User:Jonathan Cline/Notebook/Ideal Microbe: Difference between revisions
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<th>Details | <th>Details | ||
<th>Requirement | <th>Requirement | ||
<tr> | |||
<td>Genome is 100% complete | |||
<td>Complete mapping means fewer unknowns, less trial-and-error | |||
<td>MUST | |||
<tr> | |||
<td>Pathway description is over 50% complete | |||
<td>Hard to quantify; though, "a lot is known" about the internals of the host. | |||
<td>MUST | |||
<tr> | <tr> | ||
<td>Non-pathogenic | <td>Non-pathogenic |
Revision as of 20:25, 9 November 2008
Please edit this page to add ideas / thoughts / corrections
- Working in a garage-lab or skunkworks environment imposes some restrictions on choice of organisms to engineer: expensive equipment/chemicals may be unavailable, protocols may need to be simplified to reduce man-hours, etc.
- There are many choices of host organisms for engineering, each having different strengths and weaknesses.
- Host organisms can be genetically improved for fitness, if a concise set of requirements are made, for engineering the organism.
- A great example is the "eau d'e coli" project from iGEM which removed (and subsequently enhanced!) the non-desirable smelly feature of the common BioBrick host.
Requirements for The Ideal Microbe
- "Must" means that the requirement must be met for proper acceptance.
- "Should" means that the requirement should attempt to be met, however operation is not jeopardized by failure to meet the requirement.
- "Hopefully" means that the requirement isn't necessary for operation, however is nice to have.
Feature | Details | Requirement |
---|---|---|
Genome is 100% complete | Complete mapping means fewer unknowns, less trial-and-error | MUST |
Pathway description is over 50% complete | Hard to quantify; though, "a lot is known" about the internals of the host. | MUST |
Non-pathogenic | Cloning and growth is not harmful to people. | MUST |
Transformable | Accepts vectors easily, makes engineering more precise. | MUST |
BioBrick Compatibility | Existing BB parts and protocols can be used | MUST |
Shelf life at least 1 year at 4C | Allows easy archival and low cost lab setup | MUST |
Low mutation rate | Lower mutation rate makes engineering more precise. | Should |
Room Temperature reproduction | Allows low cost lab setup | Should |
Electroporation | Allows modification using alternative method | hopefully |
Cells can be freeze-dried | Allows simple shipment method and low cost lab setup | hopefully |
Public perceives host as "Friendly" | Hearing the name makes people smile rather than frown. | Should |
Doesn't smell bad | Indole production is limited or absent. | hopefully |
Looks translucent or opaque (or green?) | Doesn't invoke "yuck" when seen. | hopefully |
Gram-((negative or positive??)) | higher metabolic compatibility with existing parts, ??other?? | Should |
Suggested Microbes so far
- Acinetobacter sp. ADP1
- Lactobacillus acidophilus
- Lactobacillus casei
References
[Full Text] Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering. Nucleic Acids Research 2004 32(19):5780-5790; doi:10.1093/nar/gkh881