Publications

TitleAbstractYear
Filter
PMID(sorted ascending)
Filter
purification of filamentous bacteriophage m13 by expanded bed anion exchange chromatography.in this paper, we investigated the development of a simplified and rapid primary capture step for the recovery of m13 bacteriophage from particulate-containing feedstock. m13 bacteriophage, carrying an insert, was propagated and subsequently purified by the application of both conventional multiple steps and expanded bed anion exchange chromatography. in the conventional method, precipitation was conducted with peg/nacl, and centrifugation was also performed. in the single step expanded bed anio ...200415459653
membrane assembly of m13 major coat protein: evidence for a structural adaptation in the hinge region and a tilted transmembrane domain.new insights into the low-resolution structure of the hinge region and the transmembrane domain of the membrane-bound major coat protein of the bacteriophage m13 are deduced from a single cysteine-scanning approach using fluorescence spectroscopy. new mutant coat proteins are labeled and reconstituted into phospholipid bilayers with varying headgroup compositions (pc, pe, and pg) and thicknesses (14:1pc, 18:1pc, and 22:1pc). information about the polarity of the local environment around the labe ...200415518546
functional display of family 11 endoxylanases on the surface of phage m13.two family 11 endoxylanases (ec 3.2.1.8) were functionally displayed on the surface of bacteriophage m13. the genes encoding endo-1,4-xylanase i from aspergillus niger (exla) and endo-1,4-xylanase a from bacillus subtilis (xyna) were fused to the gene encoding the minor coat protein g3p in phagemid vector phos31. phage rescue resulted in functional monovalent display of the enzymes as was demonstrated by three independent tests. firstly, purified recombinant phage particles showed a clear hydrol ...200515639087
isotropic-cholesteric phase transition of filamentous virus suspensions as a function of rod length and charge.the viruses studied are genetically engineered, charged, semiflexible filamentous bacteriophages that are structurally identical to m13 virus, but differ either in contour length or surface charge. while varying contour length (l) we assume the persistence length (p) remains constant, and thus we alter the rod flexibility (l/p) . surface charge is altered both by changing solution ph and by comparing two viruses, fd and m13, which differ only by the substitution of one charged for one neutral am ...200415697386
localization of escherichia coli poly(a) polymerase i in cellular membrane.poly(a) polymerase i (pap i), the pcnb gene product, is the main enzyme responsible for rna polyadenylation in escherichia coli. polyadenylated rna molecules are rapidly degraded by a multiprotein complex called rna degradosome. here we demonstrate that apart from its presence in cytosol, pap i is also localized in cellular membrane. although this observation might appear surprising, it was demonstrated recently by others that e. coli rna degradosome is also associated with the cytoplasmic membr ...200515737627
protein-lipid interactions of bacteriophage m13 gene 9 minor coat protein.gene 9 protein is one of the minor coat proteins of bacteriophage m13. the protein plays a role in the assembly process by associating with the host membrane by protein-lipid interactions. the availability of chemically synthesized protein has enabled the biophysical characterization of the membrane-bound state of the protein by using model membrane systems. this paper summarizes, discusses and further interprets this work in the light of the current state of the literature, leading to new possi ...200415764365
genome-wide comparison of phage m13-infected vs. uninfected escherichia coli.to identify escherichia coli genes potentially regulated by filamentous phage infection, we used oligonucleotide microarrays. genome-wide comparison of phage m13-infected and uninfected e. coli, 2 and 20 min after infection, was performed. the analysis revealed altered transcription levels of 12 e. coli genes in response to phage infection, and the observed regulation of phage genes correlated with the known in vivo pattern of m13 mrna species. ten of the 12 host genes affected could be grouped ...200515782232
screening for pres specific binding ligands with a phage displayed peptides library.to construct a random peptide phage display library and search for peptides that specifically bind to the pres region of hepatitis b virus (hbv).200515996026
the construction of dna molecules of figure-eight structure.using dna molecules to construct a structural scaffold for nanotechnology is largely accepted. in this article, we report on two methods for constructing a figure-eight structure of dna molecules having a relatively high yield that could be used further as a scaffold for nanotechnology applications. in the first method, two plasmids were constructed that, on digestion with a restriction endonuclease producing nicks in the corresponding sites and after heating, produced complementary single-stran ...200516039974
a phage-displayed cyclic peptide that interacts tightly with the immunodominant region of hepatitis b surface antigen.the surface antigen (hbsag) of hepatitis b virus (hbv) is highly conformational and generally evokes protective humoral immune response in human. a disulfide constrained random heptapeptide library displayed on the coat protein iii of filamentous bacteriophage m13 was employed to select specific ligands that interact with hbsag subtype ad. fusion phages carrying the amino acid sequence etgakph and other related sequences were isolated. the binding site of peptide etgakph was located on the immun ...200516087122
efficient construction of a large collection of phage-displayed combinatorial peptide libraries.selections from phage-displayed combinatorial peptide libraries are an effective strategy for identifying peptide ligands to target proteins. existing protocols for constructing phage-displayed libraries utilize either ligation into double-stranded phage dna or kunkel mutagenesis with single-stranded phagemid dna. although the kunkel approach rapidly provides library sizes of up to 10(11), as many as 20% of the phagemids may be non-recombinant. with several modifications to current kunkel protoc ...200516178814
[study on screening mimicking epitope of ochratoxin a from phage display peptide library].to screen phage particles capable of mimicking ochratoxin a and establish immunoassay for ochratoxin a with it.200516229273
antagonists of hsp16.3, a low-molecular-weight mycobacterial chaperone and virulence factor, derived from phage-displayed peptide libraries.the persistence of mycobacterium tuberculosis is a major cause of concern in tuberculosis (tb) therapy. in the persistent mode the pathogen can resist drug therapy, allowing the possibility of reactivation of the disease. several protein factors have been identified that contribute to persistence, one of them being the 16-kda low-molecular-weight mycobacterial heat shock protein hsp16.3, a homologue of the mammalian eye lens protein alpha-crystallin. it is believed that hsp16.3 plays a key role ...200516269776
