[Supra-assembly of biomolecule] Year Started : 2020

Muneyoshi Ichikawa

Understanding the mechanisms of the ciliary beating at the atomic level.

Researcher
Muneyoshi Ichikawa

Tenure-track professor
School of Life Sciences
Fudan University

Outline

In this project, I will use cryo-electron microscopy to obtain high-resolution stuructures of the ciliary components. By combining with proteome analysis and modeling of the proteins, I will obtain the atomic models of these ciliary components. By fitting these atomic models into whole ciliary axonemal structure obtained by cryo-electron tomography, the atomic model of the whole ciliary axoneme will be obtained. Then, I will understand how the ciliary axoneme is stabilized by molecular dynamics simulations. I will also aim to visualize the real-time conformational change within the cilia to understand the mechanisms of ciliary beating at the atomic level.

Yuka Iwasaki

Higher order structure in heterochromatin formation

Researcher
Yuka Iwasaki

Team Leader
Center for Integrative Medical Sciences
RIKEN

Outline

Heterochromatin is vital to sustaining stable chromosome structure and gene expression patterns, and its dysregulation can cause various diseases. This project aims to characterize higher order nuclear architectural change induced upon small RNA-guided heterochromatin formation in a stepwise manner. Furthermore, I aim to engineer artificial small RNAs that can regulate heterochromatin formation.

Kenichi Umeda

Dynamic Mechanism of SMC Complex Revealed by High-Speed Atomic Force Microscopy

Researcher
Kenichi Umeda

Assistant Professor
Nano Life Science Institute (WPI NanoLSI)
Kanazawa University

Outline

Recently, it has been revealed that liquid-liquid phase separation nature of the structural maintenance of chromosomes (SMC) complexes assumes an important role in the processes of DNA condensation and sister chromatids adhesion. However, the research field of the submolecular-scale formation and destruction process of such a biomolecular liquid phase has been an unattained territory. In this study, I investigate and reveal the dynamic mechanism of SMC related to the liquid phase using newly developed high-speed atomic force microscopy combined with optical tweezers technique.

Yoichi Otsuka

Understanding Live Cell Carcinogenesis with Picofluid Mass Spectrometry Imaging

Researcher
Yoichi Otsuka

Associate Professor
Graduate School of Science Department of Physics
Osaka University

Outline

To understand the essence of cellular biological activity, it is important to measure and analyze the chemical species contained in living cells as multidimensional information to understand their biochemical significance. In this project, I will develop a mass spectrometric imaging technique utilizing pico-liquids and investigate the molecular environment in living cells based on changes in the amounts and types of specific chemical components. We will explore the changes in a variety of lipids, metabolites, and proteins inherent in cancer cells and elucidate their relationship to cell heterogeneity.

Shinji Kajimoto

Quantitative evaluation of local intracellular environments by direct observation of water in a cell

Researcher
Shinji Kajimoto

Associate Professor
Graduate School of Pharmaceutical Sciences
Tohoku University

Outline

In this project, I develop a method for label free quantitative evaluation of intracellular environments by observing water in a cell, and track local changes inside a living cell under chemical and physical stresses, which cause intracellular liquid-liquid phase separation (LLPS). Raman and Brillouin spectral imaging allows the quantitative analysis of water distribution inside a cell, intra- and extra-cellular temperature, local stiffness and so on, as well as changes in molecular structure and interaction. By applying the Raman and Brillouin imaging to living cells under various stresses, I elucidate the mechanism of intracellular droplet formation via LLPS from the molecular to macroscopic level.

Takahiro Kosugi

Understanding and controlling functions of protein complexes in cells by rational design

Researcher
Takahiro Kosugi

Assistant Professor
Institute for Molecular Science
National Institutes of Natural Sciences

Outline

Protein complexes play essential roles in cells. This project aims to understand the functions of protein complexes in cells by creating several rational designed protein complexes of which the functions are controlled and replacing native protein complexes in cells with the designed ones. Furthermore, the obtained knowledge is exploited to develop novel technology to control cells by using the designed protein complexes.

Hotaka Kobayashi

Seeing and controlling RISC function at the single mRNA level

Researcher
Hotaka Kobayashi

Associate Professor
Institute of Advanced Medical Sciences
Tokushima University

Outline

MicroRNAs, a class of small non-coding RNAs, form the ribonucleoprotein complex called RISC, which silences thousands of mRNAs. This project aims to develop novel methods to see and control the function of RISC at the single mRNA level to reveal when and where RISC works in cells.

Masashi Tachikawa

Comprehensive mathematical modeling of mitochondrial morphologies

Researcher
Masashi Tachikawa

Associate Professor
Association of International Arts and Science
Yokohama City University

Outline

Mitochondria are double-membrane-bound organelles providing important cellular functions involving bioenergetics, apoptosis and metabolism. Mitochondria exhibit complex morphology which are considered to correlate with their functions, although it remains elusive. This project aims to develop mathematical models to govern mitochondrial morphologies based on force balances in inner and outer membranes and kinetics of functional molecules, and to reveal the control principle of the morphologies.

Hirokazu Tanimoto

Experimental physics of intracellular structures

Researcher
Hirokazu Tanimoto

Associate Professor
School of Science
Yokohama City University

Outline

This study aims to elucidate physical principles organizing cellular interior by taking an advantage of direct intracellular force measurements.

