Talk:CH391L/S12/Pattern Formation

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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:29, 6 April 2012 (EDT)''':Images need citations. Chili peppers are tiny?
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:29, 6 April 2012 (EDT)''':Images need citations. Chili peppers are tiny?
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**'''[[User:Jared Ellefson|Jared Ellefson]] 18:17, 7 April 2012 (EDT)''':Fixed the chili problem. But it's not letting me add text to the figures? I'll keep working on it
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:29, 6 April 2012 (EDT)''':There's a nice presentation posted many places online, including [http://psiren.cs.nott.ac.uk/projects/synbiont/attachment/wiki/WikiAttachments/Righetti_Romero.pptx here], which seems to contain unpublished computational modeling of more complex circuits and pattern formation, but without any wet lab work.
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:29, 6 April 2012 (EDT)''':There's a nice presentation posted many places online, including [http://psiren.cs.nott.ac.uk/projects/synbiont/attachment/wiki/WikiAttachments/Righetti_Romero.pptx here], which seems to contain unpublished computational modeling of more complex circuits and pattern formation, but without any wet lab work.
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**'''[[User:Jared Ellefson|Jared Ellefson]] 18:10, 7 April 2012 (EDT)''':I think this brings up an interesting topic. How much weight should a non-tested biological model hold? Biological models sometimes don't work due to idiosyncrasies. But that said, I'd be curious to see how that circuit would work, it has a very BZ reaction feel which is cool (http://www.youtube.com/watch?v=3JAqrRnKFHo).
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:29, 6 April 2012 (EDT)''':Your references aren't working correctly: the syntax for the end of the line is pmid=12219076
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:29, 6 April 2012 (EDT)''':Your references aren't working correctly: the syntax for the end of the line is pmid=12219076
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**'''[[User:Jared Ellefson|Jared Ellefson]] 18:10, 7 April 2012 (EDT)''':Fixed
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:44, 6 April 2012 (EDT)''': Spelling: "achieved". First sentence of "Synthetic pattern formation..." needs help.
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:44, 6 April 2012 (EDT)''': Spelling: "achieved". First sentence of "Synthetic pattern formation..." needs help.
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:44, 6 April 2012 (EDT)''':Has anything "useful" ever been done with synthetic pattern formation? Do you think it would be possible to get noncircular colony growth for _E. coli_ (or noncircular spreading in soft agar) by putting one of these circuits in that would "sector" the colony and change how it spread or something like that?
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**'''[[User:Jared Ellefson|Jared Ellefson]] 18:17, 7 April 2012 (EDT)''':ok
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:44, 6 April 2012 (EDT)''':Has anything "useful" ever been done with synthetic pattern formation? Do you think it would be possible to get noncircular colony growth for ''E. coli'' (or noncircular spreading in soft agar) by putting one of these circuits in that would "sector" the colony and change how it spread or something like that?
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**'''[[User:Jared Ellefson|Jared Ellefson]] 18:10, 7 April 2012 (EDT)''':Depends on the definition of useful. I certainly foresee this being an enabling technology. But I'm not sure how useful it will be in E.coli. The real biomedical applications might start to take place once systems like this are imported into mammalian cell culture. In terms of non-circular colony growth, yeah I bet this is possible. My guess is tricky though, if you're dealing with cell survival. I'm not sure the exact parameters you are thinking of (autonomous vs non-autonomous), but I bet you could do some fun stuff with light controlling cell growth.
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**'''[[User:Jared Ellefson|Jared Ellefson]] 11:54, 9 April 2012 (EDT)''':This paper[http://pubs.acs.org/doi/pdf/10.1021/ja105431h] is pretty cool. They use DNA to form extracellular matrix-like scaffolds. In which cells can do things based on the structural characteristics of the scaffold. And this is fully programmable because it is made of DNA. 
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***'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 13:57, 9 April 2012 (EDT)''': I was thinking autonomous. Like, can you engineer a cell that forms dumbbell shaped colonies?
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*'''[[User:Ben Slater|Ben Slater]] 20:27, 8 April 2012 (EDT)''': Think it's possible to design a color bacterial photo system? As in, color output, not just input?
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**'''[[User:Jared Ellefson|Jared Ellefson]] 11:07, 9 April 2012 (EDT)''':YES! Definitely. For instance the multicolor system has two lacZ genes, one that is turned "ON" by Green and the other turned "ON" by RED. I think simply just changing the LacZ genes to GFP and mCherry for instance could give you an exact color copy of the image you display. It would be fun to just see ''how'' complicated you can build these light circuits.
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*'''[[User:Adam Meyer|Adam Meyer]] 11:21, 9 April 2012 (EDT)''':It seems as though in all the cases listed, the pattern is specified by the investigator.  Are there systems in which the investigator sets up conditions and the organisms form an optimal pattern that fits those conditions?  In other words, the pattern is not known ''a priori'' but answers some question.
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**'''[[User:Jared Ellefson|Jared Ellefson]] 11:54, 9 April 2012 (EDT)''':This paper[http://www.sciencemag.org/content/327/5964/439.full.pdf] describes pattern formation where the ''program'' is natural to the organism, but the parameters are synthetic. In the paper, a mold is grown on a plate with strategically placed food sources that resemble the Tokyo rail system. The mold then creates the most efficient pathing between the food nodes. It is really surprising that the biological map created from this highly resembles the actual engineered routes.
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***'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 13:57, 9 April 2012 (EDT)''': That's a really fun paper.

