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Aulner N, Danckaert A, Fernandes J, Nicola MA, Roux P, Salles A, Tinevez JY, Shorte SL. Fluorescence imaging host pathogen interactions: fifteen years benefit of hindsight…. Curr Opin Microbiol 2018; 43:193-198. [PMID: 29567588 DOI: 10.1016/j.mib.2018.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 01/24/2023]
Abstract
We consider in review current state-of-the-art fluorescence microscopy for investigating the host-pathogen interface. Our perspective is honed from years with literally thousands of microbiologists using the variety of imaging technologies available within our dedicated BSL2/BSL3 optical imaging research service facilities at the Institut Pasteur Paris founded from scratch in 2001. During fifteen years learning from the success and failures of introducing different fluorescence imaging technologies, methods, and technical development strategies we provide here a synopsis review of our experience to date and a synthesis of how we see the future in perspective for fluorescence imaging at the host-pathogen interface.
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Affiliation(s)
- Nathalie Aulner
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Anne Danckaert
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Julien Fernandes
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Marie-Anne Nicola
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Pascal Roux
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Audrey Salles
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Spencer L Shorte
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
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Abstract
PURPOSE OF REVIEW To provide an overview of recent research of how HIV integration relates to productive and latent infection and implications for cure strategies. RECENT FINDINGS How and where HIV integrates provides new insights into how HIV persists on antiretroviral therapy (ART). Clonal expansion of infected cells with the same integration site demonstrates that T-cell proliferation is an important factor in HIV persistence, however, the driver of proliferation remains unclear. Clones with identical integration sites harbouring defective provirus can accumulate in HIV-infected individuals on ART and defective proviruses can express RNA and produce protein. HIV integration sites differ in clonally expanded and nonexpanded cells and in latently and productively infected cells and this influences basal and inducible transcription. There is a growing number of cellular proteins that can alter the pattern of integration to favour latency. Understanding these pathways may identify new interventions to eliminate latently infected cells. SUMMARY Using advances in analysing HIV integration sites, T-cell proliferation of latently infected cells is thought to play a major role in HIV persistence. Clonal expansion has been demonstrated with both defective and intact viruses. Production of viral RNA and protein from defective viruses may play a role in driving chronic immune activation. The site of integration may determine the likelihood of proliferation and the degree of basal and induced transcription. Finally, host factors and gene expression at the time of infection may determine the integration site. Together these new insights may lead to novel approaches to elimination of latently infected cells.
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Affiliation(s)
- Jori Symons
- The Peter Doherty nstitute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria
| | - Paul U Cameron
- The Peter Doherty nstitute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Sharon R Lewin
- The Peter Doherty nstitute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
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Ospina Stella A, Turville S. All-Round Manipulation of the Actin Cytoskeleton by HIV. Viruses 2018; 10:v10020063. [PMID: 29401736 PMCID: PMC5850370 DOI: 10.3390/v10020063] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
While significant progress has been made in terms of human immunodeficiency virus (HIV) therapy, treatment does not represent a cure and remains inaccessible to many people living with HIV. Continued mechanistic research into the viral life cycle and its intersection with many aspects of cellular biology are not only fundamental in the continued fight against HIV, but also provide many key observations of the workings of our immune system. Decades of HIV research have testified to the integral role of the actin cytoskeleton in both establishing and spreading the infection. Here, we review how the virus uses different strategies to manipulate cellular actin networks and increase the efficiency of various stages of its life cycle. While some HIV proteins seem able to bind to actin filaments directly, subversion of the cytoskeleton occurs indirectly by exploiting the power of actin regulatory proteins, which are corrupted at multiple levels. Furthermore, this manipulation is not restricted to a discrete class of proteins, but rather extends throughout all layers of the cytoskeleton. We discuss prominent examples of actin regulators that are exploited, neutralized or hijacked by the virus, and address how their coordinated deregulation can lead to changes in cellular behavior that promote viral spreading.
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Affiliation(s)
- Alberto Ospina Stella
- The Kirby Institute, University of New South Wales (UNSW), Sydney NSW 2052, Australia.
| | - Stuart Turville
- The Kirby Institute, University of New South Wales (UNSW), Sydney NSW 2052, Australia.
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Milev MP, Yao X, Berthoux L, Mouland AJ. Impacts of virus-mediated manipulation of host Dynein. DYNEINS 2018. [PMCID: PMC7150161 DOI: 10.1016/b978-0-12-809470-9.00010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In general viruses' modus operandi to propagate is achieved by the co-opting host cell components, membranes, proteins, and machineries to their advantage. This is true for virtually every aspect of a virus' replication cycle from virus entry to the budding or release of progeny virus particles. In this chapter, we will discuss new information on the impacts of virus-mediated manipulation of Dynein motor complexes and associated machineries and factors. We will highlight how these host cell components impact on pathogenicity and immune responses, as many of the virus-mediated hijacked components also play pivotal roles in immune responses to pathogen insult. There are several comprehensive reviews that define virus–Dynein interactions including the first edition of this book that describes how viruses manipulate the host cell machineries their advantage. An updated table is included to summarize these virus–host interactions. Notably, barriers to intracellular translocation represent major hurdles to viral components during de novo infection and during active replication and the generation of progeny virus particles. Clearly, the subversion of host cell molecular motor protein activities takes advantage of constitutive and regulated membrane trafficking events and will target virus components to intracytoplasmic locales and membrane assembly. Broadening our understanding of the interplay between viruses, Dynein and the cytoskeleton will likely inform on new types of therapies. Continual enhancement of the breadth of new information on how viruses manipulate host cell biology will inevitably aid in the identification of new targets that can be poisoned to block old, new, and emerging viruses alike in their tracks.
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55
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Tsai CF, Lin HY, Hsu WL, Tsai CH. The novel mitochondria localization of influenza A virus NS1 visualized by FlAsH labeling. FEBS Open Bio 2017; 7:1960-1971. [PMID: 29226082 PMCID: PMC5715299 DOI: 10.1002/2211-5463.12336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/11/2022] Open
Abstract
The nonstructural protein 1 (NS1) of the influenza A virus (IAV) is a multifunctional protein that counteracts host cell antiviral responses and inhibits host cell pre‐mRNA processing. NS1 contains two nuclear localization signals that facilitate NS1 shuttling between cytoplasm and nucleus. In this study, we initially observed the novel mitochondria localization of NS1 in a subset of transfected cells. We then further monitored the localization dynamics of the NS1 protein in live cells infected with IAV expressing NS1 with insertion of a tetracysteine‐tag. The resulting mutant virus showed similar levels of infectivity and expression pattern of NS1 to those of wild‐type IAV. Pulse labeling using a biarsenical compound (fluorescein arsenical hairpin binder) allowed us to visualize the dynamic subcellular distribution of NS1 real time. We detected NS1 in mitochondria at a very early infection time point [1.5 h postinfection (hpi)] and observed the formation of a granular structure pattern in the nucleus at 4 hpi. This is the first identification of the novel mitochondria localization of NS1. The possible role of NS1 at an early infection time point is discussed.
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Affiliation(s)
- Chuan-Fu Tsai
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
| | - Hsin-Yi Lin
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health National Chung Hsing University Taichung Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
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56
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Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes. PLoS Pathog 2017; 13:e1006570. [PMID: 28827840 PMCID: PMC5578721 DOI: 10.1371/journal.ppat.1006570] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/31/2017] [Accepted: 08/05/2017] [Indexed: 11/19/2022] Open
Abstract
The dynamics and regulation of HIV-1 nuclear import and its intranuclear movements after import have not been studied. To elucidate these essential HIV-1 post-entry events, we labeled viral complexes with two fluorescently tagged virion-incorporated proteins (APOBEC3F or integrase), and analyzed the HIV-1 dynamics of nuclear envelope (NE) docking, nuclear import, and intranuclear movements in living cells. We observed that HIV-1 complexes exhibit unusually long NE residence times (1.5±1.6 hrs) compared to most cellular cargos, which are imported into the nuclei within milliseconds. Furthermore, nuclear import requires HIV-1 capsid (CA) and nuclear pore protein Nup358, and results in significant loss of CA, indicating that one of the viral core uncoating steps occurs during nuclear import. Our results showed that the CA-Cyclophilin A interaction regulates the dynamics of nuclear import by delaying the time of NE docking as well as transport through the nuclear pore, but blocking reverse transcription has no effect on the kinetics of nuclear import. We also visualized the translocation of viral complexes docked at the NE into the nucleus and analyzed their nuclear movements and determined that viral complexes exhibited a brief fast phase (<9 min), followed by a long slow phase lasting several hours. A comparison of the movement of viral complexes to those of proviral transcription sites supports the hypothesis that HIV-1 complexes quickly tether to chromatin at or near their sites of integration in both wild-type cells and cells in which LEDGF/p75 was deleted using CRISPR/cas9, indicating that the tethering interactions do not require LEDGF/p75. These studies provide novel insights into the dynamics of viral complex-NE association, regulation of nuclear import, viral core uncoating, and intranuclear movements that precede integration site selection. Although nuclear import of HIV-1 is essential for viral replication, many aspects of this process are currently unknown. Here, we defined the dynamics of HIV-1 nuclear envelope (NE) docking, nuclear import and its relationship to viral core uncoating, and intranuclear movements. We observed that HIV-1 complexes exhibit an unusually long residence time at the NE (∼1.5 hrs) compared to other cellular and viral cargos, and that HIV-1 capsid (CA) and host nuclear pore protein Nup358 are required for NE docking and nuclear import. Soon after import, the viral complexes exhibit a brief fast phase of movement, followed by a long slow phase, during which their movement is similar to that of integrated proviruses, suggesting that they rapidly become tethered to chromatin through interactions that do not require LEDGF/p75. Importantly, we found that NE association and nuclear import is regulated by the CA-cyclophilin A interaction, but not reverse transcription, and that one of the viral core uncoating steps, characterized by substantial loss of CA, occurs concurrently with nuclear import.
