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67 Publications

Showing 31-40 of 67 results
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    07/01/05 | Neurogeometry and potential synaptic connectivity.
    Stepanyants A, Chklovskii DB
    Trends in Neurosciences. 2005 Jul;28(7):387-94. doi: 10.1016/j.tins.2005.05.006

    The advent of high-quality 3D reconstructions of neuronal arbors has revived the hope of inferring synaptic connectivity from the geometric shapes of axons and dendrites, or ’neurogeometry’. A quantitative description of connectivity must be built on a sound theoretical framework. Here, we review recent developments in neurogeometry that can provide such a framework. We base the geometric description of connectivity on the concept of a ’potential synapse’–the close apposition between axons and dendrites necessary to form an actual synapse. In addition to describing potential synaptic connectivity in neuronal circuits, neurogeometry provides insight into basic features of functional connectivity, such as specificity and plasticity.

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    06/29/05 | Pneumatic capillary gun for ballistic delivery of microparticles.
    Rinberg D, Simonnet C, Groisman A
    Applied Physics Letters. 2005 Jun 29;87:014103

    A pneumatic gun for ballistic delivery of microparticles to soft targets is proposed and demonstrated. The particles are accelerated by a high-speed flow of helium in a capillary tube. Vacuum suction applied to a concentric larger diameter tube is used to divert substantially all of the flow of helium from the gun nozzle, thereby preventing the gas from hitting and damaging the target. Speed of ejection of micron-sized gold particles from the gun nozzle, and their depth of penetration into agarose gels are reported.

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    06/28/05 | Drosophila as a model for human neurodegenerative disease.
    Bilen J, Bonini NM
    Annual Review of Genetics. 2005 Jun 28;39:153-71. doi: 10.1146/annurev.genet.39.110304.095804

    Among many achievements in the neurodegeneration field in the past decade, two require special attention due to the huge impact on our understanding of molecular and cellular pathogenesis of human neurodegenerative diseases. First is defining specific mutations in familial neurodegenerative diseases and second is modeling these diseases in easily manipulable model organisms including the fruit fly, nematode, and yeast. The power of these genetic systems has revealed many genetic factors involved in the various pathways affected, as well as provided potential drug targets for therapeutics. This review focuses on fruit fly models of human neurodegenerative diseases, with emphasis on how fly models have provided new insights into various aspects of human diseases.

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    06/20/05 | Joint nonparametric alignment for analyzing spatial gene expression patterns of Drosophila imaginal discs.
    Ahammad P, Harmon C, Hammonds AS, Sastry S, Rubin GM
    IEEE Conference on Computer Vision and Pattern Recognition. 2005 Jun 20;2:755-60

    To compare spatial patterns of gene expression, one must analyze a large number of images as current methods are only able to measure a small number of genes at a time. Bringing images of corresponding tissues into alignment is a critical first step in making a meaningful comparative analysis of these spatial patterns. Significant image noise and variability in the shapes make it hard to pick a canonical shape model. In this paper, we address these problems by combining segmentation and unsupervised shape learning algorithms. We first segment images to acquire structures of interest, then jointly align the shapes of these acquired structures using an unsupervised nonparametric maximum likelihood algorithm along the lines of congealing, while simultaneously learning the underlying shape model and associated transformations. The learned transformations are applied to corresponding images to bring them into alignment in one step. We demonstrate the results for images of various classes of Drosophila imaginal discs and discuss the methodology used for a quantitative analysis of spatial gene expression patterns.

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    06/20/05 | Sparse and composite coherent lattices. (With commentary)
    Betzig E
    Physical Review A. 2005 Jun 20;71:063406

    A method is described that yields a series of (D+1)-element wave-vector sets giving rise to (D=2 or 3)-dimensional coherent sparse lattices of any desired Bravais symmetry and primitive cell shape, but of increasing period relative to the excitation wavelength. By applying lattice symmetry operations to any of these sets, composite lattices of N>D+1 waves are constructed, having increased spatial frequency content but unchanged crystal group symmetry and periodicity. Optical lattices of widely spaced excitation maxima of diffraction-limited confinement and controllable polarization can thereby be created, possibly useful for quan- tum optics, lithography, or multifocal microscopy.

    Commentary: Develops a formalism to find a set of wavevectors that create a periodic optical lattice of any desired Bravais symmetry by the mutual interference of the corresponding plane waves. Discovers two new classes of optical lattices, sparse and composite, that together permit the creation of widely spaced, tightly confined excitation maxima in 3D potentially suitable for high speed volumetric live cell imaging. The implementation of this idea was derailed by our exclusive focus on PALM at the time, and many of its goals have since been reached with our Bessel beam plane illumination microscope. Nevertheless, sparse and composite optical lattices may prove useful in atomic physics or for the fabrication of 3D nanostructures.

