akira

    2011-05-01

    We have performed extensive density functional theory (DFT) calculations, partial cross sections, dipole prepared continuum orbitals, dipole amplitudes and phase shifts, asymmetry parameters β, and molecular frame photoelectron angular distributions, to elucidate the O1s photoionization dynamics of NO2 molecule with emphasis on the shape resonances in the O1s ionization continuum. In the shape resonance region, the β parameters and photoelectron angular distributions have been compared with our experimental results. Fairly good agreement between the theory and experiment has confirmed that the DFT level calculations can well describe the photoionization dynamics of the simple molecule such as NO2. Interference due to equivalent atom photoionization is theoretically considered, and the possibility of detection of the effect in the two degenerate channels with different combinations of light polarization and photoemission direction is discussed.

  20. Examining Prebiotic Chemistry Using O(^1D) Insertion Reactions

    Science.gov (United States)

    Hays, Brian M.; Laas, Jacob C.; Weaver, Susanna L. Widicus

    2013-06-01

    Aminomethanol, methanediol, and methoxymethanol are all prebiotic molecules expected to form via photo-driven grain surface chemistry in the interstellar medium (ISM). These molecules are expected to be precursors for larger, biologically-relevant molecules in the ISM such as sugars and amino acids. These three molecules have not yet been detected in the ISM because of the lack of available rotational spectra. A high resolution (sub)millimeter spectrometer coupled to a molecular source is being used to study these molecules using O(^1D) insertion reactions. The O(^1D) chemistry is initiated using an excimer laser, and the products of the insertion reactions are adiabatically cooled using a supersonic expansion. Experimental parameters are being optimized by examination of methanol formed from O(^1D) insertion into methane. Theoretical studies of the structure and reaction energies for aminomethanol, methanediol, and methoxymethanol have been conducted to guide the laboratory studies once the methanol experiment has been optimized. The results of the calculations and initial experimental results will be presented.

  1. An open reading frame in the Escherichia coli bacteriophage lambda genome encodes a protein that functions in assembly of the long tail fibers of bacteriophage T4.

    OpenAIRE

    Montag, D.; Henning, U

    1987-01-01

    Assembly of the long tail fibers of the Escherichia coli bacteriophage T4 requires the catalytic action of two auxiliary proteins. It was found that a gene of the entirely unrelated phage lambda codes for a protein which can substitute for one of these T4 polypeptides, protein 38. The lambda gene was designated tfa (tail fiber assembly). Protein 38 consists of 183 residues, and the Tfa protein consists of 194 residues; the two polypeptides are about 40% homologous. Although the tfa gene is di...

  2. Cloning, sequencing, and recombinational analysis with bacteriophage BF23 of the bacteriophage T5 oad gene encoding the receptor-binding protein.

    OpenAIRE

    Krauel, V; Heller, K J

    1991-01-01

    Binding of bacteriophage T5 to its receptor, the Escherichia coli FhuA protein, is mediated by tail protein pb5. In this article we confirm that pb5 is encoded by the T5 oad gene and describe the isolation, expression, and sequencing of this gene. In order to locate oad precisely, we analyzed recombinants between BF23, a T5-related phage with a different host range, and plasmid clones containing segments of the T5 chromosome. This analysis also showed that oad has little or no homology with h...

  3. Bacteriophage infections of microbiota can lead to leaky gut in an experimental rodent model.

    Science.gov (United States)

    Tetz, George; Tetz, Victor

    2016-01-01

    Increased intestinal permeability and translocation of gut microbiota from the intestinal lumen to the systemic circulation predispose patients to various diseases and may be one of the main triggers thereof. The role of microbiota in increased intestinal permeability is under intensive investigation. Here, we studied alterations in the host and increased intestinal permeability as a direct effect of treatment with a bacteriophage cocktail. After 10 days of challenge, the rats showed weight loss, messy hair, and decreased activity. Additionally, they displayed a significantly elevated lactulose:mannitol ratio and the level of circulating immune complexes. To our knowledge, this study demonstrates for the first time that increased intestinal permeability may be induced by bacteriophages that affect the microbiota. PMID:27340433

  4. Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage

    International Nuclear Information System (INIS)

    Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulation of the hexamer within the procapsid. Here we use hydrogen-deuterium exchange and mass spectrometry to delineate the interactions of the P4 hexamer with the bacteriophage phi12 procapsid. P4 associates with the procapsid via its C-terminal face. The interactions also stabilize subunit interfaces within the hexamer. The conformation of the virus-bound hexamer is more stable than the hexamer in solution, which is prone to spontaneous ring openings. We propose that the stabilization within the viral capsid increases the packaging processivity and confers selectivity during RNA loading

  5. Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli

    International Nuclear Information System (INIS)

    Bacteriophage P1 has a contractile tail that targets the conserved lipopolysaccharide on the outer membrane surface of the host for initial adsorption. The mechanism by which P1 DNA enters the host cell is not well understood, mainly because the transient molecular interactions between bacteriophage and bacteria have been difficult to study by conventional approaches. Here, we engineered tiny E. coli host cells so that the initial stages of P1-host interactions could be captured in unprecedented detail by cryo-electron tomography. Analysis of three-dimensional reconstructions of frozen-hydrated specimens revealed three predominant configurations: an extended tail stage with DNA present in the phage head, a contracted tail stage with DNA, and a contracted tail stage without DNA. Comparative analysis of various conformations indicated that there is uniform penetration of the inner tail tube into the E. coli periplasm and a significant movement of the baseplate away from the outer membrane during tail contraction.

  6. Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2.

    Science.gov (United States)

    Horn, Wilf T; Tars, Kaspars; Grahn, Elin; Helgstrand, Charlotte; Baron, Andrew J; Lago, Hugo; Adams, Chris J; Peabody, David S; Phillips, Simon E V; Stonehouse, Nicola J; Liljas, Lars; Stockley, Peter G

    2006-03-01

    Sequence-specific interactions between RNA stem-loops and coat protein (CP) subunits play vital roles in the life cycles of the RNA bacteriophages, e.g., by allowing translational repression of their replicase cistrons and tagging their own RNA genomes for encapsidation. The CPs of bacteriophages Qbeta and MS2 each discriminate in favor of their cognate translational operators, even in the presence of closely related operators from other phages in vivo. Discrete mutations within the MS2 CP have been shown to relax this discrimination in vitro. We have determined the structures of eight complexes between such mutants and both MS2 and Qbeta stem-loops with X-ray crystallography. In conjunction with previously determined in vivo repression data, the structures enable us to propose the molecular basis for the discrimination mechanism. PMID:16531233

  7. Isolation and characterization of bacteriophages infecting nocardioforms in wastewater treatment plant.

    Science.gov (United States)

    Khairnar, Krishna; Pal, Preeti; Chandekar, Rajshree H; Paunikar, Waman N

    2014-01-01

    Activated sludge plants (ASP) are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages NOC1, NOC2, and NOC3 for the control of Nocardia species. The bacteriophages isolated in this study have shown promising results in controlling foam producing bacterial growth under laboratory conditions, suggesting that it may prove useful in the field as an alternative biocontrol agent to reduce the foaming problem. To the best of our knowledge to date no work has been published from India related to biological approach for the control of foaming. PMID:25140256

  8. Isolation and Characterization of Bacteriophages Infecting Nocardioforms in Wastewater Treatment Plant

    Directory of Open Access Journals (Sweden)

    Krishna Khairnar

    2014-01-01

    Full Text Available Activated sludge plants (ASP are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages NOC1, NOC2, and NOC3 for the control of Nocardia species. The bacteriophages isolated in this study have shown promising results in controlling foam producing bacterial growth under laboratory conditions, suggesting that it may prove useful in the field as an alternative biocontrol agent to reduce the foaming problem. To the best of our knowledge to date no work has been published from India related to biological approach for the control of foaming.

  9. Bacteriophage amplification assay for detection of Listeria spp. using virucidal laser treatment

    Directory of Open Access Journals (Sweden)

    I.C. Oliveira

    2012-09-01

    Full Text Available A protocol for the bacteriophage amplification technique was developed for quantitative detection of viable Listeria monocytogenes cells using the A511 listeriophage with plaque formation as the end-point assay. Laser and toluidine blue O (TBO were employed as selective virucidal treatment for destruction of exogenous bacteriophage. Laser and TBO can bring a total reduction in titer phage (ca. 10(8 pfu/mL without affecting the viability of L. monocytogenes cells. Artificially inoculated skimmed milk revealed mean populations of the bacteria as low as between 13 cfu/mL (1.11 log cfu/mL, after a 10-h assay duration. Virucidal laser treatment demonstrated better protection of Listeria cells than the other agents previously tested. The protocol was faster and easier to perform than standard procedures. This protocol constitutes an alternative for rapid, sensitive and quantitative detection of L. monocytogenes.

  10. Eradication of Salmonella Typhimurium in broiler chicks by combined use of P22 bacteriophage and probiotic

    Directory of Open Access Journals (Sweden)

    Guilherme Augusto Marietto Gonçalves

    2011-06-01

    Full Text Available It has been reported that the phage therapy is effective in controlling the number of colony-forming unit (CFU of Salmonella spp. in chicken gut. This paper describes the protective effect of phage and Lactobacilli administration on Salmonella infection in 1-day-old chicks. We administered the bacteriophage P22 in a single dose and a probiotic mixture of four species of bacteriocin-producing Lactobacillus once a day for one week. Samples were analyzed every 48 hours, and intestinal eradication of S. Typhimurium was confirmed after treatments. We observed an increase in the size of duodenal villi and cecal crypts, as well as an increase in body weight in groups that received daily doses of Lactobacilli. This study confirms the efficiency of bacteriophage therapy in controlling salmonellosis in chicks and the beneficial effect of Lactobacilli mixtures in the weight gain of the birds.

  11. Climatology of the O(1S) and O(1D) emission rates from WINDII/UARS global measurements

    Science.gov (United States)

    Zhang, Z.; Shepherd, S.

    The Wind Imaging Interferometer WINDII on the Upper Atmospheric Research Satellite UARS has provided a large number of O 1S green line 557 7 nm and O 1D red line 630 0 nm emission rate profiles during 1991-1997 of unprecedented high quality The daytime airglow emission is produced mainly by solar energy deposition and vary according to changes of the solar zenith angle and solar irradiance The nighttime airglow emission rates show strong latitudinal and local time dependences Using both daytime and nighttime measurements the directly solar excited daytime emission rates can be removed and the indirectly excited component is revealed This study presents the seasonal and latitudinal variations of the indirect component of the two airglow emission rates which may be due to tides geomagnetic effects and other physical and photochemical processes

  12. Plasmid insertion mutagenesis and lac gene fusion with mini-mu bacteriophage transposons.

    OpenAIRE

    Castilho, B A; Olfson, P; Casadaban, M J

    1984-01-01

    Small bacteriophage Mu transposable elements containing the lac operon structural genes were constructed to facilitate the isolation and use of Mu insertions and lac gene fusions. These mini-Mu elements have selectable genes for either ampicillin or kanamycin resistance and can be used to form both transcriptional and translational lac gene fusions. Some of the mini-Mu-lac elements constructed are deleted for the Mu A and B transposition genes and form stable insertions that cannot undergo tr...

  13. Antibody producing capacity to the bacteriophage phi X174 in yersinia arthritis.

    OpenAIRE

    Bucknall, R.; Leirisalo-Repo, M; Laitinen, O; Jones, J V

    1987-01-01

    Antibody production in response to the primary immunogen bacteriophage phi X174 was investigated in 14 patients with previous yersinia arthritis (YA) and in 15 controls. HLA-B27 occurred in 10 patients with YA and in three controls. After primary and secondary immunisation the antibody responses were essentially similar both in patients with YA and controls. Consequently our results suggest that antibody response to a foreign antigen does not differ between patients with YA and a normal contr...

  14. Molecular cloning of unintegrated Moloney mouse sarcoma virus DNA in bacteriophage lambda.

    OpenAIRE

    Verma, I M; Lai, M.H.; Bosselman, R A; McKennett, M. A.; Fan, H.; Berns, A

    1980-01-01

    The covalently closed circular forms of unintegrated viral DNA obtained from cells infected with Moloney mouse sarcoma virus was cloned in bacteriophage lambda. The viral DNA was cleaved with restriction endonuclease HindIII and inserted in the unique HindIII site of lambda Charon 21A DNA. Recombinant clones containing virus-reactive DNA sequences were analyzed by restriction endonuclease mapping, R-loop formation, and infectivity assays. Two of eight genome-length recombinant clones characte...

  15. Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

    OpenAIRE

    Fallico, Vincenzo

    2011-01-01

    Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2,...

  16. Enumeration of Bacteriophages and Host Bacteria in Sewage and the Activated-Sludge Treatment Process

    OpenAIRE

    Donald L. Ewert; Paynter, M. J. B.

    1980-01-01

    Bacteriophage populations in an activated-sludge sewage treatment plant were enumerated. A newly developed assay for quantitation of total phages, employing direct electron microscopic counts, was used in conjunction with the plaque assay. The total concentration of phages was significantly higher in reactor mixed liquor and effluent than in influent sewage, indicating a net production of phages within the reactor. Maximum total phage concentrations in the fluid phase of sewage, activated-slu...

  17. Extraction and Study of Bacteriophages, Used against Agents of Potato Soft Rot

    OpenAIRE

    Magda D. Davitashvili; Lela Z. Tsiklauri

    2012-01-01

    The use of specific bacteriophages and their complex mixtures against bacterial diseases is very effective. As for causative agent of potato soft rot Erwinia carotovora, specific phages (25 phages in total) were extracted from diseased potato, soil and sewage. The study of their biological properties showed the diversity of phages in terms of lytic action, virion plaque and morphology, as well as in relation to different environmental factors. Phages showed explicit antibacterial activity in ...

  18. Participation of the lytic replicon in bacteriophage P1 plasmid maintenance.

    OpenAIRE

    Yarmolinsky, M B; Hansen, E B; Jafri, S; Chattoraj, D K

    1989-01-01

    P1 bacteriophage carries at least two replicons: a plasmid replicon and a viral lytic replicon. Since the isolated plasmid replicon can maintain itself stably at the low copy number characteristic of intact P1 prophage, it has been assumed that this replicon is responsible for driving prophage replication. We provide evidence that when replication from the plasmid replicon is prevented, prophage replication continues, albeit at a reduced rate. The residual plasmid replication is due to incomp...

  19. Ecology of Anti-Biofilm Agents II: Bacteriophage Exploitation and Biocontrol of Biofilm Bacteria

    OpenAIRE

    Stephen T. Abedon

    2015-01-01

    Bacteriophages are the viruses of bacteria. In the guise of phage therapy they have been used for decades to successfully treat what are probable biofilm-containing chronic bacterial infections. More recently, phage treatment or biocontrol of biofilm bacteria has been brought back to the laboratory for more rigorous assessment as well as towards the use of phages to combat environmental biofilms, ones other than those directly associated with bacterial infections. Considered in a companion ar...

  20. Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin.

    Science.gov (United States)

    Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan

    2016-08-23

    Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents. PMID:27513288

  1. Isolation of Acanthamoeba-Specific Antibodies from a Bacteriophage Display Library

    OpenAIRE

    Khan, Naveed A.; Greenman, John; Topping, Katherine P.; Victoria C. Hough; Temple, Graham S.; Paget, Timothy A.

    2000-01-01

    Acanthamoeba causes opportunistic eye infections in humans, which can lead to severe keratitis and may ultimately result in blindness. Current methods for identifying this organism rely on culture and microscopy. In this paper, we describe the isolation of antibody fragments that can be used for the unequivocal identification of Acanthamoeba. A bacteriophage antibody display library was used to isolate antibody fragments that bind specifically to Acanthamoeba. Individual clones were studied b...

  2. Expression of the bacteriophage T4 denV structural gene in Escherichia coli

    International Nuclear Information System (INIS)

    The expression of the T4 denV gene, which previously had been cloned in plasmid constructs downstream of the bacteriophage lambda hybrid promoter-operator oLpR, was analyzed under a variety of growth parameters. Expression of the denV gene product, endonuclease V, was confirmed in DNA repair-deficient Escherichia coli (uvrA recA) by Western blot analyses and by enhancements of resistance to UV irradiation

  3. A genomic approach to understand interactions between Streptococcus pneumoniae and its bacteriophages

    OpenAIRE

    Leprohon, Philippe; Gingras, Hélène; Ouennane, Siham; Moineau, Sylvain; Ouellette, Marc

    2015-01-01

    Background Bacteriophage replication depends on bacterial proteins and inactivation of genes coding for such host factors should interfere with phage infection. To gain further insights into the interactions between S. pneumoniae and its pneumophages, we characterized S. pneumoniae mutants selected for resistance to the virulent phages SOCP or Dp-1. Results S. pneumoniae R6-SOCPR and R6-DP1R were highly resistant to the phage used for their selection and no cross-resistance between the two ph...

  4. Repair-defective mutants of Alteromonas espejiana, the host for bacteriophage PM2.

    OpenAIRE

    Zerler, B R; Wallace, S S

    1984-01-01

    The in vivo repair processes of Alteromonas espejiana, the host for bacteriophage PM2, were characterized, and UV- and methyl methanesulfonate (MMS)-sensitive mutants were isolated. Wild-type A. espejiana cells were capable of photoreactivation, excision, recombination, and inducible repair. There was no detectable pyrimidine dimer-DNA N-glycosylase activity, and pyrimidine dimer removal appeared to occur by a pathway analogous to the Escherichia coli Uvr pathway. The UV- and MMS-sensitive mu...

  5. Chemical factors influencing adsorption of bacteriophage MS2 to membrane filters.

    OpenAIRE

    Farrah, S R

    1982-01-01

    Antichaotropic salts, such as magnesium sulfate, and metal chelators, such as citrate ions, promoted adsorption of bacteriophage MS2 to membrane filters. In contrast, compounds that disrupt hydrophobic interactions, such as chaotropic salts, urea, Tween 80, and ethanol, did not promote adsorption of MS2 to membrane filters and counteracted the ability of magnesium sulfate to promote such adsorption. These results provide evidence that magnesium sulfate promotes the association of MS2 with mem...

  6. Translesion synthesis is the main component of SOS repair in bacteriophage lambda DNA.

    OpenAIRE

    Defais, M; Lesca, C; Monsarrat, B.; Hanawalt, P

    1989-01-01

    Agents that interfere with DNA replication in Escherichia coli induce physiological adaptations that increase the probability of survival after DNA damage and the frequency of mutants among the survivors (the SOS response). Such agents also increase the survival rate and mutation frequency of irradiated bacteriophage after infection of treated bacteria, a phenomenon known as Weigle reactivation. In UV-irradiated single-stranded DNA phage, Weigle reactivation is thought to occur via induced, e...

  7. Stepwise Expansion of the Bacteriophage φ6 Procapsid: Possible Packaging Intermediates

    OpenAIRE

    Nemecek, Daniel; Cheng, Naiqian; Qiao, Jian; Mindich, Leonard; Steven, Alasdair C; Heymann, J. Bernard

    2011-01-01

    The initial assembly product of bacteriophage φ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding ...

  8. Solid-state 31P NMR spectroscopy of bacteriophage M13 and tobacco mosaic virus.

    OpenAIRE

    Magusin, P.C.M.M.

    1995-01-01

    In this thesis, the results of various 31P NMR experiments observed for intact virus particles of bacteriophage M13 and Tobacco Mosaic Virus (TMV), are presented. To explain the results in a consistent way, models are developed and tested. 31P nuclei in M13 and TMV are only present in the phosphodiesters of the encapsulated nucleic acid molecule. Therefore, 31P NMR spectroscopy reveals structural and dynamic properties of the nucleic acid backbone selectively without isotope labeling, even th...

  9. Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor

    OpenAIRE

    Migliori, Amy D.; Keller, Nicholas; Alam, Tanfis I.; Mahalingam, Marthandan; Rao, Venigalla B.; Arya, Gaurav; Smith, Douglas E.

    2014-01-01

    How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here, we show that site-directed alteratio...

  10. The membrane-bound form of gene 9 minor coat protein of bacteriophage M13

    OpenAIRE

    Houbiers, M.C.

    2002-01-01

    Bacteriophage M13 is a virus that infects the bacteria Escherichia coli ( E. coli ), a single cell organism that resides in our intestines. It consists of the cytoplasm (contents) and a double membrane that keeps the contents together (the barrier to the outside world). The membrane is formed by lipid molecules which consist of a head group that very much likes water (hydrophilic) and two fatty tails that dislike water (hydrophobic). In order to avoid contact with water the fatty tails group ...

  11. Proteasome Inhibitors Enhance Bacteriophage Lambda (λ) Mediated Gene Transfer in Mammalian Cells

    OpenAIRE

    Volcy, Ketna; Dewhurst, Stephen

    2008-01-01

    Bacteriophage lambda vectors can transfer their genomes into mammalian cells, resulting in expression of phage-encoded genes. However, this process is inefficient. Experiments were therefore conducted to delineate the rate limiting step(s) involved, using a phage vector that contains a mammalian luciferase reporter gene cassette. The efficiency of phage-mediated gene transfer in mammalian cells was quantitated, in the presence or absence of pharmacologic inhibitors of cell uptake and degradat...

  12. Initiation of bacteriophage lambda DNA replication in vitro with purified lambda replication proteins.

    OpenAIRE

    Wold, M S; Mallory, J B; Roberts, J D; LeBowitz, J H; McMacken, R

    1982-01-01

    We have developed a soluble enzyme system that replicates exogenously added plasmid DNA (lambda dv) bearing the replication origin of the bacteriophage lambda chromosome. The system contains pure phage lambda O and P replication proteins and a partially purified mixture of Escherichia coli replication proteins [the enzyme system of Fuller, R.S., Kaguni, J.M. & Kornberg, A. (1981) Proc. Natl. Acad. Sci. USA 78, 7370-7374). The features of lambda dv replication in this system closely resemble t...

  13. Simultaneous display of two large proteins on the head and tail of bacteriophage lambda

    OpenAIRE

    Pavoni, Emiliano; Vaccaro, Paola; D’Alessio, Valeria; De Santis, Rita; Minenkova, Olga

    2013-01-01

    Background Consistent progress in the development of bacteriophage lambda display platform as an alternative to filamentous phage display system was achieved in the recent years. The lambda phage has been engineered to display efficiently multiple copies of peptides or even large protein domains providing a powerful tool for screening libraries of peptides, proteins and cDNA. Results In the present work we describe an original method for dual display of large proteins on the surface of lambda...

  14. The protein interaction network of bacteriophage lambda with its host Escherichia coli.

    OpenAIRE

    Blasche, Sonja; Wuchty, Stefan; Rajagopala, Seesandra V.; Uetz, Peter

    2013-01-01

    Although most of the 73 open reading frames (ORFs) in bacteriophage λ have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its host Escherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between the...

  15. Bacteriophage-Resistant Staphylococcus aureus Mutant Confers Broad Immunity against Staphylococcal Infection in Mice

    OpenAIRE

    Capparelli, Rosanna; Nocerino, Nunzia; Lanzetta, Rosa; Silipo, Alba; Amoresano, Angela; Giangrande, Chiara; Becker, Karsten; Blaiotta, Giuseppe; Evidente, Antonio; Cimmino, Alessio; Iannaccone, Marco; Parlato, Marianna; Medaglia, Chiara; Roperto, Sante; Roperto, Franco

    2010-01-01

    In the presence of a bacteriophage (a bacteria-attacking virus) resistance is clearly beneficial to the bacteria. As expected in such conditions, resistant bacteria emerge rapidly. However, in the absence of the phage, resistant bacteria often display reduced fitness, compared to their sensitive counterparts. The present study explored the fitness cost associated with phage-resistance as an opportunity to isolate an attenuated strain of S. aureus. The phage-resistant strain A172 was isolated ...

  16. Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system

    OpenAIRE

    Kiro, Ruth; Shitrit, Dror; Qimron, Udi

    2014-01-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are tar...

  17. pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

    OpenAIRE

    May, Eric R.; Arora, Karunesh; Brooks, Charles L.

    2014-01-01

    Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to sh...

  18. Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids

    OpenAIRE

    Thorsten Hugel; Jens Michaelis; Hetherington, Craig L.; Jardine, Paul J.; Shelley Grimes; Walter, Jessica M.; Wayne Falk; Anderson, Dwight L.; Carlos Bustamante

    2007-01-01

    Author Summary The life cycles of many viruses include a self-assembly stage in which a powerful molecular motor packs the DNA genome into the virus's preformed shell (the capsid). Biochemical and biophysical studies have identified essential components of the packaging machinery and measured various characteristics of the packaging process, while crystallography and electron microscopy have provided snapshots of viral structure before and after packaging. In bacteriophage ϕ29 assembly, the D...

  19. Novel bacteriophage therapy for controlling metallo-beta-lactamase producing Pseudomonas aeruginosa infection in Catfish

    OpenAIRE

    Khairnar, Krishna; Raut, Mahendra P; Rajshree H. Chandekar; Sanmukh, Swapnil G; Waman N. PAUNIKAR

    2013-01-01

    Background The bacteriophage therapy is an effective antimicrobial approach with potentially important applications in medicine and biotechnology which can be seen as an additional string in the bow. Emerging drug resistant bacteria in aquaculture industry due to unrestricted use of antibiotics warrants more sustainable and environmental friendly strategies for controlling fish infections. The isolated bacteria from fish lesions was characterised based on isolation on selective and differenti...

  20. Isolation and Characterization of Bacteriophages Infecting Nocardioforms in Wastewater Treatment Plant

    OpenAIRE

    Khairnar, Krishna; Pal, Preeti; Rajshree H. Chandekar; Waman N. PAUNIKAR

    2014-01-01

    Activated sludge plants (ASP) are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages ...

  1. Isolation and Preliminary Characterization of Twenty Bacteriophages Infecting Either Brevibacterium or Arthrobacter Strains

    OpenAIRE

    Trautwetter, Annie; Blanco, Carlos

    1988-01-01

    Thirty-seven bacteriophages plaquing on Corynebacterium, Brevibacterium, or Arthrobacter strains were isolated from soil or vegetation samples. Restriction analysis of phage DNA indicated that 20 phages were unique; one of them produced entirely turbid plaques on Brevibacterium ketoglutamicum and was characterized as temperate. All these phages were assigned to group B of the classification of Bradley (Bacteriol. Rev. 31:230-314, 1967) and had relatively narrow host ranges.

  2. A bacteriophage transcription regulator inhibits bacterial transcription initiation by σ-factor displacement

    OpenAIRE

    Liu, Bing; Shadrin, Andrey; Sheppard, Carol; Mekler, Vladimir; Xu, Yingqi; Severinov, Konstantin; Matthews, Steve; Wigneshweraraj, Sivaramesh

    2014-01-01

    Bacteriophages (phages) appropriate essential processes of bacterial hosts to benefit their own development. The multisubunit bacterial RNA polymerase (RNAp) enzyme, which catalyses DNA transcription, is targeted by phage-encoded transcription regulators that selectively modulate its activity. Here, we describe the structural and mechanistic basis for the inhibition of bacterial RNAp by the transcription regulator P7 encoded by Xanthomonas oryzae phage Xp10. We reveal that P7 uses a two-step ...

  3. Growth of Salmonella bacteriophage P22 in Escherichia coli dna(Ts) mutants.

    OpenAIRE

    Schanda-Mulfinger, U E; Schmieger, H

    1980-01-01

    Salmonella bacteriophage P22 grows in two deoxyribonucleic acid initiation mutants of Escherichia coli under nonpermissive conditions, dnaA and dnaC. Functional products of genes dnaE, dnaZ, lig, dnaK, and dnaG are indispensable for deoxyribonucleic acid replication of P22. In 11 E. coli dnaB mutants belonging to all phenotypic groups, phage were produced at 42 degrees C.

