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6th
NanoLSI
Symposium
Nanoprobe Technology
for Understanding
Molecular Systems

6th
NanoLSI
Symposium
Nanoprobe Technology for Understanding
Molecular Systems

NOVEMBER

14-15, 2022
VENUE
ANA CROWNE PLAZA HOTEL KANAZAWA, JAPANHYBRIDFLEXIBLE FORMAT

6th NanoLSI Symposium
November 14, 2022

DAY 1

8:30 AM

Reception opening and arrival tea

9:00 AM

Opening remarks: Prof. Takeshi Fukuma, Director of NanoLSI

9:10 AM

Session #1 9:10AM -11:10AM
Prof. Takeshi Fukuma & Prof. Yasufumi Takahashi
Probing Inside of Living Cells by SPM

Chairperson:
Session theme:

Prof. Ricardo Garcia (Instituto deCiencia de Materiales de Madrid, CSIC)
Advances in Single Cell Nanomechanics: Subsurface Imaging and Nanorheology
Prof. Hiroshi Uji-i (Hokkaido University)
Remote Excitation Single Cell Endoscopy
Assoc. Prof. Paolo Actis (University of Leeds)
Longitudinal Single-Cell Profiling with a Nanobiopsy Platform
Prof. Takeshi Fukuma (NanoLSI, Kanazawa University)
Intracellular Structures and Mechanics of Living Cells Investigated by Nanoendoscopy-AFM

11:10 AM
1:00 PM

Lunch

Poster session
Session #2
Chairperson:
Session theme:

1:00PM -3:00PM
Assoc. Prof. Hitoshi Asakawa & Assoc. Prof. Satoshi Arai
Molecular Assemblies and Reactions in Various Dimensional Spaces
Prof. Steven De Feyter (KU Leuven)
Formation and Functionalization of 2D Materials: A Molecular Approach
Assoc. Prof. Satoshi Arai (NanoLSI, Kanazawa University)
Subcellular Thermometry and Nanoheating Using Functional Dyes
Prof. Shiki Yagai (Chiba University)
Synthetic Supramolecular Polymers with Diverse Topological Features
Assoc. Prof. Hitoshi Asakawa (NanoLSI / NanoMaRi, Kanazawa University)
Molecular Pockets in 2D Supramolecular Assemblies Investigated by 3D-AFM

3:00 PMTea break

3:20 PM

Session #3
Chairperson:
Session theme:

3:20PM -5:20PM
Asst. Prof. Holger Flechsig
Theory and Modelling of Intracellular Dynamics
Dist. Prof. Tsvi Tlusty (Ulsan National Institute of Science and Technology)
The Collective Dynamics of Enzymatic Nano-Machines
Asst. Prof. Chiho Watanabe (Hiroshima University)
Cell-Size Space Effect on Molecular Diffusion and Liquid-Liquid Phase Separation
Dr. Tatsuo Shibata (RIKEN Center for Biosystems Dynamics Research)
Emergence of Cell Chirality from the Spatial Organization of Actin and Myosin Cytoskeleton
Prof. Ralf Metzler (University of Potsdam)
Beyond Brownian Motion: From Data to Models

5:40 PM

Banquet5:40PM -7:10PM

Banquet toast:04

Prof. Yoshihiro Fukumori, Vice Director of NanoLSI※ pre-registration required.

November 15, 2022

8:30 AM

Reception opening and arrival tea

9:00 AM

Session #4 9:00AM -11:00AM

DAY 2

Chairperson: Prof. Richard W. Wong
Session theme: Recent Advances in Nuclear Biology
Prof. Robert Goldman (Northwestern University Feinberg School of Medicine)Intermediate Filament Networks Connect the Nucleus to the Cell Cortex
Prof. Ohad Medalia (University of Zurich)
The Remarkable Structure and Mechanics of Nuclear Lamin Filaments
Assoc. Prof. Takeshi Shimi (Tokyo Institute of Technology)
The Role of A-Type Lamins in Repair of Nuclear Envelope Ruptures
Assoc. Prof. Hanae Sato (NanoLSI, Kanazawa University)
Real-Time Imaging of Transcriptional Feedback in Nonsense-Mediated mRNA Decay

11:00 AM
1:30 PM

Lunch

Poster session
Session #5 1:30PM -3:00PM

Prof. Mikihiro Shibata & Prof. Noriyuki Kodera
Chairperson:
Session theme: Nanoprobe Technology for Understanding Neurosience
Dr. Atsushi Miyawaki (RIKEN Center for Brain Science)
Cruising in the Cell
Prof. Mikihiro Shibata (NanoLSI, Kanazawa University)
Correlation between Function and Mobility of Protein Complex Revealed by HS-AFM
Prof. Yasufumi Takahashi (NanoLSI, Kanazawa University / Nagoya University)
Development of Organelle Collection Technology Using Nanopipette

3:00 PM

Closing remarks: Overall Organizer Prof. Mikihiro Shibata
Photo session

Pre-eventNovember 13, 2022 4:00 PM - 5:00 PM

Optional lab tour @ NanoLSI Building, Kakuma Campus, Kanazawa University

05

06

ABSTRACTS

P 08

Ricardo Garcia

/

P 10

Hiroshi Uji‐i/

Hokkaido University

P 12

Paolo Actis/

University of Leeds

P 14

Takeshi Fukuma/

NanoLSI, Kanazawa University

P 16

Steven De Feyter/

KU Leuven

P 18

Satoshi Arai/

NanoLSI, Kanazawa University

P 20

Shiki Yagai/

Chiba University

P 22

Hitoshi Asakawa

P 24

Tsvi Tlusty

P 26

Chiho Watanabe

/

P 28

Tatsuo Shibata/

RIKEN Center for Biosystems Dynamics Research

P 30

Ralf Metzler

University of Potsdam

P 32

Robert Goldman/

Northwestern University Feinberg School of Medicine

P 34

Ohad Medalia/

University of Zurich

P 36

Takeshi Shimi/

Tokyo Institute of Technology

P 38

Hanae Sato/

NanoLSI, Kanazawa University

P 40

Atsushi Miyawaki/

RIKEN Center for Brain Science

P 42

Mikihiro Shibata/

NanoLSI, Kanazawa University

P 44

Yasufumi Takahashi/

Instituto de Ciencia de Materiales de Madrid, CSIC/

NanoLSI / NanoMaRi, Kanazawa University

Ulsan National Institute of Science & Technology/

Hiroshima University/

NanoLSI, Kanazawa University / Nagoya University

07

Ricardo Garcia

https://wp.icmm.
csic.es/forcetool/

Professor of Nanoscience and Nanotechnology
Instituto de Ciencia de Materiales de Madrid, CSIC, Spain

E-mail: r.garcia@csic.es
Website: https://wp.icmm.csic.es/forcetool/

Research Interests
Atomic force microscopy, Nanomechanics, Biophysics, Solid-liquid interfaces, Scanning probe lithography

Education
1990

PhD in Physics, Universidad Autonoma de Madrid, Madrid, Spain

Professional Experience2014 - present
2004 - 20132002 - 2004
1994 - 2001
1991 - 19931990 - 1991

Professor of Nanoscience, Instituto de Ciencia de Materiales de Madrid/CSIC/Spain
Professor, Instituto de Microelectrónica de Madrid/CSIC/Spain
Research Scientist, Instituto de Microelectrónica de Madrid/CSIC/Spain
Tenured Scientist, Instituto de Microelectrónica de Madrid/CSIC/Spain
Post-Doctoral Associate, Institute of Molecular Biology/University of Oregon/USA
Post-Doctoral Fellow/ Dept. Chemistry/University of New Mexico/USA

Honors
2019
2016
2013
2011
2010
2007

Beller Lectureship Award, American Physical Society/USA
Nanotechnology Recognition Award, American Vacuum Society/USA
ERC Advanced Grant, European Research Council
Achievement Recognition Award, CSIC/Spain
Nanotechnology Prize, Regional Government of Madrid/Spain
Fellow, American Physical Society/USA

Publications

08

1.

Gisbert, V.G.; Benaglia, S.; Yhlig, M.R.; Proksch, R.; Garcia, R. High-speed nanomechanical mapping of the early stages of collagen
growth by bimodal force microscopy. ACS Nano 2021, 15, 1850-1857.

2.

Garcia, P.D.; Guerrero, P.D.; Garcia, R. Nanorheology of living cells measured by AFM-based force–distance curves. Nanoscale
2020, 12, 9133-9143.

3.

Garcia, R. Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications. Chemical
Society Reviews 2020, 49, 5850-5884.

4.

Uhlig, M.R.; Martin-Jimenez, D.; Garcia, R. Atomic-scale mapping of hydrophobic layers on graphene and few-layer MoS2 andWSe2 in water. Nature Communications 2019, 10, 2606.

5.

Fukuma, T. & Garcia, R. Atomic-and molecular-resolution mapping of solid–liquid interfaces by 3D atomic force microscopy. ACS
Nano 2018, 12, 11785-11797.

Advances in Single Cell Nanomechanics:
Subsurface Imaging and Nanorheology
Ricardo Garcia
Instituto de Ciencia de Materiales de Madrid, CSIC, Madrid, Spain

The development of high-resolution, label-free, quantitative and subsurface microscopy methods ofliving cells remains a formidable problem. Force microscopy-based measurements are contributing toour understanding of single cell properties. However, current AFM-methods have several limitations.
First, the spatial resolution is in the 100 nm range. Second, the description of a cell is restricted to its
elastic properties which implies that the measurements are semi-quantitative. Third, AFM does notprovide images of intracellular structures (sub-surface).
This presentation introduces an integrated approach to overcome those limitations. We present a
method to determine the complete nanomechanical response of a cell from a force-distance curve.
The method incorporates the cell’s finite-thickness, a power-law nanorheology model and thedeformation history of the cell. It transforms the experimental data into viscoelastic parameters of thecell as a function of the indentation frequency. The method enables to generate three-dimensional
maps of eukaryotic cells.

