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Drigo RAE, Habashy A, Acree C, Kim KY, Deerinck T, Patterson E, Lantier L, McGuinness O, Ellisman M. Mesoscale Metabolic Channeling Revealed by Multimodal Microscopy. Res Sq 2024:rs.3.rs-4096781. [PMID: 38699373 PMCID: PMC11065083 DOI: 10.21203/rs.3.rs-4096781/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Metabolic homeostasis within cells and tissues requires engagement of catabolic and anabolic pathways consuming nutrients needed to generate energy to drive these and other subcellular processes. However, the current understanding of cell homeostasis and metabolism, including how cells utilize nutrients, comes largely from tissue and cell models analyzed after fractionation. These bulk strategies do not reveal the spatial characteristics of cell metabolism at the single cell level, and how these aspects relate to the location of cells and organelles within the complexity of the tissue they reside within. Here we pioneer the use of high-resolution electron and stable isotope microscopy (MIMS-EM) to quantitatively map the fate of nutrient-derived 13 C atoms at subcellular scale. When combined with machine-learning image segmentation, our approach allows us to establish the cellular and organellar spatial pattern of glucose 13 C flux in hepatocytes in situ . We applied network analysis algorithms to chart the landscape of organelle-organelle contact networks and identified subpopulations of mitochondria and lipid droplets that have distinct organelle interactions and 13 C enrichment levels. In addition, we revealed a new relationship between the initiation of glycogenesis and proximity of lipid droplets. Our results establish MIMS-EM as a new tool for tracking and quantifying nutrient metabolism at the subcellular scale, and to identify the spatial channeling of nutrient-derived atoms in the context of organelle-organelle interactions in situ .
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Chaudhary P, Lockwood H, Stowell C, Bushong E, Reynaud J, Yang H, Gardiner SK, Wiliams G, Williams I, Ellisman M, Marsh-Armstrong N, Burgoyne C. Retrolaminar Demyelination of Structurally Intact Axons in Nonhuman Primate Experimental Glaucoma. Invest Ophthalmol Vis Sci 2024; 65:36. [PMID: 38407858 PMCID: PMC10902877 DOI: 10.1167/iovs.65.2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/28/2024] [Indexed: 02/27/2024] Open
Abstract
Purpose To determine if structurally intact, retrolaminar optic nerve (RON) axons are demyelinated in nonhuman primate (NHP) experimental glaucoma (EG). Methods Unilateral EG NHPs (n = 3) were perfusion fixed, EG and control eyes were enucleated, and foveal Bruch's membrane opening (FoBMO) 30° sectoral axon counts were estimated. Optic nerve heads were trephined; serial vibratome sections (VSs) were imaged and colocalized to a fundus photograph establishing their FoBMO location. The peripheral neural canal region within n = 5 EG versus control eye VS comparisons was targeted for scanning block-face electron microscopic reconstruction (SBEMR) using micro-computed tomographic reconstructions (µCTRs) of each VS. Posterior laminar beams within each µCTR were segmented, allowing a best-fit posterior laminar surface (PLS) to be colocalized into its respective SBEMR. Within each SBEMR, up to 300 axons were randomly traced until they ended (nonintact) or left the block (intact). For each intact axon, myelin onset was identified and myelin onset distance (MOD) was measured relative to the PLS. For each EG versus control SBEMR comparison, survival analyses compared EG and control MOD. Results MOD calculations were successful in three EG and five control eye SBEMRs. Within each SBEMR comparison, EG versus control eye axon loss was -32.9%, -8.3%, and -15.2% (respectively), and MOD was increased in the EG versus control SBEMR (P < 0.0001 for each EG versus control SBEMR comparison). When data from all three EG eye SBEMRs were compared to all five control eye SBEMRs, MOD was increased within the EG eyes. Conclusions Structurally intact, RON axons are demyelinated in NHP early to moderate EG. Studies to determine their functional status are indicated.
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Affiliation(s)
- Priya Chaudhary
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Howard Lockwood
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Cheri Stowell
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Eric Bushong
- National Center for Microscopy & Imaging Research, UCSD, La Jolla, California, United States
| | - Juan Reynaud
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Hongli Yang
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Stuart K Gardiner
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Galen Wiliams
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Imee Williams
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Mark Ellisman
- National Center for Microscopy & Imaging Research, UCSD, La Jolla, California, United States
| | - Nick Marsh-Armstrong
- Department of Ophthalmology, University of California, Davis, California, United States
| | - Claude Burgoyne
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
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Osorio-Rodriguez D, Metcalfe KS, McGlynn SE, Yu H, Dekas AE, Ellisman M, Deerinck T, Aristilde L, Grotzinger JP, Orphan VJ. Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation. Proc Natl Acad Sci U S A 2023; 120:e2302156120. [PMID: 38079551 PMCID: PMC10743459 DOI: 10.1073/pnas.2302156120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM-often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)-are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1-9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862-866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.
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Affiliation(s)
- Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Kyle S. Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Shawn E. McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo152-8550, Japan
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- College of Urban and Environmental Sciences, Peking University, Beijing100871, China
| | - Anne E. Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Earth System Science, Stanford University, Stanford, CA94305
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Tom Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL60208
| | - John P. Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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dos Santos C, Shrestha S, Cottam M, Perkins G, Lev-Ram V, Roy B, Acree C, Kim KY, Deerinck T, Cutler M, Dean D, Cartailler JP, MacDonald PE, Hetzer M, Ellisman M, Drigo RAE. Caloric restriction promotes beta cell longevity and delays aging and senescence by enhancing cell identity and homeostasis mechanisms. Res Sq 2023:rs.3.rs-3311459. [PMID: 37790446 PMCID: PMC10543285 DOI: 10.21203/rs.3.rs-3311459/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Caloric restriction (CR) extends organismal lifespan and health span by improving glucose homeostasis mechanisms. How CR affects organellar structure and function of pancreatic beta cells over the lifetime of the animal remains unknown. Here, we used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis link this transcriptional phenotype to transcription factors involved in beta cell identity (Mafa) and homeostasis (Atf6). Imaging metabolomics further demonstrates that CR beta cells are more energetically competent. In fact, high-resolution light and electron microscopy indicates that CR reduces beta cell mitophagy and increases mitochondria mass, increasing mitochondrial ATP generation. Finally, we show that long-term CR delays the onset of beta cell aging and senescence to promote longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cells during aging and diabetes.
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Affiliation(s)
- Cristiane dos Santos
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Shristi Shrestha
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Matthew Cottam
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Guy Perkins
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Varda Lev-Ram
- University of California San Diego, Department of Pharmacology, School of Medicine. La Jolla, CA USA
| | - Birbickram Roy
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Christopher Acree
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Keun-Young Kim
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Thomas Deerinck
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Melanie Cutler
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Danielle Dean
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | | | - Patrick E. MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Martin Hetzer
- Institute of Science and Technology Austria (ISTA), Vienna, Austria
| | - Mark Ellisman
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Rafael Arrojo e Drigo
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
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Dos Santos C, Shrestha S, Cottam M, Perkins G, Lev-Ram V, Roy B, Acree C, Kim KY, Deerinck T, Cutler M, Dean D, Cartailler JP, MacDonald PE, Hetzer M, Ellisman M, E Drigo RA. Caloric restriction promotes beta cell longevity and delays aging and senescence by enhancing cell identity and homeostasis mechanisms. bioRxiv 2023:2023.08.23.554369. [PMID: 37662336 PMCID: PMC10473730 DOI: 10.1101/2023.08.23.554369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Caloric restriction (CR) extends organismal lifespan and health span by improving glucose homeostasis mechanisms. How CR affects organellar structure and function of pancreatic beta cells over the lifetime of the animal remains unknown. Here, we used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis link this transcriptional phenotype to transcription factors involved in beta cell identity (Mafa) and homeostasis (Atf6). Imaging metabolomics further demonstrates that CR beta cells are more energetically competent. In fact, high-resolution light and electron microscopy indicates that CR reduces beta cell mitophagy and increases mitochondria mass, increasing mitochondrial ATP generation. Finally, we show that long-term CR delays the onset of beta cell aging and senescence to promote longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cells during aging and diabetes.
