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Huang Z, Sun Y, Liu S, Chen X, Ping J, Fei P, Gong Z, Zheng N. A machine learning based method for tracking of simultaneously imaged neural activity and body posture of freely moving maggot. Biochem Biophys Res Commun 2024; 727:150290. [PMID: 38941792 DOI: 10.1016/j.bbrc.2024.150290] [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: 03/12/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024]
Abstract
To understand neural basis of animal behavior, it is necessary to monitor neural activity and behavior in freely moving animal before building relationship between them. Here we use light sheet fluorescence microscope (LSFM) combined with microfluidic chip to simultaneously capture neural activity and body movement in small freely behaving Drosophila larva. We develop a transfer learning based method to simultaneously track the continuously changing body posture and activity of neurons that move together using a sub-region tracking network with a precise landmark estimation network for the inference of target landmark trajectory. Based on the tracking of each labelled neuron, the activity of the neuron indicated by fluorescent intensity is calculated. For each video, annotation of only 20 frames in a video is sufficient to yield human-level accuracy for all other frames. The validity of this method is further confirmed by reproducing the activity pattern of PMSIs (period-positive median segmental interneurons) and larval movement as previously reported. Using this method, we disclosed the correlation between larval movement and left-right asymmetry in activity of a group of unidentified neurons labelled by R52H01-Gal4 and further confirmed the roles of these neurons in bilateral balance of body contraction during larval crawling by genetic inhibition of these neurons. Our method provides a new tool for accurate extraction of neural activities and movement of freely behaving small-size transparent animals.
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Affiliation(s)
- Zenan Huang
- Zhejiang Lab, Hangzhou, 311121, China; Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, 310007, China
| | - Yixuan Sun
- Zhejiang Lab, Hangzhou, 311121, China; Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Affiliated Mental Health Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China
| | | | - Xiaopeng Chen
- Zhejiang Lab, Hangzhou, 311121, China; School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong, University of Science and Technology, Wuhan, 430074, China
| | - Junyu Ping
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong, University of Science and Technology, Wuhan, 430074, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong, University of Science and Technology, Wuhan, 430074, China
| | - Zhefeng Gong
- Zhejiang Lab, Hangzhou, 311121, China; Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Affiliated Mental Health Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Nenggan Zheng
- Zhejiang Lab, Hangzhou, 311121, China; Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, 310007, China
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Schlomann BH, Pai TW, Sandhu J, Imbert GF, Graham TGW, Garcia HG. Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612587. [PMID: 39345471 PMCID: PMC11429692 DOI: 10.1101/2024.09.12.612587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Immune responses in tissues display intricate patterns of gene expression that vary across space and time. While such patterns have been increasingly linked to disease outcomes, the mechanisms that generate them and the logic behind them remain poorly understood. As a tractable model of spatial immune responses, we investigated heterogeneous expression of antimicrobial peptides in the larval fly fat body, an organ functionally analogous to the liver. To capture the dynamics of immune response across the full tissue at single-cell resolution, we established live light sheet fluorescence microscopy of whole larvae. We discovered that expression of antimicrobial peptides occurs in a reproducible spatial pattern, with enhanced expression in the anterior and posterior lobes of the fat body. This pattern correlates with microbial localization via blood flow but is not caused by it: loss of heartbeat suppresses microbial transport but leaves the expression pattern unchanged. This result suggests that regions of the tissue most likely to encounter microbes via blood flow are primed to produce antimicrobials. Spatial transcriptomics revealed that these immune microenvironments are defined by genes spanning multiple biological processes, including lipid-binding proteins that regulate host cell death by the immune system. In sum, the larval fly fat body exhibits spatial compartmentalization of immune activity that resembles the strategic positioning of immune cells in mammals, such as in the liver, gut, and lymph nodes. This finding suggests that tissues may share a conserved spatial organization that optimizes immune responses for antimicrobial efficacy while preventing excessive self-damage.
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3
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Booth JH, Meek AT, Kronenberg NM, Pulver SR, Gather MC. Optical mapping of ground reaction force dynamics in freely behaving Drosophila melanogaster larvae. eLife 2024; 12:RP87746. [PMID: 39042447 PMCID: PMC11265794 DOI: 10.7554/elife.87746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024] Open
Abstract
During locomotion, soft-bodied terrestrial animals solve complex control problems at substrate interfaces, but our understanding of how they achieve this without rigid components remains incomplete. Here, we develop new all-optical methods based on optical interference in a deformable substrate to measure ground reaction forces (GRFs) with micrometre and nanonewton precision in behaving Drosophila larvae. Combining this with a kinematic analysis of substrate-interfacing features, we shed new light onto the biomechanical control of larval locomotion. Crawling in larvae measuring ~1 mm in length involves an intricate pattern of cuticle sequestration and planting, producing GRFs of 1-7 µN. We show that larvae insert and expand denticulated, feet-like structures into substrates as they move, a process not previously observed in soft-bodied animals. These 'protopodia' form dynamic anchors to compensate counteracting forces. Our work provides a framework for future biomechanics research in soft-bodied animals and promises to inspire improved soft-robot design.
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Affiliation(s)
- Jonathan H Booth
- SUPA, School of Physics and Astronomy, University of St AndrewsSt AndrewsUnited Kingdom
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of CologneCologneGermany
- School of Psychology and Neuroscience, University of St AndrewsSt AndrewsUnited Kingdom
- Centre of Biophotonics, University of St AndrewsSt AndrewsUnited Kingdom
| | - Andrew T Meek
- SUPA, School of Physics and Astronomy, University of St AndrewsSt AndrewsUnited Kingdom
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of CologneCologneGermany
- Centre of Biophotonics, University of St AndrewsSt AndrewsUnited Kingdom
| | - Nils M Kronenberg
- SUPA, School of Physics and Astronomy, University of St AndrewsSt AndrewsUnited Kingdom
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of CologneCologneGermany
- Centre of Biophotonics, University of St AndrewsSt AndrewsUnited Kingdom
| | - Stefan R Pulver
- School of Psychology and Neuroscience, University of St AndrewsSt AndrewsUnited Kingdom
- Centre of Biophotonics, University of St AndrewsSt AndrewsUnited Kingdom
| | - Malte C Gather
- SUPA, School of Physics and Astronomy, University of St AndrewsSt AndrewsUnited Kingdom
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of CologneCologneGermany
- Centre of Biophotonics, University of St AndrewsSt AndrewsUnited Kingdom
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McNulty P, Wu R, Yamaguchi A, Heckscher ES, Haas A, Nwankpa A, Skanata MM, Gershow M. CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595209. [PMID: 38826435 PMCID: PMC11142166 DOI: 10.1101/2024.05.22.595209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multistage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.
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Affiliation(s)
- Paul McNulty
- Department of Physics,New York University, New York, USA
| | - Rui Wu
- Department of Physics,New York University, New York, USA
| | | | - Ellie S. Heckscher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Andrew Haas
- Department of Physics,New York University, New York, USA
| | | | | | - Marc Gershow
- Department of Physics,New York University, New York, USA
- Center for Neural Science,New York University, New York, USA
- Neuroscience Institute, New York University, New York, USA
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5
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Mukherjee A, Andrés Jeske Y, Becam I, Taïeb A, Brooks P, Aouad J, Monguillon C, Conduit PT. γ-TuRCs and the augmin complex are required for the development of highly branched dendritic arbors in Drosophila. J Cell Sci 2024; 137:jcs261534. [PMID: 38606636 PMCID: PMC11128279 DOI: 10.1242/jcs.261534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Microtubules are nucleated by γ-tubulin ring complexes (γ-TuRCs) and are essential for neuronal development. Nevertheless, γ-TuRC depletion has been reported to perturb only higher-order branching in elaborated Drosophila larval class IV dendritic arborization (da) neurons. This relatively mild phenotype has been attributed to defects in microtubule nucleation from Golgi outposts, yet most Golgi outposts lack associated γ-TuRCs. By analyzing dendritic arbor regrowth in pupae, we show that γ-TuRCs are also required for the growth and branching of primary and secondary dendrites, as well as for higher-order branching. Moreover, we identify the augmin complex (hereafter augmin), which recruits γ-TuRCs to the sides of pre-existing microtubules, as being required predominantly for higher-order branching. Augmin strongly promotes the anterograde growth of microtubules in terminal dendrites and thus terminal dendrite stability. Consistent with a specific role in higher-order branching, we find that augmin is expressed less strongly and is largely dispensable in larval class I da neurons, which exhibit few higher-order dendrites. Thus, γ-TuRCs are essential for various aspects of complex dendritic arbor development, and they appear to function in higher-order branching via the augmin pathway, which promotes the elaboration of dendritic arbors to help define neuronal morphology.
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Affiliation(s)
- Amrita Mukherjee
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Yaiza Andrés Jeske
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Isabelle Becam
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Anaelle Taïeb
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Paul Brooks
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Joanna Aouad
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | | - Paul T. Conduit
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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Harken AD, Deoli NT, Perez Campos C, Ponnaiya B, Garty G, Lee GS, Casper MJ, Dhingra S, Li W, Johnson GW, Amundson SA, Grabham PW, Hillman EMC, Brenner DJ. Combined ion beam irradiation platform and 3D fluorescence microscope for cellular cancer research. BIOMEDICAL OPTICS EXPRESS 2024; 15:2561-2577. [PMID: 38633084 PMCID: PMC11019671 DOI: 10.1364/boe.522969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
To improve particle radiotherapy, we need a better understanding of the biology of radiation effects, particularly in heavy ion radiation therapy, where global responses are observed despite energy deposition in only a subset of cells. Here, we integrated a high-speed swept confocally-aligned planar excitation (SCAPE) microscope into a focused ion beam irradiation platform to allow real-time 3D structural and functional imaging of living biological samples during and after irradiation. We demonstrate dynamic imaging of the acute effects of irradiation on 3D cultures of U87 human glioblastoma cells, revealing characteristic changes in cellular movement and intracellular calcium signaling following ionizing irradiation.