References09Hiroshi Uji-i

https://www.es.
hokudai.ac.jp/labo/
lnn/Top_English.html

https://sites.google.
com/site/hiroshisgroup/

Professor
RIES, Hokkaido University, Japan
Department of Chemistry, KU Leuven

E-mail: hiroshi.ujii@es.hokudai.ac.jp, hiroshi.ujii@kuleuven.beWebsite: https://www.es.hokudai.ac.jp/labo/lnn/Top_English.html
https://sites.google.com/site/hiroshisgroup/

Research Interests
Nanoscopy, Plasmonics, Single molecule spectroscopy

Education
2002
1999

PhD, Department of Chemistry, Tohoku University, JapanMs, Department of Applied Physics, Osaka University, Japan

Professional Experience
2015 - present
2011- present
2004 - 2011

Full Professor, Research Institute for Electronic Science (RIES), Hokkaido University, Japan

2002 - 2004

Post-Doctoral Research Fellow, Katholieke Universiteit Leuven (KULeuven) Belgium

Research Professor (‘hoofddocent’), Katholieke Universiteit Leuven (KULeuven) Belgium
Senior Post-Doctoral Researcher for Center of Excellence
Katholieke Universiteit Leuven (KULeuven) Belgium

Honors
2015
2009

ERC starting grant “Plasmonics-based Energy Harvesting for Catalysis: PLASMHACAT”
PRESTO/JST

Publications
His research activity has been published in over 150 peer-reviewed international journals and three book chapters (h-index of 43 (web ofscience)).5 publications related to Endoscopy

10

1.

Nanoscale, 2022. 14, 5439 - 5446

2.

ACS Applied Nano Materials 2021, 4, 9, 9886–9894.

3.

Analytical Chemistry, 2021, 93, 12, 5037–5045

4.

Nature Communications, 2015, 6, 6287.

5.

Nano Letters, 2009, 9, 995 - 1001.

Remote Excitation Single Cell Endoscopy
Hiroshi Uji-i
RIES, Hokkaido University, Sapporo, JapanKU Leuven, Leuven, Belgium
iCeMS, Kyoto University, Kyoto, Japan

Silver nanowires (AgNWs) serve as plasmonic waveguides for propagating surface plasmon
polaritons (SPPs), allowing the spatial confinement and transfer light energy over micrometer distancethrough the structures below sub-diffraction limited diameter. In addition to this, surface plasmon
allows us to concentrate light energy in nanometer regions, such as at the nanowire end, leading to a
massive enhancement of electromagnetic filed that can be used for surface enhanced Raman
scattering (SERS) or fluorescence (SEF) spectroscopy/microscopy.
In this contribution, we will discuss noble nanoscopic techniques using a combination of SERS/SEF
detection and sub-diffraction limit SPPs waveguiding for spectroscopic/microscopic. Specifically, wedemonstrate that SPPs launched along an AgNW can remotely excite SERS [1] and SEF [2] in thevicinity of the nanowire surface due to the SPPs wave-guiding effect. The ability to transfer SERS/SEF
excitation over several microns will be discussed with respect to single-cell endoscopy, understandingof the interaction between anti-cancer drug molecules and cellular components such as DNA for
drug delivery systems [3], and surface characterization using tip-enhanced Raman/fluorescencemicroscopy [4].

References

11Paolo Actis

https://eps.leeds.
ac.uk/electronicengineering/staff/
806/dr-paolo-actis

Associate Professor of Bionanotechnology
University of Leeds, UK

E-mail: p.actis@leeds.ac.uk
Website: https://eps.leeds.ac.uk/electronic-engineering/staff/806/dr-paolo-actis

Research Interests
Single molecule analysis with nanopores, Single cell analysis, Nanoelectrochemistry

Education
2008
2005

PhD in Electrochemistry, Grenoble Institute of Technology, FR
Msc Materials Science, University of Turin, IT

Professional Experience
2021 - present
2016 - 2021
2014 - 20162012 - 20142008 - 2012

Associate Professor, University of Leeds, UK
University Academic Fellow, University of Leeds, UK
Consultant and Project Manager, Bio Nano Consulting, UK
Postdoctoral Scholar, Imperial College London, UK
Postdoctoral Scholar, University of California, Santa Cruz, US

Publications

12

1.

Nanopore Fingerprinting of Supramolecular DNA Nanostructures, S Confederat, I Sandei, G Mohanan, C Wälti, P Actis, 2022,
Biophysical Journal

2.

A subcellular cookie cutter for spatial genomics in human tissue, AG Bury, A Pyle, F Marcuccio, DM Turnbull, AE Vincent, G Hudson, P
Actis, 2022, Analytical and Bioanalytical Chemistry, 1-10

3.

Rational design of DNA nanostructures for single molecule biosensing, M Raveendran, AJ Lee, R Sharma, C Wälti, P Actis, 2020, Nature
Communications 11 (1), 1-9

4.

Macromolecular crowding enhances the detection of DNA and proteins by a solid-state nanopore, CC Chau, SE Radford, EW Hewitt, P
Actis, 2020, Nano Letters 20 (7), 5553-5561

5.

Ribosome fingerprinting with a solid-state nanopore, M Raveendran, AR Leach, T Hopes, JL Aspden, P Actis, 2020, ACS Sensors 5 (11),3533-3539

Longitudinal Single-Cell Profilingwith a Nanobiopsy Platform
Paolo Actis
School of Electronic and Electrical Engineering, University of Leeds, UK

Physiological and pathological processes within the human body are controlled by complex cell-cellinteractions within the context of a dynamic microenvironment. The ability to dynamically measurephenotypes (i.e. gene expression, protein activities, ion fluctuations, signalling) at the single cell levelis key to understanding cellular behaviour in a complex environment.
I will present the integration of nanopipettes with scanning probe microscopy techniques to enable
the extraction of genetic material from living cells. I will discuss the longitudinal profiling of brain
cancer cells to characterize the transcriptional reprogramming at the single cell level after
chemotherapy and radiotherapy.

References

13

Takeshi Fukuma

http://fukuma.w3.
kanazawa-u.ac.jp/

Professor, Doctor
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

E-mail: fukuma@staff.kanazawa-u.ac.jp
Website: http://fukuma.w3.kanazawa-u.ac.jp/

Research Interests
Atomic Force Microscopy, Nanoscale Measurement Technologies, Electrical Engineering, Interfacial Sciences, Life Sciences, Electrochemistry

Education
2003

Doctor of Engineering, Department of Electronic Science and Engineering, Kyoto University, Japan

Professional Experience2017 - present2017 - present
2012 - 20172007 - 20122005 - 2007
2001 - 2005

Director/Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Professor, Faculty of Frontier Engineering, Kanazawa University, Japan
Professor, Faculty of Electronic Eng. and Computer Sci., Kanazawa University, Japan
Associate Professor, Frontier Science Organization, Kanazawa University, Japan
Senior Scientist, Physics Department, Trinity College Dublin, Ireland
Research Fellow, Kyoto University, Japan

Honors
2018
2017
2011

15th JSPS Prize, Japan Society for the Promotion of Science
Hokkoku Bunka Award, Hokkoku Shinbun
The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology;
The Young Scientists' Prize

Publications

14

1.

Yurtsever, A.; Wang, P. X.; Priante, F.; Morais Jaques, Y.; Miyata, K.; MacLachlan, M. J.; Foster, A. S.; Fukuma, T., Probing the Structural
Details of Chitin Nanocrystal-Water Interfaces by Three-Dimensional Atomic Force Microscopy. Small Methods 2022, 2200320.

2.

Penedo, M.; Miyazawa, K.; Okano, N.; Furusho, H.; Ichikawa, T.; Alam Mohammad, S.; Miyata, K.; Nakamura, C.; Fukuma, T.,
Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM. Sci. Adv. 2021, 7 (52), eabj4990.

3.

Fukuma, T.; Garcia, R., Atomic- and Molecular-Resolution Mapping of Solid-Liquid Interfaces by 3D Atomic Force Microscopy. ACS
Nano 2018, 12 (12), 11785-11797.

Intracellular Structures and Mechanics of Living Cells
Investigated by Nanoendoscopy-AFM
Takeshi Fukuma
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Atomic force microscopy (AFM) has been a powerful tool for directly visualizing nanoscale structures,
dynamics and mechanics of biomolecular systems. However, it has been a great challenge to directly
access intracellular components of living cells since AFM was originally developed as a 2D surface
imaging tool. To overcome this limitation, we have recently developed nanoendoscopy AFM, where
we insert a needle-like probe into a living cell to perform a 2D/3D AFM measurement. With thedeveloped technique, we have demonstrated imaging of the whole cell structures, actin fibers, focal
adhesions without giving a serious damage to the living cell. In addition, the method also allowed us
to map the elasticity distribution on a nucleus to reveal its dependence on the cell cycle and cancer
progression. Owing to the capability to directly access to the intracellular component with a probe,
most of the functionality of the AFM should, in principle, be available even in a living cell. We also
combined this method with confocal or TIRF microscope. The correlative imaging by fluorescencemicroscopy and AFM allows simultaneous imaging of dynamic transports of specific molecules andstructural development of intracellular component. These methods should provide new insights into thenanodynamics and nanomechanics inside living cells.

References

15

Steven De Feyter

www.defeytergroup.org

Professor
Division of Molecular Imaging and Photonics, Department of Chemistry,
KU Leuven, Belgium

E-mail: steven.defeyter@kuleuven.beWebsite: www.defeytergroup.org

Research Interests
Scanning probe microscopy, Nano(bio)chemistry, Surface functionalization

Education
1997
1993

PhD in Chemistry (KU Leuven)
Master in Chemistry (KU Leuven)

Professional Experience
2011-present
2004 - 20111999 - 2004
1998 - 1999

Full Professor, Department of Chemistry, KU Leuven (Belgium)
Associate Professor, Department of Chemistry, KU Leuven (Belgium)
Postdoctoral Researcher, Department of Chemistry, KU Leuven (Belgium)
Postdoctoral Researcher, California Institute of Technology (USA)

Honors
2019
2018
2016
2014
2013

Lavoisier Lectures (Université Paris Diderot)
Elected member of the “European Academy of Sciences”
26th IOCF Yoshida LectureshipElected member of the Royal Flemish Academy of Belgium for Science and the Arts: Natural Sciences
European Research Council (ERC) Advanced Grant (NANOGRAPH@LSI)

Publications

16

1.

