Shaner Lab

Principal Investigator: Nathan C. Shaner, PhD  

email: nathanshaner at scintillon dot org

Research Focus: Biological tool-building (fluorescent proteins and bioluminescence)

The Shaner lab adapts naturally occurring proteins into broadly useful biological research tools.This type of work remains under-served and underfunded in the biological sciences despite its importance to the continued advancement of focused human disease research.

One of our key areas of work is engineering naturally occurring fluorescent proteins, found in many marine invertebrates such as jellyfish and corals, for use in imaging the activity within living cells. We believe our work will improve researchers’ ability to visualize processes in living cells at “superresolution,” showing much more detail than is possible with traditional microscopy.

We also aim to fully decode the bioluminescence pathways by which organisms produce light, allowing us to design ultra-sensitive biological sensors.

Shaner Lab: In-depth

Biological Tools. Many of the most useful tools in modern biomedical research are derived from naturally evolved systems. Among the most well known biological tools are the fluorescent proteins, derived from a variety of marine invertebrates such as jellyfish and corals. We are continuing to engineer improved fluorescent protein variants optimized for use in specific imaging techniques, such as the newly minted field of superresolution imaging, which uses fluorescent labels to allow reconstruction of optical images far beyond the traditional diffraction limit.

Bioluminescence. We are also interested in bioluminescence, the process by which biological organisms, such as fireflies and jellyfish, produce light. Every known bioluminescence reaction involves an enzyme (a luciferase or a photoprotein) and a small molecule substrate (a luciferin). Currently, we are working with Dr. Ute Hochgeschwender at Central Michigan University to develop luciferase-based light sources to selectively activate optogenetic actuators in vivo. This approach allows the use of optogenetic tools in intact animals without the need for invasive surgeries.

While a great many luciferases and photoproteins have been cloned, very little is understood about the biosynthesis of eukaryotic luciferins. We are using massively parallel RNA-Seq and biochemical approaches to delineate the biosynthetic pathways for a number of important eukaryotic luciferins, including firefly luciferin ("d-luciferin"), dinoflagellate luciferin, and coelenterazine (in collaboration with Dr. Steven Haddock at MBARI). Eventually, we hope to use these pathways to generate the next generation of optogenetic tools for biomedical research

Shaner Lab Grants

NIH R01 "Fluorescent Proteins for Superresolution Imaging"

NSF BRAIN EAGER "Genetically Encoded Light Sources for Non-Invasive Optogenetics"


