Evidence map›Paper›PMID 38053139›Full record

ArticleBMC research notes2023

A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint.

Maneenop Yimyaem, Kunlakanya Jitobaom, Prasert Auewarakul

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC research notes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.3field-weighted citation impact, top 35% of its field
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

2 citing papers in PubMed, 2 citations in OpenAlex.

  1. Review
  2. 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

3 authors at 1 institution in 1 country.

Maneenop YimyaemGraduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand.
Kunlakanya JitobaomDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
Prasert AuewarakulDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. prasert.aue@mahidol.ac.th.
Mahidol University · TH

Funding

National Science and Technology Development Agency P-20-52262
6 · The paper itself

Abstract

objectiveRare codons were previously shown to be enriched at the beginning of the dengue virus (DENV) open reading frame. However, the role of rare codons in regulating translation efficiency and replication of DENV remains unclear. The present study aims to clarify the significance of rare codon usage at the beginning of DENV transcripts using the codon adaptation index (CAI). METHODOLOGY: CAIs of the whole starting regions of DENV transcripts as well as 18-codon sliding windows of the regions were analyzed.

resultsOne of the intriguing findings is that those rare codons do not typically result in uniformly low CAI in the starting region with rare codons. However, it shows a notable local drop in CAI around the 50th codon in all dengue serotypes. This suggests that there may be a translational checkpoint at this site and that the rare codon usage upstream to this checkpoint may not be related to translational control.

Indexed as

Codon UsageDengue VirusCodonOpen Reading FramesCodonCodon adaptation indexRare codonTranslational checkpoint

Identifiers

PMID38053139
PMCPMC10698908
OpenAlexW4389334286

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.