Bio

Academic Appointments


Research & Scholarship

Current Research and Scholarly Interests


Prof. Smith’s laboratory explores the development, structure, function and disorders of the brain’s neural circuitry. The lab’s experimental approach has typically begun with the invention of a new optical imaging method followed by applications of that method to attack important but previous untractable experimental challenges. Early on, Smith invented a novel fiber-optic spectrometer for calcium sensing that enabled the first detection and measurement of calcium transients in vertebrate neurons, the first quantitative measurements of presynaptic Ca transients, and the extraordinarily significant discovery of Ca influx through NMDA receptor channels. Later Smith lab imaging inventions led to numerous significant neuroscience discoveries, including retrograde actin flow within neuronal growth cones, intracellular Ca waves in astrocytes, the active role of dendritic filopodia in synaptogenesis, and the packeted delivery of synaptic protein components during synaptogenesis, and to the first optical measurements of single synaptic vesicle release, the first in vivo imaging of synaptotropic dendrite growth, and the first in vivo functional imaging measurements of visual receptive field development in a vertebrate animal. Most recently, they have invented a unique high-resolution proteomic imaging method called “array tomography”, and are now working to apply this novel method to explore the molecular architecture of cortical microcircuits in mouse and human. This work is currently focused on efforts to identify the circuit loci of the specific changes in synaptic connectivity associated with specific memory traces, i.e. the physical “engrams” of experience. This work is referenced more fully in the Smith “Biosketch” and “CV” documents to be found on this web page.

Teaching

2013-14 Courses


Postdoctoral Advisees


Publications

Journal Articles


  • Automated Analysis of a Diverse Synapse Population PLOS COMPUTATIONAL BIOLOGY Busse, B., Smith, S. 2013; 9 (3)

    Abstract

    Synapses of the mammalian central nervous system are highly diverse in function and molecular composition. Synapse diversity per se may be critical to brain function, since memory and homeostatic mechanisms are thought to be rooted primarily in activity-dependent plastic changes in specific subsets of individual synapses. Unfortunately, the measurement of synapse diversity has been restricted by the limitations of methods capable of measuring synapse properties at the level of individual synapses. Array tomography is a new high-resolution, high-throughput proteomic imaging method that has the potential to advance the measurement of unit-level synapse diversity across large and diverse synapse populations. Here we present an automated feature extraction and classification algorithm designed to quantify synapses from high-dimensional array tomographic data too voluminous for manual analysis. We demonstrate the use of this method to quantify laminar distributions of synapses in mouse somatosensory cortex and validate the classification process by detecting the presence of known but uncommon proteomic profiles. Such classification and quantification will be highly useful in identifying specific subpopulations of synapses exhibiting plasticity in response to perturbations from the environment or the sensory periphery.

    View details for DOI 10.1371/journal.pcbi.1002976

    View details for Web of Science ID 000316864200047

    View details for PubMedID 23555213

  • Sub-diffraction Limit Localization of Proteins in Volumetric Space Using Bayesian Restoration of Fluorescence Images from Ultrathin Specimens PLOS COMPUTATIONAL BIOLOGY Wang, G., Smith, S. J. 2012; 8 (8)

    Abstract

    Photon diffraction limits the resolution of conventional light microscopy at the lateral focal plane to 0.61?/NA (??=?wavelength of light, NA?=?numerical aperture of the objective) and at the axial plane to 1.4n?/NA(2) (n?=?refractive index of the imaging medium, 1.51 for oil immersion), which with visible wavelengths and a 1.4NA oil immersion objective is -220 nm and -600 nm in the lateral plane and axial plane respectively. This volumetric resolution is too large for the proper localization of protein clustering in subcellular structures. Here we combine the newly developed proteomic imaging technique, Array Tomography (AT), with its native 50-100 nm axial resolution achieved by physical sectioning of resin embedded tissue, and a 2D maximum likelihood deconvolution method, based on Bayes' rule, which significantly improves the resolution of protein puncta in the lateral plane to allow accurate and fast computational segmentation and analysis of labeled proteins. The physical sectioning of AT allows tissue specimens to be imaged at the physical optimum of modern high NA plan-apochormatic objectives. This translates to images that have little out of focus light, minimal aberrations and wave-front distortions. Thus, AT is able to provide images with truly invariant point spread functions (PSF), a property critical for accurate deconvolution. We show that AT with deconvolution increases the volumetric analytical fidelity of protein localization by significantly improving the modulation of high spatial frequencies up to and potentially beyond the spatial frequency cut-off of the objective. Moreover, we are able to achieve this improvement with no noticeable introduction of noise or artifacts and arrive at object segmentation and localization accuracies on par with image volumes captured using commercial implementations of super-resolution microscopes.

    View details for DOI 10.1371/journal.pcbi.1002671

    View details for Web of Science ID 000308553500046

    View details for PubMedID 22956902

  • Astrocyte glypicans 4 and 6 promote formation of excitatory synapses via GluA1 AMPA receptors NATURE Allen, N. J., Bennett, M. L., Foo, L. C., Wang, G. X., Chakraborty, C., Smith, S. J., Barres, B. A. 2012; 486 (7403): 410-?

    Abstract

    In the developing central nervous system (CNS), the control of synapse number and function is critical to the formation of neural circuits. We previously demonstrated that astrocyte-secreted factors powerfully induce the formation of functional excitatory synapses between CNS neurons. Astrocyte-secreted thrombospondins induce the formation of structural synapses, but these synapses are postsynaptically silent. Here we use biochemical fractionation of astrocyte-conditioned medium to identify glypican 4 (Gpc4) and glypican 6 (Gpc6) as astrocyte-secreted signals sufficient to induce functional synapses between purified retinal ganglion cell neurons, and show that depletion of these molecules from astrocyte-conditioned medium significantly reduces its ability to induce postsynaptic activity. Application of Gpc4 to purified neurons is sufficient to increase the frequency and amplitude of glutamatergic synaptic events. This is achieved by increasing the surface level and clustering, but not overall cellular protein level, of the GluA1 subunit of the AMPA (?-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) glutamate receptor (AMPAR). Gpc4 and Gpc6 are expressed by astrocytes in vivo in the developing CNS, with Gpc4 expression enriched in the hippocampus and Gpc6 enriched in the cerebellum. Finally, we demonstrate that Gpc4-deficient mice have defective synapse formation, with decreased amplitude of excitatory synaptic currents in the developing hippocampus and reduced recruitment of AMPARs to synapses. These data identify glypicans as a family of novel astrocyte-derived molecules that are necessary and sufficient to promote glutamate receptor clustering and receptivity and to induce the formation of postsynaptically functioning CNS synapses.

