Autophagy in Mammalian Systems, Part B

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.

Chapter 1
LC3-based assay for monitoring autophagy
Shunsuke Kimura, Naonobu Fujita, Takeshi Noda and Tamotsu Yoshimori

Chapter 2
Analysis of autophagy using GFP-LC3 transgenic mice
Noboru Mizushima

Chapter 3
Photoactivatable GFP
Jennifer Lippincott-Schwartz and Dale Hailey

Chapter 4
Assaying for autophagic protein degradation
Fred Meijer

Chapter 5
Sequestration assays for mammalian autophagy
Per O. Seglen

Chapter 6
Incorporation of monodansylcadaverine (MDC) as an assay to assess autophagy induction and monitoring fusion with a degradative compartment
Maria Isabel Colombo

Chapter 7
The GST-BHMT assay and related assays for autophagy
Carol A. Mercer and Patrick B. Dennis

Chapter 8
Redox and autophagy-ROS as an indicator for autophagic activity
Ruth Scherz-Shouval and Zvulun Elazar

Chapter 9
FACS analysis of autophagy
Elena Shvets, Ephraim Fass and Zvulun Elazar

Chapter 10
Electron microscopy in mammals
Päivi Ylä-Anttila and Eeva-Liisa Eskelinen

Chapter 11
Monitoring mTOR activity
Ken Inoki

Chapter 12
Using p62 as a marker for autophagy.
Terje Johansen

Chapter 13
Cytosolic LC3 ratio as a quantitative index of macroautophagy
Motoni Kadowaki and Md. Razaul Karim

Chapter 14
Pexophagy in mammalian cells
Junji Ezaki,Takashi Ueno, Eiki Kominami and Masaaki Komatsu

Chapter 15
Mitophagy in mammalian cells.
Ji Zhang and Paul A. Ney

Chapter 16
Quantification of WIPI-1/Atg18 puncta formation for assessing mammalian autophagy
Tassula Proikas-Cezanne and Simon G. Pfisterer

Chapter 17
Correlative light and electron microscopy (CLEM) using GFP-LC3 and other autophagosome markers
Sharon Tooze and Minoo Razi

Chapter 18
Nanotechnology assays for autophagy
Oleksandr Seleverstov

Chapter 19
Photoconvertible KAEDA-LC3 for monitoring autophagic flux
Christoph Goemans and Aviva Tolkovsky

Chapter 20
Methods to monitor Chaperone-mediated autophagy
Ana Maria Cuervo and Susmita Kaushik

Chapter 21
Autophagy in response to Salmonella enterica serovar Typhimurium infection
Cheryl Birmingham and John Brumell

Chapter 22
Monitoring autophagy during Mycobacterium tuberculosis infection
Vojo Deretic

Chapter 23
Shigella, Listeria and Streptococcus induction of autophagy
Michinaga Ogawa,Yuko Yoshikawa, Ichiro Nakagawa,
Chihiro Sasakawa, and Trinad Chakraborty

Chapter 24
Measuring the impact of infection on autophagy in macrophages
Jean-Francois Dubuisson, Brenda Byrne and Michele Swanson

Researchers in biochemistry, cell and molecular biology, oncology, pharmacology