Welcome to my scientific journey. I’m Yao Yuan, a Ph.D. candidate at the University of Tsukuba, exploring the nexus of experimental biology and computational analysis under the guidance of Prof. Akiyoshi Fukamizu and Prof. Yasuteru Shigeta. My work, a symphony of in vitro, in silico, and in vivo approaches, aims to elucidate protein dynamics and their impact on health. Here, I’ll share the bioinformatics tools and insights developed through my research, inviting you to discover the science that fuels my passion.
Research Ability
My research philosophy,“The Experimental-Theoretical Symphony," reflects my dedication to integrating experimental biology with theoretical and computational approaches to uncover the complexities of biological systems.
in vitro:
- Utilization of Escherichia coli for protein expression, crafting mutant proteins to conduct in vitro activity assays.
- Measure binding affinities using Isothermal Titration Calorimetry (ITC)
- Complementing these studies with quantitative analysis of reaction products through LC-MS/MS.
in silico:
- Employing molecular dynamics (MD) simulations to model protein-protein interactions, serving to corroborate results obtained from in vitro activity assays.
- Developing extensive scripts for molecular docking simulations aimed at high-throughput screening of protein-small molecule interactions, which enables the systematic exploration of potential binding partners.
- Advancing RNA-seq analytical workflows through the creation of automated scripts for quality control, trimming, mapping, and extraction of reads data from large datasets of fastq files.
- Conducting comprehensive downstream RNA-seq analysis using R programming. This includes processing data for Principal Component Analysis (PCA), identifying differentially expressed genes (DEGs), and performing Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA).
- Analyzing RNA-seq data through Weighted Gene Co-expression Network Analysis (WGCNA) to construct co-expressed gene networks for genes of interest.
in vivo:
- Oversee the breeding and maintenance of mice
- Proficiency in mouse dissection, enabling detailed anatomical studies and precise organ and tissue collection
- Performing extractions of proteins, RNA, and DNA from organ tissues and cells
- Conducting quantitative PCR (qPCR) to assess gene expression levels
- Skilled in Immunoprecipitation (IP) and Western blotting techniques
- Extracting embryonic fibroblasts from mouse embryos
- Carry out cell staining and assays to evaluate cellular characteristics and functions
Publications
γ-enolase (ENO2) is methylated at the Nτ position of His-190 among enolase isozymes
Fumiya Kasai, Koichiro Kako, Syunsuke Maruhashi, Toru Uetake, Yuan Yao, Hiroaki Daitoku, Akiyoshi Fukamizu
J.Biochem,Jul.2023
Yoshiyuki Nagaoka, Yukimasa Takeishi, Yuki Miyake, Kana Takeda, Kazuhiko Okamura, Yuan Yao, Kaori Motomura, Hiroaki Daitoku, Akiyoshi Fukamizu, Mitsutoki Hatta
Molecular Biology Reports,Jan.2024
Presentations
Yuan Yao, Jun-Dal Kim, Hiroaki Daitoku, Naoto Muromachi, Koichiro Kako, Junji Ishida, Kowit Hengphasatporn, Yasuteru Shigeta, Akiyoshi Fukamizu
「Effect of H179Y substation from mouse to human PRMT1 on biological functions」, Tsukuba Conference, Sep, 2021
Yuan Yao、Naoto Muromachi、Jun-Dal Kim、Akiyoshi Fukamizu
「A study on the effect of H179Y point mutation in murine PRMT1 on biological functions」第93回日本生化学会、P-160、オンライン開催、Sep、2020年
Yuan Yao, Jun-Dal Kim, Hiroaki Daitoku, Naoto Muromachi, Koichiro Kako, Junji Ishida, Akiyoshi Fukamizu
「Study on the effect of H179Y one-point mutation in murine PRMT1 on biological functions」第94回日本生化学会、P-230、オンライン開催、Oct、2021年
Yuan Yao, Koichiro Kako, Kowit Hengphasatporn, Yasuteru Shigeta, Kaori Motomura, Jundal Kim, Akiyoshi Fukamizu
「ヒト型アルギニンメチル化酵素PRMT1遺伝子改変マウスの作出とその解析」 第95回日本生化学会，2T17e-09,口頭発表,2p-265,ポスター発表，Nov，2022
Yuan Yao, Koichiro Kako,Kaori Motomura, Jun-Dal Kim,Akiyoshi Fukamizu
「ヒト型アルギニンメチル化酵素PRMT1遺伝子改変マウスの作出とその解析」 第70回日本実験動物学会，O-50,口頭発表,May,2023
Yuan Yao, Koichiro Kako,Kaori Motomura, Jun-Dal Kim,Akiyoshi Fukamizu
「理論と実験から読み解くヒト・マウスPRMT1の一アミノ酸の相違性」日本生化学会関東支部例会,P09,ポスター発表，Jun，2023
Yuan Yao, Koichiro Kako,Kaori Motomura, Jun-Dal Kim,Akiyoshi Fukamizu
「理論と実験から読み解くヒト・マウスPRMT1の一アミノ酸の相違性」第96回日本生化学会,2P-122,ポスター発表，Nov，2023