Shintaro Ichikawa, Kazuya Ishikawa, Hitoshi Miyakawa, Yutaka Kodama# (2022) Live-cell imaging of the chloroplast outer envelope membrane using fluorescent dyes. Plant Direct, 6(11) e462
☆本論文は、市川晋太郎の卒業論文・修士論文研究

Keiko Midorikawa, Ayaka Tateishi, Kiminori Toyooka, Mayuko Sato, Takuto Imai, Yutaka Kodama, Keiji Numata (2022) Three-dimensional nanoscale analysis of light-dependent organelle changes in Arabidopsis mesophyll cells. PNAS Nexus, 1(5) pgac225

Shintaro Ichikawa*, Shota Kato*, Yuta Fujii, Kazuya Ishikawa, Keiji Numata, Yutaka Kodama# (2022) Organellar Glue: A Molecular Tool to Artificially Control Chloroplast−Chloroplast Interactions. ACS Synth. Biol.11(10) 3190-3197.
☆本論文は、市川晋太郎の卒業論文・修士論文研究
☆本論文は、藤井雄太の博士論文研究

Tatsushi Fukushima*, Yutaka Kodama# (2022) Selection of a histidine auxotrophic Marchantia polymorpha strain with an auxotrophic selective marker. Plant Biotechnol, 39(4) 345-354.
☆本論文は、福島竜志の卒業論文・修士論文研究

Simon Sau Yin Law, Geoffrey Liou, Yukiko Nagai, Joan Giménez-Dejoz, Ayaka Tateishi, Kousuke Tsuchiya, Yutaka Kodama, Tsuyohiko Fujigaya, Keiji Numata (2022) Polymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria.  Nature Communications, 13(1) 2417-2417

Kazuya Ishikawa, Ryota Konno, Satoyuki Hirano, Yuta Fujii, Masayuki Fujiwara, Yoichiro Fukao, Yutaka Kodama# (2022) The endoplasmic reticulum membrane–bending protein RETICULON facilitates chloroplast relocation movement in Marchantia polymorpha. Plant J, 111:205-216.
☆本論文は、今野涼太の卒業論文・修士論文研究
☆本論文は、平野慧潔の卒業論文・修士論文研究
☆本論文は、藤井雄太の博士論文研究

Satoyuki Hirano*, Kotoko Sasaki*, Yasuhide Osaki*, Kyoka Tahara, Hitomi Takahashi, Atsushi Takemiya, Yutaka Kodama# (2022) The localization of phototropin to the plasma membrane defines a cold-sensing compartment in Marchantia polymorpha. PNAS Nexus, pgac030.
☆本論文は、平野慧潔の卒業論文・修士論文研究
☆本論文は、佐々木琴子の卒業論文・修士論文研究
☆本論文は、大崎益秀の修士論文研究

Minoru Noguchi, Yutaka Kodama# (2022) Temperature Sensing in Plants: On the Dawn of Molecular Thermosensor Research. Plant & Cell Physiology, pcac033.
☆本論文は、野口穂の修士論文研究・博士論文研究

Chonprakun Thagun, Yoko Horii, Maai Mori, Seiya Fujita, Misato Ohtani, Kousuke Tsuchiya, Yutaka Kodama, Masaki Odahara#, Keiji Numata# (2022) Non-transgenic Gene Modulation via Spray Delivery of Nucleic Acid/Peptide Complexes into Plant Nuclei and Chloroplasts. ACS Nano, 16: 3506-3521.

Takaaki Miyamoto, Kiminori Toyooka, Jo-Ann Chuah, Masaki Odahara, Mieko Higchi-Takeuchi, Yumi Goto, Yoko Motoda, Takanori Kigawa, Yutaka Kodama, Keiji Numata# (2022) A Synthetic Multidomain Peptide That Drives a Macropinocytosis-Like Mechanism for Cytosolic Transport of Exogenous Proteins into Plants. JACS Au, 2:223-233.

2021

Kazusato Oikawa, Ayaka Tateishi, Masaki Odahara, Yutaka Kodama#, Keiji Numata# (2021) Imaging of the Entry Pathway of a Cell-Penetrating Peptide-DNA Complex From the Extracellular Space to Chloroplast Nucleoids Across Multiple Membranes in Arabidopsis Leaves. Frontiers in Plant Science, 12: 59871-759871.

