Talk:CH391L/S13/Ancestral Sequence Reconstruction

• 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?

• Benjamin Gilman 13:21, 21 February 2013 (EST): The Pauling and Zuckerkandl paper came out when the only protein sequence information we had came from limited peptide sequencing methods like Edman degradation (N-terminal sequencing). You might add something about the shift to using DNA or RNA sequences to infer protein sequence once techniques like Maxam-Gilbert and Sanger sequencing showed up in the '70s.

• 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 speciesn being sequenced today?
  • Catherine I. Mortensen 23:19, 20 February 2013 (EST): I'm not sure what the oldest intact DNA is but I did find an article about the oldest living relative to eukaryotes. It's protozoan that is thought to have evolved one billion years ago. Apparently it doesn't fit into any specific kingdom. http://www.livescience.com/19955-ancient-protist-kingdom.html
• Catherine I. Mortensen 15:05, 21 February 2013 (EST):Has anyone heard of H. Salinarum?

• 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.

• Jeffrey E. Barrick 17:16, 18 February 2013 (EST):Add a picture of the fluorescent proteins (take one from Matz Lab website?

• 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.

• Jeffrey E. Barrick 18:37, 20 February 2013 (EST):Please add the titles of papers in the bibliography on your own as is done in other topics. You might also send feedback to OWW to tell them the bibio extension is broken to see if someday they will fix it.