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Affiliation(s)
- Andrew D Harken
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Naresh T Deoli
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Citlali Perez Campos
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Brian Ponnaiya
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Guy Garty
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Grace S Lee
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Malte J Casper
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Shikhar Dhingra
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Gary W Johnson
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Sally A Amundson
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Peter W Grabham
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Elizabeth M C Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - David J Brenner
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
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7
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Cooney PC, Huang Y, Li W, Perera DM, Hormigo R, Tabachnik T, Godage IS, Hillman EMC, Grueber WB, Zarin AA. Neuromuscular basis of Drosophila larval rolling escape behavior. Proc Natl Acad Sci U S A 2023; 120:e2303641120. [PMID: 38096410 PMCID: PMC10743538 DOI: 10.1073/pnas.2303641120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
When threatened by dangerous or harmful stimuli, animals engage in diverse forms of rapid escape behaviors. In Drosophila larvae, one type of escape response involves C-shaped bending and lateral rolling followed by rapid forward crawling. The sensory circuitry that promotes larval escape has been extensively characterized; however, the motor programs underlying rolling are unknown. Here, we characterize the neuromuscular basis of rolling escape behavior. We used high-speed, volumetric, Swept Confocally Aligned Planar Excitation (SCAPE) microscopy to image muscle activity during larval rolling. Unlike sequential peristaltic muscle contractions that progress from segment to segment during forward and backward crawling, muscle activity progresses circumferentially during bending and rolling escape behavior. We propose that progression of muscular contraction around the larva's circumference results in a transient misalignment between weight and the ground support forces, which generates a torque that induces stabilizing body rotation. Therefore, successive cycles of slight misalignment followed by reactive aligning rotation lead to continuous rolling motion. Supporting our biomechanical model, we found that disrupting the activity of muscle groups undergoing circumferential contraction progression leads to rolling defects. We use EM connectome data to identify premotor to motor connectivity patterns that could drive rolling behavior and perform neural silencing approaches to demonstrate the crucial role of a group of glutamatergic premotor neurons in rolling. Our data reveal body-wide muscle activity patterns and putative premotor circuit organization for execution of the rolling escape response.
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Affiliation(s)
- Patricia C. Cooney
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Neuroscience, Columbia University, New York, NY10027
| | - Yuhan Huang
- Department of Biology, Texas A&M University, College Station, TX77843
- Zarin Laboratory, Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX77843
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Electrical Engineering, Columbia University, New York, NY10027
| | - Dulanjana M. Perera
- Department of Multidisciplinary Engineering, Texas A&M University, College Station, TX77843
| | - Richard Hormigo
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
| | - Tanya Tabachnik
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
| | - Isuru S. Godage
- Department of Multidisciplinary Engineering, Texas A&M University, College Station, TX77843
- Department of Engineering Technology and Industrial Distribution, Texas A&M University, College Station, TX77843
- J. Mike Walker ‘66 Department of Mechanical Engineering, Texas A&M University, College Station, TX77843
| | - Elizabeth M. C. Hillman
- Laboratory for Functional Optical Imaging, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Biomedical Engineering, Columbia University, New York, NY10027
- Laboratory for Functional Optical Imaging, Kavli Institute for Brain Science, Columbia University, New York, NY10032
| | - Wesley B. Grueber
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Neuroscience, Columbia University, New York, NY10027
- Department of Physiology and Cellular Biophysics, Jerome L. Greene Science Center, New York, NY10027
| | - Aref A. Zarin
- Department of Biology, Texas A&M University, College Station, TX77843
- Zarin Laboratory, Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX77843
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Schaffer ES, Mishra N, Whiteway MR, Li W, Vancura MB, Freedman J, Patel KB, Voleti V, Paninski L, Hillman EMC, Abbott LF, Axel R. The spatial and temporal structure of neural activity across the fly brain. Nat Commun 2023; 14:5572. [PMID: 37696814 PMCID: PMC10495430 DOI: 10.1038/s41467-023-41261-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/29/2023] [Indexed: 09/13/2023] Open
Abstract
What are the spatial and temporal scales of brainwide neuronal activity? We used swept, confocally-aligned planar excitation (SCAPE) microscopy to image all cells in a large volume of the brain of adult Drosophila with high spatiotemporal resolution while flies engaged in a variety of spontaneous behaviors. This revealed neural representations of behavior on multiple spatial and temporal scales. The activity of most neurons correlated (or anticorrelated) with running and flailing over timescales that ranged from seconds to a minute. Grooming elicited a weaker global response. Significant residual activity not directly correlated with behavior was high dimensional and reflected the activity of small clusters of spatially organized neurons that may correspond to genetically defined cell types. These clusters participate in the global dynamics, indicating that neural activity reflects a combination of local and broadly distributed components. This suggests that microcircuits with highly specified functions are provided with knowledge of the larger context in which they operate.
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Affiliation(s)
- Evan S Schaffer
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA.
| | - Neeli Mishra
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
| | - Matthew R Whiteway
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Statistics and the Grossman Center for the Statistics of Mind, Columbia University, New York, NY, 10027, USA
| | - Wenze Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Michelle B Vancura
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
| | - Jason Freedman
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
| | - Kripa B Patel
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Venkatakaushik Voleti
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Liam Paninski
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Statistics and the Grossman Center for the Statistics of Mind, Columbia University, New York, NY, 10027, USA
| | - Elizabeth M C Hillman
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Radiology, Columbia University, New York, NY, 10027, USA
| | - L F Abbott
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Richard Axel
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY, 10027, USA
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9
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Cooney PC, Huang Y, Li W, Perera DM, Hormigo R, Tabachnik T, Godage I, Hillman EMC, Grueber WB, Zarin AA. Neuromuscular Basis of Drosophila larval rolling escape behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526733. [PMID: 36778508 PMCID: PMC9915593 DOI: 10.1101/2023.02.01.526733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
When threatened by dangerous or harmful stimuli, animals engage in diverse forms of rapid escape behaviors. In Drosophila larvae, one type of escape response involves C-shaped bending and lateral rolling followed by rapid forward crawling. The sensory circuitry that promotes larval escape has been extensively characterized; however, the motor programs underlying rolling are unknown. Here, we characterize the neuromuscular basis of rolling escape behavior. We used high-speed, volumetric, Swept Confocally-Aligned Planar Excitation (SCAPE) microscopy to image muscle activity during larval rolling. Unlike sequential peristaltic muscle contractions that progress from segment to segment during forward and backward crawling, the muscle activity progresses circumferentially during bending and rolling escape behavior. We propose that progression of muscular contraction around the larval circumference results in a transient misalignment between weight and the ground support forces, which generates a torque that induces stabilizing body rotation. Therefore, successive cycles of slight misalignment followed by reactive aligning rotation lead to continuous rolling motion. Supporting our biomechanical model, we found that disrupting the activity of muscle groups undergoing circumferential contraction progression lead to rolling defects. We use EM connectome data to identify premotor to motor connectivity patterns that could drive rolling behavior, and perform neural silencing approaches to demonstrate the crucial role of a group of glutamatergic premotor neurons in rolling. Our data reveal body-wide muscle activity patterns and putative premotor circuit organization for execution of the rolling escape response.
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10
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Dallmann CJ, Dickerson BH, Simpson JH, Wyart C, Jayaram K. Mechanosensory Control of Locomotion in Animals and Robots: Moving Forward. Integr Comp Biol 2023; 63:450-463. [PMID: 37279901 PMCID: PMC10445419 DOI: 10.1093/icb/icad057] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/10/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023] Open
Abstract
While animals swim, crawl, walk, and fly with apparent ease, building robots capable of robust locomotion remains a significant challenge. In this review, we draw attention to mechanosensation-the sensing of mechanical forces generated within and outside the body-as a key sense that enables robust locomotion in animals. We discuss differences between mechanosensation in animals and current robots with respect to (1) the encoding properties and distribution of mechanosensors and (2) the integration and regulation of mechanosensory feedback. We argue that robotics would benefit greatly from a detailed understanding of these aspects in animals. To that end, we highlight promising experimental and engineering approaches to study mechanosensation, emphasizing the mutual benefits for biologists and engineers that emerge from moving forward together.
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Affiliation(s)
- Chris J Dallmann
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Bradley H Dickerson
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Julie H Simpson
- Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Claire Wyart
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, Paris 75005, France
| | - Kaushik Jayaram
- Paul M Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
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11
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Kohsaka H. Linking neural circuits to the mechanics of animal behavior in Drosophila larval locomotion. Front Neural Circuits 2023; 17:1175899. [PMID: 37711343 PMCID: PMC10499525 DOI: 10.3389/fncir.2023.1175899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/13/2023] [Indexed: 09/16/2023] Open
Abstract
The motions that make up animal behavior arise from the interplay between neural circuits and the mechanical parts of the body. Therefore, in order to comprehend the operational mechanisms governing behavior, it is essential to examine not only the underlying neural network but also the mechanical characteristics of the animal's body. The locomotor system of fly larvae serves as an ideal model for pursuing this integrative approach. By virtue of diverse investigation methods encompassing connectomics analysis and quantification of locomotion kinematics, research on larval locomotion has shed light on the underlying mechanisms of animal behavior. These studies have elucidated the roles of interneurons in coordinating muscle activities within and between segments, as well as the neural circuits responsible for exploration. This review aims to provide an overview of recent research on the neuromechanics of animal locomotion in fly larvae. We also briefly review interspecific diversity in fly larval locomotion and explore the latest advancements in soft robots inspired by larval locomotion. The integrative analysis of animal behavior using fly larvae could establish a practical framework for scrutinizing the behavior of other animal species.
