3rd ExCELLS Retreat for Young Scientists
第 3 回 ExCELLS 若手リトリート

February 4, 2021
Online meeting

Organizers
Hirokazu Ishii (Nemoto Lab), Takahiro Kosugi (Koga group), Masashi Tanimoto (HigashijimaLab), Taiga Takahashi (Nemoto Lab), Kei Yamamoto (Aoki Lab), Daiki Fukuhara (Okumura
group), Takaaki Sokabe, Shigenori Nonaka, Yasuhiro Go, Tadashi Sato, Tomoyo Isogai1

目次（Index）

p.3,4

連絡事項（For Your Information）

p.5,6

スケジュール（Schedule）

pp.7-16 招待講演者紹介（Biography of Invited Speakers）
p.17

ポスター発表（Poster Presentation）

p.18,19 ポスタータイトルおよび発表グループ（List of Poster）【Web 公開版のため割愛】
pp.20-22 Zoom の使い方（How to use Zoom）
pp.23-25 Slack の使い方（How to use Slack）
p.26

連絡先（Contact）

2

目的
ExCELLS を中心とした若手の異分野間交流を推進し、将来の共同研究への発展を目指す

連絡事項
言語
日本語（発表や質疑応答は英語でも構いません）
守秘義務
 発表者の許可を得ない限り、発表資料の録画や録音、画面のキャプチャ保存等は禁止します。講演およびポスター発表には未公表の内容も含まれます。発表者の研究を尊重し、リトリート外へ情報共有をしないよう配慮をお願い致します。
 Zoom 会議の ID およびパスワードは他の人に教えないようにしてください。
招待講演 各セッションが始まる前の休憩時間（最初のセッション演者はリトリート開会前）に PCの動作確認を行っていただくようお願い致します。
 発表 25 分+質疑応答 5 分です。
ポスター発表（pp.17-19）
 発表は Zoom のブレイクアウトルームおよび画面共有機能を使って行います。
（Zoom ブレイクアウトルームの使い方については pp.20-22 に記載しています）
 発表形式は自由とします（PowerPoint, Keynote などのスライドショー、一面のポスターなど） 発表資料は英語で作成してください。
 ポスター発表は 3 つのセッションに分かれています。
 前半 2 回は、事前に指定された 4 人グループで発表 10 分＋質疑応答 5 分のポスタ
ー発表を行います。
 最後の 1 回では、前半グループと後半グループに分けて 30 分ずつ発表して頂きます。このセッションでは、自分の発表時間以外は自由に移動して発表を聴いて構いません（例えば、前半グループで発表した場合、後半は自由に移動できます）。
 発表グループは、p.18,19 に記載しています。
その他
 本リトリートでは、参加者同士の交流を促進するために Slack を用いた質疑応答や情報交換を行います。使い方の詳細は pp.23-25 に記載しています。
 発言時以外はマイクミュート、カメラオフでお願い致します。ご発言時はマイクをオンに、差し支えなければカメラをオンにして下さい。

3

For Your Information
Language
Japanese (English is acceptable for the presentation and Q&A.)
Confidentiality
 Recording of the presentation materials or saving screen captures is prohibited without
the permission of the presenter.
 Do not share your Zoom conference ID and password with anyone else.
Invited talks
 Please check in your PC during a break immediately before your session starts (or before
Opening Remark for speakers of the Invited Talk Session 1).
 Presentation 25 minutes + Q&A 5 minutes.
Poster presentation (pp.17-19)
 Presentations will be held in the Zoom Breakout rooms using Share.
(Instructions on how to use the Zoom Breakout rooms are provided on pp.20-22)
 The presentation format is free (slide show using PowerPoint, Keynote, poster, etc.)
 Presentation materials should be prepared in English.
 Poster presentations are divided into three sessions.
 In the first two sessions, poster presentations will be held in groups of four for 10
minutes plus 5 minutes for questions and answers.
 In the last session, presenters will be divided into the first half and the second half for
30 minutes each. You can move around and listen to the presentations except foryour own presentation time.
 Groups of the poster presentation are described in p.18,19.
Others In this retreat, Slack is used for Q&A and information exchange to promote interaction
among participants. Details on how to use it are provided on pp.23-25.
 Please mute your microphone and turn off your camera when listening to the talk.
Please turn on the microphone when speaking and the camera if you are not concerned.

4スケジュール

2月4日

8:30

ZOOM 受付開始

8:50-9:00

開会の挨拶 （加藤 晃一）

招待講演 1 （座長: 谷本昌志）
9:00-9:30
9:30-10:00
10:00-10:30

米原 圭祐 先生（デンマーク・Nordic EMBL/オーフス大学/DANDRITE）“Visual motion processing: cell types, circuits, and computation”
中村 哲也 先生（米国・ラトガース大学）“The genetic mechanisms of the fin-to-limb transition”
廣田 佳久 先生（芝浦工業大学・シンシナティ大学）“Research Study Abroad for a Corona Period～Tips on research and life at University of Cincinnati～”

招待講演 2 （座長: 小杉貴洋）
10:45-11:15
11:15-11:45

11:45-13:00

Daniel-Adriano Silva 先生（米国・Neoleukin Therapeutics）“De Novo Design of Therapeutics During the Pandemic”
望月 建爾 先生（中国・浙江大学）“Study on Water, in China”
昼食

招待講演 3 （座長: 石井宏和）
13:00-13:30
13:30-14:00

14:00-14:05

宮﨑 牧人 先生（京都大学白眉センター）“In vitro reconstitution of cytoskeletal dynamics”
平松 弘嗣 先生（台湾・国立交通大学）“Development of LC-Raman system”
集合写真撮影ポスター発表14:10-14:15
14:15-15:15
15:15-15:30
15:30-16:30

イントロダクション
Session 1 (15 min x 4)
休憩（次のグループへ移動）
Session 2 (15 min x 4)