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Affiliation(s)
- Cristiane Dos Santos
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Shristi Shrestha
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Matthew Cottam
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Guy Perkins
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Varda Lev-Ram
- University of California San Diego, Department of Pharmacology, School of Medicine. La Jolla, CA USA
| | - Birbickram Roy
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Christopher Acree
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Keun-Young Kim
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Thomas Deerinck
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Melanie Cutler
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Danielle Dean
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | | | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Martin Hetzer
- Institute of Science and Technology Austria (ISTA), Vienna, Austria
| | - Mark Ellisman
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Rafael Arrojo E Drigo
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
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Venkatraman K, Lee CT, Garcia G, Mahapatra A, Kim K, Perkins G, Phan S, Pasolli HA, Lippincott-Schwartz J, Ellisman M, Rangamani P, Budin I. Dissecting the lipidic determinants of inner mitochondrial membrane structure. Biophys J 2023; 122:98a. [PMID: 36785115 DOI: 10.1016/j.bpj.2022.11.720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | | | | | | | - Keunyoung Kim
- University of California San Diego, La Jolla, CA, USA
| | - Guy Perkins
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Mark Ellisman
- University of California San Diego, La Jolla, CA, USA
| | | | - Itay Budin
- University of California San Diego, La Jolla, CA, USA
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Fang J, Castillon G, Phan S, McArdle S, Hariharan C, Ellisman M, Ollmann Saphire E. Ebola viral factories are biomolecular condensates with specialized assembly dynamics for viral RNA synthesis. Biophys J 2023; 122:442a. [PMID: 36784269 DOI: 10.1016/j.bpj.2022.11.2385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Jingru Fang
- Scripps Research, La Jolla, CA, USA; La Jolla Institute, La Jolla, CA, USA
| | - Guillaume Castillon
- Cellular and Molecular Medicine Electron Microscopy Core Facility, University of California San Diego, La Jolla, CA, USA; National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
| | - Sara McArdle
- Light Microscopy Core Facility, La Jolla Institute, La Jolla, CA, USA
| | | | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
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Sepulveda-Falla D, Sanchez JS, Almeida MC, Boassa D, Acosta-Uribe J, Vila-Castelar C, Ramirez-Gomez L, Baena A, Aguillon D, Villalba-Moreno ND, Littau JL, Villegas A, Beach TG, White CL, Ellisman M, Krasemann S, Glatzel M, Johnson KA, Sperling RA, Reiman EM, Arboleda-Velasquez JF, Kosik KS, Lopera F, Quiroz YT. Distinct tau neuropathology and cellular profiles of an APOE3 Christchurch homozygote protected against autosomal dominant Alzheimer's dementia. Acta Neuropathol 2022; 144:589-601. [PMID: 35838824 PMCID: PMC9381462 DOI: 10.1007/s00401-022-02467-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 01/22/2023]
Abstract
We describe in vivo follow-up PET imaging and postmortem findings from an autosomal dominant Alzheimer's disease (ADAD) PSEN1 E280A carrier who was also homozygous for the APOE3 Christchurch (APOE3ch) variant and was protected against Alzheimer's symptoms for almost three decades beyond the expected age of onset. We identified a distinct anatomical pattern of tau pathology with atypical accumulation in vivo and unusual postmortem regional distribution characterized by sparing in the frontal cortex and severe pathology in the occipital cortex. The frontal cortex and the hippocampus, less affected than the occipital cortex by tau pathology, contained Related Orphan Receptor B (RORB) positive neurons, homeostatic astrocytes and higher APOE expression. The occipital cortex, the only cortical region showing cerebral amyloid angiopathy (CAA), exhibited a distinctive chronic inflammatory microglial profile and lower APOE expression. Thus, the Christchurch variant may impact the distribution of tau pathology, modulate age at onset, severity, progression, and clinical presentation of ADAD, suggesting possible therapeutic strategies.
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Affiliation(s)
- Diego Sepulveda-Falla
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Justin S Sanchez
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Camila Almeida
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, Brazil
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research (NCMIR), San Diego School of Medicine (UCSD), University of California, La Jolla, San Diego, CA, 92093, USA
- Department of Neurosciences, San Diego School of Medicine (UCSD), University of California, La Jolla, San Diego, CA, 92093, USA
| | - Juliana Acosta-Uribe
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Clara Vila-Castelar
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Liliana Ramirez-Gomez
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana Baena
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - David Aguillon
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Nelson David Villalba-Moreno
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jessica Lisa Littau
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andres Villegas
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Thomas G Beach
- Department of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Charles L White
- Department of Pathology, Neuropathology Laboratory, University of Texas Southwestern Medical Center, Dallas, USA
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), San Diego School of Medicine (UCSD), University of California, La Jolla, San Diego, CA, 92093, USA
- Department of Neurosciences, San Diego School of Medicine (UCSD), University of California, La Jolla, San Diego, CA, 92093, USA
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Experimental Pathology Core Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Keith A Johnson
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Reisa A Sperling
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Joseph F Arboleda-Velasquez
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kenneth S Kosik
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Yakeel T Quiroz
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Grupo de Neurociencias de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia.
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Hatano A, Someya M, Tanaka H, Sakakima H, Izumi S, Hoshijima M, Ellisman M, McCulloch AD. Automated 3D reconstruction of isolated mitochondria from cardiomyocyte SBEM images. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Krishna S, Arrojo E Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer MW. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Dev Cell 2021; 56:2952-2965.e9. [PMID: 34715012 DOI: 10.1016/j.devcel.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 07/28/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]
Abstract
In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.
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Affiliation(s)
- Shefali Krishna
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rafael Arrojo E Drigo
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA; National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA
| | - Juliana S Capitanio
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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11
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Stoneham CA, Langer S, De Jesus PD, Wozniak JM, Lapek J, Deerinck T, Thor A, Pache L, Chanda SK, Gonzalez DJ, Ellisman M, Guatelli J. A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor. PLoS Pathog 2021; 17:e1009409. [PMID: 34843601 PMCID: PMC8659692 DOI: 10.1371/journal.ppat.1009409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 12/09/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
The HIV-1 accessory protein Vpu modulates membrane protein trafficking and degradation to provide evasion of immune surveillance. Targets of Vpu include CD4, HLAs, and BST-2. Several cellular pathways co-opted by Vpu have been identified, but the picture of Vpu's itinerary and activities within membrane systems remains incomplete. Here, we used fusion proteins of Vpu and the enzyme ascorbate peroxidase (APEX2) to compare the ultrastructural locations and the proximal proteomes of wild type Vpu and Vpu-mutants. The proximity-omes of the proteins correlated with their ultrastructural locations and placed wild type Vpu near both retromer and ESCRT-0 complexes. Hierarchical clustering of protein abundances across the mutants was essential to interpreting the data and identified Vpu degradation-targets including CD4, HLA-C, and SEC12 as well as Vpu-cofactors including HGS, STAM, clathrin, and PTPN23, an ALIX-like protein. The Vpu-directed degradation of BST-2 was supported by STAM and PTPN23 and to a much lesser extent by the retromer subunits Vps35 and SNX3. PTPN23 also supported the Vpu-directed decrease in CD4 at the cell surface. These data suggest that Vpu directs targets from sorting endosomes to degradation at multi-vesicular bodies via ESCRT-0 and PTPN23.
