Talk:CH391L/S13/Refactoring Operons

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:29, 1 April 2013 (EDT)''': Did pH or carbonation pose any problems when using soda as a growth medium?
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:29, 1 April 2013 (EDT)''': Did pH or carbonation pose any problems when using soda as a growth medium?
 +
**'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': Gabe, they diluted the soda into a buffered medium, so there wasn't a significant change in the pH of the growth medium. The carbonation did not seem to pose a problem either.
**'''[[User:Neil R Gottel|Neil R Gottel]] 17:50, 3 April 2013 (EDT)''':Don't know about those, but some of the energy drinks didn't work because of the other weird things they put in there (I believe 5 hour energy didn't work, but Monster was fine.
**'''[[User:Neil R Gottel|Neil R Gottel]] 17:50, 3 April 2013 (EDT)''':Don't know about those, but some of the energy drinks didn't work because of the other weird things they put in there (I believe 5 hour energy didn't work, but Monster was fine.
 +
***'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': Is this a sign that we should avoid 5 hour energy?
***'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 18:12, 4 April 2013 (EDT)''':Is it possible that the 5 hour energy didn't work because of the intense concentration of caffeine in such a small bottle...? Maybe there were just too many methylxanthines for the cell to handle?
***'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 18:12, 4 April 2013 (EDT)''':Is it possible that the 5 hour energy didn't work because of the intense concentration of caffeine in such a small bottle...? Maybe there were just too many methylxanthines for the cell to handle?
*'''[[User:Neil R Gottel|Neil R Gottel]] 17:50, 3 April 2013 (EDT)''':This refactoring stuff is pretty awesome, and it looks like several of our potential projects will require it, like our steroid and smell degradation ideas. I love how you can just simplify it down to simple diagrams. Too bad that refactored nitrogenase gene set had such poor performance, I was hoping to see it work even better than normal.
*'''[[User:Neil R Gottel|Neil R Gottel]] 17:50, 3 April 2013 (EDT)''':This refactoring stuff is pretty awesome, and it looks like several of our potential projects will require it, like our steroid and smell degradation ideas. I love how you can just simplify it down to simple diagrams. Too bad that refactored nitrogenase gene set had such poor performance, I was hoping to see it work even better than normal.
Line 6: Line 8:
*'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 21:40, 4 April 2013 (EDT)''': I can imagine a situation where this could become in handy...such as taking an operon and trying to simplify it to make it work and understanding the function and then an IDT like store where you could shop for parts would have it ready for a researcher in this refactored format. The problem is that as said in class not many people have done it, although as a tool it would become in handy. Also I don't know how many of you guys know about the coming [http://sb6.biobricks.org/registration/ Biobrick Conference], I didn't know where else to post this but looks interesting.
*'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 21:40, 4 April 2013 (EDT)''': I can imagine a situation where this could become in handy...such as taking an operon and trying to simplify it to make it work and understanding the function and then an IDT like store where you could shop for parts would have it ready for a researcher in this refactored format. The problem is that as said in class not many people have done it, although as a tool it would become in handy. Also I don't know how many of you guys know about the coming [http://sb6.biobricks.org/registration/ Biobrick Conference], I didn't know where else to post this but looks interesting.
*'''[[User:Yunle Huang|Yunle Huang]] 23:05, 4 April 2013 (EDT)''':Could you clarify the robustness assay's purpose? I had trouble understanding "tolerances of a gene or set of genes to changes in expression level".
*'''[[User:Yunle Huang|Yunle Huang]] 23:05, 4 April 2013 (EDT)''':Could you clarify the robustness assay's purpose? I had trouble understanding "tolerances of a gene or set of genes to changes in expression level".
 +
**'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': I will work on getting that updated.
*'''[[User:Yunle Huang|Yunle Huang]] 23:06, 4 April 2013 (EDT)''':I think you're missing the citation for the caffeine paper.
*'''[[User:Yunle Huang|Yunle Huang]] 23:06, 4 April 2013 (EDT)''':I think you're missing the citation for the caffeine paper.
 +
**'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': I've been trying to fix the citation list. Something weird is going on and the numbering isn't exactly as it should be.
*'''[[User:Evan J. Weaver|Evan Weaver]] 22:49, 4 April 2013 (EDT)''': How do you find out if the mutations you induce into the operon are inside the nonessential parts?
*'''[[User:Evan J. Weaver|Evan Weaver]] 22:49, 4 April 2013 (EDT)''': How do you find out if the mutations you induce into the operon are inside the nonessential parts?
 +
**'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': At the point that they are trying introducing mutations into essential genes, it is assumed that most nonessential genes and regulatory genes have been removed.
*'''[[User:Evan J. Weaver|Evan Weaver]] 22:54, 4 April 2013 (EDT)''': Under the tolerence assay section, what does inducible control mean?  Does it mean that when exposed to a stimulant, the cell creates the gene product?
*'''[[User:Evan J. Weaver|Evan Weaver]] 22:54, 4 April 2013 (EDT)''': Under the tolerence assay section, what does inducible control mean?  Does it mean that when exposed to a stimulant, the cell creates the gene product?
 +
**'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': Exactly. Expression of genes under the control of a Ptac promoter is induced when IPTG is added to the growth medium.
*'''[[User:Thomas Wall|Thomas Wall]] 15:54, 5 April 2013 (EDT)''': I don't know where to post this paper, but I thought it was super awesome.  They did a little refactoring  http://www.pnas.org/content/early/2013/03/19/1222607110.full.pdf
*'''[[User:Thomas Wall|Thomas Wall]] 15:54, 5 April 2013 (EDT)''': I don't know where to post this paper, but I thought it was super awesome.  They did a little refactoring  http://www.pnas.org/content/early/2013/03/19/1222607110.full.pdf
*'''[[User:Siddharth Das|Siddharth Das]] 13:50, 8 April 2013 (EDT)''': Apparently, the decaffeination gene was relatively huge in order to demethylase three sites of the xanthine. So, I was wondering I huge would the gene be for the steroid topic? Is it possible to do in E. coli?
*'''[[User:Siddharth Das|Siddharth Das]] 13:50, 8 April 2013 (EDT)''': Apparently, the decaffeination gene was relatively huge in order to demethylase three sites of the xanthine. So, I was wondering I huge would the gene be for the steroid topic? Is it possible to do in E. coli?
**'''[[User:Neil R Gottel|Neil R Gottel]] 16:04, 8 April 2013 (EDT)''':[http://openwetware.org/wiki/Image:Ancientcloning.jpg We can handle it.]
**'''[[User:Neil R Gottel|Neil R Gottel]] 16:04, 8 April 2013 (EDT)''':[http://openwetware.org/wiki/Image:Ancientcloning.jpg We can handle it.]
 +
***'''[[User:Max E. Rubinson|Max E. Rubinson]] 12:23, 16 April 2013 (EDT)''': Thank you Neil