    View details for DOI 10.1038/nature11059

    View details for Web of Science ID 000305466800045

    View details for PubMedID 22722203

  • Deep molecular diversity of mammalian synapses: why it matters and how to measure it NATURE REVIEWS NEUROSCIENCE O'Rourke, N. A., Weiler, N. C., Micheva, K. D., Smith, S. J. 2012; 13 (6): 365-379

    Abstract

    Pioneering studies in the middle of the twentieth century revealed substantial diversity among mammalian chemical synapses and led to a widely accepted classification of synapse type on the basis of neurotransmitter molecule identity. Subsequently, powerful new physiological, genetic and structural methods have enabled the discovery of much deeper functional and molecular diversity within each traditional neurotransmitter type. Today, this deep diversity continues to pose both daunting challenges and exciting new opportunities for neuroscience. Our growing understanding of deep synapse diversity may transform how we think about and study neural circuit development, structure and function.

    View details for DOI 10.1038/nrn3170

    View details for Web of Science ID 000304197000007

    View details for PubMedID 22573027

  • High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy NATURE PROTOCOLS Tapia, J. C., Kasthuri, N., Hayworth, K. J., Schalek, R., Lichtman, J. W., Smith, S. J., Buchanan, J. 2012; 7 (2): 193-206

    Abstract

    Conventional heavy metal poststaining methods on thin sections lend contrast but often cause contamination. To avoid this problem, we tested several en bloc staining techniques to contrast tissue in serial sections mounted on solid substrates for examination by field emission scanning electron microscopy (FESEM). Because FESEM section imaging requires that specimens have higher contrast and greater electrical conductivity than transmission electron microscopy (TEM) samples, our technique uses osmium impregnation (OTO) to make the samples conductive while heavily staining membranes for segmentation studies. Combining this step with other classic heavy metal en bloc stains, including uranyl acetate (UA), lead aspartate, copper sulfate and lead citrate, produced clean, highly contrasted TEM and scanning electron microscopy (SEM) samples of insect, fish and mammalian nervous systems. This protocol takes 7-15 d to prepare resin-embedded tissue, cut sections and produce serial section images.

    View details for DOI 10.1038/nprot.2011.439

    View details for Web of Science ID 000300402300001

    View details for PubMedID 22240582

  • Three-Dimensional Microstructural Changes in Murine Abdominal Aortic Aneurysms Quantified Using Immunofluorescent Array Tomography JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY Saatchi, S., Azuma, J., Wanchoo, N., Smith, S. J., Yock, P. G., Taylor, C. A., Tsao, P. S. 2012; 60 (2): 97-109

    Abstract

    This study investigated the spatial and temporal remodeling of blood vessel wall microarchitecture and cellular morphology during abdominal aortic aneurysm (AAA) development using immunofluorescent array tomography (IAT), a high-resolution three-dimensional (3D) microscopy technology, in the murine model. Infrarenal aortas of C57BL6 mice (N=20) were evaluated at 0, 7, and 28 days after elastase or heat-inactivated elastase perfusion. Custom algorithms quantified volume fractions (VF) of elastin, smooth muscle cell (SMC) actin, and adventitial collagen type I, as well as elastin thickness, elastin fragmentation, non-adventitial wall thickness, and nuclei amount. The 3D renderings depicted elastin and collagen type I degradation and SMC morphological changes. Elastin VF decreased 37.5% (p<0.01), thickness decreased 48.9%, and fragmentation increased 449.7% (p<0.001) over 28 days. SMC actin VF decreased 78.3% (p<0.001) from days 0 to 7 and increased 139.7% (p<0.05) from days 7 to 28. Non-adventitial wall thickness increased 61.1%, medial nuclei amount increased 159.1% (p<0.01), and adventitial collagen type I VF decreased 64.1% (p<0.001) over 28 days. IAT and custom image analysis algorithms have enabled robust quantification of vessel wall content, microstructure, and organization to help elucidate the dynamics of vascular remodeling during AAA development.

    View details for DOI 10.1369/0022155411433066

    View details for Web of Science ID 000299481300001

    View details for PubMedID 22140132

  • Bidirectional Regulation of Dendritic Voltage-Gated Potassium Channels by the Fragile X Mental Retardation Protein NEURON Lee, H. Y., Ge, W., Huang, W., He, Y., Wang, G. X., Rowson-Baldwin, A., Smith, S. J., Jan, Y. N., Jan, L. Y. 2011; 72 (4): 630-642

    Abstract

    How transmitter receptors modulate neuronal signaling by regulating voltage-gated ion channel expression remains an open question. Here we report dendritic localization of mRNA of Kv4.2 voltage-gated potassium channel, which regulates synaptic plasticity, and its local translational regulation by fragile X mental retardation protein (FMRP) linked to fragile X syndrome (FXS), the most common heritable mental retardation. FMRP suppression of Kv4.2 is revealed by elevation of Kv4.2 in neurons from fmr1 knockout (KO) mice and in neurons expressing Kv4.2-3'UTR that binds FMRP. Moreover, treating hippocampal slices from fmr1 KO mice with Kv4 channel blocker restores long-term potentiation induced by moderate stimuli. Surprisingly, recovery of Kv4.2 after N-methyl-D-aspartate receptor (NMDAR)-induced degradation also requires FMRP, likely due to NMDAR-induced FMRP dephosphorylation, which turns off FMRP suppression of Kv4.2. Our study of FMRP regulation of Kv4.2 deepens our knowledge of NMDAR signaling and reveals a FMRP target of potential relevance to FXS.

    View details for DOI 10.1016/j.neuron.2011.09.033

    View details for Web of Science ID 000297180100013

    View details for PubMedID 22099464

  • Large-Scale Automated Histology in the Pursuit of Connectomes JOURNAL OF NEUROSCIENCE Kleinfeld, D., Bharioke, A., Blinder, P., Bock, D. D., Briggman, K. L., Chklovskii, D. B., Denk, W., Helmstaedter, M., Kaufhold, J. P., Lee, W. A., Meyer, H. S., Micheva, K. D., Oberlaender, M., Prohaska, S., Reid, R. C., Smith, S. J., Takemura, S., Tsai, P. S., Sakmann, B. 2011; 31 (45): 16125-16138

    Abstract

    How does the brain compute? Answering this question necessitates neuronal connectomes, annotated graphs of all synaptic connections within defined brain areas. Further, understanding the energetics of the brain's computations requires vascular graphs. The assembly of a connectome requires sensitive hardware tools to measure neuronal and neurovascular features in all three dimensions, as well as software and machine learning for data analysis and visualization. We present the state of the art on the reconstruction of circuits and vasculature that link brain anatomy and function. Analysis at the scale of tens of nanometers yields connections between identified neurons, while analysis at the micrometer scale yields probabilistic rules of connection between neurons and exact vascular connectivity.

