IRIE lab


 

A LITTLE ABOUT OUR GROUP


Evo-Devo: Are there any general rules between ontogeny (embryogenesis) and phylogeny (evolution)? Some say that we passed through fish-like stage when we were fetus, but does this have something to do with our evolutionary history?
Evolvability: Bodyplan evolution seems to be very conservative when compared to other features (e.g. size, coat color), but why? Can we quantitate which animals, phenotypes, or developmental system tends to evolve more? Is it possible that we quantitate evolvability (or constrained status) of animal features?
Evolvedness: Which developmental systems of animal species are more evolved? Can we say tadpole stage of frogs are more ancestral, and later stages (e.g., adult) are more evolved?
Microchimerism: We are chimera by nature, having maternal cells in our body, but what are the roles of these microchimeric cells? Is there a possibility that maternal cess are involved in an onset/progress of fetal disease?

We study whatever we feel it interesting, and we welcome students with strong curiosity. We are waiting for your contact.

MAJOR FINDINGS & PRPOSED IDEAS




RULE IN
EMBRYONIC EVOLUTION
TURTLE EVOLUTION
MICROCHIMERISM &
CONGENITAL DISEASE
GENE REGULATION
AND BIRD EVOLUTION




PUBLICATIONS


The list here is not to flaunt my modest achievements, but to obtrain scientific feedbacks (preferably constructive criticism) from you.
I'm wanting to explore an exciting scientific adventure over the discussions. Thank you :)
      *: corresponding author



Remaining questions related to the hourglass model in vertebrate evolution.
Naoki Irie*
Current Opinion in Genetics & Development, 45:103-107, (2017)

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
Ryohei Seki, Cai Li, Qi Fang, Shinichi Hayashi, Shiro Egawa, Jiang Hu, Luohao Xu, Hailin Pan, Mao Kondo, Tomohiko Sato, Haruka Matsubara, Namiko Kamiyama, Keiichi Kitajima, Daisuke Saito, Yang Liu, M. Thomas P. Gilbert, Qi Zhou, Xing Xu, Toshihiko Shiroishi, Naoki Irie*, Koji Tamura* & Guojie Zhang*
Nature Communications, 114229, (2017)

Unexpected link between polyketide synthase and calcium carbonate biomineralization
Motoki Hojo, Ai Omi, Gen Hamanaka, Kazutoshi Shindo, Atsuko Shimada, Mariko Kondo, Takanori Narita, Masato Kiyomoto, Yohei Katsuyama, Yasuo Ohnishi, Naoki Irie and Hiroyuki Takeda
Zoological Letters, 1:3, (2015)

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
Richard E. Green, Edward L. Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W. Vandewege, John A. St. John, Salvador Capella-Gutiérrez, Todd A. Castoe, Colin Kern, Matthew K. Fujita, Juan C. Opazo, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Robert M. Hubley, Arian F. Smit, Roy N. Platt, Christine A. Lavoie, Meganathan P. Ramakodi, John W. Finger Jr., Alexander Suh, Sally R. Isberg, Lee Miles, Amanda Y. Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C. Burgess, Scott V. Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T. Howard, Cathy R. Gresham, Daniel G. Peterson, Jürgen Schmitz, David D. Pollock, David Haussler, Eric W. Triplett, Guojie Zhang, Naoki Irie, Erich D. Jarvis, Christopher A. Brochu, Carl J. Schmidt, Fiona M. McCarthy, Brant C. Faircloth, Federico G. Hoffmann, Travis C. Glenn, Toni Gabaldón, Benedict Paten, and David A. Ray
Science, 12 December Vol. 346 no. 6215 (2014)


The developmental hourglass model: a predictor of the basic body plan?
Naoki Irie*, and Shigeru Kuratani
Development, 141:4649-4655 (2014)

The Evolutionary Origin of the Vertebrate Body Plan: The Problem of Head Segmentation
Takayuki Onai, Naoki Irie , and Shigeru Kuratani
Annual Review of Genomics and Human Genetics, Vol. 15: 443-459 (2014)


Turtle ghrelin
Juan Pascual-Anaya, Amonida Zaddissa, Bronwen Aken, Guojie Zhang and Naoki Irie*
Nature Genetics, 46,526 (2014)


