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1
Chen, Pei-Ju, Yan Li, and Chi-Hon Lee. "Calcium Imaging of Neural Activity in Fly Photoreceptors." Cold Spring Harbor Protocols 2022, no. 7 (May 31, 2022): pdb.top107800. http://dx.doi.org/10.1101/pdb.top107800.
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Functional imaging methodologies allow researchers to simultaneously monitor the neural activities of all single neurons in a population, and this ability has led to great advances in neuroscience research. Taking advantage of a genetically tractable model organism, functional imaging in Drosophila provides opportunities to probe scientific questions that were previously unanswerable by electrophysiological recordings. Here, we introduce comprehensive protocols for two-photon calcium imaging in fly visual neurons. We also discuss some challenges in applying optical imaging techniques to study visual systems and consider the best practices for making comparisons between different neuron groups.
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Wang, Yangzhen, Feng Su, Shanshan Wang, Chaojuan Yang, Yonglu Tian, Peijiang Yuan, Xiaorong Liu, Wei Xiong, and Chen Zhang. "Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging." Bioinformatics 35, no. 17 (January 23, 2019): 3208–10. http://dx.doi.org/10.1093/bioinformatics/btz055.
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Abstract Motivation Functional imaging at single-neuron resolution offers a highly efficient tool for studying the functional connectomics in the brain. However, mainstream neuron-detection methods focus on either the morphologies or activities of neurons, which may lead to the extraction of incomplete information and which may heavily rely on the experience of the experimenters. Results We developed a convolutional neural networks and fluctuation method-based toolbox (ImageCN) to increase the processing power of calcium imaging data. To evaluate the performance of ImageCN, nine different imaging datasets were recorded from awake mouse brains. ImageCN demonstrated superior neuron-detection performance when compared with other algorithms. Furthermore, ImageCN does not require sophisticated training for users. Availability and implementation ImageCN is implemented in MATLAB. The source code and documentation are available at https://github.com/ZhangChenLab/ImageCN. Supplementary information Supplementary data are available at Bioinformatics online.
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Yang, Jian, Yong Zhang, Yuanlin Yu, and Ning Zhong. "Nested U-Net Architecture Based Image Segmentation for 3D Neuron Reconstruction." Journal of Medical Imaging and Health Informatics 11, no. 5 (May 1, 2021): 1348–56. http://dx.doi.org/10.1166/jmihi.2021.3379.
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Digital reconstruction of neurons is a critical step in studying neuronal morphology and exploring the working mechanism of the brain. In recent years, the focus of neuronal morphology reconstruction has gradually shifted from single neurons to multiple neurons in a whole brain. Microscopic images of a whole brain often have low signal-to-noise-ratio, discontinuous neuron fragments or weak neuron signals. It is very difficult to segment neuronal signals from the background of these images, which is the first step of most automatic reconstruction algorithms. In this study, we propose a Nested U-Net based Ultra-Tracer model (NUNU-Tracer) for better multiple neurons image segmentation and morphology reconstruction. The NUNU-Tracer utilizes nested U-Net (UNet++) deep network to segment 3D neuron images, reconstructs neuron morphologies under the framework of the Ultra-Tracer and prunes branches of noncurrent tracing neurons. The 3D UNet++ takes a 3D microscopic image as its input, and uses scale-space distance transform and linear fusion strategy to generate the segmentation maps for voxels in the image. It is capable of removing noise, repairing broken neurite patterns and enhancing neuronal signals. We evaluate the performance of the 3D UNet++ for image segmentation and NUNU-Tracer for neuron morphology reconstruction on image blocks and neurons, respectively. Experimental results show that they significantly improve the accuracy and length of neuron reconstructions.
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Keliris, Georgios A., Qinglin Li, Amalia Papanikolaou, Nikos K. Logothetis, and Stelios M. Smirnakis. "Estimating average single-neuron visual receptive field sizes by fMRI." Proceedings of the National Academy of Sciences 116, no. 13 (March 13, 2019): 6425–34. http://dx.doi.org/10.1073/pnas.1809612116.
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The noninvasive estimation of neuronal receptive field (RF) properties in vivo allows a detailed understanding of brain organization as well as its plasticity by longitudinal following of potential changes. Visual RFs measured invasively by electrophysiology in animal models have traditionally provided a great extent of our current knowledge about the visual brain and its disorders. Voxel-based estimates of population RF (pRF) by functional magnetic resonance imaging (fMRI) in humans revolutionized the field and have been used extensively in numerous studies. However, current methods cannot estimate single-neuron RF sizes as they reflect large populations of neurons with individual RF scatter. Here, we introduce an approach to estimate RF size using spatial frequency selectivity to checkerboard patterns. This method allowed us to obtain noninvasive, average single-neuron RF estimates over a large portion of human early visual cortex. These estimates were significantly smaller compared with prior pRF methods. Furthermore, fMRI and electrophysiology experiments in nonhuman primates demonstrated an exceptionally good match, validating the approach.
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Ning, Kefu, Xiaoyu Zhang, Xuefei Gao, Tao Jiang, He Wang, Siqi Chen, Anan Li, and Jing Yuan. "Deep-learning-based whole-brain imaging at single-neuron resolution." Biomedical Optics Express 11, no. 7 (June 8, 2020): 3567. http://dx.doi.org/10.1364/boe.393081.
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Kalaska, John F. "Emerging ideas and tools to study the emergent properties of the cortical neural circuits for voluntary motor control in non-human primates." F1000Research 8 (May 29, 2019): 749. http://dx.doi.org/10.12688/f1000research.17161.1.
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For years, neurophysiological studies of the cerebral cortical mechanisms of voluntary motor control were limited to single-electrode recordings of the activity of one or a few neurons at a time. This approach was supported by the widely accepted belief that single neurons were the fundamental computational units of the brain (the “neuron doctrine”). Experiments were guided by motor-control models that proposed that the motor system attempted to plan and control specific parameters of a desired action, such as the direction, speed or causal forces of a reaching movement in specific coordinate frameworks, and that assumed that the controlled parameters would be expressed in the task-related activity of single neurons. The advent of chronically implanted multi-electrode arrays about 20 years ago permitted the simultaneous recording of the activity of many neurons. This greatly enhanced the ability to study neural control mechanisms at the population level. It has also shifted the focus of the analysis of neural activity from quantifying single-neuron correlates with different movement parameters to probing the structure of multi-neuron activity patterns to identify the emergent computational properties of cortical neural circuits. In particular, recent advances in “dimension reduction” algorithms have attempted to identify specific covariance patterns in multi-neuron activity which are presumed to reflect the underlying computational processes by which neural circuits convert the intention to perform a particular movement into the required causal descending motor commands. These analyses have led to many new perspectives and insights on how cortical motor circuits covertly plan and prepare to initiate a movement without causing muscle contractions, transition from preparation to overt execution of the desired movement, generate muscle-centered motor output commands, and learn new motor skills. Progress is also being made to import optical-imaging and optogenetic toolboxes from rodents to non-human primates to overcome some technical limitations of multi-electrode recording technology.
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Hogg, Peter W., and Kurt Haas. "Bulk Dye Loading for In Vivo Calcium Imaging of Visual Responses in Populations of Xenopus Tectal Neurons." Cold Spring Harbor Protocols 2022, no. 1 (March 29, 2021): pdb.prot106831. http://dx.doi.org/10.1101/pdb.prot106831.
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Bulk loading of neurons with fluorescent calcium indicators in transparent albino Xenopus tadpoles offers a rapid and easy method for tracking sensory-evoked activity in large numbers of neurons within an awake developing brain circuit. In vivo two-photon time-lapse imaging of an image plane through the optic tectum allows defining receptive field properties from visual-evoked responses for studies of single-neuron and network-level encoding and plasticity. Here, we describe loading the Xenopus tadpole optic tectum with the membrane-permeable AM ester of Oregon Green 488 BAPTA-1 (OGB-1 AM) for in vivo imaging experiments.
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Koyano, Kenji W., Akinori Machino, Masaki Takeda, Teppei Matsui, Ryoko Fujimichi, Yohei Ohashi, and Yasushi Miyashita. "In vivo visualization of single-unit recording sites using MRI-detectable elgiloy deposit marking." Journal of Neurophysiology 105, no. 3 (March 2011): 1380–92. http://dx.doi.org/10.1152/jn.00358.2010.
