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Cassedy A, Mullins E, O'Kennedy R. Sowing seeds for the future: The need for on-site plant diagnostics. Biotechnol Adv 2020; 39:107358. [DOI: 10.1016/j.biotechadv.2019.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 01/28/2019] [Accepted: 02/21/2019] [Indexed: 01/09/2023]
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Dunbar CA, Callaway HM, Parrish CR, Jarrold MF. Probing Antibody Binding to Canine Parvovirus with Charge Detection Mass Spectrometry. J Am Chem Soc 2018; 140:15701-15711. [PMID: 30398860 DOI: 10.1021/jacs.8b08050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There are many techniques for monitoring and measuring the interactions between proteins and ligands. Most of these techniques are ensemble methods that can provide association constants and in some cases stoichiometry. Here we use charge detection mass spectrometry (CDMS), a single particle technique, to probe the interactions of antigen binding fragments (Fabs) from a series of antibodies with the canine parvovirus (CPV) capsid. In addition to providing the average number of bound Fabs as a function of Fab concentration (i.e., the binding curve), CDMS measurements provide information about the distribution of bound Fabs. We show that the distribution of bound ligands is much better at distinguishing between different binding models than the binding curve. The binding of Fab E to CPV is a textbook example. A maximum of 60 Fabs bind and the results are consistent with a model where all sites have the same binding affinity. However, for Fabs B, F, and 14, the distributions can only be fit by a model where there are distinct virus subpopulations with different binding affinities. This behavior can be distinguished from a situation where all CPV particles are identical, and each particle has the same distribution of sites with different binding affinities. The different responses to viral heterogeneity can be traced to the Fab binding sites. A comparison of Fab binding to new and aged CPV capsids reveals that a post-translational modification at the binding site for Fab E (M569) probably reduces the binding affinity.
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Affiliation(s)
- Carmen A Dunbar
- Department of Chemistry , Indiana University , 800 E. Kirkwood Ave. , Bloomington , Indiana 47405 , United States
| | - Heather M Callaway
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , New York 14850 , United States
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , New York 14850 , United States
| | - Martin F Jarrold
- Department of Chemistry , Indiana University , 800 E. Kirkwood Ave. , Bloomington , Indiana 47405 , United States
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Hong S, Lee C. The Current Status and Future Outlook of Quantum Dot-Based Biosensors for Plant Virus Detection. THE PLANT PATHOLOGY JOURNAL 2018; 34:85-92. [PMID: 29628814 PMCID: PMC5880352 DOI: 10.5423/ppj.rw.08.2017.0184] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/14/2018] [Accepted: 01/18/2018] [Indexed: 05/23/2023]
Abstract
Enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR), widely used for the detection of plant viruses, are not easily performed, resulting in a demand for an innovative and more efficient diagnostic method. This paper summarizes the characteristics and research trends of biosensors focusing on the physicochemical properties of both interface elements and bioconjugates. In particular, the topological and photophysical properties of quantum dots (QDs) are discussed, along with QD-based biosensors and their practical applications. The QD-based Fluorescence Resonance Energy Transfer (FRET) genosensor, most widely used in the biomolecule detection fields, and QD-based nanosensor for Rev-RRE interaction assay are presented as examples. In recent years, QD-based biosensors have emerged as a new class of sensor and are expected to open opportunities in plant virus detection, but as yet there have been very few practical applications (Table 3). In this article, the details of those cases and their significance for the future of plant virus detection will be discussed.
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Affiliation(s)
| | - Cheolho Lee
- Corresponding author. Phone) +82-2-940-7188, E-mail)
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Yamasaki T, Miyake S, Nakano S, Morimura H, Hirakawa Y, Nagao M, Iijima Y, Narita H, Ichiyama S. Development of a Surface Plasmon Resonance-Based Immunosensor for Detection of 10 Major O-Antigens on Shiga Toxin-Producing Escherichia coli, with a Gel Displacement Technique To Remove Bound Bacteria. Anal Chem 2016; 88:6711-7. [PMID: 27243947 DOI: 10.1021/acs.analchem.6b00797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A surface plasmon resonance-based immunosensor (SPR-immunosensor) was developed for the detection of Shiga toxin-producing Escherichia coli (STEC) belonging to the O-antigen groups O26, O91, O103, O111, O115, O121, O128, O145, O157, and O159. The polyclonal antibodies (PoAbs) generated against each of the STEC O-antigen types in rabbits were purified and were immobilized on the sensor chip at 0.5 mg/mL. The limit of detection for STEC O157 by the SPR-immunosensor was found to be 6.3 × 10(4) cells for 75 s. Each of the examined 10 O-antigens on the STECs was detected by the corresponding PoAb with almost no reaction to the other PoAbs. The detected STECs were sufficiently removed from the PoAbs using gelatin or agarose gel without deactivation of the PoAbs, enabling repeatable use of the sensor chip. The developed SPR-immunosensor can be applied for the detection of multiple STEC O-antigens. Furthermore, the new antigen removal technique using the gel displacement approach can be utilized with various immunosensors to improve the detection of pathogens in clinical and public health settings.