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Affiliation(s)
- Hiroshi Kohsaka
- Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo, Japan
- Department of Complexity Science and Engineering, Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
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12
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Greaney MR, Wreden CC, Heckscher ES. Distinctive features of the central synaptic organization of Drosophila larval proprioceptors. Front Neural Circuits 2023; 17:1223334. [PMID: 37564629 PMCID: PMC10410283 DOI: 10.3389/fncir.2023.1223334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
Proprioceptive feedback is critically needed for locomotor control, but how this information is incorporated into central proprioceptive processing circuits remains poorly understood. Circuit organization emerges from the spatial distribution of synaptic connections between neurons. This distribution is difficult to discern in model systems where only a few cells can be probed simultaneously. Therefore, we turned to a relatively simple and accessible nervous system to ask: how are proprioceptors' input and output synapses organized in space, and what principles underlie this organization? Using the Drosophila larval connectome, we generated a map of the input and output synapses of 34 proprioceptors in several adjacent body segments (5-6 left-right pairs per segment). We characterized the spatial organization of these synapses, and compared this organization to that of other somatosensory neurons' synapses. We found three distinguishing features of larval proprioceptor synapses: (1) Generally, individual proprioceptor types display segmental somatotopy. (2) Proprioceptor output synapses both converge and diverge in space; they are organized into six spatial domains, each containing a unique set of one or more proprioceptors. Proprioceptors form output synapses along the proximal axonal entry pathway into the neuropil. (3) Proprioceptors receive few inhibitory input synapses. Further, we find that these three features do not apply to other larval somatosensory neurons. Thus, we have generated the most comprehensive map to date of how proprioceptor synapses are centrally organized. This map documents previously undescribed features of proprioceptors, raises questions about underlying developmental mechanisms, and has implications for downstream proprioceptive processing circuits.
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Affiliation(s)
- Marie R. Greaney
- Committee on Neurobiology, The University of Chicago, Chicago, IL, United States
| | - Chris C. Wreden
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
| | - Ellie S. Heckscher
- Committee on Neurobiology, The University of Chicago, Chicago, IL, United States
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
- Institute for Neuroscience, The University of Chicago, Chicago, IL, United States
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13
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Yamaguchi A, Wu R, McNulty P, Karagyozov D, Mihovilovic Skanata M, Gershow M. Multi-neuronal recording in unrestrained animals with all acousto-optic random-access line-scanning two-photon microscopy. Front Neurosci 2023; 17:1135457. [PMID: 37389365 PMCID: PMC10303936 DOI: 10.3389/fnins.2023.1135457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
To understand how neural activity encodes and coordinates behavior, it is desirable to record multi-neuronal activity in freely behaving animals. Imaging in unrestrained animals is challenging, especially for those, like larval Drosophila melanogaster, whose brains are deformed by body motion. A previously demonstrated two-photon tracking microscope recorded from individual neurons in freely crawling Drosophila larvae but faced limits in multi-neuronal recording. Here we demonstrate a new tracking microscope using acousto-optic deflectors (AODs) and an acoustic GRIN lens (TAG lens) to achieve axially resonant 2D random access scanning, sampling along arbitrarily located axial lines at a line rate of 70 kHz. With a tracking latency of 0.1 ms, this microscope recorded activities of various neurons in moving larval Drosophila CNS and VNC including premotor neurons, bilateral visual interneurons, and descending command neurons. This technique can be applied to the existing two-photon microscope to allow for fast 3D tracking and scanning.
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Affiliation(s)
- Akihiro Yamaguchi
- Department of Physics, New York University, New York, NY, United States
| | - Rui Wu
- Department of Physics, New York University, New York, NY, United States
| | - Paul McNulty
- Department of Physics, New York University, New York, NY, United States
| | - Doycho Karagyozov
- Department of Physics, New York University, New York, NY, United States
| | | | - Marc Gershow
- Department of Physics, New York University, New York, NY, United States
- Center for Neural Science, New York University, New York, NY, United States
- Neuroscience Institute, New York University, New York, NY, United States
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14
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Hertzler JI, Bernard AR, Rolls MM. Dendrite regeneration mediates functional recovery after complete dendrite removal. Dev Biol 2023; 497:18-25. [PMID: 36870669 PMCID: PMC10073339 DOI: 10.1016/j.ydbio.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
Unlike many cell types, neurons are not typically replaced if damaged. Therefore, regeneration of damaged cellular domains is critical for maintenance of neuronal function. While axon regeneration has been documented for several hundred years, it has only recently become possible to determine whether neurons respond to dendrite removal with regeneration. Regrowth of dendrite arbors has been documented in invertebrate and vertebrate model systems, but whether it leads to functional restoration of a circuit remains unknown. To test whether dendrite regeneration restores function, we used larval Drosophila nociceptive neurons. Their dendrites detect noxious stimuli to initiate escape behavior. Previous studies of Drosophila sensory neurons have shown that dendrites of single neurons regrow after laser severing. We removed dendrites from 16 neurons per animal to clear most of the dorsal surface of nociceptive innervation. As expected, this reduced aversive responses to noxious touch. Surprisingly, behavior was completely restored 24 h after injury, at the stage when dendrite regeneration has begun, but the new arbor has only covered a small portion of its former territory. This behavioral recovery required regenerative outgrowth as it was eliminated in a genetic background in which new growth is blocked. We conclude that dendrite regeneration can restore behavior.
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Affiliation(s)
- J Ian Hertzler
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Annabelle R Bernard
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Melissa M Rolls
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.
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15
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Boivin JC, Zhu J, Ohyama T. Nociception in fruit fly larvae. FRONTIERS IN PAIN RESEARCH 2023; 4:1076017. [PMID: 37006412 PMCID: PMC10063880 DOI: 10.3389/fpain.2023.1076017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Nociception, the process of encoding and processing noxious or painful stimuli, allows animals to detect and avoid or escape from potentially life-threatening stimuli. Here, we provide a brief overview of recent technical developments and studies that have advanced our understanding of the Drosophila larval nociceptive circuit and demonstrated its potential as a model system to elucidate the mechanistic basis of nociception. The nervous system of a Drosophila larva contains roughly 15,000 neurons, which allows for reconstructing the connectivity among them directly by transmission electron microscopy. In addition, the availability of genetic tools for manipulating the activity of individual neurons and recent advances in computational and high-throughput behavior analysis methods have facilitated the identification of a neural circuit underlying a characteristic nocifensive behavior. We also discuss how neuromodulators may play a key role in modulating the nociceptive circuit and behavioral output. A detailed understanding of the structure and function of Drosophila larval nociceptive neural circuit could provide insights into the organization and operation of pain circuits in mammals and generate new knowledge to advance the development of treatment options for pain in humans.
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Affiliation(s)
- Jean-Christophe Boivin
- Department of Biology, McGill University, Montreal, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Jiayi Zhu
- Department of Biology, McGill University, Montreal, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Tomoko Ohyama
- Department of Biology, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
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16
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Niu X, Mao CX, Wang S, Wang X, Zhang Y, Hu J, Bi R, Liu Z, Shan J. α-Tubulin acetylation at lysine 40 regulates dendritic arborization and larval locomotion by promoting microtubule stability in Drosophila. PLoS One 2023; 18:e0280573. [PMID: 36827311 PMCID: PMC9955671 DOI: 10.1371/journal.pone.0280573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 01/03/2023] [Indexed: 02/25/2023] Open
Abstract
Posttranslational modification of tubulin increases the dynamic complexity and functional diversity of microtubules. Acetylation of α-tubulin at Lys-40 is a highly conserved posttranslational modification that has been shown to improve the flexibility and resilience of microtubules. Here we studied the in vivo functions of α-tubulin acetylation by knocking-out Atat, the Drosophila α-tubulin acetyltransferase, and by mutating Lys-40 to Arg in α1-tubulin. We found a reduction in the dendritic arborization of larval class I dendritic arborization (da) neurons in both mutants. The dendritic developmental defects in atat mutants could be reversed by enhancing the stability of microtubules either through knocking down the microtubule severing protein Katanin 60 or through overexpressing tubulin-specific chaperone E, suggesting that α-tubulin deacetylation impairsed dendritic morphology by decreasing the stability of microtubules. Using time-lapse recordings, we found that atat and α1-tubulinK40R mutations dramatically increased the number of dendritic protrusions that were likely to be immature dendritic precursors. Finally, we showed that both Atat and α-tubulin acetylation were required in class I da neurons to control larval locomotion. These findings add novel insight into the current knowledge of the role of α-tubulin acetylation in regulating neuronal development and functions.
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Affiliation(s)
- Xiaoxiao Niu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Chuan-Xi Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Shan Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Xiongxiong Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Youyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Juncheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Ran Bi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
| | - Zhihua Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
- * E-mail: (SJ); (ZL)
| | - Jin Shan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life science, Hubei University, Wuhan, China
- * E-mail: (SJ); (ZL)
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17
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Krämer R, Wolterhoff N, Galic M, Rumpf S. Developmental pruning of sensory neurites by mechanical tearing in Drosophila. J Cell Biol 2023; 222:213805. [PMID: 36648440 PMCID: PMC9856751 DOI: 10.1083/jcb.202205004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/24/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Mechanical forces actively shape cells during development, but little is known about their roles during neuronal morphogenesis. Developmental neurite pruning, a critical circuit specification mechanism, often involves neurite abscission at predetermined sites by unknown mechanisms. Pruning of Drosophila sensory neuron dendrites during metamorphosis is triggered by the hormone ecdysone, which induces local disassembly of the dendritic cytoskeleton. Subsequently, dendrites are severed at positions close to the soma by an unknown mechanism. We found that ecdysone signaling causes the dendrites to become mechanically fragile. Severing occurs during periods of increased pupal morphogenetic tissue movements, which exert mechanical forces on the destabilized dendrites. Tissue movements and dendrite severing peak during pupal ecdysis, a period of strong abdominal contractions, and abolishing ecdysis causes non-cell autonomous dendrite pruning defects. Thus, our data establish mechanical tearing as a novel mechanism during neurite pruning.