exploring the local conformational space of a membrane protein by site-directed spin labeling.molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called ghost, of spin label esr spectra was applied to study the structure and dynamics of membrane proteins. the new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. the method is applied to spin-labeled bacteriophage m13 major coat protein, which is used as a model membrane protein. ...200516309264
structural analysis of peptides that interact with newcastle disease virus.a peptide with the sequence ctlttklyc has previously been identified to inhibit the propagation of newcastle disease virus (ndv) in embryonated chicken eggs and tissue culture. ndv has been classified into two main groups: the velogenic group, and mesogenic with lentogenic strains as the other group based on its dissociation constants. in this study the peptide, ctlttklyc, displayed on the piii protein of a filamentous m13 phage was synthesized and mutated in order to identify the amino acid res ...200616377031
rapid preparation of stable isotope labeled peptides that bind to target proteins by a phage library system.we have developed a system for directly isolating foreign peptides displayed on the n-terminus of the major coat protein of bacteriophage m13. the phage particle in this system is formed as a mixture of wild type and modified coat proteins. the n-terminal segment of the modified coat protein was mutated for chemical cleavage, in order to obtain the displayed peptide from the major coat protein. using 13c, 15n- labeled medium, we introduced stable isotopes, 13c and/or 15n, into the coat proteins. ...200616505961
[construction of phage-displayed library by dna shuffling and the screening of potent hirudin variants].to directed promote the antithrombotic activity of hirudin in vitro with dna family shuffling method.200616507250
dna hybridization detection on electrical microarrays using coulostatic pulse technique.we demonstrated a novel application of transient coulostatic pulse technique for the detection of label free dna hybridization on nm-sized gold interdigitated ultramicroelectrode arrays (au-ida) made in silicon technology. the array consists of eight different positions with an au-ida pair at each position arranged on the si-based biochip. immobilization of capture probes onto the au-ida was accomplished by self-assembling of thiol-modified oligonucleotides. target hybridization was indicated by ...200616574397
cloning and structure determination of cdna for cutinase, an enzyme involved in fungal penetration of plants.the primary structure of cutinase, an extracellular fungal enzyme involved in the penetration of plants by pathogenic fungi, has been determined from the nucleotide sequence of cloned cdna. clones containing cdna made from poly(a)(+) rna isolated from fungal cultures induced to synthesize cutinase were screened for their ability to hybridize with the [(32)p]cdna for mrna unique to the induced culture. the 75 cdna clones thus identified were screened for the cutinase genetic code by hybrid-select ...198416593482
anchoring mechanisms of membrane-associated m13 major coat protein.bacteriophage m13 major coat protein is extensively used as a biophysical, biochemical, and molecular biology reference system for studying membrane proteins. the protein has several elements that control its position and orientation in a lipid bilayer. the n-terminus is dominated by the presence of negatively charged amino acid residues (glu2, asp4, and asp5), which will always try to extend into the aqueous phase and therefore act as a hydrophilic anchor. the amphipathic and the hydrophobic tr ...200616620800
mapping protease substrates by using a biotinylated phage substrate library.we describe a bacteriophage m13 substrate library encoding the avitag (bira substrate) and combinatorial heptamer peptides displayed at the n terminus of the mature form of capsid protein iii. phages are biotinylated efficiently (> or = 50%) when grown in e. coli cells coexpressing bira, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. we have used this library to map the specificity of human factor x ...200616628754
fret study of membrane proteins: simulation-based fitting for analysis of membrane protein embedment and association.a new formalism for the simultaneous determination of the membrane embedment and aggregation of membrane proteins is developed. this method is based on steady-state förster (or fluorescence) resonance energy transfer (fret) experiments on site-directed fluorescence labeled proteins in combination with global data analysis utilizing simulation-based fitting. the simulation of fret was validated by a comparison with a known analytical solution for energy transfer in idealized membrane systems. the ...200616632512
in vivo drafting of single-chain antibodies for regulatory duty on the sigma54-promoter pu of the tol plasmid.the identification of single-chain antibodies (scfvs) that interfere in vivo with the building of the complex that activate the prokaryotic, sigma54-dependent promoter pu of the catabolic tol plasmid pww0 is reported. to this end, a phage m13 library of scfvs was raised against the cognate prokaryotic enhancer-binding activator, xylr. the scfv pool was then expressed intracellularly in a reporter pu-lacz strain of escherichia coli designed to permit formation of intramolecular disulphide bonds i ...200616689797
inhibition of bacteriophage m13 replication with esterified milk proteins.esterified milk proteins [methylated (met) or ethylated (et) alpha-lactalbumin (ala), beta-lactoglobulin (blg), and beta-casein (bcn)], unmodified native milk proteins, and native basic proteins (calf thymus histone and hen egg white lysozyme) were tested for their antiviral activity against the bacteriophage m13 and for their influence on its replication (except bcn). all esterified milk proteins showed an antiviral activity against the bacteriophage m13, proportional to the extent of esterific ...200616719499
direct confinement of individual viruses within polyethylene glycol (peg) nanowells.individual m13 viruses were spatially confined within wells fabricated from nanomolding of a peg-based random copolymer. the viruses were selectively adhered to the region pretreated with an antibody against the virus, resulting in individual virus arrays. the polymer surface was found to be highly resistant to the attachment of the virus (approximately 0.02 microm-2), approximately 2 orders of magnitude lower than that on a bare silicon surface. the physical height of the template provided an a ...200616771579
lipid solvation effects contribute to the affinity of gly-xxx-gly motif-mediated helix-helix interactions.interactions between transmembrane helices are mediated by the concave gly-xxx-gly motif surface. whether gly residues per se are sufficient for selection of this motif has not been established. here, we used the in vivo toxcat assay to measure the relative affinities of all 18 combinations of gly, ala, and ser "small-xxx-small" mutations in glycophorin a (gpa) and bacteriophage m13 major coat protein (mcp) homodimers. affinity values were compared with the accessibility to a methylene-sized pro ...200616834324
