Southern Blotting Involves the Transfer of DNA from a Gel to a Membrane, Followed by Detection of Specific Sequences by Hybridization with a Labeled Probe
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Supplementary Materials and Method Immunostaining and Western Blot
Supplementary Materials and Method Immunostaining and Western Blot Analysis For immunofluorescence staining, mouse and human cells were fixed with 4% paraformaldehyde- PBS for 15 min. Following Triton-X100 permeabilization and blocking, cells were incubated with primary antibodies overnight at 4°C following with Alexa 594-conjugated secondary antibodies at 4°C for 1 hour (Thermo Fisher Scientific, 1:1000). Samples were mounted using VECTASHIELD Antifade Mounting Medium with DAPI (Vector Laboratories) and immunofluorescence was detected using Olympus confocal microscopy. For western blot analysis, cells were lysed on ice using RIPA buffer supplemented with protease and phosphatase inhibitors (Sigma). Primary Antibodies for Immunostaining and Western Blot Analysis: Yap (14074, Cell Signaling), pYAP (4911, Cell Signaling), Lats1 (3477, Cell Signaling), pLats1( 8654, Cell Signaling), Wnt5a (2530, Cell Signaling), cleaved Caspase-3 (9661, Cell Signaling), Ki-67 (VP-K451, Vector Laboratories), Cyr61 (sc-13100, Santa Cruz Biotechnology), CTGF (sc-14939, Santa Cruz Biotechnology), AXL (8661, Cell Signaling), pErk (4376, Cell Signaling), pMEK (4376, Cell Signaling), Ck-19 (16858-1-AP, Proteintech), Actin (A2228, Sigma Aldrich), Vinculin (V4139, Sigma Aldrich), Kras (sc-30, Santa Cruz Biotechnology). Ectopic expression of YAP1 and WNT5A in mouse and human cells To generate YAP1S127A-expressing stable Pa04C cells, Pa04C cells were transfected with a linearized pcDNA3.1 plasmid with or without YAP1 cDNA containing S127A substitution. Two days post-transfection using Lipofectamine1000, cultures were selected in G418 (Sigma) and single clones were picked and expanded for further analysis. Overexpression of YAPS127A or WNT5A in human or mouse cells other than Pa04C were acheieved with lentivral infection. Briefly, lentivirus infection was performed by transfecting 293T cells with either GFP control, YAP1S127A, or WNT5A cloned in pHAGE lentivirus vector {EF1α promoter-GW-IRES-eGFP (GW: Gateway modified)}. -
Biochemistry and the Genomic Revolution 1.1
Dedication About the authors Preface Tools and Techniques Clinical Applications Molecular Evolution Supplements Supporting Biochemistry, Fifth Edition Acknowledgments I. The Molecular Design of Life 1. Prelude: Biochemistry and the Genomic Revolution 1.1. DNA Illustrates the Relation between Form and Function 1.2. Biochemical Unity Underlies Biological Diversity 1.3. Chemical Bonds in Biochemistry 1.4. Biochemistry and Human Biology Appendix: Depicting Molecular Structures 2. Biochemical Evolution 2.1. Key Organic Molecules Are Used by Living Systems 2.2. Evolution Requires Reproduction, Variation, and Selective Pressure 2.3. Energy Transformations Are Necessary to Sustain Living Systems 2.4. Cells Can Respond to Changes in Their Environments Summary Problems Selected Readings 3. Protein Structure and Function 3.1. Proteins Are Built from a Repertoire of 20 Amino Acids 3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops 3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores 3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures 3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure Summary Appendix: Acid-Base Concepts Problems Selected Readings 4. Exploring Proteins 4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation 4.3. Immunology Provides Important Techniques with Which to Investigate Proteins 4.4. Peptides Can Be Synthesized by Automated Solid-Phase Methods 4.5. -
Blotting Techniques Blotting Is the Technique in Which Nucleic Acids Or
