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1.  Serotype- and serogroup-specific detection of African horsesickness virus using phage displayed chicken scFvs for indirect double antibody sandwich ELISAs 
Journal of Veterinary Science  2013;14(1):95-98.
There is an ongoing need for standardized, easily renewable immunoreagents for detecting African horsesickness virus (AHSV). Two phage displayed single-chain variable fragment (scFv) antibodies, selected from a semi-synthetic chicken antibody library, were used to develop double antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISAs) to detect AHSV. In the DAS-ELISAs, the scFv previously selected with directly immobilized AHSV-3 functioned as a serotype-specific reagent that recognized only AHSV-3. In contrast, the one selected with AHSV-8 captured by IgG against AHSV-3 recognized all nine AHSV serotypes but not the Bryanston strain of equine encephalosis virus. Serving as evidence for its serogroup-specificity. These two scFvs can help to rapidly confirm the presence of AHSV while additional serotype-specific scFvs may simplify AHSV serotyping.
doi:10.4142/jvs.2013.14.1.95
PMCID: PMC3615239  PMID: 23388433
African horsesickness virus; double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA); phage-displayed scFv; serotype-specific
2.  Differentiation of Candida albicans and Candida dubliniensis by Using Recombinant Human Antibody Single-Chain Variable Fragments Specific for Hyphae 
Journal of Clinical Microbiology  2003;41(3):1152-1160.
To identify antigens specific for the filamentous form of Candida albicans, a combinatorial phage display library expressing human immunoglobulin heavy and light chain variable regions was used to select phage clones capable of binding to the surfaces of viable C. albicans filaments. Eight distinct phage clones that bound specifically to filament surface antigens not expressed on blastoconidia were identified. Single-chain antibody variable fragments (scFv) derived from two of these phage clones (scFv5 and scFv12) were characterized in detail. Filament-specific antigen expression was detected by an indirect immunofluorescence assay. ScFv5 reacted with C. dubliniensis filaments, while scFv12 did not. Neither scFv reacted with C. glabrata, C. parapsilosis, C. rugosa, C. tropicalis, or Saccharomyces cerevisiae grown under conditions that stimulated filament formation in C. albicans and C. dubliniensis. Epitope detection by the two scFv was sensitive to proteinase K treatment but not to periodate treatment, indicating that the cognate epitopes were composed of protein. The antigens reactive with scFv5 and scFv12 were extractable from the cell surface with Zymolyase, but not with sodium dodecyl sulfate (SDS) and 2-mercaptoethanol, and migrated as polydisperse, high-molecular-weight bands on SDS-polyacrylamide gel electrophoresis gels. The epitopes were detected on clinical specimens obtained from infants with thrush and urinary candidiasis without passage of the organisms on laboratory media, confirming epitope expression in human infection. The availability of a monoclonal immunologic reagent that recognizes filaments from both C. albicans and C. dubliniensis and another specific only to C. albicans adds to the repertoire of potential diagnostic reagents for differentiation between these closely related species.
doi:10.1128/JCM.41.3.1152-1160.2003
PMCID: PMC150300  PMID: 12624045
3.  Magnetic bead-based phage anti-immunocomplex assay (PHAIA) for the detection of the urinary biomarker 3-phenoxybenzoic acid to assess human exposure to pyrethroid insecticides 
Analytical biochemistry  2008;386(1):45-52.
Noncompetitive immunoassays are advantageous over competitive assays for the detection of small molecular weight compounds. We recently demonstrated that phage peptide libraries can be an excellent source of immunoreagents that facilitate the development of sandwich-type noncompetitive immunoassays for the detection of small analytes, avoiding the technical challenges of producing anti-immunocomplex antibody. In this work we explore a new format that may help to optimize the performance of the phage anti-immunocomplex assay (PHAIA) technology. As a model system we used a polyclonal antibody to 3-phenoxybenzoic acid (3-PBA) and an anti-immunocomplex phage clone bearing the cyclic peptide CFNGKDWLYC. The assay setup with the biotinylated antibody immobilized onto streptavidin-coated magnetic beads significantly reduced the amount of coating antibody giving identical sensitivity (50% saturation of the signal (SC50) = 0.2–0.4 ng/ml) to the best result obtained with direct coating of the antibody on ELISA plates. The bead-based assay tolerated up to 10 and 5% of methanol and urine matrix, respectively. This assay system accurately determined the level of spiked 3-PBA in different urine samples prepared by direct dilution or clean-up with solid-phase extraction after acidic hydrolysis with overall recovery of 80–120%.