automated 10-channel capillary chip immunodetector for biological agents detection.the automated 10-channel capillary chip immunodetector (10k-idwg) is a prototype, which has been developed for automatically operated biological agents (ba) point detection. the current technology uses a chemiluminescence capillary immunoassay (eia) technique in combination with integrated microfluidics and allows the highly sensitive and rapid detection and preliminary identification of multiple ba in aqueous solutions in the laboratory. the chemiluminescence capillary eia are performed within ...200716839755
[production and characterization of the single chain antibodies against human alpha2b-interferon].a combinatorial library of single-chain antibodies (scfv) from mice immunized with human alpha2b interferon (hifn-alpha2b) was constructed. for obtaining of phage display antibodies the dna fragments of scfv were cloned into phagemid vector pcantab-5e and rescued from escherichia coli cells by infection with bacteriophage m13. bacterial clones synthesizing specific scfv against hifn-alpha2b were isolated by several rounds of affinity selection of phage library. after isolation and affinity purif ...200516846077
identification and strain differentiation of 'bacteroides fragilis group' species and prevotella bivia by pcr fingerprinting.using single consensus primers of genomic nucleotide sequences, pcr-generated fingerprints were used for identification and differentiation of the bacteroides fragilis group (b. fragilis, b. thetaiotaomicron, b. ovatus, b. distasonis, b. vulgatus) and prevotella bivia (b. bivius) by comparing the dna profiles with those of reference strains from the american type culture collection and german culture collection. when primed by a single primer phage m13 core sequence, intra-species specific diffe ...199516887529
motional restrictions of membrane proteins: a site-directed spin labeling study.site-directed mutagenesis was used to produce 27 single cysteine mutants of bacteriophage m13 major coat protein spanning the whole primary sequence of the protein. single-cysteine mutants were labeled with nitroxide spin labels and incorporated into phospholipid bilayers with increasing acyl chain length. the sdsl is combined with esr and cd spectroscopy. cd spectroscopy provided information about the overall protein conformation in different mismatching lipids. the spin label esr spectra were ...200616905615
enrichment of open reading frames presented on bacteriophage m13 using hyperphage.the enrichment of open reading frames (orfs) from large gene libraries and the presentation of the corresponding polypeptides on filamentous phage m13 (phage display) is frequently used to identify binding partners of unknown orfs. in particular phage display is a valuable tool for the identification of pathogen-related antigens and a first step for the development of new diagnostics and therapeutics. here, we introduce a significant improvement of phage-based orf enrichment by using hyperphage, ...200616989094
observation of the low frequency vibrational modes of bacteriophage m13 in water by raman spectroscopy.recently, a technique which departs radically from conventional approaches has been proposed. this novel technique utilizes biological objects such as viruses as nano-templates for the fabrication of nanostructure elements. for example, rod-shaped viruses such as the m13 phage and tobacco mosaic virus have been successfully used as biological templates for the synthesis of semiconductor and metallic nanowires.200616995944
fret study of membrane proteins: determination of the tilt and orientation of the n-terminal domain of m13 major coat protein.a formalism for membrane protein structure determination was developed. this method is based on steady-state fret data and information about the position of the fluorescence maxima on site-directed fluorescent labeled proteins in combination with global data analysis utilizing simulation-based fitting. the methodology was applied to determine the structural properties of the n-terminal domain of the major coat protein from bacteriophage m13 reconstituted into unilamellar dopc/dopg (4:1 mol/mol) ...200717114224
unit-length, single-stranded circular dnas of both polarity of begomoviruses are generated in escherichia coli harboring phage m13-cloned begomovirus genome with single copy of replication origin.replication of genomic dnas of plant-pathogenic begomoviruses has been demonstrated in prokaryotes, which supported the possibility of analyzing dna replication process of begomoviruses in bacteria. however, previous studies indicated that the replication of begomovirus dnas in prokaryotes requires tandem constructs of viral genomes with at least two copies of the origin of replication (ori). in this study, phage m13 vector harboring the unit-length genome with only a single copy of ori of a mon ...200717204346
the position of the gly-xxx-gly motif in transmembrane segments modulates dimer affinity.although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix-helix interactions between single transmembrane (tm) helices. while the stability of helix-helix partnerships mediated by the gly-xxx-gly (gg4) motif is known to be generally modulated by distal interfacial residues, it has not ...200617215886
probing the low-frequency vibrational modes of viruses with raman scattering--bacteriophage m13 in water.raman spectroscopy is used to study low-wave-number (</=20 cm(-1)) acoustic vibrations of the m13 phage. a well-defined raman line is observed at around 8.5 cm(-1). the experimental results are compared with theoretical calculations based on an elastic continuum model and appropriate raman selection rules derived from a bond polarizability model. the observed raman mode is shown to belong to one of the raman-active axial modes of the m13 phage protein coat. it is expected that the detection and ...200717477724
inactivation of viruses by coherent excitations with a low power visible femtosecond laser.resonant microwave absorption has been proposed in the literature to excite the vibrational states of microorganisms in an attempt to destroy them. but it is extremely difficult to transfer microwave excitation energy to the vibrational energy of microorganisms due to severe absorption of water in this spectral range. we demonstrate for the first time that, by using a visible femtosecond laser, it is effective to inactivate viruses such as bacteriophage m13 through impulsive stimulated raman sca ...200717550590
influence of charge and flexibility on smectic phase formation in filamentous virus suspensions.we present experimental measurements of the cholesteric-smectic phase transition of suspensions of charged semiflexible rods as a function of rod flexibility and surface charge. the rod particles consist of the bacteriophage m13 and closely related mutants, which are structurally identical to m13, but vary either in contour length and therefore ratio of persistence length to contour length, or surface charge. surface charge is altered in two ways; by changing solution ph and by comparing m13 wit ...200717677469