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Affiliation(s)
- Charlotte A. Stoneham
- Department of Medicine, University of California, San Diego School of Medicine and Veterans Affairs San Diego Healthcare System, La Jolla, California, United States of America
| | - Simon Langer
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Paul D. De Jesus
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Jacob M. Wozniak
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - John Lapek
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Thomas Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California, San Diego, School of Medicine, La Jolla, California, United States of America
| | - Andrea Thor
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California, San Diego, School of Medicine, La Jolla, California, United States of America
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Sumit K. Chanda
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - David J. Gonzalez
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California, San Diego, School of Medicine, La Jolla, California, United States of America
- Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, California, United States of America
| | - John Guatelli
- Department of Medicine, University of California, San Diego School of Medicine and Veterans Affairs San Diego Healthcare System, La Jolla, California, United States of America
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12
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Marlow J, Spietz R, Kim K, Ellisman M, Girguis P, Hatzenpichler R. Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment. Environ Microbiol 2021; 23:4756-4777. [PMID: 34346142 PMCID: PMC8456820 DOI: 10.1111/1462-2920.15667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/08/2021] [Indexed: 01/04/2023]
Abstract
Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were resin-embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%-22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.
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Affiliation(s)
- Jeffrey Marlow
- Department of Organismic and Evolutionary BiologyHarvard University16 Divinity AveCambridgeMassachusetts02138USA
| | - Rachel Spietz
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm EngineeringMontana State UniversityBozemanMontana59717USA
| | - Keun‐Young Kim
- Department of NeurosciencesUniversity of California at San Diego School of Medicine and National Center for Microscopy and Imaging Research, University of CaliforniaSan DiegoLa JollaCalifornia92093USA
| | - Mark Ellisman
- Department of NeurosciencesUniversity of California at San Diego School of Medicine and National Center for Microscopy and Imaging Research, University of CaliforniaSan DiegoLa JollaCalifornia92093USA
- Department of PharmacologyUniversity of CaliforniaSan DiegoLa JollaCalifornia92161USA
| | - Peter Girguis
- Department of Organismic and Evolutionary BiologyHarvard University16 Divinity AveCambridgeMassachusetts02138USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm EngineeringMontana State UniversityBozemanMontana59717USA
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13
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Han M, Momcilovic M, Bushong E, Stiles L, Shirihai O, Koehler C, Sadeghi S, Ellisman M, Shackelford DB. Abstract 2818: In vivo imaging of mitochondrial bioenergetics in lung cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Non-small cell lung cancer (NSCLC) is a histologically, genetically and metabolically heterogeneous disease. The mitochondria are essential regulators of cellular energy and metabolism and they play a critical role in sustaining growth and survival of lung tumor cells. However, our understanding of mitochondrial metabolism in cancer at an in vivo level has been limited thus leaving a large gap in our knowledge of how mitochondrial bioenergetics support tumor growth. To better study mitochondrial bioenergetics in lung tumors, we recently developed and validated a voltage sensitive, positron emission tomography (PET) tracer known as 4-[18F]fluorobenzyl triphenylphosphonium (18FBnTP) that we used to profile mitochondrial bioenergetics in autochthonous K-Ras driven mouse models of lung cancer (Momcilovic et al., (2019) Nature). The use of 18FBnTP PET imaging enabled us to functionally profile mitochondrial bioenergetics in live tumors and discover distinct functional mitochondrial heterogeneity conserved across different NSCLC tumor subtypes. In order to study mitochondria at the level of ultrastructure we coupled 18FBnTP PET with 3D serial block-face scanning electron microscopy (3D SBEM). By coupling these two techniques we are able to image and quantify mitochondria heterogeneity from whole tumors down to the ultrastructures of individual mitochondria within tumor cells. Our study reveals distinct organization of mitochondrial structure and function as lung tumors adapt during tumorigenesis. We anticipate that coupling 18FBnTP PET imaging with 3D SBEM will have dynamic applications beyond that of lung cancer and enrich our understanding how mitochondria impact human disease.
Citation Format: Mingqi Han, Milica Momcilovic, Eric Bushong, Linsey Stiles, Orian Shirihai, Carla Koehler, Saman Sadeghi, Mark Ellisman, David B. Shackelford. In vivo imaging of mitochondrial bioenergetics in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2818.
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Affiliation(s)
- Mingqi Han
- 1UCLA David Geffen School of Medicine, Los Angeles, CA
| | | | - Eric Bushong
- 2University of California San Diego, La Jolla, CA
| | - Linsey Stiles
- 1UCLA David Geffen School of Medicine, Los Angeles, CA
| | | | | | | | - Mark Ellisman
- 4University of California, San Diego, Los Angeles, CA
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14
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Zhu Y, Uytiepo M, Bushong E, Haberl M, Beutter E, Scheiwe F, Zhang W, Chang L, Luu D, Chui B, Ellisman M, Maximov A. Nanoscale 3D EM reconstructions reveal intrinsic mechanisms of structural diversity of chemical synapses. Cell Rep 2021; 35:108953. [PMID: 33826888 PMCID: PMC8354523 DOI: 10.1016/j.celrep.2021.108953] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/21/2021] [Accepted: 03/15/2021] [Indexed: 10/25/2022] Open
Abstract
Chemical synapses of shared cellular origins have remarkably heterogeneous structures, but how this diversity is generated is unclear. Here, we use three-dimensional (3D) electron microscopy and artificial intelligence algorithms for image processing to reconstruct functional excitatory microcircuits in the mouse hippocampus and microcircuits in which neurotransmitter signaling is permanently suppressed with genetic tools throughout the lifespan. These nanoscale analyses reveal that experience is dispensable for morphogenesis of synapses with different geometric shapes and contents of membrane organelles and that arrangement of morphologically distinct connections in local networks is stochastic. Moreover, loss of activity increases the variability in sizes of opposed pre- and postsynaptic structures without disrupting their alignments, suggesting that inherently variable weights of naive connections become progressively matched with repetitive use. These results demonstrate that mechanisms for the structural diversity of neuronal synapses are intrinsic and provide insights into how circuits essential for memory storage assemble and integrate information.
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Affiliation(s)
- Yongchuan Zhu
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marco Uytiepo
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric Bushong
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - Matthias Haberl
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - Elizabeth Beutter
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Frederieke Scheiwe
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Weiheng Zhang
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lyanne Chang
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Danielle Luu
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Brandon Chui
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92037, USA.
| | - Anton Maximov
- Department of Neuroscience, The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
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15
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Jackson D, Holcomb P, Ellisman M, Spirou G. Cover Image. Synapse 2021. [DOI: 10.1002/syn.22194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Jackson D, Holcomb P, Ellisman M, Spirou G. Two types of somatic spines provide sites for intercellular signaling during calyx of Held growth and maturation. Synapse 2020; 75:e22189. [PMID: 33025635 DOI: 10.1002/syn.22189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022]
Abstract
Dendritic spines have been described in developing and mature systems, but similar extensions from cell bodies are less studied. We utilized electron microscopy image volumes, uniquely collected across a range of early postnatal and month-old mice, to characterize and describe two types of somatic processes that extended into and under the developing calyx of Held (CH), which we named type 1 and type 2 spines. Type 1 spines occurred singly, were mostly vermiform in shape, and formed regularly spaced indentations into the CH. Type 1 spines appeared in concert with the earliest expansion of the CH by P3, peaked at P6 and returned to low density at P30. Type 2 spines were intertwined into a secondary structure called a spine mat, which has not previously been described in the CNS, and were more complex geometrically. Type 2 spines formed after the CH crossed a size threshold, reached maximum density at P9, and were absent from most CHs at P30. Both spine types, but a higher density of type 1 spines, were sites for synapse formation. Spine mats brought pre- and postsynaptic neurons and glial cells into contact, and were captured in stages of partial detachment and engulfment by the presynaptic terminal, suggesting trans-endocytosis as a mode of removal ahead of maturity. In conglomerate, these observations reveal somatic spines to be sites for chemical neurotransmission and chemical sampling among synaptic partners and glia as tissue structure transforms into mature neural circuits.
