Publications

generating thermal stable variants of protein domains through phage display.	often in protein design research, one desires to generate thermally stable variants of a protein or domain. one route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. a library of protein domain variants can be generated by mutagenic pcr, expressed on the surface of bacteriophage m13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during ...	2012	23276752
virus activated artificial ecm induces the osteoblastic differentiation of mesenchymal stem cells without osteogenic supplements.	biochemical and topographical features of an artificial extracellular matrix (aecm) can direct stem cell fate. however, it is difficult to vary only the biochemical cues without changing nanotopography to study their unique role. we took advantage of two unique features of m13 phage, a non-toxic nanofiber-like virus, to generate a virus-activated aecm with constant ordered ridge/groove nanotopography but displaying different fibronectin-derived peptides (rgd, its synergy site phsrn, and a combin ...	2013	23393624
virus-based photo-responsive nanowires formed by linking site-directed mutagenesis and chemical reaction.	owing to the genetic flexibility and error-free bulk production, bio-nanostructures such as filamentous phage showed great potential in materials synthesis, however, their photo-responsive behaviour is neither explored nor unveiled. here we show m13 phage genetically engineered with tyrosine residues precisely fused to the major coat protein is converted into a photo-responsive organic nanowire by a site-specific chemical reaction with an aromatic amine to form an azo dye structure on the surfac ...	2013	23673356
a simple and rapid method to isolate purer m13 phage by isoelectric precipitation.	m13 virus (phage) has been extensively used in phage display technology and nanomaterial templating. our research aimed to use m13 phage to template sulfur nanoparticles for making lithium ion batteries. traditional methods for harvesting m13 phage from escherichia coli employ polyethylene glycol (peg)-based precipitation, and the yield is usually measured by plaque counting. with this method, peg residue is present in the m13 phage pellet and is difficult to eliminate. to resolve this issue, a ...	2013	23807666
facile method for large scale alignment of one dimensional nanoparticles and control over myoblast orientation and differentiation.	a facile and robust method to align one-dimensional (1d) nanoparticles (nps) in large scale has been developed. using flow assembly, representative rod-like nanoparticles, including tobacco mosaic virus (tmv), gold nanorods, and bacteriophage m13, have been aligned inside glass tubes by controlling flow rate and substrate surface properties. the properties of 1d nps, such as stiffness and aspect ratio, play a critical role in the alignment. furthermore, these hierarchically organized structures ...	2013	24004197
self-assembly of rodlike virus to superlattices.	rodlike tobacco mosaic virus (tmv) has been found to assemble into superlattices in aqueous solution using the polymer methylcellulose to induce depletion and free volume entropy-based attractive forces. both transmission electron microscopy and small-angle x-ray scattering show that the superlattices form in both semidilute and concentrated regimes of polymer, where the free volume entropy and the depletion interaction are the dominant driving force, respectively. the superlattices are nacl and ...	2013	24044529
fabrication of a silica nanocable using hydroxyl-group core-engineered filamentous virus.	biological materials with surface-active proteins can be genetically modified to bind target materials. in particular, filamentous-shaped m13 bacteriophages (m13 phage) are attractive scaffolds for functional nanostructures due to their highly ordered protein-coat surface. this paper demonstrates a simple method for fabricating silica nanocables along a modified m13 phage. the m13 phage was genetically engineered to display the amino acid serine on the surface to provide hydroxyl groups for a so ...	2013	24205629
an analysis of tobacco mosaic virus replicative structures synthesized in vitro.	the rna structures synthesized in vitro by a crude enzyme complex from tobacco mosaic virus (tmv)-infected leaves have been analyzed; the major viral-specific products were similar to tmv-replicative form (rf) and-replicative intermediate (ri) in electrophoretic behavior and ribonuclease sensitivity. synthesis of these rf-like and ri-like structures neither required nor responded to added viral rna, but did require all four ribonucleotide triphosphates. enriched radiolabeled rf-like and ri-like ...	1986	24307422