  4. The mom gene of bacteriophage Mu: the mechanism of methylation-dependent expression.

    OpenAIRE

    Seiler, A.; Blöcker, H; Frank, R.; Kahmann, R

    1986-01-01

    Transcription of the DNA modification gene (mom) of bacteriophage Mu requires methylation of three GATC sites upstream of the mom promoter by the Escherichia coli deoxyadenosine methylation function (Dam). The three sites map within a 40-bp segment termed region I. Small deletions, inversions, duplications and specific point mutations have been introduced in region I. Their effect on mom expression has been studied in dam+ and dam strains. Dam-dependent expression of the mom gene requires a s...

  5. Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673▿†

    OpenAIRE

    Kropinski, Andrew M.; Arutyunov, Denis; Foss, Mary; Cunningham, Anna; Ding, Wen; Singh, Amit; Pavlov, Andrey R.; Henry, Matthew; Evoy, Stephane; Kelly, John; Szymanski, Christine M.

    2011-01-01

    Campylobacter jejuni continues to be the leading cause of bacterial food-borne illness worldwide, so improvements to current methods used for bacterial detection and disease prevention are needed. We describe here the genome and proteome of C. jejuni bacteriophage NCTC 12673 and the exploitation of its receptor-binding protein for specific bacterial detection. Remarkably, the 135-kb Myoviridae genome of NCTC 12673 differs greatly from any other proteobacterial phage genome described (includin...

  6. Regions of incompatibility in single-stranded DNA bacteriophages phi X174 and G4.

    OpenAIRE

    van der Avoort, H G; van der Ende, A.; van Arkel, G A; Weisbeek, P J

    1984-01-01

    The intracellular presence of a recombinant plasmid containing the intercistronic region between the genes H and A of bacteriophage phi X174 strongly inhibits the conversion of infecting single-stranded phi X DNA to parental replicative-form DNA. Also, transfection with single-stranded or double-stranded phi X174 DNA of spheroplasts from a strain containing such a "reduction" plasmid shows a strong decrease in phage yield. This phenomenon, the phi X reduction effect, was studied in more detai...

  7. Dissection of the DNA Mimicry of the Bacteriophage T7 Ocr Protein using Chemical Modification

    OpenAIRE

    Stephanou, Augoustinos S.; Roberts, Gareth A.; Cooper, Laurie P.; Clarke, David J.; Thomson, Andrew R.; Mackay, C. Logan; Nutley, Margaret; Cooper, Alan; Dryden, David T. F.

    2009-01-01

    The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modi...

  8. Computer Simulations of DNA Packing inside Bacteriophages: Elasticity, Electrostatics and Entropy

    OpenAIRE

    Marenduzzo, D.

    2008-01-01

    There is now a considerable literature on computer simulations of DNA packaging inside bacteriophage capsids. While most studies have reached a semiquantitative or qualitative agreement with single molecule packaging and ejection studies, several quantitative answers are to date still lacking, needing either more accurate measurements or more realistic or difficult simulations. Here, I briefly review the outstanding questions in this field and report some new numerical results on DNA packagin...

  9. Response of bacteriophage T7 biological dosimeter to dehydration and extraterrestrial solar UV radiation

    Science.gov (United States)

    Hegedüs, M.; Fekete, A.; Módos, K.; Kovács, G.; Rontó, Gy.; Lammer, H.; Panitz, C.

    2007-02-01

    The experiment "Phage and uracil response" (PUR) will be accommodated in the EXPOSE facility of the ISS. Bacteriophage T7/isolated T7 DNA will be exposed to different subsets of extreme environmental parameters in space, in order to study the Responses of Organisms to the Space Environment (ROSE). Launch into orbit is preceded by EXPOSE Experiment Verification Tests (EVT) to optimize the methods and the evaluation. Bacteriophage T7/isolated T7 DNA thin layers were exposed to vacuum ( 10-6Pa), to monochromatic (254 nm) and polychromatic (200-400 nm) UV radiation in air as well as in simulated space vacuum. Using neutral density (ND) filters dose-effect curves were performed in order to define the maximum doses tolerated. The effect of temperature fluctuation in vacuum was also studied. The structural/chemical effects on bacteriophage T7/isolated T7 DNA were analyzed by spectroscopic and microscopical methods. Characteristic changes in the absorption spectrum and in the electrophoretic pattern of phage/DNA have been detected indicating the damage of isolated and intraphage DNA. DNA damage was also determined by quantitative PCR (QPCR) using 555 and 3826 bp fragments of T7 DNA. We obtained substantial evidence that DNA lesions (e.g. strand breaks, DNA-protein cross-links, cyclobutane pirimidine dimers (CPDs) etc.) accumulate throughout exposure. Preliminary results suggest a synergistic action of space vacuum and UV radiation with DNA being the critical target.

  10. Interactions of the cell-wall glycopolymers of lactic acid bacteria with their bacteriophages

    Directory of Open Access Journals (Sweden)

    Marie-Pierre eChapot-Chartier

    2014-05-01

    Full Text Available Lactic acid bacteria (LAB are Gram positive bacteria widely used in the production of fermented food in particular cheese and yoghurts. Bacteriophage infections during fermentation processes have been for many years a major industrial concern and have stimulated numerous research efforts. Better understanding of the molecular mechanisms of bacteriophage interactions with their host bacteria is required for the development of efficient strategies to fight against infections. The bacterial cell wall plays key roles in these interactions. First, bacteriophages must adsorb at the bacterial surface through specific interactions with receptors that are cell wall components. At next step, phages must overcome the barrier constituted by cell wall peptidoglycan to inject DNA inside bacterial cell. Also at the end of the infection cycle, phages synthesize endolysins able to hydrolyze peptidoglycan and lyse bacterial cells to release phage progeny. In the last decade, concomitant development of genomics and structural analysis of cell wall components allowed considerable advances in the knowledge of their structure and function in several model LAB. Here, we describe the present knowledge on the structure of the cell wall glycopolymers of the best characterized LAB emphasizing their structural variations and we present the available data regarding their role in bacteria-phage specific interactions at the different steps of the infection cycle.

  11. Characterization of a novel Morganella morganii bacteriophage FSP1 isolated from river water.

    Science.gov (United States)

    Yamaki, Shogo; Omachi, Takuo; Kawai, Yuji; Yamazaki, Koji

    2014-10-01

    Morganella morganii has been identified as a causative agent of opportunistic infections and histamine poisoning. Bacteriophage is a virus and has recently been considered an alternative agent to antibiotics for the control of bacteria that have developed antibiotic resistance. In this study, a novel M. morganii bacteriophage isolated from river water was characterized. The isolated phage, termed FSP1, was purified by polyethylene glycol precipitation followed by cesium chloride density-gradient centrifugation. FSP1 has infectivity against only M. morganii and was identified as a Myoviridae bacteriophage through morphological analysis with transmission electron microscopy. According to the one-step growth curve, the FSP1 latent period, eclipse period, and burst size were 30, 20 min, and 42 PFU infected cell(-1) , respectively. The genome size of FSP1 was estimated to be c. 45.6-49.4 kb by restriction endonuclease analyses. Moreover, challenge testing against M. morganii in vitro revealed that FSP1 had high lytic activity and that the viable cell count of M. morganii was reduced by 6.12 log CFU mL(-1) after inoculation with FSP1 at a multiplicity of infection (MOI) = 10. These results suggested that FSP1 could be used as a biocontrol agent against M. morganii for treatment of infectious disease treatment or food decontamination. PMID:25168469

  12. Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia

    Directory of Open Access Journals (Sweden)

    Anik Kusmiatun

    2015-01-01

    Full Text Available Bacillus pumilus is a spore-forming bacteria that is rod-shaped, gram positive, and aerobic. B. pumilus produced pumilacidins, known to have toxic effects on epithelial cells. Antibiotics were usually used to treat the disease caused by bacteria. Antibiotic typing test of B. pumilus indigenous from sewage water showed that this isolate was resistant to ampicillin and clindamycin. An alternative way was by application of bacteriophages as biocontrol agents to reduce B. pumilus in environment. The aim of this study were to isolate and characterize B. pumilus bacteriophage isolated from Ciapus River in Bogor, West Java. Bacteriophages infecting B. pumilus were isolated from river water using the double agar overlay method. Phages were defined by plaque morphology, structure, host range, and characteristic of molecular weight protein phage. Phage FBa1, FBa2, and FBa3 had narrow host range and they were specific for infecting B. pumilus. Electron microscope observation showed that phage FBa1 had icosahedral head without tail (166.67 nm in diameter, so it is called phage-like particles. Characterization of phage FBa1 by SDS-PAGE showed five proteins band. Molecular weight of FBa1 proteins was 70.9, 54.9, 33.8, 28.3, and 21.4 kDa.

  13. Isolation of a novel polyvalent virulent bacteriophage of E.coli

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective: To isolate virulent bacteriophage from environment samples and explore the potential way of decontaminating the environmental wastewater. Methods: The standard plaque assay, negative staining transmission electron microscopy (TEM), genome extraction and nucleases test were used to isolate bacteriophages. Then its morphology and characteristics were examined. Results: A novel bacteriophage XY-1 was isolated from a sewage pond in a hospital. It infected and killed 6 E. coli reference strains. The phage had a round head (diameter 40-50 nm), no tail and the genome was ssRNA of approximately 5. 0 kb. It was able to reduce E. coli to an extent of 44. 63% to 67. 00% when being added into the samples of different raw sewage water, depending on the contact time, the temperature and the phage dose. Conclusion; From the morphology typical and nucleotide characteristics (RNA) of the genome of phage, phage XY-1 appears to be closely related to phage f2. It may have some effects for the control of E. coli in sewage water.

  14. The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin.

    Science.gov (United States)

    Liu, Jared; Yan, Riceley; Zhong, Qiao; Ngo, Sam; Bangayan, Nathanael J; Nguyen, Lin; Lui, Timothy; Liu, Minghsun; Erfe, Marie C; Craft, Noah; Tomida, Shuta; Li, Huiying

    2015-09-01

    The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy. PMID:25848871

  15. PCR method for detection and identification of Lactobacillus casei/paracasei bacteriophages in dairy products.

    Science.gov (United States)

    Binetti, Ana G; Capra, M Luján; Alvarez, Miguel A; Reinheimer, Jorge A

    2008-05-31

    Bacteriophage infections of starter lactic acid bacteria (LAB) pose a serious risk to the dairy industry. Nowadays, the expanding use of valuable Lactobacillus strains as probiotic starters determines an increase in the frequency of specific bacteriophage infections in dairy plants. This work describes a simple and rapid Polymerase Chain Reaction (PCR) method that detects and identifies bacteriophages infecting Lactobacillus casei/paracasei, the main bacterial species used as probiotic. Based on a highly conserved region of the NTP-binding genes belonging to the replication module of L. casei phages phiA2 and phiAT3 (the only two whose genomes are completely sequenced), a pair of primers was designed to generate a specific fragment. Furthermore, this PCR detection method proved to be a useful tool for monitoring and identifying L. casei/paracasei phages in industrial samples since specific PCR signals were obtained from phage contaminated milk (detection limit: 10(4) PFU/mL milk) and other commercial samples (fermented milks and cheese whey) that include L. casei/paracasei as probiotic starter (detection limit: 10(6) PFU/mL fermented milk). Since this method can detect the above phages in industrial samples and can be easily incorporated into dairy industry routines, it might be readily used to earmark contaminated milk for use in processes that do not involve susceptible starter organisms, or processes which involve phage-deactivating conditions. PMID:18471918

  16. Physiological and Molecular Characterization of Salmonella Bacteriophages Previously Used in Phage Therapy.

    Science.gov (United States)

    Zhang, J; Hong, Y; Fealey, M; Singh, A; Walton, K; Martin, C; Harman, N J; Mahlie, J; Ebner, P D

    2015-12-01

    The use of bacteriophages as biocontrol agents to control Salmonella in food production has gained popularity over the last two decades. Previously, our laboratory demonstrated that bacteriophages can be direct fed to limit Salmonella colonization and transmission in pigs. Here, we characterized the bacteriophages in our treatment cocktail in terms of lytic spectrum, growth kinetics, survivability under various conditions, and genomic sequencing. PCR-based fingerprinting indicated that 9 of the 10 phages, while related, were distinct isolates. Single-step growth kinetics analysis determined that the eclipse periods, latent periods, and burst sizes averaged 21.5 min, 31.5 min, and 43.3 particles, respectively. The viability of the phages was measured after exposure to various pH ranges, temperatures, digestive enzymes, UV light, and chlorinated water. Temperatures greater than 87.5°C, pH of biocontrol agent in various aspects of food production when the exact serovar or strain of contaminating Salmonella is not yet known. PMID:26613908

  17. Repair of near (365 nm)- and far (254 nm)- UV damage to bacteriophage of Escherichia coli

    International Nuclear Information System (INIS)

    Intact bacteriophages were irradiated at 365 nm or 254 nm and then analyzed for DNA photoproducts or injected into their bacterial host to test susceptibility of the damage to both phage and host-cell mediated repair systems. Both thymine dimers and single-strand breaks were induced in the phage DNA by 365 nm radiation. The dimers appeared to be the major lethal lesion in both repair deficient bacteriophage T4 and bacteriophage lambda after 254 nm or 365 nm irradiation. Damage induced in T4 by either wavelength was equally susceptible to x-gene reactivation. v-gene reactivation acted on a larger fraction of the near-UV damage. The host-cell mediated photo-reactivation system was only slightly less effective for near-UV damage but host-cell reactivation (survival of phage lambda on uvr+ and uvr- host) was effective against a far smaller section of near-UV damage than far-UV damage. Weigle-reactivation (far-UV induced) of near-UV damage to phage lambda was not observed. The results suggested that unless the near-UV damaged phage DNA is repaired immediately after injection, the lesions rapidly lose their susceptibility to repair with a consequent loss of activity of the phage particles. (author)

  18. Interaction of Bacteriophage l with Its E. coli Receptor, LamB

    Directory of Open Access Journals (Sweden)

    Sujoy Chatterjee

    2012-11-01

    Full Text Available The initial step of viral infection is the binding of a virus onto the host cell surface. This first viral-host interaction would determine subsequent infection steps and the fate of the entire infection process. A basic understating of the underlining mechanism of initial virus-host binding is a prerequisite for establishing the nature of viral infection. Bacteriophage λ and its host Escherichia coli serve as an excellent paradigm for this purpose. λ phages bind to specific receptors, LamB, on the host cell surface during the infection process. The interaction of bacteriophage λ with the LamB receptor has been the topic of many studies, resulting in wealth of information on the structure, biochemical properties and molecular biology of this system. Recently, imaging studies using fluorescently labeled phages and its receptor unveil the role of spatiotemporal dynamics and divulge the importance of stochasticity from hidden variables in the infection outcomes. The scope of this article is to review the present state of research on the interaction of bacteriophage λ and its E. coli receptor, LamB.

  19. Characterization of a new ViI-like Erwinia amylovora bacteriophage phiEa2809.

    Science.gov (United States)

    Lagonenko, Alexander L; Sadovskaya, Olga; Valentovich, Leonid N; Evtushenkov, Anatoly N

    2015-04-01

    Erwinia amylovora is a Gram-negative plant pathogenic bacteria causing fire blight disease in many Rosaceae species. A novel E. amylovora bacteriophage, phiEa2809, was isolated from symptomless apple leaf sample collected in Belarus. This phage was also able to infect Pantoea agglomerans strains. The genome of phiEa2809 is a double-stranded linear DNA 162,160 bp in length, including 145 ORFs and one tRNA gene. The phiEa2809 genomic sequence is similar to the genomes of the Serratia plymutica phage MAM1, Shigella phage AG-3, Dickeya phage vB DsoM LIMEstone1 and Salmonella phage ViI and lacks similarity to described E. amylovora phage genomes. Based on virion morphology (an icosahedral head, long contractile tail) and genome structure, phiEa2809 was classified as a member of Myoviridae, ViI-like bacteriophages group. PhiEa2809 is the firstly characterized ViI-like bacteriophage able to lyse E. amylovora. PMID:25714551

  20. Biomimetic self-templating optical structures fabricated by genetically engineered M13 bacteriophage.

    Science.gov (United States)

    Kim, Won-Geun; Song, Hyerin; Kim, Chuntae; Moon, Jong-Sik; Kim, Kyujung; Lee, Seung-Wuk; Oh, Jin-Woo

    2016-11-15

    Here, we describe a highly sensitive and selective surface plasmon resonance sensor system by utilizing self-assembly of genetically engineered M13 bacteriophage. About 2700 copies of genetically expressed peptide copies give superior selectivity and sensitivity to M13 phage-based SPR sensor. Furthermore, the sensitivity of the M13 phage-based SPR sensor was enhanced due to the aligning of receptor matrix in specific direction. Incorporation of specific binding peptide (His Pro Gln: HPQ) gives M13 bacteriophage high selectivity for the streptavidin. Our M13 phage-based SPR sensor takes advantage of simplicity of self-assembly compared with relatively complex photolithography techniques or chemical conjugations. Additionally, designed structure which is composed of functionalized M13 bacteriophage can simultaneously improve the sensitivity and selectivity of SPR sensor evidently. By taking advantages of the genetic engineering and self-assembly, we propose the simple method for fabricating novel M13 phage-based SPR sensor system which has a high sensitivity and high selectivity. PMID:27295572

  1. Complete genome sequence of the cold-active bacteriophage VMY22 from Bacillus cereus.

    Science.gov (United States)

    Qin, Kunhao; Cheng, Benxu; Zhang, Shengting; Wang, Nan; Fang, Yuan; Zhang, Qi; Kuang, Anxiu; Lin, Lianbing; Ji, Xiuling; Wei, Yunlin

    2016-06-01

    The cold-active bacteriophage VMY22, belonging to the Podoviridae family, was isolated from Mingyong Glacier in China. Sequence analysis revealed that the genome is 18,609 bp long, with an overall G + C content of 36.4 mol%, and 25 open reading frames (ORFs). The sequence contains 46 potential promoters, 6 transcription terminators, and no tRNAs. Most of the ORFs show a high degree of similarity to B103 (NC_004165). Two noteworthy findings were made. First, one of the predicted proteins, ORF 19, shows high sequence similarity to the bacteriocin biosynthesis protein from Bacillus cereus. From this information, we propose that the VMY22 phage is at an intermediate phase in its coevolution with its bacterial host. Second, seven of the hypothetical proteins appear to be unique to this cold-active B. cereus phage (i.e., not found in temperate-active B. cereus phages). These observations add to our current knowledge about the coevolution of bacteriophages and their hosts. The identification of a novel group of gene and protein structures and functions will lead to a better understanding of cold-adaptation mechanisms in bacteria and their bacteriophages. PMID:26941234

  2. Survival of Shiga toxin-producing Escherichia coli and Stx bacteriophages in moisture enhanced beef.

    Science.gov (United States)

    Langsrud, Solveig; Heir, Even; Rode, Tone Mari

    2014-07-01

    Moisture enhancement of meat through injection is a technology to improve the sensory properties and the weight of meat. However, the technology may increase the risk of food borne infections. Shiga toxin-producing Escherichia coli (STEC) or bacteriophages carrying cytotoxin genes (Shiga toxin genes, stx), which is normally only present on the surface of intact beef, may be transferred to the inner parts of the muscle during the injection process. Pathogens and bacteriophages surviving the storage period may not be eliminated in the cooking process since many consumers prefer undercooked beef. Measures to increase the microbial food safety of moisture enhanced beef may include sterilization or washing of the outer surface of the meat before injection, avoiding recycling of marinade and addition of antimicrobial agents to the marinade. This paper reviews the literature regarding microbial safety of moisture enhanced beef with special emphasis on STEC and Stx bacteriophages. Also, results from a European Union research project, ProSafeBeef (Food-CT-16 2006-36241) are presented. PMID:24134920

  3. The Resistance of Vibrio cholerae O1 El Tor Strains to the Typing Phage 919TP, a Member of K139 Phage Family.

    Science.gov (United States)

    Shen, Xiaona; Zhang, Jingyun; Xu, Jialiang; Du, Pengcheng; Pang, Bo; Li, Jie; Kan, Biao

    2016-01-01

    Bacteriophage 919TP is a temperate phage of Vibrio cholerae serogroup O1 El Tor and is used as a subtyping phage in the phage-biotyping scheme in cholera surveillance in China. In this study, sequencing of the 919TP genome showed that it belonged to the Vibrio phage K139 family. The mechanisms conferring resistance to 919TP infection of El Tor strains were explored to help understand the subtyping basis of phage 919TP and mutations related to 919TP resistance. Among the test strains resistant to phage 919TP, most contained the temperate 919TP phage genome, which facilitated superinfection exclusion to 919TP. Our data suggested that this immunity to Vibrio phage 919TP occurred after absorption of the phage onto the bacteria. Other strains contained LPS receptor synthesis gene mutations that disable adsorption of phage 919TP. Several strains resistant to 919TP infection possessed unknown resistance mechanisms, since they did not contain LPS receptor mutations or temperate K139 phage genome. Further research is required to elucidate the phage infection steps involved in the resistance of these strains to phage infection. PMID:27242744

  4. The Resistance of Vibrio cholerae O1 El Tor Strains to the Typing Phage 919TP, a Member of K139 Phage Family

    Science.gov (United States)

    Shen, Xiaona; Zhang, Jingyun; Xu, Jialiang; Du, Pengcheng; Pang, Bo; Li, Jie; Kan, Biao

    2016-01-01

    Bacteriophage 919TP is a temperate phage of Vibrio cholerae serogroup O1 El Tor and is used as a subtyping phage in the phage-biotyping scheme in cholera surveillance in China. In this study, sequencing of the 919TP genome showed that it belonged to the Vibrio phage K139 family. The mechanisms conferring resistance to 919TP infection of El Tor strains were explored to help understand the subtyping basis of phage 919TP and mutations related to 919TP resistance. Among the test strains resistant to phage 919TP, most contained the temperate 919TP phage genome, which facilitated superinfection exclusion to 919TP. Our data suggested that this immunity to Vibrio phage 919TP occurred after absorption of the phage onto the bacteria. Other strains contained LPS receptor synthesis gene mutations that disable adsorption of phage 919TP. Several strains resistant to 919TP infection possessed unknown resistance mechanisms, since they did not contain LPS receptor mutations or temperate K139 phage genome. Further research is required to elucidate the phage infection steps involved in the resistance of these strains to phage infection.

  5. Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1.

    Science.gov (United States)

    Betts, Alex; Vasse, Marie; Kaltz, Oliver; Hochberg, Michael E

    2013-11-01

    Antibiotic resistance is becoming increasingly problematic for the treatment of infectious disease in both humans and livestock. The bacterium Pseudomonas aeruginosa is often found to be resistant to multiple antibiotics and causes high patient mortality in hospitals. Bacteriophages represent a potential option to combat pathogenic bacteria through their application in phage therapy. Here, we capitalize on previous studies showing how evolution may increase phage infection capacity relative to ancestral genotypes. We passaged four different phage isolates (podoviridae, myoviridae) through six serial transfers on the ancestral strain of Pseudomonas aeruginosa PAO1. We first demonstrate that repeated serial passage on ancestral bacteria increases infection capacity of bacteriophage on ancestral hosts and on those evolved for one transfer. This result is confirmed when examining the ability of evolved phage to reduce ancestral host population sizes. Second, through interaction with a single bacteriophage for 24 h, P. aeruginosa can evolve resistance to the ancestor of that bacteriophage; this also provides these evolved bacteria with cross-resistance to the other three bacteriophages. We discuss how the evolutionary training of phages could be employed as effective means of combatting bacterial infections or disinfecting surfaces in hospital settings, with reduced risk of bacterial resistance compared with conventional methods. PMID:24187587

  6. 鹅FoxO1基因cDNA序列的克隆及组织表达%Cloning and Tissues Expression Analysis of Goose Forkhead Box O1 (FoxO1) Gene cDNA Sequence

    Institute of Scientific and Technical Information of China (English)

    杨璐; 魏守海

    2014-01-01

    为了研究鹅FoxO1(forkhead box O1)基因的功能,根据GenBank已收录的鸡(Gallus gallus)、人(Homo sapiens)和小鼠(Mus musculus)等物种FoxO1基因序列的同源保守区域,设计特异性引物,利用RT-PCR技术克隆鹅FoxO1基因cDNA序列,并对基因序列进行了生物信息学分析.结果表明,成功克隆得到了鹅FoxO1基因cDNA序列,通过BLAST比对,鹅FoxO1基因与原鸡、人、小鼠的核苷酸序列同源性分别为97%、83%、82%,FoxO1基因在四川白鹅中表达水平总体表现为:皮脂>腹脂>腿肌>胸肌>肝脏.因此,FoxO1基因在多个组织中都有表达,且表达差异较大.

  7. Photochemistry of O(1D) and O(1S) lines in the coma of 67P/Churyumov-Gerasimenko

    Science.gov (United States)

    Cessateur, Gaël; De Keyser, Johan; Maggiolo, Romain; Gibbons, Andrew; Gronoff, Guillaume; Gunell, Herbert; Dhooghe, Frederik; Loreau, Jérôme; Vaeck, Nathalie; Altwegg, Kathrin; Bieler, Andre; Briois, Christelle; Calmonte, Ursina; Combi, Michael; Fuselier, Stephen; Gombosi, Tamas; Haessig, Myrtha; Le Roy, Lena; Neefs, Eddy; Rubin, Martin

    2016-04-01

    We present here a chemistry-emission coupled model to study the production and loss mechanisms of the O(1D) and O(1S) states, for comet 67P/Churyumov-Gerasimenko. The recent discovery of O2 in significant abundance relative to water (3.80% +/- 0.85%, Bieler et al. 2015) within the coma of 67P has been taken into consideration for the first time in such models. We evaluate the effect of the presence of O2 on the green to red-doublet emission intensity ratio, which is traditionally used to assess the CO2 abundance within cometary atmospheres. Model simulations, solving the continuity equation with transport, show that not taking O2 into account leads to an underestimation of the CO2 abundance within 67P. This strongly suggests that the green to red-doublet emission intensity ratio alone is not a proper tool for determining the CO2 abundance, as previously suggested. O2 might indeed be a rather common and abundant parent species, following the re-analysis of the comet 1P/Halley data (Rubin et al. 2015). Therefore, it is likely that earlier determinations of the CO2 abundance in cometary atmospheres have to be revisited.

  8. Survival of Vibrio cholerae O1 on fomites

    DEFF Research Database (Denmark)

    Farhana, Israt; Hossain, Zenat Zebin; Tulsiani, Suhella Mohan;

    2016-01-01

    It is well established that the contamination sources of cholera causing bacteria, Vibrio cholerae, are water and food, but little is known about the transmission role of the fomites (surfaces that can carry pathogens) commonly used in households. In the absence of appropriate nutrients or growth...... conditions on fomites, bacteria have been known to assume a viable but non-culturable (VBNC) state after a given period of time. To investigate whether and when V. cholerae O1 assumes such a state, this study investigated the survival and viable quantification on a range of fomites such as paper, wood, glass......, plastic, cloth and several types of metals under laboratory conditions. The fomites were inoculated with an outbreak strain of V. cholerae and its culturability was examined by drop plate count method at 30 min intervals for up to 6 h. For molecular detection, the viable/dead stain ethidium monoazide (EMA...