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Precise localization of single-neuron activity has elucidated functional architectures of the primate cerebral cortex, related to vertically stacked layers and horizontally aligned columns. The traditional “gold standard” method for localizing recorded neuron is histological examination of electrolytic lesion marks at recording sites. Although this method can localize recorded neurons with fine neuroanatomy, the necessity for postmortem analysis prohibits its use in long-term chronic experiments. To localize recorded single-neuron positions in vivo, we introduced MRI-detectable elgiloy deposit marks, which can be created by electrolysis of an elgiloy microelectrode tip and visualized on highly contrasted magnetic resonance (MR) images. Histological analysis validated that the deposit mark centers could be localized relative to neuroanatomy in vivo with single-voxel accuracy, at an in-plane resolution of 200 μm. To demonstrate practical applications of the technique, we recorded single-neuron activity from a monkey performing a cognitive task and localized it in vivo using deposit marks (deposition: 2 μA for 3 min; scanning: fast-spin-echo sequence with 0.15 × 0.15 × 0.8 mm3 resolution, 120/4,500 ms of echo-time/repetition-time and 8 echo-train-length), as is usually performed with conventional postmortem methods using electrolytic lesion marks. Two localization procedures were demonstrated: 1) deposit marks within a microelectrode track were used to reconstruct a dozen recorded neuron positions along the track directly on MR images; 2) combination with X-ray imaging allowed estimation of hundreds of neuron positions on MR images. This new in vivo method is feasible for chronic experiments with nonhuman primates, enabling analysis of the functional architecture of the cerebral cortex underlying cognitive processes.
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Tetzlaff, Svenja, Joaquín Campos, Linh Nguyen, Christopher Strahle, Wolfgang Wick, Thomas Kuner, Frank Winkler, Claudio Acuna, and Varun Venkataramani. "CNSC-21. CHARACTERIZATION OF NEURON-TUMOR INTERACTIONS USING HUMAN CO-CULTURES." Neuro-Oncology 24, Supplement_7 (November 1, 2022): vii26. http://dx.doi.org/10.1093/neuonc/noac209.102.
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Abstract Glioblastoma are incurable brain tumors characterized by their colonization of the entire brain and their notorious therapeutic resistance. Recently, we discovered long membrane tubes called tumor microtubes contributing to invasion, network formation of tumor-tumor networks and therapeutic resistance. Subsequently, heterogeneous networks of neurons and glioblastoma cells were characterized, which can communicate by synaptic and perisynaptic contacts as well as by paracrine mechanisms. Currently used models of studying neuron-glioblastoma interactions are limited by the possibility to study glioblastoma in a defined human neuronal microenvironment. Here, we set out to derive excitatory and inhibitory neurons from embryonic stem cells via lentiviral reprogramming and co-cultured them with patient-derived glioblastoma cells. We could show that structural and functional neuron-glioblastoma synaptic contacts are formed. Functional communication between neurons and glioblastoma cells were characterized with calcium imaging, showing similar complex calcium dynamics previously characterized with in vivo imaging of patient-derived xenograft models. The single-cell glioblastoma morphology was morphometrically similar to that of human glioblastoma tissue. Tumor microtubes and the formation of tumor-tumor networks could be demonstrated. Additionally, glioblastoma invasion patterns in our human neuronal co-culture model resemble invasion patterns recently characterized with patient-derived xenograft models. Lastly, we investigated reciprocal neuron-glioblastoma interactions and longitudinally characterized neuronal activity with patch-clamp electrophysiology. In conclusion, we provide a novel human neuron-glioblastoma co-culture system allowing in-depth molecular and functional characterization for future Cancer Neuroscience studies.
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Matsuda, Takahiko, and Izumi Oinuma. "Imaging endogenous synaptic proteins in primary neurons at single-cell resolution using CRISPR/Cas9." Molecular Biology of the Cell 30, no. 22 (October 15, 2019): 2838–55. http://dx.doi.org/10.1091/mbc.e19-04-0223.
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Fluorescence imaging at single-cell resolution is a crucial approach to analyzing the spatiotemporal regulation of proteins within individual cells of complex neural networks. Here we present a nonviral strategy that enables the tagging of endogenous loci by CRISPR/Cas9-mediated genome editing combined with a nucleofection technique. The method allowed expression of fluorescently tagged proteins at endogenous levels, and we successfully achieved tagging of a presynaptic protein, synaptophysin (Syp), and a postsynaptic protein, PSD-95, in cultured postmitotic neurons. Superresolution fluorescence microscopy of fixed neurons confirmed the identical localization patterns of the tagged proteins to those of endogenous ones verified by immunohistochemistry. The system is also applicable for multiplexed labeling and live-cell imaging. Live imaging with total internal reflection fluorescence microscopy of a single dendritic process of a neuron double-labeled with Syp-mCherry and PSD-95-EGFP revealed the previously undescribed dynamic localization of the proteins synchronously moving along dendritic shafts. Our convenient and versatile strategy is potent for analysis of proteins whose ectopic expressions perturb cellular functions.
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Duncan, John. "Converging levels of analysis in the cognitive neuroscience of visual attention." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 353, no. 1373 (August 29, 1998): 1307–17. http://dx.doi.org/10.1098/rstb.1998.0285.
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Experiments using behavioural, lesion, functional imaging and single neuron methods are considered in the context of a neuropsychological model of visual attention. According to this model, inputs compete for representation in multiple visually responsive brain systems, sensory and motor, cortical and subcortical. Competition is biased by advance priming of neurons responsive to current behavioural targets. Across systems competition is integrated such that the same, selected object tends to become dominant throughout. The behavioural studies reviewed concern divided attention within and between modalities. They implicate within–modality competition as one main restriction on concurrent stimulus identification. In contrast to the conventional association of lateral attentional focus with parietal lobe function, the lesion studies show attentional bias to be a widespread consequence of unilateral cortical damage. Although the clinical syndrome of unilateral neglect may indeed be associated with parietal lesions, this probably reflects an assortment of further deficits accompanying a simple attentional imbalance. The functional imaging studies show joint involvement of lateral prefrontal and occipital cortex in lateral attentional focus and competition. The single unit studies suggest how competition in several regions of extrastriate cortex is biased by advance priming of neurons responsive to current behavioural targets. Together, the concepts of competition, priming and integration allow a unified theoretical approach to findings from behavioural to single neuron levels.
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Xu, Shengjin, Hui Yang, Vilas Menon, Andrew L. Lemire, Lihua Wang, Fredrick E. Henry, Srinivas C. Turaga, and Scott M. Sternson. "Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles." Science 370, no. 6514 (October 15, 2020): eabb2494. http://dx.doi.org/10.1126/science.abb2494.
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Brains encode behaviors using neurons amenable to systematic classification by gene expression. The contribution of molecular identity to neural coding is not understood because of the challenges involved with measuring neural dynamics and molecular information from the same cells. We developed CaRMA (calcium and RNA multiplexed activity) imaging based on recording in vivo single-neuron calcium dynamics followed by gene expression analysis. We simultaneously monitored activity in hundreds of neurons in mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker genes had predictive power for neuronal responses across 11 behavioral states. The PVH uses combinatorial assemblies of molecularly defined neuron populations for grouped-ensemble coding of survival behaviors. The neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated multiple cell types with similar responses. Our results show that molecularly defined neurons are important processing units for brain function.
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Barry, John F., Matthew J. Turner, Jennifer M. Schloss, David R. Glenn, Yuyu Song, Mikhail D. Lukin, Hongkun Park, and Ronald L. Walsworth. "Optical magnetic detection of single-neuron action potentials using quantum defects in diamond." Proceedings of the National Academy of Sciences 113, no. 49 (November 22, 2016): 14133–38. http://dx.doi.org/10.1073/pnas.1601513113.
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Magnetic fields from neuronal action potentials (APs) pass largely unperturbed through biological tissue, allowing magnetic measurements of AP dynamics to be performed extracellularly or even outside intact organisms. To date, however, magnetic techniques for sensing neuronal activity have either operated at the macroscale with coarse spatial and/or temporal resolution—e.g., magnetic resonance imaging methods and magnetoencephalography—or been restricted to biophysics studies of excised neurons probed with cryogenic or bulky detectors that do not provide single-neuron spatial resolution and are not scalable to functional networks or intact organisms. Here, we show that AP magnetic sensing can be realized with both single-neuron sensitivity and intact organism applicability using optically probed nitrogen-vacancy (NV) quantum defects in diamond, operated under ambient conditions and with the NV diamond sensor in close proximity (∼10 µm) to the biological sample. We demonstrate this method for excised single neurons from marine worm and squid, and then exterior to intact, optically opaque marine worms for extended periods and with no observed adverse effect on the animal. NV diamond magnetometry is noninvasive and label-free and does not cause photodamage. The method provides precise measurement of AP waveforms from individual neurons, as well as magnetic field correlates of the AP conduction velocity, and directly determines the AP propagation direction through the inherent sensitivity of NVs to the associated AP magnetic field vector.
