1
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Balabdaoui F, Wierzbicki T, Bao E. Reconstruction of the real 3D shape of the SARS-CoV-2 virus. Biophys J 2024; 123:1297-1310. [PMID: 38715359 PMCID: PMC11140469 DOI: 10.1016/j.bpj.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/23/2024] [Accepted: 04/19/2024] [Indexed: 05/19/2024] Open
Abstract
The photographs of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus taken by electron transmission microscopy and cryoelectron microscopy provide only a 2D silhouette. The viruses appear to look like distorted circles. The present paper questions the real shape of the SARS-CoV-2 virus and makes an attempt to give an answer. Is this a general ellipsoid, a spheroid with rotational symmetry, a sphere, or something else? The answer requires the application of tools from three different disciplines: structural mechanics, microbiology, and statistics. A total of 590 virus photographs taken from 22 recently published papers were examined. From this experimental data pool, the histogram of diameter ratios was built from the 283 measurements where the virus images could be approximated as ellipses. The curve peaks at the diameter ratio of 1.22. The transformation equation for the spatial shape to the planar shade was derived for a fixed light source of the microscope. This equation involves an unknown orientation of the viruses with respect to the microscope. Two sets of models were developed, one with a uniform distribution of the virus orientation and the other with the orientation defined by the normalized beta distribution. In both sets of models, the unknown diameter ratio of the spheroidal virus was regarded as a random realization from translated gamma distributions. The parameters of the distribution of the kernel functions were determined by minimizing the mean square difference between the predicted and measured 2D histograms. The information included in the measured histograms was found to be insufficient to find an unknown distribution of the virus's orientation. Simply too many unknown parameters render the solution physically unrealistic. The minimization procedure with a uniform probability of virus orientation predicted the peak of the aspect ratio of the 3D spheroid at 1.32. Based on this result, models of the virus will be developed in the continuation of this research for a full dynamic analysis.
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Affiliation(s)
| | | | - Emma Bao
- Duke University, Durham, North Carolina
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2
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Guo K, Grünberg R, Ren Y, Chang T, Wustoni S, Strnad O, Koklu A, Díaz-Galicia E, Agudelo JP, Druet V, Castillo TCH, Moser M, Ohayon D, Hama A, Dada A, McCulloch I, Viola I, Arold ST, Inal S. SpyDirect: A Novel Biofunctionalization Method for High Stability and Longevity of Electronic Biosensors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2306716. [PMID: 38161228 DOI: 10.1002/advs.202306716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Electronic immunosensors are indispensable tools for diagnostics, particularly in scenarios demanding immediate results. Conventionally, these sensors rely on the chemical immobilization of antibodies onto electrodes. However, globular proteins tend to adsorb and unfold on these surfaces. Therefore, self-assembled monolayers (SAMs) of thiolated alkyl molecules are commonly used for indirect gold-antibody coupling. Here, a limitation associated with SAMs is revealed, wherein they curtail the longevity of protein sensors, particularly when integrated into the state-of-the-art transducer of organic bioelectronics-the organic electrochemical transistor. The SpyDirect method is introduced, generating an ultrahigh-density array of oriented nanobody receptors stably linked to the gold electrode without any SAMs. It is accomplished by directly coupling cysteine-terminated and orientation-optimized spyTag peptides, onto which nanobody-spyCatcher fusion proteins are autocatalytically attached, yielding a dense and uniform biorecognition layer. The structure-guided design optimizes the conformation and packing of flexibly tethered nanobodies. This biolayer enhances shelf-life and reduces background noise in various complex media. SpyDirect functionalization is faster and easier than SAM-based methods and does not necessitate organic solvents, rendering the sensors eco-friendly, accessible, and amenable to scalability. SpyDirect represents a broadly applicable biofunctionalization method for enhancing the cost-effectiveness, sustainability, and longevity of electronic biosensors, all without compromising sensitivity.
