scholarly journals Overlap Intensity: An ImageJ Macro for Analyzing the HIV-1 In Situ Uncoating Assay

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1604
Author(s):  
Zachary Ingram ◽  
Hannah Matheney ◽  
Emma Wise ◽  
Courtney Weatherford ◽  
Amy E. Hulme
Keyword(s):  
Cell Imaging ◽  
High Accuracy ◽  
Analysis Software ◽  
Viral Core ◽  
Antibody Staining ◽  
Manual Counting ◽  
Manual Methods ◽  
Fixed Cell ◽  
Hiv 1

Capsid uncoating is at the crossroads of early steps in HIV-1 replication. In recent years, the development of novel assays has expanded how HIV-1 uncoating can be studied. In the in situ uncoating assay, dual fluorescently labelled virus allows for the identification of fused viral cores. Antibody staining then detects the amount of capsid associated with each viral core at different times post-infection. Following fixed cell imaging, manual counting can be used to assess the fusion state and capsid signal for each viral core, but this method can introduce bias with increased time of analysis. To address these limitations, we developed the Overlap Intensity macro in ImageJ. This macro automates the detection of viral cores and quantification of overlapping fusion and capsid signals. We demonstrated the high accuracy of the macro by comparing core detection to manual methods. Analysis of an in situ uncoating assay further verified the macro by detecting progressive uncoating as expected. Therefore, this macro improves the accessibility of the in situ uncoating assay by replacing time-consuming manual methods or the need for expensive data analysis software. Beyond the described assay, the Overlap Intensity macro includes adjustable settings for use in other methods requiring quantification of overlapping fluorescent signals.

Monitoring HIV-1 treatment in immune-cell subsets with ultrasensitive fluorescence-in-situ hybridisation

The Lancet ◽  
1999 ◽  
Vol 353 (9148) ◽  
pp. 211-212 ◽  
Author(s):  
Bruce K Patterson ◽  
Mary Ann Czerniewski ◽  
John Pottage ◽  
Michelle Agnoli ◽  
Harold Kessler ◽  
...  
Keyword(s):  
Immune Cell ◽  
In Situ Hybridisation ◽  
Fluorescence In Situ Hybridisation ◽  
Immune Cell Subsets ◽  
Hiv 1

Cost-Effective High-Speed, Three-Dimensional Live-Cell Imaging of HIV-1 Transfer at the T Cell Virological Synapse

2021 ◽  
Author(s):  
Alice Sandmeyer ◽  
Lili Wang ◽  
Wolfgang Hübner ◽  
Marcel Müller ◽  
Benjamin Chen ◽  
...  
Keyword(s):  
T Cell ◽  
Live Cell Imaging ◽  
High Speed ◽  
Cell Imaging ◽  
Three Dimensional ◽  
Cost Effective ◽  
Live Cell ◽  
Virological Synapse ◽  
Hiv 1

scholarly journals Assessment of the Accuracy of a Multi-Beam LED Scanner Sensor for Measuring Olive Canopies

Sensors ◽  
2018 ◽  
Vol 18 (12) ◽  
pp. 4406 ◽  
Author(s):  
Rafael Sola-Guirado ◽  
Sergio Bayano-Tejero ◽  
Antonio Rodríguez-Lizana ◽  
Jesús Gil-Ribes ◽  
Antonio Miranda-Fuentes
Keyword(s):  
Laboratory Test ◽  
Real Time ◽  
Relative Error ◽  
Laser Scanner ◽  
Field Tests ◽  
High Accuracy ◽  
Field Conditions ◽  
Canopy Trees ◽  
Canopy Volume

Canopy characterization has become important when trying to optimize any kind of agricultural operation in high-growing crops, such as olive. Many sensors and techniques have reported satisfactory results in these approaches and in this work a 2D laser scanner was explored for measuring canopy trees in real-time conditions. The sensor was tested in both laboratory and field conditions to check its accuracy, its cone width, and its ability to characterize olive canopies in situ. The sensor was mounted on a mast and tested in laboratory conditions to check: (i) its accuracy at different measurement distances; (ii) its measurement cone width with different reflectivity targets; and (iii) the influence of the target’s density on its accuracy. The field tests involved both isolated and hedgerow orchards, in which the measurements were taken manually and with the sensor. The canopy volume was estimated with a methodology consisting of revolving or extruding the canopy contour. The sensor showed high accuracy in the laboratory test, except for the measurements performed at 1.0 m distance, with 60 mm error (6%). Otherwise, error remained below 20 mm (1% relative error). The cone width depended on the target reflectivity. The accuracy decreased with the target density.

scholarly journals Requirement for an Intact T-Cell Actin and Tubulin Cytoskeleton for Efficient Assembly and Spread of Human Immunodeficiency Virus Type 1

2007 ◽  
Vol 81 (11) ◽  
pp. 5547-5560 ◽  
Author(s):  
Clare Jolly ◽  
Ivonne Mitar ◽  
Quentin J. Sattentau
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Cells ◽  
Plasma Membrane ◽  
T Cell ◽  
Immunodeficiency Virus ◽  
Fixed Cell ◽  
Cell Spread ◽  
Hiv 1 ◽  
Cell Cell