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Affiliation(s)
- Dakota Jackson
- Rockefeller Neuroscience Institute, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Paul Holcomb
- Rockefeller Neuroscience Institute, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA
| | - George Spirou
- Department of Medical Engineering, University of South Florida, Tampa, FL, USA
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17
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Agarwala S, Kim KY, Phan S, Ju S, Kong YE, Bushong E, Ellisman M, Tamplin O. 3047 – THE ADULT HEMATOPOIETIC STEM CELL NICHE IN ZEBRAFISH DEFINED USING CORRELATIVE LIGHT AND ELECTRON MICROSCOPY. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Abstract
Synapses are dynamic connections that underlie essential functions of the nervous system. The addition, removal, and maintenance of synapses govern the flow of information in neural circuits throughout the lifetime of an animal. While extensive studies have elucidated many intrinsic mechanisms that neurons employ to modulate their connections, increasing evidence supports the roles of non-neuronal cells, such as glia, in synapse maintenance and circuit function. We previously showed that C. elegans epidermis regulates synapses through ZIG-10, a cell-adhesion protein of the immunoglobulin domain superfamily. Here we identified a member of the Pals1/MPP5 family, MAGU-2, that functions in the epidermis to modulate phagocytosis and the number of synapses by regulating ZIG-10 localization. Furthermore, we used light and electron microscopy to show that this epidermal mechanism removes neuronal membranes from the neuromuscular junction, dependent on the conserved phagocytic receptor CED-1. Together, our study shows that C. elegans epidermis constrains synaptic connectivity, in a manner similar to astrocytes and microglia in mammals, allowing optimized output of neural circuits.
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Affiliation(s)
- Salvatore J Cherra
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Alexandr Goncharov
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA.,Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
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19
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Momcilovic M, Han M, Bushong E, Stiles L, Dubinett S, Christofk H, Shirihai O, Koehler C, Sadeghi S, Ellisman M, Shackelford D. IA08 Mapping Mitochondrial Heterogeneity in Lung Cancer. J Thorac Oncol 2020. [DOI: 10.1016/j.jtho.2019.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Wesseling JF, Phan S, Bushong EA, Siksou L, Marty S, Pérez-Otaño I, Ellisman M. Sparse force-bearing bridges between neighboring synaptic vesicles. Brain Struct Funct 2019; 224:3263-3276. [PMID: 31667576 PMCID: PMC6875159 DOI: 10.1007/s00429-019-01966-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/05/2019] [Indexed: 12/28/2022]
Abstract
Most vesicles in the interior of synaptic terminals are clustered in clouds close to active zone regions of the plasma membrane where exocytosis occurs. Electron-dense structures, termed bridges, have been reported between a small minority of pairs of neighboring vesicles within the clouds. Synapsin proteins have been implicated previously, but the existence of the bridges as stable structures in vivo has been questioned. Here we use electron tomography to show that the bridges are present but less frequent in synapsin knockouts compared to wildtype. An analysis of distances between neighbors in wildtype tomograms indicated that the bridges are strong enough to resist centrifugal forces likely induced by fixation with aldehydes. The results confirm that the bridges are stable structures and that synapsin proteins are involved in formation or stabilization.
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Affiliation(s)
- John F Wesseling
- Instituto de Neurociencias, CSIC-UMH, San Juan de Alicante, Spain. .,Departmento de Neurociencias (CIMA), Universidad de Navarra, Pamplona, Spain.
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
| | - Léa Siksou
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France.,Global Research and Development, Teva Pharmaceutical Industries Ltd, Netanya, Israel
| | - Serge Marty
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France.,Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR7225, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | | | - Mark Ellisman
- National Center for Microscopy and Imaging Research and Department of Neuroscience, University of California, San Diego, CA, USA
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21
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Spirou G, Kersting M, Bayliss T, Razzaq B, Holcomb P, Morehead M, Spencer N, Ellisman M, Manis P. New Principles for Cell and Circuit Function Revealed by Volume Nanoscale Imaging. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.201.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Paul Manis
- University of North CarolinaChapel Hill, Chapel HillNC
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22
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Zhao H, Perkins G, Yao H, Callacondo D, Appenzeller O, Ellisman M, La Spada AR, Haddad GG. Mitochondrial dysfunction in iPSC-derived neurons of subjects with chronic mountain sickness. J Appl Physiol (1985) 2018; 125:832-840. [PMID: 29357502 PMCID: PMC6734077 DOI: 10.1152/japplphysiol.00689.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 02/05/2023] Open
Abstract
Patients with chronic mountain sickness (CMS) suffer from hypoxemia, erythrocytosis, and numerous neurologic deficits. Here we used induced pluripotent stem cell (iPSC)-derived neurons from both CMS and non-CMS subjects to study CMS neuropathology. Using transmission electron microscopy, we report that CMS neurons have a decreased mitochondrial volume density, length, and less cristae membrane surface area. Real-time PCR confirmed a decreased mitochondrial fusion gene optic atrophy 1 (OPA1) expression. Immunoblot analysis showed an accumulation of the short isoform of OPA1 (S-OPA1) in CMS neurons, which have reduced ATP levels under normoxia and increased lactate dehydrogenase (LDH) release and caspase 3 activation after hypoxia. Improving the balance between the long isoform of OPA1 and S-OPA1 in CMS neurons increased the ATP levels and attenuated LDH release under hypoxia. Our data provide initial evidence for altered mitochondrial morphology and function in CMS neurons, and reveal increased cell death under hypoxia due in part to altered mitochondrial dynamics. NEW & NOTEWORTHY Induced pluripotent stem cell-derived neurons from chronic mountain sickness (CMS) subjects have altered mitochondrial morphology and dynamics, and increased sensitivity to hypoxic stress. Modification of OPA1 can attenuate cell death after hypoxic treatment, providing evidence that altered mitochondrial dynamics play an important role in increased vulnerability under stress in CMS neurons.
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Affiliation(s)
- Helen Zhao
- Department of Pediatrics (Respiratory Medicine), University of California San Diego , La Jolla, California
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, University of California San Diego , La Jolla, California
| | - Hang Yao
- Department of Pediatrics (Respiratory Medicine), University of California San Diego , La Jolla, California
| | - David Callacondo
- School of Medicine, Faculty of Health Sciences, Universidad Privada de Tacna, Tacna, Peru
- Instituto de Evaluación de Tecnologíasen Salud e Investigación (IETSI). EsSalud . Lima , Peru
| | - Otto Appenzeller
- New Mexico Health Enhancement and Marathon Clinics Research Foundation , Albuquerque, New Mexico
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California San Diego , La Jolla, California
| | - Albert R La Spada
- Department of Pediatrics (Respiratory Medicine), University of California San Diego , La Jolla, California
- Department of Neurosciences, University of California San Diego , La Jolla, California
- Department of Cellular and Molecular Medicine, University of California San Diego , La Jolla, California
- Institute for Genomic Medicine, University of California San Diego , La Jolla, California
- Sanford Consortium for Regenerative Medicine, University of California San Diego , La Jolla, California
- The Rady Children's Hospital , San Diego, California
| | - Gabriel G Haddad
- Department of Pediatrics (Respiratory Medicine), University of California San Diego , La Jolla, California
- Department of Neurosciences, University of California San Diego , La Jolla, California
- The Rady Children's Hospital , San Diego, California
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23
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Hu B, Arpag S, Zhang X, Möbius W, Werner H, Sosinsky G, Ellisman M, Zhang Y, Hamilton A, Chernoff J, Li J. Tuning PAK Activity to Rescue Abnormal Myelin Permeability in HNPP. PLoS Genet 2016; 12:e1006290. [PMID: 27583434 PMCID: PMC5008806 DOI: 10.1371/journal.pgen.1006290] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/10/2016] [Indexed: 01/31/2023] Open
Abstract
Schwann cells in the peripheral nervous systems extend their membranes to wrap axons concentrically and form the insulating sheath, called myelin. The spaces between layers of myelin are sealed by myelin junctions. This tight insulation enables rapid conduction of electric impulses (action potentials) through axons. Demyelination (stripping off the insulating sheath) has been widely regarded as one of the most important mechanisms altering the action potential propagation in many neurological diseases. However, the effective nerve conduction is also thought to require a proper myelin seal through myelin junctions such as tight junctions and adherens junctions. In the present study, we have demonstrated the disruption of myelin junctions in a mouse model (Pmp22+/-) of hereditary neuropathy with liability to pressure palsies (HNPP) with heterozygous deletion of Pmp22 gene. We observed a robust increase of F-actin in Pmp22+/- nerve regions where myelin junctions were disrupted, leading to increased myelin permeability. These abnormalities were present long before segmental demyelination at the late phase of Pmp22+/- mice. Moreover, the increase of F-actin levels correlated with an enhanced activity of p21-activated kinase (PAK1), a molecule known to regulate actin polymerization. Pharmacological inhibition of PAK normalized levels of F-actin, and completely prevented the progression of the myelin junction disruption and nerve conduction failure in Pmp22+/- mice. Our findings explain how abnormal myelin permeability is caused in HNPP, leading to impaired action potential propagation in the absence of demyelination. We call it "functional demyelination", a novel mechanism upstream to the actual stripping of myelin that is relevant to many demyelinating diseases. This observation also provides a potential therapeutic approach for HNPP.