Blotting techniques Blotting is the technique in which nucleic acids or proteins are immobilized onto a solid support generally nylon or nitrocellulose membranes. Blotting of nucleic acid is the central technique for hybridization studies. Nucleic acid labeling and hybridization on membranes have formed the basis for a range of experimental techniques involving understanding of gene expression, organization, etc. Identifying and measuring specific proteins in complex biological mixtures, such as blood, have long been important goals in scientific and diagnostic practice. More recently the identification of abnormal genes in genomic DNA has become increasingly important in clinical research and genetic counseling. Blotting techniques are used to identify unique proteins and nucleic acid sequences. They have been developed to be highly specific and sensitive and have become important tools in both molecular biology and clinical research. General principle The blotting methods are fairly simple and usually consist of four separate steps: electrophoretic separation of protein or of nucleic acid fragments in the sample; transfer to and immobilization on paper support; binding of analytical probe to target molecule on paper; and visualization of bound probe. Molecules in a sample are first separated by electrophoresis and then transferred on to an easily handled support medium or membrane. This immobilizes the protein or DNA fragments, provides a faithful replica of the original separation, and facilitates subsequent biochemical analysis. After being transferred to the support medium the immobilized protein or nucleic acid fragment is localized by the use of probes, such as antibodies or DNA, that specifically bind to the molecule of interest. Finally, the position of the probe that is bound to the immobilized target molecule is visualized usually by autoradiography. -
Southern Blotting Teacher’S Guidebook
PR139 G-Biosciences ♦ 1-800-628-7730 ♦ 1-314-991-6034 ♦ [email protected] A Geno Technology, Inc. (USA) brand name Southern Blotting Teacher’s Guidebook (Cat. # BE-315) think proteins! think G-Biosciences www.GBiosciences.com MATERIALS INCLUDED ....................................................................................................... 3 SPECIAL HANDLING INSTRUCTIONS ................................................................................... 3 ADDITIONAL EQUIPMENT REQUIRED ................................................................................ 3 TIME REQUIRED ................................................................................................................. 3 AIMS .................................................................................................................................. 4 BACKGROUND ................................................................................................................... 4 TEACHER’S PRE EXPERIMENT SET UP ................................................................................ 5 PREPARATION OF AGAROSE GEL ................................................................................... 5 PREPARE THE DNA LADDER ........................................................................................... 5 PREPARE DILUTE DNA STAINING SOLUTION .................................................................. 5 MATERIALS FOR DEMONSTRATION ................................................................................... 6 DEMONSTRATION -
Western Blotting Guidebook
Western Blotting Guidebook Substrate Substrate Secondary Secondary Antibody Antibody Primary Primary Antibody Antibody Protein A Protein B 1 About Azure Biosystems At Azure Biosystems, we develop easy-to-use, high-performance imaging systems and high-quality reagents for life science research. By bringing a fresh approach to instrument design, technology, and user interface, we move past incremental improvements and go straight to innovations that substantially advance what a scientist can do. And in focusing on getting the highest quality data from these instruments—low backgrounds, sensitive detection, robust quantitation—we’ve created a line of reagents that consistently delivers reproducible results and streamlines workflows. Providing scientists around the globe with high-caliber products for life science research, Azure Biosystems’ innovations open the door to boundless scientific insights. Learn more at azurebiosystems.com. cSeries Imagers Sapphire Ao Absorbance Reagents & Biomolecular Imager Microplate Reader Blotting Accessories Corporate Headquarters 