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NISHIDA Keiji
Engineering Biology Research Center
Professor

Researcher basic information

■ Research news
■ Research Areas
  • Environmental science/Agricultural science / Plant genetics and breeding
  • Life sciences / Evolutionary biology
  • Life sciences / Systems genomics

Research activity information

■ Award
  • 2019 神戸大学, 第11回学長表彰（財務貢献者）
    西田 敬二

  • 2019 Iue Memorial Foundation, 第43回井植文化賞（科学技術部門）
    NISHIDA Keiji

  • 2018 神戸大学, 第10回学長表彰（財務貢献者）
    西田 敬二

  • 2017 神戸大学, 第9回学長表彰（財務貢献者）
    西田 敬二

  • 2017 National Institute of Science and Technology Policy, NISTEP Award, DNA 塩基書き換えによる切らないゲノム編集(Target-AID)
    西田 敬二

  • 2016 International Botanical Congress, Excellent Scholar Award
    NISHIDA Keiji

  • 2007 The Botanical Society of Japan, 若手奨励賞
    NISHIDA Keiji

  • 2005 The Japanese Society of Plant Morphology, 奨励賞
    NISHIDA Keiji

■ Paper
  • Hitoshi Mitsunobu, Yudai Kita, Yumiko Nambu-Nishida, Shoko Miyazaki, Kensuke Nakajima, Ken-ichiro Taoka, Akihiko Kondo, Keiji Nishida
    Abstract Lactobacilli play essential roles in the food industry and have a significant potential as probiotics and therapeutic agents. Genomic and genetic information has increasingly accumulated and been linked to their various functions, to which transgenic approaches are being performed to verify crucial genes. In order to reasonably develop more useful strains, beneficial traits need to be introduced into any given strains and enhanced or combined based on such genotype characterization. However, for practical use as probiotics or foods, organisms with transgene are hardly acceptable. Here, we have introduced the base editing Target-AID system specifically for Lactobacilli, enabling precise installation of point mutations without donor DNA and at multiple genomic loci simultaneously. Lactiplantibacillus plantarum has been successfully engineered to reduce production of imidazole propionate, which has been reported to be associated with type 2 diabetes by impairing glucose tolerance and insulin signaling. Additionally, this system enabled transient knock-out of an essential gene, such as one involved in cell division, resulting in severe filamentous cell phenotype. This demonstrates Target-AID is a promising genetic tool for Lactobacilli and can accelerate both applied and fundamental research. Key points • Efficient and multiplexable cytosine base editing established in Lactobacilli. • Edited Lactobacillus reducing imidazole propionate associated with the risk of type 2 diabetes. • Transient knock-out and dissection of an essential gene function.
    Springer Science and Business Media LLC, Apr. 2025, Applied Microbiology and Biotechnology, 109(1) (1)
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Sao Mai Nguyen, Ken-ichiro Taoka, Keiji Nishida
    Springer US, Mar. 2025, Springer Protocols Handbooks, 1 - 18
    In book

  • Kousuke Seki, Kenji Komatsu, Kanami Yamaguchi, Yoshinori Murai, Keiji Nishida, Ryohei Koyama, Yuichi Uno
    We identified LsMybW as the allele responsible for the shift in color from black to white seeds in wild ancestors of lettuce to modern cultivars. Successfully selected white seeds are a key agronomic trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black-in its wild ancestor-to white seeds remains uncertain. We aimed to identify the gene/s responsible for white seed trait in lettuce. White seeds accumulated less proanthocyanidins than black seeds, similar to the phenotype observed in Arabidopsis TT2 mutants. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F2 population derived from a cross between "ShinanoPower" (white) and "Escort" (black). The white seed trait was controlled by a single recessive locus (48.055-50.197 Mbp) in linkage group 7. Using five PCR-based markers and numerous cultivars, eight candidate genes were mapped in the locus. Only the LG7_v8_49.251Mbp_HinfI marker, employing a single-nucleotide mutation in the stop codon of Lsat_1_v5_gn_7_35020.1, was completely linked to seed color phenotype. In addition, the coding region sequences for other candidate genes were identical in the resequence analysis of "ShinanoPower" and "Escort." Therefore, we proposed Lsat_1_v5_gn_7_35020.1 as the candidate gene and designated it as LsMybW (Lactuca sativa Myb White seeds), an ortholog encoding the R2R3-MYB transcription factor in Arabidopsis. When we validated the role of LsMybW through genome editing, LsMybW knockout mutants harboring an early termination codon showed a change in seed color from black to white. Therefore, LsMybW was the allele responsible for the shift in seed color. The development of a robust marker for marker-assisted selection and identification of the gene responsible for white seeds have implications for future breeding technology and physiological analysis.
    Jan. 2024, Plant cell reports, 43(2) (2), 35 - 35, English, International magazine
    Scientific journal

  • Soh Ishiguro, Kana Ishida, Rina C. Sakata, Hideto Mori, Mamoru Takana, Samuel King, Omar Bashth, Minori Ichiraku, Nanami Masuyama, Ren Takimoto, Yusuke Kijima, Arman Adel, Hiromi Toyoshima, Motoaki Seki, Ju Hee Oh, Anne-Sophie Archambault, Keiji Nishida, Akihiko Kondo, Satoru Kuhara, Hiroyuki Aburatani, Ramon I. Klein Geltink, Yasuhiro Takashima, Nika Shakiba, Nozomu Yachie
    Clonal heterogeneity underlies diverse biological processes, including cancer progression, cell differentiation, and microbial evolution. Cell tagging strategies with DNA barcodes have recently enabled analysis of clone size dynamics and clone-restricted transcriptomic landscapes of heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here, we present a new multi-kingdom genetic barcoding system, CloneSelect, in which a target cell clone can be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first barcoded and propagated so their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored throughout the experimental timecourse. This novel CRISPR-barcode genetics platform provides many new ways of analyzing and manipulating mammalian, yeast, and bacterial systems. Teaser A multi-kingdom CRISPR-activatable barcoding system enables the precise isolation of target barcode-labeled clones from a complex cell population.
    Cold Spring Harbor Laboratory, Jan. 2023

  • Sachiko Kashojiya, Yu Lu, Mariko Takayama, Hiroki Komatsu, Luyen Hieu Thi Minh, Keiji Nishida, Kenta Shirasawa, Kenji Miura, Satoko Nonaka, Jun-Ichiro Masuda, Akihiko Kondo, Hiroshi Ezura, Tohru Ariizumi
    Target activation-induced cytidine deaminase (Target-AID), a novel CRISPR/Cas9-based genome-editing tool, confers the base-editing capability on the Cas9 genome-editing system. It involves the fusion of cytidine deaminase (CDA), which catalyzes cytidine (C) to uridine (U) substitutions, to the mutated nickase-type nCas9 or deactivated-type dCas9. To confirm and extend the applicability of the Target-AID genome-editing system in tomatoes (Solanum lycopersicum L.), we transformed the model tomato cultivar "Micro-Tom" and commercial tomato cultivars using this system by targeting SlDELLA, which encodes a negative regulator of the plant phytohormone gibberellic acid (GA) signaling pathway. We confirmed that the nucleotide substitutions were induced by the Target-AID system, and we isolated mutants showing high GA sensitivity in both "Micro-Tom" and the commercial cultivars. Moreover, by successfully applying this system to ETHYLENE RECEPTOR 1 (SlETR1) with single sgRNA targeting, double sgRNA targeting, as well as dual-targeting of both SlETR1 and SlETR2 with a single sgRNA, we demonstrated that the Target-AID genome-editing system is a promising tool for molecular breeding in tomato crops. This study highlights an important aspect of the scientific and agricultural potential of the combinatorial use of the Target-AID and other base-editing systems.
    Jan. 2022, Horticulture research, 9, English, International magazine
    Scientific journal

  • Johan Hunziker, Keiji Nishida, Akihiko Kondo, Tohru Ariizumi, Hiroshi Ezura
    Our previous study demonstrated that Target-AID which is the modified CRISPR/Cas9 system enabling base-editing is an efficient tool for targeting multiple genes. Three genes, SlDDB1, SlDET1, and SlCYC-B, responsible for carotenoid accumulation were targeted, and allelic variations were previously obtained by Target-AID. In this research, we characterized the effect of new alleles on plant growth and fruit development, as well as carotenoid accumulation, individually in segregating backcross populations or combined in null self-segregant lines. Only lines carrying homozygous substitutions in the three targeted genes and the segregating backcross population of individual mutations were characterized, resulting in the isolation of two allelic versions for SlDDB1, one associated with SlDET1 and the last one with SlCYC-B. All edited lines showed variations in carotenoid accumulation, with an additive effect for each single mutation. These results suggest that Target-AID base-editing technology is an effective tool for creating new allelic variations in target genes to improve carotenoid accumulation in tomato.
    2022, Frontiers in plant science, 13, 848560 - 848560, English, International magazine
    Scientific journal

  • Kohei Kawaguchi, Rie Takei-Hoshi, Ikue Yoshikawa, Keiji Nishida, Makoto Kobayashi, Miyako Kusano, Yu Lu, Tohru Ariizumi, Hiroshi Ezura, Shungo Otagaki, Shogo Matsumoto, Katsuhiro Shiratake
    AbstractSugar content is one of the most important quality traits of tomato. Cell wall invertase promotes sucrose unloading in the fruit by maintaining a gradient of sucrose concentration between source leaves and fruits, while invertase inhibitor (INVINH) regulates this process. In this study, knock-out of cell wall INVINH in tomato (SlINVINH1) was performed by genome editing using, CRISPR/Cas9 and Target-AID technologies. Most of the genome-edited lines set higher soluble solid content (SSC) fruit than the original cultivar ‘Suzukoma’, while fruit weight was different among the genome-edited lines. From these genome-edited lines, three lines (193–3, 199–2, and 247–2), whose SSC was significantly higher than ‘Suzukoma’ and fruit weight were almost the same as the original cultivar, were selected. The fruit weight and overall plant growth of the two lines were comparable to those of the original cultivar. In contrast, the fructose and glucose contents in the mature fruits of the two lines were significantly higher than those of the original cultivar. The mature fruits of genome edited line 193–3 showed the highest sugar content, and the fructose and glucose contents were 29% and 36% higher than that of the original cultivar, respectively. Whole genome sequence data showed no off-target mutations in the genome-edited lines. Non-target metabolome analysis of mature fruits revealed that fructose was the highest loading factor in principal component analysis (PCA) between the genome-edited line and the original cultivar, and no unexpected metabolites appeared in the genome-edited line. In this study, we succeeded in producing tomato lines with high sugar content without a decrease in fruit weight and deterioration of plant growth by knock-out of SlINVINH1 using genome editing technology. This study showed that functional disruption of SlINVINH1 is an effective approach to produce tomato cultivars with high sugar content.
    Springer Science and Business Media LLC, Dec. 2021, Scientific Reports, 11(1) (1), 21534 - 21534, English, International magazine
    Scientific journal