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57
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Distinct functions of diaphanous-related formins regulate HIV-1 uncoating and transport. Proc Natl Acad Sci U S A 2017; 114:E6932-E6941. [PMID: 28760985 DOI: 10.1073/pnas.1700247114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diaphanous (Dia)-related formins (DRFs) coordinate cytoskeletal remodeling by controlling actin nucleation and microtubule (MT) stabilization to facilitate processes such as cell polarization and migration; yet the full extent of their activities remains unknown. Here, we uncover two discrete roles and functions of DRFs during early human immunodeficiency virus type 1 (HIV-1) infection. Independent of their actin regulatory activities, Dia1 and Dia2 facilitated HIV-1-induced MT stabilization and the intracellular motility of virus particles. However, DRFs also bound in vitro assembled capsid-nucleocapsid complexes and promoted the disassembly of HIV-1 capsid (CA) shell. This process, also known as "uncoating," is among the most poorly understood stages in the viral lifecycle. Domain analysis and structure modeling revealed that regions of Dia2 that bound viral CA and mediated uncoating as well as early infection contained coiled-coil domains, and that these activities were genetically separable from effects on MT stabilization. Our findings reveal that HIV-1 exploits discrete functions of DRFs to coordinate critical steps in early infection and identifies Dia family members as regulators of the poorly understood process of HIV-1 uncoating.
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58
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Abstract
Retroviruses are obligate intracellular parasites of eukaryotic cells. After reverse transcription, the viral DNA contained in the preintegration complex is delivered to the nucleus of the host cell, where it integrates. Before reaching the nucleus, the incoming particle and the preintegration complex must travel throughout the cytoplasm. Likewise, the newly synthesized viral proteins and viral particles must transit the cytoplasm during exit. The cytoplasm is a crowded environment, and simple diffusion is difficult. Therefore, viruses have evolved to utilize the cellular mechanisms of movement through the cytoplasm, where microtubules are the roads, and the ATP-dependent motors dynein and kinesin are the vehicles for retrograde and anterograde trafficking. This review will focus on how different retroviruses (Mazon-Pfizer monkey virus, prototype foamy virus, bovine immunodeficiency virus, human immunodeficiency virus type 1, and murine leukemia virus) have subjugated the microtubule-associated motor proteins for viral replication. Although there have been advances in our understanding of how retroviruses move along microtubules, the strategies are different among them. Thus, a better understanding of the mechanisms used by each retrovirus to functionally subvert microtubule motor proteins will provide important clues in the design of new antiretroviral drugs that can specifically disrupt intracellular viral trafficking.
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Affiliation(s)
- Gloria Arriagada
- Departamento de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Viña del Mar, Chile
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59
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Gao Y, Yu Y, Sanchez L, Yu Y. Seeing the unseen: Imaging rotation in cells with designer anisotropic particles. Micron 2017; 101:123-131. [PMID: 28711013 DOI: 10.1016/j.micron.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 01/27/2023]
Abstract
Cellular functions are enabled by cascades of transient biological events. Imaging and tracking the dynamics of these events have proven to be a powerful means of understanding the principles of cellular processes. These studies have typically focused on translational dynamics. By contrast, investigations of rotational dynamics have been scarce, despite emerging evidence that rotational dynamics are an inherent feature of many cellular processes and may also provide valuable clues to understanding those cell functions. Such studies have been impeded by the limited availability of suitable rotational imaging probes. This has recently changed thanks to the advances in the development of anisotropic particles for rotational imaging. In this review, we will summarize current techniques for imaging rotation using particle probes that are anisotropic in shape or optical properties. We will highlight two studies that demonstrate how these techniques can be applied to explore important facets of cellular functions.
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Affiliation(s)
- Yuan Gao
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Yanqi Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Lucero Sanchez
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States.
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60
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Wang IH, Burckhardt CJ, Yakimovich A, Morf MK, Greber UF. The nuclear export factor CRM1 controls juxta-nuclear microtubule-dependent virus transport. J Cell Sci 2017; 130:2185-2195. [PMID: 28515232 DOI: 10.1242/jcs.203794] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/12/2017] [Indexed: 12/26/2022] Open
Abstract
Transport of large cargo through the cytoplasm requires motor proteins and polarized filaments. Viruses that replicate in the nucleus of post-mitotic cells use microtubules and the dynein-dynactin motor to traffic to the nuclear membrane and deliver their genome through nuclear pore complexes (NPCs) into the nucleus. How virus particles (virions) or cellular cargo are transferred from microtubules to the NPC is unknown. Here, we analyzed trafficking of incoming cytoplasmic adenoviruses by single-particle tracking and super-resolution microscopy. We provide evidence for a regulatory role of CRM1 (chromosome-region-maintenance-1; also known as XPO1, exportin-1) in juxta-nuclear microtubule-dependent adenovirus transport. Leptomycin B (LMB) abolishes nuclear targeting of adenovirus. It binds to CRM1, precludes CRM1-cargo binding and blocks signal-dependent nuclear export. LMB-inhibited CRM1 did not compete with adenovirus for binding to the nucleoporin Nup214 at the NPC. Instead, CRM1 inhibition selectively enhanced virion association with microtubules, and boosted virion motions on microtubules less than ∼2 µm from the nuclear membrane. The data show that the nucleus provides positional information for incoming virions to detach from microtubules, engage a slower microtubule-independent motility to the NPC and enhance infection.
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Affiliation(s)
- I-Hsuan Wang
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
| | - Christoph J Burckhardt
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
- Department of Bioinformatics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Artur Yakimovich
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
| | - Matthias K Morf
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
- Molecular Life Sciences Graduate School, ETH and University of Zürich, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
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61
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Lee A, Tsekouras K, Calderon C, Bustamante C, Pressé S. Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis. Chem Rev 2017; 117:7276-7330. [PMID: 28414216 PMCID: PMC5487374 DOI: 10.1021/acs.chemrev.6b00729] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light's diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we've termed the interpretation problem.
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Affiliation(s)
- Antony Lee
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California at Berkeley, Berkeley, California 94720, United States
| | - Konstantinos Tsekouras
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | | | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California at Berkeley, Berkeley, California 94720, United States
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, United States
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute, University of California at Berkeley, Berkeley, California 94720, United States
| | - Steve Pressé
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Department of Cell and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
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62
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Smooth 2D manifold extraction from 3D image stack. Nat Commun 2017; 8:15554. [PMID: 28561033 PMCID: PMC5499208 DOI: 10.1038/ncomms15554] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/05/2017] [Indexed: 11/27/2022] Open
Abstract
Three-dimensional fluorescence microscopy followed by image processing is routinely used to study biological objects at various scales such as cells and tissue. However, maximum intensity projection, the most broadly used rendering tool, extracts a discontinuous layer of voxels, obliviously creating important artifacts and possibly misleading interpretation. Here we propose smooth manifold extraction, an algorithm that produces a continuous focused 2D extraction from a 3D volume, hence preserving local spatial relationships. We demonstrate the usefulness of our approach by applying it to various biological applications using confocal and wide-field microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation of 3D image stacks with maximum accuracy. Maximum Intensity Projection is a common tool to represent 3D biological imaging data in a 2D space, but it creates artefacts. Here the authors develop Smooth Manifold Extraction, an ImageJ/Fiji plugin, to preserve local spatial relationships when extracting the content of a 3D volume to a 2D space.
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63
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Capsid-Dependent Host Factors in HIV-1 Infection. Trends Microbiol 2017; 25:741-755. [PMID: 28528781 DOI: 10.1016/j.tim.2017.04.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 11/20/2022]
Abstract
After invasion of a susceptible target cell, HIV-1 completes the early phase of its life cycle upon integration of reverse-transcribed viral DNA into host chromatin. The viral capsid, a conical shell encasing the viral ribonucleoprotein complex, along with its constitutive capsid protein, plays essential roles at virtually every step in the early phase of the viral life cycle. Recent work has begun to reveal how the viral capsid interacts with specific cellular proteins to promote these processes. At the same time, cellular restriction factors target the viral capsid to thwart infection. Comprehensive understanding of capsid-host interactions that promote or impede HIV-1 infection may provide unique insight to exploit for novel therapeutic interventions.
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64
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Portilho DM, Persson R, Arhel N. Role of non-motile microtubule-associated proteins in virus trafficking. Biomol Concepts 2017; 7:283-292. [PMID: 27879481 DOI: 10.1515/bmc-2016-0018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/04/2016] [Indexed: 11/15/2022] Open
Abstract
Viruses are entirely dependent on their ability to infect a host cell in order to replicate. To reach their site of replication as rapidly and efficiently as possible following cell entry, many have evolved elaborate mechanisms to hijack the cellular transport machinery to propel themselves across the cytoplasm. Long-range movements have been shown to involve motor proteins along microtubules (MTs) and direct interactions between viral proteins and dynein and/or kinesin motors have been well described. Although less well-characterized, it is also becoming increasingly clear that non-motile microtubule-associated proteins (MAPs), including structural MAPs of the MAP1 and MAP2 families, and microtubule plus-end tracking proteins (+TIPs), can also promote viral trafficking in infected cells, by mediating interaction of viruses with filaments and/or motor proteins, and modulating filament stability. Here we review our current knowledge on non-motile MAPs, their role in the regulation of cytoskeletal dynamics and in viral trafficking during the early steps of infection.
