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Biotech Science

Function of 80% of the Human Genome Charted 112

Posted by Soulskill
from the scientists-are-busy-busy-people dept.
ananyo writes "In what is likely to be a historic moment in science, ENCODE, the Encyclopedia of DNA Elements, has published 30 papers in Nature, Genome Research and Genome Biology today, assigning some sort of function to roughly 80% of the genome, including more than 70,000 'promoter' regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 'enhancer' regions that regulate expression of distant genes. The project was designed to pick up where the Human Genome Project left off. Although that massive effort revealed the blueprint of human biology, it quickly became clear that the instruction manual for reading the blueprint was sketchy at best. Researchers could identify in its 3 billion letters many of the regions that code for proteins, but those make up little more than 1% of the genome, contained in around 20,000 genes. ENCODE, which started in 2003, aims to catalog the 'functional' DNA sequences between genes, learn when and in which cells they are active and trace their effects on how the genome is packaged, regulated and read. Nature has set up an ENCODE site with an explorer, that groups the papers by topic, and collects all the papers, which are available free."
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Function of 80% of the Human Genome Charted

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  • by bill_mcgonigle (4333) * on Wednesday September 05, 2012 @04:45PM (#41239185) Homepage Journal

    Just happened to hear an NPR interview on the way back to the office. The researcher described most of the 80% as regulating the expression of the protein codes. Brace yourself Slashdot: he called it the 'operating system'.

    • by vlm (69642)

      I always thought JCL on MVS was more "natural". JCL... its in my genes...

    • by fm6 (162816) on Wednesday September 05, 2012 @04:59PM (#41239343) Homepage Journal

      Yep, and the OS can get reprogrammed by viruses.

      Various fields borrow terminology from each other. Not that big a deal. My toaster has a "cancel" button. An old-fashioned "eject" would make more sense to me, but I guess mechanical terminology is less familiar to most people.

      • by tlhIngan (30335) <slashdotNO@SPAMworf.net> on Wednesday September 05, 2012 @05:17PM (#41239581)

        Yep, and the OS can get reprogrammed by viruses.

        It's also got fairly good licensing terms - I mean the OS can be replicated (it is billions of times - once for ever cell), and the OS can make copies of itself (mitosis), and even end up altering itself through random changes (mutations).

        A virus only infects one cell to duplicate itself - all the other uninfected cells have their own copy. The antivirus system basically works by killing infected cells.

        So all in all, an interesting OS - security worse than Windows (i.e., none at all - just random strings of genetic code can alter the OS - you don't neve need root! just physical access!), yet it really works by sheer number of copies.

        • > It's also got fairly good licensing terms - I mean the OS can be replicated (it is billions of times - once for ever cell), Yeah, right. But use the wrong process for replication, and you'll end up paying for it for almost two decades! How's that for vendor lock-in?
        • <blockquote>So all in all, an interesting OS - security worse than Windows (i.e., none at all - just random strings of genetic code can alter the OS - you don't neve need root! just physical access!), yet it really works by sheer number of copies.</blockquote>

          Yet just a small mutation can have disastrous consequences for the organism. Just insuring the number of copies is not enough. What is interesting is that the DNA copying process actually prevents 'forking' the source code :

          http://www.natur
      • by grcumb (781340)

        Yep, and the OS can get reprogrammed by viruses.

        Various fields borrow terminology from each other. Not that big a deal. My toaster has a "cancel" button. An old-fashioned "eject" would make more sense to me, but I guess mechanical terminology is less familiar to most people.

        I'd be a lot more impressed if your toaster had an UNDO button.

        • by fm6 (162816)

          Jeez, I can't think of any kitchen appliance that wouldn't be improved by such a feature. Alas, entropy is an issue.

      • by jedwidz (1399015)

        The real innovation wasn't the button label, but figuring out how to turn partly-toasted bread back into fresh.

    • So when is the gcc port going to be finished?

    • by MrEricSir (398214)

      Brace yourself Slashdot: he called it the 'operating system'.