presentation of the functional receptor-binding domain of the bacterial adhesin f17a-g on bacteriophage m13.bovine enterotoxigenic escherichia coli (etec) carrying f17a fimbriae attach to the intestinal epithelium by means of the f17a-g adhesin. since filamentous bacteriophages can be employed for the display of foreign peptides, we tested the applicability of this system to f17a-g. the receptor-binding domain of the f17a-g adhesin was expressed on bacteriophage m13, as an amino-terminal fusion with the phage protein piii. this domain retained its n-acetyl-beta-d: -glucosamine binding activity. the ph ...200817701282
transposon tn7 directs transposition into the genome of filamentous bacteriophage m13 using the element-encoded tnse protein.the bacterial transposon tn7 has a pathway of transposition that preferentially targets conjugal plasmids. we propose that this same transposition pathway recognizes a structure or complex found during filamentous bacteriophage replication, likely by targeting negative-strand synthesis. the ability to insert into both plasmid and bacteriophage dnas that are capable of cell-to-cell transfer would help explain the wide distribution of tn7 relatives.200717921297
covalent virus layer for mass-based biosensing.m13 virus particles were covalently attached to a planar gold-coated quartz crystal microbalance (qcm) through reaction with a self-assembled monolayer of n-hydroxysuccinimide thioctic ester, followed by incorporation of the blocking agent bovine serum albumin. this immobilization chemistry produced a phage multilayer having a coverage equivalent to approximately 6.5 close-packed monolayers of the virus. the properties of this "covalent virus surface" or cvs for the mass-based detection of a 148 ...200818198846
mapping protein-protein interactions with phage-displayed combinatorial peptide libraries.this unit describes the process and analysis of affinity selecting bacteriophage m13 from libraries displaying combinatorial peptides fused to either a minor or major capsid protein. direct affinity selection uses target protein bound to a microtiter plate followed by purification of selected phage by elisa. alternatively, there is a bead-based affinity selection method. these methods allow one to readily isolate peptide ligands that bind to a protein target of interest and use the consensus seq ...200318228422
immunoassays in nanoliter volume reactors using fluorescent particle diffusometry.a model analyte, the m13 virus, was detected through the change in the brownian motion of a population of microparticles. epi-fluorescence microscopy was used to simultaneously track antibody-coated and bare microparticles to unambiguously measure the diffusion coefficient and demonstrate multiplexed detection. the sensitivity of the diffusometry assay was high enough that individual virus-to-particle binding ratios could be detected. analysis of the experimental errors indicated that the primar ...200818294011
opto-fluidic micro-ring resonator for sensitive label-free viral detection.we have demonstrated sensitive label-free virus detection using the opto-fluidic ring resonator (ofrr) sensor. the ofrr is a novel sensing platform that integrates the microfluidics and photonic sensing technology with a low detection limit and small volume. in our experiment, filamentous bacteriophage m13 was used as a safe model system. virus samples were flowed through the ofrr whose surface was coated with m13-specific antibodies. we studied the sensor performance by monitoring in real-time ...200818299750
real-time kinetics of restriction-modification gene expression after entry into a new host cell.most type ii restriction-modification (r-m) systems produce separate restriction endonuclease (rease) and methyltransferase (mtase) proteins. after r-m system genes enter a new cell, protective mtase must appear before rease to avoid host chromosome cleavage. the basis for this apparent temporal regulation is not well understood. pvuii and some other r-m systems appear to achieve this delay by cotranscribing the rease gene with the gene for an autogenous transcription activator/repressor (the 'c ...200818334533
single-molecule dna sequencing of a viral genome.the full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. a reference sequence enables the use of short read length. we report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual dna molecules simultaneously. a dna polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual dn ...200818388294
recombinant adeno-associated viral vectors are deficient in provoking a dna damage response.adeno-associated virus type 2 (aav2) provokes a dna damage response that mimics a stalled replication fork. we have previously shown that this response is dependent on ataxia telangiectasia-mutated and rad3-related kinase and involves recruitment of dna repair proteins into foci associated with aav2 dna. here, we investigated whether recombinant aav2 (raav2) vectors are able to produce a similar response. surprisingly, the results show that both single-stranded and double-stranded green fluoresc ...200818463154
direct electrical transduction of antibody binding to a covalent virus layer using electrochemical impedance.electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kda antibody to a "covalent virus layer" (cvl) immobilized on a gold electrode. the cvl consisted of m13 phage particles covalently anchored to a 3 mm diameter gold disk electrode. the ability of the cvl to distinguish this antibody ("p-ab") from a second, nonbinding antibody ("n-ab") was evaluated as a function of the frequency and phase of the measured current relative to the applied voltage. the binding of p-ab to ...200818590279
subgenomic rnas with nucleotide sequences derived from rnas 1 and 2 of cucumber mosaic virus can act as messenger rnas in vitro.encapsidated rnas of cucumber mosaic virus (cmv) were analyzed by hybridization to specific probes after gel electrophoresis. [32p]-complementary dna (cdna) probes were prepared by transcription of genomic rna 1 and rna 2 nucleotide sequences that had been cloned in a bacteriophage m13 vector. probes that correspond to unique sequences near the 3' ends of rna 1 and rna 2 revealed over 20 smaller rnas. the subgenomic rnas derived from each genomic rna were analyzed more definitively by hybrid sel ...198518639845
on the origin of the helper component of tobacco vein mottling virus: translational initiation near the 5' terminus of the viral rna and termination by uag codons.the nature of the polypeptide products encoded by the 5'-terminal region of the rna of the potyvirus, tobacco vein mottling virus (tvmv), was investigated. single-stranded dna probes complementary to either nucleotides 1100-2100 or 2100-2820 from the 5' terminus of the rna were prepared by subcloning recombinant plasmids in bacteriophage m13. these were hybridized to tvmv rna, the dna:rna hybrids translated in a reticulocyte lysate cell-free translation system (hybrid-arrested translation), and ...198518639848
