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Article ; Online: Correction: Suppression of class I compensated cell enlargement by xs2 mutation is mediated by salicylic acid signaling.

Fujikura, Ushio / Ezaki, Kazune / Horiguchi, Gorou / Seo, Mitsunori / Kanno, Yuri / Kamiya, Yuji / Lenhard, Michael / Tsukaya, Hirokazu

PLoS genetics

2023 Volume 19, Issue 5, Page(s) e1010775

Abstract: This corrects the article DOI: 10.1371/journal.pgen.1008873.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pgen.1008873.].
Language	English
Publishing date	2023-05-19
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1010775
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice

Shimatani, Zenpei / Fujikura, Ushio / Ishii, Hisaki / Terada, Rie / Nishida, Keiji / Kondoh, Akihiko

Data in Brief. 2018 Oct., v. 20 p.1325-1331

2018

Abstract: Acetolactate synthase (ALS) catalyzes the initial step in the biosynthesis of branched-chain amino acids, and is highly conserved from bacteria to higher plants. ALS is encoded by a single copy gene in rice genome and is a target enzyme of several ... ...

Abstract	Acetolactate synthase (ALS) catalyzes the initial step in the biosynthesis of branched-chain amino acids, and is highly conserved from bacteria to higher plants. ALS is encoded by a single copy gene in rice genome and is a target enzyme of several classes of herbicides. Although ALS mutations conferring herbicide-resistance property to plants are well documented, effect of Imazamox (IMZ) on rice and the mutations in ALS correlated with IMZ tolerance were unclear. In this article, the effect of IMZ on rice calli and seedlings in tissue culture conditions were evaluated. Also, the ALSA96V mutation was confirmed to improve IMZ tolerance of rice calli. Based on these results, ALS-assisted multiplex targeted base editing in rice was demonstrated in combination with Target-AID, a CRISPR/Cas9-cytidine deaminase fusion system [1], [2].
Keywords	acetolactate synthase ; biosynthesis ; callus ; genes ; herbicide resistance ; imazamox ; mutation ; rice ; tissue culture
Language	English
Dates of publication	2018-10
Size	p. 1325-1331.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.08.124
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Suppression of class I compensated cell enlargement by xs2 mutation is mediated by salicylic acid signaling.

Fujikura, Ushio / Ezaki, Kazune / Horiguchi, Gorou / Seo, Mitsunori / Kanno, Yuri / Kamiya, Yuji / Lenhard, Michael / Tsukaya, Hirokazu

PLoS genetics

2020 Volume 16, Issue 6, Page(s) e1008873

Abstract: The regulation of leaf size has been studied for decades. Enhancement of post-mitotic cell expansion triggered by impaired cell proliferation in Arabidopsis is an important process for leaf size regulation, and is known as compensation. This suggests a ... ...

Abstract	The regulation of leaf size has been studied for decades. Enhancement of post-mitotic cell expansion triggered by impaired cell proliferation in Arabidopsis is an important process for leaf size regulation, and is known as compensation. This suggests a key interaction between cell proliferation and cell expansion during leaf development. Several studies have highlighted the impact of this integration mechanism on leaf size determination; however, the molecular basis of compensation remains largely unknown. Previously, we identified extra-small sisters (xs) mutants which can suppress compensated cell enlargement (CCE) via a specific defect in cell expansion within the compensation-exhibiting mutant, angustifolia3 (an3). Here we revealed that one of the xs mutants, namely xs2, can suppress CCE not only in an3 but also in other compensation-exhibiting mutants erecta (er) and fugu2. Molecular cloning of XS2 identified a deleterious mutation in CATION CALCIUM EXCHANGER 4 (CCX4). Phytohormone measurement and expression analysis revealed that xs2 shows hyper activation of the salicylic acid (SA) response pathway, where activation of SA response can suppress CCE in compensation mutants. All together, these results highlight the regulatory connection which coordinates compensation and SA response.
MeSH term(s)	Antiporters/genetics ; Arabidopsis/physiology ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Calcium/metabolism ; Cations, Divalent/metabolism ; Cell Enlargement ; Cell Proliferation/genetics ; Gene Expression Regulation, Plant ; Loss of Function Mutation ; Organ Size/genetics ; Plant Growth Regulators/metabolism ; Plant Leaves/cytology ; Plant Leaves/growth & development ; Plant Leaves/metabolism ; Plants, Genetically Modified ; Salicylic Acid/metabolism ; Signal Transduction/genetics
Chemical Substances	Antiporters ; Arabidopsis Proteins ; Cations, Divalent ; NPR1 protein, Arabidopsis ; Plant Growth Regulators ; Salicylic Acid (O414PZ4LPZ) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2020-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1008873
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Article: Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice.

