Table of Contents

1. Mitochondrial Dysfunction in Mitochondrial Medicine: Current Limitations, Pitfalls, and Tomorrow

Naig Gueguen, Guy Lenaers, Pascal Reynier, Volkmar Weissig, and Marvin Edeas

2. Preparation of 'Functional' Mitochondria - A Challenging Business

Stefan Lehr, Sonja Hartwig, and Jorg Kotzka

3. Isolation and Quality Control of Functional Mitochondria

Sonja Hartwig, Jorg Kotzka, and Stefan Lehr

4. Purification of Functional Platelet Mitochondria Using a Discontinuous Percoll Gradient

Jacob L. Leger, Nicolas Pichaud, and Luc H. Boudreau

5. Mechanical Permeabilization as a New Method for Assessment of Mitochondrial Function in Insect Tissues

Alessandro Gaviraghi, Yan Aveiro, Stephanie S. Carvalho, Rodiesley S. Rosa, Matheus P. Oliveira, and Marcus F. Oliveira

6. Analysis of Mitochondrial Retrograde Signaling In Yeast Model Systems

Nicoletta Guaragnella, Masa Zdralevic, Zdena Palkova, and Sergio Giannattasio

7. Native Gel Electrophoresis and Immunoblotting to Analyze Electron Transport Chain Complexes

Gisela Beutner and George A. Porter, Jr.

8. Measuring Mitochondrial Hydrogen Peroxide Levels and Glutathione Redox Equilibrium in Drosophila Neuron Subtypes Using Redox-Sensitive Fluorophores and 3D Imaging

Lori M. Buhlman, Petros P. Keoseyan, Kathryn Houlihan, and Amber N. Juba

9. Assessment of Mitochondrial Cell Metabolism By Respiratory Chain Electron Flow Assays

Flavia Radogna, Deborah Gerard, Mario Dicato, and Marc Diederich

10. Whole-Cell and Mitochondrial dNTP Pool Quantification from Cells and Tissues

Juan C. Landoni, Liya Wang, and Anu Suomalainen

11. Single Particle-Tracking Method in Fluorescence Microscopy to Monitor Bioenergetic Responses Of Individual Mitochondria

Camille Colin, Emmanuel Suraniti, Emma Abell, Audrey Semont, Neso Sojic, Philippe Diolez, and Stephane Arbault

12. Investigation of Mitochondrial ADP-ribosylation via Immunofluorescence

Ann-Katrin Hopp and Michael O. Hottiger

13. Assessment of Mitochondrial Ca²⁺ Uptake

Andras T. Deak, Claire Jean-Quartier, Alexander I. Bondarenko, Lukas N. Groschner, Roland Malli, Wolfgang F. Graier, and Markus Waldeck-Weiermair

14. Assessment of Mitochondrial Membrane Potential and NADH Redox State in Acute Brain Slices

Andrey Y. Vinokurov, Viktor V. Dremin, Gennadii A. Piavchenko, Olga A. Stelmashchuk, Plamena R. Angelova, and Andrey Y. Abramov

15. Evaluation of Mitochondria Content and Function in Live Cells by Multi-color Flow Cytometric Analysis

Hsiu-Han Fan, Tsung-Lin Tsai, Ivan L. Dzhagalov, and Chia-Lin Hsu

16. Analysis of Mitochondrial Dysfunction during Cell Death

Vladimir Gogvadze and Boris Zhivotovsky

17. Modified Blue-Native Gel Approach for Analysis of Respiratory Super-Complexes

Sergiy M. Nadtochiy, Megan Ngai, and Paul S. Brookes

18. Patch-Clamp Recording of the Activity of Ion Channels in the Inner Mitochondrial Membrane

Piotr Bednarczyk, Rafal P. Kampa, Shur Kucman, Aleksandra Sek, Agnieszka Walewska, and Piotr Koprowski

19. Assessment of Mitochondrial Protein Glutathionylation as Signaling for CO Pathway

Ana S. Almeida, Claudia Figueiredo-Pereira, and Helena L.A. Vieira

20. 3D Optical Cryo-Imaging Method: A Novel Approach To Quantify Renal Mitochondrial Bioenergetics Dysfunction

Shima Mehrvar, Amadou K. S. Camara, and Mahsa Ranji

21. Simultaneous Quantification of Mitochondrial ATP and ROS Production Using ATP Energy Clamp Methodology

Liping Yu, Brian D. Fink, and William I. Sivitz

22. High-Throughput Image Analysis of Lipid-Droplet-Bound Mitochondria

Nathanael Miller, Dane Wolf, Nour Alsabeeh, Kiana Mahdaviani, Mayuko Segawa, Marc Liesa, and Orian Shirihai

23. Cell Energy Budget Platform for Multi-Parametric Assessment of Cell and Tissue Metabolism

Dmitri B. Papkovsky and Alexander V. Zhdanov

24. Fluorescence-based Assay for Measuring OMA1 Activity

Julia Tobacyk and Lee Ann MacMillan-Crow

25. Studying Mitochondrial Network Formation by in vivo and in vitro Reconstitution Assay

Wanqing Du, Xiangjun Di, and Qian Peter Su

26. Extraction of Functional Mitochondria Based on the Membrane Stiffness

Md Habibur Rahman, Qinru Xiao, Shirui Zhao, An-Chi Wei, and Yi-Ping Ho

27. A Protocol for Untargeted Metabolomic Analysis: From Sample Preparation to Data Processing

Amanda L. Souza and Gary J. Patti

28. A Method for Analysis of Nitrotyrosine-Containing Proteins by Immunoblotting Coupled With Mass Spectrometry

Matej Kohutiar and Adam Eckhardt

29. In vivo Visualization And Quantification of Mitochondrial Morphology in C. elegans

R. de Boer, R. L. Smith, W. H. De Vos, E. M. M. Manders, andH. van der Spek

30. Assessing Impact of Platinum Complexes on Mitochondrial Functions

Suxing Jin and Xiaoyong Wang

31. In-silico Modeling of the Mitochondrial Pumping Complexes with Markov State Models

Roger Springett

32. Monitoring the Mitochondrial Presequence Import Pathway in Living Mammalian Cells with a New Molecular Biosensor

Maxime Jacoupy, Emeline Hamon-Keromen, and Olga Corti