Reviewer
Vamseedhar Rayaprolu
  • Cryo-EM Microscopist 2, Oregon Health and Sciences University
Research fields
  • Biophysics
Image-based Quantification of Direct Cell-to-cell Transmission of Bovine Viral Diarrhea Virus
Authors:  Fernando Merwaiss and Diego E. Alvarez, date: 08/05/2019, view: 4141, Q&A: 0
Different viruses rely on direct cell-to-cell transmission to propagate infection within the infected host. Measuring this mode of transmission in cultured cells is often complicated by the contribution of cell free viruses to spread, and the difficulty to distinguish between primary infected cells that produce the virus and neighboring cells that are the target of spreading. Here, we present a protocol to quantify cell-to-cell transmission of the model pestivirus bovine viral diarrhea virus that is based on the co-culture of producer cells that are infected with a reporter virus expressing mCherry and target cells that stably express GFP. Spread of cell-free viruses is blocked by the presence of a neutralizing antibody in the cell culture medium, and cell-associated transmission is unequivocally quantified by numbering cells that are positive for both GFP and mCherry using automated analysis of fluorescence microscopy images.
Analysis of Functional Virus-generated PAMP RNAs Using IFNα/β ELISA Assay
Authors:  Margit Mutso, Xiang Liu, Andres Merits and Suresh Mahalingam, date: 06/20/2019, view: 3930, Q&A: 0
Virus-generated PAMP RNAs are key factors that activate host immune response. The PAMP RNAs are therefore usually closely related with viral disease pathogenesis. Quantitative real time PCR is a conventional method to assess RNA. However, it cannot be used for detecting short dsRNAs generated by viral replicase. This protocol was established to analyze the PAMP RNAs produced by viruses which are able to induce host immune response. Classical viral PAMP RNAs and non-classical viral PAMP RNAs are analyzed separately. Briefly, to access total viral PAMP RNAs, total RNA was extracted from the virus infected cells and then transfected into Cop5 cells. Whereas, to assess non-classical viral PAMP RNAs, the constructs expressing viral replicase are transfected into Cop5 cells. The amount of IFNα/β produced by Cop5 cells, determined by ELISA, is correlated with the total and non-classical viral PAMP RNAs. Since this method is based on type I IFN response, it is therefore suitable for measuring the functional virus-generated PAMP RNAs and also for assessing the efficiency of these PAMP RNAs.
Viral Chromosome Conformation Capture (V3C) Assays for Identifying Trans-interaction Sites between Lytic Viruses and the Cellular Genome
Authors:  Kinjal Majumder, Maria Boftsi and David J Pintel, date: 03/20/2019, view: 4072, Q&A: 0
The folding mechanisms of the mammalian genome package our genetic material into the nucleus, and in doing so, dictate its appropriate replication and expression. Chromosome conformation capture technology has enabled the dissection of the folding principles of the cellular genome. This has led to a better understanding of the role played by architectural proteins in forming and dissolving 3D-chromatin-structure. These assays are based on the principle of crosslinking distant cellular sites that are proximal to each other in 3D space using formaldehyde followed by digestion of formed hybrid DNA junctions. Invading viruses, such as the lytic parvovirus Minute Virus of Mice (MVM), establish distinct replication centers within the nuclear environment at cellular sites that preferentially undergo DNA damage, but do not integrate into the cellular DNA. We have adapted chromosome conformation capture technology to study the trans-interaction between MVM and the cellular genome, which we have dubbed V3C, which can be extended to a whole-genome analysis we term V3C-seq. This protocol describes the procedure for performing, as well as analyzing V3C-seq assays, and can be adapted for mapping the cellular interaction sites of any non-integrating DNA virus.