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) infection of CD4+ T cells leads to the production of new virions that assemble at the plasma membrane. Gag and Env accumulate in the context of lipid rafts at the inner and outer leaflets of the plasma membrane, respectively, forming polarized domains from which HIV-1 buds. HIV-1 budding can result in either release of cell-free virions or direct cell-cell spread via a virological synapse (VS). The recruitment of Gag and Env to these plasma membrane caps in T cells is poorly understood but may require elements of the T-cell secretory apparatus coordinated by the cytoskeleton. Using fixed-cell immunofluorescence labeling and confocal microscopy, we observed a high percentage of HIV-1-infected T cells with polarized Env and Gag in capped, lipid raft-like assembly domains. Treatment of infected T cells with inhibitors of actin or tubulin remodeling disrupted Gag and Env compartmentalization within the polarized raft-like domains. Depolymerization of the actin cytoskeleton reduced Gag release and viral infectivity, and actin and tubulin inhibitors reduced Env incorporation into virions. Live- and fixed-cell confocal imaging and assay of de novo DNA synthesis by real-time PCR allowed quantification of HIV-1 cell-cell transfer. Inhibition of actin and tubulin remodeling in infected cells interfered with cell-cell spread across a VS and reduced new viral DNA synthesis. Based on these data, we propose that HIV-1 requires both actin and tubulin components of the T-cell cytoskeleton to direct its assembly and budding and to elaborate a functional VS.

scholarly journals The rhodopsin-retinochrome system for retinal re-isomerization predates the origin of cephalopod eyes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Oliver Vöcking ◽  
Lucas Leclère ◽  
Harald Hausen
Keyword(s):  
In Situ Hybridization ◽  
Photoreceptor Cells ◽  
Visual Cycle ◽  
Phylogenetic Distribution ◽  
Enzymatic Process ◽  
Antibody Staining ◽  
The Individual ◽  
Functional Components ◽  
Visual Rhodopsin

Abstract Background The process of photoreception in most animals depends on the light induced isomerization of the chromophore retinal, bound to rhodopsin. To re-use retinal, the all-trans-retinal form needs to be re-isomerized to 11-cis-retinal, which can be achieved in different ways. In vertebrates, this mostly includes a stepwise enzymatic process called the visual cycle. The best studied re-isomerization system in protostomes is the rhodopsin-retinochrome system of cephalopods, which consists of rhodopsin, the photoisomerase retinochrome and the protein RALBP functioning as shuttle for retinal. In this study we investigate the expression of the rhodopsin-retinochrome system and functional components of the vertebrate visual cycle in a polyplacophoran mollusk, Leptochiton asellus, and examine the phylogenetic distribution of the individual components in other protostome animals. Results Tree-based orthology assignments revealed that orthologs of the cephalopod retinochrome and RALBP are present in mollusks outside of cephalopods. By mining our dataset for vertebrate visual cycle components, we also found orthologs of the retinoid binding protein RLBP1, in polyplacophoran mollusks, cephalopods and a phoronid. In situ hybridization and antibody staining revealed that L. asellus retinochrome is co-expressed in the larval chiton photoreceptor cells (PRCs) with the visual rhodopsin, RALBP and RLBP1. In addition, multiple retinal dehydrogenases are expressed in the PRCs, which might also contribute to the rhodopsin-retinochrome system. Conclusions We conclude that the rhodopsin-retinochrome system is a common feature of mollusk PRCs and predates the origin of cephalopod eyes. Our results show that this system has to be extended by adding further components, which surprisingly, are shared with vertebrates.

scholarly journals HIV-1 uncoating occurs via a series of rapid biomechanical changes in the core related to individual stages of reverse transcription

2021 ◽  
Author(s):  
Sanela Rankovic ◽  
Akshay Deshpande ◽  
Shimon Harel ◽  
Christopher Aiken ◽  
Itay Rousso
Keyword(s):  
Reverse Transcription ◽  
Viral Genome ◽  
Morphological Changes ◽  
Viral Capsid ◽  
Target Cells ◽  
Viral Core ◽  
Successful Infection ◽  
Capsid Shell ◽  
Hiv 1

AbstractThe HIV core consists of the viral genome and associated proteins encased by a cone-shaped protein shell termed the capsid. Successful infection requires reverse transcription of the viral genome and disassembly of the capsid shell within a cell in a process known as uncoating. The integrity of the viral capsid is critical for reverse transcription, yet the viral capsid must be breached to release the nascent viral DNA prior to integration. We employed atomic force microscopy to study the stiffness changes in HIV-1 cores during reverse transcription in vitro in reactions containing the capsid-stabilizing host metabolite IP6. Cores exhibited a series of stiffness spikes, with up to three spikes typically occurring between 10-30, 40-80, and 120-160 minutes after initiation of reverse transcription. Addition of the reverse transcriptase (RT) inhibitor efavirenz eliminated the appearance of these spikes and the subsequent disassembly of the capsid, thus establishing that both result from reverse transcription. Using timed addition of efavirenz, and analysis of an RNAseH-defective RT mutant, we established that the first stiffness spike requires minus-strand strong stop DNA synthesis, with subsequent spikes requiring later stages of reverse transcription. Additional rapid AFM imaging experiments revealed repeated morphological changes in cores that were temporally correlated with the observed stiffness spikes. Our study reveals discrete mechanical changes in the viral core that are likely related to specific stages of reverse transcription. Our results suggest that reverse-transcription-induced changes in the capsid progressively remodel the viral core to prime it for temporally accurate uncoating in target cells.

scholarly journals A High-Accuracy Multiwavelength Radiometer for In Situ Measurements in the Thermal Infrared. Part II: Behavior in Field Experiments

2003 ◽  
Vol 20 (7) ◽  
pp. 1023-1033 ◽  
Author(s):  
Gérard Brogniez ◽  
Christophe Pietras ◽  
Michel Legrand ◽  
Philippe Dubuisson ◽  
Martial Haeffelin
Keyword(s):  
Field Experiments ◽  
Thermal Infrared ◽  
High Accuracy ◽  
In Situ Measurements
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