biomimetic virus-based colourimetric sensors.	many materials in nature change colours in response to stimuli, making them attractive for use as sensor platform. however, both natural materials and their synthetic analogues lack selectivity towards specific chemicals, and introducing such selectivity remains a challenge. here we report the self-assembly of genetically engineered viruses (m13 phage) into target-specific, colourimetric biosensors. the sensors are composed of phage-bundle nanostructures and exhibit viewing-angle independent col ...	2014	24448217
no effect of femtosecond laser pulses on m13, e. coli, dna, or protein.	data showing what appears to be nonthermal inactivation of m13 bacteriophage (m13), tobacco mosaic virus, escherichia coli (e. coli), and jurkatt t-cells following exposure to 80-fs pulses of laser radiation have been published. interest in the mechanism led to attempts to reproduce the results for m13 and e. coli. bacteriophage plaque-forming and bacteria colony-forming assays showed no inactivation of the microorganisms; therefore, model systems were used to see what, if any, damage might be o ...	2014	24474502
identification of peptides that bind hepatitis c virus envelope protein e2 and inhibit viral cellular entry from a phage-display peptide library.	hepatitis c virus (hcv) envelope protein e2 is required for the entry of hcv into cells. viral envelope proteins interact with cell receptors in a multistep process, which may be a promising target for the development of novel antiviral agents. in this study, a heptapeptide m13 phage-display library was screened for peptides that bind specifically to prokaryotically expressed, purified truncated hcv envelope protein e2. elisa assay was used to quantify the binding of the peptides to hcv e2 prote ...	2014	24573486
virus-templated au and au/pt core/shell nanowires and their electrocatalytic activitives for fuel cell applications.	a facile synthetic route was developed to make au nanowires (nws) from surfactant-mediated bio-mineralization of a genetically engineered m13 phage with specific au binding peptides. from the selective interaction between au binding m13 phage and au ions in aqueous solution, au nws with uniform diameter were synthesized at room temperature with yields greater than 98 % without the need for size selection. the diameters of au nws were controlled from 10 nm to 50 nm. the au nws were found to be ac ...	2012	24910712
using an aqueous two-phase polymer-salt system to rapidly concentrate viruses for improving the detection limit of the lateral-flow immunoassay.	the development of point-of-need (pon) diagnostics for viruses has the potential to prevent pandemics and protects against biological warfare threats. here we discuss the approach of using aqueous two-phase systems (atpss) to concentrate biomolecules prior to the lateral-flow immunoassay (lfa) for improved viral detection. in this paper, we developed a rapid pon detection assay as an extension to our previous proof-of-concept studies which used a micellar atps. we present our investigation of a ...	2014	24942535
dying for good: virus-bacterium biofilm co-evolution enhances environmental fitness.	commonly used in biotechnology applications, filamentous m13 phage are non-lytic viruses that infect e. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for engineering community systems. using the e. coli strain tg1, we have investigated how a selective pressure involving elevated levels of toxic chromate, mimicking that found in some superfund sites, alters population dynamics following infection with eit ...	2012	25114551
single virus detection by means of atomic force microscopy in combination with advanced image analysis.	in the present contribution virions of five different virus species, namely varicella-zoster virus, porcine teschovirus, tobacco mosaic virus, coliphage m13 and enterobacteria phage psp3, are investigated using atomic force microscopy (afm). from the resulting height images quantitative features like maximal height, area and volume of the viruses could be extracted and compared to reference values. subsequently, these features were accompanied by image moments, which quantify the morphology of t ...	2014	25196422
