Gene Engineering Division > Research tools > Biosensor & Visualization

Biosensor & Visualization

Sensor & Visualization

ATP measurement

  • QUEEN
    Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging.
    Yaginuma, H., Kawai, S., Tabata, K.V., Tomiyama, K., Kakizuka, A., Komatsuzaki, T., Noji, H., Imamura, H.
    Sci. Rep. 4: 6522 (2014). PMID 25283467.

Autophagy indicator

  • Chaperone mediated autophagy activity by the GAPDH-HT indicator by Dr. Takahiro Seki’s lab as well as fluorescent protein probes of LC3B accumulation developed by Dr. Noboru Mizushima’s lab, Dr. Itaru Hamachi’s lab and Dr. Keiji Kimura’s lab are available.

bilirubin indicator UnaG, BReleaCa

  • A dual-ligand-modulable fluorescent protein based on UnaG and calmodulin.
    Shitashima, Y., Shimozawa, T., Asahi, T., Miyawaki, A.
    Biochem. Biophys. Res. Commun. 496 (3): 872-879 (2018). PubMed PMID 29395087.

    Catalog no. Name of resource Descriptiion
    RDB15908 pRSETB-BReleaCa Bacteria expression vector of UnaG/CaM hybrid protein, BReleaCa, capable of binding to bilirubin and calcium.
    Catalog no. Name of resource Descriptiion
    RDB15909 pcDNA3-BReleaCa Expression vector of UnaG/CaM hybrid protein, BReleaCa, capable of binding to bilirubin and calcium.
  • Continuous de novo biosynthesis of haem and its rapid turnover to bilirubin are necessary for cytoprotection against cell damage.
    Takeda, T.A., Mu, A., Tai, T.T., Kitajima, S., Taketani, S.
    Sci. Rep. 5: 10488 (2015). PubMed PMID 25990790.

    Catalog no. Name of resource Descriptiion
    RDB13504 pET-His UNAG Expression clone of eel UnaG in E.coli.
  • A bilirubin-inducible fluorescent protein from eel muscle.
    Kumagai, A., Ando, R., Miyatake, H., Greimel, P., Kobayashi, T., Hirabayashi, Y., Shimogori, T., Miyawaki, A.
    Cell 153 (7): 1602-1611(2013). PubMed PMID 23768684.

    Catalog no. Name of resource Descriptiion
    RDB15703 UnaG/pcDNA3-FLAG Expression vector of eel UnaG, bilirubin-inducible fluorescent protein.
    Catalog no. Name of resource Descriptiion
    RDB15704 UnaG/pGEX-2T xpression vector of eel UnaG, bilirubin-inducible fluorescent protein.

cAMP indicator

  • Extracellular calcium influx activates adenylate cyclase 1 and potentiates insulin secretion in MIN6 cells.
    Kitaguchi, T., Oya, M., Wada, Y., Tsuboi, T., Miyawaki, A.
    Biochem. J. 450 (2): 365-373 (2013). PubMed PMID 23282092.

    Catalog no. Name of resource Descriptiion
    RDB15247 Flamindo/pcDNA3 Expression vector of yellow fluorescent biosensor for cAMP, Flamindo.

Cell cycle indicator Fucci

  • To monitor cell cycle progression in living cells, cell cycle indicator Fucci probes deveoped by Dr. Atsushi Miyawaki’s lab are available.

Caspase activity indicator

  • A high-throughput method for development of FRET-based indicators for proteolysis.
    Nagai, T., Miyawaki, A.
    Biochem. Biophys. Res. Commun. 319 (1): 72-77 (2004). PubMed PMID 15158444.

    Catalog no. Name of resource Descriptiion
    RDB15705 SCAT3.1/pcDNA4 HMB Expression vector of FRET based apoptosis probe.
  • Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer.
    Karasawa, S., Araki, T., Nagai, T., Mizuno, H., Miyawaki, A.
    Biochem. J. 381 (Pt 1): 307-312 (2004). PubMed PMID 15065984.

    Catalog no. Name of resource Descriptiion
    RDB15240 MiCy-DEVD-mKO1/pCS2 Expression vector of FRET based caspase3 activity monitoring probe.

Calcium-ion sensor

  • Fluorescent protein-based Ca2+ sensors, G-CaMPs, Yellow Cameleons and Pericams developed by Dr. Jin-ichi Nakai’s lab and Dr. Atsushi Miyawaki’s lab, which are composed with calmodulin, fluorescent protein and M13 peptide (CaM binding domain of myosin light chain kinase), are designated to visualize intracellular [Ca2+] dynamics.
  • G-CaMP
  • Pericam
  • Yellow Cameleon

Concentration of Protein in cells

  • Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it.
    Morikawa, J.T., Fujita, H., Kitamura, A., Horio, T., Yamamoto, J., Kinjo, M., Sasaki, A., Machiyama, H., Yoshizawa, K., Ichimura, T., Imada, K., Nagai, T., Watanabe, M.T.
    Sci. Rep. 6: 22342, 2016. PubMed PMID: 26956628