Session 3 (30 min x 2)
16:30-17:00
前半グループ
17:00-17:30

後半グループ

17:30-17:40

閉会の挨拶 （郷康広）

17:40-19:00

フリーディスカッション

5

Schedule
8:30
8:50-9:00

February 4th
ZOOM meeting open
Welcome & Opening Remark (Koichi Kato)

Invited Talk Session 1 (Chair: Masashi Tanimoto)
9:00-9:30

9:30-10:00
10:00-10:30

Keisuke YONEHARA（Denmark・Nordic EMBL/Aarhus University/DANDRITE）“Visual motion processing: cell types, circuits, and computation”
Tetsuya NAKAMURA（United States・Rutgers University）“The genetic mechanisms of the fin-to-limb transition”
Yoshihisa HIROTA（Shibaura Institute of Technology/University of Cincinnati）“Research Study Abroad for a Corona Period～Tips on research and life at University of Cincinnati～”

Invited Talk Session 2 (Chair: Takahiro Kosugi)
10:45-11:15
11:15-11:45

11:45-13:00

Daniel-Adriano Silva（United States・Neoleukin Therapeutics）“De Novo Design of Therapeutics During the Pandemic”
Kenji MOCHIZUKI（China・Zhejiang University）“Study on Water, in China”
Lunch

Invited Talk Session 3 (Chair: Hirokazu Ishii)
13:00-13:30
13:30-14:00

14:00-14:05

Makito MIYAZAKI（Kyoto University）“In vitro reconstitution of cytoskeletal dynamics”
Hirotsugu HIRAMATSU（Taiwan・National Chiao Tung University）“Development of LC-Raman system”
Group photo

Poster Presentation Session
14:10-14:15
14:15-15:15
15:15-15:30
15:30-16:30

Introduction
Session 1 (15 min x 4)
Break（Please move to the next group）
Session 2 (15 min x 4)

Session 3 (30 min x 2)
16:30-17:00
First group17:00-17:30
Second group17:30-17:40
17:40-19:00

Closing remark (Yasuhiro Go)Free discussion

6

Invited Speakers
米原 圭祐 先生（デンマーク・Nordic EMBL/オーフス大学/DANDRITE）
Keisuke YONEHARA（Denmark・Nordic EMBL/Aarhus University/DANDRITE）
中村 哲也 先生（米国・ラトガース大学）
Tetsuya NAKAMURA（United States・Rutgers University）
廣田 佳久 先生（芝浦工業大学・シンシナティ大学）
Yoshihisa HIROTA（Shibaura Institute of Technology/University of Cincinnati）
Daniel-Adriano Silva 先生（米国・Neoleukin Therapeutics）
Daniel-Adriano Silva（United States・Neoleukin Therapeutics）
望月 建爾 先生（中国・浙江大学）
Kenji MOCHIZUKI（China・Zhejiang University）
宮﨑 牧人 先生（京都大学白眉センター）
Makito MIYAZAKI（Kyoto University）
平松 弘嗣 先生（台湾・国立交通大学）
Hirotsugu HIRAMATSU（Taiwan・National Chiao Tung University）

7

Visual motion processing: cell types, circuits,
and computation
Keisuke Yonehara
DVM, PhD, Associate Professor, Group Leader
DANDRITE, Nordic EMBL, Aarhus University
keisuke.yonehara@dandrite.au.dk
Carrier history
20202015-

PRESTO researcher, DANDRITE, Aarhus University, DenmarkGroup leader/Associate professor, DANDRITE, Nordic EMBL, Department of Biomedicine,
Aarhus University, Aarhus, Denmark.
2009-2014 Postdoc, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland (Botond Roskalab)
2003-2008 PhD in Molecular Neurobiology, The Graduate University for Advanced Studies [SOKENDAI],
Okazaki, Japan (Masaharu Noda lab)
1997-2003 BSc and DVM in Veterinary Medical Science, The University of Tokyo, Tokyo, Japan (Masugi
Nishihara lab)

Research background
Inferring the direction of image motion is a fundamental component of visual computation and essential for
visually guided behavior. In the retina, the direction of image motion is encoded in direction-selective retinal
ganglion cells. My research group aims to understand the structure, function, development, and disease of neuralcircuits underlying retinal direction selectivity and how retinal motion signals impact central visual processing.

Message to young researchers“Push your limits” by Botond Roska. “Thinking is hard work; that’s why few do it” by Albert Einstein.
References[1] Synapse-specific direction selectivity in retinal bipolar cell axon terminals. Matsumoto A et al.,bioRxiv, doi: https://doi.org/10.1101/2020.10.12.335810[2] Binocular integration of retinal motion information underlies optic flow processing by the cortex. Rasmussen
NR, Matsumoto A, et al., Curr Biol, in press. bioRxiv, doi: https://doi.org/10.1101/2020.10.12.335810[3] Rapid ‘multi-directed’ cholinergic transmission at central synapses. Sethuramanujam S, Matsumoto A et al.,Nat Commun, in press. bioRxiv, doi: https://doi.org/10.1101/2020.04.18.048330[4] Contributions of Retinal Direction Selectivity to Central Visual Processing. Rasmussen R, Yonehara K (2020),
Curr Biol 30: PR897-R903.
[5] A segregated cortical stream for retinal direction selectivity. Rasmussen R, Matsumoto A et al., 2020, Nat
Commun 11: 831.
[6] Spatiotemporally Asymmetric Excitation Supports Mammalian Retinal Motion Sensitivity. Matsumoto A et al.,2019, Curr Biol 29: 3277-3288.
[7] Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction
Selectivity. Yonehara K, Fiscella M et al., 2016, Neuron 89: 177-193. Best of Neuron 2016[8] The first stage of cardinal direction selectivity is localized to the dendrites of retinal ganglion cells. Yonehara
K, Farrow K et al., 2013, Neuron 79: 1078-1085.
[9] Spatially asymmetric reorganization of inhibition establishes a motion-sensitive circuit. Yonehara K et al., 2011,
Nature 469: 407-410.
[10] Identification of retinal ganglion cells and their projections involved in central transmission of information about
upward and downward image motion. Yonehara K et al., 2009, PLoS One 4: e4320.

