Re: Reverse-engineering the T. rex genome

[Erik Boehm <erikboehm07@yahoo.com>]

> Phillip Bigelow wrote:
> > Gallus gallus has been mapped, but its one thing to
> map the
> > thing.  It's another challenge, entirely,
> > to correlate genes with function. 
I could further draw a distinction, and say that you sequence genomes, you 
annotate genomes, but you don't really map them.
You can map a specific gene to a specific location on a chromosome. Doing this 
usually involves an observable phenotype, which tells you something about the 
function of the gene you are mapping.

When you sequence a genome, at the most basic level, all you find is the 
nucleotide sequence, but you don't even know which of those nucleotides 
constitute a "gene" - after all for any given length of DNA you have to examine 
6 different possibilities for open reading frames.
Genes can be on either strand, and since codons are pairs of three nucleotides, 
there are three possibilities for reading frames per strand.
And its very hard to tell what codes for aa's, what produces rna transcripts 
that aren't translated (but still serve some function, and could be considered 
a gene), what nucleotides are promoters, which ones are structural, binding 
sites, which ones are merely "spacers", etc.

Very few genomes have been fully sequenced and annotated - the mitochondria 
genome is one - I could see calling it "mapped", as you can precisely identify 
where each gene is within the genome.
But the human genome - even though we (basically) know the sequence, we don't 
know where all the genes are, and thus there is still a lot of mapping to do.

 Researchers
> have
> > hardly begun on such a correlation of any of the
> > avian-specific diseases.
> > 
> > I'm no gene person, but here is my train of thought on
> the
> > matter:
> >
> > I'm no gene person, but here is my train of thought on
> the matter:
> >
> > Something makes avians uniquely suseptable to the
> bacterial infection 
> > of their jaw. 

More like a protist has developed a specific work-around to the avian immune 
system. It could even be what the protists is working around is homo
s have significantly similar function and sequence. Just a slight change at the 
right area, and you then need to change another protein that interacts with it.
Its like a lock and key.
The avian (and apparently Theropod/Coelosaur) immune system is the lock, and 
the protist has developed a key.

Particularly, plant resistance to certain fungal pathogens is particularly like 
a lock and key model. A specific plant protein recognizes a specific fungal 
protein, and confers resistance (although since the plant is specific to the 
fungus, what is the "lock" and "key" here may be reversed, when compared to 
other pathogens where the pathogen recognizes a specific host protein, and when 
the host protein changes- ie the lock changes, the pathogen "key" no longer 
works)
The fungus protein can mutate, and become pathogenic against the strain again, 
and likewise, the plant protein can mutate, and block the fungus again.
Such mutation and counter mutation could have been going on with theropods and 
protists for the last hundred million years or more.

Now you may be able to compare proteins involved in host-pathogen interactions, 
and look for differences in mammals and birds, and identify a few genes that 
are different, and conclude dinosaurs had similar genes, but its a LONG LONG 
way from reverse engineering an entire Dino genome.

Keep in mind, the trich back then wouldn't be the same as the trich now.
The "lock" has changed, the "key" has changed, you will not know the exact 
sequence, only that the sequence was similar to what you found.
Likewise, we can already make determinations on what dino DNA "was like" after 
the "soft tissue" amino acid sequence was found in a T-rex, and found to be 
similar to that of a chicken.

We can then guess that since similar proteins were encoded, the DNA was 
probably similar too.
The DNA can be more dissimilar than the protein sequence (as the same protein 
can be encoded using different codons, different promoter sequences, different 
intron content, etc) , so in the case where you identify pro
he immune system that are specific to the trich-bird pathogenisis, you will 
know even less- as you don't know how similar the trich was back then to the 
trich now, you don't know how similar the corresponding T-rex proteins were, 
and thus you know even less how similar the DNA that was needed to express 
those proteins was.



When it comes to reverse engineering a Dino, I think the closest you'd have any 
chance of getting, would be the last common ancestor of birds.

Sequence every single bird species genome, get the consensus sequences for each 
node on the tree, and determine the consensus sequence for the most basal node.
Of course, you'll never get a 100% confident consensus, and likely not even 50% 
confidence any particular nucleotide was the ancestral condition.
Synthesize that sequence, and stick it into a cell, and try to grow a new bird 
out of it.....

Then do the same with the bird + crocodile consensus sequences.

Unfortunately the sequences have diverged too much to have any hope of actually 
reconstructing the genome of the last common ancestor, but I think you could 
get close, and it would be interesting to see what sort of creature (if any, it 
may die as an empbryo) would result,
Would you get a healthy primitive looking bird (or primitive looking archosaur 
if you include croc consensus sequences), or some sort of "monster of science" 
with no relevance?