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Ling, Tong, Kevin C. Boyle, Valentina Zuckerman, Thomas Flores, Charu Ramakrishnan, Karl Deisseroth, and Daniel Palanker. "High-speed interferometric imaging reveals dynamics of neuronal deformation during the action potential." Proceedings of the National Academy of Sciences 117, no. 19 (April 27, 2020): 10278–85. http://dx.doi.org/10.1073/pnas.1920039117.
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Neurons undergo nanometer-scale deformations during action potentials, and the underlying mechanism has been actively debated for decades. Previous observations were limited to a single spot or the cell boundary, while movement across the entire neuron during the action potential remained unclear. Here we report full-field imaging of cellular deformations accompanying the action potential in mammalian neuron somas (−1.8 to 1.4 nm) and neurites (−0.7 to 0.9 nm), using high-speed quantitative phase imaging with a temporal resolution of 0.1 ms and an optical path length sensitivity of <4 pm per pixel. The spike-triggered average, synchronized to electrical recording, demonstrates that the time course of the optical phase changes closely matches the dynamics of the electrical signal. Utilizing the spatial and temporal correlations of the phase signals across the cell, we enhance the detection and segmentation of spiking cells compared to the shot-noise–limited performance of single pixels. Using three-dimensional (3D) cellular morphology extracted via confocal microscopy, we demonstrate that the voltage-dependent changes in the membrane tension induced by ionic repulsion can explain the magnitude, time course, and spatial features of the phase imaging. Our full-field observations of the spike-induced deformations shed light upon the electromechanical coupling mechanism in electrogenic cells and open the door to noninvasive label-free imaging of neural signaling.
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Huys, Quentin J. M., Misha B. Ahrens, and Liam Paninski. "Efficient Estimation of Detailed Single-Neuron Models." Journal of Neurophysiology 96, no. 2 (August 2006): 872–90. http://dx.doi.org/10.1152/jn.00079.2006.
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Biophysically accurate multicompartmental models of individual neurons have significantly advanced our understanding of the input–output function of single cells. These models depend on a large number of parameters that are difficult to estimate. In practice, they are often hand-tuned to match measured physiological behaviors, thus raising questions of identifiability and interpretability. We propose a statistical approach to the automatic estimation of various biologically relevant parameters, including 1) the distribution of channel densities, 2) the spatiotemporal pattern of synaptic input, and 3) axial resistances across extended dendrites. Recent experimental advances, notably in voltage-sensitive imaging, motivate us to assume access to: i) the spatiotemporal voltage signal in the dendrite and ii) an approximate description of the channel kinetics of interest. We show here that, given i and ii, parameters 1–3 can be inferred simultaneously by nonnegative linear regression; that this optimization problem possesses a unique solution and is guaranteed to converge despite the large number of parameters and their complex nonlinear interaction; and that standard optimization algorithms efficiently reach this optimum with modest computational and data requirements. We demonstrate that the method leads to accurate estimations on a wide variety of challenging model data sets that include up to about 104 parameters (roughly two orders of magnitude more than previously feasible) and describe how the method gives insights into the functional interaction of groups of channels.
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Ishikawa, Tomoe, and Yuji Ikegaya. "Locally sequential synaptic reactivation during hippocampal ripples." Science Advances 6, no. 7 (February 2020): eaay1492. http://dx.doi.org/10.1126/sciadv.aay1492.
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The sequential reactivation of memory-relevant neuronal ensembles during hippocampal sharp-wave (SW) ripple oscillations reflects cognitive processing. However, how a downstream neuron decodes this spatiotemporally organized activity remains unexplored. Using subcellular calcium imaging from CA1 pyramidal neurons in ex vivo hippocampal networks, we discovered that neighboring spines are activated serially along dendrites toward or away from cell bodies. Sequential spine activity was engaged repeatedly in different SWs in a complex manner. In a single SW event, multiple sequences appeared discretely in dendritic trees, but overall, sequences occurred preferentially in some dendritic branches. Thus, sequential replays of multineuronal spikes are distributed across several compartmentalized dendritic foci of a postsynaptic neuron, with their spatiotemporal features preserved.
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Peng, Hanchuan, Peng Xie, Lijuan Liu, Xiuli Kuang, Yimin Wang, Lei Qu, Hui Gong, et al. "Morphological diversity of single neurons in molecularly defined cell types." Nature 598, no. 7879 (October 6, 2021): 174–81. http://dx.doi.org/10.1038/s41586-021-03941-1.
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AbstractDendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.
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Wu, Yuxiang, Shang Wu, Xin Wang, Chengtian Lang, Quanshi Zhang, Quan Wen, and Tianqi Xu. "Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans." PLOS Computational Biology 18, no. 10 (October 10, 2022): e1010594. http://dx.doi.org/10.1371/journal.pcbi.1010594.
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Advanced volumetric imaging methods and genetically encoded activity indicators have permitted a comprehensive characterization of whole brain activity at single neuron resolution in Caenorhabditis elegans. The constant motion and deformation of the nematode nervous system, however, impose a great challenge for consistent identification of densely packed neurons in a behaving animal. Here, we propose a cascade solution for long-term and rapid recognition of head ganglion neurons in a freely moving C. elegans. First, potential neuronal regions from a stack of fluorescence images are detected by a deep learning algorithm. Second, 2-dimensional neuronal regions are fused into 3-dimensional neuron entities. Third, by exploiting the neuronal density distribution surrounding a neuron and relative positional information between neurons, a multi-class artificial neural network transforms engineered neuronal feature vectors into digital neuronal identities. With a small number of training samples, our bottom-up approach is able to process each volume—1024 × 1024 × 18 in voxels—in less than 1 second and achieves an accuracy of 91% in neuronal detection and above 80% in neuronal tracking over a long video recording. Our work represents a step towards rapid and fully automated algorithms for decoding whole brain activity underlying naturalistic behaviors.
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Faumont, Serge, and Shawn R. Lockery. "The Awake Behaving Worm: Simultaneous Imaging of Neuronal Activity and Behavior in Intact Animals at Millimeter Scale." Journal of Neurophysiology 95, no. 3 (March 2006): 1976–81. http://dx.doi.org/10.1152/jn.01050.2005.
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Genetically encoded optical probes of neuronal activity offer the prospect of simultaneous recordings of neuronal activity and behavior in intact animals. A central problem in simultaneous imaging is that the field of view of the high-power objective required for imaging the neuron is often too small to allow the experimenter to assess the overall behavioral state of the animal. Here we present a method that solves this problem using a microscope with two objectives focused on the preparation: a high-power lens dedicated to imaging the neuron and low-power lens dedicated to imaging the behavior. Images of activity and behavior are acquired simultaneously but separately using different wavelengths of light. The new approach was tested using the cameleon calcium sensor expressed in Caenorhabditis elegans sensory neurons. We show that simultaneous recordings of neuronal activity and behavior are practical in C. elegans and, moreover, that such recordings can reveal subtle, transient correlations between calcium levels and behavior that may be missed in nonsimultaneous recordings. The new method is likely to be useful whenever it would be desirable to record simultaneously at two different spatial resolutions from a single location, or from two different locations in space.
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Davis, Karen D., William D. Hutchison, Andres M. Lozano, Ronald R. Tasker, and Jonathan O. Dostrovsky. "Human Anterior Cingulate Cortex Neurons Modulated by Attention-Demanding Tasks." Journal of Neurophysiology 83, no. 6 (June 1, 2000): 3575–77. http://dx.doi.org/10.1152/jn.2000.83.6.3575.
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Recent imaging studies have implicated the anterior cingulate cortex (ACC) in various cognitive functions, including attention. However, until now, there was no evidence for changes in neuronal activity of individual ACC neurons during performance of tasks that require attention and effortful thought. We hypothesized these neurons must exist in the human ACC. In this study, we present electrophysiological data from microelectrode single neuron recordings in the human ACC of neuronal modulation during attention-demanding tasks in 19% of 36 neurons tested. These findings provide the first direct evidence of an influence of a cognitive state on the spontaneous neuronal activity of human ACC neurons.
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Zhang, Weize, Peng Pan, Xin Wang, Yixu Chen, Yong Rao, and Xinyu Liu. "Force-Controlled Mechanical Stimulation and Single-Neuron Fluorescence Imaging of Drosophila Larvae." IEEE Robotics and Automation Letters 6, no. 2 (April 2021): 3736–43. http://dx.doi.org/10.1109/lra.2021.3061874.
