Lipid Rafts in Anticancer Therapy: Theory and Practice (Review)
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Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
Anti-COPE Picoband Antibody Catalog # ABO13033
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Anti-COPE Picoband Antibody Catalog # ABO13033 Specification Anti-COPE Picoband Antibody - Product Information Application IHC Primary Accession O14579 Host Rabbit Reactivity Human, Mouse, Rat Clonality Polyclonal Format Lyophilized Description Rabbit IgG polyclonal antibody for Coatomer subunit epsilon(COPE) detection. Tested with WB, IHC-P in Human;Mouse;Rat. Figure 4. IHC analysis of COPE using Reconstitution anti-COPE antibody (ABO13033). Add 0.2ml of distilled water will yield a concentration of 500ug/ml. Anti-COPE Picoband Antibody - Additional Information Gene ID 11316 Other Names Coatomer subunit epsilon, Epsilon-coat protein, Epsilon-COP, COPE Calculated MW 34482 MW KDa Application Details Immunohistochemistry(Paraffin-embedded Section), 0.5-1 µg/ml, Human, Mouse, Rat, By Heat<br> Western blot, 0.1-0.5 µg/ml, Human, Mouse, Rat, <br> <br> Subcellular Localization Cytoplasm . Golgi apparatus membrane ; Peripheral membrane protein ; Cytoplasmic side . Cytoplasmic vesicle, COPI-coated vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Contents Each vial contains 5mg BSA, 0.9mg NaCl, 0.2mg Na2HPO4, 0.05mg NaN3. Immunogen E. coli-derived human COPE recombinant protein (Position: E80-A308). Human COPE shares 89.5% amino acid (aa) sequence identity with mouse COPE. Purification Immunogen affinity purified. Cross Reactivity No cross reactivity with other proteins. -
Role of Cholesterol in Lipid Raft Formation: Lessons from Lipid Model Systems
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1610 (2003) 174–183 www.bba-direct.com Review Role of cholesterol in lipid raft formation: lessons from lipid model systems John R. Silvius* Department of Biochemistry, McGill University, Montre´al, Que´bec, Canada H3G 1Y6 Received 21 March 2002; accepted 16 October 2002 Abstract Biochemical and cell-biological experiments have identified cholesterol as an important component of lipid ‘rafts’ and related structures (e.g., caveolae) in mammalian cell membranes, and membrane cholesterol levels as a key factor in determining raft stability and organization. Studies using cholesterol-containing bilayers as model systems have provided important insights into the roles that cholesterol plays in determining lipid raft behavior. This review will discuss recent progress in understanding two aspects of lipid–cholesterol interactions that are particularly relevant to understanding the formation and properties of lipid rafts. First, we will consider evidence that cholesterol interacts differentially with different membrane lipids, associating particularly strongly with saturated, high-melting phospho- and sphingolipids and particularly weakly with highly unsaturated lipid species. Second, we will review recent progress in reconstituting and directly observing segregated raft-like (liquid-ordered) domains in model membranes that mimic the lipid compositions of natural membranes incorporating raft domains. D 2003 Elsevier Science B.V. All rights reserved. Keywords: Sterol; Phospholipid; Sphingolipid; Lipid bilayer; Lipid monolayer; Membrane domain 1. Introduction Two major observations suggest that cholesterol–lipid interactions play an important role in the formation of rafts Cholesterol–lipid interactions have long been recognized in animal cell membranes. -
The Adaptive Remodeling of Endothelial Glycocalyx in Response to Fluid Shear Stress
City University of New York (CUNY) CUNY Academic Works Publications and Research City College of New York 2014 The Adaptive Remodeling of Endothelial Glycocalyx in Response to Fluid Shear Stress Ye Zeng CUNY City College John M. Tarbell CUNY City College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/cc_pubs/34 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] The Adaptive Remodeling of Endothelial Glycocalyx in Response to Fluid Shear Stress Ye Zeng1,2, John M. Tarbell1* 1 Department of Biomedical Engineering, The City College of New York, New York, New York, United States of America, 2 Institute of Biomedical Engineering, School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China Abstract The endothelial glycocalyx is vital for mechanotransduction and endothelial barrier integrity. We previously demonstrated the early changes in glycocalyx organization during the initial 30 min of shear exposure. In the present study, we tested the hypothesis that long-term shear stress induces further remodeling of the glycocalyx resulting in a robust layer, and explored the responses of membrane rafts and the actin cytoskeleton. After exposure to shear stress for 24 h, the glycocalyx components heparan sulfate, chondroitin sulfate, glypican-1 and syndecan-1, were enhanced on the apical surface, with nearly uniform spatial distributions close to baseline levels that differed greatly from the 30 min distributions. Heparan sulfate and glypican-1 still clustered near the cell boundaries after 24 h of shear, but caveolin-1/caveolae and actin were enhanced and concentrated across the apical aspects of the cell. -