replication of tobacco mosaic virus. viii. characterization of a third subgenomic tmv rna.in an earlier study we concluded that tobacco mosaic virus (tmv) infections engender a third subgenomic rna in infected tissue (p. palukaitis, f. garcia-arenal, m. a. sulzinski, and m. zaitlin (1983), virology 131, 533-545). this rna of approximate mw of 1.1 x 10(6), termed i1-rna, was shown to be polyribosome-associated and thus was presumed to serve as a messenger rna in vivo. upon in vitro translation of i1-rna in a rabbit reticulocyte lysate system, a major product of mw approximately 50k wa ...198518640547
lysogenisation of spiroplasma citri by a type 3 spiroplasmavirus.a short-tailed polyhedral spiroplasmavirus, ai, with a plaque morphology typical of temperate phages and a linear double-stranded dna genome which can circularise due to the presence of cohesive ends, was able to lysogenise spiroplasma citri. lysogenic sporoplasmas spontaneously released ai virus at a low level, and were immune to superinfection by the released virus, but not to infection by two serologically related viruses. these properties were retained following repeated cultivation in virus ...198518640554
single-molecule dna sequencing technologies for future genomics research.during the current genomics revolution, the genomes of a large number of living organisms have been fully sequenced. however, with the advent of new sequencing technologies, genomics research is now at the threshold of a second revolution. several second-generation sequencing platforms became available in 2007, but a further revolution in dna resequencing technologies is being witnessed in 2008, with the launch of the first single-molecule dna sequencer (helicos biosciences), which has already b ...200818722683
regional pattern of the molecular types of cryptococcus neoformans and cryptococcus gattii in brazil.the molecular types of 443 brazilian isolates of cryptococcus neoformans and cryptococcus gattii were analyzed to determine their geographic distribution within brazil and their underlying host conditions. the following data, imported from previous epidemiological studies as well as two culture collections, were analyzed for: place of isolation, source (clinical or environmental), host risk factors, species, serotype, mating type, and molecular type. molecular typing by pcr-fingerprinting using ...200818797758
oriented cell growth on self-assembled bacteriophage m13 thin films.fibrillar m13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with rgd peptides, guide cell alignment and orient the cell outgrowth along defined directions.200818956063
malassezia furfur fingerprints as possible markers for human phylogeography.malassezia furfur was the first species described within the cosmopolitan yeast genus malassezia, which now comprises 13 species. reported isolation rates of these species from healthy and diseased human skin show geographic variations. pcr-fingerprinting with the wild-type phage m13 primer (5'-gagggtggcggttct-3') was applied to investigate phylogeographic associations of m. furfur strains isolated from scandinavians residing permanently in greece, in comparison to clinical isolates from greek, ...200919020555
controllable g5p-protein-directed aggregation of ssdna-gold nanoparticles.we assembled single-stranded dna (ssdna) conjugated nanoparticles using the phage m13 gene 5 protein (g5p) as the molecular glue to bind two antiparallel noncomplementary ssdna strands. the entire process was controlled tightly by the concentration of the g5p protein and the presence of double-stranded dna. the g5p-ssdna aggregate was disintegrated by hybridization with complementary ssdna (c-ssdna) that triggers the dissociation of the complex. polyhistidine-tagged g5p was bound to nickel nitri ...200919072316
primary endemic cryptococcosis gattii by molecular type vgii in the state of pará, brazil.in order to study the infectious agents causing human disseminated cryptococcosis in the state of pará, north brazil, 56 isolates of cryptococcusspp. (54 isolated from cerebral spinal fluid and two from blood cultures) from 43 cases diagnosed between 2003-2007 were analysed. the species were determined through morphological and physiological tests and genotypes were determined by ura5-rflp and pcr-fingerprinting (wild-type phage m13). the following species and genotypes were identified: cryptoco ...200819148422
synthesis of a virus electrode for measurement of prostate specific membrane antigen.though relatively unexploited in biosensor applications, phage display technology can provide versatile recognition scaffolds for detection of cancer markers and other analytes. this chapter details protocols for covalent attachment of viruses directly to electrodes for reagent-free detection of analytes in real-time. customization of binding specificity leverages selections with large phage display libraries prior to covalent attachment of the selected virus to the electrode. the methods descri ...200919159102
peptide-mediated reduction of silver ions on engineered biological scaffolds.herein we report the spontaneous reduction of silver ions into nanostructures by yeast surface-displayed glutamic acid (e(6)) and aspartic acid (d(6)) peptides. light spectroscopy and electron microscopy reveal that silver ions are photoreduced in the presence of the polycarboxylic acid-containing peptides and ambient light, with an increase in reduction capability of e(6) expressing yeast over d(6) yeast. the importance of tethering peptides to a biological scaffold was inferred by observing th ...200819206318
membrane protein frustration: protein incorporation into hydrophobic mismatched binary lipid mixtures.bacteriophage m13 major coat protein was reconstituted in different nonmatching binary lipid mixtures composed of 14:1pc and 22:1pc lipid bilayers. challenged by this lose-lose situation of hydrophobic mismatch, the protein-lipid interactions are monitored by cd and site-directed spin-label electron spin resonance spectroscopy of spin-labeled site-specific single cysteine mutants located in the c-terminal protein domain embedded in the hydrophobic core of the membrane (i39c) and at the lipid-wat ...200919217858
from 'i' to 'l' and back again: the odyssey of membrane-bound m13 protein.the major coat protein of the filamentous bacteriophage m13 is a surprising protein because it exists both as a membrane protein and as part of the m13 phage coat during its life cycle. early studies showed that the phage-bound structure of the coat protein was a continuous i-shaped alpha-helix. however, throughout the years various structural models, both i-shaped and l-shaped, have been proposed for the membrane-bound state of the coat protein. recently, site-directed labelling approaches have ...200919362002
surface rigidity change of escherichia coli after filamentous bacteriophage infection.in this study, the feasibility using atomic force microscopy (afm) to study the interaction between bacteriophages (phages) and bacteria in situ was demonstrated here. filamentous phage m13 specifically infects the male escherichia coli, which expresses f-pili. after infection, e. coli become fragile and grows at a slower rate. afm provides a powerful tool for investigating these changes in a near-physiological environment. using high-resolution afm in phosphate-buffered saline, the damage to th ...200919366225