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HIRATA, Yoshihiro, Kaori SHIGETOMI-KURIBAYASHI, Ken-ichi HONMA, Sato HONMA, and Ryosuke ENOKI. "Fluorescent calcium imaging of suprachiasmatic single neuron on the micropattern-culture dish." Proceedings of the JSME Conference on Frontiers in Bioengineering 2016.27 (2016): B114. http://dx.doi.org/10.1299/jsmebiofro.2016.27.b114.
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Hefft, Stefan, Armin Brandt, Stefan Zwick, Dominik von Elverfeldt, Irina Mader, Joacir Cordeiro, Michael Trippel, Julie Blumberg, and Andreas Schulze-Bonhage. "Safety of Hybrid Electrodes for Single-Neuron Recordings in Humans." Neurosurgery 73, no. 1 (April 23, 2013): 78–85. http://dx.doi.org/10.1227/01.neu.0000429840.76460.8c.
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Abstract BACKGROUND: Intracranial in vivo recordings of individual neurons in humans are increasingly performed for a better understanding of the mechanisms of epileptogenesis and of the neurobiological basis of cognition. So far, information about the safety of stereotactic implantations and of magnetic resonance imaging (MRI) with hybrid depth electrodes is scarce. OBJECTIVE: The aim of this study was to assess neurosurgical safety of implantations, recordings, and imaging using hybrid electrodes in humans. METHODS: Perioperative and long-term safety of implantation of a total of 88 hybrid depth electrodes with integrated microwires was assessed retrospectively in 25 consecutive epilepsy patients who underwent implantation of electrodes from 2007 to 2011 based on electronically stored charts. Safety aspects of MRI are reported from both in vitro and in vivo investigations. Precision of electrode implantation is evaluated based on intraoperative computed tomography and pre- and postoperative MRI. RESULTS: There was no clinically relevant morbidity associated with the use of hybrid electrodes in any of the patients. Precision of recordings from the targets aimed at was similar to that of standard depth electrodes. In vitro studies demonstrated the absence of relevant heating of hybrid electrodes with newly designed connectors with MRI at 1.5 T, corresponding to well-tolerated clinical MRI in patients. CONCLUSION: Given the technical approach described here, precise targeting and safe use are possible with hybrid electrodes containing microwires for in vivo recording of human neuronal units.
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Lelito, Katherine R., and Orie T. Shafer. "Reciprocal cholinergic and GABAergic modulation of the small ventrolateral pacemaker neurons of Drosophila's circadian clock neuron network." Journal of Neurophysiology 107, no. 8 (April 15, 2012): 2096–108. http://dx.doi.org/10.1152/jn.00931.2011.
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The relatively simple clock neuron network of Drosophila is a valuable model system for the neuronal basis of circadian timekeeping. Unfortunately, many key neuronal classes of this network are inaccessible to electrophysiological analysis. We have therefore adopted the use of genetically encoded sensors to address the physiology of the fly's circadian clock network. Using genetically encoded Ca2+ and cAMP sensors, we have investigated the physiological responses of two specific classes of clock neuron, the large and small ventrolateral neurons (l- and s-LNvs), to two neurotransmitters implicated in their modulation: acetylcholine (ACh) and γ-aminobutyric acid (GABA). Live imaging of l-LNv cAMP and Ca2+ dynamics in response to cholinergic agonist and GABA application were well aligned with published electrophysiological data, indicating that our sensors were capable of faithfully reporting acute physiological responses to these transmitters within single adult clock neuron soma. We extended these live imaging methods to s-LNvs, critical neuronal pacemakers whose physiological properties in the adult brain are largely unknown. Our s-LNv experiments revealed the predicted excitatory responses to bath-applied cholinergic agonists and the predicted inhibitory effects of GABA and established that the antagonism of ACh and GABA extends to their effects on cAMP signaling. These data support recently published but physiologically untested models of s-LNv modulation and lead to the prediction that cholinergic and GABAergic inputs to s-LNvs will have opposing effects on the phase and/or period of the molecular clock within these critical pacemaker neurons.
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Hill, Evan S., Caroline Moore-Kochlacs, Sunil K. Vasireddi, Terrence J. Sejnowski, and William N. Frost. "Validation of Independent Component Analysis for Rapid Spike Sorting of Optical Recording Data." Journal of Neurophysiology 104, no. 6 (December 2010): 3721–31. http://dx.doi.org/10.1152/jn.00691.2010.
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Independent component analysis (ICA) is a technique that can be used to extract the source signals from sets of signal mixtures where the sources themselves are unknown. The analysis of optical recordings of invertebrate neuronal networks with fast voltage-sensitive dyes could benefit greatly from ICA. These experiments can generate hundreds of voltage traces containing both redundant and mixed recordings of action potentials originating from unknown numbers of neurons. ICA can be used as a method for converting such complex data sets into single-neuron traces, but its accuracy for doing so has never been empirically evaluated. Here, we tested the accuracy of ICA for such blind source separation by simultaneously performing sharp electrode intracellular recording and fast voltage-sensitive dye imaging of neurons located in the central ganglia of Tritonia diomedea and Aplysia californica, using a 464-element photodiode array. After running ICA on the optical data sets, we found that in 34 of 34 cases the intracellularly recorded action potentials corresponded 100% to the spiking activity of one of the independent components returned by ICA. We also show that ICA can accurately sort action potentials into single neuron traces from a series of optical data files obtained at different times from the same preparation, allowing one to monitor the network participation of large numbers of individually identifiable neurons over several recording episodes. Our validation of the accuracy of ICA for extracting the neural activity of many individual neurons from noisy, mixed, and redundant optical recording data sets should enable the use of this powerful large-scale imaging approach for studies of invertebrate and suitable vertebrate neuronal networks.
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Arieli, A., D. Shoham, R. Hildesheim, and A. Grinvald. "Coherent spatiotemporal patterns of ongoing activity revealed by real-time optical imaging coupled with single-unit recording in the cat visual cortex." Journal of Neurophysiology 73, no. 5 (May 1, 1995): 2072–93. http://dx.doi.org/10.1152/jn.1995.73.5.2072.
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1. We examined the spatiotemporal organization of ongoing activity in cat visual areas 17 and 18, in relation to the spontaneous activity of individual neurons. To search for coherent activity, voltage-sensitive dye signals were correlated with the activity of single neurons by the use of spike-triggered averaging. In each recording session an area of at least 2 x 2 mm of cortex was imaged, with 124 diodes. In addition, electrical recordings from two isolated units, the local field potential (LFP) from the same microelectrodes, and the surface electroencephalogram (EEG) were recorded simultaneously. 2. The optical signals recorded from the dye were similar to the LFP recorded from the same site. Optical signals recorded from different cortical sites exhibited a different time course. Therefore real-time optical imaging provides information that is equivalent in many ways to multiple-site LFP recordings. 3. The spontaneous firing of single neurons was highly correlated with the optical signals and with the LFP. In 88% of the neurons recorded during spontaneous activity, a significant correlation was found between the occurrence of a spike and the optical signal recorded in a large cortical region surrounding the recording site. This result indicates that spontaneous activity of single neurons is not an independent process but is time locked to the firing or to the synaptic inputs from numerous neurons, all activated in a coherent fashion even without a sensory input. 4. For the cases showing correlation with the optical signal, 27-36% of the optical signal during spike occurrence was directly related to the occurrence of spontaneous spikes in a single neuron, over an area of 2 x 2 mm. In the same cortical area, 43-55% of the activity was directly related to the visual stimulus. 5. Surprisingly, we found that the amplitude of this coherent ongoing activity, recorded optically, was often almost as large as the activity evoked by optimal visual stimulation. The amplitude of the ongoing activity that was directly and reproducibly related to the spontaneous spikes of a single neuron was, on average, as high as 54% of the amplitude of the visually evoked response that was directly related to optimal sensory stimulation, recorded optically. 6. Coherent activity was detected even at distant cortical sites up to 6 mm apart.(ABSTRACT TRUNCATED AT 400 WORDS)
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Broadie, Kendal, Helen Sink, David Van Vactor, Douglas Fambrough, Paul M. Whitington, Michael Bate, and Corey S. Goodman. "From growth cone to synapse: the life history of the RP3 motor neuron." Development 119, Supplement (December 1, 1993): 227–38. http://dx.doi.org/10.1242/dev.119.supplement.227.
