Activity-Regulated Cytoskeleton-Associated Protein Controls AMPAR Endocytosis Through a Direct Interaction with Clathrin-Adaptor Protein 21,2,3
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
Exogenous Antigens Gain Access to the Major Histocompatibility Complex Class I Processing Pathway in B Cells by Receptor-Mediated Uptake Byyong Ke and Judith A
Brief Definitive Report Exogenous Antigens Gain Access to the Major Histocompatibility Complex Class I Processing Pathway in B Cells by Receptor-mediated Uptake ByYong Ke and Judith A. Kapp From the Department of Pathology and Winship Cancer Center, Emory University School of Medicine, Atlanta, Georgia 30322 Summary Professional antigen-presenting cells, such as macrophages, dendritic cells, or B cells, take up soluble, exogenous antigens (Ags) and process them through the class II pathway, Several re- ports have shown that phagocytic macrophages also process particulate or soluble forms of ex- ogenous Ag via the class I pathway. By contrast, B cells normally do not process soluble, exog- enous Ag by way of the class I pathway unless Ags are directly introduced into the cytoplasm. Here we report that B cells present exogenous Ag via the class I pathway when Ags are taken up by receptor-mediated endocytosis. Thus, specialized methods of Ag uptake such as phago- cytosis or receptor-mediated endocytosis deliver exogenous Ag into the class I pathway of Ag processing and presentation. xogenous Ags are taken up nonspecifically by fluid- Materials and Methods phase pinocytosis or endocytosis, processed, and pre- E Antigens and Reagents. Chicken egg OVA, TNP, chloroquine, sented via class II pathway by professional APCs, such as brefeldin A, and phenazine methosulfate (PMS) were purchased macrophages, dendritic cells, or B cells. Exogenous Ags do from Sigma Chemical Co. (St. Louis, MO). Crystallized beef in- not enter the class I pathway of most cells (1-3). However, sulin was purchased from Lilly Research Labs (Indianapolis, IN). a small population of phagocytic macrophages can process TNP was conjugated to OVA or insulin as described (13). -
Elucidating the Signalling Pathway of Mer Tyrosine Kinase Receptor in Efferocytosis
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 8-19-2014 12:00 AM Elucidating the Signalling Pathway of Mer Tyrosine Kinase Receptor in Efferocytosis Ekenedelichukwu Azu The University of Western Ontario Supervisor Dr. Bryan Heit The University of Western Ontario Graduate Program in Microbiology and Immunology A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Ekenedelichukwu Azu 2014 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Cell Biology Commons, Immunity Commons, Molecular Biology Commons, and the Other Immunology and Infectious Disease Commons Recommended Citation Azu, Ekenedelichukwu, "Elucidating the Signalling Pathway of Mer Tyrosine Kinase Receptor in Efferocytosis" (2014). Electronic Thesis and Dissertation Repository. 2260. https://ir.lib.uwo.ca/etd/2260 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. ELUCIDATING THE SIGNALLING PATHWAY OF MER TYROSINE KINASE RECEPTOR IN EFFEROCYTOSIS Thesis format: Monograph by Ekenedelichukwu Azu Graduate Program in Microbiology and Immunology A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science The School of Graduate and Postdoctoral Studies The University of Western Ontario London, Ontario, Canada © Ekenedelichukwu Azu 2014 Abstract Efferocytosis is the clearance of apoptotic cells and is necessary for homeostasis. Mer Tyrosine Kinase (MerTK) is a crucial efferocytic receptor whose loss is associated with chronic inflammatory diseases and autoimmunity. While previous studies have shown that MerTK mediates efferocytosis through a unique mechanism that requires integrins, MerTK signalling pathway remains unknown. -
Mechanisms of Synaptic Plasticity Mediated by Clathrin Adaptor-Protein Complexes 1 and 2 in Mice