doi:10.1016/j.ab.2008.12.003
PMCID: PMC2863013  PMID: 19101498
Phage anti-immunocomplex assay; Phage peptide display; Phage ELISA; Noncompetitive immunoassay; 3-Phenoxybenzoic acid; Pyrethroid insecticides
4.  Characterization of Lactococcus lactis phage antigens. 
Phage phi 197 is representative of a widespread lactococcal phage group characterized by a particular morphology (prolate head with a noncontractile tail). In order to develop an immunoenzymatic phage detection test, fusion proteins containing beta-galactosidase fused to epitopes of phage phi 197 structural proteins were constructed by cloning random DNA fragments from the phage genome upstream of a lacZ gene on a plasmid vector. Recombinant plasmids containing certain fragments encoded the synthesis of fusion proteins which react with polyclonal antibodies against the phage and confer a Lac+ phenotype on Escherichia coli. Three different epitopes were represented; phage-specific DNA fragments encoding these epitopes were mapped at three locations on the phage genome, and their nucleotide sequences were determined. Two fused phage antigens were conformational epitopes, whereas the phage epitope of protein encoded by the recombinant plasmid designated pOA17 was a denaturation-resistant epitope. This epitope was very immunogenic. Protein encoded by plasmid pOA17 was synthesized in large amounts from a strong promoter. Antibodies raised against this hybrid protein were used to identify the 46-kDa minor phage protein which provides the epitope. Antibody cross-reactivity of phages related to phi 197 showed that this epitope is well conserved in this genetic group.
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PMCID: PMC195807  PMID: 1514794
5.  Selection of Ceratitis capitata (Diptera: Tephritidae) Specific Recombinant Monoclonal Phage Display Antibodies for Prey Detection Analysis 
PLoS ONE  2012;7(12):e51440.
Several recombinant antibodies against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), one of the most important pests in agriculture worldwide, were selected for the first time from a commercial phage display library of human scFv antibodies. The specificity and sensitivity of the selected recombinant antibodies were compared with that of a rabbit polyclonal serum raised in parallel using a wide range of arthropod species as controls. The selected recombinant monoclonal antibodies had a similar or greater specificity when compared with classical monoclonal antibodies. The selected recombinant antibodies were successfully used to detect the target antigen in the gut of predators and the scFv antibodies were sequenced and compared. These results demonstrate the potential for recombinant scFv antibodies to be used as an alternative to the classical monoclonal antibodies or even molecular probes in the post-mortem analysis studies of generalist predators.
doi:10.1371/journal.pone.0051440
PMCID: PMC3522712  PMID: 23272105
6.  Definition of conditions that enable antigen-specific activation of the majority of isolated trinitrophenol-binding B cells 
The Journal of Experimental Medicine  1982;156(6):1635-1649.
In an effort to further elucidate the early cellular events in generation of antibody responses, we have determined the requirements for antigen-specific initiation of the G0 to G1 transition by isolated trinitrophenol (TNP) -binding B lymphocytes. TNP-binding cells were isolated from normal B6D2F1 splenocyte populations using hapten affinity fractionation on disulfide-bonded TNP-gelatin-coated plates. Populations prepared in this way are greater than or equal to 96% immunoglobulin positive and 70-95% antigen binding. Isolated cells were cultured for 48 h in the presence of a variety of TNP conjugates including TNP-Brucella abortus (Ba), TNP-Ficoll, TNP-sheep erythrocytes (SRBC), TNP-human gamma globulin (HGG), or TNP-ovalbumin (OVA) before being harvested and subjected to acridine orange cell cycle analysis. As many as 80% of cells were in cycle by 48 h in response to TNP-Ba, a thymus-independent (TI1 antigen. A smaller proportion (congruent to 40%) were in cycle in response to TNP-Ficoll, a TI2 antigen. Significant activation was not detected in cultures challenged with the thymus-dependent immunogens TNP-SRBC, TNP-HGG, and TNP-OVA. Addition of interleukin 1 (IL-1), IL-2, B cell growth factor, and/or T cell- replacing factor to cultures did not facilitate responses to these immunogens, suggesting a requirement for antigen-specific T cell help for entry into cell cycle induced by thymus dependent antigens. Activation by TNP-Ba was antigen specific and independent of accessory cells, occurring with equal efficiency in bulk and single-cell cultures. Activation by TNP-Ba was inhibitable by anti-Fab and anti-mu antibodies, but not by anti-delta antibodies. Results indicate that activation of TNP-binding cells to enter cell cycle by TNP-Ba is independent of accessory cells and requires interaction of antigen with cell surface IgM. Exposure to thymus-dependent TNP-immunogens plus nonspecific helper factors is insufficient to cause entry of TNP- binding cells into cycle.
PMCID: PMC2186872  PMID: 6184434
7.  A Nanostructured Piezoelectric Immunosensor for Detection of Human Cardiac Troponin T 
Sensors (Basel, Switzerland)  2011;11(11):10785-10797.