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In Drosophila, the ability to analyze the development of individually identified neurons with a variety of imaging and biophysical techniques can be complemented by sophisticated genetics and molecular biology. This powerful combination is allowing the development and function of single neurons and their synaptic connections to be unraveled at an unparalleled level of resolution. In this article, we focus on a single, identified motoneuron — RP3 — arguably the best understood neuron in the fruitfly. Many events in the life history of RP3 are well characterized, including cell migration, axon outgrowth and pathfinding within the central nervous system, pathfinding in the periphery to its appropriate muscle target domain, the specific recognition of its muscle targets, the events of synapse formation and maturation, and its mature function in the locomotion of the fly larva. Genetic analysis has revealed mutations in a number of different genes which affect specific aspects of RP3 development from axon outgrowth to synapse formation.
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Sadovsky, Alexander J., Peter B. Kruskal, Joseph M. Kimmel, Jared Ostmeyer, Florian B. Neubauer, and Jason N. MacLean. "Heuristically optimal path scanning for high-speed multiphoton circuit imaging." Journal of Neurophysiology 106, no. 3 (September 2011): 1591–98. http://dx.doi.org/10.1152/jn.00334.2011.
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Population dynamics of patterned neuronal firing are fundamental to information processing in the brain. Multiphoton microscopy in combination with calcium indicator dyes allows circuit dynamics to be imaged with single-neuron resolution. However, the temporal resolution of fluorescent measures is constrained by the imaging frequency imposed by standard raster scanning techniques. As a result, traditional raster scans limit the ability to detect the relative timing of action potentials in the imaged neuronal population. To maximize the speed of fluorescence measures from large populations of neurons using a standard multiphoton laser scanning microscope (MPLSM) setup, we have developed heuristically optimal path scanning (HOPS). HOPS optimizes the laser travel path length, and thus the temporal resolution of neuronal fluorescent measures, using standard galvanometer scan mirrors. Minimizing the scan path alone is insufficient for prolonged high-speed imaging of neuronal populations. Path stability and the signal-to-noise ratio become increasingly important factors as scan rates increase. HOPS addresses this by characterizing the scan mirror galvanometers to achieve prolonged path stability. In addition, the neuronal dwell time is optimized to sharpen the detection of action potentials while maximizing scan rate. The combination of shortest path calculation and minimization of mirror positioning time allows us to optically monitor a population of neurons in a field of view at high rates with single-spike resolution, ∼125 Hz for 50 neurons and ∼8.5 Hz for 1,000 neurons. Our approach introduces an accessible method for rapid imaging of large neuronal populations using traditional MPLSMs, facilitating new insights into neuronal circuit dynamics.
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Laine, Romain F., Gabriele S. Kaminski Schierle, Sebastian van de Linde, and Clemens F. Kaminski. "From single-molecule spectroscopy to super-resolution imaging of the neuron: a review." Methods and Applications in Fluorescence 4, no. 2 (June 27, 2016): 022004. http://dx.doi.org/10.1088/2050-6120/4/2/022004.
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Nurminen, Lauri, Markku Kilpeläinen, Pentti Laurinen, and Simo Vanni. "Area Summation in Human Visual System: Psychophysics, fMRI, and Modeling." Journal of Neurophysiology 102, no. 5 (November 2009): 2900–2909. http://dx.doi.org/10.1152/jn.00201.2009.
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Contextual modulation is a fundamental feature of sensory processing, both on perceptual and on single-neuron level. When the diameter of a visual stimulus is increased, the firing rate of a cell typically first increases (summation field) and then decreases (surround field). Such an area summation function draws a comprehensive profile of the receptive field structure of a neuron, including areas outside the classical receptive field. We investigated area summation in human vision with psychophysics and functional magnetic resonance imaging (fMRI). The stimuli were similar to those used drifting sine wave gratings in previous macaque single-cell area summation studies. A model was developed to facilitate comparison of area summation in fMRI to area summation in psychophysics and single cells. The model consisted of units with an antagonistic receptive field structure found in single cells in the primary visual cortex. The receptive field centers of the model neurons were distributed in the region of the visual field covered by a single voxel. The measured area summation functions were qualitatively similar to earlier single-cell data. The model with parameters derived from psychophysics captured the spatial structure of the summation field in the primary visual cortex as measured with fMRI. The model also generalized to a novel situation in which the neural population was displaced from the stimulus center. The current study shows that contextual modulation arises from similar spatially antagonistic and overlapping excitatory and inhibitory mechanisms, both in single cells and in human vision.
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Valdez, André B., Megan H. Papesh, David M. Treiman, Stephen D. Goldinger, and Peter N. Steinmetz. "Encoding of Race Categories by Single Neurons in the Human Brain." NeuroSci 3, no. 3 (August 5, 2022): 419–39. http://dx.doi.org/10.3390/neurosci3030031.
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Previous research has suggested that race-specific features are automatically processed during face perception, often with out-group faces treated categorically. Functional imaging has illuminated the hemodynamic correlates of this process, with fewer studies examining single-neuron responses. In the present experiment, epilepsy patients undergoing microwire recordings in preparation for surgical treatment were shown realistic computer-generated human faces, which they classified according to the emotional expression shown. Racial categories of the stimulus faces varied independently of the emotion shown, being irrelevant to the patients’ primary task. Nevertheless, we observed race-driven changes in neural firing rates in the amygdala, anterior cingulate cortex, and hippocampus. These responses were broadly distributed, with the firing rates of 28% of recorded neurons in the amygdala and 45% in the anterior cingulate cortex predicting one or more racial categories. Nearly equal proportions of neurons responded to White and Black faces (24% vs. 22% in the amygdala and 26% vs. 28% in the anterior cingulate cortex). A smaller fraction (12%) of race-responsive neurons in the hippocampus predicted only White faces. Our results imply a distributed representation of race in brain areas involved in affective judgments, decision making, and memory. They also support the hypothesis that race-specific cues are perceptually coded even when those cues are task-irrelevant.
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Kondo, Tosho, Ihori Ebinuma, Hirotaka Tanaka, Yukitoshi Nishikawa, Takaki Komiya, Mitsuru Ishikawa, and Hideyuki Okano. "Rapid and Robust Multi-Phenotypic Assay System for ALS Using Human iPS Cells with Mutations in Causative Genes." International Journal of Molecular Sciences 24, no. 8 (April 10, 2023): 6987. http://dx.doi.org/10.3390/ijms24086987.
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Amyotrophic lateral sclerosis (ALS) is a major life-threatening disease caused by motor neuron degeneration. More effective treatments through drug discovery are urgently needed. Here, we established an effective high-throughput screening system using induced pluripotent stem cells (iPSCs). Using a Tet-On-dependent transcription factor expression system carried on the PiggyBac vector, motor neurons were efficiently and rapidly generated from iPSCs by a single-step induction method. Induced iPSC transcripts displayed characteristics similar to those of spinal cord neurons. iPSC-generated motor neurons carried a mutation in fused in sarcoma (FUS) and superoxide dismutase 1 (SOD1) genes and had abnormal protein accumulation corresponding to each mutation. Calcium imaging and multiple electrode array (MEA) recordings demonstrated that ALS neurons were abnormally hyperexcitable. Noticeably, protein accumulation and hyperexcitability were ameliorated by treatment with rapamycin (mTOR inhibitor) and retigabine (Kv7 channel activator), respectively. Furthermore, rapamycin suppressed ALS neuronal death and hyperexcitability, suggesting that protein aggregate clearance through the activation of autophagy effectively normalized activity and improved neuronal survival. Our culture system reproduced several ALS phenotypes, including protein accumulation, hyperexcitability, and neuronal death. This rapid and robust phenotypic screening system will likely facilitate the discovery of novel ALS therapeutics and stratified and personalized medicine for sporadic motor neuron diseases.
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Hockley, James R. F., Toni S. Taylor, Gerard Callejo, Anna L. Wilbrey, Alex Gutteridge, Karsten Bach, Wendy J. Winchester, David C. Bulmer, Gordon McMurray, and Ewan St John Smith. "Single-cell RNAseq reveals seven classes of colonic sensory neuron." Gut 68, no. 4 (February 26, 2018): 633–44. http://dx.doi.org/10.1136/gutjnl-2017-315631.