Shimatani, Zenpei / Fujikura, Ushio / Ishii, Hisaki / Terada, Rie / Nishida, Keiji / Kondo, Akihiko

Data in brief

2018 Volume 20, Page(s) 1325–1331

Abstract	Acetolactate synthase (ALS) catalyzes the initial step in the biosynthesis of branched-chain amino acids, and is highly conserved from bacteria to higher plants. ALS is encoded by a single copy gene in rice genome and is a target enzyme of several classes of herbicides. Although
Language	English
Publishing date	2018-08-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.08.124
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Targeted Base Editing with CRISPR-Deaminase in Tomato.

Shimatani, Zenpei / Ariizumi, Tohru / Fujikura, Ushio / Kondo, Akihiko / Ezura, Hiroshi / Nishida, Keiji

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1917, Page(s) 297–307

Abstract: The Target-AID system, consisting of a complex of cytidine deaminase and deficient CRISPR/Cas9, enables highly specific genomic nucleotide substitutions without the need for template DNA. The Cas9-fused cytidine deaminase is guided by sgRNAs and ... ...

Abstract	The Target-AID system, consisting of a complex of cytidine deaminase and deficient CRISPR/Cas9, enables highly specific genomic nucleotide substitutions without the need for template DNA. The Cas9-fused cytidine deaminase is guided by sgRNAs and catalyzes the conversion of cytosine to uracil. The resulting U-G DNA mismatches trigger nucleotide substitutions (C to T or G to A) through DNA replication and repair pathways. Target-AID also retains the benefits of conventional CRISPR/Cas9 including robustness in various organisms, high targeting efficiency, and multiplex simultaneous gene editing. Our research group recently developed plant-optimized Target-AID system and demonstrated targeted base editing in tomato and rice. In this chapter, we introduce methods for Target-AID application in tomato.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Cytidine Deaminase/genetics ; Gene Editing/methods ; Solanum lycopersicum/genetics
Chemical Substances	Cytidine Deaminase (EC 3.5.4.5)
Language	English
Publishing date	2018-11-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8991-1_22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A method using electroporation for the protein delivery of Cre recombinase into cultured Arabidopsis cells with an intact cell wall.

Furuhata, Yuichi / Sakai, Ayako / Murakami, Tomi / Morikawa, Mone / Nakamura, Chikashi / Yoshizumi, Takeshi / Fujikura, Ushio / Nishida, Keiji / Kato, Yoshio

Scientific reports

2019 Volume 9, Issue 1, Page(s) 2163

Abstract: Genome engineering in plants is highly dependent on the availability of effective molecular techniques. Despite vast quantities of research, genome engineering in plants is still limited in terms of gene delivery, which requires the use of infectious ... ...

