Bacterial Amyloids: Methods and Protocols

ISBN-13: 9781071625286 / Angielski / Twarda / 2022

Arluison, Véronique

Opis

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.

Spis treści

1. Study of Amyloid Fibers Using Atomic Force Microscopy

            Daniel G. Cava and Marisela Vélez

 

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

            Antoine Cossa and Sylvain Trépout

 

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

            Esra Yuca and Urartu Özgür Şafak Şeker

 

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, Véronique 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 Vélez

 

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 Véronique Arluison

 

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

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

 

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

            Krzysztof Kubiak, Lidia Gaffke, Karolina Pierzynowska, Zuzanna Cyske, Łukasz Grabowski, Katarzyna Kosznik-Kwaśnicka, Weronika Jaroszewicz, Alicja Węgrzyn, and Grzegorz Węgrzyn

 

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, Véronique 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 Véronique Arluison

 

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

            Josefina Marin, Paulina Aguilera, Rosalba Lagos, and Andrés 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 Andrés 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-François Berret

 

20. Probing Amyloids-DNA Interaction with Nanofluidics

            Rajib Basak, Indresh Yadav, Véronique 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, Véronique Arluison, Ana J. Pérez-Berná, Sylvain Trépout, and Eva Pereiro