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Affiliation(s)
- Bo Hu
- Department of Neurology, Center for Human Genetics Research, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Sezgi Arpag
- Department of Neurology, Center for Human Genetics Research, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Xuebao Zhang
- Department of Anatomy and Cell Biology, Wayne State University, Detroit, Michigan, United States of America
| | - Wiebke Möbius
- Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), GÖttingen, Germany
| | - Hauke Werner
- Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), GÖttingen, Germany
| | - Gina Sosinsky
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, United States of America
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, United States of America
| | - Yang Zhang
- Department of Neurology, Center for Human Genetics Research, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Audra Hamilton
- Department of Neurology, Center for Human Genetics Research, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jonathan Chernoff
- Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States of America
| | - Jun Li
- Department of Neurology, Center for Human Genetics Research, Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
- * E-mail:
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Jones C, Liu T, Cohan NW, Ellisman M, Tasdizen T. Efficient semi-automatic 3D segmentation for neuron tracing in electron microscopy images. J Neurosci Methods 2015; 246:13-21. [PMID: 25769273 DOI: 10.1016/j.jneumeth.2015.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND In the area of connectomics, there is a significant gap between the time required for data acquisition and dense reconstruction of the neural processes contained in the same dataset. Automatic methods are able to eliminate this timing gap, but the state-of-the-art accuracy so far is insufficient for use without user corrections. If completed naively, this process of correction can be tedious and time consuming. NEW METHOD We present a new semi-automatic method that can be used to perform 3D segmentation of neurites in EM image stacks. It utilizes an automatic method that creates a hierarchical structure for recommended merges of superpixels. The user is then guided through each predicted region to quickly identify errors and establish correct links. RESULTS We tested our method on three datasets with both novice and expert users. Accuracy and timing were compared with published automatic, semi-automatic, and manual results. COMPARISON WITH EXISTING METHODS Post-automatic correction methods have also been used in Mishchenko et al. (2010) and Haehn et al. (2014). These methods do not provide navigation or suggestions in the manner we present. Other semi-automatic methods require user input prior to the automatic segmentation such as Jeong et al. (2009) and Cardona et al. (2010) and are inherently different than our method. CONCLUSION Using this method on the three datasets, novice users achieved accuracy exceeding state-of-the-art automatic results, and expert users achieved accuracy on par with full manual labeling but with a 70% time improvement when compared with other examples in publication.
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Affiliation(s)
- Cory Jones
- Scientific Computing and Imaging Institute, University of Utah, United States; Department of Electrical and Computer Engineering, University of Utah, United States
| | - Ting Liu
- Scientific Computing and Imaging Institute, University of Utah, United States; School of Computing, University of Utah, United States
| | - Nathaniel Wood Cohan
- National Center for Microscopy and Imaging Research, University of California, San Diego, United States
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, United States
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah, United States; Department of Electrical and Computer Engineering, University of Utah, United States; School of Computing, University of Utah, United States.
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25
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Abstract
Total internal reflection fluorescence microscopy (TIRF), in both commercial and custom-built configurations, is widely used for high signal-noise ratio imaging. The imaging depth of traditional TIRF is sensitive to the incident angle of the laser, and normally limited to around 100 nm. In our paper, using a high refractive index material and the evanescent waves of various waveguide modes, we propose a compact and tunable ultra-short decay length TIRF system, which can reach decay lengths as short as 19 nm, and demonstrate its application for imaging fluorescent dye-labeled F-actin in HeLa cells.
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Perez A, Seyedhosseini M, Tasdizen T, Ellisman M. Automated workflows for the morphological characterization of organelles in electron microscopy image stacks (LB72). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.lb72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alex Perez
- Center for Research IN Biological Systems University of California, San DiegoLA JollaCAUnited States
| | - Mojtaba Seyedhosseini
- Scientific Computing and Imaging Institute University of UtahSalt Lake CityUTUnited States
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute University of UtahSalt Lake CityUTUnited States
| | - Mark Ellisman
- Center for Research IN Biological Systems University of California, San DiegoLA JollaCAUnited States
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27
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Das T, Hakozaki H, Nitu F, Bers D, Ellisman M, Cornea R, Hoshijima M. Correlative super‐resolution light microscopy and electron microscopy determines spatial Ryanodine receptor type 2 distribution in mouse ventricular myocytes (LB707). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.lb707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Donald Bers
- Department of Pharmacology UCDDavisCAUnited States
| | | | - Razvan Cornea
- BMBB University of MinnesotaMinneapolisMNUnited States
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28
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Xue J, Yin S, Perkins G, Ellisman M, Haddad G, Liu S, Zhou D. Mitochondrial proteomes of
Drosophila melanogaster
adapted to chronic hypoxic environment (960.7). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.960.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jin Xue
- Pediatrics University of California San DiegoLA JollaCAUnited States
| | | | - Guy Perkins
- National Center for Microscopy and Imaging Research University of California San DiegoLA JollaCAUnited States
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research University of California San DiegoLA JollaCAUnited States
| | - Gabriel Haddad
- The Rady Children's HospitalSan DiegoCAUnited States
- NeuroSciencesUniversity of California San DiegoLA JollaCAUnited States
- Pediatrics University of California San DiegoLA JollaCAUnited States
| | - Siqi Liu
- Beijing Institute of Genomics BeijingChina
| | - Dan Zhou
- Pediatrics University of California San DiegoLA JollaCAUnited States
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29
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Liu T, Seyedhosseini M, Ellisman M, Tasdizen T. WATERSHED MERGE FOREST CLASSIFICATION FOR ELECTRON MICROSCOPY IMAGE STACK SEGMENTATION. Proc IEEE Int Conf Comput Vis 2013; 2013:4069-4073. [PMID: 25484631 DOI: 10.1109/icip.2013.6738838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Automated electron microscopy (EM) image analysis techniques can be tremendously helpful for connectomics research. In this paper, we extend our previous work [1] and propose a fully automatic method to utilize inter-section information for intra-section neuron segmentation of EM image stacks. A watershed merge forest is built via the watershed transform with each tree representing the region merging hierarchy of one 2D section in the stack. A section classifier is learned to identify the most likely region correspondence between adjacent sections. The inter-section information from such correspondence is incorporated to update the potentials of tree nodes. We resolve the merge forest using these potentials together with consistency constraints to acquire the final segmentation of the whole stack. We demonstrate that our method leads to notable segmentation accuracy improvement by experimenting with two types of EM image data sets.