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Affiliation(s)
- Tomomi Yamasaki
- Advanced Science, Technology & Management Research Institute of Kyoto , Shimogyo-ku, Kyoto 600-8813, Japan
| | - Shiro Miyake
- Advanced Science, Technology & Management Research Institute of Kyoto , Shimogyo-ku, Kyoto 600-8813, Japan.,Research & Development Division, HORIBA, Ltd., Minami-ku, Kyoto 601-8510, Japan
| | - Satoshi Nakano
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine , Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Morimura
- Research & Development Division, HORIBA, Ltd., Minami-ku, Kyoto 601-8510, Japan
| | - Yuki Hirakawa
- Advanced Science, Technology & Management Research Institute of Kyoto , Shimogyo-ku, Kyoto 600-8813, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine , Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshio Iijima
- Department of Microbiology, Kobe Institute of Health , Chuo-ku, Kobe 650-0046, Japan
| | - Hiroshi Narita
- Department of Food and Nutrition, Kyoto Women's University , Higashiyama-ku, Kyoto 605-8501, Japan
| | - Satoshi Ichiyama
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine , Sakyo-ku, Kyoto 606-8507, Japan
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Tiwari PB, Üren A, He J, Darici Y, Wang X. Note: Model identification and analysis of bivalent analyte surface plasmon resonance data. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:106107. [PMID: 26521004 PMCID: PMC4617740 DOI: 10.1063/1.4933318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Surface plasmon resonance (SPR) is a widely used, affinity based, label-free biophysical technique to investigate biomolecular interactions. The extraction of rate constants requires accurate identification of the particular binding model. The bivalent analyte model involves coupled non-linear differential equations. No clear procedure to identify the bivalent analyte mechanism has been established. In this report, we propose a unique signature for the bivalent analyte model. This signature can be used to distinguish the bivalent analyte model from other biphasic models. The proposed method is demonstrated using experimentally measured SPR sensorgrams.
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Affiliation(s)
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, District of Columbia 20057, USA
| | - Jin He
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| | - Yesim Darici
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| | - Xuewen Wang
- Department of Physics, Florida International University, Miami, Florida 33199, USA
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Tian YP, Hepojoki J, Ranki H, Lankinen H, Valkonen JPT. Analysis of potato virus Y coat protein epitopes recognized by three commercial monoclonal antibodies. PLoS One 2014; 9:e115766. [PMID: 25542005 PMCID: PMC4277358 DOI: 10.1371/journal.pone.0115766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/28/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Potato virus Y (PVY, genus Potyvirus) causes substantial economic losses in solanaceous plants. Routine screening for PVY is an essential part of seed potato certification, and serological assays are often used. The commercial, commonly used monoclonal antibodies, MAb1128, MAb1129, and MAb1130, recognize the viral coat protein (CP) of PVY and distinguish PVYN strains from PVYO and PVYC strains, or detect all PVY strains, respectively. However, the minimal epitopes recognized by these antibodies have not been identified. METHODOLOGY/PRINCIPAL FINDINGS SPOT peptide array was used to map the epitopes in CP recognized by MAb1128, MAb1129, and MAb1130. Then alanine replacement as well as N- and C-terminal deletion analysis of the identified peptide epitopes was done to determine critical amino acids for antibody recognition and the respective minimal epitopes. The epitopes of all antibodies were located within the 30 N-terminal-most residues. The minimal epitope of MAb1128 was 25NLNKEK30. Replacement of 25N or 27N with alanine weakened the recognition by MAb1128, and replacement of 26L, 29E, or 30K nearly precluded recognition. The minimal epitope for MAb1129 was 16RPEQGSIQSNP26 and the most critical residues for recognition were 22I and 23Q. The epitope of MAb1130 was defined by residues 5IDAGGS10. Mutation of residue 6D abrogated and mutation of 9G strongly reduced recognition of the peptide by MAb1130. Amino acid sequence alignment demonstrated that these epitopes are relatively conserved among PVY strains. Finally, recombinant CPs were produced to demonstrate that mutations in the variable positions of the epitope regions can affect detection with the MAbs. CONCLUSIONS/SIGNIFICANCE The epitope data acquired can be compared with data on PVY CP-encoding sequences produced by laboratories worldwide and utilized to monitor how widely the new variants of PVY can be detected with current seed potato certification schemes or during the inspection of imported seed potatoes as conducted with these MAbs.
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Affiliation(s)
- Yan-Ping Tian
- Department of Agricultural Sciences, Plant Pathology Laboratory, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Peptide and Protein Laboratory, Infection Biology Research Program, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Harri Ranki
- Department of Virology, Peptide and Protein Laboratory, Infection Biology Research Program, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Hilkka Lankinen
- Department of Virology, Peptide and Protein Laboratory, Infection Biology Research Program, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, Plant Pathology Laboratory, University of Helsinki, Helsinki, Finland
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