Use of uncoated magnetic beads to capture Mycobacterium smegmatis and Mycobacterium avium paratuberculosis prior detection by mycobacteriophage D29 and real-time-PCR.

Uncoated tosyl-activated magnetic beads were evaluated to capture Mycobacterium smegmatis and Mycobacterium avium subspecies paratuberculosis (MAP) from spiked feces, milk, and urine. Centrifugation and uncoated magnetic beads recovered more than 99% and 93%, respectively, of 1.68 × 107 CFU/mL, 1.68 × 106 CFU/mL and 1.68 × 105 CFU/mL M. smegmatis cells resuspended in phosphate buffer saline. The use of magnetic beads was more efficient to concentrate cells from 1.68 × 104 CFU/mL of M. smegmatis than centrifugation. Likewise, the F57-qPCR detection of MAP cells was different whether they were recovered by beads or centrifugation; cycle threshold (Ct) was lower (p < 0.05) for the detection of MAP cells recovered by beads than centrifugation, indicative of greater recovery. Magnetic separation of MAP cells from milk, urine, and feces specimens was demonstrated by detection of F57 and IS900 sequences. Beads captured no less than 109 CFU/mL from feces and no less than 104 CFU/mL from milk and urine suspensions. In another detection strategy, M. smegmatis coupled to magnetic beads were infected by mycobacteriophage D29. Plaque forming units were observed after 24 h of incubation from urine samples containing 2 × 105 and 2 × 103 CFU/mL M. smegmatis. The results of this study provide a promising tool for diagnosis of tuberculosis and Johne's disease.

Immobilization of Intact Phage and Phage-Derived Proteins for Detection and Biocontrol Purposes.

The natural specificity of bacteriophages toward their hosts represents great potential for the development of platforms for the capture and detection of bacterial pathogens. Whole phage can carry reporter genes to alter the phenotype of the target pathogen. Phage can also act as staining agents or the progeny of the infection process can be detected. Alternatively, using phage components as probes offer advantages over whole phage particles, including smaller probe size and resilience to desiccation. Phage structures can be engineered for improved affinity, specificity, and binding properties. However, such concepts require the ability to anchor phage and phage-components onto mechanical supports such as beads or flat surfaces. The ability to orient the anchoring is desired in order to optimize binding efficiency. This chapter presents various methods that have been employed for the attachment of phage and phage components onto support structures such as beads, filters, and sensor surfaces.

Helium Ion Microscope-Assisted Nanomachining of Resonant Nanostrings.

Helium ion microscopy has recently emerged as a potent tool for the in-situ modification and imaging of nanoscale devices. For example; finely focused helium ion beams have been used for the milling of pores in suspended structures. We here report the use of helium ion milling for the post-fabrication modification of nanostrings machined from an amorphous SiCN material. The modification consisted of milling linear arrays of holes along the length of nanostrings. This milling results in a slight decrease of resonant frequency while increasing the surface to volume ratio of the device. The frequency decrease is attributed to a reduction of the effective Young's modulus of the string, which in turn reduces the tension the string is under. Such experimental observations are supported by the finite element analysis of milled and non-milled strings.

Aryl Diazonium Chemistry for the Surface Functionalization of Glassy Biosensors.

Nanostring resonator and fiber-optics-based biosensors are of interest as they offer high sensitivity, real-time measurements and the ability to integrate with electronics. However, these devices are somewhat impaired by issues related to surface modification. Both nanostring resonators and photonic sensors employ glassy materials, which are incompatible with electrochemistry. A surface chemistry approach providing strong and stable adhesion to glassy surfaces is thus required. In this work, a diazonium salt induced aryl film grafting process is employed to modify a novel SiCN glassy material. Sandwich rabbit IgG binding assays are performed on the diazonium treated SiCN surfaces. Fluorescently labelled anti-rabbit IgG and anti-rabbit IgG conjugated gold nanoparticles were used as markers to demonstrate the absorption of anti-rabbit IgG and therefore verify the successful grafting of the aryl film. The results of the experiments support the effectiveness of diazonium chemistry for the surface functionalization of SiCN surfaces. This method is applicable to other types of glassy materials and potentially can be expanded to various nanomechanical and optical biosensors.

Diazonium Chemistry for the Bio-Functionalization of Glassy Nanostring Resonator Arrays.