      A good start, but wake me up when there's a high-level language that compiles into DNA.

      • Well, I can do one better - a programming language for DNA computing (so you can not only compile to dna, but even compute with it) :

        http://research.microsoft.com/en-us/projects/dna/
      • Four codons map define an ascii char (98 bits). Some stunt earlier this summer had a book encoded into DNA. The storage potential is vast. But the encoding and decoding is as currently rather slow.
    • by Bob-taro (996889)

      Just happened to hear an NPR interview on the way back to the office. The researcher described most of the 80% as regulating the expression of the protein codes. Brace yourself Slashdot: he called it the 'operating system'.

      So, can we run Linux?

      • I developed a concept that deals with this.
        It's called "genome base one"
        it basically means all organisms on Earth, with DNA/RNA, run the same "OS" -- Genome Base One.
        We simply have different genomes, and so we are different creatures.
        but it's all the same.
        I also own the site genomebaseone.com..!
      • Imagine a beowolf cluster of us! Oh, wait, this is the internet, it's probably been done, with video.

  • by viperidaenz (2515578) on Wednesday September 05, 2012 @04:49PM (#41239221)
    Wait for the lawsuits when they come across a gene some company holds a patent for. They "invented" it you know.
    • by Anonymous Coward

      Mod the parent up -- this is exactly what will happen in the future. If you think the Apple / Samsung battle was bad just wait until major drug companies start battling over which genes their research cores "invented"

      We are entering into an interesting century that, according to law, may redefine what it means to be an individual.

    • by whydavid (2593831) on Wednesday September 05, 2012 @05:14PM (#41239553)
      This is probably the single-most important factor in determining whether or not we'll see "personalized medicine" within the next 50 years. The fact that a company owns a patent on the idea of testing the BRCA1 and BRCA2 genes for breast cancer susceptibility is absurd.
      • by Cyberax (705495)
        The company holds a patent on a specific method of testing for BRCA1/BRCA2 genes. You are free to use any other method, not infringing on their patent. The problem is that the method they've patented is fairly generic, it's possible to work around it, but not cheaply.
        • by whydavid (2593831)
          My understanding of this is quite different. Look here: http://www.genomicslawreport.com/index.php/2010/10/11/a-do-it-yourself-genomic-challenge-to-myriad-the-fda-and-the-future-of-genetic-tests/ [genomicslawreport.com] If you scroll down to "What This Means, Part I...." there is an explanation of the various patents, including a patent on the nucleotide sequence itself, and the process of comparing the sequence to known mutations. While they speculate that a whole genome sequence would get around the gene nucleotide sequence
          • by Cyberax (705495)
            No, situation is more complicated. Myriad has patented the preparation of the affected gene and then detection of mutations. So if you isolate the BRCA1/2 genes and then do testing on them, you'll be likely infringing Myriad's patent.

            However, if you sequence/genotype your genome and then check it for BRCA mutations then you're OK and do not infringe on Myriad's patent. That has been affirmed by the court decision (the very same one that upheld the patent claims on BRCA gene isolation process), because th
            • by whydavid (2593831)
              This is good news. I've studied bioinformatics, but the legal side of this is way over my head. Thanks for the insight.
  • by wonkey_monkey (2592601) on Wednesday September 05, 2012 @04:54PM (#41239273) Homepage

    In what is likely to be a historic moment in science

    I'm not knocking the achievement, but wouldn't it be a more truly historic moment when they've nailed down the function of 100% of the genome? Where was the big celebration when they got to 64.576%?

    • by vlm (69642)

      The historic part is its release day. Kind of like that other /. story where gathering 14 million or 13 million or whatever iphone UDIDs into a big pile wasn't the story, the story was releasing them for anyone to look at and download and mess with.

    • You called in sick that day.
    • Maybe not where you work, but at my office we had cake that day.

      We have cake pretty much every day, since a bunch of people I work with are insanely avid bakers.