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ObjectiveIntegration of nutritional, microbial and inflammatory events along the gut-brain axis can alter bowel physiology and organism behaviour. Colonic sensory neurons activate reflex pathways and give rise to conscious sensation, but the diversity and division of function within these neurons is poorly understood. The identification of signalling pathways contributing to visceral sensation is constrained by a paucity of molecular markers. Here we address this by comprehensive transcriptomic profiling and unsupervised clustering of individual mouse colonic sensory neurons.DesignUnbiased single-cell RNA-sequencing was performed on retrogradely traced mouse colonic sensory neurons isolated from both thoracolumbar (TL) and lumbosacral (LS) dorsal root ganglia associated with lumbar splanchnic and pelvic spinal pathways, respectively. Identified neuronal subtypes were validated by single-cell qRT-PCR, immunohistochemistry (IHC) and Ca2+-imaging.ResultsTranscriptomic profiling and unsupervised clustering of 314 colonic sensory neurons revealed seven neuronal subtypes. Of these, five neuronal subtypes accounted for 99% of TL neurons, with LS neurons almost exclusively populating the remaining two subtypes. We identify and classify neurons based on novel subtype-specific marker genes using single-cell qRT-PCR and IHC to validate subtypes derived from RNA-sequencing. Lastly, functional Ca2+-imaging was conducted on colonic sensory neurons to demonstrate subtype-selective differential agonist activation.ConclusionsWe identify seven subtypes of colonic sensory neurons using unbiased single-cell RNA-sequencing and confirm translation of patterning to protein expression, describing sensory diversity encompassing all modalities of colonic neuronal sensitivity. These results provide a pathway to molecular interrogation of colonic sensory innervation in health and disease, together with identifying novel targets for drug development.
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Campos, Pauline, Jamie J. Walker, and Patrice Mollard. "Diving into the brain: deep-brain imaging techniques in conscious animals." Journal of Endocrinology 246, no. 2 (August 2020): R33—R50. http://dx.doi.org/10.1530/joe-20-0028.
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In most species, survival relies on the hypothalamic control of endocrine axes that regulate critical functions such as reproduction, growth, and metabolism. For decades, the complexity and inaccessibility of the hypothalamic–pituitary axis has prevented researchers from elucidating the relationship between the activity of endocrine hypothalamic neurons and pituitary hormone secretion. Indeed, the study of central control of endocrine function has been largely dominated by ‘traditional’ techniques that consist of studying in vitro or ex vivo isolated cell types without taking into account the complexity of regulatory mechanisms at the level of the brain, pituitary and periphery. Nowadays, by exploiting modern neuronal transfection and imaging techniques, it is possible to study hypothalamic neuron activity in situ, in real time, and in conscious animals. Deep-brain imaging of calcium activity can be performed through gradient-index lenses that are chronically implanted and offer a ‘window into the brain’ to image multiple neurons at single-cell resolution. With this review, we aim to highlight deep-brain imaging techniques that enable the study of neuroendocrine neurons in awake animals whilst maintaining the integrity of regulatory loops between the brain, pituitary and peripheral glands. Furthermore, to assist researchers in setting up these techniques, we discuss the equipment required and include a practical step-by-step guide to performing these deep-brain imaging studies.
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Hackett, Mark J., Sally Caine, Xia Liu, Tim E. May, and Ferenc Borondics. "Development of single-beam wide-field infrared imaging to study sub-cellular neuron biochemistry." Vibrational Spectroscopy 77 (March 2015): 51–59. http://dx.doi.org/10.1016/j.vibspec.2014.12.004.
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Kayser, Christoph, Christopher I. Petkov, and Nikos K. Logothetis. "Tuning to Sound Frequency in Auditory Field Potentials." Journal of Neurophysiology 98, no. 3 (September 2007): 1806–9. http://dx.doi.org/10.1152/jn.00358.2007.
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Neurons in auditory cortex are selective for the frequency content of acoustical stimuli. Classically, this response selectivity is studied at the single-neuron level. However, current research often employs functional imaging techniques to investigate the organization of auditory cortex. The signals underlying the imaging data arise from neural mass action and reflect the properties of populations of neurons. For example, the signal used for functional magnetic resonance imaging (fMRI-BOLD) was shown to correlate with the oscillatory activity quantified by local field potentials (LFPs). This raises the questions of how the frequency selectivity in neuronal population signals compares with the tuning of spiking responses. To address this, we quantified tuning properties of auditory-evoked potentials (AEP), different frequency bands of the LFP, analog multi-unit (AMUA), and spike-sorted single- and multiunit activity in auditory cortex. The AMUA showed a close correspondence in frequency tuning to the spike-sorted activity. In contrast, for the LFP, we found a clear dissociation of high- and low-frequency bands: there was a gradual increase of tuning-curve similarity, tuning specificity, and information about the stimulus with increasing LFP frequency. Although properties of the high-frequency LFP matched those of spiking activity, the lower-frequency bands differed considerably as did the AEP. These results demonstrate that electrophysiological population responses exhibit varying degrees of frequency tuning and suggest that those functional imaging methods that are related to high-frequency oscillatory activity should well reflect the neuronal processing of sound frequency.
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Huerta, Tomas S., Bilal B. Haider, Richard Adamovich-Zeitlin, Sangeeta S. Chavan, Kevin J. Tracey, and Eric H. Chang. "Vagus nerve sensory neurons have distinct neural responses to inflammatory mediators." Journal of Immunology 208, no. 1_Supplement (May 1, 2022): 52.14. http://dx.doi.org/10.4049/jimmunol.208.supp.52.14.
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Abstract Cytokines are secreted signaling proteins that are important mediators of inflammation. While prior work has demonstrated that the level of cytokines can be regulated by nerve stimulation, the role of the nervous system in sensing these immune mediators is still poorly understood. During periods of inflammation, it has been shown that sensory signals travel up the vagus nerve to the brain. However, it is unclear how individual vagal sensory neurons encode specific immune information. Here we use in vivo calcium imaging of the nodose ganglion to monitor neural activity in individual vagus nerve sensory neurons in response to specific cytokines. Using mice that express the calcium indicator GCaMP6f in glutamatergic neurons, we imaged neurons of the nodose ganglion in situ using a 1-photon miniature microscope (Miniscope). During imaging, the proinflammatory cytokines interleukin 1β (IL-1β) and tumor necrosis factor (TNF) were applied directly to the vagus nerve. Fluorescence data was analyzed with a Python-based software CaImAn and a custom pipeline to output the single neuron activity as change in fluorescence: ΔF/F. Our results reveal that specific vagal sensory neurons respond differentially to specific immune mediators. The average amplitude, integral, and delay of TNF-responsive neurons was significantly higher than IL-1β-responsive cells (TNF vs IL-1β, p < 0.01), while having less number of peaks per response (TNF vs IL-1β, p < 0.05). This may suggest different patterns of transient neural activity associated with each particular cytokine. Further investigation into this type of neuro-immune signaling may identify novel neural targets for the treatment of inflammatory disorders. This study was funded in part by NIH/NIGMS
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Latifi, Shahrzad, Simon Mitchell, Rouhollah Habibey, Fouzhan Hosseini, Elissa Donzis, Ana María Estrada-Sánchez, H. Rezaei Nejad, Michael Levine, Peyman Golshani, and S. Thomas Carmichael. "Neuronal Network Topology Indicates Distinct Recovery Processes after Stroke." Cerebral Cortex 30, no. 12 (July 29, 2020): 6363–75. http://dx.doi.org/10.1093/cercor/bhaa191.
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Abstract Despite substantial recent progress in network neuroscience, the impact of stroke on the distinct features of reorganizing neuronal networks during recovery has not been defined. Using a functional connections-based approach through 2-photon in vivo calcium imaging at the level of single neurons, we demonstrate for the first time the functional connectivity maps during motion and nonmotion states, connection length distribution in functional connectome maps and a pattern of high clustering in motor and premotor cortical networks that is disturbed in stroke and reconstitutes partially in recovery. Stroke disrupts the network topology of connected inhibitory and excitatory neurons with distinct patterns in these 2 cell types and in different cortical areas. These data indicate that premotor cortex displays a distinguished neuron-specific recovery profile after stroke.
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Eliscovich, Carolina, Shailesh M. Shenoy, and Robert H. Singer. "Imaging mRNA and protein interactions within neurons." Proceedings of the National Academy of Sciences 114, no. 10 (February 21, 2017): E1875—E1884. http://dx.doi.org/10.1073/pnas.1621440114.
