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2432 Janelia Publications

Showing 2131-2140 of 2432 results
Bock Lab
02/01/12 | Volume electron microscopy for neuronal circuit reconstruction.
Briggman KL, Bock DD
Current Opinion in Neurobiology. 2012 Feb;22(1):154-61. doi: 10.1016/j.conb.2011.10.022

The last decade has seen a rapid increase in the number of tools to acquire volume electron microscopy (EM) data. Several new scanning EM (SEM) imaging methods have emerged, and classical transmission EM (TEM) methods are being scaled up and automated. Here we summarize the new methods for acquiring large EM volumes, and discuss the tradeoffs in terms of resolution, acquisition speed, and reliability. We then assess each method’s applicability to the problem of reconstructing anatomical connectivity between neurons, considering both the current capabilities and future prospects of the method. Finally, we argue that neuronal ’wiring diagrams’ are likely necessary, but not sufficient, to understand the operation of most neuronal circuits: volume EM imaging will likely find its best application in combination with other methods in neuroscience, such as molecular biology, optogenetics, and physiology.

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Svoboda Lab
01/26/12 | Regular spiking and intrinsic bursting pyramidal cells show orthogonal forms of experience-dependent plasticity in layer V of barrel cortex.
Jacob V, Petreanu L, Wright N, Svoboda K, Fox K
Neuron. 2012 Jan 26;73(2):391-404. doi: 10.1016/j.neuron.2011.11.034

Most functional plasticity studies in the cortex have focused on layers (L) II/III and IV, whereas relatively little is known of LV. Structural measurements of dendritic spines in vivo suggest some specialization among LV cell subtypes. We therefore studied experience-dependent plasticity in the barrel cortex using intracellular recordings to distinguish regular spiking (RS) and intrinsic bursting (IB) subtypes. Postsynaptic potentials and suprathreshold responses in vivo revealed a remarkable dichotomy in RS and IB cell plasticity; spared whisker potentiation occurred in IB but not RS cells while deprived whisker depression occurred in RS but not IB cells. Similar RS/IB differences were found in the LII/III to V connections in brain slices. Modeling studies showed that subthreshold changes predicted the suprathreshold changes. These studies demonstrate the major functional partition of plasticity within a single cortical layer and reveal the LII/III to LV connection as a major excitatory locus of cortical plasticity.

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01/17/12 | Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution.
Rego EH, Shao L, Macklin JJ, Winoto L, Johansson GA, Kamps-Hughes N, Davidson MW, Gustafsson MG
Proceedings of the National Academy of Sciences of the United States of America. 2012 Jan 17;109:E135-43. doi: 10.1073/pnas.1107547108

Using ultralow light intensities that are well suited for investigating biological samples, we demonstrate whole-cell superresolution imaging by nonlinear structured-illumination microscopy. Structured-illumination microscopy can increase the spatial resolution of a wide-field light microscope by a factor of two, with greater resolution extension possible if the emission rate of the sample responds nonlinearly to the illumination intensity. Saturating the fluorophore excited state is one such nonlinear response, and a realization of this idea, saturated structured-illumination microscopy, has achieved approximately 50-nm resolution on dye-filled polystyrene beads. Unfortunately, because saturation requires extremely high light intensities that are likely to accelerate photobleaching and damage even fixed tissue, this implementation is of limited use for studying biological samples. Here, reversible photoswitching of a fluorescent protein provides the required nonlinearity at light intensities six orders of magnitude lower than those needed for saturation. We experimentally demonstrate approximately 40-nm resolution on purified microtubules labeled with the fluorescent photoswitchable protein Dronpa, and we visualize cellular structures by imaging the mammalian nuclear pore and actin cytoskeleton. As a result, nonlinear structured-illumination microscopy is now a biologically compatible superresolution imaging method.

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Sternson Lab
01/15/12 | Regulation of neuronal input transformations by tunable dendritic inhibition.
Lovett-Barron M, Turi GF, Kaifosh P, Lee PH, Bolze F, Sun X, Nicoud Jc, Zemelman BV, Sternson SM, Losonczy A
Nature Neuroscience. 2012 Jan 15;15(3):423-30. doi: 10.1038/nn.3024

Transforming synaptic input into action potential output is a fundamental function of neurons. The pattern of action potential output from principal cells of the mammalian hippocampus encodes spatial and nonspatial information, but the cellular and circuit mechanisms by which neurons transform their synaptic input into a given output are unknown. Using a combination of optical activation and cell type-specific pharmacogenetic silencing in vitro, we found that dendritic inhibition is the primary regulator of input-output transformations in mouse hippocampal CA1 pyramidal cells, and acts by gating the dendritic electrogenesis driving burst spiking. Dendrite-targeting interneurons are themselves modulated by interneurons targeting pyramidal cell somata, providing a synaptic substrate for tuning pyramidal cell output through interactions in the local inhibitory network. These results provide evidence for a division of labor in cortical circuits, where distinct computational functions are implemented by subtypes of local inhibitory neurons.

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Ji LabBetzig LabSvoboda Lab
01/03/12 | Characterization and adaptive optical correction of aberrations during in vivo imaging in the mouse cortex.
Ji N, Sato TR, Betzig E
Proceedings of the National Academy of Sciences of the United States of America. 2012 Jan 3;109:22-7. doi: 10.1073/pnas.1109202108

The signal and resolution during in vivo imaging of the mouse brain is limited by sample-induced optical aberrations. We find that, although the optical aberrations can vary across the sample and increase in magnitude with depth, they remain stable for hours. As a result, two-photon adaptive optics can recover diffraction-limited performance to depths of 450 μm and improve imaging quality over fields of view of hundreds of microns. Adaptive optical correction yielded fivefold signal enhancement for small neuronal structures and a threefold increase in axial resolution. The corrections allowed us to detect smaller neuronal structures at greater contrast and also improve the signal-to-noise ratio during functional Ca(2+) imaging in single neurons.

