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Sample records for bacteriophage p2 capsids

  1. 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...

  2. 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.

  3. 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...

  4. 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...

  5. 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.

  6. Theory of morphological transformation of viral capsid shell during the maturation process in the HK97 bacteriophage and similar viruses

    Science.gov (United States)

    Konevtsova, O. V.; Lorman, V. L.; Rochal, S. B.

    2016-05-01

    We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group I while the radial field has the full icosahedral symmetry Ih. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure.

  7. In vitro binding of anthrax protective antigen on bacteriophage T4 capsid surface through Hoc-capsid interactions: A strategy for efficient display of large full-length proteins

    International Nuclear Information System (INIS)

    An in vitro binding system is described to display large full-length proteins on bacteriophage T4 capsid surface at high density. The phage T4 icosahedral capsid features 155 copies of a nonessential highly antigenic outer capsid protein, Hoc, at the center of each major capsid protein hexon. Gene fusions were engineered to express the 83-kDa protective antigen (PA) from Bacillus anthracis fused to the N-terminus of Hoc and the 130-kDa PA-Hoc protein was expressed in Escherichia coli and purified. The purified PA-Hoc was assembled in vitro on hoc - phage particles. Binding was specific, stable, and of high affinity. This defined in vitro system allowed manipulation of the copy number of displayed PA and imposed no significant limitation on the size of the displayed antigen. In contrast to in vivo display systems, the in vitro approach allows all the capsid binding sites to be occupied by the 130-kDa PA-Hoc fusion protein. The PA-T4 particles were immunogenic in mice in the absence of an adjuvant, eliciting strong PA-specific antibodies and anthrax lethal toxin neutralizing antibodies. The in vitro display on phage T4 offers a novel platform for potential construction of customized vaccines against anthrax and other infectious diseases

  8. Characterization of the binding sites of two proteins involved in the bacteriophage P2 site-specific recombination system.

    OpenAIRE

    Yu, A.; Haggård-Ljungquist, E

    1993-01-01

    Integration of the bacteriophage P2 genome into the Escherichia coli host chromosome occurs by site-specific recombination between the phage attP and E. coli attB sites. The phage-encoded 38-kDa protein, integrase, is known to be necessary for both phage integration as well as excision. In order to begin the molecular characterization of this recombination event, we have cloned the int gene and overproduced and partially purified the Int protein and an N-terminal truncated form of Int. Both t...

  9. 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...

  10. φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity

    Directory of Open Access Journals (Sweden)

    Kvitko Brian H

    2012-12-01

    Full Text Available Abstract Background Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237. Results We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains. Conclusions The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.

  11. 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

  12. Crystallization and preliminary crystallographic analysis of the major capsid proteins VP16 and VP17 of bacteriophage P23-77

    International Nuclear Information System (INIS)

    The major capsid proteins VP16 and VP17 of bacteriophage P23-77 have been crystallized using both recombinant and purified virus and preliminary diffraction analyses have been performed. Members of the diverse double-β-barrel lineage of viruses are identified by the conserved structure of their major coat protein. New members of this lineage have been discovered based on structural analysis and we are interested in identifying relatives that utilize unusual versions of the double-β-barrel fold. One candidate for such studies is P23-77, an icosahedral dsDNA bacteriophage that infects the extremophile Thermus thermophilus. P23-77 has two major coat proteins, namely VP16 and VP17, of a size consistent with a single-β-barrel core fold. These previously unstudied proteins have now been successfully expressed as recombinant proteins, purified and crystallized using hanging-drop and sitting-drop vapour-diffusion methods. Crystals of coat proteins VP16 and VP17 have been obtained as well as of a putative complex. In addition, virus-derived material has been crystallized. Diffraction data have been collected to beyond 3 Å resolution for five crystal types and structure determinations are in progress

  13. 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.

  14. Nonlinear Finite Element Analysis of Nanoindentation of Viral Capsids

    CERN Document Server

    Gibbons, M M; Gibbons, Melissa M.; Klug, William S.

    2006-01-01

    Recent Atomic Force Microscope (AFM) nanoindentation experiments measuring mechanical response of the protein shells of viruses have provided a quantitative description of their strength and elasticity. To better understand and interpret these measurements, and to elucidate the underlying mechanisms, this paper adopts a course-grained modeling approach within the framework of three-dimensional nonlinear continuum elasticity. Homogeneous, isotropic, elastic, thick shell models are proposed for two capsids: the spherical Cowpea Chlorotic Mottle Virus (CCMV), and the ellipsocylindrical bacteriophage $\\phi 29$. As analyzed by the finite element method, these models enable parametric characterization of the effects of AFM tip geometry, capsid dimensions, and capsid constitutive descriptions. The generally nonlinear force response of capsids to indentation is shown to be insensitive to constitutive details, and greatly influenced by geometry. Nonlinear stiffening and softening of the force response is dependent on ...

  15. 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

  16. 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.

  17. 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...

  18. 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

  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. 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.

  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. 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

  3. 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.

  4. Continuum Theory of Retroviral Capsids

    Science.gov (United States)

    Nguyen, T. T.; Bruinsma, R. F.; Gelbart, W. M.

    2006-02-01

    We present a self-assembly phase diagram for the shape of retroviral capsids, based on continuum elasticity theory. The spontaneous curvature of the capsid proteins drives a weakly first-order transition from spherical to spherocylindrical shapes. The conical capsid shape which characterizes the HIV-1 retrovirus is never stable under unconstrained energy minimization. Only under conditions of fixed volume and/or fixed spanning length can the conical shape be a minimum energy structure. Our results indicate that, unlike the capsids of small viruses, retrovirus capsids are not uniquely determined by the molecular structure of the constituent proteins but depend in an essential way on physical constraints present during assembly.

  5. Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA Origami

    Energy Technology Data Exchange (ETDEWEB)

    Stephanopoulos, Nicholas [Univ. of California, Berkeley, CA (United States); Liu, Minghui [Arizona State Univ., Tempe, AZ (United States); Tong, Gary J [Univ. of California, Berkeley, CA (United States); Li, Zhe [Arizona State Univ., Tempe, AZ (United States); Liu, Yan [Arizona State Univ., Tempe, AZ (United States); Yan, Hao [Arizona State Univ., Tempe, AZ (United States); Francis, Matthew B [Univ. of California, Berkeley, CA (United States)

    2010-06-24

    DNA origami was used as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. To do this, we first modified the interior surface of bacteriophage MS2 capsids with fluorescent dyes as a model cargo. An unnatural amino acid on the external surface was then coupled to DNA strands that were complementary to those extending from origami tiles. Two different geometries of DNA tiles (rectangular and triangular) were used. The capsids associated with tiles of both geometries with virtually 100% efficiency under mild annealing conditions, and the location of capsid immobilization on the tile could be controlled by the position of the probe strands. The rectangular tiles and capsids could then be arranged into one-dimensional arrays by adding DNA strands linking the corners of the tiles. The resulting structures consisted of multiple capsids with even spacing (~100 nm). We also used a second set of tiles that had probe strands at both ends, resulting in a one-dimensional array of alternating capsids and tiles. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multicomponent systems from biological scaffolds using the power of rationally engineered DNA nanostructures.

  6. 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...

  7. 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

  8. 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...

  9. 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

  10. 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 ...

  11. 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...

  12. 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...

  13. P2X receptors.

    Science.gov (United States)

    North, R Alan

    2016-08-01

    Extracellular adenosine 5'-triphosphate (ATP) activates cell surface P2X and P2Y receptors. P2X receptors are membrane ion channels preferably permeable to sodium, potassium and calcium that open within milliseconds of the binding of ATP. In molecular architecture, they form a unique structural family. The receptor is a trimer, the binding of ATP between subunits causes them to flex together within the ectodomain and separate in the membrane-spanning region so as to open a central channel. P2X receptors have a widespread tissue distribution. On some smooth muscle cells, P2X receptors mediate the fast excitatory junction potential that leads to depolarization and contraction. In the central nervous system, activation of P2X receptors allows calcium to enter neurons and this can evoke slower neuromodulatory responses such as the trafficking of receptors for the neurotransmitter glutamate. In primary afferent nerves, P2X receptors are critical for the initiation of action potentials when they respond to ATP released from sensory cells such as taste buds, chemoreceptors or urothelium. In immune cells, activation of P2X receptors triggers the release of pro-inflammatory cytokines such as interleukin 1β. The development of selective blockers of different P2X receptors has led to clinical trials of their effectiveness in the management of cough, pain, inflammation and certain neurodegenerative diseases.This article is part of the themed issue 'Evolution brings Ca(2+) and ATP together to control life and death'. PMID:27377721

  14. 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.

  15. 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

  16. 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.

  17. Theory of morphological transformation of viral capsid shells during maturation process

    CERN Document Server

    Konevtsova, O V; Rochal, S B

    2015-01-01

    In the frame of the Landau-Ginzburg formalism we propose a minimal phenomenological model for a morphological transformation in viral capsid shells. The transformation takes place during virus maturation process which renders virus infectious. The theory is illustrated on the example of the HK97 bacteriophage and viruses with similar morphological changes in the protective protein shell. The transformation is shown to be a structural phase transition driven by two order parameters. The first order parameter describes the isotropic expansion of the protein shell while the second one is responsible for the shape symmetry breaking and the resulting shell faceting. The group theory analysis and the resulting thermodynamic model make it possible to choose the parameter which discriminates between the icosahedral shell faceting often observed in viral capsids and the dodecahedral one observed in viruses of the Parvovirus family. Calculated phase diagram illustrates the discontinuous character of the virus morpholog...

  18. P2P financovanie

    OpenAIRE

    Dobiasová, Dana

    2015-01-01

    The aim of this bachelors thesis is to determine the effect of P2P lending on the economic indicators and the status of small and medium enterprises in the United States, specifically for the period form 2011 to 2015. To better understand the practical part, two first chapters will be focused on defining the concept of P2P lending and analysing the current situation in the United States. Besides that, it is also an emphasis on regulatory requirements which are newly starting to appear. This k...

  19. Saperi P2P

    Directory of Open Access Journals (Sweden)

    Salvatore Iaconesi

    2009-10-01

    Full Text Available Il paper presenta l'architettura filosofica e logica di un progetto ongoing per la creazione di un'infrastruttura peer to peer per la diffusione dei saperi. Tale infrastruttura p2p vuole essere la base per costruire un framework aperto e orizzontale, che ospiti pratiche innovative di creazione, condivisione e disseminazione di informazioni e conoscenza.

  20. 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...

  1. 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...

  2. Virus Capsids as Targeted Nanoscale Delivery Vessels of Photoactive Compounds for Site-Specific Photodynamic Therapy

    Science.gov (United States)

    Cohen, Brian A.

    The research presented in this work details the use of a viral capsid as an addressable delivery vessel of photoactive compounds for use in photodynamic therapy. Photodynamic therapy is a treatment that involves the interaction of light with a photosensitizing molecule to create singlet oxygen, a reactive oxygen species. Overproduction of singlet oxygen in cells can cause oxidative damage leading to cytotoxicity and eventually cell death. Challenges with the current generation of FDA-approved photosensitizers for photodynamic therapy primarily stem from their lack of tissue specificity. This work describes the packaging of photoactive cationic porphyrins inside the MS2 bacteriophage capsid, followed by external modification of the capsid with cancer cell-targeting G-quadruplex DNA aptamers to generate a tumor-specific photosensitizing agent. First, a cationic porphyrin is loaded into the capsids via nucleotide-driven packaging, a process that involves charge interaction between the porphyrin and the RNA inside the capsid. Results show that over 250 porphyrin molecules associate with the RNA within each MS2 capsid. Removal of RNA from the capsid severely inhibits the packaging of the cationic porphyrins. Porphyrin-virus constructs were then shown to photogenerate singlet oxygen, and cytotoxicity in non-targeted photodynamic treatment experiments. Next, each porphyrin-loaded capsid is externally modified with approximately 60 targeting DNA aptamers by employing a heterobifunctional crosslinking agent. The targeting aptamer is known to bind the protein nucleolin, a ubiquitous protein that is overexpressed on the cell surface by many cancer cell types. MCF-7 human breast carcinoma cells and MCF-10A human mammary epithelial cells were selected as an in vitro model for breast cancer and normal tissue, respectively. Fluorescently tagged virus-aptamer constructs are shown to selectively target MCF-7 cells versus MCF-10A cells. Finally, results are shown in which porphyrin

  3. Molecular Architecture of the Retroviral Capsid.

    Science.gov (United States)

    Perilla, Juan R; Gronenborn, Angela M

    2016-05-01

    Retroviral capsid cores are proteinaceous containers that self-assemble to encase the viral genome and a handful of proteins that promote infection. Their function is to protect and aid in the delivery of viral genes to the nucleus of the host, and, in many cases, infection pathways are influenced by capsid-cellular interactions. From a mathematical perspective, capsid cores are polyhedral cages and, as such, follow well-defined geometric rules. However, marked morphological differences in shapes exist, depending on virus type. Given the specific roles of capsid in the viral life cycle, the availability of detailed molecular structures, particularly at assembly interfaces, opens novel avenues for targeted drug development against these pathogens. Here, we summarize recent advances in the structure and understanding of retroviral capsid, with particular emphasis on assemblies and the capsid cores. PMID:27039020

  4. 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.

  5. 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.

  6. 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}.

  7. [A STUDY OF THE ISOLATED BACTERIOPHAGE ΦAB-SP7 ADSORPTION ON THE CELL SURFACE OF THE AZOSPIRILLUM BRASILENSE SP7].

    Science.gov (United States)

    Guliy, O I; Karavaeva, O A; Velikov, V A; Sokolov, O I; Pavily, S A; Larionova, O S; Burov, A M; Ignatov, O V

    2016-01-01

    The bacteriophage ΦAb-Sp7 was isolated from the cells of the Azospirillum brasilense Sp7. The morphology, size of the gram-negative colonies, and range of lytic activity against other strains and species of the genus Azospirillum was tested. The isolated phage DNA was examined using electrophoretic and restriction analysis, and the size of the genome were established. The electron microscopy. resuIts show that the phage (capsid) has a strand-like form. The electron microscopy study of the bacteriophage ΦAb-Sp7 adsorption on the A. brasilense Sp7 bacterial surface was performed. PMID:27145602

  8. 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

  9. 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.)

  10. 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.

  11. 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...

  12. Prediction of stability changes upon mutation in an icosahedral capsid.

    Science.gov (United States)

    Hickman, Samuel J; Ross, James F; Paci, Emanuele

    2015-09-01

    Identifying the contributions to thermodynamic stability of capsids is of fundamental and practical importance. Here we use simulation to assess how mutations affect the stability of lumazine synthase from the hyperthermophile Aquifex aeolicus, a T = 1 icosahedral capsid; in the simulations the icosahedral symmetry of the capsid is preserved by simulating a single pentamer and imposing crystal symmetry, in effect simulating an infinite cubic lattice of icosahedral capsids. The stability is assessed by estimating the free energy of association using an empirical method previously proposed to identify biological units in crystal structures. We investigate the effect on capsid formation of seven mutations, for which it has been experimentally assessed whether they disrupt capsid formation or not. With one exception, our approach predicts the effect of the mutations on the capsid stability. The method allows the identification of interaction networks, which drive capsid assembly, and highlights the plasticity of the interfaces between subunits in the capsid. PMID:26178267

  13. 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.

  14. 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

  15. Membrane-mediated interaction between retroviral capsids

    Science.gov (United States)

    Zhang, Rui; Nguyen, Toan

    2012-02-01

    A retrovirus is an RNA virus that is replicated through a unique strategy of reverse transcription. Unlike regular enveloped viruses which are assembled inside the host cells, the assembly of retroviral capsids happens right on the cell membrane. During the assembly process, the partially formed capsids deform the membrane, giving rise to an elastic energy. When two such partial capsids approach each other, this elastic energy changes. Or in other words, the two partial capsids interact with each other via the membrane. This membrane mediated interaction between partial capsids plays an important role in the kinetics of the assembly process. In this work, this membrane mediated interaction is calculated both analytically and numerically. It is worth noting that the diferential equation determining the membrane shape in general nonlinear and cannot be solved analytically,except in the linear region of small deformations. And it is exactly the nonlinear regime that is important for the assembly kinetics of retroviruses as it provides a large energy barrier. The theory developed here is applicable to more generic cases of membrane mediated interactions between two membrane-embedded proteins.

  16. 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.

  17. Pollution Prevention (P2) Widget

    Data.gov (United States)

    U.S. Environmental Protection Agency — The P2 (Pollution Prevention) Widget allows the user to retrieve information on reductions in waste generation, safer waste management alternatives, and effective...

  18. Dynamic pathways for viral capsid assembly

    Energy Technology Data Exchange (ETDEWEB)

    Hagan, Michael F.; Chandler, David

    2006-02-09

    We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive assembly. For some ranges of parameters, assembly is facile, while for others, assembly is dynamically frustrated by kinetic traps corresponding to malformed or incompletely formed capsids. Our simulations sample many independent trajectories at various capsomer concentrations, allowing for statistically meaningful conclusions. Depending on subunit (i.e., capsomer) geometries, successful assembly proceeds by several mechanisms involving binding of intermediates of various sizes. We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes.

  19. Second-site suppressors of HIV-1 capsid mutations: restoration of intracellular activities without correction of intrinsic capsid stability defects

    OpenAIRE

    Yang Ruifeng; Shi Jiong; Byeon In-Ja L; Ahn Jinwoo; Sheehan Jonathan H; Meiler Jens; Gronenborn Angela M; Aiken Christopher

    2012-01-01

    Abstract Background Disassembly of the viral capsid following penetration into the cytoplasm, or uncoating, is a poorly understood stage of retrovirus infection. Based on previous studies of HIV-1 CA mutants exhibiting altered capsid stability, we concluded that formation of a capsid of optimal intrinsic stability is crucial for HIV-1 infection. Results To further examine the connection between HIV-1 capsid stability and infectivity, we isolated second-site suppressors of HIV-1 mutants exhibi...

  20. 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

  1. 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

  2. Genomic Sequencing and Biological Characteristics of a Novel Escherichia Coli Bacteriophage 9g, a Putative Representative of a New Siphoviridae Genus

    Directory of Open Access Journals (Sweden)

    Eugene E. Kulikov

    2014-12-01

    Full Text Available Bacteriophage 9g was isolated from horse feces using Escherichia coli C600 as a host strain. Phage 9g has a slightly elongated capsid 62 × 76 nm in diameter and a non-contractile tail about 185 nm long. The complete genome sequence of this bacteriophage consists of 56,703 bp encoding 70 predicted open reading frames. The closest relative of phage 9g is phage PhiJL001 infecting marine alpha-proteobacterium associated with Ircinia strobilina sponge, sharing with phage 9g 51% of amino acid identity in the main capsid protein sequence. The DNA of 9g is resistant to most restriction endonucleases tested, indicating the presence of hypermodified bases. The gene cluster encoding a biosynthesis pathway similar to biosynthesis of the unusual nucleoside queuosine was detected in the phage 9g genome. The genomic map organization is somewhat similar to the typical temperate phage gene layout but no integrase gene was detected. Phage 9g efficiently forms stable associations with its host that continues to produce the phage over multiple passages, but the phage can be easily eliminated via viricide treatment indicating that no true lysogens are formed. Since the sequence, genomic organization and biological properties of bacteriophage 9g are clearly distinct from other known Enterobacteriaceae phages, we propose to consider it as the representative of a novel genus of the Siphoviridae family.

  3. Derepression of prophage P2 by satellite phage P4: cloning of the P4 epsilon gene and identification of its product.

    OpenAIRE

    Liu, T; Renberg, S K; Haggård-Ljungquist, E

    1997-01-01

    Escherichia coli phage P4 lacks all of the genetic information necessary for capsid, tail, and lysis functions. P4 is therefore dependent on a helper phage, such as P2, for lytic propagation. During P4 superinfection of a P2 lysogen, the P2 prophage is derepressed by the action of the P4-encoded epsilon gene. We have cloned the epsilon gene and identified the 10-kDa E protein. The epsilon gene product is the only P4 protein required to derepress prophage P2, which leads to in situ P2 DNA repl...

  4. 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 ...

  5. Kinetics versus Thermodynamics in Virus Capsid Polymorphism.

    Science.gov (United States)

    Moerman, Pepijn; van der Schoot, Paul; Kegel, Willem

    2016-07-01

    Virus coat proteins spontaneously self-assemble into empty shells in aqueous solution under the appropriate physicochemical conditions, driven by an interaction free energy per bond on the order of 2-5 times the thermal energy kBT. For this seemingly modest interaction strength, each protein building block nonetheless gains a very large binding free energy, between 10 and 20 kBT. Because of this, there is debate about whether the assembly process is reversible or irreversible. Here we discuss capsid polymorphism observed in in vitro experiments from the perspective of nucleation theory and of the thermodynamics of mass action. We specifically consider the potential contribution of a curvature free energy term to the effective interaction potential between the proteins. From these models, we propose experiments that may conclusively reveal whether virus capsid assembly into a mixture of polymorphs is a reversible or an irreversible process. PMID:27027925

  6. Mechanostability of Proteins and Virus Capsids

    Science.gov (United States)

    Cieplak, Marek

    2013-03-01

    Molecular dynamics of proteins within coarse grained models have become a useful tool in studies of large scale systems. The talk will discuss two applications of such modeling. The first is a theoretical survey of proteins' resistance to constant speed stretching as performed for a set of 17134 simple and 318 multidomain proteins. The survey has uncovered new potent force clamps. They involve formation of cysteine slipknots or dragging of a cystine plug through the cystine ring and lead to characteristic forces that are significantly larger than the common shear-based clamp such as observed in titin. The second application involves studies of nanoindentation processes in virus capsids and elucidates their molecular aspects by showing deviations in behavior compared to the continuum shell model. Across the 35 capsids studied, both the collapse force and the elastic stiffness are observed to vary by a factor of 20. The changes in mechanical properties do not correlate simply with virus size or symmetry. There is a strong connection to the mean coordination number , defined as the mean number of interactions to neighboring amino acids. The Young's modulus for thin shell capsids rises roughly quadratically with - 6, where 6 is the minimum coordination for elastic stability in three dimensions. Supported by European Regional Development Fund, through Innovative Economy grant Nanobiom (POIG.01.01.02-00-008/08)

  7. Capsid modification strategies for detargeting adenoviral vectors.

    Science.gov (United States)

    Parker, Alan L; Bradshaw, Angela C; Alba, Raul; Nicklin, Stuart A; Baker, Andrew H

    2014-01-01

    Adenoviral vectors hold immense potential for a wide variety of gene therapy based applications; however, their efficacy and toxicity is dictated by "off target" interactions that preclude cell specific targeting to sites of disease. A number of "off target" interactions have been described in the literature that occur between the three major capsid proteins (hexon, penton, and fiber) and components of the circulatory system, including cells such as erythrocytes, white blood cells, and platelets, as well as circulatory proteins including complement proteins, coagulation factors, von Willebrand Factor, p-selectin as well as neutralizing antibodies. Thus, to improve efficacious targeting to sites of disease and limit nonspecific uptake of virus to non-target tissues, specifically the liver and the spleen, it is necessary to develop suitable strategies for genetically modifying the capsid proteins to preclude these interactions. To this end we have developed versatile systems based on homologous recombination for modification of each of the major capsid proteins, which are described herein. PMID:24132476

  8. 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

  9. 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.

  10. 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

  11. Fv1 restriction and retrovirus vaccine immunity in Apobec3-deficient 129P2 mice.

    Directory of Open Access Journals (Sweden)

    Kalani Halemano

    Full Text Available Understanding the host genetics of the immune response in retrovirus infection models could provide insights for basic HIV vaccine discovery. In Friend retrovirus (FV infection of mice, Fv1 differentially inhibits N-tropic versus B-tropic FV infection by mediating a capsid-dependent post-entry block, Fv2 susceptibility governs splenomegaly induction, and Rfv3 resistance primes a stronger neutralizing antibody response due to more potent Apobec3 activity. Apobec3 polymorphisms in inbred mouse strains correlate with Rfv3 resistance and susceptibility, with one unresolved exception. The 129/OlaHsd (129P2 mouse strain is Fv2 and Rfv3 susceptible based on genotyping, but infection of 129P2 mice with B-tropic FV resulted in strong neutralizing antibody responses and no splenomegaly. Here we confirm that 129P2 mice are Fv1(nr/nr, explaining its resistance to B-tropic FV. Infection of 129P2 mice with NB-tropic FV, which can efficiently infect mice independent of Fv1 genotype, resulted in severe splenomegaly, high levels of viremia and weak neutralizing antibody responses regardless of Apobec3 status. Notably, high-dose B-tropic FV infection of 129P2 Apobec3-deficient mice induced significant adaptive immune responses and conferred high levels of protection following challenge with pathogenic NB-tropic FV. This immunological protection complemented previous studies that N-tropic FV can act as a live-attenuated vaccine in Fv1 (b/b mice. Altogether, the results obtained in 129P2 mice strengthen the conclusion that Rfv3 is encoded by Apobec3, and highlight Fv1 incompatibility as a retroviral vaccine paradigm in mice. Due to its susceptibility to disease that allows for pathogenic challenge studies, B-tropic FV infection of 129P2 mice may be a useful model to study the immunological pathways induced by retroviral capsid restriction.

  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. Modeling HIV-1 viral capsid nucleation by dynamical systems.

    Science.gov (United States)

    Sadre-Marandi, Farrah; Liu, Yuewu; Liu, Jiangguo; Tavener, Simon; Zou, Xiufen

    2015-12-01

    There are two stages generally recognized in the viral capsid assembly: nucleation and elongation. This paper focuses on the nucleation stage and develops mathematical models for HIV-1 viral capsid nucleation based on six-species dynamical systems. The Particle Swarm Optimization (PSO) algorithm is used for parameter fitting to estimate the association and dissociation rates from biological experiment data. Numerical simulations of capsid protein (CA) multimer concentrations demonstrate a good agreement with experimental data. Sensitivity and elasticity analysis of CA multimer concentrations with respect to the association and dissociation rates further reveals the importance of CA trimer-of- dimers in the nucleation stage of viral capsid self- assembly. PMID:26596714

  14. Large-scale functional purification of recombinant HIV-1 capsid.

    Directory of Open Access Journals (Sweden)

    Magdeleine Hung

    Full Text Available During human immunodeficiency virus type-1 (HIV-1 virion maturation, capsid proteins undergo a major rearrangement to form a conical core that protects the viral nucleoprotein complexes. Mutations in the capsid sequence that alter the stability of the capsid core are deleterious to viral infectivity and replication. Recently, capsid assembly has become an attractive target for the development of a new generation of anti-retroviral agents. Drug screening efforts and subsequent structural and mechanistic studies require gram quantities of active, homogeneous and pure protein. Conventional means of laboratory purification of Escherichia coli expressed recombinant capsid protein rely on column chromatography steps that are not amenable to large-scale production. Here we present a function-based purification of wild-type and quadruple mutant capsid proteins, which relies on the inherent propensity of capsid protein to polymerize and depolymerize. This method does not require the packing of sizable chromatography columns and can generate double-digit gram quantities of functionally and biochemically well-behaved proteins with greater than 98% purity. We have used the purified capsid protein to characterize two known assembly inhibitors in our in-house developed polymerization assay and to measure their binding affinities. Our capsid purification procedure provides a robust method for purifying large quantities of a key protein in the HIV-1 life cycle, facilitating identification of the next generation anti-HIV agents.

  15. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    Energy Technology Data Exchange (ETDEWEB)

    X Qiu; D Rau; V Parsegian; L Fang; C Knobler; W Gelbart

    2011-12-31

    Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage {lambda} with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5 x 10{sup 3} base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1 kT/bp, an order of magnitude larger than the bending energies.

  16. 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.

  17. 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

  18. Ion etching of bacteriophage lambda: evidence that the right end of the DNA is located at the outside of the phage DNA mass.

    OpenAIRE

    Brown, J.C.; Newcomb, W W

    1986-01-01

    Bacteriophage lambda was etched in an Ar+ plasma under conditions in which the capsid and some of the DNA were eroded (by sputtering) from the particle surface. Analysis of the DNA remaining in etched phage demonstrated an enrichment in sequences derived from the left end and middle of the genome; sequences from the right end were selectively lost. The results suggest that the DNA in the mature phage is arranged with its left end toward the center and its right end toward the exterior of the ...

  19. Mx oligomer: a novel capsid pattern sensor?

    Science.gov (United States)

    Kong, Jia; Ma, Min; He, Shuangyi; Qin, Xiaohong

    2016-08-01

    Myxovirus resistance proteins represent a family of interferon-induced restriction factors of the innate and adaptive immune system. Human MxB acts as a novel restriction factor with antiviral activity against a range of HIV-1 and other retroviruses mainly by inhibiting the uncoating process after reverse transcription but prior to integration. Based on published data and conservation analysis, we propose a novel hypothesis, in which MxB dimers form higher order oligomers that restrict retroviral replication by binding to the viral capsid. Insights into the mechanistic basis of structural and functional characteristics of MxB will greatly advance our understanding of MxB. PMID:27492442

  20. Studies towards the Sex Pheromone of the Green Capsid Bug

    NARCIS (Netherlands)

    Drijfhout, F.P.

    2001-01-01

    The green capsid bug, Lygocoris pabulinus (L.) (Heteroptera: Miridae) is a serious pest in fruit orchards, which is difficult to control. Because it is difficult to determine the actual population density, fruit growers apply insecticides against the green capsid bug on regular times to reduce the r

  1. 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

  2. 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.

  3. Towards P2P XML Database Technology

    NARCIS (Netherlands)

    Zhang, Y.

    2007-01-01

    To ease the development of data-intensive P2P applications, we envision a P2P XML Database Management System (P2P XDBMS) that acts as a database middle-ware, providing a uniform database abstraction on top of a dynamic set of distributed data sources. In this PhD work, we research which features suc

  4. Heteromeric assembly of P2X subunits

    Directory of Open Access Journals (Sweden)

    Ralf Hausmann

    2013-12-01

    Full Text Available Transcripts and/or proteins of P2X receptor (P2XR subunits have been found in virtually all mammalian tissues. Generally more than one of the seven known P2X subunits have been identified in a given cell type. Six of the seven cloned P2X subunits can efficiently form functional homotrimeric ion channels in recombinant expression systems. This is in contrast to other ligand-gated ion channel families, such as the Cys-loop or glutamate receptors, where homomeric assemblies seem to represent the exception rather than the rule. P2XR mediated responses recorded from native tissues rarely match exactly the biophysical and pharmacological properties of heterologously expressed homomeric P2XRs. Heterotrimerization of P2X subunits is likely to account for this observed diversity. While the existence of heterotrimeric P2X2/3Rs and their role in physiological processes is well established, the composition of most other P2XR heteromers and/or the interplay between distinct trimeric receptor complexes in native tissues is not clear. After a description of P2XR assembly and the structure of the intersubunit ATP-binding site, this review summarizes the distribution of P2XR subunits in selected mammalian cell types and the biochemically and/or functionally characterized heteromeric P2XRs that have been observed upon heterologous co-expression of P2XR subunits. We further provide examples where the postulated heteromeric P2XRs have been suggested to occur in native tissues and an overview of the currently available pharmacological tools that have been used to discriminate between homo- and heteromeric P2XRs

  5. 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.

  6. Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids

    OpenAIRE

    Li, Yen-Li; Chandrasekaran, Viswanathan; Carter, Stephen D.; Woodward, Cora L.; Christensen, Devin E; Dryden, Kelly A.; Pornillos, Owen; Yeager, Mark; Ganser-Pornillos, Barbie K.; Jensen, Grant J; Sundquist, Wesley I.

    2016-01-01

    TRIM5 proteins are restriction factors that block retroviral infections by binding viral capsids and preventing reverse transcription. Capsid recognition is mediated by C-terminal domains on TRIM5α (SPRY) or TRIMCyp (cyclophilin A), which interact weakly with capsids. Efficient capsid recognition also requires the conserved N-terminal tripartite motifs (TRIM), which mediate oligomerization and create avidity effects. To characterize how TRIM5 proteins recognize viral capsids, we developed met...

  7. Structure of the Triatoma virus capsid

    Energy Technology Data Exchange (ETDEWEB)

    Squires, Gaëlle; Pous, Joan [Laboratoire de Virologie Moléculaire et Structurale, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette CEDEX (France); Agirre, Jon [Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia (FBB) (Spain); Unidad de Biofísica (UBF, CSIC, UPV/EHU), PO Box 644, 48080 Bilbao (Spain); Rozas-Dennis, Gabriela S. [U.N.S., San Juan 670 (8000) Bahía Blanca (Argentina); U.N.S., Avenida Alem 1253 (8000) Bahía Blanca (Argentina); Costabel, Marcelo D. [U.N.S., Avenida Alem 1253 (8000) Bahía Blanca (Argentina); Marti, Gerardo A. [Centro de Estudios Parasitológicos y de Vectores (CEPAVE-CCT, La Plata, CONICET-UNLP), Calle 2 No. 584 (1900) La Plata (Argentina); Navaza, Jorge; Bressanelli, Stéphane [Laboratoire de Virologie Moléculaire et Structurale, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette CEDEX (France); Guérin, Diego M. A., E-mail: diego.guerin@ehu.es [Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia (FBB) (Spain); Unidad de Biofísica (UBF, CSIC, UPV/EHU), PO Box 644, 48080 Bilbao (Spain); Rey, Felix A., E-mail: diego.guerin@ehu.es [Laboratoire de Virologie Moléculaire et Structurale, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette CEDEX (France)

    2013-06-01

    The crystallographic structure of TrV shows specific morphological and functional features that clearly distinguish it from the type species of the Cripavirus genus, CrPV. The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.

  8. Structure of the Triatoma virus capsid

    International Nuclear Information System (INIS)

    The crystallographic structure of TrV shows specific morphological and functional features that clearly distinguish it from the type species of the Cripavirus genus, CrPV. The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed

  9. 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

  10. 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.

  11. Nanoindentation of virus capsids in a molecular model

    OpenAIRE

    Cieplak, Marek; Robbins, Mark O.

    2010-01-01

    A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that consitute the capsids and is described in terms of the C-alpha atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments...

  12. P2X receptors in neuroglia

    OpenAIRE

    Verkhratsky, Alexei; Pankratov, Yuri; Lalo, Ulyana; Nedergaard, Maiken

    2012-01-01

    Different types of ionotropic P2X purinoceptors are expressed in all major types of neuroglia, where they mediate a variety of physiological and pathological signaling. Cortical astrocytes express specific P2X1/5 heteromeric receptors that are activated by ongoing synaptic transmission and can trigger fast local signaling through elevation in cytoplasmic Ca2+ and Na+ concentrations. Oligodendrocytes express several types of P2X receptors that may control their development and mediate axonal–g...

  13. The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure

    International Nuclear Information System (INIS)

    The C-terminal domain of a bacteriophage P2 tail-spike protein, gpV, was crystallized and its structure was solved at 1.27 Å resolution. The refined model showed a triple β-helix structure and the presence of iron, calcium and chloride ions. The adsorption and infection of bacteriophage P2 is mediated by tail fibres and tail spikes. The tail spikes on the tail baseplate are used to irreversibly adsorb to the host cells. Recently, a P2 phage tail-spike protein, gpV, was purified and it was shown that a C-terminal domain, Ser87–Leu211, is sufficient for the binding of gpV to host Escherichia coli membranes [Kageyama et al. (2009 ▶), Biochemistry, 48, 10129–10135]. In this paper, the crystal structure of the C-terminal domain of P2 gpV is reported. The structure is a triangular pyramid and looks like a spearhead composed of an intertwined β-sheet, a triple β-helix and a metal-binding region containing iron, calcium and chloride ions

  14. 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...

  15. 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.

  16. 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.

  17. 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.

  18. Towards P2P XML Database Technology

    OpenAIRE

    Ying ZHANG

    2007-01-01

    To ease the development of data-intensive P2P applications, we envision a P2P XML Database Management System (P2P XDBMS) that acts as a database middle-ware, providing a uniform database abstraction on top of a dynamic set of distributed data sources. In this PhD work, we research which features such a database abstraction should offer and how it can be realised efficiently by extending and combining existing XML databases with P2P technologies. The first step in this research is a distribute...

  19. Biological Physics Prize talk: Grabbing the Cat by the Tail: Studies of DNA Packaging by Single φ 29 Bacteriophage Particles Using Optical Tweezers

    Science.gov (United States)

    Bustamante, Carlos

    2002-03-01

    I will present our recent results on the packaging of DNA by the connector motor at the base of the head of bacteriophage φ 29. As part of their infection cycle, many viruses must package their newly replicated genomes inside a protein capsid to insure its proper transport and delivery to other host cells. Bacteriophage φ 29 packages its 6.6 mm long double-stranded DNA into a 42 nm dia. x 54 nm high capsid via a portal complex that hydrolyses ATP. This process is remarkable because entropic, electrostatic, and bending energies of the DNA must be overcome to package the DNA to near-crystalline density. We have used optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force generating motor. We find that this motor can work against loads of up to ~57 picoNewtons on average, making it one of the strongest molecular motors ever reported. Movements of over 5 mm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force-velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Interestingly, the packaging rate decreases as the prohead is filled, indicating that an internal pressure builds up due to DNA compression. We estimate that at the end of the packaging the capsid pressure is ~15 MegaPascals, corresponding to an internal force of ~50 pN acting on the motor. The biological implications of this internal pressure and the mechano-chemical efficiency of the engine are discussed.

  20. Cyclophilin A interacts with diverse lentiviral capsids

    Directory of Open Access Journals (Sweden)

    Emerman Michael

    2006-10-01

    Full Text Available Abstract Background The capsid (CA protein of HIV-1 binds with high affinity to the host protein cyclophilin A (CypA. This binding positively affects some early stage of the viral life-cycle because prevention of binding either by drugs that occupy that active site of cyclophilin A, by mutation in HIV-1 CA, or RNAi that knocks down intracellular CypA level diminishes viral infectivity. The closely related lentivirus, SIVcpz also binds CypA, but it was thought that this interaction was limited to the HIV-1/SIVcpz lineage because other retroviruses failed to interact with CypA in a yeast two-hybrid assay. Results We find that diverse lentiviruses, FIV and SIVagmTAN also bind to CypA. Mutagenesis of FIV CA showed that an amino acid that is in a homologous position to the proline at amino acid 90 of HIV-1 CA is essential for FIV interactions with CypA. Conclusion These results demonstrate that CypA binding to lentiviruses is more widespread than previously thought and suggest that this interaction is evolutionarily important for lentiviral infection.

  1. Genome, Proteome and Structure of a T7-Like Bacteriophage of the Kiwifruit Canker Phytopathogen Pseudomonas Syringae pv. Actinidiae

    Directory of Open Access Journals (Sweden)

    Rebekah A. Frampton

    2015-06-01

    Full Text Available Pseudomonas syringae pv. actinidiae is an economically significant pathogen responsible for severe bacterial canker of kiwifruit (Actinidia sp.. Bacteriophages infecting this phytopathogen have potential as biocontrol agents as part of an integrated approach to the management of bacterial canker, and for use as molecular tools to study this bacterium. A variety of bacteriophages were previously isolated that infect P. syringae pv. actinidiae, and their basic properties were characterized to provide a framework for formulation of these phages as biocontrol agents. Here, we have examined in more detail φPsa17, a phage with the capacity to infect a broad range of P. syringae pv. actinidiae strains and the only member of the Podoviridae in this collection. Particle morphology was visualized using cryo-electron microscopy, the genome was sequenced, and its structural proteins were analysed using shotgun proteomics. These studies demonstrated that φPsa17 has a 40,525 bp genome, is a member of the T7likevirus genus and is closely related to the pseudomonad phages φPSA2 and gh-1. Eleven structural proteins (one scaffolding were detected by proteomics and φPsa17 has a capsid of approximately 60 nm in diameter. No genes indicative of a lysogenic lifecycle were identified, suggesting the phage is obligately lytic. These features indicate that φPsa17 may be suitable for formulation as a biocontrol agent of P. syringae pv. actinidiae.

