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? 


*How does plasmid copy number get affected by oxygen availability?  Cellular media?   
=== For biochemical assays, are sodium phosphate and potassium phosphate buffers equivalent?   2013/05/24===  
**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.
Are there reasons why it would matter whether sodium or potassium is in solution?  I tried to research this question online and haven't found anything.  I did learn [[Lidstrom:Buffers#General_Info|this]]


*How do I decide whether to gel purify after digestions (before ligations)? 
=== Why does the DNA clump when you run overloaded agarose gels? (2012/10/02) ===
**The BioBrick/Ginkgo manual doesn't instruct you to. Besty always does.
[[image:janet purification gel.jpg|thumb|center|polka-dot DNA in a 0.7% agarose gel]]


*How does colony density affect colony size?  [[image:colony_size_varies_with_colony_density.jpg|thumb|colony size varies with colony density]]
===Why do apples make people burp? ===
**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.
* (posted 5/23/2012)
** I have been wondering this for years.
 
== Old/Now uninteresting ==
=== What is the difference between Bacto yeast extract & Difco yeast extract? ===
I e-mailed BD on 2012/03/01 and asked "What is the difference between Difco Yeast Extract and Bacto Yeast Extract?  I only see Difco Yeast Extract UF in this: http://www.bd.com/ds/technicalCenter/misc/br_3_2547.pdf so it is hard to compare.  I have an old bottle of Difco Yeast extract that is not UF and I wonder if it can be substituted for Bacto Yeast extract.  It is also old (1999) -- does it go bad?"

Latest revision as of 15:23, 23 May 2015

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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

For biochemical assays, are sodium phosphate and potassium phosphate buffers equivalent? 2013/05/24

Are there reasons why it would matter whether sodium or potassium is in solution? I tried to research this question online and haven't found anything. I did learn this

Why does the DNA clump when you run overloaded agarose gels? (2012/10/02)

polka-dot DNA in a 0.7% agarose gel

Why do apples make people burp?

  • (posted 5/23/2012)
    • I have been wondering this for years.

Old/Now uninteresting

What is the difference between Bacto yeast extract & Difco yeast extract?

I e-mailed BD on 2012/03/01 and asked "What is the difference between Difco Yeast Extract and Bacto Yeast Extract? I only see Difco Yeast Extract UF in this: http://www.bd.com/ds/technicalCenter/misc/br_3_2547.pdf so it is hard to compare. I have an old bottle of Difco Yeast extract that is not UF and I wonder if it can be substituted for Bacto Yeast extract. It is also old (1999) -- does it go bad?"

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