Neurofilaments at a Glance
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ENSG Gene Encodes Effector TCR Pathway Costimulation Inhibitory/Exhaustion Synapse/Adhesion Chemokines/Receptors
ENSG Gene Encodes Effector TCR pathway Costimulation Inhibitory/exhaustion Synapse/adhesion Chemokines/receptors ENSG00000111537 IFNG IFNg x ENSG00000109471 IL2 IL-2 x ENSG00000232810 TNF TNFa x ENSG00000271503 CCL5 CCL5 x x ENSG00000139187 KLRG1 Klrg1 x ENSG00000117560 FASLG Fas ligand x ENSG00000121858 TNFSF10 TRAIL x ENSG00000134545 KLRC1 Klrc1 / NKG2A x ENSG00000213809 KLRK1 Klrk1 / NKG2D x ENSG00000188389 PDCD1 PD-1 x x ENSG00000117281 CD160 CD160 x x ENSG00000134460 IL2RA IL-2 receptor x subunit alpha ENSG00000110324 IL10RA IL-10 receptor x subunit alpha ENSG00000115604 IL18R1 IL-18 receptor 1 x ENSG00000115607 IL18RAP IL-18 receptor x accessory protein ENSG00000081985 IL12RB2 IL-12 receptor x beta 2 ENSG00000186810 CXCR3 CXCR3 x x ENSG00000005844 ITGAL CD11a x ENSG00000160255 ITGB2 CD18; Integrin x x beta-2 ENSG00000156886 ITGAD CD11d x ENSG00000140678 ITGAX; CD11c x x Integrin alpha-X ENSG00000115232 ITGA4 CD49d; Integrin x x alpha-4 ENSG00000169896 ITGAM CD11b; Integrin x x alpha-M ENSG00000138378 STAT4 Stat4 x ENSG00000115415 STAT1 Stat1 x ENSG00000170581 STAT2 Stat2 x ENSG00000126561 STAT5a Stat5a x ENSG00000162434 JAK1 Jak1 x ENSG00000100453 GZMB Granzyme B x ENSG00000145649 GZMA Granzyme A x ENSG00000180644 PRF1 Perforin 1 x ENSG00000115523 GNLY Granulysin x ENSG00000100450 GZMH Granzyme H x ENSG00000113088 GZMK Granzyme K x ENSG00000057657 PRDM1 Blimp-1 x ENSG00000073861 TBX21 T-bet x ENSG00000115738 ID2 ID2 x ENSG00000176083 ZNF683 Hobit x ENSG00000137265 IRF4 Interferon x regulatory factor 4 ENSG00000140968 IRF8 Interferon -
Supplemental Material Table of Contents
Supplemental material Table of Contents Detailed Materials and Methods ......................................................................................................... 2 Perioperative period ........................................................................................................................... 2 Ethical aspects ................................................................................................................................... 4 Evaluation of heart failure ................................................................................................................. 4 Sample preparation for ANP mRNA expression .................................................................................. 5 Sample preparation for validative qRT-PCR (Postn, Myh7, Gpx3, Tgm2) ............................................ 6 Tissue fibrosis .................................................................................................................................... 7 Ventricular remodeling and histological tissue preservation ................................................................ 8 Evaluation of the histological preservation of cardiac tissue ................................................................ 9 Sample preparation and quantitative label-free proteomics analyses .................................................. 10 Statistical methods ........................................................................................................................... 12 References ........................................................................................................................................ -
The CAP-Gly and Basic Microtubule Binding Domains of Dynactin Are
Knockdown of dynactin’s p150Glued subunit abrogates microtubule organization by Jared Todd Roeckner A Thesis Submitted to the Faculty of The Wilkes Honors College In Partial Fulfillment of the Requirements for the Degree of Bachelor of Arts in Liberal Arts and Sciences with a Concentration in Biology Wilkes Honors College of Florida Atlantic University Jupiter, Florida May 2009 Knockdown of dynactin’s p150Glued subunit abrogates microtubule organization by Jared T. Roeckner This thesis was prepared under the direction of the candidate’s thesis advisor, Dr. Nicholas Quintyne, and has been approved by the members of the supervisory committee. It was submitted to the faculty of The Honors College and was