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Ray A, Gordus A. Nonlinear integration of sensory and motor inputs by a single neuron in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.05.647390. [PMID: 40236064 PMCID: PMC11996571 DOI: 10.1101/2025.04.05.647390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Context is important for sensory integration. Rather than simply considering sensory information independently, the brain integrates this information to inform behavior, however identifying this property at the single-neuron level is not trivial. In Caenorhabditis elegans , the paired interneurons AIBL and AIBR (AIB) have a compartmentalized organization of presynapses along its singular process. Sensory and sensory interneurons primarily synapse along the proximal process, while motor and motor interneurons synapse along the distal process. Since this neuron has graded potentials, the simplest model for AIB integration is simply a convolution of its presynaptic inputs. Through a series of experiments to manipulate sensory and motor input onto AIB, we find that while AIB activity is primarily a convolution of motor inputs, its sensory responses are not integrated independently. Instead, the gain in sensory input is a function of the temporal dynamics of motor input. Sensory information is reinforced when it matches the expected behavioral response. We find this property is also observed in other whole-brain datasets. Context-dependent behavioral responses to sensory input is well-documented. Here, we show this property can be localized to single neurons in the worm nervous system. This integration property likely plays an important role in context-dependent decision-making, as well as the highly variable dynamics of the worm nervous system.
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Philbrook A, O’Donnell MP, Grunenkovaite L, Sengupta P. Cilia structure and intraflagellar transport differentially regulate sensory response dynamics within and between C. elegans chemosensory neurons. PLoS Biol 2024; 22:e3002892. [PMID: 39591402 PMCID: PMC11593760 DOI: 10.1371/journal.pbio.3002892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 10/10/2024] [Indexed: 11/28/2024] Open
Abstract
Sensory neurons contain morphologically diverse primary cilia that are built by intraflagellar transport (IFT) and house sensory signaling molecules. Since both ciliary structural and signaling proteins are trafficked via IFT, it has been challenging to decouple the contributions of IFT and cilia structure to neuronal responses. By acutely inhibiting IFT without altering cilia structure and vice versa, here we describe the differential roles of ciliary trafficking and sensory ending morphology in shaping chemosensory responses in Caenorhabditis elegans. We show that a minimum cilium length but not continuous IFT is necessary for a subset of responses in the ASH nociceptive neurons. In contrast, neither cilia nor continuous IFT are necessary for odorant responses in the AWA olfactory neurons. Instead, continuous IFT differentially modulates response dynamics in AWA. Upon acute inhibition of IFT, cilia-destined odorant receptors are shunted to ectopic branches emanating from the AWA cilia base. Spatial segregation of receptors in these branches from a cilia-restricted regulatory kinase results in odorant desensitization defects, highlighting the importance of precise organization of signaling molecules at sensory endings in regulating response dynamics. We also find that adaptation of AWA responses upon repeated exposure to an odorant is mediated by IFT-driven removal of its cognate receptor, whereas adaptation to a second odorant is regulated via IFT-independent mechanisms. Our results reveal unexpected complexity in the contribution of IFT and cilia organization to the regulation of responses even within a single chemosensory neuron type and establish a critical role for these processes in the precise modulation of olfactory behaviors.
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Affiliation(s)
- Alison Philbrook
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael P. O’Donnell
- Department of Molecular, Cellular, and Developmental Biology, Yale University, Connecticut, United States of America
| | - Laura Grunenkovaite
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
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Liu J, Bonnard E, Scholz M. Adapting and optimizing GCaMP8f for use in Caenorhabditis elegans. Genetics 2024; 228:iyae125. [PMID: 39074213 PMCID: PMC11457936 DOI: 10.1093/genetics/iyae125] [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: 06/10/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024] Open
Abstract
Improved genetically encoded calcium indicators (GECIs) are essential for capturing intracellular dynamics of both muscle and neurons. A novel set of GECIs with ultrafast kinetics and high sensitivity was recently reported by Zhang et al. (2023). While these indicators, called jGCaMP8, were demonstrated to work in Drosophila and mice, data for Caenorhabditis elegans were not reported. Here, we present an optimized construct for C. elegans and use this to generate several strains expressing GCaMP8f (fast variant of the indicator). Utilizing the myo-2 promoter, we compare pharyngeal muscle activity measured with GCaMP7f and GCaMP8f and find that GCaMP8f is brighter upon binding to calcium, shows faster kinetics, and is not disruptive to the intrinsic contraction dynamics of the pharynx. Additionally, we validate its application for detecting neuronal activity in touch receptor neurons which reveals robust calcium transients even at small stimulus amplitudes. As such, we establish GCaMP8f as a potent tool for C. elegans research which is capable of extracting fast calcium dynamics at very low magnifications across multiple cell types.
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Affiliation(s)
- Jun Liu
- Max Planck Research Group Neural Information Flow, Max Planck Institute for Neurobiology of Behavior-caesar, Bonn 53175, Germany
| | - Elsa Bonnard
- Max Planck Research Group Neural Information Flow, Max Planck Institute for Neurobiology of Behavior-caesar, Bonn 53175, Germany
- International Max Planck Research School for Brain and Behavior, Bonn 53175, Germany
| | - Monika Scholz
- Max Planck Research Group Neural Information Flow, Max Planck Institute for Neurobiology of Behavior-caesar, Bonn 53175, Germany
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Xue W, Lei Z, Liu B, Guo H, Yan W, Jin YN, Yu YV. Olfactory dysfunction as an early pathogenic indicator in C. elegans models of Alzheimer's and polyglutamine diseases. Front Aging Neurosci 2024; 16:1462238. [PMID: 39411283 PMCID: PMC11473296 DOI: 10.3389/fnagi.2024.1462238] [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: 07/09/2024] [Accepted: 09/16/2024] [Indexed: 10/19/2024] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease and polyglutamine diseases are characterized by abnormal accumulation of misfolded proteins, leading to neuronal dysfunction and subsequent neuron death. However, there is a lack of studies that integrate molecular, morphological, and functional analyses in neurodegenerative models to fully characterize these time-dependent processes. In this study, we used C. elegans models expressing Aβ1-42 and polyglutamine to investigate early neuronal pathogenic features in olfactory neurons. Both models demonstrated significant reductions in odor sensitivity in AWB and AWC chemosensory neurons as early as day 1 of adulthood, while AWA chemosensory neurons showed no such decline, suggesting cell-type-specific early neuronal dysfunction. At the molecular level, Aβ1-42 or Q40 expression caused age-dependent protein aggregation and morphological changes in neurons. By day 6, both models displayed prominent protein aggregates in neuronal cell bodies and neurites. Notably, AWB neurons in both models showed significantly shortened cilia and increased instances of enlarged cilia as early as day 1 of adulthood. Furthermore, AWC neurons expressing Aβ1-42 displayed calcium signaling defects, with significantly reduced responses to odor stimuli on day 1, further supporting early behavioral dysfunction. In contrast, AWA neuron did not exhibit reduced calcium responses, consistent with the absence of detectable decreases in olfactory sensitivity in these neurons. These findings suggest that decreased calcium signaling and dysfunction in specific sensory neuron subtypes are early indicators of neurodegeneration in C. elegans, occurring prior to the formation of visible protein aggregates. We found that the ER unfolded protein response (UPR) is significantly activated in worms expressing Aβ1-42. Activation of the AMPK pathway alleviates olfactory defects and reduces fibrillar Aβ in these worms. This study underscores the use of C. elegans olfactory neurons as a model to elucidate mechanisms of proteostasis in neurodegenerative diseases and highlights the importance of integrated approaches.
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Affiliation(s)
- Weikang Xue
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ziyi Lei
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Bin Liu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hanxin Guo
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Weiyi Yan
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Youngnam N. Jin
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yanxun V. Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
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Thurgood P, Hawke A, Low LS, Borg A, Peter K, Baratchi S, Khoshmanesh K. Tube Oscillation Drives Transitory Vortices Across Microfluidic Barriers. SMALL METHODS 2024; 8:e2301427. [PMID: 38161266 DOI: 10.1002/smtd.202301427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Here, the generation of dynamic vortices across microscale barriers using the tube oscillation mechanism is demonstrated. Using a combination of high-speed imaging and computational flow dynamics, the cyclic formation, expansion, and collapse of vortices are studied. The dynamics of vortices across circular , triangular, and blade-shape barriers are investigated at different tube oscillation frequencies. The formation of an array of synchronous vortices across parallel blade-shaped barriers is demonstrated. The transient flows caused by these dynamic vortex arrays are harnessed for the rapid and efficient mixing of blood samples . A circular barrier scribed with a narrow orifice on its shoulder is used to facilitate the injection of liquid into the microfluidic channel, and its rapid mixing with the main flow through the dynamic vortices generated across the barrier. This approach facilitates the generation of vortices with desirable configurations, sizes, and dynamics in a highly controllable, programmable, and predictable manner while operating at low static flow rates.