insertion of bacteriophage m13 coat protein into membranes. 198219431483
transmembrane helix association affinity can be modulated by flanking and noninterfacial residues.the gxxxg sequence motif mediates the association of transmembrane (tm) helices by providing a site of close contact between them. however, it is not sufficient for strong association. for example, both bacteriophage m13 major coat protein (mcp) and human erythrocyte protein glycophorin a (gpa) contain a gxxxg motif in their tm domains and form a homodimer, but the association affinity of mcp, measured by the toxcat in vivo assay, is dramatically weaker than that of gpa. even when all interfacia ...200919486666
viruses: incredible nanomachines. new advances with filamentous phages.during recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. in particular filamentous viruses, for example bacteriophage m13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. this could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproductio ...201019680644
asymmetric dipping of bacteriophage m13 coat protein with increasing lipid bilayer thickness.knowledge about the vertical movement of a protein with respect to the lipid bilayer plane is important to understand protein functionality in the biological membrane. in this work, the vertical displacement of bacteriophage m13 major coat protein in a lipid bilayer is used as a model system to study the molecular details of its anchoring mechanism in a homologue series of lipids with the same polar head group but different hydrophobic chain length. the major coat proteins were reconstituted int ...200919715663
sources of bacillus cereus contamination in a pasteurized zucchini purée processing line, differentiated by two pcr-based methods.in previous work, raw materials used for processing pasteurized zucchini purée (zucchini, milk proteins and starch) and cultivation soil of zucchinis were found to be potential sources of stored product contamination with bacillus cereus. 134 b. cereus strains originating from these sources and from the stored product were typed using coliphage m13 sequence-based polymerase chain reaction (m13-pcr) and dna amplification fingerprinting. combined patterns from the two methods were compared using d ...200319719681
replication of the single-stranded dna of the male-specific bacteriophage m13. isolation of intracellular forms of phage-specific dna.the intracellular dna has been isolated from escherichia coli f+ cells infected with the small male-specific bacteriophage m13 and fractionated on a methylated albumin-kieselguhr column. two infectious forms of phage-specific dna were isolated and identified as a double-stranded replicative form and single-stranded dna on the basis of their elution from the methylated albumin-kieselguhr column, infectivity to spheroplasts before and after heating, sedimentation at low ionic strength and buoyant ...196619768864
replication of the single-stranded dna of the male-specific bacteriophage m13: circular forms of the replicative dna.equilibrium centrifugation in caesium chloride, band sedimentation in alkaline solutions and electron microscopy have been used to study purified preparations of the m13 replicative dna. the buoyant density of the m13 replicative dna in a cscl density gradient is 1.701, compared to a density of 1-710 for escherichia coli dna. when the replicative dna is sedimented in alkaline solutions of cscl (p = 1.35), two components are observed with uncorrected s-values of 48.6 +/- 0.2 and 15.2 +/- 0.5. tre ...196619768865
molecular characterisation of sporothrix schenckii isolates from humans and cats involved in the sporotrichosis epidemic in rio de janeiro, brazil.an epidemic of sporotrichosis, a subcutaneous mycosis caused by the fungus sporothrix schenckii, is ongoing in rio de janeiro, brazil, in which cases of human infection are related to exposure to cats. in an attempt to demonstrate the zoonotic character of this epidemic using molecular methodology, we characterised by dna-based typing methods 19 human and 25 animal s. schenckii isolates from the epidemic, as well as two control strains. to analyse the isolates, the random amplified polymorphic d ...200919820840
oligovalent fab display on m13 phage improved by directed evolution.efficient display of antibody on filamentous phage m13 coat is crucial for successful biopanning selections. we applied a directed evolution strategy to improve the oligovalent display of a poorly behaving fab fragment fused to phage gene-3 for minor coat protein (g3p). the fab displaying clones were enriched from a randomly mutated fab gene library with polyclonal anti-mouse igg antibodies. contribution of each mutation to the improved phenotype of one selected mutant was studied. it was found ...201020012710
biologically templated photocatalytic nanostructures for sustained light-driven water oxidation.over several billion years, cyanobacteria and plants have evolved highly organized photosynthetic systems to shuttle both electronic and chemical species for the efficient oxidation of water. in a similar manner to reaction centres in natural photosystems, molecular and metal oxide catalysts have been used to photochemically oxidize water. however, the various approaches involving the molecular design of ligands, surface modification and immobilization still have limitations in terms of catalyti ...201020383127
purification of bacteriophage m13 by anion exchange chromatography.m13 is a non-lytic filamentous bacteriophage (phage). it has been used widely in phage display technology for displaying foreign peptides, and also for studying macromolecule structures and interactions. traditionally, this phage has been purified by cesium chloride (cscl) density gradient ultracentrifugation which is highly laborious and time consuming. in the present study, a simple, rapid and efficient method for the purification of m13 based on anion exchange chromatography was established. ...201020538529
[selecting the phage displaying tetrodotoxin mimic epitope by phage random peptide library].to screen the positive phage displaying the mimic epitope of tetrodotoxin (ttx) by using phage random peptide display library technology and to establish immunoassay for the detection of tetrodotoxin.201020568457
phage display: concept, innovations, applications and future.phage display is the technology that allows expression of exogenous (poly)peptides on the surface of phage particles. the concept is simple in principle: a library of phage particles expressing a wide diversity of peptides is used to select those that bind the desired target. the filamentous phage m13 is the most commonly used vector to create random peptide display libraries. several methods including recombinant techniques have been developed to increase the diversity of the library. on the ot ...201020659548
