CeMI Equipments List

Currently the CeMI has various types of equipments as below.

If you make a reservation of the CeMI Equipment for the first time,
read carefully the -User Application-.
If you already obtained permission for the use of the CeMI Equipment,
go to the -Online Reservation Page-.
For login, please add "@cemi.icems.kyoto-u.ac.jp" to your ID.

<About Installation Place>
- RB2 = Research Bldg.1 (2F)

- RA3 = Research Bldg.1 Annex
(3F)
- IR3 = iCeMS Research Bldg. (3F)

<Plan (pdf file)>
Research Bldg.1(2F) & Research Bldg. 1 Annex
Research Bldg.1(2F):enlarged view
Research Bldg. 1 Annex:enlarged view

No. Equipment Name Abreviation Place
Nikon Imaging-Techno Lab
1. Nikon Fast-Scan Confocal Fluorescence Microscope A1R Nikon FastConf RB2-209
2. Nikon Confocal Fluorescence Microscope A1 Nikon Conf IR-3-309
3. Nikon Long-Term Time-Lapse Fluorescence Microscope Nikon BioStation RB2-209
4. Nikon Fiber TIRF Microscope Nikon FiberTIRF RB2-203
5. Single Fluorescent-Molecule Tracking Station, High Speed SFMT-HS RB2-203
6. Single Fluorescent-Molecule Tracking Station, Bench-Test SFMT-Bench RB2-203
7. Single Fluorescent-Molecule Tracking Station, Live-cell PALM, Developmental SFMT-PALM-Dev RB2-209
Olympus MicroImaging Center
1. Olympus Confocal Fluorescence Inverted Microscope FV1000 Olympus InvConf RA3-305
2. Olympus Confocal Fluorescence Up-Right Microscope FV1000 Olympus URConf RA3-305
3. Olympus Long-Term Time-Lapse Fluorescence Microscope Olympus Time-Lapse RA3-305
4. Olympus Fiber TIRF Microscope Olympus FiberTIRF RA3-305
5. Single Fluorescent-Molecule Tracking Station, Developmental SFMT-Dev RA3-304
Leica Center
1. Leica STED-Confocal, FCS-Confocal Fluorescence Microscope Leica STEDConf RA3-301
Zeiss Center
1. Zeiss Two-photon Confocal, FCCS Confocal Fluorescence Microscope (LSM780) Zeiss 2pConf RA3-301
2. Zeiss Airyscan Super-Resolution, Confocal Fluorescence Microscope (LSM880) Zeiss LSM880Airy RA3-301
3. Zeiss Confocal Microscope (LSM710) Zeiss Conf RA3-304
Terahertz Imaging Center (Tanaka Lab)
1. Real-Time THz Near-Field Microscope THz-NF RB2-201
2. Real-Time THz Transmission Microscope THz-TR RB2-201

 

Publications List by CeMI Equipments

Nikon FastConf (A1R)
Suzuki KGN, Kasai RS, Hirosawa KM, Nemoto YL, Ishibashi M, Miwa Y, Fujiwara TK, Kusumi A (2012) Transient GPI-anchored protein homodimers are units for raft organization and function. Nat Chem Biol 8: 774-783
DOI: 10.1038/Nchembio.1028

Inaba H, Sanghamitra NJM, Fukai T, Matsumoto T, Nishijo K, Kanamaru S, Arisaka F, Kitagawa S, Ueno T (2014) Intracellular protein delivery system with protein needle-GFP construct. Chem Lett 43: 1505-1507
DOI: 10.1246/cl.140481

Sanghamitra NJM, Inaba H, Arisaka F, Ohtan Wang D, Kanamaru S, Kitagawa S, Ueno T (2014) Plasma membrane translocation of a protein needle based on a triple-stranded β-helix motif. Mol BioSyst 10: 2677-2683
DOI: 10.1039/C4MB00293H

Inaba H, Sanghamitra NJ, Fujita K, Sho T, Kuchimaru T, Kitagawa S, Kizaka-Kondoh S, Ueno T (2015) A metal carbonyl-protein needle composite designed for intracellular CO delivery to modulate NF-kB activity. Mol Biosyst 11: 3111-3118
DOI: 10.1039/C5MB00327J

