Evidence map›Paper›PMID 40883991›Full record

ArticleBiophysical journal2025

3D localization of retrovirus assembly in the presence of structured background with deep learning.

John Kohler, Kwang-Ho Hur, Elijah Wray, Jesse Donahue, Rayna Addabbo, Louis M Mansky, Joachim D Mueller

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biophysical journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

John KohlerSchool of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota.
Kwang-Ho HurSchool of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota.
Elijah WrayInstitute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota; Biomedical Engineering Graduate Program, University of Minnesota, Minneapolis, Minnesota.
Jesse DonahueSchool of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota.
Rayna AddabboSchool of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota.
Louis M ManskyInstitute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota; Biomedical Engineering Graduate Program, University of Minnesota, Minneapolis, Minnesota; Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota.
Joachim D MuellerSchool of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota; Biomedical Engineering Graduate Program, University of Minnesota, Minneapolis, Minnesota. Electronic address: jochen@umn.edu.

Funding

Minnesota Training Program in VirologyT32AI083196 · NIAID · UNIVERSITY OF MINNESOTA · PI Louis M Mansky · 2010 to 2026
$3.2M
HIV particle morphology and biogenesisR01AI177264 · NIAID · UNIVERSITY OF MINNESOTA · PI JOACHIM D MUELLER, Louis M Mansky · 2023 to 2026
$2.8M
NIAID NIH HHS R01 AI177264NIAID NIH HHS T32 AI083196
6 · The paper itself

Abstract

Human immunodeficiency virus type 1 (HIV-1) particle assembly is driven by the Gag structural polyprotein and is a crucial step in the production of new virus particles. Elucidating the details of this process is necessary to fully understand the virus replication cycle. Real-time measurements of virus particle biogenesis in living cells have proved challenging, and most of our knowledge of this process to date has come from total internal fluorescence microscopy of labeled Gag at the bottom plasma membrane (PM) of adherent cells. While the glass coverslip adjacent to the bottom PM renders this an artificial environment, fluorescence measurements at the more physiologically relevant top PM are challenging due to the three-dimensional (3D) profile at the top PM as well as the large, structured background fluorescence that arises due to cytoplasmic, unassembled Gag protein. Here, we describe an approach to 3D localization microscopy and analysis to address the challenges associated with imaging virus assembly at the top PM in live cells. Specifically, we have employed the double helix point spread function for 3D imaging with an extended depth of field combined with a deep learning pipeline to analyze images that contain heterogeneous structured backgrounds. We demonstrate the power of this approach by measuring virus assembly at the top PM of adherent cells in 3D fluorescence microscopy and observe intriguing differences in the assembly kinetics and HIV-1 Gag puncta mobility between the adherent bottom PM and the nonadherent top PM.

Indexed as

Deep LearningHIV-1Imaging, Three-DimensionalVirus AssemblyCell Membranegag Gene Products, Human Immunodeficiency VirusHumansMicroscopy, Fluorescencegag Gene Products, Human Immunodeficiency Virus

Identifiers

PMID40883991
PMCPMC12536721

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.