Presentation Information
[2ASPR-27]Lightning Talks by ECRs No.10
○Misaki Kobayashi (University of Tsukuba)
My research in the ASAP program focuses on the structural optimization of the Rubisco using in silico analysis with the goal of improving photosynthetic performance and ultimately contributing to the development of plants with enhanced water-use efficiency, a central objective of the ASAP project. To advance this research, I participated in a one-month research stay at the University of Illinois Urbana-Champaign through the ASPIRE program, where I worked with Professor Diwaker Shukla’s group.
The Shukla laboratory develops computational and AI-driven approaches to investigate molecular processes relevant to diverse fields, including medicine, climate science, and plant biology. One of the laboratory’s recent developments is EZSpecificity, a computational platform for predicting enzyme–substrate specificity. My primary objective during the visit was to learn structural prediction methods and acquire the skills necessary to utilize EZSpecificity for engineering.
My academic background is in plant biotechnology, particularly genome editing in tomato and the development of genome-editing methods using transient expression systems. Prior to this project, I had no experience in computational biology, molecular simulations, or international research stays. Consequently, I initially faced considerable challenges in learning computational workflows and structural analysis techniques. Through self-directed study and continuous discussions with collaborators, I gradually learned how to perform structural predictions, troubleshoot computational analyses, and prepare structural datasets for enzyme-specificity prediction. This experience also highlighted the importance of proactive communication and scientific discussion in an international research environment.
Although the one-month stay was not sufficient to complete the entire optimization process, I successfully established a computational workflow for engineering and learned how to prepare structural information for EZSpecificity analyses. Importantly, I have continued the project after returning to Japan through ongoing collaboration with members of the Shukla laboratory.
Beyond the technical skills acquired, this experience had a profound impact on my career perspective. Before the exchange program, I was uncertain about my future career path after completing my Ph.D. However, exposure to computational plant science significantly deepened my interest in this field and inspired me to pursue an academic career. This experience not only broadened my research expertise but also revealed to me the appeal of integrating experimental and computational approaches in plant science, serving as a catalyst for my decision to pursue an academic career and contribute to the future development of plant biotechnology research.
The Shukla laboratory develops computational and AI-driven approaches to investigate molecular processes relevant to diverse fields, including medicine, climate science, and plant biology. One of the laboratory’s recent developments is EZSpecificity, a computational platform for predicting enzyme–substrate specificity. My primary objective during the visit was to learn structural prediction methods and acquire the skills necessary to utilize EZSpecificity for engineering.
My academic background is in plant biotechnology, particularly genome editing in tomato and the development of genome-editing methods using transient expression systems. Prior to this project, I had no experience in computational biology, molecular simulations, or international research stays. Consequently, I initially faced considerable challenges in learning computational workflows and structural analysis techniques. Through self-directed study and continuous discussions with collaborators, I gradually learned how to perform structural predictions, troubleshoot computational analyses, and prepare structural datasets for enzyme-specificity prediction. This experience also highlighted the importance of proactive communication and scientific discussion in an international research environment.
Although the one-month stay was not sufficient to complete the entire optimization process, I successfully established a computational workflow for engineering and learned how to prepare structural information for EZSpecificity analyses. Importantly, I have continued the project after returning to Japan through ongoing collaboration with members of the Shukla laboratory.
Beyond the technical skills acquired, this experience had a profound impact on my career perspective. Before the exchange program, I was uncertain about my future career path after completing my Ph.D. However, exposure to computational plant science significantly deepened my interest in this field and inspired me to pursue an academic career. This experience not only broadened my research expertise but also revealed to me the appeal of integrating experimental and computational approaches in plant science, serving as a catalyst for my decision to pursue an academic career and contribute to the future development of plant biotechnology research.
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