Evidence map›Paper›PMID 25228758›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2014

Genomic donor cassette sharing during VLRA and VLRC assembly in jawless vertebrates.

Sabyasachi Das, Jianxu Li, Stephen J Holland, Lakshminarayan M Iyer, Masayuki Hirano, Michael Schorpp, L Aravind, Max D Cooper, Thomas Boehm

Open access · bronzeAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
0.7field-weighted citation impact, top 30% 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

12 citing papers in PubMed, 21 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Review
  6. Evolution of variable lymphocyte receptor B antibody loci in jawless vertebrates.Proceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  7. Review
  8. Review
  9. Zebrafish and Medaka: Two Teleost Models of T-Cell and Thymic Development.International journal of molecular sciences · 2019
    Review
  10. Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  11. Characterization of Lamprey BAFF-like Gene: Evolutionary Implications.Journal of immunology (Baltimore, Md. : 1950) · 2016
    Article
  12. 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

9 authors at 4 institutions in 2 countries.

Sabyasachi DasEmory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322;
Jianxu LiEmory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322;
Stephen J HollandDepartment of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; and.
Lakshminarayan M IyerNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.
Masayuki HiranoEmory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322;
Michael SchorppDepartment of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; and.
L AravindNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.
Max D CooperEmory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322; mdcoope@emory.edu boehm@immunbio.mpg.de.
Thomas BoehmDepartment of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; and mdcoope@emory.edu boehm@immunbio.mpg.de.
Emory University · USMax Planck Society · DENational Center for Biotechnology Information · USNational Institutes of Health · US

Funding

Evolutionary Analysis and Comparative Genomics of Protein SuperfamiliesZIALM594244 · NLM · NATIONAL LIBRARY OF MEDICINE · PI ARAVIND, L · 2009 to 2025
$20.3M
Characterization of the Lamprey Adaptive Immune SystemR01AI072435 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Max Dale Cooper · 2007 to 2026
$8.1M
Definition of an Ancient T cell-like System in LampreysR01GM100151 · NIGMS · EMORY UNIVERSITY · PI COOPER, MAX DALE · 2012 to 2016
$1.5M
Intramural NIH HHSNIAID NIH HHS AI072435NIAID NIH HHS R01 AI072435NIGMS NIH HHS GM100151NIGMS NIH HHS R01 GM100151
6 · The paper itself

Abstract

Lampreys possess two T-like lymphocyte lineages that express either variable lymphocyte receptor (VLR) A or VLRC antigen receptors. VLRA(+) and VLRC(+) lymphocytes share many similarities with the two principal T-cell lineages of jawed vertebrates expressing the αβ and γδ T-cell receptors (TCRs). During the assembly of VLR genes, several types of genomic cassettes are inserted, in step-wise fashion, into incomplete germ-line genes to generate the mature forms of antigen receptor genes. Unexpectedly, the structurally variable components of VLRA and VLRC receptors often possess partially identical sequences; this phenomenon of module sharing between these two VLR isotypes occurs in both lampreys and hagfishes. By contrast, VLRA and VLRC molecules typically do not share their building blocks with the structurally analogous VLRB receptors that are expressed by B-like lymphocytes. Our studies reveal that VLRA and VLRC germ-line genes are situated in close proximity to each other in the lamprey genome and indicate the interspersed arrangement of isotype-specific and shared genomic donor cassettes; these features may facilitate the shared cassette use. The genomic structure of the VLRA/VLRC locus in lampreys is reminiscent of the interspersed nature of the TCRA/TCRD locus in jawed vertebrates that also allows the sharing of some variable gene segments during the recombinatorial assembly of TCR genes.

Indexed as

AnimalsBase SequenceEvolution, MolecularGenetic LociGenomeHagfishesJawLampreysMolecular Sequence DataReceptors, AntigenT-LymphocytesVertebratesReceptors, Antigenadaptive immunityagnathamolecular evolutionselection

Identifiers

PMID25228758
PMCPMC4205630
OpenAlexW2087859741

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.