accepted in partial fulfillment of the Requirements for the Degree of Bachelor of Arts in Liberal Arts and Sciences. SUPERVISORY COMMITTEE: ________________________ Dr. Nicholas Quintyne ________________________ Dr. Paul Kirchman ________________________ Dean, Wilkes Honors College _________ Date ii ACKNOWLEDGEMENTS First, I would like to thank Dr. Nicholas Quintyne for allowing me to work in his lab for the last three years and overseeing and guiding my thesis research and writing. I would like to acknowledge Dr. Stephen King and Dr. Margret Kincaid at UMKC for providing us with the p150Glued knockdown plasmids. Dr. Paul Kirchman, April Mistrik, and everyone in the Quintyne lab helped me out greatly. Ed Fulton and I worked on many steps of this project together and I thank him for his help. Finally, I would like to thank my family and friends for supporting of my thesis research and my undergraduate studies as a whole. iii ABSTRACT Author: Jared Todd Roeckner Title: Knockdown of dynactin’s p150Glued subunit abrogates microtubule organization Institutions: Harriet L. -
Overview of the Cytoskeleton from an Evolutionary Perspective
Downloaded from http://cshperspectives.cshlp.org/ on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Overview of the Cytoskeleton from an Evolutionary Perspective Thomas D. Pollard1 and Robert D. Goldman2 1Departments of Molecular Cellular and Developmental Biology, Molecular Biophysics and Biochemistry, and Cell Biology ,Yale University, New Haven, Connecticut 06520-8103 2Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 Correspondence: [email protected] SUMMARY Organisms in the three domains of life depend on protein polymers to form a cytoskeleton that helps to establish their shapes, maintain their mechanical integrity, divide, and, in many cases, move. Eukaryotes have the most complex cytoskeletons, comprising three cytoskeletal poly- mers—actin filaments, intermediate filaments, and microtubules—acted on by three families of motor proteins (myosin, kinesin, and dynein). Prokaryotes have polymers of proteins ho- mologous to actin and tubulin but no motors, and a few bacteria have a protein related to intermediate filament proteins. Outline 1 Introduction—Overview of cellular 4 Overview of the evolution of the cytoskeleton functions 5 Conclusion 2 Structures of the cytoskeletal polymers References 3 Assembly of cytoskeletal polymers Editors: Thomas D. Pollard and Robert D. Goldman Additional Perspectives on The Cytoskeleton available at www.cshperspectives.org Copyright # 2018 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a030288 Cite this article as Cold Spring Harb Perspect Biol 2018;10:a030288 1 Downloaded from http://cshperspectives.cshlp.org/ on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press T.D. Pollard and R.D. Goldman 1 INTRODUCTION—OVERVIEW OF CELLULAR contrast, intermediate filaments do not serve as tracks for FUNCTIONS molecular motors (reviewed by Herrmann and Aebi 2016) but, rather, are transported by these motors. -
Genome-Wide Analyses Identify KIF5A As a Novel ALS Gene
This is a repository copy of Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/129590/ Version: Accepted Version Article: Nicolas, A, Kenna, KP, Renton, AE et al. (210 more authors) (2018) Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. Neuron, 97 (6). 1268-1283.e6. https://doi.org/10.1016/j.neuron.2018.02.027 Reuse This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) licence. This licence only allows you to download this work and share it with others as long as you credit the authors, but you can’t change the article in any way or use it commercially. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Genome-wide Analyses Identify KIF5A as a Novel ALS Gene Aude Nicolas1,2, Kevin P. Kenna2,3, Alan E. Renton2,4,5, Nicola Ticozzi2,6,7, Faraz Faghri2,8,9, Ruth Chia1,2, Janice A. Dominov10, Brendan J. Kenna3, Mike A. Nalls8,11, Pamela Keagle3, Alberto M. Rivera1, Wouter van Rheenen12, Natalie A. Murphy1, Joke J.F.A. van Vugt13, Joshua T. Geiger14, Rick A. Van der Spek13, Hannah A. Pliner1, Shankaracharya3, Bradley N. -
EB1 Proteins Regulate Microtubule Dynamics, Cell Polarity, and Chromosome Stability Jennifer S