    • I think it's more along the lines of using everything we know, they mapped everything they could. And now they're done. So current methods can explain some kind of purpose (though I'd be willing to bet some regions have additional uses beyond what was found) for 80% of the human genome. It's possible that the remaining 20% actually does nothing (we know some of it at least is leftover from retro-virus infections for instance) or that it does stuff we don't understand yet or most likely some of each. Thi

  • We were told that most of the DNA was junk; you mean the biologists wised up and figured out that nature doesn't deal in junk?

    • Re: (Score:2, Informative)

      If memory serves, 'junk' was some unfortunate-but-persistent description of non-coding regions(which are, indeed, the great majority of the genome); but that work on what exactly the regions that don't code do do has advanced considerably since then...

    • They're called non coding sequences and while many have no perceivable function, some do have regulatory functions. Not to mention that you can get a lot of neutral drift out of those regions.

    • by HeckRuler (1369601) on Wednesday September 05, 2012 @05:10PM (#41239509)
      It's time you wised up [wikipedia.org] (it's RIGHT THERE). Junk DNA is non-encoding. Meaning it doesn't get used to make proteins. This was thought to be the entire purpose of DNA, so junk DNA was like commented out code or dead code [wikipedia.org]. But we learned that this genes have other uses. Like some DNA affects the trans-coding of nearby genes. And it appears some non-encoding DNA is still selected for, so it probably has some unknown function.

      But nature most certainly deals in junk. And there is DNA in you right now that's non-encoding, non-functional, and not selected for. IE, it's junk. It just happens to be the random uninitialized value or a previous mismatch of old code that was cut long ago. Deal with it.
      • by Cyberax (705495)
        Regulatory regions are small. Together they are probably less than 0.5% of the whole DNA, while _confirmed_ junk is about 66% of the DNA.
    • by nashv (1479253)

      It's a frozen accident during early attempts to clone genes. When you were cloning genes, you got lots and lots of other non-coding regions into your test-tubes and bacteria that you weren't interested in. Hence , it was called 'junk DNA'. Hence, you know that 'junk DNA' that you get when you try to clone something? Most of the genome is made of that stuff.

      It was by no means a statement on the importance of that DNA.

      • by Cyberax (705495)
        Uhm, no. "Junk" DNA is really junk. It consists of repeating regions, transposons, inactive and decaying retroviruses, etc. It has no direct functions, and its indirect usability is questionable. For example, pufferfish has almost no junk DNA while some plants (corn, for example) have lots of it without any visible effects on mutation rates or cell viability.
        • by nashv (1479253)

          That's Francis Crick's interpretation of it. The most popular usage of the term is, however, this : Biémont, Christian; Vieira, C (2006). "Genetics: Junk DNA as an evolutionary force". Nature 443 (7111): 521–4

        • by Tharkkun (2605613)

          Uhm, no. "Junk" DNA is really junk. It consists of repeating regions, transposons, inactive and decaying retroviruses, etc. It has no direct functions, and its indirect usability is questionable. For example, pufferfish has almost no junk DNA while some plants (corn, for example) have lots of it without any visible effects on mutation rates or cell viability.

          So if this is 100% true. Let's remove all this dna and see if you continue breathing. Unfortunately you don't know for sure what's its used for so you determine it to be junk.

          • by Cyberax (705495)
            There were experiments to do exactly this (on mice, of course). We can't remove ALL the junk DNA (it's a complicated task), but they've removed around 2% of junk DNA without any visible effects.
    • by bughunter (10093)

      Maybe *you* treat *your* DNA like junk, leaving it on the floor or flushing it down the shower drain, and all that.

      Biologists treat it like mice and make it run mazes and solve puzzles. They think it's pretty smart.

  • by fm6 (162816)

    Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?