Observing Polymerization in Two-Dimensional Dynamic Covalent Polymers. G. Zhan, Z.-F. Cai, K. Strutyński, L. Yu, N. Herrmann, M.
Martínez-Abadía, M. Melle-Franco, A. Mateo-Alonso, S. De Feyter. Nature, 2022, 603, 835–840.

2.

Detection and Stabilization of a Previously Unknown 2D (Pseudo)polymorph using Lateral Nanoconfinement. A. M. Bragança, A.
Minoia, R. Steeno, J. Seibel, B. E. Hirsch, L. Verstraete, O. Ivasenko, K. Müllen, K. S. Mali, R. Lazzaroni, S. De Feyter, J. Am. Chem. Soc.,
2021, 143, 11080-11087.

3.

Multicomponent Covalent Chemical Patterning of Graphene M. C. Rodríguez González, A. Leonhardt, H. Stadler, S. Eyley, W.
Thielemans, S. De Gendt, K. S. Mali, S. De Feyter. ACS Nano, 2021, 15, 6, 10618-10627.

Formation and Functionalization of 2D Materials:
A Molecular Approach
Steven De Feyter
Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Belgium

In this presentation, I will mainly focus on the functionalization of graphite, graphene, and transition
metal dichalcogenides using molecules, though the concepts can be applied to other 2D materials
too. Nanostructuring is at the heart of all functionalization protocols that we develop because it
opens new possibilities for control and functionality. A variety of scanning probe microscopy methods
are used for visualization, characterization, and manipulation. The first approach is based onmolecular self-assembly at the interface between a liquid or air, and graphite or graphene. A second
approach is based on the covalent attachment of molecules on 2D materials via covalent chemistry. It
will be demonstrated how in addition to bottom-up strategies that provide control on the density andlayer thickness, as well as submicron to nanoscale nanostructuring, also top-down scanning probe
microscopy and optical lithography can be used to structure such covalently modified surfaces. A
third approach does not focus on the functionalization of the surface, but uses the surface as asupport for the in-plane covalent stitching of molecules, leading to the formation of on-surface 2D
dynamic covalent polymers.

References

17Satoshi Arai

https://sites.google.
com/view/satoshiarai

Associate Professor
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

E-mail: satoshi.arai@staff.kanazawa-u.ac.jp
Website: https://sites.google.com/view/satoshiarai

Research Interests
Chemical Biology, Bioimaging, Cell Engineering, Fluorescence Lifetime Microscopy

Education
2007

Doctor of Engineering, Polymer Chemistry, Waseda University

Professional Experience
2021 - present
2019 - present
2016 - 20192015 - 20192012 - 20162011 - 20122009 - 20102007 - 2009

FOREST Researcher (JST)Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Assistant Professor, Res. Inst. for Sci. and Eng., Waseda University, Singapore
PRIME Researcher (AMED)
Senior Research Fellow, WASEDA Bioscience Research Institute in Singapore, Singapore
Research Fellow, National University of Singapore , Singapore
Postdoctoral Fellow, Cooperative Bio Sci. Res. Inst., Waseda University, Japan
Research Associate, Dept. of Life Sci. and Med. Biosci., Waseda University, Japan

Honors
2014
2014
2013

The Award for Encouragement of Research in IUMRS-ICA2014
Tanaka Kikinzoku, MMS Award
The Molecular Biology Society of Japan, Travel Award

Publications

18

1.

Modulation of Local Cellular Activities using a Photothermal Dye-Based Subcellular-Sized Heat Spot, Ferdinandus, M. Suzuki, C. Q.
Vu, Y. Harada, S. R. Sarker, S. Ishiwata, T. Kitaguchi, S. Arai*, ACS Nano, 16, 6, 9004-9018 (2022)

2.

A palette of site-specific organelle fluorescent thermometers, X. Liu, T. Yamazaki (equal first), H.-Y. Kwon, S. Arai*, Y.-T. Chang*,
Materials Today Bio, 16, 100405 (2022)

3.

RGB-Color Intensiometric Indicators to Visualize Spatiotemporal Dynamics of ATP in Single Cells, S. Arai, R. Kriszt, K. Harada, L-S. Looi,
S. Matsuda, D. Wongso, S. Suo, S. Ishiura, Y-H. Tseng, M. Raghunath, T. Ito, T. Tsuboi, T. Kitaguchi, Angew. Chem. Int. Ed., 57,
10873-10878 (2018).

Subcellular Thermometry and Nanoheating
Using Functional Dyes
Satoshi Arai
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Temperature at nano- and microscale is a significant physical element to drive cellular system. To
elucidate the system thermodynamically, the development of technology to measure and regulate
subcellular temperature has been indispensable, named thermal cell engineering. Previously, using
temperature-sensitive fluorescent dyes, we reported organelle targetable fluorescent thermometersthat enable the read-out of temperature at organelles as detectable fluorescent signals such as
intensity and lifetime. Yet, targeted organelles were only limited to mitochondria and ER as
well-known heat sources in thermogenic cells. Very recently, we extended this to several organelles
including lipid droplets, golgi, plasma membrane, nucleus, and lysosome which have never beenreached by the other sensing methods. Using fluorescent lifetime imaging (FLIM), we further
demonstrated these thermometers in quantitative thermometry of heat production in brown
adipocytes.
Other than that, we have been developing local heating method at subcellular level. A key thing is afunctional photothermal dye which absorbs near-infrared (NIR) light and converts to heat efficiently.
Arrangement of the dyes to the target place, followed by NIR laser stimulation, allows to create a tinyheat spot at single cellular level. In this talk, we will share recent progress on thermal engineering inlive cell and their cellular applications.

References

19

Shiki Yagai

http://chem.tf.chiba-u.
jp/yagai/index.html

Professor, Doctor
Institute for Advanced Academic Research (IAAR)
Department of Applied Chemistry and Biotechnology, Graduate School of Engineering,
Chiba University, Japan

E-mail: yagai@faculty.chiba-u.jp
Website: http://chem.tf.chiba-u.jp/yagai/index.html

Research Interests
Self-assembled molecular materials, Supramolecular polymers

Education
2002

Doctor of Science, Graduate School of Science and Technology, Ritsumeikan University, Japan

Professional Experience
2022 - present
2021 - present2017 - 2022
2010 - 20172006 - 2010
2002 - 2006

Professor, Institute for Advanced Academic Research (IAAR), Chiba University, Japan
Visiting Professor, The University of Tokyo, Japan
Professor, Institute for Global Prominent Research (IGPR), Chiba University, Japan
Associate Professor, Graduate School of Engineering, Chiba University, Japan
PRESTO Researcher, Japan Science and Technology Agency, Japan
Assistant Professor, Faculty of Engineering, Chiba University, Japan

Honors2021
2020

Award for Creative Work for 2021, The Chemical Society of JapanThe 17th JSPS Prize, Japan Society for the Promotion of Science

Publications

20

1.

Takahashi, S.; Yagai, S., Harmonizing Topological Features of Self-Assembled Fibers by Rosette-Mediated Random Supramolecular
Copolymerization and Self-Sorting of Monomers by Photo-Cross-Linking. J. Am. Chem. Soc., 2022, 144(29), 13374-13383.

2.

Fukushima, T.; Tamaki, K.; Isobe, A.; Hirose, T.; Shimizu, N.; Takagi, H.; Haruki, R., Adachi, S.; Hollamby, M.; Yagai, S.,
Diarylethene-Powered Light-Induced Folding of Supramolecular Polymers. J. Am. Chem. Soc., 2021, 143(15), 5845-5854.

3.

Aratsu, K.; Takeya, R.; Pauw, B.R.; Hollamby, M. J.; Kitamoto, Y.; Shimizu, N.; Takagi, H.; Haruki, R.; Adachi, S.; Yagai, S.,
Supramolecular copolymerization driven by integrative self-sorting of hydrogen-bonded rosettes. Nature Commun., 2020, 11, Article
number: 1623.

4.

Datta, S.; Kato, Y.; Higashiharaguchi, S.; Aratsu, K.; Isobe, A.; Saito, T.; Prabhu, D. D.; Kitamoto, Y.; Hollamby, M. J.; Smith, A. J.;
Dalgliesh, R.; Mahmoudi, N.; Pesce, L.; Perego, C.; Pavan, G. M.; Yagai, S., Self-assembled poly-catenanes from supramoleculartoroidal building blocks. Nature, 2020, 583, 400-405.

5.

Kitamoto, Y.; Pan, Z.; Prabhu, D. D.; Isobe, A.; Ohba, T.; Shimizu, N.; Takagi, H., Haruki, R.; Adachi, S.; Yagai, S., One-shot preparation of
topologically chimeric nanofibers via a gradient supramolecular copolymerization. Nature Commun., 2019, 10, Article number: 4578.

Synthetic Supramolecular Polymers
with Diverse Topological Features
Shiki Yagai
Institute for Advanced Academic Research (IAAR), Department of Applied Chemistry and Biotechnology,
Graduate School of Engineering, Chiba University, Japan

One-dimensional molecular aggregates, known as supramolecular polymers, are emerging
next-generation polymeric materials owing to their reversible bonding. However, to compete overcovalent counterparts, development of supramolecular polymers with well-defined higher-order
structures (topologies) are desired. We have addressed this issue based on our unexpecteddiscovery a decade ago on the formation of nanorings from hydrogen-bonded macrocyclic
aggregates (rosettes) of barbituric acid-functionalized π-conjugated molecules in alkane solvent (J.
Am. Chem. Soc. 2009, 131, 5408; Angew. Chem. Int. Ed. 2012, 51, 9679). The shape persistencyof the nanoring along with its uniformity in diameter (ca. 14 nm) allowed us to propose that thegeneration of "intrinsic curvature" upon the continuous stacking of rosettes. Based on this idea, we
synthesized various π-conjugated compounds based on the above molecular design to create
curved supramolecular polymers with well-defined topological features. With the self-assembly
behaviors of these newly prepared compounds, which have been revealed particularly by direct
visualization of their supramolecular polymer chains by AFM, we can now comprehensively illustrate
new aspects of our curved supramolecular polymers including complex self-assembly pathways andenergy landscapes, dynamic topological change, topological extension by copolymerization, andtruly topological structures in molecular assembly.