  2. Genome, Proteome and Structure of a T7-Like Bacteriophage of the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae.

    Science.gov (United States)

    Frampton, Rebekah A; Acedo, Elena Lopez; Young, Vivienne L; Chen, Danni; Tong, Brian; Taylor, Corinda; Easingwood, Richard A; Pitman, Andrew R; Kleffmann, Torsten; Bostina, Mihnea; Fineran, Peter C

    2015-07-01

    Pseudomonas syringae pv. actinidiae is an economically significant pathogen responsible for severe bacterial canker of kiwifruit (Actinidia sp.). Bacteriophages infecting this phytopathogen have potential as biocontrol agents as part of an integrated approach to the management of bacterial canker, and for use as molecular tools to study this bacterium. A variety of bacteriophages were previously isolated that infect P. syringae pv. actinidiae, and their basic properties were characterized to provide a framework for formulation of these phages as biocontrol agents. Here, we have examined in more detail φPsa17, a phage with the capacity to infect a broad range of P. syringae pv. actinidiae strains and the only member of the Podoviridae in this collection. Particle morphology was visualized using cryo-electron microscopy, the genome was sequenced, and its structural proteins were analysed using shotgun proteomics. These studies demonstrated that φPsa17 has a 40,525 bp genome, is a member of the T7likevirus genus and is closely related to the pseudomonad phages φPSA2 and gh-1. Eleven structural proteins (one scaffolding) were detected by proteomics and φPsa17 has a capsid of approximately 60 nm in diameter. No genes indicative of a lysogenic lifecycle were identified, suggesting the phage is obligately lytic. These features indicate that φPsa17 may be suitable for formulation as a biocontrol agent of P. syringae pv. actinidiae. PMID:26114474

  3. The RNA core weakly influences the interactions of the bacteriophage MS2 at key environmental interfaces

    KAUST Repository

    Nguyen, Thanh H.

    2011-01-01

    The effect of the RNA core on interfacial interactions of the bacteriophage MS2 was investigated. After removal of the RNA core, empty intact capsids were characterized and compared to untreated MS2. Electron density of untreated MS2 and RNA-free MS2 were characterized by transmission electron microscopy (TEM) and synchrotron-based small angle spectroscopy (SAXS). Suspensions of both particles exhibited similar electrophoretic mobility across a range of pH values. Similar effects were observed at pH 5.9 across a range of NaCl or CaCl2 concentrations. We compared key interfacial interactions (particle-particle and particle/air-water interface) between suspensions of each type of particle using time resolved dynamic light scattering (TR-DLS) to observe and quantify aggregation kinetics and axisymmetric drop shape analysis to measure adsorption at the air-water interface. Both suspensions showed insignificant aggregation over 4 h in 600 mM NaCl solutions. In the presence of Ca2+ ions, aggregation of both types of particles was consistent with earlier aggregation studies and was characterized by both reaction-limited and diffusion-limited regimes occurring at similar [Ca2+]. However, the removal of the RNA from MS2 had no apparent effect on the aggregation kinetics of particles. Despite some differences in the kinetics of adsorption to the air-water interface, the changes in surface tension which result from particle adsorption showed no difference between the untreated MS2 and RNA-free MS2. The interactions and structure of particles at the air-water interface were further probed using interfacial dilational rheology. The surface elasticity (E s) and surface viscosity (ηs) at the interface were low for both the untreated virus and the RNA-free capsid. This observation suggests that the factors that impact the adsorption kinetics are not important for an equilibrated interface. © 2011 The Royal Society of Chemistry.

  4. RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2

    Directory of Open Access Journals (Sweden)

    Ottar Rolfsson

    2008-01-01

    Full Text Available Using a combination of biochemistry, mass spectrometry, NMR spectroscopy and cryo-electron microscopy (cryo-EM, we have been able to show that quasi-equivalent conformer switching in the coat protein (CP of an RNA bacteriophage (MS2 is controlled by a sequence-specific RNA–protein interaction. The RNA component of this complex is an RNA stem-loop encompassing just 19 nts from the phage genomic RNA, which is 3569 nts in length. This binding results in the conversion of a CP dimer from a symmetrical conformation to an asymmetric one. Only when both symmetrical and asymmetrical dimers are present in solution is assembly of the T = 3 phage capsid efficient. This implies that the conformers, we have characterized by NMR correspond to the two distinct quasi-equivalent conformers seen in the 3D structure of the virion. An icosahedrally-averaged single particle cryo-EM reconstruction of the wild-type phage (to ∼9 Å resolution has revealed icosahedrally ordered density encompassing up to 90% of the single-stranded RNA genome. The RNA is seen with a novel arrangement of two concentric shells, with connections between them along the 5-fold symmetry axes. RNA in the outer shell interacts with each of the 90 CP dimers in the T = 3 capsid and although the density is icosahedrally averaged, there appears to be a different average contact at the different quasi-equivalent protein dimers: precisely the result that would be expected if protein conformer switching is RNA-mediated throughout the assembly pathway. This unprecedented RNA structure provides new constraints for models of viral assembly and we describe experiments aimed at probing these. Together, these results suggest that viral genomic RNA folding is an important factor in efficient assembly, and further suggest that RNAs that could sequester viral CPs but not fold appropriately could act as potent inhibitors of viral assembly.

  5. Processes of CdP2 sublimation

    International Nuclear Information System (INIS)

    The process of cadmium diphosphide sublimation are studied under equilibrium conditions. Measurement of vapor pressure above cadmium diphosphide in the temperature range has shown, that the value of summary pressure is a function of monocrystal sizes: the larger the surface is, the higher is vapor pressure. An experiment is exercised on measuring summary vapor pressure above fine-dispersive CdP2 (grain size-5 mk). It is determined that the value of summary pressure above monocrystals with large surface and above fine-dispersive CdP2 is the same in the whole temperature range (740-1000 K). These data permit to state, that equilibrium between the condensated and gaseous phases takes place at evaporating fine-dispersive sample. For finding the way of thermal dissociation at cadmium diphosphide sublimation calculated are the composition of saturated vapor above it by means of the known values of Gibbs energies of solid CdP2 formation, constants of equlibrium of dissociation reaction and summary vapor pressure. The results have shown that saturated vapor above CdP2 in the temperature range practically wholly consists of P4 molecules. Pressure measured at CdP2 sublimation corresponds to three-phase equilibrium between gaseous phase and solid CdP2 and Cd2P3. Standard enthalpy of CdP2 formation has been calculated by means of reaction heat and heat of the Cd2P3 formation

  6. 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

  7. P2 performance measurement tools workbook: Draft

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    The underlying purpose of the Department of Energy`s (DOE) Waste Minimization and Pollution Prevention (WMin/P2) Program is compliance with the waste management regulations set forth by the DOE, the federal government, and individual state and local agencies 1. In addition to these regulatory mandates, the increases in waste management costs and public interest in environmental issues have created other drivers to develop and demonstrate an effective WMin/P2 Program. The Waste Minimization Division (EM-334) must have adequate methods to calculate and roll up pollution prevention (P2) progress to meet the WMin/P2 requirements; these requirements support DOE and national objectives and direct funding. This document outlines a system to evaluate DOE`s P2 progress towards the waste reduction requirements. The emphasis of these pollution prevention measurements is to evaluate whether P2 activities are effective, (i.e., has the required amount of waste been reduced as a result of the P2 activities) and to evaluate the cost management of P2 projects. The performance evaluation system presented in this document encompass these aspects: (1) site requirements that apply to all DOE waste generating organizations, (2) a baseline that is not affected by short-term waste generation, and (3) key indicators that can be rolled up across DOE sites and across specific Cognizant Secretarial Officers` (CSO) sites. In a performance-based management system, requirements are the fundamental link between the planning and measurement process. The site requirements are {open_quotes}targets{close_quotes} at the process or activity level. Measuring DOE`s P2 progress toward these requirements provides the necessary feedback to (1) compare performance with the requirements/standards (i.e., whether the reduction requirement of 50% by 1999 is achievable) (2) detect departures from planned levels of performance, and (3) restore performance to the planned levels or achieve new levels of performance.

  8. Propiedad Intelectual y Redes P2P

    OpenAIRE

    ALCAINE SÁNCHEZ, JUAN FRANCISCO

    2015-01-01

    La meta de este documento no es otra que la de presentar al lector información acerca de la legislación sobre propiedad intelectual y distintos protocolos y software P2P. Primero se mostrará información sobre las principales leyes españolas en materia de propiedad intelectual. Posteriormente se presentará información acerca de los principales protocolos P2P sus clientes a lo largo de la historia de las redes P2P. Por último, se mostrarán las alternativas de pago a la descarga no lega...

  9. The dynamics of polymer ejection from a capsid

    CERN Document Server

    Linna, R P; Kaski, K

    2013-01-01

    The polymer ejection from a capsid is an interesting biological phenomenon with relevance to modern biotechnology. Here we study the capsid ejection using Langevin dynamics and show it to be a highly out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a wall or a membrane dividing free space. We find the escape times to scale with polymer length, $\\tau \\sim N^\\alpha$. The scaling exponent varies with the initial monomer density $\\rho$ inside the capsid. For very low densities $\\rho \\le 0.002$ the polymer is only weakly confined by the capsid, and scaling with $\\alpha = 1.35$ that is very close to the one in polymer translocation was obtained. At intermediate densities we find perfect scaling with $\\alpha = 1.22$ and 1.24 for $\\rho = 0.01$ and 0.02, respectively. For $\\rho \\gtrapprox 0.25$ we find the polymers to be completely confined by the capsid and the perfect scaling be broken. Based on our measurement of short-ranged transitions, the cap...

  10. P2X and P2Y receptor signaling in red blood cells

    Science.gov (United States)

    Sluyter, Ronald

    2015-01-01

    Purinergic signaling involves the activation of cell surface P1 and P2 receptors by extracellular nucleosides and nucleotides such as adenosine and adenosine triphosphate (ATP), respectively. P2 receptors comprise P2X and P2Y receptors, and have well-established roles in leukocyte and platelet biology. Emerging evidence indicates important roles for these receptors in red blood cells. P2 receptor activation stimulates a number of signaling pathways in progenitor red blood cells resulting in microparticle release, reactive oxygen species formation, and apoptosis. Likewise, activation of P2 receptors in mature red blood cells stimulates signaling pathways mediating volume regulation, eicosanoid release, phosphatidylserine exposure, hemolysis, impaired ATP release, and susceptibility or resistance to infection. This review summarizes the distribution of P2 receptors in red blood cells, and outlines the functions of P2 receptor signaling in these cells and its implications in red blood cell biology. PMID:26579528

  11. Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

    Science.gov (United States)

    Grime, John M. A.; Dama, James F.; Ganser-Pornillos, Barbie K.; Woodward, Cora L.; Jensen, Grant J.; Yeager, Mark; Voth, Gregory A.

    2016-05-01

    The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.

  12. A study of variability of capsid protein genes of Radish mosaic virus

    OpenAIRE

    Holá, Marcela

    2008-01-01

    The part of RNA2 genome segment of several isolates of Radish mosaic virus (RaMV) including capsid protein genes was sequenced. Variability of capsid protein genes among the isolates of Radish mosaic virus was studied.

  13. Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

    Science.gov (United States)

    Grime, John M. A.; Dama, James F.; Ganser-Pornillos, Barbie K.; Woodward, Cora L.; Jensen, Grant J.; Yeager, Mark; Voth, Gregory A.

    2016-01-01

    The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies. PMID:27174390

  14. Mobile P2P Fast Similarity Search

    OpenAIRE

    Bocek, T; Hecht, F. V.; Hausheer, D; Hunt, E; Stiller, B.

    2009-01-01

    In informal data sharing environments, misspellings cause problems for data indexing and retrieval. This is even more pronounced in mobile environments, in which devices with limited input devices are used. In a mobile environment, similarity search algorithms for finding misspelled data need to account for limited CPU and bandwidth. This demo shows P2P fast similarity search (P2PFastSS) running on mobile phones and laptops that is tailored to uncertain data entry and use...

  15. Second-site suppressors of HIV-1 capsid mutations: restoration of intracellular activities without correction of intrinsic capsid stability defects

    Directory of Open Access Journals (Sweden)

    Yang Ruifeng

    2012-04-01

    Full Text Available Abstract Background Disassembly of the viral capsid following penetration into the cytoplasm, or uncoating, is a poorly understood stage of retrovirus infection. Based on previous studies of HIV-1 CA mutants exhibiting altered capsid stability, we concluded that formation of a capsid of optimal intrinsic stability is crucial for HIV-1 infection. Results To further examine the connection between HIV-1 capsid stability and infectivity, we isolated second-site suppressors of HIV-1 mutants exhibiting unstable (P38A or hyperstable (E45A capsids. We identified the respective suppressor mutations, T216I and R132T, which restored virus replication in a human T cell line and markedly enhanced the fitness of the original mutants as revealed in single-cycle infection assays. Analysis of the corresponding purified N-terminal domain CA proteins by NMR spectroscopy demonstrated that the E45A and R132T mutations induced structural changes that are localized to the regions of the mutations, while the P38A mutation resulted in changes extending to neighboring regions in space. Unexpectedly, neither suppressor mutation corrected the intrinsic viral capsid stability defect associated with the respective original mutation. Nonetheless, the R132T mutation rescued the selective infectivity impairment exhibited by the E45A mutant in aphidicolin-arrested cells, and the double mutant regained sensitivity to the small molecule inhibitor PF74. The T216I mutation rescued the impaired ability of the P38A mutant virus to abrogate restriction by TRIMCyp and TRIM5α. Conclusions The second-site suppressor mutations in CA that we have identified rescue virus infection without correcting the intrinsic capsid stability defects associated with the P38A and E45A mutations. The suppressors also restored wild type virus function in several cell-based assays. We propose that while proper HIV-1 uncoating in target cells is dependent on the intrinsic stability of the viral capsid, the

  16. 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...

  17. 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...

  18. 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...

  19. 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 ...

  20. 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

  1. 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...

  2. 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

  3. 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

  4. The Amphipathic Helix of Adenovirus Capsid Protein VI Contributes to Penton Release and Postentry Sorting

    OpenAIRE

    Martinez, Ruben; Schellenberger, Pascale; Vasishtan, Daven; Aknin, Cindy; Austin, Sisley; Dacheux, Denis; Rayne, Fabienne; Siebert, Alistair; Ruzsics, Zsolt; GRUENEWALD, Kay; Wodrich, Harald

    2014-01-01

    Nuclear delivery of the adenoviral genome requires that the capsid cross the limiting membrane of the endocytic compartment and traverse the cytosol to reach the nucleus. This endosomal escape is initiated upon internalization and involves a highly coordinated process of partial disassembly of the entering capsid to release the membrane lytic internal capsid protein VI. Using wild-type and protein VI-mutated human adenovirus serotype 5 (HAdV-C5), we show that capsid stability and membrane rup...

  5. Modelling the self-assembly of virus capsids

    International Nuclear Information System (INIS)

    We use computer simulations to study a model, first proposed by Wales (2005 Phil. Trans. R. Soc. A 363 357), for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe assembly dynamics more complex than that seen for the original T = 1 model.

  6. A Simple Model for Immature Retrovirus Capsid Assembly

    Science.gov (United States)

    Paquay, Stefan; van der Schoot, Paul; Dragnea, Bogdan

    In this talk I will present simulations of a simple model for capsomeres in immature virus capsids, consisting of only point particles with a tunable range of attraction constrained to a spherical surface. We find that, at sufficiently low density, a short interaction range is sufficient for the suppression of five-fold defects in the packing and causes instead larger tears and scars in the capsid. These findings agree both qualitatively and quantitatively with experiments on immature retrovirus capsids, implying that the structure of the retroviral protein lattice can, for a large part, be explained simply by the effective interaction between the capsomeres. We thank the HFSP for funding under Grant RGP0017/2012.

  7. 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

  8. 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

  9. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Energy Technology Data Exchange (ETDEWEB)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  10. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    International Nuclear Information System (INIS)

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it

  11. 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

  12. 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

  13. 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

  14. VIRION MORPHOLOGY AND STRUCTURAL ORGANIZATION OF POLYVALENT BACTERIOPHAGES TT10-27 AND KEY.

    Science.gov (United States)

    Faidiuk, I V; Boyko, A A; Muchnyk, F V; Tovkach, F I

    2015-01-01

    Fine ultrastructure of polyvalent bacteriophages TT10-27 and KEY isolated from affected with fire blight disease plant tissues, was studied using electron microscopy. Phages have isometric heads connected to short complex tail (TT10-27, C1-morphotype) or long non-contractile tail (KEY B-1 morphotype). Maximum diameter of TT10-27 head, measured as the distance between opposite vertices, is 71.3 nm; tail tube of 22 nm in diameter and 9.0 nm in width is framed with 12 appendages that form flabellate structure of 47.0-58.6 nm in diameter. KEY features capsid of 78.6 nm in diameter and flexible non-contractile tail of 172.5 nm long, which ends with a conical tip. Due to a number of features phage TT10-27 was assigned to a group of N4-like phages of Podoviridae family. KEY is a representative of family Siphoviridae, the least freaquent group of Erwinia amylovora phages. PMID:26214897

  15. Construction of carrier state viruses with partial genomes of the segmented dsRNA bacteriophages

    International Nuclear Information System (INIS)

    The cystoviridae are bacteriophages with genomes of three segments of dsRNA enclosed within a polyhedral capsid. Two members of this family, PHI6 and PHI8, have been shown to form carrier states in which the virus replicates as a stable episome in the host bacterium while expressing reporter genes such as kanamycin resistance or lacα. The carrier state does not require the activity of all the genes necessary for phage production. It is possible to generate carrier states by infecting cells with virus or by electroporating nonreplicating plasmids containing cDNA copies of the viral genomes into the host cells. We have found that carrier states in both PHI6 and PHI8 can be formed at high frequency with all three genomic segments or with only the large and small segments. The large genomic segment codes for the proteins that constitute the inner core of the virus, which is the structure responsible for the packaging and replication of the genome. In PHI6, a carrier state can be formed with the large and middle segment if mutations occur in the gene for the major structural protein of the inner core. In PHI8, carrier state formation requires the activity of genes 8 and 12 of segment S

  16. P2P Techniques for Decentralized Applications

    CERN Document Server

    Pacitti, Esther

    2012-01-01

    As an alternative to traditional client-server systems, Peer-to-Peer (P2P) systems provide major advantages in terms of scalability, autonomy and dynamic behavior of peers, and decentralization of control. Thus, they are well suited for large-scale data sharing in distributed environments. Most of the existing P2P approaches for data sharing rely on either structured networks (e.g., DHTs) for efficient indexing, or unstructured networks for ease of deployment, or some combination. However, these approaches have some limitations, such as lack of freedom for data placement in DHTs, and high late

  17. P2P Live Video Streaming

    OpenAIRE

    Chatzidrossos, Ilias

    2010-01-01

    The ever increasing demand for video content directed the focus of researchfrom traditional server-based schemes to peer-to-peer systems for videodelivery. In such systems, video data is delivered to the users by utilizing theresources of the users themselves, leading to a potentially scalable solution.Users connect to each other, forming a p2p overlay network on top of theInternet and exchange the video segments among themselves. The performanceof a p2p system is characterized by its capabil...

  18. Thermoelastic properties of Zn3P2

    DEFF Research Database (Denmark)

    Gerward, Leif; Olsen, J. Staun; Waśkowska, A.

    2011-01-01

    The bulk modulus and thermal expansion of Zn3P2 has been investigated at pressures up to 21GPa and temperatures down to 100K. The experimental zero-pressure bulk modulus is 80.7 ± 1.8GPa, in accordance with the bulk modulus scaling and lattice properties of the related compound Cd3P2. A tetragonal...... to orthorhombic phase transformation occurs above 11GPa with a relative volume change of-7.1%. Values for the thermal expansion coefficient are reported at 293, 200 and 100K....

  19. HIV-1 capsid is involved in post-nuclear entry steps

    OpenAIRE

    Chen, N-Y; Zhou, L.; Gane, P.J.; Opp, S.; Ball, N. J.; Nicastro, G.; Zufferey, M.; Buffone, C.; Luban, J.; Selwood, D; Diaz-Griffero, F.; Taylor, I.; Fassati, A.

    2016-01-01

    Background HIV-1 capsid influences viral uncoating and nuclear import. Some capsid is detected in the nucleus but it is unclear if it has any function. We reported that the antibiotic Coumermycin-A1 (C-A1) inhibits HIV-1 integration and that a capsid mutation confers resistance to C-A1, suggesting that capsid might affect post-nuclear entry steps. Results Here we report that C-A1 inhibits HIV-1 integration in a capsid-dependent way. Using molecular docking, we identify an extended binding poc...

  20. L2, the minor capsid protein of papillomavirus

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Joshua W. [Department of Pathology, The Johns Hopkins University, Baltimore, MD 21287 (United States); Roden, Richard B.S., E-mail: roden@jhmi.edu [Department of Pathology, The Johns Hopkins University, Baltimore, MD 21287 (United States); Department of Oncology, The Johns Hopkins University, Baltimore, MD 21287 (United States); Department of Gynecology and Obstetrics, The Johns Hopkins University, Baltimore, MD 21287 (United States)

    2013-10-15

    The capsid protein L2 plays major roles in both papillomavirus assembly and the infectious process. While L1 forms the majority of the capsid and can self-assemble into empty virus-like particles (VLPs), L2 is a minor capsid component and lacks the capacity to form VLPs. However, L2 co-assembles with L1 into VLPs, enhancing their assembly. L2 also facilitates encapsidation of the ∼8 kbp circular and nucleosome-bound viral genome during assembly of the non-enveloped T=7d virions in the nucleus of terminally differentiated epithelial cells, although, like L1, L2 is not detectably expressed in infected basal cells. With respect to infection, L2 is not required for particles to bind to and enter cells. However L2 must be cleaved by furin for endosome escape. L2 then travels with the viral genome to the nucleus, wherein it accumulates at ND-10 domains. Here, we provide an overview of the biology of L2. - Highlights: • L2 is the minor antigen of the non-enveloped T=7d icosahedral Papillomavirus capsid. • L2 is a nuclear protein that can traffic to ND-10 and facilitate genome encapsidation. • L2 is critical for infection and must be cleaved by furin. • L2 is a broadly protective vaccine antigen recognized by neutralizing antibodies.

  1. P2X Receptors and Synaptic Plasticity

    Czech Academy of Sciences Publication Activity Database

    Pankratov, Y.; Lalo, U.; Krishtal, A.; Verkhratsky, Alexei

    2009-01-01

    Roč. 158, č. 1 (2009), s. 137-148. ISSN 0306-4522 Institutional research plan: CEZ:AV0Z50390512 Keywords : ATP * P2X receptors * synaptic plasticity Subject RIV: FH - Neurology Impact factor: 3.292, year: 2009

  2. Role of electrostatic interactions in the assembly of empty spherical viral capsids

    CERN Document Server

    Siber, Antonio

    2007-01-01

    We examine the role of electrostatic interactions in the assembly of empty spherical viral capsids. The charges on the protein subunits that make the viral capsid mutually interact and are expected to yield electrostatic repulsion acting against the assembly of capsids. Thus, attractive protein-protein interactions of non-electrostatic origin must act to enable the capsid formation. We investigate whether the interplay of repulsive electrostatic and attractive interactions between the protein subunits can result in the formation of spherical viral capsids of a preferred radius. For this to be the case, we find that the attractive interactions must depend on the angle between the neighboring protein subunits (i.e. on the mean curvature of the viral capsid) so that a particular angle(s) is (are) preferred energywise. Our results for the electrostatic contributions to energetics of viral capsids nicely correlate with recent experimental determinations of the energetics of protein-protein contacts in Hepatitis B ...

  3. Antigenic properties of avian hepatitis E virus capsid protein.

    Science.gov (United States)

    Zhao, Qin; Syed, Shahid Faraz; Zhou, En-Min

    2015-10-22

    Avian hepatitis E virus (HEV) is the main causative agent of big liver and spleen disease and hepatitis-splenomegaly syndrome in chickens, and is genetically and antigenically related to mammalian HEVs. HEV capsid protein contains immunodominant epitopes and induces a protective humoral immune response. A better understanding of the antigenic composition of this protein is critically important for the development of effective vaccine and sensitive and specific serological assays. To date, six linear antigenic domains (I-VI) have been characterized in avian HEV capsid protein and analyzed for their applications in the serological diagnosis and vaccine design. Domains I and V induce strong immune response in chickens and are common to avian, human, and swine HEVs, indicating that the shared epitopes hampering differential diagnosis of avian HEV infection. Domains III and IV are not immunodominant and elicit a weak immune response. Domain VI, located in the N-terminal region of the capsid protein, can also trigger an intense immune response, but the anti-domain VI antibodies are transient. The protection analysis showed that the truncated capsid protein containing the C-terminal 268 amino acid residues expressed by the bacterial system can provide protective immunity against avian HEV infection in chickens. However, the synthetic peptides incorporating the different linear antigenic domains (I-VI) and epitopes are non-protective. The antigenic composition of avian HEV capsid protein is altogether complex. To develop an effective vaccine and accurate serological diagnostic methods, more conformational antigenic domains or epitopes are to be characterized in detail. PMID:26340899

  4. Genetic analysis and homology modeling of capsid protein of norovirus GII.14.

    Science.gov (United States)

    Chan-It, Wisoot; Thongprachum, Aksara; Okitsu, Shoko; Mizuguchi, Masashi; Ushijima, Hiroshi

    2014-02-01

    In this study, a more detailed genetic characterization of the VP1 capsid protein of uncommon norovirus (NoV) GII.14 strains reported previously in Japan and China was performed using sequence analyses and homology modeling technique. The result of genetic comparison with the M7 prototype strain of GII.14 revealed that 10 amino acid mutations were observed at the same positions across the P2 and P1-2 subdomains in both Japanese and Chinese strains. By the homology modeling of the P domain, 7 out of these 10 mutations were predicted to be located on the surface-exposed P2 and P1-2 subdomains. All GII.14 strains had an altered RGD-like motif (RGT → KGT). While the Chinese strains contained 5 random amino acid changes in the S domain and the P2 subdomain, these changes were not detected in the Japanese strains. In addition, the histo-blood group antigen (HBGA)-binding interfaces remain identical to those of the previously determined GII.4 structure (VA387), suggesting the conservation of HBGA binding profile within the GII genogroup. Taken together, this report provides supportive structural data that antigenic drifts that occurred mostly in the P2 and P1-2 subdomains might be sufficient to generate new mutants, thus permitting the GII.14 virus to escape the host pre-existing immunity. These results also suggest the need for comparing the evolutionary profiles and structural models of rare NoV genotypes to an insight into NoV evolution. PMID:24009213

  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. The P2X7 receptor

    DEFF Research Database (Denmark)

    Kvist, Torben Madsen; Schwarz, Peter; Jørgensen, Niklas Rye

    2014-01-01

    Inflammatory diseases are often multiorganic diseases with manifestations not related directly to the primary affected organ. They are often complicated by a generalized bone loss that subsequently leads to osteoporosis and bone fractures. The exact mechanism for the accompanying bone loss is not...... from an increase in bone resorption and the pro-inflammatory cytokines tumor necrosis factor alpha and interleukin 1 beta and has been shown to not only mediate the inflammatory response but also to strongly stimulate bone degradation. The purinergic P2X7 receptor is central in the processing of these...... two cytokines and in the initiation of the inflammatory response, and it is a key molecule in the regulation of both bone formation and bone resorption. The aim of this review is therefore to provide evidence-based novel hypotheses of the role of ATP-mediated purinergic signalling via the P2X7...

  7. Parallel Multimedia Algorithms in P2G

    OpenAIRE

    2011-01-01

    Multimedia applications have a history of driving the demand for computational resources. In entertainment and digital arts, computer animation is popular, but also compute-intensive. We see that there is an increasing demand on multimedia processing, yet there is a lack of support for complex multimedia workloads with real-time requirements in current parallel and distributed execution frameworks. As a result of this observation, the P2G framework was initiated. With inhe...

  8. Magnetic susceptibility of CdP2

    International Nuclear Information System (INIS)

    Measurements are made for the magnetic susceptibility of the tetragonal modification of CdP2 single crystals carried out by the Faraday method in a 77-300 K temperature range. The single crystals were grown from the vapour phase and by the Bridgman technique. Thermal treatment in vacuum and in the component vapours has shown that the difference in absolute values of the magnetic susceptibility of the initial crystals is pre ermined by structuradet and mechanical processing defects. These defects influence the redistribution of electron density and the growth of the Van-Vleck paramagnetism. Annealing of the nondoped crystals in P vapour resulted in the maximum value of magnetic susceptibility chi=-0.415x10-6 cm3/g which is taken for the lattice susceptibility. It is established that the total susceptibility of CdP2 consists of the lattice susceptibility and defect susceptibility. The Langevin diamagnetism and Van-Vleck paramagnetism are determined, the degree of CdP2 ionicity is also evaluated

  9. 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.

  10. 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

  11. The 'devil's staircase' in CdP2 and ZnP2

    International Nuclear Information System (INIS)

    The defect structures occurring in the different phases of CdP2 and ZnP2 are studied by means of electron diffraction and high resolution electron microscopy. The occurrence of numerous planar interfaces in the β-phase of CdP2 suggests a possible explanation for the series of microphases observed in this type of compound. The absence of thermal dilatation in certain small temperature ranges is explained by assuming that the thermal expansion is in fact compensated in such temperature intervals by the formation of new microphases with a different stacking resulting in smaller lattice parameters. (author)

  12. Cathodoluminescence in doped CdP2 and CdSiP2 crystals

    International Nuclear Information System (INIS)

    Some general features of the behaviour of Cu, Zn, Bi, and Mn impurities in CdSiP2 and CdP2 crystals are studied by analyzing electron beam-excited luminescence spectra measured in a temperature range of 6 to 300 K, as well as by determining their electrical parameters. The impurities are established to substitute mainly the cadmium in the crystalline lattice and to promote the formation of complexes of defects, which are radiative recombination centers. Cadmium vacancies as well participate in the defect complex formation processes. A radiation ascribed to interstitial cadmium-type defects, is discovered in CdSiP2 crystals. (author)

  13. Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: Implications for replication and genome packaging

    International Nuclear Information System (INIS)

    In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein–protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. - Highlights: • YFP fusion proteins of BMV p1a and p2a are biologically active. • Self-interaction was observed for p1a, p2a and CP. • CP interacts with p2a but not p1a. • Majority of reconstituted YFP resulting from bona fide fusion protein partners localized on ER

  14. Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: Implications for replication and genome packaging

    Energy Technology Data Exchange (ETDEWEB)

    Chaturvedi, Sonali; Rao, A.L.N., E-mail: arao@ucr.edu

    2014-09-15

    In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein–protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. - Highlights: • YFP fusion proteins of BMV p1a and p2a are biologically active. • Self-interaction was observed for p1a, p2a and CP. • CP interacts with p2a but not p1a. • Majority of reconstituted YFP resulting from bona fide fusion protein partners localized on ER.

  15. 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.)

  16. The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4

    International Nuclear Information System (INIS)

    Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.

  17. Eclogitic pyroxenes, ordered with p2 symmetry.

    Science.gov (United States)

    Clark, J R; Papike, J J

    1966-11-25

    X-ray diffraction crystal-structure analysis of omphacite from eclogite, Tiburon Peninsula, Marin County, California, shows that this clinopyroxene has P2 symmetry with a nearly ordered distribution of the multiple cation content defined by its approximate formula: (Na(o.5) Ca(o.5)) (Mg(o.4)Fe(2)+( 0.1) Al(0.4) Fe(3) +(0.1)) Si(2)0(6). Na+ and Ca(2+) tend to assume alternate locations in the structure, and ( Mg,Fe(2+)) octahedra alternate with Al(3+). or (Al,F(3+)) octahedra in chains along c. PMID:17752801

  18. MINERVA: Collaborative P2P Search (Demo)

    OpenAIRE

    Bender, Matthias; Michel, Sebastian; Triantafillou, Peter; Weikum, Gerhard; Zimmer, Christian; Böhm, Klemens; Jensen, Christian S.; Haas, Laura M.; Kersten, Martin L.; Larson, Per-Ake; Ooi, Beng Chin

    2005-01-01

    This paper proposes the live demonstration of a prototype of MINERVA, a novel P2P Web search engine. The search engine is layered on top of a DHT-based overlay network that connects an a-priori unlimited number of peers, each of which maintains a personal local database and a local search facility. Each peer posts a small amount of metadata to a physically distributed directory that is used to efficiently select promising peers from across the peer population that ca...

  19. Python passive network mapping P2NMAP

    CERN Document Server

    Hosmer, Chet

    2015-01-01

    Python Passive Network Mapping: P2NMAP is the first book to reveal a revolutionary and open source method for exposing nefarious network activity. The ""Heartbleed"" vulnerability has revealed significant weaknesses within enterprise environments related to the lack of a definitive mapping of network assets. In Python Passive Network Mapping, Chet Hosmer shows you how to effectively and definitively passively map networks. Active or probing methods to network mapping have traditionally been used, but they have many drawbacks - they can disrupt operations, crash systems, and - most important

  20. Useful scars: Physics of the capsids of archaeal viruses

    Science.gov (United States)

    Perotti, L. E.; Dharmavaram, S.; Klug, W. S.; Marian, J.; Rudnick, J.; Bruinsma, R. F.

    2016-07-01

    We propose a physical model for the capsids of tailed archaeal viruses as viscoelastic membranes under tension. The fluidity is generated by thermal motion of scarlike structures that are an intrinsic feature of the ground state of large particle arrays covering surfaces with nonzero Gauss curvature. The tension is generated by a combination of the osmotic pressure of the enclosed genome and an extension force generated by filamentous structure formation that drives the formation of the tails. In continuum theory, the capsid has the shape of a surface of constant mean curvature: an unduloid. Particle arrays covering unduloids are shown to exhibit pronounced subdiffusive and diffusive single-particle transport at temperatures that are well below the melting temperature of defect-free particle arrays on a surface with zero Gauss curvature.

  1. Electronic states of BP, BP +, BP -, B 2P 2, B2P2- and B2P2+

    Science.gov (United States)

    Linguerri, Roberto; Komiha, Najia; Oswald, Rainer; Mitrushchenkov, Alexander; Rosmus, Pavel

    2008-05-01

    Using augmented sextuple zeta basis sets and internally contracted multireference configuration interaction (MRCI) wavefunctions, potential energy, electric dipole and transition moments have been computed for the X 3Π, a 1Σ +, b 1Π and A 3Σ - states of BP, X 2Σ + and A 2Π states of BP - and X 4Σ - and A 4Π states of BP +. From these data spectroscopic constants, radiative transition probabilities and photoelectron spectra of BP - and BP have been evaluated. The non-vanishing spin-orbit coupling elements between the four low lying triplet and singlet states of the neutral BP have also been calculated from MRCI wavefunctions. The treatment of the corresponding perturbations in the manifold of dense rovibrational states in the three lowest states would require a precise knowledge of the electronic excitation energies. Our best singlet-triplet separations (X-a) are calculated to be 2412 cm -1 (MRCI) and 2482 cm -1 (restricted coupled cluster with perturbative triples (RCCSD(T))) with an estimated error bound of about ±200 cm -1. All three states have long radiative lifetimes with cascading among the rovibrational levels of different states. The ionization energy IE e of BP is calculated to be 9.22 eV (MRCI) and 9.48 eV (RCCSD(T)), the electron affinity EA e 2.51 eV (MRCI) and 2.74 eV (RCCSD(T)). The photoelectron spectra of BP and BP - have been obtained from the Franck-Condon factors of the MRCI potentials. For the UV spectroscopy the dipole allowed radiative transition probabilities are given for A 3Σ - ↔ X 3Π, b 1Π ↔ a 1Σ + of BP, A 2Π ↔ X 2Σ + of BP - and A 4Π ↔ X 4Σ - of BP +. The ionization energy IE e of B 2P 2 of 8.71 eV and the electron affinity EA e of 2.34 eV have been calculated by the RCCSD(T)/aVQZ approach. Also the harmonic vibrational wavenumbers for the electronic ground states of the ions B2P2+ and B2P2- are given.

  2. Fluctuation Pressure Assisted Ejection of DNA From Bacteriophage

    CERN Document Server

    Harrison, Michael J

    2010-01-01

    The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of parallel segments that forms an equilibrium conformation at minimum free energy, which presses tightly against internal capsid walls. Using a canonical ensemble at temperature T we calculate internal pressure fluctuations against a slowly moving or static capsid mantle for an elastic continuum model of the folded DNA bundle. It is found that fluctuating pressure on the capsid internal wall from thermal excitation of longitudinal acoustic vibrations in the bundle may have root-mean-square values which are several tens of atmospheres for typically small phage dimensions. Comparisons are given with measured data on three mutants of lambda phage with different base pair lengths and total genome ejection pressures.

  3. Fluctuation Pressure Assisted Ejection of DNA From Bacteriophage

    Science.gov (United States)

    Harrison, Michael J.

    2011-03-01

    The role of thermal pressure fluctuations excited within tightly packaged DNA while it is ejected from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of parallel segments that forms an equilibrium conformation at minimum free energy, which presses tightly against capsid walls. Using a canonical ensemble at temperature T we calculate internal pressure fluctuations against a slowly moving or static capsid mantle for an elastic continuum model of the folded DNA bundle. It is found that fluctuating pressures on the capsid from thermal excitation of longitudinal acoustic vibrations in the bundle whose wavelengths are exceeded by the bend persistence length may have root-mean-square values that are several tens of atmospheres for typically small phage dimensions. Comparisons are given with measured data on three mutants of lambda phage with different base pair lengths and total genome ejection pressures.

  4. Dilatometric study of ZnP2 and CdP2 single crystals

    International Nuclear Information System (INIS)

    Dilatometric measurements of ZnP2 and CdP2 monocrystals of tetragonal modification, grown from a vapour phase, are carried out. Hysteresis of a relative change in monocrystals length by their heating and cooling is identified. It is shown that changes in velocity during the heating or cooling process lead to deviation on the functional dependence curves. The events observed are explained by availability of a homogeneity narrow area in the zinc and cadmium diphosphides. 13 refs.; 3 figs

  5. Characterization of the in vitro HIV-1 Capsid Assembly Pathway

    OpenAIRE

    Barklis, Eric; Alfadhli, Ayna; McQuaw, Carolyn; Yalamuri, Suraj; Still, Amelia; Barklis, Robin Lid; Kukull, Ben; López, Claudia S.

    2009-01-01

    During morphogenesis of mature HIV-1 cores, the viral capsid (CA) proteins assemble conical or tubular shells around the viral ribonucleoprotein complexes. This assembly step is mimicked in vitro through reactions in which CA proteins oligomerize to form long tubes, and this process can be modeled as consisting of a slow nucleation period followed by a rapid phase of tube growth. We have developed a novel fluorescence microscopy approach to monitor in vitro assembly reactions and have employe...

