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2432 Janelia Publications

Showing 1371-1380 of 2432 results
10/10/16 | Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin.
Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R, Kokotovic M, Grimm JB, Lavis LD, Lee J, Mejia FJ, Li Y, Yao T, Ren X
eLife. 2016 Oct 10;5:. doi: 10.7554/eLife.17667

The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes.

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10/07/16 | Light sheet microscopes: Novel imaging toolbox for visualizing life's processes.
Heddleston JM, Chew T
The International Journal of Biochemistry & Cell Biology. 2016 Oct 7:. doi: 10.1016/j.biocel.2016.10.002

Capturing dynamic processes in live samples is a nontrivial task in biological imaging. Although fluorescence provides high specificity and contrast compared to other light microscopy techniques, the photophysical principles of this method can have a harmful effect on the sample. Current advances in light sheet microscopy have created a novel imaging toolbox that allows for rapid acquisition of high-resolution fluorescent images with minimal perturbation of the processes of interest. Each unique design has its own advantages and limitations. In this review, we describe several cutting edge light sheet microscopes and their optimal applications.

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Looger Lab
10/06/16 | The Oscillating Stimulus Transporter Assay, OSTA: Quantitative functional imaging of transporter protein activity in time and frequency domains.
Keller JP, Looger LL
Molecular Cell. 2016 Oct 6;64(1):199-212. doi: 10.1016/j.molcel.2016.09.001

Transmembrane transporter proteins allow the passage of essentially all biologically important molecules across the lipid membranes of cells and organelles and are therefore of central importance to all forms of life. Current methods of transporter measurement, however, are lacking in several dimensions. Herein, a method is presented in which oscillating stimuli are presented to transporter-expressing cells, and activity is measured through imaging the corresponding oscillating responses of intracellular fluorescent sensors. This approach yields continuous temporal readouts of transporter activity and can therefore be used to measure time-dependent responses to drugs and other stimuli. Because of the periodic nature of the response, temporal Fourier transforms can be used to identify and quantify regions of interest in the xy plane and to overcome noise. This technique, called the Oscillating Stimulus Transporter Assay (OSTA), should greatly facilitate both functional characterization of transporters as well as high-throughput screening of drugs for transporters of particular pathophysiological interest.

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Zlatic LabCardona LabFetter LabTruman LabScientific Computing Software
10/05/16 | Competitive disinhibition mediates behavioral choice and sequences in Drosophila.
Jovanic T, Schneider-Mizell CM, Shao M, Masson J, Denisov G, Fetter RD, Mensh BD, Truman JW, Cardona A, Zlatic M
Cell. 2016 Oct 5;167(3):858-70. doi: 10.1016/j.cell.2016.09.009

Even a simple sensory stimulus can elicit distinct innate behaviors and sequences. During sensorimotor decisions, competitive interactions among neurons that promote distinct behaviors must ensure the selection and maintenance of one behavior, while suppressing others. The circuit implementation of these competitive interactions is still an open question. By combining comprehensive electron microscopy reconstruction of inhibitory interneuron networks, modeling, electrophysiology, and behavioral studies, we determined the circuit mechanisms that contribute to the Drosophila larval sensorimotor decision to startle, explore, or perform a sequence of the two in response to a mechanosensory stimulus. Together, these studies reveal that, early in sensory processing, (1) reciprocally connected feedforward inhibitory interneurons implement behavioral choice, (2) local feedback disinhibition provides positive feedback that consolidates and maintains the chosen behavior, and (3) lateral disinhibition promotes sequence transitions. The combination of these interconnected circuit motifs can implement both behavior selection and the serial organization of behaviors into a sequence.

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10/04/16 | A near atomic structure of the active human apoptosome.
Cheng TC, Hong C, Akey IV, Yuan S, Akey CW
eLife. 2016 Oct 04;5:e17755. doi: 10.7554/eLife.17755

In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease.

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Gonen Lab
10/04/16 | Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.
Sawaya MR, Rodriguez J, Cascio D, Collazo MJ, Shi D, Reyes FE, Hattne J, Gonen T, Eisenberg DS
Proceedings of the National Academy of Sciences of the United States of America. 2016 Oct 04;113(40):11232-6. doi: 10.1073/pnas.1606287113

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.