  • Keiji Nishida, Akihiko Kondo
    Aug. 2021, The CRISPR journal, 4(4) (4), 462 - 463, English, International magazine
    Scientific journal

  • Ang Li, Hitoshi Mitsunobu, Shin Yoshioka, Suzuki Takahisa, Akihiko Kondo, Keiji Nishida
    Abstract Structure-based rational engineering of the cytosine base editing system Target-AID was performed to minimize its off-target effect and molecular size. By intensive and careful truncation, DNA-binding domain of its deaminase PmCDA1 was eliminated and additional mutations were introduced to restore enzyme function. The resulting tCDA1EQ was effective in N-terminal fusion (AID-2S) or inlaid architecture (AID-3S) with Cas9, showing minimized gRNA-independent off-targets, as assessed in yeast and human cells. Combining with the smaller Cas9 ortholog system, the smallest cytosine base editing system was created that is within the size limit of AAV vector.
    Research Square Platform LLC, Apr. 2021, Nature communications, 13(1) (1), 4531 - 4531, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Shaoze Yuan, Shunsuke Kawasaki, Islam M. Y. Abdellatif, Keiji Nishida, Akihiko Kondo, Tohru Ariizumi, Hiroshi Ezura, Kenji Miura
    KEY MESSAGE: Base editing in tomatoes was achieved by transient expression. The Solanaceae plants, particularly the tomato (Solanum lycopersicum), is of huge economic value worldwide. The tomato is a unique model plant for studying the functions of genes related to fruit ripening. Deeper understanding of tomatoes is of great importance for both plant research and the economy. Genome editing technology, such as CRISPR/Cas9, has been used for functional genetic research. However, some challenges, such as low transformation efficiency, remain with this technology. Moreover, the foreign Cas9 and gRNA expression cassettes must be removed to obtain null-segregants In this study, we used a high-level transient expression system to improve the base editing technology. A high-level transient expression system has been established previously using geminiviral replication and a double terminator. The pBYR2HS vector was used for this transient expression system. nCas9-CDA and sgRNA-SlHWS were introduced into this vector, and the protein and RNA were then transiently expressed in tomato tissues by agroinfiltration. The homozygous mutant produced by base editing was obtained in the next generation with an efficiency of about 18%. nCas9-free next-generation plants were 71%. All the homozygous base-edited plants in next generation are nCas9-free. These findings show that the high-level transient expression system is useful for base editing in tomatoes.
    Springer Science and Business Media LLC, Apr. 2021, Plant Cell Reports, 40(4) (4), 667 - 676, English, International magazine
    Scientific journal

  • Keiji Nishida, Akihiko Kondo
    In metabolic engineering, genome editing tools make it much easier to discover and evaluate relevant genes and pathways and construct strains. Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first choice for genome engineering in many organisms includingindustrially relevant ones. Targeted DNA cleavage by CRISPR-Cas provides variousgenome engineering modes such as indels, replacements, large deletions, knock-in and chromosomal rearrangements, while host-dependent differences in repair pathways need to be considered. The versatility of the CRISPR system has given rise to derivative technologies that complement nuclease-based editing, which causes cytotoxicity especially in microorganisms. Deaminase-mediated base editing installs targeted point mutations with much less toxicity. CRISPRi and CRISPRa can temporarily control gene expression without changing the genomic sequence. Multiplex, combinatorial and large scale editing are made possible by streamlined design and construction of gRNA libraries to further accelerates comprehensive discovery, evaluation and building of metabolic pathways. This review summarizes the technical basis and recent advances in CRISPR-related genome editing tools applied for metabolic engineering purposes, with representative examples of industrially relevant eukaryotic and prokaryotic organisms.
    Elsevier BV, Jan. 2021, Metabolic Engineering, 63, 141 - 147, English, International magazine
    Scientific journal

  • Johan Hunziker, Keiji Nishida, Akihiko Kondo, Sanae Kishimoto, Tohru Ariizumi, Hiroshi Ezura
    AbstractThe use of Target activation-induced cytidine deaminase (Target-AID) base-editing technology with the CRISPR-Cas 9 system fused with activation-induced cytidine deaminase (AID) resulted in the substitution of a cytidine with a thymine. In previous experiments focusing on a single target gene, this system has been reported to work in several plant species, including tomato (Solanum lycopersicum L.). In this research, we used Target-AID technology to target multiple genes related to carotenoid accumulation in tomato. We selected 3 genes, SlDDB1, SlDET1 and SlCYC-B, for their roles in carotenoid accumulation. Among 12 edited T0 lines, we obtained 10 independent T0 lines carrying nucleotide substitutions in the three targeted genes, with several allelic versions for each targeted gene. The two edited lines showed significant differences in carotenoid accumulation. These results demonstrate that Target-AID technology is a highly efficient tool for targeting multiple genes with several allelic versions.
    Springer Science and Business Media LLC, Dec. 2020, Scientific Reports, 10(1) (1), 20471 - 20471, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Yoshihito Shinozaki, Bertrand P Beauvoit, Masaru Takahara, Shuhei Hao, Kentaro Ezura, Marie-Hélène Andrieu, Keiji Nishida, Kazuki Mori, Yutaka Suzuki, Satoshi Kuhara, Hirofumi Enomoto, Miyako Kusano, Atsushi Fukushima, Tetsuya Mori, Mikiko Kojima, Makoto Kobayashi, Hitoshi Sakakibara, Kazuki Saito, Yuya Ohtani, Camille Bénard, Duyen Prodhomme, Yves Gibon, Hiroshi Ezura, Tohru Ariizumi
    Fruit set is the process whereby ovaries develop into fruits after pollination and fertilization. The process is induced by the phytohormone gibberellin (GA) in tomatoes, as determined by the constitutive GA response mutant procera However, the role of GA on the metabolic behavior in fruit-setting ovaries remains largely unknown. This study explored the biochemical mechanisms of fruit set using a network analysis of integrated transcriptome, proteome, metabolome, and enzyme activity data. Our results revealed that fruit set involves the activation of central carbon metabolism, with increased hexoses, hexose phosphates, and downstream metabolites, including intermediates and derivatives of glycolysis, the tricarboxylic acid cycle, and associated organic and amino acids. The network analysis also identified the transcriptional hub gene SlHB15A, that coordinated metabolic activation. Furthermore, a kinetic model of sucrose metabolism predicted that the sucrose cycle had high activity levels in unpollinated ovaries, whereas it was shut down when sugars rapidly accumulated in vacuoles in fruit-setting ovaries, in a time-dependent manner via tonoplastic sugar carriers. Moreover, fruit set at least partly required the activity of fructokinase, which may pull fructose out of the vacuole, and this could feed the downstream pathways. Collectively, our results indicate that GA cascades enhance sink capacities, by up-regulating central metabolic enzyme capacities at both transcriptional and posttranscriptional levels. This leads to increased sucrose uptake and carbon fluxes for the production of the constituents of biomass and energy that are essential for rapid ovary growth during the initiation of fruit set.
    Sep. 2020, Proceedings of the National Academy of Sciences of the United States of America, 117(38) (38), 23970 - 23981, English, International magazine
    Scientific journal

  • Akira Komatsu, Miki Ohtake, Zenpei Shimatani, Keiji Nishida
    When cultivated rice seed fall into fields, they may overwinter and spontaneously germinate the next spring. Such germinated plants are termed "volunteer rice." Volunteer grains originating from feed rice varieties may differ in certain traits, such as quality and taste, as compared with those of rice cultivated for human consumption, which may reduce the overall quality of the final harvested grain. Many rice varieties show resistance to benzobicyclon (BBC), a beta-triketone herbicide (bTH) that inhibits 4-hydroxyphenylpyruvate dioxygenase (HPPD). Recently, the rice gene HIS1 (HPPD INHIBITOR SENSITIVE 1) conferring resistance to BBC and other bTHs was identified. In this study, to suppress the occurrence of volunteer rice infestation, we attempted to generate a BBC-sensitive rice strain via the knockout of the HIS1 gene using genome editing techniques. The production of a his1 knockout line was carried out by the start-codon substitution or stop-codon creation using CRISPR-Cas9 cytidine deaminase fusion, which is useful as a novel amino acid sequence is not generated due to the shifting of the reading frame. The mutation frequencies of independent transgenic plants were 3.6, 13.5, 13.8, and 21.2% at four gRNAs for start-codon substitution and three stop-codon creations. The his1 knockout lines were conferred with sensitivity to BBC, re-confirming by genome editing that this is indeed the gene responsible for BBC resistance/sensitivity. The his1 knockout lines also exhibited a sensitive phenotype to other bTHs, including sulcotrione, mesotrione, tembotrione, and tefuryltrione, compared with the wild-type variety 'Nipponbare.' These results demonstrate the potential of herbicide-sensitive rice produced by genome editing technology as a material to control volunteer feed rice using pre-labeled herbicides for varieties consumed by humans.
    Frontiers Media SA, Aug. 2020, Frontiers in Plant Science, 11, 925 - 925, English, International magazine
    [Refereed]
    Scientific journal