Mechanisms of synaptic plasticity mediated by Clathrin Adaptor-protein complexes 1 and 2 in mice Dissertation for the award of the degree “Doctor rerum naturalium” at the Georg-August-University Göttingen within the doctoral program “Molecular Biology of Cells” of the Georg-August University School of Science (GAUSS) Submitted by Ratnakar Mishra Born in Birpur, Bihar, India Göttingen, Germany 2019 1 Members of the Thesis Committee Prof. Dr. Peter Schu Institute for Cellular Biochemistry, (Supervisor and first referee) University Medical Center Göttingen, Germany Dr. Hans Dieter Schmitt Neurobiology, Max Planck Institute (Second referee) for Biophysical Chemistry, Göttingen, Germany Prof. Dr. med. Thomas A. Bayer Division of Molecular Psychiatry, University Medical Center, Göttingen, Germany Additional Members of the Examination Board Prof. Dr. Silvio O. Rizzoli Department of Neuro-and Sensory Physiology, University Medical Center Göttingen, Germany Dr. Roland Dosch Institute of Developmental Biochemistry, University Medical Center Göttingen, Germany Prof. Dr. med. Martin Oppermann Institute of Cellular and Molecular Immunology, University Medical Center, Göttingen, Germany Date of oral examination: 14th may 2019 2 Table of Contents List of abbreviations ................................................................................. 5 Abstract ................................................................................................... 7 Chapter 1: Introduction ............................................................................ -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Clathrin-Mediated Endocytosis As a Marker of Cell Membrane Tension in Cultured Cells and Developing Organisms
Clathrin-Mediated Endocytosis as a Marker of Cell Membrane Tension in Cultured Cells and Developing Organisms Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Joshua Paul Ferguson, M.S., B.S. Graduate Program in Physics The Ohio State University 2018 Dissertation Committee: Dr. Comert Kural, Advisor Dr. Michael Poirier Dr. Sooryakumar Ratnasingham Dr. Ralf Bundschuh Copyrighted by Joshua Paul Ferguson 2018 Abstract Individual cells decipher and react to both their chemical and mechanical environment. Clathrin-mediated endocytosis (CME) is a major process by which cells internalize macromolecules. The triskelion-shaped clathrin protein assembles on the membrane as a spherical lattice enveloping the membrane until scission begets internalization. The membrane curvature generated by the invaginations during endocytosis associate CME with the mechanical environment of the cell. Fluorescence microscopy is used to study the dynamics of CME, and in particular to discern the time it takes for CME events to complete (i.e. their lifetime). It is our hypothesis that the lifetime of CME events relates inversely to the cell membrane tension. We will support this hypothesis with live-cell imaging on glass substrates and in living organisms. We suggest a new methodology for studying CME dynamics that enables higher spatial and temporal resolution than lifetime analysis. We will also characterize the tension response of CME by using various cell manipulation techniques. In addition, we will demonstrate the ability of CME dynamics to predict cell movement and relate gradients in clathrin coat growth rates to previously established tension gradients in cultured cells and living organisms. -
Electron Microscopy and Tomography on Endocytosis of Macrophages
1268 Microsc. Microanal. 23 (Suppl 1), 2017 doi:10.1017/S1431927617007000 © Microscopy Society of America 2017 Electron Microscopy and Tomography on Endocytosis of Macrophages I. Ratnayake1, S. P. Ahrenkiel1, A. Hoppe2 and N. Thiex 3 1. Nanoscience and Nanoengineering Ph.D. Program, South Dakota School of Mines and Technology, Rapid City, SD, USA 2. Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, USA 3. Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA Macrophages are a type of white blood cell that engulf and digest foreign substances, microbes, and cancer cells in a process called endocytosis, so macrophages act like scavengers. They are constantly roaming around, searching for and destroying dead cells and foreign particles that do not belong in the body. There are three types of endocytosis: phagocytosis, pinocytosis, and receptor-mediated endocytosis. Transmission electron microscopy (TEM) is capable of much higher magnification and greater resolving power than optical microscopy, allowing visualization of much smaller objects with finer detail. Traditional TEM techniques provide only 2D projection views of thin cellular slices. However, electron tomography (ET) technique provides a way for obtaining detailed 3D structures of sub-cellular macro- molecular objects [1]. TEM tomography of macrophages is being developed for visualization of the endocytosis process in relation to cell structure. Differences in the structural characteristics of cells undergoing phagocytosis and pinocytosis were observed by TEM. Figure 1 shows a few important components of a phagocytic macrophage cell. Figure 2 shows a comparison between the structural characteristics of phagocytosis and pinocytosis processes. The phagocytic vesicles are called “phagosomes” and are filled with engulfed solid materials where as the pinocytotic vesicles are called “macropinosomes” and are filled with fluid materials, which have been taken into the cell. -