Resonant glassy nanostrings have been employed for the detection of biomolecules. These devices offer high sensitivity and amenability to large array integration and multiplexed assays. Such a concept has however been impaired by the lack of stable and biocompatible linker chemistries. Diazonium salt reduction-induced aryl grafting is an aqueous-based process providing strong chemical adhesion. In this work, diazonium-based linker chemistry was performed for the first time on glassy nanostrings, which enabled the bio-functionalization of such devices. Large arrays of nanostrings with ultra-narrow widths down to 10 nm were fabricated employing electron beam lithography. Diazonium modification was first developed on SiCN surfaces and validated by X-ray photoelectron spectroscopy. Similarly modified nanostrings were then covalently functionalized with anti-rabbit IgG as a molecular probe. Specific enumeration of rabbit IgG was successfully performed through observation of downshifts of resonant frequencies. The specificity of this enumeration was confirmed through proper negative control experiments. Helium ion microscopy further verified the successful functionalization of nanostrings.

Low Temperature Reactive Sputtering of Thin Aluminum Nitride Films on Metallic Nanocomposites.

Piezoelectric aluminum nitride thin films were deposited on aluminum-molybdenum (AlMo) metallic nanocomposites using reactive DC sputtering at room temperature. The effect of sputtering parameters on film properties was assessed. A comparative study between AlN grown on AlMo and pure aluminum showed an equivalent (002) crystallographic texture. The piezoelectric coefficients were measured to be 0.5±0.1 C m(-2) and 0.9±0.1 C m(-2), for AlN deposited on Al/0.32Mo and pure Al, respectively. Films grown onto Al/0.32Mo however featured improved surface roughness. Roughness values were measured to be 1.3nm and 5.4 nm for AlN films grown on AlMo and on Al, respectively. In turn, the dielectric constant was measured to be 8.9±0.7 for AlN deposited on Al/0.32Mo seed layer, and 8.7±0.7 for AlN deposited on aluminum; thus, equivalent within experimental error. Compatibility of this room temperature process with the lift-off patterning of the deposited AlN is also reported.

A Review of Membrane-Based Biosensors for Pathogen Detection.

Biosensors are of increasing interest for the detection of bacterial pathogens in many applications such as human, animal and plant health, as well as food and water safety. Membranes and membrane-like structures have been integral part of several pathogen detection platforms. Such structures may serve as simple mechanical support, function as a part of the transduction mechanism, may be used to filter out or concentrate pathogens, and may be engineered to specifically house active proteins. This review focuses on membrane materials, their associated biosensing applications, chemical linking procedures, and transduction mechanisms. The sensitivity of membrane biosensors is discussed, and the state of the field is evaluated and summarized.

Mycobacteriophage cell binding proteins for the capture of mycobacteria.

Slow growing Mycobacteriumavium subsp. paratuberculosis (MAP) causes a deadly condition in cattle known as Johne's disease where asymptomatic carriers are the major source of disease transmission. MAP was also shown to be associated with chronic Crohn's disease in humans. Mycobacterium smegmatis is a model mycobacterium that can cause opportunistic infections in a number of human tissues and, rarely, a respiratory disease. Currently, there are no rapid, culture-independent, reliable and inexpensive tests for the diagnostics of MAP or M. smegmatis infections. Bacteriophages are viruses producing a number of proteins that effectively and specifically recognize the cell envelopes of their bacterial hosts. We demonstrate that the mycobacterial phage L5 minor tail protein Gp6 and lysin Gp10 are useful tools for the rapid capture of mycobacteria. Immobilized Gp10 was able to bind both MAP and M. smegmatis cells whereas Gp6 was M. smegmatis specific. Neither of the 2 proteins was able to capture E. coli, salmonella, campylobacter or Mycobacterium marinum cells. Gp6 was detected previously as a component of the phage particle and shows no homology to proteins with known function. Therefore, electrospray ionization mass spectrometry was used to determine whether recombinant Gp6 could bind to a number of chemically synthesized fragments of mycobacterial surface glycans. These findings demonstrate that mycobacteriophage proteins could be used as a pathogen capturing platform that can potentially improve the effectiveness of existing diagnostic methods.

A suggested classification for two groups of Campylobacter myoviruses.