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65
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Terrasse R, Memmi M, Palle S, Heyndrickx L, Vanham G, Pozzetto B, Bourlet T. Visualization of X4- and R5-Tropic HIV-1 Viruses Expressing Fluorescent Proteins in Human Endometrial Cells: Application to Tropism Study. PLoS One 2017; 12:e0169453. [PMID: 28060897 PMCID: PMC5218496 DOI: 10.1371/journal.pone.0169453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/16/2016] [Indexed: 12/12/2022] Open
Abstract
Worldwide most HIV infections occur through heterosexual transmission, involving complex interactions of cell-free and cell-associated particles with cells of the female genital tract mucosa. The ability of HIV-1 to “infect” epithelial cells remains poorly understood. To address this question, replicative-competent chimeric constructs expressing fluorescent proteins and harboring the envelope of X4- or R5-tropic HIV-1 strains were used to “infect” endometrial HEC1-A cells. The virus-cell interactions were visualized using confocal microscopy (CM) at various times post infection. Combined with quantification of viral RNA and total HIV DNA in infected cells, the CM pictures suggest that epithelial cells do not support a complete viral replication cycle: X4-tropic viruses are imported into the nucleus in a non-productive way, whereas R5-tropic viruses transit through the cytoplasm without replication and are preferentially transmitted to susceptible activated peripheral blood mononuclear cells. Within the limit of experiments conducted in vitro on a continued cell line, these results indicate that the epithelial mucosa may participate to the selection of HIV-1 strains at the mucosal level.
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Affiliation(s)
- Rachel Terrasse
- Groupe Immunité des Muqueuses et Agents Pathogènes EA3064, University of Lyon, Faculté de Médecine Jacques Lisfranc de Saint-Etienne, Saint-Etienne cedex 02, France
| | - Meriam Memmi
- Groupe Immunité des Muqueuses et Agents Pathogènes EA3064, University of Lyon, Faculté de Médecine Jacques Lisfranc de Saint-Etienne, Saint-Etienne cedex 02, France
| | - Sabine Palle
- Centre de Microscopie Confocale Multiphotonique, Université Jean Monnet, Pôle Optique et Vision, Saint-Etienne cedex 2, France
| | - Leo Heyndrickx
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Guido Vanham
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Faculty of Biomedical, Pharmaceutical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Bruno Pozzetto
- Groupe Immunité des Muqueuses et Agents Pathogènes EA3064, University of Lyon, Faculté de Médecine Jacques Lisfranc de Saint-Etienne, Saint-Etienne cedex 02, France
- * E-mail:
| | - Thomas Bourlet
- Groupe Immunité des Muqueuses et Agents Pathogènes EA3064, University of Lyon, Faculté de Médecine Jacques Lisfranc de Saint-Etienne, Saint-Etienne cedex 02, France
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66
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Marzook NB, Newsome TP. Viruses That Exploit Actin-Based Motility for Their Replication and Spread. Handb Exp Pharmacol 2016; 235:237-261. [PMID: 27757755 DOI: 10.1007/164_2016_41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The actin cytoskeleton is a crucial part of the eukaryotic cell. Viruses depend on host cells for their replication, and, as a result, many have developed ways of manipulating the actin network to promote their spread. This chapter reviews the various ways in which viruses utilize the actin cytoskeleton at discrete steps in their life cycle, from entry into the host cell, replication, and assembly of new progeny to virus release. Various actin inhibitors that function in different ways to affect proper actin dynamics can be used to parse the role of actin at these steps.
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Affiliation(s)
- N Bishara Marzook
- The School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Timothy P Newsome
- The School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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Dirk BS, Van Nynatten LR, Dikeakos JD. Where in the Cell Are You? Probing HIV-1 Host Interactions through Advanced Imaging Techniques. Viruses 2016; 8:v8100288. [PMID: 27775563 PMCID: PMC5086620 DOI: 10.3390/v8100288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 12/19/2022] Open
Abstract
Viruses must continuously evolve to hijack the host cell machinery in order to successfully replicate and orchestrate key interactions that support their persistence. The type-1 human immunodeficiency virus (HIV-1) is a prime example of viral persistence within the host, having plagued the human population for decades. In recent years, advances in cellular imaging and molecular biology have aided the elucidation of key steps mediating the HIV-1 lifecycle and viral pathogenesis. Super-resolution imaging techniques such as stimulated emission depletion (STED) and photoactivation and localization microscopy (PALM) have been instrumental in studying viral assembly and release through both cell-cell transmission and cell-free viral transmission. Moreover, powerful methods such as Forster resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) have shed light on the protein-protein interactions HIV-1 engages within the host to hijack the cellular machinery. Specific advancements in live cell imaging in combination with the use of multicolor viral particles have become indispensable to unravelling the dynamic nature of these virus-host interactions. In the current review, we outline novel imaging methods that have been used to study the HIV-1 lifecycle and highlight advancements in the cell culture models developed to enhance our understanding of the HIV-1 lifecycle.
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Affiliation(s)
- Brennan S Dirk
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Logan R Van Nynatten
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
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Sharaf R, Mempel TR, Murooka TT. Visualizing the Behavior of HIV-Infected T Cells In Vivo Using Multiphoton Intravital Microscopy. Methods Mol Biol 2016; 1354:189-201. [PMID: 26714713 DOI: 10.1007/978-1-4939-3046-3_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The introduction of multiphoton microscopy has dramatically broadened the scope of intravital imaging studies and has allowed researchers to validate and refine basic mechanistic concepts in many areas of biology within the context of physiologically relevant tissue microenvironments. This has also led to new insights into the behavior of immune cells at steady state, and how their behaviors are altered during an immune response. At the same time, advances in the humanized mouse model have allowed for in vivo studies of strictly human pathogens, such as HIV-1. Here, we describe in detail an intravital microscopy approach to visualize the dynamic behavior of HIV-infected T cells within the lymph nodes of live, anesthetized humanized mice.
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Affiliation(s)
- Radwa Sharaf
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy andImmunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Thorsten R Mempel
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy andImmunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Thomas T Murooka
- Departments of Immunology and Medical Microbiology, University of Manitoba, 750 McDermot Ave, Rm 433, Winnipeg, MB, Canada, R3E 0T5.
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Dharan A, Talley S, Tripathi A, Mamede JI, Majetschak M, Hope TJ, Campbell EM. KIF5B and Nup358 Cooperatively Mediate the Nuclear Import of HIV-1 during Infection. PLoS Pathog 2016; 12:e1005700. [PMID: 27327622 PMCID: PMC4915687 DOI: 10.1371/journal.ppat.1005700] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/21/2016] [Indexed: 12/23/2022] Open
Abstract
Following envelope mediated fusion, the HIV-1 core is released into the cytoplasm of the target cell and undergoes a series of trafficking and replicative steps that result in the nuclear import of the viral genome, which ultimately leads to the integration of the proviral DNA into the host cell genome. Previous studies have found that disruption of microtubules, or depletion of dynein or kinesin motors, perturb the normal uncoating and trafficking of the viral genome. Here, we show that the Kinesin-1 motor, KIF5B, induces a relocalization of the nuclear pore component Nup358 into the cytoplasm during HIV-1 infection. This relocalization of NUP358 is dependent on HIV-1 capsid, and NUP358 directly associates with viral cores following cytoplasmic translocation. This interaction between NUP358 and the HIV-1 core is dependent on multiple capsid binding surfaces, as this association is not observed following infection with capsid mutants in which a conserved hydrophobic binding pocket (N74D) or the cyclophilin A binding loop (P90A) is disrupted. KIF5B knockdown also prevents the nuclear entry and infection by HIV-1, but does not exert a similar effect on the N74D or P90A capsid mutants which do not rely on Nup358 for nuclear import. Finally, we observe that the relocalization of Nup358 in response to CA is dependent on cleavage protein and polyadenylation factor 6 (CPSF6), but independent of cyclophilin A. Collectively, these observations identify a previously unappreciated role for KIF5B in mediating the Nup358 dependent nuclear import of the viral genome during infection. Fusion of viral and target cell membranes releases the HIV-1 viral capsid, which houses the viral RNA and proteins necessary for viral reverse transcription and integration, into the cytoplasm of target cells. To complete infection, the viral capsid must ultimately traffic to the nucleus and undergo a process known as uncoating to allow the nuclear import of the viral genome into the nucleus, where it subsequently integrates into the genome of the target cell. Here, we show that the concerted actions of microtubule motor KIF5B and the nuclear pore component Nup358 cooperatively facilitate the uncoating and nuclear import of the viral genome. Moreover, we also identify the determinants in the viral capsid protein, which forms the viral capsid core, that are required for KIF5B dependent nuclear entry. These studies reveal a novel role for the microtubule motor KIF5B in the nuclear import of the viral genome and reveal potential intervention targets for therapeutic intervention.