    View details for DOI 10.1523/JNEUROSCI.4077-11.2011

    View details for Web of Science ID 000296799700012

    View details for PubMedID 22072665

  • The Use of Immunofluorescent Array Tomography to Study the Three-Dimensional Microstructure of Murine Blood Vessels CELLULAR AND MOLECULAR BIOENGINEERING Saatchi, S., Wanchoo, N., Azuma, J., Smith, S. J., Tsao, P. S., Yock, P. G., Taylor, C. A. 2011; 4 (2): 311-323
  • Characterization of genetically targeted neuron types in the zebrafish optic tectum FRONTIERS IN NEURAL CIRCUITS Robles, E., Smith, S. J., Baier, H. 2011; 5

    Abstract

    The optically transparent larval zebrafish is ideally suited for in vivo analyses of neural circuitry controlling visually guided behaviors. However, there is a lack of information regarding specific cell types in the major retinorecipient brain region of the fish, the optic tectum. Here we report the characterization of three previously unidentified tectal cell types that are specifically labeled by dlx5/6 enhancer elements. In vivo laser-scanning microscopy in conjunction with ex vivo array tomography revealed that these neurons differ in their morphologies, synaptic connectivity, and neurotransmitter phenotypes. The first type is an excitatory bistratified periventricular interneuron that forms a dendritic arbor in the retinorecipient stratum fibrosum et griseum superficiale (SFGS) and an axonal arbor in the stratum griseum centrale (SGC). The second type, a GABAergic non-stratified periventricular interneuron, extends a bushy arbor containing both dendrites and axons into the SGC and the deepest sublayers of the SFGS. The third type is a GABAergic periventricular projection neuron that extends a dendritic arbor into the SGC and a long axon to the torus semicircularis, medulla oblongata, and anterior hindbrain. Interestingly, the same axons form en passant synapses within the deepest neuropil layer of the tectum, the stratum album centrale. This approach revealed several novel aspects of tectal circuitry, including: (1) a glutamatergic mode of transmission from the superficial, retinorecipient neuropil layers to the deeper, output layers, (2) the presence of interneurons with mixed dendrite/axon arbors likely involved in local processing, and (3) a heretofore unknown GABAergic tectofugal projection to midbrain and hindbrain. These observations establish a framework for studying the morphological and functional differentiation of neural circuits in the zebrafish visual system.

    View details for DOI 10.3389/fncir.2011.00001

    View details for Web of Science ID 000289442400001

    View details for PubMedID 21390291

  • Single-Synapse Analysis of a Diverse Synapse Population: Proteomic Imaging Methods and Markers NEURON Micheva, K. D., Busse, B., Weiler, N. C., O'Rourke, N., Smith, S. J. 2010; 68 (4): 639-653

    Abstract

    A lack of methods for measuring the protein compositions of individual synapses in situ has so far hindered the exploration and exploitation of synapse molecular diversity. Here, we describe the use of array tomography, a new high-resolution proteomic imaging method, to determine the composition of glutamate and GABA synapses in somatosensory cortex of Line-H-YFP Thy-1 transgenic mice. We find that virtually all synapses are recognized by antibodies to the presynaptic phosphoprotein synapsin I, while antibodies to 16 other synaptic proteins discriminate among 4 subtypes of glutamatergic synapses and GABAergic synapses. Cell-specific YFP expression in the YFP-H mouse line allows synapses to be assigned to specific presynaptic and postsynaptic partners and reveals that a subpopulation of spines on layer 5 pyramidal cells receives both VGluT1-subtype glutamatergic and GABAergic synaptic inputs. These results establish a means for the high-throughput acquisition of proteomic data from individual cortical synapses in situ.

    View details for DOI 10.1016/j.neuron.2010.09.024

    View details for Web of Science ID 000285079500005

    View details for PubMedID 21092855

  • Array tomography: high-resolution three-dimensional immunofluorescence. Cold Spring Harbor protocols Micheva, K. D., O'Rourke, N., Busse, B., Smith, S. J. 2010; 2010 (11): pdb top89-?

    Abstract

    Array tomography, which is described in this article, is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Although the fabrication procedures can be relatively difficult, the high resolution, depth invariance, and molecular discrimination offered by array tomography justify the effort involved. Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture.

    View details for DOI 10.1101/pdb.top89

    View details for PubMedID 21041404

  • Array tomography: imaging stained arrays. Cold Spring Harbor protocols Micheva, K. D., O'Rourke, N., Busse, B., Smith, S. J. 2010; 2010 (11): pdb prot5526-?

    Abstract

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. In this protocol, tissue arrays are imaged using conventional wide-field fluorescence microscopy. Images can be captured manually or, with the appropriate software and hardware, the process can be automated.

    View details for DOI 10.1101/pdb.prot5526

    View details for PubMedID 21041399

  • Array tomography: production of arrays. Cold Spring Harbor protocols Micheva, K. D., O'Rourke, N., Busse, B., Smith, S. J. 2010; 2010 (11): pdb prot5524-?

    Abstract

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time consuming and require some practice to perfect. This protocol describes the sectioning of embedded tissues and the mounting of the serial arrays. The procedures require some familiarity with the techniques used for ultramicrotome sectioning for electron microscopy.

    View details for DOI 10.1101/pdb.prot5524

    View details for PubMedID 21041397

  • Array tomography: immunostaining and antibody elution. Cold Spring Harbor protocols Micheva, K. D., O'Rourke, N., Busse, B., Smith, S. J. 2010; 2010 (11): pdb prot5525-?

    Abstract

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. In this protocol, tissue arrays are prepared for imaging by tagging with primary antibodies against specific cellular targets, followed by labeling with fluorescent secondary antibodies. Alternatively, fluorescent proteins that have been introduced into the tissue before dissection can be used.

    View details for DOI 10.1101/pdb.prot5525

    View details for PubMedID 21041398

  • Array tomography: rodent brain fixation and embedding. Cold Spring Harbor protocols Micheva, K. D., O'Rourke, N., Busse, B., Smith, S. J. 2010; 2010 (11): pdb prot5523-?

    Abstract

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. This protocol describes the fixation and processing required to prepare tissues for immunofluorescence array tomography.

    View details for DOI 10.1101/pdb.prot5523

    View details for PubMedID 21041396

  • Array tomography: semiautomated image alignment. Cold Spring Harbor protocols Micheva, K. D., O'Rourke, N., Busse, B., Smith, S. J. 2010; 2010 (11): pdb prot5527-?

    Abstract

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving.

    View details for DOI 10.1101/pdb.prot5527

    View details for PubMedID 21041400

  • Circadian and Homeostatic Regulation of Structural Synaptic Plasticity in Hypocretin Neurons NEURON Appelbaum, L., Wang, G., Yokogawa, T., Skariah, G. M., Smith, S. J., Mourrain, P., Mignot, E. 2010; 68 (1): 87-98

    Abstract

    Neurons exhibit rhythmic activity that ultimately affects behavior such as sleep. In living zebrafish larvae, we used time-lapse two-photon imaging of the presynaptic marker synaptophysin in hypocretin/orexin (HCRT) neurons to determine the dynamics of synaptic modifications during the day and night. We observed circadian rhythmicity in synapse number in HCRT axons. This rhythm is regulated primarily by the circadian clock but is also affected by sleep deprivation. Furthermore, NPTX2, a protein implicated in AMPA receptor clustering, modulates circadian synaptic changes. In zebrafish, nptx2b is a rhythmic gene that is mostly expressed in hypothalamic and pineal gland cells. Arrhythmic transgenic nptx2b overexpression (hcrt:NPTX2b) increases synapse number and abolishes rhythmicity in HCRT axons. Finally, hcrt:NPTX2b fish are resistant to the sleep-promoting effects of melatonin. This behavioral effect is consistent with NPTX2b-mediated increased activity of HCRT circuitry. These data provide real-time in vivo evidence of circadian and homeostatic regulation of structural synaptic plasticity.