Revision as of 11:23, 16 April 2013

  • Gabriel Wu 17:29, 1 April 2013 (EDT): Did pH or carbonation pose any problems when using soda as a growth medium?
    • Max E. Rubinson 12:23, 16 April 2013 (EDT): Gabe, they diluted the soda into a buffered medium, so there wasn't a significant change in the pH of the growth medium. The carbonation did not seem to pose a problem either.
    • Neil R Gottel 17:50, 3 April 2013 (EDT):Don't know about those, but some of the energy drinks didn't work because of the other weird things they put in there (I believe 5 hour energy didn't work, but Monster was fine.
      • Max E. Rubinson 12:23, 16 April 2013 (EDT): Is this a sign that we should avoid 5 hour energy?
      • Catherine I. Mortensen 18:12, 4 April 2013 (EDT):Is it possible that the 5 hour energy didn't work because of the intense concentration of caffeine in such a small bottle...? Maybe there were just too many methylxanthines for the cell to handle?
  • Neil R Gottel 17:50, 3 April 2013 (EDT):This refactoring stuff is pretty awesome, and it looks like several of our potential projects will require it, like our steroid and smell degradation ideas. I love how you can just simplify it down to simple diagrams. Too bad that refactored nitrogenase gene set had such poor performance, I was hoping to see it work even better than normal.
    • Gabriel Wu 14:28, 5 April 2013 (EDT): From discussions with Chris Yellman (who spoke to the class earlier about genome engineering), I've learned that the Voigt lab has taken another approach to engineering the nitrogen utilization pathway. It's not yet published data, but apparently, it resulted in a greater than native pathway output.
  • Alvaro E. Rodriguez M. 21:40, 4 April 2013 (EDT): I can imagine a situation where this could become in handy...such as taking an operon and trying to simplify it to make it work and understanding the function and then an IDT like store where you could shop for parts would have it ready for a researcher in this refactored format. The problem is that as said in class not many people have done it, although as a tool it would become in handy. Also I don't know how many of you guys know about the coming Biobrick Conference, I didn't know where else to post this but looks interesting.
  • Yunle Huang 23:05, 4 April 2013 (EDT):Could you clarify the robustness assay's purpose? I had trouble understanding "tolerances of a gene or set of genes to changes in expression level".
    • Max E. Rubinson 12:23, 16 April 2013 (EDT): I will work on getting that updated.
  • Yunle Huang 23:06, 4 April 2013 (EDT):I think you're missing the citation for the caffeine paper.
    • Max E. Rubinson 12:23, 16 April 2013 (EDT): I've been trying to fix the citation list. Something weird is going on and the numbering isn't exactly as it should be.
  • Evan Weaver 22:49, 4 April 2013 (EDT): How do you find out if the mutations you induce into the operon are inside the nonessential parts?
    • Max E. Rubinson 12:23, 16 April 2013 (EDT): At the point that they are trying introducing mutations into essential genes, it is assumed that most nonessential genes and regulatory genes have been removed.
  • Evan Weaver 22:54, 4 April 2013 (EDT): Under the tolerence assay section, what does inducible control mean? Does it mean that when exposed to a stimulant, the cell creates the gene product?
    • Max E. Rubinson 12:23, 16 April 2013 (EDT): Exactly. Expression of genes under the control of a Ptac promoter is induced when IPTG is added to the growth medium.
  • Thomas Wall 15:54, 5 April 2013 (EDT): I don't know where to post this paper, but I thought it was super awesome. They did a little refactoring http://www.pnas.org/content/early/2013/03/19/1222607110.full.pdf
  • Siddharth Das 13:50, 8 April 2013 (EDT): Apparently, the decaffeination gene was relatively huge in order to demethylase three sites of the xanthine. So, I was wondering I huge would the gene be for the steroid topic? Is it possible to do in E. coli?
Personal tools