Janet B. Matsen:Open Lab Questions: Difference between revisions
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==Open Questions== | ==Open Questions== | ||
*What causes an overloaded colony PCR reaction to fail? | *What causes an overloaded colony PCR reaction to fail? | ||
*How does plasmid copy number get affected by oxygen availability? Cellular media? I have noticed that LB often gives me orders of magnitude lower plasmid yields and that growing cultures with liquid:air volumes higher than 1:5 is not good. | |||
*How do I decide whether to gel purify after digestions (before ligations)? The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does. | *How does plasmid copy number get affected by oxygen availability? Cellular media? | ||
**I have noticed that LB often gives me orders of magnitude lower plasmid yields and that growing cultures with liquid:air volumes higher than 1:5 is not good. | |||
*How do I decide whether to gel purify after digestions (before ligations)? | |||
**The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does. | |||
*How does colony density affect colony size? | |||
**I observe that when there is a large number of colonies per area on an agar plate, that the colonies are smaller. I have thought about the possibility of diffusion-limited arrival of nutrients, however, one would expect to see larger colonies on the outside of the cluster if this is the case. | |||
Revision as of 12:08, 11 March 2012
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These questions are "open" to me, not necessarily the scientific community. If you have insights or can point me toward references relevant to them, please do!
Open Questions
- What causes an overloaded colony PCR reaction to fail?
- How does plasmid copy number get affected by oxygen availability? Cellular media?
- I have noticed that LB often gives me orders of magnitude lower plasmid yields and that growing cultures with liquid:air volumes higher than 1:5 is not good.
- How do I decide whether to gel purify after digestions (before ligations)?
- The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does.
- How does colony density affect colony size?
- I observe that when there is a large number of colonies per area on an agar plate, that the colonies are smaller. I have thought about the possibility of diffusion-limited arrival of nutrients, however, one would expect to see larger colonies on the outside of the cluster if this is the case.