  • Rina C Sakata, Soh Ishiguro, Hideto Mori, Mamoru Tanaka, Kenji Tatsuno, Hiroki Ueda, Shogo Yamamoto, Motoaki Seki, Nanami Masuyama, Keiji Nishida, Hiroshi Nishimasu, Kazuharu Arakawa, Akihiko Kondo, Osamu Nureki, Masaru Tomita, Hiroyuki Aburatani, Nozomu Yachie
    We describe base editors that combine both cytosine and adenine base-editing functions. A codon-optimized fusion of the cytosine deaminase PmCDA1, the adenosine deaminase TadA and a Cas9 nickase (Target-ACEmax) showed a high median simultaneous C-to-T and A-to-G editing activity at 47 genomic targets. On-target as well as DNA and RNA off-target activities of Target-ACEmax were similar to those of existing single-function base editors.
    Jul. 2020, Nature biotechnology, 38(7) (7), 865 - 869, English, International magazine
    [Refereed]
    Scientific journal

  • Rina C Sakata, Soh Ishiguro, Hideto Mori, Mamoru Tanaka, Kenji Tatsuno, Hiroki Ueda, Shogo Yamamoto, Motoaki Seki, Nanami Masuyama, Keiji Nishida, Hiroshi Nishimasu, Kazuharu Arakawa, Akihiko Kondo, Osamu Nureki, Masaru Tomita, Hiroyuki Aburatani, Nozomu Yachie
    An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Jul. 2020, Nature biotechnology, 38(7) (7), 901 - 901, English, International magazine
    [Refereed]

  • Kenta Katayama, Hitoshi Mitsunobu, Keiji Nishida
    Technologies harnessing CRISPR systems have been rapidly evolving and expanding the capacity of researchers for understanding of mammalian cell behavior and its underlying mechanisms through genome and epigenome manipulations. In this review, we summarized the recent developments of CRISPR-based technologies for genetic and epigenetic modifications that include engineering of Cas9 for PAM simplification, non-cleaving base editing tools and alteration of gene expression. Applications such as genome-wide screening methods or CRISPR-based DNA barcoding for cellular lineage tracking are highlighted. Anticipated and upcoming development for mammalian synthetic biology that includes organelle engineering is also discussed.
    Oct. 2019, Current Opinion in Chemical Biology, 52, 79 - 84, English, International magazine
    [Refereed][Invited]
    Scientific journal

  • Shimatani, Zenpei, Ariizumi, Tohru, Fujikura, Ushio, Kondo, Akihiko, Ezura, Hiroshi, Nishida, Keiji
    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.
    Apr. 2019, Methods in molecular biology (Clifton, N.J.), 1917, 297 - 307, English, International magazine
    [Refereed]
    Scientific journal

  • Yuichi Furuhata, Ayako Sakai, Tomi Murakami, Mone Morikawa, Chikashi Nakamura, Takeshi Yoshizumi, Ushio Fujikura, Keiji Nishida, Yoshio Kato
    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.
    Feb. 2019, Scientific Reports, 9(1) (1), 2163 - 2163, English, International magazine
    [Refereed]
    Scientific journal

  • Yumiko Nambu-Nishida, Keiji Nishida, Tomohisa Hasunuma, Akihiko Kondo
    Springer Verlag, Dec. 2018, AMB Express, 8(1) (1), 56 - 56, English, International magazine
    [Refereed]
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • SHIMATANI Zenpei, FUJIKURA Ushio, ISHII Hisaki, TERADA Rie, NISHIDA Keiji, KONDO Akihiko
    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].
    Aug. 2018, Data in Brief, 20, 1325 - 1331, English, International magazine
    [Refereed]
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Shingo Tanaka, Shin Yoshioka, Keiji Nishida, Hiroshi Hosokawa, Akira Kakizuka, Shingo Maegawa
    To date, several genome editing technologies have been developed and are widely utilized in many fields of biology. Most of these technologies, if not all, use nucleases to create DNA double-strand breaks (DSBs), raising the potential risk of cell death and/or oncogenic transformation. The risks hinder their therapeutic applications in humans. Here, we show that in vivo targeted single-nucleotide editing in zebrafish, a vertebrate model organism, can be successfully accomplished with the Target-AID system, which involves deamination of a targeted cytidine to create a nucleotide substitution from cytosine to thymine after replication. Application of the system to two zebrafish genes, chordin (chd) and one-eyed pinhead (oep), successfully introduced premature stop codons (TAG or TAA) in the targeted genomic loci. The modifications were heritable and faithfully produced phenocopies of well-known homozygous mutants of each gene. These results demonstrate for the first time that the Target-AID system can create heritable nucleotide substitutions in vivo in a programmable manner, in vertebrates, namely zebrafish.
    Jul. 2018, Scientific reports, 8(1) (1), 11423 - 11423, English, International magazine
    Scientific journal

  • Arazoe T, Kondo A, Nishida K
    Since the emergence of programmable RNA-guided nucleases based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems, genome editing technologies have become a simplified and versatile tool for genome editing in various organisms and cell types. Although genome editing enables efficient genome manipulations, such as gene disruptions, gene knockins, and chromosomal translocations via DNA double-strand break (DSB) repair in eukaryotes, DSBs induced by the CRISPR/Cas system are lethal or severely toxic to many microorganisms. Therefore, in many prokaryotes, including industrially useful microbes, the CRISPR/Cas system is often used as a negative selection component in combination with recombineering or other related strategies. Novel and revolutionary technologies have been recently developed to re-write targeted nucleotides (C:G to T:A and A:T to G:C) without DSBs and donor DNA templates. These technologies rely on the recruitment of deaminases at specific target loci using the nuclease-deficient CRISPR/Cas system. Here, the authors review and compare CRISPR-based genome editing, current base editing platforms and their spectra. The authors discuss how these technologies can be applied in various aspects of microbial metabolic engineering to overcome barriers to cellular regulation in prokaryotes.
    Jun. 2018, Biotechnology journal, 13(9) (9), e1700596, English, International magazine
    [Refereed]
    Scientific journal

  • Satomi Banno, Keiji Nishida, Takayuki Arazoe, Hitoshi Mitsunobu, Akihiko Kondo
    Nature Publishing Group, Apr. 2018, Nature Microbiology, 3(4) (4), 423 - 429, English, International magazine
    [Refereed]
    Scientific journal

  • Hiroya Itoh, Ai Miura, Makoto Matsui, Takayuki Arazoe, Keiji Nishida, Toshitaka Kumagai, Masanori Arita, Koichi Tamano, Masayuki Machida, Takashi Shibata
    Springer Verlag, Feb. 2018, Applied Microbiology and Biotechnology, 102(3) (3), 1393 - 1405, English
    [Refereed]
    Scientific journal

  • Zenpei Shimatani, Ushio Fujikura, Hisaki Ishii, Yusuke Matsui, Minoru Suzuki, Yuki Ueke, Ken-ichiro Taoka, Rie Terada, Keiji Nishida, Akihiko Kondo
    Elsevier Masson SAS, 2018, Plant Physiology and Biochemistry, 131, 78 - 83, English, International magazine
    [Refereed]
    Scientific journal

  • Yamato Yoshida, Haruko Kuroiwa, Takashi Shimada, Masaki Yoshida, Mio Ohnuma, Takayuki Fujiwara, Yuuta Imoto, Fumi Yagisawa, Keiji Nishida, Shunsuke Hirooka, Osami Misumi, Yuko Mogi, Yoshihiko Akakabe, Kazunobu Matsushita, Tsuneyoshi Kuroiwa
    Dec. 2017, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(50) (50), 13284 - 13289, English, International magazine
    [Refereed]
    Scientific journal

  • Hitoshi Mitsunobu, Jun Teramoto, Keiji Nishida, Akihiko Kondo
    Oct. 2017, TRENDS IN BIOTECHNOLOGY, 35(10) (10), 983 - 996, English, International magazine
    [Refereed]
    Scientific journal

  • Yumiko Nambu-Nishida, Keiji Nishida, Tomohisa Hasunuma, Akihiko Kondo
    Aug. 2017, SCIENTIFIC REPORTS, 7(1) (1), 8993 - 8993, English, International magazine
    [Refereed]
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Targeted nucleotide substitution in mammalian cell by Target-AID
    ARAZOE TAKAHIRO, NISHIDA KEIJI, KONDO AKIHIKO
    Jun. 2017, Bio-protocol, 7, 11, English
    [Refereed]
    Scientific journal

  • Zenpei Shimatani, Sachiko Kashojiya, Mariko Takayama, Rie Terada, Takayuki Arazoe, Hisaki Ishii, Hiroshi Teramura, Tsuyoshi Yamamoto, Hiroki Komatsu, Kenji Miura, Hiroshi Ezura, Keiji Nishida, Tohru Ariizumi, Akihiko Kondo
    May 2017, NATURE BIOTECHNOLOGY, 35(5) (5), 441 - +, English, International magazine
    [Refereed]
    Scientific journal

  • Keiji Nishida, Takayuki Arazoe, Nozomu Yachie, Satomi Banno, Mika Kakimoto, Mayura Tabata, Masao Mochizuki, Aya Miyabe, Michihiro Araki, Kiyotaka Y. Hara, Zenpei Shimatani, Akihiko Kondo
    Sep. 2016, SCIENCE, 353(6305) (6305), aaf8729, English, International magazine
    [Refereed]
    Scientific journal

  • Kiyotaka Y. Hara, Naoko Aoki, Jyumpei Kobayashi, Kentaro Kiriyama, Keiji Nishida, Michihiro Araki, Akihiko Kondo
    Nov. 2015, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 99(22) (22), 9771 - 9778, English, International magazine
    [Refereed]
    Scientific journal

  • Xiaoting Ye, Kana Morikawa, Shih-Hsin Ho, Michihiro Araki, Keiji Nishida, Tomohisa Hasunuma, Kiyotaka Y. Hara, Akihiko Kondo
    Apr. 2015, Microbial Cell Factories, 14, 56 - 56, English, International magazine
    [Refereed]
    Scientific journal