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Affiliation(s)
- Rafael Krämer
- https://ror.org/00pd74e08Institute for Neurobiology, University of Münster, Münster, Germany
| | - Neele Wolterhoff
- https://ror.org/00pd74e08Institute for Neurobiology, University of Münster, Münster, Germany
| | - Milos Galic
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Sebastian Rumpf
- https://ror.org/00pd74e08Institute for Neurobiology, University of Münster, Münster, Germany
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18
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Thomson EE, Harfouche M, Kim K, Konda PC, Seitz CW, Cooke C, Xu S, Jacobs WS, Blazing R, Chen Y, Sharma S, Dunn TW, Park J, Horstmeyer RW, Naumann EA. Gigapixel imaging with a novel multi-camera array microscope. eLife 2022; 11:e74988. [PMID: 36515989 PMCID: PMC9917455 DOI: 10.7554/elife.74988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from structures that approach the cellular scale to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies with a field of view over hundreds of square centimeters at an optical resolution of 18 µm. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. Further, the MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Overall, by removing the bottlenecks imposed by single-camera image acquisition systems, the MCAM provides a powerful platform for investigating detailed biological features and behavioral processes of small model organisms across a wide range of spatial scales.
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Affiliation(s)
- Eric E Thomson
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Kanghyun Kim
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Pavan C Konda
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Catherine W Seitz
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Colin Cooke
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Shiqi Xu
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Whitney S Jacobs
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Robin Blazing
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Yang Chen
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Timothy W Dunn
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | | | - Roarke W Horstmeyer
- Ramona Optics IncDurhamUnited States
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Eva A Naumann
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
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19
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Liu Z, Zhu Y, Zhang L, Jiang W, Liu Y, Tang Q, Cai X, Li J, Wang L, Tao C, Yin X, Li X, Hou S, Jiang D, Liu K, Zhou X, Zhang H, Liu M, Fan C, Tian Y. Structural and functional imaging of brains. Sci China Chem 2022; 66:324-366. [PMID: 36536633 PMCID: PMC9753096 DOI: 10.1007/s11426-022-1408-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022]
Abstract
Analyzing the complex structures and functions of brain is the key issue to understanding the physiological and pathological processes. Although neuronal morphology and local distribution of neurons/blood vessels in the brain have been known, the subcellular structures of cells remain challenging, especially in the live brain. In addition, the complicated brain functions involve numerous functional molecules, but the concentrations, distributions and interactions of these molecules in the brain are still poorly understood. In this review, frontier techniques available for multiscale structure imaging from organelles to the whole brain are first overviewed, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), serial-section electron microscopy (ssEM), light microscopy (LM) and synchrotron-based X-ray microscopy (XRM). Specially, XRM for three-dimensional (3D) imaging of large-scale brain tissue with high resolution and fast imaging speed is highlighted. Additionally, the development of elegant methods for acquisition of brain functions from electrical/chemical signals in the brain is outlined. In particular, the new electrophysiology technologies for neural recordings at the single-neuron level and in the brain are also summarized. We also focus on the construction of electrochemical probes based on dual-recognition strategy and surface/interface chemistry for determination of chemical species in the brain with high selectivity and long-term stability, as well as electrochemophysiological microarray for simultaneously recording of electrochemical and electrophysiological signals in the brain. Moreover, the recent development of brain MRI probes with high contrast-to-noise ratio (CNR) and sensitivity based on hyperpolarized techniques and multi-nuclear chemistry is introduced. Furthermore, multiple optical probes and instruments, especially the optophysiological Raman probes and fiber Raman photometry, for imaging and biosensing in live brain are emphasized. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Zhichao Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Ying Zhu
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Liming Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Weiping Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Qiaowei Tang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Xiaoqing Cai
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Jiang Li
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Lihua Wang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Changlu Tao
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | | | - Xiaowei Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055 China
| | - Dawei Jiang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
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20
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Swope RD, Hertzler JI, Stone MC, Kothe GO, Rolls MM. The exocyst complex is required for developmental and regenerative neurite growth in vivo. Dev Biol 2022; 492:1-13. [PMID: 36162553 PMCID: PMC10228574 DOI: 10.1016/j.ydbio.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022]
Abstract
The exocyst complex is an important regulator of intracellular trafficking and tethers secretory vesicles to the plasma membrane. Understanding of its role in neuron outgrowth remains incomplete, and previous studies have come to different conclusions about its importance for axon and dendrite growth, particularly in vivo. To investigate exocyst function in vivo we used Drosophila sensory neurons as a model system. To bypass early developmental requirements in other cell types, we used neuron-specific RNAi to target seven exocyst subunits. Initial neuronal development proceeded normally in these backgrounds, however, we considered this could be due to residual exocyst function. To probe neuronal growth capacity at later times after RNAi initiation, we used laser microsurgery to remove axons or dendrites and prompt regrowth. Exocyst subunit RNAi reduced axon regeneration, although new axons could be specified. In control neurons, a vesicle trafficking marker often concentrated in the new axon, but this pattern was disrupted in Sec6 RNAi neurons. Dendrite regeneration was also severely reduced by exocyst RNAi, even though the trafficking marker did not accumulate in a strongly polarized manner during normal dendrite regeneration. The requirement for the exocyst was not limited to injury contexts as exocyst subunit RNAi eliminated dendrite regrowth after developmental pruning. We conclude that the exocyst is required for injury-induced and developmental neurite outgrowth, but that residual protein function can easily mask this requirement.
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Affiliation(s)
- Rachel D Swope
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - J Ian Hertzler
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Michelle C Stone
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Gregory O Kothe
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Melissa M Rolls
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.
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21
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Creamer MS, Chen KS, Leifer AM, Pillow JW. Correcting motion induced fluorescence artifacts in two-channel neural imaging. PLoS Comput Biol 2022; 18:e1010421. [PMID: 36170268 PMCID: PMC9518861 DOI: 10.1371/journal.pcbi.1010421] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
Imaging neural activity in a behaving animal presents unique challenges in part because motion from an animal's movement creates artifacts in fluorescence intensity time-series that are difficult to distinguish from neural signals of interest. One approach to mitigating these artifacts is to image two channels simultaneously: one that captures an activity-dependent fluorophore, such as GCaMP, and another that captures an activity-independent fluorophore such as RFP. Because the activity-independent channel contains the same motion artifacts as the activity-dependent channel, but no neural signals, the two together can be used to identify and remove the artifacts. However, existing approaches for this correction, such as taking the ratio of the two channels, do not account for channel-independent noise in the measured fluorescence. Here, we present Two-channel Motion Artifact Correction (TMAC), a method which seeks to remove artifacts by specifying a generative model of the two channel fluorescence that incorporates motion artifact, neural activity, and noise. We use Bayesian inference to infer latent neural activity under this model, thus reducing the motion artifact present in the measured fluorescence traces. We further present a novel method for evaluating ground-truth performance of motion correction algorithms by comparing the decodability of behavior from two types of neural recordings; a recording that had both an activity-dependent fluorophore and an activity-independent fluorophore (GCaMP and RFP) and a recording where both fluorophores were activity-independent (GFP and RFP). A successful motion correction method should decode behavior from the first type of recording, but not the second. We use this metric to systematically compare five models for removing motion artifacts from fluorescent time traces. We decode locomotion from a GCaMP expressing animal 20x more accurately on average than from control when using TMAC inferred activity and outperforms all other methods of motion correction tested, the best of which were ~8x more accurate than control.
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Affiliation(s)
- Matthew S Creamer
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
| | - Kevin S Chen
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
| | - Andrew M Leifer
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
- Department of Physics, Princeton University, Princeton, New Jersey, United States of America
| | - Jonathan W Pillow
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
- Department of Psychology, Princeton University, Princeton, New Jersey, United States of America
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22
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Sun X, Liu Y, Liu C, Mayumi K, Ito K, Nose A, Kohsaka H. A neuromechanical model for Drosophila larval crawling based on physical measurements. BMC Biol 2022; 20:130. [PMID: 35701821 PMCID: PMC9199175 DOI: 10.1186/s12915-022-01336-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal locomotion requires dynamic interactions between neural circuits, the body (typically muscles), and surrounding environments. While the neural circuitry of movement has been intensively studied, how these outputs are integrated with body mechanics (neuromechanics) is less clear, in part due to the lack of understanding of the biomechanical properties of animal bodies. Here, we propose an integrated neuromechanical model of movement based on physical measurements by taking Drosophila larvae as a model of soft-bodied animals. RESULTS We first characterized the kinematics of forward crawling in Drosophila larvae at a segmental and whole-body level. We then characterized the biomechanical parameters of fly larvae, namely the contraction forces generated by neural activity, and passive elastic and viscosity of the larval body using a stress-relaxation test. We established a mathematical neuromechanical model based on the physical measurements described above, obtaining seven kinematic values characterizing crawling locomotion. By optimizing the parameters in the neural circuit, our neuromechanical model succeeded in quantitatively reproducing the kinematics of larval locomotion that were obtained experimentally. This model could reproduce the observation of optogenetic studies reported previously. The model predicted that peristaltic locomotion could be exhibited in a low-friction condition. Analysis of floating larvae provided results consistent with this prediction. Furthermore, the model predicted a significant contribution of intersegmental connections in the central nervous system, which contrasts with a previous study. This hypothesis allowed us to make a testable prediction for the variability in intersegmental connection in sister species of the genus Drosophila. CONCLUSIONS We generated a neurochemical model based on physical measurement to provide a new foundation to study locomotion in soft-bodied animals and soft robot engineering.
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Affiliation(s)
- Xiyang Sun
- Department of Complexity Science and Engineering, Graduate School of Frontier Science, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yingtao Liu
- Department of Physics, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-0033, Japan
| | - Chang Liu
- Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Koichi Mayumi
- Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Kohzo Ito
- Department of Advanced Materials Science, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Akinao Nose
- Department of Complexity Science and Engineering, Graduate School of Frontier Science, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.,Department of Physics, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 133-0033, Japan
| | - Hiroshi Kohsaka
- Department of Complexity Science and Engineering, Graduate School of Frontier Science, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan. .,Division of General Education, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1, Chofugaoka, Chofu, Tokyo, 182-8585, Japan.