A piezoelectric immunosensor based on gold nanoparticles (AuNPs) co-immobilized on a dithiol-modified surface is proposed for detection of human cardiac troponin T (TnT). Anti-human troponin T (anti-TnT) antibodies were covalently immobilized on the nanostructured electrode surface by thiol-aldehyde linkages. In a homogeneous bulk solution, TnT was captured by anti-TnT immobilized on the QCM electrode. Cyclic voltammetry studies were used to characterize the AuNPs layer on the electrode surface and the anti-TnT immobilization steps. The QCM-flow immunosensor exhibited good reliability, measuring concentrations of TnT from 0.003 to 0.5 ng mL−1 in human serum with high linearity (r = 0.989; p < 0.01). The immunosensor exhibited a 7% coefficient of variation and 0.0015 ng mL−1 limit of detection, indicating a high reproducibility and sensitivity. The proposed QCM nanostructured immunosensor is easy to use and has promising potential in the diagnosis of acute myocardial infarction due to its speed and high sensitivity.
doi:10.3390/s111110785
PMCID: PMC3274313  PMID: 22346671
piezoelectric; immunosensor; gold nanoparticle; cardiac troponin T
8.  Production of Eight Different Hydride Complexes and Nitrite Release from 2,4,6-Trinitrotoluene by Yarrowia lipolytica▿ † 
Applied and Environmental Microbiology  2007;73(24):7898-7905.
2,4,6-Trinitrotoluene (TNT) transformation by the yeast strain Yarrowia lipolytica AN-L15 was shown to occur via two different pathways. Direct aromatic ring reduction was the predominant mechanism of TNT transformation, while nitro group reduction was observed to be a minor pathway. Although growth of Y. lipolytica AN-L15 was inhibited initially in the presence of TNT, TNT transformation was observed, indicating that the enzymes necessary for TNT reduction were present initially. Aromatic ring reduction resulted in the transient accumulation of eight different TNT-hydride complexes, which were characterized using high-performance liquid chromatography, UV-visible diode array detection, and negative-mode atmospheric pressure chemical ionization mass spectrometry (APCI-MS). APCI-MS analysis revealed three different groups of TNT-hydride complexes with molecular ions at m/z 227, 228, and 230, which correspond to TNT-mono- and dihydride complexes and protonated dihydride isomers, respectively. One of the three protonated dihydride complex isomers detected appears to release nitrite in the presence of strain AN-L15. This release of nitrite is of particular interest since it can provide a pathway towards complete degradation and detoxification of TNT.
doi:10.1128/AEM.01296-07
PMCID: PMC2168150  PMID: 17933928
9.  Directed evolution of an anti-human red blood cell antibody 
mAbs  2009;1(3):268-280.
We have earlier described a haemagglutination-based assay for on-site detection of antibodies to HIV using whole blood. The reagent in this assay comprises of monovalent Fab fragment of an anti-human RBC antibody fused to immunodominant antigens of HIV-1 and HIV-2. In the present work, we describe a rational and systematic method for directed evolution of scFv and Fab antihuman RBC antibody fragments. Based on homology modeling and germline sequence alignments of antibodies, target residues in the anti-RBC MAb B6 sequence were identified for mutagenesis. A combinatorial library of 107 clones was constructed and subjected to selection on whole RBC under competitive binding conditions to identify several phage-displayed B6 scFv clones with improved binding as determined in an agglutination assay. Selected VL and VH sequences were shuffled to generate a second generation phage-displayed Fab library which on panning yielded Fab clones with several fold better binding than wild type. The mutants with better binding also displayed more Fab molecules per phage particle indicating improved in vivo folding which was also confirmed by their increased periplasmic secretion compared to the wild type. The mutant Fab molecules also showed superior characteristics in large scale production by in vitro folding of LC and Fd. The biophysical measurements involving thermal and chemical denaturation and renaturation kinetics clearly showed that two of the mutant Fab molecules possessed significantly improved characteristics as compared to the wild type B6 Fab. Structural modelling revealed that B6 Fab mutants had increased hydrogen bonding resulting in increased stability. Our approach provides a novel and useful strategy to obtain recombinant antibodies with improved characteristics.
PMCID: PMC2726587  PMID: 20069755
phage display; antibody maturation; Fab; antibody folding; scFv; agglutination
10.  Enzyme immunoassay for detection of human immunodeficiency virus antigens in cell cultures. 
Journal of Clinical Microbiology  1988;26(3):453-458.
A sensitive and specific avidin-biotin enzyme immunoassay that uses immunoreagents from naturally infected individuals was formulated for the detection of human immunodeficiency virus (HIV) antigens. A total of 500 cell culture samples from 111 cultures were tested in this assay and in a reverse transcriptase (RT) assay. Of 353 samples that were positive in the immunoassay, 174 were positive and 179 were negative in the RT assay. The specificity of the immunoassay results was supported by the failure of samples to react with nonimmune serum, by the ability of an anti-HIV type 1 monoclonal antibody to block the reactivity of selected samples, and by the appearance of RT activity in samples drawn from some cultures after a longer period of cultivation. HIV antigens were detected in 174 of 176 RT-positive samples (sensitivity, 98.9%). A comparison of the kinetics of antigen production and RT activity revealed that detectable antigen levels frequently preceded the appearance of RT activity. Thus, 50% of virus-containing cultures were identified within 9 days by immunoassay compared with 14 days by RT assay. In addition, RT activity was often detected intermittently in cultures sampled on several days, whereas antigen levels did not decline after initial appearance. Enzyme immunoassays for HIV antigen detection that use easily obtained reagents and simple technologies could facilitate laboratory and clinical research which requires cultivation of viruses.