Shun Tamaki, Ryosuke Sato, Yuki Koshitsuka, Masashi Asahina, Yutaka Kodama, Takahiro Ishikawa, Tomoko Shinomura# (2021) Suppression of the Lycopene Cyclase Gene Causes Downregulation of Ascorbate Peroxidase Activity and Decreased Glutathione Pool Size, Leading to H2O2 Accumulation in Euglena gracilis. Frontiers in Plant Science, 12: 786208-786208

Kato S*, Takahashi Y*, Fujii Y*, Sasaki K, Hirano S, Okajima K & Kodama Y# (2021) The photo-thermochemical properties and functions of Marchantia phototropin encoded by an unduplicated gene in land plant evolution. J Photochem Photobiol B, 224: 112305.
☆本論文は、高橋大和の卒業論文・修士論文研究
☆本論文は、藤井雄太の博士論文研究
☆本論文は、佐々木琴子の修士論文研究
☆本論文は、平野慧潔の卒業論文研究

Takahashi H & Kodama Y# (2021) Culture-based preservation of Marchantia polymorpha gemmalings and thalli without encapsulation, drying, or freezing. Plant Biotechnol, 38:449-452.

Yokawa K & Kodama Y# (2021) A green light-excitable FRET system for monitoring intracellular calcium levels in plant cells. Plant Signal Behav, 1963104.

Kamiyama Y, Hirotani M, Ishikawa S, Minegishi F, Katagiri S, Rogan C, Takahashi F, Nomoto M, Ishikawa K, Kodama Y, Tada Y,  Takezawa D, Anderson J, Peck S, Shinozaki K & Umezawa T# (2021) Arabidopsis group C Raf-like protein kinases negatively regulate abscisic acid signaling and are direct substrates of SnRK2. Proc Natl Acad Sci U S A, 118: e2100073118.

Yong LK, Tsuboyama S, Kitamura R, Kurokura T, Suzuki T & Kodama Y# (2021) Chloroplast relocation movement in the liverwort Apopellia endiviifolia. Physiol Plant, 173:775-787.
☆本論文は、Yong Lee-Kienの修士論文・博士論文研究

Ronnie Concepcion#, Elmer Dadios, Argel Bandala, Joel Cuello, Yutaka Kodama (2021) Hybrid Genetic Programming and Multiverse-based Optimization of Pre-Harvest Growth Factors of Aquaponic Lettuce Based on Chlorophyll Concentration. Int J Adv Sci Eng Inf Technol, 11:2128-2138.

Odahara M, Watanabe K, Kawasaki R, Tsuchiya K, Tateishi A,  Motoda Y, Kigawa T, Kodama Y & Numata K# (2021) Nanoscale polyion complex vesicles for delivery of cargo proteins and Cas9 ribonucleoprotein complexes to plant cells. ACS Appl Nano Mater, 4: 5630-5635.

Oikawa K, Imai T,  Kodama K# & Numata K# (2021) Effects of mitochondria-selective fluorescent probes on mitochondrial movement in Arabidopsis mesophyll cells evaluated by using the quantification. Plant Biotechnol, 38:257-262.

Oikawa K, Imai T, Thagun C, Toyooka K, Yoshizumi T, Ishikawa K, Kodama K# & Numata K# (2021) Mitochondrial movement during its association with chloroplasts in Arabidopsis thaliana. Commun Biol, 4:292.

Yilmaz N, Kodama Y & Numata K# (2021) Lipid membrane interaction of peptide/DNA complexes designed for gene delivery. Langmuir 37:1882-1893.

2020

Takahashi H & Kodama Y# (2020) CRUNC: a cryopreservation method for unencapsulated gemmae of Marchantia polymorpha. PeerJ, 8:e10174.

Thagun C, Motoda Y, Kigawa T,  Kodama Y# & Numata K# (2020) Simultaneous introduction of multiple biomacromolecules into plant cells using a cell-penetrating peptide nanocarrier. Nanoscale, 12:18844 – 18856.

Midorikawa K, Tsuchiya K#, Law S, Miyagi Y, Asai T, Iino T, Ozeki Y, Kodama Y# & Numata K# (2020) Cellular internalization mechanism of novel Raman probes designed for plant cells.  RSC Chem Biol, 1:204-208.

