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2657 Janelia Publications

Showing 1831-1840 of 2657 results
Pastalkova Lab
07/18/15 | Oscillatory patterns in hippocampus under light and deep isoflurane anesthesia closely mirror prominent brain states in awake animals.
Lustig B, Wang Y, Pastalkova E
Hippocampus. 2015 Jul 18;26(1):102-9. doi: 10.1002/hipo.22494

The hippocampus exhibits a variety of distinct states of activity under different conditions. For instance the rhythmic patterns of activity orchestrated by the theta oscillation during running and REM sleep are markedly different from the large irregular activity (LIA) observed during awake resting and slow wave sleep. We found that under different levels of isoflurane anesthesia activity in the hippocampus of rats displays two distinct states which have several qualities that mirror the theta and LIA states. These data provide further evidence that the two states are intrinsic modes of the hippocampus; while also characterizing a preparation that could be useful for studying the natural activity states in hippocampus. This article is protected by copyright. All rights reserved.

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Druckmann Lab
01/01/10 | Over-complete representations on recurrent neural networks can support persistent percepts.
Druckmann S, Chklovskii D
Neural Information Processing Systems 23 (NIPS 2010). 2010;23:541-9

A striking aspect of cortical neural networks is the divergence of a relatively small number of input channels from the peripheral sensory apparatus into a large number of cortical neurons, an over-complete representation strategy. Cortical neurons are then connected by a sparse network of lateral synapses. Here we propose that such architecture may increase the persistence of the representation of an incoming stimulus, or a percept. We demonstrate that for a family of networks in which the receptive field of each neuron is re-expressed by its outgoing connections, a represented percept can remain constant despite changing activity. We term this choice of connectivity REceptive FIeld REcombination (REFIRE) networks. The sparse REFIRE network may serve as a high-dimensional integrator and a biologically plausible model of the local cortical circuit.

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Gonen Lab
04/02/13 | Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.
Nannenga BL, Iadanza MG, Vollmar BS, Gonen T
Current Protocols in Protein Science . 2013 Apr 2;Chapter 17:Unit 17.15. doi: 10.1002/0471140864.ps1715s72

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

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12/29/15 | P1 interneurons promote a persistent internal state that enhances inter-male aggression in Drosophila.
Hoopfer ED, Jung Y, Inagaki HK, Rubin GM, Anderson DJ
eLife. 2015 Dec 29;4:. doi: 10.7554/eLife.11346

How brains are hardwired to produce aggressive behavior, and how aggression circuits are related to those that mediate courtship, is not well understood. A large-scale screen for aggression-promoting neurons in Drosophila identified several independent hits that enhanced both inter-male aggression and courtship. Genetic intersections revealed that 8-10 P1 interneurons, previously thought to exclusively control male courtship, were sufficient to promote fighting. Optogenetic experiments indicated that P1 activation could promote aggression at a threshold below that required for wing extension. P1 activation in the absence of wing extension triggered persistent aggression via an internal state that could endure for minutes. High-frequency P1 activation promoted wing extension and suppressed aggression during photostimulation, whereas aggression resumed and wing extension was inhibited following photostimulation offset. Thus, P1 neuron activation promotes a latent, internal state that facilitates aggression and courtship, and controls the overt expression of these social behaviors in a threshold-dependent, inverse manner.

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05/01/11 | PALM and STORM: unlocking live-cell super-resolution.
Henriques R, Griffiths C, Hesper Rego E, Mhlanga MM
Biopolymers. 2011 May;95(5):322-31. doi: 10.1002/bip.21586

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.