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    06/15/05 | R-type calcium channels contribute to afterdepolarization and bursting in hippocampal CA1 pyramidal neurons.
    Metz AE, Jarsky T, Martina M, Spruston N
    J Neurosci. 2005 Jun 15;25(24):5763-73. doi: 10.1523/JNEUROSCI.0624-05.2005

    Action potentials in pyramidal neurons are typically followed by an afterdepolarization (ADP), which in many cells contributes to intrinsic burst firing. Despite the ubiquity of this common excitable property, the responsible ion channels have not been identified. Using current-clamp recordings in hippocampal slices, we find that the ADP in CA1 pyramidal neurons is mediated by an Ni2+-sensitive calcium tail current. Voltage-clamp experiments indicate that the Ni2+-sensitive current has a pharmacological and biophysical profile consistent with R-type calcium channels. These channels are available at the resting potential, are activated by the action potential, and remain open long enough to drive the ADP. Because the ADP correlates directly with burst firing in CA1 neurons, R-type calcium channels are crucial to this important cellular behavior, which is known to encode hippocampal place fields and enhance synaptic plasticity.

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    06/03/05 | Output-mode transitions are controlled by prolonged inactivation of sodium channels in pyramidal neurons of subiculum.
    Cooper DC, Chung S, Spruston N
    PLoS Biol. 2005 Jun;3(6):e175. doi: 10.1371/journal.pbio.0030175

    Transitions between different behavioral states, such as sleep or wakefulness, quiescence or attentiveness, occur in part through transitions from action potential bursting to single spiking. Cortical activity, for example, is determined in large part by the spike output mode from the thalamus, which is controlled by the gating of low-voltage-activated calcium channels. In the subiculum--the major output of the hippocampus--transitions occur from bursting in the delta-frequency band to single spiking in the theta-frequency band. We show here that these transitions are influenced strongly by the inactivation kinetics of voltage-gated sodium channels. Prolonged inactivation of sodium channels is responsible for an activity-dependent switch from bursting to single spiking, constituting a novel mechanism through which network dynamics are controlled by ion channel gating.

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    Svoboda Lab
    06/01/05 | Geometric and functional organization of cortical circuits.
    Shepherd GM, Stepanyants A, Bureau I, Chklovskii D, Svoboda K
    Nature Neuroscience. 2005 Jun;8(6):782-90. doi: 10.1016/j.tins.2005.05.006

    Can neuronal morphology predict functional synaptic circuits? In the rat barrel cortex, ’barrels’ and ’septa’ delineate an orderly matrix of cortical columns. Using quantitative laser scanning photostimulation we measured the strength of excitatory projections from layer 4 (L4) and L5A to L2/3 pyramidal cells in barrel- and septum-related columns. From morphological reconstructions of excitatory neurons we computed the geometric circuit predicted by axodendritic overlap. Within most individual projections, functional inputs were predicted by geometry and a single scale factor, the synaptic strength per potential synapse. This factor, however, varied between projections and, in one case, even within a projection, up to 20-fold. Relationships between geometric overlap and synaptic strength thus depend on the laminar and columnar locations of both the pre- and postsynaptic neurons, even for neurons of the same type. A large plasticity potential appears to be incorporated into these circuits, allowing for functional ’tuning’ with fixed axonal and dendritic arbor geometry.

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    06/01/05 | Learning in realistic networks of spiking neurons and spike-driven plastic synapses.
    Mongillo G, Curti E, Romani S, Amit DJ
    European Journal of Neuroscience. 2005 Jun;21(11):3143-60. doi: 10.1111/j.1460-9568.2005.04087.x

    We have used simulations to study the learning dynamics of an autonomous, biologically realistic recurrent network of spiking neurons connected via plastic synapses, subjected to a stream of stimulus-delay trials, in which one of a set of stimuli is presented followed by a delay. Long-term plasticity, produced by the neural activity experienced during training, structures the network and endows it with active (working) memory, i.e. enhanced, selective delay activity for every stimulus in the training set. Short-term plasticity produces transient synaptic depression. Each stimulus used in training excites a selective subset of neurons in the network, and stimuli can share neurons (overlapping stimuli). Long-term plasticity dynamics are driven by presynaptic spikes and coincident postsynaptic depolarization; stability is ensured by a refresh mechanism. In the absence of stimulation, the acquired synaptic structure persists for a very long time. The dependence of long-term plasticity dynamics on the characteristics of the stimulus response (average emission rates, time course and synchronization), and on the single-cell emission statistics (coefficient of variation) is studied. The study clarifies the specific roles of short-term synaptic depression, NMDA receptors, stimulus representation overlaps, selective stimulation of inhibition, and spike asynchrony during stimulation. Patterns of network spiking activity before, during and after training reproduce most of the in vivo physiological observations in the literature.

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    Magee Lab
    06/01/05 | Plasticity of dendritic function.
    Magee JC, Johnston D
    Current Opinion in Neurobiology. 2005 Jun;15:334-42. doi: 10.1002/cbic.201000254

    The various properties of neuronal dendrites–their morphology, active membrane and synaptic properties–all play important roles in determining the functional capabilities of central nervous system neurons. Because of their fundamental involvement in both synaptic integration and synaptic plasticity, the active dendritic properties are important for both neuronal information processing and storage. The active properties of dendrites are determined by the densities of voltage-gated ion channels located within the dendrites in addition to the biophysical characteristics of those channels. The real power of this system resides in the level of plasticity that is provided by the many forms of channel modulation known to exist in neurons. Indeed, voltage gated ion channel modulation shapes the active properties of neuronal dendrites to specific conditions, thus tailoring the functional role of the single neuron within its circuit.

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