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Viral Fossil Brought Back To Life
Posted by
samzenpus
on Wed Nov 01, 2006 09:15 PM
from the what-could-go-wrong dept.
from the what-could-go-wrong dept.
hey hey hey writes "In a controversial study, researchers have resurrected a retrovirus that infected our ancestors millions of years ago and now sits frozen in the human genome. Published online by Genome Research this week, the study may shed new light on the history of these genomic intruders, as well as their role in tumors. Although this particular virus, dubbed Phoenix, is a wimpy one, some argue that resuscitating any ancient virus is inherently risky and that the study should have undergone stricter reviews."
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Andromeda strain (Score:3, Insightful)
Really interesting (Score:2)
Re: (Score:2)
because thats what we really need... (Score:4, Funny)
I mean - I was just saying the other day to a friend, I haven't
seen a new virus in ages... just the same old ebola, HIV,
flu, H5N1, herpes... I mean YAWN. Where's the excitement in
those?
Re: (Score:2)
Very interesting (Score:5, Informative)
Viruses have a lytic cycle where they express nasty genes and build capsids inside you, and a lysogenic cycle, where they adopt a different strategy- they get into your DNA, become part of the junk DNA, and they replicate during normal cell division along with all the rest of your DNA.
Junk DNA has all sorts of nasty critters in it. One trick your body uses is to carpet especially infectious regions with methyl groups via cytosine methylation [wikipedia.org]. Basically the idea is that the methyl groups jam up the machinery that comes along to express proteins, so if the proteins are viral, you can "comment them out" that way. When a cell divides, both strands of its DNA have methylated cytosines in the same regions. After the DNA replicates you have two methylated daughter strands, each coupled with a brand new complimentary strand. This complimentary strand has no methyl groups on it. So a clever enzyme comes along, DNA methyltransferase. [wikipedia.org] It has a regulatory domain and a catalytic domain. The regulatory domain runs across the DNA feeling it for methyl groups. If it finds them on one strand, the catalytic domain deposits methyl groups on the other strand. That way, the stretch of DNA can be marked as "bad news" in a way that is heritable, despite the fact that no actual DNA sequence is being "inherited". As far as where the initial methylation signal came from, that can probably be put down to natural selection.
Re: (Score:2)
Re:Very interesting (Score:4, Interesting)
Parent
Re:Very interesting (Score:5, Informative)
Dude, I'll just refer you to the Wikipedia page on Junk DNA [wikipedia.org] (the bold tags are mine):
And I didn't even edit that on Wikipedia before replying either.
You can call it something else if you're offended, but the DNA itself won't have its feelings hurt if you call it junk.
Parent
Re: (Score:3, Interesting)
Please don't believe everything you read on wikipedia. It might have been right if I'd read that 5 years ago, but my work, and other people's work says otherwise.
Re:Very interesting (Score:5, Informative)
Well that's not the same kind of "reverse transcriptase".
TERT has the job of making DNA molecules longer after replication (telomere lengthening). It appends a sequence of 5'-TTAGGG (a telomere) over and over to the 3' end of a chromosome. To do this, it has an RNA template molecule inside itself with a sequence complimentary to TTAGGG, offset and repeated twice: 3'-CAAUCCCAAUC-5'. The left end of the template aligns to the end of the chromosome and hybridizes to the TTAGGG on the end. Then a new TTAGGG hybridizes to the second half of the template, is bound to the chromosome, and TERT disengages to repeat the process with another TTAGGG chunk. It's a pretty clever implementation actually. You could probably have it repeat any six base monomer other than TTAGGG by changing the RNA template molecule that it uses. Some other species use a different six base sequence for their telomeres.
This technically counts as converting RNA to DNA, so the enzyme is called "telomerase reverse transcriptase". But it's not appending any coding DNA, it's just adding TTAGGG over and over again to give structural integrity to the chromosome. Usually "reverse transcriptase" refers to a family of enzymes with a viral origin that share ancestry and work by converting viral coding RNA into DNA with no proofreading mechanism and a high rate of error.
It's most commonly used by retroviruses along with integrase (used by viruses to splice crud into your DNA) but retrotransposons [wikipedia.org] also use it to jump around. These are genetic parasite sequences that can move around in the genome and use reverse transcriptase to make copies of themselves. LINE (long interspersed element) is a retrotransposon about 5000 bases long that inserts copies of itself all over the place. The human genome now has about 900,000 copies of LINE- fully 21% of the genome. Another 11% of the genome is SINE (short interspersed element) elements. SINE is a 500 base or less sequence. LINE has actual coding DNA in it for something that works like integrase and reverse transcriptase. That lets it copy itself along with its adjacent sequence, and insert the copy in some random place in your DNA. SINEs don't have any coding DNA- they hitch a ride along with the LINEs when they get copied, so they're parasitizing the parasites.