  9. Analysis of a second bacteriophage hyaluronidase gene from Streptococcus pyogenes: evidence for a third hyaluronidase involved in extracellular enzymatic activity.

    OpenAIRE

    Hynes, W L; Hancock, L; Ferretti, J J

    1995-01-01

    The hyaluronidase gene (hylP2) from a second group A streptococcal bacteriophage was isolated from ATCC T-type-22 hyaluronidase-producing strain 10403, a strain known to produce increased amounts of extracellular hyaluronidase. Sequence analysis of hylP2 and alignment with the previously described bacteriophage hyaluronidase gene (hylP) showed a high degree of similarity; however, hylP2 had deletions of regions specifying 34 amino acids. Twenty-eight of the deleted amino acids were in a regio...

  10. Identification of Quaternary Structure and Functional Domains of the CI Repressor from Bacteriophage TP901-1

    DEFF Research Database (Denmark)

    Pedersen, Margit; Lo Leggio, Leila; Grossmann, J. Günter;

    2008-01-01

    The bacteriophage-encoded repressor protein plays a key role in determining the life cycle of a temperate phage following infection of a sensitive host. The repressor protein Cl, which is encoded by the temperate lactococcal phage TP901-1, represses transcription from both the lytic promoter P...... the protein is involved in the interaction with host proteins. By using small-angle X-ray scattering, we show for the first time the overall solution structure of a full-length wild-type bacteriophage repressor at low resolution revealing that the TP901-1 repressor forms a flat oligomer, most probably...

  11. Assembly-associated structural changes of bacteriophage T7 capsids. Detection by use of a protein-specific probe.

    OpenAIRE

    Khan, S. A.; Griess, G A; Serwer, P

    1992-01-01

    To detect changes in capsid structure that occur when a preassembled bacteriophage T7 capsid both packages and cleaves to mature-size longer (concatameric) DNA, the kinetics and thermodynamics are determined here for the binding of the protein-specific probe, 1,1'-bi(4-anilino)naphthalene-5,5'-di-sulfonic acid (bis-ANS), to bacteriophage T7, a T7 DNA deletion (8.4%) mutant, and a DNA-free T7 capsid (metrizamide low density capsid II) known to be a DNA packaging intermediate that has a permeab...

  12. Screening tumor-targeting bacteriophage particles by pre-clearing phage display

    International Nuclear Information System (INIS)

    Phage display technique provides a powerful approach for the discovery of new tumor-specific peptides. However, the peptides isolated through this technique usually did not possess high tumor-specific property. A pre-clearing step was introduced to increase the efficiency of biopanning by removal of particles that could interact with ubiquitously expressed cellular receptors in the non-target organs. The randomized Ph. D-CX7C phage library (Phage III) was first pre-cleared in normal mice to reduce vasculature- or organ-targeting phages to get the pre-cleared phage library, and then the tumor-targeting bacteriophage particles (Phage I) were screened from pre-clearing phage library in S180 tumor-bearing mice.The biodistribution results of 99mTc-labeled phages in mice bearing S180 tumor show that the uptake of 99mTc-labeled Phage I in tumor is high but low in normal organs, and the tumor-to-liver and tumor-to-spleen ratios of 99mTc-labeled Phage I are higher than those of 99mTc-labeled Phage II (tumor-specific phages screened from the original CX7C library) and Phage III (unscreened phages from the original CX7C library). It indicates that the yield of tumor-targeting bacteriophage particles could be improved and the non-specific binding in organs becomes weak. Consequently, the pre-clearing phage display method could improve the yield of positive hits by reducing the non-target organ accumulation of bacteriophage particles. (authors)

  13. Biochemical characterization of a thermostable HNH endonuclease from deep-sea thermophilic bacteriophage GVE2.

    Science.gov (United States)

    Zhang, Likui; Huang, Yanchao; Xu, Dandan; Yang, Lixiang; Qian, Kaicheng; Chang, Guozhu; Gong, Yong; Zhou, Xiaojian; Ma, Kesen

    2016-09-01

    His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity and are found in all kingdoms of life. Although HNH endonucleases from mesophiles have been widely investigated, the biochemical functions of HNH endonucleases from thermophilic bacteriophages remain unknown. Here, we characterized the biochemical properties of a thermostable HNH endonuclease from deep-sea thermophilic bacteriophage GVE2. The recombinant GVE2 HNH endonuclease exhibited non-specific cleavage activity at high temperature. The optimal temperature of the GVE2 HNH endonuclease for cleaving DNA was 60-65 °C, and the enzyme retained its DNA cleavage activity even after heating at 100 °C for 30 min, suggesting the enzyme is a thermostable endonuclease. The GVE2 HNH endonuclease cleaved DNA over a wide pH spectrum, ranging from 5.5 to 9.0, and the optimal pH for the enzyme activity was 8.0-9.0. Furthermore, the GVE2 HNH endonuclease activity was dependent on a divalent metal ion. While the enzyme is inactive in the presence of Cu(2+), the GVE2 HNH endonuclease displayed cleavage activity of varied efficiency with Mn(2+), Mg(2+), Ca(2+), Fe(2+), Co(2+), Zn(2+), and Ni(2+). The GVE2 HNH endonuclease activity was inhibited by NaCl. This study provides the basis for determining the role of this endonuclease in life cycle of the bacteriophage GVE2 and suggests the potential application of the enzyme in molecular biology and biotechnology. PMID:27131500

  14. Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater.

    Science.gov (United States)

    Calero-Cáceres, William; Muniesa, Maite

    2016-05-15

    The emergence and prevalence of antibiotic resistance genes (ARGs) in the environment is a serious global health concern. ARGs from bacteria can be mobilized by mobile genetic elements, and recent studies indicate that phages and phage-derived particles, among others, could play a role in the spread of ARGs through the environment. ARGs are abundant in the bacterial and bacteriophage fractions of water bodies and for successful transfer of the ARGs, their persistence in these environments is crucial. In this study, three ARGs (blaTEM, blaCTX-M and sul1) that naturally occur in the bacterial and phage fractions of raw wastewater were used to evaluate the persistence of ARGs at different temperatures (4 °C, 22 °C and 37 °C) and pH values (3, 7 and 9), as well as after various disinfection treatments (thermal treatment, chlorination and UV) and natural inactivation in a mesocosm. Gene copies (GC) were quantified by qPCR; then the logarithmic reduction and significance of the differences between their numbers were evaluated. The ARGs persisted for a long time with minimal reductions after all the treatments. In general, they showed greater persistence in the bacteriophage fraction than in the bacterial fraction. Comparisons showed that the ARGs persisted under conditions that reduced culturable Escherichia coli and infectious coliphages below the limit of detection. The prevalence of ARGs, particularly in the bacteriophage fraction, poses the threat of the spread of ARGs and their incorporation into a new bacterial background that could lead to the emergence of new resistant clones. PMID:26978717

  15. Environmental Factors Influencing Numbers of Rhizobium leguminosarum biovar trifolii and Its Bacteriophages in Two Field Soils

    OpenAIRE

    Lawson, Kerrie A.; Barnet, Yvonne M.; McGilchrist, Clyde A.

    1987-01-01

    Fluctuations in numbers of Rhizobium leguminosarum biovar trifolii and its bacteriophages in two fields with different soil types were followed during a 17-month period in 1981 and 1982. Mean levels of both phage and rhizobia varied significantly (P < 0.05) on different occasions, with rhizobial levels varying from 1.6 × 102 to 2.0 × 104 cell per g of soil and phage from 0 to 1.7 × 104 PFU/g of soil. Multivariate regression analysis showed rhizobial levels to be significantly and positively r...

  16. Extraction and Study of Bacteriophages, Used against Agents of Potato Soft Rot

    Directory of Open Access Journals (Sweden)

    Magda D. Davitashvili

    2012-12-01

    Full Text Available The use of specific bacteriophages and their complex mixtures against bacterial diseases is very effective. As for causative agent of potato soft rot Erwinia carotovora, specific phages (25 phages in total were extracted from diseased potato, soil and sewage. The study of their biological properties showed the diversity of phages in terms of lytic action, virion plaque and morphology, as well as in relation to different environmental factors. Phages showed explicit antibacterial activity in vitro in liquid and solid media, as well as during model tests of potato tubers artificial inoculation.

  17. The role of template superhelicity in the initiation of bacteriophage lambda DNA replication.

    OpenAIRE

    Alfano, C; McMacken, R

    1988-01-01

    The prepriming steps in the initiation of bacteriophage lambda DNA replication depend on the action of the lambda O and P proteins and on the DnaB helicase, single-stranded DNA binding protein (SSB), and DnaJ and DnaK heat shock proteins of the E. coli host. The binding of multiple copies of the lambda O protein to the phage replication origin (ori lambda) initiates the ordered assembly of a series of nucleoprotein structures that form at ori lambda prior to DNA unwinding, priming and DNA syn...

  18. Isolation of Acanthamoeba-Specific Antibodies from a Bacteriophage Display Library

    Science.gov (United States)

    Khan, Naveed A.; Greenman, John; Topping, Katherine P.; Hough, Victoria C.; Temple, Graham S.; Paget, Timothy A.

    2000-01-01

    Acanthamoeba causes opportunistic eye infections in humans, which can lead to severe keratitis and may ultimately result in blindness. Current methods for identifying this organism rely on culture and microscopy. In this paper, we describe the isolation of antibody fragments that can be used for the unequivocal identification of Acanthamoeba. A bacteriophage antibody display library was used to isolate antibody fragments that bind specifically to Acanthamoeba. Individual clones were studied by enzyme-linked immunosorbent assay, flow cytometry, and immunofluorescence. Four antibody clones that specifically bind to Acanthamoeba spp. were identified. PMID:10835006

  19. [Studies on the repair of damaged DNA in bacteriophage, bacterial and mammalian systems]: Final report

    International Nuclear Information System (INIS)

    This study sought to exploit the use of uv radiation as a source of genomic damage. We explored the molecular mechanism of the repair of DNA damage at a number of different levels of biological organization, by investigating bacteriophage, bacterial, yeast and mammalian cells. Not only have observations obtained in one biological system suggested specific experimental approaches in others, but we have also learned that some biochemical pathways for DNA repair are unique to specific organisms. Our studies are summarized in terms of 4 major areas of research activity that span the past 16 years. 86 refs

  20. The bacteriophage T4 regA gene: primary sequence of a translational repressor.

    OpenAIRE

    Trojanowska, M.; Miller, E S; Karam, J; Stormo, G; Gold, L

    1984-01-01

    The regA gene product of bacteriophage T4 is an autogenously controlled translational regulatory protein that plays a role in differential inhibition (translational repression) of a subpopulation of T4-encoded "early" mRNA species. The structural gene for this polypeptide maps within a cluster of phage DNA replication genes, (genes 45-44-62-regA-43-42), all but one of which (gene 43) are under regA-mediated translational control. We have cloned the T4 regA gene, determined its nucleotide sequ...

  1. Primary structure and functional analysis of the lysis genes of Lactobacillus gasseri bacteriophage phi adh.

    OpenAIRE

    Henrich, B; Binishofer, B; Bläsi, U

    1995-01-01

    The lysis genes of the Lactobacillus gasseri bacteriophage phi adh were isolated by complementation of a lambda Sam mutation in Escherichia coli. Nucleotide sequencing of a 1,735-bp DNA fragment revealed two adjacent coding regions of 342 bp (hol) and 951 bp (lys) in the same reading frame which appear to belong to a common transcriptional unit. Proteins corresponding to the predicted gene products, holin (12.9 kDa) and lysin (34.7 kDa), were identified by in vitro and in vivo expression of t...

  2. Bacteriophage lambda DNA packaging: scanning for the terminal cohesive end site during packaging.

    OpenAIRE

    Feiss, M; Widner, W

    1982-01-01

    Bacteriophage lambda packages the DNA of the related phage 21 poorly [Hohn, B. (1975) J. Mol. Biol. 98, 93--106]. To understand the nature of the packaging defect, the interaction of the cohesive end site (cos) specific for phage 21 (cos phi 21) with phage lambda terminase has been investigated. The ability of lambda terminase to cleave cos phi 21 was studied in vitro; lambda terminase cleaved cos phi 21 only 1% as well as it cleaved the phage lambda cohesive end site (cos lambda). In vitro p...

  3. Novel application of bacteriophage for controlling foaming in wastewater treatment plant- an eco-friendly approach.

    Science.gov (United States)

    Khairnar, Krishna; Chandekar, Rajshree; Nair, Aparna; Pal, Preeti; Paunikar, Waman N

    2016-01-01

    This addendum to "Novel application of bacteriophage for controlling foaming in wastewater treatment plant- an eco-friendly approach " includes characteristics of the phages NOC1, NOC2 and NOC3 not discussed in the previous paper. The phage adsorption and host interaction properties, their sensitivity to pH and temperature are inferred. NOC2 is seen to be more temperature resistant while others are not. All the phages show pH sensitivity. There is a variance observed in the behavior of these phages. Also, applicability of the phage based system to large scale reactors is studied and discussed here. PMID:26890996

  4. Cloning and expression of the gene for bacteriophage T7 RNA polymerase.

    OpenAIRE

    Davanloo, P; Rosenberg, A H; Dunn, J J; Studier, F W

    1984-01-01

    The complete coding sequence of the gene for bacteriophage T7 RNA polymerase (T7 gene 1) has been cloned in the plasmid pBR322. Large amounts of active enzyme can be accumulated in Escherichia coli when the cloned gene is transcribed from the lac UV5 promoter. A protease activity that apparently can nick the protein without causing it to fall apart can be a problem during purification, but a procedure is described that gives good yields of essentially homogeneous, highly active enzyme suitabl...

  5. Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harbouring a CRISPR-like Cas4 protein

    Directory of Open Access Journals (Sweden)

    Ian F. Connerton

    2015-01-01

    Full Text Available Campylobacter jejuni is a worldwide cause of human diarrhoeal disease. Clustered Repetitively Interspaced Palindromic Repeats (CRISPRs and associated proteins allow Bacteria and Archaea to evade bacteriophage and plasmid infection. Type II CRISPR systems are found in association with combinations of genes encoding the CRISPR-associated Cas1, Cas2, Cas4 or Csn2, and Cas9 proteins. C. jejuni possesses a minimal subtype II-C CRISPR system containing cas1, cas2, and cas9 genes whilst cas4 is notably absent. Cas4 proteins possess 5ʹ-3ʹ exonuclease activity to create recombinogenic-ends for spacer acquisition. Here we report a conserved Cas4-like protein in Campylobacter bacteriophages that creates a novel split arrangement between the bacteriophage and host that represents a new twist in the bacteriophage/host co-evolutionary arms race. The continuous association of bacteriophage and host in the carrier state life cycle of C. jejuni provided an opportunity to study spacer acquisition in this species. Remarkably all the spacer sequences observed were of host origin. We hypothesise that Campylobacter bacteriophages can use Cas4-like protein to activate spacer acquisition to use host DNA as an effective decoy to bacteriophage DNA. Bacteria that acquire self-spacers and escape phage infection must overcome CRISPR-mediated autoimmunity either by loss of the interference functions leaving them susceptible to foreign DNA incursion or tolerate changes in gene regulation.

  6. Associations between Forkhead Box O1 (FoxO1 Expression and Indicators of Hepatic Glucose Production in Transition Dairy Cows Supplemented with Dietary Nicotinic Acid.

    Directory of Open Access Journals (Sweden)

    Asako Kinoshita

    Full Text Available Forkhead box protein O1 (FoxO1 is a transcription factor which promotes hepatic glucose production (HGP by up-regulating the transcription of gluconeogenic enzymes in monogastric species. The activity of FoxO1 is inhibited by insulin-induced phosphorylation. The aims of the present study were to find associations between FoxO1 expression and variables associated with HGP as affected by feeding regimen in dairy cows during the transition period. Twenty one healthy German Holstein cows were allocated to four groups (LC-CON, HC-CON, LC-NA with 5 cows/group and HC-NA with 6 cows/group, respectively. Cows received 0 (LC-CON and HC-CON or 24 (LC-NA and HC-NA g/d nicotinic acid with high (HC or low (LC concentrate proportion from -42 days (-41.8 + 4.8; mean + standard deviation relative to expected calving date (d-42 to d24. Liver biopsy was taken at d-42, 1, 21, and 100. The total protein expression of FoxO1 (tFoxO1 and the extent of phosphorylation of FoxO1 at serine 256 (pFoxO1 were analysed semiquantitatively by Western Blotting. The expression of hepatic mRNA of FoxO1 and seven genes associated with HGP was measured by real-time RT-PCR. Mixed model and Pearson's correlation were used for statistical evaluation with the level of significance at P<0.05. No dietary effect was observed either on feed intake, energy balance, or on the concentration of blood metabolites. Neither time nor diet affected the expression of FoxO1 total protein and mRNA. A NA × concentrate interaction was found in pFoxO1. However, no corresponding dietary effect was found in the mRNA expression of investigated genes. Different patterns of correlations between FoxO1-related variables and investigated indicators for HGP were found at d21 and 100. The results indicated that the regulation of HGP did not take place on the levels of mRNA and protein expression and the phosphorylation of FoxO1 in dairy cows in early lactation.

  7. The Vibrio parahaemolyticus-infecting bacteriophage qdvp001: genome sequence and endolysin with a modular structure.

    Science.gov (United States)

    Wang, Weiyu; Li, Mengzhe; Lin, Hong; Wang, Jingxue; Mao, Xiangzhao

    2016-10-01

    Vibrio parahaemolyticus, a marine pathogen, is a causative agent of gastroenteritis in humans after consumption of contaminated seafood. In recent years, infections with V. parahaemolyticus have become an increasingly frequent factor in microbial food poisoning; therefore, it is urgent to figure out ways to control Vibrio parahaemolyticus. Endolysins, lytic enzymes encoded by bacteriophages, have been regarded as a therapeutic alternative to antibiotics in control of bacterial growth and have been successfully utilized in various areas. Here, we report the full genome sequence of the novel phage qdvp001, which lyses Vibrio parahaemolyticus 17802. The qdvp001 genome consists of a 134,742-bp DNA with a G+C content of 35.35 % and 227 putative open reading frames. Analysis revealed that the qdvp001 open reading frames encoded various putative functional proteins with a putative endolysin gene (ORF 60). No holin genes were identified in qdvp001. ORF 60 was cloned and expressed. The results showed that the purified endolysin Lysqdvp001 had a high hydrolytic activity toward Vibrio parahaemolyticus and a broader spectrum compared to that of the parental bacteriophage qdvp001. Thus, purified endolysin Lysqdvp001 has a potential to be used as an antibacterial agent in the future. PMID:27376376

  8. Bacteriophage Mediates Efficient Gene Transfer in Combination with Conventional Transfection Reagents

    Directory of Open Access Journals (Sweden)

    Amanda Donnelly

    2015-12-01

    Full Text Available The development of commercially available transfection reagents for gene transfer applications has revolutionized the field of molecular biology and scientific research. However, the challenge remains in ensuring that they are efficient, safe, reproducible and cost effective. Bacteriophage (phage-based viral vectors have the potential to be utilized for general gene transfer applications within research and industry. Yet, they require adaptations in order to enable them to efficiently enter cells and overcome mammalian cellular barriers, as they infect bacteria only; furthermore, limited progress has been made at increasing their efficiency. The production of a novel hybrid nanocomplex system consisting of two different nanomaterial systems, phage vectors and conventional transfection reagents, could overcome these limitations. Here we demonstrate that the combination of cationic lipids, cationic polymers or calcium phosphate with M13 bacteriophage-derived vectors, engineered to carry a mammalian transgene cassette, resulted in increased cellular attachment, entry and improved transgene expression in human cells. Moreover, addition of a targeting ligand into the nanocomplex system, through genetic engineering of the phage capsid further increased gene expression and was effective in a stable cell line generation application. Overall, this new hybrid nanocomplex system (i provides enhanced phage-mediated gene transfer; (ii is applicable for laboratory transfection processes and (iii shows promise within industry for large-scale gene transfer applications.

  9. Key residues of S. flexneri OmpA mediate infection by bacteriophage Sf6.

    Science.gov (United States)

    Porcek, Natalia B; Parent, Kristin N

    2015-05-22

    Many viruses, including bacteriophage, have the inherent ability to utilize several types of proteinaceous receptors as an attachment mechanism to infect cells, yet the molecular mechanisms that drive receptor binding have not been elucidated. Using bacteriophage Sf6 and its host, Shigella flexneri, we investigated how Sf6 utilizes outer membrane protein A (OmpA) for infection. Specifically, we identified that surface loops of OmpA mediate Shigella infection. We further characterized which residues in the surface loops are responsible for Sf6 binding and productive infection using a combination of in vivo and in vitro approaches including site-directed mutagenesis, phage plaque assays, circular dichroism spectroscopy, and in vitro genome ejection assays. Our data indicate that Sf6 can productively interact with other bacterial OmpAs as long as they share homology in loops 2 and 4, suggesting that these loops may determine host specificity. Our data provide a model in which Sf6 interacts with OmpA using the surface of the protein and new insights into viral attachment through binding to membrane protein receptors. PMID:25816773

  10. Small regulatory RNAs in lambdoid bacteriophages and phage-derived plasmids: Not only antisense.

    Science.gov (United States)

    Nejman-Faleńczyk, Bożena; Bloch, Sylwia; Licznerska, Katarzyna; Felczykowska, Agnieszka; Dydecka, Aleksandra; Węgrzyn, Alicja; Węgrzyn, Grzegorz

    2015-03-01

    Until recently, only two small regulatory RNAs encoded by lambdoid bacteriophages were known. These transcripts are derived from paQ and pO promoters. The former one is supposed to act as an antisense RNA for expression of the Q gene, encoding a transcription antitermination protein. The latter transcript, called oop RNA, was initially proposed to have a double role, in establishing expression of the cI gene and in providing a primer for DNA replication. Although the initially proposed mechanisms by which oop RNA could influence the choice between two alternative developmental pathways of the phage and the initiation of phage DNA replication were found not true, the pO promoter has been demonstrated to be important for both regulation of phage development and control of DNA replication. Namely, the pO-derived transcript is an antisense RNA for expression of the cII gene, and pO is a part of a dual promoter system responsible for regulation of initiation of DNA synthesis from the oriλ region. Very recent studies identified a battery of small RNAs encoded by lambdoid bacteriophages existing as prophages in chromosomes of enterohemorrhagic Escherichia coli strains. Some of them have very interesting functions, like anti-small RNAs. PMID:25111672

  11. Translesion synthesis is the main component of SOS repair in bacteriophage lambda DNA

    International Nuclear Information System (INIS)

    Agents that interfere with DNA replication in Escherichia coli induce physiological adaptations that increase the probability of survival after DNA damage and the frequency of mutants among the survivors (the SOS response). Such agents also increase the survival rate and mutation frequency of irradiated bacteriophage after infection of treated bacteria, a phenomenon known as Weigle reactivation. In UV-irradiated single-stranded DNA phage, Weigle reactivation is thought to occur via induced, error-prone replication through template lesions. Weigle reactivation occurs with higher efficiency in double-stranded DNA phages such as lambda, and we therefore asked if another process, recombination between partially replicated daughter molecules, plays a major role in this case. To distinguish between translesion synthesis and recombinational repair, we studied the early replication of UV-irradiated bacteriophage lambda in SOS-induced and uninduced bacteria. To avoid complications arising from excision of UV lesions, we used bacterial uvrA mutants, in which such excision does not occur. Our evidence suggests that translesion synthesis is the primary component of Weigle reactivation of lambda phage in the absence of excision repair. The greater efficiency in Weigle reactivation of double-stranded DNA phage could thus be attributed to some inducible excision repair unable to occur on single-stranded DNA. In addition, after irradiation, lambda phage replication seems to switch prematurely from the theta mode to the rolling circle mode

  12. Induction and characterization of a lysogenic bacteriophage of Lactococcus garvieae isolated from marine fish species.

    Science.gov (United States)

    Hoai, T D; Yoshida, T

    2016-07-01

    This study investigated the presence of prophages in Lactococcus garvieae isolated from several marine fish species in Japan. Representative strains of 16 bacterial genotypes (S1-S16) selected from more than 400 L. garvieae isolates were used to induce lysogenic bacteriophages. These strains were treated with 500 ng mL(-1) freshly prepared mitomycin C. A cross-spotting assay was performed to validate the lysogenic and indicator strains. The lysogenic strains were selected for isolation and concentration of the phages. Phage DNA was digested with EcoRI for biased sinusoidal field gel electrophoresis analysis. Polymerase chain reaction (PCR) was used to detect integrated prophage DNA. Of the 16 representative bacterial genotypes, 12 strains integrated prophages as indicated by the PCR assay, and 10 phages were detected and isolated using two indicator bacterial strains. Analysis of genomic DNA showed that these phages were homologous and named as PLgT-1. Transmission electron microscopy revealed that the morphology of PLgT-1 was consistent with the virus family Siphoviridae. PCR analysis of the prophage DNA revealed that all of the S1 genotype strains were lysogenic (30/30), but none of the S16 genotype strains were lysogenic (0/30). This is the first study to investigate lysogenic bacteriophages from L. garvieae. PMID:26471724

  13. Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes.

    Science.gov (United States)

    Subirats, Jéssica; Sànchez-Melsió, Alexandre; Borrego, Carles M; Balcázar, José Luis; Simonet, Pascal

    2016-08-01

    A metagenomics approach was applied to explore the presence of antibiotic resistance genes (ARGs) in bacteriophages from hospital wastewater. Metagenomic analysis showed that most phage sequences affiliated to the order Caudovirales, comprising the tailed phage families Podoviridae, Siphoviridae and Myoviridae. Moreover, the relative abundance of ARGs in the phage DNA fraction (0.26%) was higher than in the bacterial DNA fraction (0.18%). These differences were particularly evident for genes encoding ATP-binding cassette (ABC) and resistance-nodulation-cell division (RND) proteins, phosphotransferases, β-lactamases and plasmid-mediated quinolone resistance. Analysis of assembled contigs also revealed that blaOXA-10, blaOXA-58 and blaOXA-24 genes belonging to class D β-lactamases as well as a novel blaTEM (98.9% sequence similarity to the blaTEM-1 gene) belonging to class A β-lactamases were detected in a higher proportion in phage DNA. Although preliminary, these findings corroborate the role of bacteriophages as reservoirs of resistance genes and thus highlight the necessity to include them in future studies on the emergence and spread of antibiotic resistance in the environment. PMID:27312355

  14. Characterization of a novel non-specific nuclease from thermophilic bacteriophage GBSV1

    Directory of Open Access Journals (Sweden)

    Zhang Xiaobo

    2008-04-01

    Full Text Available Abstract Background Thermostable enzymes from thermophiles have attracted extensive studies. In this investigation, a nuclease-encoding gene (designated as GBSV1-NSN was obtained from a thermophilic bacteriophage GBSV1 for the first time. Results After recombinant expression in Escherichia coli, the purified GBSV1-NSN exhibited non-specific nuclease activity, being able to degrade various nucleic acids, including RNA, single-stranded DNA and double-stranded DNA that was circular or linear. Based on sequence analysis, the nuclease shared no homology with any known nucleases, suggesting that it was a novel nuclease. The characterization of the recombinant GBSV1-NSN showed that its optimal temperature and pH were 60°C and 7.5, respectively. The results indicated that the enzymatic activity was inhibited by enzyme inhibitors or detergents, such as ethylene diamine tetraacetic acid, citrate, dithiothreitol, β-mercaptoethanol, guanidine hydrochloride, urea and SDS. In contrast, the nuclease activity was enhanced by TritonX-100, Tween-20 or chaps to approximately 124.5% – 141.6%. The Km of GBSV1-NSN nuclease was 231, 61 and 92 μM, while its kcat was 1278, 241 and 300 s-1 for the cleavage of dsDNA, ssDNA and RNA, respectively. Conclusion Our study, therefore, presented a novel thermostable non-specific nuclease from thermophilic bacteriophage and its overexpression and purification for scientific research and applications.

