Slashdot Mirror
Viral Fossil Brought Back To Life
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."
need I say more
...a new (retro)virus.
/sarcasm
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?
Only 3% of the genome is genes, the rest is junk DNA which has a lot of interesting stuff like alternate versions of genes, commented out ideas, and coded critters like this one that sit in your DNA like "sunken ships". There are like 200 copies of reverse transcriptase in the human genome, different versions, all in this junk DNA. Reverse transcriptase has absolutely no legitimate purpose in a eukaryote. It can take a segment of RNA (usually viral RNA), convert it into DNA, and stich it into your genome. Only viruses need to do that. The RNA itself has code for reverse transcriptase, and we see it in our chromosomes all over the place, this gene that is useful to viruses and no one else. It's the most common gene in your body.
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. 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. 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.
The abstract with a link to the full pdf is available online. The pdf is available on campus from many universities. It is interesting that this is already in the news. This is not technically in print form yet, and was just posted to the journal's advance articles web site.
"Asleep at the switch? I wasn't asleep, I was drunk!" -- Homer
If human beings were designed, it seems to be a poor design to include copies of viruses in it. But we mere mortal humble human beings dont have the intellect to fathom the Divine Intentions. All we can say for sure is that, unless you pay the priest 10% of your income and get dunked in a pool you will rot in Hell.
sed -e 's/Chuck Norris/Rajnikant/g' joke > fact
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. 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.
This sig seemed like a good idea at the time....
Creating black holes for kicks? That's what they are about to do in 2008 using the Large Hadron Collider.
As a side note, tonight I am sleeping on the couch: got busted typoing a Google image search for 'Large Hadron Collider.'
Obama likes poor people so much, he wants to make more of them.
Wasn't this the plot of one of the Final Fantasy games?
I'm not sure, but I'm sure Mohinder Suresh would be interested in this information.
The theory of relativity doesn't work right in Arkansas.
Err, no, at the center of the Earth gravitational pull wouldn't be infinite. Rather, there wouldn't be any.
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 would pull equally in every direction.
What could possibly go wrong?!
"No Risk"
By no means do I suggest that these researchers necessarily acted dangerously or that their research and research like it should be stopped, but I have to say that complex efforts with potentially "devastating" [your term] results should not be reassured against with phrases like "there was no risk". Your explanation of "The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate" only inspires a dubious curiosity for how this was done.
Indeed, also hearing the allegation that "the researchers couldn't be absolutely sure about Phoenix's infectivity" and that only biosafety level 3 was used while a level 4 was recommended, a layperson is left to wonder. (What the hell is a biosafety level in the first place, ?)
These researchers are Dr. Frankensteins in their pursuit of knowledge. And let them be! The pursuit of knowledge is unquestionably good! Just let them be careful while doing it, or they may also be Dr. Frankensteins in their poor safeguarding, Unleashing The Ritz on us.
Biodiversity & Nanomachines
In support of the investigation, let me say that I recently wondered, on the tail of some ethics reading regarding ecology, what other utility values nature could provide us beyond simple resources and recreation. Thinking of how proteins are basically nanomachines; and how much of the unused portions of our genome may be disused codes for once-useful, now-retired proteins; and how hard it must be to design a working nanomachine (just look at how hemoglobin contorts so bizarrely with the simple addition of an oxygen molecule); I came to wonder whether there might be a goldmine of blueprints for tested nanomachines in us. In us and every species we destroy.
Yes, please figure out how to mine genomes for molecular machines. In the meantime we'll see about preserving all these genomes.
Ob. Plural Of 'Virus'
Don't say 'virii'. That isn't even just wrong yet. You probably mean 'viri', which is just wrong. It wasn't used in the plural (being a mass noun, not a count noun) and there may not have been a proper plural form of it in Latin. My guess is that it is actually a 4th declension neuter with a plural of 'virus' (long 'u' sound), but what the hell do I know? Well, more than someone saying 'virii', by a long shot. Be safe, inflect it in English rather than classically: viruses.
Knowing the details of the debate makes you a pedant. I mean, how important is it really? But using the certainly wrong classical form makes you ignorant.
http://en.wikipedia.org/wiki/Plural_of_virus
http://www.sysinternals.com/Utilities/RootkitRevea ler.html has a tool that can help flesh out all those registry and file system API discrepancies for further study.
Of course it's always safe to run AdAware[ http://www.lavasoft.com/ ] and if you have the budget, purchase WebRoot[ http://www.webroot.com/ ] for a fast, centralized cleaning in the enterprize environment.