Diffusion of Lipids and GPI-Anchored Proteins in Actin-Free Plasma Membrane Vesicles Measured by STED-FCS Falk Schneidera, Mathias P
bioRxiv preprint doi: https://doi.org/10.1101/076109; this version posted September 19, 2016. 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-NC-ND 4.0 International license. Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS Falk Schneidera, Mathias P. Clausena,b, Dominic Waithec, Thomas Kollera, Gunes Ozhand,e, Christian Eggelinga,c,*, Erdinc Sezgina,* a MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX39DS, Oxford, United Kingdom b MEMPHYS – Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark c Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, OX39DS, Oxford, United Kingdom d Izmir International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylul University, Inciralti- Balcova, 35340 Izmir, Turkey; e Department of Medical Biology and Genetics, Dokuz Eylul University Medical School, Inciralti-Balcova, 35340 Izmir, Turkey. Correspondence: [email protected]; [email protected] Running title: Diffusion in actin-free plasma membrane vesicles Keywords: plasma membrane biophysics, fluorescence correlation spectroscopy, lipid raft, GPI anchored proteins, STED microscopy, STED-FCS, giant plasma membrane vesicles, Abbreviations: giant plasma membrane vesicles (GPMVs), giant unilamellar vesicles (GUVs), Glycophosphatidylinositol anchored protein (GPI-AP), phospholipid (PL), Stimulated emission depletion (STED), fluorescence correlation spectroscopy (FCS) Character count: 19,026 1 bioRxiv preprint doi: https://doi.org/10.1101/076109; this version posted September 19, 2016. -
Lipid Rafts Facilitate LPS Responses 2605
Research Article 2603 Mediators of innate immune recognition of bacteria concentrate in lipid rafts and facilitate lipopolysaccharide-induced cell activation Martha Triantafilou1, Kensuke Miyake2, Douglas T. Golenbock3,* and Kathy Triantafilou1,‡ 1University of Portsmouth, School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK 2Department of Immunology, Saga Medical School, Nabeshima, Japan 3Boston University School of Medicine, Boston Medical Center, The Maxwell Finland Laboratory for Infectious Diseases, Boston, Massachusetts 02118, USA *Present address: Department of Medicine, Division of Infectious Diseases, University of Massachusetts Medical School, Worcester, MA 01665, USA ‡Author for correspondence (e-mail: [email protected]) Accepted 19 March 2002 Journal of Cell Science 115, 2603-2611 (2002) © The Company of Biologists Ltd Summary The plasma membrane of cells is composed of lateral present in microdomains following LPS stimulation. Lipid heterogeneities, patches and microdomains. These raft integrity is essential for LPS-cellular activation, since membrane microdomains or lipid rafts are enriched raft-disrupting drugs, such as nystatin or MCD, inhibit in glycosphingolipids and cholesterol and have been LPS-induced TNF-α secretion. Our results suggest that the implicated in cellular processes such as membrane sorting entire bacterial recognition system is based around the and signal transduction. In this study we investigated the ligation of CD14 by bacterial components and the importance of lipid raft formation in the innate immune recruitment of multiple signalling molecules, such as hsp70, recognition of bacteria using biochemical and fluorescence hsp90, CXCR4, GDF5 and TLR4, at the site of CD14-LPS imaging techniques. We found that receptor molecules ligation, within the lipid rafts. -
Shiga Toxin E. Coli Detection Differentiation Implications for Food
SL440 Shiga Toxin-Producing Escherichia coli: Detection, Differentiation, and Implications for Food Safety1 William J. Zaragoza, Max Teplitski, and Clifton K. Fagerquist2 Introduction for the effective detection of the Shiga-toxin-producing pathogens in a variety of food matrices. Shiga toxin is a protein found within the genome of a type of virus called a bacteriophage. These bacteriophages can There are two types of Shiga toxins—Shiga toxin 1 (Stx1) integrate into the genomes of the bacterium E. coli, giving and Shiga toxin 2 (Stx2). Stx1 is composed of several rise to Shiga toxin-producing E. coli (STEC). Even though subtypes knows as Stx1a, Stx1c, and Stx1d. Stx2 has seven most E. coli are benign or even beneficial (“commensal”) subtypes: a–g. Strains carrying all of the Stx1 subtypes affect members of our gut microbial communities, strains of E. humans, though they are less potent than that of Stx2. Stx2 coli carrying Shiga-toxin encoding genes (as well as other subtypes a,c, and d are frequently associated with human virulence determinants) are highly pathogenic in humans illness, while the other subtypes affect different animals. and other animals. When mammals ingest these bacteria, Subtypes Stx2b and Stx2e affect neonatal piglets, while STECs can undergo phage-driven lysis and deliver these target hosts for Stx2f and Stx2g subtypes are not currently toxins to mammalian guts. The Shiga toxin consists of an known (Fuller et al. 2011). Stx2f was originally isolated A subunit and 5 identical B subunits. The B subunits are from feral pigeons (Schmidt et al. 2000), and Stx2g was involved in binding to gut epithelial cells. -
The Importance of Lipid Raft Proteins for Sepsis: Could Raftlin-2 Be a New Biomarker?