  6. Extreme genetic fragility of the HIV-1 capsid

    OpenAIRE

    Rihn, S.J.; Wilson, S. J.; Loman, N. J.; Alim, M.; Bakker, S.E.; Bhella, D.; Gifford, R.J.; Rixon, F J; Bieniasz, P D

    2013-01-01

    Genetic robustness, or fragility, is defined as the ability, or lack thereof, of a biological entity to maintain function in the face of mutations. Viruses that replicate via RNA intermediates exhibit high mutation rates, and robustness should be particularly advantageous to them. The capsid (CA) domain of the HIV-1 Gag protein is under strong pressure to conserve functional roles in viral assembly, maturation, uncoating, and nuclear import. However, CA is also under strong immunological pres...

  7. Assembly of recombinant Israeli Acute Paralysis Virus capsids.

    Directory of Open Access Journals (Sweden)

    Junyuan Ren

    Full Text Available The dicistrovirus Israeli Acute Paralysis Virus (IAPV has been implicated in the worldwide decline of honey bees. Studies of IAPV and many other bee viruses in pure culture are restricted by available isolates and permissive cell culture. Here we show that coupling the IAPV major structural precursor protein ORF2 to its cognate 3C-like processing enzyme results in processing of the precursor to the individual structural proteins in a number of insect cell lines following expression by a recombinant baculovirus. The efficiency of expression is influenced by the level of IAPV 3C protein and moderation of its activity is required for optimal expression. The mature IAPV structural proteins assembled into empty capsids that migrated as particles on sucrose velocity gradients and showed typical dicistrovirus like morphology when examined by electron microscopy. Monoclonal antibodies raised to recombinant capsids were configured into a diagnostic test specific for the presence of IAPV. Recombinant capsids for each of the many bee viruses within the picornavirus family may provide virus specific reagents for the on-going investigation of the causes of honeybee loss.

  8. Cleavage sites within the poliovirus capsid protein precursors

    International Nuclear Information System (INIS)

    Partial amino-terminal sequence analysis was performed on radiolabeled poliovirus capsid proteins VP1, VP2, and VP3. A computer-assisted comparison of the amino acid sequences obtained with that predicted by the nucleotide sequence of the poliovirus genome allows assignment of the amino terminus of each capsid protein to a unique position within the virus polyprotein. Sequence analysis of trypsin-digested VP4, which has a blocked amino terminus, demonstrates that VP4 is encoded at or very near to the amino terminus of the polyprotein. The gene order of the capsid proteins is VP4-VP2-VP3-VP1. Cleavage of VP0 to VP4 and VP2 is shown to occur between asparagine and serine, whereas the cleavages that separate VP2/VP3 and VP3/VP1 occur between glutamine and glycine residues. This finding supports the hypothesis that the cleavage of VP0, which occurs during virion morphogenesis, is distinct from the cleavages that separate functional regions of the polyprotein

  9. Nanoindentation of virus capsids in a molecular model

    Science.gov (United States)

    Cieplak, Marek; Robbins, Mark O.

    2010-01-01

    A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the Cα atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments, showing an elastic region followed by an irreversible drop in force. The mechanical response of CPMV has not been studied, but the molecular model predicts an order of magnitude higher stiffness and a much shorter elastic region than for CCMV. These large changes result from small structural changes that increase the number of bonds by only 30% and would be difficult to capture in continuum models. Direct comparison of local deformations in continuum and molecular models of CCMV shows that the molecular model undergoes a gradual symmetry breaking rotation and accommodates more strain near the walls than the continuum model. The irreversible drop in force at small separations is associated with rupturing nearly all of the bonds between capsid proteins in the molecular model, while a buckling transition is observed in continuum models.

  10. 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...

  11. 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...

  12. 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

  13. 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...

  14. 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...

  15. Mutational analysis of the capsid protein of Leishmania RNA virus LRV1-4.

    OpenAIRE

    Cadd, T L; MacBeth, K; Furlong, D; Patterson, J. L.

    1994-01-01

    The virion of Leishmania RNA virus is predicted to be composed of a 742-amino-acid major capsid protein and a small percentage of capsid-polymerase fusion molecules. Recently, the capsid protein alone was expressed and shown to spontaneously assemble into viruslike particles. Since the major structural protein of the virion shell self-assembles into viruslike particles when expressed in the baculovirus expression system, assembly of the virion can be studied by mutational analysis and express...

  16. Contribution of PDZD8 to Stabilization of the Human Immunodeficiency Virus Type 1 Capsid

    OpenAIRE

    Guth, Charles Alexander; Sodroski, Joseph

    2014-01-01

    Following human immunodeficiency virus type 1 (HIV-1) entry into the host cell, the viral capsid gradually disassembles in a process called uncoating. A proper rate of uncoating is important for reverse transcription of the HIV-1 genome. Host restriction factors such as TRIM5α and TRIMCyp bind retroviral capsids and cause premature disassembly, leading to blocks in reverse transcription. Other host factors, such as cyclophilin A, stabilize the HIV-1 capsid and are required for efficient infec...

  17. Contribution of PDZD8 to Stabilization of the Human Immunodeficiency Virus (HIV-1) Capsid

    OpenAIRE

    Guth, Charles Alexander

    2013-01-01

    Following human immunodeficiency virus (HIV-1) entry into the host cell, the viral capsid gradually disassembles in a process called uncoating. A proper rate of uncoating is important for reverse transcription of the HIV-1 genome. Host restriction factors such as TRIM5alpha; and TRIMCyp bind retroviral capsids and cause premature disassembly, leading to blocks in reverse transcription. Other host factors, such as cyclophilin A, stabilize the HIV-1 capsid and are required for efficient infe...

  18. The Fate of HIV-1 Capsid: A Biochemical Assay for HIV-1 Uncoating

    OpenAIRE

    Yang, Yang; Luban, Jeremy; Diaz-Griffero, Felipe

    2014-01-01

    The uncoating process of HIV-1 is a poorly understood process, so the development of a reliable assay to study uncoating is critical for moving the field forward. Here we describe an uncoating assay that currently represents the state-of-the-art biochemical procedure for monitoring uncoating and core stability during infection. This assay is based on the biochemical separation of soluble capsid protein from particulate capsid cores and provides information about the fate of the capsid during ...

  19. The fate of HIV-1 capsid: a biochemical assay for HIV-1 uncoating.

    Science.gov (United States)

    Yang, Yang; Luban, Jeremy; Diaz-Griffero, Felipe

    2014-01-01

    The uncoating process of HIV-1 is a poorly understood process, so the development of a reliable assay to study uncoating is critical for moving the field forward. Here we describe an uncoating assay that currently represents the state-of-the-art biochemical procedure for monitoring uncoating and core stability during infection. This assay is based on the biochemical separation of soluble capsid protein from particulate capsid cores and provides information about the fate of the capsid during infection. PMID:24158811

  20. Facilitating the use of alternative capsid control methods towards sustainable production of organic cocoa in Ghana

    OpenAIRE

    Ayenor, G.K.; Huis, van, A.; Obeng-Ofori, D.; Padi, B.; Röling, N.G.

    2007-01-01

    Cocoa (Theobroma cacao L.) is an important foreign exchange earner for Ghana. However, production is constrained by a high incidence of pests and diseases. Based on farmers' needs, this study focused on the control of capsids, mainly Sahlbergella singularis Haglund and Distantiella theobroma (Distant) (both Hemiptera: Miridae). Annual crop loss caused by capsids is estimated at 25¿30%. To control capsids, formal research recommends application of synthetic insecticides four times between Augu...

  1. Three-dimensional structure determination of capsid of Aedes albopicus C6/36 cell densovirus

    Institute of Scientific and Technical Information of China (English)

    CHENG; Lingpeng; CHEN; Senxiong; Jenifer; M.Brannan; Joa

    2004-01-01

    The three-dimensional structure of capsid of Aedes albopictus C6/36 densovirus was determined to 14-(A) resolution by electron cryomicroscopy and computer reconstruction. The triangulation number of the capsid is 1. There are 12 holes in each triangular face and a spike on each 5-fold vertex. The validity of the capsid and nucleic acid densities in the reconstructions was discussed.

  2. UV-Sensitivity of Shiga Toxin-Converting Bacteriophage Virions Φ24B, 933W, P22, P27 and P32

    Directory of Open Access Journals (Sweden)

    Sylwia Bloch

    2015-09-01

    Full Text Available Shiga toxin-converting bacteriophages (Stx phages are present as prophages in Shiga toxin-producing Escherichia coli (STEC strains. Theses phages can be transmitted to previously non-pathogenic E. coli cells making them potential producers of Shiga toxins, as they bear genes for these toxins in their genomes. Therefore, sensitivity of Stx phage virions to various conditions is important in both natural processes of spreading of these viruses and potential prophylactic control of appearance of novel pathogenic E. coli strains. In this report we provide evidence that virions of Stx phages are significantly more sensitive to UV irradiation than bacteriophage λ. Following UV irradiation of Stx virions at the dose of 50 J/m2, their infectivity dropped by 1–3 log10, depending on the kind of phage. Under these conditions, a considerable release of phage DNA from virions was observed, and electron microscopy analyses indicated a large proportion of partially damaged virions. Infection of E. coli cells with UV-irradiated Stx phages resulted in significantly decreased levels of expression of N and cro genes, crucial for lytic development. We conclude that inactivation of Stx virions caused by relatively low dose of UV light is due to damage of capsids that prevents effective infection of the host cells.

  3. Vaccination against Very Virulent Infectious Bursal Disease Virus Using Recombinant T4 Bacteriophage Displaying Viral Protein VP2

    Institute of Scientific and Technical Information of China (English)

    Yong-Chang CAO; Quan-Cheng SHI; Jing-Yun MA; Qing-Mei XIE; Ying-Zuo BI

    2005-01-01

    In order to develop a desirable inexpensive, effective and safe vaccine against the very virulent infectious bursal disease virus (vvIBDV), we tried to take advantage of the emerging T4 bacteriophage surface protein display system. The major immunogen protein VP2 from the vvIBDV strain HK46 was fused to the nonessential T4 phage surface capsid protein, a small outer capsid (SOC) protein, resulting in the 49 kDa SOC-VP2 fusion protein, which was verified by sodium dodecylsulfate polyacrylamide gel electrophoresis and Western blot. Immunoelectromicroscopy showed that the recombinant VP2 protein was successfully displayed on the surface of the T4 phage. The recombinant VP2 protein is antigenic and showed reactivities to various monoclonal antibodies (mAbs) against IBDV, whereas the wild-type phage T4 could not react to any mAb. In addition, the recombinant VP2 protein is immunogenic and elicited specific antibodies in immunized specific pathogen free (SPF) chickens. More significantly, immunization of SPF chickens with the recombinant T4-VP2 phage protected them from infection by the vvIBDV strain HK46. When challenged with the vvIBDV strain HK46 at a dose of 100 of 50% lethal dose (LD50) per chicken 4 weeks after the booster was given, the group vaccinated with the T4-VP2 recombinant phage showed no clinical signs of disease or death, wh ereas the unvaccinated group and the group vaccinated with the wild-type T4phage exhibited 100% clinical signs of disease and bursal damages, and 30%-40% mortality. Collectively,the data herein showed that the T4-displayed VP2 protein might be an inexpensive, effective and safe vaccine candidate against vvIBDV.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Analysis of the mechanical properties of wild type and hyperstable mutants of the HIV-1 capsid

    OpenAIRE

    Ramalho, Ruben; Rankovic, Sanela; Zhou, Jing; Aiken, Christopher; Rousso, Itay

    2016-01-01

    Background The human immunodeficiency virus (HIV-1) capsid is a self-assembled protein shell that contains the viral genome. During the stages between viral entry into a host cell and nuclear import of the viral DNA, the capsid dissociates in a process known as uncoating, which leads to the release of the viral genetic material. Mutations that alter the stability of the capsid affect the uncoating rate and impair HIV-1 infectivity. Results To gain further insight into the role of capsid stabi...

  11. Small-Molecule Inhibition of Human Immunodeficiency Virus Type 1 Infection by Virus Capsid Destabilization▿

    OpenAIRE

    Shi, Jiong; Zhou, Jing; Shah, Vaibhav B.; Aiken, Christopher; Whitby, Kevin

    2010-01-01

    Human immunodeficiency virus type 1 (HIV-1) infection is dependent on the proper disassembly of the viral capsid, or “uncoating,” in target cells. The HIV-1 capsid consists of a conical multimeric complex of the viral capsid protein (CA) arranged in a hexagonal lattice. Mutations in CA that destabilize the viral capsid result in impaired infection owing to defects in reverse transcription in target cells. We describe here the mechanism of action of a small molecule HIV-1 inhibitor, PF-3450074...

  12. P2P变革网络

    Institute of Scientific and Technical Information of China (English)

    陈克胜

    2001-01-01

    @@ 自ARPANET以来,互联网发展史上最伟大的发明是WEB的发明,因为WEB的图形界面和易用性,使互联网迅速地得到运用.P2P(peer to peer,对等网络)是自WEB之后的又一重大发明,它使网络计算模式从集中式向分布式偏移:使现在的主/从网络架构向对等式转移:使Internet上的资源共享又被提高了一个层次,使网络就是计算机更具体化.

  13. $^3P_2$ Superfluids Are Topological

    CERN Document Server

    Mizushima, Takeshi

    2016-01-01

    We clarify the topology of the $^3P_2$ superfluidity which is expected to be realized in the cores of neutron stars and cubic odd-parity superconductors. The phase diagram includes the unitary uniaxial/biaxial nematic phases and nonunitary ferromagnetic and cyclic phases. We here show that the low-energy structures of all the phases are governed by different types of topologically protected gapless fermionic excitations: Surface Majorana fermions in nematic phases, single itinerant Majorana fermion in the ferromagnetic phase, and a quartet of itinerant Majorana fermions in the cyclic phase. Using the superfluid Fermi liquid theory, we also demonstrate that dihedral-two and -four biaxial nematic phases are thermodynamically favored in the weak coupling limit under a magnetic field. The mass acquisition of surface Majorana fermions in nematic phases is subject to symmetry.

  14. Characterization of post-translation products of herpes simplex virus gene 35 proteins binding to the surfaces of full capsids but not empty capsids

    International Nuclear Information System (INIS)

    The authors report on the properties of a genetically and immunologically related family of structural (γ) polypeptides of herpes simplex virus 1 designated as infected cell polypeptides (ICP) 35. The members of this family were identified and studied with the aid of a panel of monoclonal antibodies exemplified by H745. This monoclonal antibody reacted with six bands (ICP35a to 35f) formed by ICPs contained in either HEp-2 or Vero cell lysates electrophoretically separated in denaturing gels and transferred to nitrocell sheets. The six bands had apparent molecular weights in the range 39,000 to 50,000. Pulse-chase experiments indicate that ICP35a to 35d are cytoplasmic precursors to nuclear products. ICP35 was labeled by 32P/sub i/ added to the medium, but the extent of phosphorylation varied and may be a determinant of isoelectric properties. Iodination studies indicate that ICP35e and 35f are the predominant forms of ICP35 present on the surface of full, nuclear capsids containing DNA. None of the members of the ICP35 family were detected in empty capsids. Surface iodination labeled the major capsid protein (ICP5) of empty capsids, but not of full capsids, indicating the ICP35e of 35f coat the surface of the viral capsid and block access to sites for iodination of ICP5, the major capsid protein

  15. The tripartite capsid gene of Salmonella phage Gifsy-2 yields a capsid assembly pathway engaging features from HK97 and λ

    International Nuclear Information System (INIS)

    Phage Gifsy-2, a lambdoid phage infecting Salmonella, has an unusually large composite gene coding for its major capsid protein (mcp) at the C-terminal end, a ClpP-like protease at the N-terminus, and a ∼ 200 residue central domain of unknown function but which may have a scaffolding role. This combination of functions on a single coding region is more extensive than those observed in other phages such as HK97 (scaffold-capsid fusion) and λ (protease-scaffold fusion). To study the structural phenotype of the unique Gifsy-2 capsid gene, we have purified Gifsy-2 particles and visualized capsids and procapsids by cryoelectron microscopy, determining structures to resolutions up to 12 A. The capsids have lambdoid T = 7 geometry and are well modeled with the atomic structures of HK97 mcp and phage λ gpD decoration protein. Thus, the unique Gifsy-2 capsid protein gene yields a capsid maturation pathway engaging features from both phages HK97 and λ.

  16. Chlamydiaphage φCPG1 Capsid Protein Vp1 Inhibits Chlamydia trachomatis Growth via the Mitogen-Activated Protein Kinase Pathway.

    Science.gov (United States)

    Guo, Yuanli; Guo, Rui; Zhou, Quan; Sun, Changgui; Zhang, Xinmei; Liu, Yuanjun; Liu, Quanzhong

    2016-01-01

    Chlamydia trachomatis is the most common cause of curable bacterial sexually transmitted infections worldwide. Although the pathogen is well established, the pathogenic mechanisms remain unclear. Given the current challenges of antibiotic resistance and blocked processes of vaccine development, the use of a specific chlamydiaphage may be a new treatment solution. φCPG1 is a lytic phage specific for Chlamydia caviae, and shows over 90% nucleotide sequence identity with other chlamydiaphages. Vp1 is the major capsid protein of φCPG1. Purified Vp1 was previously confirmed to inhibit Chlamydia trachomatis growth. We here report the first attempt at exploring the relationship between Vp1-treated C. trachomatis and the protein and gene levels of the mitogen-activated/extracellular regulated protein kinase (MAPK/ERK) pathway by Western blotting and real-time PCR, respectively. Moreover, we evaluated the levels of pro-inflammatory cytokines interleukin (IL)-8 and IL-1 by enzyme-linked immunosorbent assay after Vp1 treatment. After 48 h of incubation, the p-ERK level of the Vp1-treated group decreased compared with that of the Chlamydia infection group. Accordingly, ERK1 and ERK2 mRNA expression levels of the Vp1-treated group also decreased compared with the Chlamydia infection group. IL-8 and IL-1 levels were also decreased after Vp1 treatment compared with the untreated group. Our results demonstrate that the inhibition effect of the chlamydiaphage φCPG1 capsid protein Vp1 on C. trachomatis is associated with the MAPK pathway, and inhibits production of the pro-inflammatory cytokines IL-8 and IL-1. The bacteriophages may provide insight into a new signaling transduction mechanism to influence their hosts, in addition to bacteriolysis. PMID:27089359

  17. Chlamydiaphage φCPG1 Capsid Protein Vp1 Inhibits Chlamydia trachomatis Growth via the Mitogen-Activated Protein Kinase Pathway

    Directory of Open Access Journals (Sweden)

    Yuanli Guo

    2016-04-01

    Full Text Available Chlamydia trachomatis is the most common cause of curable bacterial sexually transmitted infections worldwide. Although the pathogen is well established, the pathogenic mechanisms remain unclear. Given the current challenges of antibiotic resistance and blocked processes of vaccine development, the use of a specific chlamydiaphage may be a new treatment solution. φCPG1 is a lytic phage specific for Chlamydia caviae, and shows over 90% nucleotide sequence identity with other chlamydiaphages. Vp1 is the major capsid protein of φCPG1. Purified Vp1 was previously confirmed to inhibit Chlamydia trachomatis growth. We here report the first attempt at exploring the relationship between Vp1-treated C. trachomatis and the protein and gene levels of the mitogen-activated/extracellular regulated protein kinase (MAPK/ERK pathway by Western blotting and real-time PCR, respectively. Moreover, we evaluated the levels of pro-inflammatory cytokines interleukin (IL-8 and IL-1 by enzyme-linked immunosorbent assay after Vp1 treatment. After 48 h of incubation, the p-ERK level of the Vp1-treated group decreased compared with that of the Chlamydia infection group. Accordingly, ERK1 and ERK2 mRNA expression levels of the Vp1-treated group also decreased compared with the Chlamydia infection group. IL-8 and IL-1 levels were also decreased after Vp1 treatment compared with the untreated group. Our results demonstrate that the inhibition effect of the chlamydiaphage φCPG1 capsid protein Vp1 on C. trachomatis is associated with the MAPK pathway, and inhibits production of the pro-inflammatory cytokines IL-8 and IL-1. The bacteriophages may provide insight into a new signaling transduction mechanism to influence their hosts, in addition to bacteriolysis.

  18. Antipsychotic Drugs Inhibit Platelet Aggregation via P2Y1 and P2Y12 Receptors

    Science.gov (United States)

    Wu, Chang-Chieh; Tsai, Fu-Ming; Chen, Mao-Liang; Wu, Semon; Lee, Ming-Cheng; Tsai, Tzung-Chieh; Wang, Lu-Kai; Wang, Chun-Hua

    2016-01-01

    Antipsychotic drugs (APDs) used to treat clinical psychotic syndromes cause a variety of blood dyscrasias. APDs suppress the aggregation of platelets; however, the underlying mechanism remains unknown. We first analyzed platelet aggregation and clot formation in platelets treated with APDs, risperidone, clozapine, or haloperidol, using an aggregometer and rotational thromboelastometry (ROTEM). Our data indicated that platelet aggregation was inhibited, that clot formation time was increased, and that clot firmness was decreased in platelets pretreated with APDs. We also examined the role two major adenosine diphosphate (ADP) receptors, P2Y1 and P2Y12, play in ADP-mediated platelet activation and APD-mediated suppression of platelet aggregation. Our results show that P2Y1 receptor stimulation with ADP-induced calcium influx was inhibited by APDs in human and rats' platelets, as assessed by in vitro or ex vivo approach, respectively. In contrast, APDs, risperidone and clozapine, alleviated P2Y12-mediated cAMP suppression, and the release of thromboxane A2 and arachidonic acid by activated platelets decreased after APD treatment in human and rats' platelets. Our data demonstrate that each APD tested significantly suppressed platelet aggregation via different mechanisms. PMID:27069920

  19. P2P Technology Principles and P2P Based Software%P2P技术原理与应用软件

    Institute of Scientific and Technical Information of China (English)

    魏文; 刘羽

    2007-01-01

    P2P的对等结构是互联网本质的回归,以P2P技术为支撑的网络应用目前席卷了整个网络产业.诸如 BitTorrent、Thunder、Skype,P2P应用已成为当前网络技术领域的一颗明星.本文介绍了P2P技术基本原理和基于P2P技术的主流软件.

  20. P2X6 Knockout Mice Exhibit Normal Electrolyte Homeostasis

    Science.gov (United States)

    Viering, Daan H. H. M.; Bos, Caro; Bindels, René J. M.; Hoenderop, Joost G. J.

    2016-01-01

    ATP-mediated signaling is an important regulator of electrolyte transport in the kidney. The purinergic cation channel P2X6 has been previously localized to the distal convoluted tubule (DCT), a nephron segment important for Mg2+ and Na+ reabsorption, but its role in ion transport remains unknown. In this study, P2x6 knockout (P2x6-/-) mice were generated to investigate the role of P2X6 in renal electrolyte transport. The P2x6-/- animals displayed a normal phenotype and did not differ physiologically from wild type mice. Differences in serum concentration and 24-hrs urine excretion of Na+, K+, Mg2+ and Ca2+ were not detected between P2x6+/+, P2x6+/- and P2x6-/- mice. Quantitative PCR was applied to examine potential compensatory changes in renal expression levels of other P2x subunits and electrolyte transporters, including P2x1-5, P2x7, Trpm6, Ncc, Egf, Cldn16, Scnn1, Slc12a3, Slc41a1, Slc41a3, Cnnm2, Kcnj10 and Fxyd2. Additionally, protein levels of P2X2 and P2X4 were assessed in P2x6+/+ and P2x6-/- mouse kidneys. However, significant changes in expression were not detected. Furthermore, no compensatory changes in gene expression could be demonstrated in heart material isolated from P2x6-/- mice. Except for a significant (P<0.05) upregulation of P2x2 in the heart of P2x6-/- mice compared to the P2x6+/+ mice. Thus, our data suggests that purinergic signaling via P2X6 is not significantly involved in the regulation of renal electrolyte handling under normal physiological conditions. PMID:27254077

  1. 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

  2. 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....

  3. Human papillomavirus in anogenital cancer, with special reference to the viral capsid

    OpenAIRE

    Heino, Pirkko

    1996-01-01

    HUMAN PAPILLOMAVIRUS IN ANOGENITAL CANCER, WITH SPECIAL REFERENCE TO THE VIRAL CAPSID b y Pirkko HeinoInfection with the oncogenic types of Human Papillomavirus (HPV), particularlyHPV type 16, is the major cause of anogenital dysplasias, which are precursorlesions of anogenital cancers. Studies of the HPV capsid are of interest, since HPVcapsids are attractive...

  4. Varicella-zoster virus induces the formation of dynamic nuclear capsid aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Lebrun, Marielle [University of Liege (ULg), GIGA-Infection Immunity and Inflammation, Laboratory of Virology and Immunology, Liege (Belgium); Thelen, Nicolas; Thiry, Marc [University of Liege (ULg), GIGA-Neurosciences, Laboratory of Cellular and Tissular Biology, Liege (Belgium); Riva, Laura; Ote, Isabelle; Condé, Claude; Vandevenne, Patricia [University of Liege (ULg), GIGA-Infection Immunity and Inflammation, Laboratory of Virology and Immunology, Liege (Belgium); Di Valentin, Emmanuel [University of Liege (ULg), GIGA-Viral Vectors Platform, Liege (Belgium); Bontems, Sébastien [University of Liege (ULg), GIGA-Infection Immunity and Inflammation, Laboratory of Virology and Immunology, Liege (Belgium); Sadzot-Delvaux, Catherine, E-mail: csadzot@ulg.ac.be [University of Liege (ULg), GIGA-Infection Immunity and Inflammation, Laboratory of Virology and Immunology, Liege (Belgium)

    2014-04-15

    The first step of herpesviruses virion assembly occurs in the nucleus. However, the exact site where nucleocapsids are assembled, where the genome and the inner tegument are acquired, remains controversial. We created a recombinant VZV expressing ORF23 (homologous to HSV-1 VP26) fused to the eGFP and dually fluorescent viruses with a tegument protein additionally fused to a red tag (ORF9, ORF21 and ORF22 corresponding to HSV-1 UL49, UL37 and UL36). We identified nuclear dense structures containing the major capsid protein, the scaffold protein and maturing protease, as well as ORF21 and ORF22. Correlative microscopy demonstrated that the structures correspond to capsid aggregates and time-lapse video imaging showed that they appear prior to the accumulation of cytoplasmic capsids, presumably undergoing the secondary egress, and are highly dynamic. Our observations suggest that these structures might represent a nuclear area important for capsid assembly and/or maturation before the budding at the inner nuclear membrane. - Highlights: • We created a recombinant VZV expressing the small capsid protein fused to the eGFP. • We identified nuclear dense structures containing capsid and procapsid proteins. • Correlative microscopy showed that the structures correspond to capsid aggregates. • Procapsids and partial capsids are found within the aggregates of WT and eGFP-23 VZV. • FRAP and FLIP experiments demonstrated that they are dynamic structures.

  5. Varicella-zoster virus induces the formation of dynamic nuclear capsid aggregates

    International Nuclear Information System (INIS)

    The first step of herpesviruses virion assembly occurs in the nucleus. However, the exact site where nucleocapsids are assembled, where the genome and the inner tegument are acquired, remains controversial. We created a recombinant VZV expressing ORF23 (homologous to HSV-1 VP26) fused to the eGFP and dually fluorescent viruses with a tegument protein additionally fused to a red tag (ORF9, ORF21 and ORF22 corresponding to HSV-1 UL49, UL37 and UL36). We identified nuclear dense structures containing the major capsid protein, the scaffold protein and maturing protease, as well as ORF21 and ORF22. Correlative microscopy demonstrated that the structures correspond to capsid aggregates and time-lapse video imaging showed that they appear prior to the accumulation of cytoplasmic capsids, presumably undergoing the secondary egress, and are highly dynamic. Our observations suggest that these structures might represent a nuclear area important for capsid assembly and/or maturation before the budding at the inner nuclear membrane. - Highlights: • We created a recombinant VZV expressing the small capsid protein fused to the eGFP. • We identified nuclear dense structures containing capsid and procapsid proteins. • Correlative microscopy showed that the structures correspond to capsid aggregates. • Procapsids and partial capsids are found within the aggregates of WT and eGFP-23 VZV. • FRAP and FLIP experiments demonstrated that they are dynamic structures

  6. 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

  7. 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

  8. Compensatory Substitutions in the HIV-1 Capsid Reduce the Fitness Cost Associated with Resistance to a Capsid-Targeting Small-Molecule Inhibitor

    OpenAIRE

    Shi, Jiong; Zhou, Jing; Halambage, Upul D.; Shah, Vaibhav B.; Burse, Mallori J.; Wu, Hua; Blair, Wade S.; Butler, Scott L.; Aiken, Christopher

    2014-01-01

    The HIV-1 capsid plays multiple roles in infection and is an emerging therapeutic target. The small-molecule HIV-1 inhibitor PF-3450074 (PF74) blocks HIV-1 at an early postentry stage by binding the viral capsid and interfering with its function. Selection for resistance resulted in accumulation of five amino acid changes in the viral CA protein, which collectively reduced binding of the compound to HIV-1 particles. In the present study, we dissected the individual and combinatorial contribut...

  9. The smallest capsid protein mediates binding of the essential tegument protein pp150 to stabilize DNA-containing capsids in human cytomegalovirus.

    Directory of Open Access Journals (Sweden)

    Xinghong Dai

    2013-08-01

    Full Text Available Human cytomegalovirus (HCMV is a ubiquitous herpesvirus that causes birth defects in newborns and life-threatening complications in immunocompromised individuals. Among all human herpesviruses, HCMV contains a much larger dsDNA genome within a similarly-sized capsid compared to the others, and it was proposed to require pp150, a tegument protein only found in cytomegaloviruses, to stabilize its genome-containing capsid. However, little is known about how pp150 interacts with the underlying capsid. Moreover, the smallest capsid protein (SCP, while dispensable in herpes simplex virus type 1, was shown to play essential, yet undefined, role in HCMV infection. Here, by cryo electron microscopy (cryoEM, we determine three-dimensional structures of HCMV capsid (no pp150 and virion (with pp150 at sub-nanometer resolution. Comparison of these two structures reveals that each pp150 tegument density is composed of two helix bundles connected by a long central helix. Correlation between the resolved helices and sequence-based secondary structure prediction maps the tegument density to the N-terminal half of pp150. The structures also show that SCP mediates interactions between the capsid and pp150 at the upper helix bundle of pp150. Consistent with this structural observation, ribozyme inhibition of SCP expression in HCMV-infected cells impairs the formation of DNA-containing viral particles and reduces viral yield by 10,000 fold. By cryoEM reconstruction of the resulting "SCP-deficient" viral particles, we further demonstrate that SCP is required for pp150 functionally binding to the capsid. Together, our structural and biochemical results point to a mechanism whereby SCP recruits pp150 to stabilize genome-containing capsid for the production of infectious HCMV virion.

  10. Experimental evolution of a bacteriophage virus reveals the trajectory of adaptation across a fecundity/longevity trade-off.

    Directory of Open Access Journals (Sweden)

    Richard H Heineman

    Full Text Available 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. However, the increased resistance to urea did not generalise to increased resistance against temperature stress, highlighting that propagule durability is environment dependent. Previous comparative studies predicted that changes in propagule resistance would be mediated by changes in capsid proteins or gene deletions. In contrast, we found that point mutations in internal core protein genes (6.7 and 16 were responsible for the increased urea resistance of our evolved strain. Prior to the emergence of the 6.7 and 16 mutations, a distinct set of 5-point mutations peaked at over 20% prevalence before attenuating, suggestive of negative epistatic interactions during adaptation. Our results illustrate that parasites can adapt to specific transmission environments, and that this adaptation can impose costs on the subsequent ability to exploit host cells, potentially constraining durable parasites to lower virulence.

  11. One- and two-phonon raman scattering in ternary phosphides ZnSiP2, ZnGeP2, CdSiP2

    International Nuclear Information System (INIS)

    One- and two-phonon Raman scattering (RS) of orientated single crystals of ZnSiP2, ZnGeP2, and CdSiP2 are investigated. For the first time in ZnSiP2 the lattice vibrations B2(L/T) 146/145 and B1 466 cm-1 are observed, and the values of L-T splitting of polar modes are determined. It is concluded that in crystals of ZnGeP2, ZnSiP2, and CdSiP2 a completely symmetric component of the second-order RS spectra is formed by overtones and gives the distribution of the phonon state density of the lattice of these compounds. This distribution is determined in the main by the points GAMMA, T, N of Brillouin zone and has the general form for all compounds investigated. An estimation is given of the frequencies of inactive A2-phonons in ZnGeP2, ZnSiP2 and CdSiP2. (author)

  12. Revised Mimivirus major capsid protein sequence reveals intron-containing gene structure and extra domain

    Directory of Open Access Journals (Sweden)

    Suzan-Monti Marie

    2009-05-01

    Full Text Available Abstract Background Acanthamoebae polyphaga Mimivirus (APM is the largest known dsDNA virus. The viral particle has a nearly icosahedral structure with an internal capsid shell surrounded with a dense layer of fibrils. A Capsid protein sequence, D13L, was deduced from the APM L425 coding gene and was shown to be the most abundant protein found within the viral particle. However this protein remained poorly characterised until now. A revised protein sequence deposited in a database suggested an additional N-terminal stretch of 142 amino acids missing from the original deduced sequence. This result led us to investigate the L425 gene structure and the biochemical properties of the complete APM major Capsid protein. Results This study describes the full length 3430 bp Capsid coding gene and characterises the 593 amino acids long corresponding Capsid protein 1. The recombinant full length protein allowed the production of a specific monoclonal antibody able to detect the Capsid protein 1 within the viral particle. This protein appeared to be post-translationnally modified by glycosylation and phosphorylation. We proposed a secondary structure prediction of APM Capsid protein 1 compared to the Capsid protein structure of Paramecium Bursaria Chlorella Virus 1, another member of the Nucleo-Cytoplasmic Large DNA virus family. Conclusion The characterisation of the full length L425 Capsid coding gene of Acanthamoebae polyphaga Mimivirus provides new insights into the structure of the main Capsid protein. The production of a full length recombinant protein will be useful for further structural studies.

  13. Reactive oxygen species promote heat shock protein 90-mediated HBV capsid assembly

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yoon Sik, E-mail: yumshak@naver.com; Seo, Hyun Wook, E-mail: suruk@naver.com; Jung, Guhung, E-mail: drjung@snu.ac.kr

    2015-02-13

    Hepatitis B virus (HBV) infection induces reactive oxygen species (ROS) production and has been associated with the development of hepatocellular carcinoma (HCC). ROS are also an important factor in HCC because the accumulated ROS leads to abnormal cell proliferation and chromosome mutation. In oxidative stress, heat shock protein 90 (Hsp90) and glutathione (GSH) function as part of the defense mechanism. Hsp90 prevents cellular component from oxidative stress, and GSH acts as antioxidants scavenging ROS in the cell. However, it is not known whether molecules regulated by oxidative stress are involved in HBV capsid assembly. Based on the previous study that Hsp90 facilitates HBV capsid assembly, which is an important step for the packing of viral particles, here, we show that ROS enrich Hsp90-driven HBV capsid formation. In cell-free system, HBV capsid assembly was facilitated by ROS with Hsp90, whereas it was decreased without Hsp90. In addition, GSH inhibited the function of Hsp90 to decrease HBV capsid assembly. Consistent with the result of cell-free system, ROS and buthionine sulfoximine (BS), an inhibitor of GSH synthesis, increased HBV capsid formation in HepG2.2.15 cells. Thus, our study uncovers the interplay between ROS and Hsp90 during HBV capsid assembly. - Highlights: • We examined H{sub 2}O{sub 2} and GSH modulate HBV capsid assembly. • H{sub 2}O{sub 2} facilitates HBV capsid assembly in the presence of Hsp90. • GSH inhibits function of Hsp90 in facilitating HBV capsid assembly. • H{sub 2}O{sub 2} and GSH induce conformation change of Hsp90.

  14. Reactive oxygen species promote heat shock protein 90-mediated HBV capsid assembly

    International Nuclear Information System (INIS)

    Hepatitis B virus (HBV) infection induces reactive oxygen species (ROS) production and has been associated with the development of hepatocellular carcinoma (HCC). ROS are also an important factor in HCC because the accumulated ROS leads to abnormal cell proliferation and chromosome mutation. In oxidative stress, heat shock protein 90 (Hsp90) and glutathione (GSH) function as part of the defense mechanism. Hsp90 prevents cellular component from oxidative stress, and GSH acts as antioxidants scavenging ROS in the cell. However, it is not known whether molecules regulated by oxidative stress are involved in HBV capsid assembly. Based on the previous study that Hsp90 facilitates HBV capsid assembly, which is an important step for the packing of viral particles, here, we show that ROS enrich Hsp90-driven HBV capsid formation. In cell-free system, HBV capsid assembly was facilitated by ROS with Hsp90, whereas it was decreased without Hsp90. In addition, GSH inhibited the function of Hsp90 to decrease HBV capsid assembly. Consistent with the result of cell-free system, ROS and buthionine sulfoximine (BS), an inhibitor of GSH synthesis, increased HBV capsid formation in HepG2.2.15 cells. Thus, our study uncovers the interplay between ROS and Hsp90 during HBV capsid assembly. - Highlights: • We examined H2O2 and GSH modulate HBV capsid assembly. • H2O2 facilitates HBV capsid assembly in the presence of Hsp90. • GSH inhibits function of Hsp90 in facilitating HBV capsid assembly. • H2O2 and GSH induce conformation change of Hsp90

  15. P2P IPTV Measurement: A Comparison Study

    OpenAIRE

    Silverston, Thomas; Fourmaux, Olivier

    2006-01-01

    With the success of P2P file sharing, new emerging P2P applications arise on the Internet for streaming content like voice (VoIP) or live video (IPTV). Nowadays, there are lots of works measuring P2P file sharing or P2P telephony systems, but there is still no comprehensive study about P2P IPTV, whereas it should be massively used in the future. During the last FIFA world cup, we measured network traffic generated by P2P IPTV applications like PPlive, PPstream, TVants and Sopcast. In this pap...

  16. Characterization of the in vitro HIV-1 capsid assembly pathway.

    Science.gov (United States)

    Barklis, Eric; Alfadhli, Ayna; McQuaw, Carolyn; Yalamuri, Suraj; Still, Amelia; Barklis, Robin Lid; Kukull, Ben; López, Claudia S

    2009-03-27

    During the morphogenesis of mature human immunodeficiency virus-1 cores, viral capsid proteins assemble conical or tubular shells around viral ribonucleoprotein complexes. This assembly step is mimicked in vitro through reactions in which capsid proteins oligomerize to form long tubes, and this process can be modeled as consisting of a slow nucleation period, followed by a rapid phase of tube growth. We have developed a novel fluorescence microscopy approach to monitor in vitro assembly reactions and have employed it, along with electron microscopy analysis, to characterize the assembly process. Our results indicate that temperature, salt concentration, and pH changes have differential effects on tube nucleation and growth steps. We also demonstrate that assembly can be unidirectional or bidirectional, that growth can be capped, and that proteins can assemble onto the surfaces of tubes, yielding multiwalled or nested structures. Finally, experiments show that a peptide inhibitor of in vitro assembly also can dismantle preexisting tubes, suggesting that such reagents may possess antiviral effects against both viral assembly and uncoating. Our investigations help establish a basis for understanding the mechanism of mature human immunodeficiency virus-1 core assembly and avenues for antiviral inhibition. PMID:19356593

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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...

