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Evans EL, Pocock GM, Einsdorf G, Behrens RT, Dobson ETA, Wiedenmann M, Birkhold C, Ahlquist P, Eliceiri KW, Sherer NM. HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME. Viruses 2022; 14:903. [PMID: 35632645 PMCID: PMC9145009 DOI: 10.3390/v14050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell imaging has emerged as a powerful means to study viral replication dynamics and identify sites of virus−host interactions. Multivariate aspects of viral replication cycles yield challenges inherent to handling large, complex imaging datasets. Herein, we describe the design and implementation of an automated, imaging-based strategy, “Human Immunodeficiency Virus Red-Green-Blue” (HIV RGB), for deriving comprehensive single-cell measurements of HIV-1 unspliced (US) RNA nuclear export, translation, and bulk changes to viral RNA and protein (HIV-1 Rev and Gag) subcellular distribution over time. Differentially tagged fluorescent viral RNA and protein species are recorded using multicolor long-term (>24 h) time-lapse video microscopy, followed by image processing using a new open-source computational imaging workflow dubbed “Nuclear Ring Segmentation Analysis and Tracking” (NR-SAT) based on ImageJ plugins that have been integrated into the Konstanz Information Miner (KNIME) analytics platform. We describe a typical HIV RGB experimental setup, detail the image acquisition and NR-SAT workflow accompanied by a step-by-step tutorial, and demonstrate a use case wherein we test the effects of perturbing subcellular localization of the Rev protein, which is essential for viral US RNA nuclear export, on the kinetics of HIV-1 late-stage gene regulation. Collectively, HIV RGB represents a powerful platform for single-cell studies of HIV-1 post-transcriptional RNA regulation. Moreover, we discuss how similar NR-SAT-based design principles and open-source tools might be readily adapted to study a broad range of dynamic viral or cellular processes.
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Affiliation(s)
- Edward L. Evans
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ginger M. Pocock
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Gabriel Einsdorf
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
| | - Ellen T. A. Dobson
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
| | - Marcel Wiedenmann
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | | | - Paul Ahlquist
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Morgridge Institute for Research, Madison, WI 53715, USA
- John and Jeanne Rowe Center for Research in Virology, Madison, WI 53715, USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
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Etheridge T, Dobson ETA, Wiedenmann M, Oden N, VanVeldhuisen P, Scott IU, Ip MS, Eliceiri KW, Blodi BA, Domalpally A. Ellipsoid Zone Defects in Retinal Vein Occlusion Correlates With Visual Acuity Prognosis: SCORE2 Report 14. Transl Vis Sci Technol 2021; 10:31. [PMID: 34003964 PMCID: PMC7998009 DOI: 10.1167/tvst.10.3.31] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose To evaluate the association between ellipsoid zone (EZ) on spectral domain optical coherence tomography (SD-OCT) and visual acuity letter score (VALS) in participants with retinal vein occlusion in the Study of Comparative Treatments for Retinal Vein Occlusion 2. Methods SD-OCT scans of 362 participants were qualitatively assessed at baseline and months 1, 6, 12, and 24 for EZ status as normal, patchy, or absent. The thickness of EZ layer in the central subfield was also obtained using machine learning. Results EZ assessments were not possible at baseline due to signal blockage in >75% of eyes. At month 1, EZ was normal in 37.6%, patchy in 48.1%, and absent in 14.3%. EZ was measurable in 48.7% with a mean area of 0.07 ± 0.16 mm2. Mean VALS was better in eyes without an EZ defect compared to eyes with an EZ defect (P < 0.0001 at all visits). EZ defect at month 1 was associated with poorer VALS at all follow-up visits (P < 0.0001). Conclusions Both qualitative and quantitative assessments of EZ status strongly correlated with VALS. Absence of EZ was associated with poorer VALS at both corresponding and future visits, with larger areas of EZ loss associated with worse VALS. Translational Relevance Assessment of EZ can be used to identify patients with potentially poor response in eyes with retinal vein occlusion.
