Main description:

This detailed volume introduces different methods to assess the structure and folding of bacterial amyloids and analyze their functions, either in vitro or in vivo. Despite their initial association with neurodegenerative diseases, there is now increasing evidence of alternative roles for amyloids, with beneficial aspects for cells. In particular, prokaryotes use amyloids as functional assemblies, where they are key players in the cell's physiology. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and up-to-date, Bacterial Amyloids: Methods and Protocols is an ideal guide for experts and novices alike to further explore these crucial protein assemblies.

Contents:

1. Study of Amyloid Fibers Using Atomic Force Microscopy

Daniel G. Cava and Marisela Velez

2. Cryo-Electron Microscopy to Analyze the Structure of Bacterial Amyloids In Vitro

Antoine Cossa and Sylvain Trepout

3. Monitoring Molecular Assembly of Biofilms Using Quartz Crystal Microbalance with Dissipation (QCM-D)

Esra Yuca and Urartu OEzgur Safak Seker

4. Measuring the Size and Spontaneous Fluctuations of Amyloid Aggregates with Fluorescence Correlation Spectroscopy

Vicky Vishvakarma and Sudipta Maiti

5. Determining the Stoichiometry of Amyloid Oligomers by Single Molecule Photobleaching

Arpan Dey and Sudipta Maiti

6. Structural Information on Bacterial Amyloid and Amyloid-DNA Complex Obtained by Small-Angle Neutron/X-Ray Scattering

Tatsuhito Matsuo, Veronique Arluison, Frank Wien, and Judith Peters

7. Fiber Diffraction and Small-Angle Scattering for Structural Investigation of Bacterial Amyloids

Tatsuhito Matsuo and Judith Peters

8. Supported Lipid Bilayers (SLBs) to Study Amyloid-Lipid Membrane Interactions with Atomic Force Microscopy

Daniel G. Cava and Marisela Velez

9. Characterization of Bacterial Amyloids by Nano-Infrared Spectroscopy

Vincent Raussens and Jehan Waeytens

10. High Throughput Screening of Heterologous Functional Amyloids Using Escherichia coli

Elizabeth A. Yates, Luis A. Estrella, and Christopher R. So

11. Evaluation of Amyloid Inhibitor Efficiency to Block Bacterial Survival

Florent Busi, Florian Turbant, Jehan Waeytens, Omar El Hamoui, Frank Wien, and Veronique Arluison

12. Anti-Amyloid Drug Screening Methods Using Bacterial Inclusion Bodies

Ana B. Caballero, Patrick Gamez, Raimon Sabate, and Alba Espargaro

13. Determination of Effects and Mechanisms of Action of Bacterial Amyloids on Antibiotic Resistance

Krzysztof Kubiak, Lidia Gaffke, Karolina Pierzynowska, Zuzanna Cyske, Lukasz Grabowski, Katarzyna Kosznik-Kwasnicka, Weronika Jaroszewicz, Alicja Wegrzyn, and Grzegorz Wegrzyn

14. Design and Testing of Synthetic Catalytic Amyloids Based on the Active Site of Enzymes

Claudio Castillo-Caceres, Eva Duran-Meza, and Rodrigo Diaz-Espinoza

15. Analysis of Bacterial Amyloid Interaction with Lipidic Membrane by Orientated Circular Dichroism and Infrared Spectroscopies

Jehan Waeytens, Florian Turbant, Veronique Arluison, Vincent Raussens, and Frank Wien

16. Direct, Rapid, and Simple Evaluation of the Expression and Conformation of Beta-Amyloid in Bacterial Cells by FTIR Spectroscopy

Christophe Sandt, David Partouche, and Veronique Arluison

17. Assessment of Intracellular Amyloid Formation in Fixed and Live Bacteria Using Fluorescence Microscopy

Josefina Marin, Paulina Aguilera, Rosalba Lagos, and Andres Marcoleta

18. Identification of Aggregation-Prone and Gatekeeper Residues in Bacterial Amyloids Using Site-Directed Mutagenesis and Flow Cytometry

Paulina Aguilera, Josefina Marin, Rosalba Lagos, and Andres Marcoleta

19. Probing DNA-Amyloid Interaction and Gel Formation by Active Magnetic Wire Microrheology

Milad Radiom, Evdokia K. Oikonomou, Arnaud Grados, Mathieu Receveur, and Jean-Francois Berret

20. Probing Amyloids-DNA Interaction with Nanofluidics

Rajib Basak, Indresh Yadav, Veronique Arluison, Jeroen A. van Kan, and Johan R.C. van der Maarel

21. Evaluation of the Role of Bacterial Amyloid on Nucleoid Structure Using Cryo Soft X-Ray Tomography

Antoine Cossa, Frank Wien, Florian Turbant, Tadeusz Kaczorowski, Grzegorz Wegrzyn, Veronique Arluison, Ana J. Perez-Berna, Sylvain Trepout, and Eva Pereiro