  15. Structural basis for RNA-genome recognition during bacteriophage Qβ replication

    DEFF Research Database (Denmark)

    Olesen, Heidi Gytz; Mohr, Durita; Seweryn, Paulina; Yoshimura, Yuichi; Kutlubaeva, Zarina; Dolman, Fleur; Chelchessa, Bosene; Chetverin, Alexander B; Mulder, Frans A A; Brodersen, Ditlev E; Knudsen, Charlotte R

    2015-01-01

    Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crys......Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X...... the ability of Qβ replicase to amplify the genomic RNA in vitro. In contrast, replication of smaller replicable RNAs is not affected. Taken together, our data suggest that the β-subunit and protein S1 cooperatively bind the (+)-stranded Qβ genome during replication initiation and provide a foundation...... for understanding template discrimination during replication initiation....

  16. Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673▿†

    Science.gov (United States)

    Kropinski, Andrew M.; Arutyunov, Denis; Foss, Mary; Cunningham, Anna; Ding, Wen; Singh, Amit; Pavlov, Andrey R.; Henry, Matthew; Evoy, Stephane; Kelly, John; Szymanski, Christine M.

    2011-01-01

    Campylobacter jejuni continues to be the leading cause of bacterial food-borne illness worldwide, so improvements to current methods used for bacterial detection and disease prevention are needed. We describe here the genome and proteome of C. jejuni bacteriophage NCTC 12673 and the exploitation of its receptor-binding protein for specific bacterial detection. Remarkably, the 135-kb Myoviridae genome of NCTC 12673 differs greatly from any other proteobacterial phage genome described (including C. jejuni phages CP220 and CPt10) and instead shows closest homology to the cyanobacterial T4-related myophages. The phage genome contains 172 putative open reading frames, including 12 homing endonucleases, no visible means of packaging, and a putative trans-splicing intein. The phage DNA appears to be strongly associated with a protein that interfered with PCR amplification and estimation of the phage genome mass by pulsed-field gel electrophoresis. Identification and analyses of the receptor-binding protein (Gp48) revealed features common to the Salmonella enterica P22 phage tailspike protein, including the ability to specifically recognize a host organism. Bacteriophage receptor-binding proteins may offer promising alternatives for use in pathogen detection platforms. PMID:21965409

  17. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174

    Directory of Open Access Journals (Sweden)

    Christopher W. Baker

    2016-04-01

    Full Text Available Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones’ phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.

  18. Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17

    International Nuclear Information System (INIS)

    The C-terminal domain of the bacteriophage T7 fibre protein gp17, consisting of amino acids 371–553, has been crystallized. Diffraction data have been obtained to around 2.0 Å resolution from two different crystal forms. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress. Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of amino acids 371–553 has been expressed, purified and crystallized. Crystals of two forms were obtained, belonging to space group P212121 (unit-cell parameters a = 61.2, b = 86.0, c = 118.4 Å) and space group C2221 (unit-cell parameters a = 68.3, b = 145.6, c = 172.1 Å). They diffracted to 1.9 and 2.0 Å resolution, respectively. Both crystals are expected to contain one trimer in the asymmetric unit. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress

  19. Microbiological study of bacteriophage induction in the presence of chemical stress factors in enhanced biological phosphorus removal (EBPR).

    Science.gov (United States)

    Motlagh, Amir Mohaghegh; Bhattacharjee, Ananda S; Goel, Ramesh

    2015-09-15

    Polyphosphate accumulating organisms (PAOs) are responsible for carrying the enhanced biological phosphorus removal (EBPR). Although the EBPR process is well studied, the failure of EBPR performance at both laboratory and full-scale plants has revealed a lack of knowledge about the ecological and microbiological aspects of EBPR processes. Bacteriophages are viruses that infect bacteria as their sole host. Bacteriophage infection of polyphosphate accumulating organisms (PAOs) has not been considered as a main contributor to biological phosphorus removal upsets. This study examined the effects of different stress factors on the dynamics of bacteriophages and the corresponding effects on the phosphorus removal performance in a lab-scale EBPR system. The results showed that copper (heavy metal), cyanide (toxic chemical), and ciprofloxacin (antibiotic), as three different anthropogenic stress factors, can induce phages integrated onto bacterial genomes (i.e. prophages) in an enriched EBPR sequencing batch reactor, resulting in a decrease in the polyphosphate kinase gene ppk1 clades copy number, phosphorus accumulation capacity, and phosphorus removal performance. This study opens opportunities for further research on the effects of bacteriophages in nutrient cycles both in controlled systems such as wastewater treatment plants and natural ecosystems. PMID:26024959

  20. Prophylactic Bacteriophage Administration More Effective than Post-infection Administration in Reducing Salmonella enterica serovar Enteritidis Shedding in Quail.

    Science.gov (United States)

    Ahmadi, Mosab; Karimi Torshizi, M Amir; Rahimi, Shaban; Dennehy, John J

    2016-01-01

    Infections caused by Salmonella bacteria, often through poultry products, are a serious public health issue. Because of drawbacks associated with antibiotic prophylaxis, alternative treatments are sought. Bacterial viruses (bacteriophages) may provide an effective alternative, but concerns remain with respect to bacteriophage stability and effectiveness. To this end, we assessed the stability of a novel bacteriophage isolated from poultry excreta, siphovirus PSE, and its effectiveness in reducing Salmonella enterica serovar Enteritidis colonization in vitro and in vivo. Moreover, we sought to determine how the timing (prophylactic or therapeutic) and route (oral gavage or vent lip) of PSE administration impacted its effectiveness. Here we report that significant quantities of viable PSE bacteriophages were recovered following exposure to high and low pH, high temperatures, and bile salts, testifying to its ability to survive extreme conditions. In addition, we found that ileal lactic acid bacteria and Streptococcus spp. counts increased, but colibacilli and total aerobe counts decreased, in quail receiving phage PSE through both oral gavage and vent lip routes. In other experiments, we assessed the efficiency of PSE administration, in both prophylactic and therapeutic contexts, via either oral gavage or vent lip administration, on S. Enteritidis colonization of quail cecal tonsils. Our results demonstrate that administration of PSE as a preventive agent could reduce the S. Enteritidis colonization more effectively than post-challenge administration. Furthermore, oral administration of PSE phage is a more effective prophylactic tool for reduction of S. Enteritidis shedding in poultry than is vent lip administration. PMID:27555842

  1. A bacteriophage T4 in vitro system to clone long DNA molecules. Final report, June 1, 1990--January 31, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Rao, V.B.

    1997-09-01

    A summary is presented of the following objectives: development of a bacteriophage T4 in vitro system, and techniques to clone long segments of foreign DNA; development of a giant prohead DNA packaging system that could potentially be used to clone even a megabase size DNA; and development of techniques to rapidly map the cloned DNA inserts.

  2. Variation of resistance and infectivity between Pseudomonas fluorescens SBW25 and bacteriophage Ф2 and its therapeutic implications

    Institute of Scientific and Technical Information of China (English)

    Hanchen; Chen; Guohua; Chen

    2015-01-01

    <正>Dear Editor,Studies of the coevolutionary dynamics between Pseudomonas fluorescens SBW25 and bacteriophageФ2 can explore host resistance and parasite infectivity with applications in the ecological and therapeutic fields.Coevolutionary dynamics determine the efficacy of phage-based therapy.In the study described here,bacterial resistance and phage infectivity fluctuated with culture

  3. Effective inhibition of lytic development of bacteriophages λ, P1 and T4 by starvation of their host, Escherichia coli

    Directory of Open Access Journals (Sweden)

    Węgrzyn Alicja

    2007-02-01

    Full Text Available Abstract Background Bacteriophage infections of bacterial cultures cause serious problems in genetic engineering and biotechnology. They are dangerous not only because of direct effects on the currently infected cultures, i.e. their devastation, but also due to a high probability of spreading the phage progeny throughout a whole laboratory or plant, which causes a real danger for further cultivations. Therefore, a simple method for quick inhibition of phage development after detection of bacterial culture infection should be very useful. Results Here, we demonstrate that depletion of a carbon source from the culture medium, which provokes starvation of bacterial cells, results in rapid inhibition of lytic development of three Escherichia coli phages, λ, P1 and T4. Since the effect was similar for three different phages, it seems that it may be a general phenomenon. Moreover, similar effects were observed in flask cultures and in chemostats. Conclusion Bacteriophage lytic development can be inhibited efficiently by carbon source limitation in bacterial cultures. Thus, if bacteriophage contamination is detected, starvation procedures may be recommended to alleviate deleterious effects of phage infection on the culture. We believe that this strategy, in combination with the use of automated and sensitive bacteriophage biosensors, may be employed in the fermentation laboratory practice to control phage outbreaks in bioprocesses more effectively.

  4. Development of prototypes of bioactive packaging materials based on immobilized bacteriophages for control of growth of bacterial pathogens in foods.

    Science.gov (United States)

    Lone, Ayesha; Anany, Hany; Hakeem, Mohammed; Aguis, Louise; Avdjian, Anne-Claire; Bouget, Marina; Atashi, Arash; Brovko, Luba; Rochefort, Dominic; Griffiths, Mansel W

    2016-01-18

    Due to lack of adequate control methods to prevent contamination in fresh produce and growing consumer demand for natural products, the use of bacteriophages has emerged as a promising approach to enhance safety of these foods. This study sought to control Listeria monocytogenes in cantaloupes and RTE meat and Escherichia coli O104:H4 in alfalfa seeds and sprouts under different storage conditions by using specific lytic bacteriophage cocktails applied either free or immobilized. Bacteriophage cocktails were introduced into prototypes of packaging materials using different techniques: i) immobilizing on positively charged modified cellulose membranes, ii) impregnating paper with bacteriophage suspension, and iii) encapsulating in alginate beads followed by application of beads onto the paper. Phage-treated and non-treated samples were stored for various times and at temperatures of 4°C, 12°C or 25°C. In cantaloupe, when free phage cocktail was added, L. monocytogenes counts dropped below the detection limit of the plating technique (format (immobilized or non-immobilized (free)). In conclusion, the developed phage-based materials demonstrated significant antimicrobial effect, when applied to the artificially contaminated foods, and can be used as prototypes for developing bioactive antimicrobial packaging materials capable of enhancing the safety of fresh produce and RTE meat. PMID:26490649

  5. Prophylactic Bacteriophage Administration More Effective than Post-infection Administration in Reducing Salmonella enterica serovar Enteritidis Shedding in Quail

    Science.gov (United States)

    Ahmadi, Mosab; Karimi Torshizi, M. Amir; Rahimi, Shaban; Dennehy, John J.

    2016-01-01

    Infections caused by Salmonella bacteria, often through poultry products, are a serious public health issue. Because of drawbacks associated with antibiotic prophylaxis, alternative treatments are sought. Bacterial viruses (bacteriophages) may provide an effective alternative, but concerns remain with respect to bacteriophage stability and effectiveness. To this end, we assessed the stability of a novel bacteriophage isolated from poultry excreta, siphovirus PSE, and its effectiveness in reducing Salmonella enterica serovar Enteritidis colonization in vitro and in vivo. Moreover, we sought to determine how the timing (prophylactic or therapeutic) and route (oral gavage or vent lip) of PSE administration impacted its effectiveness. Here we report that significant quantities of viable PSE bacteriophages were recovered following exposure to high and low pH, high temperatures, and bile salts, testifying to its ability to survive extreme conditions. In addition, we found that ileal lactic acid bacteria and Streptococcus spp. counts increased, but colibacilli and total aerobe counts decreased, in quail receiving phage PSE through both oral gavage and vent lip routes. In other experiments, we assessed the efficiency of PSE administration, in both prophylactic and therapeutic contexts, via either oral gavage or vent lip administration, on S. Enteritidis colonization of quail cecal tonsils. Our results demonstrate that administration of PSE as a preventive agent could reduce the S. Enteritidis colonization more effectively than post-challenge administration. Furthermore, oral administration of PSE phage is a more effective prophylactic tool for reduction of S. Enteritidis shedding in poultry than is vent lip administration. PMID:27555842

  6. Spectroscopic analysis of the oligosaccharides produced by bacteriophage-borne enzyme action on Klebsiella K36 polysaccharide

    International Nuclear Information System (INIS)

    Mass spectral analysis of the permethylated oligossacharides obtained by bacteriophage degradation of Klebsiella K36 polysaccharide has enabled the sequence of sugar residues to be determined. 2D N.m.r. studies confirmed the inter-sugar linkages and established the anomeric configurations

  7. Utilization of Lambda bacteriophage as an Apoptin effective delivery platform to the BT-474 human breast carcinoma

    Directory of Open Access Journals (Sweden)

    Narmin Ghaderi

    2014-02-01

    Conclusion: Utilization of recombinant Lambda bacteriophage as a safe expression vector has been confirmed. Apoptin was induced apoptosis specifically in the tumors in vivo. Use of such construct is a very safe way to treat cancer in human. The results presented here reveal important features of λ nanobioparticles to serve as safe delivery and expression platform for human cancer therapy.

  8. Poly(N-isopropylacrylamide-co-allylamine) (PNIPAM-co-ALA) nanospheres for the thermally triggered release of Bacteriophage K.

    Science.gov (United States)

    Hathaway, Hollie; Alves, Diana R; Bean, Jessica; Esteban, Patricia P; Ouadi, Khadija; Sutton, J Mark; Jenkins, A Toby A

    2015-10-01

    Due to the increased prevalence of resistant bacterial isolates which are no longer susceptible to antibiotic treatment, recent emphasis has been placed on finding alternative modes of treatment of wound infections. Bacteriophage have long been investigated for their antimicrobial properties, yet the utilization of phage therapy for the treatment of wound infections relies on a suitable delivery system. Poly(N-isopropylacrylamide) (PNIPAM) is a thermally responsive polymer which undergoes a temperature dependent phase transition at a critical solution temperature. Bacteriophage K has been successfully formulated with PNIPAM nanospheres copolymerized with allylamine (PNIPAM-co-ALA). By utilizing a temperature responsive polymer it has been possible to engineer the nanospheres to collapse at an elevated temperature associated with a bacterial skin infection. The nanogels were reacted with surface deposited maleic anhydride in order to anchor the nanogels to non-woven fabric. Bacteriophage incorporated PNIPAM-co-ALA nanospheres demonstrated successful bacterial lysis of a clinically relevant bacterial isolate - Staphylococcus aureus ST228 at 37°C, whilst bacterial growth was unaffected at 25°C, thus providing a thermally triggered release of bacteriophage. PMID:26423908

  9. Bacteriophage Isolated from Feedlot Cattle Can Reduce Escherichia coli O157:H7 Populations in Ruminant Gastrointestinal Tracts

    Science.gov (United States)

    Foodborne pathogenic bacteria, such as Escherichia coli O157:H7, can live undetected in the gut of food animals and be spread to humans via consumption of contaminated meat, direct animal contact, or water runoff into drinking and crop irrigation water supplies. Bacteriophages are viruses that prey...

  10. Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34

    International Nuclear Information System (INIS)

    The crystallization of three C-terminal fragments of the bacteriophage T4 protein gp34 is reported. Diffraction data have been obtained for three native crystal forms and two selenomethionine derivatives, one of which contained high-quality anomalous signal

  11. Associations between Forkhead Box O1 (FoxO1) Expression and Indicators of Hepatic Glucose Production in Transition Dairy Cows Supplemented with Dietary Nicotinic Acid.

    Science.gov (United States)

    Kinoshita, Asako; Locher, Lena; Tienken, Reka; Meyer, Ulrich; Dänicke, Sven; Rehage, Jürgen; Huber, Korinna

    2016-01-01

    Forkhead box protein O1 (FoxO1) is a transcription factor which promotes hepatic glucose production (HGP) by up-regulating the transcription of gluconeogenic enzymes in monogastric species. The activity of FoxO1 is inhibited by insulin-induced phosphorylation. The aims of the present study were to find associations between FoxO1 expression and variables associated with HGP as affected by feeding regimen in dairy cows during the transition period. Twenty one healthy German Holstein cows were allocated to four groups (LC-CON, HC-CON, LC-NA with 5 cows/group and HC-NA with 6 cows/group, respectively). Cows received 0 (LC-CON and HC-CON) or 24 (LC-NA and HC-NA) g/d nicotinic acid with high (HC) or low (LC) concentrate proportion from -42 days (-41.8 + 4.8; mean + standard deviation) relative to expected calving date (d-42) to d24. Liver biopsy was taken at d-42, 1, 21, and 100. The total protein expression of FoxO1 (tFoxO1) and the extent of phosphorylation of FoxO1 at serine 256 (pFoxO1) were analysed semiquantitatively by Western Blotting. The expression of hepatic mRNA of FoxO1 and seven genes associated with HGP was measured by real-time RT-PCR. Mixed model and Pearson's correlation were used for statistical evaluation with the level of significance at Pdairy cows in early lactation. PMID:26800252

  12. Survival of Vibrio cholerae O1 on fomites.

    Science.gov (United States)

    Farhana, Israt; Hossain, Zenat Zebin; Tulsiani, Suhella Mohan; Jensen, Peter Kjær Mackie; Begum, Anowara

    2016-09-01

    It is well established that the contamination sources of cholera causing bacteria, Vibrio cholerae, are water and food, but little is known about the transmission role of the fomites (surfaces that can carry pathogens) commonly used in households. In the absence of appropriate nutrients or growth conditions on fomites, bacteria have been known to assume a viable but non-culturable (VBNC) state after a given period of time. To investigate whether and when V. cholerae O1 assumes such a state, this study investigated the survival and viable quantification on a range of fomites such as paper, wood, glass, plastic, cloth and several types of metals under laboratory conditions. The fomites were inoculated with an outbreak strain of V. cholerae and its culturability was examined by drop plate count method at 30 min intervals for up to 6 h. For molecular detection, the viable/dead stain ethidium monoazide (EMA) which inhibits amplification of DNA from dead cells was used in combination with real-time polymerase chain reaction (EMA-qPCR) for direct quantitative analyses of viable V. cholerae at 2, 4, 6, 24 h and 7 day time intervals. Results showed that V. cholerae on glass and aluminum surfaces lost culturability within one hour after inoculation but remained culturable on cloth and wood for up to four hours. VBNC V. cholerae on dry fomite surfaces was detected and quantified by EMA-qPCR even 7 days after inoculation. In conclusion, the prolonged survival of V. cholerae on various household fomites may play vital role in cholera transmission and needs to be further investigated. PMID:27430513

  13. Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae.

    Directory of Open Access Journals (Sweden)

    Nikolay V Volozhantsev

    Full Text Available Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium responsible for human food-borne disease as well as non-food-borne human, animal and poultry diseases. Because bacteriophages or their gene products could be applied to control bacterial diseases in a species-specific manner, they are potential important alternatives to antibiotics. Consequently, poultry intestinal material, soil, sewage and poultry processing drainage water were screened for virulent bacteriophages that lysed C. perfringens. Two bacteriophages, designated ΦCPV4 and ΦZP2, were isolated in the Moscow Region of the Russian Federation while another closely related virus, named ΦCP7R, was isolated in the southeastern USA. The viruses were identified as members of the order Caudovirales in the family Podoviridae with short, non-contractile tails of the C1 morphotype. The genomes of the three bacteriophages were 17.972, 18.078 and 18.397 kbp respectively; encoding twenty-six to twenty-eight ORF's with inverted terminal repeats and an average GC content of 34.6%. Structural proteins identified by mass spectrometry in the purified ΦCP7R virion included a pre-neck/appendage with putative lyase activity, major head, tail, connector/upper collar, lower collar and a structural protein with putative lysozyme-peptidase activity. All three podoviral bacteriophage genomes encoded a predicted N-acetylmuramoyl-L-alanine amidase and a putative stage V sporulation protein. Each putative amidase contained a predicted bacterial SH3 domain at the C-terminal end of the protein, presumably involved with binding the C. perfringens cell wall. The predicted DNA polymerase type B protein sequences were closely related to other members of the Podoviridae including Bacillus phage Φ29. Whole-genome comparisons supported this relationship, but also indicated that the Russian and USA viruses may be unique members of the sub-family Picovirinae.

  14. Purification and characterization of pili of a Vibrio cholerae non-O1 strain.

    OpenAIRE

    Yamashiro, T.; Nakasone, N; Iwanaga, M

    1993-01-01

    Pili of the Vibrio cholerae non-O1 strain V10 were purified and characterized. The V10 pili were physicochemically and immunologically different from those of the previously reported V. cholerae non-O1 strain S7, although the pili of the two strains had homologous N-terminal amino acid sequences. V10 plus antigen was detected only in V. cholerae non-O1 strains.

  15. Isolation and Characterization of a Virulent Bacteriophage AB1 of Acinetobacter baumannii

    Directory of Open Access Journals (Sweden)

    Jia Shiru

    2010-04-01

    Full Text Available Abstract Background Acinetobacter baumannii is an emerging nosocomial pathogen worldwide with increasing prevalence of multi-drug and pan-drug resistance. A. baumannii exists widely in natural environment, especially in health care settings, and has been shown difficult to be eradicated. Bacteriophages are often considered alternative agent for controlling bacterial infection and contamination. In this study, we described the isolation and characterization of one virulent bacteriophage AB1 capable of specifically infecting A. baumannii. Results A virulent bacteriophage AB1, specific for infecting a clinical strain A. baumannii KD311, was first isolated from marine sediment sample. Restriction analysis indicated that phage AB1 was a dsDNA virus with an approximate genome size of 45.2 kb to 46.9 kb. Transmission electron microscopy showed that phage AB1 had an icosahedral head with a non-contractile tail and collar or whisker structures, and might be tentatively classified as a member of the Siphoviridae family. Proteomic pattern of phage AB1, generated by SDS-PAGE using purified phage particles, revealed five major bands and six minor bands with molecular weight ranging from 14 to 80 kilo-dalton. Also determined was the adsorption rate of phage AB1 to the host bacterium, which was significantly enhanced by addition of 10 mM CaCl2. In a single step growth test, phage AB1 was shown having a latent period of 18 minutes and a burst size of 409. Moreover, pH and thermal stability of phage AB1 were also investigated. At the optimal pH 6.0, 73.2% of phages survived after 60 min incubation at 50°C. When phage AB1 was used to infect four additional clinical isolates of A. baumannii, one clinical isolate of Stenotrophomonas maltophilia, and Pseudomonas aeruginosa lab strains PAK and PAO1, none of the tested strains was found susceptible, indicating a relatively narrow host range for phage AB1. Conclusion Phage AB1 was capable of eliciting efficient lysis

  16. The Bacteriophage Carrier State of Campylobacter jejuni Features Changes in Host Non-coding RNAs and the Acquisition of New Host-derived CRISPR Spacer Sequences

    Science.gov (United States)

    Hooton, Steven P. T.; Brathwaite, Kelly J.; Connerton, Ian F.

    2016-01-01

    Incorporation of self-derived CRISPR DNA protospacers in Campylobacter jejuni PT14 occurs in the presence of bacteriophages encoding a CRISPR-like Cas4 protein. This phenomenon was evident in carrier state infections where both bacteriophages and host are maintained for seemingly indefinite periods as stable populations following serial passage. Carrier state cultures of C. jejuni PT14 have greater aerotolerance in nutrient limited conditions, and may have arisen as an evolutionary response to selective pressures imposed during periods in the extra-intestinal environment. A consequence of this is that bacteriophage and host remain associated and able to survive transition periods where the chances of replicative success are greatly diminished. The majority of the bacteriophage population do not commit to lytic infection, and conversely the bacterial population tolerates low-level bacteriophage replication. We recently examined the effects of Campylobacter bacteriophage/C. jejuni PT14 CRISPR spacer acquisition using deep sequencing strategies of DNA and RNA-Seq to analyze carrier state cultures. This approach identified de novo spacer acquisition in C. jejuni PT14 associated with Class III Campylobacter phages CP8/CP30A but spacer acquisition was oriented toward the capture of host DNA. In the absence of bacteriophage predation the CRISPR spacers in uninfected C. jejuni PT14 cultures remain unchanged. A distinct preference was observed for incorporation of self-derived protospacers into the third spacer position of the C. jejuni PT14 CRISPR array, with the first and second spacers remaining fixed. RNA-Seq also revealed the variation in the synthesis of non-coding RNAs with the potential to bind bacteriophage genes and/or transcript sequences. PMID:27047470

  17. Thermodynamic Database for the NdO(1.5)-YO(1.5)-YbO(1.5)-ScO(1.5)-ZrO2 System

    Science.gov (United States)

    Jacobson, Nathan S.; Copland, Evan H.; Kaufman, Larry

    2001-01-01

    A database for YO(1.5)-NdO(1.5)-YbO(1.5)-ScO(1.5)-ZrO2 for ThermoCalc (ThermoCalc AB, Stockholm, Sweden) has been developed. The basis of this work is the YO(1.5)-ZrO2 assessment by Y. Du, Z. Jin, and P. Huang, 'Thermodynamic Assessment of the ZrO2-YO(1.5) System'. Experimentally only the YO(1.5)-ZrO2 system has been well-studied. All other systems are only approximately known. The major simplification in this work is the treatment of each single cation unit as a component. The pure liquid oxides are taken as reference states and two term lattice stability descriptions are used for each of the components. The limited experimental phase diagrams are reproduced.

  18. Multiparametric atomic force microscopy imaging of single bacteriophages extruding from living bacteria.

    Science.gov (United States)

    Alsteens, David; Trabelsi, Heykel; Soumillion, Patrice; Dufrêne, Yves F

    2013-01-01

    Force-distance (FD) curve-based atomic force microscopy is a valuable tool to simultaneously image the structure and map the biophysical properties of biological samples at the nanoscale. Traditionally, FD-based atomic force microscopy has been severely limited by its poor temporal and lateral resolutions. Here we report the use of advanced FD-based technology combined with biochemically sensitive tips to image filamentous bacteriophages extruding from living bacteria at unprecedented speed and resolution. Directly correlated multiparametric images of the structure, adhesion and elasticity of infected bacteria demonstrate that the sites of assembly and extrusion localize at the bacterial septum in the form of soft nanodomains surrounded by stiff cell wall material. The quantitative nano-bio-imaging method presented here offers a wealth of opportunities for mapping the physical properties and molecular interactions of complex biosystems, from viruses to tissues. PMID:24336094

  19. Isolation of a lytic bacteriophage against virulent Aeromonas hydrophila from an organized equine farm.

    Science.gov (United States)

    Anand, Taruna; Vaid, Rajesh Kumar; Bera, Bidhan Ch; Singh, Jitender; Barua, Sanjay; Virmani, Nitin; K, Rajukumar; Yadav, Neeraj Kumar; Nagar, Dinesh; Singh, Raj K; Tripathi, B N

    2016-04-01

    A bacteriophage (VTCCBPA6) against a pathogenic strain of Aeromonas hydrophila was isolated from the sewage of an organized equine breeding farm. On the basis of TEM analysis, phage belonged to family Myoviridae. PCR amplification and sequence analysis of gp23 gene (encoding for major capsid protein) revealed phylogenetic resemblance to T4 like virus genus. Protein profiling by SDS-PAGE also indicated its resemblance to T4 like phage group. However, the comparison of its gp23 gene sequence with previously reported phages showed similarity with T4-like phages infecting Enterobacteriaceae instead of Aeromonas spp. Thus, to our knowledge, this report points toward the fact that a novel/evolved phage might exist in equine environment against A. hydrophila, which can be potentially used as a biocontrol agent. PMID:26748732

  20. Environmental Factors Influencing Numbers of Rhizobium leguminosarum biovar trifolii and Its Bacteriophages in Two Field Soils.