References

21

Hitoshi Asakawa

https://nanomari-na.
w3.kanazawa-u.ac.
jp/asakawa/

Associate Professor
Nanomaterials Research Institute (NanoMaRi), Kanazawa University, Japan
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

E-mail: hi_asa@staff.kanazawa-u.ac.jp
Website: https://nanomari-na.w3.kanazawa-u.ac.jp/asakawa/Research Interests
Atomic force microscopy, Molecular self-assembly, Intermolecular interactions, Molecular recognition, Interfacial science

Education
Docter of Engineering, Department of Biological Functions Engineering, Kyushu Institute ofTechnology, Japan

2007

Professional Experience
2018 - presentGroup Leader/Associate Professor, Nanomaterials Research Institute (NanoMaRi), Kanazawa
University, Japan2017 - present
2016 - present2010 - 20162008 - 2010

Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Associate Professor, Division of Material Chemistry, Kanazawa University, Japan
Assistant Professor, Bio-AFM Frontier Research Center, Kanazawa University, Japan
Postdoctoral Fellow, Frontier Science Organization, Kanazawa University, Japan

Honors2019

The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology;
The Young Scientists' Prize

2013

Nanoprobe Technology Young Scientist Award from No. 167 Committee of Japan Society for the Promotion of Science (JSPS)

Publications

22

1.

Ide, Y.; Manabe, Y.; Inaba, Y.; Kinoshita, Y.; Pirillo, J.; Hijikata, Y.; Yoneda, T.; Shivakumar, K. I.; Tanaka, S.; Asakawa, H.; et al.
Determination of the Critical Chain Length for Macromolecular Crystallization Using Structurally Flexible Polyketones. Chem. Sci. 2022,
13, 9848–9854.

2.

Lebitania, J. A.; Inada, N.; Morimoto, M.; You, J.; Shahiduzzaman, M.; Taima, T.; Hirata, K.; Fukuma, T.; Ohta, A.; Asakawa, T.;
Asakawa, H., Local Cross-Coupling Activity of Azide-Hexa(ethylene Glycol)-Terminated Self-Assembled Monolayers Investigated by
Atomic Force Microscopy. Langmuir 2021, 37, 14688–14696.

3.

Asakawa, H.; Matsui, S.; Trinh, Q. T.; Hirao, H.; Inokuma, Y.; Ogoshi, T.; Tanaka, S.; Komatsu, K.; Ohta, A.; Asakawa, T.; et al. Chiral
Monolayers with Achiral Tetrapod Molecules on Highly Oriented Pyrolytic Graphite. J. Phys. Chem. C 2020, 124, 7760–7767.

Molecular Pockets in 2D Supramolecular Assemblies
Investigated by 3D-AFM in Liquid
Hitoshi Asakawa
Nanomaterials Research Institute (NanoMaRi), Kanazawa University, Japan
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Two-dimensional (2D) supramolecular assemblies of various building blocks on surfaces have beenstudied for constructing molecular architectures. The following important tasks are to establish design
methodologies that create functions of the supramolecular assemblies and analysis methods of thefunctions. We recently proposed building blocks with a three-dimensional shape and the potential toform nanosized “molecular pockets” in the 2D supramolecular assemblies. The molecular pockets are
expected to have molecular recognition functions like macrocyclic molecules and are helpful forvarious applications such as sensing, separation, and chemical storage. The recognition function ofmolecular pockets fundamentally originates from intermolecular interactions in real space. Thus, theintermolecular interactions around pockets, as well as the molecular-scale structures, should be
investigated to understand their recognition functions. However, the direct observation ofmolecular-scale intermolecular interactions is difficult even with any analytical methods.
Three-dimensional AFM (3D-AFM) is a promising technique for analyzing the interactions aroundmolecular pockets in real space. The 3D-AFM has been developed as a unique technique tovisualize the distribution of intermolecular interactions with sub-nanometer (sub-nm) spatial resolution
and piconewton (pN) force sensitivity. The 3D-AFM images obtained in this study showed that
attractive forces are localized in the molecular pockets formed by the self-assembly of the 3D
building blocks. The characteristic attractive forces are likely caused by a decrease in the hydrogenbond networks compared with bulk water. Our results demonstrate that the 3D-AFM technique canvisualize the distribution of interaction forces related to molecular recognition and should contributeto the design of functional supramolecular assemblies.

References

23

Tsvi Tlusty

http://www.sns.ias.
edu/~tlusty/

Distinguished Professor
Physics Department, Ulsan National Institute for Science and Technology (UNIST),
Center for Soft and Living Matter, and Institute of Basic Science (IBS), Republic of Korea

E-mail: tsvitlusty@gmail.com
Website: http://www.sns.ias.edu/~tlusty/

Research Interests
Physical biology, protein dynamics and evolution, active matter, information engines, quantum concepts in dissipative matter,

Education2000 - 2004

Fellow, Center for Physics and Biology, Rockefeller University, New York.
Host: Prof. Albert Libchaber

2000

Ph.D. in Physics, Weizmann Institute. Advisor: Prof. Sam SafranProfessional Experience
2015 - present
2015 - present
2011 - 20152005 - 2013

Distinguished Professor, Department of Physics, UNIST, Ulsan
Group Leader, Center for Soft and Living Matter, Institute for Basic Science
Long-term Member, Institute of Advanced Study, Princeton.
Senior researcher, Physics of Complex Systems, Weizmann Institute.

Publications

24

1.

Piñeros, W.D. & Tlusty, T. (2022) Spontaneous Chiral Symmetry Breaking in a Random Driven Chemical System. Nature Comm. 13, 2244.

2.

Eckmann J-P, Roujemont J & Tlusty T (2019) Proteins: The physics of amorphous evolving matter. Reviews of Modern Physics. 91, 03100.

3.

Jee AY, Cho YK, Granick S & Tlusty T (2019) Catalytic enzymes are active matter. Proc Natl Acad Sci USA 115, E10812-E10821.

4.

Tlusty T Libchaber A & Eckmann JP (2017) Physical model of the sequence-to-function map of proteins, Physical Review X, 7(2): 021037.

5.

Savir Y & Tlusty T. (2013) The ribosome as an optimal decoder: a lesson in molecular recognition. Cell 153(2):471-479.

The Collective Dynamics ofEnzymatic Nano-Machines
Tsvi Tlusty
Physics Department, Ulsan National Institute for Science and Technology (UNIST),
Center for Soft and Living Matter, and Institute of Basic Science (IBS), Republic of Korea

The cellular milieu is teeming with biochemical nano-machines, in particular enzymes – catalysts thatspeed up the rate of metabolic reactions by orders of magnitude, thereby making life possible. In thistalk, we will examine the collective dynamics of these enzymatic nano-machines at multiple
spatiotemporal scales of physics and evolution.
We will first discuss the internal dynamics of enzymes. Proteins such as enzymes are a matter of dual
nature. As a physical object, an enzyme molecule is a folded chain of amino acids with multifarious
biochemistry, but it is also an instantiation along an evolutionary trajectory determined by the
enzyme’ s function. We will describe a physical framework that links the evolution of the genesequence to the emergence of large-scale dynamical modes in the enzyme, revealing basic featuresof the genotype-to-phenotype map.
Then, we will discuss how the internal dynamics of enzymes may lead to collective externalinteractions. In the classical view, catalysis is a localized chemical process where enzymes operate
independently and feel the external environment only as thermal agitation that jolts the activatedcomplex past the transition state’ s energy barrier. The cell, however, is bustling with activity thatgenerates significant athermal agitation, provoking the hypothesis we will examine that enzymatic
catalysis is a collective, many-body process in which enzymes affect each other by inducing
longrange hydrodynamic forces. To conclude, we will discuss potential ways to measure theproposed collective effects.

References25

Chiho Watanabe

https://researchmap.
jp/chiho_watanabe

Assistant Professor
Graduate School of Integrated Sciences for Life, Hiroshima University, Japan

E-mail: cwatan@hiroshima-u.ac.jp
Website: https://researchmap.jp/chiho_watanabe (Researchmap)

Research Interests
Lipid membrane, Artificial cell, Polymer solution, Water, Cell-size space effect, Neurodegenerative disease

Education
2015
2012

PhD, Universeity Paris 7, Paris Diderot, France
Master’s degree in Engineering, Tokyo University of Agriculture and Technology, Japan

Professional Experience2020 - present
2019 - 20202016 - 2018

Assistant Professor at Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
Specially Appointed Assistant Professor at Komaba Institute for Sciences (KIS), the University of Tokyo, Japan
Postdoctoral Researcher at Tokyo University of Agriculture and Technology, Japan

Honors
2021
2021
2020

17th Early Career Award in Biophysics, The Biophysical Society of Japan (BSJ)
Young Oral Presentation Award, The 72nd Divisional Meeting of Division of Colloid and Surface Chemistry
The Emerging Science Lecture Prize at the 17th Australia-Japan Colloids Symposium, Australasian Colloids and Interface Society

Publications

26

1.

Watanabe, C.; Furuki, T.; Kanakubo, Y.; Kanie, F.; Koyanagi, K.; Takeshita, J.; Yanagisawa, M. Cell-Sized Confinement Initiates Phase
Separation of Polymer Blends and Promotes Fractionation upon Competitive Membrane Wetting. ACS Materials Lett. 2022,
1742–1748. https://doi.org/10.1021/acsmaterialslett.2c00404.

2.

