Genomes and Genes
Thomas J Deerinck
Affiliation: University of California
- Multicolor and electron microscopic imaging of connexin traffickingGuido Gaietta
National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Science 296:503-7. 2002..Selective imaging by correlated optical and electron microscopy of protein molecules of known ages will clarify fundamental processes of protein trafficking in situ...
- Roles of KChIP1 in the regulation of GABA-mediated transmission and behavioral anxietyKun Xia
State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, China
Mol Brain 3:23. 2010..Our study suggests that KChIP1 is a synaptic protein that regulates behavioral anxiety by modulating inhibitory synaptic transmission, and drugs that act on KChIP1 may help to treat patients with mood disorders including anxiety...
- PKA, PKC, and AKAP localization in and around the neuromuscular junctionG A Perkins
Department of Neurosciences and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093 0608, USA
BMC Neurosci 2:17. 2001..We found previously that a new class of AKAPs, dual-specific AKAPs, denoted D-AKAP1 and D-AKAP2, bind to RIalpha in addition to the RII subunits...
- The application of fluorescent quantum dots to confocal, multiphoton, and electron microscopic imagingThomas J Deerinck
National Center of Microscopy and Imaging Research NCMIR, Center for Research on Biological Systems, University of California, San Diego UCSD School of Medicine, 1000 BSB, 9500 Gilman Drive, MC0608, La Jolla, CA 92093 0608, USA
Toxicol Pathol 36:112-6. 2008..Considerations for their application to immunolabeling for correlated light and electron microscopic analysis are discussed...
- Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopyJason Lanman
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
J Struct Biol 161:439-46. 2008..Two features of the mitochondrial modification are approximately 60 nm spherules that line the outer membrane and the large chamber created by the convolution induced in the entire organelle...
- Markers for correlated light and electron microscopyGina E Sosinsky
National Center for Microscopy and Imaging Research and Center for Research in Biological Systems, University of California, San Diego, La Jolla, California 92093, USA
Methods Cell Biol 79:575-91. 2007
- Isoform-specific PKA dynamics revealed by dye-triggered aggregation and DAKAP1alpha-mediated localization in living cellsBrent R Martin
Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Chem Biol 14:1031-42. 2007..Overall, effective separation of type I PKA is substrate dependent, whereas type II PKA dissociation relies on autophosphorylation...
- Investigating synapse formation and function using human pluripotent stem cell-derived neuronsJi Eun Kim
Neurobiology Section, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
Proc Natl Acad Sci U S A 108:3005-10. 2011..These findings establish human pluripotent stem cell-derived neurons as a viable model for the study of synaptic differentiation and function under normal and disorder-associated conditions...
- The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applicationsGina E Sosinsky
National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, 1070 Basic Science Building MC 0608, 9500 Gilman Drive, La Jolla, CA 92093 0608, USA
J Struct Biol 161:359-71. 2008....
- Light and electron microscopic localization of multiple proteins using quantum dotsThomas J Deerinck
Department of Neurosciences, The National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA
Methods Mol Biol 374:43-53. 2007..Here we demonstrate an approach using quantum dots for pre-embedding immunolabeling of multiple diverse proteins for both LM and EM that overcomes many of these problems...
- High resolution three-dimensional reconstruction of fibrotic skeletal muscle extracellular matrixAllison R Gillies
Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
J Physiol . 2016..Therapeutic strategies for skeletal muscle fibrosis should consider the organisation of the ECM to target the structures and cells contributing to fibrotic muscle function. This article is protected by copyright. All rights reserved...
- Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imagingMark H Ellisman
National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093 0608, USA
Methods Cell Biol 111:139-55. 2012..Here we review and discuss the current generation of genetic labels for direct protein identification by CLEM, addressing their relative strengths and weaknesses and in what experiments they would be most useful...
- Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopyGuido M Gaietta
National Center for Microscopy and Imaging Research, Center for Research on Biological Structure, University of California at San Diego, La Jolla, CA 92093, USA
Proc Natl Acad Sci U S A 103:17777-82. 2006..Our studies provide previously undescribed insights into Golgi disassociation and reassembly during mitosis and offer a powerful approach to follow recombinant protein distribution in 4D imaging and correlated high-resolution analysis...
- Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomographyGina E Sosinsky
National Center for Microscopy and Imaging Research, Department of Neurosciences and the Center for Research on Biological Systems, University of California, San Diego, CA, USA
Neuroinformatics 3:133-62. 2005....
