Evidence map›Paper›PMID 33468052›Full record

ArticleBMC genomics2021

Comparative whole-genome and proteomics analyses of the next seed bank and the original master seed bank of MucoRice-CTB 51A line, a rice-based oral cholera vaccine.

Ai Sasou, Yoshikazu Yuki, Ayaka Honma, Kotomi Sugiura, Koji Kashima, Hiroko Kozuka-Hata, Masanori Nojima, Masaaki Oyama, Shiho Kurokawa, Shinichi Maruyama and 6 more

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

Article in BMC genomics, 2021. 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
0.4field-weighted citation impact, top 39% 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, 3 citations in OpenAlex.

  1. Article
  2. 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

16 authors at 5 institutions in 2 countries.

Ai SasouDivision of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Yoshikazu YukiDivision of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. yukiy@ims.u-tokyo.ac.jp.
Ayaka HonmaDivision of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Kotomi SugiuraDivision of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Koji KashimaAsahi Kogyosha Co., Ltd., Tokyo, Japan.
Hiroko Kozuka-HataMedical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Masanori NojimaCenter for Translational Research, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Masaaki OyamaMedical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Shiho KurokawaDivision of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Shinichi MaruyamaAsahi Kogyosha Co., Ltd., Tokyo, Japan.
Masaharu KurodaCrop Development Division, NARO Agriculture Research Center, Niigata, Japan.
Shinjiro TanoueAstellas Pharma Inc., Tokyo, Japan.
Narushi TakamatsuAstellas Pharma Inc., Tokyo, Japan.
Kohtaro FujihashiResearch and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Eiji GotoFaculty of Horticulture, Graduate School of Horticulture, Chiba University, Chiba, Japan.
Hiroshi KiyonoDivision of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
The University of Tokyo · JPAstellas Pharma (Japan) · JPChiba University · JPNiigata Agricultural Research Institute · JPUniversity of Tokyo Hospital · JP

Funding

Japan Agency for Medical Research and Development (AMED) JP17pc0101001
6 · The paper itself

Abstract

backgroundWe have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker-free MucoRice-CTB line 51A, which has three copies of the cholera toxin B subunit (CTB) gene and two copies of an RNAi cassette inserted into the rice genome. We determined the sequence and location of the transgenes on rice chromosomes 3 and 12. The expression of alpha-amylase/trypsin inhibitor, a major allergen protein in rice, is lower in this line than in wild-type rice. Line 51A was self-pollinated for five generations to fix the transgenes, and the seeds of the sixth generation produced by T5 plants were defined as the master seed bank (MSB). T6 plants were grown from part of the MSB seeds and were self-pollinated to produce T7 seeds (next seed bank; NSB). NSB was examined and its whole genome and proteome were compared with those of MSB.

resultsWe re-sequenced the transgenes of NSB and MSB and confirmed the positions of the three CTB genes inserted into chromosomes 3 and 12. The DNA sequences of the transgenes were identical between NSB and MSB. Using whole-genome sequencing, we compared the genome sequences of three NSB with three MSB samples, and evaluated the effects of SNPs and genomic structural variants by clustering. No functionally important mutations (SNPs, translocations, deletions, or inversions of genic regions on chromosomes) between NSB and MSB samples were detected. Analysis of salt-soluble proteins from NSB and MSB samples by shot-gun MS/MS detected no considerable differences in protein abundance. No difference in the expression pattern of storage proteins and CTB in mature seeds of NSB and MSB was detected by immuno-fluorescence microscopy.

conclusionsAll analyses revealed no considerable differences between NSB and MSB samples. Therefore, NSB can be used to replace MSB in the near future.

Indexed as

Cholera VaccinesOryzaCholera ToxinPlants, Genetically ModifiedProteomicsSeed BankTandem Mass SpectrometryCholera ToxinCholera VaccinesMucoRice-CTBOral cholera vaccinePlant-made pharmaceuticalsProteomics analysisSeed bankShot-gun MS/MSTransgenic riceWhole-genome re-sequencing

Identifiers

PMID33468052
PMCPMC7814724
OpenAlexW3123667032

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.