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RNA–protein interactions are essential for proper gene expression regulation, particularly in neurons with unique spatial constraints. Currently, these interactions are defined biochemically, but a method is needed to evaluate them quantitatively within morphological context. Colocalization of two-color labels using wide-field microscopy is a method to infer these interactions. However, because of chromatic aberrations in the objective lens, this approach lacks the resolution to determine whether two molecules are physically in contact or simply nearby by chance. Here, we developed a robust super registration methodology that corrected the chromatic aberration across the entire image field to within 10 nm, which is capable of determining whether two molecules are physically interacting or simply in proximity by random chance. We applied this approach to image single-molecule FISH in combination with immunofluorescence (smFISH-IF) and determined whether the association between an mRNA and binding protein(s) within a neuron was significant or accidental. We evaluated several mRNA-binding proteins identified from RNA pulldown assays to determine which of these exhibit bona fide interactions. Surprisingly, many known mRNA-binding proteins did not bind the mRNA in situ, indicating that adventitious interactions are significant using existing technology. This method provides an ability to evaluate two-color registration compatible with the scale of molecular interactions.
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Assunção, F. B., T. L. P. D. Scoppetta, B. S. Yonekura Inada, L. D. A. Martins, E. O. Narvaez, M. D. Soldatelli, L. F. Freitas, V. H. R. Marussi, C. M. S. Campos, and L. L. F. D. Amaral. "Secondary Neurodegeneration: A General Approach to Axonal and Transaxonal Degeneration." Neurographics 11, no. 2 (March 1, 2021): 111–26. http://dx.doi.org/10.3174/ng.2000050.
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CNS WM tracts are mainly composed of axons, and when these structures undergo apoptosis or lose their integrity, neurodegeneration may occur. Secondary neuronal degeneration can be classified as axonal degeneration and involves only the first neuron in a pathway (Wallerian degeneration of the corticospinal tract being its prototype) or be classified as transaxonal degeneration and involve more than a single neuron in a common pathway, usually a closed neuronal circuit, in specific tracts, such as the dentate-rubro-olivary tract, tracts of the limbic system, corticopontocerebellar tract, cranial nerve tracts, and nigrostriatal pathway. This study aimed to review the anatomy of the main CNS tracts susceptible to secondary neuronal degeneration and to illustrate, through different imaging modalities, the findings associated with this poorly explored and understood process involved in the pathophysiologic substrate of numerous neurologic diseases.Learning Objective: Recognize the anatomy of the main CNS tracts susceptible to secondary neuronal degeneration and identify its main imaging findings in different imaging modalities.
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Krishna, Saritha, Andy Daniel, Vardhaan Ambati, Clara Seibert, and Shawn Hervey-Jumper. "CNSC-29. NKCC1 SIGNALING IN GLIOBLASTOMA REGULATES NEURONAL HYPEREXCITABILITY THROUGH GABAERGIC TONE." Neuro-Oncology 25, Supplement_5 (November 1, 2023): v29. http://dx.doi.org/10.1093/neuonc/noad179.0113.
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Abstract Over 90% of patients with glioma experience tumor-associated epilepsy, however first-line treatment fails to control seizures in most patients. Thus, there is a critical need to identify novel drivers of glioblastoma-induced neuronal hyperexcitability. We therefore used high-density electrode arrays to record local field potentials in vivo from gliomas. We then developed cerebral organoid and mouse models using primary glioblastoma cells from patients and neurons derived from induced pluripotent stem cells. Single-cell RNA sequencing (13,730 cells analyzed) in this system identified genes elevated in glioma-intrinsic neurons, including the sodium-potassium-chloride co-transporter 1 (NKCC1), which mediates chloride (Cl-) influx into cells. This elevated NKCC1 expression and subsequent increase of intracellular Cl- sets the reversal potential of GABAAR-mediated currents promoting depolarizing excitatory GABAergic responses. Electrophysiological analysis of glioma-neuron co-cultures using multi-electrode array and live-cell calcium imaging demonstrated increased network burst synchrony in the presence of NKCC1-high expressing tumor cells. Single-nucleus sequencing (54,000 cells analyzed) of embryonic neurons in co-culture with GBM cells further confirmed the elevated expression of circuit assembly genes including neuronal NKCC1. Live-cell imaging of iPSC-induced neuron organoids co-cultured with NKCC1-high-and low-GBM cells revealed increased migration and integration of NKCC1-elevated tumor cells. Mechanistic and functional studies validating therapeutic vulnerabilities to NKCC1 silencing by shRNA knockdown and by the FDA-approved diuretic drug, bumetanide was performed in vitro. The reduction in neuronal synchrony induced by NKCC1 downregulation correlated with a decrease in extracellular GABA and glutamate, suggesting a strong association between excitatory GABAergic and glutamate signaling with neuronal hypersynchrony in glioblastoma. Patient-derived xenograft in vivo experiments evaluated the effect of NKCC1 on tumor growth and progression and NKCC1-high GBM cells exhibited greater tumor burden compared to control mice. Collectively, these findings reveal a novel mechanism driving neuronal hyperactivity in glioblastoma and identifies potential therapeutic vulnerabilities for the treatment of glioma-associated epilepsy.
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Wilson, C. J., and J. C. Callaway. "Coupled Oscillator Model of the Dopaminergic Neuron of the Substantia Nigra." Journal of Neurophysiology 83, no. 5 (May 1, 2000): 3084–100. http://dx.doi.org/10.1152/jn.2000.83.5.3084.
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Calcium imaging using fura-2 and whole cell recording revealed the effective location of the oscillator mechanism on dopaminergic neurons of the substantia nigra, pars compacta, in slices from rats aged 15–20 days. As previously reported, dopaminergic neurons fired in a slow rhythmic single spiking pattern. The underlying membrane potential oscillation survived blockade of sodium currents with TTX and was enhanced by blockade of voltage-sensitive potassium currents with TEA. Calcium levels increased during the subthreshold depolarizing phase of the membrane potential oscillation and peaked at the onset of the hyperpolarizing phase as expected if the pacemaker potential were due to a low-threshold calcium current and the hyperpolarizing phase to calcium-dependent potassium current. Calcium oscillations were synchronous in the dendrites and soma and were greater in the dendrites than in the soma. Average calcium levels in the dendrites overshot steady-state levels and decayed over the course of seconds after the oscillation was resumed after having been halted by hyperpolarizing currents. Average calcium levels in the soma increased slowly, taking many cycles to achieve steady state. Voltage clamp with calcium imaging revealed the voltage dependence of the somatic calcium current without the artifacts of incomplete spatial voltage control. This showed that the calcium current had little or no inactivation and was half-maximal at −40 to −30 mV. The time constant of calcium removal was measured by the return of calcium to resting levels and depended on diameter. The calcium sensitivity of the calcium-dependent potassium current was estimated by plotting the slow tail current against calcium concentration during the decay of calcium to resting levels at −60 mV. A single compartment model of the dopaminergic neuron consisting of a noninactivating low-threshold calcium current, a calcium-dependent potassium current, and a small leak current reproduced most features of the membrane potential oscillations. The same currents much more accurately reproduced the calcium transients when distributed uniformly along a tapering cable in a multicompartment model. This model represented the dopaminergic neuron as a set of electrically coupled oscillators with different natural frequencies. Each frequency was determined by the surface area to volume ratio of the compartment. This model could account for additional features of the dopaminergic neurons seen in slices, such as slow adaptation of oscillation frequency and may produce irregular firing under different coupling conditions.
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Liang, Dandan, Zhigang Xue, Jinfeng Xue, Duanyang Xie, Ke Xiong, Huixing Zhou, Fulei Zhang, et al. "Sinoatrial node pacemaker cells share dominant biological properties with glutamatergic neurons." Protein & Cell 12, no. 7 (February 6, 2021): 545–56. http://dx.doi.org/10.1007/s13238-020-00820-9.
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AbstractActivation of the heart normally begins in the sinoatrial node (SAN). Electrical impulses spontaneously released by SAN pacemaker cells (SANPCs) trigger the contraction of the heart. However, the cellular nature of SANPCs remains controversial. Here, we report that SANPCs exhibit glutamatergic neuron-like properties. By comparing the single-cell transcriptome of SANPCs with that of cells from primary visual cortex in mouse, we found that SANPCs co-clustered with cortical neurons. Tissue and cellular imaging confirmed that SANPCs contained key elements of glutamatergic neurotransmitter system, expressing genes encoding glutamate synthesis pathway (Gls), ionotropic and metabotropic glutamate receptors (Grina, Gria3, Grm1 and Grm5), and glutamate transporters (Slc17a7). SANPCs highly expressed cell markers of glutamatergic neurons (Snap25 and Slc17a7), whereas Gad1, a marker of GABAergic neurons, was negative. Functional studies revealed that inhibition of glutamate receptors or transporters reduced spontaneous pacing frequency of isolated SAN tissues and spontaneous Ca2+ transients frequency in single SANPC. Collectively, our work suggests that SANPCs share dominant biological properties with glutamatergic neurons, and the glutamatergic neurotransmitter system may act as an intrinsic regulation module of heart rhythm, which provides a potential intervention target for pacemaker cell-associated arrhythmias.
