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Gauthey W, Randi F, Sharma AK, Kumar S, Leifer AM. Light evokes stereotyped global brain dynamics in Caenorhabditis elegans. Curr Biol 2024; 34:R14-R15. [PMID: 38194919 PMCID: PMC10783800 DOI: 10.1016/j.cub.2023.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 01/11/2024]
Abstract
Stereotyped oscillations in population neural activity recordings from immobilized Caenorhabditis elegans have garnered interest for their striking low dimensionality and their evocative state-space trajectories or manifolds. Previously these oscillations have been interpreted as intrinsically driven global motor commands. Here we test whether these oscillations are intrinsic. We show that similar oscillations are evoked by high-intensity blue light commonly used for calcium imaging. Oscillations are reduced or absent and have a lower frequency when a longer imaging wavelength is used. Under the original blue light illumination, oscillations are reduced or have a lower frequency in animals that lack GUR-3, an endogenous light- and hydrogen-peroxide-sensitive gustatory receptor. Additional experiments with hydrogen peroxide are consistent with GUR-3's involvement. We therefore propose that blue light evokes global oscillations in part through the creation of reactive oxygen species that activate the hydrogen-peroxide-sensing receptor GUR-3.
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Affiliation(s)
- Wayan Gauthey
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Francesco Randi
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Anuj K Sharma
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Sandeep Kumar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Andrew M Leifer
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA; Department of Physics, Princeton University, Princeton, NJ 08544, USA.
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Pechmann S. Single-cell expression predicts neuron-specific protein homeostasis networks. Open Biol 2024; 14:230386. [PMID: 38262604 PMCID: PMC10805596 DOI: 10.1098/rsob.230386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/17/2023] [Indexed: 01/25/2024] Open
Abstract
The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing. Here, large-scale single-cell expression data from the Allen Brain Map are analysed to investigate the transcription regulation of the core protein homeostasis network across the human brain. Remarkably, distinct expression profiles suggest specialized protein homeostasis networks with systematic adaptations in excitatory neurons, inhibitory neurons and non-neuronal cells. Moreover, several chaperones and Ubiquitin ligases are found transcriptionally coregulated with genes important for synapse formation and maintenance, thus linking protein homeostasis to the regulation of neuronal function. Finally, evolutionary analyses highlight the conservation of an elevated interaction density in the chaperone network, suggesting that one of the most exciting aspects of chaperone action may yet be discovered in their collective action at the systems level. More generally, our work highlights the power of computational analyses for breaking down complexity and gaining complementary insights into fundamental biological problems.
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Ding J, Peng L, Moon S, Lee HJ, Patel DS, Lu H. An expanded GCaMP reporter toolkit for functional imaging in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad183. [PMID: 37565483 PMCID: PMC10542313 DOI: 10.1093/g3journal/jkad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/16/2023] [Indexed: 08/12/2023]
Abstract
In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo. In particular, GCaMPs, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters is also well suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.
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Affiliation(s)
- Jimmy Ding
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lucinda Peng
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sihoon Moon
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyun Jee Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hang Lu
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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4
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Ding J, Peng L, Moon S, Lee HJ, Patel DS, Lu H. An expanded GCaMP reporter toolkit for functional imaging in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531342. [PMID: 36945463 PMCID: PMC10028802 DOI: 10.1101/2023.03.06.531342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo . In particular, GCaMP, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters are also well-suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.
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Affiliation(s)
- Jimmy Ding
- These authors contributed equally
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lucinda Peng
- These authors contributed equally
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sihoon Moon
- These authors contributed equally
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyun Jee Lee
- These authors contributed equally
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Dhaval S. Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Present address: NemaLife Inc, Lubbock, TX 79409, USA
| | - Hang Lu
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Sridhar N, Fajrial AK, Doser RL, Hoerndli FJ, Ding X. Surface acoustic wave microfluidics for repetitive and reversible temporary immobilization of C. elegans. LAB ON A CHIP 2022; 22:4882-4893. [PMID: 36377422 PMCID: PMC10091851 DOI: 10.1039/d2lc00737a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Caenorhabditis elegans is an important genetic model for neuroscience studies, used for analyses of how genes control connectivity, neuronal function, and behavior. To date, however, most studies of neuronal function in C. elegans are incapable of obtaining microscopy imaging with subcellular resolution and behavior analysis in the same set of animals. This constraint stems from the immobilization requirement for high-resolution imaging that is incompatible with behavioral analysis using conventional immobilization techniques. Here, we present a novel microfluidic device that uses surface acoustic waves (SAW) as a non-contact method to temporarily immobilize worms for a short period (30 seconds). We optimize the SAW based protocol for rapid switching between free-swimming and immobilized states, facilitating non-invasive analysis of swimming behavior as well as high-resolution synaptic imaging in the same animal. We find that the coupling of heat and acoustic pressure play a key role in the immobilization process. We introduce a proof-of-concept longitudinal study, illustrating that the device enables repeated imaging of fluorescently tagged synaptic receptors in command interneurons and analysis of swimming behavior in the same animals for three days. This longitudinal approach provides the first correlative analysis of synaptic glutamatergic receptors and swimming behavior in aging animals. We anticipate that this device will enable further longitudinal analysis of animal motility and subcellular morphological changes during development and aging in C. elegans.
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Affiliation(s)
- Nakul Sridhar
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Apresio Kefin Fajrial
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Rachel L Doser
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.
| | - Frederic J Hoerndli
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.
| | - Xiaoyun Ding
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado, USA.
- Biomedical Engineering Program, University of Colorado Boulder, Boulder, Colorado, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
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Fast, efficient, and accurate neuro-imaging denoising via supervised deep learning. Nat Commun 2022; 13:5165. [PMID: 36056020 PMCID: PMC9440141 DOI: 10.1038/s41467-022-32886-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
Volumetric functional imaging is widely used for recording neuron activities in vivo, but there exist tradeoffs between the quality of the extracted calcium traces, imaging speed, and laser power. While deep-learning methods have recently been applied to denoise images, their applications to downstream analyses, such as recovering high-SNR calcium traces, have been limited. Further, these methods require temporally-sequential pre-registered data acquired at ultrafast rates. Here, we demonstrate a supervised deep-denoising method to circumvent these tradeoffs for several applications, including whole-brain imaging, large-field-of-view imaging in freely moving animals, and recovering complex neurite structures in C. elegans. Our framework has 30× smaller memory footprint, and is fast in training and inference (50–70 ms); it is highly accurate and generalizable, and further, trained with only small, non-temporally-sequential, independently-acquired training datasets (∼500 pairs of images). We envision that the framework will enable faster and long-term imaging experiments necessary to study neuronal mechanisms of many behaviors. Volumetric functional imaging is widely used for recording neuron activities in vivo for many experimental organisms. Here the authors report supervised deep-denoising methods for improved whole-brain imaging, large field-of-view imaging in freely moving animals, and recovering complex neurite structures in C. elegans.
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