  • Shaner, N.C., Campbell, R.E., Steinbach, P.A., Giepmans, B.N., Palmer, A.E. & Tsien R.Y. (2004). "Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein." Nature Biotechnology, 22(12), 1567-72. (Download PDF)
  • Shaner, N.C., Steinbach, P.A. & Tsien, R.Y. (2005). "A guide to choosing fluorescent proteins." Nature Methods, 2(12), 905-9. (Download PDF)
  • Shu, X., Shaner, N.C., Yarbrough, C.A., Tsien, R.Y. & Remington, S.J. (2006). "Novel chromophores and buried charges control color in mFruits." Biochemistry, 45(32), 9639-47. (Download PDF)
  • Ai, H.W., Shaner, N.C., Cheng, Z., Tsien, R.Y. & Campbell, R.E. (2007). "Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins." Biochemistry, 46(20), 5904-10. (Download PDF)
  • Shaner, N.C., Patterson, G.H. & Davidson, M.W. (2007). "Advances in fluorescent protein technology." Journal of Cell Science, 120(Pt 24) 4247-60. (Download PDF)
  • Shaner, N.C., Lin, M.Z., McKeown, M.R., Steinbach, P.A., Hazelwood, K.L., Davidson, M.W. & Tsien, R.Y. (2008). "Improving the photostability of bright monomeric orange and red fluorescent proteins." Nature Methods, 5(6), 545-51. PMC2853173 (Download PDF)
  • Lin, M.Z., McKeown, M.R., Ng, H.L., Aguilera, T.A., Shaner, N.C., Campbell, R.E., Adams, S.R., Gross, L.A., Ma, W., Alber, T. & Tsien, R.Y. (2009). "Autofluoresent proteins with excitation in the optical window for intravital imaging in mammals." Chemistry & Biology, 16(11), 1169-79. PMC2814181 (Download PDF)
  • Ouyang, M., Huang, H., Shaner, N.C., Remacle, A.G., Shiryaev, S.A., Strongin, A.Y., Tsien, R.Y. & Wang, Y. (2010). "Simultaneous visualization of pro-tumorigenic Src and MT1-MMP activities with fluorescence resonance energy transfer." Cancer Research, 70(6): 2204-12. PMC2840183 (Download PDF)
  • Hoi, H., Shaner, N.C., Davidson, M.W., Cairo, C.W., Wang, J. & Campbell, R.E. (2010). "A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization."  Journal of Molecular Biology, 401(5), 776-91. (Download PDF)
  • Ewen-Campen, B., Shaner, N.C., Panfilio, K.A., Suzuki, Y., Roth, S. & Extavour, C.G. (2011). "The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus."  BMC Genomics, 12:61. PMC3040728 (Download PDF)
  • Siebert, S., Robinson, M.D., Tintori, S.C., Goetz, F., Helm, R.R., Smith, S.A., Shaner, N.C., Haddock, S.H., & Dunn, C.W. (2011). "Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows." PloS One, 6(7):e22953. PMC3146525 (Download PDF)
  • Li, H., Foss, S.M., Dobryy, Y.L., Park, C.K., Hires, S.A., Shaner, N.C., Tsien, R.Y., Osborne, L.C. & Voglmaier, S.M. (2011). "Concurrent imaging of synaptic vesicle recycling and calcium dynamics." Frontiers in Molecular Neuroscience, 4:34. PMC3206542 (Download PDF)
  • Powers, M.L., McDermott, A.G., Shaner, N.C., & Haddock, S.H. (2012). "Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: Insights into light-sensitive photoproteins." Biochemical and Biophysical Research Communications, Feb 8;431(2):360-6. PMC3570696 (Download PDF)
  • Francis, W.R., Christianson, L.M., Kiko, R., Powers, M.L., Shaner, N.C., & Haddock, S.H. (2013). "A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly." BMC Genomics, Mar 12;14(1):167. (Download PDF)
  • Shaner, N.C. (2013). "The mFruit collection of monomeric fluorescent proteins." Clin Chem 59(2):440-441. (commentary) (Download PDF)
  • Shaner, N.C., Lambert, G.G., Chammas, A., Ni, Y., Cranfill, P.J., Baird, M.A., Sell, B.R., Allen, J.R., Day, R.N., Israelsson, M., Davidson, M.W., & Wang, J. (2013) "A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum." Nature Methods, May;10(5):407-9. doi: 10.1038/nmeth.2413. (Download PDF)
  • Shaner, N.C. (2014) "Fluorescent proteins for quantitative microscopy: Important properties and practical evaluation." Methods in Cell Biology, 123:95-111. doi: 10.1016/B978-0-12-420138-5.00006-9. (Download PDF)
  • Francis, W.R., Shaner, N.C., Christianson, L.M., Powers, M.L., & Haddock, S.H. (2015) "Occurrence of Isopenicillin-N-Synthase Homologs in Bioluminescent Ctenophores and Implications for Coelenterazine Biosynthesis." PLoS One, Jun 30;10(6):e0128742. doi: 10.1371/journal.pone.0128742. (Download PDF) 
  • Fujita K, Nagai T, Shaner N, Egner A. (2015) "Special Section Guest Editorial: Protein Photonics for Imaging, Sensing, and Manipulation: Honoring Prof. Osamu Shimomura, a Pioneer of Photonics for Biomedical Research." J Biomed Opt, Oct;20(10):101201. doi: 10.1117/1.JBO.20.10.101201.
  • Tewson PH, Martinka S, Shaner NC, Hughes TE, Quinn AM. (2016) "New DAG and cAMP Sensors Optimized for Live-Cell Assays in Automated Laboratories." J Biomol Screen, Mar;21(3):298-305. doi: 10.1177/1087057115618608.
  • Clavel D, Gotthard G, von Stetten D, De Sanctis D, Pasquier H, Lambert GG, Shaner NC, Royant A. (2016) "Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution." Acta Crystallogr D Struct Biol, Dec 1;72(Pt 12):1298-1307.
  • Shen Y, Chen Y, Wu J, Shaner NC, Campbell RE. (2017) "Engineering of mCherry variants with long Stokes shift, red-shifted fluorescence, and low cytotoxicity." PLoS One, Feb 27;12(2):e0171257. doi: 10.1371/journal.pone.0171257.

Latest News

Scintillon Institute investigator Dr. Nathan Shaner, in collaboration with colleagues at the Monterey Bay Aquarium Research Institute, has published a paper in PLoS ONE describing the discovery of a major clue about how marine organisms produce light.

The Scintillion Institute’s Nathan Shaner and his collaborator Ute Hochgeschwender at Central Michigan University became recipients of a National Science Foundation (NSF) BRAIN EAGER grant for developing non-invasive optogenetics based on bioluminescence.

This project will take advantage of wild-type fluorescent proteins with novel optical properties to be cloned from a broad range of species, including several Great Barrier Reef corals made available through an international collaboration.