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Jadaa N, Aldor N, Jenik K, Oberhoffner S, Butkowsky C, Tran A, Lewis A, DeWitte-Orr SJ, Poynter S. Evaluating Cationic Nanoparticles as Carriers of Antiviral Nucleic Acids. Methods Mol Biol 2024; 2813:309-320. [PMID: 38888786 DOI: 10.1007/978-1-0716-3890-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Nanoparticle carriers enable the multivalent delivery of nucleic acids to cells and protect them from degradation. In this chapter, we present a comprehensive overview of four methodologies: electrophoretic mobility shift assay (EMSA), alamarBlue/CFDA-AM cell viability dyes, fluorescence microscopy, and antiviral assays, which collectively are tools to explore interactions between nucleic acids and nanoparticles, and their biological efficacy. These assays provide insights into binding potential, cytotoxicity, and antiviral efficacy of nucleic acid-based nanoparticle treatments furthering the development of effective antiviral therapeutics.
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Affiliation(s)
| | | | | | | | | | - Andy Tran
- Wilfrid Laurier University, Waterloo, ON, Canada
| | - Aaron Lewis
- Wilfrid Laurier University, Waterloo, ON, Canada
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Fang X, Chen J, Yan F, Wu G. Subcellular Colocalization Assay of Host Factors with Viral Replication Complex in the dsRNA Reporter Nicotiana benthamiana. Methods Mol Biol 2024; 2771:39-45. [PMID: 38285389 DOI: 10.1007/978-1-0716-3702-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
As obligate pathogens, plant viruses co-opt several host factors for viral replication. Double-stranded RNA (dsRNA) plays important roles in plants, including eliciting innate immune responses and RNA interference. dsRNA also represents the genetic entities of a number of viruses and is a marker of infection by positive-sense single-stranded RNA viruses. Previous detection methods for RNA viruses basically relied on immunological methods, but later researchers discovered that the dsRNA-binding domain of the Flock house virus B2 protein is a perfect alternative to the J2 mAb for sensitive and rapid detection of long dsRNA in vitro and in vivo, and developed B2:GFP transgenic Nicotiana benthamiana line. This method describes in detail how to visualize host factors in the viral replication complex in time and space with the help of B2:GFP transgenic plants, exemplified by Turnip mosaic virus (TuMV), a representative virus member of the Potyviruses.
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Affiliation(s)
- Xinxin Fang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China.
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China.
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Bandilla L. Versatile open-source fluorescence documentation system. HARDWAREX 2023; 15:e00450. [PMID: 37457305 PMCID: PMC10345341 DOI: 10.1016/j.ohx.2023.e00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 06/03/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
Fluorescence has long been the best method for detecting bio-molecules at high sensitivity and with the possibility of easy data analysis and is routine for gel electrophoresis and much more. However, the systems for detecting the fluorophores remain expensive and thus inaccessible to many. Most commercial systems are often only optimized for one specific application, making reuse difficult. This paper demonstrates, characterizes and evaluates an inexpensive and versatile system for the detection of fluorophores with two wavelengths using high power LEDs. The LEDs are arranged in two banks angled downward at a tray in a way that allows for bright and uniform illumination while preventing direct reflections into the camera. The emitted light is filtered through an exchangeable filter frame and can be detected using the camera of a smartphone or similar device. By using filters both in front of the LEDs and the camera, very low background and using sufficient exposure times, very high sensitivity can be achieved. The two wavelengths of excitation light and the exchangeable filters allow for optimization for the specific fluorophore used and thus highest brightness.
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Semple SL, Vo NTK, Poynter SJ, Li M, Heath DD, DeWitte-Orr SJ, Dixon B. Extracellular dsRNA induces a type I interferon response mediated via class A scavenger receptors in a novel Chinook salmon derived spleen cell line. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 89:93-101. [PMID: 30118734 DOI: 10.1016/j.dci.2018.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Despite increased global interest in Chinook salmon aquaculture, little is known of their viral immune defenses. This study describes the establishment and characterization of a continuous cell line derived from Chinook salmon spleen, CHSS, and its use in innate immune studies. Optimal growth was seen at 14-18 °C when grown in Leibovitz's L-15 media with 20% fetal bovine serum. DNA analyses confirmed that CHSS was Chinook salmon and genetically different from the only other available Chinook salmon cell line, CHSE-214. Unlike CHSE-214, CHSS could bind extracellular dsRNA, resulting in the rapid and robust expression of antiviral genes. Receptor/ligand blocking assays confirmed that class A scavenger receptors (SR-A) facilitated dsRNA binding and subsequent gene expression. Although both cell lines expressed three SR-A genes: SCARA3, SCARA4, and SCARA5, only CHSS appeared to have functional cell-surface SR-As for dsRNA. Collectively, CHSS is an excellent cell model to study dsRNA-mediated innate immunity in Chinook salmon.