Most Campylobacter bacteriophages isolated to date have long contractile tails and belong to the family Myoviridae. Based on their morphology, genome size and endonuclease restriction profile, Campylobacter phages were originally divided into three groups. The recent genome sequencing of seven virulent campylophages reveal further details of the relationships between these phages at the genome organization level. This article details the morphological and genomic features among the campylophages, investigates their taxonomic position, and proposes the creation of two new genera, the "Cp220likevirus" and "Cp8unalikevirus" within a proposed subfamily, the "Eucampyvirinae"

Phage receptor binding protein-based magnetic enrichment method as an aid for real time PCR detection of foodborne bacteria.

We present a novel phage receptor binding protein-based magnetic separation and pre-enrichment method as an alternative to the immunomagnetic separation methods by replacing antibodies with bacteriophage receptor binding proteins (RBPs). We couple the proposed RBP-based magnetic separation with real time PCR for rapid, sensitive and specific detection of Campylobacter jejuni cells in artificially contaminated skim milk, milk with 2% fat and chicken broth. Recovery rates, assessed by real time PCR, were greater than 80% for the samples spiked with as low as 100 cfu mL(-1) of C. jejuni cells. The specificity of capture was confirmed using Salmonella Typhimurium as a negative control where no bacteria were captured on the RBP-derivatized magnetic beads. The combination of RBP-based magnetic separation and real time PCR improved PCR sensitivity and allowed the detection of C. jejuni cells in milk and chicken broth samples without a time consuming pre-enrichment step through culturing. The total sample preparation and analysis time in the proposed RBP-based enrichment method coupled with real time PCR was less than 3 h.

Bacteriophage receptor binding protein based assays for the simultaneous detection of Campylobacter jejuni and Campylobacter coli.

Campylobacter jejuni and Campylobacter coli are the most common bacterial causes of foodborne gastroenteritis which is occasionally followed by a debilitating neuropathy known as Guillain-Barré syndrome. Rapid and specific detection of these pathogens is very important for effective control and quick treatment of infection. Most of the diagnostics available for these organisms are time consuming and require technical expertise with expensive instruments and reagents to perform. Bacteriophages bind to their host specifically through their receptor binding proteins (RBPs), which can be exploited for pathogen detection. We recently sequenced the genome of C. jejuni phage NCTC12673 and identified its putative host receptor binding protein, Gp047. In the current study, we localized the receptor binding domain to the C-terminal quarter of Gp047. CC-Gp047 could be produced recombinantly and was capable of agglutinating both C. jejuni and C. coli cells unlike the host range of the parent phage which is limited to a subset of C. jejuni isolates. The agglutination procedure could be performed within minutes on a glass slide at room temperature and was not hindered by the presence of buffers or nutrient media. This agglutination assay showed 100% specificity and the sensitivity was 95% for C. jejuni (n = 40) and 90% for C. coli (n = 19). CC-Gp047 was also expressed as a fusion with enhanced green fluorescent protein (EGFP). Chimeric EGFP_CC-Gp047 was able to specifically label C. jejuni and C. coli cells in mixed cultures allowing for the detection of these pathogens by fluorescent microscopy. This study describes a simple and rapid method for the detection of C. jejuni and C. coli using engineered phage RBPs and offers a promising new diagnostics platform for healthcare and surveillance laboratories.

Recent advances in bacteriophage based biosensors for food-borne pathogen detection.

Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements.

Surface-immobilization of chromatographically purified bacteriophages for the optimized capture of bacteria.

Bacteriophages offer interesting alternatives to antibodies for the specific capture and detection of pathogenic bacteria onto biosensing surfaces. Procedures for the optimal chemical immobilization of lytic bacteriophages onto surfaces are presented. More specifically, the removal of lysate contaminants from bacteriophage suspensions by size exclusion chromatography significantly increases the resultant planar surface density of immobilized bacteriophages. E. coli T4 and Salmonella enterica serovar Typhimurium P22 phage systems seem to undergo highly heterogeneous adsorption to the surface, possibly explaining the observed phage clustering at higher surface densities. The T4 phage and its E. coli host were initially employed as a model system where we discovered an optimal planar surface density of phages for best bacterial capture: 18.9 ± 0.8 phages/µm(2) capturing 18.0 ± 0.3 bacteria/100 µm(2). Phage surface clustering ultimately limits the T4 phage-immobilized surface's ability to specifically capture its host bacteria. Nevertheless, this is to our knowledge the largest surface capture density of E. coli reported using intact T4 bacteriophages. Two additional purified bacteriophage systems (P22 and Campylobacter jejuni phage NCTC 12673) were then similarly studied for their ability to capture their corresponding host bacteria (Salmonella enterica serovar Typhimurium and Campylobacter jejuni respectively) on a surface.