Kawasaki R, Tsuchiya K#, Kodama Y  & Numata K# (2020) Development of reactive oxygen species-triggered degradable nanoparticles using oligoproline-containing peptides. Biomacromolecules, 21:4116-4122.

Tanno Y, Kato S, Takahashi S, Takaichi S, Kodama Y, Sonoike K  & Shinomura T# (2020) Light dependent accumulation of β-carotene enhances photo-acclimation of Euglena gracilis. J Photochem Photobiol B Biol, 209:111950-111950.

Fujii Y*, Ogasawara Y*, Takahashi Y*, Sakata M*, Noguchi M*, Tamura  S & Kodama Y #（2020）The cold-induced switch in direction of chloroplast relocation occurs independently of changes in endogenous phototropin levels．PLOS ONE, 15:e0233302.
☆本論文は、藤井雄太の博士論文研究
☆本論文は、小笠原有香の卒業論文研究
☆本論文は、高橋大和の修士論文研究
☆本論文は、坂田桃子の博士論文研究
☆本論文は、野口穂の修士論文研究
☆本論文は、田村沙織の修士論文研究

坂田桃子、児玉豊 #（2020）タイムゲート法と光変換型蛍光タンパク質とを組み合わせた細胞内タンパク質局在過程の追跡．Plant Morphol, 32:27-30.
☆本論文は、坂田桃子の修士論文研究

Kato S, Ozasa K, Maeda M, Tanno Y, Tamaki S, Higuchi-Takeuchi M, Numata K, Kodama Y, Sato M, Toyooka K & Shinomura T# (2020) Carotenoids in the eyespot apparatus are required for triggering phototaxis in Euglena gracilis. Plant J, 100:1091-1102.

Kikuchi M, Konno N, Suzuki T, Fujii Y, Kodama Y, Isogai A & Habu N# (2020) A bacterial endo-β-1,4-glucuronan lyase, CUL-I from Brevundimonas sp. SH203, belonging to a novel polysaccharide lyase family. Protein Expr Purif, 166:105502.

Yilmaz N, Kodama Y & Numata K# (2020) Revealing the architecture of cell wall in living plant cells by bio-imaging and enzymatic degradation. Biomacromolecules, 21:95-103.

2019

Sakata M, Kimura S, Fujii Y, Sakai T & Kodama Y#  (2019) Relationship between relocation of phototropin to the chloroplast periphery and the initiation of chloroplast movement in Marchantia polymorpha. Plant Direct, 3: e00160.
☆本論文は、坂田桃子の卒業論文・修士論文研究
☆本論文は、木村俊の修士論文研究
☆本論文は、藤井雄太の博士論文研究

Hamashima N*, Xie X*, Hikawa M, Suzuki T & Kodama Y# (2019) A gain-of-function T-DNA insertion mutant of Marchantia polymorpha hyper-accumulates flavonoid riccionidin A. Plant Biotechnol,  36:201-204.
☆本論文は、濵島典子の卒業論文・修士論文研究

Shinotsuka R, Oba T#, Mitome T, Masuya T, Ito S, Murakami Y, Kagenishi T,  Kodama Y, Matsuda M, Yoshida T, Wakamori M, Ohkura M & Nakai J (2019) Synthesis of quinolyl-pyrrole derivatives as novel environment-sensitive fluorescent probes. J Photochem Photobiol A Chem,  382:111900.

児玉豊 #（2019）植物はどうやって温度を感じるのか．生物工学, 97:352.

児玉豊 #（2019）葉緑体の寒冷逃避反応．植物の生長調節, 54:44-48.

児玉豊 #（2019）タイムゲート法：植物における蛍光バイオイメージングの技術革新．OplusE, 41:401-403.

Hikawa M, Nishizawa K & Kodama Y# (2019) Prediction of prospective leaf morphology in lettuce based on intracellular chloroplast position. Sci Hortic, 251:20-24. (bioRxiv, 543538)

Midorikawa K, Kodama Y# & Numata K# (2019) Vacuum/compression infiltration-mediated permeation pathway of a peptide-pDNA complex as a non-viral carrier for gene delivery in planta. Sci Rep, 9:271.

