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2. Neurophotonic tools for microscopic measurements and manipulation: status report

Author

Abdelfattah, Ahmed S, Ahuja, Sapna, Akkin, Taner, Allu, Srinivasa Rao, Brake, Joshua, Boas, David A, Buckley, Erin M, Campbell, Robert E, Chen, Anderson I, Cheng, Xiaojun, Čižmár, Tomáš, Costantini, Irene, De Vittorio, Massimo, Devor, Anna, Doran, Patrick R, Khatib, Mirna El, Emiliani, Valentina, Fomin-Thunemann, Natalie, Fainman, Yeshaiahu, Fernandez-Alfonso, Tomas, Ferri, Christopher GL, Gilad, Ariel, Han, Xue, Harris, Andrew, Hillman, Elizabeth MC, Hochgeschwender, Ute, Holt, Matthew G, Ji, Na, Kılıç, Kıvılcım, Lake, Evelyn MR, Li, Lei, Li, Tianqi, Mächler, Philipp, Miller, Evan W, Mesquita, Rickson C, Nadella, KM Naga Srinivas, Nägerl, U Valentin, Nasu, Yusuke, Nimmerjahn, Axel, Ondráčková, Petra, Pavone, Francesco S, Campos, Citlali Perez, Peterka, Darcy S, Pisano, Filippo, Pisanello, Ferruccio, Puppo, Francesca, Sabatini, Bernardo L, Sadegh, Sanaz, Sakadzic, Sava, Shoham, Shy, Shroff, Sanaya N, Silver, R Angus, Sims, Ruth R, Smith, Spencer L, Srinivasan, Vivek J, Thunemann, Martin, Tian, Lei, Tian, Lin, Troxler, Thomas, Valera, Antoine, Vaziri, Alipasha, Vinogradov, Sergei A, Vitale, Flavia, Wang, Lihong V, Uhlířová, Hana, Xu, Chris, Yang, Changhuei, Yang, Mu-Han, Yellen, Gary, Yizhar, Ofer, and Zhao, Yongxin

Subjects
Engineering, Biomedical and Clinical Sciences, Neurosciences, Biomedical Engineering, 1.1 Normal biological development and functioning, Underpinning research, Neurological, optical imaging, molecular sensors, optogenetics, fluorescence, label free, blood flow, multimodal, Medical Biotechnology, Biomedical engineering
Abstract

Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.

Published
2022

6. Kilohertz frame-rate two-photon tomography

Author

Kazemipour, Abbas, Novak, Ondrej, Flickinger, Daniel, Marvin, Jonathan S., Abdelfattah, Ahmed S., King, Jonathan, Borden, Philip M., Kim, Jeong Jun, Al-Abdullatif, Sarah H., Deal, Parker E., Miller, Evan W., Schreiter, Eric R., Druckmann, Shaul, Svoboda, Karel, Looger, Loren L., and Podgorski, Kaspar

Published
2019
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7. A genetically encoded near-infrared fluorescent calcium ion indicator

Author

Qian, Yong, Piatkevich, Kiryl D., Mc Larney, Benedict, Abdelfattah, Ahmed S., Mehta, Sohum, Murdock, Mitchell H., Gottschalk, Sven, Molina, Rosana S., Zhang, Wei, Chen, Yingche, Wu, Jiahui, Drobizhev, Mikhail, Hughes, Thomas E., Zhang, Jin, Schreiter, Eric R., Shoham, Shy, Razansky, Daniel, Boyden, Edward S., and Campbell, Robert E.

Published
2019
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8. Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

Author

Abdelfattah, Ahmed S., primary, Zheng, Jihong, additional, Singh, Amrita, additional, Huang, Yi-Chieh, additional, Reep, Daniel, additional, Tsegaye, Getahun, additional, Tsang, Arthur, additional, Arthur, Benjamin J., additional, Rehorova, Monika, additional, Olson, Carl V.L., additional, Shuai, Yichun, additional, Zhang, Lixia, additional, Fu, Tian-Ming, additional, Milkie, Daniel E., additional, Moya, Maria V., additional, Weber, Timothy D., additional, Lemire, Andrew L., additional, Baker, Christopher A., additional, Falco, Natalie, additional, Zheng, Qinsi, additional, Grimm, Jonathan B., additional, Yip, Mighten C., additional, Walpita, Deepika, additional, Chase, Martin, additional, Campagnola, Luke, additional, Murphy, Gabe J., additional, Wong, Allan M., additional, Forest, Craig R., additional, Mertz, Jerome, additional, Economo, Michael N., additional, Turner, Glenn C., additional, Koyama, Minoru, additional, Lin, Bei-Jung, additional, Betzig, Eric, additional, Novak, Ondrej, additional, Lavis, Luke D., additional, Svoboda, Karel, additional, Korff, Wyatt, additional, Chen, Tsai-Wen, additional, Schreiter, Eric R., additional, Hasseman, Jeremy P., additional, and Kolb, Ilya, additional

