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561 results on '"Lavis, Luke D."'

2. A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging

Author

Farrants, Helen, Shuai, Yichun, Lemon, William C., Monroy Hernandez, Christian, Zhang, Deng, Yang, Shang, Patel, Ronak, Qiao, Guanda, Frei, Michelle S., Plutkis, Sarah E., Grimm, Jonathan B., Hanson, Timothy L., Tomaska, Filip, Turner, Glenn C., Stringer, Carsen, Keller, Philipp J., Beyene, Abraham G., Chen, Yao, Liang, Yajie, Lavis, Luke D., and Schreiter, Eric R.

Published
2024
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5. Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes.

Author

Brown, Timothy A, Schaefer, Katherine S, Tsang, Arthur, Yi, Hyun Ah, Grimm, Jonathan B, Lemire, Andrew L, Jradi, Fadi M, Kim, Charles, McGowan, Kevin, Ritola, Kimberly, Armstrong, Derek T, Mostafa, Heba H, Korff, Wyatt, Vale, Ronald D, and Lavis, Luke D

Subjects
Biological Sciences, Pneumonia & Influenza, Vaccine Related, Emerging Infectious Diseases, Clinical Research, Biotechnology, Biodefense, Genetics, Lung, Infectious Diseases, Prevention, Infection, Good Health and Well Being, COVID-19, Coloring Agents, Humans, Hydrogen-Ion Concentration, Molecular Diagnostic Techniques, Nucleic Acid Amplification Techniques, RNA, Viral, SARS-CoV-2, Sensitivity and Specificity, Social Structure, LAMPshade, RT-LAMP, Si-fluorescein, carbofluorescein, Technology, Medical and Health Sciences, Biological sciences
Abstract

The worldwide coronavirus disease 2019 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce 2 pH-sensitive "LAMPshade" dyes as novel readouts in an isothermal Reverse Transcriptase Loop-mediated isothermal AMPlification amplification assay for severe acute respiratory syndrome coronavirus 2 RNA. The resulting JaneliaLAMP assay is robust, simple, inexpensive, and has low technical requirements, and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

Published
2021

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

Author

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

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Behavioral and Social Science, Mental Health, Mental Illness, Networking and Information Technology R&D (NITRD), Bioengineering, Machine Learning and Artificial Intelligence, Brain Disorders, Depression, Neurosciences, 1.1 Normal biological development and functioning, Mental health, Algorithms, Amino Acid Sequence, Amygdala, Animals, Behavior, Animal, Binding Sites, Brain, Directed Molecular Evolution, HEK293 Cells, Humans, Kinetics, Linear Models, Machine Learning, Mice, Mice, Inbred C57BL, Photons, Protein Binding, Serotonin, Serotonin Plasma Membrane Transport Proteins, Sleep, Wakefulness, OSTA, SERT, fear-learning, fiber photometry, fluorescence protein sensor, iSeroSnFR, machine learning, serotonin, sleep-wake, social behaviors, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in vitro and in vivo serotonin detection, respectively.

Published
2020

8. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems

Author

Binns, Thomas C, Ayala, Anthony X, Grimm, Jonathan B, Tkachuk, Ariana N, Castillon, Guillaume A, Phan, Sebastien, Zhang, Lixia, Brown, Timothy A, Liu, Zhe, Adams, Stephen R, Ellisman, Mark H, Koyama, Minoru, and Lavis, Luke D

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, 3, 3'-Diaminobenzidine, Animals, Animals, Genetically Modified, Cell Line, Tumor, Drug Design, Humans, Larva, Ligands, Light, Microphthalmia-Associated Transcription Factor, Microscopy, Electron, Neurons, Photosensitizing Agents, Quantum Theory, Rhodamines, Singlet Oxygen, Zebrafish, Zebrafish Proteins, HaloTag, Janelia Fluor, cell ablation, electron microscopy, fluorescence, photochemistry, photosensitizer, reactive oxygen species, rhodamine
Abstract

Light-mediated chemical reactions are powerful methods for manipulating and interrogating biological systems. Photosensitizers, compounds that generate reactive oxygen species upon excitation with light, can be utilized for numerous biological experiments, but the repertoire of bioavailable photosensitizers is limited. Here, we describe the synthesis, characterization, and utility of two photosensitizers based upon the widely used rhodamine scaffold and demonstrate their efficacy for chromophore-assisted light inactivation, cell ablation in culture and in vivo, and photopolymerization of diaminobenzidine for electron microscopy. These chemical tools will facilitate a broad range of applications spanning from targeted destruction of proteins to high-resolution imaging.

Published
2020

9. 3D ATAC-PALM: super-resolution imaging of the accessible genome

Author

Xie, Liangqi, Dong, Peng, Chen, Xingqi, Hsieh, Tsung-Han S, Banala, Sambashiva, De Marzio, Margherita, English, Brian P, Qi, Yifeng, Jung, Seol Kyoung, Kieffer-Kwon, Kyong-Rim, Legant, Wesley R, Hansen, Anders S, Schulmann, Anton, Casellas, Rafael, Zhang, Bin, Betzig, Eric, Lavis, Luke D, Chang, Howard Y, Tjian, Robert, and Liu, Zhe

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Bioengineering, Chromosome Painting, DNA, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Image Processing, Computer-Assisted, In Situ Hybridization, Fluorescence, Microscopy, Sequence Analysis, DNA, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.