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01/01/12 | A lattice filter model of the visual pathway.
Gregor K, Chklovskii DB
Advances in Neural Information Processing Systems. 2012;24:1709-17

Early stages of visual processing are thought to decorrelate, or whiten, the incoming temporally varying signals. Because the typical correlation time of natural stimuli, as well as the extent of temporal receptive fields of lateral geniculate nucleus (LGN) neurons, is much greater than neuronal time constants, such decorrelation must be done in stages combining contributions of multiple neurons. We propose to model temporal decorrelation in the visual pathway with the lattice filter, a signal processing device for stage-wise decorrelation of temporal signals. The stage-wise architecture of the lattice filter maps naturally onto the visual pathway (photoreceptors -> bipolar cells -> retinal ganglion cells -> LGN) and its filter weights can be learned using Hebbian rules in a stage-wise sequential manner. Moreover, predictions of neural activity from the lattice filter model are consistent with physiological measurements in LGN neurons and fruit fly second-order visual neurons. Therefore, the lattice filter model is a useful abstraction that may help unravel visual system function.

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Druckmann Lab
01/01/12 | A mechanistic model of early sensory processing based on subtracting sparse representations.
Druckmann S, Hu T, Chklovskii D
Advances in Neural Information Processing Systems. 2012;25:1979-87

Early stages of sensory systems face the challenge of compressing information from numerous receptors onto a much smaller number of projection neurons, a so called communication bottleneck. To make more efficient use of limited bandwidth, compression may be achieved using predictive coding, whereby predictable, or redundant, components of the stimulus are removed. In the case of the retina, Srinivasan et al. (1982) suggested that feedforward inhibitory connections subtracting a linear prediction generated from nearby receptors implement such compression, resulting in biphasic center-surround receptive fields. However, feedback inhibitory circuits are common in early sensory circuits and furthermore their dynamics may be nonlinear. Can such circuits implement predictive coding as well? Here, solving the transient dynamics of nonlinear reciprocal feedback circuits through analogy to a signal-processing algorithm called linearized Bregman iteration we show that nonlinear predictive coding can be implemented in an inhibitory feedback circuit. In response to a step stimulus, interneuron activity in time constructs progressively less sparse but more accurate representations of the stimulus, a temporally evolving prediction. This analysis provides a powerful theoretical framework to interpret and understand the dynamics of early sensory processing in a variety of physiological experiments and yields novel predictions regarding the relation between activity and stimulus statistics.

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Cui Lab
01/01/12 | Complex wavefront corrections for deep tissue focusing using low coherence backscattered light.
Fiolka R, Si K, Cui M
Optics Express. 2012;20(15):16532-43. doi: 10.1364/OE.20.016532

Aberrations and random scattering severely limit optical imaging in deep tissue. Adaptive optics can in principle drastically extend the penetration depth and improve the image quality. However, for random scattering media a large number of spatial modes need to be measured and controlled to restore a diffraction limited focus. Here, we present a parallel wavefront optimization method using backscattered light as a feedback. Spatial confinement of the feedback signal is realized with a confocal pinhole and coherence gating. We show in simulations and experiments that this approach enables focusing deep into tissue over up to six mean scattering path lengths. Experimentally the technique was tested on tissue phantoms and fixed brain slices.

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01/01/12 | Design tools for artificial nervous systems.
Scheffer L
Design Automation Conference (DAC), 2012 49th ACM/EDAC/IEEE. 2012:

Electronic and biological systems both perform complex information processing, but they use very different techniques. Though electronics has the advantage in raw speed, biological systems have the edge in many other areas. They can be produced, and indeed self-reproduce, without expensive and finicky factories. They are tolerant of manufacturing defects, and learn and adapt for better performance. In many cases they can self-repair damage. These advantages suggest that biological systems might be useful in a wide variety of tasks involving information processing. So far, all attempts to use the nervous system of a living organism for information processing have involved selective breeding of existing organisms. This approach, largely independent of the details of internal operation, is used since we do not yet understand how neural systems work, nor exactly how they are constructed. However, as our knowledge increases, the day will come when we can envision useful nervous systems and design them based upon what we want them to do, as opposed to variations on what has been already built. We will then need tools, corresponding to our Electronic Design Automation tools, to help with the design. This paper is concerned with what such tools might look like.

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Baker Lab
01/01/12 | Doublesex functions early and late in gustatory sense organ development.
Mellert DJ, Robinett CC, Baker BS
PLoS One. 2012;7:e51489. doi: 10.1371/journal.pone.0051489

Somatic sexual dimorphisms outside of the nervous system in Drosophila melanogaster are largely controlled by the male- and female-specific Doublesex transcription factors (DSX(M) and DSX(F), respectively). The DSX proteins must act at the right times and places in development to regulate the diverse array of genes that sculpt male and female characteristics across a variety of tissues. To explore how cellular and developmental contexts integrate with doublesex (dsx) gene function, we focused on the sexually dimorphic number of gustatory sense organs (GSOs) in the foreleg. We show that DSX(M) and DSX(F) promote and repress GSO formation, respectively, and that their relative contribution to this dimorphism varies along the proximodistal axis of the foreleg. Our results suggest that the DSX proteins impact specification of the gustatory sensory organ precursors (SOPs). DSX(F) then acts later in the foreleg to regulate gustatory receptor neuron axon guidance. These results suggest that the foreleg provides a unique opportunity for examining the context-dependent functions of DSX.

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