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HIV Protocols

Overview of attention for book
Cover of 'HIV Protocols'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Quantifying CD4/CCR5 Usage Efficiency of HIV-1 Env Using the Affinofile System
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    Chapter 2 Measuring T Cell-to-T Cell HIV-1 Transfer, Viral Fusion, and Infection Using Flow Cytometry
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    Chapter 3 HIV-1 Capsid Stabilization Assay
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    Chapter 4 Detection and Tracking of Dual-Labeled HIV Particles Using Wide-Field Live Cell Imaging to Follow Viral Core Integrity
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    Chapter 5 HIV-1 Reverse Transcriptase-Based Assay to Determine Cellular dNTP Concentrations
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    Chapter 6 Rapid Determination of HIV-1 Mutant Frequencies and Mutation Spectra Using an mCherry/EGFP Dual-Reporter Viral Vector
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    Chapter 7 Novel Biochemical Tools for Probing HIV RNA Structure
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    Chapter 8 Analysis of HIV-1 Gag-RNA Interactions in Cells and Virions by CLIP-seq.
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    Chapter 9 Isolation of Cognate Cellular and Viral Ribonucleoprotein Complexes of HIV-1 RNA Applicable to Proteomic Discovery and Molecular Investigations
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    Chapter 10 Methods for the Analyses of Inhibitor-Induced Aberrant Multimerization of HIV-1 Integrase
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    Chapter 11 Quantification of HIV-1 Gag Localization Within Virus Producer Cells
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    Chapter 12 Methods to Study Determinants for Membrane Targeting of HIV-1 Gag In Vitro
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    Chapter 13 Visualizing the Behavior of HIV-Infected T Cells In Vivo Using Multiphoton Intravital Microscopy
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    Chapter 14 Modeling HIV-1 Mucosal Transmission and Prevention in Humanized Mice
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    Chapter 15 High-Throughput Humanized Mouse Models for Evaluation of HIV-1 Therapeutics and Pathogenesis
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    Chapter 16 Measuring the Frequency of Latent HIV-1 in Resting CD4 + T Cells Using a Limiting Dilution Coculture Assay
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    Chapter 17 LGIT In Vitro Latency Model in Primary and T Cell Lines to Test HIV-1 Reactivation Compounds
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    Chapter 18 Improved Methods to Detect Low Levels of HIV Using Antibody-Based Technologies
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    Chapter 19 Analysis of ABCA1 and Cholesterol Efflux in HIV-Infected Cells
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    Chapter 20 The Proteomic Characterization of Plasma or Serum from HIV-Infected Patients
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    Chapter 21 Proteomic Characterization of Exosomes from HIV-1-Infected Cells
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    Chapter 22 Detecting HIV-1 Tat in Cell Culture Supernatants by ELISA or Western Blot
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    Chapter 23 Protocol for Detection of HIV-Tat Protein in Cerebrospinal Fluid by a Sandwich Enzyme-Linked Immunosorbent Assay
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    Chapter 24 Measuring the Uptake and Transactivation Function of HIV-1 Tat Protein in a Trans-cellular Cocultivation Setup.
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    Chapter 25 Evaluating the Role of Viral Proteins in HIV-Mediated Neurotoxicity Using Primary Human Neuronal Cultures.
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    Chapter 26 Erratum
Attention for Chapter 8: Analysis of HIV-1 Gag-RNA Interactions in Cells and Virions by CLIP-seq.
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (52nd percentile)
  • Good Attention Score compared to outputs of the same age and source (76th percentile)

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Chapter title
Analysis of HIV-1 Gag-RNA Interactions in Cells and Virions by CLIP-seq.
Chapter number 8
Book title
HIV Protocols
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3046-3_8
Pubmed ID
Book ISBNs
978-1-4939-3045-6, 978-1-4939-3046-3
Authors

Kutluay, Sebla B, Bieniasz, Paul D, Sebla B. Kutluay, Paul D. Bieniasz, Kutluay, Sebla B., Bieniasz, Paul D.

Abstract

Next-generation sequencing-based methodologies have revolutionized the analysis of protein-nucleic acid complexes; yet these novel approaches have rarely been applied in virology. Because it has an RNA genome, RNA-protein interactions play critical roles in human immunodeficiency virus type 1 (HIV-1) replication. In many cases, the binding sites of proteins on HIV-1 RNA molecules in physiologically relevant settings are not known. Cross-linking-immunoprecipitation sequencing (CLIP-seq) methodologies, which combine immunoprecipitation of covalently crosslinked protein-RNA complexes with high-throughput sequencing, is a powerful technique that can be applied to such questions as it provides a global account of RNA sequences bound by a RNA-binding protein of interest in physiological settings at near-nucleotide resolution. Here, we describe the application of the CLIP-seq methodology to identify the RNA molecules that are bound by the HIV-1 Gag protein in cells and in virions. This protocol can easily be applied to other viral and cellular RNA-binding proteins that influence HIV-1 replication.

X Demographics

X Demographics

The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 13 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 13 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 31%
Student > Bachelor 2 15%
Professor 2 15%
Librarian 1 8%
Researcher 1 8%
Other 1 8%
Unknown 2 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 6 46%
Agricultural and Biological Sciences 4 31%
Engineering 1 8%
Unknown 2 15%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 May 2018.
All research outputs
#13,221,334
of 22,842,950 outputs
Outputs from Methods in molecular biology
#3,465
of 13,127 outputs
Outputs of similar age
#184,634
of 393,571 outputs
Outputs of similar age from Methods in molecular biology
#328
of 1,470 outputs
Altmetric has tracked 22,842,950 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,127 research outputs from this source. They receive a mean Attention Score of 3.4. This one has gotten more attention than average, scoring higher than 72% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 393,571 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 52% of its contemporaries.
We're also able to compare this research output to 1,470 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.