Editorial
Editorial: Hands-on Training Program
2024 Volume 21 Issue Supplemental2 Article ID: e212007
Details
2024 Volume 21 Issue Supplemental2 Article ID: e212007
Six hands-on training programs were conducted for young researchers in conjunction with the IUPAB2024 conference, which was held in Kyoto from June 24 to June 28 [1]. In addition to Kyoto, the programs were also held in Kanazawa, Kobe, Osaka, and Tokyo (Fig. 1a). These six programs were coordinated by Dr. Kumiko Hayashi (Univ. Tokyo), an executive committee member of the IUPAB2024 conference. This program fulfills one of IUPAB’s missions: to promote education and capacity-building programs for students and young researchers in scientifically developing countries. The Biophysical Society of Japan (BSJ) provided travel support to all participants, which is shown on the IUPAB2024 website as supporting material. BSJ provided travel support to the participants ranging from 10,000 JPY-70,000 JPY in total, depending on the recipient’s proximity to the location where the program was held.
As a result of intensified promotion on X (Fig. 1b), a total of 117 applicants applied for 70 spots. After a selection process, 66 participants from 28 countries (including Japan) were selected to join the program (Fig. 2). The organizers of each program selected participants based on factors such as their motivation to participate in the hands-on training, country, gender, and academic year. Due to differences in program content, the number of participants that could be accommodated varied by program (Fig. 2a). Sixty percent of the participants were from overseas. The gender ratio was evenly split with 50% each (Fig. 2c). In terms of participants’ careers, three-quarters were students, while one-quarter were degree holders. The students included undergraduates, master’s students, and PhD candidates. The PhD holders consisted of postdoctoral researchers and assistant professors.
Below is a brief introduction to each program. The detailed contents of the programs can be seen in references such as presentation slides, provided as supporting materials. The web page for the all six hands-on training programs is shown in 21_e212007_1.pdf. The references of the programs A, B, C, D, E, and F are included in 21_e212007_2.pdf, 21_e212007_3.pdf, 21_e212007_4.pdf, 21_e212007_5.pdf, 21_e212007_6.pdf, and 21_e212007_7.pdf, respectively.
Organizers: Takeharu Nagai, Shuichi Onami, Grant-in-Aid for Scientific Research on Innovative Area: “Singularity biology”
Venue: Osaka University and RIKEN Kobe Campus
Event date: June 18–21
In Program A, participants learned about image acquisition of ultra-large cell populations with a cutting-edge biological trans-scale scope called AMATERAS, image processing based on information engineering, and quantitative analysis of cellular dynamics and activity [2].
Program B: Visualizing the nanometer world in liquid by Bio-SPMsOrganizers: WPI-NanoLSI (Nano Life Science Institute), Kanazawa University
Venue: Kanazawa University
Event date: July 1
Program B is a one-day tour to Kanazawa University, where participants learned about Bio-SPM technologies, including super-resolution AFM (FM-AFM & 3D-AFM), high-speed AFM, SICM, and AFM for cell measurement, as well as experience SPM imaging of biological molecules or living cells.
Program C: CHARMM-GUI/GENESIS MD tutorialOrganizers: Yuji Sugita, Wonpil Im, Florence Tama, Yasuhiro Matsunaga, Kei Moritsugu
Venue: RIKEN, Kobe Campus
Event date: June 30–July 2
The CHARMM-GUI/GENESIS Workshop, held in Kobe, focused on learning MD simulations, including hands-on training with GENESIS and CHARMM-GUI.
Program D: DNA nanomachine tutorialOrganizers: Shin-ichiro M. Nomura, Grant-in-Aid for Transformative Research Areas(A) “Molecular Cybernetics”
Venue: Kansai University
Event date: June 22
Molecular robotics is an emerging academic field that seeks to create systems, referred to as robots, using molecules designed from the ground up as components. A hands-on program was offered for those interested in molecular robotics, providing an opportunity to learn the fundamentals of designing and evaluating DNA nanomachines within a short period of time. The program was open to all, regardless of specialty or background, and included learning DNA nanomachine design, visualization, and observation.
Program E: Exploring multi-cellular mechanicsOrganizers: Grant-in-Aid for Transformative Research Areas (A) “Mechanical self-transformation of living systems”
Venue: Kyoto University
Event date: June 29
This hands-on session offered an introduction to imaging and image analysis of multi-cellular systems such as tissues and embryos. Participants learned specimen handling techniques, including working with mouse embryos, and acquired skills in capturing both 2D and 3D images using light-sheet microscopy. The session also covered live-cell high-speed AFM and the microscopic observation and analysis of gut motility, with a focus on extracting biophysical parameters through image analysis.
