

On the 3.2kbytes in Influenza A - blasdel
http://www.bunniestudios.com/blog/?p=353

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jbyers
That's the most interesting not-really-about-computers article I've read on HN
in the last two years.

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rw
(awesome? bioinformatics)

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kylec
#t

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jhickner
_If you thought of organisms as computers with IP addresses, each functional
group of cells in the organism would be listening to the environment through
its own active port. So, as port 25 maps specifically to SMTP services on a
computer, port H1 maps specifically to the windpipe region on a human.
Interestingly, the same port H1 maps to the intestinal tract on a bird._

Could anyone expand a bit on this subject? I found this completely
fascinating, but I'm having trouble finding further reading on the underlying
mechanics of "ports", as the article calls them.

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imajes
As i understand it, your body is made of various different types of cells.
Now, a virus has to be able to mate with these cells to break through and then
change the RNA of the cell so it can replicate- remember, viruses are sub-cell
agents and need to cause mutations of good cells to replicate.

So given your body is made of different types of cells, viruses only have the
keys to certain cells - where there's enough in common in their RNA to mate.
This is kind of what's meant by the ports the author describes- H1N1 has
enough similar encoding to the cells in your throat, nose and sinuses to mate
and cause mutations.

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ars
I don't believe this is correct. First a virus does not cause a cell to
mutate. It's more akin to handing the cell a new set of work orders, but it
doesn't mutate the cell's DNA.

Second, I think the "port" is not that the RNA is similar, but rather the
virus has a protein key on it's surface that physically allows it to enter the
cell.

In the micro world things move by atomic forces. In this case the virus has a
protein on it's surface that is the same shape as a protein on the surface of
the cell. The same shape means the electrical charges line up, and the virus
is drawn toward the cell by electrostatic forces.

If the charge pattern does not match up, the virus will not be drawn toward
the cell. Remember the virus has no ability to move.

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arebop
Not all viruses cause mutations, but some do:
<http://en.wikipedia.org/wiki/Retrovirus>

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kqr2
Interesting use of computer analogies:

    
    
      DNA		 : Program stored on disk
      RNA		 : Program loaded in RAM
      Amino Acid	 : Pixel in a frame buffer
      Protein	 : Image output from the RNA program
      Organism	 : Computer with an IP address
      Functional     : An application which listens to a particular socket
       Group of Cells

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eru
Yes interesting. Though Proteins are much more active than images. Perhaps an
analogy with robots would be more apt.

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jballanc
Well, this doesn't really get at the heart of the article (or the matter), but
to be rather pedantic, the virus genome encodes much more than just 3.2KB.
Keep in mind that most of what the genome accomplishes is done with proteins.
In that case, you have to take codons (sets of 3 bases) and convert to one of
the 20 amino acids. This effectively takes 64 bits of information and reduces
it to 20...

 _EXCEPT_ that proteins are 3-dimensional entities. Their exact 3D
configuration is encoded in the amino acid sequence encoded by the DNA. We
still don't fully understand how this encoding works, but it is, in effect,
the most awesome compression algorithm imaginable!

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sketerpot
There's some redundancy in the mapping of codons to amino acids. Some of the
most common point mutations will cause a codon to map to the same amino acid,
or a functionally similar one. That's some information that would be lost if
you represented DNA as an amino acid sequence.

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ars
Since this virus mutates so often, shouldn't they sequence a few hundred
versions of it?

And clearly I need to install a firewall to close some of those open ports.

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robinhouston
At the institute where I work, we're sequencing H1N1 isolates from (IIRC)
fifty UK patients. There are also emergency plans to start sequencing flu
samples on a massive scale if it turns into a major epidemic. I would be
astonished if large sequencing centres in other countries were not doing
similar things.

In other words: yes you're right, and it's already being done.

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jballanc
Please, please, PLEASE Don't take the author's advice of trying to catch
H1N1!!! I realize that comment was tongue-in-cheek, but still... There are a
lot of people who do believe that they'll be better off catching it, and this
is only likely to make things worse.

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imajes
well, since most of us get flu at least once every couple of years, it's kind
of hard to avoid H1N1, the most popular form of influenza going around. Of
course, if we were to catch the very specific form of H1N1 with the genetic
coding that matches the swine flu epidemic, that'd be worse.

It's worth remembering that in almost all cases, it's not the flu that kills
you - it's the onset pneumonia, diarrhea and dehydration that takes you down.
The best survivalist method is to remind yourself how to treat cold/flu
symptoms, stock up on meds, and sweat it out. Helps if your health insurance
is up to date too. :)

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jballanc
True, many will become infected naturally. The problem is that the antigenic
shift of influenza is affected by transmission rate. That is, the more times a
virus gets passed from person to person, the more it can mutate. The vaccines
that are developed are based on a "normal" rate of antigenic shift. If large
groups of people try to get infected, there is a risk that they will throw off
this rate.

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silentOpen
_So, those of us with the mutation that causes lungs to ignore the H5 port
would have a better chance of surviving an Avian flu infection, whereas as
those of us that open port H5 on the lungs have no chance to survive make your
time / all your base pairs are belong to H5N1._

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stuntgoat
Joel, can I help you build a stackoverflow for virologists, please? I want to
call it antigenoverflow.

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flinc
the best resource on H1N1 (and virology in general) I've found to counter the
news hysteria <http://www.twiv.tv/>