The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
Zhuo Wang, Juan Pascual-Anaya, Amonida Zadissa, Wenqi Li, Yoshihito Niimura, Zhiyong Huang, Chunyi Li, Simon White, Zhiqiang Xiong, Dongming Fang, Bo Wang, Yao Ming, Yan Chen, Yuan Zheng, Shigehiro Kuraku, Miguel Pignatelli, Javier Herrero, Kathryn Beal, Masafumi Nozawa, Juan Wang, Hongyan Zhang, Lili Yu, Shuji Shigenobu, Junyi Wang, Jiannan Liu, Paul Flicek, Steve Searle, Jun Wang, Shigeru Kuratani, Ye Yin, Bronwen Aken, Guojie Zhang, Naoki Irie*
Nature Genetics, 45(6):701-706, 2013
<Corrigendum to this paper has been published on 2014 May 28th>


Emerging Questions in Materno-Fetal Microchimerism <Review Article>
Naoki Irie*
Reproductive System & Sexual Disorders, S1:002 (2011)

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis.
Naoki Irie*, Shigeru Kuratani
Nature Communications, 2 : 248., 2011 + (Erratum)


Reviews of Biliary Atresia: A New Immunological Insight on Etiopathogenesis
Toshihiro Muraji, David L. Suskind, and Naoki Irie
Expert Review of Gastroenterology & Hepatology, Dec; 3(6): 599-606. (2009)


Maternal HLA class I compatibility in patients with biliary atresia.
Naoki Irie, Toshihiro Muraji, Naoki Hosaka, Yasutsugu Takada, Seisuke Sakamoto, Kohichi Tanaka
Journal of Pediatric Gastroenterology & Nutrition, Volume 49, Issue 4, 488-492 (2009)

Maternal Microchimerism in Underlying Pathogenesis of Biliary Atresia: Quantification and Phenotypes of Maternal Cells in the Liver.
Toshihiro Muraji, Naoki Hosaka, Naoki Irie, Makiko Yoshida, Yukihiro Imai, Kohichi Tanaka, Yasutsugu Takada, Seisuke Sakamoto, Hironori Haga, Susumu Ikehara
Pediatrics, Mar 1; 121, 3 (2008)


The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information
Naoki Irie and Atsuko Sehara-Fujisawa
BMC Biology, 5:1, 12 January (2007)


Fused protein of PKC activation loop and PDK1-interacting fragment (AL-PIF) functions as a pseudosubstrate and an inhibitory molecule for PDK1 when expressed in cells
Takahiro Seki, Naoki Irie, Kyoko Nakamura, Hiroshi Sakaue, Wataru Ogawa, Masato Kasuga, Hideyuki Yamamoto, Shiho Ohmori, Naoaki Saito, and Norio Sakai
Genes to Cells, 11: pages 1051-1070, Sep (2006)


Essential roles of Meltrin beta (ADAM19) in heart development.
Kazuto Kurohara, Kouji Komatsu, Tomohiro Kurisaki, Aki Masuda, Naoki Irie, Masahide Asano, Katsuko Sudo, Yo-ichi Nabeshima, Yoichiro Iwakura, and Atsuko Sehara-Fujisawa
Developmental Biology, Volume 267, Issue 1, pages 14-28 (2004)


Subtype- and species-specific knockdown of PKC using short interfering RNA
Naoki Irie, Norio Sakai, Takehiko Ueyama, Taketoshi Kajimoto, Ysuhito Shirai, and Naoaki Saito
Biochem Biophys Res Commun, 298(5): pages 738-43 (2002)

 

 

COLLABORATORS


TURTLE GENOME PROJECT
EXPANDE PROJECT
Echinoderm PROJECT




 

BOOKS / BOOK SECTIONS



胎児期に刻まれた進化の痕跡

慶應大学出版会(入江直樹)


生体の科学 Vol.66 No.3 2015
[特集] 進化と発生からみた生命科学
発生進化の法則性と謎
-発生砂時計モデル-
(内田唯, 入江直樹)

 


