Yuji Ishitsuka

Photograph
Title Scientist
Department Singular Genomics, San Diego, CA
Email Yuji@nospam66df72a63c972.SingularGenomics.com
Biography

ABOUT

Interdisciplinary postdoctoral researcher with 10+ years of academic research experience in biophysics and nanotechnology. Expert in biophysical characterization of lipid systems and membrane proteins in vitro and in living cells proven with internationally recognized 27 scientific publications (1550+ citations). Strengths in assay development, membrane physical chemistry, DNA nanostructure, surface chemistry, microscopy and high throughput data analysis. Seeking to develop the next generation of innovative tools that can transform the lives around the world.

EDUCATION

B.S.               Chemistry (Biochemistry), Wheaton College, Wheaton, IL, 2000

M.S.               Physical chemistry, The University of Chicago, Chicago, IL, 2001

Ph.D.             Physical chemistry, The University of Chicago, Chicago, IL, 2006

Post. Doc.   Ha Group, University of Illinois at Urbana Champaign, 2006-2011

Post. Doc.   Ulrich Nienhaus group, Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany, 2011-2015

Res. Sci.      Paul R. Selvin group, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 2015-Present

PUBLICATIONS

  1. Lee S.H., Jin, C., Cai, E., Ge, P., Ishitsuka, Y., Teng, K.W., Thomaz, A.A., Nall, D.L., Baday, M., Jeyifous, O., Demonte, D., Dundas, C.M., Park, S., Delgado, J.Y., Green, W.N., Selvin, P.R.,Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes, eLife, 6:e27744, (2017).
  2. Teng, K. W. Ishitsuka, Y., Ren, P., Youn, Y., Deng, X., Ge, P., Lee, S.H., Belmont, A. S. and Selvin, P. R., Labeling Proteins Inside Living Cells Using External Fluorophores for Fluorescence Microscopy, eLife, 5:e20378,  (2016).
  3. Bergs, A., Ishitsuka, Y., Evangelinos, M., Nienhaus, G.U. and Takeshita, N., Dynamics of Actin Cables in Polarized Growth of the Filamentous Fungus Aspergillus nidulans, Front. Microbiol., 7, 682 (2016)
  4. Hense, A., Prunsche, B., Gao, P., Ishitsuka, Y., Nienhaus, K., and Nienhaus, G. U.,Monomeric Garnet, a far-red fluorescent protein for live-cell STED imaging, Scientific Reports, 5, 18006 (2015)
  5. Ishitsuka, Y., Savage, N., Li, Y., Bergs A., Grün, N., Kohler, D., Donnelly, R., Nienhaus, G. U., Fischer, R. and Takeshita N., Superresolution microscopy reveals a dynamic picture of cell polarity maintenance during directional growth, Science Advances,1, e1500947 (2015)
  6. Manck, R., Ishitsuka, Y., Herrero, S., Takeshita, N., Nienhaus, G.U. and Fischer R., Genetic evidence for a microtubule-capture mechanism during polarised growth of Aspergillus nidulans, J. Cell Science, 128, 3569–3582 (2015)
  7. Ishitsuka, Y.*, Azadfar. N.*, Kobitski, A. Y., Nienhaus, K., Johnsson, N. and Nienhaus, G. U.,Evaluation of Genetically Encoded Chemical Tags as Orthogonal Fluorophore Labeling Tools for Single-Molecule FRET Applications, J. Phys. Chem. B119, 6611-6619 (2015) *equal contributions.
  8. Saccà, B.*, Ishitsuka, Y.*, Meyer, R., Sprengel, A., Schöneweiß, E.S., Nienhaus, G.U. and Niemeyer, C.M., Reversible reconfiguration of DNA origami nanochambers monitored by single-molecule FRET, Angew. Chem. Int. Ed., 54, 1-7 (2015) *equal contributions.
  9. Ishitsuka, Y., Nienhaus, K. and Nienhaus, G.U.,Photoactivatable Fluorescent Proteins for Super-Resolution Microscopy, Methods in Mol Biol., 1148, 239-260 (2014)
  10. Takeshita, N., Mania, D., Herrero de Vega, S., Ishitsuka, Y., Nienhaus, G.U., Podolski, M., Howard, J. and Fischer, R., The cell end marker TeaA and the microtubule polymerase AlpA contribute to microtubule guidance at the hyphal tip cortex of Aspergillus nidulansfor polarity maintenance, J. Cell Science, 126, 5400–5411 (2013)
