Talk:CH391L/S12/Refactoring Genomes

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Current revision (13:48, 9 April 2012) (view source)
 
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**'''[[User:Jon M. Laurent|Jon M. Laurent]] 13:32, 9 April 2012 (EDT)''': A section on these details has been added.
**'''[[User:Jon M. Laurent|Jon M. Laurent]] 13:32, 9 April 2012 (EDT)''': A section on these details has been added.
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:11, 6 April 2012 (EDT)''':There is a 2009 book on genome refactoring that is available for [http://catalog.lib.utexas.edu/search/X?SEARCH=genome+refactoring online reading through the library]. It describes refactoring the phage M13 genome in an undergraduate lab course at MIT, and actually has some other sections of general interest for teaching synthetic biology. Definitely a good one to cite and maybe mention M13. Are there any other efforts to refactor out there, or has interest waned in this?
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:11, 6 April 2012 (EDT)''':There is a 2009 book on genome refactoring that is available for [http://catalog.lib.utexas.edu/search/X?SEARCH=genome+refactoring online reading through the library]. It describes refactoring the phage M13 genome in an undergraduate lab course at MIT, and actually has some other sections of general interest for teaching synthetic biology. Definitely a good one to cite and maybe mention M13. Are there any other efforts to refactor out there, or has interest waned in this?
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**'''[[User:Jon M. Laurent|Jon M. Laurent]] 13:32, 9 April 2012 (EDT)''':I actually had this book open and intended to cite it, but failed to remember it. I have added a small mention and citation for it. I don't know of any other specific refactoring efforts currently being undertaken (save for the assumption that the yeast refactoring is ongoing). I think maybe the synthetic genome of M. mycoides by Venters group is the only other recent big project that could be called 'refactoring' of sorts. I think that we've successfully shown that refactoring can be done successfully, so the proof-of-principle phase is more or less done. Thus (as evidenced by the yeast project), the major focus now should be, and probably is, on actual useful refactoring. The yeast project is the first step in this direction with the scramble system and removal of amber-stop codons. There are other useful things that can be done though, maybe refactoring E. coli for efficient addition and removal of useful operons, or redesigning synthetic operons, etc.
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**'''[[User:Jon M. Laurent|Jon M. Laurent]] 13:32, 9 April 2012 (EDT)''':I actually had this book open and intended to cite it, but failed to remember it. I have added a small mention and citation for it. I don't know of any other specific refactoring efforts currently being undertaken (save for the assumption that the yeast refactoring is ongoing). I think maybe the synthetic genome of M. mycoides by Venters group is the only other recent big project that could be called 'refactoring' of sorts. I think that we've successfully shown that refactoring can be done, so the proof-of-principle phase is more or less done. Thus (as evidenced by the yeast project), the major focus now should be, and probably is, on actual useful refactoring. The yeast project is the first step in this direction with the scramble system and removal of amber-stop codons. There are other useful things that can be done though, maybe refactoring E. coli for efficient addition and removal of useful operons, or redesigning synthetic operons, etc.

Current revision

  • Jeffrey E. Barrick 17:01, 2 April 2012 (EDT):Did they replace the telomeres? With what?
    • Jon M. Laurent 13:32, 9 April 2012 (EDT): Yes, they did replace the telomeres. However, they just replaced them with a telomere 'seed' sequence so that new cells would have a template on which to build new telomeres.
  • Jeffrey E. Barrick 10:11, 6 April 2012 (EDT):General note: I don't like the trend of pasting summary boxes from papers into these Wiki pages. The point of making this page is to digest information into important points and bring together different papers, not reproduce existing information. You already have much of the information in your description, anyway.
    • Jon M. Laurent 13:32, 9 April 2012 (EDT):Yeah, I see your point on this. I will remove it.
  • Jeffrey E. Barrick 10:11, 6 April 2012 (EDT):Why don't you cite a paper from sequencing T7?
  • Jeffrey E. Barrick 10:11, 6 April 2012 (EDT):Can you describe in more detail the method of genome construction they used for T7? They put the segment in a plasmid and changed it, or they PCRed each gene with primers that changed the endpoints like you have pictured? How do they recombine the genomes? Is it by infecting a cell carrying a plasmid with wild-type T7 and screening for recombinants?
    • Jon M. Laurent 13:32, 9 April 2012 (EDT): A section on these details has been added.
  • Jeffrey E. Barrick 10:11, 6 April 2012 (EDT):There is a 2009 book on genome refactoring that is available for online reading through the library. It describes refactoring the phage M13 genome in an undergraduate lab course at MIT, and actually has some other sections of general interest for teaching synthetic biology. Definitely a good one to cite and maybe mention M13. Are there any other efforts to refactor out there, or has interest waned in this?
    • Jon M. Laurent 13:32, 9 April 2012 (EDT):I actually had this book open and intended to cite it, but failed to remember it. I have added a small mention and citation for it. I don't know of any other specific refactoring efforts currently being undertaken (save for the assumption that the yeast refactoring is ongoing). I think maybe the synthetic genome of M. mycoides by Venters group is the only other recent big project that could be called 'refactoring' of sorts. I think that we've successfully shown that refactoring can be done, so the proof-of-principle phase is more or less done. Thus (as evidenced by the yeast project), the major focus now should be, and probably is, on actual useful refactoring. The yeast project is the first step in this direction with the scramble system and removal of amber-stop codons. There are other useful things that can be done though, maybe refactoring E. coli for efficient addition and removal of useful operons, or redesigning synthetic operons, etc.
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