  2. STABILITY OF P2 METHODS FOR NEUTRON TRANSPORT EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    袁光伟; 沈智军; 沈隆钧; 周毓麟

    2002-01-01

    In this paper the P2 approximation to the one-group planar neutron transport theory is discussed. The stability of the solutions for P2 equations with general boundary conditions, including the Marshak boundary condition, is proved. Moreover,the stability of the up-wind difference scheme for the P2 equation is demonstrated.

  3. 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.

  4. Purification and functional characterization of the phage P2 Ogr protein: A prokaryotic zinc-binding transcriptional activator

    International Nuclear Information System (INIS)

    These studies have focused on the mechanism underlying positive control of bacteriophage P2 and P4 late gene expression; specifically, the role played by the activator ogr gene product. The phage P2 late genes are organized into four transcriptional units. Late transcription depends on the host RNA polymerase, the phage ogr gene product, and concurrent P2 DNA replication. Ogr is a 72-residue basic protein rich in cysteine and histidine. The genetic evidence implicates a physical interaction between RNA polymerase and Ogr. The Ogr protein is also a positive regulatory factor for satellite phage P4 late gene transcription. P2 and P4 together constitute a promising model for studying viral transactivation. The authors have developed a simple purification procedure for Ogr protein synthesized from an overproducing plasmid. Inclusion bodies formed upon overproduction were denatured, and the overproduced protein was purified by one-step gel filtration chromatography. The purified Ogr was allowed to refold under optimized conditions and was subsequently shown to be able to transactivate the phage P4 late promoter Psid in an in vitro coupled transcription-translation system. Using a 65Zn blotting method and absorption spectroscopy, the author show that Ogr is a zinc-binding protein and that the conserved cysteine residues are involved in forming a complex with Zn(II). The purification procedure allows Ogr to be obtained in both high purity and yield. In addition, Ogr is characterized as to its molar extinction coefficient, molecular weight, amino acid composition, N-terminal sequence and secondary structure. Ogr is not a phage virion protein and is a low abundant protein during a phage P2 life cycle. The Ogr protein alone does not appear to bind to the phage late promoters PF and Psid, nor is it capable of directing RNA polymerase to the promoters in vitro

  5. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

    International Nuclear Information System (INIS)

    The cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body-bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations

  6. Role of dynamic capsomere supply for viral capsid self-assembly

    International Nuclear Information System (INIS)

    Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to persistent infections, capsomeres are continuously produced in the cytoplasm of the host cell while completed capsids exit the cell for a new round of infection. Here we use coarse-grained Brownian dynamics simulations of a generic patchy particle model to elucidate the role of the dynamic supply of capsomeres for the reversible self-assembly of empty T1 icosahedral virus capsids. We find that for high rates of capsomere influx only a narrow range of bond strengths exists for which a steady state of continuous capsid production is possible. For bond strengths smaller and larger than this optimal value, the reaction volume becomes crowded by small and large intermediates, respectively. For lower rates of capsomere influx a broader range of bond strengths exists for which a steady state of continuous capsid production is established, although now the production rate of capsids is smaller. Thus our simulations suggest that the importance of an optimal bond strength for viral capsid assembly typical for in vitro conditions can be reduced by the dynamic influx of capsomeres in a cellular environment. (paper)

  7. Structure of the capsid of Kilham rat virus from small-angle neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Wobbe, C.R.; Mitra, S.; Ramakrishnan, V.

    1984-12-18

    The structure of empty capsids of Kilham rat virus, an autonomous parvovirus with icosahedral symmetry, was investigated by small-angle neutron scattering. From the forward scatter, the molecular weight was determined to be 4.0 x 10(6), and from the Guinier region, the radius of gyration was found to be 105 A in D2O and 104 A in H/sub 2/O. On the basis of the capsid molecular weight and the molecular weights and relative abundances of the capsid proteins, the authors propose that the capsid has a triangulation number of 1. Extended scattering curves and mathematical modeling revealed that the capsid consists of two shells of protein, the inner shell extending from 58 to 91 A in D2O and from 50 to 91 A in H/sub 2/O and containing 11% of the capsid scattering mass, and the outer shell extending to 121 A in H/sub 2/O and D2O. The inner shell appears to have a higher content of basic amino acids than the outer shell, based on its lower scattering density in D2O than in H/sub 2/O. The authors propose that all three capsid proteins contribute to the inner shell and that this basic region serves DNA binding and partial charge neutralization functions.

  8. 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.

  9. Ebselen, a Small-Molecule Capsid Inhibitor of HIV-1 Replication.

    Science.gov (United States)

    Thenin-Houssier, Suzie; de Vera, Ian Mitchelle S; Pedro-Rosa, Laura; Brady, Angela; Richard, Audrey; Konnick, Briana; Opp, Silvana; Buffone, Cindy; Fuhrmann, Jakob; Kota, Smitha; Billack, Blase; Pietka-Ottlik, Magdalena; Tellinghuisen, Timothy; Choe, Hyeryun; Spicer, Timothy; Scampavia, Louis; Diaz-Griffero, Felipe; Kojetin, Douglas J; Valente, Susana T

    2016-04-01

    The human immunodeficiency virus type 1 (HIV-1) capsid plays crucial roles in HIV-1 replication and thus represents an excellent drug target. We developed a high-throughput screening method based on a time-resolved fluorescence resonance energy transfer (HTS-TR-FRET) assay, using the C-terminal domain (CTD) of HIV-1 capsid to identify inhibitors of capsid dimerization. This assay was used to screen a library of pharmacologically active compounds, composed of 1,280in vivo-active drugs, and identified ebselen [2-phenyl-1,2-benzisoselenazol-3(2H)-one], an organoselenium compound, as an inhibitor of HIV-1 capsid CTD dimerization. Nuclear magnetic resonance (NMR) spectroscopic analysis confirmed the direct interaction of ebselen with the HIV-1 capsid CTD and dimer dissociation when ebselen is in 2-fold molar excess. Electrospray ionization mass spectrometry revealed that ebselen covalently binds the HIV-1 capsid CTD, likely via a selenylsulfide linkage with Cys198 and Cys218. This compound presents anti-HIV activity in single and multiple rounds of infection in permissive cell lines as well as in primary peripheral blood mononuclear cells. Ebselen inhibits early viral postentry events of the HIV-1 life cycle by impairing the incoming capsid uncoating process. This compound also blocks infection of other retroviruses, such as Moloney murine leukemia virus and simian immunodeficiency virus, but displays no inhibitory activity against hepatitis C and influenza viruses. This study reports the use of TR-FRET screening to successfully identify a novel capsid inhibitor, ebselen, validating HIV-1 capsid as a promising target for drug development. PMID:26810656

  10. Structure of Tl2Mo2P2O11

    International Nuclear Information System (INIS)

    Dimolybdenum dithallium diphosphate, Tl2Mo2P2O11, is isotypic with K2Mo2P2O11. Its framework is built from the original Mo2P2O15 unit, formed by one Mo2O11 group sharing four of its corners with two PO4 tetrahedra, leading to [Mo2P2O13]∞ chains running along c. The [Mo2P2O11]∞ framework forms two different intersecting tunnels running along c and left angle 110 right angle , where the TI+ ions are located. (orig.)

  11. Research of P2P SIP technology%P2P SIP技术的研究

    Institute of Scientific and Technical Information of China (English)

    隋晋光; 鲁士文

    2007-01-01

    在阐述P2P和SIP技术的基础上,引出了一种二者融合的新技术--P2P SIP,提出了采用P2P SIP技术系统的体系结构、工作方式,并且对P2P SIP技术的安全性问题进行了分析.

  12. 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...

  13. Specific recognition and accelerated uncoating of retroviral capsids by the TRIM5α restriction factor

    OpenAIRE

    Stremlau, Matthew; Perron, Michel; Lee, Mark; Li, Yuan; Song, Byeongwoon; Javanbakht, Hassan; Diaz-Griffero, Felipe; Anderson, Donovan J.; Sundquist, Wesley I.; Sodroski, Joseph

    2006-01-01

    The host restriction factor TRIM5α mediates species-specific, early blocks to retrovirus infection; susceptibility to these blocks is determined by viral capsid sequences. Here we demonstrate that TRIM5α variants from Old World monkeys specifically associate with the HIV type 1 (HIV-1) capsid and that this interaction depends on the TRIM5α B30.2 domain. Human and New World monkey TRIM5α proteins associated less efficiently with the HIV-1 capsid, accounting for the lack of restriction in cells...

  14. Identification of Capsid Mutations That Alter the Rate of HIV-1 Uncoating in Infected Cells

    OpenAIRE

    Hulme, Amy E.; Kelley, Z; Okocha, Eneniziaogochukwu A.; Hope, Thomas J.

    2014-01-01

    After viral fusion with the cell membrane, the conical capsid of HIV-1 disassembles by a process called uncoating. We recently utilized the cyclosporine (CsA) washout assay, in which TRIM-CypA-mediated restriction of viral replication is used to detect the state of the viral capsid, to study the kinetics of uncoating in HIV-1-infected cells. Here we have extended this analysis to examine the effects of p24 capsid protein (p24CA) mutations and cellular environment on the kinetics of uncoating ...

  15. Identification of an immunodominant epitope within the capsid protein of hepatitis C virus.

    OpenAIRE

    Nasoff, M S; Zebedee, S L; Inchauspé, G; Prince, A. M.

    1991-01-01

    We have isolated cDNA clones from the 5' end of the Hutchinson strain of hepatitis C virus. Sequences encoding various segments of the HCV structural region were fused to the gene for glutathione S-transferase and analyzed for the expression of hepatitis C virus-capsid fusion proteins. With a set of these fusion proteins, both human and chimpanzee immune responses to capsid were studied. An immunodominant epitope was located within the amino-terminal portion of capsid that is preferentially r...

  16. On the geometry of regular icosahedral capsids containing disymmetrons

    CERN Document Server

    Ang, Kai-Siang

    2016-01-01

    Icosahedral virus capsids are composed of symmetrons, organized arrangements of capsomers. There are three types of symmetrons: disymmetrons, trisymmetrons, and pentasymmetrons, which have different shapes and are centered on the icosahedral 2-fold, 3-fold and 5-fold axes of symmetry, respectively. In 2010 [Sinkovits & Baker] gave a classification of all possible ways of building an icosahedral structure solely from trisymmetrons and pentasymmetrons, which requires the triangulation number T to be odd. In the present paper we incorporate disymmetrons to obtain a geometric classification of icosahedral viruses formed by regular penta-, tri-, and disymmetrons. For every class of solutions, we further provide formulas for symmetron sizes and parity restrictions on h, k, and T numbers. We also present several methods in which invariants may be used to classify a given configuration.

  17. Capsid-like Arrays in Crystals of Chimpanzee Adenovirus Hexon

    International Nuclear Information System (INIS)

    The major coat protein, hexon, from a chimpanzee adenovirus (AdC68) is of interest as a target for vaccine vector modification. AdC68 hexon has been crystallized in the orthorhombic space group C222 with unit cell dimensions of a = 90.8 Angstroms, b = 433.0 Angstroms, c = 159.3 Angstroms, and one trimer (3 x 104,942 Da) in the asymmetric unit. The crystals diffract to 2.1 Angstroms resolution. Initial studies reveal that the molecular arrangement is quite unlike that in hexon crystals for human adenovirus. In the AdC68 crystals, hexon trimers are parallel and pack closely in two-dimensional continuous arrays similar to those formed on electron microscope grids. The AdC68 crystals are the first in which adenovirus hexon has molecular interactions that mimic those used in constructing the viral capsid

  18. 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

  19. 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

  20. 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

  1. 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...

  2. 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.

  3. Enterovirus 71 viral capsid protein linear epitopes: Identification and characterization

    Directory of Open Access Journals (Sweden)

    Gao Fan

    2012-01-01

    Full Text Available Abstract Background To characterize the human humoral immune response against enterovirus 71 (EV71 infection and map human epitopes on the viral capsid proteins. Methods A series of 256 peptides spanning the capsid proteins (VP1, VP2, VP3 of BJ08 strain (genomic C4 were synthesized. An indirect enzyme-linked immunosorbent assay (ELISA was carried out to detect anti-EV71 IgM and IgG in sera of infected children in acute or recovery phase. The partially overlapped peptides contained 12 amino acids and were coated in the plate as antigen (0.1 μg/μl. Sera from rabbits immunized with inactivated BJ08 virus were also used to screen the peptide panel. Results A total of 10 human anti-EV71 IgM epitopes (vp1-14 in VP1; vp2-6, 21, 40 and 50 in VP2 and vp3-10, 12, 15, 24 and 75 in VP3 were identified in acute phase sera. In contrast, only one anti-EV71 IgG epitope in VP1 (vp1-15 was identified in sera of recovery stage. Four rabbit anti-EV71 IgG epitopes (vp1-14, 31, 54 and 71 were identified and mapped to VP1. Conclusion These data suggested that human IgM epitopes were mainly mapped to VP2 and VP3 with multi-epitope responses occurred at acute infection, while the only IgG epitope located on protein VP1 was activated in recovery phase sera. The dynamic changes of humoral immune response at different stages of infection may have public health significance in evaluation of EV71 vaccine immunogenicity and the clinical application of diagnostic reagents.

  4. AAV8 capsid variable regions at the two-fold symmetry axis contribute to high liver transduction by mediating nuclear entry and capsid uncoating

    International Nuclear Information System (INIS)

    Adeno-associated virus serotype 8 (AAV8) is a promising vector for liver-directed gene therapy. Although efficient uncoating of viral capsids has been implicated in AAV8's robust liver transduction, much about the biology of AAV8 hepatotropism remains unclear. Our study investigated the structural basis of AAV8 liver transduction efficiency by constructing chimeric vector capsids containing sequences derived from AAV8 and AAV2 – a highly homologous yet poorly hepatotropic serotype. Engineered vectors containing capsid variable regions (VR) VII and IX from AAV8 in an AAV2 backbone mediated near AAV8-like transduction in mouse liver, with higher numbers of chimeric genomes detected in whole liver cells and isolated nuclei. Interestingly, chimeric capsids within liver nuclei also uncoated similarly to AAV8 by 6 weeks after administration, in contrast with AAV2, of which a significantly smaller proportion were uncoated. This study links specific AAV capsid regions to the transduction ability of a clinically relevant AAV serotype. - Highlights: • We construct chimeric vectors to identify determinants of AAV8 liver transduction. • An AAV2-based vector with 17 AAV8 residues exhibited high liver transduction in mice. • This vector also surpassed AAV2 in cell entry, nuclear entry and onset of expression. • Most chimeric vector particles were uncoated at 6 weeks, like AAV8 and unlike AAV2. • Chimera retained heparin binding and was antigenically distinct from AAV2 and AAV8

  5. AAV8 capsid variable regions at the two-fold symmetry axis contribute to high liver transduction by mediating nuclear entry and capsid uncoating

    Energy Technology Data Exchange (ETDEWEB)

    Tenney, Rebeca M.; Bell, Christie L.; Wilson, James M., E-mail: wilsonjm@mail.med.upenn.edu

    2014-04-15

    Adeno-associated virus serotype 8 (AAV8) is a promising vector for liver-directed gene therapy. Although efficient uncoating of viral capsids has been implicated in AAV8's robust liver transduction, much about the biology of AAV8 hepatotropism remains unclear. Our study investigated the structural basis of AAV8 liver transduction efficiency by constructing chimeric vector capsids containing sequences derived from AAV8 and AAV2 – a highly homologous yet poorly hepatotropic serotype. Engineered vectors containing capsid variable regions (VR) VII and IX from AAV8 in an AAV2 backbone mediated near AAV8-like transduction in mouse liver, with higher numbers of chimeric genomes detected in whole liver cells and isolated nuclei. Interestingly, chimeric capsids within liver nuclei also uncoated similarly to AAV8 by 6 weeks after administration, in contrast with AAV2, of which a significantly smaller proportion were uncoated. This study links specific AAV capsid regions to the transduction ability of a clinically relevant AAV serotype. - Highlights: • We construct chimeric vectors to identify determinants of AAV8 liver transduction. • An AAV2-based vector with 17 AAV8 residues exhibited high liver transduction in mice. • This vector also surpassed AAV2 in cell entry, nuclear entry and onset of expression. • Most chimeric vector particles were uncoated at 6 weeks, like AAV8 and unlike AAV2. • Chimera retained heparin binding and was antigenically distinct from AAV2 and AAV8.

  6. 基于P2P的SIP网络研究%Research of SIP Internet based on P2P

    Institute of Scientific and Technical Information of China (English)

    李桂林; 李建华

    2007-01-01

    在现有P2P应用和SIP协议特点的基础上,提出了分层P2P-SIP网络设计方案,详细分析了P2P-SIP节点的实现机制.该设计采用P2P技术提高传统SIP网络的可靠性、自组织性,并解决了异构P2P-SIP网络互通问题.

  7. P2X1 receptors and the endothelium

    Directory of Open Access Journals (Sweden)

    LS Harrington

    2005-03-01

    Full Text Available Adenosine triphosphate (ATP is now established as a principle vaso-active mediator in the vasculature. Its actions on arteries are complex, and are mediated by the P2X and P2Y receptor families. It is generally accepted that ATP induces a bi-phasic response in arteries, inducing contraction via the P2X and P2Y receptors on the smooth muscle cells, and vasodilation via the actions of P2Y receptors located on the endothelium. However, a number of recent studies have placed P2X1 receptors on the endothelium of some arteries. The use of a specific P2X1 receptor ligand, a, b methylene ATP has demonstrated that P2X1 receptors also have a bi-functional role. The actions of ATP on P2X1 receptors is therefore dependant on its location, inducing contraction when located on the smooth muscle cells, and dilation when expressed on the endothelium, comparable to that of P2Y receptors.

  8. P2X receptors: New players in cancer pain

    Institute of Scientific and Technical Information of China (English)

    Alessia; Franceschini; Elena; Adinolfi

    2014-01-01

    Pain is unfortunately a quite common symptom for cancer patients. Normally pain starts as an episodic experience at early cancer phases to become chronic in later stages. In order to improve the quality of life of oncological patients, anti-cancer treatments are often accompanied by analgesic therapies. The P2 X receptor are adenosine triphosphate(ATP) gated ion channels expressed by several cells including neurons, cancer and immune cells. Purinergic signaling through P2 X receptors recently emerged as possible common pathway for cancer onset/growth and pain sensitivity. Indeed, tumor microenvironment is rich in extracellular ATP, which has a role in both tumor development and pain sensation. The study of the different mechanisms by which P2 X receptors favor cancer progression and relative pain, represents an interesting challenge to design integrated therapeutic strategies for oncological patients. This review summarizes recent findings linking P2 X receptors and ATP to cancer growth, progression and related pain. Special attention has been paid to the role of P2X2, P2X3, P2X4 and P2X7 in the genesisof cancer pain and to the function of P2X7 in tumor growth and metastasis. Therapeutic implications of the administration of different P2 X receptor blockers to alleviate cancer-associated pain sensations contemporarily reducing tumor progression are also discussed.

  9. Molecular evolution of the capsid gene in human norovirus genogroup II

    Science.gov (United States)

    Kobayashi, Miho; Matsushima, Yuki; Motoya, Takumi; Sakon, Naomi; Shigemoto, Naoki; Okamoto-Nakagawa, Reiko; Nishimura, Koichi; Yamashita, Yasutaka; Kuroda, Makoto; Saruki, Nobuhiro; Ryo, Akihide; Saraya, Takeshi; Morita, Yukio; Shirabe, Komei; Ishikawa, Mariko; Takahashi, Tomoko; Shinomiya, Hiroto; Okabe, Nobuhiko; Nagasawa, Koo; Suzuki, Yoshiyuki; Katayama, Kazuhiko; Kimura, Hirokazu

    2016-01-01

    Capsid protein of norovirus genogroup II (GII) plays crucial roles in host infection. Although studies on capsid gene evolution have been conducted for a few genotypes of norovirus, the molecular evolution of norovirus GII is not well understood. Here we report the molecular evolution of all GII genotypes, using various bioinformatics techniques. The time-scaled phylogenetic tree showed that the present GII strains diverged from GIV around 1630CE at a high evolutionary rate (around 10−3 substitutions/site/year), resulting in three lineages. The GII capsid gene had large pairwise distances (maximum > 0.39). The effective population sizes of the present GII strains were large (>102) for about 400 years. Positive (20) and negative (over 450) selection sites were estimated. Moreover, some linear and conformational B-cell epitopes were found in the deduced GII capsid protein. These results suggested that norovirus GII strains rapidly evolved with high divergence and adaptation to humans. PMID:27384324

  10. Pt, Co-Pt and Fe-Pt alloy nanoclusters encapsulated in virus capsids

    Science.gov (United States)

    Okuda, M.; Eloi, J.-C.; Jones, S. E. Ward; Verwegen, M.; Cornelissen, J. J. L. M.; Schwarzacher, W.

    2016-03-01

    Nanostructured Pt-based alloys show great promise, not only for catalysis but also in medical and magnetic applications. To extend the properties of this class of materials, we have developed a means of synthesizing Pt and Pt-based alloy nanoclusters in the capsid of a virus. Pure Pt and Pt-alloy nanoclusters are formed through the chemical reduction of [PtCl4]- by NaBH4 with/without additional metal ions (Co or Fe). The opening and closing of the ion channels in the virus capsid were controlled by changing the pH and ionic strength of the solution. The size of the nanoclusters is limited to 18 nm by the internal diameter of the capsid. Their magnetic properties suggest potential applications in hyperthermia for the Co-Pt and Fe-Pt magnetic alloy nanoclusters. This study introduces a new way to fabricate size-restricted nanoclusters using virus capsid.

  11. Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion.

    Science.gov (United States)

    Bosse, Jens B; Hogue, Ian B; Feric, Marina; Thiberge, Stephan Y; Sodeik, Beate; Brangwynne, Clifford P; Enquist, Lynn W

    2015-10-20

    The nuclear chromatin structure confines the movement of large macromolecular complexes to interchromatin corrals. Herpesvirus capsids of approximately 125 nm assemble in the nucleoplasm and must reach the nuclear membranes for egress. Previous studies concluded that nuclear herpesvirus capsid motility is active, directed, and based on nuclear filamentous actin, suggesting that large nuclear complexes need metabolic energy to escape nuclear entrapment. However, this hypothesis has recently been challenged. Commonly used microscopy techniques do not allow the imaging of rapid nuclear particle motility with sufficient spatiotemporal resolution. Here, we use a rotating, oblique light sheet, which we dubbed a ring-sheet, to image and track viral capsids with high temporal and spatial resolution. We do not find any evidence for directed transport. Instead, infection with different herpesviruses induced an enlargement of interchromatin domains and allowed particles to diffuse unrestricted over longer distances, thereby facilitating nuclear egress for a larger fraction of capsids. PMID:26438852

  12. Modeling Load Balancing in Heterogeneous Unstructured P2P Systems

    Directory of Open Access Journals (Sweden)

    Zhi J. Li

    2005-01-01

    Full Text Available Load balancing is a generally concerned problem in peer-to-peer (P2P systems. Many researches on load balancing in the structured P2P systems have been launched currently, such as Chord or other DHTs. Although the researches on load balancing in unstructured P2P systems are emerged nowadays, the simple mechanisms achieved can only perform effectively in uniform environment. In this study, the influence on load balancing of the heterogeneity existed universally in unstructured P2P systems are analyzed, the unstructured P2P systems and their load balancing and the heterogeneity are modeled. Based on the formal model, the load balancing is analyzed quantitatively under static and dynamic environment and the typical load balancing algorithms are also analyzed. Some important conclusions are drawn which can be used in new models of load balancing in unstructured P2P systems.

  13. Research and Development of P2P Worms

    Institute of Scientific and Technical Information of China (English)

    Li You; Zhi-Guang Qin

    2011-01-01

    With the development and the application of many popular peer-to-peer (P2P) systems such as eMule and BitTorrent,worms probably employ the features of these P2P networks to put them at risk.Some features,such as the local routing table and the application routing mechanism,are helpful to quickly distribute the P2P worms into the networks.This paper aims to give a comprehensive survey of P2P worms.The definition and the classification of P2P worms are discussed firstly.Then,the research and development of P2P worms, including experimental analysis,propagation modeling,and defensive approaches,are addressed and analyzed in detail.

  14. Supporting Collaboration and Creativity Through Mobile P2P Computing

    Science.gov (United States)

    Wierzbicki, Adam; Datta, Anwitaman; Żaczek, Łukasz; Rzadca, Krzysztof

    Among many potential applications of mobile P2P systems, collaboration applications are among the most prominent. Examples of applications such as Groove (although not intended for mobile networks), collaboration tools for disaster recovery (the WORKPAD project), and Skype's collaboration extensions, all demonstrate the potential of P2P collaborative applications. Yet, the development of such applications for mobile P2P systems is still difficult because of the lack of middleware.

  15. X-Ray Structures of Native HIV-1 Capsid Protein Reveal Conformational Variability

    OpenAIRE

    Gres, Anna T.; Kirby, Karen A.; KewalRamani, Vineet N.; Tanner, John J.; Pornillos, Owen; Sarafianos, Stefan G.

    2015-01-01

    The detailed molecular interactions between Human Immunodeficiency Virus type 1 (HIV-1) capsid protein (CA) hexamers have been elusive in the context of a native protein. We report crystal structures describing novel interactions between CA monomers related by 6-fold symmetry within a hexamer (intra-hexamer) and by 3-fold and 2-fold symmetry between neighboring hexamers (inter-hexamer). These structures help elucidate how CA builds a hexagonal lattice, the foundation of the mature capsid. Lat...

  16. TRIM5α Disrupts the Structure of Assembled HIV-1 Capsid Complexes In Vitro▿

    OpenAIRE

    Black, Lesa R.; Aiken, Christopher

    2010-01-01

    The host restriction factor TRIM5α provides intrinsic defense against retroviral infections in mammalian cells. TRIM5α blocks infection by targeting the viral capsid after entry but prior to completion of reverse transcription, but whether this interaction directly alters the structure of the viral capsid is unknown. A previous study reported that rhesus macaque TRIM5α protein stably associates with cylindrical complexes formed by assembly of recombinant HIV-1 CA-NC protein in vitro and that ...

  17. Role of the Capsid Helix 4-5 Loop in Equine Infectious Anemia Virus Infection

    OpenAIRE

    Bollman, Brooke Ann

    2012-01-01

    The lentiviral capsid core, which encapsulates the viral RNA genome, is delivered into the target cell cytoplasm during the viral entry process. In the cytoplasm, the conical core undergoes morphological changes, which are termed uncoating. Proper uncoating has been shown to be critical for the infectivity of the lentivirus HIV-1. In addition, the HIV-1 capsid protein is critical for the process of nuclear import of the preintegration complex (PIC). The lentivirus equine infectious anemia...

  18. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6

    Science.gov (United States)

    Bhattacharya, Akash; Alam, Steven L.; Fricke, Thomas; Zadrozny, Kaneil; Sedzicki, Jaroslaw; Taylor, Alexander B.; Demeler, Borries; Pornillos, Owen; Ganser-Pornillos, Barbie K.; Diaz-Griffero, Felipe; Ivanov, Dmitri N.; Yeager, Mark

    2014-01-01

    Upon infection of susceptible cells by HIV-1, the conical capsid formed by ∼250 hexamers and 12 pentamers of the CA protein is delivered to the cytoplasm. The capsid shields the RNA genome and proteins required for reverse transcription. In addition, the surface of the capsid mediates numerous host–virus interactions, which either promote infection or enable viral restriction by innate immune responses. In the intact capsid, there is an intermolecular interface between the N-terminal domain (NTD) of one subunit and the C-terminal domain (CTD) of the adjacent subunit within the same hexameric ring. The NTD–CTD interface is critical for capsid assembly, both as an architectural element of the CA hexamer and pentamer and as a mechanistic element for generating lattice curvature. Here we report biochemical experiments showing that PF-3450074 (PF74), a drug that inhibits HIV-1 infection, as well as host proteins cleavage and polyadenylation specific factor 6 (CPSF6) and nucleoporin 153 kDa (NUP153), bind to the CA hexamer with at least 10-fold higher affinities compared with nonassembled CA or isolated CA domains. The crystal structure of PF74 in complex with the CA hexamer reveals that PF74 binds in a preformed pocket encompassing the NTD–CTD interface, suggesting that the principal inhibitory target of PF74 is the assembled capsid. Likewise, CPSF6 binds in the same pocket. Given that the NTD–CTD interface is a specific molecular signature of assembled hexamers in the capsid, binding of NUP153 at this site suggests that key features of capsid architecture remain intact upon delivery of the preintegration complex to the nucleus. PMID:25518861

  19. Trapping of Hepatitis B Virus capsid assembly intermediates by phenylpropenamide assembly accelerators

    OpenAIRE

    Katen, Sarah P.; Chirapu, Srinivas Reddy; Finn, M.G.; Zlotnick, Adam

    2010-01-01

    Understanding the biological self-assembly process of virus capsids is key to understanding the viral life cycle, as well as serving as a platform for the design of assembly-based antiviral drugs. Here we identify and characterize the phenylpropenamide family of small molecules, known to have antiviral activity in vivo, as assembly effectors of the Hepatitis B Virus (HBV) capsid. We have found two representative phenylpropenamides to be assembly accelerators, increasing the rate of assembly w...

  20. A Beta-Herpesvirus with Fluorescent Capsids to Study Transport in Living Cells

    OpenAIRE

    Jens B Bosse; Rudolf Bauerfeind; Leonhard Popilka; Lisa Marcinowski; Martina Taeglich; Christophe Jung; Hannah Striebinger; Jens von Einem; Ulrike Gaul; Paul Walther; Koszinowski, Ulrich H.; Zsolt Ruzsics

    2012-01-01

    Fluorescent tagging of viral particles by genetic means enables the study of virus dynamics in living cells. However, the study of beta-herpesvirus entry and morphogenesis by this method is currently limited. This is due to the lack of replication competent, capsid-tagged fluorescent viruses. Here, we report on viable recombinant MCMVs carrying ectopic insertions of the small capsid protein (SCP) fused to fluorescent proteins (FPs). The FPs were inserted into an internal position which allowe...

  1. P2P技术分析和大数据P2P识别方案设想

    Institute of Scientific and Technical Information of China (English)

    廖江

    2014-01-01

    As P2P mechanism has been widely used in lots of Internet applications, the traffic characterized by P2P features dominates the capacity of the carriers' bandwidth, which is one of the main driving factors to the surprising development of the bandwidth. This ar-ticle summarizes the features of P2P mechanism and the P2P traffic, also the developing technologies of P2P identifying and controlling. A kind of technology of Deep Flow Identify based on big data technology is provided in order to help the ISP network OAM.%P2P技术广泛应用于各种Internet应用,P2P方式产生的流量是运营商网络中主要成分之一,并促进宽带网络超常规发展。本文汇总分析P2P技术特点、P2P流量特点及P2P流量识别和控制技术,提出基于大数据系统进行深度流量分析(DFI)的思路,以进一步提高对网络流量的掌控力度,支撑企业流量经营工作。

  2. Characterization of P2P IPTV Traffic: Scaling Analysis

    OpenAIRE

    Silverston, Thomas; Fourmaux, Olivier; Salamatian, Kave

    2007-01-01

    P2P IPTV applications arise on the Internet and will be massively used in the future. It is expected that P2P IPTV will contribute to increase the overall Internet traffic. In this context, it is important to measure the impact of P2P IPTV on the networks and to characterize this traffic. Dur- ing the 2006 FIFA World Cup, we performed an extensive measurement campaign. We measured network traffic generated by broadcasting soc- cer games by the most popular P2P IPTV applications, namely PPLive...

  3. Search by shortcuts in P2P scientific collaboration system

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A P2P scientific collaboration is a P2P network whose members can share documents, co-compile papers and codes, and communicate with each other instantly. From the simulation experiment we found that P2P collaboration system is a power-law network with a tail between -2 and -3.We utilized the algorithm that searches by high-degree shortcuts to improve the scalability of p2p collaboration system. The experimental result shows that the algorithm works better than random walk algorithm.

  4. In vivo encapsulation of nucleic acids using an engineered nonviral protein capsid.

    Science.gov (United States)

    Lilavivat, Seth; Sardar, Debosmita; Jana, Subrata; Thomas, Geoffrey C; Woycechowsky, Kenneth J

    2012-08-15

    In Nature, protein capsids function as molecular containers for a wide variety of molecular cargoes. Such containers have great potential for applications in nanotechnology, which often require encapsulation of non-native guest molecules. Charge complementarity represents a potentially powerful strategy for engineering novel encapsulation systems. In an effort to explore the generality of this approach, we engineered a nonviral, 60-subunit capsid, lumazine synthase from Aquifex aeolicus (AaLS), to act as a container for nucleic acid. Four mutations were introduced per subunit to increase the positive charge at the inner surface of the capsid. Characterization of the mutant (AaLS-pos) revealed that the positive charges lead to the uptake of cellular RNA during production and assembly of the capsid in vivo. Surprisingly, AaLS-pos capsids were found to be enriched with RNA molecules approximately 200-350 bases in length, suggesting that this simple charge complementarity approach to RNA encapsulation leads to both high affinity and a degree of selectivity. The ability to control loading of RNA by tuning the charge at the inner surface of a protein capsid could illuminate aspects of genome recognition by viruses and pave the way for the development of improved RNA delivery systems. PMID:22827162

  5. Epitopes expressed in different adenovirus capsid proteins induce different levels of epitope-specific immunity.

    Science.gov (United States)

    Krause, Anja; Joh, Ju H; Hackett, Neil R; Roelvink, Peter W; Bruder, Joseph T; Wickham, Thomas J; Kovesdi, Imre; Crystal, Ronald G; Worgall, Stefan

    2006-06-01

    On the basis of the concept that the capsid proteins of adenovirus (Ad) gene transfer vectors can be genetically manipulated to enhance the immunogenicity of Ad-based vaccines, the present study compared the antiantigen immunogenicity of Ad vectors with a common epitope of the hemagglutinin (HA) protein of the influenza A virus incorporated into the outer Ad capsid protein hexon, penton base, fiber knob, or protein IX. Incorporation of the same epitope into the different capsid proteins provided insights into the correlation between epitope position and antiepitope immunity. Following immunization of three different strains of mice (C57BL/6, BALB/c, and CBA) with either an equal number of Ad particles (resulting in a different total HA copy number) or different Ad particle numbers (to achieve the same HA copy number), the highest primary (immunoglobulin M [IgM]) and secondary (IgG) anti-HA humoral and cellular CD4 gamma interferon and interleukin-4 responses against HA were always achieved with the Ad vector carrying the HA epitope in fiber knob. These observations suggest that the immune response against an epitope inserted into Ad capsid proteins is not necessarily dependent on the capsid protein number and imply that the choice of incorporation site in Ad capsid proteins in their use as vaccines needs to be compared in vivo. PMID:16699033

  6. An alphavirus temperature-sensitive capsid mutant reveals stages of nucleocapsid assembly

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yan, E-mail: yzheng15@students.kgi.edu; Kielian, Margaret, E-mail: margaret.kielian@einstein.yu.edu

    2015-10-15

    Alphaviruses have a nucleocapsid core composed of the RNA genome surrounded by an icosahedral lattice of capsid protein. An insertion after position 186 in the capsid protein produced a strongly temperature-sensitive growth phenotype. Even when the structural proteins were synthesized at the permissive temperature (28 °C), subsequent incubation of the cells at the non-permissive temperature (37 °C) dramatically decreased mutant capsid protein stability and particle assembly. Electron microscopy confirmed the presence of cytoplasmic nucleocapsids in mutant-infected cells cultured at the permissive temperature, but these nucleocapsids were not stable to sucrose gradient separation. In contrast, nucleocapsids isolated from mutant virus particles had similar stability to that of wildtype virus. Our data support a model in which cytoplasmic nucleocapsids go through a maturation step during packaging into virus particles. The insertion site lies in the interface between capsid proteins in the assembled nucleocapsid, suggesting the region where such a stabilizing transition occurs. - Highlights: • We characterize an alphavirus capsid insertion mutation. • These capsid mutants are highly temperature sensitive for growth. • The insertion affects nucleocapsid stability. • Results suggest that the nucleocapsid is stabilized during virus budding.

  7. Compensatory Substitutions in the HIV-1 Capsid Reduce the Fitness Cost Associated with Resistance to a Capsid-Targeting Small-Molecule Inhibitor

    Science.gov (United States)

    Shi, Jiong; Zhou, Jing; Halambage, Upul D.; Shah, Vaibhav B.; Burse, Mallori J.; Wu, Hua; Blair, Wade S.; Butler, Scott L.