    View details for DOI 10.1016/j.neuron.2010.09.006

    View details for Web of Science ID 000283704200010

    View details for PubMedID 20920793

  • Visualizing the Distribution of Synapses from Individual Neurons in the Mouse Brain PLOS ONE Li, L., Tasic, B., Micheva, K. D., Ivanov, V. M., Spletter, M. L., Smith, S. J., Luo, L. 2010; 5 (7)

    Abstract

    Proper function of the mammalian brain relies on the establishment of highly specific synaptic connections among billions of neurons. To understand how complex neural circuits function, it is crucial to precisely describe neuronal connectivity and the distributions of synapses to and from individual neurons.In this study, we present a new genetic synaptic labeling method that relies on expression of a presynaptic marker, synaptophysin-GFP (Syp-GFP) in individual neurons in vivo. We assess the reliability of this method and use it to analyze the spatial patterning of synapses in developing and mature cerebellar granule cells (GCs). In immature GCs, Syp-GFP is distributed in both axonal and dendritic regions. Upon maturation, it becomes strongly enriched in axons. In mature GCs, we analyzed synapses along their ascending segments and parallel fibers. We observe no differences in presynaptic distribution between GCs born at different developmental time points and thus having varied depths of projections in the molecular layer. We found that the mean densities of synapses along the parallel fiber and the ascending segment above the Purkinje cell (PC) layer are statistically indistinguishable, and higher than previous estimates. Interestingly, presynaptic terminals were also found in the ascending segments of GCs below and within the PC layer, with the mean densities two-fold lower than that above the PC layer. The difference in the density of synapses in these parts of the ascending segment likely reflects the regional differences in postsynaptic target cells of GCs.The ability to visualize synapses of single neurons in vivo is valuable for studying synaptogenesis and synaptic plasticity within individual neurons as well as information flow in neural circuits.

    View details for DOI 10.1371/journal.pone.0011503

    View details for Web of Science ID 000279715300014

    View details for PubMedID 20634890

  • Sleep-wake regulation and hypocretin-melatonin interaction in zebrafish PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Appelbaum, L., Wang, G. X., Maro, G. S., Mori, R., Tovin, A., Marin, W., Yokogawa, T., Kawakami, K., Smith, S. J., Gothilf, Y., Mignot, E., Mourrain, P. 2009; 106 (51): 21942-21947

    Abstract

    In mammals, hypocretin/orexin (HCRT) neuropeptides are important sleep-wake regulators and HCRT deficiency causes narcolepsy. In addition to fragmented wakefulness, narcoleptic mammals also display sleep fragmentation, a less understood phenotype recapitulated in the zebrafish HCRT receptor mutant (hcrtr-/-). We therefore used zebrafish to study the potential mediators of HCRT-mediated sleep consolidation. Similar to mammals, zebrafish HCRT neurons express vesicular glutamate transporters indicating conservation of the excitatory phenotype. Visualization of the entire HCRT circuit in zebrafish stably expressing hcrt:EGFP revealed parallels with established mammalian HCRT neuroanatomy, including projections to the pineal gland, where hcrtr mRNA is expressed. As pineal-produced melatonin is a major sleep-inducing hormone in zebrafish, we further studied how the HCRT and melatonin systems interact functionally. mRNA level of arylalkylamine-N-acetyltransferase (AANAT2), a key enzyme of melatonin synthesis, is reduced in hcrtr-/- pineal gland during the night. Moreover, HCRT perfusion of cultured zebrafish pineal glands induces melatonin release. Together these data indicate that HCRT can modulate melatonin production at night. Furthermore, hcrtr-/- fish are hypersensitive to melatonin, but not other hypnotic compounds. Subthreshold doses of melatonin increased the amount of sleep and consolidated sleep in hcrtr-/- fish, but not in the wild-type siblings. These results demonstrate the existence of a functional HCRT neurons-pineal gland circuit able to modulate melatonin production and sleep consolidation.

    View details for DOI 10.1073/pnas.906637106

    View details for Web of Science ID 000272994200086

    View details for PubMedID 19966231

  • Classical MHCI Molecules Regulate Retinogeniculate Refinement and Limit Ocular Dominance Plasticity NEURON Datwani, A., McConnell, M. J., Kanold, P. O., Micheva, K. D., Busse, B., Shamloo, M., Smith, S. J., Shatz, C. J. 2009; 64 (4): 463-470

    Abstract

    Major histocompatibility complex class I (MHCI) genes were discovered unexpectedly in healthy CNS neurons in a screen for genes regulated by neural activity. In mice lacking just 2 of the 50+ MHCI genes H2-K(b) and H2-D(b), ocular dominance (OD) plasticity is enhanced. Mice lacking PirB, an MHCI receptor, have a similar phenotype. H2-K(b) and H2-D(b) are expressed not only in visual cortex, but also in lateral geniculate nucleus (LGN), where protein localization correlates strongly with synaptic markers and complement protein C1q. In K(b)D(b-/-) mice, developmental refinement of retinogeniculate projections is impaired, similar to C1q(-/-) mice. These phenotypes in K(b)D(b-/-) mice are strikingly similar to those in beta2 m(-/-)TAP1(-/-) mice, which lack cell surface expression of all MHCIs, implying that H2-K(b) and H2-D(b) can account for observed changes in synapse plasticity. H2-K(b) and H2-D(b) ligands, signaling via neuronal MHCI receptors, may enable activity-dependent remodeling of brain circuits during developmental critical periods.

    View details for DOI 10.1016/j.neuron.2009.10.015

    View details for Web of Science ID 000272378900005

    View details for PubMedID 19945389

  • Gabapentin Receptor alpha 2 delta-1 Is a Neuronal Thrombospondin Receptor Responsible for Excitatory CNS Synaptogenesis CELL Eroglu, C., Allen, N. J., Susman, M. W., O'Rourke, N. A., Park, C. Y., Oezkan, E., Chakraborty, C., Mulinyawe, S. B., Annis, D. S., Huberman, A. D., Green, E. M., Lawler, J., Dolmetsch, R., Garcia, K. C., Smith, S. J., Luo, Z. D., Rosenthal, A., Mosher, D. F., Barres, B. A. 2009; 139 (2): 380-392

    Abstract

    Synapses are asymmetric cellular adhesions that are critical for nervous system development and function, but the mechanisms that induce their formation are not well understood. We have previously identified thrombospondin as an astrocyte-secreted protein that promotes central nervous system (CNS) synaptogenesis. Here, we identify the neuronal thrombospondin receptor involved in CNS synapse formation as alpha2delta-1, the receptor for the anti-epileptic and analgesic drug gabapentin. We show that the VWF-A domain of alpha2delta-1 interacts with the epidermal growth factor-like repeats common to all thrombospondins. alpha2delta-1 overexpression increases synaptogenesis in vitro and in vivo and is required postsynaptically for thrombospondin- and astrocyte-induced synapse formation in vitro. Gabapentin antagonizes thrombospondin binding to alpha2delta-1 and powerfully inhibits excitatory synapse formation in vitro and in vivo. These findings identify alpha2delta-1 as a receptor involved in excitatory synapse formation and suggest that gabapentin may function therapeutically by blocking new synapse formation.