Watanabe, C.; Tanaka, S.; Löffler, R. J. G.; Hanczyc, M. M.; Górecki, J. Dynamic Ordering Caused by a Source-Sink Relation between
Two Droplets. Soft Matter 2022. https://doi.org/10.1039/D2SM00497F.

3.

Watanabe, C.; Yanagisawa, M. Evaporation Patterns of Dextran–Poly(Ethylene Glycol) Droplets with Changes in Wettability andCompatibility. Life 2022, 12 (3), 373. https://doi.org/10.3390/life12030373.

4.

Harusawa, K.; Watanabe, C.; Kobori, Y.; Tomita, K.; Kitamura, A.; Kinjo, M.; Yanagisawa, M. Membrane Surface Modulates Slow
Diffusion in Small Crowded Droplets. Langmuir 2021, 37 (1), 437–444. https://doi.org/10.1021/acs.langmuir.0c03086.

5.

Watanabe, C.; Kobori, Y.; Yamamoto, J.; Kinjo, M.; Yanagisawa, M. Quantitative Analysis of Membrane Surface and Small
Confinement Effects on Molecular Diffusion. J. Phys. Chem. B 2020, 124 (6), 1090–1098.
https://doi.org/10.1021/acs.jpcb.9b10558.

Cell-Size Space Effect on Molecular Diffusionand Liquid-Liquid Phase Separation
Chiho Watanabe
Graduate School of Integrated Sciences for Life, Hiroshima University, Japan

Cells typically have a size of a few to several tens of micrometers and contain a solution with large
amounts of biopolymers covered with a cell membrane (lipid membrane). There is interest in how
cell-size spatial confinement affects the internal solution behavior that often differs from those in bulk
systems. We attempted to decipher the cell-size space effect (CSE) by using polymeric droplets (w/oemulsions) as artificial cells, which can realize macromolecular crowding and cell-size confinement
by lipid membranes, which are the characteristics of real cells. Specifically, we studied cell-size
confinement effects on 1) molecular diffusion, which is the basis of solution properties, and 2)
liquid-liquid phase separation (LLPS), which has attracted attention in recent years from experiments.
Molecular diffusion was measured by fluorescence correlation spectroscopy (FCS), and it was foundthat the diffusion coefficient is slower in cell-size droplets than in larger ones. In addition, we foundthat phase separation is induced through cell-sized confinement of polymer mixtures, which are in a
one-phase state in larger droplets or bulk solutions of microliters or larger. Furthermore, it was
indicated that the membrane interfacial properties are important for both phenomena. We would liketo introduce these physico-chemical studies on the cell-size space effect.

References

27

Tatsuo Shibata

http://www.qbic.
riken.jp/phb/

Team Leader
Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, Japan

E-mail: tatsuo.shibata@riken.jp
Website: http://www.qbic.riken.jp/phb/

Research Interests
Biophysics of cells and development, Cell and tissue chirality, Collective cell migration

Education
1999
1994

Ph.D. Graduate School of Arts and Sciences, The University of Tokyo, Japan
B.S. Faculty of Science, Kyoto University, Japan

Professional Experience
2018 - present
2015 - 20182010 - 20142005 - 2010
2002 - 2005
2001 - 2003
1999 - 2001

Team Leader, Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, Japan
Team Leader, Laboratory for Physical Biology, RIKEN Quantitative Biology Center, Japan
Unit Leader, Laboratory for Physical Biology, RIKEN Center for Developmental Biology, Japan
Associate Professor, Department of Mathematical and Life Sciences, Hiroshima University, Japan
Lecturer, Department of Mathematical and Life Sciences, Hiroshima University, Japan
Research Scientist and Humboldt Research Fellowship, Fritz Haber Institute of Max Planck Society, Germany
Postdoctoral Research Fellow, Research Institute for Mathematical Sciences, Kyoto University, Japan

Honors2010

The Young Scientists’ Prize, the Commendation for Science and Technology, the MEXT

Publications

28

1.

Sato, K., Hiraiwa, T. & Shibata, T. Cell Chirality Induces Collective Cell Migration in Epithelial Sheets. Physical Review Letters
115,188102 (2015).

2.

Nishikawa, M., Hörning, M., Ueda, M. & Shibata, T. Excitable Signal Transduction Induces Both Spontaneous and Directional Cell
Asymmetries in the Phosphatidylinositol Lipid Signaling System for Eukaryotic Chemotaxis. Biophys J 106, 723–734 (2014).

3.

Arai, Y., Shibata, T., Matsuoka, S., Sato, M. J., Yanagida, T. & Ueda, M. Self-organization of the phosphatidylinositol lipids signaling
system for random cell migration. PNAS 107, 12399–12404 (2010).

4.

Shibata, T. & Fujimoto, K. Noisy signal amplification in ultrasensitive signal transduction. PNAS 102, 331–336 (2005).

5.

Shibata, T. & Kaneko, K. Collective Chaos. Physical Review Letters 81, 4116–4119 (1998).

Emergence of Cell Chirality from the Spatial
Organization of Actin and Myosin Cytoskeleton
Tatsuo Shibata
Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, JapanThe chirality or left-right asymmetry of the morphogenesis and arrangement of organ is essential for
their function and development. The chirality of organ and tissue is derived from the chirality of thecells that compose of them, and the cellular chirality emerges by organizing the molecular chirality
within the cell. However, the principle of how molecular chirality is organized to lead to cellularchirality is still unclear. To address this question, we experimentally study the dynamical chiralbehaviors of single epithelial cells and provide a theoretical understanding of how the chiralbehaviors at the single-cell level arise from the molecular-level chirality. We first found that thenucleus rotates, and the cytoplasm circulates in the clockwise direction, which is driven by the actin
and myosin cytoskeleton. During the rotation, the actin and myosin cytoskeleton organizes in avortex-like chiral orientational order, which apparently drives the rotation. However, when theformation of stress fibers was repressed by drug treatment, the vortex-like chiral order disappearedand concentric achiral order emerged while the cells still rotate. Hence, the cell can rotate without
any macroscopic chiral order of the cytoskeleton. To elucidate the mechanism of these chiral rotation
with and without macroscopic chiral orientational order of the cytoskeleton, we analyzed ahydrodynamic model considering the effect of chirality of cytoskeleton. Our experiment and theory
suggest that the cell chirality emerges as a collective behavior of chiral molecules even without any
macroscopic chiral orientational order of the cytoskeleton.

References

29

Ralf Metzler

http://www.agnld.
uni-potsdam.de/

Chair Professor for Theoretical Physics
Institute of Physics & Astronomy, University of Potsdam, Germany

E-mail: ralf.metzler@uni-potsdam.de
Website: http://www.agnld.uni-potsdam.de/Research Interests
Stochastic processes, nonequilibrium statistical physics, search processes, molecular reactions,soft and biological mat- ter, data science,machine learning, Bayesian analysis

Education
1996

Doctor of Natural Science, Physics Dept, University of Ulm, Germany

Professional Experience
2011 - present
2007 - 2011
2006 - 2007
2002 - 2006

Chair Professor for Theoretical Physics, University of Potsdam, Germany
Professor ("Extraordinarius") for Complex Bio Materials, Technical University of Munich (TUM), Germany
Associate Professor and Canada Research Chair in Biological Physics, University of Ottawa, Canada
Assistant Professor, NORDITA-Nordic Institute for Theoretical Physics, Copenhagen, Denmark

Honors2023

Distinguished Visiting Professor, Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India

2023

Heilbronn distinguished visiting fellowship (Mathematics of Movement programme at Isaac Newton Institue), Heilbronn
Institute for Mathematical Research

2022

APCTP Distinguished Fellow (Senior Advisory Group Scientist), Asia Pacific Center for Theoretical Physics, Pohang, Korea

2020

Higgs Associate, Higgs Centre for Theoretical Physics, University of Edinburgh, Scotland

2017

SigmaPhi Prize 2017 for outstanding achievements in Statistical Physics

2010

Finland Distinguished Professor (FiDiPro) at Tampere University of Technology, Academy of Finland

2006

Canada Research Chair in Biological Physics, Government of Canada

2000

Emmy Noether fellowship, German Science Foundation

1998

Amos de Shalit named fellowship, Minerva German-Israeli binational Foundation

1998

Feodor Lynen fellowship, Alexander von Humboldt Foundation

Continue to next page30

Beyond Brownian Motion: From Data to Models
Ralf Metzler
Institute of Physics & Astronomy, University of Potsdam, Germany

After a brief historical introduction to Brownian motion I will address recent experimental andsimulations results on diffusive transport in complex systems, ranging from dynamics in single
molecules, motion of molecules and tracers in living biological cells, to ants and birds. The main
characteristic of these system is the occurrence of non-Gaussian displacement distributions and/or
anomalous diffusion of the form <r 2 (t)> ~ t α with α ≠ 1. Due to the non-universality of such kind of
stochastic dynamics, it is important to know the precise underlying physical process [1]. I will discuss
several examples. Data-science methods help us in identifying such physical processes encoded inexperimental records and to extract physical parameters. I will provide an overview over different
approaches and their performance in the context of diffusive motion [2,3].

References

Publications
1.

G. Muñoz-Gil et al., Objective comparison of methods to decode anomalous diffusion, Nature Comm. 12, 6253 (2021)

2.

E. Yamamoto, T. Akimoto, A. Mitsutake, and R. Metzler, Universal relation between instantaneous diffusivity and radius of
gyration of proteins in aqueous solution, Phys. Rev. Lett. 126, 128101 (2021)

3.

D. Krapf et al, Spectral Content of a Single Non-Brownian Trajectory, Phys. Rev. X 9, 011019 (2019)

4.

A. V. Chechkin, F. Seno, R. Metzler, and I. M. Sokolov, Brownian yet non-Gaussian diffusion: from superstatistics tosubordination of diffusing diffusivities, Phys. Rev. X 7, 021002 (2017)

5.

A. Godec and R. Metzler, Universal proximity effect in target search kinetics in the few encounter limit, Phys. Rev. X 6,041037 (2016)

6.