    2014-01-01

    ABSTRACT The HIV-1 capsid plays multiple roles in infection and is an emerging therapeutic target. The small-molecule HIV-1 inhibitor PF-3450074 (PF74) blocks HIV-1 at an early postentry stage by binding the viral capsid and interfering with its function. Selection for resistance resulted in accumulation of five amino acid changes in the viral CA protein, which collectively reduced binding of the compound to HIV-1 particles. In the present study, we dissected the individual and combinatorial contributions of each of the five substitutions Q67H, K70R, H87P, T107N, and L111I to PF74 resistance, PF74 binding, and HIV-1 infectivity. Q67H, K70R, and T107N each conferred low-level resistance to PF74 and collectively conferred strong resistance. The substitutions K70R and L111I impaired HIV-1 infectivity, which was partially restored by the other substitutions at positions 67 and 107. PF74 binding to HIV-1 particles was reduced by the Q67H, K70R, and T107N substitutions, consistent with the location of these positions in the inhibitor-binding pocket. Replication of the 5Mut virus was markedly impaired in cultured macrophages, reminiscent of the previously reported N74D CA mutant. 5Mut substitutions also reduced the binding of the host protein CPSF6 to assembled CA complexes in vitro and permitted infection of cells expressing the inhibitory protein CPSF6-358. Our results demonstrate that strong resistance to PF74 requires accumulation of multiple substitutions in CA to inhibit PF74 binding and compensate for fitness impairments associated with some of the sequence changes. IMPORTANCE The HIV-1 capsid is an emerging drug target, and several small-molecule compounds have been reported to inhibit HIV-1 infection by targeting the capsid. Here we show that resistance to the capsid-targeting inhibitor PF74 requires multiple amino acid substitutions in the binding pocket of the CA protein. Three changes in CA were necessary to inhibit binding of PF74 while maintaining viral

  8. P2P本质特征视角对P2P发展愿景的研究%The Research on P2P Development Vision from the Perspective of the Nature of P2P

    Institute of Scientific and Technical Information of China (English)

    陆岷峰; 李琴

    2015-01-01

    关于P2P,从产生到爆发性成长其争论之声从没停止过,由于对其认识上的不统一,导致对P2P的评价不一致,其发展目标、社会认同、成长方式及未来愿景也各不相同。从P2P本质特征分析入手,掌握P2P的基本特征,便于抓住事物的本质和主要矛盾,从而对P2P未来的发展前景作出科学的判断,对保持这一新生事物的发展才能提供一个良好的环境。 P2P其特征有本质和非本质之分,本质特征是“互联网+民间借贷”,非本质特征有互联网金融、信用中介、民间借贷等,P2P的本质特征已经充分表明其有美好的发展愿景,P2P有着巨大的需求市场和广泛的供给市场,同时也适应了金融市场多元化需求的大的发展趋势,现实中存在的问题是当前P2P所面临的监管、信任机制等不完善造成的,这并不否定P2P生命力及生存发展的本身。%The argument about P2P has never stopped from P2P’ emergence to its rapid growth. The different understanding to P2P leads to the different evaluation on P2P, and its development goals, social recognition, growth methods and future vision are also different. From the analysis on the nature of P2P, the paper thinks that mastering the basic features of P2P means mastering the essence and the principal contradiction of P2P, therefore the scientific judgment can be made on the development vision of P2P in the future, and a good environment can be provided to keep the development of the new-born thing. P2P is characterized with essential nature and non-essential nature, and its essential nature is“Internet+informal lending”, while the non-essential nature includes the Internet fi-nance, credit intermediary, informal lending etc. The essential nature of P2P has fully shown that P2P has a good development vision, has a huge market demand and a wide range of market supply, and has adapted to the development trend of the diversified

  9. ZrCu2P2 and HfCu2P2 phosphides and their crystal structure

    International Nuclear Information System (INIS)

    Isostructural ZrCu2P2 and HfCu2P2 compounds are prepared for the first time. X-ray diffraction analysis (of powder, DRON-2.0 diffractometer, FeKsub(α) radiation) was used to study crystal structure of HfCu2P2 phosphide belonging to the CaAl2Si2 structural type (sp. group P anti 3 m 1, R=0.095). Lattice parameters the compounds are as follows: for ZrCu2P2 a=0.3810(1), c=0.6184(5); for HfCu2P2 a=0.3799(1), c=0.6160(2) (nm). Atomic parameters in the HfCu2P2 structure and interatomic distances are determined

  10. P2X7 Receptors in Neurological and Cardiovascular Disorders

    Directory of Open Access Journals (Sweden)

    Stephen D. Skaper

    2009-01-01

    Full Text Available P2X receptors are ATP-gated cation channels that mediate fast excitatory transmission in diverse regions of the brain and spinal cord. Several P2X receptor subtypes, including P2X7, have the unusual property of changing their ion selectivity during prolonged exposure to ATP, which results in a channel pore permeable to molecules as large as 900 daltons. The P2X7 receptor was originally described in cells of hematopoietic origin, and mediates the influx of Ca2+ and Na+ and Ca2+ and Na+ ions as well as the release of proinflammatory cytokines. P2X7 receptors may affect neuronal cell death through their ability to regulate the processing and release of interleukin-1, a key mediator in neurodegeneration, chronic inflammation, and chronic pain. Activation of P2X7, a key mediator in neurodegeneration, chronic inflammation, and chronic pain. Activation of P2X7 receptors provides an inflammatory stimulus, and P2X7 receptor-deficient mice have substantially attenuated inflammatory responses, including models of neuropathic and chronic inflammatory pain. Moreover, P2X7 receptor activity, by regulating the release of proinflammatory cytokines, may be involved in the pathophysiology of depression. Apoptotic cell death occurs in a number of vascular diseases, including atherosclerosis, restenosis, and hypertension, and may be linked to the release of ATP from endothelial cells, P2X7 receptor activation, proinflammatory cytokine production, and endothelial cell apoptosis. In this context, the P2X7 receptor may be viewed as a gateway of communication between the nervous, immune, and cardiovascular systems.

  11. 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...

  12. 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...

  13. 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...

  14. 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.

  15. AlvisP2P: Scalable Peer-to-Peer Text Retrieval in a Structured P2P Network

    OpenAIRE

    Luu, Toan; Skobeltsyn, Gleb; Klemm, Fabius; Puh, Maroje; Podnar Zarko, Ivana; Rajman, Martin; Aberer, Karl

    2008-01-01

    In this paper we present the AlvisP2P IR engine, which enables efficient retrieval with multi-keyword queries from a global document collection available in a P2P network. In such a network, each peer publishes its local index and invests a part of its local computing resources (storage, CPU, bandwidth) to maintain a fraction of a global P2P index. This investment is rewarded by the network-wide accessibility of the local documents via the global search facility. The AlvisP2P engine uses an o...

  16. Morphisms from P2 to Gr(2,C4)

    CERN Document Server

    Mazouni, A El; Nagaraj, D S

    2009-01-01

    In this note we study morphisms from P2 to Gr(2,C4) from the point of view of the cohomology class they represent in the Grassmannian. This leads to some new result about projection of d-uple imbedding of P2 to P5.

  17. Cooling of Neutron Stars and 3P_2 neutron gap

    OpenAIRE

    Grigorian, H.; Voskresensky, D.N.(National Research Nuclear University (MEPhI), Moscow, 115409, Russia)

    2005-01-01

    We study the dependence of the cooling of isolated neutron stars on the magnitude of the $3P_2$ neutron gap. It is demonstrated that our ``Nuclear medium cooling scenario'' is in favor of a suppressed value of the $3P_2$ neutron gap.

  18. The role of P2X receptors in bone biology

    DEFF Research Database (Denmark)

    Jørgensen, N R; Syberg, S; Ellegaard, M

    2015-01-01

    come from studies on murine knockout models and from pharmacologic studies on cells and animals. More recently, the role of P2X receptors in human bone diseases has been documented. Loss-of-functions polymorphisms in the P2X7 receptorare associated with bone loss and increased fracture risk. Very...

  19. 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.

  20. Limited cross-reactivity of mouse monoclonal antibodies against Dengue virus capsid protein among four serotypes

    Directory of Open Access Journals (Sweden)

    Noda M

    2012-11-01

    Full Text Available Megumi Noda,1 Promsin Masrinoul,1 Chaweewan Punkum,1 Chonlatip Pipattanaboon,2,3 Pongrama Ramasoota,2,4 Chayanee Setthapramote,2,3 Tadahiro Sasaki,6 Mikiko Sasayama,1 Akifumi Yamashita,1,5 Takeshi Kurosu,6 Kazuyoshi Ikuta,6 Tamaki Okabayashi11Mahidol-Osaka Center for Infectious Diseases, 2Center of Excellence for Antibody Research, 3Department of Microbiology and Immunology, 4Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, Thailand; 5Graduate School of Life Science, Tohoku University, Sendai, Miyagi, 6Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, JapanBackground: Dengue illness is one of the important mosquito-borne viral diseases in tropical and subtropical regions. Four serotypes of dengue virus (DENV-1, DENV-2, DENV-3, and DENV-4 are classified in the Flavivirus genus of the family Flaviviridae. We prepared monoclonal antibodies against DENV capsid protein from mice immunized with DENV-2 and determined the cross-reactivity with each serotype of DENV and Japanese encephalitis virus.Methods and results: To clarify the relationship between the cross-reactivity of monoclonal antibodies and the diversity of these viruses, we examined the situations of flaviviruses by analyses of phylogenetic trees. Among a total of 60 prepared monoclonal antibodies specific for DENV, five monoclonal antibodies stained the nuclei of infected cells and were found to be specific to the capsid protein. Three were specific to DENV-2, while the other two were cross-reactive with DENV-2 and DENV-4. No monoclonal antibodies were cross-reactive with all four serotypes. Phylogenetic analysis of DENV amino acid sequences of the capsid protein revealed that DENV-2 and DENV-4 were clustered in the same branch, while DENV-1 and DENV-3 were clustered in the other branch. However, these classifications of the capsid protein were different from those of the

  1. The NTD-CTD intersubunit interface plays a critical role in assembly and stabilization of the HIV-1 capsid

    OpenAIRE

    Yufenyuy, Ernest L; Aiken, Christopher

    2013-01-01

    Background Lentiviruses exhibit a cone-shaped capsid composed of subunits of the viral CA protein. The intrinsic stability of the capsid is critical for HIV-1 infection, since both stabilizing and destabilizing mutations compromise viral infectivity. Structural studies have identified three intersubunit interfaces in the HIV-1 capsid, two of which have been previously studied by mutational analysis. In this present study we analyzed the role of a third interface, that which is formed between ...

  2. Charting the Structure and Energetics of Packaged DNA in Bacteriophages

    Science.gov (United States)

    Qiu, Xiangyun; Rau, Donald C.; Parsegian, V. Adrian; Fang, Li Tai; Knobler, Charles M.; Gelbart, William M.

    2009-03-01

    Many bacterial viruses resort to pressure in order to infect bacteria, e.g., lambda phage stores its dsDNA genome at surprisingly high pressure and then uses this pressure to drive delivery of the genome. We report on a biophysical interrogation of the DNA configuration and pressure in lambda phage by combining structural and thermodynamic measurements with theoretical modeling. Changes in DNA organization in the capsid are monitored using solution small angle x-ray scattering (SAXS). We vary the DNA-DNA repulsion and DNA bending contributions to the capsid pressure by changing salt concentrations and packaged length, and augment SAXS data with osmotic stress measurements to elicit the evolving structure and energetics of the packaged DNA.

  3. Polymer ejection from bacteriophages is fully determined by confinement energy

    CERN Document Server

    Piili, J

    2015-01-01

    The ejection dynamics through a nanoscale pore of a flexible polymer that is initially strongly confined inside a spherical capsid is examined. By extensive simulations using the stochastic rotation dynamics method we show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers under constant initial monomer density. This dependence is a consequence of the excess free energy of the polymer due to confinement growing exponentially with the initial monomer number inside the capsid, which we address to strong monomer-monomer interactions. Consequently, for sufficiently strong initial confinement and long polymers ejection times for polymers of different lengths depend linearly on the length. At polymer lengths amenable to computer simulations the dependence is superlinear due to the finite-size effect related to the retraction of polymer tails at final stages of ejection.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. Modeling capsid self-assembly: design and analysis

    International Nuclear Information System (INIS)

    A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible and an explicit solvent is optionally included. Model design, simulation methodology and analysis techniques are discussed. The analysis focuses on the growth pathways and the nature of the intermediate states, properties that are hard to access experimentally. Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered

  10. Codon Optimization of Human Parvovirus B19 Capsid Genes Greatly Increases Their Expression in Nonpermissive Cells▿ †

    OpenAIRE

    Zhi, Ning; Wan, Zhihong; Liu, Xiaohong; Wong, Susan; Kim, Dong Joo; Young, Neal S.; Kajigaya, Sachiko

    2010-01-01

    Parvovirus B19 (B19V) is pathogenic for humans and has an extreme tropism for human erythroid progenitors. We report cell type-specific expression of the B19V capsid genes (VP1 and VP2) and greatly increased B19V capsid protein production in nonpermissive cells by codon optimization. Codon usage limitation, rather than promoter type and the 3′ untranslated region of the capsid genes, appears to be a key factor in capsid protein production in nonpermissive cells. Moreover, B19 virus-like parti...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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-...

  3. Small-molecule inhibition of human immunodeficiency virus type 1 infection by virus capsid destabilization.

    Science.gov (United States)

    Shi, Jiong; Zhou, Jing; Shah, Vaibhav B; Aiken, Christopher; Whitby, Kevin

    2011-01-01

    Human immunodeficiency virus type 1 (HIV-1) infection is dependent on the proper disassembly of the viral capsid, or "uncoating," in target cells. The HIV-1 capsid consists of a conical multimeric complex of the viral capsid protein (CA) arranged in a hexagonal lattice. Mutations in CA that destabilize the viral capsid result in impaired infection owing to defects in reverse transcription in target cells. We describe here the mechanism of action of a small molecule HIV-1 inhibitor, PF-3450074 (PF74), which targets CA. PF74 acts at an early stage of HIV-1 infection and inhibits reverse transcription in target cells. We show that PF74 binds specifically to HIV-1 particles, and substitutions in CA that confer resistance to the compound prevent binding. A single point mutation in CA that stabilizes the HIV-1 core also conferred strong resistance to the virus without inhibiting compound binding. Treatment of HIV-1 particles or purified cores with PF74 destabilized the viral capsid in vitro. Furthermore, the compound induced the rapid dissolution of the HIV-1 capsid in target cells. PF74 antiviral activity was promoted by binding of the host protein cyclophilin A to the HIV-1 capsid, and PF74 and cyclosporine exhibited mutual antagonism. Our data suggest that PF74 triggers premature HIV-1 uncoating in target cells, thereby mimicking the activity of the retrovirus restriction factor TRIM5α. This study highlights uncoating as a step in the HIV-1 life cycle that is susceptible to small molecule intervention. PMID:20962083

  4. Small-Molecule Inhibition of Human Immunodeficiency Virus Type 1 Infection by Virus Capsid Destabilization▿

    Science.gov (United States)

    Shi, Jiong; Zhou, Jing; Shah, Vaibhav B.; Aiken, Christopher; Whitby, Kevin

    2011-01-01

    Human immunodeficiency virus type 1 (HIV-1) infection is dependent on the proper disassembly of the viral capsid, or “uncoating,” in target cells. The HIV-1 capsid consists of a conical multimeric complex of the viral capsid protein (CA) arranged in a hexagonal lattice. Mutations in CA that destabilize the viral capsid result in impaired infection owing to defects in reverse transcription in target cells. We describe here the mechanism of action of a small molecule HIV-1 inhibitor, PF-3450074 (PF74), which targets CA. PF74 acts at an early stage of HIV-1 infection and inhibits reverse transcription in target cells. We show that PF74 binds specifically to HIV-1 particles, and substitutions in CA that confer resistance to the compound prevent binding. A single point mutation in CA that stabilizes the HIV-1 core also conferred strong resistance to the virus without inhibiting compound binding. Treatment of HIV-1 particles or purified cores with PF74 destabilized the viral capsid in vitro. Furthermore, the compound induced the rapid dissolution of the HIV-1 capsid in target cells. PF74 antiviral activity was promoted by binding of the host protein cyclophilin A to the HIV-1 capsid, and PF74 and cyclosporine exhibited mutual antagonism. Our data suggest that PF74 triggers premature HIV-1 uncoating in target cells, thereby mimicking the activity of the retrovirus restriction factor TRIM5α. This study highlights uncoating as a step in the HIV-1 life cycle that is susceptible to small molecule intervention. PMID:20962083

  5. Structural Studies of Adeno-Associated Virus Serotype 8 Capsid Transitions Associated with Endosomal Trafficking

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Hyun-Joo; Gurda, Brittney L.; McKenna, Robert; Potter, Mark; Byrne, Barry; Salganik, Maxim; Muzyczka, Nicholas; Agbandje-McKenna, Mavis (Florida)

    2012-09-17

    The single-stranded DNA (ssDNA) parvoviruses enter host cells through receptor-mediated endocytosis, and infection depends on processing in the early to late endosome as well as in the lysosome prior to nuclear entry for replication. However, the mechanisms of capsid endosomal processing, including the effects of low pH, are poorly understood. To gain insight into the structural transitions required for this essential step in infection, the crystal structures of empty and green fluorescent protein (GFP) gene-packaged adeno-associated virus serotype 8 (AAV8) have been determined at pH values of 6.0, 5.5, and 4.0 and then at pH 7.5 after incubation at pH 4.0, mimicking the conditions encountered during endocytic trafficking. While the capsid viral protein (VP) topologies of all the structures were similar, significant amino acid side chain conformational rearrangements were observed on (i) the interior surface of the capsid under the icosahedral 3-fold axis near ordered nucleic acid density that was lost concomitant with the conformational change as pH was reduced and (ii) the exterior capsid surface close to the icosahedral 2-fold depression. The 3-fold change is consistent with DNA release from an ordering interaction on the inside surface of the capsid at low pH values and suggests transitions that likely trigger the capsid for genome uncoating. The surface change results in disruption of VP-VP interface interactions and a decrease in buried surface area between VP monomers. This disruption points to capsid destabilization which may (i) release VP1 amino acids for its phospholipase A2 function for endosomal escape and nuclear localization signals for nuclear targeting and (ii) trigger genome uncoating.

  6. 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

  7. P2MP MPLS-Based Hierarchical Service Management System

    Science.gov (United States)

    Kumaki, Kenji; Nakagawa, Ikuo; Nagami, Kenichi; Ogishi, Tomohiko; Ano, Shigehiro

    This paper proposes a point-to-multipoint (P2MP) Multi-Protocol Label Switching (MPLS) based hierarchical service management system. Traditionally, general management systems deployed in some service providers control MPLS Label Switched Paths (LSPs) (e.g., RSVP-TE and LDP) and services (e.g., L2VPN, L3VPN and IP) separately. In order for dedicated management systems for MPLS LSPs and services to cooperate with each other automatically, a hierarchical service management system has been proposed with the main focus on point-to-point (P2P) TE LSPs in MPLS path management. In the case where P2MP TE LSPs and services are deployed in MPLS networks, the dedicated management systems for P2MP TE LSPs and services must work together automatically. Therefore, this paper proposes a new algorithm that uses a correlation between P2MP TE LSPs and multicast VPN services based on a P2MP MPLS-based hierarchical service management architecture. Also, the capacity and performance of the proposed algorithm are evaluated by simulations, which are actually based on certain real MPLS production networks, and are compared to that of the algorithm for P2P TE LSPs. Results show this system is very scalable within real MPLS production networks. This system, with the automatic correlation, appears to be deployable in real MPLS production networks.

  8. P2X4 receptors and neuropathic pain

    Directory of Open Access Journals (Sweden)

    Makoto Tsuda

    2013-10-01

    Full Text Available Neuropathic pain, a debilitating pain condition, is a common consequence of damage to the nervous system. Neuropathic pain is often resistant to currently available analgesics. A growing body of evidence indicates that spinal microglia react and undergo a series of changes that directly influence the establishment of neuropathic pain states. After nerve injury, P2X4 receptors (P2X4Rs are upregulated in spinal microglia by several factors at the transcriptional and translational levels. Those include the CC chemokine CCL21 derived from damaged neurons, the extracellular matrix protein fibronectin in the spinal cord, and the transcription factor interferon regulatory factor 8 expressed in microglia. P2X4R expression in microglia is also regulated at the post-translational level by signaling from other cell-surface receptors such as CC chemokine receptor CCR2. Importantly, inhibiting the function or expression of P2X4Rs and P2X4R-regulating molecules suppresses the aberrant excitability of dorsal horn neurons and neuropathic pain. These findings indicate that P2X4R-positive microglia are a central player in mechanisms for neuropathic pain. Thus, microglial P2X4Rs are a potential target for treating the chronic pain state.

  9. Queries mining for efficient routing in P2P communities

    CERN Document Server

    Ismail, Anis; Durand, Nicolas; Nachouki, Gilles; Hajjar, Mohammad

    2011-01-01

    Peer-to-peer (P2P) computing is currently attracting enormous attention. In P2P systems a very large number of autonomous computing nodes (the peers) pool together their resources and rely on each other for data and services. Peer-to-peer (P2P) Data-sharing systems now generate a significant portion of Internet traffic. Examples include P2P systems for network storage, web caching, searching and indexing of relevant documents and distributed network-threat analysis. Requirements for widely distributed information systems supporting virtual organizations have given rise to a new category of P2P systems called schema-based. In such systems each peer exposes its own schema and the main objective is the efficient search across the P2P network by processing each incoming query without overly consuming bandwidth. The usability of these systems depends on effective techniques to find and retrieve data; however, efficient and effective routing of content-based queries is a challenging problem in P2P networks. This wo...

  10. Measurement and Analysis of P2P IPTV Program Resource

    OpenAIRE

    Wenxian Wang; Xingshu Chen; Haizhou Wang; Qi Zhang; Cheng Wang

    2014-01-01

    With the rapid development of P2P technology, P2P IPTV applications have received more and more attention. And program resource distribution is very important to P2P IPTV applications. In order to collect IPTV program resources, a distributed multi-protocol crawler is proposed. And the crawler has collected more than 13 million pieces of information of IPTV programs from 2009 to 2012. In addition, the distribution of IPTV programs is independent and incompact, resulting in chaos of program na...

  11. Comparing Pedophile Activity in Different P2P Systems

    OpenAIRE

    Raphaël Fournier; Thibault Cholez; Matthieu Latapy; Isabelle Chrisment; Clémence Magnien; Olivier Festor; Ivan Daniloff

    2014-01-01

    International audience Peer-to-peer (P2P) systems are widely used to exchange content over the Internet. Knowledge of pedophile activity in such networks remains limited, despite having important social consequences. Moreover, though there are different P2P systems in use, previous academic works on this topic focused on one system at a time and their results are not directly comparable. We design a methodology for comparing KAD and eDonkey, two P2P systems among the most prominent ones an...

  12. The role of P2X receptors in bone biology

    DEFF Research Database (Denmark)

    Jørgensen, N R; Syberg, S; Ellegaard, M

    2015-01-01

    receptors regulate bone metabolism and especially for the P2X7 receptor an impressive amount of evidence has now documented its expression in osteoblasts, osteoclasts, and osteocytes as well as important functional roles in proliferation, differentiation, and function of the cells of bone. Key evidence has...... come from studies on murine knockout models and from pharmacologic studies on cells and animals. More recently, the role of P2X receptors in human bone diseases has been documented. Loss-of-functions polymorphisms in the P2X7 receptorare associated with bone loss and increased fracture risk. Very...

  13. Code wars 10 years of P2P software litigation

    CERN Document Server

    Giblin, Rebecca

    2011-01-01

    Code Wars recounts the legal and technological history of the first decade of the P2P file sharing era, focusing on the innovative and anarchic ways in which P2P technologies evolved in response to decisions reached by courts with regard to their predecessors. With reference to US, UK, Canadian and Australian secondary liability regimes, this insightful book develops a compelling new theory to explain why a decade of ostensibly successful litigation failed to reduce the number, variety or availability of P2P file sharing applications - and highlights ways the law might need to change if it is

  14. Evolution of pro-protamine P2 genes in primates.

    Science.gov (United States)

    Retief, J D; Dixon, G H

    1993-06-01

    Protamines P1 and P2 form a family of small basic peptides that represent the major sperm proteins in placental mammals. In human and mouse protamine P2 is one of the most abundant sperm proteins. The protamine P2 gene codes for a P2 precursor, pro-P2 which is later processed by proteolytic cleavages in its N-terminal region to form the mature P2 protamines. We have used polymerase chain amplification to directly sequence the pro-P2 genes of the five major primate families: red howler (Alouatta seniculus) is a New World monkey (Cebidae); the two macaque species, Macaca mulatta and M. nemistrina are Old World monkeys (Cercopithecidae), the gibbon, Hylobates lar, represents one branch of the apes (Hylobatidae); the orangutan, Pongo pygmaeus, gorilla, Gorilla gorilla and two species of chimpanzee Pan paniscus and Pan troglodytes represent a second ape family (Pongidae). These pro-P2 genes are compared with that of human [Domenjoud, L., Nussbaum, G., Adham, I. M., Greeske, G. & Engel, W. (1990) Genomics 8, 127-133]. The overall size and organization of the genes are conserved within the group. The mean length of pro-P2 is 101 residues, with an increase to 102 in M. nemistrina and a decrease to 99 residues in red howler (A. seniculus). In gorilla and red howler one of two 79-bp tandem repeats that occurs 3' of the gene is deleted. Of the 101 deduced amino acids examined, an amino acid change occurs in one or more primates at 45 positions. Considering only the most recently diverged group, the human/gorilla/chimpanzee clade, this represents a very high mutation rate of 0.99 changes/100 sites in 10(6) years. This rapid mutation rate is characteristic of both members of the protamine gene family, P1 and P2. Consideration of the variable nature of the sequences at the multiple sites of proteolysis during the processing of the pro-P2 indicates either that there are several processing enzymes of differing specificities, or more likely that the folded structure of the pro-P2

  15. 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...

  16. TCLM-P2P: Task Collaboration Logic Model Oriented to P2P Community%TCLM-P2P:面向P2P社区的任务协作逻辑模型

    Institute of Scientific and Technical Information of China (English)

    王杨; 王汝传; 严远亭; 韩志杰; 赵保华

    2012-01-01

    P2P网络中广泛存在的“free riding”现象使其在任务协作领域的应用受到了极大制约.为了实现P2P网络环境下的有效任务协作,提出了一种具有激励机制的任务协作逻辑模型.基于Agent理论,首先给出了对等体、半对等体、P2P社区等概念;然后在合同网的框架下提出了面向P2P网络社区的任务协作逻辑模型TCLM-P2P(task collaborative logic model oriented to P2P community).相对于传统的任务协作模型,在合理的前提假设条件下,模型给出了模型公理和协作规则.该模型通过基于虚拟积分的协作算法实现了具有激励机制的P2P网络中的任务分配与协作.原型系统的实现及仿真实验结果表明TCLM-P2P模型具有可行性和有效性:不仅能够激励自利节点主动参与到任务分配与协作中;同时也能在一定程度上抑制节点的free riding行为,从而保障了P2P系统的有序工作.%Traditional P2P networks mainly are applied to file sharing and instant message fields. However, how to perform the task collaboration based on P2P community is a challenging job. The former research work indicated that the task collaboration in P2P network had been greatly restricted by free riding behaviors. To realize effective task allocating and task collaborating in P2P network environment, this paper presents a task collaboration logic model oriented to P2P community. Based on agent and multi-agent theory, the paper firstly introduces some concepts including the peer body, half-peer body and P2P community; then the TCLM-P2P is presented including some collaboration axioms and rulers. In order to enhance the incentive mechanism, virtual score becomes the main goal which each peer endeavor pursues. In addition, based on the contract net protocol, a task collaboration algorithm is presented. The proposed algorithm is composed of two phases. One is the task collaboration and the other is the task second bid when some peers fail

  17. Relevance of capsid structure in the buckling and maturation of spherical viruses

    International Nuclear Information System (INIS)

    The shape and mechanical properties of viral capsids play an important role in several biological processes during the virus life cycle. In particular, to become infective, many viruses require a maturation stage where the capsid undergoes a buckling transition, from an initial spherical procapsid into a final icosahedral faceted shell. Here we study, using a minimal physical model, how the capsid shape and the buckling transition depend on the triangulation number T and the icosahedral class P of the virus structure. We find that, for small shells, capsids with P = 1 are most likely to produce polyhedral shapes that minimize their energy and accumulated stress, whereas viruses with P = 3 prefer to remain spherical. For big capsids, all shells are more stable adopting an icosahedral shape, in agreement with continuum elastic theory. Moreover, spherical viruses show a buckling transition to polyhedral shells under expansion, in consonance with virus maturation. The resulting icosahedral shell is mechanically stiffer, tolerates larger expansions and withstands higher internal pressures before failing, which could explain why some dsDNA viruses, which rely on the pressurization of their genetic material to facilitate the infection, undergo a buckling transition. We emphasize that the results are general and could also be applied to non-biological systems. (paper)

  18. A molecular thermodynamic model for the stability of hepatitis B capsids

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jehoon; Wu, Jianzhong, E-mail: jwu@engr.ucr.edu [Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521 (United States)

    2014-06-21

    Self-assembly of capsid proteins and genome encapsidation are two critical steps in the life cycle of most plant and animal viruses. A theoretical description of such processes from a physiochemical perspective may help better understand viral replication and morphogenesis thus provide fresh insights into the experimental studies of antiviral strategies. In this work, we propose a molecular thermodynamic model for predicting the stability of Hepatitis B virus (HBV) capsids either with or without loading nucleic materials. With the key components represented by coarse-grained thermodynamic models, the theoretical predictions are in excellent agreement with experimental data for the formation free energies of empty T4 capsids over a broad range of temperature and ion concentrations. The theoretical model predicts T3/T4 dimorphism also in good agreement with the capsid formation at in vivo and in vitro conditions. In addition, we have studied the stability of the viral particles in response to physiological cellular conditions with the explicit consideration of the hydrophobic association of capsid subunits, electrostatic interactions, molecular excluded volume effects, entropy of mixing, and conformational changes of the biomolecular species. The course-grained model captures the essential features of the HBV nucleocapsid stability revealed by recent experiments.

  19. X-Ray Structures of the Hexameric Building Block of the HIV Capsid

    Energy Technology Data Exchange (ETDEWEB)

    Pornillos, Owen; Ganser-Pornillos, Barbie K.; Kelly, Brian N.; Hua, Yuanzi; Whitby, Frank G.; Stout, C. David; Sundquist, Wesley I.; Hill, Christopher P.; Yeager, Mark; (Scripps); (Utah)

    2009-09-11

    The mature capsids of HIV and other retroviruses organize and package the viral genome and its associated enzymes for delivery into host cells. The HIV capsid is a fullerene cone: a variably curved, closed shell composed of approximately 250 hexamers and exactly 12 pentamers of the viral CA protein. We devised methods for isolating soluble, assembly-competent CA hexamers and derived four crystallographically independent models that define the structure of this capsid assembly unit at atomic resolution. A ring of six CA N-terminal domains form an apparently rigid core, surrounded by an outer ring of C-terminal domains. Mobility of the outer ring appears to be an underlying mechanism for generating the variably curved lattice in authentic capsids. Hexamer-stabilizing interfaces are highly hydrated, and this property may be key to the formation of quasi-equivalent interactions within hexamers and pentamers. The structures also clarify the molecular basis for capsid assembly inhibition and should facilitate structure-based drug design strategies.

  20. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

    Science.gov (United States)

    Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun

    2016-03-01

    The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.

  1. Modulation of P2X3 and P2X2/3 Receptors by Monoclonal Antibodies.

    Science.gov (United States)

    Shcherbatko, Anatoly; Foletti, Davide; Poulsen, Kris; Strop, Pavel; Zhu, Guoyun; Hasa-Moreno, Adela; Melton Witt, Jody; Loo, Carole; Krimm, Stellanie; Pios, Ariel; Yu, Jessica; Brown, Colleen; Lee, John K; Stroud, Robert; Rajpal, Arvind; Shelton, David

    2016-06-01

    Purinergic homomeric P2X3 and heteromeric P2X2/3 receptors are ligand-gated cation channels activated by ATP. Both receptors are predominantly expressed in nociceptive sensory neurons, and an increase in extracellular ATP concentration under pathological conditions, such as tissue damage or visceral distension, induces channel opening, membrane depolarization, and initiation of pain signaling. Hence, these receptors are considered important therapeutic targets for pain management, and development of selective antagonists is currently progressing. To advance the search for novel analgesics, we have generated a panel of monoclonal antibodies directed against human P2X3 (hP2X3). We have found that these antibodies produce distinct functional effects, depending on the homomeric or heteromeric composition of the target, its kinetic state, and the duration of antibody exposure. The most potent antibody, 12D4, showed an estimated IC50 of 16 nm on hP2X3 after short term exposure (up to 18 min), binding to the inactivated state of the channel to inhibit activity. By contrast, with the same short term application, 12D4 potentiated the slow inactivating current mediated by the heteromeric hP2X2/3 channel. Extending the duration of exposure to ∼20 h resulted in a profound inhibition of both homomeric hP2X3 and heteromeric hP2X2/3 receptors, an effect mediated by efficient antibody-induced internalization of the channel from the plasma membrane. The therapeutic potential of mAb12D4 was assessed in the formalin, complete Freund's adjuvant, and visceral pain models. The efficacy of 12D4 in the visceral hypersensitivity model indicates that antibodies against P2X3 may have therapeutic potential in visceral pain indications. PMID:27129281

  2. P2P Concept Search: Some Preliminary Results

    OpenAIRE

    Giunchiglia, Fausto; Kharkevich, Uladzimir; Noori, S.R.H

    2009-01-01

    Concept Search extends syntactic search, i.e., search based on the computation of string similarity between words, with semantic search, i.e., search based on the computation of semantic relations between complex concepts. It allows us to deal with ambiguity of natural language. P2P Concept Search extends Concept Search by allowing distributed semantic search over structured P2P network. The key idea is to exploit distributed, rather than centralized, background knowledge and indices.

  3. Evaluating MDC with Incentives in P2PTV Systems

    OpenAIRE

    González Cela, Alberto José; Ríos, André; Enero, Guillermo; Oller Arcas, Antonio; Alcober Segura, Jesús Ángel

    2010-01-01

    The popularity of P2P video streaming is raising the interest of broadcasters, operators and service providers. Concretely, mesh-pull based P2P systems are the most extended ones. Despite these systems address scalability efficiently, they still present limitations that difficult them to offer the same user experience in comparison with traditional TV. These ones are mainly the free-riding effect, long start-up delays and the impact of churn and bandwidth heterogeneity. In this paper we study...

  4. Mobile P2P Web Services Using SIP

    OpenAIRE

    Guido Gehlen; Fahad Aijaz; Yi Zhu; Bernhard Walke

    2007-01-01

    Telecommunication networks and the Internet are growing together. Peer-to-Peer (P2P) services which are originally offered by network providers, like telephony and messaging, are provided through VoIP and Instant Messaging (IM) by Internet service providers, too. The IP Multimedia Subsystem (IMS) is the answer of the telecommunication industry to this trend and aims at providing Internet P2P and multimedia services controlled by the network operators. The IMS provides mobility and session man...

  5. Meeting of the ITER SWG-P2 in Vienna

    International Nuclear Information System (INIS)

    The Special Working Group established under Protocol 2 to the ITER IDA Agreement (SWG-P2) met at the IAEA in Vienna in 6-9 December 1999. This report contains excerpts from the report of the ITER SWG-P2 to the ITER Council on the Joint Implementation of ITER, detailing benefits, contributions, the legal framework, siting, licensing and decommissioning as well as procurement, staffing and intellectual property rights

  6. Survey on Scheduling Technologies of P2P Media Streaming

    OpenAIRE

    Guangxue Yue; Nanqing Wei; Jiansheng Liu; Xiaofeng Xiong; Linquan Xie

    2011-01-01

    P2P streaming media applications grows rapidly. Scheduling technologies are the key of streaming research. After review the history of distribution systems. We studied the main data distribution topology and P2P streaming scheduling technologies. Compared current scheduling algorithms. Finally made a conclusion and forecasted scheduling in the mesh-tree distribution structure, heterogeous network, alone with security in scheduling will be the hotspots in the near future.

  7. The Physical Mirror Equivalence for the Local P^2

    CERN Document Server

    Cacciatori, Sergio Luigi; Guerra, Stefano

    2013-01-01

    In this paper we consider the total space of the canonical bundle of P^2 and we use a proposal by Hosono, together with results in Seidel and Auroux-Katzarkov-Orlov, to deduce the right physical mirror equivalence between D^b(K_{P^2}) and the derived Fukaya category of its mirror. By construction, our equivalence is compatible with the mirror map between moduli spaces and with the computation of Gromov--Witten invariants.

  8. Accelerated FoxP2 evolution in echolocating bats.

    Science.gov (United States)

    Li, Gang; Wang, Jinhong; Rossiter, Stephen J; Jones, Gareth; Zhang, Shuyi

    2007-01-01

    FOXP2 is a transcription factor implicated in the development and neural control of orofacial coordination, particularly with respect to vocalisation. Observations that orthologues show almost no variation across vertebrates yet differ by two amino acids between humans and chimpanzees have led to speculation that recent evolutionary changes might relate to the emergence of language. Echolocating bats face especially challenging sensorimotor demands, using vocal signals for orientation and often for prey capture. To determine whether mutations in the FoxP2 gene could be associated with echolocation, we sequenced FoxP2 from echolocating and non-echolocating bats as well as a range of other mammal species. We found that contrary to previous reports, FoxP2 is not highly conserved across all nonhuman mammals but is extremely diverse in echolocating bats. We detected divergent selection (a change in selective pressure) at FoxP2 between bats with contrasting sonar systems, suggesting the intriguing possibility of a role for FoxP2 in the evolution and development of echolocation. We speculate that observed accelerated evolution of FoxP2 in bats supports a previously proposed function in sensorimotor coordination. PMID:17878935

  9. Characterization of P2P IPTV Traffic: Scaling Analysis

    CERN Document Server

    Silverston, Thomas; Salamatian, Kave

    2007-01-01

    P2P IPTV applications arise on the Internet and will be massively used in the future. It is expected that P2P IPTV will contribute to increase the overall Internet traffic. In this context, it is important to measure the impact of P2P IPTV on the networks and to characterize this traffic. During the 2006 FIFA World Cup, we performed an extensive measurement campaign. We measured network traffic generated by broadcasting soccer games by the most popular P2P IPTV applications, namely PPLive, PPStream, SOPCast and TVAnts. From the collected data, we characterized the P2P IPTV traffic structure at different time scales. To the best of our knowledge, this is the first work, which presents a complete multiscale analysis of the P2P IPTV traffic. Our observations show that the network traffic has not the same scale behavior whether the applications use TCP or UDP. For all the applications, the download traffic is different from the upload traffic and the signaling traffic has an impact on the download traffic.

  10. Improving P2P live-content delivery using SVC

    Science.gov (United States)

    Schierl, T.; Sánchez, Y.; Hellge, C.; Wiegand, T.

    2010-07-01

    P2P content delivery techniques for video transmission have become of high interest in the last years. With the involvement of client into the delivery process, P2P approaches can significantly reduce the load and cost on servers, especially for popular services. However, previous studies have already pointed out the unreliability of P2P-based live streaming approaches due to peer churn, where peers may ungracefully leave the P2P infrastructure, typically an overlay networks. Peers ungracefully leaving the system cause connection losses in the overlay, which require repair operations. During such repair operations, which typically take a few roundtrip times, no data is received from the lost connection. While taking low delay for fast-channel tune-in into account as a key feature for broadcast-like streaming applications, the P2P live streaming approach can only rely on a certain media pre-buffer during such repair operations. In this paper, multi-tree based Application Layer Multicast as a P2P overlay technique for live streaming is considered. The use of Flow Forwarding (FF), a.k.a. Retransmission, or Forward Error Correction (FEC) in combination with Scalable video Coding (SVC) for concealment during overlay repair operations is shown. Furthermore the benefits of using SVC over the use of AVC single layer transmission are presented.

  11. Network Awareness in P2P-TV Applications

    Science.gov (United States)

    Traverso, Stefano; Leonardi, Emilio; Mellia, Marco; Meo, Michela

    The increasing popularity of applications for video-streaming based on P2P paradigm (P2P-TV) is raising the interest of both broadcasters and network operators. The former see a promising technology to reduce the cost of streaming content over the Internet, while offering a world-wide service. The latter instead fear that the traffic offered by these applications can grow without control, affecting other services, and possibly causing network congestion and collapse. The “Network-Aware P2P-TV Application over Wise Networks” FP7 project aims at studying and developing a novel P2P-TV application offering the chance to broadcast high definition video to broadcasters and to carefully manage the traffic offered by peers to the network, therefore avoiding worries to Internet providers about network overload. In such context, we design a simulator to evaluate performance of different P2P-TV solutions, to compare them both considering end-users’ and network providers’ perspectives, such as quality of service perceived by subscribers and link utilization. In this paper, we provide some results that show how effective can be a network aware P2P-TV system.

