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information biology laboratory
Elucidation of life system using model organism C. elegans

content of reseach

As the decoding of various genome sequences including the human genome has been completed. Recently, the central paradigm of biology is recognized, "Biological information is from DNA to RNA, then to protein, and thus forms cells and individuals". It is essential for the cells formation that two kinds of molecules, “lipids” and “carbohydrates” in addition to protein. And their lipids and carbohydrates are deeply involved in precursors of bioenergy, signal transduction molecules, metabolism, construction of biostructure, and biodiversity. Therefore, it is necessary to expand the core paradigm to include lipids, carbohydrates and complex carbohydrates (glycolipids, glycoproteins, etc...) in order to understand individuals and understand them in an integrated manner (Figure 1). In our laboratory, our goal is to "recreate (reproduce) the life activity program". For that purpose, we are conducting research focusing on the four themes of "understanding of biogeneration system" and "understanding of synthesis pathway and function of glycolipid", "identification of lipid mediator and understanding of physiological function" and "understanding of robustness of metabolic reaction network".

menber

Professor Masahiro ITO

maito●sk.ritsumei.ac.jp(● change to "@")

Lecture(2020 academic year)

【department of university】
Programminig language,Bio algorithm, etc...

Assistant professor Yukihiko KUBOTA

yukubota●fc.ritsumei.ac.jp (● change to "@")

Lecture(2020 academic year)

【department of university】
Biochemistry, Practice of molecular biology, etc..
  • D3

    M. Fahmi

    research theme

    Prediction of protein protein interaction from evolutionary biology

  • M2

    N. Ohta

    research theme

    Analysis of the PAF1 complex during Caenorhabditis elegans oogenesis

  • M2

    G. Yasui

    research theme

    In silico analysis of Rett syndrome-related proteins by data science

  • M1

    A. Ezaki

    research theme

    Elucidation of Gonadal elongation control mechanism by histone deacetylase HDA-2 complex in C.elegans

  • M1

    H. Kitagawa

    research theme

    Phylogenetic profiling analysis of ORF8 interacting proteins in SARS-CoV2

  • M1

    T. Hamasaki

    research theme

    Comparative analysis of cell-type-specific functions of the transcription factor HDA-1 complex during gonadal development in C.elegans

  • Bachelor

    Adachi

    research theme

    Dry research

  • Bachelor

    T.Unno

    research theme

    Wet research

  • Bachelor

    K.Kamashita

    research theme

    Dry research

  • Bachelor

    Y.Takatsuka

    research theme

    Wet research

  • Bachelor

    Y.Takeda

    research theme

    Dry research

  • Bachelor

    Y.Tanaka

    research theme

    Dry research

  • Bachelor

    C.Hamaoka

    research theme

    Dry research

  • Bachelor

    K.Hamanishi

    research theme

    Dry research

  • Bachelor

    S.Yamanaka

    research theme

    Wet research

  • Clerk

    Y. Iwamoto

    research theme

    Recruiting now

achievements

Publication

・Kojima H, Shinohara R, Itonori S, Ito M. Characterization of a Novel Rhamnose-containing Acidic Glycosphingolipid from the Ascidian Halocynthia aurantium. J Oleo Sci. 2017 Mar 1;66(3):285-295. doi: 10.5650/jos.ess16150. Epub 2017 Feb 10.

・Tomono T, Kojima H, Fukuchi S, Tohsato Y, Ito M. Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. Biophys Physicobiol. 2015 Nov 12;12:57-68. doi: 10.2142/biophysico.12.0_57. eCollection 2015.

・Tohsato Y, Ikuta K, Shionoya A, Mazaki Y, Ito M. Parameter optimization and sensitivity analysis for large kinetic models using a real-coded genetic algorithm. Gene. 2013 Apr 10;518(1):84-90. doi: 10.1016/j.gene.2012.11.080. Epub 2012 Dec 27.

・Fahmi M, Ito M. Evolutionary Approach of Intrinsically Disordered CIP/KIP Proteins. Sci Rep. 2019 Feb 7;9(1):1575. doi: 10.1038/s41598-018-37917-5.

・Kubota Y, Nishiwaki K, Ito M, Sugimoto A. The Role of Tissue Inhibitors of Metalloproteinases in Organ Development and Regulation of ADAMTS Family Metalloproteinases in Caenorhabditis elegans. Genetics. 2019 Jun;212(2):523-535. doi: 10.1534/genetics.119.301795. Epub 2019 Apr 16.