Mini-Review EB1 Proteins Regulate Microtubule Dynamics, Cell Polarity, and Chromosome Stability Jennifer S. Tirnauer* and Barbara E. Bierer‡ *Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115; and ‡Laboratory of Lymphocyte Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 The EB1 family represents a highly conserved group of screen for mutations that caused chromosome loss (Bein- proteins, present in yeast through humans, that localize to hauer et al., 1997). Caenorhabditis elegans has two EB1 re- spindle and cytoplasmic microtubules, especially at their lated genes (GenBank accession numbers VW02B12L.3 distal tips. The budding yeast homologue of EB1, Bim1p, and Y59A8B.P; these data were produced by the C. ele- regulates microtubule stability and is important for posi- gans Sequencing Group at the Sanger Centre and can be tioning the mitotic spindle, anchoring it to the bud through obtained from http://www.sanger.ac.uk/Projects/C_elegans/), astral microtubule attachment to the cortical protein and Drosophila melanogaster has at least three EB1 family Kar9p. Bim1p interacts functionally with dynactin in a late members (GenBank accession numbers [Benson et al., mitotic cell cycle checkpoint. EB1 proteins in human cells 2000] AAD27859, AAF46575, and AAF57623). The num- interact physically with the adenomatous polyposis coli ber of EB1 proteins in humans is unknown, but to date (APC) tumor suppressor protein, targeting APC to micro- EB1, EB2, EB3, and EBF3 have been reported, along with tubule plus ends, and with members of the dynactin com- the highly related RP1, RP2, and RP3 proteins (Su et al., plex. -
Rapid Transport of Neural Intermediate Filament Protein
Research Article 2345 Rapid transport of neural intermediate filament protein Brian T. Helfand*, Patty Loomis*, Miri Yoon and Robert D. Goldman‡ Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Ward 11-145, Chicago, IL 60611, USA *These authors contributed equally to this work ‡Author for correspondence (e-mail: [email protected]) Accepted 1 April 2003 Journal of Cell Science 116, 2345-2359 © 2003 The Company of Biologists Ltd doi:10.1242/jcs.00526 Summary Peripherin is a neural intermediate filament protein that is motors, conventional kinesin and cytoplasmic dynein. Our expressed in peripheral and enteric neurons, as well as in data demonstrate that peripherin particles and squiggles PC12 cells. A determination of the motile properties of can move as components of a rapid transport system peripherin has been undertaken in PC12 cells during capable of delivering cytoskeletal subunits to the most different stages of neurite outgrowth. The results reveal distal regions of neurites over relatively short time periods. that non-filamentous, non-membrane bound peripherin particles and short peripherin intermediate filaments, termed ‘squiggles’, are transported at high speed Movies available online throughout PC12 cell bodies, neurites and growth cones. These movements are bi-directional, and the majority Key words: Intermediate filaments, Peripherin, Dynein, Kinesin, require microtubules along with their associated molecular Cytoskeleton Introduction 2000; Wang and Brown, 2001; Wang et al., 2000). It has also The morphology of the typical neuron consists of a cell body been shown that non-membrane bound particles containing with unusually long cytoplasmic processes. The longest of non-filamentous forms of NF proteins and kinesin can move these is the axon. -
Cytoskeleton and Cell Motility
Cytoskeleton and Cell Motility Thomas Risler1 1Laboratoire Physicochimie Curie (CNRS-UMR 168), Institut Curie, Section de Recherche, 26 rue d’Ulm, 75248 Paris Cedex 05, France (Dated: January 23, 2008) PACS numbers: 1 Article Outline Glossary I. Definition of the Subject and Its Importance II. Introduction III. The Diversity of Cell Motility A. Swimming B. Crawling C. Extensions of cell motility IV. The Cell Cytoskeleton A. Biopolymers B. Molecular motors C. Motor families D. Other cytoskeleton-associated proteins E. Cell anchoring and regulatory pathways F. The prokaryotic cytoskeleton V. Filament-Driven Motility A. Microtubule growth and catastrophes B. Actin gels C. Modeling polymerization forces D. A model system for studying actin-based motility: The bacterium