  • Fumi Yagisawa, Takayuki Fujiwara, Mio Ohnuma, Haruko Kuroiwa, Keiji Nishida, Yuuta Imoto, Yamato Yoshida, Tsuneyoshi Kuroiwa
    Aug. 2013, Protoplasma, 250(4) (4), 943 - 948, English, International magazine
    [Refereed]
    Scientific journal

  • Yuuta Imotoa, Haruko Kuroiwaa, Yamato Yoshida, Mio Ohnuma, Takayuki Fujiwara, Masaki Yoshida, Keiji Nishida, Fumi Yagisawa, Shunsuke Hirooka, Shin-Ya Miyagishima, Osami Misumi, Shigeyuki Kawano, Tsuneyoshi Kuroiwa
    Jun. 2013, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110(23) (23), 9583 - 9588, English, International magazine
    [Refereed]
    Scientific journal

  • Fumi Yagisawa, Takayuki Fujiwara, Haruko Kuroiwa, Keiji Nishida, Yuuta Imoto, Tsuneyoshi Kuroiwa
    Oct. 2012, PROTOPLASMA, 249(4) (4), 1129 - 1135, English, International magazine
    [Refereed]
    Scientific journal

  • Keiji Nishida, Pamela A. Silver
    Feb. 2012, PLOS BIOLOGY, 10(2) (2), e1001269, English, International magazine
    [Refereed]
    Scientific journal

  • Involvement of Elongation Factor-1 alpha in Cytokinesis without Actomyosin Contractile Ring in the Primitive Red Alga Cyanidioschyzon merolae
    Yuuta Imoto, Keiji Nishida, Fumi Yagisawa, Yamato Yoshida, Mio Ohnuma, Masaki Yoshida, Takayuki Fujiwara, Haruko Kuroiwa, Shigeyuki Kawano, Tsuneyoshi Kuroiwa
    Dec. 2011, CYTOLOGIA, 76(4) (4), 431 - 437, English
    [Refereed]
    Scientific journal

  • Involvement of elongation
    Imoto, U, Nishida, K, Yagisawa, F, Yoshida, Y, Ohnuma, M, Yoshida, M, Fujiwara, T, Kuroiwa, H, Kawano, S, Kuroiwa, T
    2011, Cytologia, 76, 431 - 437, English
    [Refereed]
    Scientific journal

  • The Vacuole Binding to Mitochondria by VIG1 Contributes an Equal Inheritance of the Vacuoles in Cyanidioschyzon merolae
    Takayuki Fujiwara, Fumi Yagisawa, Mio Ohnuma, Yamato Yoshida, Masaki Yoshida, Keiji Nishida, Osami Misumi, Haruko Kuroiwa, Tsuneyoshi Kuroiwa
    Jun. 2010, CYTOLOGIA, 75(2) (2), 189 - 194, English
    [Refereed]
    Scientific journal

  • The Vacuole Binding to Mitochondria by VIG1 Contributes an Equal Inheritance of the Vacuoles in Cyanidioschyzon merolae
    FUJIWARA Takayuki, YAGISAWA Fumi, OHNUMA Mio, YOSHIDA Yamato, YOSHIDA Masaki, NISHIDA Keiji, MISUMI Osami, KUROIWA Haruko, KUROIWA Tsuneyoshi
    Jun. 2010, Cytologia, 69(1) (1), 97 - 100, English
    [Refereed]
    Scientific journal

  • The coiled-coil protein VIG1 is essential for tethering vacuoles to mitochondria during vacuole inheritance of Cyanidioschyzon merolae
    FUJIWARA Takayuki, KUROIWA Haruko, YAGISAWA Fumi, OHNUMA Mio, YOSHIDA Yamato, YOSHIDA Masaki, NISHIDA Keiji, MISUMI Osami, WATANABE Satoru, TANAKA Kan, KUROIWA Tsuneyoshi
    Mar. 2010, Plant Cell, 22(3) (3), 772 - 781, English
    [Refereed]
    Scientific journal

  • Fumi Yagisawa, Keiji Nishida, Masaki Yoshida, Mio Ohnuma, Takashi Shimada, Takayuki Fujiwara, Yamato Yoshida, Osami Misumi, Haruko Kuroiwa, Tsuneyoshi Kuroiwa
    Dec. 2009, PLANT JOURNAL, 60(5) (5), 882 - 893, English, International magazine
    [Refereed]
    Scientific journal

  • Shunsuke Hirooka, Osami Misumi, Masaki Yoshida, Toshiyuki Mori, Keiji Nishida, Fumi Yagisawa, Yamato Yoshida, Takayuki Fujiwara, Haruko Kuroiwa, Tsuneyoshi Kuroiwa
    Dec. 2009, PLANT CELL REPORTS, 28(12) (12), 1881 - 1893, English, International magazine
    [Refereed]
    Scientific journal

  • Periodic gene expression patterns during the highly synchronized cell nucleus and organelle division cycles in the unicellular red alga Cyanidioschyzon merolae
    FUJIWARA Takayuki, MISUMI Osami, TASHIRO Kousuke, YOSHIDA Yamato, NISHIDA Keiji, YAGISAWA Fumi, IMAMURA Sousuke, YOSHIDA Masaki, MORI Toshiyuki, TANAKA Kan, KUROIWA Haruko, KUROIWA Tsuneyoshi
    Feb. 2009, DNA Research, 16(1) (1), 59 - 72, English
    [Refereed]
    Scientific journal

  • Fujiwara, T, Misumi, O, Tashiro, K, Yoshida, Y, Nishida, K, Yagisawa, F, Imamura, S, Yoshida, M, Mori, T, Tanaka, K, Kuroiwa, H, Kuroiwa, T
    Previous cell cycle studies have been based on cell-nuclear proliferation only. Eukaryotic cells, however, have double membranes-bound organelles, such as the cell nucleus, mitochondrion, plastids and single-membrane-bound organelles such as ER, the Golgi body, vacuoles (lysosomes) and microbodies. Organelle proliferations, which are very important for cell functions, are poorly understood. To clarify this, we performed a microarray analysis during the cell cycle of Cyanidioschyzon merolae. C. merolae cells contain a minimum set of organelles that divide synchronously. The nuclear, mitochondrial and plastid genomes were completely sequenced. The results showed that, of 158 genes induced during the S or G2-M phase, 93 were known and contained genes related to mitochondrial division, ftsZ1-1, ftsz1-2 and mda1, and plastid division, ftsZ2-1, ftsZ2-2 and cmdnm2. Moreover, three genes, involved in vesicle trafficking between the single-membrane organelles such as vps29 and the Rab family protein, were identified and might be related to partitioning of single-membrane-bound organelles. In other genes, 46 were hypothetical and 19 were hypothetical conserved. The possibility of finding novel organelle division genes from hypothetical and hypothetical conserved genes in the S and G2-M expression groups is discussed.
    2009, DNA Res., 74(1) (1), 1 - 72, English, International magazine
    [Refereed]
    Scientific journal

  • Novel Dynamics of FtsZ Ring Before Plastid Abscission
    Yamato Yoshida, Keiji Nishida, Tsuneyoshi Kuroiwa, Shigeyuki Kawano
    Jun. 2008, CYTOLOGIA, 73(2) (2), 197 - 201, English
    [Refereed]
    Scientific journal

  • Osami Misumi, Yamato Yoshida, Keiji Nishida, Takayuki Fujiwara, Takayuki Sakajiri, Syunsuke Hirooka, Yoshiki Nishimura, Tsuneyoshi Kuroiwa
    Mar. 2008, JOURNAL OF PLANT RESEARCH, 121(2) (2), 251 - 251, English
    [Refereed]

  • Osami Misumi, Yamato Yoshida, Keiji Nishida, Takayuki Fujiwara, Takayuki Sakajiri, Syunsuke Hirooka, Yoshiki Nishimura, Tsuneyoshi Kuroiwa
    Springer Japan, 2008, Journal of Plant Research, 121(1) (1), 1 - 17, English, Domestic magazine
    [Refereed]
    Scientific journal

  • Fumi Yagisawa, Keiji Nishida, Haruko Kuroiwa, Toshiyuki Nagata, Tsuneyoshi Kuroiwa
    Sep. 2007, PLANTA, 226(4) (4), 1017 - 1029, English, International magazine
    [Refereed]
    Scientific journal

  • Hisayoshi Nozaki, Hiroyoshi Takano, Osami Misumi, Kimihiro Terasawa, Motomichi Matsuzaki, Shinichiro Maruyama, Keiji Nishida, Fumi Yagisawa, Yamato Yoshida, Takayuki Fujiwara, Susumu Takio, Katsunori Tamura, Sung Jin Chung, Soichi Nakamura, Haruko Kuroiwa, Kan Tanaka, Naoki Sato, Tsuneyoshi Kuroiwa
    Jul. 2007, BMC BIOLOGY, 5, 28 - 28, English, International magazine
    [Refereed]
    Scientific journal

  • Keiji Nishida, Fumi Yagisawa, Haruko Kuroiwa, Yamato Yoshida, Tsuneyoshi Kuroiwa
    Mar. 2007, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104(11) (11), 4736 - 4741, English, International magazine
    [Refereed]
    Scientific journal

  • Isolated chloroplast division machinery can actively constrict after stretching
    YOSHIDA Yamato, KUROIWA Haruko, MISUMI Osami, NISHIDA Keiji, YAGISAWA Fumi, FUJIWARA Takayuki, NANAMIYA Hideaki, KAWAMURA Fujio, KUROIWA Tsuneyoshi
    Chloroplast division involves plastid-dividing, dynamin, and FtsZ (PDF) rings. We isolated intact supertwisted (or spiral) and circular PDF machineries from chloroplasts of the red alga Cyanidioschyzon merolae. After individual intact PDF machineries were stretched to four times their original lengths with optical tweezers, they spontaneously returned to their original sizes. Dynamin-released PDF machineries did not retain the spiral structure and could not be stretched. Thus, dynamin may generate the motive force for contraction by filament sliding in dividing chloroplasts, in addition to pinching-off the membranes.
    Sep. 2006, Science, 313(5792) (5792), 1435 - 1438, English, International magazine
    [Refereed]
    Scientific journal