development and evaluation of single domain antibodies for vaccinia and the l1 antigen.	there is ongoing interest to develop high affinity, thermal stable recognition elements to replace conventional antibodies in biothreat detection assays. as part of this effort, single domain antibodies that target vaccinia virus were developed. two llamas were immunized with killed viral particles followed by boosts with the recombinant membrane protein, l1, to stimulate the immune response for envelope and membrane proteins of the virus. the variable domains of the induced heavy chain antibodi ...	2014	25211488
accelerated detection of viral particles by combining ac electric field effects and micro-raman spectroscopy.	a detection method that combines electric field-assisted virus capture on antibody-decorated surfaces with the "fingerprinting" capabilities of micro-raman spectroscopy is demonstrated for the case of m13 virus in water. the proof-of-principle surface mapping of model bioparticles (protein coated polystyrene spheres) captured by an ac electric field between planar microelectrodes is presented with a methodology for analyzing the resulting spectra by comparing relative peak intensities. the same ...	2015	25580902
detection of viruses by counting single fluorescent genetically biotinylated reporter immunophage using a lateral flow assay.	we demonstrated a lateral flow immunoassay (lfa) for detection of viruses using fluorescently labeled m13 bacteriophage as reporters and single-reporter counting as the readout. avitag-biotinylated m13 phage were functionalized with antibodies using avidin-biotin conjugation and fluorescently labeled with alexafluor 555. individual phage bound to target viruses (here ms2 as a model) captured on an lfa membrane strip were imaged using epi-fluorescence microscopy. using automated image processing, ...	2015	25581289
the nmr-rosetta capsid model of m13 bacteriophage reveals a quadrupled hydrophobic packing epitope.	filamentous phage are elongated semiflexible ssdna viruses that infect bacteria. the m13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. here we present a structural model for the capsid of intact m13 bacteriophage using rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state nmr experimental data. the c5 subunit symmetry observed in fiber diffraction studies was enforced during model building. the structure c ...	2015	25587134
m13 bacteriophage and adeno-associated virus hybrid for novel tissue engineering material with gene delivery functions.		2016	26010471
virus-templated fret platform for the rational design of ratiometric fluorescent nanosensors.	we report here the construction of a bacteriophage m13-templated supramolecular nanosystem, i.e. m13-β-cd/ada-fitc/ada-rhb, which can be used as effective ratiometric fluorescent sensors for intracellular sensing.	2015	26012560
using the m13 phage as a biotemplate to create mesoporous structures decorated with gold and platinum nanoparticles.	by taking advantage of the physical and chemical properties of the m13 bacteriophage, we have used this virus to synthesize mesoporous silica structures. major coat protein p8 was chemically modified by attaching thiol groups. as we show, the resulting thiolated phage can be used as a biotemplate able to direct the formation of mesoporous silica materials. simultaneously, this thiol functionality acts as an anchor for binding metal ions, such as au(3+) and pt(4+), forming reactive m13-metal ioni ...	2015	26275033
cell-adhesive rgd peptide-displaying m13 bacteriophage/plga nanofiber matrices for growth of fibroblasts.	m13 bacteriophages can be readily fabricated as nanofibers due to non-toxic bacterial virus with a nanofiber-like shape. in the present study, we prepared hybrid nanofiber matrices composed of poly(lactic-co-glycolic acid, plga) and m13 bacteriophages which were genetically modified to display the rgd peptide on their surface (rgd-m13 phage).	2014	26331065
virus based full colour pixels using a microheater.	mimicking natural structures has been received considerable attentions, and there have been a few practical advances. tremendous efforts based on a self-assembly technique have been contributed to the development of the novel photonic structures which are mimicking nature's inventions. we emulate the photonic structures from an origin of colour generation of mammalian skins and avian skin/feathers using m13 phage. the structures can be generated a full range of rgb colours that can be sensitivel ...	2015	26334322
injected phage-displayed-vp28 vaccine reduces shrimp litopenaeus vannamei mortality by white spot syndrome virus infection.	white spot syndrome virus (wssv) is the most important viral pathogen for the global shrimp industry causing mass mortalities with huge economic losses. recombinant phages are capable of expressing foreign peptides on viral coat surface and act as antigenic peptide carriers bearing a phage-displayed vaccine. in this study, the full-length vp28 protein of wssv, widely known as potential vaccine against infection in shrimp, was successfully cloned and expressed on m13 filamentous phage. the functi ...	2016	27241285
