Design of optogenetic tools
Michael Rappleye, Sarah J. Wait, Justin Daho Lee, Jamison C. Siebart, Lily Torp, Netta Smith, Jeanot Muster, Kenneth A. Matreyek, Douglas M. Fowler, and Andre Berndt. Optogenetic Microwell Array Screening System: A High-Throughput Engineering Platform for Genetically Encoded Fluorescent Indicators.
ACS Sensors, 2023 Nov 24;8(11):4233-4244. doi: 10.1021/acssensors.3c01573. Epub 2023 Nov 13.
Andre Berndt, Denise Cai, Adam Cohen, Barbara Juarez, Jaume Taura Iglesias, Hejian Xiong, Zhenpeng Qin, Lin Tian and Paul A. Slesinger. Current Status and Future Strategies for Advancing Functional Circuit Mapping In Vivo.
Journal of Neuroscience 8 November 2023, 43 (45) 7587-7598; DOI: https://doi.org/10.1523/JNEUROSCI.1391-23.2023
Sarah J. Wait, Michael Rappleye, Justin Daho Lee, Netta Smith, Andre Berndt, Machine Learning Ensemble Directed Engineering of Genetically Encoded Fluorescent Calcium Indicators
https://www.biorxiv.org/content/10.1101/2023.04.13.536801v1, doi: https://doi.org/10.1101/2023.04.13.536801
Michael Rappleye, Adam Gordon-Fennel, Daniel C. Castro, Avi K. Matarasso, Catalina A. Zamorano, Sarah J. Wait, Justin D. Lee, Jamison C. Siebart, Azra Suko, Netta Smith, Jeanot Muster, Kenneth A Matreyek, Douglas M. Fowler, Garrett D. Stuber, Michael R. Bruchas, Andre Berndt: Opto-MASS: a high-throughput engineering platform for genetically encoded fluorescent sensors enabling all-optical in vivo detection of monoamines and opioids https://www.biorxiv.org/content/10.1101/2022.06.01.494241v2; doi: https://doi.org/10.1101/2022.06.01.494241
Berndt A*, Lee SY*, Wietek J*, Ramakrishnan C, Steinberg EE, Rashid AJ, Kim H, Park S, Santoro A, Frankland PW, Iyer S, Pak S, Delp SL, Malenka RC, Josselyn S, Carlen M, Hegemann P, and Deisseroth K: Determinants of channelrhodopsin ion selectivity: structural principles for optogenetics. PNAS (2016)
Tee BC*, Chortos A*, Berndt A*, Nguyen AK, Tom A, McGuire A, Lin ZC, Tien K, Bae WG, Wang H, Mei P, Chou HH, Cui B, Deisseroth K, Ng TN, Bao Z: A skin-inspired organic digital mechanoreceptor. Science (2015) [pdf]
Rajasethupathy P, Sankaran S, Marshel JH, Kim CK, Ferenczi E, Lee SY, Berndt A, Ramakrishnan C, Jaffe, Lo M, Liston C, Deisseroth K: Projections from neocortex mediate top-down control of memory retrieval. Nature (2015)
Berndt A*, Lee SY*, Ramakrishnan C and Deisseroth K: Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science (2014)
Berndt A*, Schoenenberger P*, Mattis J, Tye KM, Deisseroth K, Hegemann P and Oertner TG: High efficiency channelrhodopsins for fast neuronal stimulation at low light levels. PNAS (2011)
Gunaydin LA*, Yizhar O*, Berndt A*, Sohal VS, Deisseroth K and Hegemann P: Ultrafast optogenetic control. Nature Neuroscience (2010) [pdf]
Berndt A*, Yizhar O*, Gunaydin LA*, Hegemann P and Deisseroth K: Bi-stable neural state switches. Nature Neuroscience (2009) [pdf]
molecular mechanism of light-activated cation channels
Kato HE, Kim YS, Paggi JM, Evans KE, Allen WE, Richardson C, Inoue K, Ito S, Ramakrishnan C, Fenno LE, Yamashita K, Hilger D, Lee SY, Berndt A, Shen K, Kandori H, Dror RO, Kobilka BK, Deisseroth K. Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature (2018)
Eisenhauer K, Kuhne J, Ritter E, Berndt A, Wolf S, Freier E, Bartl F, Hegemann P, Gerwert K: In channelrhodopsin-2 Glu-90 is crucial for ion selectivity and is deprotonated during the
photocycle. The Journal of Biological Chemistry (2012)
Gradmann D, Berndt A, Schneider F and Hegemann P: Rectification of the channelrhodopsin early conductance. Biophysical Journal (2011)
Stehfest K, Ritter E, Berndt A, Bartl F and Hegemann P: The branched photocycle of the slow cycling channelrhodopsin-2 mutant C128T. Journal of Molecular Biology (2010) [pdf]
Berndt A*, Prigge M*, Gradmann D and Hegemann P: Two open states with progressive proton selectivities in the branched channelrhodopsin-2 photocycle. Biophysical Journal (2010)
Ritter E, Stehfest K, Berndt A, Hegemann P and Bartl FJ: Monitoring light-induced structural changes of Channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy. The Journal of Biological Chemistry (2008)
Collaborative research projects
Rongfeng K. Hu, Patrick B. Chen, André Berndt, David J. Anderson, Weizhe Hong: Improved Version of ChETA Promotes Aggression in the Medial Amygdala
bioRxiv 2022.06.05.493862; doi: https://doi.org/10.1101/2022.06.05.493862
Klima JC, Doyle LA, Lee JD*, Rappleye M, Gagnon LA, Lee MY, Barros EP, Vorobieva AA, Dou J, Bremner S, Quon JS, Chow CM, Carter L, Mack DL, Amaro RE, Vaughan JC, Berndt A, Stoddard BL, Baker D: Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nature Communications (2021)
Iyer SM, Vesuna S, Ramakrishnan C, Huynh K, Young S, Berndt A, Lee SY, Gorini CJ, Deisseroth K, Delp SL: Optogenetic and chemogenetic strategies for sustained inhibition of pain. Scientific Reports (2016)
Ferenczi EA, Vierock J, Atsuta-Tsunoda K, Tsunoda SP, Ramakrishnan C, Gorini C, Thompson K, Lee SY, Berndt A, Perry C, Minniberger S, Vogt A, Mattis J, Prakash R, Delp S, Deisseroth K, Hegemann P: Optogenetic approaches addressing extracellular modulation of neural excitability. Scientific Reports (2016)
Kim CK, Yang SJ, Pichamoorthy N, Young NP, Kauvar I, Jennings JH, Lerner TN, Berndt A, Lee SY, Ramakrishnan C, Davidson TJ, Inoue M, Bito H, Deisseroth K: Simultaneous fast measurement of circuit dynamics at multiple sites across the mammalian brain. Nature Neuroscience (2016)
Kim CK, Miri A, Leung LC, Berndt A, Mourrain P, Tank DW, Burdine RD: Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping. Frontiers in Neural Circuits (2014)
Fenno LE, Mattis J, Ramakrishnan C, Hyun M, Lee SY, He M, Tucciarone J, Selimbeyoglu A, Berndt A, Grosenick L, Zalocusky KA, Bernstein H, Diester I, Boyce FM, Bass CE, Neve R, Huang ZJ and Deisseroth K: INTRSECT: single-component targeting of cells using multiple-feature Boolean logic. Nature Methods (2014)
* co-first author