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Affiliation(s)
- Adarsh Dharan
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, Chicago, Illinois, United States of America
| | - Sarah Talley
- Integrative Cell Biology Program, Stritch School of Medicine, Loyola University, Chicago, Illinois, United States of America
| | - Abhishek Tripathi
- Burn and Shock Trauma Research Institute, Department of Surgery, Stritch School of Medicine, Loyola University, Chicago, Illinois, United States of America
| | - João I. Mamede
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Matthias Majetschak
- Burn and Shock Trauma Research Institute, Department of Surgery, Stritch School of Medicine, Loyola University, Chicago, Illinois, United States of America
| | - Thomas J. Hope
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, Chicago, Illinois, United States of America
- Integrative Cell Biology Program, Stritch School of Medicine, Loyola University, Chicago, Illinois, United States of America
- * E-mail:
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70
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Sakin V, Paci G, Lemke EA, Müller B. Labeling of virus components for advanced, quantitative imaging analyses. FEBS Lett 2016; 590:1896-914. [PMID: 26987299 DOI: 10.1002/1873-3468.12131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 12/31/2022]
Abstract
In recent years, investigation of virus-cell interactions has moved from ensemble measurements to imaging analyses at the single-particle level. Advanced fluorescence microscopy techniques provide single-molecule sensitivity and subdiffraction spatial resolution, allowing observation of subviral details and individual replication events to obtain detailed quantitative information. To exploit the full potential of these techniques, virologists need to employ novel labeling strategies, taking into account specific constraints imposed by viruses, as well as unique requirements of microscopic methods. Here, we compare strengths and limitations of various labeling methods, exemplify virological questions that were successfully addressed, and discuss challenges and future potential of novel approaches in virus imaging.
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Affiliation(s)
- Volkan Sakin
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
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Calderon CP. Motion blur filtering: A statistical approach for extracting confinement forces and diffusivity from a single blurred trajectory. Phys Rev E 2016; 93:053303. [PMID: 27301001 DOI: 10.1103/physreve.93.053303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 12/13/2022]
Abstract
Single particle tracking (SPT) can aid in understanding a variety of complex spatiotemporal processes. However, quantifying diffusivity and confinement forces from individual live cell trajectories is complicated by inter- and intratrajectory kinetic heterogeneity, thermal fluctuations, and (experimentally resolvable) statistical temporal dependence inherent to the underlying molecule's time correlated confined dynamics experienced in the cell. The problem is further complicated by experimental artifacts such as localization uncertainty and motion blur. The latter is caused by the tagged molecule emitting photons at different spatial positions during the exposure time of a single frame. The aforementioned experimental artifacts induce spurious time correlations in measured SPT time series that obscure the information of interest (e.g., confinement forces and diffusivity). We develop a maximum likelihood estimation (MLE) technique that decouples the above noise sources and systematically treats temporal correlation via time series methods. This ultimately permits a reliable algorithm for extracting diffusivity and effective forces in confined or unconfined environments. We illustrate how our approach avoids complications inherent to mean square displacement or autocorrelation techniques. Our algorithm modifies the established Kalman filter (which does not handle motion blur artifacts) to provide a likelihood based time series estimation procedure. The result extends A. J. Berglund's motion blur model [Phys. Rev. E 82, 011917 (2010)PLEEE81539-375510.1103/PhysRevE.82.011917] to handle confined dynamics. The approach can also systematically utilize (possibly time dependent) localization uncertainty estimates afforded by image analysis if available. This technique, which explicitly treats confinement and motion blur within a time domain MLE framework, uses an exact likelihood (time domain methods facilitate analyzing nonstationary signals). Our estimator is demonstrated to be consistent over a wide range of exposure times (5 to 100 ms), diffusion coefficients (1×10^{-3} to 1μm^{2}/s), and confinement widths (100 nm to 2μm). We demonstrate that neglecting motion blur or confinement can substantially bias estimation of kinetic parameters of interest to researchers. The technique also permits one to check statistical model assumptions against measured individual trajectories without "ground truth." The ability to reliably and consistently extract motion parameters in trajectories exhibiting confined and/or non-stationary dynamics, without exposure time artifacts corrupting estimates, is expected to aid in directly comparing trajectories obtained from different experiments or imaging modalities. A Python implementation is provided (open-source code will be maintained on GitHub; see also the Supplemental Material with this paper).
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Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology. Viruses 2016; 8:v8050127. [PMID: 27164126 PMCID: PMC4885082 DOI: 10.3390/v8050127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/31/2016] [Accepted: 04/29/2016] [Indexed: 12/13/2022] Open
Abstract
Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. Notably, the development of replicating-competent reporter-expressing viruses (RCREVs) has provided an excellent option to detect directly viral replication without the use of secondary labeling, which represents a significant advance in virology. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. However, there remain various challenges associated with RCREVs, including pathogenicity alterations due to the insertion of a reporter gene, instability or loss of the reporter gene expression, or attenuation of reporter signals in vivo. Despite all these limitations, RCREVs have become powerful tools for both basic and applied virology with the development of new technologies for generating RCREVs, the inventions of novel reporters and the better understanding of regulation of viral replication.
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73
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Florian PE, Rouillé Y, Ruta S, Nichita N, Roseanu A. Recent advances in human viruses imaging studies. J Basic Microbiol 2016; 56:591-607. [DOI: 10.1002/jobm.201500575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Paula Ecaterina Florian
- Department of ; Ligand-Receptor Interactions; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| | - Yves Rouillé
- Center for Infection and Immunity of Lille (CIIL); Inserm U1019; CNRS UMR8204; Institut Pasteur de Lille; Université Lille Nord de France; Lille France
| | - Simona Ruta
- Department of Emergent Diseases; Stefan S. Nicolau Institute of Virology; Bucharest 030304 Romania
| | - Norica Nichita
- Department of Viral Glycoproteins; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| | - Anca Roseanu
- Department of ; Ligand-Receptor Interactions; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
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Oum YH, Desai TM, Marin M, Melikyan GB. Click labeling of unnatural sugars metabolically incorporated into viral envelope glycoproteins enables visualization of single particle fusion. J Virol Methods 2016; 233:62-71. [PMID: 27033181 DOI: 10.1016/j.jviromet.2016.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
Enveloped viruses infect target cells by fusing their membrane with cellular membrane through a process that is mediated by specialized viral glycoproteins. The inefficient and highly asynchronous nature of viral fusion complicates studies of virus entry on a population level. Single virus imaging in living cells has become an important tool for delineating the entry pathways and for mechanistic studies of viral fusion. We have previously demonstrated that incorporation of fluorescent labels into the viral membrane and trapping fluorescent proteins in the virus interior enables the visualization of single virus fusion in living cells. Here, we implement a new approach to non-invasively label the viral membrane glycoproteins through metabolic incorporation of unnatural sugars followed by click-reaction with organic fluorescent dyes. This approach allows for efficient labeling of diverse viral fusion glycoproteins on the surface of HIV pseudoviruses. Incorporation of a content marker into surface-labeled viral particles enables sensitive detection of single virus fusion with live cells.
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Affiliation(s)
- Yoon Hyeun Oum
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA
| | - Tanay M Desai
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA
| | - Mariana Marin
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA
| | - Gregory B Melikyan
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA; Children's Healthcare of Atlanta, Atlanta, GA, USA.
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75
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SUN2 Overexpression Deforms Nuclear Shape and Inhibits HIV. J Virol 2016; 90:4199-4214. [PMID: 26865710 DOI: 10.1128/jvi.03202-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/03/2016] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED In a previous screen of putative interferon-stimulated genes, SUN2 was shown to inhibit HIV-1 infection in an uncharacterized manner. SUN2 is an inner nuclear membrane protein belonging to the linker of nucleoskeleton and cytoskeleton complex. We have analyzed here the role of SUN2 in HIV infection. We report that in contrast to what was initially thought, SUN2 is not induced by type I interferon, and that SUN2 silencing does not modulate HIV infection. However, SUN2 overexpression in cell lines and in primary monocyte-derived dendritic cells inhibits the replication of HIV but not murine leukemia virus or chikungunya virus. We identified HIV-1 and HIV-2 strains that are unaffected by SUN2, suggesting that the effect is specific to particular viral components or cofactors. Intriguingly, SUN2 overexpression induces a multilobular flower-like nuclear shape that does not impact cell viability and is similar to that of cells isolated from patients with HTLV-I-associated adult T-cell leukemia or with progeria. Nuclear shape changes and HIV inhibition both mapped to the nucleoplasmic domain of SUN2 that interacts with the nuclear lamina. This block to HIV replication occurs between reverse transcription and nuclear entry, and passaging experiments selected for a single-amino-acid change in capsid (CA) that leads to resistance to overexpressed SUN2. Furthermore, using chemical inhibition or silencing of cyclophilin A (CypA), as well as CA mutant viruses, we implicated CypA in the SUN2-imposed block to HIV infection. Our results demonstrate that SUN2 overexpression perturbs both nuclear shape and early events of HIV infection. IMPORTANCE Cells encode proteins that interfere with viral replication, a number of which have been identified in overexpression screens. SUN2 is a nuclear membrane protein that was shown to inhibit HIV infection in such a screen, but how it blocked HIV infection was not known. We show that SUN2 overexpression blocks the infection of certain strains of HIV before nuclear entry. Mutation of the viral capsid protein yielded SUN2-resistant HIV. Additionally, the inhibition of HIV infection by SUN2 involves cyclophilin A, a protein that binds the HIV capsid and directs subsequent steps of infection. We also found that SUN2 overexpression substantially changes the shape of the cell's nucleus, resulting in many flower-like nuclei. Both HIV inhibition and deformation of nuclear shape required the domain of SUN2 that interacts with the nuclear lamina. Our results demonstrate that SUN2 interferes with HIV infection and highlight novel links between nuclear shape and viral infection.
