Talk:CH391L/S13/Metagenomics & Bioprospecting

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*'''[[User:Kevin Baldridge|Kevin Baldridge]] 01:55, 19 February 2013 (EST)''':The introduction is great and really helpful. However there is a little bit of redundancy, the sentences at the ends of the first two paragraphs in particular.
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 01:55, 19 February 2013 (EST)''':The introduction is great and really helpful. However there is a little bit of redundancy, the sentences at the ends of the first two paragraphs in particular.
**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:58, 20 February 2013 (EST)''':Please finish merging in whatever additional content was there from last year's topic. You also need at least one more image.
**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:58, 20 February 2013 (EST)''':Please finish merging in whatever additional content was there from last year's topic. You also need at least one more image.
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*'''[[User:Siddharth Das|Siddharth Das]] 21:11, 2/21/2013 (EST)''': You provided an thorough overview of both metagenomics and bioprospecting. Nevertheless, I was wondering if you could expand on the virology section. I don't seem to remember this was a heavily touched upon subject in your presentation and wonder if its needed since it repeats ideas from your intro.
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*'''[[User:Thomas Wall|Thomas Wall]] 23:07, 2/21/2013 (EST)''': This topic is pretty close to my heart having worked on several projects of this nature, check me out http://aem.asm.org/content/75/9/2735
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 22:36, 24 February 2013 (EST)''':Neat paper topic!
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*'''[[User:Thomas Wall|Thomas Wall]] 23:25, 2/21/2013 (EST)''': At the SGI christmas party one year they had a video of Craig Venter on his boat with the SNL song "I'm on a boat" playing, it was pretty hilarious, sadly I can't find it online, but I will continue to look.
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 21:40, 24 February 2013 (EST)''':Seems to have been [http://www.youtube.com/watch?v=ORTyaK3d4eA&feature=player_embedded removed from YouTube].
==Metabolic Engineering==
==Metabolic Engineering==
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:58, 20 February 2013 (EST)''':It would be interesting to go back and trace the discovery of those genes.
**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:58, 20 February 2013 (EST)''':It would be interesting to go back and trace the discovery of those genes.
**'''[[User:Benjamin Gilman|Benjamin Gilman]] 17:39, 21 February 2013 (EST)''': My understanding is that taxol is currently made by growing ''taxus''(yew tree family) cells in suspension along with the fungus that completes the synthesis, not unlike what happens in actual tree bark.  Does anyone know if a similar strategy has ever been used with engineered organisms to synthesize a product in cases where a single species couldn't be coaxed into completing the synthesis?   
**'''[[User:Benjamin Gilman|Benjamin Gilman]] 17:39, 21 February 2013 (EST)''': My understanding is that taxol is currently made by growing ''taxus''(yew tree family) cells in suspension along with the fungus that completes the synthesis, not unlike what happens in actual tree bark.  Does anyone know if a similar strategy has ever been used with engineered organisms to synthesize a product in cases where a single species couldn't be coaxed into completing the synthesis?   
 +
***'''[[User:Thomas Wall|Thomas Wall]] 23:14, 2/21/2013 (EST)''': I have been chomping at the bit to do a synthetic biology project like this for no less than two years
*'''[[User:Gabriel Wu|Gabriel Wu]] 18:26, 18 February 2013 (EST)''': A short interesting article about the difference between microbial production (synthetic biology style) versus chemical synthesis. [http://www.nature.com/nature/journal/v492/n7428/full/492188a.html]
*'''[[User:Gabriel Wu|Gabriel Wu]] 18:26, 18 February 2013 (EST)''': A short interesting article about the difference between microbial production (synthetic biology style) versus chemical synthesis. [http://www.nature.com/nature/journal/v492/n7428/full/492188a.html]
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*'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 19:32, 21 February 2013 (EST)''':Hey Jeff, It could be nice if you invited [http://bk21.ajou.ac.kr/nanomed/english/professor/professor03_09.jsp Dr. Pyung Cheon Lee]  to talk, since he does work in metabolic engineering.  
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*'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 19:32, 21 February 2013 (EST)''':Hey Jeff, It could be nice if you invited [http://bk21.ajou.ac.kr/nanomed/english/professor/professor03_09.jsp Dr. Pyung Cheon Lee]  to talk, since he does work in metabolic engineering.
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**'''[[User:Kevin Baldridge|Kevin Baldridge]] 10:24, 25 February 2013 (EST)''':Unless I'm missing something he's not exactly local? If you are looking for metabolic engineering work, you might look a little closer to home in [http://www.che.utexas.edu/faculty-staff/faculty-directory/alper/ Dr. Hal Alper's] group
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***'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 10:30, 25 February 2013 (EST)''':Dr. Alper talked to class last year, which was great. Alvaro didn't mention that Dr. Lee is visiting my lab for the year. Both do fun things.
==Human Microbiome Project (HMP)==
==Human Microbiome Project (HMP)==
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:43, 18 February 2013 (EST)''': The first major paper release of the Human Microbiome Project (HMP) has been published. There were two big papers in Nature in June, 2012 [http://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Nature_HMP_061312.pdf 1], [http://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Nature_HMP_Framework_061312.pdf 2]. These papers accompanied a coordinated release of about a dozen papers in various PLoS journals [http://www.genome.gov/27549115].
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:43, 18 February 2013 (EST)''': The first major paper release of the Human Microbiome Project (HMP) has been published. There were two big papers in Nature in June, 2012 [http://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Nature_HMP_061312.pdf 1], [http://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Nature_HMP_Framework_061312.pdf 2]. These papers accompanied a coordinated release of about a dozen papers in various PLoS journals [http://www.genome.gov/27549115].