binding of the dimeric deinococcus radiodurans single-stranded dna binding protein to single-stranded dna.deinococcus radiodurans single-stranded (ss) dna binding protein (drssb) originates from a radiation-resistant bacterium and participates in dna recombination, replication, and repair. although it functions as a homodimer, it contains four dna binding domains (ob-folds) and thus is structurally similar to the escherichia coli ssb (ecossb) homotetramer. we examined the equilibrium binding of drssb to ssdna for comparison with that of ecossb. we find that the occluded site size of drssb on poly(dt ...201020795631
enhancing the lateral-flow immunoassay for viral detection using an aqueous two-phase micellar system.availability of a rapid, accurate, and reliable point-of-care (poc) device for detection of infectious agents and pandemic pathogens, such as swine-origin influenza a (h1n1) virus, is crucial for effective patient management and outbreak prevention. due to its ease of use, rapid processing, and minimal power and laboratory equipment requirements, the lateral-flow (immuno)assay (lfa) has gained much attention in recent years as a possible solution. however, since the sensitivity of lfa has been s ...201020865404
m13-microsatellite pcr and rdna sequence markers for identification of trichoderma (hypocreaceae) species in saudi arabian soil.seven fungal isolates were identified as pan-global hypocrea/trichoderma species, from section trichoderma, on the basis of their morphology. these species were h. lixii/t. harzianum and h. orientalis/t. longibrachiatum. pcr-based markers with primer m13 (core sequence of phage m13) and internal-transcribed spacer sequences of ribosomal dna were used to confirm the identity of the two trichoderma species. sequence identification was performed using the trichokey version 2.0 barcode program and t ...201020957605
phenotypic and genotypic characteristics of mycobacterium isolates from fighting fish betta spp. in malaysia.mycobacteriosis due to mycobacteria is one of the most common bacterial diseases in ornamental fish. we describe here the phenotypic and genotypic characteristics of mycobacterium isolates from fighting fish betta spp. using atcc mycobacterium marinum, mycobacterium fortuitum and mycobacterium chelonae as references. a total of four isolates (m1, m2, m3, m4) were obtained from four out of 106 fish samples using selective agar, and identified to mycobacterium genus using acid-fast staining and 16 ...201020971487
novel peptide inhibiting both tem-1 β-lactamase and penicillin-binding proteins.9g4h9, a catalytic antibody displaying β-lactamase-like activity, has been developed by the anti-idiotypic approach using β-lactamase as the first antigen. thus 9g4h9 represents the 'internal image' of β-lactamase. we selected a cyclic peptide anchored to a bacteriophage m13 library using 9g4h9 as the target. pep90 is a cyclic heptapeptide enclosed between two cysteine residues. we showed that pep90 could inhibit both tem-1 β-lactamase (k(i)  = 333 μm) and several penicillin-binding proteins (ic ...201021044268
selective cloning, characterization, and production of the culicoides nubeculosus salivary gland allergen repertoire associated with equine insect bite hypersensitivity.salivary gland proteins of culicoides spp. have been suggested to be among the main allergens inducing ige-mediated insect bite hypersensitivity (ibh), an allergic dermatitis of the horse. the aim of our study was to identify, produce and characterize ige-binding salivary gland proteins of culicoides nubeculosus relevant for ibh by phage surface display technology. a cdna library constructed with mrna derived from c. nubeculosus salivary glands was displayed on the surface of filamentous phage m ...201021071100
characterisation of methacrylate monoliths for bacteriophage purification.binding of three different bacteriophages (phages), namely t7, lambda and m13 on methacrylate monoliths was investigated. phage m13 exhibited the highest dynamic binding capacity of 4.5×10(13) pfu/ml while t7 and lambda showed capacity of 1×10(13) pfu/ml, all corresponding to values of around 1mg/ml. interestingly, capacity for lambda phage was increased 5-fold by increasing nacl concentration in a loaded sample from 0 to 0.2m while there was a constant capacity decrease for t7 and m13 phages. u ...201021238969
study of robustness of filamentous bacteriophages for industrial applications.the development of a whole new class of industrial agents, such as biologically based nanomaterials and viral vectors, has raised many challenges for their large-scale manufacture, principally due to the lack of essential physical data and bioprocessing knowledge. a new example is the promise of filamentous bacteriophages and their derivatives. as a result, there is now an increasing need for the establishment of strong biochemical engineering foundations to serve as a guide for future manufactu ...201121328313
screening of specific binding peptide targeting blood vessel of human esophageal cancer in vivo in mice.cancer of the esophagus and gastroesophageal junction remains a virulent malignancy with poor prognosis. rapid progresses were made in chemotherapeutic agents and the development of molecular markers allowed better identification of candidates for targeted therapy. this study aimed to identify the candidate peptides used for anti-angiogenic therapy of esophageal cancer by in vivo screening c7c peptide library for peptides binding specifically to blood vessels of human esophageal cancer.201121362285
synthetic inter-species cooperation of host and virus for targeted genetic evolution.cooperative inter-species interaction is another way of evolution in nature. such cooperation leading to mutual benefits provides a new view on the interaction of biological systems, and engineering such inter-species interaction offers an opportunity for diverse potential applications in biotechnology. here we show a synthetic system with artificially created inter-species cooperation of host and virus. a genetically engineered host (escherichia coli) provides nutrients and energies necessary f ...201121396406
genotypic characterization of cutaneous leishmaniasis at al baha and al qasim provinces (saudi arabia).fifty samples of skin ulcers were collected from the western region of saudi arabia kingdom (al baha and al qasim) to study genotypic characterization of cutaneous leishmaniasis in this area. thirty-six samples were recorded as leishmania isolates. the same isolates were subsequently tested with fingerprinting with single arbitrary primers. the primers used derived from the core sequence of the phage m13, and the repeat sequences (gtg)5 and (gaca)4. the 36 isolates were all identified as leishma ...201121417928
identification and safety evaluation of bacillus species occurring in high numbers during spontaneous fermentations to produce gergoush, a traditional sudanese bread snack.gergoush is a naturally fermented sudanese bread snack produced in three fermentation steps (primary starter, adapted starter and final dough), followed by three baking steps for a half to one hour at above 200 °c. this study examines the microbiota of two sets of fermentations performed at a traditional production site in khartoum, sudan in 2006 and 2009, respectively. in 2006 four different milk/legume based primary starters (faba bean, chick pea, lentil and white bean) were sampled in order t ...201121429611