Nikon FiberTIRF
Kafer GR, Li X, Horii T, Suetake I, Tajima S, Hatada I, Carlton PM (2016) 5-Hydroxymethylcytosine marks sites of DNA damage and promotes genome stability. Cell Rep 14: 1283-1292
DOI: 10.1016/j.celrep.2016.01.035

Nikon SFMT-HS
Shibata ACE, Fujiwara TK, Chen LM, Suzuki KGN, Ishikawa Y, Nemoto YL, Miwa Y, Kalay Z, Chadda R, Naruse K, Kusumi A (2012) Archipelago architecture of the focal adhesion: Membrane molecules freely enter and exit from the focal adhesion zone. Cytoskeleton 69: 380-392
DOI: 10.1002/Cm.21032

Shibata ACE, Chen LMH, Nagai R, Ishidate F, Chadda R, Miwa Y, Naruse K, Shirai YM, Fujiwara TK, Kusumi A (2013) Rac1 recruitment to the archipelago structure of the focal adhesion through the fluid membrane as revealed by single-molecule analysis. Cytoskeleton 70: 161-177
DOI: 10.1002/Cm.21097

Nikon SFMT-PALM-DEV
Fujiwara TK, Iwasawa K, Kalay Z, Tsunoyama TA, Watanabe Y, Umemura YM, Murakoshi H, Suzuki KGN, Nemoto YL, Morone N, Kusumi A (2016) Confined diffusion of transmembrane proteins and lipids induced by the same actin meshwork lining the plasma membrane. Mol Biol Cell 27: 1101-1119
DOI: 10.1091/mbc.E15-04-0186

Sotoma S, Iimura J, Igarashi R, Hirosawa KM, Ohnishi H, Mizukami S, Kikuchi K, Fujiwara TK, Shirakawa M, Tochio M (2016) Selective labeling of proteins on living cell membranes using fluorescent nanodiamond probes. Nanomaterials 6: 56
DOI: 10.3390/nano6040056

Olympus InvConf
Komura N, Suzuki KGN, Ando H, Konishi M, Ikeda M, Imamura A, Chadda R, Fujiwara TK, Tsuboi H, Sheng R, Cho W, Furukawa Koichi, Furukawa Keiko, Yamauchi Y, Ishida H, Kusumi A (2016) Raft-based interactions of gangliosides with a GPI-anchored receptor. Nat Chem Biol 12:402-410
DOI:10.1038/nchembio.2059

Olympus InvConf & URConf (FV1000D), Nikon FastConf (A1R), and Leica STEDConf (SP5 STED)
Sugimura K, Ishihara S (2013) The mechanical anisotropy in a tissue promotes ordering in hexagonal cell packing. Development 140: 4091-4101
DOI: 10.1242/Dev.094060

Olympus InvConf & URConf (FV1000D)
Ishihara S, Sugimura K (2012) Bayesian inference of force dynamics during morphogenesis. J Theor Biol 313: 201-211
DOI: 10.1016/j.jtbi.2012.08.017

Ishihara S, Sugimura K, Cox SJ, Bonnet I, Bellaiche Y, Graner F (2013) Comparative study of non-invasive force and stress inference methods in tissue. Eur Phys J E Soft Matter 36: 9859 Cover page , DOI: 10.1140/Epje/I2013-13045-8

Olympus InvConf & Zeiss 2pConf (LSM780 NLO/ConfoCor3)
Oomoto I, Suzuki-Hirano A, Umeshima H, Han YW, Yanagisawa H, Carlton P, Harada Y, Kengaku M, Okamoto A, Shimogori T, Wang, DO (2015) ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues. Nucleic Acids Res 43: e126
DOI: 10.1093/nar/gkv614

Zeiss 2pConf (LSM780 NLO/ConfoCor3)
Diring S, Wang DO, Kim C, Kondo M, Chen Y, Kitagawa S, Kamei K, Furukawa S (2013) Localized cell stimulation by nitric oxide using a photoactive porous coordination polymer platform. Nat Commun 4: 2684
DOI: 10.1038/Ncomms3684

