May 2024
We are proud to announce several award winners:
Undergraduate research assistant Vedant Chavan won a Mary Gate research scholarship
Undergraduate research assistant Mikayla Gargantiel won a stipend from the UW Center of Excellence in Neurobiology of Addiction, Pain, and Emotion to support the development of novel fluorescent opioid sensors this summer.
Graduate Student Sarah Wait won the Scientific Achievement Award from the UW Molecular Engineering & Sciences Scientific Graduate Program.
Graduate Student Aida Moghadasi won a research fellowship from UW’s Institute for Stem Cell and Regenerative Medicine.
PI Andre Berndt won the Excellence in Research Award from the UW Department of Bioengineering.
Congratulations Everyone!
April 2024
We published two preprints on BioRxiv on the engineering of genetically encoded fluorescent hydrogen peroxide sensors:
Far-red and sensitive sensor for monitoring real time H2O2 dynamics with subcellular resolution and in multi-parametric imaging applications. https://doi.org/10.1101/2024.02.06.579232
Structure-guided engineering of a fast genetically encoded sensor for real-time H2O2 monitoring. https://www.biorxiv.org/content/10.1101/2024.01.31.578117v1
March 2024
Our paper “Machine Learning Ensemble Directed Engineering of Genetically Encoded Fluorescent Calcium Indicators“ has been published in Nature Computational Science. Graduate Student Sarah Wait used machine learning to develop record-setting fluorescent calcium indicators eGCaMP+ and eGCaMP2+. https://www.nature.com/articles/s43588-024-00611-w.
The constructs are available on Addgene: https://www.addgene.org/Andre_Berndt/
UW press release: https://newsroom.uw.edu/news-releases/ai-shown-to-dramatically-speed-protein-engineering
November 2023
The annual SfN meeting in Washington D.C. was a great success. Justin Lee, Sarah Wait, Lily Torp, and Aida Moghadasi presented their work on hydrogen peroxide sensors, machine learning-based design of calcium indicators, high-throughput screening of sensor proteins and automated cell segmentation and tracking.
We are also welcoming a new lab member, Yuxuan Wang, who joins the lab as a 1st year Bioengineering Ph.D. student.
Andre Berndt co-hosted a mini-symposium on Current Status and Future Strategies for Advancing Functional Circuit Mapping In Vivo together with Prof Paul Schlesinger (Icahn School of Medicine at Mount Sinai). Speakers included Dr. Denise Cai (Icahn School of Medicine at Mount Sinai), Dr. Jaume Taura (Icahn School of Medicine at Mount Sinai), Dr. Barbara Juarez (University of Maryland Baltimore), Dr. Lin Tian (UC Davis), and Dr. Adam Cohen (Harvard University).
Our joint symposium has been featured in a special review issue of the Journal of Neuroscience. DOI: https://doi.org/10.1523/JNEUROSCI.1391-23.2023
Our manuscript on our high-throughput screening platform, the Optogenetic Microwell Array Screening System, has been published in ACS Sensors, 2023 Nov 24;8(11):4233-4244. doi: 10.1021/acssensors.3c01573. Epub 2023 Nov 13.
August 2023
Our summer trip led us to a guided night kayak tour in the Salish Sea near Bellingham, WA, to observe bioluminescence in marine dinoflagellates. This was close to where the original green fluorescent protein was identified in jellyfish. Memories for a lifetime!
We also welcomed Shajesh Sharma (1st year Bioengineering Ph.D. student) and Vedant Chavan (Bioengineering undergraduate researcher) as well as Aida Moghadasi, who transitioned to become a 1st year Bioengineering Ph.D. student, and Shani Zuniga, who joins the lab as a postbaccalaureate researcher.
July 2023
Over the summer, our lab hosted an undergraduate researcher, Tamilore Dairo, from Mercer University. Tamilore explored new ways to engineer fluorescent opioid sensors. Her work could lead to more efficient and selective opioid sensors for use in neuroscience research.
May 2023
The National Institutes of Health (NIH) Brain Initiative has awarded us a $2.6 million grant. Our team consists of the labs of Andre Berndt (Assistant Professor of Bioengineering), Michael Bruchas (Professor of Anesthesiology and Pharmacology), and Marta Soden (Research Assistant Professor of Pharmacology). We aim to advance the understanding of neuropeptide modulation in the brain, specifically the dynamics of opioid neuropeptides. They play a crucial role in many behaviors, such as exploration, stress response, memory formation, and learning, and they are also strongly linked to many pathophysiological conditions. Despite their importance, our understanding of neuropeptides is blurred by the difficulty in isolating their functions within the brain due to the lack of precise monitoring techniques. A significant obstacle is the slow throughput of current engineering approaches for developing novel fluorescent sensors for neuropeptide detection. To address this, we aim to utilize an efficient platform for neuropeptide sensor engineering that can screen thousands of sensor variants rapidly and efficiently. We will utilize this high-throughput platform called Opto-MASS to engineer ligand-selective fluorescent biosensors capable of monitoring endogenous and exogenous opioid dynamics in the brains of animal models. This innovative research could revolutionize our understanding of brain circuits and behaviors impacted by opioids. It could provide critical insights into conditions like stress, anxiety, and opioid abuse, presenting a promising path toward developing treatments for these conditions.