8

The genetic mechanisms of the fin-to-limb
transition
Tetsuya Nakamura
Assistant professor
Department of Genetics, Rutgers the State University of New Jersey
nakamura@dls.rutgers.edu
Lab website: http://nakamuralab.com
Carrier history
2018-Present

Assistant Professor, Rutgers the State University of New Jersey

2012-2017

Postdoctoral Researcher, University of Chicago
Supported by fellowships of JSPS, Uehara memorial foundation, andMarine Biological Laboratory

2008-2012

Assistant Professor, Osaka University

2007-2008

Postdoctoral Scholar, Osaka University
Supported by JSPS fellowship

2002-2007

Graduate student, Osaka University
Supported by JSPS fellowshipResearch background
During the water-to-land transition, a number of body structures were modified and new structures evolved as
can be seen such as in the skull, jaw, shoulder, lung, and appendages. Whereas these morphological changes arecentral to the evolution of tetrapods, little research has been done to discern their developmental bases andidentify the contribution to the evolutionary mechanisms. Bridging functional genomics, embryology, andcomparative anatomy, we currently identify the genetic mechanisms underlying the appendage evolution fromfish to tetrapods, namely the fin-to-limb transition.

Message to young researchers
Of particular importance for young scientists is experiencing different scientific culture in US or Europe at least
for a couple of years. Although state-of-the-art equipment and technique are available in Japan, learning how to
conduct science in western countries would help you success as scientists. Just come to US or Europe and workwith many outstanding researchers. I promise that working abroad changes your life!
References[1] Turner N, Mikalauskaite D, Barone K, Flaherty K, Senevirathne G, Adachi N, Shubin NH and Nakamura T.
The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids
Proc Biol Sci. 2019 Nov 6;286(1914):20191571.
[2] Nakamura T, Gerhke AR, Lemberg J, Szymaszek J, Shubin NH.
Digits and fin rays share common developmental histories.
Nature. 2016 Aug 17;537(7619):225-228.
[3] Nakamura T, Klomp J, Pieretti J., Schneider I.,Gerhke AR., Shubin NH.
Molecular mechanisms underlying the exceptional adaptations of batoid fins.
Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15940-5.

9Research Study Abroad for a Corona Period～Tips on research and life at University of Cincinnati～

Yoshihisa Hirota Ph.D.
Position：Associate Professor (SIT), Visiting Scholar (UC)
Affiliation：Shibaura Institute of Technology (SIT)
University of Cincinnati (UC)
Email address：hirotay@shibaura-it.ac.jp (SIT)
hirotaya@ucmail.uc.edu (UC)
Carrier history
2004-2006
2006-2008
2008-20102010-20132012-20132013-20142013-20142013-20142014-20162016-20192019-present
2019-2020
2020-2021

Undergraduate thesis research, Kobe Pharmaceutical University, Japan
Master thesis research, Kobe Pharmaceutical University Graduate School, Japan
Researcher, Production Technology Research Institute, Kyowa Kirin Co. Ltd
Doctoral thesis research, Kobe Pharmaceutical University Graduate School, Japan
Research Fellow DC2, Japan Society for the Promotion of Science, Japan
Research Fellow PD, Japan Society for the Promotion of Science, Japan
Postdoctoral Research Fellow, Kobe Pharmaceutical University, Japan
Special researcher, ERATO Murata Research Center for Lipid Active Structure Project
Osaka University, Japan
Assistant Professor, Faculty of Pharmacy, Suzuka University of Medical Sciences,Japan
Assistant Professor (Tenure Track), Department of Bioscience and Engineering,
Shibaura Institute of Technology, Japan
Associate Professor (Principal Investigator), Department of Bioscience and Engineering,
Shibaura Institute of Technology, Japan
Visiting Lecturer, Division of Antiviral Chemotherapy, Center for Chronic Viral
Diseases, Kagoshima University, Japan
Visiting Scholar, College of Medicine, University of Cincinnati, U.S.A.

Research backgroundMolecular nutrition research with a focus on lipid-soluble vitamins (especially Vitamins K and D)
Physiological function analysis of GTP sensor PI5P4Kb

Message to young researchers
Thank you for your interest. I would like to share with you “How I decided to study abroad” and “What I enjoyed
and what I found difficult during Corona”. I will try to provide as much useful information as possible to young
researchers. If you have any questions, please feel free to contact me! I am looking forward to meeting you. To
the young researchers, “Enjoy your research”!
References (+: Co-first authors; *: Corresponding author)[1] Nakagawa K., Hirota Y., Okano T., et al, Nature, 468, 117-121 (2010).
[2] Hirota Y., Okano T., et al, J. Biol. Chem., 288, 33071-33080 (2013).
[3] Hirota Y#. and Suhara Y#. Int. J. Mol. Sci., 20, pii: E3006 (2019).
[4] Yoshimura H+., Hirota Y+., Suhara Y., et al, Bioorg. Med. Chem. Lett., 30, 127059 (2020).
[5] Nishikawa M., Hirota Y., Sakaki T., et al, Sci. Rep., 10, 5677 (2020).
[6] Sato T+., Hirota Y+., Suhara Y., et al, J. Med. Chem., 64, in press (2021).
[7] Ikeda Y., Hirota Y., Sasaki AT., et al, J. Biochem., 169, in press (2021).