    • Re:Junk DNA? (Score:4, Interesting)

      by afidel (530433) on Wednesday September 05, 2012 @05:14PM (#41239549)

      Uh, it was called into question over a decade ago. No scientific paper or journal article ever referred to it as "junk" DNA, it was called non-encoding regions and it was understood fairly early on that at least some of the area held a regulatory function. What wasn't realized until the human genome project concluded was just how little of the genome was encoding and how massively important the regulatory regions were (the human body creates a heck of a lot more than 10,000 different proteins so the regulatory regions must be more than simple on/off switches but must also have the ability to affect structural changes in the protein encoding sequence),

    • by whydavid (2593831)
      Strictly speaking, it is still universally believed that 'many' non-coding genes are historical junk with no current function, and experiments on organisms with much simpler DNA than ours bears this out (in short, they will scramble suspected 'useless' sections of DNA and look for changes in function; impossible to do in humans, but relatively simple for c. elegans). If you are talking about the antiquated view of _all_ non-coding genes as "junk DNA:" This is not the usual belief, at least not in the mole
      • by fm6 (162816)

        So, non-coding genes don't create any external proteins, but do help make the genome as a whole work? That still does away with the concept of junk DNA.

        • by whydavid (2593831)
          If you read what I wrote closely, you would see that what you are suggesting is widely believed to be _not_ true for most non-coding genes. "Junk" DNA is alive and well, though the nice thing about science as opposed to religion is that you won't see a lot of crying if someone conclusively proves that every last nucleotide serves a purpose...but the weight of evidence doesn't support such a conclusion today.
        • by tbird81 (946205)

          Some DNA codes for proteins.
          Some DNA doesn't code for proteins, but regulates expression of other parts of the DNA.
          Some DNA has other functions, (e.g to do with mitosis, RNAs etc.)
          Some DNA has no function, and is just there because there is no selection pressure to remove it - this can be called junk DNA.

    • Re:Junk DNA? (Score:5, Insightful)

      by robotkid (681905) <alanc2052@y a h o o . c om> on Wednesday September 05, 2012 @05:26PM (#41239693)

      Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?

      I don't think any serious molecular biologist ever thought the majority of DNA had no function, just as no neuroscientist ever believed that we only use 10% of our brain, but that's precisely the sort of sound bite that, when uttered in a press release somewhere, echos around the public consciousness forever and never dies because it provides a conveniently sciency premise for the next batch of rebooted superhero origin stories. The distinction is that before this study, we knew non-coding DNA was involved in regulation but not to what extent; i.e. there were plenty of specific anecdotal findings but nothing this systematic and large scale.

      As for the significance of this sort of work, yes, it exactly like release day for a major software package, it's an anticipatory excitement and not a "we finally found the Higgs Boson after decades of searching" type of achievement. Molecular biologists and geneticists everywhere can now do a simple web search see how this affects the system they are working on without needing to perpetually beg the labs that possess the specialized high-throughput instrumentation to do a one-off experiment just for their favorite gene. . .

      • by Cyberax (705495)
        Actually, most molecular biologists KNOW that the majority of _eukaryotic_ DNA has no function. It's junk, deal with it. Fairly small parts of non-coding DNA perform useful functions: gene expression regulation (less than 0.1% of total DNA), mechanic 'handles' for cell replication machinery (about 5% of DNA), various RNA enzymes (less than 1%), etc. But most of it is still junk.
        • by robotkid (681905)

          Actually, most molecular biologists KNOW that the majority of _eukaryotic_ DNA has no function. It's junk, deal with it. Fairly small parts of non-coding DNA perform useful functions: gene expression regulation (less than 0.1% of total DNA), mechanic 'handles' for cell replication machinery (about 5% of DNA), various RNA enzymes (less than 1%), etc. But most of it is still junk.

          Sure, it'll never add up to an actual majority of the genome, but do you seriously believe the proportions you quote will still be valid in say, 5, 10 years? Just because something doesn't light up on your nifty hidden markov models doesn't mean there aren't any more epigenetic or non-coding regulatory bits hidden between those mountains of retrotransposon corpses just waiting to be discovered.

          Show me a viable cell line with a 90% of the genome removed and then I'll believe you. Until then. . .