  12. P2P Data Management in Mobile Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Nida Sahar Sayeda

    2013-04-01

    Full Text Available The rapid growth in wireless technologies has made wireless communication an important source for transporting data across different domains. In the same way, there are possibilities of many potential applications that can be deployed using WSNs (Wireless Sensor Networks. However, very limited applications are deployed in real life due to the uncertainty and dynamics of the environment and scare resources. This makes data management in WSN a challenging area to find an approach that suits its characteristics. Currently, the trend is to find efficient data management schemes using evolving technologies, i.e. P2P (Peer-to-Peer systems. Many P2P approaches have been applied in WSNs to carry out the data management due to similarities between WSN and P2P. With the similarities, there are differences too that makes P2P protocols inefficient in WSNs. Furthermore, to increase the efficiency and to exploit the delay tolerant nature of WSNs, where ever possible, the mobile WSNs are gaining importance. Thus, creating a three dimensional problem space to consider, i.e. mobility, WSNs and P2P. In this paper, an efficient algorithm is proposed for data management using P2P techniques for mobile WSNs. The real world implementation and deployment of proposed algorithm is also presented

  13. Accelerated FoxP2 evolution in echolocating bats.

    Directory of Open Access Journals (Sweden)

    Gang Li

    Full Text Available FOXP2 is a transcription factor implicated in the development and neural control of orofacial coordination, particularly with respect to vocalisation. Observations that orthologues show almost no variation across vertebrates yet differ by two amino acids between humans and chimpanzees have led to speculation that recent evolutionary changes might relate to the emergence of language. Echolocating bats face especially challenging sensorimotor demands, using vocal signals for orientation and often for prey capture. To determine whether mutations in the FoxP2 gene could be associated with echolocation, we sequenced FoxP2 from echolocating and non-echolocating bats as well as a range of other mammal species. We found that contrary to previous reports, FoxP2 is not highly conserved across all nonhuman mammals but is extremely diverse in echolocating bats. We detected divergent selection (a change in selective pressure at FoxP2 between bats with contrasting sonar systems, suggesting the intriguing possibility of a role for FoxP2 in the evolution and development of echolocation. We speculate that observed accelerated evolution of FoxP2 in bats supports a previously proposed function in sensorimotor coordination.

  14. Potential energy curves for P2 and P2+ constructed from a strictly N-representable natural orbital functional

    CERN Document Server

    Piris, Mario

    2016-01-01

    The potential energy curves of P2 and P2+ have been calculated using an approximate, albeit strictly N-representable, energy functional of the one-particle reduced density matrix: PNOF5. Quite satisfactory accord is found for the equilibrium bond lengths and dissociation energies for both species. The predicted vertical ionization energy for P2 by means of the extended Koopmans' theorem is 10.57 eV in good agreement with the experimental data. Comparison of the vibrational energies and anharmonicities with their corresponding experimental values supports the quality of the resultant potential energy curves.

  15. 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...

  16. 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

  17. Extreme genetic fragility of the HIV-1 capsid.

    Science.gov (United States)

    Rihn, Suzannah J; Wilson, Sam J; Loman, Nick J; Alim, Mudathir; Bakker, Saskia E; Bhella, David; Gifford, Robert J; Rixon, Frazer J; Bieniasz, Paul D

    2013-01-01

    Genetic robustness, or fragility, is defined as the ability, or lack thereof, of a biological entity to maintain function in the face of mutations. Viruses that replicate via RNA intermediates exhibit high mutation rates, and robustness should be particularly advantageous to them. The capsid (CA) domain of the HIV-1 Gag protein is under strong pressure to conserve functional roles in viral assembly, maturation, uncoating, and nuclear import. However, CA is also under strong immunological pressure to diversify. Therefore, it would be particularly advantageous for CA to evolve genetic robustness. To measure the genetic robustness of HIV-1 CA, we generated a library of single amino acid substitution mutants, encompassing almost half the residues in CA. Strikingly, we found HIV-1 CA to be the most genetically fragile protein that has been analyzed using such an approach, with 70% of mutations yielding replication-defective viruses. Although CA participates in several steps in HIV-1 replication, analysis of conditionally (temperature sensitive) and constitutively non-viable mutants revealed that the biological basis for its genetic fragility was primarily the need to coordinate the accurate and efficient assembly of mature virions. All mutations that exist in naturally occurring HIV-1 subtype B populations at a frequency >3%, and were also present in the mutant library, had fitness levels that were >40% of WT. However, a substantial fraction of mutations with high fitness did not occur in natural populations, suggesting another form of selection pressure limiting variation in vivo. Additionally, known protective CTL epitopes occurred preferentially in domains of the HIV-1 CA that were even more genetically fragile than HIV-1 CA as a whole. The extreme genetic fragility of HIV-1 CA may be one reason why cell-mediated immune responses to Gag correlate with better prognosis in HIV-1 infection, and suggests that CA is a good target for therapy and vaccination strategies

  18. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

    International Nuclear Information System (INIS)

    CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer

  19. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

    Energy Technology Data Exchange (ETDEWEB)

    Parent, Kristin N., E-mail: kparent@msu.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Tang, Jinghua; Cardone, Giovanni [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Gilcrease, Eddie B. [University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112 (United States); Janssen, Mandy E.; Olson, Norman H. [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Casjens, Sherwood R., E-mail: sherwood.casjens@path.utah.edu [University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112 (United States); Baker, Timothy S., E-mail: tsb@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); University of California, San Diego, Division of Biological Sciences, La Jolla, CA, 92093 (United States)

    2014-09-15

    CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer.

  20. Ergothioneine, histidine, and two naturally occurring histidine dipeptides as radioprotectors against gamma-irradiation inactivation of bacteriophages T4 and P22

    International Nuclear Information System (INIS)

    Bacteriophages P22, T4+, and T4os (osmotic shock-resistant mutant with altered capsids) were diluted in 0.85% NaCl and exposed to gamma irradiation (2.79 Gy/min) at room temperature (24 degrees C). T4+ was more sensitive to inactivation than was P22, and the T4os mutant was even more sensitive than T4+. Catalase exhibited a strong protective effect and superoxide dismutase a weaker protection, indicating that H2O2 or some product derived therefrom was predominant in causing inactivation of plaque formation. Low but significant (0.1-0.3 mM) reduced glutathione (GSH) enhanced phage inactivation, but a higher (1 mM) GSH concentration protected. A similar effect was found for the polyamine, spermidine. In contrast, 0.1 mM L-ergothioneine (2-thiol-L-histidine betaine) exhibited strong protection and 1 mM afforded essentially complete protection. L-Ergothioneine is present in millimolar concentrations in some fungi and is conserved up to millimolar concentrations in critical tissues when consumed by man. L-Histidine and two histidine-containing dipeptides, carnosine and anserine, protected at a concentration of 1 mM, a level at which they are present in striated muscles of various animals

  1. Ergothioneine, histidine, and two naturally occurring histidine dipeptides as radioprotectors against gamma-irradiation inactivation of bacteriophages T4 and P22

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, P.E.; Hartman, Z.; Citardi, M.J.

    1988-05-01

    Bacteriophages P22, T4+, and T4os (osmotic shock-resistant mutant with altered capsids) were diluted in 0.85% NaCl and exposed to gamma irradiation (2.79 Gy/min) at room temperature (24 degrees C). T4+ was more sensitive to inactivation than was P22, and the T4os mutant was even more sensitive than T4+. Catalase exhibited a strong protective effect and superoxide dismutase a weaker protection, indicating that H/sub 2/O/sub 2/ or some product derived therefrom was predominant in causing inactivation of plaque formation. Low but significant (0.1-0.3 mM) reduced glutathione (GSH) enhanced phage inactivation, but a higher (1 mM) GSH concentration protected. A similar effect was found for the polyamine, spermidine. In contrast, 0.1 mM L-ergothioneine (2-thiol-L-histidine betaine) exhibited strong protection and 1 mM afforded essentially complete protection. L-Ergothioneine is present in millimolar concentrations in some fungi and is conserved up to millimolar concentrations in critical tissues when consumed by man. L-Histidine and two histidine-containing dipeptides, carnosine and anserine, protected at a concentration of 1 mM, a level at which they are present in striated muscles of various animals.

  2. Theatrical distribution and P2P movie piracy: a survey of P2P networks in Hungary using transactional data

    OpenAIRE

    Bodó, B.; Lakatos, Z.

    2012-01-01

    This article examines what appears to be the most important factor shaping file sharing: the failure of traditional cultural markets to efficiently supply the demand in the online environment. Its findings are based on tracking the traffic of movies on three Hungarian P2P networks. This dataset is then matched with cinematic distribution data of the films tracked in P2P transactions. Central to our analysis is the assessment of two piracy paradigms: substitution and shortage, that is, whether...

  3. In vitro assembly of polymorphic virus-like particles from the capsid protein of a nodavirus.

    Science.gov (United States)

    Bajaj, Saumya; Banerjee, Manidipa

    2016-09-01

    Viral capsid proteins are programmed to assemble into homogeneous structures in native environments; but the molecular details of these assembly pathways are seldom clearly understood. In order to define the chain of events in the construction of a minimal system, we attempted controlled assembly of the capsid protein of a small insect nodavirus, Flock House Virus (FHV). Bacterial expression of the FHV capsid protein, and subsequent in vitro assembly, generated a heterogeneous population of closed particles. We show that in spite of the altered structure, these particles are capable of membrane disruption, like native viruses, and of incorporating and delivering foreign cargo to specific locations. The unique structure and characteristics of these particles extends our understanding of nodavirus assembly. Additionally, the establishment of a bacterial production system, and methods for in vitro assembly and packaging are of considerable benefit for biotechnological applications of FHV. PMID:27289029

  4. Hepatitis B Virus Core Protein Phosphorylation Sites Affect Capsid Stability and Transient Exposure of the C-terminal Domain.

    Science.gov (United States)

    Selzer, Lisa; Kant, Ravi; Wang, Joseph C-Y; Bothner, Brian; Zlotnick, Adam

    2015-11-20

    Hepatitis B virus core protein has 183 amino acids divided into an assembly domain and an arginine-rich C-terminal domain (CTD) that regulates essential functions including genome packaging, reverse transcription, and intracellular trafficking. Here, we investigated the CTD in empty hepatitis B virus (HBV) T=4 capsids. We examined wild-type core protein (Cp183-WT) and a mutant core protein (Cp183-EEE), in which three CTD serines are replaced with glutamate to mimic phosphorylated protein. We found that Cp183-WT capsids were less stable than Cp183-EEE capsids. When we tested CTD sensitivity to trypsin, we detected two different populations of CTDs differentiated by their rate of trypsin cleavage. Interestingly, CTDs from Cp183-EEE capsids exhibited a much slower rate of proteolytic cleavage when compared with CTDs of Cp183-WT capsids. Cryo-electron microscopy studies of trypsin-digested capsids show that CTDs at five-fold symmetry vertices are most protected. We hypothesize that electrostatic interactions between glutamates and arginines in Cp183-EEE, particularly at five-fold, increase capsid stability and reduce CTD exposure. Our studies show that quasi-equivalent CTDs exhibit different rates of exposure and thus might perform distinct functions during the hepatitis B virus lifecycle. Our results demonstrate a structural role for CTD phosphorylation and indicate crosstalk between CTDs within a capsid particle. PMID:26405031

  5. Breaking a virus: Identifying molecular level failure modes of a viral capsid by multiscale modeling

    Science.gov (United States)

    Krishnamani, V.; Globisch, C.; Peter, C.; Deserno, M.

    2016-07-01

    We use coarse-grained (CG) simulations to study the deformation of empty Cowpea Chlorotic Mottle Virus (CCMV) capsids under uniaxial compression, from the initial elastic response up to capsid breakage. Our CG model is based on the MARTINI force field and has been amended by a stabilizing elastic network, acting only within individual proteins, that was tuned to capture the fluctuation spectrum of capsid protein dimers, obtained from all atom simulations. We have previously shown that this model predicts force-compression curves that match AFM indentation experiments on empty CCMV capsids. Here we investigate details of the actual breaking events when the CCMV capsid finally fails. We present a symmetry classification of all relevant protein contacts and show that they differ significantly in terms of stability. Specifically, we show that interfaces which break readily are precisely those which are believed to form last during assembly, even though some of them might share the same contacts as other non-breaking interfaces. In particular, the interfaces that form pentamers of dimers never break, while the virtually identical interfaces within hexamers of dimers readily do. Since these units differ in the large-scale geometry and, most noticeably, the cone-angle at the center of the 5- or 6-fold vertex, we propose that the hexameric unit fails because it is pre-stressed. This not only suggests that hexamers of dimers form less frequently during the early stages of assembly; it also offers a natural explanation for the well-known β-barrel motif at the hexameric center as a post-aggregation stabilization mechanism. Finally, we identify those amino acid contacts within all key protein interfaces that are most persistent during compressive deformation of the capsid, thereby providing potential targets for mutation studies aiming to elucidate the key contacts upon which overall stability rests.

  6. Human immunodeficiency virus type 1 capsid protein is a substrate of the retroviral proteinase while integrase is resistant toward proteolysis

    International Nuclear Information System (INIS)

    The capsid protein of human immunodeficiency virus type 1 was observed to undergo proteolytic cleavage in vitro when viral lysate was incubated in the presence of dithiothreitol at acidic pH. Purified HIV-1 capsid protein was also found to be a substrate of the viral proteinase in a pH-dependent manner; acidic pH (<7) was necessary for cleavage, and decreasing the pH toward 4 increased the degree of processing. Based on N-terminal sequencing of the cleavage products, the capsid protein was found to be cleaved at two sites, between residues 77 and 78 as well as between residues 189 and 190. Oligopeptides representing these cleavage sites were also cleaved at the expected peptide bonds. The presence of cyclophilin A decreased the degree of capsid protein processing. Unlike the capsid protein, integrase was found to be resistant toward proteolysis in good agreement with its presence in the preintegration complex

  7. P2P Simulator for Queries Routing Using Data Mining

    Directory of Open Access Journals (Sweden)

    Anis ISMAIL

    2011-09-01

    Full Text Available Data mining is used to extract hidden information from large databases. In Peer-to-Peer context, achallenging problem is how to find the appropriate Peer to deal with a given query without overlyconsuming bandwidth. Different methods proposed routing strategies of queries taking into account theP2P network at hand. An unstructured P2P system based on an organization of Peers around Super-Peersthat are connected to Super-Super-Peer according to their semantic domains is considered. This paperintegrates Decision Trees in P2P architectures for predicting Query-Suitable Super-Peers representing acommunity of Peers, where one among them is able to answer the given query. In fact, by analyzing thequeries’ log file, a predictive model that avoids flooding queries in the P2P networks constructed bypredicting the appropriate Super-Peer, and hence the Peer to answer the query. The proposed architectureis based on a Decision Tree (Base-Knowledge - BK. The efficiency of these architectures is discussedconsidering architecture without knowledge (Baseline using only the flooding queries method to answerqueries. The advantage of this knowledge based model is the robustness in Queries routing mechanism andscalability in P2P Network.

  8. A Framework For Concept Drifting P2P Traffic Identification

    Directory of Open Access Journals (Sweden)

    Guanghui Yan

    2013-08-01

    Full Text Available Identification of network traffic using port-based or payload-based analysis is becoming increasing difficult with many Peer-to-Peer (P2P application using dynamic ports, masquerading techniques, and encryption to avoid detection. To overcome this problem, several machine learning technique were proposed to classify P2P traffics. But in the real P2P network environment, new communities of peers often attend and old communities of peers often leave. It requires the identification methods to be capable of coping with concept drift, and updating the model incrementally. In this paper, we present a concept-adapting algorithm CluMC which is based on streaming data mining techniques to identify P2P applications in Internet traffic. The CluMC use micro-cluster structures which contain potential micro-cluster structures and outlier micro-cluster structures to classify the P2P traffic and discover the concept drift with limited memory. Our performance study over a number of real data sets that we captured at a main gateway router demonstrates the effectiveness and efficiency of our method.

  9. Variations of P2 in subpulse drifting pulsars

    Science.gov (United States)

    Yuen, R.; Melrose, D. B.; Samsuddin, M. A.; Tu, Z. Y.; Han, X. H.

    2016-06-01

    We develop a model for subpulse separation period, P2, taking into account both the apparent motion of the visible point as a function of pulsar phase, ψ, and the possibility of abrupt jumps between different rotation states in non-corotating pulsar magnetospheres. We identify three frequencies: (i) the spin frequency of the star, (ii) the drift frequency of the magnetospheric plasma in the source region and (iii) the angular frequency of the visible point around its trajectory. We show how the last of these, which is neglected in traditional models by implicitly assuming the line of sight through the centre of the star, affects the interpretation of P2. We attribute the subpulse structure to emission from m antinodes distributed uniformly in azimuthal angle about the magnetic axis. We show that variations of P2 as a function of rotational phase or observing frequency arise naturally when the motion of the visible point is taken into account. We discuss possible application of our model in signifying overall field-line distortion at the emitting region. Abrupt changes in P2 can occur during state switching in the magnetosphere. We demonstrate that the unique value of P2 in each rotation state can be used, in principle, to relate the rotation state of the magnetospheres to subpulse drifting.

  10. Behavioural Correlation for Detecting P2P Bots

    CERN Document Server

    Al-Hammadi, Yousof

    2010-01-01

    In the past few years, IRC bots, malicious programs which are remotely controlled by the attacker through IRC servers, have become a major threat to the Internet and users. These bots can be used in different malicious ways such as issuing distributed denial of services attacks to shutdown other networks and services, keystrokes logging, spamming, traffic sniffing cause serious disruption on networks and users. New bots use peer to peer (P2P) protocols start to appear as the upcoming threat to Internet security due to the fact that P2P bots do not have a centralized point to shutdown or traceback, thus making the detection of P2P bots is a real challenge. In response to these threats, we present an algorithm to detect an individual P2P bot running on a system by correlating its activities. Our evaluation shows that correlating different activities generated by P2P bots within a specified time period can detect these kind of bots.

  11. Effects of antidepressants on P2X7 receptors.

    Science.gov (United States)

    Wang, Wei; Xiang, Zheng-Hua; Jiang, Chun-Lei; Liu, Wei-Zhi; Shang, Zhi-Lei

    2016-08-30

    Antidepressants including paroxetine, fluoxetine and desipramine are commonly used for treating depression. P2×7 receptors are member of the P2X family. Recent studies indicate that these receptors may constitute a novel potential target for the treatment of depression. In the present study, we examined the action of these antidepressants on cloned rat P2×7 receptors that were stably expressed in human embryonic kidney (HEK) 293 cells by using the whole-cell patch-clamp technique, and found that paroxetine at a dose of 10µM could significantly reduce the inward currents evoked by the P2×7 receptors agonist BzATP by pre-incubation for 6-12 but not by acute application (10µM) or pre-incubation for 2-6h at a dose of 1µM, 3µM or 10µM paroxetine. Neither fluoxetine nor desipramine had significant effects on currents evoked by BzATP either applied acutely or by pre-incubation at various concentrations. These results suggest that the sensitivity of rat P2×7 receptors to antidepressants is different, which may represent an unknown mechanism by which these drugs exert their therapeutic effects and side effects. PMID:27318632

  12. Contribution of MxB Oligomerization to HIV-1 Capsid Binding and Restriction

    OpenAIRE

    Buffone, Cindy; Schulte, Bianca; OPP, Silvana; Diaz-Griffero, Felipe

    2015-01-01

    The alpha interferon (IFN-α)-inducible restriction factor myxovirus B (MxB) blocks HIV-1 infection after reverse transcription but prior to integration. MxB binds to the HIV-1 core, which is composed of capsid protein, and this interaction leads to inhibition of the uncoating process of HIV-1. Previous studies suggested that HIV-1 restriction by MxB requires binding to capsid. This work tests the hypothesis that MxB oligomerization is important for the ability of MxB to bind to the HIV-1 core...

  13. HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358

    OpenAIRE

    Bichel, Katsiaryna; Price, Amanda J.; Schaller, Torsten; Towers, Greg J.; Freund, Stefan MV; James, Leo C.

    2013-01-01

    BACKGROUND: Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells. Infection of non-dividing cells requires transport through the nuclear pore but how this is mediated is unknown. RESULTS: Here we present the crystal structure of the N-terminal capsid domain of HIV-1 in complex with the cyclophilin domain of nuclear pore protein NUP358. The structure reveals that HIV-1 is positio...

  14. Rhesus TRIM5α Disrupts the HIV-1 Capsid at the Inter­Hexamer Interfaces

    OpenAIRE

    Zhao, Gongpu; Ke, Danxia; Vu, Thomas; Ahn, Jinwoo; Shah, Vaibhav B.; Yang, Ruifeng; Aiken, Christopher; Charlton, Lisa M.; Gronenborn, Angela M.; Zhang, Peijun

    2011-01-01

    TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5αrh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully und...

  15. Group theory of icosahedral virus capsid vibrations: a top-down approach.

    Science.gov (United States)

    Peeters, Kasper; Taormina, Anne

    2009-02-21

    We explore the use of a top-down approach to analyse the dynamics of icosahedral virus capsids and complement the information obtained from bottom-up studies of viral vibrations available in the literature. A normal mode analysis based on protein association energies is used to study the frequency spectrum, in which we reveal a universal plateau of low-frequency modes shared by a large class of Caspar-Klug capsids. These modes break icosahedral symmetry and are potentially relevant to the genome release mechanism. We comment on the role of viral tiling theory in such dynamical considerations. PMID:19014954

  16. Isolation of an Intertypic Poliovirus Capsid Recombinant from a Child with Vaccine-Associated Paralytic Poliomyelitis

    OpenAIRE

    Martín, Javier; Samoilovich, Elena; Dunn, Glynis; Lackenby, Angie; Feldman, Esphir; Heath, Alan; Svirchevskaya, Ekaterina; Cooper, Gill; Yermalovich, Marina; Minor, Philip D.

    2002-01-01

    The isolation of a capsid intertypic poliovirus recombinant from a child with vaccine-associated paralytic poliomyelitis is described. Virus 31043 had a Sabin-derived type 3-type 2-type 1 recombinant genome with a 5′-end crossover point within the capsid coding region. The result was a poliovirus chimera containing the entire coding sequence for antigenic site 3a derived from the Sabin type 2 strain. The recombinant virus showed altered antigenic properties but did not acquire type 2 antigeni...

  17. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6

    OpenAIRE

    Bhattacharya, Akash; Alam, Steven L; Fricke, Thomas; Zadrozny, Kaneil; Sedzicki, Jaroslaw; Taylor, Alexander B.; Demeler, Borries; Pornillos, Owen; Ganser-Pornillos, Barbie K.; Diaz-Griffero, Felipe; Dmitri N Ivanov; Yeager, Mark

    2014-01-01

    Events that occur between entry of the HIV-1 capsid into the cytoplasm of the target cell and the delivery of the viral genetic material into the nucleus constitute some of the less well understood processes in the viral life cycle. We demonstrated that PF74, a small-molecule inhibitor of HIV-1, and the host proteins CPSF6 and NUP153 bind to a preformed pocket within the CA protein hexamers that exist within the assembled capsid. Our results suggest that key features of the CA hexameric latti...

  18. Nanoindentation of 35 Virus Capsids in a Molecular Model: Relating Mechanical Properties to Structure

    OpenAIRE

    Cieplak, Marek; Robbins, Mark O.

    2013-01-01

    A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries T = 1, T = 2, T = 3, pseudo T = 3, T = 4, and T = 7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the C atoms associated with each amino acid. The number of these atoms ranges between 8 460 (for SPMV – satellite panicum mosaic virus) and 135 780 (for NBV – nudaureli virus). Nanoindentation by a broad AFM tip is modeled as comp...

  19. Synthesis of Amylose-b-P2 VP Block Copolymers.

    Science.gov (United States)

    Kumar, Kamlesh; Woortman, Albert J J; Loos, Katja

    2015-12-01

    A new class of rod-coil block copolymers is synthesized by chemoenzymatic polymerization. In the first step, maltoheptaose, which acts as a primer for the synthesis of amylose, is attached to poly(2-vinyl pyridine) (P2 VP). The enzymatic polymerization of maltoheptaose is carried out by phosphorylase to obtain amylose-b-P2 VP block copolymers. The block copolymer is characterized by Fourier transform infrared spectroscopy, nuclear magnetic resonance, gel permeation chromatography, and wide-angle X-ray scattering techniques. The designed molecules combine the inclusion complexation ability of amylose with the supramolecular complexation ability of P2 VP and therefore this kind of rod-coil block copolymers can be used to generate well-organized novel self-assembled structures. PMID:26437256

  20. Compromising Tor Anonymity Exploiting P2P Information Leakage

    CERN Document Server

    Manils, Pere; Blond, Stevens Le; Kaafar, Mohamed Ali; Castelluccia, Claude; Legout, Arnaud; Dabbous, Walid

    2010-01-01

    Privacy of users in P2P networks goes far beyond their current usage and is a fundamental requirement to the adoption of P2P protocols for legal usage. In a climate of cold war between these users and anti-piracy groups, more and more users are moving to anonymizing networks in an attempt to hide their identity. However, when not designed to protect users information, a P2P protocol would leak information that may compromise the identity of its users. In this paper, we first present three attacks targeting BitTorrent users on top of Tor that reveal their real IP addresses. In a second step, we analyze the Tor usage by BitTorrent users and compare it to its usage outside of Tor. Finally, we depict the risks induced by this de-anonymization and show that users' privacy violation goes beyond BitTorrent traffic and contaminates other protocols such as HTTP.

  1. Model of Controlling the Hubs in P2P Networks

    Directory of Open Access Journals (Sweden)

    Yuhua Liu

    2009-06-01

    Full Text Available Research into the hubs in Peer-to-Peer (P2P networks, and present a new method to avoid generating the hubs in the networks by controlling the logical topology structure of P2P networks. We firstly introduce the controlling ideas about hierarchizing the hubs. Then, we disclose and interpret the controlling model, and give out the concrete method to carry it out. Finally, we validate our controlling model via simulations and the simulation results demonstrate that our work is effective to control the hubs in P2P networks. Thus, this model can improve the network competence to defend against coordinated attacks, promote the network robustness, and ensure the network would develop continually and healthily.

  2. 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.

  3. 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...

  4. [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

  5. 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.

  6. 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.)

  7. P2P STREAMING MEDIA INDUSTRY IN CHINA

    OpenAIRE

    Dai, Steffi (Wenjing)

    2009-01-01

    The peer-to-peer (P2P) streaming media industry opened up a new era for the cyber age, has had a significant effect on many people?s leisure time, and has changed the way many people use entertainment. Over the past few years, this industry has developed dramatically in China, and it is thriving. In terms of the current situation, the P2P streaming media industry holds typical Chinese features that both enrich the audience?s cultural life, and have some impact on other kinds of mass media. Th...

  8. Specific Inhibitors of HIV Capsid Assembly Binding to the C-Terminal Domain of the Capsid Protein: Evaluation of 2-Arylquinazolines as Potential Antiviral Compounds

    Czech Academy of Sciences Publication Activity Database

    Machara, A.; Lux, V.; Kožíšek, Milan; Grantz Šašková, Klára; Štěpánek, O.; Kotora, M.; Parkan, Kamil; Pávová, Marcela; Glass, B.; Sehr, P.; Lewis, J.; Müller, B.; Kräusslich, H. G.; Konvalinka, Jan

    2016-01-01

    Roč. 59, č. 2 (2016), s. 545-558. ISSN 0022-2623 R&D Projects: GA ČR GA13-19561S EU Projects: European Commission(XE) 201095 - HIV ACE Institutional support: RVO:61388963 Keywords : HIV-1 assembly * capsid * high-throughput screening * AlphaScreen assay Subject RIV: CE - Biochemistry Impact factor: 5.447, year: 2014

  9. P2X and P2Y Receptors—Role in the Pathophysiology of the Nervous System

    Directory of Open Access Journals (Sweden)

    Kamila Puchałowicz

    2014-12-01

    Full Text Available Purinergic signalling plays a crucial role in proper functioning of the nervous system. Mechanisms depending on extracellular nucleotides and their P2 receptors also underlie a number of nervous system dysfunctions. This review aims to present the role of purinergic signalling, with particular focus devoted to role of P2 family receptors, in epilepsy, depression, neuropathic pain, nervous system neoplasms, such as glioma and neuroblastoma, neurodegenerative diseases like Parkinson’s disease, Alzheimer’s disease and multiple sclerosis. The above-mentioned conditions are associated with changes in expression of extracellular ectonucleotidases, P2X and P2Y receptors in neurons and glial cells, as well as releasing considerable amounts of nucleotides from activated or damaged nervous tissue cells into the extracellular space, which contributes to disturbance in purinergic signalling. The numerous studies indicate a potential possibility of using synthetic agonists/antagonists of P2 receptors in treatment of selected nervous system diseases. This is of particular significance, since numerous available agents reveal a low effectiveness and often produce side effects.

  10. 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

  11. 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.

  12. 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

  13. P2X receptor channels in endocrine glands

    Czech Academy of Sciences Publication Activity Database

    Stojilkovic, S. S.; Zemková, Hana

    2013-01-01

    Roč. 2, č. 4 (2013), s. 173-180. ISSN 2190-460X R&D Projects: GA ČR(CZ) GBP304/12/G069 Institutional support: RVO:67985823 Keywords : ATP * purinergic P2X receptor channels * pituitary * endocrine glands Subject RIV: ED - Physiology

  14. Measurement and analysis of P2P IPTV program resource.

    Science.gov (United States)

    Wang, Wenxian; Chen, Xingshu; Wang, Haizhou; Zhang, Qi; Wang, Cheng

    2014-01-01

    With the rapid development of P2P technology, P2P IPTV applications have received more and more attention. And program resource distribution is very important to P2P IPTV applications. In order to collect IPTV program resources, a distributed multi-protocol crawler is proposed. And the crawler has collected more than 13 million pieces of information of IPTV programs from 2009 to 2012. In addition, the distribution of IPTV programs is independent and incompact, resulting in chaos of program names, which obstructs searching and organizing programs. Thus, we focus on characteristic analysis of program resources, including the distributions of length of program names, the entropy of the character types, and hierarchy depth of programs. These analyses reveal the disorderly naming conventions of P2P IPTV programs. The analysis results can help to purify and extract useful information from chaotic names for better retrieval and accelerate automatic sorting of program and establishment of IPTV repository. In order to represent popularity of programs and to predict user behavior and popularity of hot programs over a period, we also put forward an analytical model of hot programs. PMID:24772008

  15. Comparing Pedophile Activity in Different P2P Systems

    Directory of Open Access Journals (Sweden)

    Raphaël Fournier

    2014-07-01

    Full Text Available Peer-to-peer (P2P systems are widely used to exchange content over the Internet. Knowledge of pedophile activity in such networks remains limited, despite having important social consequences. Moreover, though there are different P2P systems in use, previous academic works on this topic focused on one system at a time and their results are not directly comparable. We design a methodology for comparing KAD and eDonkey, two P2P systems among the most prominent ones and with different anonymity levels. We monitor two eDonkey servers and the KAD network during several days and record hundreds of thousands of keyword-based queries. We detect pedophile-related queries with a previously validated tool and we propose, for the first time, a large-scale comparison of pedophile activity in two different P2P systems. We conclude that there are significantly fewer pedophile queries in KAD than in eDonkey (approximately 0.09% vs. 0.25%.

  16. Pollution Prevention Successes Database (P2SDb) user guide

    International Nuclear Information System (INIS)

    When Pollution Prevention Opportunity Assessments (P2OAs) were launched at the Hanford Site during the summer of 1994, the first comment received from those using them expressed the desire for a method to report assessments electronically. As a temporary measure, macros were developed for use on word processing systems, but a more formal database was obviously needed. Additionally, increased DOE and Washington state reporting requirements for pollution prevention suggested that a database system would streamline the reporting process. The Pollution Prevention Group of Westinghouse Hanford Company (WHC) contracted with the Data Automation Engineering Department from ICF Kaiser Hanford Company (ICFKH) to develop the system. The scope was to develop a database that will track P2OAs conducted by the facilities and contractors at the Hanford Site. It will also track pollution prevention accomplishments that are not the result of P2OAs and document a portion of the Process Waste Assessments conducted in the past. To accommodate the above criteria, yet complete the system in a timely manner, the Pollution Prevention Successes Database (P2SDb) is being implemented in three phases. The first phase will automate the worksheets to provide both input and output of the data associated with the worksheets. The second phase will automate standard summary reports and ad hoc reports. The third phase will provide automated searching of the database to facilitate the sharing of pollution prevention experiences among various users. This User's Guide addresses only the Phase 1 system

  17. P2P Domain Classification using Decision Tree

    CERN Document Server

    Ismail, Anis

    2011-01-01

    In Peer-to-Peer context, a challenging problem is how to find the appropriate peer to deal with a given query without overly consuming bandwidth? Different methods proposed routing strategies of queries taking into account the P2P network at hand. This paper considers an unstructured P2P system based on an organization of peers around Super-Peers that are connected to Super-Super- Peer according to their semantic domains; By analyzing the queries log file, a predictive model that avoids flooding queries in the P2P network is constructed after predicting the appropriate Super-Peer, and hence the peer to answer the query. A challenging problem in a schema-based Peer-to-Peer (P2P) system is how to locate peers that are relevant to a given query. In this paper, architecture, based on (Super-)Peers is proposed, focusing on query routing. The approach to be implemented, groups together (Super-)Peers that have similar interests for an efficient query routing method. In such groups, called Super-Super-Peers (SSP), Su...

  18. Characteristics of new P2Y12 inhibitors: selection of P2Y12 inhibitors in clinical practice.

    Science.gov (United States)

    Golino, Paolo

    2013-12-01

    The options for antithrombotic therapy have recently been expanded, facilitating optimal tailored treatment. Dual antiplatelet therapy with aspirin and an approved adenosine diphosphate P2Y12 receptor antagonist is recommended for the management of patients with acute coronary syndromes (ACS). However, there are a number of controversies: which P2Y12 inhibitor to choose; how long should antiplatelet therapy be used so as to prevent thrombotic events and minimize bleeding risks; whether to use drug-eluting (DES) or bare-metal stents (BMS) and how to manage the individual variability in response to clopidogrel. Clopidogrel in combination with aspirin has been the standard dual antiplatelet regimen for ACS. The new, more potent P2Y12 inhibitors, prasugrel and ticagrelor, have shown improved antithrombotic effects compared with clopidogrel in patients with ACS (with or without ST-segment elevation myocardial infarction) in landmark trials, even if they were associated with an increased risk of major bleeding. Different pharmacogenetic and pharmacodynamic characteristics may explain, in part, the different pharmacologic and clinical responses to these antiplatelet agents. Importantly, both clopidogrel and prasugrel are prodrugs, i.e., they need to be converted in vivo into active metabolites that selectively and irreversibly bind the P2Y12 receptor. Unlike clopidogrel, however, common functional cytochrome P450 genetic variants do not affect prasugrel active metabolite levels or inhibition of platelet aggregation. In contrast, ticagrelor is not a prodrug (i.e., does not require hepatic metabolism to exert its antiplatelet effect) and represents the first oral P2Y12 receptor antagonist that is reversibly bound. Similar to prasugrel, ticagrelor achieves greater and more rapid inhibition of platelet function than clopidogrel. Evidence suggests that the new P2Y12 antagonists may offer improved antithrombotic effects compared with clopidogrel in selected patients for the

  19. 力竭运动对大鼠大脑P2X2、P2X4和P2X6受体表达的影响%Effect of Exhaustive Exercise on the Expression of Brain P2X2,P2X4,and P2X6 Receptors in Rats

    Institute of Scientific and Technical Information of China (English)

    周未艾; 李硕; 陈海涛

    2012-01-01

    目的:探讨一次和反复力竭游泳运动后大鼠大脑ATP受体P2X之三个亚型P2X2、P2X4和P2X6的时相性变化特点.方法:健康成年雄性SD大鼠68只,分为一次力竭游泳运动组和反复力竭游泳运动组及安静对照组,反复力竭组大鼠每日负重3%体重进行力竭游泳运动,共训练2周.运动组分别于力竭运动后即刻、4小时、12小时和24小时取材,采用实时荧光定量PCR方法测定力竭运动后大鼠P2X2、P2X4和P2X6受体亚型mRNA水平.结果:(1)反复力竭运动后12小时组P2X2相对表达率达到峰值,与反复力竭其它各组及安静对照组、一次力竭12小时组均有显著差异(P<0.01).(2)一次力竭即刻组P2X4相对表达率与安静对照组、4小时组、12小时组比较有显著统计学差异(分别为P< 0.01、P<0.05、P< 0.01).(3)反复力竭运动后12小时组P2X6相对表达率达到峰值.结论:3种受体亚型在一次力竭运动和反复力竭运动后12小时出现峰值或峰值趋势,提示在力竭运动后12小时,这3种P2X受体亚型所参与的中枢神经生理生化活动在此时可能会达到一个活跃期.%Objective The main purpose of this study is to investigate the variation in P2X2,P2X4 and P2X6 receptors in rats brain at different time points after single bout exhaustive exercise and repeated exhaustive exercise. Methods Sixty-eight male SD rats were divided randomly into the single bout exhaustive swimming group (SE), repeated exhausting swimming (RE), and sedentary group (C). The rats in group RE with weight-bearing 3% of body weight swan to exhaustion each day for a total of two weeks. The brain tissue of the rats was removed at 0 hr,4 hr,12 hr and 24 hr after the last exhaustive swimming. The mRNA levels of P2X2,P2X4 and P2X6 receptors in the brain tissue were observed through real-time quantitative PCR method. Results (l)The peak relative expression rate of the P2X2 in the group RE revealed at 12 hr after exhaustive

  20. Functionalized Congeners of P2Y1 Receptor Antagonists:

    Energy Technology Data Exchange (ETDEWEB)

    de Castro, Sonia [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Maruoka, Hiroshi [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Hong, Kunlun [ORNL; Kilbey, II, S Michael [ORNL; Costanzi, Stefano [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Hechler, Béatrice [University of Strasbourg; Gachet, Christian [EFS-Alsace, Strasbourg, France; Harden, T. Kendall [University of North Carolina School of Medicine; Jacobson, Kenneth A. [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health

    2010-01-01

    The P2Y{sub 1} receptor is a prothrombotic G protein-coupled receptor (GPCR) activated by ADP. Preference for the North (N) ring conformation of the ribose moiety of adenine nucleotide 3',5'-bisphosphate antagonists of the P2Y{sub 1} receptor was established by using a ring-constrained methanocarba (a bicyclo[3.1.0]hexane) ring as a ribose substitute. A series of covalently linkable N{sup 6}-methyl-(N)-methanocarba-2'-deoxyadenosine-3',5'-bisphosphates containing extended 2-alkynyl chains was designed, and binding affinity at the human (h) P2Y{sub 1} receptor determined. The chain of these functionalized congeners contained hydrophilic moieties, a reactive substituent, or biotin, linked via an amide. Variation of the chain length and position of an intermediate amide group revealed high affinity of carboxylic congener 8 (K{sub i} 23 nM) and extended amine congener 15 (K{sub i} 132 nM), both having a 2-(1-pentynoyl) group. A biotin conjugate 18 containing an extended {epsilon}-aminocaproyl spacer chain exhibited higher affinity than a shorter biotinylated analogue. Alternatively, click coupling of terminal alkynes of homologous 2-dialkynyl nucleotide derivatives to alkyl azido groups produced triazole derivatives that bound to the P2Y{sub 1} receptor following deprotection of the bisphosphate groups. The preservation of receptor affinity of the functionalized congeners was consistent with new P2Y{sub 1} receptor modeling and ligand docking. Attempted P2Y{sub 1} antagonist conjugation to PAMAM dendrimer carriers by amide formation or palladium-catalyzed reaction between an alkyne on the dendrimer and a 2-iodopurine-derivatized nucleotide was unsuccessful. A dialkynyl intermediate containing the chain length favored in receptor binding was conjugated to an azide-derivatized dendrimer, and the conjugate inhibited ADP-promoted human platelet aggregation. This is the first example of attaching a strategically functionalized P2Y receptor

  1. Pressure study of UCu2P2, UCuP2 and UCuAs2 ferromagnets

    International Nuclear Information System (INIS)

    The effect of hydrostatic pressure on the Curie temperature of single-crystalline UCu2P2, UCuP2 and UCuAs2 compounds was measured up to 1.0 GPa by means of a.c. magnetic susceptibility. For the former compound TC increases linearly with pressure at the rate of (10 ± 1) K/GPa, whereas for the remaining two ternaries it is nearly unaffected by pressure. The obtained data are discussed in the frame of localized magnetism in these compounds. (author)

  2. Physical Ingredients Controlling Stability and Structural Selection of Empty Viral Capsids.

    Science.gov (United States)

    Aznar, María; Reguera, David

    2016-07-01

    One of the crucial steps in the viral replication cycle is the self-assembly of its protein shell. Typically, each native virus adopts a unique architecture, but the coat proteins of many viruses have the capability to self-assemble in vitro into different structures by changing the assembly conditions. However, the mechanisms determining which of the possible capsid shapes and structures is selected by a virus are still not well-known. We present a coarse-grained model to analyze and understand the physical mechanisms controlling the size and structure selection in the assembly of empty viral capsids. Using this model and Monte Carlo simulations, we have characterized the phase diagram and stability of T = 1,3,4,7 and snub cube shells. In addition, we have studied the tolerance of different shells to changes in physical parameters related to ambient conditions, identifying possible strategies to induce misassembly or failure. Finally, we discuss the factors that select the shape of a capsid as spherical, faceted, elongated, or decapsidated. Our model sheds important light on the ingredients that control the assembly and stability of viral shells. This knowledge is essential to get capsids with well-defined size and structure that could be used for promising applications in medicine or bionanotechnology. PMID:27114062

  3. Facilitating the use of alternative capsid control methods towards sustainable production of organic cocoa in Ghana

    NARCIS (Netherlands)

    Ayenor, G.K.; Huis, van A.; Obeng-Ofori, D.; Padi, B.; Röling, N.G.