6747 Sierra Court Phone: (925) 307-7127 Please send purchase orders to: Suite A-B (9am–4pm Pacific time) [email protected] Dublin, CA 94568 To dial from outside of the US: For product inquiries, please email USA +1 925 307 7127 [email protected] FAX: (925) 905-1816 www.azurebiosystems.com • [email protected] Copyright © 2018 Azure Biosystems. All rights reserved. The Azure Biosystems logo, Azure Biosystems™, cSeries™, Sapphire™ and Radiance™ are trademarks of Azure Biosystems, Inc. More information about Azure Biosystems intellectual property assets, including patents, trademarks and copyrights, is available at www.azurebiosystems.com or by contacting us by phone or email. All other trademarks are property of their respective owners. -
Bioanalytical Chemistry 4. Gel Electrophoresis
73 Bioanalytical chemistry 4. Gel Electrophoresis Required reading: Sections 9.1, 9.2.3, 9.2.4, 9.5.1, 10.1 to 10.7, 11.1 to 11.5, and 15.5 of Mikkelsen and Cortón, Bioanalytical Chemistry Some objectives for this section ⇒ You will know what DNA agarose gel electrophoresis is ⇒ You will know what the difference between normal and pulsed field electrophoresis of DNA ⇒ You will know what SDS-PAGE is. ⇒ You will understand how the basis for molecular basis for size-based separation of proteins by SDS- PAGE. ⇒ You will know what IEF is. ⇒ You will know how SDS-PAGE and IEF can be combined in 2-dimensional gel electroophoresis ⇒ You will know what a Western Blot is. ⇒ You will appreciate how these techniques can be used in the analysis of DNA and proteins. Primary Source Material • Chapter 4 and 6 of Biochemistry: Berg, Jeremy M.; Tymoczko, John L.; and Stryer, Lubert (NCBI bookshelf). • Chapter 3 and 7 of Molecular Cell Biology 4th ed. (Ch. 9, 5th ed.): Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E. (NCBI bookshelf). • Chapter 12 of Introduction to Genetic Analysis Anthony: J.F. Griffiths, Jeffrey H. Miller, David T. Suzuki, Richard C. Lewontin, William M. Gelbart (NCBI bookshelf). • Some animations are from http://www.wiley-vch.de/books/info/3-527-30300-6/. • http://www.piercenet.com/ Electrophoresis 74 The velocity of migration (v) of a molecule in an electric field depends on the electric field strength (E), the net charge on the protein (z), and the frictional coefficient (f). -
Clinical Molecular Genetics in the Uk C.1975–C.2000
CLINICAL MOLECULAR GENETICS IN THE UK c.1975–c.2000 The transcript of a Witness Seminar held by the History of Modern Biomedicine Research Group, Queen Mary, University of London, on 5 February 2013 Edited by E M Jones and E M Tansey Volume 48 2014 ©The Trustee of the Wellcome Trust, London, 2014 First published by Queen Mary, University of London, 2014 The History of Modern Biomedicine Research Group is funded by the Wellcome Trust, which is a registered charity, no. 210183. ISBN 978 0 90223 888 6 All volumes are freely available online at www.history.qmul.ac.uk/research/modbiomed/ wellcome_witnesses/ Please cite as: Jones E M, Tansey E M. (eds) (2014) Clinical Molecular Genetics in the UK c.1975–c.2000. Wellcome Witnesses to Contemporary Medicine, vol. 48. London: Queen Mary, University of London. CONTENTS What is a Witness Seminar? v Acknowledgements E M Tansey and E M Jones vii Illustrations and credits ix Abbreviations xi Ancillary guides xiii Introduction Professor Bob Williamson xv Transcript Edited by E M Jones and E M Tansey 1 Appendix 1 Photograph, with key, of delegates attending The Molecular Biology of Thalassaemia conference in Kolimbari, Crete, 1978 88 Appendix 2 Extracts from the University of Leiden postgraduate course Restriction Fragment Length Polymorphisms and Human Genetics, 1982 91 Appendix 3 Archival material of the Clinical Molecular Genetics Society 95 Biographical notes 101 References 113 Index 131 Witness Seminars: Meetings and Publications 143 WHAT IS A WITNESS SEMINAR? The Witness Seminar is a specialized form of oral history, where several individuals associated with a particular set of circumstances or events are invited to meet together to discuss, debate, and agree or disagree about their memories. -
Journal of Biomedical Discovery and Collaboration
