Archaea: Methods and Protocols

1. Archaea: a goldmine for molecular biologists and evolutionists

Patrick Forterre

Part I: Genetic manipulation of Archaea

2. Progress and challenges in archaeal genetic manipulation

3. Genetic manipulation of Haloferax species

Ambika Dattani, Catherine Harrison, and Thorsten Allers

4. CRISPR interference as a tool to Repress Gene Expression in Haloferax volcanii

Thandi S. Schwarz, Sandra S. Schreiber, and Anita Marchfelder

5. Transformation Techniques for the Anaerobic Hyperthermophile Thermococcus kodakarensis

Geraldy L. S. Liman, Meghan E. Stettler and Thomas J. Santangelo

6. Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea

Johanna Thomsen, Katrin Weidenbach, William W. Metcalf and Ruth A. Schmitz

7. An interdomain conjugation protocol for plasmid-DNA transfer into Methanothermobacter thermautotrophicus Δ
H

Christian Fink, Largus T. Angenen, and Bastian Molitor

8. Methods for Markerless Gene Deletion and Plasmid-Based Expression in Sulfolobus acidocaldarius

Xing Ye, Alejandra Recalde, Sonja-Verena Albers and Marleen van Wolferen

9. A Rapid Targeted Gene Inactivation Approach in Sulfolobus islandicus

Changyi Zhang, Serina M. Taluja, Emily N. Hallett, and Rachel J. Whitaker

10. Transposon Insertion Mutagenesis in hyperthermophilic crenarchaeon Sulfolobus islandicus

Changyi Zhang and Rachel J. Whitaker

11. Reprogramming CRISPR-mediated RNA interference for silencing of essential genes in Sulfolobales

Erika Wimmer, Isabelle Anna Zink and Christa Schleper

Part II: Molecular Biology of Archaea

12. Progress and challenges in archaeal molecular biology

13. ChIP-seq Occupancy Mapping of the Archaeal Transcription Machinery

Fabian Blombach, Kathy L. Smollett, and Finn Werner

14. Conversion of ribosome-protected mRNA to DNA and deep sequencing for ribosome profiling in Haloferax volcanii

Diego Rivera Gelsinger, Emma Dallon, and Jocelyne DiRuggiero

15. Small RNA-sequencing library preparation for the halophilic archaeon Haloferax volcanii

Diego Rivera Gelsinger and Jocelyne DiRuggiero

16. Quantitative Mass Spectrometry by SILAC in Haloferax volcanii - Ricardo L. Couto-Rodriguez, Daniel Gal, Lana J. McMillan, Jin Koh, Sixue Chen, and Julie A. Maupin-Furlow

Roberto A. Paggi, Stefan P. Albaum, Ansgar Poetsch, and Micaela Cerletti

18. Proteomic sample preparation and data analysis in line with the Archaeal Proteome

Stefan Schulze and Mechthild Pohlschroder.

19. In vivo protein crosslinking and co-immunoprecipitation in Haloferax volcanii

Roberto A. Paggi, Rosana E. De Castro and Micaela Cerletti

20. Proteolytic activity assays in haloarchaea

Roberto Alejandro Paggi, Mara Ins. Gimnez, and Rosana Esther De Castro

21. Carotenoids from Haloarchaea: Extraction, fractionation and characterization

Mara Sandra Churio, Micaela Cerletti, and Rosana Esther De Castro

22. Metal nanoparticles biosynthesis using the halophilic archaeon Haloferax volcanii Mariana Ins Costa and Mara Ins Gimnez

23. Simplified enzymatic synthesis of 2-keto-3-deoxy-D-gluconate from D-glucon