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76
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Cheng Z, Hoffmann A. A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection. J Theor Biol 2016; 395:87-96. [PMID: 26860658 DOI: 10.1016/j.jtbi.2016.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
Abstract
Although HIV viremia in infected patients proceeds in a manner that may be accounted for by deterministic mathematical models, single virus-cell encounters following initial HIV exposure result in a variety of outcomes, only one of which results in a productive infection. The development of single molecule tracking techniques in living cells allows studies of intracellular transport of HIV, but it remains less clear what its impact may be on viral integration efficiency. Here, we present a stochastic intracellular mathematical model of HIV replication that incorporates microtubule transport of viral components. Using this model, we could study single round infections and observe how viruses entering cells reach one of three potential fates - degradation of the viral RNA genome, formation of LTR circles, or successful integration and establishment of a provirus. Our model predicts global trafficking properties, such as the probability and the mean time for a HIV viral particle to reach the nuclear pore. Interestingly, our model predicts that trafficking determines neither the probability or time of provirus establishment - instead, they are a function of vRNA degradation and reverse transcription reactions. Thus, our spatio-temporal model provides novel insights into the HIV infection process and may constitute a useful tool for the identification of promising drug targets.
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Affiliation(s)
- Zhang Cheng
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), and Institute for Quantitative and Computational Biosciences (QCB), UC, Los Angeles, CA 92093, United States.
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), and Institute for Quantitative and Computational Biosciences (QCB), UC, Los Angeles, CA 92093, United States.
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Caly L, Kassouf VT, Moseley GW, Diefenbach RJ, Cunningham AL, Jans DA. Fast track, dynein-dependent nuclear targeting of human immunodeficiency virus Vpr protein; impaired trafficking in a clinical isolate. Biochem Biophys Res Commun 2016; 470:735-740. [PMID: 26792716 DOI: 10.1016/j.bbrc.2016.01.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/08/2016] [Indexed: 12/23/2022]
Abstract
Nuclear import of the accessory protein Vpr is central to infection by human immunodeficiency virus (HIV). We previously identified the Vpr F72L mutation in a HIV-infected, long-term non-progressor, showing that it resulted in reduced Vpr nuclear accumulation and altered cytoplasmic localisation. Here we demonstrate for the first time that the effects of nuclear accumulation of the F72L mutation are due to impairment of microtubule-dependent-enhancement of Vpr nuclear import. We use high resolution imaging approaches including fluorescence recovery after photobleaching and other approaches to document interaction between Vpr and the dynein light chain protein, DYNLT1, and impaired interaction of the F72L mutant with DYNLT1. The results implicate MTs/DYNLT1 as drivers of Vpr nuclear import and HIV infection, with important therapeutic implications.
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Affiliation(s)
- Leon Caly
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia
| | - Vicki T Kassouf
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Gregory W Moseley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia
| | - Russell J Diefenbach
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Anthony L Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - David A Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
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Manzo C, Garcia-Parajo MF. A review of progress in single particle tracking: from methods to biophysical insights. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:124601. [PMID: 26511974 DOI: 10.1088/0034-4885/78/12/124601] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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79
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Elis E, Ehrlich M, Bacharach E. Dynamics and restriction of murine leukemia virus cores in mitotic and interphase cells. Retrovirology 2015; 12:95. [PMID: 26577111 PMCID: PMC4650138 DOI: 10.1186/s12977-015-0220-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/22/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Murine leukemia viruses (MLVs) naturally infect unsynchronized T and B lymphocytes, thus, the incoming virus encounters both interphase and mitotic cells. While it is well accepted that MLV requires cell division to complete its replication cycle, it is not known if ab initio infection of mitotic cells can result in productive infection. This question is highly relevant since the milieu of mitotic cells is markedly different from this of interphase cells; e.g. lacking radial microtubule network and intact nuclear envelope. To follow MLV infection in mitotic and interphase cells in real-time, we employed our recently developed infectious MLV particles with labeled cores, cellular models expressing fluorescence markers of different intracellular compartments and protocols for reversible mitotic arrest of MLV-susceptible cells. RESULTS Multi-wavelength live cell imaging was employed to simultaneously visualize GFP-labeled MLV cores, DiD-labeled viral or cellular membranes, and fluorescently-labeled microtubules or chromosomes. Cells were imaged either at interphase or upon mitotic arrest with microtubule poisons. Analysis of virus localization and trajectories revealed entry by endocytosis at interphase and mitosis, and correlation between viral mobility parameters and presence or absence of polymerized interphase microtubules. The success of infection of viruses that entered cells in mitosis was evidenced by their ability to reverse transcribe, their targeting to condensed chromosomes in the absence of radial microtubule network, and gene expression upon exit from mitosis. Comparison of infection by N, B or NB -tropic viruses in interphase and mitotic human cells revealed reduced restriction of the N-tropic virus, for infection initiated in mitosis. CONCLUSIONS The milieu of the mitotic cells supports all necessary requirements for early stages of MLV infection. Such milieu is suboptimal for restriction of N-tropic viruses, most likely by TRIM5α.
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Affiliation(s)
- Efrat Elis
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Marcelo Ehrlich
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Eran Bacharach
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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80
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Desai TM, Marin M, Sood C, Shi J, Nawaz F, Aiken C, Melikyan GB. Fluorescent protein-tagged Vpr dissociates from HIV-1 core after viral fusion and rapidly enters the cell nucleus. Retrovirology 2015; 12:88. [PMID: 26511606 PMCID: PMC4625717 DOI: 10.1186/s12977-015-0215-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/16/2015] [Indexed: 02/06/2023] Open
Abstract
Background HIV-1 Vpr is recruited into virions during assembly and appears to remain associated with the viral core after the reverse transcription and uncoating steps of entry. This feature has prompted the use of fluorescently labeled Vpr to visualize viral particles and to follow trafficking of post-fusion HIV-1 cores in the cytoplasm. Results Here, we tracked single pseudovirus entry and fusion and observed that fluorescently tagged Vpr gradually dissociates from post-fusion viral cores over the course of several minutes and accumulates in the nucleus. Kinetics measurements showed that fluorescent Vpr released from the cores very rapidly entered the cell nucleus. More than 10,000 Vpr molecules can be delivered into the cell nucleus within 45 min of infection by HIV-1 particles pseudotyped with the avian sarcoma and leukosis virus envelope glycoprotein. The fraction of Vpr from cell-bound viruses that accumulated in the nucleus was proportional to the extent of virus-cell fusion and was fully blocked by viral fusion inhibitors. Entry of virus-derived Vpr into the nucleus occurred independently of envelope glycoproteins or target cells. Fluorescence correlation spectroscopy revealed two forms of nuclear Vpr—monomers and very large complexes, likely involving host factors. The kinetics of viral Vpr entering the nucleus after fusion was not affected by point mutations in the capsid protein that alter the stability of the viral core. Conclusions The independence of Vpr shedding of capsid stability and its relatively rapid dissociation from post-fusion cores suggest that this process may precede capsid uncoating, which appears to occur on a slower time scale. Our results thus demonstrate that a bulk of fluorescently labeled Vpr incorporated into HIV-1 particles is released shortly after fusion. Future studies will address the question whether the quick and efficient nuclear delivery of Vpr derived from incoming viruses can regulate subsequent steps of HIV-1 infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0215-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tanay M Desai
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA.
| | - Mariana Marin
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA.
| | - Chetan Sood
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA.
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Fatima Nawaz
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Gregory B Melikyan
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, USA.
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81
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Trinh LA, Fraser SE. Imaging the Cell and Molecular Dynamics of Craniofacial Development: Challenges and New Opportunities in Imaging Developmental Tissue Patterning. Curr Top Dev Biol 2015; 115:599-629. [PMID: 26589939 DOI: 10.1016/bs.ctdb.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of the vertebrate head requires cell-cell and tissue-tissue interactions between derivatives of the three germ layers to coordinate morphogenetic movements in four dimensions (4D: x, y, z, t). The high spatial and temporal resolution offered by optical microscopy has made it the main imaging modularity for capturing the molecular and cellular dynamics of developmental processes. In this chapter, we highlight the challenges and new opportunities provided by emerging technologies that enable dynamic, high-information-content imaging of craniofacial development. We discuss the challenges of varying spatial and temporal scales encountered from the biological and technological perspectives. We identify molecular and fluorescence imaging technology that can provide solutions to some of the challenges. Application of the techniques described within this chapter combined with considerations of the biological and technical challenges will aid in formulating the best image-based studies to extend our understanding of the genetic and environmental influences underlying craniofacial anomalies.
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Affiliation(s)
- Le A Trinh
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Scott E Fraser
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
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82
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Abstract
In a mature, infectious HIV-1 virion, the viral genome is housed within a conical capsid core made from the viral capsid (CA) protein. The CA protein and the structure into which it assembles facilitate virtually every step of infection through a series of interactions with multiple host cell factors. This Review describes our understanding of the interactions between the viral capsid core and several cellular factors that enable efficient HIV-1 genome replication, timely core disassembly, nuclear import and the integration of the viral genome into the genome of the target cell. We then discuss how elucidating these interactions can reveal new targets for therapeutic interactions against HIV-1.