Published
2023
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9. Correction to: A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578

Author

Shen, Yi, Dana, Hod, Abdelfattah, Ahmed S., Patel, Ronak, Shea, Jamien, Molina, Rosana S., Rawal, Bijal, Rancic, Vladimir, Chang, Yu-Fen, Wu, Lanshi, Chen, Yingche, Qian, Yong, Wiens, Matthew D., Hambleton, Nathan, Ballanyi, Klaus, Hughes, Thomas E., Drobizhev, Mikhail, Kim, Douglas S., Koyama, Minoru, Schreiter, Eric R., and Campbell, Robert E.

Published
2019
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10. A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578

Author

Shen, Yi, Dana, Hod, Abdelfattah, Ahmed S., Patel, Ronak, Shea, Jamien, Molina, Rosana S., Rawal, Bijal, Rancic, Vladimir, Chang, Yu-Fen, Wu, Lanshi, Chen, Yingche, Qian, Yong, Wiens, Matthew D., Hambleton, Nathan, Ballanyi, Klaus, Hughes, Thomas E., Drobizhev, Mikhail, Kim, Douglas S., Koyama, Minoru, Schreiter, Eric R., and Campbell, Robert E.

Published
2018
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11. Optimization of genetically encoded voltage and calcium indicators for in vivo imaging

Author

Hasseman, Jeremy, Abdelfattah, Ahmed S., Arthur, Ben, Cox, Jim D., Guo, Caiying, Jayaraman, Vivek, Kolb, Ilya, Korff, Wyatt, Lee, Albert K, Lee, Jae Sung, Looger, Loren, Lopez, Crystal, Pachitariu, Marius, Reep, Daniel, Schreiter, Eric R., Spruston, Nelson, Svoboda, Karel, Tebo, Alison G., Turner, Glenn C., Tsang, Arthur, Tsegaye, Getahun, Wang, Tim, Zhang, Yan, and Zheng, Jihong

Subjects
Animal cell and molecular biology, Neurosciences not elsewhere classified, Medical molecular engineering of nucleic acids and proteins, Proteins and peptides, Plant cell and molecular biology
Abstract

The GENIE Project Team at HHMI Janelia Research Campus have developed a multiple genetically-encoded fluorescent indicators including the jGCaMP8 Calcium indicator family, the Voltron and Positron voltage indicators, and animal models incorporating these indicators. This poster provides updates on developments in each tool and how to obtain them. Chemigenetic voltage indicator improvement: Voltron2 showed a 65% increase in 1AP sensitivity and 3x better subthreshold membrane potential detection. Mutations in the voltage-sensing domain (Ace2N) were swapped between various types of voltage indicators and compared with patch-clamp. A new positive-going variant, Positron2, showed a 300% improvement in sensitivity. jGCaMP8s and 8m transgenic mice: TetO-jGCaMP8s mouse has ~5X increased SNR compared to TetO-GCaMP6s. Sensitivity and fast kinetics match AAV performance. TIGRE jGCaMP8s/m knock-in mice stably expressed in targeted neuronal subpopulations with reduced tetTA toxicity effects. Mice available soon from JAX.