Program F: Real-time single-molecule experiments with optical tweezers and correlated fluorescence microscopyOrganizers: LUMICKS, the Institute for Quantitative Bioscience, The University of Tokyo
Venue: Institute for Quantitative Bioscience, The University of Tokyo
Event date: June 22–23
Witness the seamless integration of optical tweezers and fluorescence microscopy into a single state-of-the-art system: the C-Trap! This one-day workshop in Tokyo included a brief introduction to the developments and applications of optical tweezers and correlated microscopy in biological research by Institute for Quantitative Biosciences, The University of Tokyo and LUMICKS. It was followed by a live demonstration where molecular interactions and protein activity of model systems were visualized in real-time, at the single-molecule level and with unparalleled resolution. Participants were able to get some hands-on experience with single-molecule assays themselves!
In Figures 3-8, the scenes of lectures, trainings, and students’ presentations for each hands-on program are shown.
Other than program F, which was hosted by the company, sessions related to the hands-on training program was held at the IUPAB 2024 conference. The sessions’ information is listed below. A commemorative photo with the session speakers and the audience was taken before/after each session (Fig. 9).
Venue: Room C-2, ICC Kyoto
Event date: 16:00–18:20, June 25
1. Automated trans-scale scope opens up a new horizon in life science research
Chair/Speaker: Takeharu Nagai (Osaka University)
2. Activatable Raman probes for multiplexed vibrational imaging in live cells and tissues
Speaker: Mako Komiya (Tokyo Institute of Technology)
3. Engineering high performance biosensors to analyze signaling and metabolism in live cells
Speaker: Robert E. Campbell (The University of Tokyo)
4. Analyzing the invisible: Advanced techniques in microscopy and spectroscopy for internal state characterization
Speaker: Imari Sao (National Institute of Information)
5. Cell tracking and data management for AMATERAS
Speaker: Shuichi Onami (RIKEN Center for Biosystems Dynamics Research)
Program B: Visualizing the Nanometer World in Liqui by Bio-SPMsVenue: Room E, ICC Kyoto
Event date: 10:00–12:20, June 27
Chair: Noriyuki Kodera (Kanazawa University)
1. Visualizing nanoscale dynamics and mechanics in living cells by nanoendoscopy AFM
Speaker: Takeshi Fukuma (Kanazawa University)
2. Nanoscale analysis of microbial cell walls using AFM
Speaker: Keisuke Miyazawa (Kanazawa University)
3. Visualizing surface dynamics of living cells at nanometer scale resolution with scanning ion conductance microscopy
Speaker: Shinji Watanabe (Nano Life Science Institute, Kanazawa University)
4. Biological nanopore probes for scanning ion conductance microscopy
Speaker: Kan Shoji (Nagaoka University of Technology)
5. Single-molecule imaging of AMPA-type glutamate receptors by high-speed atomic force microscopy
Speaker: Mikihito Shibata (Kanazawa University)
6. HS-AFM analysis of microtubule-binding proteins in solution
Speaker: Ikuko Hayashi (Yokohama City University)
Program C: CHARMM-GUI/GENESIS MD TutorialVenue: Room C-2, ICC Kyoto
Event date: 10:00–12:20, June 28
Chair: Yuji Sugita (RIKEN)
1. Three routes to molecular movies
Speaker: Helmut Grubmüller (Max Planck Institute for Multidisciplinary Sciences)
2. Modeling multi-state structure of proteins and simulating their conformational transitions
Speaker: Chen Song (Peking University)
3. Multiscale simulations of enzyme mechanisms: bridging catalysis, conformational changes and ligand release
Speaker: Kwangho Nam (University of Texas at Arlington)
4. Exploring allosteric changes in the conformational landscape of Src kinase upon substrate binding by GENESIS
Speaker: Song-ho Chong (Kumamoto University)
5. Computational exploration of chromatin structure and dynamics: from single nucleosomes to entire genes
Speaker: Giovanni Brandani (Kyoto University)