g5, a phage single-stranded dna-binding protein, fused with a nuclear localization signal, attenuates symptoms and reduces begomovirus-betasatellite accumulation in transgenic plants.	cotton leaf curl disease is caused by several monopartite begomoviruses and is the major threat to cotton production in the indian subcontinent. the disease has been shown to be associated with four distinct species, including cotton leaf curl kokhran virus (clcukov), and a specific betasatellite-cotton leaf curl multan betasatellite (clcumub). transgenic nicotiana benthamiana plants were produced which constitutively express the escherichia coli phage m13 encoded, sequence nonspecific single-st ...	2016	27364491
simulation of the m13 life cycle ii: investigation of the control mechanisms of m13 infection and establishment of the carrier state.	bacteriophage m13 is a true parasite of bacteria, able to co-opt the infected cell and control the production of progeny across many cellular generations. here, our genetically-structured simulation of m13 is applied to quantitatively dissect the interplay between the host cellular environment and the controlling interactions governing the phage life cycle during the initial establishment of infection and across multiple cell generations. multiple simulations suggest that phage-encoded feedback ...	2017	27569186
direct detection and measurement of wall shear stress using a filamentous bio-nanoparticle.	the wall shear stress (wss) that a moving fluid exerts on a surface affects many processes including those relating to vascular function. wss plays an important role in normal physiology (e.g. angiogenesis) and affects the microvasculature's primary function of molecular transport. points of fluctuating wss show abnormalities in a number of diseases; however, there is no established technique for measuring wss directly in physiological systems. all current methods rely on estimates obtained from ...	2015	27570611
hierarchical self-assembly of responsive organoplatinum(ii) metallacycle-tmv complexes with turn-on fluorescence.	here we report that the rod-like tobacco mosaic virus (tmv), having a negatively charged surface, can be assembled into three-dimensional micrometer-sized bundle-like superstructures via multiple electrostatic interactions with a positively charged molecular "glue", namely, a tetraphenylethylene (tpe)-based discrete organoplatinum(ii) metallacycle (tpe-pt-mc). due to the nanoconfinement effect in the resultant tmv/tpe-pt-mc complexes and the aggregation-induced emission (aie) activity of the tpe ...	2016	27608138
simulation of the m13 life cycle i: assembly of a genetically-structured deterministic chemical kinetic simulation.	to expand the quantitative, systems level understanding and foster the expansion of the biotechnological applications of the filamentous bacteriophage m13, we have unified the accumulated quantitative information on m13 biology into a genetically-structured, experimentally-based computational simulation of the entire phage life cycle. the deterministic chemical kinetic simulation explicitly includes the molecular details of dna replication, mrna transcription, protein translation and particle as ...	2017	27644585
design and engineering of a transmissible antiviral defense.	we propose, model, and implement a novel system of population-level intervention against a virus. one context is a treatment against a chronic infection such as hiv. the underlying principle is a form of virus 'wars' in which a benign, transmissible agent is engineered to protect against infection by and spread of a lethal virus. in our specific case, the protective agent consists of two entities, a benign virus and a gene therapy vector mobilized by the benign virus.	2016	27752283
identification of the cell binding domain in nipah virus g glycoprotein using a phage display system.	nipah virus (niv) is a highly pathogenic zoonotic paramyxovirus with unusual broad host tropism and is designated as a category c pathogen by the u.s. national institute of allergy and infectious diseases. niv infection is initiated after binding of the viral g glycoprotein to the host cell receptor. the aim of this study was to map the niv g glycoprotein cell binding domain using a phage display system. the niv g extracellular domain was truncated and displayed as attachment proteins on m13 pha ...	2017	28082163