View metadata, citation and similar papers at core.ac.uk brought to you by CORE Journal of Biomedical Discovery and provided by PubMed Central Collaboration BioMed Central Case Study Open Access The emergence and diffusion of DNA microarray technology Tim Lenoir*† and Eric Giannella† Address: Jenkins Collaboratory for New Technologies in Society, Duke University, John Hope Franklin Center, 2204 Erwin Road, Durham, North Carolina 27708-0402, USA Email: Tim Lenoir* - [email protected]; Eric Giannella - [email protected] * Corresponding author †Equal contributors Published: 22 August 2006 Received: 09 August 2006 Accepted: 22 August 2006 Journal of Biomedical Discovery and Collaboration 2006, 1:11 doi:10.1186/1747-5333-1-11 This article is available from: http://www.j-biomed-discovery.com/content/1/1/11 © 2006 Lenoir and Giannella; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The network model of innovation widely adopted among researchers in the economics of science and technology posits relatively porous boundaries between firms and academic research programs and a bi-directional flow of inventions, personnel, and tacit knowledge between sites of university and industry innovation. Moreover, the model suggests that these bi-directional flows should be considered as mutual stimulation of research and invention in both industry and academe, operating as a positive feedback loop. One side of this bi-directional flow – namely; the flow of inventions into industry through the licensing of university-based technologies – has been well studied; but the reverse phenomenon of the stimulation of university research through the absorption of new directions emanating from industry has yet to be investigated in much detail. -
Permease from Escherichia Coli
Plasticity of lipid-protein interactions in the function and topogenesis of the membrane protein lactose permease from Escherichia coli Mikhail Bogdanova,1, Philip Heacocka, Ziqiang Guanb, and William Dowhana,1 aDepartment of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX, 77030; and bDepartment of Biochemistry, Duke University Medical Center, Durham, NC 27710 Edited by William T. Wickner, Dartmouth Medical School, Hanover, NH, and approved July 15, 2010 (received for review May 9, 2010) Phosphatidylcholine (PC) has been widely used in place of naturally N-terminal two-TM helical hairpin of PheP and GabP are in- occurring phosphatidylethanolamine (PE) in reconstitution of verted with respect to their orientation in PE-containing cells bacterial membrane proteins. However, PC does not support native and the remaining TMs. These permeases do not carry out pro- structure or function for several reconstituted transport proteins. ton-coupled energy-dependent uphill transport of substrate in Lactose permease (LacY) of Escherichia coli, when reconstituted cells lacking PE, but still display energy-independent downhill in E. coli phospholipids, exhibits energy-dependent uphill and transport. LacY reconstituted into total E. coli phospholipids car- energy-independent downhill transport function and proper con- ries out uphill transport with domains C6 and P7 on opposite formation of periplasmic domain P7, which is tightly linked to sides of the membrane bilayer as observed in wild-type cells uphill transport function. LacY expressed in cells lacking PE and (9). Leaving out PE during reconstitution results in only downhill containing only anionic phospholipids exhibits only downhill trans- transport with domains C6 and P7 residing on the same side of port and lacks native P7 conformation. -
Protein Blotting Guide