6. WHAT CAN CHARMM-GUI DO FOR YOU?
Chair/Speaker: Wonpil Im (Lehigh University)
Program D: DNA Nanomachine TutorialVenue: Room C-2, ICC Kyoto
Event date: 14:30–16:50, June 24
Chair: Shin-ichiro Nomura (Tohoku University)
1. DNA origami-based integrated molecular systems and functional nanomachine
Speaker: Masayuki Endo (Kansai University)
2. Nanomechanical DNA origami devices
Speaker: Akinori Kuzuya (Kansai University)
3. Multi-reconfigurable and multi-responsive DNA origami nanodevices
Speaker: Yuki Suzuki (Mei University)
4. Online user interface of computational tools for accelerating DNA nanotechnology research
Speaker: Ibuki Kawamata (Kyoto University)
5. Long DNA strands’ insertion into DNA droplets as a potential model for chromatin condensates studies
Pick-up speaker: Nathan Nunes Evangelista (Tokyo Institute of Technology)
6. DNA nanopore sensor for cell secretion measurement
Pick-up speaker: Hiromu Akai (Nagoya University of Technology)
Program E: Exploring Multi-cellular MechanicsVenue: Room A, ICC Kyoto
Event date: 10:00–12:20, June 28
Chair: Tatsuo Shibata (RIKEN)
Chair: Shige H. Yoshimura (Kyoto University)
1. Active cytoskeleton controlled through force and shape
Speaker: Yusuke Maeda (Kyushu University)
2. Cellular-level left-right asymmetry, cell chirality, induces the chiral collective rotation of multicellular colony
Speaker: Tomoki Ishibashi (RIKEN)
3. Analysis of differential grouth in curved surface morphogenesis through constructing a conformal map
Pick-up speaker: Kentaro Morikawa (Kyoto University)
4. Tiling mechanisms of the compound eye through geometrical tessellation
Chair/Speaker: Makoto Sato (Kanazawa University)
5. Mechanical waves decode positional information to calibrate wound healing response in zebrafish
Speaker: Fu-Lai Wen (National Taipei University of Education)
6. PIEZO1-mediated mechanosensing regulates the fate of neural progenitor cells during cerebral development
Speaker: Mayumi Okamoto (Nara Women’s University)
After the hands-on training programs, we invited participants to write experience reports. Eleven participants wrote experience reports as Commentary and Perspective of BPPB, which are also scheduled to be included in the IUPAB 2024 special issue. (Some of the experience reports have not been published yet.)
• Single-Molecule Manipulation with C-Trap: An Impressive Training Experience
Yuze Sun (National University of Singapore) [3]
• GENESIS and CHARMM-GUI: Advances and Applications from Hands-on Training Program C at RIKEN
Nor Sulong (University Malaya, University College MAIWP International), Vannajan Lee (University Malaya) [4]
• Constructing virtual DNA-nanomachines
Nathan Nunes Evangelista (Tokyo Institute of Technology), Masahiro Takinoue (Tokyo Institute of Technology) [5]
• Feeling a nanoworld with optical tweezers: Hands on training at IUPAB 2024
Zuzana Johanovská (Institute of Physics of Charles University) [6]
• IUPAB and BSJ meeting Kyoto: reflections on hands-on workshop “Real-time single-molecule experiments with optical tweezers and correlated fluorescence microscopy” with Lumicks C-trap, emphasising the importance of practicing international and interdisciplinary science
Karina New (Universidad de Chile) [7]
• Using interactive deep learning to track cells: a report on a 3-day hands-on training program at IUPAB 2024
Lissy Hartmann (University of Technology Sydney), Samara Bridge (University of Technology Sydney) [8]
• Experience of Hands-on training program on DNA Nanomachine at IUPAB2024
Koki Yoshida (Tokyo Institute of Technology) [9]
• Experience Report of Hands-on Training Program E: Exploring Multi-cellular Mechanics
Asuka Sakazume (Ochanomizu University) [10]
• DNA nanomachine tutorial
Hong T. Vu (University of Nottingham) [11]
The hands-on programs were a first at the IUPAB Congress, but they received high praise from the participants. We hope that such initiatives to nurture young researchers will continue in the future.
I would like to acknowledge all the organizations of the six hands-on programs, particularly those who supported me from the preparation period, including Dr. Nagai, Dr. Onami, Dr. Kodera, Dr. Sugita, Dr. Kobayashi, Dr. Nomura, Dr. Yoshimura, Dr. Wang, and Dr. Chaubet. My gratitude also extends to the IUPAB2024 public relations office (Dr. Mita) and the IUPAB2024 Secretariat (Convention Linkage Inc.). I am also thankful to the president, Dr. Noji, and the IUPAB2024 committee members for their valuable discussions on this project. Lastly, I would like to express my appreciation to the Biophysical Society of Japan for their support.