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83
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The evolution of structured illumination microscopy in studies of HIV. Methods 2015; 88:20-7. [DOI: 10.1016/j.ymeth.2015.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 02/04/2023] Open
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84
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Lawley SD, Tuft M, Brooks HA. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042709. [PMID: 26565274 DOI: 10.1103/physreve.92.042709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 06/05/2023]
Abstract
Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.
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Affiliation(s)
- Sean D Lawley
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Marie Tuft
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Heather A Brooks
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
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85
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Calderon CP, Bloom K. Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments. PLoS One 2015; 10:e0137633. [PMID: 26384324 PMCID: PMC4575198 DOI: 10.1371/journal.pone.0137633] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 08/20/2015] [Indexed: 12/14/2022] Open
Abstract
Understanding the basis for intracellular motion is critical as the field moves toward a deeper understanding of the relation between Brownian forces, molecular crowding, and anisotropic (or isotropic) energetic forcing. Effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state changes, e.g., changes induced by dynamic micro-environments, photobleaching, and other heterogeneity inherent in biological processes. This study discusses limitations in currently popular analysis methods (e.g., mean square displacement-based analyses) and how new techniques can be used to systematically analyze Single Particle Tracking (SPT) data experiencing abrupt state changes in time or space. The approach is to track GFP tagged chromatids in metaphase in live yeast cells and quantitatively probe the effective forces resulting from dynamic interactions that reflect the sum of a number of physical phenomena. State changes can be induced by various sources including: microtubule dynamics exerting force through the centromere, thermal polymer fluctuations, and DNA-based molecular machines including polymerases and protein exchange complexes such as chaperones and chromatin remodeling complexes. Simulations aiming to show the relevance of the approach to more general SPT data analyses are also studied. Refined force estimates are obtained by adopting and modifying a nonparametric Bayesian modeling technique, the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT applications. The HDP-SLDS method shows promise in systematically identifying dynamical regime changes induced by unobserved state changes when the number of underlying states is unknown in advance (a common problem in SPT applications). We expand on the relevance of the HDP-SLDS approach, review the relevant background of Hierarchical Dirichlet Processes, show how to map discrete time HDP-SLDS models to classic SPT models, and discuss limitations of the approach. In addition, we demonstrate new computational techniques for tuning hyperparameters and for checking the statistical consistency of model assumptions directly against individual experimental trajectories; the techniques circumvent the need for "ground-truth" and/or subjective information.
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Affiliation(s)
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States of America
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86
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Perillo EP, Liu YL, Huynh K, Liu C, Chou CK, Hung MC, Yeh HC, Dunn AK. Deep and high-resolution three-dimensional tracking of single particles using nonlinear and multiplexed illumination. Nat Commun 2015. [PMID: 26219252 PMCID: PMC4532916 DOI: 10.1038/ncomms8874] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Molecular trafficking within cells, tissues and engineered three-dimensional multicellular models is critical to the understanding of the development and treatment of various diseases including cancer. However, current tracking methods are either confined to two dimensions or limited to an interrogation depth of ∼15 μm. Here we present a three-dimensional tracking method capable of quantifying rapid molecular transport dynamics in highly scattering environments at depths up to 200 μm. The system has a response time of 1 ms with a temporal resolution down to 50 μs in high signal-to-noise conditions, and a spatial localization precision as good as 35 nm. Built on spatiotemporally multiplexed two-photon excitation, this approach requires only one detector for three-dimensional particle tracking and allows for two-photon, multicolour imaging. Here we demonstrate three-dimensional tracking of epidermal growth factor receptor complexes at a depth of ∼100 μm in tumour spheroids. Existing single-particle tracking techniques are limited in terms of penetration depth, tracking range or temporal resolution. Here, Perillo et al. demonstrate three-dimensional particle tracking up to 200-μm depth, with 35-nm spatial localization and 50-μs resolution using multiplexed two-photon excitation.
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Affiliation(s)
- Evan P Perillo
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Yen-Liang Liu
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Khang Huynh
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Cong Liu
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Chao-Kai Chou
- 1] Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holocombe, Boulevard, Unit 108, Houston, Texas 77030-4009, USA [2] Center for Molecular Medicine and Graduate Institute of Cancer Biology, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Mien-Chie Hung
- 1] Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holocombe, Boulevard, Unit 108, Houston, Texas 77030-4009, USA [2] Center for Molecular Medicine and Graduate Institute of Cancer Biology, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Andrew K Dunn
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
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87
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Real-time Imaging of Rabies Virus Entry into Living Vero cells. Sci Rep 2015; 5:11753. [PMID: 26148807 PMCID: PMC4493577 DOI: 10.1038/srep11753] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 06/04/2015] [Indexed: 12/15/2022] Open
Abstract
Understanding the mechanism of rabies virus (RABV) infection is vital for prevention and therapy of virulent rabies. However, the infection mechanism remains largely uncharacterized due to the limited methods and viral models. Herein, we utilized a powerful single-virus tracking technique to dynamically and globally visualize the infection process of the live attenuated rabies vaccine strain-SRV9 in living Vero cells. Firstly, it was found that the actin-enriched filopodia is in favor of virus reaching to the cell body. Furthermore, by carrying out drug perturbation experiments, we confirmed that RABV internalization into Vero cells proceeds via classical dynamin-dependent clathrin-mediated endocytosis with requirement for intact actin, but caveolae-dependent endocytosis is not involved. Then, our real-time imaging results unambiguously uncover the characteristics of viral internalization and cellular transport dynamics. In addition, our results directly and quantitatively reveal that the intracellular motility of internalized RABV particles is largely microtubule-dependent. Collectively, our work is crucial for understanding the initial steps of RABV infection, and elucidating the mechanisms of post-infection. Significantly, the results provide profound insight into development of novel and effective antiviral targets.
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88
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Smal I, Meijering E. Quantitative comparison of multiframe data association techniques for particle tracking in time-lapse fluorescence microscopy. Med Image Anal 2015; 24:163-189. [PMID: 26176413 DOI: 10.1016/j.media.2015.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 04/29/2015] [Accepted: 06/17/2015] [Indexed: 02/08/2023]
Abstract
Biological studies of intracellular dynamic processes commonly require motion analysis of large numbers of particles in live-cell time-lapse fluorescence microscopy imaging data. Many particle tracking methods have been developed in the past years as a first step toward fully automating this task and enabling high-throughput data processing. Two crucial aspects of any particle tracking method are the detection of relevant particles in the image frames and their linking or association from frame to frame to reconstruct the trajectories. The performance of detection techniques as well as specific combinations of detection and linking techniques for particle tracking have been extensively evaluated in recent studies. Comprehensive evaluations of linking techniques per se, on the other hand, are lacking in the literature. Here we present the results of a quantitative comparison of data association techniques for solving the linking problem in biological particle tracking applications. Nine multiframe and two more traditional two-frame techniques are evaluated as a function of the level of missing and spurious detections in various scenarios. The results indicate that linking techniques are generally more negatively affected by missing detections than by spurious detections. If misdetections can be avoided, there appears to be no need to use sophisticated multiframe linking techniques. However, in the practically likely case of imperfect detections, the latter are a safer choice. Our study provides users and developers with novel information to select the right linking technique for their applications, given a detection technique of known quality.
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Affiliation(s)
- Ihor Smal
- Biomedical Imaging Group Rotterdam, Erasmus MC-University Medical Center Rotterdam, Departments of Medical Informatics and Radiology, P.O. Box 2040, Rotterdam 3000 CA, The Netherlands.
| | - Erik Meijering
- Biomedical Imaging Group Rotterdam, Erasmus MC-University Medical Center Rotterdam, Departments of Medical Informatics and Radiology, P.O. Box 2040, Rotterdam 3000 CA, The Netherlands
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89
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Malikov V, da Silva ES, Jovasevic V, Bennett G, de Souza Aranha Vieira DA, Schulte B, Diaz-Griffero F, Walsh D, Naghavi MH. HIV-1 capsids bind and exploit the kinesin-1 adaptor FEZ1 for inward movement to the nucleus. Nat Commun 2015; 6:6660. [PMID: 25818806 PMCID: PMC4380233 DOI: 10.1038/ncomms7660] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 02/17/2015] [Indexed: 12/11/2022] Open
Abstract
Intracellular transport of cargos, including many viruses, involves directed movement on microtubules mediated by motor proteins. Although a number of viruses bind motors of opposing directionality, how they associate with and control these motors to accomplish directed movement remains poorly understood. Here we show that human immunodeficiency virus type 1 (HIV-1) associates with the kinesin-1 adaptor protein, Fasiculation and Elongation Factor zeta 1 (FEZ1). RNAi-mediated FEZ1 depletion blocks early infection, with virus particles exhibiting bi-directional motility but no net movement to the nucleus. Furthermore, both dynein and kinesin-1 motors are required for HIV-1 trafficking to the nucleus. Finally, the ability of exogenously expressed FEZ1 to promote early HIV-1 infection requires binding to kinesin-1. Our findings demonstrate that opposing motors both contribute to early HIV-1 movement and identify the kinesin-1 adaptor, FEZ1 as a capsid-associated host regulator of this process usurped by HIV-1 to accomplish net inward movement towards the nucleus.
