Janet B. Matsen:Open Lab Questions

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(Open Questions)
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(For biochemical assays, are sodium phosphate and potassium phosphate buffers equivalent?)
 
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==Open Questions==
==Open Questions==
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=== Why does the DNA clump when you run overloaded agarose gels? (2012/10/02) ===
 
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[[image:janet purification gel.jpg|thumb|center|include small not-overloaded lanes when running purification gels]]
 
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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? (7/13/2012) ===
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=== For biochemical assays, are sodium phosphate and potassium phosphate buffers equivalent?   2013/05/24===
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**[http://partsregistry.org/Help:Transformation_Protocol| Example protocol] showing ice incubation
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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]]
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** Mila weighing in: "This waiting period is part of the protocol. Not sure anyone knows what exactly happens but likely DNA just needs this time to land onto a cell. Longer time does not do much for the efficiency of the transformation. However the efficiency of the cells is determined by something upstream, by how the cells were grown and chemically treated. This is the most important part of the transformation process.."
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** [http://www.madsci.org/posts/archives/oct2000/971308650.Mi.r.html online]: ""After making the cells leaky, the DNA is added to the cells and allowed to sit on ice for 10-20 minutes. This allows the DNA to get past the cell membrane, and gives enough time for lots of cells to recieve the DNA and to make certain all of the DNA gets in the cells. After this, in order to make the cells keep the DNA, and to make certain they survive, (Being leaky is not a good thing) the cells are heat shocked for several seconds to 'turn on' (induce) heat shock genes which aid in survival and recovery. After that, the cells are incubated to start growing and plated on selective media to recover those cells that actually recieved the DNA.
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** It is simple to do an experiment where you transform some without waiting and some after waiting, of course.
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===What causes an overloaded colony PCR reaction to fail? ===  
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=== What is the difference between Bacto yeast extract & Difco yeast extract? ===  
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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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*How does plasmid copy number get affected by oxygen availability? Cellular media?   
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=== Why does the DNA clump when you run overloaded agarose gels? (2012/10/02) ===
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**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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[[image:janet purification gel.jpg|thumb|center|polka-dot DNA in a 0.7% agarose gel]]
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===Is it important to let chemically competent cells sit on ice 20-30 min after adding DNAWhat does this do? (7/13/2012) ===
 +
*[http://partsregistry.org/Help:Transformation_Protocol| Example protocol] showing ice incubation
 +
* Mila weighing in: "This waiting period is part of the protocol. Not sure anyone knows what exactly happens but likely DNA just needs this time to land onto a cell. Longer time does not do much for the efficiency of the transformation. However the efficiency of the cells is determined by something upstream, by how the cells were grown and chemically treated. This is the most important part of the transformation process.."
 +
* [http://www.madsci.org/posts/archives/oct2000/971308650.Mi.r.html online]: ""After making the cells leaky, the DNA is added to the cells and allowed to sit on ice for 10-20 minutes. This allows the DNA to get past the cell membrane, and gives enough time for lots of cells to recieve the DNA and to make certain all of the DNA gets in the cells. After this, in order to make the cells keep the DNA, and to make certain they survive, (Being leaky is not a good thing) the cells are heat shocked for several seconds to 'turn on' (induce) heat shock genes which aid in survival and recovery. After that, the cells are incubated to start growing and plated on selective media to recover those cells that actually recieved the DNA.
 +
* It is simple to do an experiment where you transform some without waiting and some after waiting, of course.
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*How does colony density affect colony size? [[image:colony_size_varies_with_colony_density.jpg|thumb|center|colony size varies with colony density]]
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===How does oxygen limitation cause lower plasmid copy number? What about the growth medium?  ===
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**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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*TB gives ''way'' higher yield than LB
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*Growing cultures with liquid:air volumes higher than 1:5 is very bad for plasmid yield.
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*Why do apples make people burp? (posted 5/23/2012)
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===Why do apples make people burp? ===
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* (posted 5/23/2012)
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** I have been wondering this for years.

Current revision

Return to Janet

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!

Contents

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

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?"

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

polka-dot DNA in a 0.7% agarose gel
polka-dot DNA in a 0.7% agarose gel

Is it important to let chemically competent cells sit on ice 20-30 min after adding DNA? What does this do? (7/13/2012)

  • Example protocol showing ice incubation
  • Mila weighing in: "This waiting period is part of the protocol. Not sure anyone knows what exactly happens but likely DNA just needs this time to land onto a cell. Longer time does not do much for the efficiency of the transformation. However the efficiency of the cells is determined by something upstream, by how the cells were grown and chemically treated. This is the most important part of the transformation process.."
  • online: ""After making the cells leaky, the DNA is added to the cells and allowed to sit on ice for 10-20 minutes. This allows the DNA to get past the cell membrane, and gives enough time for lots of cells to recieve the DNA and to make certain all of the DNA gets in the cells. After this, in order to make the cells keep the DNA, and to make certain they survive, (Being leaky is not a good thing) the cells are heat shocked for several seconds to 'turn on' (induce) heat shock genes which aid in survival and recovery. After that, the cells are incubated to start growing and plated on selective media to recover those cells that actually recieved the DNA.
  • It is simple to do an experiment where you transform some without waiting and some after waiting, of course.

How does oxygen limitation cause lower plasmid copy number? What about the growth medium?

  • TB gives way higher yield than LB
  • Growing cultures with liquid:air volumes higher than 1:5 is very bad for plasmid yield.

Why do apples make people burp?

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