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Affiliation(s)
- Peter Thurgood
- School of Engineering, RMIT University, Melbourne, VIC, 3000, Australia
| | - Adam Hawke
- School of Engineering, RMIT University, Melbourne, VIC, 3000, Australia
| | - Lee Sheer Low
- School of Engineering, RMIT University, Melbourne, VIC, 3000, Australia
| | - Aimee Borg
- School of Engineering, RMIT University, Melbourne, VIC, 3000, Australia
| | - Karlheinz Peter
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- Department of Cardiometabolic Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sara Baratchi
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- Department of Cardiometabolic Health, The University of Melbourne, Parkville, VIC, 3010, Australia
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Vaidehi Narayanan H, Xiang MY, Chen Y, Huang H, Roy S, Makkar H, Hoffmann A, Roy K. Direct observation correlates NFκB cRel in B cells with activating and terminating their proliferative program. Proc Natl Acad Sci U S A 2024; 121:e2309686121. [PMID: 39024115 PMCID: PMC11287273 DOI: 10.1073/pnas.2309686121] [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: 07/19/2023] [Accepted: 05/28/2024] [Indexed: 07/20/2024] Open
Abstract
Antibody responses require the proliferative expansion of B cells controlled by affinity-dependent signals. Yet, proliferative bursts are heterogeneous, varying between 0 and 8 divisions in response to the same stimulus. NFκB cRel is activated in response to immune stimulation in B cells and is genetically required for proliferation. Here, we asked whether proliferative heterogeneity is controlled by natural variations in cRel abundance. We developed a fluorescent reporter mTFP1-cRel for the direct observation of cRel in live proliferating B cells. We found that cRel is heterogeneously distributed among naïve B cells, which are enriched for high expressors in a heavy-tailed distribution. We found that high cRel expressors show faster activation of the proliferative program, but do not sustain it well, with population expansion decaying earlier. With a mathematical model of the molecular network, we showed that cRel heterogeneity arises from balancing positive feedback by autoregulation and negative feedback by its inhibitor IκBε, confirmed by mouse knockouts. Using live-cell fluorescence microscopy, we showed that increased cRel primes B cells for early proliferation via higher basal expression of the cell cycle driver cMyc. However, peak cMyc induction amplitude is constrained by incoherent feedforward regulation, decoding the fold change of cRel activity to terminate the proliferative burst. This results in a complex nonlinear, nonmonotonic relationship between cRel expression and the extent of proliferation. These findings emphasize the importance of direct observational studies to complement gene knockout results and to learn about quantitative relationships between biological processes and their key regulators in the context of natural variations.
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Affiliation(s)
- Haripriya Vaidehi Narayanan
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Mark Y. Xiang
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Yijia Chen
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Helen Huang
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Sukanya Roy
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT84112
| | - Himani Makkar
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT84112
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Koushik Roy
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT84112
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Haley JA, Chalasani SH. C. elegans foraging as a model for understanding the neuronal basis of decision-making. Cell Mol Life Sci 2024; 81:252. [PMID: 38849591 PMCID: PMC11335288 DOI: 10.1007/s00018-024-05223-1] [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: 12/14/2023] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 06/09/2024]
Abstract
Animals have evolved to seek, select, and exploit food sources in their environment. Collectively termed foraging, these ubiquitous behaviors are necessary for animal survival. As a foundation for understanding foraging, behavioral ecologists established early theoretical and mathematical frameworks which have been subsequently refined and supported by field and laboratory studies of foraging animals. These simple models sought to explain how animals decide which strategies to employ when locating food, what food items to consume, and when to explore the environment for new food sources. These foraging decisions involve integration of prior experience with multimodal sensory information about the animal's current environment and internal state. We suggest that the nematode Caenorhabditis elegans is well-suited for a high-resolution analysis of complex goal-oriented behaviors such as foraging. We focus our discussion on behavioral studies highlighting C. elegans foraging on bacteria and summarize what is known about the underlying neuronal and molecular pathways. Broadly, we suggest that this simple model system can provide a mechanistic understanding of decision-making and present additional avenues for advancing our understanding of complex behavioral processes.
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Affiliation(s)
- Jessica A Haley
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Sreekanth H Chalasani
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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8
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Banse SA, Jarrett CM, Robinson KJ, Blue BW, Shaw EL, Phillips PC. The egg-counter: a novel microfluidic platform for characterization of Caenorhabditis elegans egg-laying. LAB ON A CHIP 2024; 24:2975-2986. [PMID: 38738514 PMCID: PMC11131562 DOI: 10.1039/d3lc01073b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/20/2024] [Indexed: 05/14/2024]
Abstract
Reproduction is a fundamental process that shapes the demography of every living organism yet is often difficult to assess with high precision in animals that produce large numbers of offspring. Here, we present a novel microfluidic research platform for studying Caenorhabditis elegans' egg-laying. The platform provides higher throughput than traditional solid-media behavioral assays while providing a very high degree of temporal resolution. Additionally, the environmental control enabled by microfluidic animal husbandry allows for experimental perturbations difficult to achieve with solid-media assays. We demonstrate the platform's utility by characterizing C. elegans egg-laying behavior at two commonly used temperatures, 15 and 20 °C. As expected, we observed a delayed onset of egg-laying at 15 °C degrees, consistent with published temperature effects on development rate. Additionally, as seen in solid media studies, egg laying output was higher under the canonical 20 °C conditions. While we validated the Egg-Counter with a study of temperature effects in wild-type animals, the platform is highly adaptable to any nematode egg-laying research where throughput or environmental control needs to be maximized without sacrificing temporal resolution.
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Affiliation(s)
- Stephen A Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Cody M Jarrett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Kristin J Robinson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Benjamin W Blue
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Emily L Shaw
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
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Raghuram V, Datye AD, Fried SI, Timko BP. Transparent and Conformal Microcoil Arrays for Spatially Selective Neuronal Activation. DEVICE 2024; 2:100290. [PMID: 39184953 PMCID: PMC11343507 DOI: 10.1016/j.device.2024.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Micromagnetic stimulation (μMS) using small, implantable microcoils is a promising method for achieving neuronal activation with high spatial resolution and low toxicity. Herein, we report a microcoil array for localized activation of cortical neurons and retinal ganglion cells. We developed a computational model to relate the electric field gradient (activating function) to the geometry and arrangement of microcoils, and selected a design that produced an anisotropic region of activation <50 μm wide. The device was comprised of an SU-8/Cu/SU-8 tri-layer structure, which was flexible, transparent and conformal and featured four individually-addressable microcoils. Interfaced with cortex or retina explants from GCaMP6-expressing mice, we observed that individual neurons localized within 40 μm of a microcoil tip could be activated repeatedly and in a dose- (power-) dependent fashion. These results demonstrate the potential of μMS devices for brain-machine interfaces and could enable routes toward bioelectronic therapies including prosthetic vision devices.
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Affiliation(s)
- Vineeth Raghuram
- Dept. of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Boston Veterans Affairs Healthcare System, Boston, MA 02130, USA
- Dept. of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Aditya D. Datye
- Dept. of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Shelley I. Fried
- Dept. of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Boston Veterans Affairs Healthcare System, Boston, MA 02130, USA
- Dept. of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Brian P. Timko
- Dept. of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Lead Contact
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Lee SA, Cho Y, Schafer WR, Lu H. Dynamic temperature control in microfluidics for in vivo imaging of cold-sensing in C. elegans. Biophys J 2024; 123:947-956. [PMID: 38449311 PMCID: PMC11052694 DOI: 10.1016/j.bpj.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/26/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024] Open
Abstract
The ability to perceive temperature is crucial for most animals. It enables them to maintain their body temperature and swiftly react to noxiously cold or hot objects. Caenorhabditis elegans is a powerful genetic model for the study of thermosensation as its simple nervous system is well characterized and its transparent body is suited for in vivo functional imaging of neurons. The behavior triggered by experience-dependent thermosensation has been well studied in C. elegans under temperature-gradient environments. However, how C. elegans senses temperature via its nervous system is not well understood due to the limitations of currently available technologies. One major bottleneck is the difficulty in creating fast temperature changes, especially cold stimuli. Here, we developed a microfluidic-based platform that allowed the in vivo functional imaging of C. elegans responding to well-controlled temporally varying temperature stimulation by rapidly switching fluid streams at different temperatures. We used computational models to enable rational design and optimization of experimental conditions. We validated the design and utility of our system with studies of the functional role of thermosensory neurons. We showed that the responses of PVD polymodal nociceptor neurons observed in previous studies can be recapitulated. Further, we highlighted how this platform may be used to dissect neuronal circuits with an example of activity recording in PVC interneurons. Both of these neuron types show sensitization phenotypes. We envision that both the engineered system and the findings in this work will spur further studies of molecular and cellular mechanisms underlying cold-sensing through the nervous system.
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Affiliation(s)
- Sol Ah Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta Georgia
| | - Yongmin Cho
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta Georgia
| | - William R Schafer
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta Georgia.
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Bottom-Tanzer S, Corella S, Meyer J, Sommer M, Bolaños L, Murphy T, Quiñones S, Heiney S, Shtrahman M, Whalen M, Oren R, Higley MJ, Cardin JA, Noubary F, Armbruster M, Dulla C. Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model. Cereb Cortex 2024; 34:bhae038. [PMID: 38365273 PMCID: PMC11486687 DOI: 10.1093/cercor/bhae038] [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: 10/16/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Traumatic brain injury (TBI) is the leading cause of death in young people and can cause cognitive and motor dysfunction and disruptions in functional connectivity between brain regions. In human TBI patients and rodent models of TBI, functional connectivity is decreased after injury. Recovery of connectivity after TBI is associated with improved cognition and memory, suggesting an important link between connectivity and functional outcome. We examined widespread alterations in functional connectivity following TBI using simultaneous widefield mesoscale GCaMP7c calcium imaging and electrocorticography (ECoG) in mice injured using the controlled cortical impact (CCI) model of TBI. Combining CCI with widefield cortical imaging provides us with unprecedented access to characterize network connectivity changes throughout the entire injured cortex over time. Our data demonstrate that CCI profoundly disrupts functional connectivity immediately after injury, followed by partial recovery over 3 weeks. Examining discrete periods of locomotion and stillness reveals that CCI alters functional connectivity and reduces theta power only during periods of behavioral stillness. Together, these findings demonstrate that TBI causes dynamic, behavioral state-dependent changes in functional connectivity and ECoG activity across the cortex.
