title: Plaque2.0-A High-Throughput Analysis Framework to Score Virus-Cell Transmission and Clonal Cell Expansion.
abstract: Classical plaque assay measures the propagation of infectious agents across a monolayer of cells. It is dependent on cell lysis, and limited by user-specific settings and low throughput. Here, we developed Plaque2.0, a broadly applicable, fluorescence microscopy-based high-throughput method to mine patho-biological clonal cell features. Plaque2.0 is an open source framework to extract information from chemically fixed cells by immuno-histochemistry or RNA in situ hybridization, or from live cells expressing GFP transgene. Multi-parametric measurements include infection density, intensity, area, shape or location information at single plaque or population levels. Plaque2.0 distinguishes lytic and non-lytic spread of a variety of DNA and RNA viruses, including vaccinia virus, adenovirus and rhinovirus, and can be used to visualize simultaneous plaque formation from co-infecting viruses. Plaque2.0 also analyzes clonal growth of cancer cells, which is relevant for cell migration and metastatic invasion studies. Plaque2.0 is suitable to quantitatively analyze virus infections, vector properties, or cancer cell phenotypes.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Artur
authors.initials: A
authors.lastname: Yakimovich
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Vardan
authors.initials: V
authors.lastname: Andriasyan
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Robert
authors.initials: R
authors.lastname: Witte
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: I-Hsuan
authors.initials: IH
authors.lastname: Wang
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Vibhu
authors.initials: V
authors.lastname: Prasad
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Maarit
authors.initials: M
authors.lastname: Suomalainen
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Urs F
authors.initials: UF
authors.lastname: Greber
mesh_terms: D000256:Adenoviridae / Q000502:physiology; D000818:Animals; D002452:Cell Count; D002460:Cell Line; D049109:Cell Proliferation; D002999:Clone Cells; D018920:Coculture Techniques; D005838:Genotype; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008856:Microscopy, Fluorescence; D009369:Neoplasms / Q000473:pathology; D010641:Phenotype; D010850:Picornaviridae Infections / Q000821:virology; D012229:Rhinovirus / Q000235:genetics; D012984:Software; D059008:Time-Lapse Imaging; D014616:Vaccinia virus; D010948:Viral Plaque Assay / Q000379:methods*; D014780:Viruses / Q000378:metabolism*