2018

児玉豊 #（2018）植物が温度を感じる仕組み〜ようやく発見！植物の温度センサー分子〜．化学と生物, 57:21-28.

Tsuboyama S & Kodama Y# (2018) Highly efficient G-AgarTrap-mediated transformation of the Marchantia polymorpha model strains Tak-1 and Tak-2. Plant Biotechnol, 35:399-403.
☆本論文は、田中（坪山）祥子の博士論文研究

Tsuboyama S, Nonaka S, Ezura H & Kodama Y# (2018) Improved G-AgarTrap: A highly efficient transformation method for intact gemmalings of the liverwort Marchantia polymorpha. Sci Rep, 8:10800.
☆本論文は、田中（坪山）祥子の博士論文研究

Konno R, Tanaka H & Kodama Y# (2018) SKLPT imaging: efficient in vivo pre-evaluation of genome-editing modules using fluorescent protein with peroxisome targeting signal. Biochem Biophys Res Commun, 503:235-241.
☆本論文は、今野涼太の卒業論文研究・修士論文研究

Tanaka H*, Suzuki R*, Okabe N, Suzuki T & Kodama Y# (2018) Salinity stress-responsive transcription factors in the liverwort Marchantia polymorpha. Plant Biotechnol, 35:281-284.
☆本研究は、高大連携事業（グローバルサイエンスキャンパス：iPU）として実施されました。鈴木凛さん、岡部菜々子さんは、横浜サイエンスフロンティア高等学校の所属です。

沼田圭司#、土屋康佑、児玉豊 （2018）オルガネラ反応クラスターが切り拓くバイオマス社会．植物の生長調節, 53：80-83.

Yoshizumi T, Oikawa K, Chuah JA, Kodama Y, & Numata K# (2018) Selective gene delivery for integrating exogenous DNA into plastid and mitochondrial genomes using peptide-DNA complexes. Biomacromolecules, 19:1582-1591.

Tsuboyama-Tanaka S & Kodama Y# (2018) AgarTrap protocols on your benchtop: simple methods for Agrobacterium-mediated genetic transformation of the liverwort Marchantia polymorpha. Plant Biotechnol, 35:93-99. (Review)
☆本論文は、田中（坪山）祥子の修士論文研究・博士論文研究

Fujii Y*, Yoshimura A* & Kodama Y# (2018) A novel orange-colored bimolecular fluorescence complementation (BiFC) assay using monomeric Kusabira-Orange protein. Biotechniques, 64:153–161.
☆本論文は、藤井雄太の修士論文研究・博士論文研究
☆本論文は、吉村彩香の卒業論文研究

Fujii Y & Kodama Y# (2018) Refinements to light sources used to analyze the chloroplast cold-avoidance response over the past century. Plant Signal Behav, e1411452. (Article Addendum)
☆本論文は、藤井雄太の博士論文研究

2017

Ushijima T*, Hanada K*, Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY, Tada Y, Suzuki Y & Matsushita T# (2017) Light controls protein localization through phytochrome-mediated alternative promoter selection. Cell, 171:1316–1325.

Osaki Y & Kodama Y# (2017) Particle bombardment and subcellular protein localization analysis in the aquatic plant Egeria densa. PeerJ, 5:e3779
☆本論文は、大崎益秀の修士論文研究

Fujii Y, Tanaka H, Konno N, Ogasawara Y, Hamashima N, Tamura S, Hasegawa S, Hayasaki Y, Okajima K & Kodama Y# (2017) Phototropin perceives temperature based on the lifetime of its photoactivated state. Proc Natl Acad Sci U S A, 114:9206–9211.
Recommended by F1000
☆本論文は、藤井雄太の修士論文・博士論文研究
☆本論文は、小笠原有香の卒業論文研究
☆本論文は、濵島典子の卒業論文・修士論文研究
☆本論文は、田村沙織の卒業論文・修士論文研究

Tanaka H, Sato M, Ogasawara Y, Hamashima N, Buchner O, Holzinger A, Toyooka K & Kodama Y# (2017) Chloroplast aggregation during the cold-positioning response in the liverwort Marchantia polymorpha L. J Plant Res, 130:1061–1070.
☆本論文は、小笠原有香の卒業論文研究
☆本論文は、濵島典子の卒業論文・修士論文研究

Hoshino S#, Takisawa R & Kodama Y (2017) Swarm robotics systems based on collective behavior of chloroplasts. J Robot Mechatron, 29:602–612.