Abstract	Genome engineering in plants is highly dependent on the availability of effective molecular techniques. Despite vast quantities of research, genome engineering in plants is still limited in terms of gene delivery, which requires the use of infectious bacteria or harsh conditions owing to the difficulty delivering biomaterial into plant cells through the cell wall. Here, we describe a method that uses electroporation-mediated protein delivery into cultured Arabidopsis thaliana cells possessing an intact cell wall, and demonstrate Cre-mediated site-specific recombination. By optimizing conditions for the electric pulse, protein concentration, and electroporation buffer, we were able to achieve efficient and less-toxic protein delivery into Arabidopsis thaliana cells with 83% efficiency despite the cell wall. To the best of our knowledge, this is the first report demonstrating the electroporation-mediated protein delivery of Cre recombinase to achieve nucleic acid-free genome engineering in plant cells possessing an intact cell wall.
MeSH term(s)	Arabidopsis/metabolism ; Arabidopsis/radiation effects ; Cell Wall/metabolism ; Cell Wall/radiation effects ; Electroporation/methods ; Endocytosis ; Integrases/metabolism ; Plant Cells/metabolism ; Plant Cells/radiation effects ; Protein Transport
Chemical Substances	Cre recombinase (EC 2.7.7.-) ; Integrases (EC 2.7.7.-)
Language	English
Publishing date	2019-02-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-38119-9
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Article ; Online: Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology.

Omidbakhshfard, Mohammad Amin / Proost, Sebastian / Fujikura, Ushio / Mueller-Roeber, Bernd

Molecular plant

2015 Volume 8, Issue 7, Page(s) 998–1010

Abstract: Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes ... ...

Abstract	Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.
MeSH term(s)	Flowers/growth & development ; Plant Development ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Plants/genetics ; Plants/metabolism ; Transcription Factors/chemistry ; Transcription Factors/metabolism
Chemical Substances	Plant Proteins ; Transcription Factors
Language	English
Publishing date	2015-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2393618-6
ISSN	1752-9867 ; 1674-2052
ISSN (online)	1752-9867
ISSN	1674-2052
DOI	10.1016/j.molp.2015.01.013
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Article ; Online: The coordination of ploidy and cell size differs between cell layers in leaves.

Katagiri, Yohei / Hasegawa, Junko / Fujikura, Ushio / Hoshino, Rina / Matsunaga, Sachihiro / Tsukaya, Hirokazu

Development (Cambridge, England)

2016 Volume 143, Issue 7, Page(s) 1120–1125

Abstract: Growth and developmental processes are occasionally accompanied by multiple rounds of DNA replication, known as endoreduplication. Coordination between endoreduplication and cell size regulation often plays a crucial role in proper organogenesis and cell ...

Abstract	Growth and developmental processes are occasionally accompanied by multiple rounds of DNA replication, known as endoreduplication. Coordination between endoreduplication and cell size regulation often plays a crucial role in proper organogenesis and cell differentiation. Here, we report that the level of correlation between ploidy and cell volume is different in the outer and inner cell layers of leaves of Arabidopsis thaliana using a novel imaging technique. Although there is a well-known, strong correlation between ploidy and cell volume in pavement cells of the epidermis, this correlation was extremely weak in palisade mesophyll cells. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells. We therefore propose that the correlation between ploidy and cell volume is regulated by cell identity.
MeSH term(s)	Arabidopsis/growth & development ; Arabidopsis Proteins/biosynthesis ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Cell Differentiation/genetics ; Cell Size ; Endoreduplication/genetics ; Gene Expression Regulation, Plant ; Homeodomain Proteins/biosynthesis ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Mesophyll Cells/cytology ; Mesophyll Cells/metabolism ; Plant Epidermis/cytology ; Plant Epidermis/growth & development ; Plant Leaves/cytology ; Plant Leaves/growth & development ; Plants, Genetically Modified/metabolism ; Ploidies
Chemical Substances	ATML1 protein, Arabidopsis ; Arabidopsis Proteins ; Homeodomain Proteins
Language	English
Publishing date	2016-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.130021
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Article ; Online: GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia.

Omidbakhshfard, Mohammad Amin / Fujikura, Ushio / Olas, Justyna Jadwiga / Xue, Gang-Ping / Balazadeh, Salma / Mueller-Roeber, Bernd

PLoS genetics

2018 Volume 14, Issue 7, Page(s) e1007484

Abstract: Leaf growth is a complex process that involves the action of diverse transcription factors (TFs) and their downstream gene regulatory networks. In this study, we focus on the functional characterization of the Arabidopsis thaliana TF GROWTH-REGULATING ... ...