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PMCID: PMC266312  PMID: 2451678
11.  Virus-Based Chemical and Biological Sensing 
Viruses have recently proven useful for the detection of target analytes such as explosives, proteins, bacteria, viruses, spores, and toxins with high selectivity and sensitivity. Bacteriophages (often shortened to phages), viruses that specifically infect bacteria, are currently the most studied viruses, mainly because target-specific nonlytic phages (and the peptides and proteins carried by them) can be identified by using the well-established phage display technique, and lytic phages can specifically break bacteria to release cell-specific marker molecules such as enzymes that can be assayed. In addition, phages have good chemical and thermal stability, and can be conjugated with nanomaterials and immobilized on a transducer surface in an analytical device. This Review focuses on progress made in the use of phages in chemical and biological sensors in combination with traditional analytical techniques. Recent progress in the use of virus—nanomaterial composites and other viruses in sensing applications is also high-lighted.
doi:10.1002/anie.200900231
PMCID: PMC2771072  PMID: 19662666
bacteria; biosensing; phages; sensors; viruses
12.  Specific suppression of allograft rejection by trinitrophenyl (TNP)- induced suppressor cells in recipients treated with TNP-haptenated donor alloantigens 
The Journal of Experimental Medicine  1985;162(5):1409-1420.
Suppressor T cells, activated by injection of trinitrobenzene sulphonic acid in DA rats, prevented rejection of LEW kidney allografts in a donor-specific manner when adoptively transferred into syngeneic recipients along with trinitrophenyl (TNP)-haptenated LEW alloantigen. TNP-haptenated third-party alloantigen was ineffective in this system. The donor-specific suppression was dependent, too, on the haptenic portion of the chemically modified alloantigen. Hence, fluorescein isothiocyanate-donor antigen did not lead to suppression in the presence of TNP-reactive suppressor cells. There is, however, some crossreaction between DNP- and TNP-haptenated alloantigens so that TNP- reactive cells and DNP-donor antigen suppressed rejection whereas DNP- reactive cells and TNP-donor antigen did not prevent graft rejection. The suppressor cells were sensitive to cyclophosphamide and radiation but were resistant to hydrocortisone. They appear to be T cells of the OX8 (suppressor/cytotoxic) phenotype since they are positive for the pan T cell antigen W3/13, are Ig negative, and do not carry the W3/25 (T helper cell) marker. However, these suppressor cells are adherent to nylon wool. They are found mainly in the spleen, are detected there within 2 d of TNBS injection, and can persist for up to 12 wk. We propose that these cells are first-order T suppressor (Ts1) cells that act in the afferent phase of the response to a renal allograft.
PMCID: PMC2187922  PMID: 2932517
13.  Development of Phage-Based Single Chain Fv Antibody Reagents for Detection of Yersinia pestis 
PLoS ONE  2011;6(12):e27756.
Background
Most Yersinia pestis strains are known to express a capsule-like antigen, fraction 1 (F1). F1 is encoded by the caf1 gene located on the large 100-kb pFra plasmid, which is found in Y. pestis but not in closely related species such as Yersinia enterocolytica and Yersinia pseudotuberculosis. In order to find antibodies specifically binding to Y. pestis we screened a large single chain Fv antibody fragment (scFv) phage display library using purified F1 antigen as a selection target. Different forms of the selected antibodies were used to establish assays for recombinant F1 antigen and Y. pestis detection.
Methods
Phage antibody panning was performed against F1 in an automated fashion using the Kingfisher magnetic bead system. Selected scFvs were screened for F1-binding specificity by one-step alkaline phosphatase enzyme linked immunosorbant assay (ELISA), and assayed for binding to recombinant antigen and/or Y. pestis by flow cytometry and whole-cell ELISA.
Results
Seven of the eight selected scFvs were shown to specifically bind both recombinant F1 and a panel of F1-positive Yersinia cells. The majority of the soluble scFvs were found to be difficult to purify, unstable and prone to cross-reactivity with F1-negative Yersinia strains, whereas phage displayed scFvs were found to be easy to purify/label and remarkably stable. Furthermore direct fluorescent labeling of phage displaying scFv allowed for an easy one-step flow cytometry assay. Slight cross-reactivity was observed when fixed cells were used in ELISA.
Conclusions
Our high throughput methods of selection and screening allowed for time and cost effective discovery of seven scFvs specifically binding Y. pestis F1 antigen. We describe implementation of different methods for phage-based immunoassay. Based on the success of these methods and the proven stability of phage, we indicate that the use of phage-displayed, rather than phage-free proteins, might generally overcome the shortcomings of scFv antibodies.
doi:10.1371/journal.pone.0027756
PMCID: PMC3234238  PMID: 22174746
14.  Assessment of T-dependent and T-independent immune responses in cattle using a B cell ELISPOT assay 
Veterinary Research  2012;43(1):68.