    Science.gov (United States)

    Lawson, K A; Barnet, Y M; McGilchrist, C A

    1987-05-01

    Fluctuations in numbers of Rhizobium leguminosarum biovar trifolii and its bacteriophages in two fields with different soil types were followed during a 17-month period in 1981 and 1982. Mean levels of both phage and rhizobia varied significantly (P soil and phage from 0 to 1.7 x 10 PFU/g of soil. Multivariate regression analysis showed rhizobial levels to be significantly and positively related to vegetation height and solar radiation, but not to mean temperature, precipitation, soil matric potential, or soil type. Rhizobiophage concentrations were significantly and positively related to soil matric potential and vegetation height. They were reduced in the silty clay loam soil, although the presence of 34% clay did not prevent phage multiplication and the occurrence of high phage levels. PMID:16347339

  1. Characterization of the novel T4-like Salmonella enterica bacteriophage STP4-a and its endolysin.

    Science.gov (United States)

    Li, Meng; Li, Mengzhe; Lin, Hong; Wang, Jingxue; Jin, Yanqiu; Han, Feng

    2016-02-01

    While screening for new antimicrobial agents for multidrug-resistant Salmonella enterica, the novel lytic bacteriophage STP4-a was isolated and characterized. Phage morphology revealed that STP4-a belongs to the family Myoviridae. Bacterial challenge assays showed that different serovars of Salmonella enterica were susceptible to STP4-a infection. The genomic characteristics of STP4-a, containing 159,914 bp of dsDNA with an average GC content of 36.86 %, were determined. Furthermore, the endolysin of STP4-a was expressed and characterized. The novel endolysin, LysSTP4, has hydrolytic activity towards outer-membrane-permeabilized S. enterica and Escherichia coli. These results provide essential information for the development of novel phage-based biocontrol agents against S. enterica. PMID:26563319

  2. Isolation of Balamuthia mandrillaris-specific antibody fragments from a bacteriophage antibody display library.

    Science.gov (United States)

    Siddiqui, Ruqaiyyah; Kulsoom, Huma; Lalani, Salima; Khan, Naveed Ahmed

    2016-07-01

    Balamuthia mandrillaris is a protist pathogen that can cause encephalitis with a mortality rate of more than 95%. Early diagnosis followed by aggressive treatment is a pre-requisite for successful prognosis. Current methods for identifying this organism rely on culture and microscopy, antibody-based methods using animals, or involve the use of molecular tools that are expensive. Here, we describe the isolation of antibody fragments that can be used for the unequivocal identification of B. mandrillaris. B. mandrillaris-specific antibody fragments were isolated from a bacteriophage antibody display library. Individual clones were studied by enzyme-linked immunosorbent assay, and immunofluorescence. Four antibody clones showed specific binding to B. mandrillaris. The usefulness of phage antibody display technology as a diagnostic tool for isolating antibody fragments against B. mandrillaris antigens and studying their biological role(s) is discussed further. PMID:27055361

  3. Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor

    Science.gov (United States)

    Migliori, Amy D.; Keller, Nicholas; Alam, Tanfis I.; Mahalingam, Marthandan; Rao, Venigalla B.; Arya, Gaurav; Smith, Douglas E.

    2014-06-01

    How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.

  4. Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis.

    Science.gov (United States)

    Sauder, Amber Brooke; Quinn, McKenzie Rea; Brouillette, Alexis; Caruso, Steven; Cresawn, Steven; Erill, Ivan; Lewis, Lynn; Loesser-Casey, Kathryn; Pate, Morgan; Scott, Crystal; Stockwell, Stephanie; Temple, Louise

    2016-02-01

    Bacillus thuringiensis Kurstaki, a bacterium that is a source of biopesticides and a safe simulant for pathogenic Bacillus species, was used to isolate seven unique bacteriophages. The phage genomes were sequenced and ranged in size from 158,100 to 163,019bp encoding 290-299 genes, and the GC content of ~38% was similar to that of the host bacterium. All phages had terminal repeats 2-3kb long. Three of the phages encoded tRNAs and three contained a self-splicing intron in the DNA polymerase gene. They were categorized as a single cluster (>60% nucleotide conservation) containing three subclusters (>80% nucleotide conservation), supported by genomic synteny and phylogenetic analysis. Considering the published genomes of phages that infect the genus Bacillus and noting the ability of many of the Bacillus cereus group phages to infect multiple species, a clustering system based on gene content is proposed. PMID:26773385

  5. Simulation experiments of the effect of space environment on bacteriophage and DNA thin films

    Science.gov (United States)

    Fekete, A.; Ronto, Gy; Hegedus, M.; Modos, K.; Berces, A.; Kovacs, G.; Lammer, H.; Panitz, C.

    2004-01-01

    The main goal of PUR experiment (phage and uracil response) is to examine and quantify the effect of specific space conditions on nucleic acid models. To achieve this an improved method was elaborated for the preparation of DNA and bacteriophage thin films. The homogeneity of the films was controlled by UV spectroscopy and microscopy. To provide experimental evidence for the hypothesis that interplanetary transfer of the genetic material is possible, phage T7 and isolated T7 DNA thin films have been exposed to selected space conditions: intense UVC radiation (lambda=254 nm) and high vacuum (10(-4) Pa). The effects of DNA hydration, conformation and packing on UV radiation damage were examined. Characteristic changes in the absorption spectrum, in the electrophoretic pattern of DNA and the decrease of the amount of PCR products have been detected indicating the photodamage of isolated and intraphage DNA. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

  6. Picosecond laser UV inactivation of lambda bacteriophage and various Escherichia coli strains

    International Nuclear Information System (INIS)

    In this work the authors studied inactivation of bacteriophage lambda11 and three strains of Escherichia coli K12 under high-intensity picosecond laser UV irradiation. With the rise of UV irradiation intensity from 1010 W/m2 to 1013 W/m2 the photoresistance of these objects sharply increased: for lambda11 phage by 33-67 times depending on host-cell strain chosen, for different strains of E. coli by 13-476 times. Under picosecond UV irradiation of lambda11 the single-quantum and two-quantum photolesions made comparable contributions to the total lethal photoproduct. In the case of E. coli it was mainly two-quantum photolesions that brought about picosecond UV inactivation. (Auth.)

  7. Inactivation of bacteriophage lambda by near-ultraviolet irradiation in the presence of chlorpromazine

    International Nuclear Information System (INIS)

    Bacteriophage lambdasub(vir) was inactivated when it was irradiated with near-UV light in the presence of chlorpromazine. DNA strand breakage in the treated phage was indicated by alkaline sucrose gradient centrifugation. The number of the breaks was increased with increasing fluence. Although the inactivation rate was enhanced with a decreasing salt concentration in the reaction mixture and under a nitrogen atmosphere, the number of the strand breaks was not altered in either case. Therefore, the DNA strand breakage is not a sole lethal damage in the treated phage. The addition of NaN3 repressed the inactivation and the reaction in a D2O medium enhanced the inactivation even if the reaction mixture was irradiated under anaerobic conditions. Under anaerobic conditions, the inactivation occurs presumably via a radical mechanism. (author)

  8. Entropy Production Rate Changes in Lysogeny/Lysis Switch Regulation of Bacteriophage Lambda

    International Nuclear Information System (INIS)

    According to the chemical kinetic model of lysogeny/lysis switch in Escherichia coli (E. coli) infected by bacteriophage λ, the entropy production rates of steady states are calculated. The results show that the lysogenic state has lower entropy production rate than lytic state, which provides an explanation on why the lysogenic state of λ phage is so stable. We also notice that the entropy production rates of both lysogenic state and lytic state are lower than that of saddle-point and bifurcation state, which is consistent with the principle of minimum entropy production for living organism in nonequilibrium stationary state. Subsequently, the relations between CI and Cro degradation rates at two bifurcations and the changes of entropy production rate with CI and Cro degradation are deduced. The theory and method can be used to calculate entropy change in other molecular network. (interdisciplinary physics and related areas of science and technology)

  9. Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids.

    Directory of Open Access Journals (Sweden)

    Thorsten Hugel

    2007-03-01

    Full Text Available The bacteriophage phi29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of a portal motor complex. Several mechanical models for the generation of these high forces by the motor complex predict coupling of DNA translocation to rotation of the head-tail connector dodecamer. Putative connector rotation is investigated here by combining the methods of single-molecule force spectroscopy with polarization-sensitive single-molecule fluorescence. In our experiment, we observe motor function in several packaging complexes in parallel using video microscopy of bead position in a magnetic trap. At the same time, we follow the orientation of single fluorophores attached to the portal motor connector. From our data, we can exclude connector rotation with greater than 99% probability and therefore answer a long-standing mechanistic question.

  10. Structure, Dynamics, and Assembly of Filamentous Bacteriophages by Nuclear Magnetic Resonance Spectroscopy

    Science.gov (United States)

    Opella, Stanley J.; Zeri, Ana Carolina; Park, Sang Ho

    2008-05-01

    Filamentous bacteriophages serve as model systems for the development and implementation of spectroscopic methods suitable for biological supramolecular assemblies. Not only are their coat proteins small and readily prepared in the laboratory, but they also have two primary roles as membrane proteins and as the principal structural element of the virus particles. As a bacterial system, they are readily labeled with stable isotopes, and this has opened possibilities for the many nuclear magnetic resonance (NMR) studies described in this review. In particular, solid-state NMR of aligned samples has been used to determine the three-dimensional structures of both the membrane-bound forms of coat proteins in phospholipid bilayers and structural forms in virus particles, which has led to an analysis of the assembly mechanism for virus particles as they are extruded through the cell membrane.

  11. pH-induced stability switching of the bacteriophage HK97 maturation pathway.

    Science.gov (United States)

    May, Eric R; Arora, Karunesh; Brooks, Charles L

    2014-02-26

    Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to shifting the stability between the states along the pathway under differing pH conditions. We further analyze these data to establish the connection between critical residues and important structural motifs which undergo reorganization during maturation. We go on to show how DNA packaging can induce spontaneous reorganization of the capsid during maturation. PMID:24495192

  12. Tripartite associations among bacteriophage WO, Wolbachia, and host affected by temperature and age in Tetranychus urticae.

    Science.gov (United States)

    Lu, Ming-Hong; Zhang, Kai-Jun; Hong, Xiao-Yue

    2012-11-01

    A phage density model of cytoplasmic incompatibility (CI), which means lytic phages reduce bacterial density associated with CI, significantly enhances our understanding of the tripartite associations among bacteriophage WO, Wolbachia and host. However, WO may alternate between lytic and lysogenic life cycles or change phage production under certain conditions including temperature, host age and host species background. Here, extreme temperatures can induce an alteration in the life cycle of WO and change the tripartite associations among WO, Wolbachia and CI. Based on the accumulation of the WO load, WO can transform into the lytic life cycle with increasing age. These findings confirmed that the environment plays an important role in the associations among WO, Wolbachia and host. PMID:22669278

  13. Repair of ultraviolet light-induced DNA damage in cholera bacteriophages

    International Nuclear Information System (INIS)

    DNA repair-proficient and -deficient strains of Vibrio cholerae were used to examine host cell reactivation, Weigle reactivation and photoreactivation of u.v.-irradiated cholera bacteriophages. U.v. light-induced DNA damage in phages of different morphological and serological groups could be efficiently photoreactivated. Host cell reactivation of irradiated phages of different groups was different on the same indicator host. Phage phi149 was the most sensitive, and phi138 the most resistant to u.v. irradiation. While phi138 showed appreciable host cell reactivation, this was minimal for phi149. Attempts to demonstrate Weigle reactivation of u.v.-irradiated cholera phages were not successful, although u.v.-induced filamentation of host cells was observed. (author)

  14. Recovery status of bacteriophages of different livestock farms of Veterinary College, Adhartal, Jabalpur, India

    Directory of Open Access Journals (Sweden)

    Sanjay Shukla and S. D. Hirpurkar

    2011-06-01

    Full Text Available Study was conducted to know the presence of bacteriophage in sewage material which can play a very important role during therapy against the some antibiotic resistance organisms. During study waste water samples were collected from different depths of the wastewater collection tanks located in livestock farms of different species (Cattle, pig, goat and poultry. These samples were subjected primarily to rapid detection by streak plate method for the detection of lytic activity followed by primary isolation of phage against two most common bacteria of environment, namely, B. subtilis and E. coli by Double agar layer (DAL method. Recovery of phages was maximum from pig feces (67% followed by dairy cattle farm waste (63%, buffalo farm waste (50%, goat farm waste (13%. [Vet. World 2011; 4(3.000: 117-119

  15. The nucleotide sequence of threonine transfer RNA coded by bacteriophage T4

    International Nuclear Information System (INIS)

    The nucleotide sequence of a low molecular weight RNA coded by bacteriophage T4 (and previously identified as species α) has been determined. The molecule is of particular biological interest for its associated biosynthetic properties. This RNA is 76 nucleotides in length, contains eight modified bases, and can be arranged in a cloverleaf configuration common to tRNAs. The anticodon sequence is UGU, which corresponds to the threonine-specific codons ACsub(G)sup(A). The nucleotide sequence was determined primarily by nearest-neighbour analysis of RNA synthesized in vitro using [α-32P] nucleoside triphosphates. Using the single-strand specific nuclease S1, two in vivo labelled half-molecules were generated and analysed. This information together with restrictions imposed by nearest-neighbour data, provided a unique linear sequence of nucleotides with the features of secondary structure common to tRNA molecules. (author)

  16. Growth of Vibrio cholerae O1 Ogawa Eltor in freshwater.

    Science.gov (United States)

    Vital, Marius; Füchslin, Hans Peter; Hammes, Frederik; Egli, Thomas

    2007-07-01

    Growth of Vibrio cholerae O1 Ogawa Eltor was studied with a growth assay in which autoclaved and filtered (0.22 microm) freshwater was inoculated at low cell density (5 x 10(3) cells ml(-1)) and proliferation was followed with flow cytometry. Against the common view, V. cholerae was able to grow extensively in different kinds of freshwater. The bacterium multiplied in river water, lake water and effluent of a wastewater treatment plant up to a cell density of 1.55 x 10(6) cells ml(-1). In these samples, apparent assimilable organic carbon (AOC(app)) concentrations ranged from 52 up to 800 microg l(-1) and the results demonstrate a positive trend between the AOC(app) concentration and final cell concentration, suggesting that AOC was a key parameter governing growth of V. cholerae. No growth was observed in waters (tap and bottled drinking water) containing less than approximately 60 microg AOC(app) l(-1). When pure cultures of V. cholerae were grown on identical lake water at different temperatures (20, 25 and 30 degrees C) the maximum specific growth rates (micromax) achieved were 0.22 h(-1), 0.32 h(-1) and 0.45 h(-1), respectively. In addition, growth was characterized in lake water samples amended with different concentrations of NaCl. The highest micromax of V. cholerae was recorded at moderate salinity levels (5 g NaCl l(-1), micromax=0.84 h(-1)), whereas at 30 g NaCl l(-1) (micromax=0.30 h(-1)) or 0 g NaCl l(-1) (micromax)=0.40 h(-1)) specific growth rates were significantly reduced. In the water tested here, micro(max) of V. cholerae was always around 50 % of that exhibited by a freshwater community of indigenous bacteria enriched from the water sampling site. Direct batch competition experiments between V. cholerae and the lake water bacterial community were performed at different temperatures in which V. cholerae was enumerated in the total community using fluorescent-surface antibodies. In all cases V. cholerae was able to grow and constituted around 10

  17. A Novel Bacteriophage Targeting Cronobacter sakazakii Is a Potential Biocontrol Agent in Foods.

    Science.gov (United States)

    Lee, Ju-Hoon; Bai, Jaewoo; Shin, Hakdong; Kim, Yeran; Park, Bookyung; Heu, Sunggi; Ryu, Sangryeol

    2016-01-01

    Cronobacter sakazakii is an important pathogen that causes high mortality in infants. Due to its occasional antibiotic resistance, a bacteriophage approach might be an alternative effective method for the control of this pathogen. To develop a novel biocontrol agent using bacteriophages, the C. sakazakii-infecting phage CR5 was newly isolated and characterized. Interestingly, this phage exhibited efficient and relatively durable host lysis activity. In addition, a specific gene knockout study and subsequent complementation experiment revealed that this phage infected the host strain using the bacterial flagella. The complete genome sequence analysis of phage CR5 showed that its genome contains 223,989 bp of DNA, including 231 predicted open reading frames (ORFs), and it has a G+C content of 50.06%. The annotated ORFs were classified into six functional groups (structure, packaging, host lysis, DNA manipulation, transcription, and additional functions); no gene was found to be related to virulence or toxin or lysogen formation, but >80% of the predicted ORFs are unknown. In addition, a phage proteomic analysis using SDS-PAGE and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revealed that seven phage structural proteins are indeed present, supporting the ORF predictions. To verify the potential of this phage as a biocontrol agent against C. sakazakii, it was added to infant formula milk contaminated with a C. sakazakii clinical isolate or food isolate, revealing complete growth inhibition of the isolates by the addition of phage CR5 when the multiplicity of infection (MOI) was 10(5). PMID:26497465

  18. Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples.

    Science.gov (United States)

    Colomer-Lluch, Marta; Jofre, Juan; Muniesa, Maite

    2011-01-01

    Antibiotic resistance is an increasing global problem resulting from the pressure of antibiotic usage, greater mobility of the population, and industrialization. Many antibiotic resistance genes are believed to have originated in microorganisms in the environment, and to have been transferred to other bacteria through mobile genetic elements. Among others, β-lactam antibiotics show clinical efficacy and low toxicity, and they are thus widely used as antimicrobials. Resistance to β-lactam antibiotics is conferred by β-lactamase genes and penicillin-binding proteins, which are chromosomal- or plasmid-encoded, although there is little information available on the contribution of other mobile genetic elements, such as phages. This study is focused on three genes that confer resistance to β-lactam antibiotics, namely two β-lactamase genes (blaTEM and blaCTX-M9) and one encoding a penicillin-binding protein (mecA) in bacteriophage DNA isolated from environmental water samples. The three genes were quantified in the DNA isolated from bacteriophages collected from 30 urban sewage and river water samples, using quantitative PCR amplification. All three genes were detected in the DNA of phages from all the samples tested, in some cases reaching 104 gene copies (GC) of blaTEM or 102 GC of blaCTX-M and mecA. These values are consistent with the amount of fecal pollution in the sample, except for mecA, which showed a higher number of copies in river water samples than in urban sewage. The bla genes from phage DNA were transferred by electroporation to sensitive host bacteria, which became resistant to ampicillin. blaTEM and blaCTX were detected in the DNA of the resistant clones after transfection. This study indicates that phages are reservoirs of resistance genes in the environment. PMID:21390233

  19. Interplay of bacteria, bacteriophage, and Berea sandstone rock in relation to enhanced oil recovery

    Energy Technology Data Exchange (ETDEWEB)

    Chang, P.L.

    1986-01-01

    Much research and development is needed to recovery oil reserves presently unattainable, and biologically enhanced oil recovery is a technology that may be used for this purpose. To address the problem of bacterial contamination in an oil field injection well region, each end of a Teflon-sleeved Berea sandstone rock was connected to a flask containing nutrient medium. By inoculation one flask with Escherichia coli B, observations of the bacterial growth in the uninoculated flask resulting from the transport and establishment of cells across the rock could be made. Differences in bacterial populations occurred depending on whether bacteriophage T4D was first adsorbed to the rock. The results of these experiments indicate that the inhibition of bacterial establishment within a rock matrix is possible via lytic interaction. Some nonlytic effects are also implied by experiments with B/4 cells, which are T4D-resistant mutants of E. coli B. A 10 to 40% retention of T4 by the rock occurred when it was loaded with 10/sup 5/ to 10/sup 6/ PFU. Also proposed is a lysogenic system for possible use in biologically enhanced oil recovery techniques. In addition to the model bacteria and phage system described above, measurements of the passage of Pseudomonas putida. 12633 and a phage-resistant mutant through Berea sandstone rock were also made. When bacteriophage gh-1 was adsorbed within the rock matrix, a reduction in the passage of the susceptible but no the resistant cells through the rock was observed. The use of P. putida and gh-1 represents a more realistic group of experiments since these pseudomonas are ubiquitous soil bacteria commonly found in oil rock regions. Preliminary work on the degradation of certain nitrogen compounds in the context of biologically enhanced oil recovery is also described in this dissertation.

  20. The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22.

    Directory of Open Access Journals (Sweden)

    Justin C Leavitt

    Full Text Available The P22-like bacteriophages have short tails. Their virions bind to their polysaccharide receptors through six trimeric tailspike proteins that surround the tail tip. These short tails also have a trimeric needle protein that extends beyond the tailspikes from the center of the tail tip, in a position that suggests that it should make first contact with the host's outer membrane during the infection process. The base of the needle serves as a plug that keeps the DNA in the virion, but role of the needle during adsorption and DNA injection is not well understood. Among the P22-like phages are needle types with two completely different C-terminal distal tip domains. In the phage Sf6-type needle, unlike the other P22-type needle, the distal tip folds into a "knob" with a TNF-like fold, similar to the fiber knobs of bacteriophage PRD1 and Adenovirus. The phage HS1 knob is very similar to that of Sf6, and we report here its crystal structure which, like the Sf6 knob, contains three bound L-glutamate molecules. A chimeric P22 phage with a tail needle that contains the HS1 terminal knob efficiently infects the P22 host, Salmonella enterica, suggesting the knob does not confer host specificity. Likewise, mutations that should abrogate the binding of L-glutamate to the needle do not appear to affect virion function, but several different other genetic changes to the tip of the needle slow down potassium release from the host during infection. These findings suggest that the needle plays a role in phage P22 DNA delivery by controlling the kinetics of DNA ejection into the host.

  1. Bacteriophage Can Prevent Encrustation and Blockage of Urinary Catheters by Proteus mirabilis.

    Science.gov (United States)

    Nzakizwanayo, Jonathan; Hanin, Aurélie; Alves, Diana R; McCutcheon, Benjamin; Dedi, Cinzia; Salvage, Jonathan; Knox, Karen; Stewart, Bruce; Metcalfe, Anthony; Clark, Jason; Gilmore, Brendan F; Gahan, Cormac G M; Jenkins, A Toby A; Jones, Brian V

    2015-01-01

    Proteus mirabilis forms dense crystalline biofilms on catheter surfaces that occlude urine flow, leading to serious clinical complications in long-term catheterized patients, but there are presently no truly effective approaches to control catheter blockage by this organism. This study evaluated the potential for bacteriophage therapy to control P. mirabilis infection and prevent catheter blockage. Representative in vitro models of the catheterized urinary tract, simulating a complete closed drainage system as used in clinical practice, were employed to evaluate the performance of phage therapy in preventing blockage. Models mimicking either an established infection or early colonization of the catheterized urinary tract were treated with a single dose of a 3-phage cocktail, and the impact on time taken for catheters to block, as well as levels of crystalline biofilm formation, was measured. In models of established infection, phage treatment significantly increased time taken for catheters to block (∼3-fold) compared to untreated controls. However, in models simulating early-stage infection, phage treatment eradicated P. mirabilis and prevented blockage entirely. Analysis of catheters from models of established infection 10 h after phage application demonstrated that phage significantly reduced crystalline biofilm formation but did not significantly reduce the level of planktonic cells in the residual bladder urine. Taken together, these results show that bacteriophage constitute a promising strategy for the prevention of catheter blockage but that methods to deliver phage in sufficient numbers and within a key therapeutic window (early infection) will also be important to the successful application of phage to this problem. PMID:26711744

  2. Mutant bacteriophages, Frank Macfarlane Burnet, and the changing nature of "genespeak" in the 1930s.

    Science.gov (United States)

    Sankaran, Neeraja

    2010-01-01

    In 1936, Frank Macfarlane Burnet published a paper entitled "Induced lysogenicity and the mutation of bacteriophage within lysogenic bacteria," in which he demonstrated that the introduction of a specific bacteriophage into a bacterial strain consistently and repeatedly imparted a specific property - namely the resistance to a different phage - to the bacterial strain that was originally susceptible to lysis by that second phage. Burnet's explanation for this change was that the first phage was causing a mutation in the bacterium which rendered it and its successive generations of offspring resistant to lysogenicity. At the time, this idea was a novel one that needed compelling evidence to be accepted. While it is difficult for us today to conceive of mutations and genes outside the context of DNA as the physico-chemical basis of genes, in the mid 1930s, when this paper was published, DNA's role as the carrier of hereditary information had not yet been discovered and genes and mutations were yet to acquire physical and chemical forms. Also, during that time genes were considered to exist only in organisms capable of sexual modes of replication and the status of bacteria and viruses as organisms capable of containing genes and manifesting mutations was still in question. Burnet's paper counts among those pieces of work that helped dispel the notion that genes, inheritance and mutations were tied to an organism's sexual status. In this paper, I analyze the implications of Burnet's paper for the understanding of various concepts - such as "mutation," and "gene," - at the time it was published, and how those understandings shaped the development of the meanings of these terms and our modern conceptions thereof. PMID:20665082

  3. A modified MS2 bacteriophage plaque reduction assay for the rapid screening of antiviral plant extracts

    Directory of Open Access Journals (Sweden)

    Ian Cock

    2010-01-01

    Full Text Available Introduction: Traditional methods of screening plant extracts and purified components for antiviral activity require up to a week to perform, prompting the need to develop more rapid quantitative methods to measure the ability of plant based preparations to block viral replication. We describe an adaption of an MS2 plaque reduction assay for use in S. aureus. Results: MS2 bacteriophage was capable of infecting and replicating in B. cereus, S. aureus and F+ E. coli but not F- E. coli. Indeed, both B. cereus and S. aureus were more sensitive to MS2 induced lysis than F+ E. coli. When MS2 bacteriophage was mixed with Camellia sinensis extract (1 mg/ml, Scaevola spinescens extract (1 mg/ml or Aloe barbadensis juice and the mixtures inoculated into S. aureus, the formation of plaques was reduced to 8.9 ± 3.8%, 5.4 ± 2.4% and 72.7 ± 20.9% of the untreated MS2 control values respectively. Conclusions: The ability of the MS2 plaque reduction assay to detect antiviral activity in these known antiviral plant preparations indicates its suitability as an antiviral screening tool. An advantage of this assay compared with traditionally used cytopathic effect reduction assays and replicon based assays is the more rapid acquisition of results. Antiviral activity was detected within 24 h of the start of testing. The MS2 assay is also inexpensive and non-pathogenic to humans making it ideal for initial screening studies or as a simulant for pathogenic viruses.