DOI: 10.14744/ejmi.2018.69875 EJMI 2018;2(2):95–100 Research Article The Importance of Lipid Raft Proteins for Sepsis: Could Raftlin-2 be a New Biomarker? Hilmi Erdem Sumbul,1 Emre Karakoc,2 Murat Erdogan,2 Ozlem Ozkan Kuscu,2 Filiz Kibar,3 Salih Cetiner,4 Tugba Korkmaz,2 Merve Yahsi,2 Firat Kocabas2 1Department of Internal Medicine, Health Science University, Adana City Training and Research Hospital, Adana, Turkey 2Department of Internal Medicine, Cukurova University, Adana, Turkey 3Department of Microbiology, Cukurova University, Adana, Turkey 4Department of Biochemistry, Cukurova University, Adana, Turkey Abstract Objectives: Bacterial infections and sepsis are common problems in patients receiving intensive care unit treatment. Raftlin-2 is a protein with an important role in lipid rafts, and the aim of this study was to compare raftlin-2 micro pro- tein blood levels in a healthy control group with a patient group with septicemia. Methods: A prospective, controlled study was conducted in the intensive care unit (ICU) of a university hospital and a control group was selected from healthy individuals. There were 64 ICU patients and 74 individuals in the control group. Blood samples were taken from the study group before the start of antibiotic therapy. The C-reactive protein, procalci- tonin, lactate, biochemistry, and raftlin-2 levels of the patient and control groups were compared. Results: There was a statistically significant difference between the lactate levels in the healthy group and the patient group with septicemia, but not in the raftlin-2 protein level. The p-values were calculated at 0.350 for raftlin-2 and 0.007 for lactate. -
In Vivo Mapping of a GPCR Interactome Using Knockin Mice
In vivo mapping of a GPCR interactome using knockin mice Jade Degrandmaisona,b,c,d,e,1, Khaled Abdallahb,c,d,1, Véronique Blaisb,c,d, Samuel Géniera,c,d, Marie-Pier Lalumièrea,c,d, Francis Bergeronb,c,d,e, Catherine M. Cahillf,g,h, Jim Boulterf,g,h, Christine L. Lavoieb,c,d,i, Jean-Luc Parenta,c,d,i,2, and Louis Gendronb,c,d,i,j,k,2 aDépartement de Médecine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; bDépartement de Pharmacologie–Physiologie, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; cFaculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; dCentre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; eQuebec Network of Junior Pain Investigators, Sherbrooke, QC J1H 5N4, Canada; fDepartment of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA 90095; gSemel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095; hShirley and Stefan Hatos Center for Neuropharmacology, University of California, Los Angeles, CA 90095; iInstitut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; jDépartement d’Anesthésiologie, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; and kQuebec Pain Research Network, Sherbrooke, QC J1H 5N4, Canada Edited by Brian K. Kobilka, Stanford University School of Medicine, Stanford, CA, and approved April 9, 2020 (received for review October 16, 2019) With over 30% of current medications targeting this family of attenuates pain hypersensitivities in several chronic pain models proteins, G-protein–coupled receptors (GPCRs) remain invaluable including neuropathic, inflammatory, diabetic, and cancer pain therapeutic targets. -
The Popeye Domain Containing Genes and Their Function in Striated Muscle