    2007-01-01

    Cocoa (Theobroma cacao L.) is an important foreign exchange earner for Ghana. However, production is constrained by a high incidence of pests and diseases. Based on farmers' needs, this study focused on the control of capsids, mainly Sahlbergella singularis Haglund and Distantiella theobroma (Distan

  4. Porcine circovirus-2 capsid protein induces cell death in PK15 cells

    International Nuclear Information System (INIS)

    Studies have shown that Porcine circovirus (PCV)-2 induces apoptosis in PK15 cells. Here we report that cell death is induced in PCV2b-infected PK15 cells that express Capsid (Cap) protein and this effect is enhanced in interferon gamma (IFN-γ)-treated cells. We further show that transient PCV2a and 2b-Cap protein expression induces cell death in PK15 cells at rate similar to PCV2 infection, regardless of Cap protein localization. These data suggest that Cap protein may have the capacity to trigger different signaling pathways involved in cell death. Although further investigation is needed to gain deeper insights into the nature of the pathways involved in Cap-induced cell death, this study provides evidence that PCV2-induced cell death in kidney epithelial PK15 cells can be mapped to the Cap protein and establishes the need for future research regarding the role of Cap-induced cell death in PCV2 pathogenesis. - Highlights: • IFN-γ enhances PCV2 replication that leads to cell death in PK15 cells. • IFN-γ enhances nuclear localization of the PCV2 Capsid protein. • Transient PCV2a and 2b-Capsid protein expression induces cell death. • Cell death is not dictated by specific Capsid protein sub-localization

  5. Novel system for analysis of interactions between HIV-1 capsid protein molecules

    Czech Academy of Sciences Publication Activity Database

    Wildová, Marcela; Pichová, Iva; Rumlová, Michaela

    Praha : JPM, 2004 - (Hunter, E.; Ruml, T.; Pichová, I.; Rumlová, M.; Sakalian, M.). s. 53 ISBN 80-86313-13-1. [The Retrovirus Assembly Meeting. 02.10.2004-06.10.2004, Praha] Keywords : capsid protein * HIV-1 Subject RIV: CE - Biochemistry

  6. Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure.

    Science.gov (United States)

    Cieplak, Marek; Robbins, Mark O

    2013-01-01

    A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries T = 1, T = 2, T = 3, pseudo T = 3, T = 4, and T = 7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the C[Formula: see text] atoms associated with each amino acid. The number of these atoms ranges between 8 460 (for SPMV - satellite panicum mosaic virus) and 135 780 (for NBV - nudaureli virus). Nanoindentation by a broad AFM tip is modeled as compression between two planes: either both flat or one flat and one curved. Plots of the compressive force versus plate separation show a variety of behaviors, but in each case there is an elastic region which extends to a characteristic force [Formula: see text]. Crossing [Formula: see text] results in a drop in the force and irreversible damage. Across the 35 capsids studied, both [Formula: see text] and the elastic stiffness are observed to vary by a factor of 20. The changes in mechanical properties do not correlate simply with virus size or symmetry. There is a strong connection to the mean coordination number [Formula: see text], defined as the mean number of interactions to neighboring amino acids. The Young's modulus for thin shell capsids rises roughly quadratically with [Formula: see text], where 6 is the minimum coordination for elastic stability in three dimensions. PMID:23785395

  7. Porcine circovirus-2 capsid protein induces cell death in PK15 cells

    Energy Technology Data Exchange (ETDEWEB)

    Walia, Rupali; Dardari, Rkia, E-mail: rdardari@ucalgary.ca; Chaiyakul, Mark; Czub, Markus

    2014-11-15

    Studies have shown that Porcine circovirus (PCV)-2 induces apoptosis in PK15 cells. Here we report that cell death is induced in PCV2b-infected PK15 cells that express Capsid (Cap) protein and this effect is enhanced in interferon gamma (IFN-γ)-treated cells. We further show that transient PCV2a and 2b-Cap protein expression induces cell death in PK15 cells at rate similar to PCV2 infection, regardless of Cap protein localization. These data suggest that Cap protein may have the capacity to trigger different signaling pathways involved in cell death. Although further investigation is needed to gain deeper insights into the nature of the pathways involved in Cap-induced cell death, this study provides evidence that PCV2-induced cell death in kidney epithelial PK15 cells can be mapped to the Cap protein and establishes the need for future research regarding the role of Cap-induced cell death in PCV2 pathogenesis. - Highlights: • IFN-γ enhances PCV2 replication that leads to cell death in PK15 cells. • IFN-γ enhances nuclear localization of the PCV2 Capsid protein. • Transient PCV2a and 2b-Capsid protein expression induces cell death. • Cell death is not dictated by specific Capsid protein sub-localization.

  8. Probing the biophysical interplay between a viral genome and its capsid

    Science.gov (United States)

    Snijder, J.; Uetrecht, C.; Rose, R. J.; Sanchez-Eugenia, R.; Marti, G. A.; Agirre, J.; Guérin, D. M. A.; Wuite, G. J. L.; Heck, A. J. R.; Roos, W. H.

    2013-06-01

    The interaction between a viral capsid and its genome governs crucial steps in the life cycle of a virus, such as assembly and genome uncoating. Tuning cargo-capsid interactions is also essential for successful design and cargo delivery in engineered viral systems. Here we investigate the interplay between cargo and capsid for the picorna-like Triatoma virus using a combined native mass spectrometry and atomic force microscopy approach. We propose a topology and assembly model in which heterotrimeric pentons that consist of five copies of structural proteins VP1, VP2 and VP3 are the free principal units of assembly. The interpenton contacts are established primarily by VP2. The dual role of the genome is first to stabilize the densely packed virion and, second, on an increase in pH to trigger uncoating by relaxing the stabilizing interactions with the capsid. Uncoating occurs through a labile intermediate state of the virion that reversibly disassembles into pentons with the concomitant release of protein VP4.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Subunit Folds and Maturation Pathway of a dsRNA Virus Capsid

    Czech Academy of Sciences Publication Activity Database

    Němeček, D.; Bouřa, Evžen; Wu, W.; Cheng, N.; Plevka, P.; Qiao, J.; Mindich, L.; Heymann, J. B.; Hurley, J. H.; Steven, A. C.

    2013-01-01

    Roč. 21, č. 8 (2013), s. 1374-1383. ISSN 0969-2126 Institutional support: RVO:61388963 Keywords : RNA bacteriophage phi-6 * minus-strand synthesis * cryoelectron microscopy * angstrom resolution * atomic-structure Subject RIV: CE - Biochemistry Impact factor: 6.794, year: 2013

  14. [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

  15. 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

  16. Functional characterization of Kaposi's sarcoma-associated herpesvirus small capsid protein by bacterial artificial chromosome-based mutagenesis

    International Nuclear Information System (INIS)

    A systematic investigation of interactions amongst KSHV capsid proteins was undertaken in this study to comprehend lesser known KSHV capsid assembly mechanisms. Interestingly the interaction patterns of the KSHV small capsid protein, ORF65 suggested its plausible role in viral capsid assembly pathways. Towards further understanding this, ORF65-null recombinant mutants (BAC-Δ65 and BAC-stop65) employing a bacterial artificial chromosome (BAC) system were generated. No significant difference was found in both overall viral gene expression and lytic DNA replication between stable monolayers of 293T-BAC36 (wild-type) and 293T-BAC-ORF65-null upon induction with 12-O-tetradecanoylphorbol-13-acetate, though the latter released 30-fold fewer virions to the medium than 293T-BAC36 cells. Sedimentation profiles of capsid proteins of ORF65-null recombinant mutants were non-reflective of their organization into the KSHV capsids and were also undetectable in cytoplasmic extracts compared to noticeable levels in nuclear extracts. These observations collectively suggested the pivotal role of ORF65 in the KSHV capsid assembly processes.

  17. Theatrical distribution and P2P movie piracy: a survey of P2P networks in Hungary using transactional data

    NARCIS (Netherlands)

    B. Bodó; Z. Lakatos

    2012-01-01

    This article examines what appears to be the most important factor shaping file sharing: the failure of traditional cultural markets to efficiently supply the demand in the online environment. Its findings are based on tracking the traffic of movies on three Hungarian P2P networks. This dataset is t

  18. A hydrophobic domain within the small capsid protein of Kaposi's sarcoma-associated herpesvirus is required for assembly.

    Science.gov (United States)

    Capuano, Christopher M; Grzesik, Peter; Kreitler, Dale; Pryce, Erin N; Desai, Keshal V; Coombs, Gavin; McCaffery, J Michael; Desai, Prashant J

    2014-08-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) capsids can be produced in insect cells using recombinant baculoviruses for protein expression. All six capsid proteins are required for this process to occur and, unlike for alphaherpesviruses, the small capsid protein (SCP) ORF65 is essential for this process. This protein decorates the capsid shell by virtue of its interaction with the capsomeres. In this study, we have explored the SCP interaction with the major capsid protein (MCP) using GFP fusions. The assembly site within the nucleus of infected cells was visualized by light microscopy using fluorescence produced by the SCP-GFP polypeptide, and the relocalization of the SCP to these sites was evident only when the MCP and the scaffold protein were also present - indicative of an interaction between these proteins that ensures delivery of the SCP to assembly sites. Biochemical assays demonstrated a physical interaction between the SCP and MCP, and also between this complex and the scaffold protein. Self-assembly of capsids with the SCP-GFP polypeptide was evident. Potentially, this result can be used to engineer fluorescent KSHV particles. A similar SCP-His6 polypeptide was used to purify capsids from infected cell lysates using immobilized affinity chromatography and to directly label this protein in capsids using chemically derivatized gold particles. Additional studies with SCP-GFP polypeptide truncation mutants identified a domain residing between aa 50 and 60 of ORF65 that was required for the relocalization of SCP-GFP to nuclear assembly sites. Substitution of residues in this region and specifically at residue 54 with a polar amino acid (lysine) disrupted or abolished this localization as well as capsid assembly, whereas substitution with non-polar residues did not affect the interaction. Thus, this study identified a small conserved hydrophobic domain that is important for the SCP-MCP interaction. PMID:24824860

  19. Rhesus TRIM5α Disrupts the HIV-1 Capsid at the Inter­Hexamer Interfaces

    Science.gov (United States)

    Zhao, Gongpu; Ke, Danxia; Vu, Thomas; Ahn, Jinwoo; Shah, Vaibhav B.; Yang, Ruifeng; Aiken, Christopher; Charlton, Lisa M.; Gronenborn, Angela M.; Zhang, Peijun

    2011-01-01

    TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5αrh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5αrh containing coiled-coil and SPRY domains (CC-SPRYrh). Concentration-dependent binding of CC-SPRYrh to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRYrh, but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5αrh on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction. PMID:21455494

  20. The Dual Role of an ESCRT-0 Component HGS in HBV Transcription and Naked Capsid Secretion.

    Directory of Open Access Journals (Sweden)

    Shu-Fan Chou

    2015-10-01

    Full Text Available The Endosomal Sorting Complex Required for Transport (ESCRT is an important cellular machinery for the sorting and trafficking of ubiquitinated cargos. It is also known that ESCRT is required for the egress of a number of viruses. To investigate the relationship between ESCRT and hepatitis B virus (HBV, we conducted an siRNA screening of ESCRT components for their potential effect on HBV replication and virion release. We identified a number of ESCRT factors required for HBV replication, and focused our study here on HGS (HRS, hepatocyte growth factor-regulated tyrosine kinase substrate in the ESCRT-0 complex. Aberrant levels of HGS suppressed HBV transcription, replication and virion secretion. Hydrodynamic delivery of HGS in a mouse model significantly suppressed viral replication in the liver and virion secretion in the serum. Surprisingly, overexpression of HGS stimulated the release of HBV naked capsids, irrespective of their viral RNA, DNA, or empty contents. Mutant core protein (HBc 1-147 containing no arginine-rich domain (ARD failed to secrete empty virions with or without HGS. In contrast, empty naked capsids of HBc 1-147 could still be promoted for secretion by HGS. HGS exerted a strong positive effect on the secretion of naked capsids, at the expense of a reduced level of virions. The association between HGS and HBc appears to be ubiquitin-independent. Furthermore, HBc is preferentially co-localized with HGS near the cell periphery, instead of near the punctate endosomes in the cytoplasm. In summary, our work demonstrated the importance of an optimum level of HGS in HBV propagation. In addition to an effect on HBV transcription, HGS can diminish the pool size of intracellular nucleocapsids with ongoing genome maturation, probably in part by promoting the secretion of naked capsids. The secretion routes of HBV virions and naked capsids can be clearly distinguished based on the pleiotropic effect of HGS involved in the ESCRT-0 complex.

  1. Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins

    Directory of Open Access Journals (Sweden)

    Katarzyna eBozek

    2012-06-01

    Full Text Available Human immunodeficiency virus type 2 (HIV-2 and simian immunodeficiency virus isolated from a macaque monkey (SIVmac are assumed to have originated from simian immunodeficiency virus isolated from sooty mangabey (SIVsm. Despite their close similarity in genome structure, HIV-2 and SIVmac show different sensitivities to TRIM5α, a host restriction factor against retroviruses. The replication of HIV-2 strains is potently restricted by rhesus (Rh monkey TRIM5α, while that of SIVmac strain 239 (SIVmac239 is not. Viral capsid protein is the determinant of this differential sensitivity to TRIM5α, as the HIV-2 mutant carrying SIVmac239 capsid protein evaded Rh TRIM5α-mediated restriction. However, the molecular determinants of this restriction mechanism are unknown. Electrostatic potential on the protein-binding site is one of the properties regulating protein-protein interactions. In this study, we investigated the electrostatic potential on the interaction surface of capsid protein of HIV-2 strain GH123 and SIVmac239. Although HIV-2 GH123 and SIVmac239 capsid proteins share more than 87% amino acid identity, we observed a large difference between the two molecules with the HIV-2 GH123 molecule having predominantly positive and SIVmac239 predominantly negative electrostatic potential on the surface of the loop between α-helices 4 and 5 (L4/5. As L4/5 is one of the major determinants of Rh TRIM5α sensitivity of these viruses, the present results suggest that the binding site of the Rh TRIM5α may show complementarity to the HIV-2 GH123 capsid surface charge distribution.

  2. Baculovirus expression of erythrovirus V9 capsids and screening by ELISA: serologic cross-reactivity with erythrovirus B19

    DEFF Research Database (Denmark)

    Heegaard, Erik D; Qvortrup, Klaus; Christensen, Jesper

    2002-01-01

    categorize V9 as an acute B19-like infection. Sequencing, combined with PCR studies, have since demonstrated the need for specific and differentiated techniques when examining samples for possible B19 or V9 viremia. The antigenic properties of the V9 capsid proteins have not been characterized previously. To...... address this question, V9 VP1 and VP2 open reading frames were cloned and expressed in insect cells using a baculovirus vector. Large quantities of purified recombinant V9 capsid protein were produced and electron micrographs revealed self-assembly of V9 VP1/VP2 and VP2 capsids into empty icosahedral...

  3. Supporting seamless mobility for P2P live streaming.

    Science.gov (United States)

    Kim, Eunsam; Kim, Sangjin; Lee, Choonhwa

    2014-01-01

    With advent of various mobile devices with powerful networking and computing capabilities, the users' demand to enjoy live video streaming services such as IPTV with mobile devices has been increasing rapidly. However, it is challenging to get over the degradation of service quality due to data loss caused by the handover. Although many handover schemes were proposed at protocol layers below the application layer, they inherently suffer from data loss while the network is being disconnected during the handover. We therefore propose an efficient application-layer handover scheme to support seamless mobility for P2P live streaming. By simulation experiments, we show that the P2P live streaming system with our proposed handover scheme can improve the playback continuity significantly compared to that without our scheme. PMID:24977171

  4. Addressing the P2P Bootstrap Problem for Small Networks

    CERN Document Server

    Wolinsky, David Isaac; Boykin, P Oscar; Figueiredo, Renato

    2010-01-01

    P2P overlays provide a framework for building distributed applications consisting of few to many resources with features including self-configuration, scalability, and resilience to node failures. Such systems have been successfully adopted in large-scale services for content delivery networks, file sharing, and data storage. In small-scale systems, they can be useful to address privacy concerns and for network applications that lack dedicated servers. The bootstrap problem, finding an existing peer in the overlay, remains a challenge to enabling these services for small-scale P2P systems. In large networks, the solution to the bootstrap problem has been the use of dedicated services, though creating and maintaining these systems requires expertise and resources, which constrain their usefulness and make them unappealing for small-scale systems. This paper surveys and summarizes requirements that allow peers potentially constrained by network connectivity to bootstrap small-scale overlays through the use of e...

  5. Firefox为P2P加速

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    一家名为Allpeers的英国公司开发了一款免费的P2P插件,可以将Firefox浏览器“变成一个”“多媒体共享发电站”,该公司表示,这个插件能够充分发挥Firefox和Bit-Torrent的强项。

  6. Behavioural Correlation for Detecting P2P Bots

    OpenAIRE

    Al-Hammadi, Yousof; Aickelin, Uwe

    2010-01-01

    In the past few years, IRC bots, malicious programs which are remotely controlled by the attacker through IRC servers, have become a major threat to the Internet and users. These bots can be used in different malicious ways such as issuing distributed denial of services attacks to shutdown other networks and services, keystrokes logging, spamming, traffic sniffing cause serious disruption on networks and users. New bots use peer to peer (P2P) protocols start to appear ...

  7. On Reducing Delays in P2P Live Streaming Systems

    OpenAIRE

    Huang, Fei

    2010-01-01

    In the recent decade, peer-to-peer (P2P) technology has greatly enhanced the scalability of multimedia streaming on the Internet by enabling efficient cooperation among end-users. However, existing streaming applications are plagued by the problems of long playback latency and long churn-induced delays. First of all, many streaming applications, such as IPTV and video conferencing, have rigorous constraints on end-to-end delays. Moreover, churn-induced delays, including delays from channel sw...

  8. Addressing the P2P Bootstrap Problem for Small Networks

    OpenAIRE

    Wolinsky, David Isaac; Juste, Pierre St.; Boykin, P. Oscar; Figueiredo, Renato

    2010-01-01

    P2P overlays provide a framework for building distributed applications consisting of few to many resources with features including self-configuration, scalability, and resilience to node failures. Such systems have been successfully adopted in large-scale services for content delivery networks, file sharing, and data storage. In small-scale systems, they can be useful to address privacy concerns and for network applications that lack dedicated servers. The bootstrap problem, finding an existi...

  9. An Efficient Secure Multicast Communication for P2P Network

    Directory of Open Access Journals (Sweden)

    Huaiqing Lin

    2011-03-01

    Full Text Available A new algorithm for efficient key management for secure group communication in P2P network is presented. The protocol avoids the escrow problem in identity-based cryptosystem and the secure delivery of private keys. It has two rounds and requires constant pairing operation per user. The security of protocol is based on some underlying problems closely related to the Bilinear Diffie-Hellman Problem are computationally hard.  

  10. Sheaves on P2 and generalized Appell functions

    CERN Document Server

    Manschot, Jan

    2014-01-01

    A closed expression is given for the generating functions of (virtual) Poincar\\'e polynomials of moduli spaces of semi-stable sheaves on the projective plane $\\mathbb{P}^2$ with arbitrary rank and Chern classes. To classify and study these generating functions, the notion of Appell functions with signature $(n_+,n_-)$ is introduced. For $n_-=1$, these novel functions reduce to the known class of Appell functions with multiple variables or higher level.

  11. P2X receptor channels in endocrine glands

    OpenAIRE

    Stojilkovic, Stanko S.; Zemkova, Hana

    2013-01-01

    The endocrine system is the system of ductless glands and single cells that synthetize hormones and release them directly into the bloodstream. Regulation of endocrine system is very complex and ATP and its degradable products ADP and adenosine contribute to its regulation acting as extracellular messengers for purinergic receptors. These include P2X receptors, a family of ligand-gated ion channels which expression and roles in endocrine tissues are reviewed here. There are seven mammalian pu...

  12. Theoretical photoionization processes for aluminum-like P2+

    Science.gov (United States)

    Wang, HongBin; Jiang, Gang; Duan, Jie

    2016-05-01

    The theoretical photoionization cross sections for the ground and metastable states of Al-like P2+ are first time investigated in the photon energy range of 30-43.5 eV by the Dirac R-matrix method, and a good agreement between the dipole length and velocity form is achieved. The effects of the partial photoionization on the total PI of ground and metastable states are discussed. Our theoretical results are consistent with the latest experimental measurement, only some discrepancies are found. The channel coupling effects play an important role in the photoionization of Al-like P2+. The resonance energies and quantum defects are obtained, where a comparison between the theoretical and experimental data is made. It is worth noting that the theoretical resonance is as large as 0.28 eV. Our results can serve as a reference to further study the PI of Al-like P2+ in theory and experiment and be regarded as a supplement for Opacity Project TOP base results.

  13. A P2P streaming service architecture with distributed caching

    Institute of Scientific and Technical Information of China (English)

    GUO Pan-hong; YANG Yang; LI Xin-you

    2007-01-01

    Multimedia streaming served through peer-to-peer (P2P) networks is booming nowadays. However, the end-to-end streaming quality is generally unstable due to the variability of the state of serve-peers. On the other hand, proxy caching is a bandwidth-efficient scheme for streaming over the Internet, whereas it is a substantially expensive method needing dedicated powerful proxy servers. In this paper, we present a P2P cooperative streaming architecture combined with the advantages of both P2P networks and multimedia proxy caching techniques to improve the streaming quality of participating clients. In this framework, a client will simultaneously retrieve contents from the server and other peers that have viewed and cached the same title before. In the meantime, the client will also selectively cache the aggregated video content so as to serve still future clients. The associate protocol to facilitate the multi-path streaming and a distributed utility-based partial caching scheme are detailedly discussed. We demonstrate the effectiveness of this proposed architecture through extensive simulation experiments on large, Internet-like topologies.

  14. The trafficking and targeting of P2X receptors

    Directory of Open Access Journals (Sweden)

    Ruth Dorothy Murrell-Lagnado

    2013-11-01

    Full Text Available The functional expression of P2X receptors at the plasma membrane is dependent on their trafficking along secretory and endocytic pathways. There are seven P2X receptor subunits, and these differ in their subcellular distributions because they have very different trafficking properties. Some are retained within the endoplasmic reticulum (ER, while others are predominantly at the cell surface or within endosomes and lysosomes. Changes in recruitment of receptors to and from the plasma membrane provides a way of rapidly up- or down-regulating the cellular response to ATP. An additional layer of regulation is the targeting of these receptors within the membranes of each compartment, which affects their stability, function and the nature of the effector proteins with which they form signaling complexes. The trafficking and targeting of P2X receptors is regulated by their interactions with other proteins and with lipids and we can expect this to vary in a cell-type specific manner, giving rise to differences in receptor activity and function.

  15. BQP_p = PP for integer p > 2

    CERN Document Server

    Bebel, Joseph

    2011-01-01

    There's something really strange about quantum mechanics. It's not just that cats can be dead and alive at the same time, and that entanglement seems to violate the principle of locality; quantum mechanics seems to be what Aaronson calls "an island in theoryspace", because even slight perturbations to the theory of quantum mechanics seem to generate absurdities. In [Aar 04] and [Aar 05], he explores these perturbations and the corresponding absurdities in the context of computation. In particular, he shows that a quantum theory where the measurement probabilities are computed using p-norm instead of the standard 2-norm has the effect of blowing up the class BQP (the class of problems that can be efficiently solved on a quantum computer) to at least PP (the class of problems that can be solved in probabilistic polynomial time). He showed that PP \\subseteq BQP_p \\subseteq PSPACE for all constants p != 2, and that BQP_p = PP for even integers p > 2. Here, we show that this equality holds for all integers p > 2.

  16. Variations of $P_2$ in subpulse drifting pulsars

    CERN Document Server

    Yuen, R; Samsuddin, M A; Tu, Z Y; Han, X H

    2016-01-01

    We develop a model for subpulse separation period, $P_2$, taking into account both the apparent motion of the visible point as a function of pulsar phase, $\\psi$, and the possibility of abrupt jumps between different rotation states in non-corotating pulsar magnetospheres. We identify three frequencies: (i) the spin frequency of the star, (ii) the drift frequency of the magnetospheric plasma in the source region, and (iii) the angular frequency of the visible point around its trajectory. We show how the last of these, which is neglected in traditional models by implicitly assuming the line of sight through the center of the star, affects the interpretation of $P_2$. We attribute the subpulse structure to emission from $m$ anti-nodes distributed uniformly in azimuthal angle about the magnetic axis. We show that variations of $P_2$ as a function of rotational phase or observing frequency arise naturally when the motion of the visible point is taken into account. We discuss possible application of our model in s...

  17. P2X7 receptors in satellite glial cells mediate high functional expression of P2X3 receptors in immature dorsal root ganglion neurons

    Directory of Open Access Journals (Sweden)

    Chen Yong

    2012-02-01

    Full Text Available Abstract Background The purinergic P2X3 receptor (P2X3R expressed in the dorsal root ganglion (DRG sensory neuron and the P2X7 receptor (P2X7R expressed in the surrounding satellite glial cell (SGC are two major receptors participating in neuron-SGC communication in adult DRGs. Activation of P2X7Rs was found to tonically reduce the expression of P2X3Rs in DRGs, thus inhibiting the abnormal pain behaviors in adult rats. P2X receptors are also actively involved in sensory signaling in developing rodents. However, very little is known about the developmental change of P2X7Rs in DRGs and the interaction between P2X7Rs and P2X3Rs in those animals. We therefore examined the expression of P2X3Rs and P2X7Rs in postnatal rats and determined if P2X7R-P2X3R control exists in developing rats. Findings We immunostained DRGs of immature rats and found that P2X3Rs were expressed only in neurons and P2X7Rs were expressed only in SGCs. Western blot analyses indicated that P2X3R expression decreased while P2X7R expression increased with the age of rats. Electrophysiological studies showed that the number of DRG neurons responding to the stimulation of the P2XR agonist, α,β-meATP, was higher and the amplitudes of α,β-meATP-induced depolarizations were larger in immature DRG neurons. As a result, P2X3R-mediated flinching responses were much more pronounced in immature rats than those found in adult rats. When we reduced P2X7R expression with P2X7R-siRNA in postnatal and adult rats, P2X3R-mediated flinch responses were greatly enhanced in both rat populations. Conclusions These results show that the P2X7R expression increases as rats age. In addition, P2X7Rs in SGCs exert inhibitory control on the P2X3R expression and function in sensory neurons of immature rats, just as observed in adult rats. Regulation of P2X7R expression is likely an effective way to control P2X3R activity and manage pain relief in infants.

  18. 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.

  19. [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

  20. 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.)

  1. 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

  2. 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...

  3. 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...

  4. 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.

  5. 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...

  6. 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...

  7. 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.

  8. High-Resolution X-Ray Structure and Functional Analysis of the Murine Norovirus 1 Capsid Protein Protruding Domain

    Energy Technology Data Exchange (ETDEWEB)

    Taube, Stefan; Rubin, John R.; Katpally, Umesh; Smith, Thomas J.; Kendall, Ann; Stuckey, Jeanne A.; Wobus, Christiane E. (Michigan); (Danforth)

    2010-07-23

    Murine noroviruses (MNV) are closely related to the human noroviruses (HuNoV), which cause the majority of nonbacterial gastroenteritis. Unlike HuNoV, MNV grow in culture and in a small-animal model that represents a tractable model to study norovirus biology. To begin a detailed investigation of molecular events that occur during norovirus binding to cells, the crystallographic structure of the murine norovirus 1 (MNV-1) capsid protein protruding (P) domain has been determined. Crystallization of the bacterially expressed protein yielded two different crystal forms (Protein Data Bank identifiers [PDB ID], 3LQ6 and 3LQE). Comparison of the structures indicated a large degree of structural mobility in loops on the surface of the P2 subdomain. Specifically, the A{prime}-B{prime} and E{prime}-F{prime} loops were found in open and closed conformations. These regions of high mobility include the known escape mutation site for the neutralizing antibody A6.2 and an attenuation mutation site, which arose after serial passaging in culture and led to a loss in lethality in STAT1{sup -/-} mice, respectively. Modeling of a Fab fragment and crystal structures of the P dimer into the cryoelectron microscopy three-dimensional (3D) image reconstruction of the A6.2/MNV-1 complex indicated that the closed conformation is most likely bound to the Fab fragment and that the antibody contact is localized to the A{prime}-B{prime} and E{prime}-F{prime} loops. Therefore, we hypothesize that these loop regions and the flexibility of the P domains play important roles during MNV-1 binding to the cell surface.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. [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

  14. Deletion of P2X2 and P2X3 receptor subunits does not alter motility of the mouse colon

    Directory of Open Access Journals (Sweden)

    JamesJGalligan

    2010-03-01

    Full Text Available Purinergic P2X receptors contribute to neurotransmission in the gut. P2X receptors are ligand-gated cation channels that mediate synaptic excitation in subsets of enteric neurons. The present study evaluated colonic motility in vitro and in vivo in wild type (WT and P2X2 and P2X3 subunit knockout (KO mice. The muscarinic receptor agonist, bethanechol (0.3-3 micromolar, caused similar contractions of the longitudinal muscle in colon segments from WT, P2X2 and P2X3 subunit KO mice. Nicotine (1-300 micromolar, acting at neuronal nicotinic receptors, caused similar longitudinal muscle relaxations in colonic segments from WT and P2X2 and P2X3 subunit KO mice. Nicotine-induced relaxations were inhibited by nitro-L-arginine (NLA, 100 micromolar and apamin (0.1 micromolar which block inhibitory neuromuscular transmission. ATP (1-1000 micromolar caused contractions only in the presence of NLA and apamin. ATP-induced contractions were similar in colon segments from WT, P2X2 and P2X3 KO mice. The mouse colon generates spontaneous migrating motor complexes (MMCs in vitro. The MMC frequency was higher in P2X2 KO compared to WT tissues; other parameters of the MMC were similar in colon segments from WT, P2X2 and P2X3 KO mice. 5-Hydroxytryptophan-induced fecal output was similar in WT, P2X2 and P2X3 KO mice. These data indicate that nicotinic receptors are located predominately on inhibitory motor neurons supplying the longitudinal muscle in the mouse colon. P2X2 or P2X3 subunit containing receptors are not localized to motorneurons supplying the longitudinal muscle. Synaptic transmission mediated by P2X2 or P2X3 subunit containing receptors is not required for propulsive motility in the mouse colon.

  15. Assembly and characterization of foot-and-mouth disease virus empty capsid particles expressed within mammalian cells

    DEFF Research Database (Denmark)

    Gullberg, Maria; Muszynski, Bartosz; Organtini, Lindsey J.; Ashley, Robert E.; Hafenstein, Susan L.; Belsham, Graham J.; Polacek, Charlotta

    The foot-and-mouth disease virus (FMDV) structural protein precursor, P1-2A, is cleaved by the virus-encoded 3C protease (3Cpro) into the capsid proteins VP0, VP1 and VP3 (and 2A). In some systems, it is difficult to produce large amounts of these processed capsid proteins since 3Cpro can be toxic...... for cells. The expression level of 3Cpro activity has now been reduced relative to the P1-2A, and the effect on the yield of processed capsid proteins and their assembly into empty capsid particles within mammalian cells has been determined. Using a vaccinia-virus-based transient expression system, P1...

  16. 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

  17. 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

  18. 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

  19. 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...

  20. Impact of chemical and structural anisotropy on the electrophoretic mobility of spherical soft multilayer particles: the case of bacteriophage MS2.

    Science.gov (United States)

    Langlet, Jérémie; Gaboriaud, Fabien; Gantzer, Christophe; Duval, Jérôme F L

    2008-04-15

    by the external proteic capsid but also by the chemical composition and hydrodynamic flow permeation of/within the inner RNA-protein bound layer and bulk RNA part of the bacteriophage. The impact of virus aggregation, as revealed by decreasing diffusion coefficients for decreasing pH values, is also discussed. PMID:18192368

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. Final Design of the SLAC P2 Marx Klystron Modulator

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, M.A.; Benwell, A.; Burkhart, C.; Larsen, R.; MacNair, D.; Nguyen, M.; Olsen, J.; /SLAC

    2011-11-08

    The SLAC P2 Marx has been under development for two years, and follows on the P1 Marx as an alternative to the baseline klystron modulator for the International Linear Collider. The P2 Marx utilizes a redundant architecture, air-insulation, a control system with abundant diagnostic access, and a novel nested droop correction scheme. This paper is an overview of the design of this modulator. There are several points of emphasis for the P2 Marx design. First, the modulator must be compatible with the ILC two-tunnel design. In this scheme, the modulator and klystron are located within a service tunnel with limited access and available footprint for a modulator. Access to the modulator is only practical from one side. Second, the modulator must have high availability. Robust components are not sufficient alone to achieve availability much higher than 99%. Therefore, redundant architectures are necessary. Third, the modulator must be relatively low cost. Because of the large number of stations in the ILC, the investment needed for the modulator components is significant. High-volume construction techniques which take advantage of an economy of scale must be utilized. Fourth, the modulator must be simple and efficient to maintain. If a modulator does become inoperable, the MTTR must be small. Fifth, even though the present application for the modulator is for the ILC, future accelerators can also take advantage of this development effort. The hardware, software, and concepts developed in this project should be designed such that further development time necessary for other applications is minimal.

  8. Expression of Norwalk virus capsid protein in transgenic tobacco and potato and its oral immunogenicity in mice.

    OpenAIRE

    Mason, H S; Ball, J M; Shi, J. J.; Jiang, X.; Estes, M K; Arntzen, C J

    1996-01-01

    Alternatives to cell culture systems for production of recombinant proteins could make very safe vaccines at a lower cost. We have used genetically engineered plants for expression of candidate vaccine antigens with the goal of using the edible plant organs for economical delivery of oral vaccines. Transgenic tobacco and potato plants were created that express the capsid protein of Norwalk virus, a calicivirus that causes epidemic acute gastroenteritis in humans. The capsid protein could be e...

  9. Gestor de almacenamiento en redes P2P

    OpenAIRE

    Olías de Lima Pancorbo, Carlos

    2009-01-01

    El objetivo del proyecto consiste en la implementación de un sistema de archivos distribuido mediante P2P, basándose en el entorno de desarrollo .NET. Para dicho desarrollo, la primera parte del proyecto consiste en la familiarización con un nuevo lenguaje de desarrollo integrado en la plataforma Visual Studio: Visual Basic.NET. En segundo lugar, una vez adquiridos los conocimientos necesarios para el desarrollo de aplicaciones en dicha plataforma, se implementará un Sistema de Archivos Distr...

  10. Random walk search in unstructured P2P

    Institute of Scientific and Technical Information of China (English)

    Jia Zhaoqing; You Jinyuan; Rao Ruonan; Li Minglu

    2006-01-01

    Unstructured P2P has power-law link distribution, and the random walk in power-law networks is analyzed. The analysis results show that the probability that a random walker walks through the high degree nodes is high in the power-law network, and the information on the high degree nodes can be easily found through random walk. Random walk spread and random walk search method (RWSS) is proposed based on the analysis result. Simulation results show that RWSS achieves high success rates at low cost and is robust to high degree node failure.