  4. Structure of the Bacteriophage [phi]KZ Lytic Transglycosylase gp144

    Energy Technology Data Exchange (ETDEWEB)

    Fokine, Andrei; Miroshnikov, Konstantin A.; Shneider, Mikhail M.; Mesyanzhinov, Vadim V.; Rossmann, Michael G. (SOIBC); (Purdue)

    2008-04-02

    Lytic transglycosylases are enzymes that act on the peptidoglycan of bacterial cell walls. They cleave the glycosidic linkage between N-acetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anhydromuramoyl product. The x-ray structure of the lytic transglycosylase gp144 from the Pseudomonas bacteriophage {phi}KZ has been determined to 2.5-{angstrom} resolution. This protein is probably employed by the bacteriophage in the late stage of the virus reproduction cycle to destroy the bacterial cell wall to release the phage progeny. {phi}KZ gp144 is a 260-residue {alpha}-helical protein composed of a 70-residue N-terminal cell wall-binding domain and a C-terminal catalytic domain. The fold of the N-terminal domain is similar to the peptidoglycan-binding domain from Streptomyces albus G d-Ala-d-Ala carboxypeptidase and to the N-terminal prodomain of human metalloproteinases that act on extracellular matrices. The C-terminal catalytic domain of gp144 has a structural similarity to the catalytic domain of the transglycosylase Slt70 from Escherichia coli and to lysozymes. The gp144 catalytic domain has an elongated groove that can bind at least five sugar residues at sites A-E. As in other lysozymes, the peptidoglycan cleavage (catalyzed by Glu{sup 115} in gp144) occurs between sugar-binding subsites D and E. The x-ray structure of the {phi}KZ transglycosylase complexed with the chitotetraose (N-acetylglucosamine){sub 4} has been determined to 2.6-{angstrom} resolution. The N-acetylglucosamine residues of the chitotetraose bind in sites A-D.

  5. Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007

    Directory of Open Access Journals (Sweden)

    Goddeeris Bruno M

    2009-12-01

    Full Text Available Abstract Background Over the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is paucity of information concerning the diversity and occurrence of mobile genetic elements in Vibrio cholerae strains implicated in these outbreaks. A total of 65 Vibrio cholerae O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs, conjugative plasmids and for their genotypic relatedness. Results All the strains were haemolytic on 5% sheep blood and positive for the Vibrio cholerae El Tor-specific haemolysin toxin gene (hylA by PCR. They all contained strB, sulII, floR and the dfrA1 genes encoding resistance to streptomycin, sulfamethoxazole, chloramphenicol and trimethoprim respectively. These genes, together with an ICE belonging to the SXT/R391 family were transferable to the rifampicin-resistant E. coli C600 en bloc. All the strains were negative for integron class 1, 2 and 3 and for transposase gene of transposon Tn7 but were positive for integron class 4 and the trpM gene of transposon Tn21. No plasmids were isolated from any of the 65 strains. All the strains were also positive for all V. cholera El Tor pathogenic genes except the NAG- specific heat-stable toxin (st gene. None of the strains were positive for virulence genes associated with the V. cholerae classical biotype. All the strains were positive for El Tor-specific CTXphi bacteriophage rstrR repressor gene (CTXETΦ but negative for the Classical, Calcutta, and the Environmental repressor types. Pulse Field Gel Electrophoresis (PFGE showed that regardless of the year of isolation, all the strains bearing the SXT element were clonally related. Conclusions This study demonstrates that the V. cholerae O1 strains carrying an SXT/R391-like

  6. 26 CFR 31.3402(o)-1 - Extension of withholding to supplemental unemployment compensation benefits.

    Science.gov (United States)

    2010-04-01

    ... unemployment compensation benefits. 31.3402(o)-1 Section 31.3402(o)-1 Internal Revenue INTERNAL REVENUE SERVICE... of withholding to supplemental unemployment compensation benefits. (a) In general. Withholding of income tax is required under section 3402(o) with respect to payments of supplemental...

  7. O1群霍乱弧菌与人类疾病

    Institute of Scientific and Technical Information of China (English)

    王树坤; 李万林

    2001-01-01

    O1群霍乱弧菌(vibrio choleraer non-O1,简称非01菌)能引起人类散发腹泻已获得世界认同,但仅O1群霍乱弧菌(vibrio choleraer non-O1,简称01菌)能引起霍乱流行的看法一直沿袭到1992年,这年在印度和孟加拉国出现了由非O1菌的O139血清群霍乱弧菌(vibrio choleraer O139)引起的一次流行。

  8. Structures and rearrangement reactions of 4-aminophenol(H2O)1+ and 3-aminophenol(H2O)1+ clusters

    Science.gov (United States)

    Gerhards, M.; Jansen, A.; Unterberg, C.; Gerlach, A.

    2005-08-01

    In this paper the structures of 4-aminophenol(H2O)1+ and 3-aminophenol(H2O)1+ clusters are investigated in molecular beam experiments by different IR/UV-double resonance techniques as well as the mass analyzed threshold ionization spectroscopy yielding both inter- and intramolecular vibrations of the ionic and neutral species. Possible structures are extensively calculated at the level of density functional theory (DFT) or at the ab initio level of theory. From the experimental and theoretical investigations it can be concluded that in the case of 4-aminophenol(H2O)1 one O H⋯O hydrogen-bonded structure exists in the neutral cluster but two structures containing either an O H⋯O or a N H⋯O hydrogen-bonded arrangement are observed in the spectra of the ionic species. This observation is a result of an intramolecular rearrangement reaction within the ion which can only take place if high excess energies are used. A reaction path via the CH bonds is calculated and explains the experimental observations. In the case of 3-aminophenol(H2O)1+ only one O H⋯O bound structure is observed both in the neutral and ionic species. Ab initio and DFT calculations show that due to geometrical and energetical reasons a rearrangement cannot be observed in the 3-aminophenol(H2O)1+ cluster ion.

  9. Temperate bacteriophage ΦO18P from an Aeromonas media isolate: Characterization and complete genome sequence

    International Nuclear Information System (INIS)

    A group of 74 Aeromonas isolates from surface water of three ponds in Bielefeld, Germany was screened for prophage induction after UV irradiation. The phage ΦO18P was induced from the Aeromonas media isolate O18. ΦO18P belongs to the Myoviridae phage family. The complete nucleotide sequence of the double stranded DNA genome of bacteriophage ΦO18P consists of 33,985 bp. The genome has 5' protruding cohesive ends of 16 bases. On the ΦO18P genome 46 open reading frames (orfs) were identified which are organized in the modules integration and regulation, replication, head, packaging, tail and lysis. Additionally the phage DNA includes a methylase gene. Comparison of the genome architecture with those of other bacteriophages revealed significant similarities to the P2 phage family and especially to the prophages of Aeromonas salmonicida and the Vibrio cholerae phage K139

  10. Bacteriophage: laboratorial diagnosis and phage therapy Bacteriofagos: diagnóstico laboratorial e terapia fágica

    Directory of Open Access Journals (Sweden)

    Joas L. Da Silva

    2009-09-01

    Full Text Available Bacteriophages have been researched as a new alternative to antibiotics. These viruses inject their genetic material into bacteria and use their host machinery to multiply themselves. The research of bacteriophages in Brazil will certainly provide low-cost treatment of multidrug resistant bacteria, new microbiological diagnosis and advantages for the Brazilian food industry.Bacteriófagos têm sido pesquisados como uma alternativa ao uso de antibióticos. Estes vírus infectam as bactérias e utilizam a maquinaria celular para multiplicar o próprio material genético. O estudo de bacteriófagos no Brasil levará ao desenvolvimento de tratamentos de baixo custo, novos testes diagnósticos e vantagens para a industria alimentícia.

  11. Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.

    Science.gov (United States)

    Agirrezabala, Xabier; Velázquez-Muriel, Javier A; Gómez-Puertas, Paulino; Scheres, Sjors H W; Carazo, José M; Carrascosa, José L

    2007-04-01

    The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. Tailed bacteriophages are emerging as one such family, and we have studied the possible existence of the HK97-like fold in bacteriophage T7. The procapsid structure at approximately 10 A resolution was used to obtain a quasi-atomic model by fitting a homology model of the T7 capsid protein gp10 that was based on the atomic structure of the HK97 capsid protein. A number of fold similarities, such as the fitting of domains A and P into the L-shaped procapsid subunit, are evident between both viral systems. A different feature is related to the presence of the amino-terminal domain of gp10 found at the inner surface of the capsid that might play an important role in the interaction of capsid and scaffolding proteins. PMID:17437718

  12. The life cycles of the temperate lactococcal bacteriophage phiLC3 monitored by a quantitative PCR method.

    Science.gov (United States)

    Lunde, M; Blatny, J M; Kaper, F; Nes, I F; Lillehaug, D

    2000-11-01

    We present here a new and general approach for monitoring the life cycles of temperate bacteriophages which establish lysogeny by inserting their genomes site-specifically into the bacterial host chromosome. The method is based on quantitative amplification of specific DNA sites involved in various cut-and-join events during the life cycles of the phages (i.e. the cos, attP, attB, attL and attR sites) with the use of sequence-specific primers. By comparing the amounts of these specific DNA sites at different intervals, we were able to follow the development of the lytic and lysogenic life cycles of the temperate lactococcal bacteriophage phiLC3 after infection of its bacterial host Lactococcus lactis ssp. cremoris IMN-C18. PMID:11040439

  13. Genomic structure of bacteriophage 6H and its distribution as prophage in Flavobacterium psychrophilum strains

    DEFF Research Database (Denmark)

    Castillo Bermúdez, Daniel Elías; Espejo, Romilio; Middelboe, Mathias

    2014-01-01

    for the presence of four phage 6H genes (integrase, tail tape protein and two hypothetical proteins) by PCR showed the presence of these prophage genes in 80% of the isolates. In conclusion, we hypothesize that bacteriophage 6H belongs to an abundant group of temperate phages which has lysogenized a large fraction......Flavobacterium psychrophilum is currently one of the most devastating fish pathogens worldwide causing considerable economic losses in salmonid aquaculture. Recently, attention has been drawn to the use of phages for controlling F. psychrophilum, and phages infecting the pathogen have been isolated....... Here, we present the genome sequence of F. psychrophilum bacteriophage 6H and its distribution as prophage in F. psychrophilum isolates. The DNA sequence revealed a genome of 46 978 bp containing 63 predicted ORFs, of which 13% was assigned a putative function, including an integrase. Sequence analysis...

  14. Interrupted thymidylate synthase gene of bacteriophages T2 and T6 and other potential self-splicing introns in the T-even bacteriophages

    International Nuclear Information System (INIS)

    Southern hybridization analyses of procaryotic DNA from Escherchia coli, λ bacteriophage, and T1 to T7 phages were carried out. The hybridization probes used consisted of DNA restriction fragments derived from the T4 phage intron-containing thymidylate synthase gene (td) and short synthetic oligodeoxynucleotides defining specific exon and intron regions of the gene. It was shown that intact as well as restricted DNA from the T-even phages hybridized not only to both T4 phage td intron- and exon-specific probes but also to probes defining the td 5' (exon I-intron) and 3' (intron-exon II) presplice junctions. These data strongly suggest that, analogous to the T4 phage, only the T2 and T6 phages among the procaryotes tested contain interrupted td genes. The td intervening sequence in each phage is roughly 1 kilobase pair (kb) in size and interrupts the td gene at a site analogous to that in the T4 phage. This was confirmed by data from Northern (RNA) hybridization analysis of td-specific in vitro transcripts of these phage DNAs. [α-32P]GTP in vitro labeling of total RNA from T4 phage-infected cells produced five species of labeled RNAs that were 1, 0.9, 0.83, 0.75, and 0.6 kb in size. Only the 1-, 0.9-, and 0.75-kb species were labeled in RNA from T2- or T6-infected cells. The commonly present 1-kb RNA is the excised td intron, which exists in both linear and circular forms in the respective T-even-phage-infected cells, while the 0.6-kb RNA unique to T4 may be the excised intron derived from the ribonucleotide reductase small subunit gene (nrdB) of the phage. The remaining labeled RNA species are likely candidates for other self-splicing introns

  15. Structure and Energetics of Encapsidated DNA in Bacteriophage HK97 Studied by Scanning Calorimetry and Cryo-electron Microscopy

    OpenAIRE

    Duda, Robert L.; Ross, Philip D.; Cheng, Naiqian; Firek, Brian A.; Hendrix, Roger W.; Conway, James F; Steven, Alasdair C.

    2009-01-01

    Encapsidation of duplex DNA by bacteriophages represents an extreme case of genome condensation, reaching near-crystalline concentrations of DNA. The HK97 system is well suited to study this phenomenon in view of detailed knowledge of its capsid structure. To characterize the interactions involved, we combined calorimetry with cryo-EM and native gel electrophoresis. We found that, as in other phages, HK97 DNA is organized in coaxially wound nested shells. When scanned in buffer containing 1mM...

  16. Peering down the barrel of a bacteriophage portal - the genome packaging and release valve in P22

    OpenAIRE

    Tang, Jinghua; Lander, Gabriel C.; Olia, Adam; Li, Rui; Casjens, Sherwood; Prevelige, Peter; Cingolani, Gino; Baker, Timothy S.; Johnson, John E.

    2011-01-01

    The encapsidated genome in all double strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein dodecamer in place of five coat protein subunits. The portal orchestrates DNA packaging and exit, through a series of varying interactions with the scaffolding, terminase, and closure proteins. Here we report an asymmetric cryo-EM reconstruction of the entire P22 virion at 7.8-Å resolution. X-ray cr...

  17. Development and Optimization of a Novel Immunomagnetic Separation- Bacteriophage Assay for Detection of Salmonella enterica Serovar Enteritidis in Broth

    OpenAIRE

    Favrin, Stacy J.; Jassim, Sabah A.; Griffiths, Mansel W

    2001-01-01

    Salmonella is the second-leading cause of food-borne illness in most developed countries, causing diarrhea, cramps, vomiting, and often fever. Many rapid methods are available for detection of Salmonella in foods, but these methods are often insensitive or expensive or require a high degree of technical ability to perform. In this paper we describe development and characterization of a novel assay that utilizes the normal infection cycle of bacteriophage SJ2 for detection of Salmonella enteri...

  18. The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination.

    OpenAIRE

    Regeard Christophe; DuBow Michael S; Deschavanne Patrick

    2010-01-01

    Abstract Background Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification. Results Here, we proposed to use genome sequence signatur...

  19. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.

    OpenAIRE

    Boeke, J D; Model, P

    1982-01-01

    Gene III protein of bacteriophage f1 is inserted into the host cell membrane where it is assembled into phage particles. A truncated form of gene III protein, encoded by a recombinant plasmid and lacking the carboxyl terminus, does not remain in the membrane but instead appears to slip through it. Fusion of a hydrophobic "membrane anchor" from another membrane protein, the gene VIII protein, to the truncated gene III protein (by manipulation of the recombinant plasmid) restores membrane ancho...

  20. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

    OpenAIRE

    Koskella, B; Parr, N.

    2015-01-01

    © 2015 The Authors. Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host–parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation...

  1. Changes in Protein Domains outside the Catalytic Site of the Bacteriophage Qβ Replicase Reduce the Mutagenic Effect of 5-Azacytidine

    OpenAIRE

    Cabanillas, Laura; Sanjuán, Rafael; Lázaro, Ester

    2014-01-01

    The high genetic heterogeneity and great adaptability of RNA viruses are ultimately caused by the low replication fidelity of their polymerases. However, single amino acid substitutions that modify replication fidelity can evolve in response to mutagenic treatments with nucleoside analogues. Here, we investigated how two independent mutants of the bacteriophage Qβ replicase (Thr210Ala and Tyr410His) reduce sensitivity to the nucleoside analogue 5-azacytidine (AZC). Despite being located outsi...

  2. Complete Genome Sequence and Characterization of the Lysis System of the Temperate Clostridium perfringens Bacteriophage Phi 3626

    OpenAIRE

    Zimmer, Markus

    2005-01-01

    Two temperate viruses f3626 and f8533 have been isolated from lysogenic Clostridium perfringens strains. Phage f3626 was chosen for a detailed analysis, and was inspected by electron microscopy, protein profiling, and host range determination. For the first time, the nucleotide sequence of a bacteriophage infecting a Clostridium species was determined. The virus belongs to the Siphoviridae family of the tailed phages, in the order Caudovirales. Its genome consists of a linear dsDNA molecules ...

  3. Site-specificity of abnormal excision: the mechanism of formation of a specialized transducing bacteriophage lambda plac5.

    OpenAIRE

    Shpakovski, G V; Berlin, Y A

    1984-01-01

    Molecular mechanism of the specialized transducing bacteriophage lambda plac5 formation has been studied. Phage-bacterial DNA junctions in lambda plac5 DNA are localized and primary structure of regions of the abnormal excisional recombination leading to the phage formation is elucidated; the crossover region proved to be comparable with the central part of attP and attB sites (the core and the adjacent tetranucleotide) in length and degree of homology. Bacterial insert in lambda plac5 DNA is...

  4. Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1

    OpenAIRE

    Betts, Alex; Vasse, Marie; Kaltz, Oliver; Hochberg, Michael E.

    2013-01-01

    Antibiotic resistance is becoming increasingly problematic for the treatment of infectious disease in both humans and livestock. The bacterium Pseudomonas aeruginosa is often found to be resistant to multiple antibiotics and causes high patient mortality in hospitals. Bacteriophages represent a potential option to combat pathogenic bacteria through their application in phage therapy. Here, we capitalize on previous studies showing how evolution may increase phage infection capacity relative t...

  5. Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons.

    OpenAIRE

    Groisman, E A; Casadaban, M J

    1987-01-01

    An in vivo cloning system that uses derivatives of the Escherichia coli bacteriophage Mu with plasmid replicons has been extended to five different species of the family Enterobacteriaceae. Mu and these mini-Mu replicon elements were introduced into strains of E. coli, Shigella flexneri, Salmonella typhimurium, Citrobacter freundii, and Proteus mirabilis by infection, by transformation, or by conjugation with newly constructed broad-host-range plasmids containing insertions of these elements....

  6. Methylation dependent expression of the mom gene of bacteriophage Mu: deletions downstream from the methylation sites affect expression.

    OpenAIRE

    Adley, C C; Bukhari, A I

    1984-01-01

    The expression of the DNA modification gene (mom) of bacteriophage Mu requires the cellular deoxyadenosine methylase (dam) and a transactivation factor from the phage. By hypothesis, the transcription of mom is activated by methylation of three GATC sequences upstream from the mom gene. We have introduced small deletions at a fourth GATC site located about 140 base pairs downstream from the primary methylation region. Some of the deletions severely affect the mom gene expression. We propose f...

  7. Experimental Evolution of a Bacteriophage Virus Reveals the Trajectory of Adaptation across a Fecundity/Longevity Trade-Off

    OpenAIRE

    Heineman, Richard H.; Brown, Sam P.

    2012-01-01

    Life history theory attempts to account for how organisms lead their lives, balancing the conflicting demands of reproduction and survival. Here, we track the genomic and phenotypic evolution of the bacteriophage virus T7 across a postulated fecundity/longevity constraint. We adapted T7 to a challenging survival environment (6M urea). Our evolved strain displayed a significant improvement in propagule survival, coupled with a significant loss of fecundity (reduced growth rate on host cells). ...

  8. Complete nucleotide sequence and genome analysis of bacteriophage BFK20 — A lytic phage of the industrial producer Brevibacterium flavum

    Czech Academy of Sciences Publication Activity Database

    Bukovska, G.; Klucar, L.; Vlček, Čestmír; Adamovic, J.; Turna, J.; Timko, J.

    2006-01-01

    Roč. 348, č. 1 (2006), s. 57-71. ISSN 0042-6822 Grant ostatní: Slovenská akademie věd(SK) VEGA2/5068/25; Science and Technology Assistance Agency(SK) APVT-51-025004 Institutional research plan: CEZ:AV0Z50520514 Keywords : Bacteriophage * Complete genome sequence * Sequence analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.525, year: 2006

  9. Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses

    Directory of Open Access Journals (Sweden)

    Ghose Chandrabali

    2006-01-01

    Full Text Available Abstract Background Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can be used to determine ancestral relationships. The well-studied model of tail morphology in bacteriophage classification was used for comparison with nucleotide usage patterns. Tetranucleotide usage deviation (TUD patterns were chosen since they have previously been shown to contain phylogenetic signal similar to that of 16S rRNA. Results We found that bacteriophages have unique TUD patterns, representing genomic signatures that are relatively conserved among those with similar host range. Analysis of TUD-based phylogeny indicates that host influences are important in bacteriophage evolution, and phylogenies containing both phages and their hosts support their co-evolution. TUD-based phylogeny of eukaryotic viruses indicates that they cluster largely based on nucleic acid type and genome size. Similarities between eukaryotic virus phylogenies based on TUD and gene content substantiate the TUD methodology. Conclusion Differences between phenotypic and TUD analysis may provide clues to virus ancestry not previously inferred. As such, TUD analysis provides a complementary approach to morphology-based systems in analysis of virus evolution.

  10. Q69, an E. faecalis-infecting bacteriophage, as a biocontrol agent for reducing tyramine in dairy products

    Directory of Open Access Journals (Sweden)

    Victor eLadero

    2016-04-01

    Full Text Available Biogenic amines (BAs are low molecular weight nitrogenous compounds with biological activity, formed from amino acids by decarboxylation. BAs are naturally present in all living organisms playing essential roles. However, their accumulation in food through the metabolic activity of certain microorganisms constitutes a toxicological hazard. Among foods, cheeses accumulate some of the highest concentrations of BAs since they provide an ideal environment for their accumulation. Most of the methods proposed for reducing BAs in cheese, such as milk pasteurisation, have not only failed to completely solve the problem, they also affect non-BA producing lactic acid bacteria (LAB, i.e., the bacteria that participate in the development of the organoleptic characteristics of cheese. Novel technologies specifically targeted against BA producers are therefore needed to control BA accumulation. Bacteriophages have been proposed as agents for specifically controlling the presence of foodborne pathogens in food. Due to its specificity, they could be used as a biotechnological tool targeted to reduce the population of BA-producing bacteria. The present work reports the isolation, from cheese, and the characterisation of bacteriophage Q69, which infects specifically Enterococcus faecalis, the species mainly responsible of the accumulation of the BA tyramine in foods. Furthermore, its capacity to reduce the accumulation of tyramine in different conditions –including a model cheese- was proven. The obtained results open up the possibility of use bacteriophages to prevent BA accumulation in fermented foods.

  11. Q69 (an E. faecalis-Infecting Bacteriophage) As a Biocontrol Agent for Reducing Tyramine in Dairy Products.

    Science.gov (United States)

    Ladero, Victor; Gómez-Sordo, Carolina; Sánchez-Llana, Esther; Del Rio, Beatriz; Redruello, Begoña; Fernández, María; Martín, M Cruz; Alvarez, Miguel A

    2016-01-01

    Biogenic amines (BAs) are low molecular weight nitrogenous compounds with biological activity, formed from amino acids by decarboxylation. BAs are naturally present in all living organisms playing essential roles. However, their accumulation in food through the metabolic activity of certain microorganisms constitutes a toxicological hazard. Among foods, cheeses accumulate some of the highest concentrations of BAs since they provide an ideal environment for their accumulation. Most of the methods proposed for reducing BAs in cheese, such as milk pasteurization, have not only failed to completely solve the problem, they also affect non-BA producing lactic acid bacteria, i.e., the bacteria that participate in the development of the organoleptic characteristics of cheese. Novel technologies specifically targeted against BA producers are therefore needed to control BA accumulation. Bacteriophages have been proposed as agents for specifically controlling the presence of foodborne pathogens in food. Due to its specificity, they could be used as a biotechnological tool targeted to reduce the population of BA-producing bacteria. The present work reports the isolation, from cheese, and the characterization of bacteriophage Q69, which infects specifically Enterococcus faecalis, the species mainly responsible of the accumulation of the BA tyramine in foods. Furthermore, its capacity to reduce the accumulation of tyramine in different conditions -including a model cheese- was proven. The obtained results open up the possibility of use bacteriophages to prevent BA accumulation in fermented foods. PMID:27092117

  12. A Metagenomic approach to characterize temperate bacteriophage populations from cystic fibrosis and non-cystic fibrosis bronchiectasis patients

    Directory of Open Access Journals (Sweden)

    Mohammad Adnan Tariq

    2015-02-01

    Full Text Available Pseudomonas aeruginosa (Pa, normally a soil commensal, is an important opportunistic pathogen in Cystic Fibrosis (CF and non-Cystic Fibrosis Bronchiectasis (nCFBR. Persistent infection correlates with accelerated decline in lung function and early mortality. The horizontal transfer of DNA by temperate bacteriophages can add gene function and selective advantages to their bacterial host within the constrained environment of the lower lung. In this study, we chemically induce temperate bacteriophages from clonal cultures of Pa and identify their mixed viral communities employing metagenomic approaches. We compared 92 temperate phage metagenomes stratified from these clinical backgrounds (47 CF and 45 nCFBR Pa isolates using MG-RAST and GeneWise2. KEGG analysis shows the complexity of temperate phage accessory gene carriage increases with duration and severity of the disease. Furthermore we identify the presence of Ig-like motifs within phage structural genes linked to bacterial adhesion and carbohydrate binding including Big_2, He_Pig and Fn3. This study provides the first clinical support to the proposed bacteriophage adherence to mucus (BAM model and the evolution of phages interacting at these mucosal surfaces over time.

  13. A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients.

    Science.gov (United States)

    Tariq, Mohammad A; Everest, Francesca L C; Cowley, Lauren A; De Soyza, Anthony; Holt, Giles S; Bridge, Simon H; Perry, Audrey; Perry, John D; Bourke, Stephen J; Cummings, Stephen P; Lanyon, Clare V; Barr, Jeremy J; Smith, Darren L

    2015-01-01

    Pseudomonas aeruginosa (Pa), normally a soil commensal, is an important opportunistic pathogen in Cystic Fibrosis (CF) and non-Cystic Fibrosis Bronchiectasis (nCFBR). Persistent infection correlates with accelerated decline in lung function and early mortality. The horizontal transfer of DNA by temperate bacteriophages can add gene function and selective advantages to their bacterial host within the constrained environment of the lower lung. In this study, we chemically induce temperate bacteriophages from clonal cultures of Pa and identify their mixed viral communities employing metagenomic approaches. We compared 92 temperate phage metagenomes stratified from these clinical backgrounds (47 CF and 45 nCFBR Pa isolates) using MG-RAST and GeneWise2. KEGG analysis shows the complexity of temperate phage accessory gene carriage increases with duration and severity of the disease. Furthermore, we identify the presence of Ig-like motifs within phage structural genes linked to bacterial adhesion and carbohydrate binding including Big_2, He_Pig, and Fn3. This study provides the first clinical support to the proposed bacteriophage adherence to mucus (BAM) model and the evolution of phages interacting at these mucosal surfaces over time. PMID:25741327

  14. Q69 (an E. faecalis-Infecting Bacteriophage) As a Biocontrol Agent for Reducing Tyramine in Dairy Products

    Science.gov (United States)

    Ladero, Victor; Gómez-Sordo, Carolina; Sánchez-Llana, Esther; del Rio, Beatriz; Redruello, Begoña; Fernández, María; Martín, M. Cruz; Alvarez, Miguel A.