Takamatsu S, Onoguchi K, Onomoto K, Narita R, Takahasi K, Ishidate F, Fujiwara TK, Yoneyama M, Kato H, Fujita T (2013) Functional characterization of domains of IPS-1 using an inducible oligomerization system. PLoS One 8: e53578
DOI: 10.1371/journal.pone.0053578

Imayoshi I, Isomura A, Harima Y, Kawaguchi K, Kori H, Miyachi H, Fujiwara T, Ishidate F, Kageyama R (2013) Oscillatory control of factors determining multipotency and fate in mouse neural progenitors. Science 342: 1203-1208
DOI: 10.1126/science.1242366

Yoshii T, Ikeda M, Hamachi I (2014) Two-photon-responsive supramolecular hydrogel for controlling materials motion in micrometer space. Angew Chem 126: 7392-7395
DOI: 10.1002/ange.201404158

Sadaie W, Harada Y, Matsuda M, Aoki K (2014) Quantitative in vivo FCCS analyses highlight the importance of competitive effects in the regulation of protein-protein interactions. Mol Cell Biol 34: 3272-3290
DOI: 10.1128/MCB.00087-14

Nakatsuji H, Numata T, Morone N, Kaneko S, Mori Y, Imahori H, Murakami T (2015) Thermosensitive ion channel activation in single neuronal cells by using surface-engineered plasmonic nanoparticles. Angew Chem Int Edit 54: 11725-11729
DOI: 10.1002/anie.201505534

Oh SW, Onomoto K, Wakimoto M, Onoguchi K, Ishidate F, Fujiwara T, Yoneyama M, Kato H, Fujita T (2016) Leader-containing uncapped viral transcript activates RIG-I in antiviral stress granules. PLoS Pathog 12: e1005444
DOI: 10.1371/journal.ppat.1005444

Takano Y, Numata T, Fujishima K, Miyake K, Nakao K, Grove WD, Inoue R, Kengaku M, Sakaki S, Mori Y, Murakami T, Imahori H (2016) Optical control of neuronal firing via photoinduced electron transfer in donor–acceptor conjugates. Chem Sci 7: 3331-3337
DOI: 10.1039/C5SC04135J

Hamamatsu EMCCD camera (ImagEM)
Yoshikawa N, Hirori H, Watanabe H, Aoki T, Ihara T, Kusuda R, Wolpert C, Fujiwara TK, Kusumi A, Kanemitsu Y, Tanaka K (2013) Biexciton state causes photoluminescence fluctuations in CdSe/ZnS core/shell quantum dots at high photoexcitation densities. Phys Rev B 88: 155440
DOI: 10.1103/Physrevb.88.155440

Tracking and data analysis software developed at the CeMI
Tanaka KA, Suzuki KG, Shirai YM, Shibutani ST, Miyahara MS, Tsuboi H, Yahara M, Yoshimura A, Mayor S, Fujiwara TK, Kusumi A (2010) Membrane molecules mobile even after chemical fixation. Nat Methods 7: 865-866
DOI: 10.1038/nmeth.f.314

Kasai RS, Suzuki KG, Prossnitz ER, Koyama-Honda I, Nakada C, Fujiwara TK, Kusumi A (2011) Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging. J Cell Biol 192: 463-480
DOI: 10.1083/jcb.201009128

Koyama-Honda I, Itakura E, Fujiwara TK, Mizushima N (2013) Temporal analysis of recruitment of mammalian ATG proteins to the autophagosome formation site. Autophagy 9: 1491-1499
DOI: 10.4161/auto.25529

Nishimura H, Ritchie K, Kasai RS, Goto M, Morone N, Sugimura H, Tanaka K, Sase I, Yoshimura A, Nakano Y, Fujiwara TK, Kusumi A (2013) Biocompatible fluorescent silicon nanocrystals for single-molecule tracking and fluorescence imaging. J Cell Biol 202: 967-983
DOI: 10.1083/jcb.201301053

Hiramoto-Yamaki N, Tanaka KA, Suzuki KG, Hirosawa KM, Miyahara MS, Kalay Z, Tanaka K, Kasai RS, Kusumi A, Fujiwara TK (2014) Ultrafast diffusion of a fluorescent cholesterol analog in compartmentalized plasma membranes. Traffic 15: 583-612
DOI: 10.1111/tra.12163

 

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