On-demand Labeling of SNAP-tagged Viral Protein for Pulse-Chase Imaging, Quench-Pulse-Chase Imaging, and Nanoscopy-based Inspection of Cell Lysates
Authors:  Roland Remenyi, Raymond Li and Mark Harris, date: 02/20/2019, view: 5144, Q&A: 0
Advanced labeling technologies allow researchers to study protein turnover inside intact cells and to track the labeled protein in downstream applications. In the context of a viral infection, the combination of imaging and fluorescent labeling of viral proteins sheds light on their biological activity and interaction with the host cell. Initial approaches have fused fluorescent proteins such as green fluorescent protein (GFP) to the viral protein-of-interest. In contrast, self-labeling enzyme tags such as the commercial SNAP-tag, a modified version of human O6-alkylguanine-DNA-alkyltransferase, covalently link synthetic ligands, which users can add on demand. The first two protocols presented here build on previously published protocols for fluorescent labeling in pulse-chase and quench-pulse-chase experiments; the combination of fluorescent labeling with advanced light microscopy visualizes the dynamic turnover of the SNAP-tagged viral protein in intact mammalian cells. A third protocol also outlines how to inspect cellular lysates microscopically for detergent-resistant assemblies of the labeled viral protein. These protocols showcase the flexibility of the SNAP-based labeling system for tracking a viral protein-of-interest in live cells, intact fixed cells, and cell lysates. Moreover, the protocols employ recently developed commercial microscopes (e.g., Airyscan microscopy) that balance resolution, speed, phototoxicity, photobleaching, and ease-of-use.
Detection of Ligand-binding to Membrane Proteins by Capacitance Measurements
Authors:  Verena Burtscher, Matej Hotka and Walter Sandtner, date: 01/05/2019, view: 5107, Q&A: 0
In multi-cellular organisms, cells communicate with each other utilizing chemical messengers. For many of these messenger molecules, the membrane is an insurmountable barrier. Yet, they act by binding to surface proteins often triggering a cascade of reactions inside the cell. Accordingly, studying ligand-receptor interactions at the cellular surface is key to understanding important aspects of membrane biology. However, despite a multitude of approaches to study membrane features, there is a need for developing techniques that can measure ligand binding with high temporal resolution and on a single cellular level. We recently developed a label-free approach to study ligand binding in real time. This methodology capitalizes on changes of the membrane’s surface potential induced by the adsorption of a charged ligand. The resulting apparent alteration of membrane capacitance is measurable by capacitance recordings. Herein, we describe the implementation of the same using recordings obtained from HEK293 cells stably expressing the human serotonin transporter (SERT), which were challenged with the inhibitor cocaine.
Quantitation of Regulatory Activity for the Complement Alternative Pathway Using an Adaptation of the AP50 in vitro Assay
Authors:  Sheila Cabezas Falcon, David L Gordon and Jillian M Carr, date: 12/20/2018, view: 5252, Q&A: 2
Complement pathways function to identify and remove pathogens and infected cells. There are three complement pathways: the classical, lectin and alternative pathway (AP). While all pathways are activated following pathogen stimuli, the AP is constitutively active and tightly controlled by activators (e.g., Factor B, Factor D) and negative regulators (e.g., Factor H). Complement activity can be measured by well-established methods that are often used in a diagnostic setting to determine the CH50 (50% complement hemolytic activity) or AP50, specifically to measure AP activity. The protocol here has adapted the traditional AP50 method designed to measure AP activity in human sera, to measure the positive or negative AP regulatory activity within a given test sample. The assay relies on the ability of AP components in human serum to lyse rabbit erythrocytes under in vitro conditions specific for the AP with subsequent release of hemoglobin that is quantitated by measurement of optical density. Our method has added test substances, such as cell culture media with defined changes in individual complement components and determined the ability to either promote or inhibit AP activity in vitro. Thus, this protocol reflects the overall functional ability of a sample to effect AP activity and can be used in the research laboratory to determine AP regulatory activity in a complex biological sample, or to test the ability of drugs or novel biomolecules to regulate AP activity.