Bacteriophage based probes for pathogen detection.

Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.

Genome and proteome of Campylobacter jejuni bacteriophage NCTC 12673.

Campylobacter jejuni continues to be the leading cause of bacterial food-borne illness worldwide, so improvements to current methods used for bacterial detection and disease prevention are needed. We describe here the genome and proteome of C. jejuni bacteriophage NCTC 12673 and the exploitation of its receptor-binding protein for specific bacterial detection. Remarkably, the 135-kb Myoviridae genome of NCTC 12673 differs greatly from any other proteobacterial phage genome described (including C. jejuni phages CP220 and CPt10) and instead shows closest homology to the cyanobacterial T4-related myophages. The phage genome contains 172 putative open reading frames, including 12 homing endonucleases, no visible means of packaging, and a putative trans-splicing intein. The phage DNA appears to be strongly associated with a protein that interfered with PCR amplification and estimation of the phage genome mass by pulsed-field gel electrophoresis. Identification and analyses of the receptor-binding protein (Gp48) revealed features common to the Salmonella enterica P22 phage tailspike protein, including the ability to specifically recognize a host organism. Bacteriophage receptor-binding proteins may offer promising alternatives for use in pathogen detection platforms.

Specific detection of Campylobacter jejuni using the bacteriophage NCTC 12673 receptor binding protein as a probe.

Campylobacter jejuni is found in the intestines of poultry, cattle, swine, wild birds and pet animals and is the major cause of foodborne gastroenteritis in developed countries. We report the use of the receptor binding protein (RBP) of Campylobacter bacteriophage NCTC 12673 for the specific capture of Campylobacter jejuni bacteria using RBP-derivatized capturing surfaces. The Gp48 RBP was expressed as a glutathione S-transferase-Gp48 (GST-Gp48) fusion protein and immobilized onto surface plasmon resonance (SPR) surfaces using glutathione self-assembled monolayers (GSH SAM). Bovine serum albumin (BSA) was used to block any non-specific binding. Glutathione SAM leads to an oriented attachment of the protein, resulting in a two- to three-fold improvement of bacterial capture when compared to dithiobis(succinimidyl propionate) (DTSP) SAM-based unoriented attachment. The specificity of recognition was confirmed using Salmonella enterica subsp. enterica serovar Typhimurium as a negative control, which indeed showed negligible binding. The detection limit of the RBP-derivatized SPR surfaces was found to be 10(2) cfu/ml. Finally, GST-Gp48 was also immobilized onto magnetic beads that were successfully used to capture and pre-concentrate the host pathogen from suspension.

Bacteriophage tailspike proteins as molecular probes for sensitive and selective bacterial detection.

We report the use of genetically engineered tailspike proteins (TSPs) from the P22 bacteriophage for the sensitive and selective detection of Salmonella enterica serovar Typhimurium. High yields of two mutant TSPs, one with an N-terminal cysteine (N-Cys) and another with a C-terminal cysteine (C-Cys), have been obtained using recombinant protein expression and purification in Escherichia coli. The mutant TSPs did not have the native endorhamnosidase enzymatic activity of intact P22 phage as well as wild type TSPs (wtTSPs). We have used the Cys-tag to immobilize these TSPs onto gold coated surfaces using thiol-chemistry. Our results demonstrate that the N-Cys configuration of TSPs gives a bacterial capture density of 25.87 ± 0.61 bacteria/100 µm(2) while the C-Cys configuration shows a density of 8.57 ± 0.19 bacteria/100 µm(2). This confirms that the appropriate orientation of the TSPs on the surface is important for efficient capture of the host bacteria. The bacterial capture density of the mutant N-Cys TSP was also 6-fold better than that obtained for intact P22 phage as well as wtTSPs. Bovine-serum albumin was used as a protective layer to prevent any non-specific binding of the bacteria onto the gold substrate. The recognition specificity was confirmed using 3 strains of E. coli which showed negligible binding. In addition, the host bacteria did not show any binding in the absence of the TSPs on the surface. We further show a selective real-time analytical detection of Salmonella by N-Cys mTSP-immobilized on gold coated SF-10 glass plates using surface plasmon resonance. The sensitivity of detection was found to be 10(3)cfu/ml of bacteria.