・Nomoto Y, Kubota Y, Ohnishi Y Kasahara K, Tomita A, Oshime T, Yamashita H, Fahmi M, Ito M. Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. PLoS One. 2019 Sep 10;14(9):e0215187. doi: 10.1371/journal.pone.0215187. eCollection 2019.

・Fahmi M, Yasui G, Seki K, Katayama S, Kaneko-Kawano T, Inazu T, Kubota Y, Ito M. In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. Int J Mol Sci. 2019 Nov 8;20(22). pii: E5593. doi: 10.3390/ijms20225593.

・Nakamura T, Fahmi M, Tanaka J, Seki K, Kubota Y, Ito M. Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico. Int J Mol Sci. 2019 Dec 13;20(24). pii: E6290. doi: 10.3390/ijms20246290.

・Fahmi M, Kubota Y, Ito M. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV. Infection, Genetics and Evolution. Short communicationAvailable online 3 March 2020.

acquisition of research funds in this year's

MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2015-2019) & Takeda Science Foundation(2019-2021)
Sientific research towards cause investigation and development of therapies for rare and intractable diseases

Prize

Travel follow ship Future of the nematodes studiesin 2018year
Yusuke Nomoto, Yuto Ohnishi
Poster award 2019 Rare disease conferens & International rare disease symposium
Kaito Seki

Join the conference

第6回リン化合物討論会(第33回C-P化合物研究会)(12/20)
[Oral presentation]
・リン酸化以外の翻訳後修飾である糖鎖修飾の進化解析
  Takahiro Nakamura, Jun Tanaka, Masahiro Ito
[Oral presentation]
・初期胚発生におけるセリンスレオニンキナーゼを制御する遺伝子カスケード
  Yusuke Nomoto, Yuto Ohnishi, Masahiro Ito
[Oral presentation]
・C. elegansの初期胚におけるHDAC複合体の転写共役因子依存的な転写調節
  Yuto Ohnishi, Yusuke Nomoto, Masahiro Ito, Yukihiko Kubota
The 41st Annual Meeting of Molecular Biology Society of Japan(11/28-30)
[Poster session]
・Evolutionary Dynamics of Intrinsically Disordered CIP/KIP Family Proteins
  Muhamad Fahmi, Masahiro Ito
[Poster session]
・Evolutionary classification of whole human glycoside hydrolase by phylogenetic profiling
  Takahiro Nakamura, Jun Tanaka, Masahiro Ito
[Poster session]
・Gene cascade analysis with the polarity mediator mex-3 as the top in the Caenorhabditis elegans early embryonic stage
  Yusuke Nomoto, Yuto Ohnishi, Masahiro Ito
[Poster session]
・Transcriptional regulation by HDAC complex depending on transcriptional co-repressor during early embryogenesis in C. elegans
  Yuto Ohnishi, Yusuke Nomoto, Masahiro Ito, Yukihiko Kubota
[Poster session]
・Distribution analysis of missense mutations and adjacent amino acids in intractable diseases
  Kaito Seki, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Functional analysis of PAF-1 complex during Caenorhabditis elegans oogenesis
  Natumi Ohta, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Functional clarification of Rett syndrome causative protein CDKL5 by phylogenetic profiling
  Gen Yasui, Takahiro Nakamura, Yukihiko Kubota, Masahiro Ito
Future of the nematodes studies(9/14-15)
[Poster session]
・Evolutionary classification of human glycoside hydrolase by phylogenetic profiling
  Takahiro Nakamura, Jun Tanaka, Hisao Kojima, Masahiro Ito
[Oral presentation]
・Gene cascade prediction using RNA-Seq data and the WormBase database
  Yusuke Nomoto, Yuto Ohnishi, Masahiro Ito
[Oral presentation]
・Comparative RNA-Seq analysis of HDAC complex scaffold protein during early embryogenesis in Caenorhabditis elegans
  Yuto Ohnishi, Yusuke Nomoto, Masahiro Ito
[Poster session]
・線虫C. elegansは、ヒト稀少・難病の原因となる点突然変異は類似しているのか?
  Kaito Seki, Masahiro Ito
[Poster session]
・Evolution and Comparative Genomics
  Muhamad Fahmi, Masahiro Ito
2018 International Society for Computational Biology(Chicago, USA 2018/07/6-10)
[Poster session]
・Evolutionary classification of human glycoside hydrolase by phylogenetic profiling
  Takahiro Nakamura, Jun Tanaka, Hisao Kojima, Masahiro Ito
[Poster session]
・Gene cascade prediction using RNA-Seq data and the WormBase database
  Yusuke Nomoto, Yuto Ohnishi, Masahiro Ito
[Poster session]
・Comparative RNA-Seq analysis of HDAC complex scaffold protein during early embryogenesis in Caenorhabditis elegans
  Yuto Ohnishi, Yusuke Nomoto, Masahiro Ito
[Poster session]
・Distribution analysis of missense mutations and adjacent amino acids in intractable diseases
  Kaito Seki, Masahiro Ito
[Poster session]
・Evolution and Comparative Genomics
  Muhamad Fahmi, Masahiro Ito