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Affiliation(s)
- Keying Guo
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yuxiang Ren
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tianrui Chang
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Shofarul Wustoni
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ondrej Strnad
- Computer, Electrical and Mathematical Science and Engineering, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Anil Koklu
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Escarlet Díaz-Galicia
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jessica Parrado Agudelo
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Victor Druet
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tania Cecilia Hidalgo Castillo
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Maximilian Moser
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - David Ohayon
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Adel Hama
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ashraf Dada
- King Faisal Specialist Hospital & Research Centre (KFSH-RC), Jeddah, 21499, Saudi Arabia
| | - Iain McCulloch
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Ivan Viola
- Computer, Electrical and Mathematical Science and Engineering, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, F-34090, France
| | - Sahika Inal
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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3
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Nonn A, Kiss B, Pezeshkian W, Tancogne-Dejean T, Cerrone A, Kellermayer M, Bai Y, Li W, Wierzbicki T. Inferring mechanical properties of the SARS-CoV-2 virus particle with nano-indentation tests and numerical simulations. J Mech Behav Biomed Mater 2023; 148:106153. [PMID: 37865016 DOI: 10.1016/j.jmbbm.2023.106153] [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] [Received: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/23/2023]
Abstract
The pandemic caused by the SARS-CoV-2 virus has claimed more than 6.5 million lives worldwide. This global challenge has led to accelerated development of highly effective vaccines tied to their ability to elicit a sustained immune response. While numerous studies have focused primarily on the spike (S) protein, less is known about the interior of the virus. Here we propose a methodology that combines several experimental and simulation techniques to elucidate the internal structure and mechanical properties of the SARS-CoV-2 virus. The mechanical response of the virus was analyzed by nanoindentation tests using a novel flat indenter and evaluated in comparison to a conventional sharp tip indentation. The elastic properties of the viral membrane were estimated by analytical solutions, molecular dynamics (MD) simulations on a membrane patch and by a 3D Finite Element (FE)-beam model of the virion's spike protein and membrane molecular structure. The FE-based inverse engineering approach provided a reasonable reproduction of the mechanical response of the virus from the sharp tip indentation and was successfully verified against the flat tip indentation results. The elastic modulus of the viral membrane was estimated in the range of 7-20 MPa. MD simulations showed that the presence of proteins significantly reduces the fracture strength of the membrane patch. However, FE simulations revealed an overall high fracture strength of the virus, with a mechanical behavior similar to the highly ductile behavior of engineering metallic materials. The failure mechanics of the membrane during sharp tip indentation includes progressive damage combined with localized collapse of the membrane due to severe bending. Furthermore, the results support the hypothesis of a close association of the long membrane proteins (M) with membrane-bound hexagonally packed ribonucleoproteins (RNPs). Beyond improved understanding of coronavirus structure, the present findings offer a knowledge base for the development of novel prevention and treatment methods that are independent of the immune system.
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Affiliation(s)
- Aida Nonn
- CMM Lab, Faculty of Mechanical Engineering, OTH Regensburg, 93053, Regensburg, Germany.
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, H-1094, Hungary; ELKH-SE Biophysical Virology Research Group, Budapest, H-1094, Hungary
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
| | | | - Albert Cerrone
- Computational Hydraulics Laboratory, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Miklos Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, H-1094, Hungary; ELKH-SE Biophysical Virology Research Group, Budapest, H-1094, Hungary
| | - Yuanli Bai
- Department of Mechanical and Aerospace of Engineering, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL, 32816, USA
| | - Wei Li
- Impact and Crashworthiness Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tomasz Wierzbicki
- Impact and Crashworthiness Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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4
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Cardoso-Lima R, Santos-Oliveira R, Souza PFN, Barbosa LRS, Wuite GJL, Alencar LMR. Physical virology: how physics is enabling a better understanding of recent viral invaders. Biophys Rev 2023; 15:611-623. [PMID: 37681101 PMCID: PMC10480132 DOI: 10.1007/s12551-023-01075-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/04/2023] [Indexed: 09/09/2023] Open
Abstract
The world is frequently afflicted by several viral outbreaks that bring diseases and health crises. It is vital to comprehend how viral assemblies' fundamental components work to counteract them. Determining the ultrastructure and nanomechanical characteristics of viruses from a physical standpoint helps categorize their mechanical characteristics, offers insight into new treatment options, and/or shows weak spots that can clarify methods for medication targeting. This study compiles the findings from studies on the ultrastructure and nanomechanical behavior of SARS-CoV-2, ZIKV (Zika virus), and CHIKV (Chikungunya virus) viral particles. With results that uncovered aspects of the organization and the spatial distribution of the proteins on the surface of the viral particle as well as the deformation response of the particles when applied a recurring loading force, this review aims to provide further discussion on the mechanical properties of viral particles at the nanoscale, offering new prospects that could be employed for designing strategies for the prevention and treatment of viral diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-023-01075-4.