  • Kuroiwa T, Nishida K, Yoshida Y, Fujiwara T, Mori T, Kuroiwa H, Misumi O
    Mitochondria are derived from free-living alpha-proteobacteria that were engulfed by eukaryotic host cells through the process of endosymbiosis, and therefore have their own DNA which is organized using basic proteins to form organelle nuclei (nucleoids). Mitochondria divide and are split amongst the daughter cells during cell proliferation. Their division can be separated into two main events: division of the mitochondrial nuclei and division of the matrix (the so-called mitochondrial division, or mitochondriokinesis). In this review, we first focus on the cytogenetical relationships between mitochondrial nuclear division and mitochondriokinesis. Mitochondriokinesis occurs after mitochondrial nuclear division, similar to bacterial cytokinesis. We then describe the fine structure and dynamics of the mitochondrial division ring (MD ring) as a basic morphological background for mitochondriokinesis. Electron microscopy studies first identified a small electron-dense MD ring in the cytoplasm at the constriction sites of dividing mitochondria in the slime mold Physarum polycephalum, and then two large MD rings (with outer cytoplasmic and inner matrix sides) in the red alga Cyanidioschyzon merolae. Now MD rings have been found in all eukaryotes. In the third section, we describe the relationships between the MD ring and the FtsZ ring descended from ancestral bacteria. Other than the GTPase, FtsZ, mitochondria have lost most of the proteins required for bacterial cytokinesis as a consequence of endosymbiosis. The FtsZ protein forms an electron transparent ring (FtsZ or Z ring) in the matrix inside the inner MD ring. For the fourth section, we describe the dynamic association between the outer MD ring with a ring composed of the eukaryote-specific GTPase dynamin. Recent studies have revealed that eukaryote-specific GTPase dynamins form an electron transparent ring between the outer membrane and the MD ring. Thus, mitochondriokinesis is thought to be controlled by a mitochondrial division (MD) apparatus including a dynamic trio, namely the FtsZ, MD and dynamin rings, which consist of a chimera of rings from bacteria and eukaryotes in primitive organisms. Since the genes for the MD ring and dynamin rings are not found in the prokaryotic genome, the host genomes may make these rings to actively control mitochondrial division. In the fifth part, we focus on the dynamic changes in the formation and disassembly of the FtsZ, MD and dynamin rings. FtsZ rings are digested during a later period of mitochondrial division and then finally the MD and dynamin ring apparatuses pinched off the daughter mitochondria, supporting the idea that the host genomes are responsible for the ultimate control of mitochondrial division. We discuss the evolution, from the original vesicle division (VD) apparatuses to VD apparatuses including classical dynamin rings and MD apparatuses. It is likely that the MD apparatuses involving the dynamic trio evolved into the plastid division (PD) apparatus in Bikonta, while in Opisthokonta, the MD apparatus was simplified during evolution and may have branched into the mitochondrial fusion apparatus. Finally, we describe the possibility of intact isolation of large MD/PD apparatuses, the identification of all their proteins and their related genes using C. merolae genome information and TOF-MS analyses. These results will assist in elucidating the universal mechanism and evolution of MD, PD and VD apparatuses.
    May 2006, Biochimica et biophysica acta, 1763(5-6) (5-6), 510 - 521, English, International magazine
    [Refereed]
    Scientific journal

  • Fumi Yagisawa, Keiji Nishida, Haruko Kuroiwa, Toshiyuki Nagata, Tsuneyoshi Kuroiwa
    Sep. 2005, Cytologia, 70(3) (3), 351 - 354, English
    [Refereed]
    Scientific journal

  • K Nishida, F Yagisawa, H Kuroiwa, T Nagata, T Kuroiwa
    May 2005, MOLECULAR BIOLOGY OF THE CELL, 16(5) (5), 2493 - 2502, English, International magazine
    [Refereed]
    Scientific journal

  • O Misumi, M Matsuzaki, H Nozaki, S Miyagishima, T Mori, K Nishida, F Yagisawa, Y Yoshida, H Kuroiwa, T Kuroiwa
    Feb. 2005, PLANT PHYSIOLOGY, 137(2) (2), 567 - 585, English, International magazine
    [Refereed]
    Scientific journal

  • F Yagisawa, K Nishida, O Misumi, H Kuroiwa, T Nagata, T Kuroiwa
    2005, PLANT AND CELL PHYSIOLOGY, 46, S68 - S68, English
    [Refereed]

  • Triple immunofluorescent labeling of FtsZ, dynamin, and EF-Tu reveals a loose association between the inner and outer membrane mitochondrial division machinery in the red alga Cyanidioschyzon merolae
    NISHIDA Keiji, MISUMI Osami, YAGISAWA Fumi, KUROIWA Haruko, NAGATA Toshiyuki, KUROIWA Tsuneyoshi
    In the mitochondria of primitive eukaryotes, FtsZ and dynamin are part of the machinery involved in division of the inner and outer membranes, respectively. These genes also commonly function in the same manner during chloroplast division. In this study, a relationship between the localization of the inner and outer division machinery was directly shown for the first time. Triple immunofluorescent labeling was performed in the red alga Cyanidioschyzon merolae by a device using narrow bandpass filter sets and bright photostable dyes. FtsZ (CmFtsZ1) and dynamin (CmDnm1) localizations were examined simultaneously throughout the mitochondrial division cycle with an alternative mitochondrial marker protein, the mitochondrial translation elongation factor EF-Tu, whose localization was also shown to be identical to the mitochondrial matrix. FtsZ and dynamin did not necessarily co-localize when both were recruited to the mitochondrial constriction site, indicating that inner and outer dividing machineries are not in tight association during the late stage of division.
    Jul. 2004, Journal of Histochemistry & Cytochemistry, 52(7) (7), 843 - 849, English, International magazine
    [Refereed]
    Scientific journal

  • M Matsuzaki, O Misumi, T Shin-I, S Maruyama, M Takahara, SY Miyagishima, T Mori, K Nishida, F Yagisawa, K Nishida, Y Yoshida, Y Nishimura, S Nakao, T Kobayashi, Y Momoyama, T Higashiyama, A Minoda, M Sano, H Nomoto, K Oishi, H Hayashi, F Ohta, S Nishizaka, S Haga, S Miura, T Morishita, Y Kabeya, K Terasawa, Y Suzuki, Y Ishii, S Asakawa, H Takano, N Ohta, H Kuroiwa, K Tanaka, N Shimizu, S Sugano, N Sato, H Nozaki, N Ogasawara, Y Kohara, T Kuroiwa
    Apr. 2004, NATURE, 428(6983) (6983), 653 - 657, English, International magazine
    [Refereed]
    Scientific journal

  • SY Miyagishima, H Nozaki, K Nishida, K Nishida, M Matsuzaki, T Kuroiwa
    Mar. 2004, JOURNAL OF MOLECULAR EVOLUTION, 58(3) (3), 291 - 303, English, International magazine
    [Refereed]
    Scientific journal

  • Fumi Yagisawa, Keiji Nishida, Yukio Okano, Ayumi Minoda, Kan Tanaka, Tsuneyoshi Kuroiwa
    Mar. 2004, Cytologia, 69(1) (1), 97 - 100, English
    [Refereed]
    Scientific journal

  • SY Miyagishima, K Nishida, T Kuroiwa
    Sep. 2003, TRENDS IN PLANT SCIENCE, 8(9) (9), 432 - 438, English, International magazine
    [Refereed]
    Scientific journal

  • S Miyagishima, K Nishida, T Mori, M Matsuzaki, T Higashiyama, H Kuroiwa, T Kuroiwa
    Mar. 2003, PLANT CELL, 15(3) (3), 655 - 665, English, International magazine
    [Refereed]
    Scientific journal

  • K Nishida, M Takahara, S Miyagishima, H Kuroiwa, M Matsuzaki, T Kuroiwa
    Feb. 2003, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(4) (4), 2146 - 2151, English, International magazine
    [Refereed]
    Scientific journal

■ MISC
  • 米村 洋而, 西田 敬二
    東京 : 医歯薬出版, 01 Feb. 2025, 医学のあゆみ, 292(5) (5), 350 - 356, Japanese

  • 塩基編集ツールの開発と応用—特集 ゲノム編集医療 : 技術開発・治療応用戦略を中心に
    光延 仁志, 西田 敬二
    大阪 : メディカルドゥ, Oct. 2020, 遺伝子医学 = Gene & medicine, 10(4) (4), 22 - 27, Japanese

  • 一塩基レベルでの精密なゲノム編集技術—Precise genome editing technology at the single nucleotide level—第5土曜特集 ゲノム編集の未来 ; ゲノム編集の原理とツール開発
    森田 健太郎, 西田 敬二
    東京 : 医歯薬出版, 30 May 2020, 医学のあゆみ, 273(9) (9), 739 - 743, Japanese

  • A COMPUTATIONAL TOOL TO DESIGN UNIQUE GUIDE RNAS FOR TARGET-AID MEDIATED GENOME-WIDE BASE EDITING
    Kenta Katayama, Jun Teramoto, Akihiko Kondo, Keiji Nishida
    Nov. 2019, Frontiers in Genome Engineering 2019
    [Refereed]
    Summary international conference

  • 植物ミトコンドリアにおけるゲノム編集の成功
    片山 健太, 日高 朋美, 風間 智彦, 鳥山 欽哉, 有村 慎一, 西田 敬二
    Sep. 2019, 日本植物学会第83回大会

  • MitoTALENによる植物ミトコンドリアゲノム編集の成功
    片山健太, 風間智彦, 鳥山欽哉, 有村慎一, 近藤昭彦, 西田敬二
    Jun. 2019, 第19回日本蛋白質科学会年会・第71回日本細胞生物学会大会 合同年次大会
    Summary national conference

  • DNA塩基書き換えによる切らないゲノム編集Target-AID—DNA base editing Target-AID as non-cleaving genome editing technology—特集 未来を切り拓く先端的な生命科学への挑戦
    西田 敬二
    東京 : 農林水産・食品産業技術振興協会, May 2019, JATAFFジャーナル = JATAFF journal : 農林水産技術, 7(5) (5), 17 - 21, Japanese