A Role for Amphiphysin in AP-1/Clathrin Coat Formation
A Role for Amphiphysin in AP-1/Clathrin Coat Formation Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Sonja Huser Studer aus Knonau (ZH) Basel, 2012 Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Martin Spiess Prof. Anne Spang Basel, den 11. Dezember 2012 Prof. Dr. Jörg Schibler Acknowledgements I would like to thank Prof. Martin Spiess for giving me the opportunity to work on this project, for continuous support, and for many fruitful discussions. Special thanks go to Dr. Gregor Suri, who initially started this project, and to Dr. Pascal Crottet for his help and expertise during experiments and for being a walking encyclopedia. Many thanks go to Nicole Beuret for her professional technical advice and assistance and for her patience to answer the countless questions. I would also like to thank the past and present lab members for creating a great working atmosphere, for scientific and other discussions, and for their support at all times: Cristina Baschong, Dr. Julia Birk, Dominik Buser, Erhan Demirci, Dr. Michael Friberg, Franziska Hasler, Dr. David Hirschmann, Tina Junne, Simone Kälin, Dr. Lucyna Kocik, Dr. Deyan Mihov, and Dr. Barry Shortt. Summary Transport of cargo within the endocytic and secretory pathway is generally mediated by coated vesicles. Clathrin, in combination with different adaptor proteins, is the major coat protein for vesicle formation at the plasma membrane, endosomes, and the trans-Golgi network (TGN). Best characterized is the formation of clathrin coats for endocytosis at the plasma membrane involving the adaptor protein complex AP-2. -
Sorting Nexin 9 in Clathrin-Mediated Endocytosis
UMEÅ UNIVERSITY MEDICAL DISSERTATIONS New Series No. 875; ISSN 0346-6612; ISBN 91-7305-599-9 Department of Medical Biochemistry and Biophysics Umeå University, Sweden Editor: The Dean of the Faculty of Medicine Sorting Nexin 9 in Clathrin-mediated Endocytosis Richard Lundmark Department of Medical Biochemistry and Biophysics Umeå University, Sweden Umeå 2004 © Richard Lundmark ISBN 91-7305-599-9 Printed in Sweden at Solfjädern Offset AB Umeå 2004 Tillägnad min älskade familj Samuel, Elias och Ida TABLE OF CONTENTS ABBREVIATIONS ...................................................................................................................2 ABSTRACT...............................................................................................................................3 PUBLICATION LIST ...............................................................................................................4 OVERVIEW ..............................................................................................................................5 1. INTRODUCTION .................................................................................................................5 2. ADAPTOR PROTEIN COMPLEXES..................................................................................6 3. CLATHRIN ...........................................................................................................................6 4. ENDOCYTOSIS....................................................................................................................7 -
Studies on the Inhibition of Endosome Fusion by Gtpγs-Bound ARF
Journal of Cell Science 112, 3477-3485 (1999) 3477 Printed in Great Britain © The Company of Biologists Limited 1999 JCS0438 Studies on the inhibition of endosome fusion by GTPγS-bound ARF Arwyn T. Jones1, David J. Spiro1, Tomas Kirchhausen2, Paul Melançon3 and Marianne Wessling-Resnick1,* 1Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA 2Department of Cell Biology, Harvard Medical School, Center for Blood Research, Boston, MA 02115, USA 3Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada *Author for correspondence (e-mail: [email protected]) Accepted 28 July; published on WWW 30 September 1999 SUMMARY Using a cell free assay, we have previously shown that ARF independent of endosomal acidification since assays is not required for endosome fusion but that inhibition of performed in the presence of the vacuolar ATPase inhibitor fusion by GTPγS is dependent on a cytosolic pool of ARFs. bafilomycin A1 are equally sensitive to GTPγS-bound