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Affiliation(s)
- Ruana Cardoso-Lima
- Physics Department, Laboratory of Biophysics and Nanosystems, Federal University of Maranhão, São Luís, MA Brazil
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ralph Santos-Oliveira
- Brazilian Nuclear Energy Commission, Nuclear Engineering Institute, Rio de Janeiro, 21941906 Brazil
- Laboratory of Nanoradiopharmacy, Rio de Janeiro State University, Rio de Janeiro, 23070200 Brazil
| | - Pedro Filho Noronha Souza
- Department of Biochemistry, Federal University of Ceará, Fortaleza, CE Brazil
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE Brazil
| | - Leandro R. S. Barbosa
- Department of General Physics, Institute of Physics, University of São Paulo, São Paulo, SP 05508-000 Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-100 Brazil
| | - Gijs J. L. Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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5
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Kouril D, Strnad O, Mindek P, Halladjian S, Isenberg T, Groller ME, Viola I. Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023; 29:1733-1747. [PMID: 34822330 DOI: 10.1109/tvcg.2021.3130670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present a method for producing documentary-style content using real-time scientific visualization. We introduce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology, created through adaptable methods instead of the rigid traditional production pipeline. Our work is motivated by the rapid evolution of scientific visualization and it potential in science dissemination. Without some form of explanation or guidance, however, novices and lay-persons often find it difficult to gain insights from the visualization itself. We integrate such knowledge using the verbal channel and provide it along an engaging visual presentation. To realize the synthesis of a molecumentary, we provide technical solutions along two major production steps: (1) preparing a story structure and (2) turning the story into a concrete narrative. In the first step, we compile information about the model from heterogeneous sources into a story graph. We combine local knowledge with external sources to complete the story graph and enrich the final result. In the second step, we synthesize a narrative, i.e., story elements presented in sequence, using the story graph. We then traverse the story graph and generate a virtual tour, using automated camera and visualization transitions. We turn texts written by domain experts into verbal representations using text-to-speech functionality and provide them as a commentary. Using the described framework, we synthesize fly-throughs with descriptions: automatic ones that mimic a manually authored documentary or semi-automatic ones which guide the documentary narrative solely through curated textual input.
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6
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Alharbi R, Strnad O, Luidolt LR, Waldner M, Kouril D, Bohak C, Klein T, Groller E, Viola I. Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023; 29:1860-1875. [PMID: 34882555 DOI: 10.1109/tvcg.2021.3133592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immersive virtual reality environments are gaining popularity for studying and exploring crowded three-dimensional structures. When reaching very high structural densities, the natural depiction of the scene produces impenetrable clutter and requires visibility and occlusion management strategies for exploration and orientation. Strategies developed to address the crowdedness in desktop applications, however, inhibit the feeling of immersion. They result in nonimmersive, desktop-style outside-in viewing in virtual reality. This article proposes Nanotilus-a new visibility and guidance approach for very dense environments that generates an endoscopic inside-out experience instead of outside-in viewing, preserving the immersive aspect of virtual reality. The approach consists of two novel, tightly coupled mechanisms that control scene sparsification simultaneously with camera path planning. The sparsification strategy is localized around the camera and is realized as a multi-scale, multi-shell, variety-preserving technique. When Nanotilus dives into the structures to capture internal details residing on multiple scales, it guides the camera using depth-based path planning. In addition to sparsification and path planning, we complete the tour generation with an animation controller, textual annotation, and text-to-visualization conversion. We demonstrate the generated guided tours on mesoscopic biological models - SARS-CoV-2 and HIV. We evaluate the Nanotilus experience with a baseline outside-in sparsification and navigational technique in a formal user study with 29 participants. While users can maintain a better overview using the outside-in sparsification, the study confirms our hypothesis that Nanotilus leads to stronger engagement and immersion.
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7
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Afzal S, Ghani S, Hittawe MM, Rashid SF, Knio OM, Hadwiger M, Hoteit I. Visualization and Visual Analytics Approaches for Image and Video Datasets: A Survey. ACM T INTERACT INTEL 2023. [DOI: 10.1145/3576935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Image and video data analysis has become an increasingly important research area with applications in different domains such as security surveillance, healthcare, augmented and virtual reality, video and image editing, activity analysis and recognition, synthetic content generation, distance education, telepresence, remote sensing, sports analytics, art, non-photorealistic rendering, search engines, and social media. Recent advances in Artificial Intelligence (AI) and particularly deep learning have sparked new research challenges and led to significant advancements, especially in image and video analysis. These advancements have also resulted in significant research and development in other areas such as visualization and visual analytics, and have created new opportunities for future lines of research. In this survey paper, we present the current state of the art at the intersection of visualization and visual analytics, and image and video data analysis. We categorize the visualization papers included in our survey based on different taxonomies used in visualization and visual analytics research. We review these papers in terms of task requirements, tools, datasets, and application areas. We also discuss insights based on our survey results, trends and patterns, the current focus of visualization research, and opportunities for future research.