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Affiliation(s)
- Samantha Bottom-Tanzer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
- MD/PhD Program, Tufts University School of Medicine, Boston, MA 02111, United States
- Neuroscience Program, Tufts Graduate School of Biomedical Sciences, Boston, MA 02111, United States
| | - Sofia Corella
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
- MD/PhD Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
| | - Jochen Meyer
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mary Sommer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
| | - Luis Bolaños
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Timothy Murphy
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sadi Quiñones
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
- Neuroscience Program, Tufts Graduate School of Biomedical Sciences, Boston, MA 02111, United States
| | - Shane Heiney
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, United States
| | - Matthew Shtrahman
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, United States
| | - Michael Whalen
- Department of Pediatrics, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115, United States
| | - Rachel Oren
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, United States
| | - Michael J Higley
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States
| | - Jessica A Cardin
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States
| | - Farzad Noubary
- Department of Health Sciences, Northeastern University, Boston, MA 02115, United States
| | - Moritz Armbruster
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
| | - Chris Dulla
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
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12
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Pu L, Wang J, Lu Q, Nilsson L, Philbrook A, Pandey A, Zhao L, Schendel RV, Koh A, Peres TV, Hashi WH, Myint SL, Williams C, Gilthorpe JD, Wai SN, Brown A, Tijsterman M, Sengupta P, Henriksson J, Chen C. Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans. Nat Commun 2023; 14:8410. [PMID: 38110404 PMCID: PMC10728192 DOI: 10.1038/s41467-023-44177-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
G protein-coupled receptors (GPCRs) mediate responses to various extracellular and intracellular cues. However, the large number of GPCR genes and their substantial functional redundancy make it challenging to systematically dissect GPCR functions in vivo. Here, we employ a CRISPR/Cas9-based approach, disrupting 1654 GPCR-encoding genes in 284 strains and mutating 152 neuropeptide-encoding genes in 38 strains in C. elegans. These two mutant libraries enable effective deorphanization of chemoreceptors, and characterization of receptors for neuropeptides in various cellular processes. Mutating a set of closely related GPCRs in a single strain permits the assignment of functions to GPCRs with functional redundancy. Our analyses identify a neuropeptide that interacts with three receptors in hypoxia-evoked locomotory responses, unveil a collection of regulators in pathogen-induced immune responses, and define receptors for the volatile food-related odorants. These results establish our GPCR and neuropeptide mutant libraries as valuable resources for the C. elegans community to expedite studies of GPCR signaling in multiple contexts.
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Affiliation(s)
- Longjun Pu
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Jing Wang
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Qiongxuan Lu
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Lars Nilsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Alison Philbrook
- Department of Biology, MS 008, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Anjali Pandey
- Department of Biology, MS 008, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Lina Zhao
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan Koh
- MRC Laboratory of Medical Sciences, London, W12 0HS, UK
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - Tanara V Peres
- MRC Laboratory of Medical Sciences, London, W12 0HS, UK
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - Weheliye H Hashi
- MRC Laboratory of Medical Sciences, London, W12 0HS, UK
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - Si Lhyam Myint
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Chloe Williams
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | | | - Sun Nyunt Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Andre Brown
- MRC Laboratory of Medical Sciences, London, W12 0HS, UK
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Piali Sengupta
- Department of Biology, MS 008, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Johan Henriksson
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
- Integrated Science Lab (Icelab), Umeå University, Umeå, Sweden.
| | - Changchun Chen
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
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13
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Banse SA, Jarrett CM, Robinson KJ, Blue BW, Shaw EL, Phillips PC. The Egg-Counter: A novel microfluidic platform for characterization of Caenorhabditis elegans egg-laying. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555781. [PMID: 37732270 PMCID: PMC10508723 DOI: 10.1101/2023.09.01.555781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Reproduction is a fundamental process that shapes the demography of every living organism yet is often difficult to assess with high precision in animals that produce large numbers of offspring. Here, we present a novel microfluidic research platform for studying Caenorhabditis elegans' egg-laying. The platform provides higher throughput than traditional solid-media assays while providing a very high degree of temporal resolution. Additionally, the environmental control enabled by microfluidic animal husbandry allows for experimental perturbations difficult to achieve with solid-media assays. We demonstrate the platform's utility by characterizing C. elegans egg-laying behavior at two commonly used temperatures, 15 and 20°C. As expected, we observed a delayed onset of egg-laying at 15°C degrees, consistent with published temperature effects on development rate. Additionally, as seen in solid media studies, egg laying output was higher under the canonical 20°C conditions. While we validated the Egg-Counter with a study of temperature effects in wild-type animals, the platform is highly adaptable to any nematode egg-laying research where throughput or environmental control needs to be maximized without sacrificing temporal resolution.
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Affiliation(s)
- Stephen A. Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Cody M. Jarrett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Kristin J. Robinson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Benjamin W. Blue
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Emily L. Shaw
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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14
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Pritz C, Itskovits E, Bokman E, Ruach R, Gritsenko V, Nelken T, Menasherof M, Azulay A, Zaslaver A. Principles for coding associative memories in a compact neural network. eLife 2023; 12:e74434. [PMID: 37140557 PMCID: PMC10159626 DOI: 10.7554/elife.74434] [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: 10/04/2021] [Accepted: 03/08/2023] [Indexed: 05/05/2023] Open
Abstract
A major goal in neuroscience is to elucidate the principles by which memories are stored in a neural network. Here, we have systematically studied how four types of associative memories (short- and long-term memories, each as positive and negative associations) are encoded within the compact neural network of Caenorhabditis elegans worms. Interestingly, sensory neurons were primarily involved in coding short-term, but not long-term, memories, and individual sensory neurons could be assigned to coding either the conditioned stimulus or the experience valence (or both). Moreover, when considering the collective activity of the sensory neurons, the specific training experiences could be decoded. Interneurons integrated the modulated sensory inputs and a simple linear combination model identified the experience-specific modulated communication routes. The widely distributed memory suggests that integrated network plasticity, rather than changes to individual neurons, underlies the fine behavioral plasticity. This comprehensive study reveals basic memory-coding principles and highlights the central roles of sensory neurons in memory formation.
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Affiliation(s)
- Christian Pritz
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Eyal Itskovits
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Eduard Bokman
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Rotem Ruach
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Vladimir Gritsenko
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Tal Nelken
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Mai Menasherof
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Aharon Azulay
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Alon Zaslaver
- Department of Genetics, Silberman Institute for Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
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15
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Yuan H, Yuan W, Duan S, Jiao K, Zhang Q, Lim EG, Chen M, Zhao C, Pan P, Liu X, Song P. Microfluidic-Assisted Caenorhabditis elegans Sorting: Current Status and Future Prospects. CYBORG AND BIONIC SYSTEMS 2023; 4:0011. [PMID: 37287459 PMCID: PMC10243201 DOI: 10.34133/cbsystems.0011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/15/2023] [Indexed: 07/30/2023] Open
Abstract
Caenorhabditis elegans (C. elegans) has been a popular model organism for several decades since its first discovery of the huge research potential for modeling human diseases and genetics. Sorting is an important means of providing stage- or age-synchronized worm populations for many worm-based bioassays. However, conventional manual techniques for C. elegans sorting are tedious and inefficient, and commercial complex object parametric analyzer and sorter is too expensive and bulky for most laboratories. Recently, the development of lab-on-a-chip (microfluidics) technology has greatly facilitated C. elegans studies where large numbers of synchronized worm populations are required and advances of new designs, mechanisms, and automation algorithms. Most previous reviews have focused on the development of microfluidic devices but lacked the summaries and discussion of the biological research demands of C. elegans, and are hard to read for worm researchers. We aim to comprehensively review the up-to-date microfluidic-assisted C. elegans sorting developments from several angles to suit different background researchers, i.e., biologists and engineers. First, we highlighted the microfluidic C. elegans sorting devices' advantages and limitations compared to the conventional commercialized worm sorting tools. Second, to benefit the engineers, we reviewed the current devices from the perspectives of active or passive sorting, sorting strategies, target populations, and sorting criteria. Third, to benefit the biologists, we reviewed the contributions of sorting to biological research. We expect, by providing this comprehensive review, that each researcher from this multidisciplinary community can effectively find the needed information and, in turn, facilitate future research.
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Affiliation(s)
- Hang Yuan
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
| | - Wenwen Yuan
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Electrical and Electronic Engineering,
University of Liverpool, Liverpool, UK
| | - Sixuan Duan
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Electrical and Electronic Engineering,
University of Liverpool, Liverpool, UK
| | - Keran Jiao
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Chemistry,
Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Quan Zhang
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
| | - Eng Gee Lim
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Electrical and Electronic Engineering,
University of Liverpool, Liverpool, UK
| | - Min Chen
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Electrical and Electronic Engineering,
University of Liverpool, Liverpool, UK
| | - Chun Zhao
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Electrical and Electronic Engineering,
University of Liverpool, Liverpool, UK
| | - Peng Pan
- Department of Mechanical & Industrial Engineering,
University of Toronto, Toronto, Canada
| | - Xinyu Liu
- Department of Mechanical & Industrial Engineering,
University of Toronto, Toronto, Canada
| | - Pengfei Song
- School of Advanced Technology,
Xi'an Jiaotong - Liverpool University, Suzhou, China
- Department of Electrical and Electronic Engineering,
University of Liverpool, Liverpool, UK
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16
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Lin A, Qin S, Casademunt H, Wu M, Hung W, Cain G, Tan NZ, Valenzuela R, Lesanpezeshki L, Venkatachalam V, Pehlevan C, Zhen M, Samuel AD. Functional imaging and quantification of multineuronal olfactory responses in C. elegans. SCIENCE ADVANCES 2023; 9:eade1249. [PMID: 36857454 PMCID: PMC9977185 DOI: 10.1126/sciadv.ade1249] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/01/2023] [Indexed: 05/21/2023]
Abstract
Many animals perceive odorant molecules by collecting information from ensembles of olfactory neurons, where each neuron uses receptors that are tuned to recognize certain odorant molecules with different binding affinity. Olfactory systems are able, in principle, to detect and discriminate diverse odorants using combinatorial coding strategies. We have combined microfluidics and multineuronal imaging to study the ensemble-level olfactory representations at the sensory periphery of the nematode Caenorhabditis elegans. The collective activity of C. elegans chemosensory neurons reveals high-dimensional representations of olfactory information across a broad space of odorant molecules. We reveal diverse tuning properties and dose-response curves across chemosensory neurons and across odorants. We describe the unique contribution of each sensory neuron to an ensemble-level code for volatile odorants. We show that a natural stimuli, a set of nematode pheromones, are also encoded by the sensory ensemble. The integrated activity of the C. elegans chemosensory neurons contains sufficient information to robustly encode the intensity and identity of diverse chemical stimuli.