10

De Novo Design of Therapeutics During thePandemic
Daniel Adriano Silva Manzano
V.P. Head of Research and Co-Founder
Neoleukin Therapeutics, Inc.
dadriano@neoleukin.com

Career history
2019-present. V.P. head of research & co-founder . Neoleukin Therapeutics, Inc., Seattle, WA, USA.
− Responsible for Neoleukin research programs; leading a research group of ~30 full time members.
2018-2019. Faculty. Acting instructor and translational investigator. Department of Biochemistry, Institute forProtein Design,
University of Washington, Seattle, WA, USA.
− Development of the Neoleukin platform for the de novo design of cytokine mimics.
− Development of computational algorithms for the de novo design of protein interfaces.

Research background2013-2018. Postdoctoral. Senior research fellow . Advisor: Dr. David Baker, University of Washington, Seattle,
WA, USA.
− High throughput design of de novo proteins.
− Design of protein-protein interfaces.
− Development of computational algorithms for de novo protein design.
2010-2013. Postdoctoral. Research associate. Advisor: Dr. Xuhui Huang, Hong Kong University of Scienceand Technology, Hong
Kong SAR, Hong Kong.
− Fundamental mechanisms of transcription in the RNA Polymerase II by multiscale computer simulations.
− Ligand binding mechanisms in periplasmic binding proteins by molecular dynamics simulations and Markov
State Models.
− Mechanisms of electron transfer in the photosynthetic complex II by combining Molecular mechanics,
Quantum mechanics, andMarkov Models.
2006-2010. Undergraduate, Master and PhD. UNAM, Mexico City, Mexico :− (Ph.D) Thesis: In silico characterization of the molecular basis of ligand binding in the periplasmic protein
LAO.
− (Master) Thesis: Computational redesign of the periplasmic protein LAO to bind non-natural ligands.
− (Bachelor) Thesis: The role of electrostatics in ligand binding by the periplasmic protein LAO.

Message to young researchers“Be thoughtful, logical and persevere following your dreams.”

11

References
https://scholar.google.com/citations?user=3_MEiYkAAAAJ&hl=en ; *Equally-contributing first author;§
Co-corresponding author[1] Linsky, T.W., Vergara, R., Codina, N., Nelson, J.W., Walker, M.J., Su, W., Barnes, C.O., Hsiang, T.Y., EsserNobis, K., Yu, K. and Reneer, Z.B., Hou Y-J., Priya T., Mitsumoto M., Pong A., Lau U.Y., Mason M.L., Chen J.,
Chen A., Berrocal T., Peng H., Clairmont N.S., Castellanos J., Lin, Y.-R., Josephson-Day A., Baric R.S., Fuller
D.H., Walkey C.D., Ross T.M., Swanson R., Bjorkman P.J., Gale Jr. M., Blancas-Mejia L.M., Yen H.-L. andSilva D.-A . De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2 (2020). Science,
370(6521), pp.1208-1214. DOI: 0.1126/science.abe0075[2] Leman, J.K., Weitzner, B.D., Lewis, S.M., Adolf-Bryfogle, J., Alam, N., Alford, R.F., Aprahamian, M., Baker,
D., Barlow, K.A., Barth, P., Basanta, B., Et al. Macromolecular modeling and design in Rosetta: recent methods
and frameworks (2020). Nature Methods, pp.1-14. DOI: 10.1038/s41592-020-0848-2[3] Quijano-Rubio A., Ulge U.-Y., Walkey C.-D.§ and Silva D.-A§ . The advent of de novo proteins for cancer
immunotherapy (2020). Current Opinion in Chemical Biology. DOI: 10.1016/j.cbpa.2020.02.002[4] Koepnick, B., Flatten, J., Husain, T., Ford, A., Silva, D.A., Bick, M.J., Bauer, A., Liu, G., Ishida, Y., Boykov, A.
and Estep, R.D. De novo protein design by citizen scientists (2019). Nature, p.1. DOI: 10.1038/s41586-0191274-4[5] Silva, D.A.*,§ , Yu S.*, Ulge U.*, Spangler J.B.*, Jude K.M., Labão-Almeida C., Ali L. R., Quijano-Rubio A.,
Ruterbusch M., Leung I., Biary T., Crowley S., Marcos E., Walkey C. D. , Weitzner B. D. , Pardo-Avila F., Carter
L., Stewart L., Riddell S., Pepper M., Bernardes G. J.L., Dougan M., Garcia K.C.§ and Baker D.§. De novo designof potent and selective mimics of IL-2/IL-15 (2019). Nature, 565(7738), p.186. DOI: 10.1038/s41586-018-08307[6] Marcos, E.*,§ , Silva, D.A.*,§ . Essentials of de novo protein design: Methods and applications (2018). WIREs
Computational Molecular Science, DOI:10.1002/wcms.1374[7] Silva, D.A., Stewart, L., Lam, K.H., Jin, R. and Baker, D. Structures and disulfide cross ‐ linking of de novo
designed therapeutic mini ‐ proteins (2018). The FEBS journal, DOI: 10.1111/febs.14394[8] Hosseinzadeh P., Bhardwaj G., Mulligan V.K., Shortridge M.D., Craven T.W. , Pardo-Avila F., Rettie S.A., Kim
D.E., Silva D.A., Ibrahim Y.M., Webb I.K., Cort J.R., Adkins J.N., Varani G., Baker D. Comprehensive
computational design of ordered peptide macrocycles (2017). Science, 15/Dec/2017 , 1461-1466. DOI:
10.1126/science.aap7577[9] Chevalier A.*, Silva D.A.*, Rocklin G.J.*, Derrick R.H., Vergara R., Murapa P., Bernard S.M., Zhang L., Lam
K-H, Yao G, Bahl C.D. , Miyashita S.I., Goreshnik I, Fuller J.T., Koday M.T., Jenkins C., Colvin T., Carter L.,
Bohn A., Bryan C.M., Fernández-Velasco D.A., Stewart L., Dong M., Huang X., Jin R., Wilson I. A. , Fuller
D.H. and Baker D., Massively parallel de novo protein design for targeted therapeutics (2017). Nature,
550(7674), p.74. DOI: 10.1038/nature23912[10] Dang, B., Wu, H., Mulligan, V.K., Mravic, M., Wu, Y., Lemmin, T., Ford, A., Silva, D.A., Baker, D. and DeGrado,
W.F. De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures (2017) .
Proceedings of the National Academy of Sciences, 114 (41), pp.10852-10857. DOI: 10.1073/pnas.1710695114[11] Marcos, E.*, Basanta, B.*, Chidyausiku, T.M., Tang, Y., Oberdorfer, G., Liu, G., Swapna, G.V.T., Guan, R., Silva,
D.A., Dou, Pereira, J.H., Xiao R., Sankaran B., Zwart P.H., Montelione G.T. and Baker D., Principles fordesigning proteins with cavities formed by curvedβsheets (2017). Science, 355(6321), pp.201-206. DOI:
10.1126/science.aah7389[12] Da, L.T., Pardo-Avila, F., Xu, L., Silva, D.A ., Zhang, L., Gao, X., Wang, D. and Huang, X., Bridge helix bending
promotes RNA polymerase II backtracking through a critical and conserved threonine residue (2016).Naturecommunications, 7. DOI: 10.1038/ncomms11244[13] Berger, S., Procko, E., Margineantu, D., Lee, E.F., Shen, B.W., Zelter, A., Silva, D.A., Chawla, K., Herold, M.J.,
Garnier, J.M. and Johnson, R., MacCoss M.J., Lessene G., Davis T.N., Stayton P.S., Stoddard B.L., Fairlie W.D.,
Hockenbery D.M. and Baker D., Computationally designed high specificity inhibitors delineate the roles of BCL2
family proteins in cancer (2016). eLife, 5, p.e20352. DOI: 10.7554/eLife.20352[14] Zhang, L., Silva, D.A. , Pardo-Avila, F., Wang, D. and Huang, X., Structural Model of RNA Polymerase II
Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes (2015). PLoS
computational biology, 11(7), p.e1004354. DOI:10.1371/journal.pcbi.1004354[15] Zhang, L., Silva, D.A. , Zhang, H., Yue, A., Yan, Y. and Huang, X., Dynamic protein conformations preferentiallydrive energy transfer along the active chain of the photosystem II reaction centre (2014) . Naturecommunications, 5. DOI: 10.1038/ncomms5170