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Affiliation(s)
- Shehzad Afzal
- King Abdullah University of Science & Technology, Saudi Arabia
| | - Sohaib Ghani
- King Abdullah University of Science & Technology, Saudi Arabia
| | | | | | - Omar M Knio
- King Abdullah University of Science & Technology, Saudi Arabia
| | - Markus Hadwiger
- King Abdullah University of Science & Technology, Saudi Arabia
| | - Ibrahim Hoteit
- King Abdullah University of Science & Technology, Saudi Arabia
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8
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Yu D, Ian O, Jie L, Xiaoru Y, Vinh NQ. User-centered visual explorer of in-process comparison in spatiotemporal space. J Vis (Tokyo) 2023; 26:403-421. [PMID: 36406961 PMCID: PMC9645334 DOI: 10.1007/s12650-022-00882-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 08/13/2022] [Accepted: 09/09/2022] [Indexed: 11/11/2022]
Abstract
Abstract We propose a user-centered visual explorer (UcVE) for progressive comparing multiple visualization units in spatiotemporal space. We create unique unit visualization with the customizable aggregated view based on the visual metaphor of flower bursts. Each visualization unit is encoded with the abstraction of spatiotemporal properties. To reduce user cognition load, UcVE allows users to visualize, save, and track in-the-process exploration results. In coordination of storage sequence and block tracking views, UcVE can facilitate comparison with multiple visualization units concurrently, selected from historical and current exploration results. UcVE offers a flexible geo-based layout, with aggregation functions and temporal views of the timeline with categorized events, to maximize the user's exploration capabilities. Finally, we demonstrate the usefulness by using COVID-19 datasets, case studies with different user scenarios, and expert feedback. Graphical abstract
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Affiliation(s)
- Dong Yu
- School of Computer Science, University of Technology Sydney, Ultimo, Australia
| | - Oppermann Ian
- School of Computer Science, University of Technology Sydney, Ultimo, Australia
| | - Liang Jie
- School of Computer Science, University of Technology Sydney, Ultimo, Australia
| | - Yuan Xiaoru
- Key Laboratory of Machine Perception (Ministry of Education), and School of AI, Peking University, Beijing, China
- National Engineering Laboratory for Big Data Analysis and Application, Peking University, Beijing, China
| | - Nguyen Quang Vinh
- School of Computing, Engineering and Mathematics, Western Sydney University, Sydney, Australia
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9
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Slater A, Nair N, Suétt R, Mac Donnchadha R, Bamford C, Jasim S, Livingstone D, Hutchinson E. Visualising Viruses. J Gen Virol 2022; 103:001730. [PMID: 35082014 PMCID: PMC8895616 DOI: 10.1099/jgv.0.001730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/22/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses pose a challenge to our imaginations. They exert a highly visible influence on the world in which we live, but operate at scales we cannot directly perceive and without a clear separation between their own biology and that of their hosts. Communication about viruses is therefore typically grounded in mental images of virus particles. Virus particles, as the infectious stage of the viral replication cycle, can be used to explain many directly observable properties of transmission, infection and immunity. In addition, their often striking beauty can stimulate further interest in virology. The structures of some virus particles have been determined experimentally in great detail, but for many important viruses a detailed description of the virus particle is lacking. This can be because they are challenging to describe with a single experimental method, or simply because of a lack of data. In these cases, methods from medical illustration can be applied to produce detailed visualisations of virus particles which integrate information from multiple sources. Here, we demonstrate how this approach was used to visualise the highly variable virus particles of influenza A viruses and, in the early months of the COVID-19 pandemic, the virus particles of the then newly characterised and poorly described SARS-CoV-2. We show how constructing integrative illustrations of virus particles can challenge our thinking about the biology of viruses, as well as providing tools for science communication, and we provide a set of science communication resources to help visualise two viruses whose effects are extremely apparent to all of us.