ARF. Since ARF is proposed to function in intracellular Finally, in contrast to reported effects on lysosomes, we membrane traffic by promoting vesicle biogenesis, and demonstrate that ARF-GTPγS does not induce endosomal components of clathrin- and COP-coated vesicles have been lysis. These combined data argue that sequestration of localized on endosomal structures, we investigated whether known coat proteins to membranes by activated ARF is not ARF-mediated inhibition of early endosome fusion involves involved in the inhibition of early endosome fusion and that the recruitment or irreversible association of these proteins its capacity to inhibit fusion involves other specific onto endosomal membranes. -
Dynamics of Clathrin-Mediated Endocytosis and Its Requirement for Organelle Biogenesis in Dictyostelium
Research Article 5721 Dynamics of clathrin-mediated endocytosis and its requirement for organelle biogenesis in Dictyostelium Laura Macro, Jyoti K. Jaiswal* and Sanford M. Simon` Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA *Present address: Center for Genetic Medicine Research, Children’s National Medical Center, Washington DC, DC 20010, USA `Author for correspondence ([email protected]) Accepted 21 August 2012 Journal of Cell Science 125, 5721–5732 ß 2012. Published by The Company of Biologists Ltd doi: 10.1242/jcs.108837 Summary The protein clathrin mediates one of the major pathways of endocytosis from the extracellular milieu and plasma membrane. In single-cell eukaryotes, such as Saccharomyces cerevisiae, the gene encoding clathrin is not an essential gene, raising the question of whether clathrin conveys specific advantages for multicellularity. Furthermore, in contrast to mammalian cells, endocytosis in S. cerevisiae is not dependent on either clathrin or adaptor protein 2 (AP2), an endocytic adaptor molecule. In this study, we investigated the requirement for components of clathrin-mediated endocytosis (CME) in another unicellular organism, the amoeba Dictyostelium. We identified a heterotetrameric AP2 complex in Dictyostelium that is similar to that which is found in higher eukaryotes. By simultaneously imaging fluorescently tagged clathrin and AP2, we found that, similar to higher eukaryotes, these proteins colocalized to membrane puncta that move into the cell together. In addition, the contractile vacuole marker protein, dajumin-green fluorescent protein (GFP), is trafficked via the cell membrane and internalized by CME in a clathrin-dependent, AP2-independent mechanism. This pathway is distinct from other endocytic mechanisms in Dictyostelium. -
Mediate Endocytosis and Phagocytosis
Proc. Nati. Acad. Sci. USA Vol. 89, pp. 5030-5034, June 1992 Immunology Two forms of the low-affinity Fc receptor for IgE differentially mediate endocytosis and phagocytosis: Identification of the critical cytoplasmic domains (CD23/endocytosis/phagocytosis) AKIRA YOKOTA*, KAzUNORI YUKAWA*, AKITSUGU YAMAMOTOt, KENJI SUGIYAMA*, MASAKI SUEMURAt, YUTAKA TASHIROt, TADAMITSU KISHIMOTO*t, AND HITOSHI KIKUTANI* *Institute for Molecular and Cellular Biology, Osaka University, 1-3, Yamada-oka, Suita, Osaka 565, Japan; *Department of Medicine III, Osaka University Medical School, 1-1-50, Fukushima, Fukushima-ku, Osaka 553, Japan; and tDepartment of Physiology, Kansai Medical University, Moriguchi-shi, Osaka 570, Japan Contributed by Tadamitsu Kishimoto, February 21, 1992 ABSTRACT We have previously identified two species of FceRIIb may be involved in B-cell function and IgE-mediated the low-affinity human Fc receptor for IgE, FceRIIa and immunity, respectively. FceRIIb, which differ only in a short stretch of amino acids at In this paper, we have attempted to elucidate the molecular the N-terminal cytoplasmic end. Their differential expressions basis ofthe functional difference between these two forms of on B cells and monocytes suggest that FceRlla and FceRIIb are receptor molecules by using stable transfectants expressing involved in B-cell function and IgE-mediated immunity, re- either human wild-type or mutated FceRII and have demon- spectively. Here we show that FceRII-mediated endocytosis is strated that endocytosis is mediated only through FceRIIa observed only in FceRlia-expressing cells, whereas IgE- and that phagocytosis is mediated only through FceRIIb. dependent phagocytosis isobserved only in FceRIEb-expressing Furthermore, the minimum amino acid residues necessary cells, demonstrating the functional difference between FceRIIa for endocytosis and phagocytosis have been determined.