    View details for DOI 10.1016/j.cell.2009.09.025

    View details for Web of Science ID 000270857500020

    View details for PubMedID 19818485

  • Oligomeric amyloid beta associates with postsynaptic densities and correlates with excitatory synapse loss near senile plaques PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Koffie, R. M., Meyer-Luehmann, M., Hashimoto, T., Adams, K. W., Mielke, M. L., Garcia-Alloza, M., Micheva, K. D., Smith, S. J., Kim, M. L., Lee, V. M., Hyman, B. T., Spires-Jones, T. L. 2009; 106 (10): 4012-4017

    Abstract

    Synapse loss correlates with a cognitive decline in Alzheimer's disease (AD), but whether this is caused by fibrillar deposits known as senile plaques or soluble oligomeric forms of amyloid beta (Abeta) is controversial. By using array tomography, a technique that combines ultrathin sectioning of tissue with immunofluorescence, allowing precise quantification of small structures, such as synapses, we have tested the hypothesis that oligomeric Abeta surrounding plaques contributes to synapse loss in a mouse model of AD. We find that senile plaques are surrounded by a halo of oligomeric Abeta. Analysis of >14,000 synapses (represented by PSD95-stained excitatory synapses) shows that there is a 60% loss of excitatory synapses in the halo of oligomeric Abeta surrounding plaques and that the density increases to reach almost control levels in volumes further than 50 microm from a plaque in an approximately linear fashion (linear regression, r(2) = 0.9; P < 0.0001). Further, in transgenic cortex, microdeposits of oligomeric Abeta associate with a subset of excitatory synapses, which are significantly smaller than those not in contact with oligomeric Abeta. The proportion of excitatory synapses associated with Abeta correlates with decreasing density (correlation, -0.588; P < 0.0001). These data show that senile plaques are a potential reservoir of oligomeric Abeta, which colocalizes with the postsynaptic density and is associated with spine collapse, reconciling the apparently competing schools of thought of "plaque" vs. "oligomeric Abeta" as the synaptotoxic species in the brain of AD patients.

    View details for DOI 10.1073/pnas.0811698106

    View details for Web of Science ID 000264036900066

    View details for PubMedID 19228947

  • ELASTIC SOURCE SELECTION FOR IN VIVO IMAGING OF NEURONAL ENSEMBLES 2009 IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING: FROM NANO TO MACRO, VOLS 1 AND 2 Grosenick, L., Anderson, T., Smith, S. J. 2009: 1263-1266
  • Seeing Circuits Assemble NEURON Lichtman, J. W., Smith, S. J. 2008; 60 (3): 441-448

    Abstract

    Developmental neurobiology has been greatly invigorated by a recent string of breakthroughs in molecular biology and optical physics that permit direct in vivo observation of neural circuit assembly. The imaging done thus far suggests that as brains are built, a significant amount of unbuilding is also occurring. We offer the view that this tumult is the result of the intersecting behaviors of the many single-celled creatures (i.e., neurons, glia, and progenitors) that inhabit brains. New tools will certainly be needed if we wish to monitor the myriad cooperative and competitive interactions at play in the cellular society that builds brains.

    View details for DOI 10.1016/j.neuron.2008.10.040

    View details for Web of Science ID 000260983800015

    View details for PubMedID 18995818

  • Low-frequency noise characterization of near-IR VCSELs for functional brain imaging PHOTONIC THERAPEUTICS AND DIAGNOSTICS IV Lee, T. T., Lim, P. G., Harris, J. S., Shenoy, K. V., Smith, S. J. 2008; 6842

    View details for DOI 10.1117/12.764143

    View details for Web of Science ID 000255314100050

  • The classical complement cascade mediates CNS synapse elimination CELL Stevens, B., Allen, N. J., Vazquez, L. E., Howell, G. R., Christopherson, K. S., Nouri, N., Micheva, K. D., Mehalow, A. K., Huberman, A. D., Stafford, B., Sher, A., Litke, A. M., Lambris, J. D., Smith, S. J., John, S. W., Barres, B. A. 2007; 131 (6): 1164-1178

    Abstract

    During development, the formation of mature neural circuits requires the selective elimination of inappropriate synaptic connections. Here we show that C1q, the initiating protein in the classical complement cascade, is expressed by postnatal neurons in response to immature astrocytes and is localized to synapses throughout the postnatal CNS and retina. Mice deficient in complement protein C1q or the downstream complement protein C3 exhibit large sustained defects in CNS synapse elimination, as shown by the failure of anatomical refinement of retinogeniculate connections and the retention of excess retinal innervation by lateral geniculate neurons. Neuronal C1q is normally downregulated in the adult CNS; however, in a mouse model of glaucoma, C1q becomes upregulated and synaptically relocalized in the adult retina early in the disease. These findings support a model in which unwanted synapses are tagged by complement for elimination and suggest that complement-mediated synapse elimination may become aberrantly reactivated in neurodegenerative disease.

    View details for DOI 10.1016/j.cell.2007.10.036

    View details for Web of Science ID 000252217100023

    View details for PubMedID 18083105

  • Circuit reconstruction tools today CURRENT OPINION IN NEUROBIOLOGY Smith, S. J. 2007; 17 (5): 601-608

    Abstract

    To understand how a brain processes information, we must understand the structure of its neural circuits-especially circuit interconnection topologies and the cell and synapse molecular architectures that determine circuit-signaling dynamics. Our information on these key aspects of neural circuit structure has remained incomplete and fragmentary, however, because of limitations of the best available imaging methods. Now, new transgenic tool mice and new image acquisition tools appear poised to permit very significant advances in our abilities to reconstruct circuit connection topologies and molecular architectures.