    2016-01-01

    Biogenic amines (BAs) are low molecular weight nitrogenous compounds with biological activity, formed from amino acids by decarboxylation. BAs are naturally present in all living organisms playing essential roles. However, their accumulation in food through the metabolic activity of certain microorganisms constitutes a toxicological hazard. Among foods, cheeses accumulate some of the highest concentrations of BAs since they provide an ideal environment for their accumulation. Most of the methods proposed for reducing BAs in cheese, such as milk pasteurization, have not only failed to completely solve the problem, they also affect non-BA producing lactic acid bacteria, i.e., the bacteria that participate in the development of the organoleptic characteristics of cheese. Novel technologies specifically targeted against BA producers are therefore needed to control BA accumulation. Bacteriophages have been proposed as agents for specifically controlling the presence of foodborne pathogens in food. Due to its specificity, they could be used as a biotechnological tool targeted to reduce the population of BA-producing bacteria. The present work reports the isolation, from cheese, and the characterization of bacteriophage Q69, which infects specifically Enterococcus faecalis, the species mainly responsible of the accumulation of the BA tyramine in foods. Furthermore, its capacity to reduce the accumulation of tyramine in different conditions –including a model cheese- was proven. The obtained results open up the possibility of use bacteriophages to prevent BA accumulation in fermented foods. PMID:27092117

  15. Solar influence on the O(1S) and O(1D) dayglow emission rates: Global-scale measurements by WINDII on UARS

    Science.gov (United States)

    Zhang, S.; Sheperd, G.

    More than 130,000 emission rate profiles of the O(^1D) dayglow (630 nm) and 500,000 of the O(^1S) (557.7nm) dayglow were observed by WINDII on UARS during 1991-1997, which provides an unprecedented and unigue database for studying the mechanisms and global climatology of the two airglow layers, and the energy balance and effects of dynamics and solar storms on the atmosphere-ionosphere-magnetosphere system. Empirical models are derived from WINDII measurements for the two emission rates as functions of the solar zenith angle and solar irradiance using the F10.7 cm flux as a proxy.

  16. FoxO1 mediates insulin-dependent regulation of hepatic VLDL production in mice

    OpenAIRE

    Kamagate, Adama; Qu, Shen; Perdomo, German; Su, Dongming; Kim, Dae Hyun; Slusher, Sandra; Meseck, Marcia; Dong, H. Henry

    2008-01-01

    Excessive production of triglyceride-rich VLDL is attributable to hypertriglyceridemia. VLDL production is facilitated by microsomal triglyceride transfer protein (MTP) in a rate-limiting step that is regulated by insulin. To characterize the underlying mechanism, we studied hepatic MTP regulation by forkhead box O1 (FoxO1), a transcription factor that plays a key role in hepatic insulin signaling. In HepG2 cells, MTP expression was induced by FoxO1 and inhibited by exposure to insulin. This ...

  17. Non-O1, non-O139 Vibrio cholerae bacteraemia in a cirrhotic patient

    OpenAIRE

    Petsaris, O.; Nousbaum, J B; Quilici, M L; Le Coadou, G; PAYAN, C; Abalain, M L

    2010-01-01

    Vibrio cholerae serogroups O1 or O139 are the aetiological agents of cholera. The pathogenicity of non-O1, non-O139 V. cholerae is less well known. These worldwide bacteria are responsible for gastrointestinal infections or, more rarely, bacteraemia in patients with an underlying disease, leading to life-threatening complications. We report a case of non-O1, non-O139 V. cholerae bacteraemia due to a haemolytic strain in a cirrhotic patient. Early antibiotherapy allowed a good outcome. The aim...

  18. Human immune response to Vibrio cholerae O1 whole cells and isolated outer membrane antigens.

    OpenAIRE

    Richardson, K; Kaper, J B; Levine, M M

    1989-01-01

    The serum immunoglobulin G (IgG) and mucosal secretory IgA (SIgA) response of human volunteers challenged with Vibrio cholerae O1 was analyzed for reactivity to V. cholerae O1 antigens by the immunoblot technique. Components of both in vitro- and in vivo (rabbit ligated ileal loop)-grown V. cholerae O1 were separated by sodium dodecyl sulfate-urea-polyacrylamide gel electrophoresis. Postchallenge serum IgG reacted uniquely with 15 antigens and with greater intensity than did prechallenge seru...

  19. Construction of an infectious cDNA clone of foot-and-mouth disease virus type O1BFS 1860 and its use in the preparation of candidate vaccine

    Indian Academy of Sciences (India)

    M Hema; D Chandran; S B Nagendrakumar; M Madhanmohan; V A Srinivasan

    2009-03-01

    Foot-and-mouth disease virus (FMDV) serotype O is the most predominant among the endemic serotypes in India. A stable, full-length cDNA clone of FMDV type O1BFS 1860 preceded by a bacteriophage T7 polymerase promoter was assembled in a plasmid vector pGEMR-7Zf(–). An ∼8.2 kb PCR product was amplified from the cDNA clone and a full-length RNA was generated from it by in vitro transcription. Transfection of BHK-21 cells with the in vitro transcripts resulted in the production of infectious recombinant FMDV particles as evidenced by cytopathic effects (CPE). Further, characterization of the recombinant virus by immunofluorescence, microneutralization test (MNT), antigen ELISA, RT-PCR, plaque assay and electron microscopy revealed similarity to the parental strain. The immunogenicity of an oil-adjuvant vaccine prepared using the inactivated recombinant virus was tested in guinea pigs and cattle. Neutralizing antibodies were produced in both vaccinated guinea pigs and cattle. Vaccinated animals were protected on challenge. The results demonstrated that the recombinant virus was as stable and effective as the parental strain for the preparation of inactivated vaccine, suggesting the potential application of this strategy to make genetically engineered FMDV vaccines.

  20. Construction of an infectious cDNA clone of foot-and-mouth disease virus type O 1 BFS 1860 and its use in the preparation of candidate vaccine.

    Science.gov (United States)

    Hema, M; Chandran, D; Nagendrakumar, S B; Madhanmohan, M; Srinivasan, V A

    2009-03-01

    Foot-and-mouth disease virus (FMDV) serotype O is the most predominant among the endemic serotypes in India. A stable,full-length cDNA clone of FMDV type O 1 BFS 1860 preceded by a bacteriophage T7 polymerase promoter was assembled in a plasmid vector pGEM R- - 7Zf(-). An 8.2 kb PCR product was amplified from the cDNA clone and a full-length RNA was generated from it by in vitro transcription.Transfection of BHK-21 cells with the in vitro transcripts resulted in the production of infectious recombinant FMDV particles as evidenced by cytopathic effects (CPE). Further, characterization of the recombinant virus by immunofluorescence, microneutralization test (MNT), antigen ELISA,RT-PCR, plaque assay and electron microscopy revealed similarity to the parental strain. The immunogenicity of an oil-adjuvant vaccine prepared using the inactivated recombinant virus was tested in guinea pigs and cattle. Neutralizing antibodies were produced in both vaccinated guinea pigs and cattle. Vaccinated animals were protected on challenge. The results demonstrated that the recombinant virus was as stable and effective as the parental strain for the preparation of inactivated vaccine, suggesting the potential application of this strategy to make genetically engineered FMDV vaccines. PMID:19430118

  1. Raman spectra in iron-based quaternary CeO1-xFxFeAs and LaO1-xFxFeAs

    International Nuclear Information System (INIS)

    Raman spectra have been measured on iron-based quaternary CeO1-xFxFeAs and LaO1-xFxFeAs with different amounts of fluorine doping at room temperatures. A group analysis has been made to clarify the optical modes. Based on first-principle calculations, the observed phonon modes can be assigned accordingly. In LaO1-xFxFeAs, the Eg and A1g modes related to the vibrations of La are suppressed with increasing F doping. However, F doping only has a small effect on the Eg and A1g modes of Fe and As. The Raman modes of La and As are absent in rare-earth substituted CeO1-xFxFeAs, and the Eg mode of oxygen, corresponding to the in-plane vibration of oxygen, moves to around 450 cm-1 and shows a very sharp peak. The electronic scattering background is low, and electron-phonon coupling is not evident for the observed phonon modes. Three features are found above 500 cm-1, which may be associated with multi-phonon processes. Nevertheless, it is also possible that they are related to magnetic fluctuations or interband transitions of d orbitals, considering their energies.

  2. FELIX: a volumetric 3D laser display

    Science.gov (United States)

    Bahr, Detlef; Langhans, Knut; Gerken, Martin; Vogt, Carsten; Bezecny, Daniel; Homann, Dennis

    1996-03-01

    In this paper, an innovative approach of a true 3D image presentation in a space filling, volumetric laser display will be described. The introduced prototype system is based on a moving target screen that sweeps the display volume. Net result is the optical equivalent of a 3D array of image points illuminated to form a model of the object which occupies a physical space. Wireframe graphics are presented within the display volume which a group of people can walk around and examine simultaneously from nearly any orientation and without any visual aids. Further to the detailed vector scanning mode, a raster scanned system and a combination of both techniques are under development. The volumetric 3D laser display technology for true reproduction of spatial images can tremendously improve the viewers ability to interpret data and to reliably determine distance, shape and orientation. Possible applications for this development range from air traffic control, where moving blips of light represent individual aircrafts in a true to scale projected airspace of an airport, to various medical applications (e.g. electrocardiography, computer-tomography), to entertainment and education visualization as well as imaging in the field of engineering and Computer Aided Design.

  3. Alfred Felix Landon Beeston (1911-1995

    Directory of Open Access Journals (Sweden)

    Alfred Felix Landon Beeston

    1997-08-01

    Full Text Available AutobiographieNé le 23 février 1911, c'est au Collège de Westminter que je fis mes études secondaires, avec une formation approfondie en latin et en grec. A temps perdu j'appris tout seul l'allemand, afin de pouvoir pratiquer dans cette langue un travail d'érudition ; j'acquis de la même façon des notions d'arabe. Toujours enclin à opter pour l'insolite, l'exotique, j'avais songé, il fut un temps, à me lancer dans le sanscrit ou le chinois ; mais je ne puis aujourd'hui me rappeler ce qui, fin...

  4. Utility of lytic bacteriophage in the treatment of multidrug-resistant Pseudomonas aeruginosa septicemia in mice

    Directory of Open Access Journals (Sweden)

    Vinodkumar C

    2008-07-01

    Full Text Available Drug resistance is the major cause of increase in morbidity and mortality in neonates. One thousand six hundred forty-seven suspected septicemic neonates were subjected for microbiological analysis over a period of 5 years. Forty-two P. aeruginosa were isolated and the antibiogram revealed that 28 P. aeruginosa were resistant to almost all the common drugs used (multidrug-resistant. The emergence of antibiotic-resistant bacterial strains is one of the most critical problems of modern medicine. As a result, a novel and most effective approaches for treating infection caused by multidrug-resistant bacteria are urgently required. In this context, one intriguing approach is to use bacteriophages (viruses that kill bacteria in the treatment of infection caused by drug-resistant bacteria. In the present study, the utility of lytic bacteriophages to rescue septicemic mice with multidrug-resistant (MDR P. aeruginosa infection was evaluated. MDR P. aeruginosa was used to induce septicemia in mice by intraperitoneal (i.p. injection of 10 7 CFU. The resulting bacteremia was fatal within 48 hrs. The phage strain used in this study had lytic activity against a wide range of clinical isolates of MDR P. aeruginosa. A single i.p. injection of 3 x 10 9 PFU of the phage strain, administered 45 min after the bacterial challenge, was sufficient to rescue 100% of the animals. Even when treatment was delayed to the point where all animals were moribund, approximately 50% of them were rescued by a single injection of this phage preparation. The ability of this phage to rescue septicemic mice was demonstrated to be due to the functional capabilities of the phage and not to a nonspecific immune effect. The rescue of septicemic mice could be affected only by phage strains able to grow in vitro on the bacterial host used to infect the animals and when such strains are heat-inactivated, they lose their ability to rescue the infected mice. Multidrug-resistant bacteria have

  5. Recombination-dependent DNA replication stimulated by double-strand breaks in bacteriophage T4.

    Science.gov (United States)

    Kreuzer, K N; Saunders, M; Weislo, L J; Kreuzer, H W

    1995-12-01

    We analyzed the mechanism of recombination-dependent DNA replication in bacteriophage T4-infected Escherichia coli using plasmids that have sequence homology to the infecting phage chromosome. Consistent with prior studies, a pBR322 plasmid, initially resident in the infected host cell, does not replicate following infection by T4. However, the resident plasmid can be induced to replicate when an integrated copy of pBR322 vector is present in the phage chromosome. As expected for recombination-dependent DNA replication, the induced replication of pBR322 required the phage-encoded UvsY protein. Therefore, recombination-dependent plasmid replication requires homology between the plasmid and phage genomes but does not depend on the presence of any particular T4 DNA sequence on the test plasmid. We next asked whether T4 recombination-dependent DNA replication can be triggered by a double-strand break (dsb). For these experiments, we generated a novel phage strain that cleaves its own genome within the nonessential frd gene by means of the I-TevI endonuclease (encoded within the intron of the wild-type td gene). The dsb within the phage chromosome substantially increased the replication of plasmids that carry T4 inserts homologous to the region of the dsb (the plasmids are not themselves cleaved by the endonuclease). The dsb stimulated replication when the plasmid was homologous to either or both sides of the break but did not stimulate the replication of plasmids with homology to distant regions of the phage chromosome. As expected for recombination-dependent replication, plasmid replication triggered by dsbs was dependent on T4-encoded recombination proteins. These results confirm two important predictions of the model for T4-encoded recombination-dependent DNA replication proposed by Gisela Mosig (p. 120-130, in C. K. Mathews, E. M. Kutter, G. Mosig, and P. B. Berget (ed.), Bacteriophage T4, 1983). In addition, replication stimulated by dsbs provides a site

  6. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation.

    Science.gov (United States)

    Shea, M A; Ackers, G K

    1985-01-20

    A quantitative model has been developed for processes in the bacteriophage lambda that control the switchover from lysogenic to lytic modes of growth. These processes include the interactions of cI repressor and cro proteins at the three DNA sites of the right operator, OR, the binding of RNA polymerase at promoters PR and PRM, the synthesis of cI repressor and cro proteins, and the degradative action of recA during induction of lysis. The model is comprised of two major physical-chemical components: a statistical thermodynamic theory for relative probabilities of the various molecular configurations of the control system; and a kinetic model for the coupling of these probabilities to functional events, including synthesis of regulatory proteins cI and cro. Using independently evaluated interaction constants and rate parameters, the model was found capable of predicting essential physiological characteristics of the system over an extended time. Sufficiency of the model to predict known physiological properties lends credence to the physical-chemical assumptions used in its construction. Several major physiological characteristics were found to arise as "system properties" through the non-linear, time-dependent, feedback-modulated combinations of molecular interactions prescribed by the model. These include: maintenance of the lysogenic state in the absence of recA-mediated cI repressor degradation; induction of lysis and the phenomenon of subinduction; and autogenous negative control of cro. We have used the model to determine the roles, within the composite system, of several key molecular processes previously characterized by studies in vitro. These include: co-operativity in cI repressor binding to DNA; interactions between repressors and RNA polymerase (positive control); and the monomer-dimer association of cI repressor molecules. A major role of cI repressor co-operativity is found to be that of guaranteeing stability of the lysogenic state against minor

  7. Characterization of bacteriophage KVP40 and T4 RNA ligase 2

    International Nuclear Information System (INIS)

    Bacteriophage T4 RNA ligase 2 (Rnl2) exemplifies a subfamily of RNA strand-joining enzymes that includes the trypanosome RNA editing ligases. A homolog of T4 Rnl2 is encoded in the 244-kbp DNA genome of vibriophage KVP40. We show that the 335-amino acid KVP40 Rnl2 is a monomeric protein that catalyzes RNA end-joining through ligase-adenylate and RNA-adenylate (AppRNA) intermediates. In the absence of ATP, pre-adenylated KVP40 Rnl2 reacts with an 18-mer 5'-PO4 single-strand RNA (pRNA) to form an 18-mer RNA circle. In the presence of ATP, Rnl2 generates predominantly AppRNA. Isolated AppRNA can be circularized by KVP40 Rnl2 in the absence of ATP. The reactivity of phage Rnl2 and the distribution of the products are affected by the length of the pRNA substrate. Whereas 18-mer and 15-mer pRNAs undergo intramolecular sealing by T4 Rnl2 to form monomer circles, a 12-mer pRNA is ligated intermolecularly to form dimers, and a 9-mer pRNA is unreactive. In the presence of ATP, the 15-mer and 12-mer pRNAs are converted to AppRNAs, but the 9-mer pRNA is not. A single 5' deoxynucleotide substitution of an 18-mer pRNA substrate has no apparent effect on the 5' adenylation or circularization reactions of T4 Rnl2. In contrast, a single deoxyribonucleoside at the 3' terminus strongly and selectively suppresses the sealing step, thereby resulting in accumulation of high levels of AppRNA in the absence of ATP. The ATP-dependent 'capping' of RNA with AMP by Rnl2 is reminiscent of the capping of eukaryotic mRNA with GMP by GTP:RNA guanylyltransferase and suggests an evolutionary connection between bacteriophage Rnl2 and eukaryotic RNA capping enzymes

  8. Two-stage, self-cycling process for the production of bacteriophages

    Directory of Open Access Journals (Sweden)

    Cooper David G

    2010-11-01

    Full Text Available Abstract Background A two-stage, self-cycling process for the production of bacteriophages was developed. The first stage, containing only the uninfected host bacterium, was operated under self-cycling fermentation (SCF conditions. This automated method, using the derivative of the carbon dioxide evolution rate (CER as the control parameter, led to the synchronization of the host bacterium. The second stage, containing both the host and the phage, was operated using self-cycling infection (SCI with CER and CER-derived data as the control parameters. When each infection cycle was terminated, phages were harvested and a new infection cycle was initiated by adding host cells from the SCF (first stage. This was augmented with fresh medium and the small amount of phages left from the previous cycle initiated the next infection cycle. Both stages were operated independently, except for this short period of time when the SCF harvest was added to the SCI to initiate the next cycle. Results It was demonstrated that this mode of operation resulted in stable infection cycles if the growth of the host cells in the SCF was synchronized. The final phage titers obtained were reproducible among cycles and were as good as those obtained in batch productions performed under the same conditions (medium, temperature, initial multiplicity of infection, etc.. Moreover, phages obtained in different cycles showed no important difference in infectivity. Finally, it was shown that cell synchronization of the host cells in the first stage (SCF not only maintained the volumetric productivity (phages per volume but also led to higher specific productivity (phage per cell per hour in the second stage (SCI. Conclusions Production of bacteriophage T4 in the semi-continuous, automated SCF/SCI system was efficient and reproducible from cycle to cycle. Synchronization of the host in the first stage prior to infection led to improvements in the specific productivity of phages in

  9. Bacteriophage and lytic enzymes - can they help us in the war with antibiotic resistant bacteria

    International Nuclear Information System (INIS)

    Drug-resistant pathogens are a growing menace to all people, regardless of age, or socioeconomic background. They endanger people industrial societies like the United States, as well as in less developed nations and are even causing problems in military field hospitals. From Streptococcus pneumoniae to Staphylococcus, C. difficile, and multidrug-resistant TB, the list is growing. The threat of engineered microorganisms further complicates the interaction between man and Mother Nature. Additionally, although antibiotics were specifically designed for treating human health emergencies, their use for raising livestock animals has expanded. In the US, large amounts of antibiotics are routinely mixed into feed in order to promote growth rather than combat disease and as prophylactic treatment to offset unnatural diets and unhealthy living conditions. U.S.-raised animals in the 1950s received 2 million pounds per year of antibiotics in their feed compared to 50 million pounds today-a 2,500-percent increase. A large percentage of these drugs pass into the environment. In fact, prior to 1995, when fluoroquinolones were first approved to treat poultry, very few fluoroquinolone-resistant Campylobacter were found in people with foodborne diseases in the United States. After the approval, however, many more fluoroquinolone-resistant bacteria were found in humans and in poultry from slaughter plants and retail stores. The threat to our food supply becomes a threat to security. What can be done? One approach is to treat bacterial diseases by the use of bacteriophages. Phages are very small viruses that destroy by lysing select bacteria. The idea of using phage as a therapy for infectious bacterial diseases was first proposed by d'Herelle around World War I and over 80 years bacteriophage has been a key tool of healthcare professionals within Eastern Europe. More recently professionals in the USA and Western Europe have isolated and developed specific lytic components which have

  10. $O(1/M^{3})$ effects for heavy-light mesons in lattice NRQCD

    CERN Document Server

    Lewis, R; Lewis, Randy

    1998-01-01

    The masses of spin-singlet and spin-triplet S-wave mesons containing a single heavy quark are computed in the quenched approximation. The light quark action and gauge field action are both classically-improved and tadpole-improved, and the couplings to the heavy quark are organized by the 1/M expansion of tadpole-improved NRQCD. At each of two lattice spacings, near 0.22fm and 0.26fm, meson masses are obtained for heavy quarks spanning the region between charmed and bottom mesons. Results up to O(1/M), O(1/M^2) and O(1/M^3) are displayed separately, so that the convergence of the heavy quark expansion can be discussed. Also, the effect of each term in the O(1/M^3) contribution is computed individually. For bottom mesons the 1/M-expansion appears to be satisfactory, but the situation for charmed mesons is less favorable.

  11. Pulmonary Cholera Due to Infection with a Non-O1 Vibrio cholerae Strain

    OpenAIRE

    Shannon, Jack D.; Kimbrough, Robert C.

    2006-01-01

    We present 2 cases of primary pulmonary non-O1 Vibrio cholerae infection. We believe that these are the first documented cases of primary pulmonary infection due to this organism from a freshwater source.

  12. O(1/M3) effects for heavy-light mesons in lattice NRQCD

    International Nuclear Information System (INIS)

    The masses of spin-singlet and spin-triplet S-wave mesons containing a single heavy quark are computed in the quenched approximation. The light quark action and gauge field action are both classically-improved and tadpole-improved, and the couplings to the heavy quark are organized by the 1/M expansion of tadpole-improved NRQCD. At each of two lattice spacings, near 0.22fm and 0.26fm, meson masses are obtained for heavy quarks spanning the region between charmed and bottom mesons. Results up to O(1/M), O(1/M2)and O(1/M3) are displayed separately, so that the convergence of the heavy quark expansion can be discussed. Also, the effect of each term in the O(1/M3) contribution is computed individually. For bottom mesons the 1/M-expansion appears to be satisfactory, but the situation for charmed mesons is less clear

  13. Poly[[tetraaquabis(μ-hydroxyacetato-κ4O1,O2:O1,O1′-μ2-sulfato-κ2O:O′-dicadmium(II] monohydrate

    Directory of Open Access Journals (Sweden)

    Urszula Rychlewska

    2009-06-01

    Full Text Available The title compound, {[Cd2(C2H3O32(SO4(H2O4]·H2O}n, was obtained unintentionally in a transmetallation reaction. The crystal structure contains a two-dimensional metal–organic framework based on CdII–(μ-hydroxyacetato-κ4O1,O2:O1,O1′–CdII zigzag chains joined together by bridging SO4 anions. The resulting layers are shifted with respect to each other and are stacked along the c axis. Their construction is supported by hydrogen bonds between water molecules and between water molecules and carboxylate or sulfate groups. Neighbouring layers are bridged by hydrogen bonds between the hydroxyl substituent and a sulfate anion. The sulfate anion and solvent water molecule are located on twofold axes. The results demonstrate that care must be taken when preparing ethylenediaminetetraacetic acid-type complexes by transmetallation, in order to avoid precipitation of metal complexes with the α-hydroxyacetate ligand.

  14. Neuraminidase production by Vibrio cholerae O1 and other diarrheagenic bacteria.

    OpenAIRE

    Kabir, S; Ahmad, N.; Ali, S.

    1984-01-01

    Vibrio cholerae O1 strains belonging to both biotypes (classical and El Tor) and both serotypes (Ogawa and Inaba) produced neuraminidase which was released rather than cell bound. Classical strains made more neuraminidase than did El Tor strains. About one-third of V. cholerae non-O1 strains and one-fourth of Aeromonas hydrophila strains were neuraminidase positive. Strains of enterotoxigenic Escherichia coli, Vibrio parahaemolyticus, and Shigella spp. did not produce detectable neuraminidase.

  15. Model for Atomic Oxygen Visible Line Emissions in Comet C/1995 O1 Hale-Bopp

    CERN Document Server

    Raghuram, Susarla

    2012-01-01

    We have recently developed a coupled chemistry-emission model for the green and red-doublet emissions of atomic oxygen on comet Hyakutake. In the present work we applied our model to comet Hale-Bopp, which had an order of magnitude higher H2O production rate than comet Hyakutake, to evaluate the photochemistry associated with the production and loss of O(1S) and O(1D) atoms and emission processes of green and red-doublet lines. We present the wavelength-dependent photo-attenuation rates for different photodissociation processes forming O(1S) and O(1D). The calculated radiative efficiency profiles of O(1S) and O(1D) atoms show that in comet Hale-Bopp the green and red-doublet emissions are emitted mostly above radial distances of 10^3 and 10^4 km, respectively. The model calculated [OI] 6300 A emission surface brightness and average intensity over the Fabry-P{\\'e}rot spectrometer field of view are consistent with the observation of Morgenthaler et al. (2001), while the intensity ratio of green to red-doublet e...

  16. Dynamics of reactions O((1)D)+C(6)H(6) and C(6)D(6).

    Science.gov (United States)

    Chen, Hui-Fen; Liang, Chi-Wei; Lin, Jim J; Lee, Yuan-Pern; Ogilvie, J F; Xu, Z F; Lin, M C

    2008-11-01

    The reaction between O((1)D) and C(6)H(6) (or C(6)D(6)) was investigated with crossed-molecular-beam reactive scattering and time-resolved Fourier-transform infrared spectroscopy. From the crossed-molecular-beam experiments, four product channels were identified. The major channel is the formation of three fragments CO+C(5)H(5)+H; the channels for formation of C(5)H(6)+CO and C(6)H(5)O+H from O((1)D)+C(6)H(6) and OD+C(6)D(5) from O((1)D)+C(6)D(6) are minor. The angular distributions for the formation of CO and H indicate a mechanism involving a long-lived collision complex. Rotationally resolved infrared emission spectra of CO (1ratio of [CO]/[OH]=2.1+/-0.4 for O((1)D)+C(6)H(6) and [CO]/[OD]>2.9 for O((1)D)+C(6)D(6) is consistent with the expectation for an abstraction reaction. The mechanism of the reaction may be understood from considering the energetics of the intermediate species and transition states calculated at the G2M(CC5) level of theory for the O((1)D)+C(6)H(6) reaction. The experimentally observed branching ratios and deuterium isotope effect are consistent with those predicted from calculations. PMID:19045343

  17. The susceptibility of Pseudomonas aeruginosa strains from cystic fibrosis patients to bacteriophages.

    Directory of Open Access Journals (Sweden)

    Christiane Essoh

    Full Text Available Phage therapy may become a complement to antibiotics in the treatment of chronic Pseudomonas aeruginosa infection. To design efficient therapeutic cocktails, the genetic diversity of the species and the spectrum of susceptibility to bacteriophages must be investigated. Bacterial strains showing high levels of phage resistance need to be identified in order to decipher the underlying mechanisms. Here we have selected genetically diverse P. aeruginosa strains from cystic fibrosis patients and tested their susceptibility to a large collection of phages. Based on plaque morphology and restriction profiles, six different phages were purified from "pyophage", a commercial cocktail directed against five different bacterial species, including P. aeruginosa. Characterization of these phages by electron microscopy and sequencing of genome fragments showed that they belong to 4 different genera. Among 47 P. aeruginosa strains, 13 were not lysed by any of the isolated phages individually or by pyophage. We isolated two new phages that could lyse some of these strains, and their genomes were sequenced. The presence/absence of a CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and Crisper associated genes was investigated to evaluate the role of the system in phage resistance. Altogether, the results show that some P. aeruginosa strains cannot support the growth of any of the tested phages belonging to 5 different genera, and suggest that the CRISPR-Cas system is not a major defence mechanism against these lytic phages.

