Hideaki Kato

Development of magnetogenetics technologies

Research Director

Hideaki Kato

Collaborator

Teruhiro Okuyama	Associate Professor Institute for Quantitative Biosciences The University of Tokyo
Susumu Yoshizawa	Associate Professor Graduate School of Frontier Sciences The University of Tokyo

Outline

We aim to pioneer a novel cell manipulation technique termed magnetogenetics. Our primary focus will be on analyzing the molecular mechanisms of magnetic receptors found in nature. Based on our findings, we will create magnetogenetics tools to control various cell activities. To evaluate the effectiveness of these tools, we will conduct experiments on both cultured cells and living animals.

Kotaro Kimura

Session with the worm’s brain through ultra-fast optical call & response

Research Director

Kotaro Kimura

Collaborator

Hiromasa Oku	Professor Faculty of Informatics Gunma University
Yuki Tsukada	Senior Assistant Professor Department of Biosciences and Informatics Keio University

Outline

The essence of brain function is the coordination of distributed and autonomous activities in various multiple regions, but our understanding of this remains limited. In this project, we regard the distributed and autonomous activities of the brain as a jazz session in which multiple autonomous performers cooperate to compose music, and aim to establish techniques where researchers engage with brain activity through a ‘call & response’ strategy, steering brain functions in desired directions, starting with studies on nematode C. elegans, which have simple brains.

Hirohide Saito

Construction of Functional RNA/RNP Evolution Platform and Development of Cell Regulation Technology

Research Director

Hirohide Saito

Collaborator

Shungo Adachi	Chief Research Institute National Cancer Center Japan Research Institute
Michiaki Hamada	Professor Faculty of Science and Engineering Waseda University
Hirohide Saito	Professor Institute for Quantitative Biosciences (IQB) The University of Tokyo／ Professor Center for iPS Cell Research and Application (CiRA) Kyoto University

Outline

In this study, we utilize AI models, synthetic biology, and large-scale analysis techniques to discover and create RNAs and RNPs with new functions. In particular, we have developed a unique AI model called “RNA & RNP Generator” to search for and generate RNAs & RNPs that express desired functions. These findings will be applied to gene expression regulation and cellular manipulation techniques. Through this research, we aim to build an “RNA & RNP Evolution Platform” that combines experimentation and AI, and we will develop cellular control mechanisms and manipulation techniques based on RNA & RNP.

Moritoshi Sato

Opto-microorganism development for optogenetic intervention and application in vivo

Research Director

Moritoshi Sato

Collaborator

Makoto Takeda	Professor Graduate School of Medicine The University of Tokyo
Masayuki Yazawa	Associate Professor Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai

Outline

We will develop opto-microorganisms that can be manipulated by light and demonstrate their potential for applications such as cancer drug discovery and drug discovery for infectious diseases by performing significant functional modification of microorganisms using directed evolution and by introducing novel optical manipulation technologies.

Kumiko Tsukui

Manipulating parasites

Research Director

Kumiko Tsukui

Collaborator

Shiroh Iwanaga	Professor Research Institute for Microbial Diseases Osaka University
Hirotaka Kanuka	Professor School of Medicine Jikei University
Haruhiko Maruyama	Professor Faculty of Medicine University of Miyazaki

Outline

We aim to establish manipulation methods for two protozoa and three helminths, and confer useful functions along with taking advantage of their characteristics. Parasites have coevolved with their hosts and acquired ingenious strategies, which allow for completing a unique parasitic life cycle. Their diverse survival strategies are attractive from perspectives of basic and applied science, but there are still technical issues to be clarified. In this research project, to break through these issues, we attempt to develop genome editing technology in parasite species, for which manipulation techniques are still underdeveloped, which enable us to utilize the parasite’s survival strategies. We expect that our developed technologies will open new avenues in parasite biology, which will be useful for future science.

Hiroshi Nishimasu

Genome eingineering using novel DNA recombinases

Research Director

Hiroshi Nishimasu

Collaborator

Sadao Ota	Associate Professor Research Center for Advanced Science and Technology The University of Tokyo
Kotaro Tsuboyama	lecturer Institute of Industrial Science The University of Tokyo
Hirofumi Nishizono	Lecturer Medical Research Institute Kanazawa Medical University

Outline

In this study, we will perform genome mining, functional analysis, and cryo-EM structural analysis of various DNA recombinases to elucidate their DNA recombination mechanisms. In addition, we will attempt structure-based molecular engineering to create recombinase variants with improved functionality and develop efficient DNA knock-in technologies. Finally, we aim to establish therapeutic methods for genetic diseases caused by large-scale genome deletions.

Nozomu Yachie

DNA Event Recorder Cell

Research Director

Nozomu Yachie

Collaborator

Daichi Inoue	Professor Graduate School of Frontier Biosciences Osaka University
Ryosuke Kojima	Associate Professor Graduate School of Medicine The University of Tokyo
A. Etsuo Susaki	Professor Graduate School of Medicine Juntendo University
Toshiro Moroishi	Professor Faculty of Life Sciences Kumamoto University

Outline

A significant challenge that modern biology faces is the inability to directly observe the sequence of events that occur within cellular structures. Current methods used to observe the molecular profiles of cells require the destruction of the samples at the time of observation. To tackle this challenge, we aim to establish “DNA event recording” systems, by which high-resolution molecular and cellular information from individual cells within a multicellular organism can be progressively stored on synthetic “DNA tapes.” Such a system permits the historical information of cells to be read out through high-throughput DNA sequencing. Our goal is to obtain a high-content map of the developmental cell lineage and cell differentiation trajectories throughout the entire process of mouse development.