Daichi M. Sakamoto

HOBBIES & INTERESTS

Basketball, physical fitness, sauna/spa, travel, movie, anime, science, business, adventure, beautiful views, communication with people

EDUCATION

Ph.D. (April 2020 – March 2024)

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Japan

Research title: Whole-body and whole-organ imaging of hypoxia using fluorescent molecular probe compatible with tissue clearing

Supervisor: Prof. Shinsuke Sando

M.Eng. (April 2018 – March 2020)

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Japan

Supervisor: Prof. Shinsuke Sando

B.Sc. (April 2014 – March 2018)

Chemistry Course, College of Science, Ibaraki University, Japan

Research title: Development of a green and sustainable synthetic method of thiazole by the dehydration condensation/cycloisomerization reaction of propargyl alcohol and thioamide

Supervisor: Associate Prof. Hirotaka Kagoshima

PUBLICATIONS

• B. Yi, H. Yatabe, D. M. Sakamoto, I. Tamura, Y. Saito, N. Yamada, R. Ashikaga, M. Kuroda, S. I. Kubota, K. Tainaka, and S. Sando "Imaging heterogeneous patterns of Aminopeptidase N activity in hierarchical tissue structures through high-resolution whole-organ 3D mapping" Angew. Chem. Int. Ed., 2025, e202504668. https://onlinelibrary.wiley.com/doi/10.1002/anie.202504668

• I. Tamura, D. M. Sakamoto, B. Yi, Y Saito, N. Yamada, J. Morimoto, Y. Takakusagi, M. Kuroda, S. I. Kubota, H. Harada, K. Tainaka, and S. Sando "Click3D: Click reaction across deep tissues for whole-organ 3D fluorescence imaging" Sci. Adv., 2024, 10, eado8471. https://www.science.org/doi/10.1126/sciadv.ado8471

• I. Tamura, D. M. Sakamoto, B. Yi, Y. Saito, N. Yamada, Y. Takakusagi, and S. Sando "Pimonidazole-alkyne conjugate for sensitive detection of hypoxia by Cu-catalyzed click reaction"Anal. Sci., 2024, 40, 1061-1070. https://link.springer.com/article/10.1007/s44211-024-00520-y

• D. M. Sakamoto, I. Tamura, B. Yi, S. Hasegawa, Y. Saito, N. Yamada, Y. Takakusagi, S. I. Kubota, M. Kobayashi, H. Harada, K. Hanaoka, M. Taki, M. Nangaku, K. Tainaka, and S. Sando "Whole-body and whole-organ 3D imaging of hypoxia using an activatable covalent fluorescent probe compatible with tissue clearing" ACS Nano, 2024, 18, 5167-5179. https://pubs.acs.org/doi/full/10.1021/acsnano.3c12716

• R. Nakahara, S. Aki, M. Sugaya, H. Hirose, M. Kato, K. Maeda, D. M. Sakamoto, Y. Kojima, M. Nishida, R. Ando, M. Muramatsu, M. Pan, R. Tsuchida, Y. Matsumura, H. Yanai, H. Takano, R. Yao, S. Sando, M. Shibuya, J. Sakai, T. Kodama, H. Kidoya, T. Shimamura, and T. Osawa “Hypoxia activates SREBP2 through golgi disassembly in bone marrow-derived cells for tumorigenesis” EMBO J., 2023, e114032. https://doi.org/10.15252/embj.2023114032

CONFERENCE PRESENTATIONS

• The 17th Symposium on Biorelevant Chemistry, Chiba, Japan, September 2023.

• Pacifichem 2021, Online, Dec. 2021.

• The 11th CSJ Chemistry Festa, Online, Japan, October 2021.

• The 15th Symposium on Biorelevant Chemistry, Online, Japan, September 2021.

• The Chemical Society of Japan, 101st Annual Meeting, Online, Japan, March 2021.

• The 8th CSJ Chemistry Festa, Funabashi, Japan, October 2018.

EMPLOYMENT EXPERIENCE

• Postdoctoral Scholar, Kaneko group, University of California, Los Angeles (June 2025 – present)

• Postdoctoral Research Associate, Conway group, University of Oxford (April 2024 – May 2025)

• Research assistant, Sando laboratory, The University of Tokyo (April 2020 – March 2024)

• Research assistant, Institute for Open Innovation, The University of Tokyo (April 2023 – June 2023) 

• Research assistant, Graduate School of Engineering, the University of Tokyo Doctoral Student Special Incentives Program (April 2020 – March 2024)

• Teaching assistant, First-Year Seminar, The University of Tokyo (April 2020 – March 2021)

HONORS & AWARDS

• Full Loan Repayment Exemption of JASSO Type 1 (interest-free) Scholarship (4,392,000 JPY) for Outstanding Academic Achievements, 2024.

• Grant-in-aid from The Toyobo Biotechnology Foundation, 2023. (declined)

• Outstanding Candidates, Research assistant, Graduate School of Engineering, the University of Tokyo Doctoral Student Special Incentives Program, 2022.

• Best Poster Award, The 11th CSJ Chemistry Festa, Online, Japan, October 2021. (Winner’s comment in Journal of the Chemical Society of Japan: chemistry and industrial chemistry, 2022 January issue)

• Excellent Presentation Award, Undergraduate thesis presentation, Chemistry Course, College of Science, Ibaraki University, March 2017.

• Academic Excellence Award, Chemistry Course, College of Science, Ibaraki University, March 2016.

• Academic Excellence Award, Chemistry Course, College of Science, Ibaraki University, March 2015.

RESEARCH SKILLS

Organic chemical synthesis

• General liquid-phase synthesis method, scaling up, and process design for a wide range of molecules.

• Purification with silica gel column chromatography, preparative thin-layer chromatography (PTLC), gel permeation chromatography (GPC), high performance liquid chromatography (HPLC), recrystallization, distillation.

• Identification and characterization of isolated compounds with nuclear magnetic resonance (NMR), electrospray ionization high resolution mass spectrometry (ESI-HRMS), fluorescence and absorbance spectroscopy.

• General solid-phase synthesis method for oligo peptide and peptoid.

In vitro experiments

• Confocal laser scanning microscopy (CLSM)

• Flow cytometry (FCM)

• Spheroid culture

• Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)

• Cytotoxicity assay

• Cell membrane permeability assay

• Enzyme assay

• DNA/RNA/protein extraction

• Polymerase chain reaction (PCR)

• Plasmid construction and transfection

Animal experiments

• Intravenous injection

• Frozen tissue sectioning

• Perfusion fixation

• Bio-distribution analysis

• Model mice preparation (tumor-bearing, cancer metastasis, hypoxemia, hyperoxemia, inflammation, ischemia by vessels ligation)

• In vivo imaging system (IVIS) fluorescence imaging

Tissue clearing

• Whole-body/whole-organ clearing

• Whole-body/whole-organ gel embedding

• 3D single-cell quantitative analysis with Imaris software