Published
2022
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12. Author Correction: Kilohertz frame-rate two-photon tomography

Author

Kazemipour, Abbas, Novak, Ondrej, Flickinger, Daniel, Marvin, Jonathan S., Abdelfattah, Ahmed S., King, Jonathan, Borden, Philip M., Kim, Jeong Jun, Al-Abdullatif, Sarah H., Deal, Parker E., Miller, Evan W., Schreiter, Eric R., Druckmann, Shaul, Svoboda, Karel, Looger, Loren L., and Podgorski, Kaspar

Published
2019
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14. Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

Author

Abdelfattah, Ahmed S, primary, Zheng, Jihong, additional, Reep, Daniel, additional, Tsegaye, Getahun, additional, Tsang, Arthur, additional, Arthur, Benjamin J, additional, Rehorova, Monika, additional, Olson, Carl VL, additional, Huang, Yi-Chieh, additional, Shuai, Yichun, additional, Koyama, Minoru, additional, Moya, Maria V, additional, Weber, Timothy D, additional, Lemire, Andrew L, additional, Baker, Christopher A, additional, Falco, Natalie, additional, Zheng, Qinsi, additional, Grimm, Jonathan B, additional, Yip, Mighten C, additional, Walpita, Deepika, additional, Forest, Craig R, additional, Chase, Martin, additional, Campagnola, Luke, additional, Murphy, Gabe, additional, Wong, Allan M, additional, Mertz, Jerome, additional, Economo, Michael N, additional, Turner, Glenn, additional, Lin, Bei-Jung, additional, Chen, Tsai-Wen, additional, Novak, Ondrej, additional, Lavis, Luke D, additional, Svoboda, Karel, additional, Korff, Wyatt, additional, Schreiter, Eric R, additional, Hasseman, Jeremy P, additional, and Kolb, Ilya, additional

Published
2021
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15. Far-red fluorescent genetically encoded calcium ion indicators

Author

Dalangin, Rochelin, primary, Drobizhev, Mikhail, additional, Molina, Rosana S., additional, Aggarwal, Abhi, additional, Patel, Ronak, additional, Abdelfattah, Ahmed S., additional, Zhao, Yufeng, additional, Wu, Jiahui, additional, Podgorski, Kaspar, additional, Schreiter, Eric R., additional, Hughes, Thomas E., additional, Campbell, Robert E., additional, and Shen, Yi, additional

Published
2020
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18. Bright and tunable far-red chemigenetic indicators

Author

Deo, Claire, primary, Abdelfattah, Ahmed S., additional, Bhargava, Hersh K., additional, Berro, Adam J., additional, Falco, Natalie, additional, Moeyaert, Benjamien, additional, Chupanova, Mariam, additional, Lavis, Luke D., additional, and Schreiter, Eric R., additional

Published
2020
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20. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Author

Abdelfattah, Ahmed S., primary, Kawashima, Takashi, additional, Singh, Amrita, additional, Novak, Ondrej, additional, Liu, Hui, additional, Shuai, Yichun, additional, Huang, Yi-Chieh, additional, Campagnola, Luke, additional, Seeman, Stephanie C., additional, Yu, Jianing, additional, Zheng, Jihong, additional, Grimm, Jonathan B., additional, Patel, Ronak, additional, Friedrich, Johannes, additional, Mensh, Brett D., additional, Paninski, Liam, additional, Macklin, John J., additional, Murphy, Gabe J., additional, Podgorski, Kaspar, additional, Lin, Bei-Jung, additional, Chen, Tsai-Wen, additional, Turner, Glenn C., additional, Liu, Zhe, additional, Koyama, Minoru, additional, Svoboda, Karel, additional, Ahrens, Misha B., additional, Lavis, Luke D., additional, and Schreiter, Eric R., additional

Published
2019
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22. Wide-Area All-Optical Neurophysiology in Acute Brain Slices

Author

Farhi, Samouil L., primary, Parot, Vicente J., additional, Grama, Abhinav, additional, Yamagata, Masahito, additional, Abdelfattah, Ahmed S., additional, Adam, Yoav, additional, Lou, Shan, additional, Kim, Jeong Jun, additional, Campbell, Robert E., additional, Cox, David D., additional, and Cohen, Adam E., additional

Published
2019
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24. Wide-area all-optical neurophysiology in acute brain slices

Author

Farhi, Samouil L., primary, Parot, Vicente J., additional, Grama, Abhinav, additional, Yamagata, Masahito, additional, Abdelfattah, Ahmed S., additional, Adam, Yoav, additional, Lou, Shan, additional, Jun Kim, Jeong, additional, Campbell, Robert E., additional, Cox, David D., additional, and Cohen, Adam E., additional

Published
2018
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25. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Author

