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Prehistoric Gene Reawakened To Battle HIV 360

Posted by kdawson
from the learning-from-our-distant-cousins dept.
Linuss points out research published in PLoS Biology that demonstrates the reawakening of latent human cells' ability to manufacture an HIV defense. A group of scientists led by Nitya Venkataraman began with the knowledge that Old World monkeys have a built-in immunity to HIV: a protein that can prevent HIV from entering cell walls and starting an infection. They examined the human genome for any evidence of a latent gene that could manufacture such a protein, and found the capability in a stretch of what has been dismissively termed "junk DNA." "In this work, we reveal that, upon correction of the premature termination codon in theta-defensin pseudogenes, human myeloid cells produce cyclic, antiviral peptides (which we have termed 'retrocyclins'), indicating that the cells retain the intact machinery to make cyclic peptides. Furthermore, we exploited the ability of aminoglycoside antibiotics to read-through the premature termination codon within retrocyclin transcripts to produce functional peptides that are active against HIV-1. Given that the endogenous production of retrocyclins could also be restored in human cervicovaginal tissues, we propose that aminoglycoside-based topical microbicides might be useful in preventing sexual transmission of HIV-1."
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Prehistoric Gene Reawakened To Battle HIV

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  • by ringbarer (545020) on Friday August 07, 2009 @12:23PM (#28987151) Homepage Journal

    Praise Raptor Jesus!

  • by Snotman (767894) on Friday August 07, 2009 @12:27PM (#28987201)
    AIDS is pwned. Good for us and our "junk" DNA. One man's junk is another man's treasure!
    • by Anonymous Coward on Friday August 07, 2009 @12:30PM (#28987239)

      Just don't stick your junk in the wrong treasure and you'll be fine.

    • by kalirion (728907) on Friday August 07, 2009 @12:30PM (#28987243)

      One man's junk is another man's treasure!

      I'll just treasure my own junk, thank you very much.

    • by Chris Burke (6130)

      Yeah, turns out there's all kinds of amazing opportunities [dresdencodak.com] hidden in our junk DNA. A cure for AIDS, and chances to Win Fabulous Prizes!

    • by Garbad Ropedink (1542973) on Friday August 07, 2009 @01:17PM (#28987801)

      Unfortunately no. By using the 'pwned' in reference to a potentially major scientific breakthrough you've actually made AIDS mutate to become airborne and highly contagious.

      It's called the 'Nantucket Principle'. Where using idiotic phrases in reference to intelligent work causes the work to be destroyed.

      Another case of this principle at work was when the Wright brothers tried their first airplane prototype. Just before they were going to do their first test flight Orville said something to the effect of 'We are going to codfloddle this strumpet!' which caused Bernoulli's principle to completely change, setting flight back many years.

      So you have to watch it.

    • by icebike (68054) on Friday August 07, 2009 @01:53PM (#28988261)

      Junk DNA is one of the greatest misnomers in genetics. It basically arose because people didn't understand the purpose of a particular gene, or they found (as in this case) that a sequence was prematurely terminated due to an encoding error, which could only be detected via comparison to another working copy from another source.

      This opens up a new field of bug detection: looking for broken code, figuring out what patch is needed and then figuring out what you could do with the repaired gene. This is going to call for vast amounts of computer simulations.

      In this case we were led to a solution to the breakage by a similar gene in another species. But there must be millions of broken genes laying about that might re-enable some traits, anything from gills to the ability to smell tyrannosaur breath. (Pedants: Look, its a joke, please don't bother pointing out the time line here, Ok?).

      There seems a tendency to assume all "lost things", (genes, knowledge, secrets of the universe, methods of building pyramids, etc) are of immense value, and far superior to knowledge we have today. (Slashdotters will surely have a term for this.) Not everything lost is desirable. This is one example that may well be.

      Many species might be expected to genetically re-energize, by natural means, any lost protection in the face of a re-appearing threat. That might take eons. If this discovery leads to a treatment, it will be signal the dawn of genetic dumpster diving on a huge scale.

