Registry use workshop videos
The following website contains really good videos that teach how to efficiently use registry. It could be useful to explore these videos before starting the extensive search for coding sequences. It provides answers to:
- 4 searches to choos from - which one should I use?
- how to add parts to registry?
- what are the requirements of judging parts?
- what are the safety concerns?
Ideally, we would use B. subtilis because it is a well characterised gram positive bacterium that does quorum sensing using small peptides as autoinducers. These small peptides could be produced as a result of cleavage of a membrane-anchored protein by a protease from the parasite which we want to detect.
However, there are issues regarding the extracellular proteases produced by gram positive bacteria. These could interfere with the system and could result in false positives.
Surpulus information on B. Subtilis chassis Subti-Wiki
E.coli was also considered as a possible option. Despite the G-ve outer membraine, there are strains that have been made more permeable through knockout of Lipid A biosynthesis in lipolysaccharides (lpxA,lpxD []). There are also proteins that can disrupt membraraines when they are inserted in them, thus making them more permeable. These chages in permeability are likely due to transient ruptures of outer membraine and so unlikely to make a very responsive or robust detecton organism [].