Janet B. Matsen:Open Lab Questions

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(Open Questions)
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**The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does.
**The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does.
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*How does colony density affect colony size?  [[image:colony_size_varies_with_colony_density]]
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*How does colony density affect colony size?  [[image:colony_size_varies_with_colony_density|thumb|]]
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[[Image:Yellow_primers.jpg|thumb|normal oligos have a yellow color that is visible with large synthesis scales]]
**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.
**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 15:03, 14 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.
normal oligos have a yellow color that is visible with large synthesis scales
normal oligos have a yellow color that is visible with large synthesis scales
    • 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.
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