  • Nishida Keiji
    Pesticide Science Society of Japan, 20 Feb. 2019, Japanese Journal of Pesticide Science, 44(1) (1), 59 - 64, Japanese

  • ゲノム編集による微生物の遺伝子改変 : 微生物モノづくりの革新—特集 ゲノム編集
    西田 敬二
    東京 : エヌ・ティー・エス, Nov. 2018, 遺伝 : 生物の科学, 72(6) (6), 572 - 577, Japanese

  • ナイスステップな研究者から見た変化の新潮流 神戸大学大学院 科学技術イノベーション研究科教授/株式会社バイオパレット取締役 西田敬二氏インタビュー : DNA塩基書き換えによる切らないゲノム編集(Target-AID)
    西田 敬二, 犬塚 隆志, 重茂 浩美, 佐藤 博俊
    東京 : 文部科学省科学技術学術政策研究所科学技術動向研究センター, 2018, STI horizon = STIホライズン : イノベーションの新地平を拓く, 4(2) (2), 13 - 16, Japanese

  • 進展するゲノム編集（＜特集＞生命をつくる：ゲノム編集の時代）
    NISHIDA KEIJI
    東京 : 東京化学同人, Jan. 2018, 現代化学, 1月号(562) (562), 26 - 29, Japanese
    Introduction scientific journal

  • 哺乳動物の全細胞系譜追跡にむけたDNAバーコード技術の開発
    増山 七海, 石黒 宗, 森 秀人, 増井 修, 関 元昭, 松尾 采佳, 西田 敬二, 栫 健太郎, 近藤 昭彦, 冨田 勝, 油谷 浩幸, 古関 明彦, 谷内江 望
    生命科学系学会合同年次大会運営事務局, Dec. 2017, 生命科学系学会合同年次大会, 2017年度, [2P - 1314], English

  • 22653 大変形弾性部材を組み込んだ高力ボルト摩擦接合ダンパーの基礎的研究
    中村 建人, 西田 銀次, 澤田 樹一郎, 黒川 善幸, 平井 敬二, 中野 翔平
    日本建築学会, 20 Jul. 2017, 構造III, (2017) (2017), 1305 - 1306, Japanese

  • Keiji Nishida, Zenpei Shimatani, Akihiko Kondo
    Current genome editing tools are based on the artificial programmable nucleases, which induce DNA double strand break which may cause formation of insertion and deletion at the target site. For more precise modification, homologous templates are needed to be co-introduced to induce homology-mediated transformation at the cleaved site, although success rate for this is not always high enough, especially in planta. In place of the nuclease-based, conventional genome editing technology, deaminase-mediated genome editing has been developed and applied to plants. Target-AID and Base Editor, which employ cytidine deaminase PmCDA1 and rApobec respectively tethered to nuclease-deficient CRISPR-Cas9 system, can specifically deaminate cytidines to form uracil on DNA, which mainly causes C to T mutagenesis. These systems were optimized for expression in plants and successfully demonstrated in rice, wheat, corn and tomato using agrobacterium-mediated transformation or particle bombardment. Advanced technology such as DNA-free transformation will be addressed in the future studies.
    The Japanese Society for Chemical Regulation of Plants, Jun. 2017, Regulation of Plant Growth & Development, 52(1) (1), 15 - 18, Japanese
    Introduction scientific journal

  • ミトコンドリア分裂リングを形成する新規ミトコンドリア分裂遺伝子MDR1の同定と機能解析
    吉田大和, 黒岩晴子, 嶋田崇史, 吉田昌樹, 大沼みお, 藤原崇之, 井元祐太, 八木沢芙美, 西田敬二, 廣岡俊亮, 三角修己, 茂木祐子, 赤壁善彦, 松下一信, 黒岩常祥
    2017, 日本原生生物学会大会講演要旨集, 50th, 20, Japanese

  • 微生物でのゲノム編集の利用と拡大技術
    KONDO Akihiko, 西田敬二, 荒添貴之
    裳華房, 2016, ゲノム編集入門, 第3章, 40 - 55, Japanese
    [Refereed]
    Introduction scientific journal

  • 1P-079 Development of non-nuclease genome editing tool
    Nishida Keiji, Banno Satomi, Kondo Akihiko
    日本生物工学会, 2015, 日本生物工学会大会講演要旨集, 67, 108 - 108, Japanese

  • 単膜系オルガネラ分裂リングの同定‐ゲノム科学を基盤としたペルオキシソーム分裂装置(POD machinery)の微細構造と分子機構の解析
    井元祐太, 井元祐太, 黒岩晴子, 黒岩晴子, 吉田大和, 大沼みお, 大沼みお, 藤原崇之, 吉田昌樹, 西田敬二, 八木沢芙美, 廣岡俊亮, 廣岡俊亮, 宮城島進也, 宮城島進也, 三角修己, 三角修己, 河野重行, 河野重行, 黒岩常祥, 黒岩常祥
    15 May 2014, 日本細胞生物学会大会要旨集, 66th, 103, Japanese

  • 原始紅藻シゾンにおけるペルオキシソーム分裂装置(Pod‐machinery)の構造と分子機構の解明
    井元祐太, 黒岩晴子, 井元祐太, 黒岩晴子, 吉田大和, 大沼みお, 大沼みお, 藤原崇之, 吉田昌樹, 西田敬二, 八木沢芙美, 廣岡俊亮, 宮城島進也, 三角修己, 黒岩常祥, 河野重行, 廣岡俊亮, 宮城島進也, 三角修己, 黒岩常祥, 河野重行
    Apr. 2014, Plant Morphol, 26(1) (1), 72, Japanese

  • ポストゲノミクスを基盤としたペルオキシソーム分裂装置(Pod‐machinery)の構造同定と分子機構の解明
    井元祐太, 黒岩晴子, 吉田大和, 大沼みお, 藤原崇之, 吉田昌樹, 西田敬二, 八木沢芙美, 廣岡俊亮, 宮城島進也, 三角修己, 黒岩常祥, 河野重行
    20 Aug. 2013, 日本植物学会大会研究発表記録, 77th, 201, Japanese

  • ミトコンドリア‐マイクロボディ複合体分裂後における非収縮環依存型細胞質分裂機構の解明
    井元祐太, 井元祐太, 井元祐太, 西田敬二, 八木沢芙美, 吉田大和, 大沼みお, 大沼みお, 吉田昌樹, 藤原崇之, 黒岩晴子, 黒岩晴子, 黒岩常祥, 黒岩常祥, 河野重行, 河野重行
    Apr. 2013, Plant Morphol, 25(1) (1), 112, Japanese

  • ミトコンドリア‐マイクロボディ複合体の分裂分配後における非アクトミオシン依存型細胞質分裂機構の解明
    井元祐太, 西田敬二, 八木沢芙美, 吉田大和, 大沼みお, 吉田昌樹, 藤原崇之, 黒岩晴子, 黒岩常祥, 河野重行
    14 Sep. 2012, 日本植物学会大会研究発表記録, 76th, 139, Japanese

  • Takayuki Fujiwara, Haruko Kuroiwa, Fumi Yagisawa, Mio Ohnuma, Yamato Yoshida, Masaki Yoshida, Keiji Nishida, Osami Misumi, Satoru Watanabe, Kan Tanaka, Tsuneyoshi Kuroiwa
    Mar. 2010, PLANT CELL, 22(3) (3), 772 - 781, English, International magazine

  • Imoto Y, Fujiwara T, Misumi O, Nishida K, Kuroiwa H, Kuroiwa T
    2010, Protoplasma, 241, 63 - 74

  • 原始紅藻Cyanidioschyzon merolaeにおける液胞タンパク質の同定
    八木沢芙美, 西田敬二, 吉田昌樹, 黒岩晴子, 黒岩常祥
    Apr. 2009, Plant Morphol, 21(1) (1), 98, Japanese

  • N Usio, Yonekura Ryuji, Iwasaki Keiji, Nishida Mutsumi, Kawamura Kouichi, Kawai Hiroshi
    分子遺伝マーカーに基づく集団遺伝解析は、外来生物の起源推定、分散様式の解明、さらには遺伝的多様性の評価において有効である。また、外部形態だけで判定不能な隠蔽種の探索、侵入回数の推定、ならびに在来種との交雑の有無や遺伝子浸透の程度の把握が可能となる。これらの知見は、外来生物のリスク評価のみならず管理(生態系管理)に活用することも可能と思われる。一般に、外来生物の管理は、意図的導入の抑制、新たな侵入や分布拡大の防止などの「予防策」と定着した外来生物を間引いたり根絶したりするための「駆除策」の2つに分けられる。外来生物の起源や拡散様式、遺伝的多様性などの情報は、予防策を立案する上で有用な情報を提供すると考えられる。しかし、当面の大きな課題は、これらの学術的知見を直に反映させることができる外来生物管理体制を産・官・学やNPOが一体となって早急に作り上げることができるかどうかである。一方、駆除策への適用可能性としては、これまでに希少種の保全遺伝学的研究で得られた知見に基づき、隔離性の高い小集団を駆除単位として策定するとともに、駆除の効果を遺伝的ボトルネックの有無から判定する方法が有効であると考えられる。
    The Ecological Society of Japan, 2009, JAPANESE JOURNAL OF ECOLOGY, 59(2) (2), 161 - 166, Japanese

  • Yagisawa, F, Nishida, K, Yoshida, M, Misumi, O, Yoshida, Y, Fujiwara, T, Kuroiwa, H, Kuroiwa, T
    2009, Plant J, 60, 882 - 892

  • 原子紅藻Cyanidioschyzon merolaeにおける液胞タンパク質の同定
    八木沢芙美, 西田敬二, 吉田昌樹, 黒岩晴子, 黒岩常祥
    25 Sep. 2008, 日本植物学会大会研究発表記録, 72nd, 165, Japanese

  • T. Kuroiwa, O. Misumi, K. Nishida, F. Yagisawa, Y. Yoshida, T. Fujiwara, H. Kuroiwa
    2008, INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY, VOL 271, 271, 97 - 152, English