April 2023
We published a preprint on the poiwer and utility of machine learngin for the engineering of fluorescent sensor proteins.
Machine Learning Ensemble Directed Engineering of Genetically Encoded Fluorescent Calcium Indicators, Sarah J. Wait, Michael Rappleye, Justin Daho Lee, Netta Smith, Andre Berndt
doi: https://doi.org/10.1101/2023.04.13.536801
March 2023
The Berndt lab, together with Michael Bruchas (Professor of Anesthesiology, Pharmacology, and Bioengineering), in partnership with researchers from Washington University in St. Louis and the Weizman Institute in Israel, have received a $5 million NIH U01 grant to develop new tools for neuromodulation of the brain using optical methods. The technology will lead to new techniques for spatial and temporal control of neuromodulator signaling in the brain. The light sensitive tools developed will have multi-functional abilities to allow for discrete control over time and space of critical receptor signaling pathways in the awake- behaving brain. These new optogenetic tools will allow neuroscientists and biologists to have unprecedented resolution in uncovering the basis for brain diseases, and have translational potential for delivery of new treatments for brain disorders.
November 2022
The Annual Meeting of the Society of Neuroscience is back in person! Michael Rappleye, Sarah Wait and Justin Lee presented their research on high-throughput sensor engineering, machine learning based protein design and reactive oxygen species sensors in San Diego.
August 2022
We are welcoming two new lab members, Lily Torp (1st year Bioengineering Ph.D. student) and Aida Moghadasi (postbaccalaureate researcher). As per tradition we celebrated by hiking, this time to Mount Rainier on a sunny but windy day.
PI Andre Berndt received the prestigious McKnight Technological Innovations in Neuroscience Award. Very honored and very humbling to be part of this community. UW medicine news story here: https://newsroom.uw.edu/postscript/uw-biosensor-research-wins-prestigious-innovation-honor
Justin Lee won a prestigious Ruth L. Kirschstein Predoctoral Individual National Research Service Award for his work on developing reactive oxygen species sensors to monitor opioid receptor activation in brain tissue. First for the lab. Congratulations, Justin!
Graduate student Justin Lee and PI Andre Berndt joined the Chehalis STEM camp together with faculty and trainees from UW ISCRM. Two days full of experiments and discussion with encouraged high school students. Great fun!
July 2022 - The Optogenetic Gordon Research Conference in Maine was a total success. Our graduate student Michael Rappleye won a Poster Award for his work on a high-throughput protein engineering platform. Congrats, Mike! Well deserved!
July 2022 - Our BBQ with the lab and friends was great. Seattle even treated us with spells of dry weather between the rain! Enough to throw a frisbee. Thanks everyone for coming!
June 2022 - The lab, including our grad students Sarah Wait, Justin Lee and Michael Rappleye went on its first “Summer” hike together on the Olympic Peninsula. Crampons and Ice Axes would have been appropriate. The Pacific Northwest is great!
June 2022 - Our first manuscript on the high throughput engineering pipeline for fluorescent sensor proteins is available on BioRxiv. The project was led by Bioengineering PhD candidate Michael Rappleye. He also developed optimized sensor proteins for dopamine and opioids. The sensors have been validated in mouse models by the groups of Dr. Michael Bruchas and Garret Stuber. We received additional support for the pipeline development from Dr. Douglas Fowler’s group and his former postdoc Kenneth A Matreyek. A truly fantastic interdisciplinary effort.
https://doi.org/10.1101/2022.06.01.494241
June 2022 - Weizhe Hong’s group from UCLA published a manuscript that cautions against the use of ChETA channelrhodopsin in every cell type and in every use scenario. We agree! The biophysical properties of cells and channelrhodopsins matter to achieve significant population responses. ChETA works best in small, fast-firing interneurons (e.g. cortical PV) but the firing probabilities drop significantly especially in larger cell types due to small ChETA photocurrents. The ChETA variant T159C (ChETA2.0) restores photocurrents and population responses and is a great choice for most applications as demonstrated by Dr. Hong and his group.
https://doi.org/10.1101/2022.06.05.493862
May 2022 - The UW Insitute for Stem Cells and Regenerative Medicine held its annual research symposium. Justin gave a fantastic talk on the various use scenarios of his fluorescent sensors for reactive oxygen species. One of them is the multiplexed and simultaneous measurement of ROS and calcium for example in stem cell-derived neurons and cardiomyocytes.
May 2022 - Michael Rappleye won a Poster Award for his presentation of the Opto-Mass protein engineering pipeline.
April 2022 - Shani Zuniga won a Mary Gates Research Scholarship to support her work on reactive oxygen species. Congrats, Shani!
April 2022 - The great news continues with Sarah Wait who will receive a graduate research scholarship from the National Science Foundation. This is a fantastic achievement! Congrats, Sarah!