    View details for DOI 10.1016/j.conb.2007.11.004

    View details for Web of Science ID 000252835100015

    View details for PubMedID 18082394

  • Array tomography: A new tool for Imaging the molecular architecture and ultrastructure of neural circuits NEURON Micheva, K. D., Smith, S. J. 2007; 55 (1): 25-36

    Abstract

    Many biological functions depend critically upon fine details of tissue molecular architecture that have resisted exploration by existing imaging techniques. This is particularly true for nervous system tissues, where information processing function depends on intricate circuit and synaptic architectures. Here, we describe a new imaging method, called array tomography, which combines and extends superlative features of modern optical fluorescence and electron microscopy methods. Based on methods for constructing and repeatedly staining and imaging ordered arrays of ultrathin (50-200 nm), resin-embedded serial sections on glass microscope slides, array tomography allows for quantitative, high-resolution, large-field volumetric imaging of large numbers of antigens, fluorescent proteins, and ultrastructure in individual tissue specimens. Compared to confocal microscopy, array tomography offers the advantage of better spatial resolution, in particular along the z axis, as well as depth-independent immunofluorescent staining. The application of array tomography can reveal important but previously unseen features of brain molecular architecture.

    View details for DOI 10.1016/j.neuron.2007.06.014

    View details for Web of Science ID 000248010700006

    View details for PubMedID 17610815

  • Integrated semiconductor optical sensors for cellular and neural imaging APPLIED OPTICS Levi, O., Lee, T. T., Lee, M. M., Smith, S. J., Harris, J. S. 2007; 46 (10): 1881-1889

    Abstract

    We review integrated optical sensors for functional brain imaging, localized index-of-refraction sensing as part of a lab-on-a-chip, and in vivo continuous monitoring of tumor and cancer stem cells. We present semiconductor-based sensors and imaging systems for these applications. Measured intrinsic optical signals and tissue optics simulations indicate the need for high dynamic range and low dark-current neural sensors. Simulated and measured reflectance spectra from our guided resonance filter demonstrate the capability for index-of-refraction sensing on cellular scales, compatible with integrated biosensors. Finally, we characterized a thermally evaporated emission filter that can be used to improve sensitivity for in vivo fluorescence sensing.

    View details for Web of Science ID 000245290300035

    View details for PubMedID 17356634

  • Pregabalin reduces the release of synaptic vesicles from cultured hippocampal neurons MOLECULAR PHARMACOLOGY Micheva, K. D., Taylor, C. P., Smith, S. J. 2006; 70 (2): 467-476

    Abstract

    Pregabalin [S-[+]-3-isobutylGABA or (S)-3-(aminomethyl)-5-methylhexanoic acid, Lyrica] is an anticonvulsant and analgesic medication that is both structurally and pharmacologically related to gabapentin (Neurontin; Pfizer Inc., New York, NY). Previous studies have shown that pregabalin reduces the release of neurotransmitters in several in vitro preparations, although the molecular details of these effects are less clear. The present study was performed using living cultured rat hippocampal neurons with the synaptic vesicle fluorescent dye probe FM4-64 to determine details of the action of pregabalin to reduce neurotransmitter release. Our results indicate that pregabalin treatment, at concentrations that are therapeutically relevant, slightly but significantly reduces the emptying of neurotransmitter vesicles from presynaptic sites in living neurons. Dye release is reduced in both glutamic acid decarboxylase (GAD)-immunoreactive and GAD-negative (presumed glutamatergic) synaptic terminals. Furthermore, both calcium-dependent release and hyperosmotic (calcium-independent) dye release are reduced by pregabalin. The effects of pregabalin on dye release are masked in the presence of l-isoleucine, consistent with the fact that both of these compounds have a high binding affinity to the calcium channel alpha(2)-delta protein. The effect of pregabalin is not apparent in the presence of an N-methyl-d-aspartate (NMDA) antagonist [D(-)-2-amino-5-phosphonopentanoic acid], suggesting that pregabalin action depends on NMDA receptor activation. Finally, the action of pregabalin on dye release is most apparent before and early during a train of electrical stimuli when vesicle release preferentially involves the readily releasable pool.

    View details for DOI 10.1124/mol.106.023309

    View details for Web of Science ID 000239117900007

    View details for PubMedID 16641316

  • Evidence from in vivo imaging that synaptogenesis guides the growth and branching of axonal arbors by two distinct mechanisms JOURNAL OF NEUROSCIENCE Meyer, M. P., Smith, S. J. 2006; 26 (13): 3604-3614

    Abstract

    To explore the relationship between axon arbor growth and synaptogenesis, developing retinal ganglion cell (RGC) axon arbors in zebrafish optic tectum were imaged in vivo at high temporal and spatial resolution using two-photon microscopy. Individual RGC axons were dually labeled by expression of a cytosolic red fluorescent protein (DsRed Express) to mark arbor structure and a fusion of the synaptic vesicle protein synaptophysin with green fluorescent protein (Syp:GFP) to mark presynaptic vesicles. Analysis of time-lapse sequences acquired at 10 min intervals revealed unexpectedly rapid kinetics of both axon branch and vesicle cluster turnover. Nascent axonal branches exhibited short average lifetimes of 19 min, and only 17% of newly extended axonal processes persisted for periods exceeding 3 h. The majority (70%) of Syp:GFP puncta formed on newly extended axonal processes. Syp:GFP puncta also exhibited short average lifetimes of 30 min, and only 34% of puncta were stabilized for periods exceeding 3 h. Moreover, strongly correlated dynamics of Syp:GFP puncta and branch structure suggest that synaptogenesis exerts strong influences on both the extension and the selective stabilization of nascent branches. First, new branches form almost exclusively at newly formed Syp:GFP puncta. Second, stabilized nascent branches invariably bear Syp:GFP puncta, and the detailed dynamics of branch retraction suggest strongly that nascent synapses can act at branch tips to arrest retraction. These observations thus provide evidence that synaptogenesis guides axon arbor growth by first promoting initial branch extension and second by selective branch stabilization.

    View details for DOI 10.1523/JNEUROSCI.0223-06.2006

    View details for Web of Science ID 000236363400027

    View details for PubMedID 16571769

  • Integrated semiconductor optical sensors for chronic, minimally-invasive imaging of brain function 2006 28TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-15 Lee, T. T., Levi, O., Cang, J., Kaneko, M., Stryker, M. P., Smith, S. J., Shenoy, K. V., Harris, J. S. 2006: 2443-2446
  • Integrated semiconductor optical sensors for chronic, minimally-invasive imaging of brain function. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference Lee, T. T., Levi, O., Cang, J., Kaneko, M., Stryker, M. P., Smith, S. J., Shenoy, K. V., Harris, J. S. 2006; 1: 1025-1028

    Abstract

    Intrinsic optical signal (IOS) imaging is a widely accepted technique for imaging brain activity. We propose an integrated device consisting of interleaved arrays of gallium arsenide (GaAs) based semiconductor light sources and detectors operating at telecommunications wavelengths in the near-infrared. Such a device will allow for long-term, minimally invasive monitoring of neural activity in freely behaving subjects, and will enable the use of structured illumination patterns to improve system performance. In this work we describe the proposed system and show that near-infrared IOS imaging at wavelengths compatible with semiconductor devices can produce physiologically significant images in mice, even through skull.