Understanding the mechanisms that maintain protective antibody levels after immunisation is important for vaccine design. In this study, we have determined the kinetics of plasma and memory B cells detectable in the blood of cattle immunised with model T-dependent or T-independent antigens. Immunisation with the T-D antigen resulted in an expansion of TNP-specific plasma cells post-TNP primary and booster immunisations, which was associated with increased titres of TNP-specific IgG antibodies. Although no TNP-specific memory B cells were detected in the T-D group following the primary immunisation, we detected an increase in the number of TNP-specific memory B cells post-TNP boost. In contrast, no TNP-specific plasma or memory B cells were detected after primary or secondary immunisation with the T-I antigen. We then investigated if immunisation with a third party antigen (tetanus toxin fragment C, TTC) would result in a bystander stimulation and increase the number of TNP-specific plasma and memory B cells in the T-D and/or T-I group. TTC immunisation in the T-D group resulted in a small increase in the number of TNP-specific plasma cells post-TTC primary immunisation and boost, and in an increase in the number of TNP-specific memory B cells post-TTC boost. This bystander effect was not observed in the animals previously immunised with the T-I antigen. In conclusion, the present study characterised for the first time the B cell response in cattle to immunisation with T-D and T-I antigens and showed that bystander stimulation of an established T-D B cell memory response may occur in cattle.
doi:10.1186/1297-9716-43-68
PMCID: PMC3487944  PMID: 23050495
15.  Recombinant Single-Chain Variable Fragment Antibodies Directed against Clostridium difficile Toxin B Produced by Use of an Optimized Phage Display System 
Recombinant antibody cloning and phage display technologies were used to produce single-chain antibodies (scFv) against Clostridium difficile toxin B. The starting material was the mouse B cell hybridoma line 5A8, which generates a monoclonal antibody against the toxin. The integrated cloning, screening, and phage display system of Krebber et al. (J. Immunol. Methods 201:35-55, 1997) allowed us to rapidly obtain toxin B-binding scFv sequences derived from the hybridoma cell line. The best candidate scFv sequences, based on preliminary enzyme-linked immunosorbent assay (ELISA) screening data were then subcloned into the compatible expression vector. Recombinant single-chain antibodies were expressed in Escherichia coli. A 29-kDa band was observed on polyacrylamide gel electrophoresis as predicted. The expressed product was characterized by immunoblotting and detection with an anti-FLAG antibody. The toxin B-binding function of the single-chain antibody was shown by a sandwich ELISA. The antibody was highly specific for toxin B and did not cross-react with material isolated from a toxin B-negative C. difficile strain. The sensitivity of the soluble single-chain antibody is significantly higher than the original monoclonal antibody based on ELISA data and could detect a minimum of 10 ng of toxin B/well. Competitive ELISAs established that the affinity of the 5A8 parent antibody and the best representative (clone 10) of the single-chain antibodies were similar and in the range of 10−8 M. We propose that recombinant antibody technology is a rapid and effective approach to the development of the next generation of immunodiagnostic reagents.
doi:10.1128/CDLI.10.4.587-595.2003
PMCID: PMC164272  PMID: 12853390
16.  Fabrication of an SPR Sensor Surface with Antifouling Properties for Highly Sensitive Detection of 2,4,6-Trinitrotoluene Using Surface-Initiated Atom Transfer Polymerization 
Sensors (Basel, Switzerland)  2013;13(7):9294-9304.
In this study, we modified a surface plasmon resonance immunosensor chip with a polymer using surface-initiated atom transfer polymerization (SI-ATRP) for the highly sensitive detection of 2,4,6-trinitrotoluene (TNT). To immobilize a TNT analogue on the polymer, mono-2-(methacryloyloxy)ethylsuccinate (MES), which has a carboxyl group, was used in this study. However, the anti-TNT antibody may adsorb non-specifically on the polymer surface by an electrostatic interaction because MES is negatively charged. Therefore, a mixed monomer with MES and diethylaminoethylmethacrylate (DEAEM), which has a tertiary amino group and is positively charged, was prepared to obtain electroneutrality for suppressing the nonspecific adsorption. The detection of TNT was performed by inhibition assay using the polymer surface. To ensure high sensitivity to TNT, the affinity between the surface and the antibody was optimized by controlling the density of the initiator for ATRP by mixing two types of self-assembled monolayer reagents. As a result, a limit of detection of 5.7 pg/mL (ppt) for TNT was achieved using the optimized surface.
doi:10.3390/s130709294
PMCID: PMC3758649  PMID: 23877126
trinitrotoluene; surface plasmon resonance; immunosensor; surface initiated atom transfer polymerization; self-assembled monolayer; nonspecific adsorption
17.  Landscape Phage as a Molecular Recognition Interface for Detection Devices 
Microelectronics journal  2008;39(2):202-207.
