Evidence map›Paper›PMID 41427412›Full record

ArticlebioRxiv : the preprint server for biology2025

An integrated workflow for structural virology with a 100 keV electron microscope.

Rasangi Pathirage, Moumita Dutta, Ruth J Parsons, Muralikrishna Lella, Emma Atwood, Qianyi E Zhang, Aaron May, Alexis Johnson, Xiao Huang, Jordan Flemming and 34 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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. Review
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

44 authors.

Rasangi PathirageDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Moumita DuttaDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Ruth J ParsonsDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Muralikrishna LellaDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Emma AtwoodDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Qianyi E ZhangDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Aaron MayDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Alexis JohnsonDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Xiao HuangDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Jordan FlemmingDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Ujjwal KumarDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Bahjat F MarayatiDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
M Ariel SpurrierDepartment of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
Coco LiuDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Junlin ZhuoDepartment of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Ki SongDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Radha Devkota AdhikariDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Salam SammourDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Victor IlevbareDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Carter AbramDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Michael DiazDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Albert GuzmanMaterial and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA.
Jay RaiMaterial and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA.
Ashwin N SkellyDepartments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Michael P HogartyDepartments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Kara AnastiDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Max PurroDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Myles LindsayDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Munir AlamDuke University, Department of Medicine, Durham, NC 27710, USA.
Drew WeissmanDepartments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Alon HerschchornDivision of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
Beatrice H HahnDepartments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
George M ShawDepartments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Amit SharmaNorth Carolina State University, College of Veterinary Medicine, Raleigh, NC 27607.
Nicholas S HeatonDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Robert J EdwardsDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Rory HendersonDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.ORCID 0000-0002-4301-6382
Thomas DennyDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Kevin O SaundersDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Janet SilicianoDepartment of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Robert SilicianoDepartment of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Barton F HaynesDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Katarzyna JanowskaDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.
Priyamvada AcharyaDuke University, Duke Human Vaccine Institute, Durham NC 27710, USA.ORCID 0000-0002-0089-277X

Funding

Nonhuman primate studies for development of a prototype HIV vaccine that induces broadly neutralizing antibodiesUM1AI144371 · NIAID · DUKE UNIVERSITY · PI HAYNES, BARTON F. · 2019 to 2025
$190.4M
Project 3 - Dynamics of latent HIV-1 reservoirs: High resolution antigenic mapping and strategies to block reboundU54AI170752 · NIAID · DUKE UNIVERSITY · PI Priyamvada Acharya · 2022 to 2026
$32.0M
Dissecting the mechanisms of HIV resistance in vivo to broadly neutralizing antibodiesU01AI169587 · NIAID · UNIVERSITY OF MINNESOTA · PI Priyamvada Acharya, Brandon James DeKosky · 2022 to 2026
$7.8M
Targeting early metastable intermediates of the SARS-CoV-2 spike for vaccine and therapeutics developmentR01AI145687 · NIAID · DUKE UNIVERSITY · PI Priyamvada Acharya · 2019 to 2026
$6.9M
THE ATHEROSCLEROSIS RISK IN COMMUNITIES (ARIC) STUDY - FIELD CENTER - TASK ORDER 01, TASK AREA A75N92022D00003 · NHLBI · UNIVERSITY OF MINNESOTA · PI LUTSEY, PAMELA · 2022 to 2025
$5.1M
Effect of natural and engineered variations on structure and biophysics of SARS-CoV-2 spikeR01AI165947 · NIAID · DUKE UNIVERSITY · PI Priyamvada Acharya, Rory Henderson · 2022 to 2026
$3.8M
Structural characterization of Fab-dimerized glycan-reactive antibodies that neutralize HIV-1R01AI165147 · NIAID · DUKE UNIVERSITY · PI ACHARYA, PRIYAMVADA, WILLIAMS, WILTON B · 2021 to 2025
$3.4M
Determinants of retroviral replication in non-native hosts for modeling HIV infectionR01AI172615 · NIAID · OHIO STATE UNIVERSITY · PI Amit Sharma · 2023 to 2026
$3.1M
Dissecting the Conformational Flexibility of HIV-1 Envelope GlycoproteinsR01AI167653 · NIAID · UNIVERSITY OF MINNESOTA · PI HERSCHHORN, ALON · 2022 to 2025
$2.9M
Data commons for 'omic, microscopy and analysis core facilitiesS10OD018164 · OD · DUKE UNIVERSITY · PI WRAY, GREGORY A. · 2014 to 2014
$598k
NHLBI NIH HHS 75N92022D00003NIAID NIH HHS R01 AI145687NIAID NIH HHS R01 AI165147NIAID NIH HHS R01 AI165947NIAID NIH HHS R01 AI167653NIAID NIH HHS R01 AI172615NIAID NIH HHS U01 AI169587NIAID NIH HHS U54 AI170752NIAID NIH HHS UM1 AI144371NIDA NIH HHS 75N95022D00003NIEHS NIH HHS 75N96022D00003NIH HHS S10 OD018164ORFDO NIH HHS 75N99022D00003
6 · The paper itself

Abstract

Cryo-EM has revolutionized structural biology, especially for flexible and heterogeneous samples, although access to high end microscopes that enable these studies remains a bottleneck. While 300 keV microscopes have been the go-to for high-resolution structural determination, they are expensive and restricted to institutional and national facilities needing specialized expertise, with access falling far short of the demand. Here, we present the user-managed operation of a cheaper 100 keV electron microscope within a structural biology laboratory enabling close integration with protein production, biochemical and biophysical studies. We provide details and considerations for the installation of the microscope, its day-to-day maintenance, and operations. Using virus surface glycoproteins as case studies, we illustrate the workflow from grid screening, data collection, and data processing, and provide examples of data quality. This user-administered setup provides a training platform for researchers at all levels, with beginners in cryo-EM achieving proficiency to independently operate the microscope within a month of regular use and training. We have demonstrated routine high-quality low-resolution reconstructions using a Ceta CMOS camera and high-resolution reconstructions enabling building of atomic models using a Falcon C direct detector. While there are several examples of facilities that manage cryo-EM and individual laboratories leveraging cryo-EM, we provide here the first demonstration of a modern group independently doing both successfully, something that has been talked about frequently but rarely seen.

Identifiers

PMID41427412
PMCPMC12713605

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.