title: Sensitive red protein calcium indicators for imaging neural activity.
abstract: Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Hod
authors.initials: H
authors.lastname: Dana
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.|Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Boaz
authors.initials: B
authors.lastname: Mohar
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Yi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Sujatha
authors.initials: S
authors.lastname: Narayan
authors.affiliation: Howard Hughes Medical Institute, The Rockefeller University, New York, United States.
authors.forename: Andrew
authors.initials: A
authors.lastname: Gordus
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Jeremy P
authors.initials: JP
authors.lastname: Hasseman
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Getahun
authors.initials: G
authors.lastname: Tsegaye
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Graham T
authors.initials: GT
authors.lastname: Holt
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Amy
authors.initials: A
authors.lastname: Hu
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Deepika
authors.initials: D
authors.lastname: Walpita
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Ronak
authors.initials: R
authors.lastname: Patel
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: John J
authors.initials: JJ
authors.lastname: Macklin
authors.affiliation: Howard Hughes Medical Institute, The Rockefeller University, New York, United States.
authors.forename: Cornelia I
authors.identifier: 0000-0002-8484-0618
authors.initials: CI
authors.lastname: Bargmann
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Misha B
authors.identifier: 0000-0002-3457-4462
authors.initials: MB
authors.lastname: Ahrens
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Eric R
authors.initials: ER
authors.lastname: Schreiter
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Vivek
authors.initials: V
authors.lastname: Jayaraman
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Loren L
authors.initials: LL
authors.lastname: Looger
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Karel
authors.identifier: 0000-0002-6670-7362
authors.initials: K
authors.lastname: Svoboda
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Douglas S
authors.identifier: 0000-0001-9029-314X
authors.initials: DS
authors.lastname: Kim
mesh_terms: D000818:Animals; D015374:Biosensing Techniques / Q000379:methods*; D017173:Caenorhabditis elegans; D002118:Calcium / Q000032:analysis*; D002478:Cells, Cultured; D004330:Drosophila; D000069416:Intravital Microscopy / Q000379:methods*; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D009474:Neurons / Q000737:chemistry* / Q000502:physiology*; D009482:Neurophysiology / Q000379:methods*; D015027:Zebrafish; D000097573:Red Fluorescent Protein
chemical_list: D002118:Calcium; D008164:Luminescent Proteins; D000097573:Red Fluorescent Protein
keywords: C. elegans; D. melanogaster; GECI; calcium imaging; fluorescent probes; mouse; neuroscience; protein engineering; zebrafish