Filamentous phages are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. Libraries of random peptides fused to pVIII domains were used for selection of phages probes specific for a panel of test antigens and biological threat agents. Because the viral carrier in the phage borne bio-selective probes is infective, they can be cloned individually and propagated indefinitely without needs of their chemical synthesis or reconstructing. As a new bioselective material, landscape phages combine unique characteristics of affinity reagents and self assembling proteins. Biorecognition layers formed by the phage-derived probes bind biological agents with high affinity and specificity and generate detectable signals in analytical platforms. The performance of phage-derived materials as biorecognition interface was illustrated by detection of Bacillus anthracis spores and Salmonella typhimurium cells. With further refinement, the phage-derived analytical platforms for detecting and monitoring of numerous threat agents may be developed, since phage interface against any bacteria, virus or toxin may be readily selected from the landscape phage libraries. As an interface in the field-use detectors, they may be superior to antibodies, since they are inexpensive, highly specific and strong binders, resistant to high temperatures and environmental stresses.
doi:10.1016/j.mejo.2006.11.007
PMCID: PMC2565273  PMID: 19190724
Biosensor; sensor; molecular recognition; interface; bacteriophage; landscape phage; phage display; phage library; Bacillus anthracis; Salmonella typhimurium; nanotechnology; ELISA; quartz crystal microbalance
18.  Thirteen Virulent and Temperate Bacteriophages of Lactobacillus bulgaricus and Lactobacillus lactis Belong to a Single DNA Homology Group 
Thirteen virulent phages and two temperate phages of two closely related bacterial species (Lactobacillus lactis and L. bulgaricus) were compared for their protein composition, their antigenic properties, their restriction endonuclease patterns, and their DNA homology. The immunoblotting studies and the DNA-DNA hybridizations showed that the phages could be differentiated into two groups. One group contained 2 temperate phages of L. bulgaricus and 11 virulent phages of L. lactis. Inside each group, at least two common proteins of identical sizes could be detected for each phage. These proteins were able to cross-react in immunoblotting experiments with an antiserum raised against one phage of the same group. Temperate phage DNAs showed partial homology with DNAs from some virulent phages. These homologies seem to be located on the region coding for the structural proteins since recombinant plasmids coding for one of the major phage proteins of one phage were able to hybridize with the DNAs from phages of the same group. These results suggest that temperate and virulent phages may be related to one another.
Images
PMCID: PMC239119  PMID: 16347174
19.  Phage display mediated immuno-PCR 
Nucleic Acids Research  2006;34(8):e62.
Immuno-PCR (IPCR) is a powerful detection technology in immunological study and clinical diagnosis due to its ultrasensitivity. Here we introduce a new strategy termed phage display mediated immuno-PCR (PD-IPCR). Instead of utilization of monoclonal antibody (mAb) and chemically bond DNA that required in the conventional IPCR, a recombinant phage particle is applied as a ready reagent for IPCR experiment. The surface displayed single chain variable fragment (scFv) and phage DNA themselves can directly serve as detection antibody and PCR template, respectively. The aim of the design is to overcome shortcoming of low detection sensitivity of scFv so as to largely facilitate the real application of scFv in immunoassay. The idea has been demonstrated by applying hantaan virus nucleocapsid protein (NP) and prion protein (PrP) as detection targets in three experimental protocols (indirect, sandwich and real-time PD-IPCR assays). The detection sensitivity was increased 1000- to 10 000-folds compared with conventional enzyme-linked immunosorbent assays (ELISAs). This proof-of-concept study may serve as a new model to develop an easy to operate, low cost and ultrasensitive immunoassay method for broad applications.
doi:10.1093/nar/gkl260
PMCID: PMC1458518  PMID: 16682441
20.  Intraspecific Epitopic Variation in a Carbohydrate Antigen Exposed on the Surface of Trichostrongylus colubriformis Infective L3 Larvae 
PLoS Pathogens  2009;5(9):e1000597.
The carbohydrate larval antigen, CarLA, is present on the exposed surface of all strongylid nematode infective L3 larvae tested, and antibodies against CarLA can promote rapid immune rejection of incoming Trichostrongylus colubriformis larvae in sheep. A library of ovine recombinant single chain Fv (scFv) antibody fragments, displayed on phage, was prepared from B cell mRNA of field-immune sheep. Phage displaying scFvs that bind to the surface of living exsheathed T. colubriformis L3 larvae were identified, and the majority of worm-binding scFvs recognized CarLA. Characterization of greater than 500 worm surface binding phage resulted in the identification of nine different anti-CarLA scFvs that recognized three distinct T. colubriformis CarLA epitopes based on blocking and additive ELISA. All anti-CarLA scFvs were specific to the T. colubriformis species of nematode. Each of the three scFv epitope classes displayed identical Western blot recognition patterns and recognized the exposed surface of living T. colubriformis exsheathed L3 larvae. Surprisingly, each of the anti-CarLA scFvs was able to bind to only a subset of worms. Double-labelling indirect immunofluorescence revealed that the three classes of anti-CarLA scFvs recognize distinct, non-overlapping, T. colubriformis sub-populations. These results demonstrate that individual T. colubriformis L3 larvae display only one of at least three distinct antigenic forms of CarLA on their surface at any given time, and suggest that antigenic variation within CarLA is likely a mechanism of immune evasion in strongylid nematodes.