- Tetracysteine genetic tags complexed with biarsenical ligands as a tool for investigating gap junction structure and dynamicsGina E Sosinsky
National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
Cell Commun Adhes 10:181-6. 2003....
- Click-EM for imaging metabolically tagged nonprotein biomoleculesJohn T Ngo
Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
Nat Chem Biol 12:459-65. 2016..We describe the application of click-EM in imaging metabolically tagged DNA, RNA and lipids in cultured cells and neurons and highlight its use in tracking peptidoglycan synthesis in the Gram-positive bacterium Listeria monocytogenes. ..
- Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopyHorng D Ou
Molecular and Cell Biology Laboratory, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
Methods 90:39-48. 2015....
- Design and synthesis of a minimal bacterial genomeClyde A Hutchison
J Craig Venter Institute, La Jolla, CA 92037, USA
Science 351:aad6253. 2016..Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design...
- Three-dimensional reconstruction of skeletal muscle extracellular matrix ultrastructureAllison R Gillies
1Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093 0863, USA
Microsc Microanal 20:1835-40. 2014..Perimysial collagen structures in the ECM may provide a target for clinical therapies aimed at reducing skeletal muscle fibrosis and stiffness. ..
- Loss of acinar cell IKKα triggers spontaneous pancreatitis in miceNing Li
Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, UCSD, La Jolla, California 92093 0723, USA
J Clin Invest 123:2231-43. 2013....
- Fibrinogen-induced perivascular microglial clustering is required for the development of axonal damage in neuroinflammationDimitrios Davalos
Gladstone Institute of Neurological Disease, University of California, San Francisco, 1650 Owens Street, San Francisco, CA 94158, USA
Nat Commun 3:1227. 2012..Thus, early and progressive perivascular microglial clustering triggered by fibrinogen leakage upon blood-brain barrier disruption contributes to axonal damage in neuroinflammatory disease...
- A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressorsHorng D Ou
Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
Cell 151:304-19. 2012..E4-ORF3 assembly creates avidity-driven interactions with PML and an emergent MRN binding interface. This reveals an elegant structural solution whereby a small protein forms a multivalent matrix that traps disparate tumor suppressors...
- Spinophilin facilitates dephosphorylation of doublecortin by PP1 to mediate microtubule bundling at the axonal wristStephanie L Bielas
Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
Cell 129:579-91. 2007..These findings suggest that spatially restricted adaptor-specific MAP reactivation through dephosphorylation is important in organization of the neuronal cytoskeleton...
- STIM1 is a Ca2+ sensor that activates CRAC channels and migrates from the Ca2+ store to the plasma membraneShenyuan L Zhang
Department of Physiology and Biophysics and Center for Immunology, University of California, Irvine, California 92697, USA
Nature 437:902-5. 2005..We propose that STIM1 functions as the missing link between Ca2+ store depletion and SOC influx, serving as a Ca2+ sensor that translocates upon store depletion to the plasma membrane to activate CRAC channels...
- Structure-function studies of blood and air capillaries in chicken lung using 3D electron microscopyJohn B West
Department of Medicine, and National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA 92093 0623, USA
Respir Physiol Neurobiol 170:202-9. 2010..These EM studies show the supporting structures in greater detail than has previously been possible, particularly in 3D, and they allow a more complete analysis of the mechanical forces affecting avian pulmonary capillaries...
- Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dotsBen N G Giepmans
Department of Neurosciences, National Center for Microscopy and Imaging Research, and Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, 92093 0608, USA
Nat Methods 2:743-9. 2005..We provide examples of double and triple immunolabeling using light, electron and correlated microscopy in rat cells and mouse tissue. We conclude that QDs aid precise high-throughput determination of protein distribution...
- Regulation of membrane trafficking and subcellular organization of endocytic compartments revealed with FM1-43 in resting and activated human T cellsAlla F Fomina
Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
Exp Cell Res 291:150-66. 2003..The present study demonstrates the utility of FM1-43 as a marker of membrane trafficking in T cells and reveals possible mechanisms of its modulation during T cell activation...
- Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptorsWilliam Ju
Nancy Friend Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, 1201 Welch Road, Stanford University School of Medicine, Palo Alto, California 94304, USA
Nat Neurosci 7:244-53. 2004....
- Hypophosphorylated SR splicing factors transiently localize around active nucleolar organizing regions in telophase daughter nucleiPaula A Bubulya
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
J Cell Biol 167:51-63. 2004..This work demonstrates a previously unrecognized role of NAPs in splicing factor trafficking and nuclear speckle biogenesis...