The Experts below are selected from a list of 234 Experts worldwide ranked by ideXlab platform
Chen Zhaobin - One of the best experts on this subject based on the ideXlab platform.
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Study of the resistance of Bacteriophage MS2 to Nanometer titanium dioxide.
Modern Preventive Medicine, 2010Co-Authors: Wu Bingting, Chen ZhaobinAbstract:[Objective] To investigate the inactivation efficacy of Nano-titanium dioxide solution to Bacteriophage MS2,and thus to preliminarily illustrate the resistance of Bacteriophage against Nano-titanium dioxide.[Methods] Applied the quantitative suspension inactivated experimental to specify the inactivated effect of Nano-titanium dioxide to Bacteriophage.Bistratal agar method was adopted in identification of neutralizer and detection of Bacteriophage.[Results] ① UV-radiation group 800mg /L concentration of Nano-titanium dioxide acting on Bacteriophage MS2 for 5 minutes or 200mg /L concentration of Nanotitanium dioxide acting on Bacteriophage MS2 for 10 minutes could reach the level of disinfection.②Natural light-radiation Group 1000mg /L concentration of Nano-titanium dioxide acting on Bacteriophage MS2 for 5 minutes or 200mg /L concentration of Nano-titanium dioxide acting on Bacteriophage MS2 for 20 minutes could reach the level of disinfection.[Conclusion] Radiated by violet ray or natural light,Nano-titanium dioxide can make Bacteriophage MS2 inactivated in short time to reach the level of disinfection.The increase the concentration of Nano-titanium dioxide solution can enhance it inactivated effect on Bacteriophage MS2.The resistance of Bacteriophage against Nano-titanium dioxide is feeble.
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THE EXPERIMENTAL STUDY ON THE INACTIVATION EFFECT OF SILVER NANOPARTICLES AQUEOUS SOLUTION WITH ORGANIC INTERFERING SUBSTANCE TO Bacteriophage MS2
Modern Preventive Medicine, 2008Co-Authors: Chen ZhaobinAbstract:[Objective]To investigate the inactivation efficacy of silver nanoparticles(Ag-NPs)aqueous solution to Bacteriophage MS2 by adding organic interfering substance(BSA)or not,and thus to offer some basic information for the practical application of silver nanoparticles in life and environment.[Methods]To determine the logarithm inactivation value(LIV)of Ag-NPs for Bacteriophage MS2,suspension quantitative inactivation test were carried out.[Results]While without BSA,MS2 was exposed to 100mg/L Ag-NPs for 60 minutes and 400mg/L for 20 minutes,the LIV to Bacteriophage MS2 were 4.01log10 and 4.12log10,respectively;But with BSA(3%),even MS2 was exposed to 400mg/L Ag-NPs for 1440min,the LIV was only 3.61log10,and to 800mg/L Ag-NPs for 90min,LIV was 4.02log10.[Conclusion]The existing of the organic interfering substance in environment could greatly cut down the inactivation effect of the solution of silver nanoparticles to Bacteriophage MS2.
Constantinos V Chrysikopoulos - One of the best experts on this subject based on the ideXlab platform.
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Bacteriophage MS2 and titanium dioxide heteroaggregation: Effects of ambient light and the presence of quartz sand.
Colloids and surfaces. B Biointerfaces, 2019Co-Authors: Vasiliki I. Syngouna, Constantinos V ChrysikopoulosAbstract:Nanoparticles (NPs) are used in numerous applications and have been observed to accumulate in natural water bodies, including aquifers where they can interact with suspended colloids and viruses. This study examines the attachment of Bacteriophage MS2 onto titanium dioxide (TiO2) anatase NPs using three different MS2 concentrations. Batch experiments, were conducted at room temperature to investigate the effect of ambient light and the presence of quartz sand on MS2 and TiO2 NPs heteroaggregation. Appropriate attachment isotherms were determined. Extended DLVO (XDLVO) theory was used to quantify the various interaction energy profiles. The results of batch experiments demonstrated that MS2 attachment onto TiO2 NPs was favored in the presence of sand under ambient light, while under dark conditions no clear trend was observed. Estimated XDLVO interaction energy profiles indicated that hydrophobic interactions may play a major role and influence the aggregation and heteroaggregation of MS2 and TiO2 NPs, as well as the simultaneous attachment of MS2 and TiO2 NPs onto quartz sand.
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Evaluation of the Factors Controlling the Time-Dependent Inactivation Rate Coefficients of Bacteriophage MS2 and PRD1
Environmental science & technology, 2006Co-Authors: Robert Anders, Constantinos V ChrysikopoulosAbstract:Static and dynamic batch experiments were conducted to study the effects of temperature and the presence of sand on the inactivation of Bacteriophage MS2 and PRD1. The experimental data suggested that the inactivation process can be satisfactorily represented by a pseudo-first-order expression with time-dependent rate coefficients. The time-dependent rate coefficients were used to determine pertinent thermodynamic properties required for the analysis of the molecular processes involved in the inactivation of each Bacteriophage. A combination of high temperature and the presence of sand appears to produce the greatest disruption to the surrounding protein coat of MS2. However, the lower activation energies for PRD1 indicate a weaker dependence of the inactivation rate on temperature. Instead, the presence of air-liquid and air-solid interfaces appears to produce the greatest damage to specific viral components that are related to infection. These results indicate the importance of using thermodynamic parameters based on the time-dependent inactivation model to better predict the inactivation of viruses in groundwater.