[screening of polypeptides binding to porcine reproductive and respiratory syndrome virus by phage display library].to find specific polypeptides that bind porcine reproductive and respiratory syndrome virus (prrsv) with high affinity and inhibit replication of prrsv, we screened ligands on intact prrsv virion by phage display library.201121465799
virus-templated self-assembled single-walled carbon nanotubes for highly efficient electron collection in photovoltaic devices.the performance of photovoltaic devices could be improved by using rationally designed nanocomposites with high electron mobility to efficiently collect photo-generated electrons. single-walled carbon nanotubes exhibit very high electron mobility, but the incorporation of such nanotubes into nanocomposites to create efficient photovoltaic devices is challenging. here, we report the synthesis of single-walled carbon nanotube-tio(2) nanocrystal core-shell nanocomposites using a genetically enginee ...201121516089
anti-heparan sulfate peptides that block herpes simplex virus infection in vivo.heparan sulfate (hs) and its highly modified form, 3-o sulfated heparan sulfate (3-os hs) contribute strongly to herpes simplex virus type-1 (hsv-1) infection in vitro. here we report results from a random m13-phage display library screening to isolate 12-mer peptides that bind specifically to hs, 3-os hs, and block hsv-1 entry. the screening identified representative candidates from two-different groups of anti-hs peptides with high positive charge densities. group 1 represented by g1 peptide ( ...201121596749
variable epitope libraries: new vaccine immunogens capable of inducing broad human immunodeficiency virus type 1-neutralizing antibody response.the extreme antigenic variability of human immunodeficiency virus (hiv) leads to immune escape of the virus, representing a major challenge in the design of effective vaccine. we have developed a novel concept for immunogen construction based on introduction of massive mutations within the epitopes targeting antigenically variable pathogens and diseases. previously, we showed that these immunogens carrying large combinatorial libraries of mutated epitope variants, termed as variable epitope libr ...201121600948
inhibition of bacterial conjugation by phage m13 and its protein g3p: quantitative analysis and model.conjugation is the main mode of horizontal gene transfer that spreads antibiotic resistance among bacteria. strategies for inhibiting conjugation may be useful for preserving the effectiveness of antibiotics and preventing the emergence of bacterial strains with multiple resistances. filamentous bacteriophages were first observed to inhibit conjugation several decades ago. here we investigate the mechanism of inhibition and find that the primary effect on conjugation is occlusion of the conjugat ...201121637841
visualizing cell extracellular matrix (ecm) deposited by cells cultured on aligned bacteriophage m13 thin films.topographical features ranging from micro- to nanometers can affect cell orientation and migratory pathways, which are important factors in tissue engineering and tumor migration. in our previous study, a convective assembly of bacteriophage m13 resulted in thin films which could be used to control the alignment of cells. however, several questions regarding its underlying reasons to dictate cell alignment remained unanswered. here, we further study the nanometer topographical features generated ...201121678980
virus-mediated fcc iron nanoparticle induced synthesis of uranium dioxide nanocrystals.a reducing system involving m13 virus-mediated fcc fe nanoparticles was employed to achieve uranium reduction and synthesize uranium dioxide nanocrystals. here we show that metastable face-centered cubic (fcc) fe nanoparticles were fabricated around the surface of the m13 virus during the specific adsorption of the virus towards fe ions under a reduced environment. the fcc phase of these fe nanoparticles was confirmed by careful tem characterization. moreover, this virus-mediated fcc fe nanopart ...200821730559
[preparation and characterization of the recombinant protein containing immunomimetic peptide of benzo[a]pyrene].two recombinant plasmids were constructed. the first plasmid contained the hybrid gene composed of immunomimetic peptide of benzo[a]pyrene, of the protein piii of bacteriophage m13 and of cellulose binding domain encoding sequences. the second plasmid contained the hybrid gene composed of the signal peptide of the protein piii of bacteriophage m13, of immunomimetic peptide of benzo[a]pyrene, of the protein pill of bacteriophage m13 and of cellulose binding domain sequences. the obtained recombin ...201121789801
RNA-binding domain in the nucleocapsid protein of gill-associated nidovirus of penaeid shrimp.Gill-associated virus (GAV) infects Penaeus monodon shrimp and is the type species okavirus in the Roniviridae, the only invertebrate nidoviruses known currently. Electrophoretic mobility shift assays (EMSAs) using His(6)-tagged full-length and truncated proteins were employed to examine the nucleic acid binding properties of the GAV nucleocapsid (N) protein in vitro. The EMSAs showed full-length N protein to bind to all synthetic single-stranded (ss)RNAs tested independent of their sequence. Th ...201121857914
phage displayed hbv core antigen with immunogenic activity.hepatitis b is a major public health problem worldwide, which may lead to chronic liver diseases such as cirrhosis and hepatocellular carcinoma. the hepatitis b core antigen (hbcag) is one of the major viral proteins, which forms the inner core of hepatitis b virus (hbv) particles. in this study, filamentous bacteriophage m13 was genetically modified to display the polypeptides of hbcag in order to develop an alternative carrier system. hbcag gene was inserted into the minor coat protein (piii) ...201121915589
engineered phage-based therapeutic materials inhibit chlamydia trachomatis intracellular infection.developing materials that are effective against sexually transmitted pathogens such as chlamydia trachomatis (ct) and hiv-1 is challenging both in terms of material selection and improving bio-membrane and cellular permeability at desired mucosal sites. here, we engineered the prokaryotic bacterial virus (m13 phage) carrying two functional peptides, integrin binding peptide (rgd) and a segment of the polymorphic membrane protein d (pmpd) from ct, as a phage-based material that can ameliorate ct ...201222494890
virus-poly(3,4-ethylenedioxythiophene) biocomposite films.virus-poly(3,4-ethylenedioxythiophene) (virus-pedot) biocomposite films are prepared by electropolymerizing 3,4-ethylenedioxythiophene (edot) in aqueous electrolytes containing 12 mm liclo(4) and the bacteriophage m13. the concentration of virus in these solutions, [virus](soln), is varied from 3 to 15 nm. a quartz crystal microbalance is used to directly measure the total mass of the biocomposite film during its electrodeposition. in combination with a measurement of the electrodeposition charg ...201222856875
Displaying items 701 - 800 of 832