Current revision

  • Jeffrey E. Barrick 10:29, 6 April 2012 (EDT):Images need citations. Chili peppers are tiny?
    • Jared Ellefson 18:17, 7 April 2012 (EDT):Fixed the chili problem. But it's not letting me add text to the figures? I'll keep working on it
  • Jeffrey E. Barrick 10:29, 6 April 2012 (EDT):There's a nice presentation posted many places online, including here, which seems to contain unpublished computational modeling of more complex circuits and pattern formation, but without any wet lab work.
    • Jared Ellefson 18:10, 7 April 2012 (EDT):I think this brings up an interesting topic. How much weight should a non-tested biological model hold? Biological models sometimes don't work due to idiosyncrasies. But that said, I'd be curious to see how that circuit would work, it has a very BZ reaction feel which is cool (http://www.youtube.com/watch?v=3JAqrRnKFHo).
  • Jeffrey E. Barrick 10:29, 6 April 2012 (EDT):Your references aren't working correctly: the syntax for the end of the line is pmid=12219076
  • Jeffrey E. Barrick 10:44, 6 April 2012 (EDT): Spelling: "achieved". First sentence of "Synthetic pattern formation..." needs help.
  • Jeffrey E. Barrick 10:44, 6 April 2012 (EDT):Has anything "useful" ever been done with synthetic pattern formation? Do you think it would be possible to get noncircular colony growth for E. coli (or noncircular spreading in soft agar) by putting one of these circuits in that would "sector" the colony and change how it spread or something like that?
    • Jared Ellefson 18:10, 7 April 2012 (EDT):Depends on the definition of useful. I certainly foresee this being an enabling technology. But I'm not sure how useful it will be in E.coli. The real biomedical applications might start to take place once systems like this are imported into mammalian cell culture. In terms of non-circular colony growth, yeah I bet this is possible. My guess is tricky though, if you're dealing with cell survival. I'm not sure the exact parameters you are thinking of (autonomous vs non-autonomous), but I bet you could do some fun stuff with light controlling cell growth.
    • Jared Ellefson 11:54, 9 April 2012 (EDT):This paper[1] is pretty cool. They use DNA to form extracellular matrix-like scaffolds. In which cells can do things based on the structural characteristics of the scaffold. And this is fully programmable because it is made of DNA.
      • Jeffrey E. Barrick 13:57, 9 April 2012 (EDT): I was thinking autonomous. Like, can you engineer a cell that forms dumbbell shaped colonies?
  • Ben Slater 20:27, 8 April 2012 (EDT): Think it's possible to design a color bacterial photo system? As in, color output, not just input?
    • Jared Ellefson 11:07, 9 April 2012 (EDT):YES! Definitely. For instance the multicolor system has two lacZ genes, one that is turned "ON" by Green and the other turned "ON" by RED. I think simply just changing the LacZ genes to GFP and mCherry for instance could give you an exact color copy of the image you display. It would be fun to just see how complicated you can build these light circuits.
  • Adam Meyer 11:21, 9 April 2012 (EDT):It seems as though in all the cases listed, the pattern is specified by the investigator. Are there systems in which the investigator sets up conditions and the organisms form an optimal pattern that fits those conditions? In other words, the pattern is not known a priori but answers some question.
    • Jared Ellefson 11:54, 9 April 2012 (EDT):This paper[2] describes pattern formation where the program is natural to the organism, but the parameters are synthetic. In the paper, a mold is grown on a plate with strategically placed food sources that resemble the Tokyo rail system. The mold then creates the most efficient pathing between the food nodes. It is really surprising that the biological map created from this highly resembles the actual engineered routes.
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