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Card Lab
10/03/16 | Comparative approaches to escape.
Peek MY, Card GM
Current Opinion in Neurobiology. 2016 Oct 3;41:167-173. doi: 10.1016/j.conb.2016.09.012

Neural circuits mediating visually evoked escape behaviors are promising systems in which to dissect the neural basis of behavior. Behavioral responses to predator-like looming stimuli, and their underlying neural computations, are remarkably similar across species. Recently, genetic tools have been applied in this classical paradigm, revealing novel non-cortical pathways that connect loom processing to defensive behaviors in mammals and demonstrating that loom encoding models from locusts also fit vertebrate neural responses. In both invertebrates and vertebrates, relative spike-timing in descending pathways is a mechanism for escape behavior choice. Current findings suggest that experimentally tractable systems, such as Drosophila, may be applicable models for sensorimotor processing and persistent states in higher organisms.

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Pastalkova Lab
09/28/16 | Synchronized excitability in a network enables generation of internal neuronal sequences.
Yingxue W, Roth Z, Pastalkova E
eLife. 2016 Sep 28;5:. doi: 10.7554/eLife.20697

Hippocampal place field sequences are supported by sensory cues and network internal mechanisms. In contrast, sharp-wave (SPW) sequences, theta sequences and episode-field sequences are internally generated. The relationship of these sequences to memory is unclear. SPW sequences have been shown to support learning and have been assumed to also support episodic memory. Conversely, we demonstrate these SPW sequences were present even after episodic memory in trained rats was impaired and after other internal sequences - episode-field and theta sequences - were eliminated. SPW sequences did not support memory despite continuing to 'replay' all task-related sequences - place-field and episode-field sequences. Sequence replay occurred selectively during a synchronous increase of population excitability -- SPWs. Similarly, theta sequences depended on the presence of repeated synchronized waves of excitability - theta oscillations. Thus, we suggest that either intermittent or rhythmic synchronized changes of excitability trigger sequential firing of neurons, which in turn supports learning and/or memory.

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09/26/16 | Flight of the dragonflies and damselflies.
Bomphrey RJ, Nakata T, Henningsson P, Lin H
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 2016 Sep 26;371(1704):. doi: 10.1098/rstb.2015.0389

This work is a synthesis of our current understanding of the mechanics, aerodynamics and visually mediated control of dragonfly and damselfly flight, with the addition of new experimental and computational data in several key areas. These are: the diversity of dragonfly wing morphologies, the aerodynamics of gliding flight, force generation in flapping flight, aerodynamic efficiency, comparative flight performance and pursuit strategies during predatory and territorial flights. New data are set in context by brief reviews covering anatomy at several scales, insect aerodynamics, neuromechanics and behaviour. We achieve a new perspective by means of a diverse range of techniques, including laser-line mapping of wing topographies, computational fluid dynamics simulations of finely detailed wing geometries, quantitative imaging using particle image velocimetry of on-wing and wake flow patterns, classical aerodynamic theory, photography in the field, infrared motion capture and multi-camera optical tracking of free flight trajectories in laboratory environments. Our comprehensive approach enables a novel synthesis of datasets and subfields that integrates many aspects of flight from the neurobiology of the compound eye, through the aeromechanical interface with the surrounding fluid, to flight performance under cruising and higher-energy behavioural modes.This article is part of the themed issue 'Moving in a moving medium: new perspectives on flight'.

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09/14/16 | Effect of magnetic nanoparticle shape on flux amplification in inductive coil magnetic resonance detection.
Barbic M, El Bidweihy H
Journal of Applied Physics. 2016 Sep 14:104506-1-7. doi: 10.1063/1.4962451

We model and analyze the effect of particle shape on the signal amplification in inductive coil magnetic resonance detection using the reversible transverse magnetic susceptibility of oriented magnetic nanostructures. Utilizing the single magnetic domain Stoner-Wohlfarth model of uniform magnetization rotation, we reveal that different ellipsoidal particle shapes can have a pronounced effect on the magnetic flux enhancement in detection configurations typical of magnetic resonance settings. We compare and contrast the prolate ellipsoids, oblate ellipsoids, and exchange-biased spheres and show that the oblate ellipsoids and exchange-biased spheres have a significantly higher flux amplification effect than the prolate ellipsoids considered previously. In addition, oblate ellipsoids have a much broader polarizing magnetic fieldrange over which their transverse flux amplification is significant. We show the dependence of transverse flux amplification on magnetic resonance bias field and discuss the resulting signal-to-noise ratio of inductive magnetic resonance detection due to the magnetic nanoparticle-filled core of the magnetic resonance detection coil.

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