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Bulumulla, Chandima, Andrew T. Krasley, and Abraham G. Beyene. "Carbon Nanotube Sensors Enable Visualization of Dopamine Neuromodulation at the Resolution of a Single Chemical Synapse." ECS Meeting Abstracts MA2023-01, no. 9 (August 28, 2023): 1120. http://dx.doi.org/10.1149/ma2023-0191120mtgabs.
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Among the organs in our body, the brain easily remains the most intriguing in terms of its complexity and function. Nerve cells, which are the functional building blocks of the brain, operate in complex networks that underpin most of the brain’s capabilities, including ability to learn, remember, initiate and orchestrate complex movement. In systems neuroscience, behavioral assays and large-scale neuronal activity recording have broadened our understanding of the role that specific brain regions and neuronal circuits play in a behaving animal. An equally exciting aspect of neuroscience concerns itself with the cellular and molecular underpinnings of nerve cell function. Unique among all the organs, the brain’s constituent cells, neurons, need to communicate with another in intricate networks that are responsible for circuit function, and most of this communication is enabled by chemical cues that are released between neurons. Better understanding of neuronal communication via chemical release from synapses requires technologies that can help us visualize and measure the spatial and temporal dynamics of these chemical signals. Our lab seeks to address this challenge by developing optical biosensors with ultra-low detection capabilities, high spatial resolution and signal-to-noise ratio. To study chemical synapses at high spatial resolution, we use primary dopamine neuron cultures derived from rats and mice as a model system. Dopamine neuron signaling is critical for learning and motor control, and its aberration is implicated in a wide range of neurological and psychiatric disorders. Furthermore, dopamine is a neuromodulator, and it is a neurochemical that is predicted to be highly diffusive in its spatial signaling. Our lab and several others have developed ssDNA functionalized SWCNT optical sensors to study catecholaminergic neurotransmitters, including dopamine. In a recent publication we reported an assay to study dopamine effluxes from primary dopaminergic neurons using a chemi-sensitive 2D substrate (DopaFilm). DopaFilm is fabricated from solution phase SWCNT-sensors in two simple steps: (1) surface functionalization of glass coverslips using silane chemistry to anchor nanosensors (2) drop casting of nanotube sensor solution to create the 2D nanofilm followed by passivation with a thin layer of poly(D-lysine). Primary dopamine neurons plated on DopaFilm are allowed to grow and mature (2 – 6 weeks depending on the experiment). Dopamine release activity can be imaged by recording the NIR emission (900-1400 nm) and at excitation with a 785nm laser. With this technology we were able to faithfully measure dopamine concentrations as low as 1nM with DopaFilm, which has an apparent dissociation constant of 268nM. In 2D cultures, we routinely observed spontaneous and evoked dendritic and axonal DA release events with bouton level spatial resolutions and sub-second temporal resolutions. With signal-to-noise ratios above 50 and comparable on and off-kinetics to latest genetically encoded dopamine sensors (dLight1 and GRABDA), DopaFilm is by far the most sensitive technology to study dopamine chemical signaling with the resolution of a single synapse. The technology allows the study of an entire neuron at the resolution of a single synapse. We combine functional imaging data with pharmacological and genetic perturbations to dissect the role that circuit effects and specific genes (proteins) play in dopamine synthesis, packaging, and release. Additionally, by taking advantage of the NIR emission of SWCNTs, we are able to multiplex dopamine release imaging with Ca2+ activity in orthogonal channels, a feat that is yet to be demonstrated with any competing technology.
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Bowman, Adam J., Cheng Huang, Mark J. Schnitzer, and Mark A. Kasevich. "Wide-field fluorescence lifetime imaging of neuron spiking and subthreshold activity in vivo." Science 380, no. 6651 (June 23, 2023): 1270–75. http://dx.doi.org/10.1126/science.adf9725.
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The development of voltage-sensitive fluorescent probes suggests fluorescence lifetime as a promising readout for electrical activity in biological systems. Existing approaches fail to achieve the speed and sensitivity required for voltage imaging in neuroscience applications. We demonstrated that wide-field electro-optic fluorescence lifetime imaging microscopy (EO-FLIM) allows lifetime imaging at kilohertz frame-acquisition rates, spatially resolving action potential propagation and subthreshold neural activity in live adult Drosophila . Lifetime resolutions of <5 picoseconds at 1 kilohertz were achieved for single-cell voltage recordings. Lifetime readout is limited by photon shot noise, and the method provides strong rejection of motion artifacts and technical noise sources. Recordings revealed local transmembrane depolarizations, two types of spikes with distinct fluorescence lifetimes, and phase locking of spikes to an external mechanical stimulus.
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Zaslaver, Alon, Idan Liani, Oshrat Shtangel, Shira Ginzburg, Lisa Yee, and Paul W. Sternberg. "Hierarchical sparse coding in the sensory system of Caenorhabditis elegans." Proceedings of the National Academy of Sciences 112, no. 4 (January 12, 2015): 1185–89. http://dx.doi.org/10.1073/pnas.1423656112.
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Animals with compact sensory systems face an encoding problem where a small number of sensory neurons are required to encode information about its surrounding complex environment. Using Caenorhabditis elegans worms as a model, we ask how chemical stimuli are encoded by a small and highly connected sensory system. We first generated a comprehensive library of transgenic worms where each animal expresses a genetically encoded calcium indicator in individual sensory neurons. This library includes the vast majority of the sensory system in C. elegans. Imaging from individual sensory neurons while subjecting the worms to various stimuli allowed us to compile a comprehensive functional map of the sensory system at single neuron resolution. The functional map reveals that despite the dense wiring, chemosensory neurons represent the environment using sparse codes. Moreover, although anatomically closely connected, chemo- and mechano-sensory neurons are functionally segregated. In addition, the code is hierarchical, where few neurons participate in encoding multiple cues, whereas other sensory neurons are stimulus specific. This encoding strategy may have evolved to mitigate the constraints of a compact sensory system.
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Lagache, Thibault, Alison Hanson, Jesús E. Pérez-Ortega, Adrienne Fairhall, and Rafael Yuste. "Tracking calcium dynamics from individual neurons in behaving animals." PLOS Computational Biology 17, no. 10 (October 8, 2021): e1009432. http://dx.doi.org/10.1371/journal.pcbi.1009432.
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Measuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic monitoring of neuronal activity and their subsequent functional characterization. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correction and Concatenation or EMC2) that compensates for the intermittent disappearance of moving neurons by integrating local deformation information from detectable neurons. We demonstrate the accuracy and versatility of our algorithm using calcium imaging data from two-photon volumetric microscopy in visual cortex of awake mice, and from confocal microscopy in behaving Hydra, which experiences major body deformation during its contractions. We quantify the performance of our algorithm using ground truth manual tracking of neurons, along with synthetic time-lapse sequences, covering a wide range of particle motions and detectability parameters. As a demonstration of the utility of the algorithm, we monitor for several days calcium activity of the same neurons in layer 2/3 of mouse visual cortex in vivo, finding significant turnover within the active neurons across days, with only few neurons that remained active across days. Also, combining automatic tracking of single neuron activity with statistical clustering, we characterize and map neuronal ensembles in behaving Hydra, finding three major non-overlapping ensembles of neurons (CB, RP1 and RP2) whose activity correlates with contractions and elongations. Our results show that the EMC2 algorithm can be used as a robust and versatile platform for neuronal tracking in behaving animals.
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Sawada, H., F. Udaka, Y. Kishi, N. Seriu, T. Mezaki, M. Kameyama, M. Honda, and M. Tomonobu. "Single photon emission computed tomography in motor neuron disease with dementia." Neuroradiology 30, no. 6 (December 1988): 577–78. http://dx.doi.org/10.1007/bf00339706.
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Somogyvári, Zoltán, Dorottya Cserpán, István Ulbert, and Péter Érdi. "Micro-Electric Imaging: Inverse Solution for Localization of Single Neuron Currents Based on Extracellular Potential Measurements." Procedia Computer Science 7 (2011): 348–50. http://dx.doi.org/10.1016/j.procs.2011.09.086.
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Ge, Lihong, and Yang Tian. "Fluorescence Lifetime Imaging of p-tau Protein in Single Neuron with a Highly Selective Fluorescent Probe." Analytical Chemistry 91, no. 5 (February 2019): 3294–301. http://dx.doi.org/10.1021/acs.analchem.8b03992.
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