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Cui Lab
10/22/12 | Parallel wavefront measurements in ultrasound pulse guided digital phase conjugation.
Fiolka R, Si K, Cui M
Optics Express. 2012 Oct 22;20(22):24827-34. doi: http://dx.doi.org/10.1364/OE.20.024827

Ultrasound pulse guided digital phase conjugation has emerged to realize fluorescence imaging inside random scattering media. Its major limitation is the slow imaging speed, as a new wavefront needs to be measured for each voxel. Therefore 3D or even 2D imaging can be time consuming. For practical applications on biological systems, we need to accelerate the imaging process by orders of magnitude. Here we propose and experimentally demonstrate a parallel wavefront measurement scheme towards such a goal. Multiple focused ultrasound pulses of different carrier frequencies can be simultaneously launched inside a scattering medium. Heterodyne interferometry is used to measure all of the wavefronts originating from every sound focus in parallel. We use these wavefronts in sequence to rapidly excite fluorescence at all the voxels defined by the focused ultrasound pulses. In this report, we employed a commercially available sound transducer to generate two sound foci in parallel, doubled the wavefront measurement speed, and reduced the mechanical scanning steps of the sound transducer to half.

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Cui Lab
03/15/11 | Parallel wavefront optimization method for focusing light through random scattering media.
Cui M
Optics Letters. 2011 Mar 15;36(6):870-2. doi: 10.1364/OL.36.000870

A parallel wavefront optimization method is demonstrated experimentally to focus light through random scattering media. The simultaneous modulation of multiple phase elements, each at a unique frequency, enables a parallel determination of the optimal wavefront. Compared to a pixel-by-pixel measurement, the reported parallel method uses the target signal in a highly efficient way. With 441 phase elements, a high-quality focus was formed through a glass diffuser with a peak-to-background ratio of \~{}270. The accuracy and repeatability of the system were tested through experiments.

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Sternson Lab
12/05/13 | Parallel, redundant circuit organization for homeostatic control of feeding behavior.
Betley JN, Cao ZF, Ritola KD, Sternson SM
Cell. 2013 Dec 5;155(6):1337-50. doi: 10.1016/j.cell.2013.11.002

Neural circuits for essential natural behaviors are shaped by selective pressure to coordinate reliable execution of flexible goal-directed actions. However, the structural and functional organization of survival-oriented circuits is poorly understood due to exceptionally complex neuroanatomy. This is exemplified by AGRP neurons, which are a molecularly defined population that is sufficient to rapidly coordinate voracious food seeking and consumption behaviors. Here, we use cell-type-specific techniques for neural circuit manipulation and projection-specific anatomical analysis to examine the organization of this critical homeostatic circuit that regulates feeding. We show that AGRP neuronal circuits use a segregated, parallel, and redundant output configuration. AGRP neuron axon projections that target different brain regions originate from distinct subpopulations, several of which are sufficient to independently evoke feeding. The concerted anatomical and functional analysis of AGRP neuron projection populations reveals a constellation of core forebrain nodes, which are part of an extended circuit that mediates feeding behavior.

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04/25/19 | Parametric amplification of reversible transverse susceptibility in single domain magnetic nanoparticles.
El Bidweihy H, Smith RD, Barbic M
AIP Advances. 2019 Apr 25;9:045031. doi: 10.1063/1.5079980

We propose, model, and experimentally demonstrate the enhancement of reversible transverse susceptibility in single domain magnetic nanoparticles through the principle of parametric amplification. It has previously been demonstrated that properly oriented anisotropic single domain magnetic nanoparticles have an appreciable peak in transverse susceptibility at the particle anisotropy field. Here we show theoretically and experimentally that an additional parametric AC magnetic field applied at a proper phase and at twice the frequency (2f) of the transverse field further enhances transverse susceptibility peaks through the process of parametric amplification. We model this effect numerically and describe it through the energy formalism of the single magnetic domain Stoner-Wohlfarth model. The proper phase relationships of the transverse and parametric fields to obtain either parametric amplification or attenuation of the transverse susceptibility signals are also described. We experimentally demonstrate such parametric tuning of transverse susceptibility in single domain magnetic nanoparticles of a commercial audio tape in a prototypical inductive transverse susceptibility set-up.
 

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Svoboda Lab
11/23/18 | Paring down to the essentials.
Wang T
Science (New York, N.Y.). 2018 Nov 23;362(6417):904. doi: 10.1126/science.aav6872