    Catalog no. Name of resource Descriptiion
    RDB14203 pPAL7_GimRET (CFP-YFP1G/pPAL7) Expression vector of GimRET (Glycine inserted mutant FRET probe) for E. coli.
    RDB14204 pGimRET (CFP-YFP1G/pECFP) Expression vector of GimRET (Glycine inserted mutant FRET probe) for mammalian cells.

pH sensor

  • Dual-color-emitting green fluorescent protein used as pH indicators from the sea cactus Cavernularia obesa developed by Dr. Katsunori Ogoh of the Olympus corporation.
    Ogoh, K. et al. Dual-color-emitting green fluorescent protein from the sea cactus Cavernularia obesa and its use as a pH indicator for fluorescence microscopy. Luminescence 28 (4): 582-591, 2013.

    Catalog no. Name of clone Characteristic misc.
    RDB14368 pCoGFP-wt wild type
    RDB14369 pCoGFP-mam From blue to green at pH 5 – 6
    RDB14370 pCoGFP-V0 From blue to green at pH 5 – 6
    RDB14371 pCoGFP-V1 From blue to green at pH 6 – 7
    RDB14372 pCoGFP-V2 From blue to green at pH 7 – 8
    RDB14373 pCoGFP-V3 From blue to green at pH 9 – 10
    RDB14374 pCoGFP-V4 From blue to green at pH 9 – 10

RA indicator

  • Visualization of an endogenous retinoic acid gradient across embryonic development.
    Shimozono, S., Iimura, T., Kitaguchi, T., Higashijima, S., Miyawaki, A.
    Nature 496 (7445): 363-366 (2013). PubMed PMID 23563268.

    Catalog no. Name of resource Descriptiion
    RDB15249 GEPRA-B Genetically encoded indicator for RA, GEPRA, having ligand binding domain from the RAR-beta.
    RDB15250 GEPRA-G Genetically encoded indicator for RA, GEPRA, having ligand binding domain from the RAR-gamma.
    RDB15251 GEPRA-AA Genetically encoded indicator for RA, GEPRA. Low-affinity verson of the GEPRA-B.
    RDB15252 GEPRA-B/ pT2KXIGdeltain Expression vector of genetically encoded indicator for RA, GEPRA. For generation of transgenic zebrafish.
    RDB15253 GEPRA-G/ pT2KXIGdeltain Expression vector of genetically encoded indicator for RA, GEPRA. For generation of transgenic zebrafish.
    RDB15254 GEPRA-AA/ pT2KXIGdeltain Expression vector of genetically encoded indicator for RA, GEPRA. For generation of transgenic zebrafish. Low-affinity verson of the GEPRA-B.

Rab11: active Rab11 visualization

  • RBD11, a bioengineered Rab11-binding module for visualizing and analyzing endogenous Rab11.
    Osaki F, Matsui T, Hiragi S, Homma Y, Fukuda M.
    J. Cell Sci. 134 (7): jcs257311 (2021). PubMed PMID 33712449.

    Catalog no. Name of resource Descriptiion
    RDB18788 pMRX-puro-EGFP-RBD11 Retroviral expression vector for visualization of active Rab11: mouse Rab11-specific binding domain (RBD11) tagged with EGFP.
    RDB18789 pMRX-puro-EGFP-RBD11-mut Retroviral expression vector of negative control for visualization of active Rab11: mouse Rab11-specific binding domain (RBD11) mutant tagged with EGFP.
    RDB18790 pMRX-puro-EGFP-2xRBD11 Retroviral expression vector of negative control for visualization of active Rab11: mouse Rab11-specific binding domain (RBD11) mutant tagged with EGFP.
    RDB18791 pMRX-puro-EGFP-2xRBD11-mut Retroviral expression vector of negative control for visualization of active Rab11: mouse Rab11-specific binding domain (RBD11) mutant tagged with EGFP.
    RDB18792 pMRX-puro-EGFP-FM-RBD11 Retroviral expression vector of active Rab11 trapper: FM-tagged mouse Rab11-specific binding domain (RBD 11) tagged with EGFP.
    RDB18793 pMRX-puro-EGFP-FM-RBD11-mut Retroviral expression vector of negative control of active Rab11 trapper: FM-tagged mouse Rab11-specific binding domain (RBD 11) mutant tagged with EGFP.

Sphingolipid marker

  • Lipid rafts are small lipid domains on the cell membrane and are thought to play an important role in signal transduction, endocytosis and more. We provide fluorescent probes for sphingomyelin and cholesterol lipid domains.
  • Nakanori: sphingomyelin and cholesterol lipid domain (lipid raft)
  • D4 toxin: cholesterol rich domain
  • lysenin: sphingomyelin

Voltage indicator

  • Improving membrane voltage measurements using FRET with new fluorescent proteins.
    Tsutsui, H., Karasawa, S., Okamura, Y., Miyawaki, A.
    Nat. Methods 5 (8): 683-685 (2008). PubMed PMID 18622396.

