Evidence map›Paper›PMID 22718821›Full record

ArticleJournal of virology2012

Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1.

Daniel Malouli, Ernesto S Nakayasu, Kasinath Viswanathan, David G Camp, W L William Chang, Peter A Barry, Richard D Smith, Klaus Früh

Abstract read
In one paragraph

Article in Journal of virology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.

0numbers the graph read from it
0cells of the map it votes in
40citing 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

40 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Article
  5. Article
  6. Article
  7. CD8Science advances · 2024
    Article
  8. HCMV-secreted glycoprotein gpUL4 inhibits TRAIL-mediated apoptosis and NK cell activation.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Review
  19. Article
  20. 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

8 authors.

Daniel MalouliVaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA.
Ernesto S Nakayasu
Kasinath Viswanathan
David G Camp
W L William Chang
Peter A Barry
Richard D Smith
Klaus Früh

Funding

Upgrade of confocal microscopy at the Oregon National Primate Research CenterP51OD011092 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI Bonnie J. Nagel · 2012 to 2026
$203.9M
WORKSHOP AND TRAINING ACTIVITIESP41RR018522 · NCRR · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI SMITH, RICHARD D · 2003 to 2011
$25.1M
Equipment Supplement Request for a Research Resource for Ultra-sensitive High Throughput ProteomicsP41GM103493 · NIGMS · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI SMITH, RICHARD D · 2012 to 2022
$22.6M
Virology and Immunology MonitoringP01AI094417 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI KAHL, CHRISTOPH ADRIAN · 2011 to 2016
$20.5M
Evasion of Antigen Presentation by Rhesus CytomegalovirusR01AI059457 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI FRUH, KLAUS J · 2005 to 2021
$6.2M
DevelopmentalP30AI082151 · NIAID · RUSH UNIVERSITY MEDICAL CENTER · PI LANDAY, ALAN L · 2009 to 2014
$4.6M
Development and In Vivo Characterization of Safety-Enhanced RhCMV/SIV VectorsR01AI095113 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI PICKER, LOUIS J. · 2011 to 2015
$4.1M
Modulation of Innate Immune Responses by CytomegalovirusR01AI070890 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI FRUH, KLAUS J · 2008 to 2012
$2.4M
Evasion of Antigen Presentation by Rhesus CytomegalovirusR56AI059457 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI FRUH, KLAUS J · 2016 to 2016
$567k
NCRR NIH HHS 5P41RR018522-10NCRR NIH HHS P41 RR018522NIAID NIH HHS AI059457-06NIAID NIH HHS AI094417NIAID NIH HHS AI095113NIAID NIH HHS P01 AI094417NIAID NIH HHS P30AI082151NIAID NIH HHS R01 AI059457NIAID NIH HHS R01 AI070890NIAID NIH HHS R01 AI095113NIAID NIH HHS R56 AI059457NIGMS NIH HHS 8 P41 GM103493-10NIGMS NIH HHS P41 GM103493NIH HHS P51 OD011092NIH HHS P51OD011092
6 · The paper itself

Abstract

Cytomegaloviruses are highly host restricted, resulting in cospeciation with their hosts. As a natural pathogen of rhesus macaques (RM), rhesus cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). Most in vivo experiments performed with RhCMV employed strain 68-1 cloned as a bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown, and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs with an arbitrary cutoff of 300 bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV, we reevaluated the RhCMV 68-1 BAC genome by whole-genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By comparing the RhCMV genome to those of several related Old World monkey (OWM) CMVs, we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis suggests a high degree of ORF conservation among OWM CMVs, thus decreasing the likelihood that ORFs found only in RhCMV comprise true genes. Moreover, virion proteomics independently validated the revised ORF predictions, since only proteins that were conserved across OWM CMVs could be detected. Taken together, these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes, and OWMs than previously assumed.

Indexed as

Open Reading FramesAmino Acid SequenceAnimalsBase SequenceCell LineCercopithecidaeChromosomes, Artificial, BacterialCytomegalovirusCytomegalovirus InfectionsEvolution, MolecularGenome, ViralHumansMacaca mulattaMolecular Sequence DataPhylogenyPrimate DiseasesViral Proteins

Identifiers

PMID22718821
PMCPMC3416160

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.