Author Summary
Strongylid nematode worm parasites currently infect hundreds of millions of people, and most farmed animals, causing enormous morbidity and economic loss. These parasites commonly produce chronic gastrointestinal infections that are highly refractory to immune clearance mechanisms. Mucosal antibodies against a carbohydrate surface antigen (CarLA) can cause rapid expulsion of incoming larval nematodes. Sheep develop strong anti-strongylid immunity following long-term grazing on contaminated pasture. From these sheep, we identified and characterized recombinant antibodies that recognize CarLA on living L3 stage infective larvae of the strongylid parasite, Trichostrongylus colubriformis. The selected antibodies are specific only to larvae of the T. colubriformis species and, surprisingly, recognize only a subset of these worms. Three different anti-CarLA antibody classes were found and each recognizes different, non-overlapping subsets of worms which, together, comprise virtually the entire population. These results are the first demonstration of “intraspecific epitopic variation” within strongylid nematodes and suggest that these parasites have a mechanism that permits the surface presentation of at least three different antigenic forms of CarLA to avoid immune clearance.
doi:10.1371/journal.ppat.1000597
PMCID: PMC2742895  PMID: 19779563
21.  Human rotavirus antigen detection by enzyme-immunoassay with antisera against Nebraska calf diarrhoea virus. 
Journal of Clinical Pathology  1981;34(6):680-685.
A four-layer solid phase enzyme-immunoassay (EIA) with antisera against Nebraska calf diarrhoea virus (NCDV) as immunoreagents was developed to detect human rotavirus antigens from stool specimens of patients with acute rotavirus gastroenteritis. Polystyrene beads were used as the solid phase, guinea-pig and rabbit anti-NCDV immunoglobulin as the catching and secondary antibody, and peroxidase-conjugated swine anti-rabbit immunoglobulin as the indicator antibody. A comparison of the developed NCDV-EIA with an identical EIA, using antisera against human rotavirus (HRV-EIA) instead of NCDV antisera, was made with 216 stool specimens positive or negative for rotavirus. A complete agreement was obtained between the two methods provided that appropriate confirmatory tests were included. The developed NCDV-EIA was as sensitive and specific for rotavirus as the HRV-EIA, and it allowed the detection of both established rotavirus types 1 and 2 from stools with equal sensitivity. The difficulties in cultivating human rotavirus in vitro for immunisation and the relative ease of growing NCDV in widely-used continuous cell lines make NCDV a good alternative in the preparation of the highly specific and sensitive rotavirus antisera required in immunoassays, and facilitate the setting-up methods for the routine diagnosis of rotavirus gastroenteritis by EIA or RIA in diagnostic virus laboratories.
PMCID: PMC493649  PMID: 6265506
22.  A Nanosensor for TNT Detection Based on Molecularly Imprinted Polymers and Surface Enhanced Raman Scattering 
Sensors (Basel, Switzerland)  2011;11(3):2700-2714.
We report on a new sensor strategy that integrates molecularly imprinted polymers (MIPs) with surface enhanced Raman scattering (SERS). The sensor was developed to detect the explosive, 2,4,6-trinitrotoluene (TNT). Micron thick films of sol gel-derived xerogels were deposited on a SERS-active surface as the sensing layer. Xerogels were molecularly imprinted for TNT using non-covalent interactions with the polymer matrix. Binding of the TNT within the polymer matrix results in unique SERS bands, which allow for detection and identification of the molecule in the MIP. This MIP-SERS sensor exhibits an apparent dissociation constant of (2.3 ± 0.3) × 10−5 M for TNT and a 3 μM detection limit. The response to TNT is reversible and the sensor is stable for at least 6 months. Key challenges, including developing a MIP formulation that is stable and integrated with the SERS substrate, and ensuring the MIP does not mask the spectral features of the target analyte through SERS polymer background, were successfully met. The results also suggest the MIP-SERS protocol can be extended to other target analytes of interest.
doi:10.3390/s110302700
PMCID: PMC3231613  PMID: 22163761
molecular imprinting; surface enhanced Raman scattering; sensor; explosives detection
23.  Construction of non-covalent single-chain Fv dimers for hepatocellular carcinoma and their biological functions 
World Journal of Hepatology  2010;2(5):185-191.
AIM: To create new diabodies with improved binding activity to antigen of the variable light - variable heavy (VH-VL) oriented single-chain Fv dimers genes (scFv).