Abdelfattah, Ahmed S., primary, Kawashima, Takashi, additional, Singh, Amrita, additional, Novak, Ondrej, additional, Liu, Hui, additional, Shuai, Yichun, additional, Huang, Yi-Chieh, additional, Grimm, Jonathan B., additional, Patel, Ronak, additional, Friedrich, Johannes, additional, Mensh, Brett D., additional, Paninski, Liam, additional, Macklin, John J., additional, Podgorski, Kaspar, additional, Lin, Bei-Jung, additional, Chen, Tsai-Wen, additional, Turner, Glenn C., additional, Liu, Zhe, additional, Koyama, Minoru, additional, Svoboda, Karel, additional, Ahrens, Misha B., additional, Lavis, Luke D., additional, and Schreiter, Eric R., additional

Published
2018
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26. A general approach to engineer positive-going eFRET voltage indicators.

Author

Abdelfattah, Ahmed S., Valenti, Rosario, Zheng, Jihong, Wong, Allan, GENIE Project Team, Chuong, Amy S., Hasseman, Jeremy P., Jayaraman, Vivek, Kolb, Ilya, Korff, Wyatt, Lavis, Luke D., Liang, Yajie, Looger, Loren L., Merryweather, Derek, Reep, Daniel, Spruston, Nelson, Svoboda, Karel, Tsang, Arthur, Tsegaye, Getahun, and Turner, Glenn

Subjects
FLUORESCENCE resonance energy transfer, RHODOPSIN, MEMBRANE potential, ELECTRIC potential, FLUORESCENT proteins
Abstract

Imaging membrane voltage from genetically defined cells offers the unique ability to report spatial and temporal dynamics of electrical signaling at cellular and circuit levels. Here, we present a general approach to engineer electrochromic fluorescence resonance energy transfer (eFRET) genetically encoded voltage indicators (GEVIs) with positive-going fluorescence response to membrane depolarization through rational manipulation of the native proton transport pathway in microbial rhodopsins. We transform the state-of-the-art eFRET GEVI Voltron into Positron, with kinetics and sensitivity equivalent to Voltron but flipped fluorescence signal polarity. We further apply this general approach to GEVIs containing different voltage sensitive rhodopsin domains and various fluorescent dye and fluorescent protein reporters. Genetically encoded voltage indicators (GEVIs) allow visualisation of fast action potentials in neurons but most are bright at rest and dimmer during an action potential. Here, the authors engineer electrochromic FRET GEVIs with fast, bright and positive-going fluorescence signals for in vivo imaging. [ABSTRACT FROM AUTHOR]

Published
2020
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29. A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein

Author

Shen, Yi, primary, Dana, Hod, additional, Abdelfattah, Ahmed S., additional, Patel, Ronak, additional, Shea, Jamien, additional, Molina, Rosana S., additional, Rawal, Bijal, additional, Rancic, Vladimir, additional, Chang, Yu-Fen, additional, Wu, Lanshi, additional, Chen, Yingche, additional, Qian, Yong, additional, Wiens, Matthew D., additional, Hambleton, Nathan, additional, Ballanyi, Klaus, additional, Hughes, Thomas E., additional, Drobizhev, Mikhail, additional, Kim, Douglas S., additional, Koyama, Minoru, additional, Schreiter, Eric R., additional, and Campbell, Robert E., additional

Published
2017
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31. A Bright and Fast Red Fluorescent Protein Voltage Indicator That Reports Neuronal Activity in Organotypic Brain Slices

Author

Abdelfattah, Ahmed S., primary, Farhi, Samouil L., additional, Zhao, Yongxin, additional, Brinks, Daan, additional, Zou, Peng, additional, Ruangkittisakul, Araya, additional, Platisa, Jelena, additional, Pieribone, Vincent A., additional, Ballanyi, Klaus, additional, Cohen, Adam E., additional, and Campbell, Robert E., additional

Published
2016
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32. A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.

Author

Shen, Yi, Dana, Hod, Abdelfattah, Ahmed S., Patel, Ronak, Shea, Jamien, Molina, Rosana S., Rawal, Bijal, Rancic, Vladimir, Chang, Yu-Fen, Wu, Lanshi, Chen, Yingche, Qian, Yong, Wiens, Matthew D., Hambleton, Nathan, Ballanyi, Klaus, Hughes, Thomas E., Drobizhev, Mikhail, Kim, Douglas S., Koyama, Minoru, and Schreiter, Eric R.