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Affiliation(s)
- Tyler Etheridge
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ellen T A Dobson
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Neal Oden
- The Emmes Company, LLC, Rockville, MD, USA
| | | | - Ingrid U Scott
- Departments of Ophthalmology and Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Michael S Ip
- Doheny Eye Institute, University of California Los Angeles Stein Eye Institute, Los Angeles, CA, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Barbara A Blodi
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Amitha Domalpally
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
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Etheridge T, Dobson ETA, Wiedenmann M, Papudesu C, Scott IU, Ip MS, Eliceiri KW, Blodi BA, Domalpally A. A semi-automated machine-learning based workflow for ellipsoid zone analysis in eyes with macular edema: SCORE2 pilot study. PLoS One 2020; 15:e0232494. [PMID: 32353052 PMCID: PMC7192485 DOI: 10.1371/journal.pone.0232494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background and objective To develop a semi-automated, machine-learning based workflow to evaluate the ellipsoid zone (EZ) assessed by spectral domain optical coherence tomography (SD-OCT) in eyes with macular edema secondary to central retinal or hemi-retinal vein occlusion in SCORE2 treated with anti-vascular endothelial growth factor agents. Methods SD-OCT macular volume scans of a randomly selected subset of 75 SCORE2 study eyes were converted to the Digital Imaging and Communications in Medicine (DICOM) format, and the EZ layer was segmented using nonproprietary software. Segmented layer coordinates were exported and used to generate en face EZ thickness maps. Within the central subfield, the area of EZ defect was measured using manual and semi-automated approaches via a customized workflow in the open-source data analytics platform, Konstanz Information Miner (KNIME). Results A total of 184 volume scans from 74 study eyes were analyzed. The mean±SD area of EZ defect was similar between manual (0.19±0.22 mm2) and semi-automated measurements (0.19±0.21 mm2, p = 0.93; intra-class correlation coefficient = 0.90; average bias = 0.01, 95% confidence interval of limits of agreement -0.18–0.20). Conclusions A customized workflow generated via an open-source data analytics platform that applied machine-learning methods demonstrated reliable measurements of EZ area defect from en face thickness maps. The result of our semi-automated approach were comparable to manual measurements.
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Affiliation(s)
- Tyler Etheridge
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Ellen T. A. Dobson
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, United States of America
| | | | - Chandana Papudesu
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Ingrid U. Scott
- Departments of Ophthalmology and Public Health Sciences, Penn State College of Medicine, Hershey, PA, United States of America
| | - Michael S. Ip
- Doheny Eye Institute, University of California Los Angeles Stein Eye Institute, Los Angeles, CA, United States of America
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Barbara A. Blodi
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Amitha Domalpally
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- * E-mail:
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Matuschek G, Wiedenmann M, Kettrup A. Determination of the partial pressure of single low volatile compounds in mixtures. Anal Bioanal Chem 1996; 354:833-5. [PMID: 15048397 DOI: 10.1007/s0021663540833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/1995] [Revised: 12/07/1995] [Accepted: 12/12/1995] [Indexed: 11/25/2022]
Abstract
A new measuring system for the determination of the vapour pressure of single compounds in mixtures is introduced. A coupling system consisting of a quadrupol mass spectrometer and a vapour pressure balance was used for these measurements. Some calibration measurements and investigations of mixtures are discussed.
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Affiliation(s)
- G Matuschek
- Institut für Okologische Chemie, GSF-Forschungszentrum für Umwelt und Gesundheit, Postfach 1129, D-85758, Oberschleissheim, Germany
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Eder E, Wiedenmann M, Deininger C, Kütt W. The relationship between mutagenicity in His G46 Salmonella and the O6-guanine alkylation in bacterial DNA by monofunctional methanesulphonates. Toxicol In Vitro 1990; 4:167-74. [DOI: 10.1016/0887-2333(90)90017-n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/1989] [Revised: 09/26/1989] [Indexed: 11/25/2022]
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Abstract
No mutagenicity or an uncertain mutagenic response has been reported in the literature for methyl methanesulphonate (MMS) in S. typhimurium strain TA1535 when using the plate assay. In our studies we found a reproducible mutagenic activity of 62 revertants/mumole and plate for MMS in strain TA1535 when using the preincubation assay. A dose-dependent increase in revertants was, however, observed only at fairly high doses (exceeding 4 mumole). Two different slopes were observed in the dose-response curve when testing MMS with strain TA100. Slope A is dependent on the error-prone response, possible only in strain TA100 due to the pKm101 plasmid (R factor) but not possible in strain TA1535 due to its umuDC deficiency. Slope B observed at higher doses (as in strain TA1535) could be explained through a GC----AT transition initiated by the O6-methylation of guanine. Our findings demonstrate that MMS induces back mutation in S. typhimurium strains carrying the hisG46 missense mutation due to the formation of O6-methylguanine. In the case of strain TA100 the pKm101 plasmid-mediated error-prone mechanism is, however, the predominant process in MMS mutagenesis which leads to a higher mutagenic response at much lower doses than the GT----AT transition in strain TA1535.
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Affiliation(s)
- E Eder
- Institute of Toxicology, University of Würzburg, F.R.G
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Hoffman C, Bastian H, Wiedenmann M, Deininger C, Eder E. Detection of acrolein congener-DNA adducts isolated from cellular systems. Arch Toxicol Suppl 1989; 13:219-23. [PMID: 2673145 DOI: 10.1007/978-3-642-74117-3_34] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C Hoffman
- Institute of Toxicology, University of Würzburg, Fed. Rep. Germany
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