12

[16] Silva, D.A. , Weiss, D. R., Avila, F. P., Da, L. T., Levitt, M., Wang, D.†and Huang, X.†., Millisecond dynamics
of RNA polymerase II translocation at atomic resolution (2014). Proceedings of the National Academy of
Sciences, 111(21), 7665-7670. DOI:0.1073/pnas.1315751111[17] Pulido, N.O., Silva, D.A. , Tellez, L.A., Pérez-Hernández, G., García-Hernández, E., Sosa-Peinado, A. andFernández-Velasco, D.A., On the molecular basis of the high affinity binding of basic amino acids to LAOBP, aperiplasmic binding protein from Salmonella typhimurium (2015). Journal of Molecular Recognition, 28(2),pp.108-116. DOI: 10.1002/jmr.2434[18] Sheong, F. K., Silva, D. A., Meng, L., Zhao, Y., & Huang, X., Automatic state Partitioning for Multi-body systems(APM): An Efficient Algorithm for Constructing Markov State Models to Elucidate Conformational Dynamics
of Multi-body Systems (2014). Journal of chemical theory and computation, 11(1), pp.17-27. DOI:
10.1021/ct5007168[19] Gu, S., Silva, D.A., Meng, L., Yue, A. and Huang, X., Quantitatively Characterizing the Ligand Binding
Mechanisms of Choline Binding Protein Using Markov State Model Analysis (2014). PLoS computational
biology, 10(8), e1003767. DOI: 10.1371/journal.pcbi.1003767[20] Zhang, L., Silva, D. A. , Zhang, H., Yue, A., Yan, Y., & Huang, X., Dynamic protein conformations preferentiallydrive energy transfer along the active chain of the photosystem II reaction centre (2014) . Naturecommunications, 5. DOI: 10.1038/ncomms5170[21] Yao, Y., Cui, R. Z., Bowman, G. R., Silva, D. A. , Sun, J., & Huang, X., Hierarchical Nyström methods forconstructing Markov state models for conformational dynamics (2013). The Journal of chemical physics,
138(17), 174106. DOI: 10.1063/1.4802007[22] Zhang L, Silva DA, Yan Y, Huang X. Force field development for cofactors in the photosystem II (2012). Journalof Computational Chemistry. 33 (25), 1969-1980. DOI: 10.1002/jcc.23016[23] Hong Y, Meng L, Chen S, Leung C, Da L, Faisal M, Silva DA, Liu J, Lam J, Huang X, Tang B. Monitoring andInhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission
Characteristics (2012), Journal of the American Chemical Society, 134(3):1680-9. DOI: 10.1021/ja208720a[24] Cui RZ, Silva DA, Song J, Bowman GR, Zhuang W, Huang X., Bridging the gap between optical spectroscopic
experiments and computer simulations for fast protein folding dynamics (2012), Current Physical Chemistry,2(1): 45-58. DOI: 10.2174/1877946811202010045[25] Silva D.A., Bowman GR, Sosa-Peinado A, and Huang X., A Role for Both Conformational Selection and Induced
Fit in Ligand Binding by the LAO Protein (2011). PLOS Computational Biology, 7(5):e1002054. DOI:
10.1371/journal.pcbi.1002054[26] Liu X, Bushnell DA, Silva D.A., Huang X, and Kornberg R.D., Initiation Complex Structure and Promoter
Proofreading (2011). Science, 333(6042):633-7. DOI: 10.1126/science.1206629[27] Silva D.A., Dominguez-Ramirez L, Rojo-Dominguez A, and Sosa-Peinado A., Conformational dynamics of Llysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity (2011). Proteins, 79(7):20972108. DOI: 10.1002/prot.23030[28] Zhuang W, Cui RZ, Silva DA, and Huang X., Simulating the T-Jump- Triggered Unfolding Dynamics of trpzip2
Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach(2011). The Journal of Physical Chemistry B, 115(18):5415-5424. DOI: 10.1021/jp109592b[29] Martínez-Becerra F, Silva DA, Domínguez-Ramírez L, Mendoza-Hernández G, López- Vidal Y, Soldevila G,
and García-Zepeda EA., Analysis of the antimicrobial activities of a chemokine-derived peptide (CDAP-4) on
Pseudomonas aeruginosa (2007). Biochemical and Biophysical Research Communications, 355(2):352-358.
DOI: 10.1016/j.bbrc.2007.01.188
Book chapters:* Equally-contributing first author[1] Silva D.A. , Correia B.E. and Procko E., Motif-driven design of protein-protein interfaces. Methods in Molecular
Biology; Barry Stoddard and David Baker (Editors). Computational Design of Ligand Binding Proteins, pp.285304. DOI: 10.1007/978-1-4939-3569-7_17[2] Da L.T.*, Sheong F.K.*, Silva D.A.* and Huang X. Application of Markov State Models to Simulate Long
Timescale Dynamics of Biological Macromolecules. Springer. Protein Conformational Dynamics. Springer
International Publishing, 2014. 29-66. . DOI: 10.1007/978-3-319-02970-2_2[3] Sosa-Peinado A, Silva-Manzano D.A., González-Andrade M., and Pérez-Hernández G. Recent advances inbiophysical techniques to determine the dynamics of proteins in solution. Advances in Protein Physical
Chemistry; Garcia-Hernandez, E. and D. Alejandro Fernandez-Velasco (Editors). Research Signpost, Kerala,
India, 2008. ISBN: 978-81-7895-324-3

