Optogenetics

Optogenetics uses light sensitive proteins called opsins to modulate and monitor the activity of neurons and other cellular states. We are working to extend the properties of opsins through protein engineering.

Gradinaru lab publications in Pubmed and BioRxiv.

2021

Dorsal raphe dopamine neurons signal motivational salience dependent on internal state, expectation, and behavioral context

February 9, 2021, Journal of Neuroscience

Jounhong Ryan Cho, Xinhong Chen, Anat Kahan, J. Elliott Robinson, Daniel A. Wagenaar and Viviana Gradinaru.

2020

Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning

December 16, 2020, Cell

Elizabeth K. Unger, Jacob P. Keller, Michael Altermatt, Ruqiang Liang, Aya Matsui, Chunyang Dong, Olivia J. Hon, Zi Yao, Junqing Sun, Samba Banala, Meghan E. Flanigan, David A. Jaffe, Samantha Hartanto, Jane Carlen, Grace O. Mizuno, Phillip M. Borden, Amol V. Shivange, Lindsay P. Cameron, Steffen Sinning, Suzanne M. Underhill, David E. Olson, Susan G. Amara, Duncan Temple Lang, Gary Rudnick, Jonathan S. Marvin, Luke D. Lavis, Henry A. Lester, Veronica A. Alvarez, Andrew J. Fisher, Jennifer A. Prescher, Thomas L. Kash, Vladimir Yarov-Yarovoy, Viviana Gradinaru, Loren L. Looger, and Lin Tian.

Negative feedback control of neuronal activity by microglia

September 30, 2020, Nature

Ana Badimon, Hayley J Strasburger, Pinar Ayata, Xinhong Chen, Aditya Nair, Ako Ikegami, Philip Hwang, Andrew T Chan, Steven M Graves, Joseph O Uweru, Carola Ledderose, Munir Gunes Kutlu, Michael A Wheeler, Anat Kahan, Masago Ishikawa, Ying-Chih Wang, Yong-Hwee E Loh, Jean X Jiang, D James Surmeier, Simon C Robson, Wolfgang G Junger, Robert Sebra, Erin S Calipari, Paul J Kenny, Ukpong B Eyo, Marco Colonna, Francisco J Quintana, Hiroaki Wake, Viviana Gradinaru, Anne Schaefer

Dorsal raphe dopamine neurons signal motivational salience dependent on internal and external states

July 27, 2020, BioRxiv

Jounhon Ryan Cho, Xinhong Chen, Anat Kahan, J. Elliott Robinson, Daniel A. Wagenaar, Viviana Gradinaru

RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations

March 23, 2020, Nature Methods
Shenqin Yao, Peng Yuan, Ben Ouellette, Thomas Zhou, Marty Mortrud, Pooja Balaram, Soumya Chatterjee, Yun Wang, Tanya L. Daigle, Bosiljka Tasic, Xiuli Kuang, Hui Gong, Qingming Luo, Shaoqun Zeng, Andrew Curtright, Ajay Dhaka, Anat Kahan, Viviana Gradinaru, Radosław Chrapkiewicz, Mark Schnitzer, Hongkui Zeng, Ali Cetin

2019

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics

October 14, 2019, Nature Methods
Claire N. Bedbrook, Kevin K. Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold

The Serotonergic Raphe Promote Sleep in Zebrafish and Mice

June 24, 2019, Neuron
Grigorios Oikonomou, Michael Altermatt, Rong-wei Zhang, Gerard M. Coughlin, Christin Montz, Viviana Gradinaru, David A. Prober

Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies

April 26, 2019, Nature Communications
Pradeep S. Rajendran, Rosemary C. Challis, Charless C. Fowlkes, Peter Hanna, John D. Tompkins, Maria C. Jordan, Sarah Hiyari, Beth A. Gabris-Weber, Alon Greenbaum, Ken Y. Chan, Benjamin E. Deverman, Heike Münzberg, Jeffrey L. Ardell, Guy Salama, Viviana Gradinaru, Kalyanam Shivkumararticle

2017

Deep tissue optical focusing and optogenetic modulation with time-reversed ultrasonically encoded light

December 8, 2017, Science Advances
Haowen Ruan, Joshua Brake, J. Elliott Robinson, Yan Liu, Mooseok Jang, Cheng Xiao, Chunyi Zhou, Viviana Gradinaru, Changhuei Yang

Overriding sleep

October 26, 2017, Science
Viviana Gradinaru

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

October 23, 2017, PLOS Computational Biology
Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold

Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?

September 25, 2017, BMC Biology
Alon Greenbaum, Min J. Jang, Collin Challis, Viviana Gradinaru

Dorsal Raphe Dopamine Neurons Modulate Arousal and Promote Wakefulness by Salient Stimuli

June 8, 2017, Neuron
Jounhong Ryan Cho, Jennifer B. Treweek, J. Elliott Robinson, Cheng Xiao, Lindsay R. Bremner, Alon Greenbaum, Viviana Gradinaru

Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins

March 10, 2017, Proceedings of the National Academy of Sciences
Claire N. Bedbrook, Austin J. Rice, Kevin K. Yang, Xiaozhe Ding, Siyuan Chen, Emily M. LeProust, Viviana Gradinaru, Frances H. Arnold

Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore

March 2, 2017, Cell Chemical Biology
Lukas Herwig, Austin J. Rice, Claire N. Bedbrook, Ruijie K. Zhang, Antti Lignell, Jackson K.B. Cahn, Hans Renata, Sheel C. Dodani, Inha Cho, Long Cai, Viviana Gradinaru, Frances H. Arnold

Global Representations of Goal-Directed Behavior in Distinct Cell Types of Mouse Neocortex

May 17, 2017, Neuron
William E. Allen, Isaac V. Kauvar, Michael Z. Chen, Ethan B. Richman, Samuel J. Yang, Ken Chan, Viviana Gradinaru, Benjamin E. Deverman, Liqun Luo, Karl Deisseroth

2016

Fluorescent boost for voltage sensors

January 26, 2016, Nature
Viviana Gradinaru, Nicholas C. Flytzanis

2014

Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons

September 15, 2014, Nature Communications
Nicholas C. Flytzanis, Claire N. Bedbrook, Hui Chiu, Martin K. M. Engqvist, Cheng Xiao, Ken Y. Chan, Paul W. Sternberg, Frances H. Arnold, Viviana Gradinaru

Directed evolution of a far-red fluorescent rhodopsin

August 25, 2014, Proceedings of the National Academy of Sciences
R. S. McIsaac, M. K. M. Engqvist, T. Wannier, A. Z. Rosenthal, L. Herwig, N. C. Flytzanis, E. S. Imasheva, J. K. Lanyi, S. P. Balashov, V. Gradinaru, F. H. Arnold