  • The Dilemma (Score:5, Funny)

    by geegel (1587009) on Friday August 07, 2009 @12:28PM (#28987213)
    I don't know what's scarier: the fact that a story with this sort of language made it to the front page or the fact that I understood it completely.
  • Maybe I just haven't been keeping up with the news on HIV research, but this would seem to be a truly novel approach to preventing transmission. Excellent work!
  • by TheTick21 (143167) on Friday August 07, 2009 @12:29PM (#28987229) Homepage

    /* This code commented out because I'm sure they're going to change their mind and I don't want to redo all the work. */

    • by AdmiralXyz (1378985) on Friday August 07, 2009 @12:53PM (#28987539)

      I've been known to break things by commenting out important sections, but causing AIDS?? Someone is about to have a hell of a performance review.

      • by Andr T. (1006215)
        It happens all the time [linuxjournal.com], or so it seems.
      • Re: (Score:2, Funny)

        by TheTick21 (143167)

        I just want to know how this bug got out of testing. You'd think "causes AIDS" would be a showstopper. They probably figured they could patch before the clients noticed.

    • Re: (Score:3, Funny)

      by cabjf (710106)
      /* This code has been commented out because it causes major bugs in the system. Will fix later. */
    • Re: (Score:3, Funny)

      by Anonymous Coward

      /* This code commented out because I'm sure they're going to change their mind and I don't want to redo all the work. */

      CTACGCTACTAC#if0CTGACGTCA#endifCTGACA

  • by turthalion (891782) on Friday August 07, 2009 @12:30PM (#28987249) Homepage

    So how long till we're all having hot monkey sex with each other? Count me out of turning on any monkey genes in *my* DNA, thank you.

    I've seen this [wikipedia.org] episode of ST:TNG, so I *know* how this is all going to end.

  • We still have a lot of our DNA not yet "activated", from what little I know about genetics, every living organism share more or less the same DNA with less than 1% of differences, its which parts that are activated and which ones that are dormant that specify what the being will look like. This also means we're still babies in terms of our evolution.

    Correct me if I am wrong.

    I for one can't wait for this to happen:
    "I dunno how much AIDS scares y'all, but I got a theory: the day they come out with a cure for

    • Re:This is good news (Score:5, Informative)

      by pauljlucas (529435) on Friday August 07, 2009 @12:39PM (#28987349) Homepage Journal

      We still have a lot of our DNA not yet "activated" ...

      If we have it, it must have evolved for a reason. Currently inactive DNA was active in the past. There's just no evolutionary pressure for it to be removed, so it sticks around.

      [E]very living organism share [sic] more or less the same DNA with less than 1% of differences ...

      Nope: We have a greater-than-1% difference with chimps, our closest living relatives. The Amoeba dubia [wikipedia.org] has more than 200 times the amount of DNA than humans.

      • Nope: We have a greater-than-1% difference with chimps, our closest living relatives.

        Apparently not:http://www.sciencedaily.com/releases/2009/06/090618084304.htm [sciencedaily.com]

        Apparently we didn't look at enough DNA before
      • Re:This is good news (Score:5, Informative)

        by atfrase (879806) on Friday August 07, 2009 @01:14PM (#28987771)

        If we have it, it must have evolved for a reason. Currently inactive DNA was active in the past. There's just no evolutionary pressure for it to be removed, so it sticks around.

        You're sort of getting at how evolution works, but I have to nitpick your word choices. The whole idea is that evolution is random and patterns only emerge when those random mutations lead to statistically significant implications for survival and reproduction.

        So it's misleading to say anything "evolved for a reason" because evolution isn't an intelligent process -- it doesn't do things because of reasons. It's also not exactly true that "[c]urrently inactive DNA was active in the past" because every generation is bound to produce lots of random genetic mutations which have no impact on our survival, in many cases because they have no impact on our physiology whatsoever. The commented (computer) code analogy is very apt here.