13

Study on Water, in China
Kenji Mochizuki
ZJU 100 Young Professor
Department of Chemistry, Zhejiang University, Chinakenji_mochizuki@zju.edu.cn
Carrier history
KM has focused on the molecular mechanism of natural phenomena related to water and ice, using computer
simulations and statistical mechanics. He received his PhD from SOKENDAI in 2014, where he investigated
the trigger for homogeneous ice melting [1]. During his PhD, he spent six months in University of Cambridgefor collaborative research. He then became a research assistant professor at Okayama University, where heworked on the influence of extreme confinement on the phase behavior of water [2]. In 2016, he stayed at Purdue
University for one year, where he tried an experimental approach, Raman-MCR, to elucidate the hydration shelltransformation around stimuli-sensitive polymers [3]. In 2017, he joined University of Utah as a JSPS Overseas
Research Fellow, where he returned to a computer chemist and studied the promotion/inhibition of ice nucleation
by macromolecules [4][5]. After working as an assistant professor at Shinshu University for two and a half years[6], he was promoted to a tenure-track professor at Zhejiang University in 2020.

Research background
Water/Ice is a unique material and has been a subject of broad interest across many natural science disciplines
and various industries (e.g., desalination and cryo-preservation). Ice exhibits an extraordinarily richpolymorphism due to its three-dimensional hydrogen bond network. The hunt for new ice phases is still ongoing;
the latest one, ice XVIII, was experimentally discovered in 2019 and computer simulations have predicted manyother potential ices. The dynamical mechanism of freezing/melting also remains to be studied, and computer
simulations are encouraged to provide insights into the microscopic aspects of ice/liquid nucleation, because ofits minute time and length scale. Furthermore, there is growing interest in how macromolecules, such as
antifreeze proteins, control nucleation/growth of ice, and how water changes its structural and dynamical
properties under nanoscale confinement, such as carbon nanotubes and metal-organic frameworks. Therefore,
although water has been studied for more than a century, our understanding of phase diagram and phasetransition dynamics of water is far from complete, so that there is still room for further research.

Message to young researchers
Daily tasks for a researcher, conducting experiments/simulations and writing papers, are the same in any country.
Thus, your scientific training as a PhD candidate or postdoctoral fellow enables you to work abroad, and there
should be more opportunities if you look around the world.
References[1] K. Mochizuki, M. Matsumoto, I. Ohmine, Nature, 498, 350-354 (2013)[2] K. Mochizuki, K. Koga, Proc. Natl. Acad. Sci. USA, 112, 8221-8226 (2015)[3] K. Mochizuki, S. R. Pattenaude, D. Ben-Amotz, J. Am. Chem. Soc., 138, 9045-9048 (2016)[4] K. Mochizuki, Y. Qiu, V. Molinero, J. Am. Chem. Soc., 139, 17003–17006 (2017)[5] K. Mochizuki, V. Molinero, J. Am. Chem. Soc., 140, 4803-4811(2018)[6] K. Mochizuki, J. Phys. Chem. B, 124, 9951-9957 (2020)14

In vitro reconstitution of cytoskeletal dynamics
Pleaseattachyourface photo.

Makito Miyazaki
Associate Professor
The Hakubi Center for Advanced Research & Department of Physics, Kyoto
University
miyazaki.makito.3s@kyoto-u.ac.jp

Carrier history
03/2011
Ph.D., Department of Physics, Kyoto University
04/2011 – 03/2015 Post-Doctoral Fellow, Department of Physics, Waseda University
04/2015 – 09/2017 Assistant Professor, Department of Physics, Waseda University
10/2017 – present
Associate Professor, The Hakubi Center for Advanced Research & Department of Physics,
Kyoto University
10/2018 – present
Invited Researcher, Institut Curie
12/2020 – present
PRESTO Researcher (Area: Supra-assembly of biomolecule)Research backgroundThe cytoskeleton is an essential intracellular structure that regulates various key functions of animal cells
including motility, division, and polarity establishment. Using an in vitro reconstitution approach, in
combination with single-molecule manipulation, live cell imaging, and physical modeling, our team aim tounderstand the self-assembly mechanism of cytoskeletal networks and the regulatory mechanism of various
cellular functions controlled by the cytoskeleton.

