Archaea : methods and protocols
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書誌事項
Archaea : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2522）（Springer protocols）
Humana Press, c2022
- hbk.
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内容説明・目次
内容説明
This volume provides an overview of well-established methods optimized for diverse archaeal model organisms and is a source of protocols facilitating access to the molecular and cellular biology characterization of these fascinating organisms. Chapters are divided into five parts detailing available genetic tools, molecular and cellular biology methods, strategies to study the ecophysiology of archaea, and classroom protocol. Each main thematic part is also introduced by future-oriented and authoritative primers. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.
Authoritative and cutting-edge, Archaea: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.
目次
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
Catherine Harrison and Thorsten Allers
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 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
Finn Werner
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
17. Proteome turnover analysis in Haloferax volcanii by a heavy isotope multilabelling approach
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, Maria Ines. Gimenez, and Rosana Esther De Castro
21. Carotenoids from Haloarchaea: Extraction, fractionation and characterization
Maria Sandra Churio, Micaela Cerletti, and Rosana Esther De Castro
22. Metal nanoparticles biosynthesis using the halophilic archaeon Haloferax volcanii Mariana Ines Costa and Maria Ines Gimenez
23. Simplified enzymatic synthesis of 2-keto-3-deoxy-D-gluconate from D-gluconate using the gluconate dehydratase from Thermoproteus tenax
Svenja Hoefmann, Promise Aku Dziwornu, Thomas Klaus, Thomas Knura, Roland Wohlgemuth, Christopher Brasen, and Bettina Siebers
PART III: Cellular Biology of Archaea
24. Progress and Challenges in Archaeal Cellular Biology Analysis
Marleen van Wolferen and Sonja-Verena Albers
25. Methods to Analyze Motility in Eury- And Crenarchaea
Megha Patro, Marleen van Wolferen, Xing Ye, Sonja-Verena Albers, and Tessa E.F. Quax
26. Immersed Liquid Biofilm and Honeycomb Pattern Formations in Haloferax volcanii
Zuha Mutan, Heather Schiller, Stefan Schulze, and Mechthild Pohlschroder
27. Cost-effective and Versatile Analysis of Archaeal Surface Adhesion Under Shaking and Standing Conditions
Stefan Schulze, Heather Schiller, Zuha Mutan, Jordan Solomonic, Orkan Telhan, and Mechthild Pohlschroder
28. Cell Adhesion and Biofilm Formation Analysis
Debora Nercessian and Juan Pablo Busalmen
29. BrdU incorporation and labelling of nascent DNA to Investigate Archaeal Replication using super-resolution imaging
Roxane Lestini, Yoann Collien, Debora Olivier, Nicolas Olivier, and Hannu Myllykallio
30. Isolation, Purification, and Characterization of Membrane Vesicles from Haloarchaea
Joshua Mills and Susanne Erdmann
31. Archaeal Viruses: Production of Virus Particles and Vesicle-Like Viruses and Purification Using Asymmetrical Flow Field-Flow Fractionation
Katri Eskelin and Hanna M. Oksanen
Part IV: Environmental Biology
32. Progress and Challenges in Studying the Ecophysiology of Archaea
Panagiotis S. Adam, Till L. V. Bornemann, and Alexander J. Probst
33. Reconstruction of Archaeal Genomes Assembly from Short-Read Metagenomes
Till L. V. Bornemann, Panagiotis S. Adam, and Alexander J. Probst
Part V: Outreach protocol
34. Outreach: Accessible and Insightful Scientific Learning Experiences Using the Microorganism Haloferax volcanii
Heather Schiller, Criston Young, Stefan Schulze, and Mechthild Pohlschroder
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