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Affiliation(s)
- Albert Lin
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Shanshan Qin
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Helena Casademunt
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Min Wu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Wesley Hung
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Gregory Cain
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nicolas Z. Tan
- Department of Physics, Northeastern University, Boston, MA, USA
| | | | - Leila Lesanpezeshki
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Cengiz Pehlevan
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Aravinthan D.T. Samuel
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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17
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Cheng D, Lee JS, Brown M, Ebert MS, McGrath PT, Tomioka M, Iino Y, Bargmann CI. Insulin/IGF signaling regulates presynaptic glutamate release in aversive olfactory learning. Cell Rep 2022; 41:111685. [DOI: 10.1016/j.celrep.2022.111685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/06/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
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18
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Sterin I, Santos AC, Park S. Neuronal Activity Reporters as Drug Screening Platforms. MICROMACHINES 2022; 13:1500. [PMID: 36144123 PMCID: PMC9504476 DOI: 10.3390/mi13091500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Understanding how neuronal activity changes and detecting such changes in both normal and disease conditions is of fundamental importance to the field of neuroscience. Neuronal activity plays important roles in the formation and function of both synapses and circuits, and dysregulation of these processes has been linked to a number of debilitating diseases such as autism, schizophrenia, and epilepsy. Despite advances in our understanding of synapse biology and in how it is altered in disease, the development of therapeutics for these diseases has not advanced apace. Many neuronal activity assays have been developed over the years using a variety of platforms and approaches, but major limitations persist. Current assays, such as fluorescence indicators are not designed to monitor neuronal activity over a long time, they are typically low-throughput or lack sensitivity. These are major barriers to the development of new therapies, as drug screening needs to be both high-throughput to screen through libraries of compounds, and longitudinal to detect any effects that may emerge after continued application of the drug. This review will cover existing assays for measuring neuronal activity and highlight a live-cell assay recently developed. This assay can be performed with easily accessible lab equipment, is both scalable and longitudinal, and can be combined with most other established methods.
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Affiliation(s)
- Igal Sterin
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ana C. Santos
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Sungjin Park
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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19
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Lawler DE, Albrecht DR. Monitoring neural activity during sleep/wake events in adult C. elegans by automated sleep detection and stimulation. STAR Protoc 2022; 3:101532. [PMID: 35834387 PMCID: PMC9293671 DOI: 10.1016/j.xpro.2022.101532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 11/20/2022] Open
Abstract
Sleep in adult C. elegans occurs spontaneously, making timing of individual sleep/wake state transitions unpredictable. This protocol presents a closed-loop system to automatically detect sleep state transitions, trigger stimulation, and record evoked neural responses. This allows users to assess functional consequences of behavioral states in an unbiased manner and identify state-dependent neuromodulation. This closed-loop system is flexible and can be configured to detect any visible events, such as behavior patterns or optical reporters, and measure corresponding evoked neural responses. For complete details on the use and execution of this protocol, please refer to Lawler et al. (2021). Protocol to assess neural activity changes between sleep and wake states in C. elegans Closed-loop system automatically detects sleep state and triggers neural stimulation Microfluidic arenas enable recording of freely moving behavior and neural responses Image analysis software extracts sleep-dependent neural changes
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Daniel E Lawler
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Dirk R Albrecht
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, USA; Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA.
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20
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Ruach R, Yellinek S, Itskovits E, Deshe N, Eliezer Y, Bokman E, Zaslaver A. A negative feedback loop in the GPCR pathway underlies efficient coding of external stimuli. Mol Syst Biol 2022; 18:e10514. [PMID: 36106925 PMCID: PMC9476886 DOI: 10.15252/msb.202110514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Efficient navigation based on chemical cues is an essential feature shared by all animals. These cues may be encountered in complex spatiotemporal patterns and with orders of magnitude varying intensities. Nevertheless, sensory neurons accurately extract the relevant information from such perplexing signals. Here, we show how a single sensory neuron in Caenorhabditis elegans animals can cell-autonomously encode complex stimulus patterns composed of instantaneous sharp changes and of slowly changing continuous gradients. This encoding relies on a simple negative feedback in the G-protein-coupled receptor (GPCR) signaling pathway in which TAX-6/Calcineurin plays a key role in mediating the feedback inhibition. This negative feedback supports several important coding features that underlie an efficient navigation strategy, including exact adaptation and adaptation to the magnitude of the gradient's first derivative. A simple mathematical model explains the fine neural dynamics of both wild-type and tax-6 mutant animals, further highlighting how the calcium-dependent activity of TAX-6/Calcineurin dictates GPCR inhibition and response dynamics. As GPCRs are ubiquitously expressed in all sensory neurons, this mechanism may be a general solution for efficient cell-autonomous coding of external stimuli.
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Affiliation(s)
- Rotem Ruach
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
| | - Shai Yellinek
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
| | - Eyal Itskovits
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
| | - Noa Deshe
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
| | - Yifat Eliezer
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
| | - Eduard Bokman
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
| | - Alon Zaslaver
- Department of Genetics, Silberman Institute of Life Science, Edmond J. Safra CampusThe Hebrew UniversityJerusalemIsrael
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21
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McLachlan IG, Kramer TS, Dua M, DiLoreto EM, Gomes MA, Dag U, Srinivasan J, Flavell SW. Diverse states and stimuli tune olfactory receptor expression levels to modulate food-seeking behavior. eLife 2022; 11:e79557. [PMID: 36044259 PMCID: PMC9433090 DOI: 10.7554/elife.79557] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/19/2022] [Indexed: 12/24/2022] Open
Abstract
Animals must weigh competing needs and states to generate adaptive behavioral responses to the environment. Sensorimotor circuits are thus tasked with integrating diverse external and internal cues relevant to these needs to generate context-appropriate behaviors. However, the mechanisms that underlie this integration are largely unknown. Here, we show that a wide range of states and stimuli converge upon a single Caenorhabditis elegans olfactory neuron to modulate food-seeking behavior. Using an unbiased ribotagging approach, we find that the expression of olfactory receptor genes in the AWA olfactory neuron is influenced by a wide array of states and stimuli, including feeding state, physiological stress, and recent sensory cues. We identify odorants that activate these state-dependent olfactory receptors and show that altered expression of these receptors influences food-seeking and foraging. Further, we dissect the molecular and neural circuit pathways through which external sensory information and internal nutritional state are integrated by AWA. This reveals a modular organization in which sensory and state-related signals arising from different cell types in the body converge on AWA and independently control chemoreceptor expression. The synthesis of these signals by AWA allows animals to generate sensorimotor responses that reflect the animal's overall state. Our findings suggest a general model in which sensory- and state-dependent transcriptional changes at the sensory periphery modulate animals' sensorimotor responses to meet their ongoing needs and states.
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Affiliation(s)
- Ian G McLachlan
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Talya S Kramer
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
- MIT Biology Graduate Program, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Malvika Dua
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Elizabeth M DiLoreto
- Department of Biology and Biotechnology, Worcester Polytechnic InstituteWorcesterUnited States
| | - Matthew A Gomes
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ugur Dag
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic InstituteWorcesterUnited States
| | - Steven W Flavell
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
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22
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Lagoy RC, Larsen E, Lawler D, White H, Albrecht DR. Microfluidic Devices for Behavioral Analysis, Microscopy, and Neuronal Imaging in Caenorhabditis elegans. Methods Mol Biol 2022; 2468:293-318. [PMID: 35320572 DOI: 10.1007/978-1-0716-2181-3_16] [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] [Indexed: 06/14/2023]
Abstract
Microfluidic devices offer several advantages for C. elegans research, particularly for presenting precise physical and chemical environments, immobilizing animals during imaging, quantifying behavior, and automating screens. However, challenges to their widespread adoption in the field include increased complexity over conventional methods, operational problems (such as clogging, leaks, and bubbles), difficulty in obtaining or fabricating devices, and the need to characterize biological results obtained from new assay formats. Here we describe the preparation and operation of simple, reusable microfluidic devices for quantifying behavioral responses to chemical patterns, and single-use devices to arrange animals for time-lapse microscopy and to measure neuronal activity. We focus on details that eliminate or reduce the frustrations commonly experienced by new users of microfluidic devices.
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Affiliation(s)
- Ross C Lagoy
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Eric Larsen
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Dan Lawler
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Hamilton White
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dirk R Albrecht
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA.
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23
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A single chemosensory GPCR is required for a concentration-dependent behavioral switching in C. elegans. Curr Biol 2021; 32:398-411.e4. [PMID: 34906353 DOI: 10.1016/j.cub.2021.11.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/15/2021] [Accepted: 11/12/2021] [Indexed: 12/19/2022]
Abstract
Animals detect and discriminate countless environmental chemicals for their well-being and survival. Although a single chemical can trigger opposing behavioral responses depending on its concentration, the mechanisms underlying such a concentration-dependent switching remain poorly understood. Here, we show that C. elegans exhibits either attraction or avoidance of the bacteria-derived volatile chemical dimethyl trisulfide (DMTS) depending on its concentration. This behavioral switching is mediated by two different types of chemosensory neurons, both of which express the DMTS-sensitive seven-transmembrane G protein-coupled receptor (GPCR) SRI-14. These two sensory neurons share downstream interneurons that process and translate DMTS signals via distinct glutamate receptors to generate the appropriate behavioral outcome. Thus, our results present one mechanism by which an animal connects two distinct types of chemosensory neurons detecting a common ligand to alternate downstream circuitry, thus efficiently switching between specific behavioral programs based on ligand concentration.