    View details for PubMedID 17946016

  • Strong effects of subphysiological temperature on the function and plasticity of mammalian presynaptic terminals JOURNAL OF NEUROSCIENCE Micheva, K. D., Smith, S. J. 2005; 25 (33): 7481-7488

    Abstract

    Most cellular processes are known to be strongly temperature dependent. Nevertheless, a large fraction of studies of mammalian synaptic function have been and are performed near room temperature (i.e., at least 10 degrees C below physiological temperature). Here, we examined the effects of temperature on presynaptic function in primary cultures of rat hippocampal neurons. FM dyes, VAMP (vesicle-associated membrane protein)-GFP (green fluorescent protein) transfection, and HRP uptake were used to quantify various aspects of synaptic vesicle recycling. Our results show that there are very substantial differences in synaptic vesicle recycling at physiological temperature as opposed to the common, lower experimental temperatures. At 37 degrees C, compared with 23 degrees C, the speed of both exocytosis and endocytosis was higher. The size of the recycling vesicle pool (in both number of vesicles and spatial extent) was twofold larger at 37 degrees C. In addition, although repeated 10 Hz electrical stimulation caused an NMDA receptor-dependent enlargement (averaging 170%) of the measurable recycling vesicle pool at 23 degrees C, the same stimulus repetition had no effect at 37 degrees C. These results show that it is potentially misleading to extend conclusions drawn about vesicle function or presynaptic plasticity at lowered experimental temperature to physiological conditions and that much new experimental work at the higher physiological temperature range will be needed to understand the true parameters of presynaptic functions.

    View details for DOI 10.1523/JNEUROSCI.1801-05.2005

    View details for Web of Science ID 000231264500001

    View details for PubMedID 16107635

  • Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Okumoto, S., Looger, L. L., Micheva, K. D., Reimer, R. J., Smith, S. J., Frommer, W. B. 2005; 102 (24): 8740-8745

    Abstract

    Glutamate is the predominant excitatory neurotransmitter in the mammalian brain. Once released, its rapid removal from the synaptic cleft is critical for preventing excitotoxicity and spillover to neighboring synapses. Despite consensus on the role of glutamate in normal and disease physiology, technical issues limit our understanding of its metabolism in intact cells. To monitor glutamate levels inside and at the surface of living cells, genetically encoded nanosensors were developed. The fluorescent indicator protein for glutamate (FLIPE) consists of the glutamate/aspartate binding protein ybeJ from Escherichia coli fused to two variants of the green fluorescent protein. Three sensors with lower affinities for glutamate were created by mutation of residues peristeric to the ybeJ binding pocket. In the presence of ligands, FLIPEs show a concentration-dependent decrease in FRET efficiency. When expressed on the surface of rat hippocampal neurons or PC12 cells, the sensors respond to extracellular glutamate with a reversible concentration-dependent decrease in FRET efficiency. Depolarization of neurons leads to a reduction in FRET efficiency corresponding to 300 nM glutamate at the cell surface. No change in FRET was observed when cells expressing sensors in the cytosol were superfused with up to 20 mM glutamate, consistent with a minimal contribution of glutamate uptake to cytosolic glutamate levels. The results demonstrate that FLIPE sensors can be used for real-time monitoring of glutamate metabolism in living cells, in tissues, or in intact organisms, providing tools for studying metabolism or for drug discovery.

    View details for Web of Science ID 000229807200061

    View details for PubMedID 15939876

  • Regulation of axon growth in vivo by activity-based competition NATURE Hua, J. Y., Smear, M. C., Baier, H., Smith, S. J. 2005; 434 (7036): 1022-1026

    Abstract

    The formation of functional neural networks requires precise regulation of the growth and branching of the terminal arbors of axons, processes known to be influenced by early network electrical activity. Here we show that a rule of activity-based competition between neighbouring axons appears to govern the growth and branching of retinal ganglion cell (RGC) axon arbors in the developing optic tectum of zebrafish. Mosaic expression of an exogenous potassium channel or a dominant-negative SNARE protein was used to suppress electrical or neurosecretory activity in subsets of RGC axons. Imaging in vivo showed that these forms of activity suppression strongly inhibit both net growth and the formation of new branches by individually transfected RGC axon arbors. The inhibition is relieved when the activity of nearby 'competing' RGC axons is also suppressed. These results therefore identify a new form of activity-based competition rule that might be a key regulator of axon growth and branch initiation.

    View details for DOI 10.1038/nature03409

    View details for Web of Science ID 000228524600039

    View details for PubMedID 15846347

  • Functional imaging reveals rapid development of visual response properties in the zebrafish tectum NEURON Niell, C. M., Smith, S. J. 2005; 45 (6): 941-951

    Abstract

    The visual pathway from the retina to the optic tectum in fish and frogs has long been studied as a model for neural circuit formation. Although morphological aspects, such as axonal and dendritic arborization, have been well characterized, less is known about how this translates into functional properties of tectal neurons during development. We developed a system to provide controlled visual stimuli to larval zebrafish, while performing two-photon imaging of tectal neurons loaded with a fluorescent calcium indicator, allowing us to determine visual response properties in intact fish. In relatively mature larvae, we describe receptive field sizes, visual topography, and direction and size selectivity. We also characterize the onset and development of visual responses, beginning when retinal axons first arborize in the tectum. Surprisingly, most of these properties are established soon after dendrite growth and synaptogenesis begin and do not require patterned visual experience or a protracted period of refinement.

    View details for DOI 10.1016/j.neuron.2005.01.047

    View details for Web of Science ID 000228031300014

    View details for PubMedID 15797554

  • Greater than 10(6) optical isolation in integrated optoelectronic fluorescence sensor. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference Thrush, E., Levi, O., Cook, L., Smith, S., Harris, J. 2004; 3: 2080-2081

    Abstract

    Integrated optoelectronic sensors hold much potential for bio-medical applications. Our work focuses on the use of semiconductor lasers, photodetectors and filters to create a monolithically integrated near-infrared fluorescence sensor. Previous research has found that the close integration of these components results in large laser background levels from spontaneous emission emitted from the side of the laser and limits sensor sensitivity. This work presents an improved optical blocking structure between the laser and photodetector which results in greater than 10(6) optical isolation. This level of isolation will allow for sensitive fluorescence detection and shows that optoelectronic components can be successfully integrated for such purposes.

    View details for PubMedID 17272131

  • Optical detection of a quantal presynaptic membrane turnover NATURE Ryan, T. A., Reuter, H., Smith, S. J. 1997; 388 (6641): 478-482

    Abstract

    Exploration of the mechanisms and plasticity of synaptic transmission has been hindered by the lack of a method to measure single vesicle turnover directly in individual presynaptic boutons at isolated nerve terminals. Although postsynaptic electrical recordings have provided a wealth of invaluable basic information about quantal presynaptic processes, this approach has often proved difficult to apply at most central nervous system synapses. Here we describe the direct optical detection of single quantal events in individual presynaptic boutons of cultured hippocampal neurons. Using the fluorescent dye FM 1-43 as a tracer for presynaptic endocytosis, we have characterized both evoked and spontaneous components of presynaptic function at the level of individual quanta. Our results are consistent with quantal interpretations of previous electrophysiological analyses and provide new information about the unitary membrane recycling event and its coupling to individual action potential stimuli, about spontaneous vesicle turnover at individual boutons, and about the numbers of vesicles recycling at individual boutons.

