Author Topic: .delgene in Real Life  (Read 3128 times)

Offline Peksa

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.delgene in Real Life
« on: May 01, 2008, 07:14:15 PM »
DB DNA is somewhat based on what real organisms can do and the things real organsims can do never cease to suprise me, so I'm wondering if there's match for .delgene in real biology? And is there some mechanism that could be described as .addgene?

Offline bacillus

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.delgene in Real Life
« Reply #1 on: May 02, 2008, 12:20:23 AM »
A virus in DB is kind of what .addgene would look like. I think real-life viruses break down a cell's DNA and use the snippets to replicate their own; kind of like harvesting amino acids by using .delgene, then rebuilding them into a virus by using .mkvirus.
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Offline EricL

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.delgene in Real Life
« Reply #2 on: May 02, 2008, 12:47:33 AM »
As far as I know, biological genomes don't self edit themsleves but as Bacillus points out, viruses will insert themselves in a host cell's DNA and hijack it's machinery to do it's bidding.  And of course mutations can disable or copy whole genes or even larger multi gene sequences.  This is how most if not all genes came to be I.e. first they were a duplicate copy of another gene created via a copy mutation and then selection modified them over time to do something else.
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Offline Numsgil

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.delgene in Real Life
« Reply #3 on: May 02, 2008, 01:34:28 AM »
My understanding is that a cell really has no machinery to repair itself after virus insertion (the only real reason to have a .delgene), and the usual strategy is suicide if it gets that far.  Which is why the genome is so highly protected in most cells.

Offline shvarz

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.delgene in Real Life
« Reply #4 on: May 02, 2008, 01:28:49 PM »
Bacteria have ways to specifically delete unwanted genes. They have methylases that "label" their own DNA with methyl groups. And they have restrictases that will destroy any DNA that does not have these "labels".

We have mechanisms that edit our genomic DNA in a very precise and specific way. This is used in immune system, where random fragments of DNA are snipped out to create a diverse set of new genes. Here's an example:
Say your genome is ABCabcdefg12345. In immune cells this mechanism would cut out a single capital letter, single lower-case letter and a single number and put them together. Thus different cells will have different final genes:
Aa2
Cf5
Be5
Ag1
etc.
These genes code for antibodies and therefore each cell has a different antibody gene, which can recognize a different pathogen.

Most viruses that we encounter don't destroy our DNA and they don't add to our DNA. They replicate as separate fragments of DNA or RNA. Only some viruses integrate their genome into ours. Most famous of those are retroviruses and our genomes are full of them. But majority of viruses don't do that.
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Offline bacillus

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.delgene in Real Life
« Reply #5 on: May 02, 2008, 07:32:02 PM »
But the labelling's more of a maintenance thing than a self-induced mutation thing, isn't it?
« Last Edit: May 02, 2008, 07:33:04 PM by bacillus »
"They laughed at Columbus, they laughed at Fulton, they laughed at the Wright brothers. But they also laughed at Bozo the Clown."
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Offline shvarz

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« Reply #6 on: May 02, 2008, 07:54:40 PM »
Yes, it's maintenance of "own" and detection of "foreign". Still, it's very similar to the way some anti-viral strategies in DB are done - counting the "correct" number of own genes and deleting anything that looks like foreign piece.

The example with immune system is the example of self-induced deletion mutation.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline bacillus

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.delgene in Real Life
« Reply #7 on: May 02, 2008, 09:10:37 PM »
The marker is a very interesting idea; a bot could mark its position in a specific memory location, and then the last genes can use those loactions to check whether any genes have viruses inbetween, then delete them.
"They laughed at Columbus, they laughed at Fulton, they laughed at the Wright brothers. But they also laughed at Bozo the Clown."
- Carl Sagan

Offline Peksa

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.delgene in Real Life
« Reply #8 on: May 05, 2008, 07:16:07 PM »
I take it that there are some immune systemic stem cells that reproduce endlessly and the new cells have just one type of antibody? I've wondered how immune system produces so many different types of antibodies. Two birds with one stone, it seems.

Offline shvarz

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« Reply #9 on: June 04, 2008, 12:40:33 AM »
By the way, bacteria and their viruses can also generate diversity in their DNA "at will":
http://biology.plosjournals.org/perlserv/?...0060131#special
"Never underestimate the power of stupid things in big numbers" - Serious Sam