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Early breakthrough of colloids and Bacteriophage MS2 in a water‐saturated sand column
Water Resources Research, 2004Co-Authors: Arturo A Keller, Sanya Sirivithayapakorn, Constantinos V ChrysikopoulosAbstract:[1] We conducted column-scale experiments to observe the effect of transport velocity and colloid size on early breakthrough of free moving colloids, to relate previous observations at the pore scale to a larger scale. The colloids used in these experiments were Bacteriophage MS2 (0.025 μm), and 0.05- and 3-μm spherical polystyrene beads, and were compared with a conservative nonsorbing tracer (KCl). The results show that early breakthrough of colloids increases with colloid size and water velocity, compared with the tracer. These results are in line with our previous observations at the pore scale that indicated that larger colloids are restricted by the size exclusion effect from sampling all paths, and therefore they tend to disperse less and move in the faster streamlines, if they are not filtered out. The measured macroscopic dispersion coefficient decreases with colloid size due to the preferential flow paths, as observed at the pore scale. Dispersivity, typically considered only a property of the medium, is in this case also a function of colloid size, in particular at low Peclet numbers due to the size exclusion effect. Other parameters for colloid transport, such as collector efficiency and colloid filtration rates, were also estimated from the experimental breakthrough curve using a numerical fitting routine. In general, we found that the estimated filtration parameters follow the clean bed filtration model, although with a lower filtration efficiency overall.
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early breakthrough of colloids and Bacteriophage MS2 in a water saturated sand column
Water Resources Research, 2004Co-Authors: Arturo A Keller, Sanya Sirivithayapakorn, Constantinos V ChrysikopoulosAbstract:[1] We conducted column-scale experiments to observe the effect of transport velocity and colloid size on early breakthrough of free moving colloids, to relate previous observations at the pore scale to a larger scale. The colloids used in these experiments were Bacteriophage MS2 (0.025 μm), and 0.05- and 3-μm spherical polystyrene beads, and were compared with a conservative nonsorbing tracer (KCl). The results show that early breakthrough of colloids increases with colloid size and water velocity, compared with the tracer. These results are in line with our previous observations at the pore scale that indicated that larger colloids are restricted by the size exclusion effect from sampling all paths, and therefore they tend to disperse less and move in the faster streamlines, if they are not filtered out. The measured macroscopic dispersion coefficient decreases with colloid size due to the preferential flow paths, as observed at the pore scale. Dispersivity, typically considered only a property of the medium, is in this case also a function of colloid size, in particular at low Peclet numbers due to the size exclusion effect. Other parameters for colloid transport, such as collector efficiency and colloid filtration rates, were also estimated from the experimental breakthrough curve using a numerical fitting routine. In general, we found that the estimated filtration parameters follow the clean bed filtration model, although with a lower filtration efficiency overall.
Neil A. Ranson - One of the best experts on this subject based on the ideXlab platform.
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direct evidence for packaging signal mediated assembly of Bacteriophage MS2
Journal of Molecular Biology, 2016Co-Authors: Ottar Rolfsson, Reidun Twarock, Neil A. Ranson, Stefani Middleton, Iain W Manfield, Simon J White, Baochang Fan, Robert Vaughan, Eric C Dykeman, James FordAbstract:Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of Bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2
Computational and Mathematical Methods in Medicine, 2008Co-Authors: Ottar Rolfsson, Katerina Toropova, Gabriella Basnak, Victoria L. Morton, Simona Francese, Gary S. Thompson, Stephen W. Homans, Alison E. Ashcroft, Nicola J. Stonehouse, Neil A. RansonAbstract: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 A 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.
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The three-dimensional structure of genomic RNA in Bacteriophage MS2: implications for assembly.
Journal of molecular biology, 2007Co-Authors: Katerina Toropova, Gabriella Basnak, Reidun Twarock, Peter G. Stockley, Neil A. RansonAbstract:Using cryo-electron microscopy, single particle image processing and three-dimensional reconstruction with icosahedral averaging, we have determined the three-dimensional solution structure of Bacteriophage MS2 capsids reassembled from recombinant protein in the presence of short oligonucleotides. We have also significantly extended the resolution of the previously reported structure of the wild-type MS2 virion. The structures of recombinant MS2 capsids reveal clear density for bound RNA beneath the coat protein binding sites on the inner surface of the T=3 MS2 capsid, and show that a short extension of the minimal assembly initiation sequence that promotes an increase in the efficiency of assembly, interacts with the protein capsid forming a network of bound RNA. The structure of the wild-type MS2 virion at approximately 9 A resolution reveals icosahedrally ordered density encompassing approximately 90% of the single-stranded RNA genome. The genome in the wild-type virion is arranged as two concentric shells of density, connected along the 5-fold symmetry axes of the particle. This novel RNA fold provides new constraints for models of viral assembly.