        However, what you're hinting at isn't just that "we have it", it's more precisely that "we all have it." The fact that a large portion of the human population all has the same inactive DNA in this position does imply that it was active in the past, and that it was beneficial in the past, because that's the only way the same DNA could end up in every person's genome. If it had never been active or useful, then we would all have had to (randomly) mutate the same useless code in that spot, which would be statistically very improbable.

      • Re: (Score:2, Funny)

        The Amoeba dubia [wikipedia.org] has more than 200 times the amount of DNA than humans.

        Slut!!

      • Re: (Score:3, Funny)

        by kungfugleek (1314949)
        But the Amoeba Dubya has a 0% difference with chimps!

        Sorry, I'll show myself out.

    • We still have a lot of our DNA not yet "activated", from what little I know about genetics, every living organism share more or less the same DNA with less than 1% of differences, its which parts that are activated and which ones that are dormant that specify what the being will look like. This also means we're still babies in terms of our evolution.

      Correct me if I am wrong.

      1. I'm pretty sure there's a lot more than 1% difference between us and anything except (maybe) some of the great apes.
      2. "Babies in terms of our evolution" seems to imply there's some kind of predefined ladder we're climbing as we evolve, which isn't how it works.

      I for one can't wait for this to happen:
      "I dunno how much AIDS scares y'all, but I got a theory: the day they come out with a cure for AIDS, a guaranteed one-shot cure, on that day there's gonna be fucking in the streets, man." - Bill hicks

      Yeah, I think Bill's pretty much right on that one--there's definitely going to be some partying going on out there if this is a sure cure.

    • by furby076 (1461805)
      The rhythm method will be back in style!!!! OH YEA!
    • every living organism share more or less the same DNA with less than 1% of differences,

      You've got the general idea, but the specifics are off. IIRC, we share 99.9% of our DNA with bonobos and gorillas, slightly less with chimps, less with other mammals, and so on and so forth as you get further and further away from our "branch" of the evolutionary tree. I believe we share something like 12% of our DNA with the banana. But yeah, there's a lot of commonality there.

    • by idlemachine (732136) on Friday August 07, 2009 @02:00PM (#28988363)

      We still have a lot of our DNA not yet "activated"[...] This also means we're still babies in terms of our evolution.

      Fire up Windows.

      Now fire up every single application you have installed.

      While you're at it, download and load every single Windows application ever.

      Getting a lot done?

      Maybe activating the "full potential" of Windows isn't all that useful.

  • by R2.0 (532027) on Friday August 07, 2009 @12:31PM (#28987267)

    We reactivated this gene in the lab, and it seemed to work. There's a type of antibiotic that seems to reactivate the gene as well. So applying the antibiotic topically (read "like spermicidal foam/gel) should reactivate the gene in a woman's naughtybits and so fight the virus.

    Focused on the woman - good idea. But how does science focus on the man? How about "STOP FUCKING PEOPLE WHO AREN'T YOUR WIFE/GIRLFRIED/SIGNIFIGANT OTHER!"

    • by Krneki (1192201) on Friday August 07, 2009 @12:55PM (#28987567)
      Men were not made for monogamy, your stupid culture made you believe so.
      • Re: (Score:3, Funny)

        by Anonymous Coward

        Men were not made for monogamy, your stupid culture made you believe so.

        Is that what you tell all the girls?

    • Since most humans have more than one SO in their lifetimes (even in the context of strictly respected serial monogamy), your advice is stupid. A similar advice was spouted when AIDS was called GRID [wikipedia.org]: "stop fucking gay men"

      I'll leave the proof for you to do as an exercise.

      In other news, spermicidal gel can be applied on a penis too.

  • by xednieht (1117791) on Friday August 07, 2009 @12:37PM (#28987321) Homepage
    Minor side effect of re-activating the sequence - you become very hairy, lose the ability to walk upright, and have a curious craving to pick through other's hair in search of lice.
  • what is an 'old world' monkey?

  • I'm just saying...