  • 細胞周期によるミトコンドリア分裂の制御機構
    西田敬二, 八木沢芙美, 黒岩晴子, 吉田大和, 吉田昌樹, 黒岩常祥
    06 Sep. 2007, 日本植物学会大会研究発表記録, 71st, 146, Japanese

  • 原始紅藻におけるリソソーム様構造の解析
    八木沢芙美, 西田敬二, 吉田昌樹, 黒岩晴子, 黒岩常祥
    06 Sep. 2007, 日本植物学会大会研究発表記録, 71st, 145, Japanese

  • 葉緑体分裂(PDF)マシンのプロテオーム解析による構成タンパク質プロファイリングと機能解析
    吉田大和, 諌山拓也, 廣岡俊亮, 若松佑樹, 西田敬二, 吉田昌樹, 黒岩晴子, 河野重行, 黒岩常祥
    06 Sep. 2007, 日本植物学会大会研究発表記録, 71st, 146, Japanese

  • The first 100% complete eukaryotic genome sequences from the red alga Cyanidioschyzon merolae 10D.
    Nozaki, H, Takano, H, Misumi, O, Terasawa, K, Matuzaki, M, Maruyama, S, Nishida, K, Yagisawa, F, Yoshida, Y, Fujiwara, T, Takio, S, Tamura, K, Chung j-Chung, Nakamura, S, Kuroiwa, H, Tanaka, K, Sato, N, Kuroiwa, T
    2007, BMC Biology, 5, No28

  • Tsuneyoshi Kuroiwa, Keiji Nishida, Yamato Yoshida, Takayuki Fujiwara, Toshiyuki Mori, Haruko Kuroiwa, Osami Misumi
    May 2006, BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1763(5-6) (5-6), 510 - 521, English
    Book review

  • 単細胞紅藻Cyanidioschyzon merolaeにおけるリソソーム様構造の動態と同定
    八木沢芙美, 西田敬二, 三角修己, 黒岩晴子, 長田敏行, 黒岩常祥
    Mar. 2005, 日本植物生理学会年会要旨集, 46th, 145, Japanese

  • 原始紅藻におけるミトコンドリア分裂機構の解析
    西田敬二, 八木沢芙美, 黒岩晴子, 長田敏行, 黒岩常祥
    Mar. 2005, 日本植物生理学会年会要旨集, 46th, 145, Japanese

  • K Nishida, F Yagisawa, H Kuroiwa, T Nagata, T Kuroiwa
    2005, PLANT AND CELL PHYSIOLOGY, 46, S68 - S68, English
    Summary international conference

  • NISHIDA Keiji, NAGATA Toshiyuki, KUROIWA Tsuneyoshi
    Summary: Mitochondrial and chloroplast division controls the number and morphology of organelles, but how cells regulate organelle division remains to be clarified. Here, we show that each step of mitochondrial and chloroplast division is closely associated with the cell cycle in Cyanidioschyzon merolae. Electron microscopy revealed direct associations between the spindle pole bodies and mitochondria, suggesting that mitochondrial distribution is physically coupled with mitosis. Mitochondrial final severance was suppressed during S phase and once induced in M phase, when dynamin was specifically recruited. Although microtubule was not directly required for the organelles division, spatial interaction between microtubule and dynamin implied to be working on a possible checkpoint for spindle elongation. Chloroplast division was induced during S phase and suppressed during M phase, which was thought to be as a consequence of synthesis and degradation of dynamin and FtsZ. Molecular networks between cell cycle and the organelles division is discussed.
    The Japanese Society of Plant Morphology, 2005, PLANT MORPHOLOGY, 17(1) (1), 51 - 55, English
    Introduction scientific journal

  • K Nishida, O Misumi, F Yagisawa, H Kuroiwa, T Nagata, T Kuroiwa
    Jul. 2004, JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY, 52(7) (7), 843 - 849, English

  • 西田敬二, 宮城島進也, 黒岩晴子, 黒岩常祥
    Through the evolution of eukaryote, division machineries of endosymbiont organelles plastid and mitochondria have been developed into amalgamation of bacterial division system and host eukaryotic controller. Despite differences in roles and morphology of the organelles, recent studies have revealed that these organelles have developed very similar division mechanisms, composed of three rings, in the early stage of evolution. A primitive red alga Cyanidioschyzon merolae has been established as a basic model of organelle division, whose organelles exhibit simplest morphology, synchronized division as well as observable division apparatuses; plastid dividing (PD) ring or mitochondrion dividing (MD) ring. In addition to the rings, the both organelles emplay two GTPases, FtsZ of bacterial remnant and eukaryotic dynamin as distinct dividing rings. Through detailed localizing studies of these proteins and apparatuses, roles of, FtsZ, PD or MD, and dynamin are thought to be placement, constriction and severance at division site, respectively.
    The Japanese Society of Plant Physiologists, 20 Mar. 2004, 日本植物生理学会年会要旨集, 45th, 92 - S079, Japanese

  • Three dividing rings common to mitochondria and plastid
    K Nishida, S Miyagishima, H Kuroiwa, T Kuroiwa
    2004, PLANT AND CELL PHYSIOLOGY, 45, S20 - S20, English
    Summary international conference

  • Analysis on mitochondrial division mechanism in a primitive alga
    K Nishida, S Miyagishima, H Kuroiwa, T Kuroiwa
    2004, PLANT AND CELL PHYSIOLOGY, 45, S217 - S217, English
    Summary international conference

  • FtsZリングおよび色素体分裂リングからなる葉緑体分裂装置複合体の構造解析
    宮城島進也, 西田敬二, 森稔幸, 黒岩晴子, 黒岩常祥
    20 Sep. 2002, 日本植物学会大会研究発表記録, 66th, 168, Japanese

  • 細胞核はどのように色素体とミトコンドリアの増殖を制御してきたか
    黒岩常祥, 黒岩晴子, 宮城島進也, 高原学, 森稔幸, 桃山ゆう, 八木沢芙美, 西田敬二, 丸山真一朗
    20 Sep. 2002, 日本植物学会大会研究発表記録, 66th, 166, Japanese

  • 細胞内共生のメカニズム,DynaminとFtsZが関わる原始紅藻のミトコンドリア分裂機構の解析
    西田敬二, 高原学, 宮城島進也, 黒岩晴子, 黒岩常祥
    20 Sep. 2002, 日本植物学会大会研究発表記録, 66th, 167, Japanese

  • ムライトと硫酸塩の反応について—〔耐火物技術協会〕第39回原料専門委員会資料
    佐藤 敬二郎, 西田 晴夫, 田口 武士
    資料形態 : テキストデータ プレーンテキスト コレクション : 国立国会図書館デジタルコレクション > デジタル化資料 > 雑誌
    東京 : 耐火物技術協会, May 1983, 耐火物, 35(304) (304), p281 - 284, Japanese

■ Books And Other Publications
  • 最新のゲノム編集技術と用途展開
    大西美輪, 光延仁志, 西田敬二
    第2編 第5章 DNA二重鎖切断を伴わない塩基編集技術, Feb. 2021

  • 最新のゲノム編集技術と用途展開
    西田敬二, 近藤昭彦
    第3編 第9章 バクテリアでのゲノム編集の有用性, Feb. 2021

  • ゲノム編集入門 : ZFN・TALEN・CRISPR-Cas9
    山本, 卓(理学), 石野, 良純, 近藤, 昭彦, 西田, 敬二, 荒添, 貴之, 丹羽, 隆介, 坂本, 尚昭, 泰松, 清人, 川原, 敦雄, 鈴木, 賢一, 宮坂, 佳樹, 真下, 知士, 安本, 周平, 村中, 俊哉, 宮本, 達雄, 田中, 伸和
    裳華房, Dec. 2016, Japanese, ISBN: 9784785358662

  • 『All About ゲノム編集』, 第1章 3) 切断を伴わないゲノム編集ツール開発（デアミナーゼ他）
    NISHIDA KEIJI
    Single work, 羊土社, Dec. 2016, Japanese
    Scholarly book

  • ゲノム編集入門, 第3章 微生物でのゲノム編集の利用と拡大技術
    NISHIDA KEIJI
    Single work, 裳華房, Dec. 2016, Japanese
    Scholarly book

■ Lectures, oral presentations, etc.
  • 塩基編集技術による次世代育種
    西田 敬二
    2019 年植物科学シンポジウム 「SDGs に向けた植物科学の展開」, Dec. 2019, Japanese, Domestic conference
    Nominated symposium

  • 塩基編集技術の開発と育種応用
    西田 敬二
    日本農芸化学会関西支部 支部例会（第511回講演会）, Dec. 2019, Japanese, Domestic conference
    [Invited]
    Invited oral presentation

  • Base editing, gene conversion and local diversification without DNA double strand break
    Keiji Nishida
    Frontiers in Genome Engineering 2019, Nov. 2019, English, International conference
    Oral presentation

  • 塩基編集技術Base editing の開発と展望
    西田 敬二
    Bio Japan 2019, Oct. 2019, Japanese, International conference
    [Invited]
    Invited oral presentation

  • Genome engineering by base editing in various organisms
    Keiji Nishida
    2019 Asian Synthetic Biology Association (ASBA) Meeting, Oct. 2019, English, International conference
    Oral presentation

  • Development of base editing tools for efficient and precise genome engineering
    Keiji Nishida
    日本遺伝学会第91回大会, Sep. 2019, English, International conference
    Invited oral presentation

  • セルロース系バイオマスを原料とするカフェ酸発酵のためのゲノム編集による大腸菌代謝改変の作 製と培養法の検討
    KAWAGUCHI HIDEO, MIYAZAKI SHOKO, TERAMOTO JUN, NISHIDA KEIJI, 南 博道, 佐塚 隆志, KONDO AKIHIKO
    第71回日本生物工学会大会, Sep. 2019, Japanese, 岡山大学, Domestic conference
    Oral presentation

  • Potential of base editing technology for gene therapy
    Keiji Nishida
    第25回日本遺伝子細胞治療学会学術集会, Jul. 2019, Japanese, Domestic conference
    [Invited]
    Invited oral presentation