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24
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Sakelaris BG, Li Z, Sun J, Banerjee S, Booth V, Gourgou E. Modelling learning in C. elegans chemosensory and locomotive circuitry for T-maze navigation. Eur J Neurosci 2021; 55:354-376. [PMID: 34894022 PMCID: PMC9269982 DOI: 10.1111/ejn.15560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 11/11/2021] [Accepted: 11/21/2021] [Indexed: 11/30/2022]
Abstract
Recently, a new type of Caenorhabditis elegans associative learning was reported, where nematodes learn to reach a target arm in an empty T‐maze, after they have successfully located reward (food) in the same side arm of a similar, baited, training maze. Here, we present a simplified mathematical model of C. elegans chemosensory and locomotive circuitry that replicates C. elegans navigation in a T‐maze and predicts the underlying mechanisms generating maze learning. Based on known neural circuitry, the model circuit responds to food‐released chemical cues by modulating motor neuron activity that drives simulated locomotion. We show that, through modulation of interneuron activity, such a circuit can mediate maze learning by acquiring a turning bias, even after a single training session. Simulated nematode maze navigation during training conditions in food‐baited mazes and during testing conditions in empty mazes is validated by comparing simulated behaviour with new experimental video data, extracted through the implementation of a custom‐made maze tracking algorithm. Our work provides a mathematical framework for investigating the neural mechanisms underlying this novel learning behaviour in C. elegans. Model results predict neuronal components involved in maze and spatial learning and identify target neurons and potential neural mechanisms for future experimental investigations into this learning behaviour.
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Affiliation(s)
| | - Zongyu Li
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor
| | - Jiawei Sun
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor
| | - Shurjo Banerjee
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor
| | - Victoria Booth
- Department of Mathematics, University of Michigan, Ann Arbor.,Department of Anesthesiology, University of Michigan, Ann Arbor
| | - Eleni Gourgou
- Department of Mechanical Engineering, University of Michigan, Ann Arbor.,Institute of Gerontology, Medical School, University of Michigan, Ann Arbor
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25
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Lanza E, Di Rocco M, Schwartz S, Caprini D, Milanetti E, Ferrarese G, Lonardo MT, Pannone L, Ruocco G, Martinelli S, Folli V. C. elegans-based chemosensation strategy for the early detection of cancer metabolites in urine samples. Sci Rep 2021; 11:17133. [PMID: 34429473 PMCID: PMC8385061 DOI: 10.1038/s41598-021-96613-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023] Open
Abstract
Chemosensory receptors play a crucial role in distinguishing the wide range of volatile/soluble molecules by binding them with high accuracy. Chemosensation is the main sensory modality in organisms lacking long-range sensory mechanisms like vision/hearing. Despite its low number of sensory neurons, the nematode Caenorhabditis elegans possesses several chemosensory receptors, allowing it to detect about as many odorants as mammals. Here, we show that C. elegans displays attraction towards urine samples of women with breast cancer, avoiding control ones. Behavioral assays on animals lacking AWC sensory neurons demonstrate the relevance of these neurons in sensing cancer odorants: calcium imaging on AWC increases the accuracy of the discrimination (97.22%). Also, chemotaxis assays on animals lacking GPCRs expressed in AWC allow to identify receptors involved in binding cancer metabolites, suggesting that an alteration of a few metabolites is sufficient for the cancer discriminating behavior of C. elegans, which may help identify a fundamental fingerprint of breast cancer.
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Affiliation(s)
- Enrico Lanza
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy
| | - Martina Di Rocco
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy ,grid.416651.10000 0000 9120 6856Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy ,grid.7841.aDepartment of Biochemical Science “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Silvia Schwartz
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy
| | - Davide Caprini
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy
| | - Edoardo Milanetti
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy ,grid.7841.aDepartment of Physics, Sapienza Università di Roma, Rome, 00185 Italy
| | - Giuseppe Ferrarese
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy
| | | | - Luca Pannone
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, RM 00165 Italy
| | - Giancarlo Ruocco
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy
| | - Simone Martinelli
- grid.416651.10000 0000 9120 6856Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Viola Folli
- grid.25786.3e0000 0004 1764 2907Istituto Italiano di Tecnologia, Center for Life Nano Science, Rome, 00161 Italy
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26
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Caprini D, Schwartz S, Lanza E, Milanetti E, Lucente V, Ferrarese G, Chiodo L, Nicoletti M, Folli V. A Shearless Microfluidic Device Detects a Role in Mechanosensitivity for AWC ON Neuron in Caenorhabditis elegans. Adv Biol (Weinh) 2021; 5:e2100927. [PMID: 34423577 DOI: 10.1002/adbi.202100927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/03/2021] [Indexed: 11/08/2022]
Abstract
AWC olfactory neurons are fundamental for chemotaxis toward volatile attractants in Caenorhabditis elegans. Here, it is shown that AWCON responds not only to chemicals but also to mechanical stimuli caused by fluid flow changes in a microfluidic device. The dynamics of calcium events are correlated with the stimulus amplitude. It is further shown that the mechanosensitivity of AWCON neurons has an intrinsic nature rather than a synaptic origin, and the calcium transient response is mediated by TAX-4 cGMP-gated cation channel, suggesting the involvement of one or more "odorant" receptors in AWCON mechano-transduction. In many cases, the responses show plateau properties resembling bistable calcium dynamics where neurons can switch from one stable state to the other. To investigate the unprecedentedly observed mechanosensitivity of AWCON neurons, a novel microfluidic device is designed to minimize the fluid shear flow in the arena hosting the nematodes. Animals in this device show reduced neuronal activation of AWCON neurons. The results observed indicate that the tangential component of the mechanical stress is the main contributor to the mechanosensitivity of AWCON . Furthermore, the microfluidic platform, integrating shearless perfusion and calcium imaging, provides a novel and more controlled solution for in vivo analysis both in micro-organisms and cultured cells.
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Affiliation(s)
- Davide Caprini
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy
| | - Silvia Schwartz
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy
| | - Enrico Lanza
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy
| | - Edoardo Milanetti
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy.,Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, 00185, Italy
| | - Valeria Lucente
- CREST OPTICS S.p.A., Via di Torre Rossa 66, Rome, 00165, Italy
| | - Giuseppe Ferrarese
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy.,Department of Engineering, Campus Bio-Medico University, Via Álvaro del Portillo 21, Rome, 00128, Italy
| | - Letizia Chiodo
- Department of Engineering, Campus Bio-Medico University, Via Álvaro del Portillo 21, Rome, 00128, Italy
| | - Martina Nicoletti
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy.,Department of Engineering, Campus Bio-Medico University, Via Álvaro del Portillo 21, Rome, 00128, Italy
| | - Viola Folli
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome, 00161, Italy
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27
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Zhou X, Belavek KJ, Miller EW. Origins of Ca 2+ Imaging with Fluorescent Indicators. Biochemistry 2021; 60:3547-3554. [PMID: 34251789 DOI: 10.1021/acs.biochem.1c00350] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In 1980, Roger Tsien published a paper, in this journal [Tsien, R. Y. (1980) Biochemistry, 19 (11), 2396], titled "New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis, and properties of prototype structures". These new buffers included 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid, or BAPTA, which is still widely used today. And so, the world was set alight with new ways in which to visualize Ca2+. The ability to watch fluctuations in intracellular Ca2+ revolutionized the life sciences, although the fluorescent indicators used today, particularly in neurobiology, no longer rely exclusively on BAPTA but on genetically encoded fluorescent Ca2+ indicators. In this Perspective, we reflect on the origins of Ca2+ imaging with a special focus on the contributions made by Roger Tsien, from the early concept of selective Ca2+ binding described in Biochemistry to optical Ca2+ indicators based on chemically synthesized fluorophores to genetically encoded fluorescent Ca2+ indicators.
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28
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Emmons SW, Yemini E, Zimmer M. Methods for analyzing neuronal structure and activity in Caenorhabditis elegans. Genetics 2021; 218:6303616. [PMID: 34151952 DOI: 10.1093/genetics/iyab072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
The model research animal Caenorhabditis elegans has unique properties making it particularly advantageous for studies of the nervous system. The nervous system is composed of a stereotyped complement of neurons connected in a consistent manner. Here, we describe methods for studying nervous system structure and function. The transparency of the animal makes it possible to visualize and identify neurons in living animals with fluorescent probes. These methods have been recently enhanced for the efficient use of neuron-specific reporter genes. Because of its simple structure, for a number of years, C. elegans has been at the forefront of connectomic studies defining synaptic connectivity by electron microscopy. This field is burgeoning with new, more powerful techniques, and recommended up-to-date methods are here described that encourage the possibility of new work in C. elegans. Fluorescent probes for single synapses and synaptic connections have allowed verification of the EM reconstructions and for experimental approaches to synapse formation. Advances in microscopy and in fluorescent reporters sensitive to Ca2+ levels have opened the way to observing activity within single neurons across the entire nervous system.
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Affiliation(s)
- Scott W Emmons
- Department of Genetics and Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 1041, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Manuel Zimmer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria and.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
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29
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Han X, Su Y, White H, O'Neill KM, Morgan NY, Christensen R, Potarazu D, Vishwasrao HD, Xu S, Sun Y, Huang SY, Moyle MW, Dai Q, Pommier Y, Giniger E, Albrecht DR, Probst R, Shroff H. A polymer index-matched to water enables diverse applications in fluorescence microscopy. LAB ON A CHIP 2021; 21:1549-1562. [PMID: 33629685 PMCID: PMC8058278 DOI: 10.1039/d0lc01233e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.