    View details for Web of Science ID A1997XN55300050

    View details for PubMedID 9242407

  • Quantitative analysis of cadherin-catenin-actin reorganization during development of cell-cell adhesion JOURNAL OF CELL BIOLOGY Adams, C. L., NELSON, W. J., Smith, S. J. 1996; 135 (6): 1899-1911

    Abstract

    Epithelial cell-cell adhesion requires interactions between opposing extracellular domains of E-cadherin, and among the cytoplasmic domain of E-cadherin, catenins, and actin cytoskeleton. Little is known about how the cadherin-catenin-actin complex is assembled upon cell-cell contact, or how these complexes initiate and strengthen adhesion. We have used time-lapse differential interference contrast (DIC) imaging to observe the development of cell-cell contacts, and quantitative retrospective immunocytochemistry to measure recruitment of proteins to those contacts. We show that E-cadherin, alpha-catenin, and beta-catenin, but not plakoglobin, coassemble into Triton X-100 insoluble (TX-insoluble) structures at cell-cell contacts with kinetics similar to those for strengthening of E-cadherin-mediated cell adhesion (Angres, B., A. Barth, and W.J. Nelson. 1996. J. Cell Biol. 134:549-557). TX-insoluble E-cadherin, alpha-catenin, and beta-catenin colocalize along cell-cell contacts in spatially discrete micro-domains which we designate "puncta," and the relative amounts of each protein in each punctum increase proportionally. As the length of the contact increases, the number of puncta increases proportionally along the contact and each punctum is associated with a bundle of actin filaments. These results indicate that localized clustering of E-cadherin/catenin complexes into puncta and their association with actin is involved in initiating cell contacts. Subsequently, the spatial ordering of additional puncta along the contact may be involved in zippering membranes together, resulting in rapid strengthening of adhesion.

    View details for Web of Science ID A1996WA87900019

    View details for PubMedID 8991100

  • Evidence for a role of dendritic filopodia in synaptogenesis and spine formation NEURON Ziv, N. E., Smith, S. J. 1996; 17 (1): 91-102

    Abstract

    Axo-dendritic synaptogenesis was examined in live hippocampal cell cultures using the fluorescent dyes DiO to label dendrites and FM 4-64 to label functional presynaptic boutons. As the first functional synaptic boutons appeared in these cultures, numerous filopodia (up to 10 micron long) were observed to extend transiently (mean lifetime 9.5 min) from dendritic shafts. With progressively increasing numbers of boutons, there were coincident decreases in numbers of transient filopodia and increases in numbers of stable dendritic spines. Dendritic filopodia were observed to initiate physical contacts with nearby axons. This sometimes resulted in filopodial stabilization and formation of functional presynaptic boutons. These findings suggest that dendritic filopodia may actively initiate synaptogenic contacts with nearby (5-10 micron) axons and thereafter evolve into dendritic spines.

    View details for Web of Science ID A1996UY98100010

    View details for PubMedID 8755481

  • Potentiation of evoked vesicle turnover at individually resolved synaptic boutons NEURON Ryan, T. A., Ziv, N. E., Smith, S. J. 1996; 17 (1): 125-134

    Abstract

    We have studied synaptic plasticity in hippocampal cell cultures using a new imaging approach that allows unambiguous discrimination of presynaptic function at the level of single synaptic boutons. Employing a protocol designed to test for use-dependent plasticity resembling N-methyl-D-aspartate receptor-dependent long-term potentiation (NMDA-type LTP), we find that brief tetanic stimuli induce a potentiation of evoked synaptic vesicle turnover that lasts for at least 1 hr. Induction of this clearly presynaptic potentiation is blocked by putative postsynaptic glutamate receptor antagonists, suggesting that a retrograde induction signal might be involved. Potentiation appears to occur approximately equally at boutons of low and high initial release probabilities, and evidently does not involve an increase in the size of the total recycling synaptic vesicle pool.

    View details for Web of Science ID A1996UY98100013

    View details for PubMedID 8755484

  • The dynamics of dendritic structure in developing hippocampal slices JOURNAL OF NEUROSCIENCE Dailey, M. E., Smith, S. J. 1996; 16 (9): 2983-2994

    Abstract

    Time-lapse fluorescence confocal microscopy was used to directly visualize the formation and dynamics of postsynaptic target structures (i.e., dendritic branches and spines) on pyramidal neurons within developing tissue slices. Within a 2 week period of time, pyramidal neurons in cultured slices derived from early postnatal rat (postnatal days 2-7) developed complex dendritic arbors bearing numerous postsynaptic spines. At early stages (1-2 d in vitro), many fine filopodial protrusions on dendrite shafts rapidly extended (maximum rate approximately 2.5 microM/minute) and retracted (median filopodial lifetime, 10 min), but some filopodia transformed into growth cones and nascent dendrite branches. As dendritic arbors matured, the population of fleeting lateral filopodia was replaced by spine-like structures having a low rate of turnover. This developmental progression involved a transitional stage in which dendrites were dominated by persistent (up to 22 hr) but dynamic spiny protrusions (i.e., protospines) that showed substantial changes in length and shape on a timescale of minutes. These observations reveal a highly dynamic state of postsynaptic target structures that may actively contribute to the formation and plasticity of synaptic connections during CNS development.

    View details for Web of Science ID A1996UF71100012

    View details for PubMedID 8622128

  • THE KINETICS OF SYNAPTIC VESICLE RECYCLING MEASURED AT SINGLE PRESYNAPTIC BOUTONS NEURON Ryan, T. A., Reuter, H., Wendland, B., Schweizer, F. E., Tsien, R. W., Smith, S. J. 1993; 11 (4): 713-724

    Abstract

    We used the fluorescent membrane probe FM 1-43 to label recycling synaptic vesicles within the presynaptic boutons of dissociated hippocampal neurons in culture. Quantitative time-lapse fluorescence imaging was employed in combination with rapid superfusion techniques to study the dynamics of synaptic vesicles within single boutons. This approach enabled us to measure exocytosis and to analyze the kinetics of endocytosis and the preparation of endocytosed vesicles for re-release (repriming). Our measurements indicate that under sustained membrane depolarization, endocytosis persists much longer than exocytosis, with a t1/2 approximately 60 s (approximately 24 degrees C); once internalized, vesicles become reavailable for exocytosis in approximately 30 s. Furthermore, we have shown that endocytosis is not dependent on membrane potential and, unlike exocytosis, that it is independent of extracellular Ca2+.

    View details for Web of Science ID A1993MD06800014

    View details for PubMedID 8398156

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