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Affiliation(s)
- Viacheslav Malikov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Eveline Santos da Silva
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Vladimir Jovasevic
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Geoffrey Bennett
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | | | - Bianca Schulte
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Mojgan H Naghavi
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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90
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Medyukhina A, Timme S, Mokhtari Z, Figge MT. Image-based systems biology of infection. Cytometry A 2015; 87:462-70. [PMID: 25641512 DOI: 10.1002/cyto.a.22638] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 12/21/2022]
Abstract
The successful treatment of infectious diseases requires interdisciplinary studies of all aspects of infection processes. The overarching combination of experimental research and theoretical analysis in a systems biology approach can unravel mechanisms of complex interactions between pathogens and the human immune system. Taking into account spatial information is especially important in the context of infection, since the migratory behavior and spatial interactions of cells are often decisive for the outcome of the immune response. Spatial information is provided by image and video data that are acquired in microscopy experiments and that are at the heart of an image-based systems biology approach. This review demonstrates how image-based systems biology improves our understanding of infection processes. We discuss the three main steps of this approach--imaging, quantitative characterization, and modeling--and consider the application of these steps in the context of studying infection processes. After summarizing the most relevant microscopy and image analysis approaches, we discuss ways to quantify infection processes, and address a number of modeling techniques that exploit image-derived data to simulate host-pathogen interactions in silico.
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Affiliation(s)
- Anna Medyukhina
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany
| | - Sandra Timme
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany.,Applied Systems Biology, Friedrich Schiller University, Jena, Germany
| | - Zeinab Mokhtari
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany.,Applied Systems Biology, Friedrich Schiller University, Jena, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany.,Applied Systems Biology, Friedrich Schiller University, Jena, Germany
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91
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Abstract
Super-resolution light microscopy including pointillist methods based on single molecule localization (e.g., PALM/STORM) allow to image protein structures much smaller than the diffraction limit (200-300 nm). However, commonly used labeling strategies such as antibodies or protein fusions have several important drawbacks, including the risk to alter the function or distribution of the imaged proteins. We recently demonstrated that pointillist imaging can be performed using the alternative labeling technique known as FlAsH, which better preserves protein function, is compatible with live cell imaging, and may help reach single nanometer resolution. We applied FlAsH-PALM to visualize HIV integrase in isolated virions or infected cells, allowing us to obtain sub-diffraction resolution images of this enzyme's spatial distribution and analyze HIV morphology without altering viral replication. The technique should also prove useful to image delicate proteins in intracellular vesicles and organelles at high resolution. Here, we present a detailed protocol in order to facilitate the application of FLAsH-PALM to other proteins and biological structures.
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92
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Li H, Chen D, Xu G, Yu B, Niu H. Three dimensional multi-molecule tracking in thick samples with extended depth-of-field. OPTICS EXPRESS 2015; 23:787-794. [PMID: 25835838 DOI: 10.1364/oe.23.000787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a non-z-scanning multi-molecule tracking system with nano-resolution in all three dimensions and extended depth of field (DOF), which based on distorted grating (DG) and double-helix point spread function (DH-PSF) combination microscopy (DDCM). The critical component in DDCM is a custom designed composite phase mask (PM) combining the functions of DG and DH-PSF. The localization precision and the effective DOF of the home-built DDCM system based on the designed PM were tested. Our experimental results show that the three-dimensional (3D) localization precision for the three diffraction orders of the grating are σ(-1st)(x, y, z) = (6.5 nm, 9.2nm, 23.4 nm), σ(0th)(x, y, z) = (3.7 nm, 2.8nm, 10.3 nm), and σ(+1s)(x, y, z) = (5.8 nm, 6.9 nm, 18.4 nm), respectively. Furthermore, the total effective DOF of the DDCM system is extended to 14 μm. Tracking experiment demonstrated that beads separated over 12 μm along the axial direction at some instants can be localized and tracked successfully.
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93
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Fernandez J, Portilho DM, Danckaert A, Munier S, Becker A, Roux P, Zambo A, Shorte S, Jacob Y, Vidalain PO, Charneau P, Clavel F, Arhel NJ. Microtubule-associated proteins 1 (MAP1) promote human immunodeficiency virus type I (HIV-1) intracytoplasmic routing to the nucleus. J Biol Chem 2014; 290:4631-4646. [PMID: 25505242 DOI: 10.1074/jbc.m114.613133] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After cell entry, HIV undergoes rapid transport toward the nucleus using microtubules and microfilaments. Neither the cellular cytoplasmic components nor the viral proteins that interact to mediate transport have yet been identified. Using a yeast two-hybrid screen, we identified four cytoskeletal components as putative interaction partners for HIV-1 p24 capsid protein: MAP1A, MAP1S, CKAP1, and WIRE. Depletion of MAP1A/MAP1S in indicator cell lines and primary human macrophages led to a profound reduction in HIV-1 infectivity as a result of impaired retrograde trafficking, demonstrated by a characteristic accumulation of capsids away from the nuclear membrane, and an overall defect in nuclear import. MAP1A/MAP1S did not impact microtubule network integrity or cell morphology but contributed to microtubule stabilization, which was shown previously to facilitate infection. In addition, we found that MAP1 proteins interact with HIV-1 cores both in vitro and in infected cells and that interaction involves MAP1 light chain LC2. Depletion of MAP1 proteins reduced the association of HIV-1 capsids with both dynamic and stable microtubules, suggesting that MAP1 proteins help tether incoming viral capsids to the microtubular network, thus promoting cytoplasmic trafficking. This work shows for the first time that following entry into target cells, HIV-1 interacts with the cytoskeleton via its p24 capsid protein. Moreover, our results support a role for MAP1 proteins in promoting efficient retrograde trafficking of HIV-1 by stimulating the formation of stable microtubules and mediating the association of HIV-1 cores with microtubules.
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Affiliation(s)
- Juliette Fernandez
- From INSERM U941, Institut Universitaire d'Hématologie de l'Hôpital Saint-Louis, 75010 Paris, France
| | - Débora M Portilho
- From INSERM U941, Institut Universitaire d'Hématologie de l'Hôpital Saint-Louis, 75010 Paris, France
| | | | - Sandie Munier
- the Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, CNRS UMR3569, Institut Pasteur, 75015 Paris, France
| | - Andreas Becker
- From INSERM U941, Institut Universitaire d'Hématologie de l'Hôpital Saint-Louis, 75010 Paris, France
| | - Pascal Roux
- Imagopole, Institut Pasteur, 75015 Paris, France
| | - Anaba Zambo
- From INSERM U941, Institut Universitaire d'Hématologie de l'Hôpital Saint-Louis, 75010 Paris, France
| | | | - Yves Jacob
- the Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, CNRS UMR3569, Institut Pasteur, 75015 Paris, France
| | - Pierre-Olivier Vidalain
- Unité de Génomique Virale et Vaccination, CNRS UMR3569, Institut Pasteur, 75015 Paris, France, and
| | - Pierre Charneau
- the Unité de Virologie Moléculaire et Vaccinologie, Institut Pasteur, 75015 Paris, France
| | - François Clavel
- From INSERM U941, Institut Universitaire d'Hématologie de l'Hôpital Saint-Louis, 75010 Paris, France
| | - Nathalie J Arhel
- From INSERM U941, Institut Universitaire d'Hématologie de l'Hôpital Saint-Louis, 75010 Paris, France,.
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94
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Calderon CP. Data-driven techniques for detecting dynamical state changes in noisily measured 3D single-molecule trajectories. Molecules 2014; 19:18381-98. [PMID: 25397733 PMCID: PMC6271607 DOI: 10.3390/molecules191118381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 11/16/2022] Open
Abstract
Optical microscopes and nanoscale probes (AFM, optical tweezers, etc.) afford researchers tools capable of quantitatively exploring how molecules interact with one another in live cells. The analysis of in vivo single-molecule experimental data faces numerous challenges due to the complex, crowded, and time changing environments associated with live cells. Fluctuations and spatially varying systematic forces experienced by molecules change over time; these changes are obscured by "measurement noise" introduced by the experimental probe monitoring the system. In this article, we demonstrate how the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS) of Fox et al. [IEEE Transactions on Signal Processing 59] can be used to detect both subtle and abrupt state changes in time series containing "thermal" and "measurement" noise. The approach accounts for temporal dependencies induced by random and "systematic overdamped" forces. The technique does not require one to subjectively select the number of "hidden states" underlying a trajectory in an a priori fashion. The number of hidden states is simultaneously inferred along with change points and parameters characterizing molecular motion in a data-driven fashion. We use large scale simulations to study and compare the new approach to state-of-the-art Hidden Markov Modeling techniques. Simulations mimicking single particle tracking (SPT) experiments are the focus of this study.
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95
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Lien CH, Lin CY, Chen SJ, Chien FC. Dynamic particle tracking via temporal focusing multiphoton microscopy with astigmatism imaging. OPTICS EXPRESS 2014; 22:27290-9. [PMID: 25401879 DOI: 10.1364/oe.22.027290] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A three-dimensional (3D) single fluorescent particle tracking strategy based on temporal focusing multiphoton excitation microscopy (TFMPEM) combined with astigmatism imaging is proposed for delivering nanoscale-level axial information that reveals 3D trajectories of single fluorospheres in the axially-resolved multiphoton excitation volume without z-axis scanning. Whereas other scanning spatial focusing multiphoton excitation schemes induce optical trapping interference, temporal focusing multiphoton excitation produces widefield illumination with minimum optical trapping force on the fluorospheres. Currently, the lateral and axial positioning resolutions of the dynamic particle tracking approach are about 14 nm and 21 nm in standard deviation, respectively. Furthermore, the motion behavior and diffusion coefficients of fluorospheres in glycerol solutions with different concentrations are dynamically measured at a frame rate up to 100 Hz. This TFMPEM with astigmatism imaging holds great promise for exploring dynamic molecular behavior deep inside biotissues via its superior penetration, reduced trapping effect, fast frame rate, and nanoscale-level positioning.