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Affiliation(s)
- Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hamilton White
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kate M O'Neill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA and Institute for Physical Science and Technology, University of Maryland College Park, College Park, MD 20742, USA
| | - Nicole Y Morgan
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Deepika Potarazu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen Xu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shar-Yin Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dirk R Albrecht
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Roland Probst
- ACUITYnano, Innovation in Biomedical Imaging, North Bethesda, MD 20850, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA and Marine Biological Laboratory Fellows Program, Woods Hole, MA 02543, USA
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30
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Hino T, Hirai S, Ishihara T, Fujiwara M. EGL-4/PKG regulates the role of an interneuron in a chemotaxis circuit of C. elegans through mediating integration of sensory signals. Genes Cells 2021; 26:411-425. [PMID: 33817914 DOI: 10.1111/gtc.12849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Interneurons, innervated by multiple sensory neurons, need to integrate information from these sensory neurons and respond to sensory stimuli adequately. Mechanisms how sensory information is integrated to form responses of interneurons are not fully understood. In Caenorhabditis elegans, loss-of-function mutations of egl-4, which encodes a cGMP-dependent protein kinase (PKG), cause a defect in chemotaxis to odorants. Our genetic and imaging analyses revealed that the response property of AIY interneuron to an odorant is reversed in the egl-4 mutant, while the responses of two upstream olfactory neurons, AWA and AWC, are largely unchanged. Cell- ablation experiments show that AIY in the egl-4 mutant functions to suppress chemotaxis. Furthermore, the reversal of AIY response occurs only in the presence of sensory signals from both AWA and AWC. These results suggest that sensory signals are inadequately integrated in the egl-4 mutant. We also show that egl-4 expression in AWA and another sensory neuron prevents the reversed AIY response and restores chemotaxis in the egl-4 mutants. We propose that EGL-4/PKG, by suppressing aberrant integration of signals from olfactory neurons, converts the response property of an interneuron to olfactory stimuli and maintains the role of the interneuron in the circuit to execute chemotactic behavior.
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Affiliation(s)
- Takahiro Hino
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Shota Hirai
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Takeshi Ishihara
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Manabi Fujiwara
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
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31
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Ferkey DM, Sengupta P, L’Etoile ND. Chemosensory signal transduction in Caenorhabditis elegans. Genetics 2021; 217:iyab004. [PMID: 33693646 PMCID: PMC8045692 DOI: 10.1093/genetics/iyab004] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Chemosensory neurons translate perception of external chemical cues, including odorants, tastants, and pheromones, into information that drives attraction or avoidance motor programs. In the laboratory, robust behavioral assays, coupled with powerful genetic, molecular and optical tools, have made Caenorhabditis elegans an ideal experimental system in which to dissect the contributions of individual genes and neurons to ethologically relevant chemosensory behaviors. Here, we review current knowledge of the neurons, signal transduction molecules and regulatory mechanisms that underlie the response of C. elegans to chemicals, including pheromones. The majority of identified molecules and pathways share remarkable homology with sensory mechanisms in other organisms. With the development of new tools and technologies, we anticipate that continued study of chemosensory signal transduction and processing in C. elegans will yield additional new insights into the mechanisms by which this animal is able to detect and discriminate among thousands of chemical cues with a limited sensory neuron repertoire.
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Affiliation(s)
- Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Noelle D L’Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
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32
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Automated Functional Screening for Modulators of Optogenetically Activated Neural Responses in Living Organisms. Methods Mol Biol 2021. [PMID: 32865748 DOI: 10.1007/978-1-0716-0830-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
All-optical methods of probing in vivo brain function are advantageous for their compatibility with automated microscopy and fast spatial targeting of neural circuit excitation and response. Recent advances in optogenetic technologies allow simultaneous light activation of specific neurons and optical readout of neural activity via fluorescent calcium reporters, providing an attractive opportunity for high-throughput screening assays that directly assess dynamic neural function in vivo. Here we describe a method to automatically record optogenetically activated neural responses in living, hydrogel-embedded organisms over many hours in a multiwell plate format. This method is suitable for screening the neural effects of hundreds of chemical compounds and assessing the time course of bioactivity over 12 h or more. As examples, we show the suppression of neural responses over time with various concentrations of two voltage-gated calcium channel blockers and a full-plate screen of 320 chemicals with positive and negative controls in a single experiment.
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33
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Neuroscience Research using Small Animals on a Chip: From Nematodes to Zebrafish Larvae. BIOCHIP JOURNAL 2021. [DOI: 10.1007/s13206-021-00012-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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34
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Neural and behavioral control in Caenorhabditis elegans by a yellow-light-activatable caged compound. Proc Natl Acad Sci U S A 2021; 118:2009634118. [PMID: 33542099 DOI: 10.1073/pnas.2009634118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Caenorhabditis elegans is used as a model system to understand the neural basis of behavior, but application of caged compounds to manipulate and monitor the neural activity is hampered by the innate photophobic response of the nematode to short-wavelength light or by the low temporal resolution of photocontrol. Here, we develop boron dipyrromethene (BODIPY)-derived caged compounds that release bioactive phenol derivatives upon illumination in the yellow wavelength range. We show that activation of the transient receptor potential vanilloid 1 (TRPV1) cation channel by spatially targeted optical uncaging of the TRPV1 agonist N-vanillylnonanamide at 580 nm modulates neural activity. Further, neuronal activation by illumination-induced uncaging enables optical control of the behavior of freely moving C. elegans without inducing a photophobic response and without crosstalk between uncaging and simultaneous fluorescence monitoring of neural activity.
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35
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Sleep Analysis in Adult C. elegans Reveals State-Dependent Alteration of Neural and Behavioral Responses. J Neurosci 2021; 41:1892-1907. [PMID: 33446520 PMCID: PMC7939084 DOI: 10.1523/jneurosci.1701-20.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 01/26/2023] Open
Abstract
Sleep, a state of quiescence associated with growth and restorative processes, is conserved across species. Invertebrates including the nematode Caenorhabditis elegans exhibit sleep-like states during development, satiety, and stress. Here, we describe behavior and neural activity during sleep and awake states in adult C. elegans hermaphrodites using new microfluidic methods. We observed effects of fluid flow, oxygen, feeding, odors, and genetic perturbations on long-term sleep behavior over 12 h. We developed a closed-loop sleep detection system to automatically deliver chemical stimuli to assess sleep-dependent changes to evoked neural responses in individual animals. Sleep increased the arousal threshold to aversive stimulation, yet the associated sensory neuron and first-layer interneuron responses were unchanged. This localizes adult sleep-dependent neuromodulation within interneurons presynaptic to the premotor interneurons, rather than afferent sensory circuits. However, sleep prolonged responses in appetitive chemosensory neurons, suggesting that sleep modulates responsiveness specifically across sensory systems rather than broadly damping global circuit activity. SIGNIFICANCE STATEMENT Much is known about molecular mechanisms that facilitate sleep control. However, it is unclear how these pathways modulate neural circuit-level sensory processing or how misregulation of neural activity contributes to sleep disorders. The nematode Caenorhabditis elegans provides the ability to study neural circuitry with single-neuron resolution, and recent studies examined sleep states between developmental stages and when stressed. Here, we examine an additional form of spontaneous sleep in adult C. elegans at the behavioral and neural activity levels. Using a closed-loop system, we show that delayed behavioral responses to aversive chemical stimulation during sleep arise from sleep-dependent sensorimotor modulation localized presynaptic to the premotor circuit, rather than early sensory circuits.
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36
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Ashraf M, Mohanan S, Sim BR, Tam A, Rahemipour K, Brousseau D, Thibault S, Corbett AD, Bub G. Random access parallel microscopy. eLife 2021; 10:56426. [PMID: 33432922 PMCID: PMC7843131 DOI: 10.7554/elife.56426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 01/11/2021] [Indexed: 11/26/2022] Open
Abstract
We introduce a random-access parallel (RAP) imaging modality that uses a novel design inspired by a Newtonian telescope to image multiple spatially separated samples without moving parts or robotics. This scheme enables near-simultaneous image capture of multiple petri dishes and random-access imaging with sub-millisecond switching times at the full resolution of the camera. This enables the RAP system to capture long-duration records from different samples in parallel, which is not possible using conventional automated microscopes. The system is demonstrated by continuously imaging multiple cardiac monolayer and Caenorhabditis elegans preparations.
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Affiliation(s)
- Mishal Ashraf
- Department of Physiology, MGill University, Montreal, Canada
| | - Sharika Mohanan
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Byu Ri Sim
- Department of Physiology, MGill University, Montreal, Canada
| | - Anthony Tam
- Department of Physiology, MGill University, Montreal, Canada
| | | | - Denis Brousseau
- Department of Physics, Engineering Physics and Optics, Université Laval, Laval, Canada
| | - Simon Thibault
- Department of Physics, Engineering Physics and Optics, Université Laval, Laval, Canada
| | - Alexander D Corbett
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Gil Bub
- Department of Physiology, MGill University, Montreal, Canada
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37
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Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O. NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell 2021; 184:272-288.e11. [PMID: 33378642 PMCID: PMC10494711 DOI: 10.1016/j.cell.2020.12.012] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering a multicolor transgene called NeuroPAL (a neuronal polychromatic atlas of landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that resolves all neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. We showcase three applications that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding for these stimuli.
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Affiliation(s)
- Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Amin Nejatbakhsh
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Erdem Varol
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Ruoxi Sun
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Gonzalo E Mena
- Department of Statistics and Data Science Initiative, Harvard University, Cambridge, MA 02138, USA
| | - Aravinthan D T Samuel
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Liam Paninski
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | | | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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Tanimoto Y, Kimura KD. Calcium Imaging of Neuronal Activity under Gradually Changing Odor Stimulation in Caenorhabditis elegans. Bio Protoc 2021; 11:e3866. [PMID: 33732757 PMCID: PMC7952960 DOI: 10.21769/bioprotoc.3866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/13/2018] [Accepted: 10/21/2020] [Indexed: 11/02/2022] Open
Abstract
Olfactory behavior is among the most fundamental animal behaviors both in the wild and in the laboratory. To elucidate the neural mechanisms underlying olfactory behavior, it is critical to measure neural responses to odorant concentration changes resembling those that animals actually sense during olfactory behavior. However, reproducing the dynamically changing olfactory stimuli to an animal during such measurements of neural activity is technically challenging. Here, we describe technical details and protocols for odor stimulation during calcium imaging of the sensory neurons of the nematode Caenorhabditis elegans. In this system, the neuronal activity of C. elegans is measured using ratiometric calcium imaging during exposure to quantitatively controlled olfactory stimuli over time. Temporal changes in odor concentrations around the animal are precisely controlled according to a predesigned temporal odor gradient to reproduce a realistic odor concentration change during olfactory behavior in a behavioral arena. By monitoring neural activity in response to the realistic olfactory stimulus, it is possible to elucidate the mechanisms by which olfactory input is processed by neural activities and reflected in behavioral output.