Listeria mono- cytogenes E. Another example of filament-driven amoeboid motility: The nematode sperm cell VI. Motor-Driven Motility A. Generic considerations 2 B. Phenomenological description close to thermodynamic equilibrium C. Hopping and transport models D. The two-state model E. Coupled motors and spontaneous oscillations F. Axonemal beating VII. Putting It Together: Active Polymer Solutions A. Mesoscopic approaches B. Microscopic approaches C. Macroscopic phenomenological approaches: The active gels D. Comparisons of the different approaches to describing active polymer solutions VIII. Extensions and Future Directions Acknowledgments Bibliography Glossary Cell Structural and functional elementary unit of all life forms. The cell is the smallest unit that can be characterized as living. Eukaryotic cell Cell that possesses a nucleus, a small membrane-bounded compartment that contains the genetic material of the cell. Cells that lack a nucleus are called prokaryotic cells or prokaryotes. Domains of life archaea, bacteria and eukarya - or in English eukaryotes, and made of eukaryotic cells - which constitute the three fundamental branches in which all life forms are classified. -
Dynein Activators and Adaptors at a Glance Mara A
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs227132. doi:10.1242/jcs.227132 CELL SCIENCE AT A GLANCE Dynein activators and adaptors at a glance Mara A. Olenick and Erika L. F. Holzbaur* ABSTRACT ribonucleoprotein particles for BICD2, and signaling endosomes for Cytoplasmic dynein-1 (hereafter dynein) is an essential cellular motor Hook1. In this Cell Science at a Glance article and accompanying that drives the movement of diverse cargos along the microtubule poster, we highlight the conserved structural features found in dynein cytoskeleton, including organelles, vesicles and RNAs. A long- activators, the effects of these activators on biophysical parameters, standing question is how a single form of dynein can be adapted to a such as motor velocity and stall force, and the specific intracellular wide range of cellular functions in both interphase and mitosis. functions they mediate. – Recent progress has provided new insights dynein interacts with a KEY WORDS: BICD2, Cytoplasmic dynein, Dynactin, Hook1, group of activating adaptors that provide cargo-specific and/or Microtubule motors, Trafficking function-specific regulation of the motor complex. Activating adaptors such as BICD2 and Hook1 enhance the stability of the Introduction complex that dynein forms with its required activator dynactin, leading Microtubule-based transport is vital to cellular development and to highly processive motility toward the microtubule minus end. survival. Microtubules provide a polarized highway to facilitate Furthermore, activating adaptors mediate specific interactions of the active transport by the molecular motors dynein and kinesin. While motor complex with cargos such as Rab6-positive vesicles or many types of kinesins drive transport toward microtubule plus- ends, there is only one major form of dynein, cytoplasmic dynein-1, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, which drives the trafficking of a wide array of minus-end-directed USA. -
Disrupted Neuronal Trafficking in Amyotrophic Lateral Sclerosis
Acta Neuropathologica (2019) 137:859–877 https://doi.org/10.1007/s00401-019-01964-7 REVIEW Disrupted neuronal trafcking in amyotrophic lateral sclerosis Katja Burk1,2 · R. Jeroen Pasterkamp3 Received: 12 October 2018 / Revised: 19 January 2019 / Accepted: 19 January 2019 / Published online: 5 February 2019 © The Author(s) 2019 Abstract Amyotrophic lateral sclerosis (ALS) is a progressive, adult-onset neurodegenerative disease caused by degeneration of motor neurons in the brain and spinal cord leading to muscle weakness. Median survival after symptom onset in patients is 3–5 years and no efective therapies are available to treat or cure ALS. Therefore, further insight is needed into the molecular and cellular mechanisms that cause motor neuron degeneration and ALS. Diferent ALS disease mechanisms have been identi- fed and recent evidence supports a prominent role for defects in intracellular transport. Several diferent ALS-causing gene mutations (e.g., in