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23
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Agrawal S, Tuthill JC. The two-body problem: Proprioception and motor control across the metamorphic divide. Curr Opin Neurobiol 2022; 74:102546. [PMID: 35512562 DOI: 10.1016/j.conb.2022.102546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/11/2022] [Accepted: 03/27/2022] [Indexed: 11/17/2022]
Abstract
Like a rocket being propelled into space, evolution has engineered flies to launch into adulthood via multiple stages. Flies develop and deploy two distinct bodies, linked by the transformative process of metamorphosis. The fly larva is a soft hydraulic tube that can crawl to find food and avoid predators. The adult fly has a stiff exoskeleton with articulated limbs that enable long-distance navigation and rich social interactions. Because the larval and adult forms are so distinct in structure, they require distinct strategies for sensing and moving the body. The metamorphic divide thus presents an opportunity for comparative analysis of neural circuits. Here, we review recent progress toward understanding the neural mechanisms of proprioception and motor control in larval and adult Drosophila. We highlight commonalities that point toward general principles of sensorimotor control and differences that may reflect unique constraints imposed by biomechanics. Finally, we discuss emerging opportunities for comparative analysis of neural circuit architecture in the fly and other animal species.
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Affiliation(s)
- Sweta Agrawal
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
| | - John C Tuthill
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
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24
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Patel KB, Liang W, Casper MJ, Voleti V, Li W, Yagielski AJ, Zhao HT, Perez Campos C, Lee GS, Liu JM, Philipone E, Yoon AJ, Olive KP, Coley SM, Hillman EMC. High-speed light-sheet microscopy for the in-situ acquisition of volumetric histological images of living tissue. Nat Biomed Eng 2022; 6:569-583. [PMID: 35347275 PMCID: PMC10353946 DOI: 10.1038/s41551-022-00849-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Histological examinations typically require the excision of tissue, followed by its fixation, slicing, staining, mounting and imaging, with timeframes ranging from minutes to days. This process may remove functional tissue, may miss abnormalities through under-sampling, prevents rapid decision-making, and increases costs. Here, we report the feasibility of microscopes based on swept confocally aligned planar excitation technology for the volumetric histological imaging of intact living tissue in real time. The systems' single-objective, light-sheet geometry and 3D imaging speeds enable roving image acquisition, which combined with 3D stitching permits the contiguous analysis of large tissue areas, as well as the dynamic assessment of tissue perfusion and function. Implemented in benchtop and miniaturized form factors, the microscopes also have high sensitivity, even for weak intrinsic fluorescence, allowing for the label-free imaging of diagnostically relevant histoarchitectural structures, as we show for pancreatic disease in living mice, for chronic kidney disease in fresh human kidney tissues, and for oral mucosa in a healthy volunteer. Miniaturized high-speed light-sheet microscopes for in-situ volumetric histological imaging may facilitate the point-of-care detection of diverse cellular-level biomarkers.
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Affiliation(s)
- Kripa B Patel
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Wenxuan Liang
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Malte J Casper
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Venkatakaushik Voleti
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Alexis J Yagielski
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Hanzhi T Zhao
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Citlali Perez Campos
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Grace Sooyeon Lee
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Joyce M Liu
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Elizabeth Philipone
- Department of Oral and Maxillofacial Pathology, Columbia University Irving Medical Center, New York, NY, USA
| | - Angela J Yoon
- Department of Oral and Maxillofacial Pathology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth P Olive
- Division of Digestive and Liver Disease, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Shana M Coley
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Elizabeth M C Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology and the Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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25
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Bittern J, Praetz M, Baldenius M, Klämbt C. Long-Term Observation of Locomotion of Drosophila Larvae Facilitates Feasibility of Food-Choice Assays. Adv Biol (Weinh) 2022; 6:e2100938. [PMID: 34365739 DOI: 10.1002/adbi.202100938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/20/2021] [Indexed: 01/27/2023]
Abstract
Animal behavior is reflected by locomotor patterns. To decipher the underlying neural circuitry locomotion has to be monitored over often longer time periods. Here a simple adaptation is described to constrain movement of third instar Drosophila larvae to a defined area and use Frustrated total internal reflection based imaging method (FIM) imaging to monitor larval movements up to 1 h. It is demonstrated that the combination of FIM imaging and long analysis periods facilitates the conduction of food choice assays and provides the means to easily quantify food preferences.
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Affiliation(s)
- Jonas Bittern
- Institut für Neuro-und Verhaltensbiologie, Badestr. 9, 48149, Münster, Germany
| | - Marit Praetz
- Institut für Neuro-und Verhaltensbiologie, Badestr. 9, 48149, Münster, Germany
| | - Marie Baldenius
- Institut für Neuro-und Verhaltensbiologie, Badestr. 9, 48149, Münster, Germany
| | - Christian Klämbt
- Institut für Neuro-und Verhaltensbiologie, Badestr. 9, 48149, Münster, Germany
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26
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Heckman EL, Doe CQ. Presynaptic contact and activity opposingly regulate postsynaptic dendrite outgrowth. eLife 2022; 11:82093. [PMID: 36448675 PMCID: PMC9728994 DOI: 10.7554/elife.82093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The organization of neural circuits determines nervous system function. Variability can arise during neural circuit development (e.g. neurite morphology, axon/dendrite position). To ensure robust nervous system function, mechanisms must exist to accommodate variation in neurite positioning during circuit formation. Previously, we developed a model system in the Drosophila ventral nerve cord to conditionally induce positional variability of a proprioceptive sensory axon terminal, and used this model to show that when we altered the presynaptic position of the sensory neuron, its major postsynaptic interneuron partner modified its dendritic arbor to match the presynaptic contact, resulting in functional synaptic input (Sales et al., 2019). Here, we investigate the cellular mechanisms by which the interneuron dendrites detect and match variation in presynaptic partner location and input strength. We manipulate the presynaptic sensory neuron by (a) ablation; (b) silencing or activation; or (c) altering its location in the neuropil. From these experiments we conclude that there are two opposing mechanisms used to establish functional connectivity in the face of presynaptic variability: presynaptic contact stimulates dendrite outgrowth locally, whereas presynaptic activity inhibits postsynaptic dendrite outgrowth globally. These mechanisms are only active during an early larval critical period for structural plasticity. Collectively, our data provide new insights into dendrite development, identifying mechanisms that allow dendrites to flexibly respond to developmental variability in presynaptic location and input strength.
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Affiliation(s)
- Emily L Heckman
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
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27
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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28
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Kilo L, Stürner T, Tavosanis G, Ziegler AB. Drosophila Dendritic Arborisation Neurons: Fantastic Actin Dynamics and Where to Find Them. Cells 2021; 10:2777. [PMID: 34685757 PMCID: PMC8534399 DOI: 10.3390/cells10102777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 01/27/2023] Open
Abstract
Neuronal dendrites receive, integrate, and process numerous inputs and therefore serve as the neuron's "antennae". Dendrites display extreme morphological diversity across different neuronal classes to match the neuron's specific functional requirements. Understanding how this structural diversity is specified is therefore important for shedding light on information processing in the healthy and diseased nervous system. Popular models for in vivo studies of dendrite differentiation are the four classes of dendritic arborization (c1da-c4da) neurons of Drosophila larvae with their class-specific dendritic morphologies. Using da neurons, a combination of live-cell imaging and computational approaches have delivered information on the distinct phases and the time course of dendrite development from embryonic stages to the fully developed dendritic tree. With these data, we can start approaching the basic logic behind differential dendrite development. A major role in the definition of neuron-type specific morphologies is played by dynamic actin-rich processes and the regulation of their properties. This review presents the differences in the growth programs leading to morphologically different dendritic trees, with a focus on the key role of actin modulatory proteins. In addition, we summarize requirements and technological progress towards the visualization and manipulation of such actin regulators in vivo.
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Affiliation(s)
- Lukas Kilo
- Dendrite Differentiation, German Center for Neurodegenerative Diseases, 53115 Bonn, Germany; (L.K.); (G.T.)
| | - Tomke Stürner
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK;
| | - Gaia Tavosanis
- Dendrite Differentiation, German Center for Neurodegenerative Diseases, 53115 Bonn, Germany; (L.K.); (G.T.)
- LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Anna B. Ziegler
- Institute of Neuro- and Behavioral Biology, University of Münster, 48149 Münster, Germany
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29
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Lesar A, Tahir J, Wolk J, Gershow M. Switch-like and persistent memory formation in individual Drosophila larvae. eLife 2021; 10:e70317. [PMID: 34636720 PMCID: PMC8510578 DOI: 10.7554/elife.70317] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/27/2021] [Indexed: 11/15/2022] Open
Abstract
Associative learning allows animals to use past experience to predict future events. The circuits underlying memory formation support immediate and sustained changes in function, often in response to a single example. Larval Drosophila is a genetic model for memory formation that can be accessed at molecular, synaptic, cellular, and circuit levels, often simultaneously, but existing behavioral assays for larval learning and memory do not address individual animals, and it has been difficult to form long-lasting memories, especially those requiring synaptic reorganization. We demonstrate a new assay for learning and memory capable of tracking the changing preferences of individual larvae. We use this assay to explore how activation of a pair of reward neurons changes the response to the innately aversive gas carbon dioxide (CO2). We confirm that when coupled to CO2 presentation in appropriate temporal sequence, optogenetic reward reduces avoidance of CO2. We find that learning is switch-like: all-or-none and quantized in two states. Memories can be extinguished by repeated unrewarded exposure to CO2 but are stabilized against extinction by repeated training or overnight consolidation. Finally, we demonstrate long-lasting protein synthesis dependent and independent memory formation.
