Protocols

The Society of Archaeal Biology plays a central role in consolidating efforts to construct a comprehensive informational resource for archaeal research. Our database of protocols is meant to serve as a community-wide repository, offering researchers a platform to access and explore a diverse array of methodological guidelines to advance the understanding of archaeal biology.

We encourage all researchers to contribute by submitting their protocols, fostering collaboration and enriching the collective knowledge base. By sharing expertise and innovative techniques, you'd be directly contributing to the archaeal research community, propelling the field forward, and uncovering the mysteries of these often-overlooked microorganisms.

You can filter the database by phylogeny or by method. As the database grows, we will look to build out a sophisticated search function.

Recent protocols

20240315--dulermo--genomic-dna-extraction-of-pure-thermococcales-cultures.pdf

Genomic DNA extraction of pure Thermococcales cultures

This protocol is adapted from a lab protocol made by Axel Thiel. The goal of this protocol was to simplify it to faster obtain genomic DNA from cell cultures. This protocol can be used for Thermococcales but could be used for other archaea. The protocol is adapted for small culture volume (1 mL to 20 mL) of cells in the stationary phase of growth; for example, 1mL of culture is enough to obtain genomic DNA for PCR whereas 20 mL is necessary to send sufficient genomic DNA for sequencing.

Archaeal Viruses: Production of Virus Particles and Vesicle-like Viruses and Purification Using Asymmetrical Flow Field-Flow Fractionation

Asymmetrical flow field-flow fractionation (AF4) is a separation method based on hydrodynamic size of the sample components. It can separate a broad size range of components (~103 to 109 Da; particle diameter from ~1 nm to ~1 μm), but is especially well suited for high molecular weight samples such as virus-sized particles and extracellular vesicles. Separation takes place in an open channel where the flows control sample elution. Separation does not involve stationary phase, allowing gentle separation and good recoveries.

Isolation, Purification, and Characterization of Membrane Vesicles from Haloarchaea

Membrane vesicles (MVs), also described as extracellular vesicles (EVs), exosomes, or outer membrane vesicles (OMVs), are nano-sized (10–300 nm) spherical, membrane-bound structures deriving from the cell envelope. MVs have been studied extensively in both eukaryotic and prokaryotic systems, revealing a plethora of unique functions including cell-to-cell communication and protection of the cell. They are able to encapsulate specific cargos from nucleic acids to proteins, thereby concentrating cargo and providing protection from the extracellular environment.

BrdU Incorporation and Labeling of Nascent DNA to Investigate Archaeal Replication Using Super-Resolution Imaging

The labeling and specific detection of nascent DNA by the incorporation of thymidine analogs provide crucial information about DNA replication dynamics without requiring the intracellular expression of fluorescent proteins. After cell fixation and permeabilization, specific detection of thymidine analogs by antibodies can be performed using super-resolution imaging techniques.