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Affiliation(s)
- Ting Liu
- Scientific Computing and Imaging Institute, University of Utah
| | | | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah
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30
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Jones C, Sayedhosseini M, Ellisman M, Tasdizen T. Neuron Segmentation in Electron Microscopy Images Using Partial Differential Equations. Proc IEEE Int Symp Biomed Imaging 2013; 2013:1457-1460. [PMID: 25143802 PMCID: PMC4136503 DOI: 10.1109/isbi.2013.6556809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In connectomics, neuroscientists seek to identify the synaptic connections between neurons. Segmentation of cell membranes using supervised learning algorithms on electron microscopy images of brain tissue is often done to assist in this effort. Here we present a partial differential equation with a novel growth term to improve the results of a supervised learning algorithm. We also introduce a new method for representing the resulting image that allows for a more dynamic thresholding to further improve the result. Using these two processes we are able to close small to medium sized gaps in the cell membrane detection and improve the Rand error by as much as 9% over the initial supervised segmentation.
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Affiliation(s)
- Cory Jones
- Scientific Computing and Imaging Institute, University of Utah
| | | | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Univeristy of California, San Diego
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah
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31
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Jones C, Liu T, Ellisman M, Tasdizen T. Semi-Automatic Neuron Segmentation in Electron Microscopy Images Via Sparse Labeling. Proc IEEE Int Symp Biomed Imaging 2013; 2013:1304-1307. [PMID: 25143801 DOI: 10.1109/isbi.2013.6556771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We introduce a novel method for utilizing user input to sparsely label membranes in electron microscopy images. Using gridlines as guides, the user marks where the guides cross the membrane to generate a sparsely labeled image. We use a best path algorithm to connect each of the sparse membrane labels. The resulting segmentation has a significantly better Rand error than automatic methods while requiring as little as 2% of the image to be labeled.
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Affiliation(s)
- Cory Jones
- Scientific Computing and Imaging Institute, University of Utah
| | - Ting Liu
- Scientific Computing and Imaging Institute, University of Utah
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Univeristy of California, San Diego
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah
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32
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Liu T, Jurrus E, Seyedhosseini M, Ellisman M, Tasdizen T. Watershed Merge Tree Classification for Electron Microscopy Image Segmentation. Proc IAPR Int Conf Pattern Recogn 2012; 2012:133-137. [PMID: 25485310 PMCID: PMC4256108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Automated segmentation of electron microscopy (EM) images is a challenging problem. In this paper, we present a novel method that utilizes a hierarchical structure and boundary classification for 2D neuron segmentation. With a membrane detection probability map, a watershed merge tree is built for the representation of hierarchical region merging from the watershed algorithm. A boundary classifier is learned with non-local image features to predict each potential merge in the tree, upon which merge decisions are made with consistency constraints to acquire the final segmentation. Independent of classifiers and decision strategies, our approach proposes a general framework for efficient hierarchical segmentation with statistical learning. We demonstrate that our method leads to a substantial improvement in segmentation accuracy.
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Affiliation(s)
- Ting Liu
- Scientific Computing and Imaging Institute, University of Utah
| | | | | | - Mark Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah
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33
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Burgers PP, Ma Y, Margarucci L, Mackey M, van der Heyden MAG, Ellisman M, Scholten A, Taylor SS, Heck AJR. A small novel A-kinase anchoring protein (AKAP) that localizes specifically protein kinase A-regulatory subunit I (PKA-RI) to the plasma membrane. J Biol Chem 2012; 287:43789-97. [PMID: 23115245 DOI: 10.1074/jbc.m112.395970] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Protein kinase A-anchoring proteins (AKAPs) provide spatio-temporal specificity for the omnipotent cAMP-dependent protein kinase (PKA) via high affinity interactions with PKA regulatory subunits (PKA-RI, RII). Many PKA-RII-AKAP complexes are heavily tethered to cellular substructures, whereas PKA-RI-AKAP complexes have remained largely undiscovered. Here, using a cAMP affinity-based chemical proteomics strategy in human heart and platelets, we uncovered a novel, ubiquitously expressed AKAP, termed small membrane (sm)AKAP due to its specific localization at the plasma membrane via potential myristoylation/palmitoylation anchors. In vitro binding studies revealed specificity of smAKAP for PKA-RI (K(d) = 7 nM) over PKA-RII (K(d) = 53 nM) subunits, co-expression of smAKAP with the four PKA R subunits revealed an even more exclusive specificity of smAKAP for PKA-RIα/β in the cellular context. Applying the singlet oxygen-generating electron microscopy probe miniSOG indicated that smAKAP is tethered to the plasma membrane and is particularly dense at cell-cell junctions and within filopodia. Our preliminary functional characterization of smAKAP provides evidence that, like PKA-RII, PKA-RI can be tightly tethered by a novel repertoire of AKAPs, providing a new perspective on spatio-temporal control of cAMP signaling.
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Affiliation(s)
- Pepijn P Burgers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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34
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Phan S, Lawrence A, Molina T, Lanman J, Berlanga M, Terada M, Kulungowski A, Obayashi J, Ellisman M. TxBR montage reconstruction for large field electron tomography. J Struct Biol 2012; 180:154-64. [PMID: 22749959 DOI: 10.1016/j.jsb.2012.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/05/2012] [Accepted: 06/12/2012] [Indexed: 11/18/2022]
Abstract
Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a consequence, are rather difficult to generate directly. Various techniques have been developed towards generating those views, from increasing the sensor array size to implementing serial sectioning and montaging. Datasets and reconstructions obtained by the latter techniques generate multiple three-dimensional (3D) reconstructions, that need to be combined together to provide all the multiscale information. In this work, we show how to implement montages within TxBR, a tomographic reconstruction software package. This work involves some new application of mathematical concepts related to volume preserving transformations and issues of gauge ambiguity, which are essential problems arising from the nature of the observation in an electron microscope. The purpose of TxBR is to handle those issues as generally as possible in order to correct for most distortions in the 3D reconstructions and allow for a seamless recombination of ET montages.
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Affiliation(s)
- Sébastien Phan
- National Center For Microscopy and Imaging Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA
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35
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Guo J, Yan Q, Sosinsky G, Ellisman M, Suter U, Li J. Virtual Demyelination and Tight Junction Defect in PMP22 Deficiency (S27.004). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.s27.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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36
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Guo J, Yan Q, Sosinsky G, Ellisman M, Suter U, Li J. Virtual Demyelination and Tight Junction Defect in PMP22 Deficiency (IN1-1.003). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.in1-1.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Astakhov V, Bandrowski A, Gupta A, Kulungowski AW, Grethe JS, Bouwer J, Molina T, Rowley V, Penticoff S, Terada M, Wong W, Hakozaki H, Kwon O, Martone ME, Ellisman M. Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics. ACTA ACUST UNITED AC 2012; 9:1595-1603. [PMID: 28479932 PMCID: PMC5415345 DOI: 10.1016/j.procs.2012.04.175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report on progress of employing the Kepler workflow engine to prototype “end-to-end” application integration workflows that concern data coming from microscopes deployed at the National Center for Microscopy Imaging Research (NCMIR). This system is built upon the mature code base of the Cell Centered Database (CCDB) and integrated rule-oriented data system (IRODS) for distributed storage. It provides integration with external projects such as the Whole Brain Catalog (WBC) and Neuroscience Information Framework (NIF), which benefit from NCMIR data. We also report on specific workflows which spawn from main workflows and perform data fusion and orchestration of Web services specific for the NIF project. This “Brain data flow” presents a user with categorized information about sources that have information on various brain regions.
