Janet B. Matsen:Open Lab Questions

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(Open Questions)
(Open Questions)
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==Open Questions==
==Open Questions==
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*Is it important to let chemically competent cells sit on ice 20-30 min after adding DNA?  What does this do?
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**[http://partsregistry.org/Help:Transformation_Protocol| Example protocol] showing ice incubation
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*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?   
*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.
**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.
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*How do I decide whether to gel purify after digestions (before ligations)? 
 
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**The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does.
 
*How does colony density affect colony size?  [[image:colony_size_varies_with_colony_density.jpg|thumb|colony size varies with colony density]]
*How does colony density affect colony size?  [[image:colony_size_varies_with_colony_density.jpg|thumb|colony size varies with colony density]]

Revision as of 13:49, 14 July 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

  • Is it important to let chemically competent cells sit on ice 20-30 min after adding DNA? What does this do?
  • 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 does colony density affect colony size?
    colony size varies with colony density
    colony size varies with colony density
    • 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.
  • Why do apples make people burp? (posted 5/23/2012)
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