The turtle evolution - a conundrum in vertebrate Evo-Devo.
“New Principles in Developmental Processes" Springer, 2014. (Naoki Irie, Hiroshi Nagashima, Shigeru Kuratani)

細胞工学 2014年 1月号 p.84-88 <秀潤社>
[特集] 生命システムのロバストネスとは何か?
「胚発生のロバストネスは進化にバイアスをかけているか?」(入江直樹)

National Geographic Nov. 2013
"Shell Life" by Johnna Rizzo

 


遺伝 2013年 3月号
「脊椎動物ファイロタイプとボディプラン進化」 (入江直樹, 倉谷滋)
2013.Mar. Vol.67, No.2, p.178-182


物理科学月刊誌 パリティ 2013年1月号 p.66-68
[特集] 物理科学、この1年 <丸善出版>
進化と発生の関係性定式化にみる生物のやわらかさ」(入江直樹) 
"Special Number: Physics of this year"

実験医学 2011年 7月号 <羊土社出版>
次世代シークエンサー活用術 (八谷剛史、入江直樹、荒川和晴)
Experimental Medicine 2011 July
Effective utilization of next-generation sequencers

実験医学 2011年4月号 <羊土社出版>
母児間マイクロキメリズムが問いかける自己と他者 免疫学・再生医学・臨床医学への展開 (入江直樹、連利博) 2011 Vol.29 No.6 955-960
Experimental Medicine 2011 <YODOSHA>

実験医学 2008年 3月号 p555-560 <羊土社出版> 
ImageJを用いた組織切片画像の三次元データ化 (入江直樹、小松紘司、瀬原淳子)
(3D transformation of serial section data using ImageJ )

発生生物学がわかる <羊土社出版> 2003/12, p83-88
第5章 中胚葉系器官形成 1) 筋肉系形成 (入江直樹、瀬原淳子)

Newspaper / Press Releases / Other


  • 日本経済新聞、財形新聞、日本の研究.com (2017 Feb.7)
  • Yahoo!ニュース、BIGLOBEニュース、日経バイオテクONLINE、ライブドアニュース、ニフティニュース、ギズモードジャパン、Beagle-HC (2017 Feb.8)
  • Quantitative Biology: Dynamics of living systems (Frontier, 2016 Jun.02)
  • 日経サイエンス 2013 8月号 「国内ニュースウォッチ」
  • 日経新聞、朝日新聞、毎日新聞、産経新聞、読売新聞、NNNニュース (2013.Apr.29)
  • 研コミュ白書 NGS現場の会 (荒川和晴、入江直樹、谷上賢瑞、中村昇太)
    細胞工学 vol.31 No.9 (2012) p.1060-1063
  • NIKKEI Newspaper
    日本経済新聞 (日曜朝刊・科学欄) ~ナゾ科学~ 阿修羅や八岐大蛇、なぜいない? 2011.Jul.10 (in Japanese)
  • RIKEN Research [PDF] 2011.June Vol.6 Num. 6
  • 科学新聞 4月15日夕刊:「脊椎動物の進化的に保存された発生段階は咽頭胚期 –理研スパコン使って明らかに-」
  • RIKEN News 2011.Mar.30 (in Japanese)
  • 新学術領域・複合適応形質進化の遺伝子基盤解明 ニュースレター Vol.2 No. S1 号外 [PDF] (in Japanese)

     

FOLLOW YOUR CURIOSITY


 

LAB MEMBERS





Naoki Irie

CV
Associate Professor
mail


Masahiro Uesaka

CV
PostDoc
mail


Yui Uchida


D1 (JSPS DC1 researcher)
mail


Flore Castellan


D1
mail

Saori Kurihara


M2

mail

Kana Fujimoto


M1

mail

PROTOCOLS


Xenopus tropicalis IVF (In vitro fertilization)




HONGO, TOKYO, JAPAN.


 


THANKS FOR VISITING US


See you again

Contact Information


113-0033
7-3-1 Bunkyo-ku, Hongo 3cho-me, Tokyo, Japan
University of Tokyo, School of Science, Bld.2

Map


IRIE lab. - University of Tokyo, School of Science, Department of Biological Sciences