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209 Publications

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    07/28/16 | A practical guide to light sheet microscopy.
    Bennett DV, Ahrens MB
    Methods in Molecular Biology (Clifton, N.J.). 2016;1451:321-31. doi: 10.1007/978-1-4939-3771-4_22

    Light sheet fluorescence microscopy is an efficient method for imaging large volumes of biological tissue, including brains of larval zebrafish, at high spatial and fairly high temporal resolution with minimal phototoxicity.Here, we provide a practical guide for those who intend to build a light sheet microscope for fluorescence imaging in live larval zebrafish brains or other tissues.

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    Pavlopoulos Lab
    07/28/16 | Non-insect crustacean models in developmental genetics including an encomium to Parhyale hawaiensis.
    Stamataki E, Pavlopoulos A
    Current Opinion in Genetics & Development. 2016 Jul 28;39:149-156. doi: 10.1016/j.gde.2016.07.004

    The impressive diversity of body plans, lifestyles and segmental specializations exhibited by crustaceans (barnacles, copepods, shrimps, crabs, lobsters and their kin) provides great material to address longstanding questions in evolutionary developmental biology. Recent advances in forward and reverse genetics and in imaging approaches applied in the amphipod Parhyale hawaiensis and other emerging crustacean model species have made it possible to probe the molecular and cellular basis of crustacean diversity. A number of biological and technical qualities like the slow tempo and holoblastic cleavage mode, the stereotypy of many cellular processes, the functional and morphological diversity of limbs along the body axis, and the availability of various experimental manipulations, have made Parhyale a powerful system to study normal development and regeneration.

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    Gonen Lab
    07/25/16 | Atomic resolution structure determination by the cryo-EM method MicroED.
    Liu S, Hattne J, Reyes FE, Sanchez-Martinez S, de la Cruz MJ, Shi D, Gonen T
    Protein Science : a Publication of the Protein Society. 2016 Jul 25;26(1):8-15. doi: 10.1002/pro.2989

    The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future. This article is protected by copyright. All rights reserved.

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    07/25/16 | Super-resolution spectroscopic microscopy via photon localization.
    Dong B, Almassalha L, Urban BE, Nguyen T, Khuon S, Chew T, Backman V, Sun C, Zhang HF
    Nature Communications. 2016 Jul 25;7:12290. doi: 10.1038/ncomms12290

    Traditional photon localization microscopy analyses only the spatial distributions of photons emitted by individual molecules to reconstruct super-resolution optical images. Unfortunately, however, the highly valuable spectroscopic information from these photons have been overlooked. Here we report a spectroscopic photon localization microscopy that is capable of capturing the inherent spectroscopic signatures of photons from individual stochastic radiation events. Spectroscopic photon localization microscopy achieved higher spatial resolution than traditional photon localization microscopy through spectral discrimination to identify the photons emitted from individual molecules. As a result, we resolved two fluorescent molecules, which were 15 nm apart, with the corresponding spatial resolution of 10 nm-a four-fold improvement over photon localization microscopy. Using spectroscopic photon localization microscopy, we further demonstrated simultaneous multi-colour super-resolution imaging of microtubules and mitochondria in COS-7 cells and showed that background autofluorescence can be identified through its distinct emission spectra.

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    Gonen LabDruckmann Lab
    07/22/16 | Accurate design of megadalton-scale two-component icosahedral protein complexes.
    Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D
    Science (New York, N.Y.). 2016 Jul 22;353(6297):389-94. doi: 10.1126/science.aaf8818

    Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

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    07/22/16 | Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme".
    Wang F, Ranjan A, Wei D, Wu C
    Science. 2016 Jul 22;353(6297):358. doi: 10.1126/science.aad5921

    Watanabe et al (Reports, 12 April 2013, p. 195) study the yeast SWR1/SWR-C complex responsible for depositing the histone variant H2A.Z by replacing nucleosomal H2A with H2A.Z. They report that reversal of H2A.Z replacement is mediated by SWR1 and related INO80 on an H2A.Z nucleosome carrying H3K56Q. Using multiple assays and reaction conditions, we find no evidence of such reversal of H2A.Z exchange.