Gas sensing properties of single conducting polymer nanowires and the effect of temperature.

We measured the electronic properties and gas sensing responses of template-grown poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate) (PEDOT/PSS)-based nanowires. The nanowires had a 'striped' structure (gold-PEDOT/PSS-gold), and were typically 8 microm long (1 microm-6 microm-1 microm for the sections, respectively) and 220 nm in diameter. Single-nanowire devices were contacted with pre-fabricated gold electrodes using dielectrophoretic assembly. A polymer conductivity of 11.5 +/- 0.7 S cm(-1) and a contact resistance of 27.6 +/- 4 kOmega were inferred from measurements on nanowires of varying length and diameter. The nanowire sensors detected a variety of odors, with rapid response and recovery (seconds). The response (DeltaR/R) varied as a power law with analyte concentration. The power law exponent was found to increase with the molecular weight of the analyte and as a function of temperature. The detection limits are set by noise intrinsic to the device and are at the ppm level even for very volatile analytes.

Electronic structure, binding energy, and solvation structure of the streptavidin-biotin supramolecular complex: ONIOM and 3D-RISM study.

We studied the electronic structure of the binding site of the streptavidin-biotin complex by using the ONIOM method at the HF/STO-3G:UFF level and obtained the solvation structure of the complex by using the statistical-mechanical, three-dimensional molecular theory of solvation (aka three-dimensional reference interaction site model, 3D-RISM-KH). All the streptavidin residues located within 3 A of the biotin residue were included in the quantum mechanical (QM) layer. In total, 16 residues including biotin with 274 atoms were in the QM layer, in which five residues are responsible for the hydrophobic interactions and nine residues for the hydrogen-bonding/electrostatic interaction with biotin. We found a geometry change of the urea moiety of the biotin bound in the network of van der Waals and polar interactions. Compared to the isolated biotin, the bridging C-C bond of the biotin urea moiety in the binding site increases in length as a result of the pi-sigma interaction with the surrounding streptavidin Trp residues. This extends the previous picture of the geometry change from the ureido group to the whole bicyclic urea moiety. We have evaluated the performance of 15 density functional methods and 11 basis sets by single point calculation for the binding energy of the optimized cooperative binding complex structure. Closest to the experimental value of 18.3 kcal/mol is the binding free energy of 19.6 kcal/mol obtained for the AN model at B3LYP/6-31G(d):UFF//HF/STO-3G:UFF level. The hybrid DFT methods with enhanced assessment for nonbonded interactions such as PBE1PBE, MPW1B95, and MPWB1K can also give accurate binding energy with the use of diffuse functionals (i.e., mPWB1K/6-31+G(d)). The 3D hydration structure of the unliganded streptavidin and the streptavidin-biotin complex obtained by using the 3D-RISM-KH molecular theory of solvation shows there is one immobilized water molecule at the biotin urea moiety, acting as a water bridge between the sulfur and the nitrogen of the NH group close to Ser45. This suggests that, in the docking process, biotin replaces six of the seven water molecules attached to the unliganded streptavidin binding site, and one remaining water molecule is squeezed into the gap between the Btn, Tyr43, Ser45, Trp92, and Trp79 residues in the binding pocket.

Single-crystal, Si nanotubes, and their mechanical resonant properties.

Single-crystalline Si nanotubes (NTs) were fabricated using vapor-liquid-solid grown, Ge nanowires (NWs) as a template upon which a Si shell was deposited to first grow Ge-core, Si-shell NWs. The tips of these NWs were removed, enabling exposure of the Ge core to H(2)SO(4) and H(2)O(2). After removing the Ge core, single-crystalline Si NTs remained. In addition to growing these Ge-core, Si-shell NWs from a Si (111) substrate, these NWs were also grown horizontally from a vertical Si surface to enable the fabrication of horizontal NTs after focused ion-beam cutting and etching steps. The resonant properties of the Ge-core, Si-shell NW, and the Si NT after the cutting and etching steps were measured and found to have a quality factor, Q, of approximately 1800.