Subjects
FLUORESCENT proteins, PROTEIN structure, CALCIUM ions, EXCITATION (Physiology), SEA anemones
Abstract

Background: Genetically encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores. Results: Here we report the development, structure, and validation of a new RFP-based GECI, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We have characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem-cell-derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo. Conclusion: K-GECO1 is the archetype of a new lineage of GECIs based on the RFP eqFP578 scaffold. It offers high sensitivity and fast kinetics, similar or better than those of current state-of-the-art indicators, with diminished lysosomal accumulation and minimal blue-light photoactivation. Further refinements of the K-GECO1 lineage could lead to further improved variants with overall performance that exceeds that of the most highly optimized red GECIs. [ABSTRACT FROM AUTHOR]

Published
2018
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33. A long Stokes shift red fluorescent Ca2+ indicator protein for two-photon and ratiometric imaging

Author

Wu, Jiahui, primary, Abdelfattah, Ahmed S., additional, Miraucourt, Loïs S., additional, Kutsarova, Elena, additional, Ruangkittisakul, Araya, additional, Zhou, Hang, additional, Ballanyi, Klaus, additional, Wicks, Geoffrey, additional, Drobizhev, Mikhail, additional, Rebane, Aleksander, additional, Ruthazer, Edward S., additional, and Campbell, Robert E., additional

Published
2014
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37. An Expanded Palette of Genetically Encoded Ca 2+ Indicators

Author

Zhao, Yongxin, primary, Araki, Satoko, additional, Wu, Jiahui, additional, Teramoto, Takayuki, additional, Chang, Yu-Fen, additional, Nakano, Masahiro, additional, Abdelfattah, Ahmed S., additional, Fujiwara, Manabi, additional, Ishihara, Takeshi, additional, Nagai, Takeharu, additional, and Campbell, Robert E., additional

Published
2011
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40. Correction to: A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.

Author

Shen, Yi, Dana, Hod, Abdelfattah, Ahmed S., Patel, Ronak, Shea, Jamien, Molina, Rosana S., Rawal, Bijal, Rancic, Vladimir, Chang, Yu-Fen, Wu, Lanshi, Chen, Yingche, Qian, Yong, Wiens, Matthew D., Hambleton, Nathan, Ballanyi, Klaus, Hughes, Thomas E., Drobizhev, Mikhail, Kim, Douglas S., Koyama, Minoru, and Schreiter, Eric R.

Subjects
SEA anemones, FLUORESCENT proteins, RED
Abstract

In the online version of the article [1], Figure S1 was mistakenly replaced with Figure 1. [ABSTRACT FROM AUTHOR]

Published
2019
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41. An Expanded Palette of Genetically Encoded Ca2+ Indicators.

Author

Yongxin Zhao, Araki, Satoko, Jiahui Wu, Teramoto, Takayuki, Yu-Fen Chang, Nakano, Masahiro, Abdelfattah, Ahmed S., Fujiwara, Manabi, Ishihara, Takeshi, Nagai, Takeharu, and Campbell, Robert E.

Subjects
*IMAGING systems in biology, *CALCIUM ions, *FLUORESCENCE, *CHIMERISM, *CELLULAR signal transduction, *BIOINDICATORS
Abstract

Engineered fluorescent protein (FP) chimeras that modulate their fluorescence in response to changes in calcium ion (Ca2+) concentration are powerful tools for visualizing intracellular signaling activity. However, despite a decade of availability, the palette of single FP-based Ca2+ indicators has remained limited to a single green hue. We have expanded this palette by developing blue, improved green, and red intensiometric indicators, as well as an emission ratiometric indicator with an 11,000% ratio change. This series enables improved single-color Ca2+ imaging in neurons and transgenic Caenorhabditis elegans. In HeLa cells, Ca2+ was imaged in three subcellular compartments, and, in conjunction with a cyan FP-yellow FP-based indicator, Ca2+ and adenosine 5'-triphosphate were simultaneously imaged. This palette of indicators paints the way to a colorful new era of Ca2+ imaging. [ABSTRACT FROM AUTHOR]

Published
2011
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