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96
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Entry of a novel marine DNA virus, Singapore grouper iridovirus, into host cells occurs via clathrin-mediated endocytosis and macropinocytosis in a pH-dependent manner. J Virol 2014; 88:13047-63. [PMID: 25165116 DOI: 10.1128/jvi.01744-14] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Iridoviruses are nucleocytoplasmic DNA viruses which cause great economic losses in the aquaculture industry but also show significant threat to global biodiversity. However, a lack of host cells has resulted in poor progress in clarifying iridovirus behavior. We investigated the crucial events during virus entry using a combination of single-virus tracking and biochemical assays, based on the established virus-cell infection model for Singapore grouper iridovirus (SGIV). SGIV infection in host cells was strongly inhibited when cells were pretreated with drugs blocking clathrin-mediated endocytosis, including sucrose and chlorpromazine. Inhibition of key regulators of macropinocytosis, including Na(+)/H(+) exchanger, Rac1 GTPase, p21-activated kinase 1 (PAK1), protein kinase C (PKC), and myosin II, significantly reduced SGIV uptake. Cy5-labeled SGIV particles were observed to colocalize with clathrin and macropinosomes. In contrast, disruption of cellular cholesterol by methyl-β-cyclodextrin and nystatin had no effect on virus infection, suggesting that SGIV entered grouper cells via the clathrin-mediated endocytic pathway and macropinocytosis but not via caveola-dependent endocytosis. Furthermore, inhibitors of endosome acidification such as chloroquine and bafilomycin A1 blocked virus infection, indicating that SGIV entered cells in a pH-dependent manner. In addition, SGIV particles were observed to be transported along both microtubules and actin filaments, and intracellular SGIV motility was remarkably impaired by depolymerization of microtubules or actin filaments. The results of this study for the first time demonstrate that not only the clathrin-dependent pathway but also macropinocytosis are involved in fish DNA enveloped virus entry, thus providing a convenient tactic for exploring the life cycle of DNA viruses. IMPORTANCE Virus entry into host cells is critically important for initiating infections and is usually recognized as an ideal target for the design of antiviral strategies. Iridoviruses are large DNA viruses which cause serious threats to ecological diversity and the aquaculture industry worldwide. However, the current understanding of iridovirus entry is limited and controversial. Singapore grouper iridovirus (SGIV) is a novel marine fish DNA virus which belongs to genus Ranavirus, family Iridoviridae. Here, using single-virus tracking technology in combination with biochemical assays, we investigated the crucial events during SGIV entry and demonstrated that SGIV entered grouper cells via the clathrin-mediated endocytic pathway in a pH-dependent manner but not via caveola-dependent endocytosis. Furthermore, we propose for the first time that macropinocytosis is involved in iridovirus entry. Together, this work not only contributes greatly to understating iridovirus pathogenesis but also provides an ideal model for exploring the behavior of DNA viruses in living cells.
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97
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Francis AC, Di Primio C, Quercioli V, Valentini P, Boll A, Girelli G, Demichelis F, Arosio D, Cereseto A. Second generation imaging of nuclear/cytoplasmic HIV-1 complexes. AIDS Res Hum Retroviruses 2014; 30:717-26. [PMID: 24798748 DOI: 10.1089/aid.2013.0277] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ability to visualize fluorescent HIV-1 particles within the nuclei of infected cells represents an attractive tool to study the nuclear biology of the virus. To this aim we recently developed a microscopy-based fluorescent system (HIV-IN-EGFP) that has proven valid to efficiently visualize HIV-1 complexes in the nuclear compartment and to examine the nuclear import efficiency of the virus. The power of this method to investigate viral events occurring between the cytoplasmic and the nuclear compartment is further shown in this study through the analysis of HIV-IN-EGFP in cells expressing the TRIMCyp restriction factor. In these cells the HIV-IN-EGFP complexes are not detected in the nuclear compartment, while treatment with MG132 reveals an accumulation of HIV-1 complexes in the cytoplasm. However, the Vpr-mediated transincorporation strategy used to incorporate IN fused to EGFP (IN-EGFP) impaired viral infectivity. To optimize the infectivity of the HIV-IN-EGFP, we used mutated forms of IN (E11K and K186E) known to stabilize the IN complexes and to partially restore viral infectivity in transcomplementation experiments. The fluorescent particles produced with the modified IN [HIV-IN(K)EGFP_IN(E)] show almost 30% infectivity as compared to wild-type NL4.3. Detailed confocal microscopy analysis revealed that the newly generated viral particles resulted in HIV-1 complexes significantly smaller in size, thus requiring the use of brighter fluorophores for nuclear visualization [HIV-IN(K)sfGFP_IN(E)]. The second-generation visualization system HIV-IN(K)sfGFP_IN(E), in addition to allowing direct visualization of HIV-1 nuclear entry and other viral events related to nuclear import, preserves intact viral properties in terms of nuclear entry and improved infectivity.
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Affiliation(s)
| | | | | | - Paola Valentini
- Center for Bio-Molecular Nanotechnologies, Istituto Italiano di Tecnologia (IIT), Arnesano (Lecce), Italy
| | - Annegret Boll
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Girelli
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Demichelis
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Daniele Arosio
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche & Fondazione Bruno Kessler, Trento, Italy
| | - Anna Cereseto
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
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98
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Lanzanò L, Gratton E. Orbital Single Particle Tracking on a commercial confocal microscope using piezoelectric stage feedback. Methods Appl Fluoresc 2014; 2. [PMID: 25419461 DOI: 10.1088/2050-6120/2/2/024010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Single Particle Tracking (SPT) is a technique used to locate fluorescent particles with nanometer precision. In the orbital tracking method the position of a particle is obtained analyzing the distribution of intensity along a circular orbit scanned around the particle. In combination with an active feedback this method allows tracking of particles in 2D and 3D with millisecond temporal resolution. Here we describe a SPT setup based on a feedback approach implemented with minimal modification of a commercially available confocal laser scanning microscope, the Zeiss LSM 510, in combination with an external piezoelectric stage scanner. The commercial microscope offers the advantage of a user-friendly software interface and pre-calibrated hardware components. The use of an external piezo-scanner allows the addition of feedback into the system but also represents a limitation in terms of its mechanical response. We describe in detail this implementation of the orbital tracking method and discuss advantages and limitations. As an example of application to live cell experiments we perform the 3D tracking of acidic vesicles in live polarized epithelial cells.
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Affiliation(s)
- Luca Lanzanò
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States
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99
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Li Y, Shen L, Li C, Huang J, Zhao B, Sun Y, Li S, Luo Y, Qiu HJ. Visualization of the Npro protein in living cells using biarsenically labeling tetracysteine-tagged classical swine fever virus. Virus Res 2014; 189:67-74. [PMID: 24815879 DOI: 10.1016/j.virusres.2014.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 12/20/2022]
Abstract
Real-time fluorescence imaging of viral proteins in living cells is a valuable means to study virus-host interactions, and tetracysteine (TC)-biarsenical technology has been used in several viruses but not in classical swine fever virus (CSFV). Here, we generated CSFV mutants vSMTC385 or vSMTC412 bearing the small TC tag (CCPGCC) in the N-terminal region of the N(pro) protein. The mutants showed growth characteristics indistinguishable from that of the wild-type virus, and retained similar N(pro) subcellular localization to that of the parent virus. Furthermore, labeling with membrane-permeable biarsenical dye resulted in the fluorescent N(pro) protein in the context of virus infection. Finally, we showed that N(pro) was localized in the cytoplasm of CSFV-infected cells at 27 h post-infection (hpi) and present in the nucleus at 48 hpi, and the nuclear import and export was clearly observed from 36.5 to 37 hpi. Interestingly, our results demonstrated that N(pro) transported across the nuclear pores by passive diffusion, which might be prevented by exogenous interferon regulatory factor 3 interacting with N(pro). Taken together, biarsenical labeling allows real-time visualization of the nucleus import and export of the fluorescent N(pro) protein in CSFV-infected living cells.
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Affiliation(s)
- Yongfeng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Liang Shen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Chao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Junhua Huang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Bibo Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yuan Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Su Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yuzi Luo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China.
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100
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Calderon CP, Weiss LE, Moerner WE. Robust hypothesis tests for detecting statistical evidence of two-dimensional and three-dimensional interactions in single-molecule measurements. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052705. [PMID: 25353827 DOI: 10.1103/physreve.89.052705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Indexed: 06/04/2023]
Abstract
Experimental advances have improved the two- (2D) and three-dimensional (3D) spatial resolution that can be extracted from in vivo single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of forces experienced by biomolecules in their native environment. Situations where such force information is relevant range from mitosis to directed transport of protein cargo along cytoskeletal structures. Models commonly applied to quantify single-molecule dynamics assume that effective forces and velocity in the x,y (or x,y,z) directions are statistically independent, but this assumption is physically unrealistic in many situations. We present a hypothesis testing approach capable of determining if there is evidence of statistical dependence between positional coordinates in experimentally measured trajectories; if the hypothesis of independence between spatial coordinates is rejected, then a new model accounting for 2D (3D) interactions can and should be considered. Our hypothesis testing technique is robust, meaning it can detect interactions, even if the noise statistics are not well captured by the model. The approach is demonstrated on control simulations and on experimental data (directed transport of intraflagellar transport protein 88 homolog in the primary cilium).
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Affiliation(s)
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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