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Affiliation(s)
- Amanda Lesar
- Department of Physics, New York UniversityNew YorkUnited States
| | - Javan Tahir
- Department of Physics, New York UniversityNew YorkUnited States
| | - Jason Wolk
- Department of Physics, New York UniversityNew YorkUnited States
| | - Marc Gershow
- Department of Physics, New York UniversityNew YorkUnited States
- Center for Neural Science, New York UniversityNew YorkUnited States
- NYU Neuroscience Institute, New York University Langone Medical CenterNew YorkUnited States
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30
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Lagache T, Hanson A, Pérez-Ortega JE, Fairhall A, Yuste R. Tracking calcium dynamics from individual neurons in behaving animals. PLoS Comput Biol 2021; 17:e1009432. [PMID: 34624016 PMCID: PMC8528277 DOI: 10.1371/journal.pcbi.1009432] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/20/2021] [Accepted: 09/08/2021] [Indexed: 12/03/2022] Open
Abstract
Measuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic monitoring of neuronal activity and their subsequent functional characterization. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correction and Concatenation or EMC2) that compensates for the intermittent disappearance of moving neurons by integrating local deformation information from detectable neurons. We demonstrate the accuracy and versatility of our algorithm using calcium imaging data from two-photon volumetric microscopy in visual cortex of awake mice, and from confocal microscopy in behaving Hydra, which experiences major body deformation during its contractions. We quantify the performance of our algorithm using ground truth manual tracking of neurons, along with synthetic time-lapse sequences, covering a wide range of particle motions and detectability parameters. As a demonstration of the utility of the algorithm, we monitor for several days calcium activity of the same neurons in layer 2/3 of mouse visual cortex in vivo, finding significant turnover within the active neurons across days, with only few neurons that remained active across days. Also, combining automatic tracking of single neuron activity with statistical clustering, we characterize and map neuronal ensembles in behaving Hydra, finding three major non-overlapping ensembles of neurons (CB, RP1 and RP2) whose activity correlates with contractions and elongations. Our results show that the EMC2 algorithm can be used as a robust and versatile platform for neuronal tracking in behaving animals.
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Affiliation(s)
- Thibault Lagache
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Alison Hanson
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Psychiatry, New York State Psychiatric Institute, Columbia University, New York, New York, United States of America
| | - Jesús E Pérez-Ortega
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Adrienne Fairhall
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, United States of America
- UW Computational Neuroscience Center, University of Washington, Seattle, Washington, United States of America
| | - Rafael Yuste
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Donostia International Physics Center, San Sebastian, Spain
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31
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Chen X, Ping J, Sun Y, Yi C, Liu S, Gong Z, Fei P. Deep-learning on-chip light-sheet microscopy enabling video-rate volumetric imaging of dynamic biological specimens. LAB ON A CHIP 2021; 21:3420-3428. [PMID: 34486609 DOI: 10.1039/d1lc00475a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Volumetric imaging of dynamic signals in a large, moving, and light-scattering specimen is extremely challenging, owing to the requirement on high spatiotemporal resolution and difficulty in obtaining high-contrast signals. Here we report that through combining a microfluidic chip-enabled digital scanning light-sheet illumination strategy with deep-learning based image restoration, we can realize isotropic 3D imaging of a whole crawling Drosophila larva on an ordinary inverted microscope at a single-cell resolution and a high volumetric imaging rate up to 20 Hz. Enabled with high performances even unmet by current standard light-sheet fluorescence microscopes, we in toto record the neural activities during the forward and backward crawling of a 1st instar larva, and successfully correlate the calcium spiking of motor neurons with the locomotion patterns.
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Affiliation(s)
- Xiaopeng Chen
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Junyu Ping
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | | | - Chengqiang Yi
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | | | - Zhefeng Gong
- Zhejiang Lab, Hangzhou, 311121, China.
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Zhejiang Lab, Hangzhou, 311121, China.
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32
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Abstract
In animals, proper locomotion is crucial to find mates and foods and avoid predators or dangers. Multiple sensory systems detect external and internal cues and integrate them to modulate motor outputs. Proprioception is the internal sense of body position, and proprioceptive control of locomotion is essential to generate and maintain precise patterns of movement or gaits. This proprioceptive feedback system is conserved in many animal species and is mediated by stretch-sensitive receptors called proprioceptors. Recent studies have identified multiple proprioceptive neurons and proprioceptors and their roles in the locomotion of various model organisms. In this review we describe molecular and neuronal mechanisms underlying proprioceptive feedback systems in C. elegans, Drosophila, and mice.
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Affiliation(s)
- Kyeong Min Moon
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
| | - Jimin Kim
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
| | - Yurim Seong
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
| | - Byung-Chang Suh
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
| | - KyeongJin Kang
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
- KBRI (Korea Brain Research Institute), Daegu 41068, Korea
| | - Han Kyoung Choe
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
- KBRI (Korea Brain Research Institute), Daegu 41068, Korea
| | - Kyuhyung Kim
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea
- KBRI (Korea Brain Research Institute), Daegu 41068, Korea
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33
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Elliott AD, Berndt A, Houpert M, Roy S, Scott RL, Chow CC, Shroff H, White BH. Pupal behavior emerges from unstructured muscle activity in response to neuromodulation in Drosophila. eLife 2021; 10:68656. [PMID: 34236312 PMCID: PMC8331185 DOI: 10.7554/elife.68656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Identifying neural substrates of behavior requires defining actions in terms that map onto brain activity. Brain and muscle activity naturally correlate via the output of motor neurons, but apart from simple movements it has been difficult to define behavior in terms of muscle contractions. By mapping the musculature of the pupal fruit fly and comprehensively imaging muscle activation at single-cell resolution, we here describe a multiphasic behavioral sequence in Drosophila. Our characterization identifies a previously undescribed behavioral phase and permits extraction of major movements by a convolutional neural network. We deconstruct movements into a syllabary of co-active muscles and identify specific syllables that are sensitive to neuromodulatory manipulations. We find that muscle activity shows considerable variability, with sequential increases in stereotypy dependent upon neuromodulation. Our work provides a platform for studying whole-animal behavior, quantifying its variability across multiple spatiotemporal scales, and analyzing its neuromodulatory regulation at cellular resolution. How do we find out how the brain works? One way is to use imaging techniques to visualise an animal’s brain in action as it performs simple behaviours: as the animal moves, parts of its brain light up under the microscope. For laboratory animals like fruit flies, which have relatively small brains, this lets us observe their brain activity right down to the level of individual brain cells. The brain directs movements via collective activity of the body’s muscles. Our ability to track the activity of individual muscles is, however, more limited than our ability to observe single brain cells: even modern imaging technology still cannot monitor the activity of all the muscle cells in an animal’s body as it moves about. Yet this is precisely the information that scientists need to fully understand how the brain generates behaviour. Fruit flies perform specific behaviours at certain stages of their life cycle. When the fly pupa begins to metamorphose into an adult insect, it performs a fixed sequence of movements involving a set number of muscles, which is called the pupal ecdysis sequence. This initial movement sequence and the rest of metamorphosis both occur within the confines of the pupal case, which is a small, hardened shell surrounding the whole animal. Elliott et al. set out to determine if the fruit fly pupa’s ecdysis sequence could be used as a kind of model, to describe a simple behaviour at the level of individual muscles. Imaging experiments used fly pupae that were genetically engineered to produce an activity-dependent fluorescent protein in their muscle cells. Pupal cases were treated with a chemical to make them transparent, allowing easy observation of their visually ‘labelled’ muscles. This yielded a near-complete record of muscle activity during metamorphosis. Initially, individual muscles became active in small groups. The groups then synchronised with each other over the different regions of the pupa’s body to form distinct movements, much as syllables join to form words. This synchronisation was key to progression through metamorphosis and was co-ordinated at each step by specialised nerve cells that produce or respond to specific hormones. These results reveal how the brain might direct muscle activity to produce movement patterns. In the future, Elliott et al. hope to compare data on muscle activity with comprehensive records of brain cell activity, to shed new light on how the brain, muscles, and other factors work together to control behaviour.
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Affiliation(s)
- Amicia D Elliott
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States.,National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Adama Berndt
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Matthew Houpert
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Snehashis Roy
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Robert L Scott
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
| | - Carson C Chow
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Benjamin H White
- National Institute of Mental Health, National Institutes of Health, Bethesda, United States
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Hunter I, Coulson B, Zarin AA, Baines RA. The Drosophila Larval Locomotor Circuit Provides a Model to Understand Neural Circuit Development and Function. Front Neural Circuits 2021; 15:684969. [PMID: 34276315 PMCID: PMC8282269 DOI: 10.3389/fncir.2021.684969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
It is difficult to answer important questions in neuroscience, such as: "how do neural circuits generate behaviour?," because research is limited by the complexity and inaccessibility of the mammalian nervous system. Invertebrate model organisms offer simpler networks that are easier to manipulate. As a result, much of what we know about the development of neural circuits is derived from work in crustaceans, nematode worms and arguably most of all, the fruit fly, Drosophila melanogaster. This review aims to demonstrate the utility of the Drosophila larval locomotor network as a model circuit, to those who do not usually use the fly in their work. This utility is explored first by discussion of the relatively complete connectome associated with one identified interneuron of the locomotor circuit, A27h, and relating it to similar circuits in mammals. Next, it is developed by examining its application to study two important areas of neuroscience research: critical periods of development and interindividual variability in neural circuits. In summary, this article highlights the potential to use the larval locomotor network as a "generic" model circuit, to provide insight into mammalian circuit development and function.
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Affiliation(s)
- Iain Hunter
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Bramwell Coulson
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Aref Arzan Zarin
- Department of Biology, The Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, United States
| | - Richard A Baines
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
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35
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Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL. In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor. Cell Rep 2021; 35:109284. [PMID: 34161775 DOI: 10.1016/j.celrep.2021.109284] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 03/06/2020] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Glucose is arguably the most important molecule in metabolism, and its dysregulation underlies diabetes. We describe a family of single-wavelength genetically encoded glucose sensors with a high signal-to-noise ratio, fast kinetics, and affinities varying over four orders of magnitude (1 μM to 10 mM). The sensors allow mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed ∼3-fold faster glucose changes in astrocytes. In larval Drosophila central nervous system explants, intracellular neuronal glucose fluxes suggested a rostro-caudal transport pathway in the ventral nerve cord neuropil. In zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory and pharmacological perturbations produced large changes in the brain. These sensors will enable rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.