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Affiliation(s)
- V Astakhov
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - A Bandrowski
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - A Gupta
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - A W Kulungowski
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - J S Grethe
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - J Bouwer
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - T Molina
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - V Rowley
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - S Penticoff
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - M Terada
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - W Wong
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - H Hakozaki
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - O Kwon
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
| | - M E Martone
- Neuroscience Information Framework, Calit2 University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093-0436, USA
| | - M Ellisman
- National Center for Microscopy Imaging Research, Basic Science Building 1000 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0608, USA
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Wong JIS, Baddeley D, Bushong EA, Ellisman M, Hoshijima M, Soeller C. 3D Imaging of Nanoscopic Membrane Systems Regulating Cardiac Excitation-Contraction Coupling: Multi-Color Optical Super-Resolution and Serial Block-Face Scanning Electron Microscopy. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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39
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Kett LR, Boassa D, Ho CCY, Rideout HJ, Hu J, Terada M, Ellisman M, Dauer WT. LRRK2 Parkinson disease mutations enhance its microtubule association. Hum Mol Genet 2011; 21:890-9. [PMID: 22080837 DOI: 10.1093/hmg/ddr526] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dominant missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic causes of Parkinson disease (PD) and genome-wide association studies identify LRRK2 sequence variants as risk factors for sporadic PD. Intact kinase function appears critical for the toxicity of LRRK2 PD mutants, yet our understanding of how LRRK2 causes neurodegeneration remains limited. We find that most LRRK2 PD mutants abnormally enhance LRRK2 oligomerization, causing it to form filamentous structures in transfections of cell lines or primary neuronal cultures. Strikingly, ultrastructural analyses, including immuno-electron microscopy and electron microscopic tomography, demonstrate that these filaments consist of LRRK2 recruited onto part of the cellular microtubule network in a well-ordered, periodic fashion. Like LRRK2-related neurodegeneration, microtubule association requires intact kinase function and the WD40 domain, potentially linking microtubule binding and neurodegeneration. Our observations identify a novel effect of LRRK2 PD mutations and highlight a potential role for microtubules in the pathogenesis of LRRK2-related neurodegeneration.
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Affiliation(s)
- Lauren R Kett
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
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40
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Yamaguchi R, Janssen E, Perkins G, Ellisman M, Kitada S, Reed JC. Efficient elimination of cancer cells by deoxyglucose-ABT-263/737 combination therapy. PLoS One 2011; 6:e24102. [PMID: 21949692 PMCID: PMC3176271 DOI: 10.1371/journal.pone.0024102] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 07/31/2011] [Indexed: 01/30/2023] Open
Abstract
As single agents, ABT-263 and ABT-737 (ABT), molecular antagonists of the Bcl-2 family, bind tightly to Bcl-2, Bcl-xL and Bcl-w, but not to Mcl-1, and induce apoptosis only in limited cell types. The compound 2-deoxyglucose (2DG), in contrast, partially blocks glycolysis, slowing cell growth but rarely causing cell death. Injected into an animal, 2DG accumulates predominantly in tumors but does not harm other tissues. However, when cells that were highly resistant to ABT were pre-treated with 2DG for 3 hours, ABT became a potent inducer of apoptosis, rapidly releasing cytochrome c from the mitochondria and activating caspases at submicromolar concentrations in a Bak/Bax-dependent manner. Bak is normally sequestered in complexes with Mcl-1 and Bcl-xL. 2DG primes cells by interfering with Bak-Mcl-1 association, making it easier for ABT to dissociate Bak from Bcl-xL, freeing Bak to induce apoptosis. A highly active glucose transporter and Bid, as an agent of the mitochondrial apoptotic signal amplification loop, are necessary for efficient apoptosis induction in this system. This combination treatment of cancer-bearing mice was very effective against tumor xenograft from hormone-independent highly metastasized chemo-resistant human prostate cancer cells, suggesting that the combination treatment may provide a safe and effective alternative to genotoxin-based cancer therapies.
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Affiliation(s)
- Ryuji Yamaguchi
- Program of Cell Death and Apoptosis, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.
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41
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Petrilli⁎ AM, Song W, Bossy B, Liot G, Lubitz S, de Assis V, Johnson J, Poquiz P, Tjong J, Pouladi M, Hayden MR, Masliah E, Ellisman M, Rouiller I, Perkins G, Bossy-Wetzel E. Mutant Huntington interaction with DRP1 impairs the mitochondrial fission and fusion balance and mediates neuronal injury. Mitochondrion 2011. [DOI: 10.1016/j.mito.2011.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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42
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Song W, Chen J, Petrilli A, Liot G, Klinglmayr E, Zhou Y, Poquiz P, Tjong J, Pouladi MA, Hayden MR, Masliah E, Ellisman M, Rouiller I, Schwarzenbacher R, Bossy B, Perkins G, Bossy-Wetzel E. Mutant huntingtin binds the mitochondrial fission GTPase dynamin-related protein-1 and increases its enzymatic activity. Nat Med 2011; 17:377-82. [PMID: 21336284 PMCID: PMC3051025 DOI: 10.1038/nm.2313] [Citation(s) in RCA: 406] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/18/2011] [Indexed: 02/07/2023]
Abstract
Huntington disease (HD) is an inherited and incurable neurodegenerative disorder caused by an abnormal polyglutamine (polyQ) expansion in huntingtin (HTT). PolyQ length determines disease onset and severity with a longer expansion causing earlier onset. The mechanisms of mutant HTT-mediated neurotoxicity remain unclear; however, mitochondrial dysfunction is a key event in HD pathogenesis1,2. Here we tested whether mutant HTT impairs the mitochondrial fission/fusion balance and thereby causes neuronal injury. We show that mutant HTT triggers mitochondrial fragmentation in neurons and fibroblasts of HD individuals in vitro and HD mice in vivo before the presence of neurological deficits and HTT aggregates. Interestingly, mutant HTT abnormally interacts with the mitochondrial fission GTPase dynamin-related protein 1 (DRP1) in HD mice and individuals which in turn stimulates its enzymatic activity. Importantly, mutant HTT-mediated mitochondrial fragmentation, defects in anterograde and retrograde mitochondrial transport, and neuronal cell death are all rescued by reducing DRP1 GTPase activity with the dominant-negative DRP1K38A mutant. Thus, DRP1 might represent a new therapeutic target to combat neurodegeneration in HD.
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Affiliation(s)
- Wenjun Song
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res 2010; 39:D546-51. [PMID: 21045053 PMCID: PMC3013694 DOI: 10.1093/nar/gkq1102] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.
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Affiliation(s)
- Shulei Sun
- The CAMERA Project, Center for Research on Biological Systems and California Institute of Telecommunication and Information Technology, University of California San Diego, 9500 Gilman Drive, Mail Code 0446, California 92093-5004, USA.
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De Jaco A, Lin MZ, Dubi N, Comoletti D, Miller MT, Camp S, Ellisman M, Butko MT, Tsien RY, Taylor P. Neuroligin trafficking deficiencies arising from mutations in the alpha/beta-hydrolase fold protein family. J Biol Chem 2010; 285:28674-82. [PMID: 20615874 DOI: 10.1074/jbc.m110.139519] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Despite great functional diversity, characterization of the alpha/beta-hydrolase fold proteins that encompass a superfamily of hydrolases, heterophilic adhesion proteins, and chaperone domains reveals a common structural motif. By incorporating the R451C mutation found in neuroligin (NLGN) and associated with autism and the thyroglobulin G2320R (G221R in NLGN) mutation responsible for congenital hypothyroidism into NLGN3, we show that mutations in the alpha/beta-hydrolase fold domain influence folding and biosynthetic processing of neuroligin3 as determined by in vitro susceptibility to proteases, glycosylation processing, turnover, and processing rates. We also show altered interactions of the mutant proteins with chaperones in the endoplasmic reticulum and arrest of transport along the secretory pathway with diversion to the proteasome. Time-controlled expression of a fluorescently tagged neuroligin in hippocampal neurons shows that these mutations compromise neuronal trafficking of the protein, with the R451C mutation reducing and the G221R mutation virtually abolishing the export of NLGN3 from the soma to the dendritic spines. Although the R451C mutation causes a local folding defect, the G221R mutation appears responsible for more global misfolding of the protein, reflecting their sequence positions in the structure of the protein. Our results suggest that disease-related mutations in the alpha/beta-hydrolase fold domain share common trafficking deficiencies yet lead to discrete congenital disorders of differing severity in the endocrine and nervous systems.