Fluorescence Titrations to Determine the Binding Affinity of Cyclic Nucleotides to SthK Ion Channels
Authors:  Philipp A.M. Schmidpeter and Crina M. Nimigean, date: 10/05/2018, view: 7881, Q&A: 0
The cyclic-nucleotide modulated ion channel family includes cyclic nucleotide-gated (CNG) and hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels, which play essential roles in visual and olfactory signaling and the heart pacemaking activity. Functionally, these channels have been extensively characterized by electrophysiological techniques from protein heterologously expressed in Xenopus oocytes and mammalian cells. On the other hand, expression and purification of these proteins for biophysical and structural analyses in vitro is problematic and expensive and, accordingly, only limited information on the purified channels is available in the literature. Here we describe a protocol for binding studies of fluorescently labeled cyclic nucleotides to a homologue of eukaryotic CNG channels. Furthermore, we describe how to directly probe binding of unlabeled cyclic nucleotides in a competition assay. The use of fluorescence as a sensitive probe for ligand binding reduces the amount of protein needed and enables fast and easy measurements using standard laboratory equipment.
Retroviral Capsid Core Stability Assay
Authors:  Tyler Milston Renner, Kasandra Bélanger and Marc-André Langlois, date: 09/20/2018, view: 4915, Q&A: 0
Structural stability of the capsid core is a critical parameter for the productive infection of a cell by a retrovirus. Compromised stability can lead to premature core disassembly, exposure of replication intermediates to cytosolic nucleic acid sensors that can trigger innate antiviral responses, and failure to integrate the proviral genome into the host DNA. Thus, core stability is a critical feature of viral replicative fitness. While there are several well-described techniques to assess viral capsid core stability, most are generally time and labor intensive. Recently, our group compared the relative stability of murine leukemia virus capsid cores using an in vitro detergent-based approach combined with ultracentrifugation against the popular fate of capsid assay. We found that both methods reached similar conclusions, albeit the first method was a significantly simpler and faster way to assess relative capsid core stability when comparing viral mutants exhibiting differences in core stability.
Selective Isolation of Retroviruses from Extracellular Vesicles by Intact Virion Immunoprecipitation
Authors:  Tyler Milston Renner, Kasandra Bélanger and Marc-André Langlois, date: 09/05/2018, view: 10520, Q&A: 0
There exists a wide variety of techniques to isolate and purify viral particles from cell culture supernatants. However, these techniques vary greatly in ease of use, purity, yield and impact on viral structural integrity. Most importantly, it is becoming evident that secreted extracellular vesicles (EVs) co-purify with retroviruses using nearly all purification methods due to nearly indistinguishable biophysical characteristics such as size, buoyant density and nucleic acid content. Recently, our group has illustrated a means of isolating intact and highly enriched retroviral virions from EV-containing cell supernatants using an immunoprecipitation approach targeting the viral envelope glycoprotein of the Moloney Murine Leukemia Virus (Renner et al., 2018). This technique, that we call intact virion immunoprecipitation (IVIP), enabled us to characterize the accessibility of epitopes on the surface of these retroviruses and assess the orientation of the virus-encoded integral membrane protein Glycogag (gPr80) in the viral envelope. Proper implementation of this protocol enables fast, simple and reproducible preparations of intact and highly purified retroviral particles devoid of detectable EV contaminants.
Analysis of the Effect of Sphingomyelinase on Rubella Virus Infectivity in Two Cell Lines
Authors:  Noriyuki Otsuki, Masafumi Sakata, Yoshio Mori, Kiyoko Okamoto and Makoto Takeda, date: 09/05/2018, view: 5033, Q&A: 0
Rubella is a mildly contagious disease characterized by low-grade fever and a morbilliform rash caused by the rubella virus (RuV). Viruses often use cellular phospholipids for infection. We studied the roles of cellular sphingomyelin in RuV infection. Treatment of cells with sphingomyelinase (SMase) inhibited RuV infection in rabbit kidney-derived RK13 cells and African green monkey (Cercopithecus aethiops) kidney-derived Vero cells. Our data further demonstrated that RuV used cellular sphingomyelin and cholesterol for its binding to cells and membrane fusion at the step of virus entry. Detailed protocols of our assays, which assess the effects of SMase treatment on RuV infectivity in RK13 and Vero cells, are described.
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