Message to young researchers
I think the most important thing is to find fun in your daily work and enjoy doing experiments.
I would also recommend finding what you are good at in the early stage of your carrier.
References (‡ equal contribution, *corresponding author)[1] R. Sakamoto‡, M. Tanabe‡, T. Hiraiwa, K. Suzuki, S. Ishiwata, Y. T. Maeda, and M. Miyazaki*, “Tug-of-war
between actomyosin-driven antagonistic forces determines the positioning symmetry in cell-sized
confinement”, Nat. Commun. 11, 3063 (2020).
[2] K. Suzuki, M. Miyazaki*, J. Takagi, T. Itabashi, and S. Ishiwata, “Spatial confinement of active microtubule
networks induces large-scale rotational cytoplasmic flow”, Proc. Natl. Acad. Sci. USA 114, 2922–2927(2017).
[3] M. Miyazaki, M. Chiba, H. Eguchi, T. Ohki, and S. Ishiwata*, “Cell-sized spherical confinement induces the
spontaneous formation of contractile actomyosin rings in vitro”, Nat. Cell Biol. 17, 480–489 (2015).
[4] M. Chiba‡, M. Miyazaki‡, and S. Ishiwata*, “Quantitative analysis of the lamellarity of giant liposomes
prepared by the inverted emulsion method”, Biophys. J. 107, 346–354 (2014).

15

Development of LC-Raman system
Hirotsugu HIRAMATSU
Assistant Professor
Department of Applied Chemistry, National Chiao Tung University
hiramatu@nctu.edu.tw

Carrier history
2002.3
2002.42005.92016.8

PhD (Chemistry), The University of Tokyo
Postdoctoral fellow, Okazaki Institute for Integrative Bioscience
Assistant Professor, Graduate School of Pharmaceutical Sciences, Tohoku University
Assistant Professor, Department of Applied Chemistry, National Chiao Tung University

Research background
Dr Hiramatsu has the experience of structural chemistry and molecular spectroscopy. He received his PhD
degree with a dissertation entitled" development of infrared electroabsorption spectroscopy and its application
to molecular structures in liquids." He started applying vibrational spectroscopy to biomolecules, in particular
proteins, during a postdoc period. Since then, he has tackled to several problems on the protein structure and itschanges. Recent research efforts are directed toward elucidating the relationship between structure and(dys)function of proteins and developing new applications of vibrational spectroscopy for biomolecules.
Message to young researchers
When I was a postdoctoral fellow at the Okazaki Institute for Integrative Bioscience in Yamate campus (20022005), I wondered if I would be able to continue my research and what would happen to me in the future. I
remember strolling along the railway tracks of Meitetsu line on Saturday evenings with a vague sense of anxiety
in my heart. With the kind support of the professors, colleagues, and junior colleagues, fortunately, I havecontinued my research until today. What I would like to say to myself at that time and to you today is that yourfuture is leading somewhere in any way. Note that there is no guarantee that the desired position will be favorable
as you imagine, and you may fit a place you arrive unexpectedly. To get success in your place (now and in the
future), please first hone your capabilities. That is to accumulate something within yourself to communicate toothers. Next, please consider the efficient way to deliver the information. This term is your outer surface andincludes logical explanations, foreign languages, and so on. Finally, please think about the factor of "luck." Theysay this factor is always not controllable, but whether you judge a certain situation as "lucky" or not is subjective
and controllable. Please enjoy the daily life and your research while considering, worrying, and preparing forthe future.

References[1] S. -H. Chen and H. Hiramatsu, J. Phys. Chem. B 123 (2019) 10663.
[2] Y. -H. Lo and H. Hiramatsu, Anal. Chem. 92 (2020) 14601.
[3] C. -I. Wen, C. -N. Yu, N. Thirumalaivasan and H. Hiramatsu, J. Raman Spectrosc. in press (2020)[10.1002/JRS.6039]

16

ポスター発表 （若手研究者の議論の場）
Poster Presentation (Discussion Session for Young Researchers) 若手研究者（大学院生、研究員、助教など）のための議論の場です。”若手研究者”の方は奮って参加ください。
This session is for young researchers (graduate students, post doctoral fellows, assistantprofessors, etc.).
 ブレイクアウトルームにて行います。ブレイクアウトルームの説明（p. 21,22)を参照。
Breakout rooms are used for this session. (See the details of breakout rooms p. 21,22)
 Session1,2 では、発表者は決められたルームへ移動してください。その他の方は好きなルームに移動してください。これまでに出会ったことの無い分野の異なる研究者との交流を楽しんでください。
Session1,2: Speakers talk in their assigned rooms and others discuss in the rooms theywant.
 Session3 は前後半に分かれています。1-XX の発表者は前半に決められたルームへ、2-XXの発表者は後半に決められたルームで講演してください。聴講者は好きな部屋に移動してください。共同研究を一緒にできそうな研究者の話を聞いて、共同研究の種を探してみてください。
Session3: This session is separated into two parts. Speakers 1-XX talk in their assigned
rooms at first half and speakers 2-XX talk in their assigned rooms at second half. Others
discuss in the rooms they want.
 閉会後の Free discussion では自由にブレイクアウトルームを使ってください。さらに交流したい研究者同士が誘いあって好きなブレイクルームに移動してください。共同研究
したい者同士も誘い合ってブレイクアウトルームに移動し、次年度の ExCELLS 若手奨励
研究への申請にむけた共同研究の話し合い場として利用してください。
After closing this retreat, we keep breakout rooms. We can discuss more in breakout rooms.