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Affiliation(s)
- Antonella De Jaco
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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Anderson D, Buccigrossi R, Ellisman M, Eppig J, Evans-Kavaldjian H, Grethe J, Hamel R, Kemnitz J, Martone M, Pohland K, Preuss N, Sullivan M, Turner J, Wagner K, Westerfield M, Yurt H. The initiative to Link Animal Models to Human DIsease (LAMHDI) (144.12). The Journal of Immunology 2010. [DOI: 10.4049/jimmunol.184.supp.144.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
We report a new Web-based resource (LAMHDI) integrating information about animal models for human disease research. This NCRR supported resource provides a simple interface to existing animal model information for the biomedical research community. It provides more efficient access to animal model information, better categorizes and organizes existing data, facilitates interactions between researchers and resource providers, and promotes broader and more applicable use of animal models for human disease research. Approach Phase 1: A first-generation prototype is available at www.LAMHDI.org. This portal provides searchable access to existing mouse and zebrafish databases through an integrated search engine, as well as linked access to information about a variety of other species including nonhuman primates and rats. The portal also allows researchers to contribute data on animal models, thereby extending the impact of existing information through direct posting by the research community. Phase 2: The second generation will add extensive new information for additional animal model species and will increase the depth and connectivity of the data through development of semantic datastores. A sophisticated software architecture will support intelligent relational searches across diverse datasets to highlight associations between diseases, animal models, and biologic pathways.
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Affiliation(s)
- David Anderson
- 1University of Washington, Washington National Primate Research Center, Seattle, WA
| | | | | | | | | | | | | | | | | | | | - Nina Preuss
- 2Turner Consulting Group, Washington D.C., DC
| | | | | | | | | | - Hakan Yurt
- 2Turner Consulting Group, Washington D.C., DC
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Pamenter M, Gu X, Yoon M, Perkins G, Ellisman M, Haddad G. 4,4‐diisothiocyanatostilbenedisulphonic acid (DIDS) is cytotoxic and does not provide protection against ischemic insults in cultured neurons or astrocytes. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.604.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Guy Perkins
- National Center for Microscopy and Imaging Research
| | | | - Gabriel Haddad
- Pediatrics
- NeuroscienceUniversity of California San DiegoLa JollaCA
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Hauser J, Ellisman M, Steinau HU, Stefan E, Dudda M, Hauser M. Ultrasound enhanced endocytotic activity of human fibroblasts. Ultrasound Med Biol 2009; 35:2084-92. [PMID: 19828232 DOI: 10.1016/j.ultrasmedbio.2009.06.1090] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 05/29/2009] [Accepted: 06/08/2009] [Indexed: 05/19/2023]
Abstract
Although various in vitro studies have shown that low-intensity pulsed ultrasound influences cytoskeletal components and biochemical pathways, the exact biologic mechanisms are still not fully understood. In this study, we analysed the effect of therapeutic ultrasound on the endocytotic activity of human foreskin fibroblasts. Fibroblasts were incubated with two different endocytotic markers (transferrin Alexa 488 and Lucifer yellow; Sigma Bioprobes, Eugene, OR, USA). To evaluate the amount of internalized markers in sonicated and nonsonicated control cells, confocal microscopy and plate reader experiments were performed. Additionally, the structural integrity of the cell membrane was monitored by electron-microscopy. After ultrasound treatment a clear increase (1.6-fold/Lucifer yellow and 1.4-fold/transferrin Alexa 488) of fluorescent marker uptake was detected. Confocal microscopy and plate reader experiments revealed that whole populations of sonicated fibroblasts showed a significant higher fluorescence compared with cells not sonicated (p<0.05; t-test for unpaired samples). The electron microscopic analysis of the cells showed no signs of structural membrane damage or a loosening of the membrane integrity. However, an exceedingly high amount of endocytotic vesicles and clathrin coated pits were observed in the sonicated group.
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Affiliation(s)
- Joerg Hauser
- Department of Plastic Surgery, BG-Kliniken Bergmannsheil, Ruhr-University-Bochum, Bochum, Germany.
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Ellisman M, Hutton T, Kirkland A, Lin A, Lin C, Molina T, Peltier S, Singh R, Tang K, Trefethen A, Wallom D, Xiong X. The OptIPuter microscopy demonstrator: enabling science through a transatlantic lightpath. Philos Trans A Math Phys Eng Sci 2009; 367:2645-2653. [PMID: 19487201 PMCID: PMC3268213 DOI: 10.1098/rsta.2009.0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The OptIPuter microscopy demonstrator project has been designed to enable concurrent and remote usage of world-class electron microscopes located in Oxford and San Diego. The project has constructed a network consisting of microscopes and computational and data resources that are all connected by a dedicated network infrastructure using the UK Lightpath and US Starlight systems. Key science drivers include examples from both materials and biological science. The resulting system is now a permanent link between the Oxford and San Diego microscopy centres. This will form the basis of further projects between the sites and expansion of the types of systems that can be remotely controlled, including optical, as well as electron, microscopy. Other improvements will include the updating of the Microsoft cluster software to the high performance computing (HPC) server 2008, which includes the HPC basic profile implementation that will enable the development of interoperable clients.
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Affiliation(s)
- M. Ellisman
- National Centre for Microscopy and Imaging Research, University of CaliforniaSan Diego, CA 92093, USA
| | - T. Hutton
- National Centre for Microscopy and Imaging Research, University of CaliforniaSan Diego, CA 92093, USA
| | - A. Kirkland
- Materials Science, University of OxfordOxford 0X1 3PH, UK
| | - A. Lin
- National Centre for Microscopy and Imaging Research, University of CaliforniaSan Diego, CA 92093, USA
| | - C. Lin
- Materials Science, University of OxfordOxford 0X1 3PH, UK
| | - T. Molina
- National Centre for Microscopy and Imaging Research, University of CaliforniaSan Diego, CA 92093, USA
| | - S. Peltier
- National Centre for Microscopy and Imaging Research, University of CaliforniaSan Diego, CA 92093, USA
| | - R. Singh
- National Centre for Microscopy and Imaging Research, University of CaliforniaSan Diego, CA 92093, USA
| | - K. Tang
- Oxford e-Research Centre, University of OxfordOxford OX1 3QG, UK
| | - A.E. Trefethen
- Oxford e-Research Centre, University of OxfordOxford OX1 3QG, UK
| | - D.C.H. Wallom
- Oxford e-Research Centre, University of OxfordOxford OX1 3QG, UK
| | - X. Xiong
- Oxford e-Research Centre, University of OxfordOxford OX1 3QG, UK
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Larson S, Aprea C, Maynard S, Imam F, Ellisman M, Martone M. A multi-scale spatial and semantic knowledge framework for neuroanatomy. Front Neuroinform 2009. [DOI: 10.3389/conf.neuro.11.2009.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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50
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Buccigrossi R, Ellisman M, Grethe J, Haselgrove C, Kennedy DN, Martone M, Preuss N, Reynolds K, Sullivan M, Turner J, Wagner K. The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). AMIA Annu Symp Proc 2008:1000. [PMID: 18999128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 06/17/2008] [Indexed: 05/27/2023]
Abstract
The Neuroimaging Informatics Tools and Resources Clearinghouse, NITRC is a newly established Web site for organizing knowledge about the resources publicly available functional MRI and related structural imaging analysis. Based on GForge, it provides a common environment for downloading, discussion, education, rating, and documentation for a growing number of resources. Its design and current status is presented.
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