Slashdot Mirror
Integrated HIV Successfully Cut Out of Human Genome
Chris writes "German scientists have succeeded in snipping HIV out of human cells after it has integrated itself into a patient's DNA. The procedure is a breakthrough in bio-technology and fuels hope of a cure for AIDS. The group is only cautiously optimistic, though, as treating a full-on infection would be substantially different than succeeding in a controlled lab environment. 'Researchers ... began with the bacterial enzyme Cre recombinase, which exchanges any two pieces of DNA flanked on either end by a certain pattern of nucleotides (DNA subunits) known as loxP. HIV does not naturally contain loxP sites, so the team created a hybrid of the two DNA molecules, which they used to select a series of mutated Cre enzymes that were increasingly able to recognize the combined DNA. The final enzyme, Tre, removed all traces of HIV from cultured human cervical cells after about three months, the researchers report online today in Science.'"
Can someone translate Doogie Howser's summary to English for us?
Alright, I must be crazy. I was just thinking about HIV in the shower, and a similar idea came to my mind. Now it wasn't identical-that would have been freaky-but similar enough to make my hair stand up when I read the first /. entry this morning
They are about 26 different stains of HIV. Article didn't mention it but I am curious if each strain might require a different technique or if this is strain independent? Either way pretty cool stuff.
Did they do it with an iPhone?
They used the transporter and the pattern from when the person beamed down on the away mission...
I read about this in PhysOrg yesterday and they speak more about something the last paragraph of Scientific American only mentions. The fact that they wouldn't use this enzyme to remove HIV infections but instead to figure out which cells have been infected. The biggest problem in treating HIV is that it can go dormant and undetected for so long during which the host can infect others. It sounds horrible, but even being able to destroy all the cells infected with the virus is worth something though it may often prove fatal to the host. I don't think this is a 'cure' or 'vaccine' merely something that makes HIV treatments much much more effective.
My work here is dung.
HIV does not naturally contain loxP sites, so the team created a hybrid of the two DNA molecules, which they used to select a series of mutated Cre enzymes that were increasingly able to recognize the combined DNA.
So...this technique won't work at all in the real world. It won't even work with actual HIV even in the lab.
It's interesting research for its own sake, but in this case it has absolutely nothing to do with HIV. They simply found an interesting way to remove an arbitrary snippet of DNA. In fact, to make it work with HIV, they had to cheat and add tags to the HIV sequence.
This is like saying I could break into a bank vault after I replaced the lock with one I knew the combination to. It says nothing about the bank, only that I possess the capability to manipulate locks.
Think of this as an initial proof-of-concept. Fiddling with DNA is extremely useful - correcting genetic diseases and curing all sorts of viruses that hang out in your cells comes to mind (e.g. herpes). You could even look at curing cancer, since that's typically due to genetic mutations that could be potentially removed, making cells non-cancerous again.
Eventually, you'll want to be able to recognize and remove longer strands of DNA. I'd also worry about the efficiency - randomly removing strands of DNA from healthy cells is a good way to cause big problems. Existing gene therapies that use viruses to deliver the payload sometimes go astray and cause cancer, which is no good.
An extremely cool piece of engineering. Probably impossible to apply large scale. If applied large scale,
I believe the risks of faulty snippet cutting would be quite significant:
Assume the protein mutates every so slightly, or just assembles in a slightly different conformation, which would accept a slightly different DNA sequence, with a single nucleotide wrong compared to loxP (lets call this sequence loxP*). Maybe this loxP* appears somewhere else in this persons genome (or even the loxP). Then she will be in big trouble. As we all know every individiual has a unique genome, and therefore it is difficult to test if the loxP or the loxP* exists anywhere in the full genome. It not enough just to check the genome of this person either, has every person has several millions of mutations in the active cells in their body (part of the immune system).
Error:
"Good news everyone!"
"the team created a hybrid of the two DNA molecules"
...and they named it Farfegnugen.
Kinda makes me wonder why we never thought of this before...
Although I feel this may also be "cheating", as Mr. Underbridge points out, I don't care. It gets us in the door, allows us to wedge it open, and take out what we want. I look it it more like "painting" a tank with a laser target so the smart-bomb knows where to strike. This is still a pretty good milestone. Maybe, just maybe, in my lifetime, we'll see this disease destroyed. I would like to live to see that.