FUS, TDP-43, or C9ORF72) have been linked to defects in neuronal trafcking and a picture is emerging on how these defects may trigger disease. This review summarizes and discusses these recent fndings. An overview of how endosomal and receptor trafcking are afected in ALS is followed by a description on dysregulated autophagy and ER/ Golgi trafcking. Finally, changes in axonal transport and nucleocytoplasmic transport are discussed. Further insight into intracellular trafcking defects in ALS will deepen our understanding of ALS pathogenesis and will provide novel avenues for therapeutic intervention. Keywords Amyotrophic lateral sclerosis · Motor neuron · Trafcking · Cytoskeleton · Rab Introduction onset is about 10 years earlier [44]. As disease progresses, corticospinal motor neurons, projecting from the motor cor- Amyotrophic lateral sclerosis (ALS) is a fatal disease char- tex to the brainstem and spinal cord, and bulbar and spinal acterized by the degeneration of upper and lower motor motor neurons, projecting to skeletal muscles, degenerate. -
The Universal Mechanism of Intermediate Filament Transport
bioRxiv preprint doi: https://doi.org/10.1101/251405; this version posted January 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 The universal mechanism of intermediate filament transport. 2 3 Amélie Robert1, Peirun Tian1, Stephen A. Adam1, Robert D. Goldman1 and Vladimir I. Gelfand1* 4 5 1Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern 6 University, Chicago, IL 60611, USA. 7 8 *Corresponding author. 9 Address: Department of Cell and Molecular Biology, Feinberg School of Medicine, 10 Northwestern University, 303 E. Chicago Ave. Ward 11-100, Chicago, IL 60611-3008 11 E-mail address: [email protected] 12 Phone: (312) 503-0530 13 Fax: (312) 503-7912 14 15 1 bioRxiv preprint doi: https://doi.org/10.1101/251405; this version posted January 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 16 ABSTRACT 17 Intermediate filaments (IFs) are a major component of the cytoskeleton that regulates a wide 18 range of physiological properties in eukaryotic cells. In motile cells, the IF network has to adapt 19 to constant changes of cell shape and tension. In this study, we used two cell lines that express 20 vimentin and keratins 8/18 to study the dynamic behavior of these IFs. -
Neurofilaments and Neurofilament Proteins in Health and Disease
Downloaded from http://cshperspectives.cshlp.org/ on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Neurofilaments and Neurofilament Proteins in Health and Disease Aidong Yuan,1,2 Mala V. Rao,1,2 Veeranna,1,2 and Ralph A. Nixon1,2,3 1Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York 10962 2Department of Psychiatry, New York University School of Medicine, New York, New York 10016 3Cell Biology, New York University School of Medicine, New York, New York 10016 Correspondence: [email protected], [email protected] SUMMARY Neurofilaments (NFs) are unique among tissue-specific classes of intermediate filaments (IFs) in being heteropolymers composed of four subunits (NF-L [neurofilament light]; NF-M [neuro- filament middle]; NF-H [neurofilament heavy]; and a-internexin or peripherin), each having different domain structures and functions. Here, we review how NFs provide structural support for the highly asymmetric geometries of neurons and, especially, for the marked radial expan- sion of myelinated axons crucial for effective nerve conduction velocity. NFs in axons exten- sively cross-bridge and interconnect with other non-IF components of the cytoskeleton, including microtubules, actin filaments, and other fibrous cytoskeletal elements, to establish a regionallyspecialized networkthat undergoes exceptionallyslow local turnoverand serves as a docking platform to organize other organelles and proteins. We also discuss how a small pool of oligomeric and short filamentous precursors in the slow phase of axonal transport maintains this network. A complex pattern of phosphorylation and dephosphorylation events on each subunit modulates filament assembly, turnover, and organization within the axonal cytoskel- eton. Multiple factors, and especially turnover rate, determine the size of the network, which can vary substantially along the axon.