Parent
Revival being controversial? (Score:2)
Revival or restoration... I think that a fully restored 1967 Hemi Barracuda is a very nice car!
Anyways, I was more expecting that the focus of controversy here would be evidence or other implications indicative of Nature's myriad ways to encourage evolution.
Link to the Original Article in Genome Research (Score:3, Informative)
Not very Intelligent design (Score:3, Insightful)
Re:Not very Intelligent design (Score:5, Informative)
My problem with evolution is that it doesn't explain the beginning.
Then you need not have a problem with evolution. Evolution and abiogenesis (life from non-life) are two separate questions and topics. Evolution tells us that descent with modification is the current best explanation for the species and forms we see today. It does not purport to tell us what the first life form(s)? were or how they came to be. That is a separate and far more speculative field of study.
Even Darwin understood this way back when. His first attempt to systemize evolution was NOT called "Origin of Life". It was called "Origin of Species". Evolution operates on extant forms of life. If it operates in the processes that lead to life starting in the first place, the mechanisms involved are likely different from the ones creationists and (reputable) biologists argue all the time. Evolution presupposes entities capable of self-reproduction. You need replicators of some sort to even talk about evolution in the first place. Once the first replicator either spontaneously arrives or is created (and no this need not be dismissed out of hand but if the only case for it is faith-based then we aren't talking science.....) then evolution can take over and eventually bring about forms vastly more varied and different from the starting point.
Parent
HERVs: 8% of Human Genome (Score:5, Interesting)
In this particular case, there were 30 copies of the virus in the genome. They worked backward to create the original virus. The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate. So there was no risk.
In the human genome, the researchers point out, are the pieces from other viruses. 8% of the human genome codes for HERV proteins or their regulatory subunits [nature.com]. If these pieces are activated, they can reassemble to create a new, working virus. This happens naturally.
All of these HERVs are viruses that, throughout human evolution, we and our ancestors have more or less come to terms with. At some point, many of them were probably devastating. But those that caught the virus, survived, and reproduced were able to mitigate the effects of the virus. These are viruses we've reached a "détente" with. They no longer rampage through the population. In fact, some of the proteins they produce are vital to our survival. One of these retroviral proteins permits implantation of the placenta. Without it, we'd all have placentas that don't attach to the uterine lining -- like mice, which as a result, aren't very complex when they have to be born.
Yes, HERVs are related to cancer. This occurs naturally. They act in a transposon-like manner, and they can pop into areas where they either damage mechanisms that prevent cancer or control cell replication. If we don't study these viral remains, we won't learn about them, won't learn what we can safely disable further -- and what we don't dare eliminate from our genome because we are dependent upon it.
These researchers were not Dr. Frankensteins, messing with things man was not meant to know. They were careful, they were deliberate, and theya re beginning the investigation into what could be an incredibly crucial topic in molecular biology.
Remember -- these are viruses that we learned to live with, more or less. By studying them, we can learn to mitigate the damage they still present.
Re:HERVs: 8% of Human Genome (Score:4, Interesting)
Parent
Re:HERVs: 8% of Human Genome (Score:5, Funny)
Hell yes! I removed all that crap and compiled my DNA with -O4 -funfold-proteins -march=ubermensch and now I can flip a VW bus with one hand and paint fences with my mind! w00t!
Parent
Re: (Score:3, Insightful)
Life will find a way.... have you learnt nothing?
Re:HERVs: 8% of Human Genome (Score:4, Funny)
Parent
Here's an anolgy (Score:2)
Way ahead of you (Score:4, Funny)
As a side note, tonight I am sleeping on the couch: got busted typoing a Google image search for 'Large Hadron Collider.'
Parent
Re: (Score:3, Informative)
The mistake you're making is trying to do the calculation with Earth's mass and zero radius. But the thing is the gravity doesn't come from a tiny point in the center, that's just a simplification. As you go inside the earth, there's going to be more and more matter over you pulling in the opposite direction. Were you to end up in the center there would be no gravity at all, as the matter around you wo
not sure... (Score:4, Funny)
I'm not sure, but I'm sure Mohinder Suresh would be interested in this information.
Parent
Re: (Score:2)