Talk:CH391L/S13/Ancestral Sequence Reconstruction

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(Questioning the validity of this technique since Jeff brought up many objections.)
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*'''[[User:Gabriel Wu|Gabriel Wu]] 17:08, 18 February 2013 (EST)''': Separate topic on sequencing wooly mammoths and neanderthals?
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:08, 18 February 2013 (EST)''': Separate topic on sequencing wooly mammoths and neanderthals?
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 18:30, 20 February 2013 (EST)''':We could call that topic '''Ancestral organism resurrection'''. It could also talk about synthesizing the 1918 Spanish flu. Here's a [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819212/ review] that might help with that topic.
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 17:10, 18 February 2013 (EST)''':On the topic of general to specific evolution, is there any consideration for hypermodified amino acids? Maybe the ancient proteins had post-translational modifications in the proteins that adjusted the specificity, but we don't know about it from the genetic sequence for the protein.
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 17:10, 18 February 2013 (EST)''':On the topic of general to specific evolution, is there any consideration for hypermodified amino acids? Maybe the ancient proteins had post-translational modifications in the proteins that adjusted the specificity, but we don't know about it from the genetic sequence for the protein.
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 17:16, 18 February 2013 (EST)''':Add a picture of the fluorescent proteins (take one from Matz's website?
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 17:16, 18 February 2013 (EST)''':Add a picture of the fluorescent proteins (take one from [http://www.bio.utexas.edu/research/matz_lab/matzlab/Welcome.html Matz Lab  website]?  
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:20, 18 February 2013 (EST)''': From Andre: Discussion of Red Queen hypothesis and how ancestral gene reconstruction can show us evolution of interactions between host and virus proteins.
*'''[[User:Gabriel Wu|Gabriel Wu]] 17:20, 18 February 2013 (EST)''': From Andre: Discussion of Red Queen hypothesis and how ancestral gene reconstruction can show us evolution of interactions between host and virus proteins.
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 18:30, 20 February 2013 (EST)''':If it's specific proteins I'd put it in this topic. If it's whole viruses, I'd kick to it a whole-organism topic.
*'''[[User:Siddharth Das|Siddharth Das]] 19:24, 19 February 2012(EST)''': With even the most powerful statistics tools and rigorous mathematics, how useful is this technology in terms of evolutionary studies, since it seems the genes themselves are inaccurate representations (varying mutation rate for the past million year, etc)? Furthermore, is it safe to assume that the genetic code was as conserved as it is today? There are exceptions even now; for example, in the fungus Candida, CUG codes for serine instead of leucine. On a different note, the wiki is very well organized.
*'''[[User:Siddharth Das|Siddharth Das]] 19:24, 19 February 2012(EST)''': With even the most powerful statistics tools and rigorous mathematics, how useful is this technology in terms of evolutionary studies, since it seems the genes themselves are inaccurate representations (varying mutation rate for the past million year, etc)? Furthermore, is it safe to assume that the genetic code was as conserved as it is today? There are exceptions even now; for example, in the fungus Candida, CUG codes for serine instead of leucine. On a different note, the wiki is very well organized.

Revision as of 19:30, 20 February 2013

  • Gabriel Wu 16:59, 18 February 2013 (EST): Remove the cost and methods of gene synthesis (or just reference the dna assembly section we've already gone over). Expand the codon optimization section (unless this fits better in somewhere else).
  • Gabriel Wu 16:59, 18 February 2013 (EST): How does Pauling's proposal for ancestral gene construction relate to the actual discovery of DNA structure?
  • Kevin Baldridge 17:00, 18 February 2013 (EST):How do the methods here compare with those used for phylogenetic placement based on ribosomal RNA sequences?
  • Gabriel Wu 17:06, 18 February 2013 (EST): Can you include a little more detail in your figures? At least give some detail about the methods used to determine time and explain the acronyms (e.g. PNCA, GNCA, etc).
  • Gabriel Wu 17:06, 18 February 2013 (EST): What's the oldest intact DNA? What's the oldest species being sequenced today?
  • Gabriel Wu 17:08, 18 February 2013 (EST): Separate topic on sequencing wooly mammoths and neanderthals?
    • Jeffrey E. Barrick 18:30, 20 February 2013 (EST):We could call that topic Ancestral organism resurrection. It could also talk about synthesizing the 1918 Spanish flu. Here's a review that might help with that topic.
  • Kevin Baldridge 17:10, 18 February 2013 (EST):On the topic of general to specific evolution, is there any consideration for hypermodified amino acids? Maybe the ancient proteins had post-translational modifications in the proteins that adjusted the specificity, but we don't know about it from the genetic sequence for the protein.
  • Gabriel Wu 17:20, 18 February 2013 (EST): From Andre: Discussion of Red Queen hypothesis and how ancestral gene reconstruction can show us evolution of interactions between host and virus proteins.
    • Jeffrey E. Barrick 18:30, 20 February 2013 (EST):If it's specific proteins I'd put it in this topic. If it's whole viruses, I'd kick to it a whole-organism topic.
  • Siddharth Das 19:24, 19 February 2012(EST): With even the most powerful statistics tools and rigorous mathematics, how useful is this technology in terms of evolutionary studies, since it seems the genes themselves are inaccurate representations (varying mutation rate for the past million year, etc)? Furthermore, is it safe to assume that the genetic code was as conserved as it is today? There are exceptions even now; for example, in the fungus Candida, CUG codes for serine instead of leucine. On a different note, the wiki is very well organized.
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