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    07/21/16 | Dopaminergic neurons write and update memories with cell-type-specific rules.
    Aso Y, Rubin GM
    eLife. 2016 Jul 21;5:e16135. doi: 10.7554/eLife.16135

    Associative learning is thought to involve parallel and distributed mechanisms of memory formation and storage. In Drosophila, the mushroom body (MB) is the major site of associative odor memory formation. Previously we described the anatomy of the adult MB and defined 20 types of dopaminergic neurons (DANs) that each innervate distinct MB compartments (Aso et al., 2014a; Aso et al., 2014b). Here we compare the properties of memories formed by optogenetic activation of individual DAN cell types. We found extensive differences in training requirements for memory formation, decay dynamics, storage capacity and flexibility to learn new associations. Even a single DAN cell type can either write or reduce an aversive memory, or write an appetitive memory, depending on when it is activated relative to odor delivery. Our results show that different learning rules are executed in seemingly parallel memory systems, providing multiple distinct circuit-based strategies to predict future events from past experiences.

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    07/19/16 | Ribosome•RelA structures reveal the mechanism of stringent response activation.
    Loveland AB, Bah E, Madireddy R, Zhang Y, Brilot AF, Grigorieff N, Korostelev AA
    Elife. 2016 07 19;5:. doi: 10.7554/eLife.17029

    Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding.

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    07/18/16 | Whole-animal imaging with high spatio-temporal resolution.
    Chhetri R, Amat F, Wan Y, Höckendorf B, Lemon WC, Keller PJ
    Proceedings of SPIE. 2016 Jul 18;9720:97200R. doi: 10.1117/12.2212564

    We developed isotropic multiview (IsoView) light-sheet microscopy in order to image fast cellular dynamics, such as cell movements in an entire developing embryo or neuronal activity throughput an entire brain or nervous system, with high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To achieve high temporal resolution and high spatial resolution at the same time, IsoView microscopy rapidly images large specimens via simultaneous light-sheet illumination and fluorescence detection along four orthogonal directions. In a post-processing step, these four views are then combined by means of high-throughput multiview deconvolution to yield images with a system resolution of ≤ 450 nm in all three dimensions. Using IsoView microscopy, we performed whole-animal functional imaging of Drosophila embryos and larvae at a spatial resolution of 1.1-2.5 μm and at a temporal resolution of 2 Hz for up to 9 hours. We also performed whole-brain functional imaging in larval zebrafish and multicolor imaging of fast cellular dynamics across entire, gastrulating Drosophila embryos with isotropic, sub-cellular resolution. Compared with conventional (spatially anisotropic) light-sheet microscopy, IsoView microscopy improves spatial resolution at least sevenfold and decreases resolution anisotropy at least threefold. Compared with existing high-resolution light-sheet techniques, such as lattice lightsheet microscopy or diSPIM, IsoView microscopy effectively doubles the penetration depth and provides subsecond temporal resolution for specimens 400-fold larger than could previously be imaged.

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    07/12/16 | Forced chromatin looping raises fetal hemoglobin in adult sickle cells to higher levels than pharmacologic inducers.
    Breda L, Motta I, Lourenco S, Gemmo C, Deng W, Rupon JW, Abdulmalik OY, Manwani D, Blobel GA, Rivella S
    Blood. 2016 Jul 12:. doi: 10.1182/blood-2016-01-691089

    Overcoming the silencing of the fetal γ-globin gene has been a long standing goal in the treatment of sickle cell disease (SCD). The major transcriptional enhancer of the β-globin locus, called LCR, dynamically interacts with the developmental stage-appropriate β-type globin genes via chromatin looping, a process requiring the protein Ldb1. In adult erythroid cells the LCR can be re-directed from the adult β- to the fetal γ-globin promoter by tethering Ldb1 to the human γ-globin promoter with custom designed zinc finger proteins (ZF-Ldb1), leading to reactivation of γ-globin gene expression. To compare this approach to pharmacological reactivation of fetal hemoglobin (HbF), hematopoietic cells from SCD patients were treated with a lentivirus expressing the ZF-Ldb1 or with chemical HbF inducers. The HbF increase in cells treated with ZF-Ldb1 was more than double of that observed with decitabine and pomalidomide; butyrate had an intermediate effect while tranylcypromine and hydroxyurea showed relatively low HbF reactivation. ZF-Ldb1 showed comparatively little toxicity, and reduced sickle Hb (HbS) synthesis as well as sickling of SCD erythroid cells under hypoxic conditions. The efficacy and low cytotoxicity of lentiviral-mediated ZF-Ldb1 gene transfer compared to the drug regimens support its therapeutic potential for the treatment of SCD.

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