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Affiliation(s)
- S L Semple
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - N T K Vo
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - S J Poynter
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - M Li
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - D D Heath
- Great Lakes Institute of Environmental Research, University of Windsor, 2990 Riverside Drive, West Windsor, Ontario, N9C 1A2, Canada
| | - S J DeWitte-Orr
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada; Department of Health Sciences, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada
| | - B Dixon
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada.
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Poynter SJ, DeWitte-Orr SJ. Understanding Viral dsRNA-Mediated Innate Immune Responses at the Cellular Level Using a Rainbow Trout Model. Front Immunol 2018; 9:829. [PMID: 29740439 PMCID: PMC5924774 DOI: 10.3389/fimmu.2018.00829] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/20/2022] Open
Abstract
Viruses across genome types produce long dsRNA molecules during replication [viral (v-) dsRNA]. dsRNA is a potent signaling molecule and inducer of type I interferon (IFN), leading to the production of interferon-stimulated genes (ISGs), and a protective antiviral state within the cell. Research on dsRNA-induced immune responses has relied heavily on a commercially available, and biologically irrelevant dsRNA, polyinosinic:polycytidylic acid (poly I:C). Alternatively, dsRNA can be produced by in vitro transcription (ivt-) dsRNA, with a defined sequence and length. We hypothesized that ivt-dsRNA, containing legitimate viral sequence and length, would be a more appropriate proxy for v-dsRNA, compared with poly I:C. This is the first study to investigate the effects of v-dsRNA on the innate antiviral response and to compare v-dsRNA to ivt-dsRNA-induced responses in fish cells, specifically rainbow trout. Previously, class A scavenger receptors (SR-As) were found to be surface receptors for poly I:C in rainbow trout cells. In this study, ivt-dsRNA binding was blocked by poly I:C and v-dsRNA, as well as SR-A competitive ligands, suggesting all three dsRNA molecules are recognized by SR-As. Downstream innate antiviral effects were determined by measuring IFN and ISG transcript levels using qRT-PCR and antiviral assays. Similar to what has been shown previously with ivt-dsRNA, v-dsRNA was able to induce IFN and ISG transcript production between 3 and 24 h, and its effects were length dependent (i.e., longer v-dsRNA produced a stronger response). Interestingly, when v-dsRNA and ivt-dsRNA were length and sequence matched both molecules induced statistically similar IFN and ISG transcript levels, which resulted in similar antiviral states against two aquatic viruses. To pursue sequence effects further, three ivt-dsRNA molecules of the same length but different sequences (including host and viral sequences) were tested for their ability to induce IFN/ISG transcripts and an antiviral state. All three induced responses similarly. This study is the first of its kind to look at the effects v-dsRNA in fish cells as well as to compare ivt-dsRNA to v-dsRNA, and suggests that ivt-dsRNA may be a good surrogate for v-dsRNA in the study of dsRNA-induced responses and potential future antiviral therapies.
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Affiliation(s)
- Sarah J. Poynter
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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Monsion B, Incarbone M, Hleibieh K, Poignavent V, Ghannam A, Dunoyer P, Daeffler L, Tilsner J, Ritzenthaler C. Efficient Detection of Long dsRNA in Vitro and in Vivo Using the dsRNA Binding Domain from FHV B2 Protein. FRONTIERS IN PLANT SCIENCE 2018; 9:70. [PMID: 29449856 PMCID: PMC5799278 DOI: 10.3389/fpls.2018.00070] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/12/2018] [Indexed: 05/17/2023]
Abstract
Double-stranded RNA (dsRNA) plays essential functions in many biological processes, including the activation of innate immune responses and RNA interference. dsRNA also represents the genetic entity of some viruses and is a hallmark of infections by positive-sense single-stranded RNA viruses. Methods for detecting dsRNA rely essentially on immunological approaches and their use is often limited to in vitro applications, although recent developments have allowed the visualization of dsRNA in vivo. Here, we report the sensitive and rapid detection of long dsRNA both in vitro and in vivo using the dsRNA binding domain of the B2 protein from Flock house virus. In vitro, we adapted the system for the detection of dsRNA either enzymatically by northwestern blotting or by direct fluorescence labeling on fixed samples. In vivo, we produced stable transgenic Nicotiana benthamiana lines allowing the visualization of dsRNA by fluorescence microscopy. Using these techniques, we were able to discriminate healthy and positive-sense single-stranded RNA virus-infected material in plants and insect cells. In N. benthamiana, our system proved to be very potent for the spatio-temporal visualization of replicative RNA intermediates of a broad range of positive-sense RNA viruses, including high- vs. low-copy number viruses.
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Affiliation(s)
- Baptiste Monsion
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Marco Incarbone
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Kamal Hleibieh
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Vianney Poignavent
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Ahmed Ghannam
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Patrice Dunoyer
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Laurent Daeffler
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Jens Tilsner
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Christophe Ritzenthaler
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
- *Correspondence: Christophe Ritzenthaler
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