17

ポスタータイトルおよび発表グループ（List of Poster）

18

19

Zoom の使い方（How to use Zoom）
注意事項（Information）


必ず参加登録と同じ氏名でご入室ください
Sign in to the Zoom meeting with the registered name.



Zoom 上で表示されているお名前をもとに、参加登録の有無を確認したのちに入室を許可します。情報セキュリティーの観点から、同定できないお名前での入室は許可しない場合があります。（Zoom アプリ右上のご自身のアイコンをクリックし、「設定」→「プロフィール」→「プロファイルを編集します」に進むとお名前の変更が可能です。ウェ
ブブラウザから入室の際は、都度お名前を入力可能です。）
We accept to enter the meeting by matching your name on Zoom with the registered
name.



若手研究者の方は氏名の後に(Y)を、シニア研究者の方は名前の後に(S)をつけてください。例えば、「石井宏和(Y)」、「郷康広(S)」としてください。(Y)のついていない方はシニア研究者と判断します。
Young researchers: please attach (Y) to the last of your name.
Senior researchers: please attach (S) to the last of your name.



一度入室されたあとは、Zoom の接続を切断せず、カメラとマイクをオフにしてください（再度接続いただく際は、再度お名前の照合を行います）
After you sign in the Zoom meeting, please keep the connection and turn off your cameraand microphone.



録画・録音は禁止します。
Recording prohibited.



問題があった場合は、緊急連絡先（hi@nips.ac.jp , +81-564-59-5255）、もしくは Slackの#help チャンネルまでご連絡ください。
If you have any problems, please contact to hi@nips.ac.jp or #help channel on Slack.

20

質問の仕方 How to ask your questions
1. 発表後、チャットに「質問」とご記入ください。
After invited talks, please write "Question" in the chat if you have a question.
2. 座長が順に指名いたします（“若手研究者”からの質問を優先します）。ミュート解除してご質問ください。
After the chair calls you (young researchers have priority), please unmute and ask yourquestion.

ブレイクアウトルームについて What are Breakout Rooms?
オンライン上で個別の部屋を作ります。
Breakout rooms allow you to split your Zoom meeting.

21

「ブレイクアウトルーム」の入り方 How to enter Breakout Rooms
ブレイクアウトルームをクリック

参加する部屋を選ぶ Select the rooms you want to enter.

「ブレイクアウトルーム」の退出 How to leave Breakout Rooms「ルームを退出する」をクリック「ブレイクアウトルームを退出する」をクリック

22

Slack の使い方 How to use Slack
本リトリートでは、参加者同士の議論・交流を促進するために、Zoom と並行して Slack を用いた質疑応答や情報交換を行います。また、開催後にも Slack は残しますので、今後の議論や交流のためにぜひご活用ください。
In this retreat, we will use “Slack” in parallel with Zoom for Q&A and discussion. We will keepa Slack group after the event, so please use it for future discussions and interactions.

https://excellsretreat2020.slack.com

各チャンネルの用途 What each channel is used for：•#announce：当日のスケジュール進行や連絡事項について、Zoom と並行してスタッ
フが随時アナウンスします。
Staff will make announcements about the day's schedule and information in parallelwith Zoom.

•#help：Zoom の接続トラブルや Slack の不明点などを、お気軽にご質問ください。
当日はスタッフが常時対応いたします。
Please feel free to ask questions about any troubles with Zoom or questions about
Slack. Our staff will be available on the day.

•#discussion：招待講演やポスターセッションの終了後、全体で引き続き議論したい
場合にお気軽にご記入ください。発表中の質問は、Zoom のチャット機能を使用してください。
If you want to continue the discussion after the invited talks or poster sessions, pleasefeel free to use this channel. If you have any questions during the presentation, please
use the Zoom chat function.

23

Slack では個人間でのダイレクトメッセージも可能です。より踏み込んだ議論をしたい場合
や、共同研究の相談などにぜひご活用ください。
Slack also allows for direct messages between individuals. Please make use of this service
when you want to have more in-depth discussions about joint research.
また、リトリート当日は終了後もディスカッションを継続できるよう、Zoom のサブグルー
プを開放しております。Slack や Zoom の個人チャットでお誘い合わせの上、ぜひご活用く
ださい。
Also, on the day of the retreat, we will open Zoom sub-groups to continue the discussion after
the retreat. Please use it after inviting us through personal chat on Slack or Zoom.

24注意事項 Information：
Slack の表示名は、参加登録時の氏名と同じにしてください。
Please make sure that your Slack display name is the same as your name on the registrationform.
1. 右上のアイコンをクリック Click on the icon in the upper right corner
2. Edit profile をクリック Click on “Edit profile”
3. 参加登録時の氏名を入力 Enter your name as you registered25

Contact
石井宏和 Hirokazu Ishii
Biophotonics Research Group, Exploratory Research Center on Life andLiving Systems (ExCELLS),
Division of Biophotonics, National Institute for Physiological Sciences(concurrent),
National Institute of Natural Sciences
Higashiyama 5-1, Myodaiji, Okazaki 444-8787, JAPANhi@nips.ac.jp , +81-564-59-5255

世話人
石井宏和（根本研）、小杉貴洋（古賀 G）、谷本昌志（東島研）、髙橋泰伽（根本研）
山本啓（青木研）、福原大輝（奥村 G）、曽我部隆彰、野中茂紀、郷康広、佐藤匡史、
磯貝知世
Organizers
Hirokazu Ishii (Nemoto Lab), Takahiro Kosugi (Koga group), Masashi Tanimoto (HigashijimaLab), Taiga Takahashi (Nemoto Lab), Kei Yamamoto (Aoki Lab), Daiki Fukuhara (Okumura
group), Takaaki Sokabe, Shigenori Nonaka, Yasuhiro Go, Tadashi Sato, Tomoyo Isogai26