Electrophoresis and Blotting Protein Blotting Guide BEGIN Protein Blotting Guide Theory and Products Part 1 Theory and Products 5 Chapter 5 Detection and Imaging 29 Total Protein Detection 31 Transfer Buffer Formulations 58 5 Chapter 1 Overview of Protein Blotting Anionic Dyes 31 Towbin Buffer 58 Towbin Buffer with SDS 58 Transfer 6 Fluorescent Protein Stains 31 Stain-Free Technology 32 Bjerrum Schafer-Nielsen Buffer 58 Detection 6 Colloidal Gold 32 Bjerrum Schafer-Nielsen Buffer with SDS 58 CAPS Buffer 58 General Considerations and Workflow 6 Immunodetection 32 Dunn Carbonate Buffer 58 Immunodetection Workflow 33 0.7% Acetic Acid 58 Chapter 2 Methods and Instrumentation 9 Blocking 33 Protein Blotting Methods 10 Antibody Incubations 33 Detection Buffer Formulations 58 Electrophoretic Transfer 10 Washes 33 General Detection Buffers 58 Tank Blotting 10 Antibody Selection and Dilution 34 Total Protein Staining Buffers and Solutions 59 Semi-Dry Blotting 11 Primary Antibodies 34 Substrate Buffers and Solutions 60 Microfiltration (Dot Blotting) Species-Specific Secondary Antibodies 34 Stripping Buffer 60 Antibody-Specific Ligands 34 Blotting Systems and Power Supplies 12 Detection Methods 35 Tank Blotting Cells 12 Colorimetric Detection 36 Part 3 Troubleshooting 63 Mini Trans-Blot® Cell and Criterion™ Blotter 12 Premixed and Individual Colorimetric Substrates 38 Transfer 64 Trans-Blot® Cell 12 Immun-Blot® Assay Kits 38 Electrophoretic Transfer 64 Trans-Blot® Plus Cell 13 Immun-Blot Amplified AP Kit 38 Microfiltration 65 Semi-Dry Blotting Cells -
Western Blot Handbook
Novus-lu-2945 Western Blot Handbook Learn more | novusbio.com Learn more | novusbio.com INTRODUCTION TO WESTERN BLOTTING Western blotting uses antibodies to identify individual proteins within a cell or tissue lysate. Antibodies bind to highly specific sequences of amino acids, known as epitopes. Because amino acid sequences vary from protein to protein, western blotting analysis can be used to identify and quantify a single protein in a lysate that contains thousands of different proteins First, proteins are separated from each other based on their size by SDS-PAGE gel electrophoresis. Next, the proteins are transferred from the gel to a membrane by application of an electrical current. The membrane can then be processed with primary antibodies specific for target proteins of interest. Next, secondary antibodies bound to enzymes are applied and finally a substrate that reacts with the secondary antibody-bound enzyme is added for detection of the antibody/protein complex. This step-by-step guide is intended to serve as a starting point for understanding, performing, and troubleshooting a standard western blotting protocol. Learn more | novusbio.com Learn more | novusbio.com TABLE OF CONTENTS 1-2 Controls Positive control lysate Negative control lysate Endogenous control lysate Loading controls 3-6 Sample Preparation Lysis Protease and phosphatase inhibitors Carrying out lysis Example lysate preparation from cell culture protocol Determination of protein concentration Preparation of samples for gel loading Sample preparation protocol 7 -
Blotting Techniques
BLOTTING TECHNIQUES Dr.Ramesh C.K. Associate Professor and Chairman Department of Biotechnology Sahyadri Science College Shimoga - 577 203 Karnataka, India BLOTTING TECHNIQUES Southern Blot Northern blot Western blot It is used to detect It is used to detect It is used to detect the DNA. the RNA. proteins. SOUTHERN BLOTTING A technique for identifying specific sequences of DNA in which DNA fragments are separated by electrophoresis, transferred to a membrane, and identified with a suitable probe. Detects restriction fragments following a restriction enzyme digest of genomic DNA (RFLPs) Named after British biochemist Edwin Southern (alive and publishing!) Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol Biol. 1975 Nov 5;98(3):503-17. History/Background • ‘Southern’ hybridization named after Sir Edwin Southern • Developed in 1975 • One of the most highly cited scientific publications “Used to detect the DNA” • This method Involves: Separation Transfer Hybridization. • This DNA can be: • Single gene • Part of a larger piece of DNA……..viral genome “The key to this method is Hybridization” Hybridization “Process of forming a dsDNA molecule between a ssDNA probe and a ss-target DNA” PRINCIPLE The mixture of molecules is separated. Immobilized on a matrix. Probe addition to the matrix to bind to the molecules. Unbound probes are removed. “The place where the probe is connected corresponds to the location of the immobilized target molecule.” Steps The DNA is digested Fragments Gel electrophoresis Transfer to membrane Probing Autoradiogram I. DNA Purification – Isolate the DNA in question from the rest of the cellular material in the nucleus.