          • by Cyberax (705495)
            Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functi
            • by robotkid (681905)

              Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functionality.

              There was a few surprising discoveries, sure. RNA enzymes were a real shock, for example. All in all, about just about 15-20% of human DNA now has 'putative junk' status that might be changed later with new discoveries.

              You've listed the things we know are useless and pointed out that it adds up to >66%. No argument there. You also hypothesize that there's room for an order-of-magnitude increase in the things that *might* be useful from future, surprising discoveries. That's entirely my point!!

              Exactly why are we arguing again?

              I can't help but point out, though, that the RNA world folks were all saying "I told you so" when the RNA bits were discovered . . .

            • by mc6809e (214243)

              Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functi

              • by Cyberax (705495)
                Well, we can detect which parts of DNA are transcribed and/or affect transcription. There are multiple ways to do that - we might miss some fine details, but we're pretty sure we're not missing any elephants in the room.

                We also know how LINEs and SINEs work on molecular level (i.e. how they propagate within the genome) and we've discovered several mechanisms that inhibit their propagation.
      • by fm6 (162816)

        That 10% of the brain thing was the usual pop culture nonsense, but I've heard a lot of reputable scientists talk about junk DNA.

        • by robotkid (681905)

          That 10% of the brain thing was the usual pop culture nonsense, but I've heard a lot of reputable scientists talk about junk DNA.

          Yeah the analogy is imperfect but they are both rooted in the common assumption that if we can't assign a function to something then it doesn't do anything at all - which is troubling to me because we don't even know what alot of the "real" genes do yet to do an accurately accounting how much is NOT useful.

          So while it'll probably remain true that "junk DNA" will outnumber "useful" DNA in the final accounting (80% is surely a headline-grabbing overreach), there will also continue to be a steady progression o

    • It is being selected for to last for some function or another. The truly junk portions probably mutate rapidly within and across species. The so-called "10,000 human genome" database will help elucidate this.
      • by fm6 (162816)

        You know, I'm grateful to all the people who want to correct my ignorance about "junk" DNA. But I wish the ones who've joined the conversation late would read the previous comments,.

  • by realxmp (518717) on Wednesday September 05, 2012 @05:09PM (#41239499)
    Imagine you were given a slightly buggy 3.2Gig piece of software used to run a group of factories and to managing communications between them. You were told to debug this piece of software, but you had no source code, only the machine code only. You could of course observe it's behaviour and set up situations in various factories to see how it behaved. To complicate matters further, you realised that the factories were all performing different functions and making different things but they were all running the same software, but it wasn't immediately obvious why they behaved differently. This is pretty much a huge oversimplification of the challenge that faces modern genetics. We have the assembler language, but we're still not sure entirely what bits are coding sections, which are data sections and which sections are marked up to act as configurations sections. It's a huge task and I love it.
    • by HeckRuler (1369601) on Wednesday September 05, 2012 @05:28PM (#41239721)
      Furthermore a long time ago some hackers [wikipedia.org] got in and mucked about committing changes the the trunk. They didn't seem to break anything vital so it was just left alone and we hope it doesn't bite us in the ass before we retire.

      Oh yeah, btw, we use a distributed revision control with about 7 Billion [wikipedia.org] branches and no one true trunk (although a lot of people claim otherwise). There's a lot of wanton merging (giggity) and branching, and it seems like every time that happens there's a chance that the revision control just fucks something up [wikipedia.org] and makes a mess of it all.
  • by anubi (640541) on Wednesday September 05, 2012 @05:17PM (#41239571) Journal
    The sky will be the limit.

    The understanding of how DNA works, ( and correspondingly, how to hack it ) is the ultimate reverse-engineering accomplishment.

    Life is a textbook, full of worked examples. We are at the stage we realize there is an alphabet, the letters mean something, and have the definition of a few words. Kindergarten stuff.

    If we play our cards right, and don't spend all our resources fighting amongst ourselves, the future is incredibly bright. We have worked examples of damn near everything we need... photosynthesis ( solar powered CO2 sequestration and energy storage ) for starters. We have bioluminescence, electric eels, and all sorts of sensor examples.