Bleh, TFS sounded like the virus/mutation conversation from Bladerunner to me.
This is a big deal because it shows that this technique which has been used for years to cut out fragments of the genome for replication (via PCR and other methods) could be used to remove the viral elements from a genome. It's a big deal research-wise, but the major problem that will hinder this application from practical application is that HIV hybridizes EXTREMELY fast. Using an artificial bacterial enzyme to remove dna fragments requires a specific nucleotide sequence that it targets. Since HIV "changes appearance" (it actually mutates) at a super accelerated rate (100,000+ faster than animal genome) it makes treating (in this case removing) the virus very difficult. This is the same reason that current HIV treatments are effective at first, but slowly become less and less effective as the virus hybridizes. I'm not sure about needing a different enzyme for every strain of HIV, but that certainly makes sense. I don't claim to be an expert on this topic, but I certainly find it interesting. Just my 2 cents...
Could this lead to people getting away with murder because they can alter their DNA ?
Could this lead to people being framed for murder due to spoofed DNA ?
This sounds like it could destroy the credibility of DNA evidence for high-profile cases in the future.
Wanna fight ? Bend over, stick your head up your ass, and fight for air.
This weeks Escape Pod Podcast (hosted by Steve Eley) is called the Giving Plague and touches on viruses, HIV, and the potential symbiotic relationship and borg like integration viruses can have with Human cells.
One of the thoughts is that viruses actually benefit the race in the long term, as we will eventually form a symbiotic relationship with the majority of them. (uses e-coli in our gut as an example), but how one day someone will be resistant to AIDS and that will make the human race stronger.
A good listen if you're fascinated by this topic. check it out. non-disclaimer: I'm just a fan.
I'm surprised that (at least reading at +3) I haven't seen any comments about the fearful implications of this.
Let's see - if I understand correctly, we've developed the capability to engineer something that can go in and ERASE very specific segments of people's DNA? I'm sure the biowarfare guys are going to have a field day with that. I'm a little concerned about the outlook for the rest of us, however. The White Plague, anyone?
-Styopa
It has one serious side effect, it temporarily turns you into a rabbi.
It is by the juice of the coffee bean that thoughts acquire speed, the teeth acquire stains. The stains become a warning
Ok, this is my wild idea.
We know that we can "reboot" the immune system by destroying the bone marrow and repopulating it with new one coming from a donor.
Now lets say that we do an autotransplant. First we take a sample from the donor and then this sample is treated with the enzyme so all of the HIV's DNA is removed. Next, we introduce a gene on this cultured cells that will produce the enzyme, thus rendering them immune to infection. Next we destroy the donor's bone marrow and implant the new one.
There will be infected T cells left behind, but they won't reproduce as they are outside the bone marrow and they would eventually die.
Could this ever work?
When his defense asked, "Which computer has Jon Johansen trespassed upon?" the answer was: "His own."
They've done it in vitro in a lab. Which is a good start, but that doesn't mean you can now safely screw anything that walks.
They probably haven't developed anything which they could conceivably be administered to a living organism yet - let alone tried administering it to one. Then you've got a battery of tests to make sure it's safe and effective - there's probably at least another 10 years before this could really be a treatment.
The great majority of potential treatments never make it through that development/testing process.
"HIV does not naturally contain loxP sites, so the team created a hybrid of the two DNA molecules, which they used to select a series of mutated Cre enzymes that were increasingly able to recognize the combined DNA." - They are not looking for the HIV DNA but they are finding it by looking for where it is not and then cutting it out. To prove they removed it they first had to mark it so they could prove it. Any effective treatment later would be difficult because you are are removing chunks of DNA from cells you "assume" are viral DNA. This sounds very important though. (I'm not a molecular biologist)
Regardless of the hybridization that HIV may undergoes the point here is that they engineered a way to recognize the HIV DNA because it "lacks" something that is found on normal DNA in this case a particular sequence that marks the point where HIV DNA is inserted into the normal DNA sequence. My take on this is that is akin to:
Think of a DNA sequence like a hotdog. (I know simple, simple) Take the hotdog and slice it in the middle, then take another hot dog and add a section of the second hotdog to the first. This simulates the HIV sequence hiding in the host cell's DNA. Now look at it. We can find the area where it is spliced because we can see the cut marks. Even if we switch from differing brands and types of hotdogs we will still be able to identify where the viral "hotdog" was inserted and is hiding by looking for the cut "ends" of the normal hotdog and remove the "invading" hotdog piece in the middle. and splice the original hotdog back together.