  11. P2P流行意味着IPTV末落?

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    十年前微软Venus计划启动了IPTV,的进程,随时随地点播音视频是当初IPTV的梦想,十年后随着宽带的普及,没有人想到在中国P2P居然占据了一半以上的带宽,IPTV还没有普及就有消亡的危险,毕竟随时随地已经实现了。

  12. Crystallogenesis of bacteriophage P22 tail accessory factor gp26 at acidic and neutral pH

    International Nuclear Information System (INIS)

    The crystallogenesis of bacteriophage P22 tail-fiber gp26 is described. To study possible pH-induced conformational changes in gp26 structure, native trimeric gp26 has been crystallized at acidic pH (4.6) and a chimera of gp26 fused to maltose-binding protein (MBP-gp26) has been crystallized at neutral and alkaline pH (7-10). Gp26 is one of three phage P22-encoded tail accessory factors essential for stabilization of viral DNA within the mature capsid. In solution, gp26 exists as an extended triple-stranded coiled-coil protein which shares profound structural similarities with class I viral membrane-fusion protein. In the cryo-EM reconstruction of P22 tail extracted from mature virions, gp26 forms an ∼220 Å extended needle structure emanating from the neck of the tail, which is likely to be brought into contact with the cell’s outer membrane when the viral DNA-injection process is initiated. To shed light on the potential role of gp26 in cell-wall penetration and DNA injection, gp26 has been crystallized at acidic, neutral and alkaline pH. Crystals of native gp26 grown at pH 4.6 diffract X-rays to 2.0 Å resolution and belong to space group P21, with a dimer of trimeric gp26 molecules in the asymmetric unit. To study potential pH-induced conformational changes in the gp26 structure, a chimera of gp26 fused to maltose-binding protein (MBP-gp26) was generated. Hexagonal crystals of MBP-gp26 were obtained at neutral and alkaline pH using the high-throughput crystallization robot at the Hauptman–Woodward Medical Research Institute, Buffalo, NY, USA. These crystals diffract X-rays to beyond 2.0 Å resolution. Structural analysis of gp26 crystallized at acidic, neutral and alkaline pH is in progress

  13. Simultaneous Visualization of Parental and Progeny Viruses by a Capsid-Specific HaloTag Labeling Strategy.

    Science.gov (United States)

    Liu, An-An; Zhang, Zhenfeng; Sun, En-Ze; Zheng, Zhenhua; Zhang, Zhi-Ling; Hu, Qinxue; Wang, Hanzhong; Pang, Dai-Wen

    2016-01-26

    Real-time, long-term, single-particle tracking (SPT) provides us an opportunity to explore the fate of individual viruses toward understanding the mechanisms underlying virus infection, which in turn could lead to the development of therapeutics against viral diseases. However, the research focusing on the virus assembly and egress by SPT remains a challenge because established labeling strategies could neither specifically label progeny viruses nor make them distinguishable from the parental viruses. Herein, we have established a temporally controllable capsid-specific HaloTag labeling strategy based on reverse genetic technology. VP26, the smallest pseudorabies virus (PrV) capsid protein, was fused with HaloTag protein and labeled with the HaloTag ligand during virus replication. The labeled replication-competent recombinant PrV harvested from medium can be applied directly in SPT experiments without further modification. Thus, virus infectivity, which is critical for the visualization and analysis of viral motion, is retained to the largest extent. Moreover, progeny viruses can be distinguished from parental viruses using diverse HaloTag ligands. Consequently, the entire course of virus infection and replication can be visualized continuously, including virus attachment and capsid entry, transportation of capsids to the nucleus along microtubules, docking of capsids on the nucleus, endonuclear assembly of progeny capsids, and the egress of progeny viruses. In combination with SPT, the established strategy represents a versatile means to reveal the mechanisms and dynamic global picture of the life cycle of a virus. PMID:26720596

  14. Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus capsid mechanics from nanomanipulation in vitro and in silico

    CERN Document Server

    Kononova, Olga; Brasch, Melanie; Cornelissen, Jeroen; Dima, Ruxandra I; Marx, Kenneth A; Wuite, Gijs J L; Roos, Wouter H; Barsegov, Valeri

    2015-01-01

    Physical properties of capsids of plant and animal viruses are important factors in capsid self-assembly, survival of viruses in the extracellular environment, and their cell infectivity. Virus shells can have applications as nanocontainers and delivery vehicles in biotechnology and medicine. Combined AFM experiments and computational modeling on sub-second timescales of the indentation nanomechanics of Cowpea Chlorotic Mottle Virus (CCMV) capsid show that the capsid's physical properties are dynamic and local characteristics of the structure, which depend on the magnitude and geometry of mechanical input. Surprisingly, under large deformations the CCMV capsid transitions to the collapsed state without substantial local structural alterations. The enthalpy change in this deformation state dH = 11.5 - 12.8 MJ/mol is mostly due to large-amplitude out-of-plane excitations, which contribute to the capsid bending, and the entropy change TdS = 5.1 - 5.8 MJ/mol is mostly due to coherent in-plane rearrangements of pr...

  15. IRES mediated expression of viral 3C protease for enhancing the yield of FMDV empty capsids using baculovirus system.

    Science.gov (United States)

    Vivek Srinivas, V M; Basagoudanavar, Suresh H; Hosamani, Madhusudan

    2016-03-01

    For expression of FMDV empty capsids, high protease activity associated with 3C co-expressed with P1 polyprotein has been reported to adversely affect the yields of capsids. Limiting the levels of 3Cpro relative to P1-2A polypeptide is thus critical to enhance the yields. In this study, FMDV internal ribosome entry site (IRES) sequence which serves as an alternative to the CAP-dependent translation initiation mechanism, was used for controlled translation of 3C protease. Baculovirus expressing bicistronic cDNA cassette containing two open reading frames-FMDV capsid gene (P1-2A) and 3Cpro intervened by IRES was prepared. Analysis of the expression in insect cells infected with baculovirus showed increased accumulation of processed capsids. Recombinant capsids showed higher immunoreactivity similar to the whole virus antigen, when reacted with polyclonal antibodies against the purified whole virus 146S particles. Thus, inclusion of the IRES upstream of 3Cpro facilitated reduced expression of the protease in baculovirus expression system, without causing significant proteolysis, thereby contributing to improved yields of the processed capsid antigens. PMID:26775685

  16. Microplate-based assay for identifying small molecules that bind a specific intersubunit interface within the assembled HIV-1 capsid.

    Science.gov (United States)

    Halambage, Upul D; Wong, Jason P; Melancon, Bruce J; Lindsley, Craig W; Aiken, Christopher

    2015-09-01

    Despite the availability of >30 effective drugs for managing HIV-1 infection, no current therapy is curative, and long-term management is challenging owing to the emergence and spread of drug-resistant mutants. Identification of drugs against novel HIV-1 targets would expand the current treatment options and help to control resistance. The highly conserved HIV-1 capsid protein represents an attractive target because of its multiple roles in replication of the virus. However, the low antiviral potencies of the reported HIV-1 capsid-targeting inhibitors render them unattractive for therapeutic development. To facilitate the identification of more-potent HIV-1 capsid inhibitors, we developed a scintillation proximity assay to screen for small molecules that target a biologically active and specific intersubunit interface in the HIV-1 capsid. The assay, which is based on competitive displacement of a known capsid-binding small-molecule inhibitor, exhibited a signal-to-noise ratio of >9 and a Z factor of >0.8. In a pilot screen of a chemical library containing 2,400 druglike compounds, we obtained a hit rate of 1.8%. This assay has properties that are suitable for screening large compound libraries to identify novel HIV-1 capsid ligands with antiviral activity. PMID:26077250

  17. Sur l'\\'equation $X^2-\\varepsilon_2\\varepsilon_{p_1p_2}\\varepsilon_{2p_1p_2}=0$

    OpenAIRE

    Azizi, Abdelmalek; Zekhnini, Abdelkader; Taous, Mohammed

    2015-01-01

    Let $p_1\\equiv p_2\\equiv5 \\pmod8$ be prime numbers such that $\\left(\\frac{p_1}{p_2}\\right)=-1$. Let $\\mathbb{L}=Q(\\sqrt2, \\sqrt{p_1p_2})$ Our goal is to resolve the equation $X^2-\\varepsilon_2\\varepsilon_{p_1p_2}\\varepsilon_{2p_1p_2}=0$ in $\\mathbb{L}$, where $\\varepsilon_j$ are fundamental units of real quadratic subfields of $Q(\\sqrt2, \\sqrt{p_1p_2})$.

  18. 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

  19. Biological Effect of Muller's Ratchet: Distant Capsid Site Can Affect Picornavirus Protein Processing▿

    OpenAIRE

    Escarmís, Cristina; Perales, Celia; Domingo, Esteban

    2009-01-01

    Repeated bottleneck passages of RNA viruses result in accumulation of mutations and fitness decrease. Here, we show that clones of foot-and-mouth disease virus (FMDV) subjected to bottleneck passages, in the form of plaque-to-plaque transfers in BHK-21 cells, increased the thermosensitivity of the viral clones. By constructing infectious FMDV clones, we have identified the amino acid substitution M54I in capsid protein VP1 as one of the lesions associated with thermosensitivity. M54I affects ...

  20. Thermodynamic characterization of the peptide assembly inhibitor binding to HIV-1 capsid protein

    Czech Academy of Sciences Publication Activity Database

    Kožíšek, Milan; Durčák, Jindřich; Konvalinka, Jan

    2013-01-01

    Roč. 10, Suppl. 1 (2013), S37-S37. ISSN 1742-4690. [Frontiers of Retrovirology: Complex retorviruses, retroelements and their hosts. 16.09.2013-18.09.2013, Cambridge] R&D Projects: GA ČR GA13-19561S Institutional support: RVO:61388963 Keywords : HIV -1 capsid protein * CAI Subject RIV: EE - Microbiology, Virology http://www.retrovirology.com/content/10/S1/P108

  1. Enhancing the Clinical Potential of AAV Vectors by Capsid Engineering to Evade Pre-Existing Immunity

    OpenAIRE

    Bartel, Melissa; Schaffer, David; Büning, Hildegard

    2011-01-01

    Vectors based on adeno-associated viruses (AAV) have shown considerable promise in both preclinical models and increasingly in clinical trials. However, one formidable challenge is pre-existing immunity due to widespread exposure to numerous AAV variants and serotypes within the human population, which affect efficacy of clinical trials due to the accompanying high levels of anti-capsid neutralizing antibodies. Transient immunosuppression has promise in mitigating cellular and humoral respons...

  2. Enhancing the clinical potential of AAV vectors by capsid engineering to evade pre-existing immunity

    OpenAIRE

    DavidSchaffer; HildegardBüning

    2011-01-01

    Vectors based on adeno-associated viruses have shown considerable promise in both preclinical models and increasingly in clinical trials. However, one formidable challenge is pre-existing immunity due to widespread exposure to numerous AAV variants and serotypes within the human population, which affect efficacy of clinical trials due to the accompanying high levels of anti-capsid neutralizing antibodies. Transient immunosuppression has promise in mitigating cellular and humoral responses ind...

  3. HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention

    OpenAIRE

    Blair, Wade S.; Pickford, Chris; Irving, Stephen L.; Brown, David G.; Anderson, Marie; Bazin, Richard; Cao, Joan; Ciaramella, Giuseppe; Isaacson, Jason; Jackson, Lynn; Hunt, Rachael; Kjerrstrom, Anne; Nieman, James A.; Patick, Amy K.; Perros, Manos

    2010-01-01

    Despite a high current standard of care in antiretroviral therapy for HIV, multidrug-resistant strains continue to emerge, underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic. We report a new class of small molecule antiretroviral compounds that directly target HIV-1 capsid (CA) via a novel mechanism of action. The compounds exhibit potent antiviral activity against HIV-1 laboratory strains, clinical isolates, and HIV-2, a...

  4. Multiple roles of the capsid protein in the early steps of HIV-1 infection.

    OpenAIRE

    Fassati, A.

    2012-01-01

    The early steps of HIV-1 infection starting after virus entry into cells up to integration of its genome into host chromosomes are poorly understood. From seminal work showing that HIV-1 and oncoretroviruses follow different steps in the early stages post-entry, significant advances have been made in recent years and an important role for the HIV-1 capsid (CA) protein, the constituent of the viral core, has emerged. CA appears to orchestrate several events, such as virus uncoating, recognitio...

  5. TRIM5alpha disrupts the structure of assembled HIV-1 capsid complexes in vitro.

    Science.gov (United States)

    Black, Lesa R; Aiken, Christopher

    2010-07-01

    The host restriction factor TRIM5alpha provides intrinsic defense against retroviral infections in mammalian cells. TRIM5alpha blocks infection by targeting the viral capsid after entry but prior to completion of reverse transcription, but whether this interaction directly alters the structure of the viral capsid is unknown. A previous study reported that rhesus macaque TRIM5alpha protein stably associates with cylindrical complexes formed by assembly of recombinant HIV-1 CA-NC protein in vitro and that restriction leads to accelerated HIV-1 uncoating in target cells. To gain further insight into the mechanism of TRIM5alpha-dependent restriction, we examined the structural effects of TRIM5 proteins on preassembled CA-NC complexes by electron microscopy. Incubation of assembled complexes with lysate of cells expressing the restrictive rhesus TRIM5alpha protein resulted in marked disruption of the normal cylindrical structure of the complexes. In contrast, incubation with lysate of control cells or cells expressing comparable levels of the nonrestrictive human TRIM5alpha protein had little effect on the complexes. Incubation with lysate of cells expressing the TRIMCyp restriction factor also disrupted the cylinders. The effect of TRIMCyp was prevented by the addition of cyclosporine, which inhibits binding of TRIMCyp to the HIV-1 capsid. Thus, disruption of CA-NC cylinders by TRIM5alpha and TRIMCyp was correlated with the specificity of restriction. Collectively, these results suggest that TRIM5alpha-dependent restriction of HIV-1 infection results from structural perturbation of the viral capsid leading to aberrant HIV-1 uncoating in target cells. PMID:20410272

  6. Development and Evaluation of an Enzyme-Linked Immunosorbent Assay for Dengue Capsid

    OpenAIRE

    Selvarajah, Suganya; Chatterji, Udayan; Kuhn, Richard; Kinney, Richard; Vasudevan, Subhash G.; Gallay, Philippe

    2012-01-01

    The astonishing speed with which Dengue has spread across the world and the severity of its infection make Dengue a prime threat to human life worldwide. Unfortunately, to date there are no effective vaccines or treatments against Dengue. Since only a few assays permit rapid and sensitive detection of Dengue, we developed a specific antigen capture enzyme-linked immunosorbent assay (ELISA) for the abundant structural Dengue-2 capsid protein. We showed that the ELISA allows rapid and sensitive...

  7. HPV L1-Capsid Protein Detection and Progression of Anal Squamous Neoplasia

    OpenAIRE

    Hernandez, Jonathan; Elahi, Abul; Siegel, Erin; Coppola, Domenico; Riggs, Bridgett; Shibata, David

    2011-01-01

    The progression of cervical intraepithelial lesions to invasive cancer is associated with corresponding reductions in human papillomavirus (HPV) L1-capsid antigen (L1) expression. We sought to determine whether a similar loss of L1 occurs during anal carcinogenesis using immunohistochemistry on paraffin-embedded sections as well as INNO-LiPA HPV Genotyping (Innogenetics, Gent, Belgium) technology to determine HPV infection status. We analyzed 31 squamous cell carcinomas (SCCs), 26 SCCs in sit...

  8. Improved serodiagnosis of hepatitis C virus infection with synthetic peptide antigen from capsid protein.

    OpenAIRE

    Hosein, B; Fang, C T; Popovsky, M A; J. Ye; Zhang, M; WANG, C. Y.

    1991-01-01

    Cloning and expression of hepatitis C virus have allowed the development of immunoassays to detect hepatitis C virus infection. However, currently available recombinant fusion protein C100-3 assays, based on a nonstructural protein of the virus, are limited in sensitivity, particularly for detecting acute infection. In this report seroconversion panels showed that an assay based on synthetic peptides, derived from immunodominant regions of both capsid and nonstructural proteins, accelerated h...

  9. Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle▿

    OpenAIRE

    Bourne, Christina; Lee, Sejin; Venkataiah, Bollu; Lee, Angela; Korba, Brent; Finn, M. G.; Zlotnick, Adam

    2008-01-01

    The relationship between the physical chemistry and biology of self-assembly is poorly understood, but it will be critical to quantitatively understand infection and for the design of antivirals that target virus genesis. Here we take advantage of heteroaryldihydropyrimidines (HAPs), which affect hepatitis B virus (HBV) assembly, to gain insight and correlate in vitro assembly with HBV replication in culture. Based on a low-resolution crystal structure of a capsid-HAP complex, a closely relat...

  10. Characterization of the DNA-binding properties of the polyomavirus capsid protein VP1.

    OpenAIRE

    Moreland, R B; Montross, L; Garcea, R L

    1991-01-01

    The major capsid protein of polyomavirus, VP1, has been expression cloned in Escherichia coli, and the recombinant VP1 protein has been purified to near homogeneity (A. D. Leavitt, T. M. Roberts, and R. L. Garcea, J. Biol. Chem. 260:12803-12809, 1985). With this recombinant protein, a nitrocellulose filter transfer assay was developed for detecting DNA binding to VP1 (Southwestern assay). In optimizing conditions for this assay, dithiothreitol was found to inhibit DNA binding significantly. W...

  11. Interactions of the HSV-1 UL25 Capsid Protein with Cellular Microtubule-associated Protein

    Institute of Scientific and Technical Information of China (English)

    Lei GUO; Ying ZHANG; Yan-chun CHE; Wen-juan WU; Wei-zhong LI; Li-chun WANG; Yun LIAO; Long-ding LIU; Qi-han LI

    2008-01-01

    An interaction between the HSV-1 UL25 capsid protein and cellular microtubule-associated protein was found using a yeast two-hybrid screen and β-D-galactosidase activity assays. Immunofluorescence microscopy of the UL25 protein demonstrated its co-localization with cellular microtubule-associated protein in the plasma membrane. Further investigations with deletion mutants suggest that UL25 is likely to have a function in the nucleus.

  12. Analysis of mouse polyomavirus mutants with lesions in the minor capsid proteins

    Czech Academy of Sciences Publication Activity Database

    Mannová, P.; Liebl, D.; Krauzewitz, N.; Fejtová, A.; Štokrová, Jitka; Palková, Z.; Griffin, B. E.; Forstová, J.

    2002-01-01

    Roč. 83, - (2002), s. 2309-2319. ISSN 0022-1317 R&D Projects: GA ČR GA204/00/0271 Grant ostatní: HHMI USA(US) 75195-540501 Institutional research plan: CEZ:AV0Z5052915; CEZ:MSM 113100003 Keywords : polyomavirus * minor capsid proteins * mutation Subject RIV: EE - Microbiology, Virology Impact factor: 3.300, year: 2002

  13. Exploring the Symmetry and Mechanism of Virus Capsid Maturation Via an Ensemble of Pathways

    OpenAIRE

    May, Eric R.; Feng, Jun; Brooks, Charles L.

    2012-01-01

    Many icosahedral viruses undergo large-scale conformational transitions between icosahedrally symmetric conformations during their life cycles. However, whether icosahedral symmetry is maintained along the transition pathways for this process is unknown. By employing a simplified and directed structure-based potential we compute an ensemble of transition pathways for the maturation transition of bacteriophage HK97. We observe localized symmetry-breaking events, but find that the large-scale d...

  14. Discovery of dual inhibitors targeting both HIV-1 capsid and human cyclophilin A to inhibit the assembly and uncoating of the viral capsid.

    Science.gov (United States)

    Li, Jiebo; Tan, Zhiwu; Tang, Shixing; Hewlett, Indira; Pang, Ruifang; He, Meizi; He, Shanshan; Tian, Baohe; Chen, Kan; Yang, Ming

    2009-04-15

    HIV-1 assembly and disassembly (uncoating) processes are critical for the HIV-1 replication. HIV-1 capsid (CA) and human cyclophilin A (CypA) play essential roles in these processes. We designed and synthesized a series of thiourea compounds as HIV-1 assembly and disassembly dual inhibitors targeting both HIV-1 CA protein and human CypA. The SIV-induced syncytium antiviral evaluation indicated that all of the inhibitors displayed antiviral activities in SIV-infected CEM cells at the concentration of 0.6-15.8 microM for 50% of maximum effective rate. Their abilities to bind CA and CypA were determined by ultraviolet spectroscopic analysis, fluorescence binding affinity and PPIase inhibition assay. Assembly studies in vitro demonstrated that the compounds could potently disrupt CA assembly with a dose-dependent manner. All of these molecules could bind CypA with binding affinities (Kd values) of 51.0-512.8 microM. Fifteen of the CypA binding compounds showed potent PPIase inhibitory activities (IC(50) valuesHIV-1 Protease or to HIV-1 Integrase in the enzyme assays. These results suggested that 15 compounds could block HIV-1 replication by inhibiting the PPIase activity of CypA to interfere with capsid disassembly and disrupting CA assembly. PMID:19328002

  15. Enhancing the clinical potential of AAV vectors by capsid engineering to evade pre-existing immunity

    Directory of Open Access Journals (Sweden)

    DavidSchaffer

    2011-10-01

    Full Text Available Vectors based on adeno-associated viruses have shown considerable promise in both preclinical models and increasingly in clinical trials. However, one formidable challenge is pre-existing immunity due to widespread exposure to numerous AAV variants and serotypes within the human population, which affect efficacy of clinical trials due to the accompanying high levels of anti-capsid neutralizing antibodies. Transient immunosuppression has promise in mitigating cellular and humoral responses induced by vector application in naïve hosts, but cannot overcome the problem that pre-existing neutralizing antibodies pose towards the goal of safe and efficient gene delivery. Shielding of AAV from antibodies, however, may be possible by covalent attachment of polymers to the viral capsid or by encapsulation of vectors inside biomaterials. In addition, there has been considerable progress in using rational mutagenesis, combinatorial libraries, and directed evolution approaches to engineer capsid variants that are not recognized by anti-AAV antibodies generally present in the human population. While additional progress must be made, such strategies, alone or in combination with immunosuppression to avoid de novo induction of antibodies, have strong potential to significantly enhance the clinical efficacy of AAV vectors.

  16. Outer capsid proteins induce the formation of pores in epithelial cells

    International Nuclear Information System (INIS)

    Two mechanisms of entrance in cell of the rotavirus, during the infection, were proposed: a direct entrance through the plasmatic membrane or by means of endocytosis. In the two cases, a permeabilization mechanism of the membrane (cellular or of the endocytic vesicle, respectively) should occur. It has been shown that the rotavirus induces permeabilization of liposomes and of membrane vesicles. In this work, are studied the changes of intact cells permeability, measuring the entrance of e tide bromides. Viral particles of double capsid of the RF stump produce an increase of the cells membrane MA104 permeability, while the simple capsid ones don't induce effect. This phenomenon requires the particles trypsinization, and occurs in a means where the concentration of free Ca is lower to 1 micromolar. The temporary course of the fluorescence increase is sigmoid. The latency, the speed and the width depend on the relationship of virus / cell, and it can be observed up to 100% of permeabilization in relation to the effect of digitonin. The pores induced in the membrane by the rotavirus are irreversible. The permeabilizer effect of the rotavirus on the membrane was observed in other cellular lines as Hela and HT29, but not in the L929 ones. These results suggest that one or more proteins of the external capsid are responsible s of the effect. These could be involved in the penetration process of the virus towards the cytoplasm and could be one of the restrictive factor of the cell infection by means of the virus

  17. Conversion of a dodecahedral protein capsid into pentamers via minimal point mutations.

    Science.gov (United States)

    Chen, Hsiao-Nung; Woycechowsky, Kenneth J

    2012-06-12

    Protein self-assembly relies upon the formation of stabilizing noncovalent interactions across subunit interfaces. Identifying the determinants of self-assembly is crucial for understanding structure-function relationships in symmetric protein complexes and for engineering responsive nanoscale architectures for applications in medicine and biotechnology. Lumazine synthases (LS's) comprise a protein family that forms diverse quaternary structures, including pentamers and 60-subunit dodecahedral capsids. To improve our understanding of the basis for this difference in assembly, we attempted to convert the capsid-forming LS from Aquifex aeolicus (AaLS) into pentamers through a small number of rationally designed amino acid substitutions. Our mutations targeted side chains at ionic (R40), hydrogen bonding (H41), and hydrophobic (L121 and I125) interaction sites along the interfaces between pentamers. We found that substitutions at two or three of these positions could reliably generate pentameric variants of AaLS. Biophysical characterization indicates that this quaternary structure change is not accompanied by substantial changes in secondary or tertiary structure. Interestingly, previous homology-based studies of the assembly determinants in LS's had identified only one of these four positions. The ability to control assembly state in protein capsids such as AaLS could aid efforts in the development of new systems for drug delivery, biocatalysis, or materials synthesis. PMID:22606973

  18. Stability of Norwalk virus capsid protein interfaces evaluated by in-silico nanoindentation

    Directory of Open Access Journals (Sweden)

    Kevin J Boyd

    2015-07-01

    Full Text Available Norwalk virus causes severe gastroenteritis for which there is currently no specific anti-viral therapy. A stage of the infection process is uncoating of the protein capsid to expose the viral genome and allow for viral replication. A mechanical characterization of the Norwalk virus may provide important information relating to the mechanism of uncoating. The mechanical strength of the Norwalk virus has previously been investigated using atomic force microscopy (AFM nanoindentation experiments. Those experiments cannot resolve specific molecular interactions, and therefore we have employed a molecular modeling approach to gain insights into the potential uncoating mechanism of the Norwalk capsid. In this study, we perform simulated nanoindentation using a coarse-grained structure based model, which provides an estimate of the spring constant in good agreement with the experimentally determined value. We further analyze the fracture mechanisms and determine weak interfaces in the capsid structure which are potential sites to inhibit uncoating by stabilization of these weak interfaces. We conclude by identifying potential target sites at the junction of a weak protein-protein interface.

  19. Perspective on Adeno-Associated Virus Capsid Modification for Duchenne Muscular Dystrophy Gene Therapy.

    Science.gov (United States)

    Nance, Michael E; Duan, Dongsheng

    2015-12-01

    Duchenne muscular dystrophy (DMD) is a X-linked, progressive childhood myopathy caused by mutations in the dystrophin gene, one of the largest genes in the genome. It is characterized by skeletal and cardiac muscle degeneration and dysfunction leading to cardiac and/or respiratory failure. Adeno-associated virus (AAV) is a highly promising gene therapy vector. AAV gene therapy has resulted in unprecedented clinical success for treating several inherited diseases. However, AAV gene therapy for DMD remains a significant challenge. Hurdles for AAV-mediated DMD gene therapy include the difficulty to package the full-length dystrophin coding sequence in an AAV vector, the necessity for whole-body gene delivery, the immune response to dystrophin and AAV capsid, and the species-specific barriers to translate from animal models to human patients. Capsid engineering aims at improving viral vector properties by rational design and/or forced evolution. In this review, we discuss how to use the state-of-the-art AAV capsid engineering technologies to overcome hurdles in AAV-based DMD gene therapy. PMID:26414293

  20. Solid-to-fluid DNA transition inside HSV-1 capsid close to the temperature of infection

    Energy Technology Data Exchange (ETDEWEB)

    Sae-Ueng, Udom; Li, Dong; Zuo, Xiaobing; Huffman, Jamie B.; Homa, Fred L.; Rau, Donald; Evilevitch, Alex

    2014-10-01

    DNA in the human Herpes simplex virus type 1 (HSV-1) capsid is packaged to a tight density. This leads to tens of atmospheres of internal pressure responsible for the delivery of the herpes genome into the cell nucleus. In this study we show that, despite its liquid crystalline state inside the capsid, the DNA is fluid-like, which facilitates its ejection into the cell nucleus during infection. We found that the sliding friction between closely packaged DNA strands, caused by interstrand repulsive interactions, is reduced by the ionic environment of epithelial cells and neurons susceptible to herpes infection. However, variations in the ionic conditions corresponding to neuronal activity can restrict DNA mobility in the capsid, making it more solid-like. This can inhibit intranuclear DNA release and interfere with viral replication. In addition, the temperature of the human host (37 °C) induces a disordering transition of the encapsidated herpes genome, which reduces interstrand interactions and provides genome mobility required for infection.

  1. Hierarchical Assembly of Plasmonic Nanostructures using Virus Capsid Scaffolds on DNA Origami Tiles

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Debin; Capehart, Stacy L.; Pal, Suchetan; Liu, Minghui; Zhang, Lei; Schuck, P. J.; Liu, Yan; Yan, Hao; Francis, Matthew B.; De Yoreo, James J.

    2014-07-07

    Plasmonic nanoarchitectures using biological scaffolds have shown the potential to attain controllable plasmonic fluorescence via precise spatial arrangement of fluorophores and plasmonic antennae. However, previous studies report a predominance of fluorescence quenching for small metal nanoparticles (less than ~60 nm) due to their small scattering cross-sections. In this work, we report the design and performance of fluorescent plasmonic structures composed of fluorophore-modified virus capsids and gold nanoparticles (AuNPs) assembled on DNA origami tiles. The virus capsid creates a scaffold for control over the three dimensional arrangement of the fluorophores, whereas the DNA origami tile provides precise control over the distance between the capsid and the AuNP. Using finite-difference time-domain (FDTD) numerical simulations and multimodal single-particle imaging measurements, we show that the judicial design of these structures places the dye molecules near the hot spot of the AuNP. This effectively increases the fluorescence intensity in the quenching regime of the AuNP, with an enhancement factor that increases with increasing AuNP size. This strategy of using biological scaffolds to control fluorescence paves the way for exploring the parameters that determine plasmonic fluorescence. It may lead to a better understanding of the antenna effects of photon absorption and emission, enabling the construction of multicomponent plasmonic systems.

  2. Transient Bluetongue virus serotype 8 capsid protein expression in Nicotiana benthamiana

    Directory of Open Access Journals (Sweden)

    Albertha R. van Zyl

    2016-03-01

    Full Text Available Bluetongue virus (BTV causes severe disease in domestic and wild ruminants, and has recently caused several outbreaks in Europe. Current vaccines include live-attenuated and inactivated viruses; while these are effective, there is risk of reversion to virulence by mutation or reassortment with wild type viruses. Subunit or virus-like particle (VLP vaccines are safer options: VLP vaccines produced in insect cells by expression of the four BTV capsid proteins are protective against challenge; however, this is a costly production method. We investigated production of BTV VLPs in plants via Agrobacterium-mediated transient expression, an inexpensive production system very well suited to developing country use. Leaves infiltrated with recombinant pEAQ-HT vectors separately encoding the four BTV-8 capsid proteins produced more proteins than recombinant pTRA vectors. Plant expression using the pEAQ-HT vector resulted in both BTV-8 core-like particles (CLPs and VLPs; differentially controlling the concentration of infiltrated bacteria significantly influenced yield of the VLPs. In situ localisation of assembled particles was investigated by using transmission electron microscopy (TEM and it was shown that a mixed population of core-like particles (CLPs, consisting of VP3 and VP7 and VLPs were present as paracrystalline arrays in the cytoplasm of plant cells co-expressing all four capsid proteins.

  3. Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study

    International Nuclear Information System (INIS)

    In this work, we report on simulations of double-stranded DNA (dsDNA) ejection from bacteriophage ϕ29 into a bacterial cell. The ejection was studied with a coarse-grained model, in which viral dsDNA was represented by beads on a torsion-less string. The bacteriophage’s capsid and the bacterial cell were defined by sets of spherical constraints. To account for the effects of the viscous medium inside the bacterial cell, the simulations were carried out using a Langevin dynamics protocol. Our simplest simulations (involving constant viscosity and no external biasing forces) produced results compatible with the push–pull model of DNA ejection, with an ejection rate significantly higher in the first part of ejection than in the latter parts. Additionally, we performed more complicated simulations, in which we included additional factors such as external forces, osmotic pressure, condensing agents and ejection-dependent viscosity. The effects of these factors (independently and in combination) on the thermodynamics and kinetics of DNA ejection were studied. We found that, in general, the dependence of ejection forces and ejection rates on the amount of DNA ejected becomes more complex if the ejection is modeled with a broader, more realistic set of parameters and influences (such as variation in the solvent’s viscosity and the application of an external force). However, certain combinations of factors and numerical parameters led to the opposition of some ejection-driving and ejection-inhibiting influences, ultimately causing an apparent simplification of the ejection profiles. (paper)

  4. Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174.

    Directory of Open Access Journals (Sweden)

    Celeste J Brown

    Full Text Available Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying adaptation. Although dissecting these molecular mechanisms is expensive and time-consuming, general patterns can be detected from repeated experiments, illuminating the biological processes involved in evolutionary adaptation. The bacteriophage φX174 was grown for 50 days in replicate chemostats under two culture conditions: Escherichia coli C as host growing at 37°C and Salmonella typhimurium as host growing at 43.5°C. After 50 days, greater than 20 substitutions per chemostat had risen to detectable levels. Of the 97 substitutions, four occurred in all four chemostats, five arose in both culture conditions, eight arose in only the high temperature S. typhimurium chemostats, and seven arose only in the E. coli chemostats. The remaining substitutions were detected only in a single chemostat, however, almost half of these have been seen in other similar experiments. Our findings support previous studies that host recognition and capsid stability are two biological processes that are modified during adaptation to novel hosts and high temperature. Based upon the substitutions shared across both environments, it is apparent that genome replication and packaging are also affected during adaptation to the chemostat environment, rather than to temperature or host per se. This environment is characterized by a large number of phage and very few hosts, leading to competition among phage within the host. We conclude from these results that adaptation to a high density environment selects for changes in genome replication at both protein and DNA sequence levels.

  5. 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

  6. Protonic Conduction in TiP2O7

    Science.gov (United States)

    Nalini, V.; Norby, T.; Anuradha, A. M.

    2006-06-01

    TiP2O7 was synthesized by reacting TiO2 and 85 % H3PO4 and characterized by XRD, TEM and SEM. The electrical conductivity of the sample was examined at 500-1000 °C under various p(O2), p(H2O), and p(D2O) conditions. The conductivity of the material in wet atmospheres was higher than that under D2O-containing and dry atmospheres, indicating that protonic conduction was dominant in this material in wet atmospheres. The conductivity was mainly independent of p(O2) at 500-900 °C under oxidizing conditions, confirming predominant ionic (protonic) conduction.

  7. Acoustics of the Sodium Loop Safety Facility P2 experiment

    International Nuclear Information System (INIS)

    In the highly instrumented P2 experiment to simulate an unprotected loss of flow in an LMBFR core, two high-temperature sodium-immersed microphones were used to obtain the acoustic scenario of the 9-second flow coastdown, boiling sodium coolant, fuel failure, and re-establishment of flow after reactor scram. Acoustic data from this and previous experiments indicate that singular larger voids are formed in the sodium boiling process. These singular larger voids were observed to collapse upon contacting the subcooled sodium or structures, at repetition rates comparable to formation rates of sodium vapor bubbles. The acoustic observations were made in the presence of sodium exposed to argon cover gas at LMFBR operating conditions, and in the presence of fission gas from fuel pin failure. 6 refs

  8. Content Distribution Mechanism in Mobile P2P Network

    Directory of Open Access Journals (Sweden)

    Degui Zeng

    2014-05-01

    Full Text Available As content distribution in mobile P2P network facing architecture instability, the limited ability of a single node, low efficiency of content distribution and other problems, this paper proposes a new mobile network structure and content distribution mechanism strategy, the new mobile network structure will be divided into multiple subnets network for partition management. Each subnet manages information routing and dissemination strategies through a super-node. The transfer of information between subnets can be achieved by transitional node in cross region. Thus the information transfer is achieved in the entire network. Content distribution strategies using part of network coding mechanism for data compression, improve the efficiency of information transmission and download success rate. Finally, experimental verification, the experimental results show that: the proposed new mobile network structure and content distribution mechanisms strategies can reduce the disturbance of download success rate caused by fixed point, reduce the data transmission delay, and effectively improve the hit rate

  9. P2P Approach for Web Services Publishing and Discovery

    Science.gov (United States)

    Islam, Mohmammad Towhidul; Akon, Mursalin; Shen, Xuemin (Sherman)

    Web service is an emerging paradigm for distributing business applications from different platforms to a wide variety of clients. The critical factor in seamlessly accessing web services is to discover the appropriate service and the related service providers. Unfortunately, current web service technologies use centralized directory to keep the service index, which is not scalable and at the same time vulnerable to single point of failure. Peer to peer system is a popular decentralized architecture which can be used for key look up service with scalability and self organization. Thus there is an opportunity to intersect the P2P framework with web services to provide the scalable solution. In this chapter, we discuss the key methods to deploy web services using the peer-to-peer technology.

  10. Adaptive Streaming of Scalable Videos over P2PTV

    Directory of Open Access Journals (Sweden)

    Youssef Lahbabi

    2015-01-01

    Full Text Available In this paper, we propose a new Scalable Video Coding (SVC quality-adaptive peer-to-peer television (P2PTV system executed at the peers and at the network. The quality adaptation mechanisms are developed as follows: on one hand, the Layer Level Initialization (LLI is used for adapting the video quality with the static resources at the peers in order to avoid long startup times. On the other hand, the Layer Level Adjustment (LLA is invoked periodically to adjust the SVC layer to the fluctuation of the network conditions with the aim of predicting the possible stalls before their occurrence. Our results demonstrate that our mechanisms allow quickly adapting the video quality to various system changes while providing best Quality of Experience (QoE that matches current resources of the peer devices and instantaneous throughput available at the network state.

  11. Action of Natural Products on P2 Receptors: A Reinvented Era for Drug Discovery

    Directory of Open Access Journals (Sweden)

    Luiz Alves

    2012-11-01

    Full Text Available Natural products contribute significantly to available drug therapies and have been a rich source for scientific investigation. In general, due to their low cost and traditional use in some cultures, they are an object of growing interest as alternatives to synthetic drugs. With several diseases such as cancer, and inflammatory and neuropathic diseases having been linked to the participation of purinergic (P2 receptors, there has been a flurry of investigations on ligands within natural products. Thirty-four different sources of these compounds have been found so far, that have shown either agonistic or antagonistic effects on P2 receptors. Of those, nine different plant sources demonstrated effects on P2X2, P2X3, P2X7, and possibly P2Y12 receptor subtypes. Microorganisms, which represent the largest group, with 26 different sources, showed effects on both receptor subtypes, ranging from P2X1 to P2X4 and P2X7, and P2Y1, P2Y2, P2Y4, and P2Y6. In addition, there were seventeen animal sources that affected P2X7 and P2Y1 and P2Y12 receptors. Natural products have provided some fascinating new mechanisms and sources to better understand the P2 receptor antagonism. Moreover, current investigations should clarify further pharmacological mechanisms in order to consider these products as potential new medicines.

  12. Analysis of the Pure Distributed P2P Network%纯分布式P2P网络结构浅析

    Institute of Scientific and Technical Information of China (English)

    刘凯; 张华

    2012-01-01

      As a network model,P2P(Peer-to-Peer) is now widely used. Unstructured and structured P2P networks are two typi⁃cal topologies in P2P networking. Unstructured P2P use flooding method and structured P2P uses Distributed Hash Table meth⁃od. This paper gives an analysis of two kinds of P2P networks and a comparison to the typical case of structured P2P and unstruc⁃tured P2P in implementation process,and then proposes a summary of their advantages and disadvantages.%  P2P(Peer-to-Peer)是现今广泛使用的一种网络模型,非结构化 P2P 模型和结构化 P2P 模型是其中两种基本拓扑结构。非结构化模型一般使用洪泛方法实现,结构化P2P网络一般使用分布式哈希表构建。该文在分析两种P2P网络的基础上,对比了结构化P2P模型和非结构化P2P模型中的典型案例的实现过程,并对其优缺点进行了总结。

  13. 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

  14. 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

  15. 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

  16. 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

  17. Length quantization of DNA partially expelled from heads of a bacteriophage T3 mutant

    International Nuclear Information System (INIS)

    DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel electrophoretic band formation. We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). Three tail gene mutations, but no head gene mutations, are present. A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNA missing 3.7–12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection. - Graphical abstract: Highlights: • We implement directed evolution- and DNA-sequencing-based phage assembly genetics. • We purify stable, mutant phage heads with a partially leaked mature DNA molecule. • Native gels and DNase-protection show leaked DNA segments to have quantized lengths. • Native gels after DNase I-removal of leaked DNA reveal the capsids to vary in radius. • Thus, we hypothesize leaked DNA quantization via variably quantized capsid radius

  18. Length quantization of DNA partially expelled from heads of a bacteriophage T3 mutant

    Energy Technology Data Exchange (ETDEWEB)

    Serwer, Philip, E-mail: serwer@uthscsa.edu [Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900 (United States); Wright, Elena T. [Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900 (United States); Liu, Zheng; Jiang, Wen [Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 (United States)

    2014-05-15

    DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel electrophoretic band formation. We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). Three tail gene mutations, but no head gene mutations, are present. A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNA missing 3.7–12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection. - Graphical abstract: Highlights: • We implement directed evolution- and DNA-sequencing-based phage assembly genetics. • We purify stable, mutant phage heads with a partially leaked mature DNA molecule. • Native gels and DNase-protection show leaked DNA segments to have quantized lengths. • Native gels after DNase I-removal of leaked DNA reveal the capsids to vary in radius. • Thus, we hypothesize leaked DNA quantization via variably quantized capsid radius.

  19. 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

  20. 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