J.-H. Jeon, M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen, Protein crowding in lipid bilayers gives rise to
non-Gaussian anomalous lateral diffusion of phospholipids and proteins, Phys. Rev. X 6, 021006 (2016)

7.

J. Shin, A. G. Cherstvy, and R. Metzler, Sensing viruses by mechanical tension of DNA in responsive hydrogels, Phys. Rev. X
4, 021002 (2014)

8.

J. H. P. Schulz, E. Barkai, and R. Metzler, Aging renewal theory and application to random walks, Phys. Rev. X 4, 011028 (2014)31

Robert D Goldman

https://labs.feinberg.
northwestern.edu/
goldman/Professor of Cell and Developmental Biology
The Stephen Walter Ranson Professor Emeritus
Feinberg School of Medicine, Northwestern University, USA

E-mail: r-goldman@northwestern.edu
Website: https://labs.feinberg.northwestern.edu/goldman/

Research Interests
Cell Biology: Cytoskeleton, Intermediate Filaments, Nuclear Lamins and Nuclear Architecture

Education
1967

Ph.D. in Biology, Princeton University, USA

Professional Experience
2021 - present

Professor of Cell and Developmental Biology, Stephen Walter Ranson Professor Emeritus,
Feinberg School of Medicine, Northwestern University, USA

1981 - 2021

The Stephen Walter Ranson Professor and Chairman
Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern
University, USA

1981 - 1991
1977 - 1981
1973 - 1974
1969 - 1973
1967 - 1969

Program Leader, Cell Biology, Northwestern University Cancer Center, USA

1967 - 1968

American Cancer Society, Eleanor Roosevelt Postdoctoral Fellow at the Royal Postgraduate
Medical School, London, England

Professor of Biological Sciences, Carnegie-Mellon University, USA
Associate Professor of Biological Sciences, Carnegie-Mellon University, USA
Assistant Professor of Biology, Case Western Reserve University, USA
American Cancer Society, Eleanor Roosevelt Postdoctoral Fellow at the Medical ResearchCouncil Institute of Virology, Glasgow, Scotland

Publications

32

1.

Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.
Vahabikashi, A.; Sivagurunathan, S.; Nicdao, FAS.; Han, YL.; Park, CY.; Kittisopikul, M, Wong, X.; Tran, JR.; Gundersen, GG.; Reddy,
KL.; Luxton, GWG.; Guo, M.; Fredberg, JJ.; Zheng, Y.; Adam, SA.; Goldman, RD. Proc Natl Acad Sci U S A. 2022 Apr 26;119(17):e2121816119.

2.

Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. Kittisopikul, M.; Shimi, T.;
Tatli, M.; Tran, JR.; Zheng, Y.; Medalia, O.; Jaqaman, K.; Adam, SA.; Goldman, RD. J Cell Biol. 2021 Apr 5;220(4):e202007082.

3.

Structural organization of nuclear lamins A, C, B1, and B2 revealed by superresolution microscopy.
Shimi, T.; Kittisopikul, M.; Tran, J.; Goldman, AE.; Adam, SA.; Zheng, Y.; Jaqaman, K.; Goldman, RD. Mol Biol Cell. 2015 Nov 5;26
(22):4075-86.

Intermediate Filament Networks
Connect the Nucleus to the Cell Cortex
Robert D Goldman
Feinberg School of Medicine, Northwestern University, USA

Recent insights into the interactions of the nuclear and cytoplasmic Intermediate Filament (IF) systems
demonstrate their functions in integrating the global response of mesenchymal cells to mechanicalstress. Within the nucleus, each of the Type V IF proteins, lamins A, C, B1, and B2 assembles into a
distinct meshwork. These meshworks are interspersed with nuclear pore complexes to form thenuclear lamina (NL). The lamin complex connects the inner nuclear membrane to chromatin. Evidence
will be presented showing that the lamin meshworks are also connected to a juxtanuclear cage ofType III vimentin IFs (VIFs) located at the outer membrane of the nuclear envelope and that this cageconnects to an extensive cytoplasmic network of VIFs associated with the cell surface. Our data showthat the lamin meshworks are connected to the juxtanuclear cage of VIFs by specific components of
the linker of nucleoskeleton and cytoskeleton (LINC) complex containing proteins spanning the innerand outer nuclear membranes. In the cortical region, VIFs are found deep within bundles of F-actin(stress fibers), thereby forming interpenetrating networks (IPNs). Using super-resolution microscopic
techniques combined with live cell imaging, cryo-EMT, fluorescence recovery after photobleaching,atomic force microscopy, optical tweezer microrheology, traction force microscopy and particle
tracking microrheology, we demonstrate that VIFs function in regulating the stiffness of the cell surface,
the cytoplasm, overall cell contractility, adhesion and motility. These results are supported byanalyses of reconstituted cytoskeletal networks prepared from purified proteins. Overall, these results
alter the commonly held view that the contractile and adhesive properties of mammalian cells aresolely regulated by F-actin and its associated proteins. This work involves collaborations with theLaboratories of David Weitz at Harvard University, Ming Guo at MIT, Paul Janmey at the Universityof Pennsylvania and Ohad Medalia at the University of Zurich. The work is supported by the NIH.

References33

Ohad Medalia

https://www.bioc.uzh.
ch/en/research/research-groups/medalia/

Professor of Biochemistry
Department of Biochemistry, University of Zurich, Switzerland

E-mail: omedalia@bioc.uzh.ch
Website: https://www.bioc.uzh.ch/en/research/research-groups/medalia/

Research Interests
The structure and mechanical properties of the nuclear envelope, Nuclear lamins, Structural analysis of intermediate filaments, Cryo-electron tomography

Education
2001

Ph. D. in Chemistry, Department of Organic Chemistry. The Weizmann Institute of Science, Israel

1994

B. Sc. In Chemistry. Faculty of Chemistry, Tel-Aviv University, Israel

Professional Experience2017 - present
2011 - 20172011 - 20152005 - 20092005 - 2009

Professor, Department of Biochemistry, University of Zurich, Switzerland
Associated Professor, Department of Biochemistry, University of Zurich, Switzerland
Adjunct Professor, Ben Gurion University, Israel
Visiting Scientists, Max-Planck Institute of Biochemistry, Germany
Senior Lecturer, Ben Gurion University, Israel

Honors
2019
2014
2010
2009
2009
2008
2004
2003
2001
2001
2001
2000
1999

ERC Synergy Grant
The Charles University, Medical Faculty Medal of Honor
Toronto Prize
The ARCHES Award
ERC Starting Grant
The FEI European Microscopy Award
The Alon Fellowship
Max-Planck Institute for Biochemistry Junior Research Award
The Elchanan E. Bondi Memorial Prize for Ph. D. students.
The Rothschild Fellowship
The European Commission Individual Fellowship
The Lev Margulis Young Investigators Award of Merit
The Wolf Foundation Fellowship- for Excellent Ph.D students.

Continue to next page
34

The Remarkable Structure and Mechanicsof Nuclear Lamin Filaments
Ohad Medalia
Department of Biochemistry, University of Zurich, Switzerland

Lamins are nuclear intermediate filaments (IFs) of metazoan cells. They assemble into fibrous
structures that are positioned between the inner nuclear membrane and the peripheral chromatin,
although a small fraction of lamins is present in the nucleoplasm. Lamins are required to maintain
nuclear structure and, together with many interaction partners, are involved in most nuclear activities.
Mutations in lamins cause a group of >14 distinct diseases called laminopathies, it is not clear how
lamins are organized in vivo and how these mutations affect lamin functions. Understanding how
lamins are assembled, and how mutations in lamins and lamin binding proteins affect lamin filament
assembly and cellular localization is essential for understanding the their modus operandi.
Moreover, lamins are intimately interacting with chromatin.
Using variety of microscopy modalities, such as protein design, atomic force microscopy, molecular
dynamics (MD) simulations, quotative fluorescence and cryo-electron microscopy, we provided
unprecedented understanding of the remarkable structure and mechanical properties of nuclear
Lamins. The results of this study indicate the unique mechanical and functional properties of lamins.

Publications
1.

Schuller, A., Wojtynek, M., Mankus D.,Tatli M., Kronenberg-Tenga R., Regmi S., Dasso M., Weis K., Medalia, O.*,
Schwartz, TU*. (2021) The cellular environment shapes the nuclear pore complex architecture. Nature, 598(7882):667-671.

2.

Turgay Y, Eibauer M, Goldman AE, Shimi T, Khayat M, Ben-Harush K, Dubrovsky-Gaupp A, Sapra KT, Goldman RD,
Medalia O. (2017) The molecular architecture of lamins in somatic cells. Nature 543(7644):261-264.

3.

Patla, I., Volberg, T., Elad, N., Hirschfeld-Warneken, V., Grasshof, C., Fässler, R., Spatz, J., Geiger, B., and Medalia, O.,(2010) Dissecting the molecular architecture of integrin-mediated focal adhesion by cryo-eelectron tomography. Nat.
Cell.Biol. 12(9):909-15

4.

Beck, M., Lucic, V., Förster, F., Baumeister, W. and Medalia, O., (2007) Snapshots of Nuclear Pore Complexes in Action
Captured by Cryoelectron Tomography. Nature. 449(7162):611-5

5.

Medalia, O., Weber, I., Frangakis, A.S., Nicastro, D. Gerisch, G., and Baumeister, W. (2002) MacromolecularArchitecture in Eukaryotic Cells Visualized by Cryo-electron Tomography. Science. 298, 1209-1213.