    Catalog no. Name of resource Descriptiion
    RDB15262 Mermaid Voltage indicator Mermaid.
  • Improved detection of electrical activity with a voltage probe based on a voltage-sensing phosphatase.
    Tsutsui, H., Jinno, Y., Tomita, A., Niino, Y., Yamada, Y., Mikoshiba, K., Miyawaki, A., Okamura, Y.
    J. Physiol. 591 (18): 4427-4437 (2013). PubMed PMID 23836686.

    Catalog no. Name of resource Descriptiion
    RDB15263 Mermaid2 Voltage probe Mermaid2.

Notch signaling reporter

  • The pRBS-EGFP and RBP-J-Venus expression clones deposited by Dr. Makoto Mark Taketo and Dr. Kenji Tanigaki, respectively, allow you monitoring the state of activation of the Notch signaling by fluorescence in living cells.

Epigenetics reporter

  • Visualization of histone acetylation: The Histac fluorescent probes deposited by Dr. Kazuki Sasaki allow you monitoring the state of activity of acetylation of histone H4 by fluorescence in living cells.
  • Visualization of methylated DNA: The EGFP-MBD-nls protein recognizes the methylated DNA and you can follow status of the DNA methylation in situ under physiological conditions using the pEGFP-MBD-nls expression clone.

Visualization of Organelles

  • Organelle marker/subcellular localization
    • We are providing genetic resources for visualization of organelles such as mitochondria and nucleus. Each clone contains an organelle localization signal sequence fused with fluorescent proteins or epitope tags. Organelles can be detected by fluorescence or by detecting epitope tags with antibodies.
  • Fluorescent protein probe that can visualize the multiple inter-organelle contact sites in cells
    • Divided GFP-fragment have a feature that they emit fluorescence again by reconstitution when each fragment is in close proximity. When labelled organelles such as mitochondria and ERs by the divided GFPs exist together, the contact sites in cells are visualized by the reconstituted fluorescent protein. The vectors of fluorescent protein probes developed by Dr. Yasushi Tamura of the Yamagata University, Dr. Toshiya Endo of the Kyoto Sangyo University and their colleague are available from the DNA Bank.
    • Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system.
      Kakimoto, Y., Tashiro, S., Kojima, R., Morozumi, Y., Endo, T., Tamura, Y.
      Sci. Rep. 8 (1): 6175 (2018). PubMed PMID 29670150.

References

Fluorescent protein resource

  • Sea cactus therostable GFP
  • Azami Green (AG, hmAG1, hmAG407)
  • cjBlue (cjBlue, cjBlue Y64L)
  • Cy11.5
  • Dronpa-Green (Dronpa, Dronpa2, Dronpa3, 22G)
  • Kaede
  • Keima-red (dKeima, dKeima570, mKeima, tdKeima)
  • Kikume Green-Red (KikGR, mKikGR, mKikGR13.2, Xpa)
  • Kusabira Green Orange (mK-GO)
  • Kusabira Orange (KO1, hmKO1, hmKO2, hmKO-K)
  • Midoriishi-Cyan (MiCy, mMiCy1)
  • Venus (Venus, mVenus, cp49Venus, cp145Venus, cp157Venus, cp173Venus, cp195Venus, cp229Venus)
  • Destabilized FPs
  • Knock in markers with CRISPR/Cas9 genome editing

Luminescent protein

  • Nano-lantern luminescent and fluorescent protein
    • Nano lantern (NL) consists of Renilla luciferase and adjacent fluorescence protein. The chemiluminescence of the luciferase provides light source for excitation and enables the fluorescence protein to be observed. Three colors of NLs, yellow, cyan and orange, have been developed. NLs do not require external light source and overcome problems such as autofluorescence, phototoxicity, and photobleaching.
  • Higher intensity luciferases having Green-, Yellow- or Red-emission by using D-luciferin
    • These luciferases have at most four-time maximum luminous intensity than that of widely used luciferase of the Photinus pyralis, a common North American firefly. Further more, Green-, Yellow- or Red-emission can be obtained by using D-luciferin as a substrate of each luciferase.
  • AkaLuc luciferase providing brighter and red-shifted luminescence
    • The artificial bioluminescence system AkaBLI enables noninvasive signal observation in deep tissue of living animals. It was developed by Dr. Atsushi Miyawaki and Dr. Satoshi Iwano of the RIKEN Center for Brain Science, and Dr. Shojiro Maki of the University of Electro-Communications. The AkaBLI consists of an artificial substrate AkaLumine with improved tissue permeability and an artificial luciferase Akaluc optimized to AkaLumine. The intensity of the luminescence of AkaBLI system is 100 to 1000 folds brighter than the conventional systems.

 

(GRP0058e 2019.01.24 T.M.)

2021.09.09



 

Comments are closed.