  18. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages.

    Science.gov (United States)

    Goldfain, Aaron M; Garmann, Rees F; Jin, Yan; Lahini, Yoav; Manoharan, Vinothan N

    2016-07-01

    A complete understanding of the cellular pathways involved in viral infections will ultimately require a diverse arsenal of experimental techniques, including methods for tracking individual viruses and their interactions with the host. Here we demonstrate the use of holographic microscopy to track the position, orientation, and DNA content of unlabeled bacteriophages (phages) in solution near a planar, functionalized glass surface. We simultaneously track over 100 individual λ phages at a rate of 100 Hz across a 33 μm × 33 μm portion of the surface. The technique determines the in-plane motion of the phage to nanometer precision, and the height of the phage above the surface to 100 nm precision. Additionally, we track the DNA content of individual phages as they eject their genome following the addition of detergent-solubilized LamB receptor. The technique determines the fraction of DNA remaining in the phage to within 10% of the total 48.5 kilobase pairs. Analysis of the data reveals that under certain conditions, λ phages move along the surface with their heads down and intermittently stick to the surface by their tails, causing them to stand up. Furthermore, we find that in buffer containing high concentrations of both monovalent and divalent salts, λ phages eject their entire DNA in about 7 s. Taken together, these measurements highlight the potential of holographic microscopy to resolve the fast kinetics of the early stages of phage infection. PMID:27063451

  19. Bacteriophage adsorption during transport through porous media: Chemical perturbations and reversibility

    Science.gov (United States)

    Bales, R.C.; Hinkle, S.R.; Kroeger, T.W.; Stocking, K.; Gerba, C.P.

    1991-01-01

    In a series of seven column experiments, attachment of the bacteriophage PRD-1 and MS-2 to silica beads at pH's 5.0-5.5 was at least partially reversible; however, release of attached phage was slow and breakthrough curves exhibited significant tailing. Rate coefficients for attachment and detachment were on the order of 10-4 and 10-6-10-4 s-1, respectively. Corresponding time scales were hours for attachment and days for detachment. The sticking efficiency (??) for phage attachment was near 0.01. The rate of phage release was enhanced by raising pH and introducing surface-active chemical species, illustrating the importance of chemical perturbations in promoting biocolloid transport. In a series of batch experiments, MS-2 adsorbed strongly to a hydrophobic surface, octadecyltrichlorosilane-bonded silica, at both pH's 5 and 7. Adsorption to the unbonded silica at pH 5 was linear, but was 2.5 (with Ca2+) to 0.25% (without Ca2+) of that to the bonded surface. Neither MS-2 nor PRD-1 adsorbed to unbonded silica at pH 7. Hydrophobic effects appear to be important for adsorption of even relatively hydrophilic biocolloids. ?? 1991 American Chemical Society.

  20. Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa.

    Science.gov (United States)

    Latino, Libera; Midoux, Cédric; Hauck, Yolande; Vergnaud, Gilles; Pourcel, Christine

    2016-05-01

    Coevolution between bacteriophages (phages) and their prey is the result of mutualistic interactions. Here, we show that pseudolysogeny is a frequent outcome of infection by virulent phages of Pseudomonas aeruginosa and that selection of resistant bacterial mutants is favoured by continuous production of phages. We investigated the frequency and characteristics of P. aeruginosa strain PAO1 variants resisting infection by different combinations of virulent phages belonging to four genera. The frequency of resistant bacteria was 10- 5 for single phage infection and 10- 6 for infections with combinations of two or four phages. The genome of 27 variants was sequenced and the comparison with the genome of the parental PAO1 strain allowed the identification of point mutations or small indels. Four additional variants were characterized by a candidate gene approach. In total, 27 independent mutations were observed affecting 14 genes and a regulatory region. The mutations affected genes involved in biosynthesis of type IV pilus, alginate, LPS and O-antigen. Half of the variants possessed changes in homopolymer tracts responsible for frameshift mutations and these phase variation mutants were shown to be unstable. Eleven double mutants were detected. The presence of free phage DNA was observed in association with exclusion of superinfection in half of the variants and no chromosomal mutation could be found in three of them. Upon further growth of these pseudolysogens, some variants with new chromosomal mutations were recovered, presumably due to continuous evolutionary pressure. PMID:26921273

  1. Display of Peptides and Proteins on the Surface of Bacteriophage λ

    Science.gov (United States)

    Sternberg, Nat; Hoess, Ronald H.

    1995-02-01

    The display of peptides or proteins on the surface of viruses is an important technology for studying peptides or proteins and their interaction with other molecules. Here we describe a display vehicle based on bacteriophage λ that incorporates a number of features distinct from other currently used display systems. Fusions of peptides or protein domains have been made to the amino terminus of the 11-kDa D protein of the λ capsid. These fusions assemble onto the viral capsid and appear to be accessible to ligand interactions, based on the ability of a monoclonal antibody to recognize an epitope fused to the D protein on phage heads. To produce large D fusion display libraries and yet avoid the cumbersome task of cloning many fragments into λ DNA, we have used the Cre-loxP site-specific recombination system in vivo to incorporate plasmids encoding the D fusions into the phage genome. Finally, we show that D fusion proteins can be added in vitro to phage lacking D protein and be assembled onto the viral capsid.

  2. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein

    DEFF Research Database (Denmark)

    Bendtsen, Jannick Dyrløv; Nilsson, A.S.; Lehnherr, H.

    2002-01-01

    Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and...... does not represent a recent acquirement of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein....... Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary...

  3. Key players in the genetic switch of bacteriophage TP901-1.

    Science.gov (United States)

    Alsing, Anne; Pedersen, Margit; Sneppen, Kim; Hammer, Karin

    2011-01-19

    After infection of a sensitive host temperate phages may enter either a lytic or a lysogenic pathway leading to new phage assembly or silencing as a prophage, respectively. The decision about which pathway to enter is centered in the genetic switch of the phage. In this work, we explore the bistable genetic switch of bacteriophage TP901-1 through experiments and statistical mechanical modeling. We examine the activity of the lysogenic promoter P(R) at different concentrations of the phage repressor, CI, and compare the effect of CI on P(R) in the presence or absence of the phage-encoded MOR protein expressed from the lytic promoter P(L). We find that the presence of large amounts of MOR prevents repression of the P(R) promoter, verifying that MOR works as an antirepressor. We compare our experimental data with simulations based on previous mathematical formulations of this switch. Good agreement between data and simulations verify the model of CI repression of P(R). By including MOR in the simulations, we are able to discard a model that assumes that CI and MOR do not interact before binding together at the DNA to repress P(R). The second model of Pr repression assumes the formation of a CI:MOR complex in the cytoplasm. We suggest that a CI:MOR complex may exist in different forms that either prevent or invoke P(R) repression, introducing a new twist on mixed feedback systems. PMID:21244827

  4. The genome of bacteriophage phiKMV, a T7-like virus infecting Pseudomonas aeruginosa

    International Nuclear Information System (INIS)

    The complete DNA sequence of a new lytic T7-like bacteriophage phiKMV is presented. It is the first genome sequence of a member of the Podoviridae that infects Pseudomonas aeruginosa. The linear G + C-rich (62.3%) double-stranded DNA genome of 42,519 bp has direct terminal repeats of 414 bp and contains 48 open reading frames that are all transcribed from the same strand. Despite absence of homology at the DNA level, 11 of the 48 phiKMV-encoded putative proteins show sequence similarity to known T7-type phage proteins. Eighteen open reading frame products have been assigned, including an RNA polymerase, proteins involved in DNA replication, as well as structural, phage maturation, and lysis proteins. Surprisingly, the major capsid protein completely lacks sequence homology to any known protein. Also, the strong virulence toward many clinical P. aeruginosa isolates and a short replication time make phiKMV attractive for phage therapy or a potential source for antimicrobial proteins

  5. Structural remodeling of bacteriophage T4 and host membranes during infection initiation.

    Science.gov (United States)

    Hu, Bo; Margolin, William; Molineux, Ian J; Liu, Jun

    2015-09-01

    The first stages of productive bacteriophage infections of bacterial host cells require efficient adsorption to the cell surface followed by ejection of phage DNA into the host cytoplasm. To achieve this goal, a phage virion must undergo significant structural remodeling. For phage T4, the most obvious change is the contraction of its tail. Here, we use skinny E. coli minicells as a host, along with cryo-electron tomography and mutant phage virions, to visualize key structural intermediates during initiation of T4 infection. We show for the first time that most long tail fibers are folded back against the tail sheath until irreversible adsorption, a feature compatible with the virion randomly walking across the cell surface to find an optimal site for infection. Our data confirm that tail contraction is triggered by structural changes in the baseplate, as intermediates were found with remodeled baseplates and extended tails. After contraction, the tail tube penetrates the host cell periplasm, pausing while it degrades the peptidoglycan layer. Penetration into the host cytoplasm is accompanied by a dramatic local outward curvature of the cytoplasmic membrane as it fuses with the phage tail tip. The baseplate hub protein gp27 and/or the ejected tape measure protein gp29 likely form the transmembrane channel for viral DNA passage into the cell cytoplasm. Building on the wealth of prior biochemical and structural information, this work provides new molecular insights into the mechanistic pathway of T4 phage infection. PMID:26283379

  6. Assembly and dynamics of the bacteriophage T4 homologous recombination machinery

    Directory of Open Access Journals (Sweden)

    Morrical Scott W

    2010-12-01

    Full Text Available Abstract Homologous recombination (HR, a process involving the physical exchange of strands between homologous or nearly homologous DNA molecules, is critical for maintaining the genetic diversity and genome stability of species. Bacteriophage T4 is one of the classic systems for studies of homologous recombination. T4 uses HR for high-frequency genetic exchanges, for homology-directed DNA repair (HDR processes including DNA double-strand break repair, and for the initiation of DNA replication (RDR. T4 recombination proteins are expressed at high levels during T4 infection in E. coli, and share strong sequence, structural, and/or functional conservation with their counterparts in cellular organisms. Biochemical studies of T4 recombination have provided key insights on DNA strand exchange mechanisms, on the structure and function of recombination proteins, and on the coordination of recombination and DNA synthesis activities during RDR and HDR. Recent years have seen the development of detailed biochemical models for the assembly and dynamics of presynaptic filaments in the T4 recombination system, for the atomic structure of T4 UvsX recombinase, and for the roles of DNA helicases in T4 recombination. The goal of this chapter is to review these recent advances and their implications for HR and HDR mechanisms in all organisms.

  7. Sequence specificity of mutagenesis in the cI gene of bacteriophage lambda

    International Nuclear Information System (INIS)

    Studies of DNA base sequence alterations have shown that for every agent the mutagenic process is specific with respect to the types of base changes induced and the location of the changes in the DNA. Analysis of the types of mutations produced by mutagenic agents can provide insight into the mechanism of mutation and can suggest which DNA lesions may be involved in the actual mutagenic event. We have developed a system for the analysis of chemically induced base sequence alterations in the cI repressor gene of bacteriophage lambda using DNA sequencing techniques. To illustrate the utility of this type of analysis, we present the results obtained with ultraviolet light (UV). Irradiation of target DNA with UV alone, or UV followed by photoreactivating light (which removes dimers), produces mostly transitions at pyrimidine-pyrimidine sites. Conversely, irradiation with 313 nm light plus acetophenone (which produces only thymine dimers) produces mostly transversions at low efficiency. This and other evidence suggests that the actual premutagenic UV lesion in E. coli may not be pyrimidine-pyrimidine dimers, but rather pyr(6-4)pyo photoproducts

  8. Host DNA replication or excision repair requirement for ultraviolet induction of bacteriophage lambda lysogens

    International Nuclear Information System (INIS)

    It is stated that the mechanism for prophage induction by radiation, or chemical agents, is not known, although a variety of hypothesis have been advanced during recent years. Biochemical data have been described that seem to favour the suggestion that DNA intermediates in the repair of DNA damage compete with prophage operators for repressor binding. When sufficient repressor is bound none remains for prophage repression and induction occurs. If this is so the prediction may be made that induction should not occur in the absence of normal repair processes. Some experimental work is described with a view to testing and verifying this prediction. A bacteriophage lambda lysogen was used in the work. Irradiation was at 420C, and samples were removed at intervals and assayed for free plaque-forming units, little induction was observed over a wide range of UV doses in non-replicating non-excising lysogens, in contradiction with some earlier results. Competition between prophage operators and repair intermediates for lambda repressor appears to be the simplest way to account for the observed results, although other possibilities are discussed. (U.K.)

  9. Class I self-splicing introns are found in the T-even bacteriophage family

    International Nuclear Information System (INIS)

    The thymidylate synthase gene (td) and ribonucleotide reductase B2 subunit gene (nrdB) EMBO both of bacteriophage T4 in origin, are procaryotic intron-containing protein-encoding genes. To screen for other procaryotic introns, southern hybridization analysis of several procaryotic genomes was carried out, using T4 phage td DNA restriction fragments and synthetic oligodeoxynucleotides defining strategic td exon and intron regions. Furthermore, the labeling pattern of total RNA with [α-32P]GTP, a typical reaction of self-splicing RNAs (class I), was examined. Experimental data implicate multiple self-splicing introns only in the T-even phages: five (1, 0.9, 0.83, 0.75 and 0.6 kb) in T4 and three (1, 0.9 and 0.75 kb) each in T2 and T6 phages. Northern hybridization analysis of total RNA extracted from T-even phage-infected cells confirms that the 1 kb RNA from each phage is in fact the excised intron segment from the precursor RNA transcribed from an intron-containing td gene in each case. This RNA cyclizes to form a contiguous circular molecule. The 0.6 kb RNA is most likely the T4 phage nrdB intron which seems to be absent from the corresponding gene in T2 and T6. The remaining RNA species are candidates for other self-splicing introns in these phages

  10. Global analysis of host response to induction of a latent bacteriophage

    Directory of Open Access Journals (Sweden)

    Keasling Jay D

    2007-08-01

    Full Text Available Abstract Background The transition from viral latency to lytic growth involves complex interactions among host and viral factors, and the extent to which host physiology is buffered from the virus during induction of lysis is not known. A reasonable hypothesis is that the virus should be evolutionarily selected to ensure host health throughout induction to minimize its chance of reproductive failure. To address this question, we collected transcriptional profiles of Escherichia coli and bacteriophage lambda throughout lysogenic induction by UV light. Results We observed a temporally coordinated program of phage gene expression, with distinct early, middle and late transcriptional classes. Our study confirmed known host-phage interactions of induction of the heat shock regulon, escape replication, and suppression of genes involved in cell division and initiation of replication. We identified 728 E. coli genes responsive to prophage induction, which included pleiotropic stress response pathways, the Arc and Cpx regulons, and global regulators crp and lrp. Several hundred genes involved in central metabolism, energy metabolism, translation and transport were down-regulated late in induction. Though statistically significant, most of the changes in these genes were mild, with only 140 genes showing greater than two-fold change. Conclusion Overall, we observe that prophage induction has a surprisingly low impact on host physiology. This study provides the first global dynamic picture of how host processes respond to lambda phage induction.

  11. Direct positive selection for improved nitroreductase variants using SOS triggering of bacteriophage lambda lytic cycle.

    Science.gov (United States)

    Guise, C P; Grove, J I; Hyde, E I; Searle, P F

    2007-04-01

    Expression of prodrug-activating enzymes that convert non-toxic substrates to cytotoxic derivatives is a promising strategy for cancer gene therapy. However, their catalytic activity with unnatural, prodrug substrates is often suboptimal. Efforts to improve these enzymes have been limited by the inability to select directly for increased prodrug activation. We have focussed on developing variants of Escherichia coli (E. coli) nitroreductase (NTR) with improved ability to activate the prodrug 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954), and describe here a novel, direct, positive selection for improved enzymes that exploits the alternative life cycles of bacteriophage lambda. In lambda lysogens of E. coli, the activation of the prodrug CB1954 by NTR triggers the SOS response to DNA damage, switching integrated lambda prophages into lytic cycle. This provides a direct, positive selection for phages encoding improved NTR variants, as, upon limiting exposure of lysogenized E. coli to CB1954, only those encoding the most active enzyme variants are triggered into lytic cycle, allowing their selective recovery. We exemplify the selection by isolating highly improved 'turbo-NTR' variants from a library of 6.8 x 10(5) clones, conferring up to 50-fold greater sensitivity to CB1954 than the wild type. Carcinoma cells infected with adenovirus expressing T41Q/N71S/F124T-NTR were sensitized to CB1954 concentrations 40- to 80-fold lower than required with WT-NTR. PMID:17301844

  12. Inactivation of indispensable bacterial proteins by early proteins of bacteriophages: implication in antibacterial drug discovery.

    Science.gov (United States)

    Sau, S; Chattoraj, P; Ganguly, T; Chanda, P K; Mandal, N C

    2008-06-01

    Bacteriophages utilize host bacterial cellular machineries for their own reproduction and completion of life cycles. The early proteins that phage synthesize immediately after the entry of their genomes into bacterial cells participate in inhibiting host macromolecular biosynthesis, initiating phage-specific replication and synthesizing late proteins. Inhibition of synthesis of host macromolecules that eventually leads to cell death is generally performed by the physical and/or chemical modification of indispensable host proteins by early proteins. Interestingly, most modified bacterial proteins were shown to take part actively in phage-specific transcription and replication. Research on phages in last nine decades has demonstrated such lethal early proteins that interact with or chemically modify indispensable host proteins. Among the host proteins inhibited by lethal phage proteins, several are not inhibited by any chemical inhibitor available today. Under the context of widespread dissemination of antibiotic-resistant strains of pathogenic bacteria in recent years, the information of lethal phage proteins and cognate host proteins could be extremely invaluable as they may lead to the identification of novel antibacterial compounds. In this review, we summarize the current knowledge about some early phage proteins, their cognate host proteins and their mechanism of action and also describe how the above interacting proteins had been exploited in antibacterial drug discovery. PMID:18537683

  13. Initiation of bacteriophage Φ29 DNA packaging studied by optical tweezers manipulation of single DNA molecules

    Science.gov (United States)

    Rickgauer, John Peter; Fuller, Derek N.; Hu, Bo; Grimes, Shelley; Jardine, Paul J.; Anderson, Dwight L.; Smith, Douglas E.

    2006-08-01

    A key step in the life cycle of many viruses, including bacteriophages, adenoviruses, and herpesviruses, is the packaging of replicated viral genomes into pre-assembled proheads by the action of ATP-dependent portal motor complexes. Here we present a method that allows the initiation of packaging by single complexes to be studied using optical tweezers. A procedure is developed for assembling phage Φ29 prohead-motor complexes, which are demonstrated to bind and begin translocation of a target DNA molecule within only a few seconds. We show that the Φ29 DNA terminal protein (gene product 3), which functions to prime DNA replication, also has a dramatic effect on packaging. The DNA tether length measured immediately after binding varied from ~30-100% of the full length, yet shortened monotonically, indicating that packaging does not strictly begin at the terminal end of the DNA. Removal of the terminal protein eliminated this variability, causing packaging to initiate at or very near the end of the DNA. These findings, taken together with electron microscopy data, suggest that rather than simply threading into the portal, the motor captures and dynamically tensions a DNA loop, and that the function of the terminal protein is to load DNA segments on both sides of the loop junction onto separate DNA translocating units.

  14. Lytic bacteriophages in Veterinary Medicine: a therapeutic option against bacterial pathogens?

    Directory of Open Access Journals (Sweden)

    C Borie

    2014-01-01

    Full Text Available The high prevalence of certain bacterial diseases in animals and their economic impact at the productive and public health levels, have directed attention towards the search for new methods of control and prevention, alternative or complementary, that aim to mitigate their adverse effects. This scenario is further complicated by the permanent and rising presence of pathogenic bacteria that are resistant to many antibiotics, limiting the choice of control strategies. In the continuous search for new therapies, there is a renewed interest on the application of bacteriophages, viruses that kill bacteria, as potential antimicrobial agents. Phage therapy in animal production, pets and experimental models of human infection have been discussed in veterinary medicine for 3 decades, with encouraging results in terms of reducing mortality, the severity of the clinical state and bacterial counts at tissue level. These benefits have been achieved thanks to increased knowledge of the biology of phages, better technology that allows their purification and their inherent advantages in terms of their safety for animals. Currently, phage research continues to open new horizons for both the medical industry and the food industry, considering the use of phages in the stages of "farm to fork", with promising results if used as an intervention in animals since their arrival to the slaughter house.

  15. The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism.

    Directory of Open Access Journals (Sweden)

    Jann T Martinsohn

    2008-05-01

    Full Text Available Genome mosaicism in temperate bacterial viruses (bacteriophages is so great that it obscures their phylogeny at the genome level. However, the precise molecular processes underlying this mosaicism are unknown. Illegitimate recombination has been proposed, but homeologous recombination could also be at play. To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into lambda. High yields of recombinants between 22% diverged genes have been obtained when the virus Red Gam pathway was active, and 100 fold less when the host Escherichia coli RecABCD pathway was active. The recombination editing proteins, MutS and UvrD, showed only marginal effects on lambda recombination. Thus, escape from host editing contributes to the high proficiency of virus recombination. Moreover, our bioinformatics study suggests that homeologous recombination between similar lambdoid viruses has created part of their mosaicism. We therefore propose that the remarkable propensity of the lambda-encoded Red and Gam proteins to recombine diverged DNA is effectively contributing to mosaicism, and more generally, that a correlation may exist between virus genome mosaicism and the presence of Red/Gam-like systems.

  16. Expression of a cloned denV gene of bacteriophage T4 in Escherichia coli

    International Nuclear Information System (INIS)

    A 713-base-pair Hae III fragment from bacteriophage T4 encompassing the denV gene with its preceding promoter has been cloned in a pBR322-derived positive-selection vector and introduced into a variety of DNA repair-deficient uvr and rec and uvr,rec Escherichia coli strains. The denV gene was found to be expressed, probably from its own promoter, causing pyrimidine dimer incision-deficient uvrA, uvrB, uvrC strains to be rescued by the denV gene. A uvrD (DNA helicase II) strain was also complemented, but to a lesser extent. A wild-type strain did not seem to be affected at the UV doses tested. Surprisingly, all recA, recB, and recC strains tested also showed an increased UV resistance, perhaps by reinforcement of the intact uvr system in these strains. Complementation of denV- T4 strains and host-cell reactivation of lambda phage was also observed in denV+ E. coli strains. Equilibrium sedimentation showed that DNA repair synthesis occurred in a UV-irradiated uvrA E. coli strain carrying the cloned denV gene. Southern blotting confirmed earlier results that the denV gene is located at 64 kilobases on the T4 map. Phage T2 (denV-) did not hybridize to a denV-specific probe

  17. Expression of a cloned denV gene of bacteriophage T4 in Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Valerie, K.; Henderson, E.E.; de Riel, J.K.

    1985-07-01

    A 713-base-pair Hae III fragment from bacteriophage T4 encompassing the denV gene with its preceding promoter has been cloned in a pBR322-derived positive-selection vector and introduced into a variety of DNA repair-deficient uvr and rec and uvr,rec Escherichia coli strains. The denV gene was found to be expressed, probably from its own promoter, causing pyrimidine dimer incision-deficient uvrA, uvrB, uvrC strains to be rescued by the denV gene. A uvrD (DNA helicase II) strain was also complemented, but to a lesser extent. A wild-type strain did not seem to be affected at the UV doses tested. Surprisingly, all recA, recB, and recC strains tested also showed an increased UV resistance, perhaps by reinforcement of the intact uvr system in these strains. Complementation of denV- T4 strains and host-cell reactivation of lambda phage was also observed in denV+ E. coli strains. Equilibrium sedimentation showed that DNA repair synthesis occurred in a UV-irradiated uvrA E. coli strain carrying the cloned denV gene. Southern blotting confirmed earlier results that the denV gene is located at 64 kilobases on the T4 map. Phage T2 (denV-) did not hybridize to a denV-specific probe.

  18. Preparation and properties of bacteriophage-borne enzyme degrading bacterial exopolysaccharide

    Institute of Scientific and Technical Information of China (English)

    Mou Haijin; Wang Jingxue; Jiang Xiaolu; Liu Zhihong

    2008-01-01

    Bacteriophages infected different serotypes of Klebsiella were isolated from sewage. Among them, a heat-stable polysaccharide depolymerase enzyme which could degrade bacterial exopolysaccharide effectively was prepared from the phage infecting Klebsiella K13. Treatment at 60 ℃ for 30 min could inactivate most of the K13 phage, with the titration decreasing from 6.4×108 PFU/mL to 1.6×106 PFU/mL. However, no obvious loss of phage enzyme activity was found after this treatment. The optimum hydrolytic temperature of phage enzyme was 60 ℃, with an activity 57% higher than that at 30 ℃. The addition of phage enzyme could result in a rapid decrease of viscosity of exopolysaccharide (EPS) solution within minutes, indicating that K13 phage polysaccharide depolymerase acts as a kind of endo-glycanohydrolase. HPLC and reducing sugar analysis showed that the hydrolysis of EPS approached approximately the maximum at 4h when the final concentration of phage was 6.0 × 108 PFU/mL. The results showed that Klebsiella K13 phage depolymerase enzyme could be used as a good tool for the preparation of EPS oligosaccharide.

  19. Engineering bacteriophage for a pragmatic low-resource setting bacterial diagnostic platform.

    Science.gov (United States)

    Talbert, Joey N; Alcaine, Samuel D; Nugen, Sam R

    2016-04-01

    Bacteriophages represent multifaceted building blocks that can be incorporated as substitutes for, or in unison with other detection methods, to create powerful new diagnostics for the detection of bacteria. The ease of phage manipulation, production, and detection speed clearly highlights that there remains unrealized opportunities to leverage these phage-based components in diagnostics amenable to resource-limited settings. The passage of regulations like the Food Safety Modernization act, and the ever increasing extent of global trade and travel, will create further demand for these types of diagnostics. While phage-based diagnostics have begun to entering the market place, further research is needed to ensure the potential benefits of phage-based technologies for public health are fully realized. We are just beginning to explore the possibilities that phage-based detection can offer us in the future. The combination of engineered phages as well as engineered enzymes could result in ultrasensitive detection systems for low-resource settings. Because the reporter enzyme is synthesized in vivo, we need to consider the options outside of normal enzyme reporters. In this case, common enzyme issues such as purification and long-term stability are less important. Phage-based diagnostics were conceptualized from out-of-the box thinking and the evolution of these systems should be as well. PMID:27246532

  20. Porous silicon membrane-modified electrodes for label-free voltammetric detection of MS2 bacteriophage.

    Science.gov (United States)

    Reta, Nekane; Michelmore, Andrew; Saint, Christopher; Prieto-Simón, Beatriz; Voelcker, Nicolas H

    2016-06-15

    A proof of concept for the label-free detection of bacteriophage MS2, a model indicator of microbiological contamination, is validated in this work as a porous silicon (pSi) membrane-based electrochemical biosensor. PSi membranes were used to afford nanochannel architectures. The sensing mechanism was based on the nanochannel blockage caused by MS2 binding to immobilized capture antibodies. This blockage was quantified by measuring the oxidation current of the electroactive species reaching the electrode surface, by means of differential pulse voltammetry (DPV). The immunosensor showed a limit of detection of 6pfu/mL in buffer, allowing the detection of MS2 to levels commonly found in real-world applications, and proved to be unaffected by matrix effects when analyzing MS2 in reservoir water. This platform enables the straightforward, direct and sensitive detection of a broad range of target analytes and constitutes a promising approach towards the development of portable electronic point of sample analysis devices. PMID:26803413