35

Takeshi Shimi

http://kimura-lab.
bio.titech.ac.jp/

https://www.youtube.
com/watch?v=
NthDgpIe_8o&ab_
channel=wrhiofficeSpecially Appointed Associate Professor/Dr.
Institute of Innovative Research, Tokyo Institute of Technology, Japan

E-mail: shimi.t.aa@m.titech.ac.jp
Website: http://kimura-lab.bio.titech.ac.jp/
Research Video: https://www.youtube.com/watch?v=NthDgpIe_8o&ab_channel=wrhioffice

Research Interests
Structure, dynamics and functions of the nuclear envelope, particularly lamina/lamins

Education
2005

Ph.D. in Biology, Osaka University Graduate School of Science, Japan

Professional Experience
2018 - present
2016 - 20182015 - 20162012 - 2015
2006 - 20122005 - 2006

Specially Appointed Associate Professor, Institute of Innovative Research, Tokyo Institute of Technology, Japan
Research Assistant Professor, Northwestern University, USA
Staff Scientist, The University of Chicago, USA
Research Assistant Professor, Northwestern University, USA
Postdoctoral Research Fellow, Northwestern University, USA
Postdoctoral Research Fellow, Advanced ICT Research Institute, Japan

Publications

36

1.

Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS. Kono, Y.; Adam, SA.; Reddy KL.;
Zheng, Y.; Medalia O.; Goldman RD.; Kimura H.; Shimi, T., J Cell Biol. 2022 (In press)

2.

Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. Kittisopikul, M*.; Shimi, T*.;
Tatli, M.; Tran, JR.; Zheng, Y.; Medalia, O.; Jaqaman, K.; Adam, SA.; Goldman, RD., (*equal contribution). J Cell Biol. 2021 Apr 5;220(4):e202007082.

3.

Structural organization of nuclear lamins A, C, B1, and B2 revealed by superresolution microscopy.
Shimi, T*.; Kittisopikul, M*.; Tran, J.; Goldman, AE.; Adam, SA.; Zheng, Y.; Jaqaman, K.; Goldman, RD., (*equal contribution). Mol Biol
Cell. 2015 Nov 5;26(22):4075-86.

The Role of A-Type Lamins in Repairof Nuclear Envelope Ruptures
Takeshi Shimi
Institute of Innovative Research, Tokyo Institute of Technology, JapanThe nuclear lamina (NL) lines the inner nuclear membrane of the nuclear envelope (NE) to maintain
nuclear structure in mammalian cells. The major NL component, the nuclear lamins contribute to theprotection against NE rupture induced by mechanical stress. However, the specific role of the laminsin repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence andlive-cell imaging revealed that among all the lamin isoforms (LA, LB1, LB2, and LC), only
nucleoplasmic LC rapidly accumulated at sites of NE rupture induced by laser microirradiation andsingle-cell compression in mouse embryonic fibroblasts. The recruitment of LC from the nucleoplasm
to the rupture sites required the binding of the immunoglobulin-like fold domain to Barrier-toautointegration factor (BAF). BAF accumulation at the rupture sites and DNA sensing of cytoplasmic
cyclic GMP-AMP synthase (cGAS) were partially dependent on LA/C. These results suggest that
nucleoplasmic LC, BAF, and cGAS concertedly accumulate for rapid repair of NE ruptures.

References

37

Hanae Satohttps://nanolsi.kanazawa-u.ac.jp/en/research/
researchers/hanae-sato

Associate Professor
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

E-mail: hanae-sato@staff.kanazawa-u.ac.jp
Website: https://nanolsi.kanazawa-u.ac.jp/en/research/researchers/hanae-sato

Research Interests
Transcription, Translation, mRNA decay

Education
2006

Ph.D. in Biochemistry University of Tokyo, Department of Biophysics and Biochemistry, Tokyo, Japan

Professional Experience
2022 - present
2022 - 2022
2021 - 2022

Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan2017 - 2021
2016 - 2017

Faculty Associate, Department of Anatomy & Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA

Research Assistant Professor, Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
Research Assistant Professor, Department of Anatomy & Structural Biology, Albert Einstein College ofMedicine, Bronx, NY, USA

Faculty Associate, Department of Cell Biology/Stem Cell Institute and Anatomy & Structural Biology, Albert Einstein
College of Medicine, Bronx, NY, USA

Honors2019

Aegean Conference Travel Award, 3rd International Conference on the Long and the Short of Non-Coding
RNAs, Crete, Greece

20192009 - 2011

Travel Award, RNA 2019 Meeting, Kraków, Poland
JSPS Postdoctoral Fellowship for Research Abroad, Japan Society for the Promotion of Science (JSPS), Japan

Publications
Li W*, Maekiniemi A*, Sato H, Osman C, Singer RH (2022) An improved imaging system that corrects MS2-induced RNA destabilization.
Nature Methods in press. (*contributed equally)
Sato H and Singer RH (2021) Cellular variability of nonsense-mediated mRNA decay. Nature communications 12:7203.
Sato H*, Das S*, Singer RH, Vera M. (2020) Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics
of Gene Expression. Annual Review of Biochemistry 89:159-187 (*contributed equally)
Sato H, Wu B, Delahaye F, Singer RH, Greally JM. (2019) Retargeting of macroH2A following mitosis to cytogenetic-scale
heterochromatic domains. J Cell Biol. 218:1810-1823.

38

Real-Time Imaging of Transcriptional Feedbackin Nonsense-Mediated mRNA Decay
Hanae Sato
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Nonsense-mediated mRNA decay (NMD) is a translation-coupled mRNA decay pathway triggeredby a premature termination codon (PTC). Although only cytoplasmic ribosomes define the in-frame
stop codon, unexpected transcriptional changes at the PTC-containing gene have been reported
previously. While this observation implies PTC detection at the transcription site prior to thecytoplasmic translation or crosstalk between cytoplasmic decay and transcription, it has never beenaddressed with high temporal and spatial resolution. Here we utilize a real-time imaging approachthat allows simultaneous detection of transcription sites expressing either wild-type or NMD-targeted
β -globin reporter genes in the same cell to capture the transcriptional dynamics at thePTC-containing gene allele. Our study provides a robust link between cytoplasmic decay andtranscription in the nucleus.

References

39

Atsushi Miyawaki

https://cfds.riken.jp/

Team Leader
RIKEN Center for Brain Science, JapanRIKEN Center for Advanced Photonics, Japan

E-mail: miyawaki-lab.ast@ml.riken.jp
Website: https://cfds.riken.jp/

Research Interests
Bioimaging

Education
1991
1987

Ph.D. Osaka University School of Medicine, Japan, field of study: Signal Transduction
M.D. Keio University School of Medicine, Japan, field of study: Medicine

Professional Experience
2022 - present2013 - present
2012 - present2010 - 20112010 - present

Visiting Professor, Institute for Life and Medical Sciences, Kyoto University, Japan

2009 - present
2008 - 20182007 - 20102007 - present
2006 - 2011
2006
2006 - 2013

Visiting Professor, Keio University School of Medicine, Japan

2005 - 20102004 - 20091999 - present

Visiting Professor, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan

1997 - 1998
1995 - 1997
1993 - 1998
1991 - 1993

Research Pharmacologist, The University of California, San Diego, USA

Team Leader, Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Japan
Visiting Professor, Graduate School of Nanobioscience, Yokohama City University, Japan
Visiting Professor, Faculty of Science, Toho University, Japan
Director, RIKEN CBS-Olympus Collaboration Center, Japan (previously named RIKEN BSI-Olympus
Collaboration Center)

Deputy Director, RIKEN Brain Science Institute, Japan
Deputy Director, BSI Olympus Collaboration Center
Visiting Professor, Graduate School of Advanced Science and Engineering, Waseda University, Japan
Visiting Professor, National Institute for Basic Biology, The National Institute of Natural Sciences, Japan
Visiting Professor, Tokyo University of Science, Japan
Research Director,ERATO MIYAWAKI Life Function Dynamics Project, Japan Science and Technology
Agency, Japan

Group Director, Advanced Technology Development Group, RIKEN Brain Science Institute, Japan
Laboratory Head, Lab for Cell Function Dynamics, RIKEN Center for Brain Science, Japan(previously named RIKEN Brain Science Institute)

HFSP, Long-Term Fellowship, The University of California, San Diego, USA
Assistant Professor, The Institute of Medical Science, The University of Tokyo, Japan
Researcher, The Institute of Medical Science, The University of Tokyo, Japan

Continue to next page40

Cruising in the Cell
Atsushi Miyawaki
RIKEN Center for Brain Science, Japan,
RIKEN Center for Advanced Photonics, JapanThe behavior of biochemical molecules moving around in cells makes me think of a school of whales
wandering in the ocean, captured by the Argus system on the artificial satellite. When bringing awhale back into the sea --- with a transmitter on its dorsal fin, every staff member hopes that it will
return safely to a school of its species. A transmitter is now minute in size, but it was not this way
before. There used to be some concern that a whale fitted with a transmitter could be given the cold
shoulder and thus ostracized by other whales for “wearing something annoying.” How is whale’ s
wandering related to the tide or a shoal of small fish? What kind of interaction is there among
different species of whales? We human beings have attempted to fully understand this fellow creaturein the sea both during and since the age of whale fishing.
In a live cell imaging experiment, a luminescent probe replaces a transmitter. We label a luminescentprobe on a specific region of a biological molecule and bring it back into a cell. We can thenvisualize how the biological molecule behaves in response to external stimulation. Since
luminescence is a physical phenomenon, we can extract various kinds of information by making fulluse of its characteristics.
Cruising inside cells in a supermicro corps, gliding down in a microtubule like a roller coaster,
pushing our ways through a jungle of chromatin while hoisting a flag of nuclear localization signal --we are reminded to retain a playful and adventurous perspective at all times. What matters ismobilizing all capabilities of science and giving full play to our imagination. We believe that suchserendipitous findings can arise out of such a sportive mind, a frame of mind that prevails whenenjoying whale-watching.