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Affiliation(s)
- Annabel Slater
- School of Life Sciences, University of Glasgow, Glasgow, UK
| | - Naina Nair
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
| | - Rachael Suétt
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
| | | | - Connor Bamford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Present address: Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, Ireland
| | - Seema Jasim
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Daniel Livingstone
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
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10
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Machado MR, Pantano S. Fighting viruses with computers, right now. Curr Opin Virol 2021; 48:91-99. [PMID: 33975154 DOI: 10.1016/j.coviro.2021.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/20/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The synergistic conjunction of various technological revolutions with the accumulated knowledge and workflows is rapidly transforming several scientific fields. Particularly, Virology can now feed from accurate physical models, polished computational tools, and massive computational power to readily integrate high-resolution structures into biological representations of unprecedented detail. That preparedness allows for the first time to get crucial information for vaccine and drug design from in-silico experiments against emerging pathogens of worldwide concern at relevant action windows. The present work reviews some of the main milestones leading to these breakthroughs in Computational Virology, providing an outlook for future developments in capacity building and accessibility to computational resources.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
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11
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Gardner A, Autin L, Fuentes D, Maritan M, Barad BA, Medina M, Olson AJ, Grotjahn DA, Goodsell DS. CellPAINT: Turnkey Illustration of Molecular Cell Biology. FRONTIERS IN BIOINFORMATICS 2021; 1. [PMID: 34790910 PMCID: PMC8594902 DOI: 10.3389/fbinf.2021.660936] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CellPAINT is an interactive digital tool that allows non-expert users to create illustrations of the molecular structure of cells and viruses. We present a new release with several key enhancements, including the ability to generate custom ingredients from structure information in the Protein Data Bank, and interaction, grouping, and locking functions that streamline the creation of assemblies and illustration of large, complex scenes. An example of CellPAINT as a tool for hypothesis generation in the interpretation of cryoelectron tomograms is presented. CellPAINT is freely available at http://ccsb.scripps.edu/cellpaint.
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Affiliation(s)
- Adam Gardner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Daniel Fuentes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Martina Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Benjamin A. Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Michaela Medina
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Arthur J. Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - David S. Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- *Correspondence: David S. Goodsell
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12
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Vasconcelos GL, Macêdo AMS, Duarte-Filho GC, Brum AA, Ospina R, Almeida FAG. Power law behaviour in the saturation regime of fatality curves of the COVID-19 pandemic. Sci Rep 2021; 11:4619. [PMID: 33633290 PMCID: PMC7907114 DOI: 10.1038/s41598-021-84165-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
We apply a versatile growth model, whose growth rate is given by a generalised beta distribution, to describe the complex behaviour of the fatality curves of the COVID-19 disease for several countries in Europe and North America. We show that the COVID-19 epidemic curves not only may present a subexponential early growth but can also exhibit a similar subexponential (power-law) behaviour in the saturation regime. We argue that the power-law exponent of the latter regime, which measures how quickly the curve approaches the plateau, is directly related to control measures, in the sense that the less strict the control, the smaller the exponent and hence the slower the diseases progresses to its end. The power-law saturation uncovered here is an important result, because it signals to policymakers and health authorities that it is important to keep control measures for as long as possible, so as to avoid a slow, power-law ending of the disease. The slower the approach to the plateau, the longer the virus lingers on in the population, and the greater not only the final death toll but also the risk of a resurgence of infections.
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Affiliation(s)
- Giovani L Vasconcelos
- Departamento de Física, Universidade Federal do Paraná, 81531-990, Curitiba, Paraná, Brazil.
| | - Antônio M S Macêdo
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901, Recife, Pernambuco, Brazil
| | - Gerson C Duarte-Filho
- Departamento de Física, Universidade Federal de Sergipe, 49100-000, São Cristóvão, Sergipe, Brazil
| | - Arthur A Brum
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901, Recife, Pernambuco, Brazil
| | - Raydonal Ospina
- Departamento de Estatística, Universidade Federal de Pernambuco, 50740-540, Recife, Pernambuco, Brazil
| | - Francisco A G Almeida
- Departamento de Física, Universidade Federal de Sergipe, 49100-000, São Cristóvão, Sergipe, Brazil
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Life cycle of SARS-CoV-2: from sketch to visualization in atomistic resolution. COMPUTER GRAPHICS FORUM : JOURNAL OF THE EUROPEAN ASSOCIATION FOR COMPUTER GRAPHICS 2021; 40:426-427. [PMID: 33821066 PMCID: PMC8014676 DOI: 10.1111/cgf.14200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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