  11. Li, Y., Ishitsuka, Y., Hedde, P.N. and Nienhaus, G.U., Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,ACS Nano,7, 5207-5214 (2013)
  12. Lai, Y., Diao, J., Liu, Y., Ishitsuka, Y., Su, Z., Schulten, K., Ha, T., Shin, Y.K., Fusion pore formation and expansion induced by Ca2+and synaptotagmin 1, Proc. Natl. Acad. Sci. USA 22, 1333-13338 (2013)
  13. Klapper, Y., Vrânceanu, M., Ishitsuka, Y., Evans, D, Scheider, D., Nienhaus, G.U. and Leneweit, G. J., Surface energy of phospholipid bilayers and the correlation to their hydration.Colloid Interface Sci.15, 267-274 (2013)
  14. Diao, J., Ishitsuka, Y., Lee, H., Joo, C., Su, Z., Syed, S., Shin, Y.K., Yoon, T.Y., and Ha, T., A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins,Nature Protocol7, 921-934 (2011)
  15. Diao, J.*, Ishitsuka, Y.*and Bae, W., Single-molecule FRET study of SNARE-mediated membrane fusion, Biosciences Report 31, 457-463 (2011) *Co-corresponding authors
  16. Jain, A., Liu,R., Ramani, B., Arauz, E., Ishitsuka, Y., Ragunathan, K., Chen, J., Xiang, Y.K. and Ha, T.,  Probing cellular protein complexes using single-molecule pull-down, Nature 473, 484-488 (2011)
  17. Ishitsuka, Y., Okumus, B., Arslan, S., Chen, K.H. and Ha, T.,Temperature-Independent Porous Nanocontainers for Single-Molecule Fluorescence Studies, Analytical Chemistry 82, 9694-9701 (2010)
  18. Diao, J.*, Su Z.*, Ishitsuka, Y.*, Lu B., Lee, K.S., Lai, Y., Shin, Y.K. and Ha, T., A single-vesicle content mixing assay for SNARE-mediated membrane fusion, Nature Communications1, 54 (2010) *equal contributions
  19. Su, Z., Ishitsuka, Y., Ha, T. and Shin, Y.K., The SNARE complex from yeast is partially unstructured on the membrane, Structure16, 1138-1146 (2008)
  20. Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C. and Ha, T., Advances in single-molecule fluorescence methods for molecular biology, Annual Review of Biochemistry77, 51-76 (2008)
  21. Neville, F., Ishitsuka, Y., Hodges, C.S., Konovalov, O., Waring, A.J., Lehrer, R.I., Lee, K.C. and Gidalevitz, D., Protegrin interaction with lipid monolayers: grazing incidence X-ray diffraction and X-ray reflectivity study, Soft Matter4, 1665-1674 (2008)
  22. Danauskas, S.M., Ratajczak, M.K., Ishitsuka, Y., Gebhardt, J., Schultz, D., Meron, M., Lin, B. and Lee, K.C., Monitoring X-Ray Beam Damage on Lipid Films by an Integrated Brewster Angle Micrscope/X-Ray Diffractometer, Review of Scientific Instruments78, 103705-103709 (2007)
  23. Lam, K.L., Ishitsuka, Y., Cheng, Y., Chien, K., Waring, A.J., Lehrer, R.I. and Lee, K.C.,Mechanism of Membrane Disruption by Antimicrobial Peptide Protegrin-1, J. Phys. Chem. B110, 21282-21286 (2006)
  24. Ishitsuka, Y., Pham, D., Waring, A.J., Lehrer, R.I. and Lee, K.C., Insertion Selectivity of Antimicrobial Peptide Protegrin-1 into Lipid Monolayers: Effect of Head Group Electrostatic and Tail Group Packing, Biochimica et Biophysica Acta1758, 1450-1560 (2006)
  25. Ishitsuka, Y., Arnt, L., Ratajczek, M.K., Frey, S., Majewski, J., Kjaer, K., Tew, G.N. and Lee, K.C., Amphiphilic Poly(phenyleneethynylene)s Can Mimic Antimicrobial Peptide Membrane Disordering Effect by Membrane Insertion, Journal of American Chemical Society128, 13123-13129 (2006)
  26. Neville, F., Cahuzac, M., Konovalov, O., Lee, K.C., Ishitsuka, Y., Kuzmenko, I., Kale, G.M. and Gidalevitz, D., Lipid head group discrimination by antimicrobial peptide LL-37: Insight into mechanism of action, Biophys. J.90, 1275-1287 (2006)
  27. Gidalevitz, D.*, Ishitsuka, Y.*, Muresan, A.S., Konovalov, O., Waring, A.J., Lehrer, R.I., and Lee, K.C., Interaction of Antimicrobial Peptide Protegrin with Biomembranes, Proc. Natl. Acad. Sci. USA100, 6302-6307 (2003) *equal contributions