Honors2021 Highly Cited Researchers 2021, Clarivate Analytics Recognition of ranking among the top 1% of researchers for most cited
documents in Cross-Field, 2021 Japan Academy Prize, 2021 Keio Medical Science Prize (Keio University Medical Science Fund),2020 Takeda Medicine Prize (Takeda Science Foundation), 2017 Uehara Prize, 2017 Medal with Purple Ribbon, 2015 Shimadzu
Prize, 2015 The Thirty-Seventh Annual W. Alden Spencer Award, 2014 Arthur Kornberg Memorial Award, 2013 Fujihara Award,
2012 Inoue Prize for Science, 2008 The Commendation for Science and Technology by the Minister of Education, Culture, Sports,
Science and Technology, 2007 Keio University Sanshikai Kitazato Award, 2007 Tsukahara Nakaakira Award, 2006 Japan Society
for the Promotion of Science Prize, 2006 Harvard University, Department of Chemistry and Chemical Biology, Woodward Visiting
Scholar, 2004 The 4th Yamazaki-Teiichi Prize Winner Biological Science & Technology.

Publications
1.

Masahiko Hirano, Ryoko Ando, Satoshi Shimozono, Mayu Sugiyama, Noriyo Takeda, Hiroshi Kurokawa, Ryusaku Deguchi,
Kazuki Endo, Kei Haga, Reiko Takai-Todaka, Shunsuke Inaura, Yuta Matsumura, Hiroshi Hama, YasushiOkada, Takahiro
Fujiwara, Takuya Morimoto, Kazuhiko Katayama, Atsushi Miyawaki “A highly photostable and bright green fluorescentprotein” Nat Biotechnol.2022 Apr 25. doi: 10.1038/s41587-022-01278-2.

2.

Michikawa T, Yoshida T, Kuroki S, Ishikawa T, Kakei S, Kimizuka R, Saito A, Yokota H, Shimizu A, Itohara S, Miyawaki
A.” Distributed sensory coding by cerebellar complex spikes in units of cortical segments.” Cell Rep.,2021 Nov 9;37
(6):109966. doi: 10.1016/j.celrep.2021.109966.

3.

KatayamaH., HamaH., NagasawaK., KurokawaH., SugiyamaM., AndoR., FunataM., YoshidaN., HommaM., NishimuraT.,
TakahashiM., IshidaY., HiokiH., TsujihataY., Miyawaki A.(2020)Visualizing and modulating mitophagy for therapeutic studies ofneurodegeneration. Cell, 2020 May 28;181(5):1176-1187.e16. doi: 10.1016/j.cell.2020.04.025.Epub 2020 May 20.

4.

AndoR., Sakaue-Sawano A., Shoda K., Miyawaki A. (2020) Two new coral fluorescent proteins of distinct colors for sharp
visualization of cell-cycle progression. bioRxiv,015156.doi: https://doi.org/10.1101/2020.03.30.015156
41

Mikihiro Shibata

https://bioafminfi.w3.
kanazawa-u.ac.jp/

Professor
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

E-mail: msshibata@staff.kanazawa-u.ac.jp
Website: https://bioafminfi.w3.kanazawa-u.ac.jp/

Research Interests
Life Sciences, Neurobiology, High-Speed Atomic Force Microscopy, Membrane Proteins

Education
Doctor of Engineering, Department of Materials Science and Engineering, Nagoya Institute ofTechnology

2007

Professional Experience
2021 - present2017 - 2021
2016 - 20172015 - 20162013 - 20152011 - 20132008 - 2011

Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Associate Professor, Institute for Frontier Science Initiative, Kanazawa University, Japan
Postdoctoral Fellow, Department of Physics, Kanazawa University, Japan
Postdoctoral Research Fellow, Max Planck Florida Institute for Neuroscience, USA
JSPS Postdoctoral Fellow for Research Abroad, Duke University Medical School, USA
Research Fellow of JSPS (SPD), Kanazawa University, Japan

Honors2018

The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology;
The Young Scientists' Prize2009

Young Researchers’ Prize of the Biophysical Society of Japan

Publications

42

1.

L. Puppulin*, D. Kanayama, N. Terasaka, K. Sakai, N. Kodera, K. Umeda, A. Sumino, A. Marchesi, W. Weilin, H. Tanaka, T. Fukuma,
H. Suga, K. Matsumoto, & M. Shibata*. Macrocyclic peptide-conjugated tip for fast and selective molecular recognition imaging by
high-speed atomic force microscopy. ACS Applied Materials & Interfaces, 13, 46, 54817–54829 (2021).

2.

M. Shibata, K. Inoue, K. Ikeda, M. Konno, M. Singh, C. Kataoka, R. Abe-Yoshizumi, H. Kandori, & T. Uchihashi. Oligomeric states of
microbial rhodopsins determined by high-speed atomic force microscopy and circular dichroic spectroscopy. Sci. Rep. 8(1) 8262 (11pages) (2018).

3.

M. Shibata*, H. Nishimasu*, N. Kodera, S. Hirano, T. Ando, T. Uchihashi, & O. Nureki*. Real-space and real-time dynamics of
CRISPR-Cas9 visualized by high-speed atomic force microscopy. Nat. Commun. 8(1) 1430 (9 pages) (2017).

Correlation Between Function and Mobilityof Protein Complex Revealed by HS-AFM
Mikihiro Shibata
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Structural biology has long contributed to our understanding of how proteins work by providing
detailed structures. However, the reported structures have been restricted to static information.
High-speed atomic force microscopy (HS-AFM) allows direct visualization of individual proteins inaction at sub-nanometer resolution under near physiological conditions. Our HS-AFM studies
performed in past few years have provided new mechanistic insight into the functional mechanism ofproteins. For example, HS-AFM movies of bacteriorhodopsin (bR), functions as a light-driven proton
pump, clearly showed that a cytoplasmic portion of bR displaced toward adjacent bR molecules at ~0.7 nm by light [1]. In addition, oligomeric structures of various microbial rhodopsins were directly
visualized and the stoichiometry of membrane proteins were determined in a lipid environment [2-4].
HS-AFM movies of CRISPR-Cas9, which has been widely used for genome editing tools, visualized
the real-space and real-time DNA cleavage by Cas9 [5]. Moreover, HS-AFM movies of hepatocyte
growth factor (HGF) with a macrocyclic peptide HiP-8 showed that binding of HiP-8 to HGF
restricted the flexibility of domains of HGF into static closed conformations, resulting in allostericinhibition [6]. Thus, HS-AFM is a powerful approach to directly visualize protein dynamics in liquid
environment. In this symposium, I would like to introduce our recent HS-AFM results ofcalcium/calmodulin-dependent protein kinase II.

References

43Yasufumi Takahashi

http://takahashi.w3.
kanazawa-u.ac.jp/
index.html

Professor
Department of Electronics, Graduate School of Engineering,Nagoya University, Japan
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

E-mail: takahashi.yasufumi.v5@f.mail.nagoya-u.ac.jp
Website: http://takahashi.w3.kanazawa-u.ac.jp/index.html

Research Interests
Scanning ion conductance microscopy, Single cell analysis, Live cell imaging

Education
2009

Doctor of Philosophy, Graduate School of Environmental Studies, Tohoku University

Professional Experience2020 - present
2020 - present2017 - 20202015 - 20172011 - 20132010 - 2011

Professor, Department of Electronics, Graduate School of Engineering,Nagoya University, Japan
Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Associate Professor, Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan
Associate Professor, Division of Electrical Engineering and Computer Science, Kanazawa University, Japan
Assistance Professor, Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Japan
JSPS Postdoctral Fellowship for Research Abroad, Division of Medicine, Imperial College London, UK

Honors2022

Horiba Masao Award

2020

Nakatani Foundation Incentive Award

2016

The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology;
The Young Scientists’ Prize

Publications

44

1.

Zhang, Y.; Takahashi, Y. et al., Nat. Commun., 2019, 10, 5610.

2.

Nashimoto, Y.; Takahashi, Y. et al. Acs Nano 2016, 10 (7), 6915-22.

3.

Zhang, Y. et al. Acs Nano 2016, 10 (3), 3214-21.

4.

Takahashi, Y.; et al. Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (29), 11540-11545.

5.

Takahashi, Y.; et al. Angew. Chem. Int. Ed. 2011, 50 (41), 9638-9642.

Development of Organelle Collection Technology
Using Nanopipette
Yasufumi Takahashi
Department of Electronics, Graduate School of Engineering, Nagoya University, Japan
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan

Super-resolution microscopy visualized nanoscale dynamics of proteins within the live cell. However,
it is difficult to distinguish more than seven fluoresecent proteins due to color restrictions, and acomprehensive evaluation technique for proteins and lipids is required. Scanning ion conductancemicroscopy (SICM) uses a nanopipette for detecting ion current and is an effective tool for live cell
topography imaging. The topography information of SICM is also effective to navigate thenanopipette on the sample surface for detecting the chemical and ejecting/collecting the chemical ata local region on a cell with nanoscale accuracy. Previously, we fabricated nanopipette-based
electrochemical and nanopore sensors to achieve oxygen, catecholamine, H 2 O 2 , and pH
imaging.1,3,4,5 However, it is difficult to detect proteins and lipids using electrochemical sensors.
The local cytosol collection is also an important application for SICM to reveal the localization ofmRNAs at a single-cell level. Since the fine structure of the nanopipette is difficult to control withconventional pressure, we have established a cytosol collection technique that utilizes changes ininterfacial tension by potential. 2 This system successfully detected local differences in Actb mRNA
expression levels within a single mouse fibroblast cell. However, proteins and lipids analysis remains
challenging due to collection volume issues. Machine learning and artificial intelligence have made it
possible to perform general human visual recognition and comprehensive judgment and haveproduced significant results in the structural analysis of membrane proteins. We have developed amachine learning-based single cell recognition and collection system. This auto-collection system not
only improves throughput but also has the potential to discover proteins that are expressed in aposition-specific manner and molecules related to protein-protein interactions by using AI technology
to perform identification equivalent to humans. The collected cytosol will be analyzed by NanoESI.

References

45

MEMO

46

Organized by
Nano Life Science Institute, Kanazawa University

Co-Organized by
Cancer Research Institute, Kanazawa University
Institute for Frontier Science Initiative, Kanazawa University

Contact
Secretariat
NanoLSI Administration Officenanolsi-office@adm.kanazawa-u.ac.jp

Websitehttps://nanolsi.kanazawa-u.ac.jp/6th-sympo/