    Seriously, I tried to read the article, but sentences like, "this treatment induced the production of intact, bioactive retrocyclin-1 peptide by human epithelial cells and cervicovaginal tissues," just make my eyes glaze over and think that the peers reviewing this journal are way out of my league.
  • Not surprised (Score:5, Informative)

    by DahGhostfacedFiddlah (470393) on Friday August 07, 2009 @12:39PM (#28987361) Homepage

    It seems to me that we carry a "catalog" of genes that are not currently useful, but have been useful in the past. It's not as if evolution destroys genes - for the most part it tends to make them inactive.

    • And sometimes, it makes them active again.
      Given time, there is a high probability that this capacity would have re-evolved, assuming that there is a selective advantage.

  • Huh? What? (Score:3, Funny)

    by DeathMagnetic (1365763) on Friday August 07, 2009 @12:42PM (#28987391)

    In this work, we reveal that, upon correction of the premature termination codon in theta-defensin pseudogenes, human myeloid cells produce cyclic, antiviral peptides (which we have termed "retrocyclins"), indicating that the cells retain the intact machinery to make cyclic peptides. Furthermore, we exploited the ability of aminoglycoside antibiotics to read-through the premature termination codon within retrocyclin transcripts to produce functional peptides that are active against HIV-1. Given that the endogenous production of retrocyclins could also be restored in human cervicovaginal tissues, we propose that aminoglycoside-based topical microbicides might be useful in preventing sexual transmission of HIV-1.

    Woah, I think I'm going to need a car analogy...

    • Re: (Score:3, Insightful)

      by badboy_tw2002 (524611)

      In this work, we reveal that coating the inside of your car's tail pipe reacts with the metal to prevent tail pipe wevils, (Highly Infectious Vermin) from nesting and eventually breaking down your entire car's resistance from rust.

    • Re:Huh? What? (Score:5, Interesting)

      by oracleofbargth (16602) on Friday August 07, 2009 @01:14PM (#28987763) Homepage

      Woah, I think I'm going to need a car analogy...

      Say your car door doesn't have any manual door locks, since it was built to be all automatic, but you lost the remote a long time ago. Your car could easily be broken into or stolen, now that you can't lock the door. So, you have someone read through the engineering manual for the car to find the code the remote used, and build another one to let you lock the doors again.

  • there's a whole bunch of crap down there i needed at one time, and mostly have forgotten about. there's also a small chance i'll need something down there again, but usefulness is so marginal. but every now and then i'll notice a glimmer of something in the corner i had totally forgotten, and i go "holy crap! this is incredibly important!"

  • by JoshDM (741866) on Friday August 07, 2009 @01:00PM (#28987623) Homepage Journal

    a caveman could do it.

  • by mea37 (1201159) on Friday August 07, 2009 @01:01PM (#28987637)

    ...and I know really it's too early to know, but the big question on my mind is: what sort of treatment are we talking about here?

    Can a cure for AIDS be derived from this? Or will it be a matter of "if we catch an HIV infection early, we can clear it up and minimize the damage"? Or is it only useful as a preventative measure, which seems to be where the quote in TFS is headed?

    If it's only useful as a preventative measure, then there are two big issues.

    One is how prone it would be to user error. If it's a "follow these steps every time you're going to put yourself at risk" kind of thing, then there's a concern that the increase in people's willingness to put themselves at risk exceeds the practical efficacy of the prevention. OTOH, if it's a "go to your doctor once (or once every X time period) for a professioally-administered round of protection", then that's probably less an issue.

    The other is... look, I'm all for scientific progress, and I think we should research the hell out of this, but let's not jump the gun. As evidenced by the fact that we call potentially-functional strecthes of DNA "junk", we do not understand what they do. If prehistoric animals used this sequence and we don't, there is probably a reason, be it small or large. Maybe it's as simple as "it takes cellular resources and the risk of an HIV-like attack had subsided below the break-even point" - and if that turns out to be the case, FULL SPEED AHEAD! Or maybe evolutionary pressures put the protein in disfavor because it interferes with some other aspect of modern human biology, or has some secondary effect that is harmful. Now it's hard to imagine that would weigh in as "more severe than an active HIV infection", so it might still be a useful treatment for a known case of AIDS if it can be used in that way (depending on cost/benefit vs. other AIDS treatments); but not necessarily a good preventative measure if that were to turn out to be the case.