Current revision

  • Gabriel Wu 18:03, 18 February 2013 (EST): We've talked a lot about DNA synthesis. I don't know if we need an entire talk on sequencing technologies (we certainly could, but may be beyond the scope), but, if anyone needs a little primer on it. It's a little dated, but still relevant on the fundamentals [1].
    • Jeffrey E. Barrick 12:58, 20 February 2013 (EST):I'd say it's probably beyond the scope of our course to go too much into sequencing tech, but it's good stuff to know. Thanks for posting the link.
  • Kevin Baldridge 01:55, 19 February 2013 (EST):The introduction is great and really helpful. However there is a little bit of redundancy, the sentences at the ends of the first two paragraphs in particular.
    • Jeffrey E. Barrick 12:58, 20 February 2013 (EST):Please finish merging in whatever additional content was there from last year's topic. You also need at least one more image.
  • Siddharth Das 21:11, 2/21/2013 (EST): You provided an thorough overview of both metagenomics and bioprospecting. Nevertheless, I was wondering if you could expand on the virology section. I don't seem to remember this was a heavily touched upon subject in your presentation and wonder if its needed since it repeats ideas from your intro.
  • Thomas Wall 23:07, 2/21/2013 (EST): This topic is pretty close to my heart having worked on several projects of this nature, check me out http://aem.asm.org/content/75/9/2735
  • Thomas Wall 23:25, 2/21/2013 (EST): At the SGI christmas party one year they had a video of Craig Venter on his boat with the SNL song "I'm on a boat" playing, it was pretty hilarious, sadly I can't find it online, but I will continue to look.

Metabolic Engineering

  • Gabriel Wu 18:22, 18 February 2013 (EST): The story of taxol is interesting and important. Unfortunately, it hasn't been as successful at commercialization--at least not yet. Another rather impressive story that so far has been more successful commercially is the microbial production of the antimalarial artemisinin. By expressing plant genes in yeast, researchers are able to economically produce large amounts artemisinin precursor. The most recent publication in this field is here. An older, but clearer explanation is here.
    • Jeffrey E. Barrick 12:58, 20 February 2013 (EST):It would be interesting to go back and trace the discovery of those genes.
    • Benjamin Gilman 17:39, 21 February 2013 (EST): My understanding is that taxol is currently made by growing taxus(yew tree family) cells in suspension along with the fungus that completes the synthesis, not unlike what happens in actual tree bark. Does anyone know if a similar strategy has ever been used with engineered organisms to synthesize a product in cases where a single species couldn't be coaxed into completing the synthesis?
      • Thomas Wall 23:14, 2/21/2013 (EST): I have been chomping at the bit to do a synthetic biology project like this for no less than two years
  • Gabriel Wu 18:26, 18 February 2013 (EST): A short interesting article about the difference between microbial production (synthetic biology style) versus chemical synthesis. [2]
  • Alvaro E. Rodriguez M. 19:32, 21 February 2013 (EST):Hey Jeff, It could be nice if you invited Dr. Pyung Cheon Lee to talk, since he does work in metabolic engineering.
    • Kevin Baldridge 10:24, 25 February 2013 (EST):Unless I'm missing something he's not exactly local? If you are looking for metabolic engineering work, you might look a little closer to home in Dr. Hal Alper's group
      • Jeffrey E. Barrick 10:30, 25 February 2013 (EST):Dr. Alper talked to class last year, which was great. Alvaro didn't mention that Dr. Lee is visiting my lab for the year. Both do fun things.

Human Microbiome Project (HMP)

  • Gabriel Wu 17:43, 18 February 2013 (EST): The first major paper release of the Human Microbiome Project (HMP) has been published. There were two big papers in Nature in June, 2012 1, 2. These papers accompanied a coordinated release of about a dozen papers in various PLoS journals [3].
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