The end result is that the virus does not "destroy" the T-Cell when it activates and replicates itself. Given that a hiding virus DNA strand in a T-Cell is eventually a "killed" t-cell I see the development of this bacteria DNA cutter will develop rapidly. Fascinating stuff...
I, for one, welcome our new Tre-enzyme mutant HIV-resistant overlords...
-S
Scientists were also overheard talking about the optimal delivery mechanism for this gene splicing technology being a radioactive spider. Further field tests are needed.
I'm a fiscal conservative, it's a pity we don't have a political party anymore
So they can regex DNA now. Sweet.
We don't get laid and we don't inject drugs. How is a nerd supposed to get AIDS (Anal Intercourse Death Syndrome)?
Oh wait, I must have read the article wrong. There must be a new Windows threat called the Heuristic Interloping Vector, Antagonistic Insecurity Device for Suckers. So, is this a virus, a trojan, or a worm? I mean, the article says it's a virus but they call trojans "viruses" all the time. Any crackers out there care to explain this to me?
Wish yourself Outside and create the recolada.
-- My Sig is a P228.
From what I read in a newspaper article (in spanish though).
Says (for all of you non-spanish speakers) there is "slight hope" for treatment to exist in 10 years.
and the "complicated" treatment would be (according to newspaper and my weird translation).
"..to obtain stem cells from the patient's blood, 'clean' them of the virus in the lab. Then these treated cells would be reintroduced into the patient and should regenerate their immune system.
Although, by this method it is highly unlikely that it will be possible to completely remove the virus from the patient, Hauber does hope that there would be enough removal of the virus to control the infection.
'This is high-technology medicine, and can't be administered in form of a pill (duh', indicated the scientist. In case mutations occured in the ends of the sequence of the virus, recombinases could be adapted quickly.."
It also mentions that the treatment would be cheaper compared to current treatments that supposedly range around $20,000 usd yearly.
This claims that it is blank plague survivors. Somewhere else, I read that it was small pox survivors. Whichever it is, some people with a certain mutation are pretty much immune to aids.
This approach is not really that useful in terms of coming up with a cure for HIV. The reason is that the complexity to excise a specific sequence of that length is WELL beyond our knowledge.
But this will hopefully lead to a real "cure" in being able to mutate it to being none-lethal or even quiescence. It struck me back in the early 80's, that about the only way is to insert a virus inside this virus and break the formation of the protein chain.
I prefer the "u" in honour as it seems to be missing these days.
... it would be move valuable than gold! If you could suddenly change peoples dna, not only would this be dangerous as to where it goes, but it could be invaluable. People who have genetic diseases could all be cured, by replacing parts of their dna. People who wanted sex changes could have their dna changed also. The scary part is that people who did not like a certain race of people could change that race genetically. The possiblities are endless.
Only 'flamers' flame!
Does slashdot hate my posts?
I mod down anyone who says "I will be modded down for this", regardless of the rest of their comment
The problem with the incentive model that you're describing is that it would need to be universally implemented or the prize has to be comparable to the profits the researching company could expect to earn from the discovery. If the incentive is tied to a clause that requires a particular pricing model, then the company will always look to see whether they can make a greater profit by declining the prize and using the same pricing models they've been using.
Virtue finds and chooses the mean.
Aristotle, Ethica Nichomachea
One would assume that there are a few critical sequences in the virus, without which it would not function or evolve around. Could the structure of its protein shell be corrupted to cause it to immediately fall apart, a la penicillin? Could changes be made to ensure that it would remain forever dormant?
It would seem that, with this technique, a little sabotage might get nearly the same benefit as cleaning it all out, for much less effort and risk.
I hate to break it to you, but AIDS is a lifestyle disease too. People choose to have sex with whomever they please and some of those people have AIDS. If they choose to do it without a condom the probability of them contracting it increases further. (I said increases because you can still get it from them even if you're using a condom). It's a *choice*.
If you're born with AIDS, that's unfortunate. I'm sorry that your parents were selfish. No, you do not deserve to die, but your short life is the result of poor choices made by your parents.