22nd International C.elegans Conference (Los Angeles 2019/6/20-24)
[Poster session]
・Analysis of the PAF1 complex during Caenorhabditis elegans oogenesis
  Natsumi Ota,Masahiro Ito, Yukihiko Kubota
The 13th International Workshop on Advanced Genomics(13AGW)(Tokyo 2019/06/25-27)
[Poster session]
・The evolutionary dynamics of intrinsically disordered CIP/KIP family proteins in vertebrates
  Muhamad Fahmi, Masahiro Ito
[Poster session]
・Evolutionary analysis of CDKL5 related protein by phylogenetic profiling
  Gen Yasui, Takahiro Nakamura, Muhamad Fahmi, Yukihiko Kubota, Masahiro Ito
2019 International Society for Computational Biology(Basel, Switzerland 2019/07/21-25)
[Poster session]
・Assessment of the evolution of RETT syndrome-related proteins disordered regions and the implications of their point mutations
  Muhamad Fahmi, Gen Yasui, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Phylogenetic profiling analysis of Rett syndrome-related proteins
  Gen Yasui, Takahiro Nakamura, Muhamad Fahmi, Yukihiko Kubota, Masahiro Ito
Future of the nematodes studies(Nagoya University, Aich 2019/8/21-22)
[Poster session]
・稀少疾患原因遺伝子における変異解析
  Kaito Seki, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Analysis of the PAF1 complex during Caenorhabditis elegans oogenesis
  Natsumi Ota,Masahiro Ito, Yukihiko Kubota
[Poster session]
・Evolutionary and functional assessment of Rett syndrome-related proteins
  Gen Yasui, Takahiro Nakamura, Muhamad Fahmi, Yukihiko Kubota, Masahiro Ito
2019 Rare disease conferens & International rare disease symposium(Ritsumeikan University:BKC 2019/08/30)
[Poster session]
・Missense mutation analysis for rare disease-causing proteins
  Kaito Seki, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Functional analysis of PAF1 complex using Caenorhabditis elegans
  Natsumi Ota,Masahiro Ito, Yukihiko Kubota
[Poster session]
・Systematic analysis of Rett syndrome-related proteins by data science
  Gen Yasui, Takahiro Nakamura, Muhamad Fahmi, Yukihiko Kubota, Masahiro Ito
The 42nd Annual Meeting of the Molecular Biology Society of Japan(Fukuoka 2019/12/3-6)
[Poster session]
・Rett Syndrome-causing proteins and their pathogenic missense point mutations: structural order disorder, post-translational modifications, and evolutionary rates
  Muhamad Fahmi, Gen Yasui, Kaito Seki, Syouichi Katayama, Takako Kaneko-Kawano, Tetsuya Inazu, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Missense mutations in interictally disorder regions in the causative proteins of rare diseases
  Kaito Seki, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Functional analysis of PAF1 complex in Caenorhabditis elegans
  Natsumi Ota,Masahiro Ito, Yukihiko Kubota
[Poster session]
・Systematic analysis of Rett syndrome-related proteins by data science
  Gen Yasui, Takahiro Nakamura, Muhamad Fahmi, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Evolutionary analysis of causative genes related to rare diseases by phylogenetic profiling
  Hiromu Kitagawa, Gen Yasui, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Evolutionary and intrinsically disordered regions analysis to human complex lipid-metabolism related proteins
  Erika Seki, Chiharu Iwanami, Gen Yasui, Yukihiko Kubota, Masahiro Ito
[Poster session]
・Transcriptional analysis of HDAC complex in Caenorhabditis elegans of embryo development
  Tasuku Hamasaki, Yuto Ohnishi, Masahiro Ito, Yukihiko Kubota, Masahiro Ito

access

The B402 room on the 4th floor of the Biolink,
Ritsumeikan University Biwako, Kusatsu campus.
It is a individual laboratory(link 40 buldings below).
This laboratory is in front of the elevator on the 4th floor.
Phone number:077-561-5301
phone extention:4402(individual laboratory),4415(laboratory)
map of Ritsumeikan University

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