November 2021 - Mike and I will present our work on the high-throughput engineering platform during the virtual SfN event (Nov 8th-11th). Previews are available starting on Nov. 3. Poster
P936. Probe Design and Engineering: Sensors
Session Time: November 9, 2021 8:30 am - 9:30 am (Chicago time)
Virtual Only, registration requiredNovember 2021- The Bioengineering Department has a new chair! (link). We welcome Princess Imoukhuede who will move to UW from the McKelvey School of Engineering at Washington University in St. Louis. Dr. Imoukhuede will start her new position and hold the Hunter and Dorothy Simpson Endowed Chair and Professorship, effective Jan. 1, 2022.
October 2021 Jamison won the Levinson Emerging Scholars Award to support him to continue his research training during the 2021-22 academic year. Congratulations, Jamison!
September 2021 - Shani Zuniga joins our lab as an undergraduate researcher. Welcome, Shani!
September 2021 - Sarah won the UW Herbold Fellowship for data science and computation. Congratulations, Sarah! This award supports her work on developing machine learning algorithms for analyzing functional datasets of mutational proteins sensor libraries.
June 2021 - Jamison Siebart won a stipend from the NIDA-funded UW NAPE center for developing fluorescent sensors for endogenous opioid release. Congratulations, Jamison!
June 2021 - After an extremely difficult year, Yihan Wang graduated with a Masters’ degree in Bioengineering from our lab. Yihan’s contributions were critical in the development and validation of our new fluorescent sensor proteins for reactive oxygen species. Congratulations Yihan and good luck with your new job!
March 2021- Sarah Wait will join our lab as a graduate student from the Molecular Engineering program. Welcome to the crew, Sarah! Sarah is interested in using machine learning to analyze data collected with our high-throughput engineering platform. This data can be used to derive general engineering principles for highly dynamic sensor proteins.
March 2021 - Jaminson Siebart won a Mary Gates undergraduate research fellowship. Congratulations, Jamison! That is well deserved!
September 23rd, 2020 - The Berndt lab welcomes Jamison Siebart who will join us again as an undergraduate researcher this fall. Also, Yihan Wang will re-join our lab as a Bioengineering Master student to continue work on her capstone project. It is great to have you back!
June 1st, 2020 - Amanda Nguyen won an undergraduate stipend from the UW Institute for Stem Cell and Regenerative Medicine. Fantastic job, Amanda!
June 1st, 2020 - Justin Lee won a predoctoral fellowship from the UW Institute for Stem Cell and Regenerative Medicine. Congratulations, Justin! He will engineer technology for detecting oxidative stress in stem-cell derived models for Alzheimer’s disease.
May 1st, 2020 - Our lab won a NAPE pilot award for the development of fluorescent sensors that can detect neuropeptides in the brain of behaving mice and rats.
March 22nd, 2020 - Yihan Wang won a Mary Gates Fellowship for her work on sensor technology detecting oxidative stress in cells and tissue. Congratulations, Yihan!
December 1st, 2019 - Our lab won the NARSAD Young Investigator Award from the Brain and Behavior Research Foundation. This project will focus on elucidating brain the differentiation, migration, and maturation of neuronal precursor cells and neurons in the developing brain of zebrafish.
June 1st, 2020, We have been awarded with an pilot grant from the UW Royalty Research Fund. We will invest the grant into improving screening technology for the development of molecular biosensors.
June 1st, 2019 - Our undergraduate student Yihan Wang won a summer research stipend from the UW Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE). She will study the mechanisms of fluorescent sensors for reactive oxygen species. Congratulations Yihan!
August 1st, 2018 - Lylah Deady joins our lab as a new postdoc in a joint project with John Tuthill's lab at the Department for Physiology and Biophysics. Welcome to Seattle, Lylah! Her project aims to reveal the mechanisms of proprioception by using optogenetic techniques for controlling and monitoring neurotransmission.
July, 1st, 2018 - Our lab has been awarded with the Innovation Pilot Award from the Institute for Stem Cell and Regenerative Medicine. The awarded project aims to elucidate the mechanisms of embryonic and adult neurogenesis.
June, 16th, 2018 - Mike Rappleye won a predoctoral fellowship from the Institute for Stem Cell and Regenerative Medicine. Congratulations! Mike will design fluorescent sensors for detecting excitatory and inhibitory neurotransmission.
June 12th, 2018 - Our lab has been awarded with the Fay/Frank Seed Grant from the Brain Research Foundation. The goal of the awarded project is to quantify the impaired excitatory/inhibitory balance of brain activity in rodent models for neurological disorders.
April 1st, 2018 - Justin Lee joins our lab as a research assistant. Justin will become a graduate Ph.D. student in the Molecular Engineering program in fall 2018.
January 1st, 2018 - Michael Rappleye joins our lab as a graduate Ph.D. student in Bioengineering. Welcome Mike!
December 15th, 2017 - Andre Berndt talks at the Allen Institute for Brain Science on how molecular engineering advances research in neuroscience.
November 9th, 2017 - The Allen Institute for Brain Science announces Andre Berndt as a 2017 Next Generation Leader