AIDS is the most ridiculous disease ever. It could have died out ages ago if the few people that initially had it (or HIV) would have just stopped having sex.
Looks like there's a flaw in God's plan to kill gay people with Aids. Sweet!
Today, Satan and the Demons sing, and the angels cry.
If only Yahweh had designed his murderous bug with a little more forethought.
(-1: Post disagrees with my already-settled worldview) is not a valid mod option.
too bad I don't have a cervix :(
I don't understand that (this is an honest assertion, not a troll).
Why you don't just s/medical insurance/healthcare tax/? You already pay for it... it shouldn't bother you to s/insurance company profit/other people health/.
I guess it isn't that simple, and that maybe even using those profits to cover other's health may not be enough... but do you really prefer to pay someone's profit, rather than paying a bit more for someone's health or life?
Awesome explanation. The story didn't make any sense to me until I read your explanation of evoloving Cre into something useful for this purpose. Thank you. This is the most nerdly thing I've read all day.
But I have to say that I disagree about needing to be careful about the number of infections in the host cell. HIV infects differentiated cells that do not naturally reproduce, so mutagenesis leading to cancer is unlikely, and killing infected cells is very nearly as useful as curing them. The body can/will always make more.
IMO, this would be less of a problem if the United States had socialized medical care like the rest of the modern world. However, since this isn't the case the wealthier people in the US accidentally promote R&D into non live saving medicine because it suits them more, and they're willing to pay. If medical care were socialized, there'd be less of a lure to develop so many "useless" medicines, and more of a lure to develop live saving medicine.
m Article.pdf is an older article that talks about some of it, http://www.futurepundit.com/archives/003979.html is newer and has newer refernces.
/. tend to think about the absurdity of software patents, but medical patents can be far more deadly and really need a review when they're used to prevent delivery of medication to people too poor to pay for medicine.
/. we see an apparent focus on software patents. That combined with their "relative newness" makes it seem they are easier to fight.
Yeah because socialized countries have developed cures for all those "poor people" cures. I must have missed the memo that France cured TB and AIDS, Germany cured Malaria, and Cuba's been busy curing the common cold.
In reality, outside of bash-a-country-fests, the facts are that the US dominates in medical research - both in discoveries as well as spending.Over the last 22 Nobel prizes in Medicine, only 7 went to people not working in the US. http://ostina.org/downloads/pdfs/bridgesvol7_Boeh
The US spends about 100 Billion dollars per year on medical research, and over half of it is private enterprise. To contrast, Europe spends single-digit billions. IN 2000 for example, Europe spent combined 3.7B versus some 90B by the US. Private spending in the US outstrips total spending in Europe. And the US has a smaller population. Which also means the US spends more per-capita than does Europe.
This is for research, not overall medical expenses.
In cancer research in the EU, over half of the spending came from charitable organizations. IN terms of cancer research spending the US easily spends more than double the EU. An interesting note is that the EU states contributed about 1.2B in noncommercial cancer research funding, and about 1.0B in tobacco subsidies (data for 2004).
Spending is IMO a poor measure, but for many it seems to matter so I list it. By that measure the US trounces any socialist country in medical research. The US also spends more on medical research as a percentage of GDP than socialist countries; 5 times as much as the EU and 7 times as much as Europe.
A decent measure is discoveries and treatments. Again, the US puts out far more discoveries and treatments per year than any socialist country.
I know people on
I suspect most of us are actually on about patents overall being bad in many ways, but since we are on
My Suburban burns less gasoline than your Prius.
...it'll be so expensive that only a few rich patients will afford to buy it, effectively allowing the poor to continue spreading the virus. What a fantastic way to stop an epidemy.
Will this cure AIDS, yes AIDS. FULL BLOWN AIDS! Can be sure this will cure not just HIV, but FULL... BLOWN... AIDS!!!!!!
I wonder if this will appear in the next release of Norton AntiVirus.....
Knowing Google's lust for data collection, the Soviet Union is still alive and well inside the psyche of Sergey Brin....
As far as I know retro viruses do not integrate themselves at totally random places in the genome, but there are preferred areas. So would it be possible to manufacture an artificial retro virus, which preferably integrates itself within the sequence the HIV virus adds to the human genome, rendering it inert this way?
Does anyone know if they used the resources from a grid computing project like World Community Grid?