Journal of Cardiovascular Development and Disease Review The Popeye Domain Containing Genes and Their Function in Striated Muscle Roland F. R. Schindler 1, Chiara Scotton 2, Vanessa French 1, Alessandra Ferlini 2 and Thomas Brand 1,* 1 Developmental Dynamics, Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Hill End Road, Harefield UB9 6JH, UK; [email protected] (R.F.R.S.); [email protected] (V.F.) 2 Department of Medical Sciences, Medical Genetics Unit, University of Ferrara, Ferrara 44121, Italy; [email protected] (C.S.); fl[email protected] (A.F.) * Correspondence: [email protected]; Tel.: +44-189-582-8900 Academic Editors: Robert E. Poelmann and Monique R.M. Jongbloed Received: 26 April 2016; Accepted: 13 June 2016; Published: 15 June 2016 Abstract: The Popeye domain containing (POPDC) genes encode a novel class of cAMP effector proteins, which are abundantly expressed in heart and skeletal muscle. Here, we will review their role in striated muscle as deduced from work in cell and animal models and the recent analysis of patients carrying a missense mutation in POPDC1. Evidence suggests that POPDC proteins control membrane trafficking of interacting proteins. Furthermore, we will discuss the current catalogue of established protein-protein interactions. In recent years, the number of POPDC-interacting proteins has been rising and currently includes ion channels (TREK-1), sarcolemma-associated proteins serving functions in mechanical stability (dystrophin), compartmentalization (caveolin 3), scaffolding (ZO-1), trafficking (NDRG4, VAMP2/3) and repair (dysferlin) or acting as a guanine nucleotide exchange factor for Rho-family GTPases (GEFT). -
Shedding and Uptake of Gangliosides and Glycosylphosphatidylinositol-Anchored Proteins ⁎ Gordan Lauc A,B, , Marija Heffer-Lauc C
Biochimica et Biophysica Acta 1760 (2006) 584–602 http://www.elsevier.com/locate/bba Review Shedding and uptake of gangliosides and glycosylphosphatidylinositol-anchored proteins ⁎ Gordan Lauc a,b, , Marija Heffer-Lauc c a Department of Chemistry and Biochemistry, University of Osijek School of Medicine, J. Huttlera 4, 31000 Osijek, Croatia b Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia c Department of Biology, University of Osijek School of Medicine, J. Huttlera 4, 31000 Osijek, Croatia Received 30 September 2005; received in revised form 22 November 2005; accepted 23 November 2005 Available online 20 December 2005 Abstract Gangliosides and glycosylphosphatidylinositol (GPI)-anchored proteins have very different biosynthetic origin, but they have one thing in common: they are both comprised of a relatively large hydrophilic moiety tethered to a membrane by a relatively small lipid tail. Both gangliosides and GPI-anchored proteins can be actively shed from the membrane of one cell and taken up by other cells by insertion of their lipid anchors into the cell membrane. The process of shedding and uptake of gangliosides and GPI-anchored proteins has been independently discovered in several disciplines during the last few decades, but these discoveries were largely ignored by people working in other areas of science. By bringing together results from these, sometimes very distant disciplines, in this review, we give an overview of current knowledge about shedding and uptake of gangliosides and GPI-anchored proteins. Tumor cells and some pathogens apparently misuse this process for their own advantage, but its real physiological functions remain to be discovered. -
1529.Full.Pdf
Intracellular Lipid Flux and Membrane Microdomains as Organizing Principles in Inflammatory Cell Signaling This information is current as Michael B. Fessler and John S. Parks of September 24, 2021. J Immunol 2011; 187:1529-1535; ; doi: 10.4049/jimmunol.1100253 http://www.jimmunol.org/content/187/4/1529 Downloaded from References This article cites 92 articles, 48 of which you can access for free at: http://www.jimmunol.org/content/187/4/1529.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on September 24, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Intracellular Lipid Flux and Membrane Microdomains as Organizing Principles in Inflammatory Cell Signaling Michael B. Fessler* and John S. Parks† Lipid rafts and caveolae play a pivotal role in organiza- remodeling of raft lipid is not only necessary in many sig- tion of signaling by TLR4 and several other immune naling cascades, but that primary perturbations of raft lipid receptors.