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Affiliation(s)
- Jacob P Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Haluk Lacin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - William C Lemon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Soomin Kim
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Richard T Lee
- Harvard Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA; The Cardiovascular Division, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Cambridge, MA, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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36
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Tavosanis G. Dendrite enlightenment. Curr Opin Neurobiol 2021; 69:222-230. [PMID: 34134010 DOI: 10.1016/j.conb.2021.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/18/2022]
Abstract
Neuronal dendrites acquire complex morphologies during development. These are not just the product of cell-intrinsic developmental programs; rather they are defined in close interaction with the cellular environment. Thus, to understand the molecular cascades that yield appropriate morphologies, it is essential to investigate them in vivo, in the actual complex tissue environment encountered by the differentiating neuron in the developing animal. Particularly, genetic approaches have pointed to factors controlling dendrite differentiation in vivo. These suggest that localized and transient molecular cascades might underlie the formation and stabilization of dendrite branches with neuron type-specific characteristics. Here, I highlight the need for studies of neuronal dendrite differentiation in the animal, the challenges provided by such an approach, and the promising pathways that have recently opened.
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Affiliation(s)
- Gaia Tavosanis
- German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, Bonn, 53127, Germany; LIMES Institute, University of Bonn, Carl-Troll-Str. 3, Bonn, 53115, Germany.
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37
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Liu S, Wang S, Zou L, Xiong W. Mechanisms in cochlear hair cell mechano-electrical transduction for acquisition of sound frequency and intensity. Cell Mol Life Sci 2021; 78:5083-5094. [PMID: 33871677 PMCID: PMC11072359 DOI: 10.1007/s00018-021-03840-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Sound signals are acquired and digitized in the cochlea by the hair cells that further transmit the coded information to the central auditory pathways. Any defect in hair cell function may induce problems in the auditory system and hearing-based brain function. In the past 2 decades, our understanding of auditory transduction has been substantially deepened because of advances in molecular, structural, and functional studies. Results from these experiments can be perfectly embedded in the previously established profile from anatomical, histological, genetic, and biophysical research. This review aims to summarize the progress on the molecular and cellular mechanisms of the mechano-electrical transduction (MET) channel in the cochlear hair cells, which is involved in the acquisition of sound frequency and intensity-the two major parameters of an acoustic cue. We also discuss recent studies on TMC1, the molecule likely to form the MET channel pore.
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Affiliation(s)
- Shuang Liu
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Shufeng Wang
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Linzhi Zou
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Wei Xiong
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China.
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China.
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38
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Feng C, Cleary JM, Kothe GO, Stone MC, Weiner AT, Hertzler JI, Hancock WO, Rolls MM. Trim9 and Klp61F promote polymerization of new dendritic microtubules along parallel microtubules. J Cell Sci 2021; 134:jcs258437. [PMID: 34096607 PMCID: PMC8214762 DOI: 10.1242/jcs.258437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/04/2021] [Indexed: 02/03/2023] Open
Abstract
Axons and dendrites are distinguished by microtubule polarity. In Drosophila, dendrites are dominated by minus-end-out microtubules, whereas axons contain plus-end-out microtubules. Local nucleation in dendrites generates microtubules in both orientations. To understand why dendritic nucleation does not disrupt polarity, we used live imaging to analyze the fate of microtubules generated at branch points. We found that they had different rates of success exiting the branch based on orientation: correctly oriented minus-end-out microtubules succeeded in leaving about twice as often as incorrectly oriented microtubules. Increased success relied on other microtubules in a parallel orientation. From a candidate screen, we identified Trim9 and kinesin-5 (Klp61F) as machinery that promoted growth of new microtubules. In S2 cells, Eb1 recruited Trim9 to microtubules. Klp61F promoted microtubule growth in vitro and in vivo, and could recruit Trim9 in S2 cells. In summary, the data argue that Trim9 and kinesin-5 act together at microtubule plus ends to help polymerizing microtubules parallel to pre-existing ones resist catastrophe.
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Affiliation(s)
- Chengye Feng
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph M. Cleary
- Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory O. Kothe
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michelle C. Stone
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexis T. Weiner
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - James I. Hertzler
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - William O. Hancock
- Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Melissa M. Rolls
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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39
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Abstract
Sound-induced mechanical stimuli are detected by elaborate mechanosensory transduction (MT) machinery in highly specialized hair cells of the inner ear. Genetic studies of inherited deafness in the past decades have uncovered several molecular constituents of the MT complex, and intense debate has surrounded the molecular identity of the pore-forming subunits. How the MT components function in concert in response to physical stimulation is not fully understood. In this review, we summarize and discuss multiple lines of evidence supporting the hypothesis that transmembrane channel-like 1 is a long-sought MT channel subunit. We also review specific roles of other components of the MT complex, including protocadherin 15, cadherin 23, lipoma HMGIC fusion partner-like 5, transmembrane inner ear, calcium and integrin-binding family member 2, and ankyrins. Based on these recent advances, we propose a unifying theory of hair cell MT that may reconcile most of the functional discoveries obtained to date. Finally, we discuss key questions that need to be addressed for a comprehensive understanding of hair cell MT at molecular and atomic levels.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Jeffrey R Holt
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA;
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40
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Mongeau JM, Schweikert LE, Davis AL, Reichert MS, Kanwal JK. Multimodal integration across spatiotemporal scales to guide invertebrate locomotion. Integr Comp Biol 2021; 61:842-853. [PMID: 34009312 DOI: 10.1093/icb/icab041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Locomotion is a hallmark of organisms that has enabled adaptive radiation to an extraordinarily diverse class of ecological niches, and allows animals to move across vast distances. Sampling from multiple sensory modalities enables animals to acquire rich information to guide locomotion. Locomotion without sensory feedback is haphazard, therefore sensory and motor systems have evolved complex interactions to generate adaptive behavior. Notably, sensory-guided locomotion acts over broad spatial and temporal scales to permit goal-seeking behavior, whether to localize food by tracking an attractive odor plume or to search for a potential mate. How does the brain integrate multimodal stimuli over different temporal and spatial scales to effectively control behavior? In this review, we classify locomotion into three ordinally ranked hierarchical layers that act over distinct spatiotemporal scales: stabilization, motor primitives, and higher-order tasks, respectively. We discuss how these layers present unique challenges and opportunities for sensorimotor integration. We focus on recent advances in invertebrate locomotion due to their accessible neural and mechanical signals from the whole brain, limbs and sensors. Throughout, we emphasize neural-level description of computations for multimodal integration in genetic model systems, including the fruit fly, Drosophila melanogaster, and the yellow fever mosquito, Aedes aegypti. We identify that summation (e.g. gating) and weighting-which are inherent computations of spiking neurons-underlie multimodal integration across spatial and temporal scales, therefore suggesting collective strategies to guide locomotion.
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Affiliation(s)
- Jean-Michel Mongeau
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lorian E Schweikert
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL 33181. University of North Carolina Wilmington, Department of Biology and Marine Biology, Wilmington, NC, U.S.A
| | | | - Michael S Reichert
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Jessleen K Kanwal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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41
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Jékely G, Godfrey-Smith P, Keijzer F. Reafference and the origin of the self in early nervous system evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190764. [PMID: 33550954 PMCID: PMC7934971 DOI: 10.1098/rstb.2019.0764] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Discussions of the function of early nervous systems usually focus on a causal flow from sensors to effectors, by which an animal coordinates its actions with exogenous changes in its environment. We propose, instead, that much early sensing was reafferent; it was responsive to the consequences of the animal's own actions. We distinguish two general categories of reafference-translocational and deformational-and use these to survey the distribution of several often-neglected forms of sensing, including gravity sensing, flow sensing and proprioception. We discuss sensing of these kinds in sponges, ctenophores, placozoans, cnidarians and bilaterians. Reafference is ubiquitous, as ongoing action, especially whole-body motility, will almost inevitably influence the senses. Corollary discharge-a pathway or circuit by which an animal tracks its own actions and their reafferent consequences-is not a necessary feature of reafferent sensing but a later-evolving mechanism. We also argue for the importance of reafferent sensing to the evolution of the body-self, a form of organization that enables an animal to sense and act as a single unit. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Peter Godfrey-Smith
- School of History and Philosophy of Science, University of Sydney, New South Wales 2006, Australia
| | - Fred Keijzer
- Department of Theoretical Philosophy, University of Groningen, Groningen, The Netherlands
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42
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Chaudhary S, Lee SA, Li Y, Patel DS, Lu H. Graphical-model framework for automated annotation of cell identities in dense cellular images. eLife 2021; 10:e60321. [PMID: 33625357 PMCID: PMC8032398 DOI: 10.7554/elife.60321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers' experiences. Here, we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in Caenorhabditis elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.
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Affiliation(s)
- Shivesh Chaudhary
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Sol Ah Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Yueyi Li
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
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Gowda SBM, Salim S, Mohammad F. Anatomy and Neural Pathways Modulating Distinct Locomotor Behaviors in Drosophila Larva. BIOLOGY 2021; 10:90. [PMID: 33504061 PMCID: PMC7910854 DOI: 10.3390/biology10020090] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/07/2020] [Accepted: 12/30/2020] [Indexed: 11/17/2022]
Abstract
The control of movements is a fundamental feature shared by all animals. At the most basic level, simple movements are generated by coordinated neural activity and muscle contraction patterns that are controlled by the central nervous system. How behavioral responses to various sensory inputs are processed and integrated by the downstream neural network to produce flexible and adaptive behaviors remains an intense area of investigation in many laboratories. Due to recent advances in experimental techniques, many fundamental neural pathways underlying animal movements have now been elucidated. For example, while the role of motor neurons in locomotion has been studied in great detail, the roles of interneurons in animal movements in both basic and noxious environments have only recently been realized. However, the genetic and transmitter identities of many of these interneurons remains unclear. In this review, we provide an overview of the underlying circuitry and neural pathways required by Drosophila larvae to produce successful movements. By improving our understanding of locomotor circuitry in model systems such as Drosophila, we will have a better understanding of how neural circuits in organisms with different bodies and brains lead to distinct locomotion types at the organism level. The understanding of genetic and physiological components of these movements types also provides directions to understand movements in higher organisms.
