Peroxisomes: Methods and Protocols

ISBN-13: 9781071630471 / Angielski

Michael Schrader

Opis

This fully updated volume assembles a comprehensive collection of methods, techniques, and strategies to investigate the molecular and cellular biology of peroxisomes in different organisms. Peroxisome research is on the rise, as novel functions and proteins of this dynamic organelle are still being discovered through studies in model systems including humans, mice, flies, plants, fungi, and yeast, and this progress is reflected in the chapters included in this collection. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and up-to-date, Peroxisomes: Methods and Protocols, Second Edition serves as an ideal guide for researchers working on peroxisome- and organelle-based research questions.

Spis treści

1. Isolation of Mammalian Peroxisomes by Density Gradient Centrifugation

            Andreas Manner and Markus Islinger

 

2. Analysis of Yeast Peroxisomes via Spatial Proteomics

            Hirakjyoti Das, Alexandros Zografakis, Silke Oeljeklaus, and Bettina Warscheid

 

3. Isolation of Glycosomes from Trypanosoma brucei

            Chethan K. Krishna, Laura Franke, Ralf Erdmann, and Vishal C. Kalel

 

4. Immunolabeling for Detection of Endogenous and Overexpressed Peroxisomal Proteins in Mammalian Cells

            Tina A. Schrader, Ruth E. Carmichael, and Michael Schrader

 

5. Super-Resolution Imaging of Peroxisomal Proteins Using STED Nanoscopy

            Eline M.F. de Lange and Rifka Vlijm

 

6. Direct Stochastic Optical Reconstruction Microscopy (dSTORM) of Peroxisomes

            Teresa Klein, Markus Sauer, Süleyman Ergün, and Srikanth Karnati

 

7. Correlative Light- and Electron Microscopy in Peroxisome Research

            Rinse de Boer and Ida J. van der Klei

 

8. Ultrastructural Analysis and Quantification of Peroxisome-Organelle Contacts

            Christian Hacker, Tina A. Schrader, and Michael Schrader

 

9. Detection of Peroxisomal Proteins during Mycobacterial Infection

            Ananyaashree Behera, Mainak Biswas, Süleyman Ergün, Srikanth Karnati, and Avinash Sonawane

 

10. Proximity-Ligation Assay to Detect Peroxisome-Organelle Interaction

            Maki Kamoshita and Michael Schrader

 

11. Assay of Reactive Oxygen/Nitrogen Species (ROS/RNS) in Arabidopsis Peroxisomes through Fluorescent Protein Containing a Type 1-Peroxisomal Targeting Signal (PTS1)

            Francisco J. Corpas and José M. Palma

 

12. Identification of Peroxisome-Derived Hydrogen Peroxide-Sensitive Target Proteins Using a YAP1C-Based Genetic Probe

            Celien Lismont, Iulia Revenco, Cláudio F. Costa, Hongli Li, Mohamed A. F. Hussein, Paul P. Van Veldhoven, Rita Derua, and Marc Fransen

 

13. Assessment of the Peroxisomal Redox State in Living Cells Using NADPH- and NAD⁺/NADH-Specific Fluorescent Protein Sensors

            Cláudio F. Costa, Hongli Li, Mohamed A. F. Hussein, Yi Yang, Celien Lismont, and Marc Fransen

 

14. Live-Cell Imaging of Peroxisomal Calcium Levels and Dynamics

            Yelena Sargsyan and Sven Thoms

 

15. Analysis of Peroxisome Biogenesis by Phos-Tag SDS-PAGE

            Kanji Okumoto and Yukio Fujiki

 

16. Targeted Modifications of the Yeast Genome to Study Peroxisomes

            Lakhan Ekal and Ewald Hettema

 

17. Applying CRISPR-Cas9 Genome Editing to Study Genes Involved in Peroxisome Biogenesis or Peroxisomal Functions

            Serhii Chornyi, Janet Koster, and Hans R. Waterham

 

18. Generation of Reporter Cell Lines for Endogenous Expression Analysis of Peroxisomal Proteins

            Beatriz S.C. Silva, Tina A. Schrader, Michael Schrader, and Ruth E. Carmichael

 

19. Peroxisomes and Viruses: Overview on Current Knowledge and Experimental Approaches

            Vanessa Ferreira, Ana Rita Ferreira, and Daniela Ribeiro

 

20. Tools to Investigate the Peroxisome-Dependent Antiviral Response

            Bruno Ramos, Ana Rita Ferreira, and Daniela Ribeiro

 

21. Determining the Importance of Peroxisomal Proteins for Viral Infections in Cultured Mammalian Cells

            Mariana Marques, Ana Rita Ferreira, and Daniela Ribeiro

 

22. Characterization of Yeast Peroxisomes: Enrichment of Peroxisomal Fractions and Analysis of b-Oxidation Activity

            Carlo van Roermund and Ewald Hettema

 

23. A Cell-Free In Vitro Import System for Peroxisomal Proteins Containing a Type 2 Targeting Signal (PTS2)

            Maria J. Ferreira, Tony A. Rodrigues, Ana G. Pedrosa, Tânia Francisco, and Jorge E. Azevedo

 

24. Assessing Peroxisomal Protein Interaction by Immunoprecipitation

            Suzan Kors and Michael Schrader

 

25. Purification of a Recombinant Human PEX1/PEX6 AAA+ ATPase Complex from HEK293TT Cells

            Saroj Pandey and Gabriele Dodt

 

26. Affinity Purification of Soluble and Membrane-Bound Protein Complexes by a FlpIn Strategy

            Rebecca Peschel, Nadine Schmidt, Wolfgang Schliebs, and Ralf Erdmann

 

27. Utilization of Nonstop mRNA to Assess Ribosome-Associated Nascent Polypeptide Chains in Early Topogenesis of Peroxisomal Proteins

            Markus Rudowitz, Luis Daniel Cruz Zaragoza, Wolfgang Girzalsky, and Ralf Erdmann

 

28. Computational Evaluation of Peroxisomal Targeting Signals in Metazoa

            Markus Kunze

 

29. Computational Approaches for Peroxisomal Protein Localization

            Marco Anteghini and Vitor A.P. Martins dos Santos

 

30. Estimating the Interaction Strength between PTS1-Peptides and Their Receptor PEX5 in Living Cells Using Flow-Cytometer-Based FRET (flowFRET) Measurements

            Bernhard Hochreiter, Johannes A. Schmid, Johannes Berger, and Markus Kunze

 

31. Using the Super Folder GFP (sfGFP) System to Study Plant Peroxisomal Protein Import

            Yousef Al-Hajaya, Chi-Chuan Lin, and Alison Baker

 

32. Biochemical Fractionation of Trypanosomes for the Analysis of Glycosomal Protein Import Defects

            Shih-En Chou, Vishal C. Kalel, and Ralf Erdmann

 

33. Manipulation and Visualization of Peroxisomes in Drosophila

            Kazuki Ueda, Julie Haskins, and Andrew James Simmonds

 

34. Mouse Models to Study Peroxisomal Functions and Disorders: Overview, Caveats, and Recommendations

            Sai Kocherlakota, Daniëlle Swinkels, Paul P. Van Veldhoven, and Myriam Baes