David S. Peabody - One of the best experts on this subject based on the ideXlab platform.
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Display of single-chain variable fragments on Bacteriophage MS2 virus-like particles.
Journal of nanobiotechnology, 2017Co-Authors: Christopher A. Lino, Jerri C. Caldeira, David S. PeabodyAbstract:Virus-like particles (VLPs) of the RNA Bacteriophage MS2 have many potential applications in biotechnology. MS2 VLPs provide a platform for peptide display and affinity selection (i.e. biopanning). They are also under investigation as vehicles for targeted drug delivery, using display of receptor-specific peptides or nucleic acid aptamers to direct their binding to specific cell-surface receptors. However, there are few molecules more suited to the precise targeting and binding of a cellular receptor than antibodies. Here we describe a strategy for display of four different functional single-chain variable fragments (scFvs) on the surface of the MS2 VLP. Each scFv is validated both for its presence on the surface of the VLP and for its ability to bind its cognate antigen. This work demonstrates the suitability of the MS2 VLP platform to display genetically fused scFvs, allowing for many potential applications of these VLPs and paving the way for future work with libraries of scFvs displayed in a similar manner on the VLP surface. These libraries can then be biopanned and novel scFv binders to targets can be readily discovered.
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Peptide Epitope Identification by Affinity Selection on Bacteriophage MS2 Virus-Like Particles
Journal of molecular biology, 2011Co-Authors: Bryce Chackerian, Jerri C. Caldeira, Julianne Peabody, David S. PeabodyAbstract:Filamentous phages are now the most widely used vehicles for phage display and provide efficient means for epitope identification. However, the peptides they display are not very immunogenic because they normally fail to present foreign epitopes at the very high densities required for efficient B-cell activation. Meanwhile, systems based on virus-like particles (VLPs) permit the engineered high-density display of specific epitopes but are incapable of peptide library display and affinity selection. We developed a new peptide display platform based on VLPs of the RNA Bacteriophage MS2. It combines the high immunogenicity of MS2 VLPs with the affinity selection capabilities of other phage display systems. Here, we describe plasmid vectors that facilitate the construction of high-complexity random sequence peptide libraries on MS2 VLPs and that allow control of the stringency of affinity selection through the manipulation of display valency. We used the system to identify epitopes for several previously characterized monoclonal antibody targets and showed that the VLPs thus obtained elicit antibodies in mice whose activities mimic those of the selecting antibodies.
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The RNA binding site of Bacteriophage MS2 coat protein.
The EMBO journal, 1993Co-Authors: David S. PeabodyAbstract:The coat protein of the RNA Bacteriophage MS2 binds a specific stem-loop structure in viral RNA to accomplish encapsidation of the genome and translational repression of replicase synthesis. In order to identify the structural components of coat protein required for its RNA binding function, a series of repressor-defective mutants has been isolated. To ensure that the repressor defects were due to substitution of binding site residues, the mutant coat proteins were screened for retention of the ability to form virus-like particles. Since virus assembly presumably requires native structure, this approach eliminated mutants whose repressor defects were secondary consequences of protein folding or stability defects. Each of the variant coat proteins was purified and its ability to bind operator RNA in vitro was measured. DNA sequence analysis identified the nucleotide and amino acid substitutions responsible for reduced RNA binding affinity. Localization of the substituted sites in the three-dimensional structure of coat protein reveals that amino acid residues on three adjacent strands of the coat protein beta-sheet are required for translational repression and RNA binding. The sidechains of the affected residues form a contiguous patch on the interior surface of the viral coat.
Christopher H. S. Aylett - One of the best experts on this subject based on the ideXlab platform.
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Bacteriophage MS2 displays unreported capsid variability assembling t 4 and mixed capsids
Molecular Microbiology, 2020Co-Authors: Natàlia De Martin Garrido, Michael A. Crone, Kailash Ramlaul, P.a. Simpson, Paul S. Freemont, Christopher H. S. AylettAbstract:Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 A and 6 A respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.
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Bacteriophage MS2 displays unreported capsid variability assembling T = 4 and mixed capsids.
Molecular microbiology, 2019Co-Authors: Natàlia De Martin Garrido, Michael A. Crone, Kailash Ramlaul, P.a. Simpson, Paul S. Freemont, Christopher H. S. AylettAbstract:Bacteriophage MS2 is a positive-sense, single-stranded RNA virus encapsulated in an asymmetric T = 3 pseudo-icosahedral capsid. It infects Escherichia coli through the F-pilus, in which it binds through a maturation protein incorporated into its capsid. Cryogenic electron microscopy has previously shown that its genome is highly ordered within virions, and that it regulates the assembly process of the capsid. In this study, we have assembled recombinant MS2 capsids with non-genomic RNA containing the capsid incorporation sequence, and investigated the structures formed, revealing that T = 3, T = 4 and mixed capsids between these two triangulation numbers are generated, and resolving structures of T = 3 and T = 4 capsids to 4 A and 6 A respectively. We conclude that the basic MS2 capsid can form a mix of T = 3 and T = 4 structures, supporting a role for the ordered genome in favouring the formation of functional T = 3 virions.