    • Re: (Score:3, Interesting)

      by jhfry (829244)

      I'm guessing that it's a one time treatment.

      Essentially its a cream/lotion that can be applied topically to trigger a genetic mutation of cells. These cells then reproduce in the typical fashion, which would maintain the same genetic code.

      I think they use a creme because all they really need effected are the parts that may be exposed to the virus. Otherwise they would use an engineered virus to deliver the mutation to your entire body.

      I'm just guessing, I could be way off base here.

      • Re: (Score:3, Informative)

        Unfortunately no. They're not actually changing the DNA. The cream/lotion concept (which they don't actually have yet) would contain the special molecule they tested that is built to help a cell read past the premature terminator in the gene sequence, so it can successfully build the proteins we're talking about. It's hitting the Retry button on the Abort, Retry, Fail prompt and successfully getting past the bad sector. But it's a local, temporary thing.

        In theory, yes, a retrovirus could be engineered t

  • The PLoS article [plosbiology.org]

    I've always been fascinated by "junk DNA." It *can't* be junk; there is so much we don't know here... In fact, the definition of "junk DNA" is something along the lines of "DNA we have not yet identified" Evolution would not have allowed for the repeated (and repeated and repeated) replication of so much code if it wouldn't have been more costly to simply ignore it. More and more researchers think that these are sequences which had a use in regulation, spacing, etc, and which can be put tog

    • Well no, not useful new ways. Useful OLD ways. The process involves reactivating gene sequences that all humans currently carry in disabled form. They've been around a long time. Our copy just has a premature terminator in the sequence that prevents it from working. The article demonstrates that they've found a way to read past the terminator to pick up the rest of the sequence and produce fully viable human-grown retrocyclins, which kill HIV. Rather than putting together raw material, these researche
  • by Anonymous Coward

    I can only imagine the cognitive dissonance in an HIV-infected creationist when s/he finds out about this!

  • For designing us with immunity but not turning it on so that the hemophiliacs (which you also must have intentionally designed in) can die horrible deaths.

  • Not called junk DNA (Score:5, Informative)

    by 140Mandak262Jamuna (970587) on Friday August 07, 2009 @01:20PM (#28987851) Journal
    The summary says "dismissively called junk DNA". That language does not occur in the serious study done by Nitya Venkataraman. I found the passage in the article, it says n "Previous reports revealed that aminoglycoside antibiotics could suppress the termination codon of pseudogenes and disease-associated nonsense mutations [19â"25]. In bacteria, "

    People be careful when you summarize research in evolution. Creationists are known to quote mine and they repeatedly quote the mistaken summary (like the one posted here in slashdot) but attribute it, wrongly and knowlingly to the science article. No matter how many times you correct they continue to persist in their misrepresentation. Finding pseudogene is quite common and it actually strengthens the argument for a common ancestor. Like all mammals can make their own Vitamin C. But we primates cant. The gene to make the vitamin exists as a mutated pseudogene in our genome. Such pseudogenes are quite common.

    But somehow in the mind of a creationist, gaining understanding of the original function of a pseudogene is somehow an evidence against evolution. Don't feed these trolls with sloppy summaries.

    I am very sure, creationists will trumpet "Scientists have pie in their face. New function found in junk DNA. Death of Evolution is neigh. Halleluja!" quoting this very summary.

    • Pseudogenes are one flavor of what is widely termed "junk DNA." There are several varieties of junk DNA including pseudogenes, introns, transposons and retroposons... and many pseudogenes, introns, transposons and retroposons are identified (and their functions better understood) regularly.

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