Higa T, Hasegawa S, Hayasaki Y, Kodama Y & Wada M# (2017) Temperature-dependent signal transmission in chloroplast accumulation response. J Plant Res, 130:1061-1070.

2016

Numata K#, Horii Y, Motoda Y, Hirai T, Nishitani C, Watanabe S, Kigawa T & Kodama Y (2016) Direct introduction of neomycin phosphotransferase II protein into apple leaves to confer kanamycin resistance. Plant Biotechnol, 33:403-407.

Kimura S  & Kodama Y# (2016) Actin-dependence of the chloroplast cold positioning response in the liverwort Marchantia polymorpha L. PeerJ, 4:e2513.
☆本論文は、木村俊の卒業論文・修士論文研究

Iizasa S#, Iizasa E, Matsuzaki S, Tanaka H, Kodama Y, Watanabe K & Nagano Y# (2016) Arabidopsis LBP/BPI related-1 and -2 bind to LPS directly and regulate PR1 expression. Sci Rep, 6:27527.

藤井雄太, 児玉豊# (2016) 誤解しないBiFC法のすゝめ：蛍光タンパク質を使ったタンパク質間相互作用イメージング． 植物の生長調節, 51：48-51.
☆本論文は、藤井雄太の卒業論文・修士論文研究

Ng KK, Motoda Y, Watanabe S, Othman AS, Kigawa T, Kodama Y &  Numata K# (2016) Intracellular delivery of proteins via fusion peptides in intact plants. PLoS ONE, 11:e0154081.

Kodama Y# (2016) Time gating of chloroplast autofluorescence allows clearer fluorescence imaging in planta. PLoS ONE, 11: e0152484.

2015

Tsuboyama-Tanaka S,  Nonaka S & Kodama Y# (2015) A highly efficient AgarTrap method for genetic transformation of mature thalli of the liverwort Marchantia polymorpha L. Plant Biotechnol, 32:333-336.
☆本論文は、田中（坪山）祥子の修士論文研究

田中（坪山）祥子, 児玉豊# (2015) アガートラップ法：寒天に捕らえたゼニゴケを簡単に形質転換する．植物の生長調節, 50：83-86. 
☆本論文は、田中（坪山）祥子の修士論文研究

Fujii Y & Kodama Y# (2015) In planta comparative analysis of improved green fluorescent proteins with reference to fluorescence intensity and bimolecular fluorescence complementation ability. Plant Biotechnol, 32:81-87.
☆本論文は、藤井雄太の卒業論文・修士論文研究

Lakshmanan M, Yoshizumi T, Sudesh K, Kodama Y & Numata K# (2015) Double stranded DNA introduction into intact plant using peptide-DNA complexes. Plant Biotechnol, 32:39-45.

Chuah JA, Yoshizumi T, Kodama Y & Numata K# (2015) Gene introduction into the mitochondria of Arabidopsis thaliana via peptide-based carriers. Sci Rep, 5:7751.

Tsuboyama-Tanaka S &  Kodama Y# (2015) AgarTrap-mediated genetic transformation using intact gemmae/gemmalings of the liverwort Marchantia polymorpha L. J Plant Res, 128:337-344.
☆本論文は、田中（坪山）祥子の修士論文研究

2014

Numata K#, Ohtani M, Yoshizumi T, Demura T & Kodama Y (2014) Local gene silencing in plants via synthetic dsRNA and carrier peptide. Plant Biotechnol J, 12:1027-1034.

Tsuboyama S & Kodama Y# (2014) AgarTrap: a simplified Agrobacterium-mediated transformation method for sporelings of the liverwort Marchantia polymorpha L. Plant Cell Physiol, 55:229-236.
☆本論文は、坪山祥子の修士論文研究

2013

Ogasawara Y, Ishizaki K, Kohchi T & Kodama Y# (2013) Cold-induced organelle relocation in the liverwort Marchantia polymorpha L. Plant Cell Environ, 36:1520-1528.
☆本論文は、小笠原有香の卒業論文研究

See also AoB Blog “When the going gets tough….. the organelles get going”
See also AoB Blog “Relocation, relocation, relocation…”

Lakshmanan M, Kodama Y, Yoshizumi T, Sudesh K & Numata K# (2013) Rapid and efficient gene delivery into plant cells using designed peptide carriers. Biomacromolecules, 14:10-16.