Abstract	Leaf growth is a complex process that involves the action of diverse transcription factors (TFs) and their downstream gene regulatory networks. In this study, we focus on the functional characterization of the Arabidopsis thaliana TF GROWTH-REGULATING FACTOR9 (GRF9) and demonstrate that it exerts its negative effect on leaf growth by activating expression of the bZIP TF OBP3-RESPONSIVE GENE 3 (ORG3). While grf9 knockout mutants produce bigger incipient leaf primordia at the shoot apex, rosette leaves and petals than the wild type, the sizes of those organs are reduced in plants overexpressing GRF9 (GRF9ox). Cell measurements demonstrate that changes in leaf size result from alterations in cell numbers rather than cell sizes. Kinematic analysis and 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay revealed that GRF9 restricts cell proliferation in the early developing leaf. Performing in vitro binding site selection, we identified the 6-base motif 5'-CTGACA-3' as the core binding site of GRF9. By global transcriptome profiling, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) we identified ORG3 as a direct downstream, and positively regulated target of GRF9. Genetic analysis of grf9 org3 and GRF9ox org3 double mutants reveals that both transcription factors act in a regulatory cascade to control the final leaf dimensions by restricting cell number in the developing leaf.
MeSH term(s)	14-3-3 Proteins/genetics ; 14-3-3 Proteins/metabolism ; Arabidopsis/physiology ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Binding Sites/genetics ; Cell Proliferation/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant/physiology ; Gene Knockout Techniques ; Gene Regulatory Networks/physiology ; Plant Leaves/cytology ; Plant Leaves/growth & development ; Plants, Genetically Modified ; Protein Binding/genetics
Chemical Substances	14-3-3 Proteins ; Arabidopsis Proteins ; Basic Helix-Loop-Helix Transcription Factors ; GRF9 protein, Arabidopsis ; bHLH39 protein, Arabidopsis
Language	English
Publishing date	2018-07-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1007484
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Article ; Online: Variation in Splicing Efficiency Underlies Morphological Evolution in Capsella.

Fujikura, Ushio / Jing, Runchun / Hanada, Atsushi / Takebayashi, Yumiko / Sakakibara, Hitoshi / Yamaguchi, Shinjiro / Kappel, Christian / Lenhard, Michael

Developmental cell

2018 Volume 44, Issue 2, Page(s) 192–203.e5

Abstract: Understanding the molecular basis of morphological change remains a central challenge in evolutionary-developmental biology. The transition from outbreeding to selfing is often associated with a dramatic reduction in reproductive structures and functions, ...

Abstract	Understanding the molecular basis of morphological change remains a central challenge in evolutionary-developmental biology. The transition from outbreeding to selfing is often associated with a dramatic reduction in reproductive structures and functions, such as the loss of attractive pheromones in hermaphroditic Caenorhabditis elegans and a reduced flower size in plants. Here, we demonstrate that variation in the level of the brassinosteroid-biosynthesis enzyme CYP724A1 contributes to the reduced flower size of selfing Capsella rubella compared with its outbreeding ancestor Capsella grandiflora. The primary transcript of the C. rubella allele is spliced more efficiently than that of C. grandiflora, resulting in higher brassinosteroid levels. These restrict organ growth by limiting cell proliferation. More efficient splicing of the C. rubella allele results from two de novo mutations in the selfing lineage. Thus, our results highlight the potentially widespread importance of differential splicing efficiency and higher-than-optimal hormone levels in generating phenotypic variation.
MeSH term(s)	Alleles ; Brassinosteroids/biosynthesis ; Capsella/anatomy & histology ; Capsella/genetics ; Capsella/growth & development ; Chromosomes, Plant ; Cytochrome P-450 Enzyme System/biosynthesis ; Cytochrome P-450 Enzyme System/genetics ; Evolution, Molecular ; Exons ; Flowers/anatomy & histology ; Flowers/genetics ; Flowers/growth & development ; Mutation ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; RNA Splicing
Chemical Substances	Brassinosteroids ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2018--22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2017.11.022
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