Masaki Tsuchiya

A flow cytometry-based method using chemical labeling for genetic dissection of cellular lipid dynamics

Researcher
Masaki Tsuchiya

Associate Professor
School of Pharmaceutical Sciences
University of Shizuoka

Outline

Translocation of lipid molecules across and between cellular membranes is critical for many biological functions. However, due to technological difficulties in directly detecting lipids in a cellular context, molecular machineries that govern intracellular lipid transport remain elusive. In this project, I aim to develop a novel method to quantify lipid dynamics at subcellular resolution in living cells. By using chemical tools to fluorescently label lipids at the organelle level, I will construct a flow cytometry-based platform for high-throughput measurement of lipid distribution within cells. Coupled with CRISPR screening, this technology can allow for the unbiassed discovery and comprehensive assessment of genes underlying cellular lipid dynamics and localization.

Ryo Nishihara

Development of peptide probes containing luminescent reaction sites

Researcher
Ryo Nishihara

Senior Researcher
Health and Medical Research Institute‚Äč
National Institute of Advanced Industrial Science and Technology (AIST)

Outline

This project aims to develop novel peptide probes containing luciferase activity based on the amino acid sequences involved in bioluminescence reactions, which were originally found in proteins present in non-luminous organisms. In addition, bioluminescence emission color and intensity will be controlled by combining novel peptide probes with rationally designed and synthesized luciferin molecules. With the use of such novel bioluminescence probes, I aim to establish a bioluminescence imaging platform that can monitor dynamic structural changes in intracellular proteins.

Taki Nishimura

Elucidating the molecular machinery underlying dynamic organelle network formation

Researcher
Taki Nishimura


PRESTO Researcher, Japan Science and Technology Agency

Outline

Organelle contact sites provide an optimal environment for individual organelles to communicate with each other and exchange small molecules, such as ions and lipids. However, it is still challenging to analyze the formation of physiological contact sites in live cells and to measure their impact on changes in membrane lipid organization. To overcome the difficulties, in this study, a detection tool for contact sites will be newly developed based on a reversible split-fluorophore. A method strategy to generate a lipid probe on demand will be also established. Thus, this research aims to deepen the understanding of organelle network formation by developing tools for the detection of organelle contact sites and membrane lipids in live cells.

Makito Miyazaki

Dissecting the regulatory mechanism of the actin cytoskeleton using an in vitro reconstitution approach

Researcher
Makito Miyazaki

Team Leader
Center for Biosystems Dynamics Research
RIKEN

Outline

The actin cytoskeleton is an essential intracellular structure that regulates various key functions of animal cells including motility, division, and polarity establishment. In this project, using an in vitro reconstitution approach, I aim to understand the regulatory mechanism of cellular functions controlled by the actin cytoskeleton. This project will contribute to the development of a novel method to manipulate key functions of living cells by perturbing the actin cytoskeletal dynamics.

Yamato Yoshida

Insights into molecular mechanisms of organelle division rings

Researcher
Yamato Yoshida

Associate Professor
Graduate School of Science
The University of Tokyo

Outline

Due to their evolutionary origin, mitochondria and plastid do not multiply de novo but through the division of pre-existing these organelles. Proliferation of these organelles is executed by ring-shaped cellular machineries termed the mitochondrial-division machinery and the plastid-division machinery. However, the mechanical details of the division machineries are still not fully understood. In particular, the kinetics and dynamics of the division machineries are almost completely unknown. The project aims two goals; (1) insights into molecular mechanisms of the division machineries using quantitative high-resolution imaging approaches; (2) comprehensive identification of genes which are involved in organelle proliferation processes by system-wide approaches. Expected findings from the project will be a trigger to know how eukaryotic cells generate and permanently maintain membrane-bounded organelles.

Masataka Yanagawa

Multicolor single molecule imaging of GPCR signalosome dynamics

Researcher
Masataka Yanagawa

Associate Professor
Graduate School of Pharmaceutical Sciences
Tohoku University

Outline

GPCRs control multiple signaling pathways via higher-order structures (signalosomes) with various signaling molecules in cell. Recently, the biased signaling by drugs has been reported in many GPCRs as targets, which is a key concept in current drug discovery. However, the mechanism of the biased signaling is unclear. In this project, developing a multicolor single molecule imaging system, I will analyze the dynamics changes of GPCR signalosome upon ligand stimulation. This project will provide a novel insight into the molecular mechanism of the biased signaling by GPCRs.

Takeshi Yokoyama

Comprehensive understanding of ribosomes with their dynamic structures and subcellular distributions.

Researcher
Takeshi Yokoyama

Assistant professor
Graduate School of Life Sciences
Tohoku University

Outline

Various macromolecular assemblies coordinately function in maintaining cellular homeostasis. The ribosome is the RNA-based supercomplex, which is resposnsible for protein synthesis. This project aims to develop a comprehensive understanding of translational machineries in their native environment by using cryo-electron microscopy, obtaining high resolution structures of ribosomes with their cellular coordinates. The development of the RNA engineering-based new technology makes possible to determine the coodinate of translating ribsomes on spesific mRNAs in the cell. The goal of this project is to visualize their dynamic behavior at high resolution in native environment, which leads to new biological insights.

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