Kodama Y# & Hu C-D# (2013) Bimolecular fluorescence complementation (BiFC) analysis of protein-protein interaction: How to calculate signal-to-noise ratio. Methods Cell Biol, 113:107-121. (Protocol)

2012

Kodama Y# & Hu C-D# (2012) Bimolecular fluorescence complementation (BiFC): A 5-year update and future perspectives. Biotechniques, 53:285–298. (Review)

2005-2011 (Prior to working as a PI)

Kodama Y, Suetsugu N & Wada M# (2011) Novel protein-protein interaction family proteins involved in chloroplast movement response. Plant Signal Behav, 6:483-490. (Review)

Kodama Y# (2011) A bright green-colored bimolecular fluorescence complementation assay in living plant cells. Plant Biotechnol, 28:95-98.

Kodama Y# & Hu C-D# (2010) An improved bimolecular fluorescence complementation assay with a high signal-to-noise ratio. Biotechniques, 49:793-805.
See also BioSpotlight in BioTechniques “Venus rising”

Kodama Y*, Suetsugu N*, Kong S-G & Wada M# (2010) Two interacting coiled-coil proteins, WEB1 and PMI2, maintain the chloroplast photorelocation movement velocity in Arabidopsis. Proc Nat Acad Sci USA, 107:19591-19596.

Kodama Y & Wada M# (2009) Simultaneous visualization of two protein complexes in a single plant cell by using multicolor fluorescence complementation analysis. Plant Mol Biol, 70:211-217.

Kodama Y*, Tamura T*, Hirasawa W*, Nakamura K & Sano H# (2009) A novel protein phosphorylation pathway involved in osmotic-stress response in tobacco plants. Biochimie, 91:533-539.

Kodama Y, Tsuboi H, Kagawa T & Wada M# (2008) Low temperature-induced chloroplast relocation mediated by a blue light receptor, phototropin 2, in fern gametophytes. J Plant Res, 121:441-448.

See also Awards for excellence in Journal of Plant Research “Best Paper Awards 2009”

Kodama Y*, Shinya T* & Sano H# (2008) Dimerization of N-methyltransferases involved in caffeine biosynthesis. Biochimie, 90:547-551.

Kodama Y & Sano H# (2007) Functional diversification of a basic helix-loop-helix protein due to alternative transcription during generation of amphidiploidy in tobacco plants. Biochem J, 403:493-499.

See also Commentary Article in Biochemical Journal “Evolutionary tinkering: birth of a novel chloroplast protein”

Kodama Y# (2007) Plastidic proteins containing motifs of nuclear transcription factors. Plant Biotechnol, 24:165-170. (Review)

Kodama Y# & Sano H (2007) A comparative analysis of basic helix-loop-helix proteins, AtPTF1 and NtWIN4, with reference to plastid localization. Plant Biotechnol, 24:335-338.

Yano A, Kodama Y, Koike A, Shinya T, Kim H-J, Matsumoto M, Ogita S, Wada Y, Ohad N & Sano H# (2006) Interaction between methylated-DNA binding protein and Ran GTPase during cell division in tobacco cultured cells. Ann Bot, 98:1179-1187.

See also ContentSnapshots in Annals of Botany “Functions of methyl DNA-binding protein during cell division”

Kodama Y & Sano H# (2006) Evolution of a basic helix-loop-helix protein from the transcriptional repressor to a plastid-resident regulatory factor – involvement in hypersensitive cell death in tobacco plants. J Biol Chem, 281:35369-35380.

Yap Y-K*, Kodama Y*, Waller F*, Chung K-M*, Ueda H*, Nakamura K*, Oldsen M, Yoda H, Yamaguchi Y & Sano H# (2005) Activation of a novel transcription factor through phosphorylation by WIPK, a wound-induced mitogen-activated protein kinase in tobacco plants. Plant Physiol, 139:127-137.