Published
2020

11. Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

Author

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

Published
2023
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18. Robust model-based analysis of single-particle tracking experiments with Spot-On.

Author

Hansen, Anders S, Woringer, Maxime, Grimm, Jonathan B, Lavis, Luke D, Tjian, Robert, and Darzacq, Xavier

Subjects
Cytological Techniques, Internet, Image Processing, Computer-Assisted, Intravital Microscopy, Single Molecule Imaging, biophysics, computational biology, dynamics, human, kinetic modeling, mouse, single molecule, single particle tracking, structural biology, super-resolution, systems biology, transcription factor, Image Processing, Computer-Assisted, Biochemistry and Cell Biology
Abstract

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.

Published
2018

20. Back to the future -- 20 years of progress and developments in photonic microscopy and biological imaging.

Author

Erard, Marie, Favard, Cyril, Lavis, Luke D., Recher, Gaëlle, Rigneault, Hervé, and Sage, Daniel

Subjects
BIOTIC communities, STEREOLOGY, ARTIFICIAL intelligence, IMAGE analysis, MOLECULAR interactions
Abstract

In 2023, the ImaBio consortium (imabio-cnrs.fr), an interdisciplinary life microscopy research group at the Centre National de la Recherche Scientifique, celebrated its 20th anniversary. ImaBio contributes to the biological imaging community through organization of MiFoBio conferences, which are interdisciplinary conferences featuring lectures and hands-on workshops that attract specialists from around the world. MiFoBio conferences provide the community with an opportunity to reflect on the evolution of the field, and the 2023 event offered retrospective talks discussing the past 20 years of topics in microscopy, including imaging of multicellular assemblies, image analysis, quantification of molecular motions and interactions within cells, advancements in fluorescent labels, and laser technology for multiphoton and label-free imaging of thick biological samples. In this Perspective, we compile summaries of these presentations overviewing 20 years of advancements in a specific area of microscopy, each of which concludes with a brief look towards the future. The full presentations are available on the ImaBio YouTube channel (youtube.com/@gdrimabio5724). [ABSTRACT FROM AUTHOR]

Published
2024
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22. Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore

Author

Fiore, Antonio, primary, Yu, Guoqiang, additional, Northey, Jason J., additional, Patel, Ronak, additional, Ravenscroft, Thomas A., additional, Ikegami, Richard, additional, Kolkman, Wiert, additional, Kumar, Pratik, additional, Grimm, Jonathan B., additional, Dilan, Tanya L., additional, Ruetten, Virginia M.S., additional, Ahrens, Misha B., additional, Shroff, Hari, additional, Lavis, Luke D., additional, Wang, Shaohe, additional, Weaver, Valerie M., additional, and Pedram, Kayvon, additional

Published
2024
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24. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Author

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

Published
2019

29. A series of spontaneously blinking dyes for super-resolution microscopy

Author

Holland, Katie L., primary, Plutkis, Sarah E., additional, Daugird, Timothy A., additional, Sau, Abhishek, additional, Grimm, Jonathan B., additional, English, Brian P., additional, Zheng, Qinsi, additional, Dave, Sandeep, additional, Rahman, Fariha, additional, Xie, Liangqi, additional, Dong, Peng, additional, Tkachuk, Ariana N., additional, Brown, Timothy A., additional, Singer, Robert H., additional, Liu, Zhe, additional, Galbraith, Catherine G., additional, Musser, Siegfried M., additional, Legant, Wesley R., additional, and Lavis, Luke D., additional

Published
2024
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40. Optimized Red-Absorbing Dyes for Imaging and Sensing

Author

Grimm, Jonathan B., primary, Tkachuk, Ariana N., additional, Patel, Ronak, additional, Hennigan, S. Thomas, additional, Gutu, Alina, additional, Dong, Peng, additional, Gandin, Valentina, additional, Osowski, Anastasia M., additional, Holland, Katie L., additional, Liu, Zhe J., additional, Brown, Timothy A., additional, and Lavis, Luke D., additional

Published
2023
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45. A modular chemigenetic calcium indicator enables in vivo functional imaging with near-infrared light

Author

Farrants, Helen, primary, Shuai, Yichun, additional, Lemon, William C, additional, Hernandez, Christian Monroy, additional, Yang, Shang, additional, Patel, Ronak, additional, Qiao, Guanda, additional, Frei, Michelle S, additional, Grimm, Jonathan B, additional, Hanson, Timothy L, additional, Tomaska, Filip, additional, Turner, Glenn C, additional, Stringer, Carsen, additional, Keller, Philipp J, additional, Beyene, Abraham G, additional, Chen, Yao, additional, Liang, Yajie, additional, Lavis, Luke D, additional, and Schreiter, Eric R, additional

Published
2023
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