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Affiliation(s)
- Yuki Tanimoto
- Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Koutarou D. Kimura
- Graduate School of Science, Osaka University, Toyonaka, Japan
- Graduate School of Science, Nagoya City University, Nagoya, Japan
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39
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Wan J, Lu H. Enabling high-throughput single-animal gene-expression studies with molecular and micro-scale technologies. LAB ON A CHIP 2020; 20:4528-4538. [PMID: 33237042 PMCID: PMC7769683 DOI: 10.1039/d0lc00881h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene expression and regulation play diverse and important roles across all living systems. By quantifying the expression, whether in a sample of single cells, a specific tissue, or in a whole animal, one can gain insights into the underlying biology. Many biological questions now require single-animal and tissue-specific resolution, such as why individuals, even within an isogenic population, have variations in development and aging across different tissues and organs. The popular techniques that quantify the transcriptome (e.g. RNA-sequencing) process populations of animals and cells together and thus, have limitations in both individual and spatial resolution. There are single-animal assays available (e.g. fluorescent reporters); however, they suffer other technical bottlenecks, such as a lack of robust sample-handling methods. Microfluidic technologies have demonstrated various improvements throughout the years, and it is likely they can enhance the impact of these single-animal gene-expression assays. In this perspective, we aim to highlight how the engineering/method-development field have unique opportunities to create new tools that can enable us to robustly answer the next set of important questions in biology that require high-density, high-quality gene expression data.
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Affiliation(s)
- Jason Wan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA.
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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40
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Randi F, Leifer AM. Measuring and modeling whole-brain neural dynamics in Caenorhabditis elegans. Curr Opin Neurobiol 2020; 65:167-175. [PMID: 33279794 PMCID: PMC7801769 DOI: 10.1016/j.conb.2020.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 11/19/2022]
Abstract
The compact nervous system of the nematode Caenorhabditis elegans makes it a powerful playground to study how neural dynamics constrained by neuroanatomy generate neural function and behavior. The ability to record neural activity from the whole brain simultaneously in this worm has opened several research avenues and is providing insights into brain-wide neural coding of locomotion, sleep, and other behaviors. We review these findings and the development of new methods, including new microscopes, new genetic tools, and new modeling approaches. We conclude with a discussion of the role of theory in interpreting or driving new experiments in C. elegans and potential paths forward.
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Affiliation(s)
- Francesco Randi
- Department of Physics, Princeton University, Jadwin Hall, Princeton, NJ 08544, USA
| | - Andrew M Leifer
- Department of Physics, Princeton University, Jadwin Hall, Princeton, NJ 08544, USA; Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
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41
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Abstract
In the last decade, microfluidic methods have proven to be powerful tools for Caenorhabditis elegans research, offering advanced manipulation of worms and precise control of experimental conditions. The advantages of microfluidic chips include their capability of immobilization, automated sorting, and longitudinal measurement, and more. In this review, we focus on control components that are widely used in the design of microfluidic devices, and discuss their functions and working principles that enable advanced manipulation on a chip. Understanding these components will ease the onboarding of researchers inexperienced with microfluidics and help them bring the power of microfluidics to new applications.
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Affiliation(s)
- Erel Levine
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Kyung Suk Lee
- Department of Physics Education, Kongju National University, Gongju, South Korea
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42
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Doser RL, Amberg GC, Hoerndli FJ. Reactive Oxygen Species Modulate Activity-Dependent AMPA Receptor Transport in C. elegans. J Neurosci 2020; 40:7405-7420. [PMID: 32847966 PMCID: PMC7511182 DOI: 10.1523/jneurosci.0902-20.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/26/2020] [Accepted: 08/16/2020] [Indexed: 12/22/2022] Open
Abstract
The AMPA subtype of synaptic glutamate receptors (AMPARs) plays an essential role in cognition. Their function, numbers, and change at synapses during synaptic plasticity are tightly regulated by neuronal activity. Although we know that long-distance transport of AMPARs is essential for this regulation, we do not understand the associated regulatory mechanisms of it. Neuronal transmission is a metabolically demanding process in which ATP consumption and production are tightly coupled and regulated. Aerobic ATP synthesis unavoidably produces reactive oxygen species (ROS), such as hydrogen peroxide, which are known modulators of calcium signaling. Although a role for calcium signaling in AMPAR transport has been described, there is little understanding of the mechanisms involved and no known link to physiological ROS signaling. Here, using real-time in vivo imaging of AMPAR transport in the intact C. elegans nervous system, we demonstrate that long-distance synaptic AMPAR transport is bidirectionally regulated by calcium influx and activation of calcium/calmodulin-dependent protein kinase II. Quantification of in vivo calcium dynamics revealed that modest, physiological increases in ROS decrease calcium transients in C. elegans glutamatergic neurons. By combining genetic and pharmacological manipulation of ROS levels and calcium influx, we reveal a mechanism in which physiological increases in ROS cause a decrease in synaptic AMPAR transport and delivery by modulating activity-dependent calcium signaling. Together, our results identify a novel role for oxidant signaling in the regulation of synaptic AMPAR transport and delivery, which in turn could be critical for coupling the metabolic demands of neuronal activity with excitatory neurotransmission.SIGNIFICANCE STATEMENT Synaptic AMPARs are critical for excitatory synaptic transmission. The disruption of their synaptic localization and numbers is associated with numerous psychiatric, neurologic, and neurodegenerative conditions. However, very little is known about the regulatory mechanisms controlling transport and delivery of AMPAR to synapses. Here, we describe a novel physiological signaling mechanism in which ROS, such as hydrogen peroxide, modulate AMPAR transport by modifying activity-dependent calcium signaling. Our findings provide the first evidence in support of a mechanistic link between physiological ROS signaling, AMPAR transport, localization, and excitatory transmission. This is of fundamental and clinical significance since dysregulation of intracellular calcium and ROS signaling is implicated in aging and the pathogenesis of several neurodegenerative disorders, including Alzheimer's and Parkinson's disease.
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Affiliation(s)
- Rachel L Doser
- Department of Biomedical Science, Colorado State University, Fort Collins, Colorado 80523
| | - Gregory C Amberg
- Department of Biomedical Science, Colorado State University, Fort Collins, Colorado 80523
| | - Frederic J Hoerndli
- Department of Biomedical Science, Colorado State University, Fort Collins, Colorado 80523
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43
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Zhao Y, Demirci U, Chen Y, Chen P. Multiscale brain research on a microfluidic chip. LAB ON A CHIP 2020; 20:1531-1543. [PMID: 32150176 DOI: 10.1039/c9lc01010f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One major challenge in current brain research is generating an integrative understanding of the brain's functions and disorders from its multiscale neuronal architectures and connectivity. Thus, innovative neurotechnology tools are urgently required for deciphering the multiscale functional and structural organizations of the brain at hierarchical scales from the molecular to the organismal level by multiple brain research initiatives launched by the European Union, United States, Australia, Canada, China, Korea, and Japan. To meet this demand, microfluidic chips (μFCs) have rapidly evolved as a trans-scale neurotechnological toolset to enable multiscale studies of the brain due to their unique advantages in flexible microstructure design, multifunctional integration, accurate microenvironment control, and capacity for automatic sample processing. Here, we review the recent progress in applying innovative μFC-based neuro-technologies to promote multiscale brain research and uniquely focus on representative applications of μFCs to address challenges in brain research at each hierarchical level. We discuss the current trend of combinational applications of μFCs with other neuro- and biotechnologies, including optogenetics, brain organoids, and 3D bioprinting, for better multiscale brain research. In addition, we offer our insights into the existing outstanding questions at each hierarchical level of brain research that could potentially be addressed by advancing microfluidic techniques. This review will serve as a timely guide for bioengineers and neuroscientists to develop and apply μFC-based neuro-technologies for promoting basic and translational brain research.
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Affiliation(s)
- Yanan Zhao
- Department of Biomedical Engineering, Wuhan University School of Basic Medical Sciences, 115 Donghu Road, Wuhan 430071, China.
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44
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Gonzales DL, Badhiwala KN, Avants BW, Robinson JT. Bioelectronics for Millimeter-Sized Model Organisms. iScience 2020; 23:100917. [PMID: 32114383 PMCID: PMC7049667 DOI: 10.1016/j.isci.2020.100917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 01/27/2023] Open
Abstract
Advances in microfabrication technologies and biomaterials have enabled a growing class of electronic devices that can stimulate and record bioelectronic signals. Many of these devices have been developed for humans or vertebrate animals, where miniaturization allows for implantation within the body. There are, however, another class of bioelectronic interfaces that exploit microfabrication and nanoelectronics to record signals from tiny, millimeter-sized organisms. In these cases, rather than implanting a device inside an animal, animals themselves are loaded in large numbers into bioelectronic devices for neural circuit and behavioral interrogation. These scalable interfaces provide platforms to develop new therapeutics as well as better understand basic principles of bioelectronic communication, neuroscience, and behavior. Here we review recent progress in these bioelectronic technologies and describe how they can complement on-chip optical, mechanical, and chemical interrogation methods to achieve high-throughput, multimodal studies of millimeter-sized small animals.