    I figure we have been given a huge shipment of arduinos with all sorts of accessories, and we have now figured out how to make the light blink.

    We don't know how its wired yet, how the compiler works, and just now figuring out some of what makes the hardware work.

    If our society will value knowledge above greed and accounting, if there is anything limiting our potential, I have yet to see it. However if greed and accounting is all we know, we will soon run into all sorts of limits, imposed only by our inability to adapt. First of these will be exhaustion of the earth's fossil fuels, followed by food and water famines. We will be like the chick that hatched, but failed to scratch, find food, and thrive, living off the energy stored in the egg - until it is depleted.

    The earth is our egg.

    I value highly the knowledge our species acquires. It is our survival.
    • by rubycodez (864176)

      it is more likely that a "defense contractor" with politicians in its pocket will develop awesome bioweapons that will, in a war started for profit or power, extinquish most or all of mankind. Death will be the limit

  • We need to ban patenting of any of this. Our genetic code is our heritage. Companies, and thus people, should not be able to patent genes or their uses. If they want to be rewarded then they need to implement actual therapy and earn their money from that, without any patenting involved.

    • by danhuby (759002)

      I would have thought genes have a good deal of 'prior art'.

      • by pubwvj (1045960)

        One would think so but the patent office clerks are giving patents on genes.

        The clerks also give out a lot of patents for obvious things. Just about everything is obvious. Dozens of people come up with the same ideas. Ideas are a dime a dozen. It is implementation, production, marketing and sales of the idea that is what has value.

  • I'm confused. I thought the non-encoding (junk) DNA was not selected for. That is random mutations were passed on because they evidently did not effect the organism's survival or reproduction. Coding DNA ( genes ) accumulated fewer mutations because mutations adversely effected it or it's offspring's survival.

    Now it appears that that non-encoding DNA is important, but seems to be less effected by mutations. Am I missing something?

    • by rnaiguy (1304181)
      Just because it doesn't code for protein doesn't mean it isn't turned into RNA, or bound by some protein to regulate some other part of the DNA. Some of it is selected for, we just didn't know where to look to find conservation, or the nature of that conservation. It's easy to pick out regions coding for protein because there are some fairly strict rules for these, so it's easy to find conservation. For some of these non-coding regions, the precise sequence and location is not important, and many similar se
    • by Cyberax (705495)
      SOME non-coding DNA has useful functions. Turns out, there's quite a few "RNA enzymes" there and gene expression regulators. They are much more difficult to find then simple genes, because genes generally have predictable "headers". However, most of non-coding is still junk.
  • It will eventually become clear what genes encode the proto-concepts in the brain for mother, father, food, water, etc. Not only that but the concept of the Sun, Moon, and stars will likely have been encoded in there as well. Extrapolate from that notion, you can get Jungian archetypes, a whole catalog of fetishes, and most certainly the predilection towards religiosity.

    Bene Gesserit meetup this Sunday.

  • Whoops... forgot to log in before posting. The publication of the ENCODE data is a big deal, make no doubt about it. But it has been overhyped and misreported in the popular press. Interestingly, this is not the fault of science journalists, but rather a consequence of the lead scientists in charge of publicity for this project. UC Berkeley biologist Michael Eisen has a couple [michaeleisen.org] blog posts [michaeleisen.org] addressing this issue, as does University of Guelph biologist T. Ryan Gregory [ev
  • Whoops... forgot to log in before posting.

    The publication of the ENCODE data is a big deal, make no doubt about it. But it has been overhyped and misreported in the popular press. Interestingly, this is not the fault of science journalists, but rather a consequence of the lead scientists in charge of publicity for this project. UC Berkeley biologist Michael Eisen has a couple [michaeleisen.org] blog posts [michaeleisen.org] addressing this issue, as does University of Guelph biologist T. Ryan Gregory. [evolverzone.com]

    Two of the main criticisms directed at

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