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Affiliation(s)
| | | | - Farhan Mohammad
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Doha 34110, Qatar; (S.B.M.G.); (S.S.)
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Barwich AS. Imaging the living brain: An argument for ruthless reductionism from olfactory neurobiology. J Theor Biol 2021; 512:110560. [PMID: 33359241 DOI: 10.1016/j.jtbi.2020.110560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
Should theories of "higher-level" cognitive effects originate in "lower-level" molecular mechanisms? This paper supports reductionist explanations of sensory perception via molecular mechanisms in neurobiology. It shows that molecular and cellular mechanisms must constitute the material foundation to derive better theories and models for neuroscience. In support of "bottom-up theorizing", I explore the recent application of a new real-time molecular imaging technique (SCAPE microscopy) to mixture coding in olfaction. Seemingly emergent "higher-level" psychological effects in odor perception, irreducible to the physical stimulus, are linked back to underlying molecular mechanisms at the receptor level. The SCAPE study has notable theoretical impact. It provides a possible answer to the neurocomputational challenge in olfaction from combinatorial coding at the periphery: how does the brain discriminate different complex mixtures from widespread and overlapping receptor activation? The failure of previous reductionist structure-odor explanations is shown to reside in misconceptualizations of the critical causal elements involved. Causally fundamental features are not of parts independently of a mechanism. Components and their relevant features are units via their causal role within a mechanism. Here, new technologies allow revisiting our understanding of the ontology and levels of organization of a system.
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Affiliation(s)
- Ann-Sophie Barwich
- Indiana University Bloomington, History and Philosophy of Science and Medicine, Cognitive Science, Bloomington, IN, United States.
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Development of motor circuits: From neuronal stem cells and neuronal diversity to motor circuit assembly. Curr Top Dev Biol 2020; 142:409-442. [PMID: 33706923 DOI: 10.1016/bs.ctdb.2020.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this review, we discuss motor circuit assembly starting from neuronal stem cells. Until recently, studies of neuronal stem cells focused on how a relatively small pool of stem cells could give rise to a large diversity of different neuronal identities. Historically, neuronal identity has been assayed in embryos by gene expression, gross anatomical features, neurotransmitter expression, and physiological properties. However, these definitions of identity are largely unlinked to mature functional neuronal features relevant to motor circuits. Such mature neuronal features include presynaptic and postsynaptic partnerships, dendrite morphologies, as well as neuronal firing patterns and roles in behavior. This review focuses on recent work that links the specification of neuronal molecular identity in neuronal stem cells to mature, circuit-relevant identity specification. Specifically, these studies begin to address the question: to what extent are the decisions that occur during motor circuit assembly controlled by the same genetic information that generates diverse embryonic neuronal diversity? Much of the research addressing this question has been conducted using the Drosophila larval motor system. Here, we focus largely on Drosophila motor circuits and we point out parallels to other systems. And we highlight outstanding questions in the field. The main concepts addressed in this review are: (1) the description of temporal cohorts-novel units of developmental organization that link neuronal stem cell lineages to motor circuit configuration and (2) the discovery that temporal transcription factors expressed in neuronal stem cells control aspects of circuit assembly by controlling the size of temporal cohorts and influencing synaptic partner choice.
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Nanda S, Bhattacharjee S, Cox DN, Ascoli GA. Distinct Relations of Microtubules and Actin Filaments with Dendritic Architecture. iScience 2020; 23:101865. [PMID: 33319182 PMCID: PMC7725934 DOI: 10.1016/j.isci.2020.101865] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/09/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022] Open
Abstract
Microtubules (MTs) and F-actin (F-act) have long been recognized as key regulators of dendritic morphology. Nevertheless, precisely ascertaining their distinct influences on dendritic trees have been hampered until now by the lack of direct, arbor-wide cytoskeletal quantification. We pair live confocal imaging of fluorescently labeled dendritic arborization (da) neurons in Drosophila larvae with complete multi-signal neural tracing to separately measure MTs and F-act. We demonstrate that dendritic arbor length is highly interrelated with local MT quantity, whereas local F-act enrichment is associated with dendritic branching. Computational simulation of arbor structure solely constrained by experimentally observed subcellular distributions of these cytoskeletal components generated synthetic morphological and molecular patterns statistically equivalent to those of real da neurons, corroborating the efficacy of local MT and F-act in describing dendritic architecture. The analysis and modeling outcomes hold true for the simplest (class I), most complex (class IV), and genetically altered (Formin3 overexpression) da neuron types.
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Affiliation(s)
- Sumit Nanda
- Center for Neural Informatics, Structures, & Plasticity and Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA 22030, USA
| | | | - Daniel N. Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA 30303, USA
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Structures, & Plasticity and Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA 22030, USA
- Bioengineering Department, Volgenau School of Engineering, George Mason University, Fairfax, VA 22032, USA
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47
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Marcovich I, Holt JR. Evolution and function of Tmc genes in mammalian hearing. CURRENT OPINION IN PHYSIOLOGY 2020. [DOI: 10.1016/j.cophys.2020.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Eschbach C, Zlatic M. Useful road maps: studying Drosophila larva's central nervous system with the help of connectomics. Curr Opin Neurobiol 2020; 65:129-137. [PMID: 33242722 PMCID: PMC7773133 DOI: 10.1016/j.conb.2020.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/21/2020] [Accepted: 09/24/2020] [Indexed: 12/16/2022]
Abstract
The larva of Drosophila melanogaster is emerging as a powerful model system for comprehensive brain-wide understanding of the circuit implementation of neural computations. With an unprecedented amount of tools in hand, including synaptic-resolution connectomics, whole-brain imaging, and genetic tools for selective targeting of single neuron types, it is possible to dissect which circuits and computations are at work behind behaviors that have an interesting level of complexity. Here we present some of the recent advances regarding multisensory integration, learning, and action selection in Drosophila larva.
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Affiliation(s)
- Claire Eschbach
- Department of Zoology, University of Cambridge, United Kingdom.
| | - Marta Zlatic
- Department of Zoology, University of Cambridge, United Kingdom; MRC Laboratory of Molecular Biology, United Kingdom.
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Ferreira Castro A, Baltruschat L, Stürner T, Bahrami A, Jedlicka P, Tavosanis G, Cuntz H. Achieving functional neuronal dendrite structure through sequential stochastic growth and retraction. eLife 2020; 9:e60920. [PMID: 33241995 PMCID: PMC7837678 DOI: 10.7554/elife.60920] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/15/2020] [Indexed: 02/06/2023] Open
Abstract
Class I ventral posterior dendritic arborisation (c1vpda) proprioceptive sensory neurons respond to contractions in the Drosophila larval body wall during crawling. Their dendritic branches run along the direction of contraction, possibly a functional requirement to maximise membrane curvature during crawling contractions. Although the molecular machinery of dendritic patterning in c1vpda has been extensively studied, the process leading to the precise elaboration of their comb-like shapes remains elusive. Here, to link dendrite shape with its proprioceptive role, we performed long-term, non-invasive, in vivo time-lapse imaging of c1vpda embryonic and larval morphogenesis to reveal a sequence of differentiation stages. We combined computer models and dendritic branch dynamics tracking to propose that distinct sequential phases of stochastic growth and retraction achieve efficient dendritic trees both in terms of wire and function. Our study shows how dendrite growth balances structure-function requirements, shedding new light on general principles of self-organisation in functionally specialised dendrites.
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Affiliation(s)
- André Ferreira Castro
- Frankfurt Institute for Advanced StudiesFrankfurt am MainGermany
- Ernst Strüngmann Institute (ESI) for Neuroscience in cooperation with Max Planck SocietyFrankfurt am MainGermany
- Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | | | - Tomke Stürner
- Center for Neurodegenerative Diseases (DZNE)BonnGermany
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | | | - Peter Jedlicka
- Frankfurt Institute for Advanced StudiesFrankfurt am MainGermany
- Faculty of Medicine, ICAR3R – Interdisciplinary Centre for 3Rs in Animal Research, Justus Liebig University GiessenGiessenGermany
- Neuroscience Center, Institute of Clinical Neuroanatomy, Goethe UniversityFrankfurt am MainGermany
| | - Gaia Tavosanis
- Center for Neurodegenerative Diseases (DZNE)BonnGermany
- LIMES Institute, University of BonnBonnGermany
| | - Hermann Cuntz
- Frankfurt Institute for Advanced StudiesFrankfurt am MainGermany
- Ernst Strüngmann Institute (ESI) for Neuroscience in cooperation with Max Planck SocietyFrankfurt am MainGermany
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50
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Mishra S, van Rees WM, Mahadevan L. Coordinated crawling via reinforcement learning. J R Soc Interface 2020; 17:20200198. [PMID: 32842883 PMCID: PMC7482564 DOI: 10.1098/rsif.2020.0198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/27/2020] [Indexed: 11/12/2022] Open
Abstract
Rectilinear crawling locomotion is a primitive and common mode of locomotion in slender soft-bodied animals. It requires coordinated contractions that propagate along a body that interacts frictionally with its environment. We propose a simple approach to understand how this coordination arises in a neuromechanical model of a segmented, soft-bodied crawler via an iterative process that might have both biological antecedents and technological relevance. Using a simple reinforcement learning algorithm, we show that an initial all-to-all neural coupling converges to a simple nearest-neighbour neural wiring that allows the crawler to move forward using a localized wave of contraction that is qualitatively similar to what is observed in Drosophila melanogaster larvae and used in many biomimetic solutions. The resulting solution is a function of how we weight gait regularization in the reward, with a trade-off between speed and robustness to proprioceptive noise. Overall, our results, which embed the brain-body-environment triad in a learning scheme, have relevance for soft robotics while shedding light on the evolution and development of locomotion.
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Affiliation(s)
- Shruti Mishra
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Wim M. van Rees
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - L. Mahadevan
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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