User:Jonathan Cline/Notebook/Ideal Microbe: Difference between revisions
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<td>Transformable | <td>Transformable | ||
<td>Accepts vectors easily, makes engineering more precise. | <td>Accepts vectors easily, makes engineering more precise. | ||
<td>MUST | |||
<tr> | |||
<td>12 hr per dish growth rate | |||
<td>At ideal temperature, complete dish growth of wild type host. | |||
<td>MUST | <td>MUST | ||
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<td>Should | <td>Should | ||
<td><td>ADP: Neg<br>Acido: Pos<br>Casei: Pos | <td><td>ADP: Neg<br>Acido: Pos<br>Casei: Pos | ||
<tr> | |||
<td>((Aerobic -or- Anerobic preference??)) | |||
<td> | |||
<td>(?) | |||
</table> | </table> | ||
Revision as of 20:38, 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 | Candidates | |
|---|---|---|---|---|
| Genome is 100% complete | Complete mapping means fewer unknowns, less trial-and-error, improved accuracy | MUST | ADP: Yes Acido: Yes Casei: Yes | |
| 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 | ADP: Yes Acido: Yes Casei: Yes | |
| Transformable | Accepts vectors easily, makes engineering more precise. | MUST | ||
| 12 hr per dish growth rate | At ideal temperature, complete dish growth of wild type host. | MUST | ||
| BioBrick Compatibility | Existing BB parts and protocols can be used | MUST | ADP: Yes Acido: ? Casei: ? | |
| 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 | ADP: No Acido: Yes Casei: Yes | |
| Doesn't smell bad | Indole production is limited or absent. | hopefully | ADP: No Acido: Maybe Casei: Maybe | |
| 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 | ADP: Neg Acido: Pos Casei: Pos | |
| ((Aerobic -or- Anerobic preference??)) | (?) |
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