  • 抗体生産性に関わる遺伝子探索のためのPichia pastorisゲノム編集技術の構築
    YAMADA KENTO, NANBU-NISHIDA YUMIKO, ITO YOICHIRO, NISHIDA KEIJI, ISHII JUN, KONDO AKIHIKO
    生物工学若手研究者の集い 夏のセミナー2019, Jul. 2019, Japanese, 琵琶湖国定公園 近江白浜 政府登録旅館 白浜荘, Domestic conference
    Poster presentation

  • Target-AID
    Keiji Nishida
    協和発酵バイオ株式会社セミナー, May 2019, Japanese, Domestic conference
    [Invited]
    Public discourse

  • 塩基編集 Base editing の開発と応用
    西田 敬二
    2019年度東大医科研大学院セミナー, May 2019, Japanese, Domestic conference
    Public discourse

  • Geneme engineering by base editing for various applications
    Keiji Nishida
    the 10th International Symposium of Innovative BioProduction Kobe (iBioK), Jan. 2019, English, International conference
    Invited oral presentation

  • Caffeic acid production from lignocellulosic biomass by metabolically engineered Eshrichaia coli
    KAWAGUCHI Hideo, SAZUKA Takashi, KATSUYAMA Yohei, TERAMOTO Jun, NISHIDA Keiji, MINAMI Hiromichi, OGINO Chiaki, OHNISHI Yasuo, KONDO Akihiko
    The 24th Symposium of Young Asian Biological Engineers’ Community (YABEC 2018), Nov. 2018, English, National Taiwan University, International conference
    Oral presentation

  • 新たなゲノム編集技術の開発
    西田 敬二
    生命科学系フロンティアミーティング 2018, Oct. 2018, Japanese, Domestic conference
    Oral presentation

  • point mutagenesis via base-specific RRISPR-editing
    Keiji Nishida
    CRISPRing 学会, Sep. 2018, English, International conference

  • 塩基編集技術Target-AIDの工学的応用
    NISHIDA KEIJI
    第70回日本生物工学会大会, Sep. 2018, Japanese, 関西大学 千里山キャンパス, Domestic conference
    Oral presentation

  • Target-AID を利用したゲノム編集による高収率ブタ ノール発酵性クロストリジウム属微生物の育種
    向山正治, 市毛栄太, 田中 勉, 西田敬二, 近藤 昭彦
    第70回日本生物工学会大会, Sep. 2018, Japanese, 関西大学 千里山キャンパス, Domestic conference
    Poster presentation

  • ゲノムを切らずに書き換える新たなゲノム編集技術の開発
    西田 敬二
    フロンティアサロン, Jul. 2018, Japanese, Domestic conference
    [Invited]
    Invited oral presentation

  • 切らないゲノム編集技術の開発と産業応用の可能性
    西田 敬二
    リンク公開フォーラム, Jul. 2018, Japanese, Domestic conference
    [Invited]
    Nominated symposium

  • 塩基編集技術の開発
    西田 敬二
    第5回 Kobe Plant Science研究会, Jun. 2018, Japanese, Domestic conference

  • 塩基編集技術の開発と応用展開
    西田 敬二
    日本ゲノム編集学会第3回大会, Jun. 2018, Japanese, 広島国際会議場, Domestic conference
    Oral presentation

  • Genome engineering by DNA base editing
    Keiji Nishida
    Biosystems Design 4.0, May 2018, English, International conference

  • ピンポイント塩基編集による次世代育種の可能性
    西田 敬二
    日本農薬学会第43回大会, May 2018, Japanese, Domestic conference

  • Base editing from Bacteria to Plants
    Keiji Nishida
    Cold Spring Harbor Asia, Apr. 2018, English, International conference

  • 植物ゲノムの塩基編集技術
    西田 敬二
    第二回植物病理を紡ぐ会, Mar. 2018, Japanese, Domestic conference
    [Invited]
    Invited oral presentation

  • Genome Editing with Non-Nuclease Editors from Bacteria to Plants
    Keiji Nishida
    Keystone Symposia, Jan. 2018, English, International conference
    [Invited]
    Invited oral presentation

  • 点変異導入型のゲノム編集技術Target-AIDの開発
    NISHIDA KEIJI
    第83回酵母研究会講演会, Sep. 2017, Japanese, 京都大学, Domestic conference
    Oral presentation

  • Target-AID を利用したゲノム編集による高収率ブタ ノール発酵性クロストリジウム属微生物の育種
    向山正治, 市毛栄太, 田中 勉, 西田敬二, 近藤 昭彦
    第69回日本生物工学会大会, Sep. 2017, Japanese, 早稲田大学 西早稲田キャンパス, Domestic conference
    Oral presentation

  • 様々な生物に応用可能なピンポイントゲノム編集技術
    西田 敬二
    合成生物工学シンポジウム, Aug. 2017, Japanese, 神戸大学百年記念館六甲ホール, Domestic conference
    Oral presentation

  • Development of a Targeted Nucleotide Editing Tool Target-AID and its Applications
    NISHIDA Keiji
    BioKorea 2017, Apr. 2017, English, COEX, Korea, International conference
    Oral presentation

  • 塩基変換による切らないゲノム編集
    NISHIDA KEIJI, 荒添 貴之, 坂野 聡美, KONDO AKIHIKO
    日本農芸化学2017年度大会シンポジウム, Mar. 2017, Japanese, 京都女子大学, Domestic conference
    Oral presentation

  • より精密なゲノムデザイン改変を可能とする点変異ゲノム編集
    西田 敬二
    第2回デザイン生命工学研究会大会, Mar. 2017, Japanese, 神戸大学統合研究拠点コンベンションホール, Domestic conference
    Oral presentation

  • ゲノム編集による Kluyveromyces marxianus の自在な 遺伝子改変
    南部-西田由美子, 西田敬二, 蓮沼 誠久, 近藤 昭彦
    日本農芸化学2017年度大会, Mar. 2017, Japanese, 日本農芸化学会, 京都女子大学, Domestic conference
    Oral presentation

  • Target-AID を利用したゲノム編集による高収率ブタ ノール発酵性クロストリジウム属微生物の育種
    向山正治, 市毛栄太, 田中 勉, 西田敬二, 近藤 昭彦
    日本農芸化学2017年度大会, Mar. 2017, Japanese, 日本農芸化学会, 京都女子大学, Domestic conference
    Oral presentation

  • Targeted point mutagenesis in various organisms
    Keiji Nishida
    the 8th International Symposium of Innovative BioProduction Kobe (iBioK), Feb. 2017, English, International conference
    Invited oral presentation

  • Targeted nucleotide substitution as a new mode of genome editing
    NISHIDA Keiji
    iBio-P, Dec. 2016, English, Haeundae Grand Hotel, Pusan Korea, International conference
    Oral presentation

  • 麹菌におけるゲノムを切らずに書き換える新規ゲノム編集ツールの確立
    荒添 貴之, 西田 敬二, 田畑 麻由良, 若井 暁, 荻野 千秋, 秦 洋二, 近藤 昭彦
    第16回糸状菌分子生物学カンファレンス, Nov. 2016, Japanese, 宇治おうばくプラザ, Domestic conference
    Poster presentation

  • 切らないゲノム編集の拡大応用
    NISHIDA KEIJI
    第6回合成生物工学シンポジウム, Jul. 2016, Japanese, 神戸大学百年記念館六甲ホール, Domestic conference
    Oral presentation

  • Genome editing mediated by base-exchange without cleaving DNA
    Keiji Nishida
    the 7th International Symposium of Innovative BioProduction Kobe (iBioK), Jan. 2016, English, International conference
    Invited oral presentation

  • ゲノムを切らずに書き換える新たなゲノム編集技術の開発
    Nishida Keiji, Itano Satomi, Kondou Akihiko
    第67回日本生物工学会大会 国際シンポジウム, Oct. 2015, Japanese, Domestic conference
    Oral presentation

  • Engineering and analyzing the sixth sense in yeast
    NISHIDA KEIJI, KONDO AKIHIKO, Pamela Silver
    第36回日本分子生物学会年会, Dec. 2013, Japanese, 日本分子生物学会, 神戸市, Biological systems are made to sense and respond to various physicochemical stimuli. Among those magneto-sensing is rare and sporadic in biology although magnetism is a major property in physics. The reason why magneto-sensing is not common is suggested to be not because it was biologically incompatible but because it was not so useful in natural environment. Expressing magneti, Domestic conference
    [Invited]
    Nominated symposium

  • Towards gene-specific hyperevolution
    NISHIDA KEIJI
    The eve of the Yeast Renaissance, Dec. 2013, Japanese, Okayama City, Domestic conference
    [Invited]
    Invited oral presentation

■ Research Themes
■ Industrial Property Rights
  • 標的化したDNA配列の核酸塩基を特異的に変換するゲノム配列の改変方法及びそれに用いる分子複合体
    NISHIDA KEIJI, KONDO AKIHIKO, 小嶋 聡美
    特願2017-164703, 04 Mar. 2015, 大学長, 特許6462069, 11 Jan. 2019
    Patent right

  • 標的化したDNA配列の核酸塩基を特異的に変換するゲノム配列の改変方法及びそれに用いる分子複合体 （シンガポール）
    NISHIDA KEIJI, KONDO AKIHIKO, 小嶋 聡美
    11201609211V, 04 Mar. 2015, 大学長, 11201609211V, 12 Jan. 2018
    Patent right

  • 標的化したDNA配列の核酸塩基を特異的に変換するゲノム配列の改変方法及びそれに用いる分子複合体
    NISHIDA KEIJI, KONDO AKIHIKO, 小嶋 聡美
    特願2016-506541, 04 Mar. 2015, 大学長, 特許6206893, 15 Sep. 2017
    Patent right

  • 脱塩基反応により標的化したDNA配列に特異的に変異を導入する、ゲノム配列の改変方法、並びにそれに用いる分子複合体
    NISHIDA KEIJI, KONDO AKIHIKO
    特願2016-516997, 02 Nov. 2015, 大学長, 特許6153180, 09 Jun. 2017
    Patent right

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