METHODS: The linker between VH and VL genes was shortened to 3-5 amino acid residues and cloned into the vector pCANTAB5E. The recombinant plasmids were transformed into TG1 cells and sequenced. The positive transformed cells were infected by M13K07 helper phage to form human recombinant phage antibodies. Expressed products were identified by SDS-PAGE, Western blotting, size exclusion gel chromatography (SEC), ELISA and immunohistochemistry.
RESULTS: Three scFv (scFv-3, scFv-4, scFv-5) were constructed successfully with binding ability to hepatocellular carcinoma 3.5-6 fold greater than their parental scFv. The single-chain Fv dimer (scFv-5, termed BDM3) with the best binding ability was successfully expressed in Yeast pichlia, as shown by. SDS-PAGE and Western blotting. SEC results suggested the molecular weight of the expressed products was about 61 kDa. Expressed products showed significantly stronger binding to hepatocellular carcinoma cells than scFv, still having 50% binding activity even after 16 h incubation as 37°C. The purified dimers were bound specifically to the tumor antigen of HCC.
CONCLUSION: we have generated scFv dimers by shortening a series of linkers to 3-5 amino acid residues in VH-linker-VL orientation, resulting in highly stable and affinity-improved dimeric molecules. These will become an attractive targeting moiety in immunotherapeutic and diagnostic applications for HCC.
doi:10.4254/wjh.v2.i5.185
PMCID: PMC2998965  PMID: 21160994
Diabody; Antibody-targeted; Specificity; Affinity; Stability
24.  Molecular characterization of murine humoral immune response to botulinum neurotoxin type A binding domain as assessed by using phage antibody libraries. 
Infection and Immunity  1997;65(9):3743-3752.
To produce antibodies capable of neutralizing botulinum neurotoxin type A (BoNT/A), the murine humoral immune response to BoNT/A binding domain (H(C)) was characterized at the molecular level by using phage antibody libraries. Mice were immunized with BoNT/A H(C), the spleens were harvested, and single-chain Fv (scFv) phage antibody libraries were constructed from the immunoglobulin heavy and light chain variable region genes. Phage expressing BoNT/A binding scFv were isolated by selection on immobilized BoNT/A and BoNT/A H(C). Twenty-eight unique BoNT/A H(C) binding scFv were identified by enzyme-linked immunosorbent assay and DNA sequencing. Epitope mapping using surface plasmon resonance in a BIAcore revealed that the 28 scFv bound to only 4 nonoverlapping epitopes with equilibrium constants (Kd) ranging from 7.3 x 10(-8) to 1.1 x 10(-9) M. In a mouse hemidiaphragm assay, scFv binding epitopes 1 and 2 significantly prolonged the time to neuroparalysis, 1.5- and 2.7-fold, respectively, compared to toxin control. scFv binding to epitopes 3 and 4 showed no protection against neuroparalysis. A combination of scFv binding epitopes 1 and 2 had an additive effect on time to neuroparalysis, which increased to 3.9-fold compared to the control. The results suggest that there are two "productive" receptor binding sites on H(C) which lead to toxin internalization and toxicity. Blockade of these two epitopes with monoclonal antibodies may provide effective immunoprophylaxis or therapy against BoNT/A intoxication.
PMCID: PMC175534  PMID: 9284147
25.  Noncompetitive Phage Anti-Immunocomplex Real-Time PCR (PHAIA-PCR) for Sensitive Detection of Small Molecules 
Analytical chemistry  2010;83(1):246-253.
Immuno-PCR (IPCR) is an analytical technology based on the excellent affinity and specificity of antibodies combined with the powerful signal amplification of PCR, providing superior sensitivity to classical immunoassays. Here we present a novel type of immuno PCR (IPCR) termed phage anti-immunocomplex real time PCR (PHAIA-PCR) for the detection of small molecules. Our method utilizes a phage anti-immunocomplex assay (PHAIA) technology in which a short peptide loop displayed on the surface of the M13 bacteriophage binds specifically to the antibody-analyte complex allowing the non-competitive detection of small analytes. The phagemid DNA encoding this peptide can be amplified by PCR, and thus, this method eliminates hapten functionalization or bio-conjugation of a DNA template while providing improved sensitivity. As a proof of concept, two PHAIA-PCRs were developed for the detection of 3-PBA, a major urinary metabolite of pyrethroid insecticide and for molinate, a herbicide implicated in fish kills. Our results demonstrate that phage DNA can be a versatile material for IPCR development, enabling universal amplification when the common element of the phagemid is targeted, or specific amplification when the real time PCR probe is designed to anneal the DNA encoding the peptide. Using magnetic beads for rapid separation of reactants, the PHAIA-PCRs proved to be 10-fold more sensitive than conventional PHAIA and significantly faster. The assay was validated with both agricultural drain water and human urine samples showing its robustness for rapid monitoring of human exposure or environmental contamination.
doi:10.1021/ac102353z
PMCID: PMC3031424  PMID: 21141939

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