Autophagy in Mammalian Systems

Part B

Edited by

  • Daniel Klionsky, Life Sciences Institute, University of Michigan, USA

This is the companion volume to Daniel Klionsky’s Autophagy: Lower Eukaryotes, which features the basic methods in autophagy covering yeasts and alternative fungi (aspergillus, podospora, magnaporthe). Klionsky is one of the leading authorities in the field. He is the editor-in-chief of Autophagy. The November 2007 issue of Nature Reviews highlighted his article, “Autophagy: From phenomenology to molecular understanding in less than a decade.” He is currently editing guidelines for the field, with 230 contributing authors, that will publish in Autophagy.Particularly in times of stress, like starvation and disease, higher organisms have an internal mechanism in their cells for chewing up and recycling parts of themselves. The process of internal “house cleaning” in the cell is called autophagy - literally self-eating. Breakthroughs in understanding the molecular basis of autophagy came after the cloning of ATG1 (autophagy-related gene 1) in yeast. (To date, 30 additional yeast genes have been identified.) These ATG genes in yeast were the stepping stones to the explosion of research into the molecular analysis of autophagy in higher eukaryotes. In the future, this research will help to design clinical approaches that can turn on autophagy and halt tumor growth.
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Researchers in biochemistry, cell and molecular biology, oncology, pharmacology


Book information

  • Published: January 2009
  • ISBN: 978-0-12-374547-7

Table of Contents

Chapter 1LC3-based assay for monitoring autophagyShunsuke Kimura, Naonobu Fujita, Takeshi Noda and Tamotsu YoshimoriChapter 2Analysis of autophagy using GFP-LC3 transgenic miceNoboru MizushimaChapter 3Photoactivatable GFPJennifer Lippincott-Schwartz and Dale HaileyChapter 4Assaying for autophagic protein degradationFred MeijerChapter 5Sequestration assays for mammalian autophagyPer O. SeglenChapter 6Incorporation of monodansylcadaverine (MDC) as an assay to assess autophagy induction and monitoring fusion with a degradative compartmentMaria Isabel ColomboChapter 7The GST-BHMT assay and related assays for autophagyCarol A. Mercer and Patrick B. DennisChapter 8Redox and autophagy-ROS as an indicator for autophagic activityRuth Scherz-Shouval and Zvulun ElazarChapter 9FACS analysis of autophagyElena Shvets, Ephraim Fass and Zvulun ElazarChapter 10Electron microscopy in mammalsPäivi Ylä-Anttila and Eeva-Liisa EskelinenChapter 11Monitoring mTOR activityKen InokiChapter 12Using p62 as a marker for autophagy.Terje JohansenChapter 13Cytosolic LC3 ratio as a quantitative index of macroautophagyMotoni Kadowaki and Md. Razaul KarimChapter 14Pexophagy in mammalian cellsJunji Ezaki,Takashi Ueno, Eiki Kominami and Masaaki KomatsuChapter 15Mitophagy in mammalian cells.Ji Zhang and Paul A. NeyChapter 16Quantification of WIPI-1/Atg18 puncta formation for assessing mammalian autophagyTassula Proikas-Cezanne and Simon G. PfistererChapter 17Correlative light and electron microscopy (CLEM) using GFP-LC3 and other autophagosome markersSharon Tooze and Minoo RaziChapter 18Nanotechnology assays for autophagyOleksandr SeleverstovChapter 19Photoconvertible KAEDA-LC3 for monitoring autophagic fluxChristoph Goemans and Aviva TolkovskyChapter 20Methods to monitor Chaperone-mediated autophagyAna Maria Cuervo and Susmita KaushikChapter 21Autophagy in response to Salmonella enterica serovar Typhimurium infectionCheryl Birmingham and John BrumellChapter 22Monitoring autophagy during Mycobacterium tuberculosis infectionVojo DereticChapter 23Shigella, Listeria and Streptococcus induction of autophagyMichinaga Ogawa,Yuko Yoshikawa, Ichiro Nakagawa,Chihiro Sasakawa, and Trinad ChakrabortyChapter 24Measuring the impact of infection on autophagy in macrophagesJean-Francois Dubuisson, Brenda Byrne and Michele Swanson