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Affiliation(s)
- Daniel L Gonzales
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr., West Lafayette, IN 47907, USA
| | - Krishna N Badhiwala
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA
| | - Benjamin W Avants
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX 77005, USA
| | - Jacob T Robinson
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA; Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX 77005, USA; Applied Physics Program, Rice University, 6100 Main St., Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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45
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Cho Y, Lee SA, Chew YL, Broderick K, Schafer WR, Lu H. Multimodal Stimulation in a Microfluidic Device Facilitates Studies of Interneurons in Sensory Integration in C. elegans. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905852. [PMID: 32003130 PMCID: PMC7720847 DOI: 10.1002/smll.201905852] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Animals' perception and behavior involve integration of multiple sensory modalities. Caenorhabditis elegans is a useful model for studying multimodal sensory integration, as it has well-characterized neuronal circuits in a relatively simple nervous system. However, most studies based on functional imaging have only been conducted on single modal stimuli, because well-controlled multimodal experiments for C. elegans are technically difficult. For instance, no single systems currently deliver precise stimuli with spatial, temporal, and intensity control, despite prior hypotheses that interneurons do integrate these sensory inputs to control behavior. Here, a microfluidic platform that can easily deliver spatially and temporally controlled combination stimuli to C. elegans is presented. With this platform, both sensory and interneuron activity is measured in response to mechanical and chemical stimulations in a quantitative and high-throughput manner. It is found that the activity of command interneuron PVC can be modulated by prior stimulation both within the same and across different modalities. The roles of monoaminergic and peptidergic signaling are further examined on the process of multimodal integration through PVC activity. The approach exemplified here is envisioned to be broadly applicable in different contexts to elucidate underlying mechanisms and identify genes affecting multisensory integration.
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Affiliation(s)
- Yongmin Cho
- School of Chemical & Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGA30332USA
- Present address:
Department of Systems BiologyHarvard Medical SchoolBostonMA02115USA
| | - Sol Ah Lee
- School of Chemical & Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGA30332USA
| | - Yee Lian Chew
- Neurobiology DivisionMedical Research Council Laboratory of Molecular BiologyCambridgeCB2 0QHUK
- Present address:
Molecular Horizons and School of Chemistry and Molecular BioscienceUniversity of Wollongong & Illawarra Health and Medical Research InstituteWollongongNSW2522Australia
| | - Kirby Broderick
- School of Chemical & Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGA30332USA
| | - William R. Schafer
- Neurobiology DivisionMedical Research Council Laboratory of Molecular BiologyCambridgeCB2 0QHUK
| | - Hang Lu
- School of Chemical & Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGA30332USA
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46
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Krenger R, Cornaglia M, Lehnert T, Gijs MAM. Microfluidic system for Caenorhabditis elegans culture and oxygen consumption rate measurements. LAB ON A CHIP 2020; 20:126-135. [PMID: 31729516 DOI: 10.1039/c9lc00829b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mitochondrial respiration is a key signature for the assessment of mitochondrial functioning and mitochondrial dysfunction is related to many diseases including metabolic syndrome and aging-associated conditions. Here, we present a microfluidic Caenorhabditis elegans culture system with integrated luminescence-based oxygen sensing. The material used for the fabrication of the microfluidic chip is off-stoichiometry dual-cure thiol-ene-epoxy (OSTE+), which is well-suited for reliably recording on-chip oxygen consumption rates (OCR) due to its low gas permeability. With our microfluidic approach, it was possible to confine a single nematode in a culture chamber, starting from the L4 stage and studying it over a time span of up to 6 days. An automated protocol for successive worm feeding and OCR measurements during worm development was applied. We found an increase of OCR values from the L4 larval stage to adulthood, and a continuous decrease as the worm further ages. In addition, we performed a C. elegans metabolic assay in which exposure to the mitochondrial uncoupling agent FCCP increased the OCR by a factor of about two compared to basal respiration rates. Subsequent treatment with sodium azide inhibited completely mitochondrial respiration.
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Affiliation(s)
- Roger Krenger
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Matteo Cornaglia
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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47
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Bhardwaj A, Pandey P, Babu K. Control of Locomotory Behavior of Caenorhabditis elegans by the Immunoglobulin Superfamily Protein RIG-3. Genetics 2020; 214:135-145. [PMID: 31740450 PMCID: PMC6944407 DOI: 10.1534/genetics.119.302872] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/15/2019] [Indexed: 12/23/2022] Open
Abstract
Cell surface immunoglobulin superfamily (IgSF) proteins play important roles in the development and function of the nervous system . Here we define the role of a Caenorhabditis elegans IgSF protein, RIG-3, in the function of the AVA command interneuron. This study reveals that RIG-3 regulates the abundance of the glutamate receptor subunit, GLR-1, in the AVA command interneuron and also regulates reversal behavior in C. elegans The mutant strain lacking rig-3 (rig-3 (ok2156)) shows increased reversal frequency during local search behaviors. Genetic and behavioral experiments suggest that RIG-3 functions through GLR-1 to regulate reversal behavior. We also show that the increased reversal frequency seen in rig-3 mutants is dependent on the increase in GLR-1 abundance at synaptic inputs to AVA, suggesting that RIG-3 alters the synaptic strength of incoming synapses through GLR-1 Consistent with the imaging experiments, altered synaptic strength was also reflected in increased calcium transients in rig-3 mutants when compared to wild-type control animals. Our results further suggest that animals lacking rig-3 show increased AVA activity, allowing the release of FLP-18 neuropeptide from AVA, which is an activity-dependent signaling molecule. Finally, we show that FLP-18 functions through the neuropeptide receptor, NPR-5, to modulate reversal behavior in C. elegans.
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Affiliation(s)
- Ashwani Bhardwaj
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Manauli 140306, India
| | - Pratima Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Manauli 140306, India
| | - Kavita Babu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Manauli 140306, India
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, India
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48
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Midkiff D, San-Miguel A. Microfluidic Technologies for High Throughput Screening Through Sorting and On-Chip Culture of C. elegans. Molecules 2019; 24:molecules24234292. [PMID: 31775328 PMCID: PMC6930626 DOI: 10.3390/molecules24234292] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
The nematode Caenorhabditis elegans is a powerful model organism that has been widely used to study molecular biology, cell development, neurobiology, and aging. Despite their use for the past several decades, the conventional techniques for growth, imaging, and behavioral analysis of C. elegans can be cumbersome, and acquiring large data sets in a high-throughput manner can be challenging. Developments in microfluidic “lab-on-a-chip” technologies have improved studies of C. elegans by increasing experimental control and throughput. Microfluidic features such as on-chip control layers, immobilization channels, and chamber arrays have been incorporated to develop increasingly complex platforms that make experimental techniques more powerful. Genetic and chemical screens are performed on C. elegans to determine gene function and phenotypic outcomes of perturbations, to test the effect that chemicals have on health and behavior, and to find drug candidates. In this review, we will discuss microfluidic technologies that have been used to increase the throughput of genetic and chemical screens in C. elegans. We will discuss screens for neurobiology, aging, development, behavior, and many other biological processes. We will also discuss robotic technologies that assist in microfluidic screens, as well as alternate platforms that perform functions similar to microfluidics.
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49
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Levy S, Bargmann CI. An Adaptive-Threshold Mechanism for Odor Sensation and Animal Navigation. Neuron 2019; 105:534-548.e13. [PMID: 31761709 DOI: 10.1016/j.neuron.2019.10.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 05/31/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023]
Abstract
Identifying the environmental information and computations that drive sensory detection is key for understanding animal behavior. Using experimental and theoretical analysis of AWCON, a well-described olfactory neuron in C. elegans, here we derive a general and broadly useful model that matches stimulus history to odor sensation and behavioral responses. We show that AWCON sensory activity is regulated by an absolute signal threshold that continuously adapts to odor history, allowing animals to compare present and past odor concentrations. The model predicts sensory activity and probabilistic behavior during animal navigation in different odor gradients and across a broad stimulus regime. Genetic studies demonstrate that the cGMP-dependent protein kinase EGL-4 determines the timescale of threshold adaptation, defining a molecular basis for a critical model feature. The adaptive threshold model efficiently filters stimulus noise, allowing reliable sensation in fluctuating environments, and represents a feedforward sensory mechanism with implications for other sensory systems.
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Affiliation(s)
- Sagi Levy
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Cornelia I Bargmann
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Chan Zuckerberg Initiative, Palo Alto, CA 94301, USA
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50
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Dobosiewicz M, Liu Q, Bargmann CI. Reliability of an interneuron response depends on an integrated sensory state. eLife 2019; 8:e50566. [PMID: 31718773 PMCID: PMC6894930 DOI: 10.7554/elife.50566] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
The central nervous system transforms sensory information into representations that are salient to the animal. Here we define the logic of this transformation in a Caenorhabditis elegans integrating interneuron. AIA interneurons receive input from multiple chemosensory neurons that detect attractive odors. We show that reliable AIA responses require the coincidence of two sensory inputs: activation of AWA olfactory neurons that are activated by attractive odors, and inhibition of one or more chemosensory neurons that are inhibited by attractive odors. AWA activates AIA through an electrical synapse, while the disinhibitory pathway acts through glutamatergic chemical synapses. AIA interneurons have bistable electrophysiological properties consistent with their calcium dynamics, suggesting that AIA activation is a stereotyped response to an integrated stimulus. Our results indicate that AIA interneurons combine sensory information using AND-gate logic, requiring coordinated activity from multiple chemosensory neurons. We propose that AIA encodes positive valence based on an integrated sensory state.
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Affiliation(s)
- May Dobosiewicz
- Lulu and Anthony Wang Laboratory of Neural Circuits and BehaviorThe Rockefeller UniversityNew YorkUnited States
| | - Qiang Liu
- Lulu and Anthony Wang Laboratory of Neural Circuits and BehaviorThe Rockefeller UniversityNew YorkUnited States
| | - Cornelia I Bargmann
- Lulu and Anthony Wang Laboratory of Neural Circuits and BehaviorThe Rockefeller UniversityNew YorkUnited States
- Chan Zuckerberg InitiativePalo AltoUnited States
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