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Science Technology

Desktop Biodetectors 66

Posted by michael
from the two-steps-toward-gattaca-one-step-back dept.
IvyMike writes: "EE Times has an interesting article on the development of desktop biodetectors that could quickly detect the presence of pathogens like anthrax and smallpox. It uses some pretty cool technology to identify the target pathogen's DNA. Too bad we don't have these things today."
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Desktop Biodetectors

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  • A machine where I put in some biomaterial and have it tell me what bacteria I have and what antibodic has traditionally been used to fight it. It'd help me decide if I need to go to the doctors or not.

    Perhaps these devices already exist and or they're too expensive for the home market? Or does it all basically boil down to having to do a culture, and compare how the bateria/virus looks compared to a catalog of specimins?
    • The best thing about such a device is that it could justify its cost.

      A $500 "detect Anthrax" device wouldn't yield much value for a large portion of the population. But... a $500 device that could detect and identify a wide variety of microorganisms might be very useful -- and worthwhile -- indeed.

      Maybe it'd be like running "top" -- instead of giving you information about processes taking up system resources, you could get information about microorganism activity in the environment (or your body, given an appropriate sample...).

      ID NAME EST COUNT/CU CENT % OF TOTAL
      787 Staphlo 2324572 12.2%
      8901 Antrax 253334 1.3%
      143 E. Coli 289217 1.4%
      1589 Ebola 16333 .035%

      • Staph and E.Coli exist in the regular human body. Problems exist when their counts get unbalanced. For example, you eat some tainted eggs and your E.Coli levels go through the roof. If the system just showed numbers like this, you would have alot of hypochondriacs worried about nothing.


        However, your ebola count would be a problem. That 0.035% ebola count would probably kill you. Unless, of course, you were lucky enough to get the Reston strain of it, which so far has shown to be non-pathogenic in humans (ie we can't get it).

      • $ killall ebola
        Permission denied
        $ su
        Password:
        # killall ebola
        # killall ebola
        # killall -KILL ebola
        deathstar kernel: Unable to handle kernel NULL pointer dereference at virtual address 00000134
        deathstar kernel: current->tss.cr3 = 2526c000, %%cr3 = 2526c000
        deathstar kernel: *pde = 00000000
        deathstar kernel: Oops: 0002
        deathstar kernel: CPU: 1
        deathstar kernel: EIP: 0010:[decontaminate+188/344]
        deathstar kernel: EFLAGS: 00010206
        deathstar kernel: eax: 00000100 ebx: df622e40 ecx: df622e40 edx: efd0ba10
        deathstar kernel: esi: df622e40 edi: 00000000 ebp: c07ff820 esp: d5469d70
        deathstar kernel: ds: 0018 es: 0018 ss: 0018
        deathstar kernel: Process ebola (pid: 6913, process nr: 59, stackpage=d5469000)
  • I sneeze without covering my mouth. Suddenly lights and sirens go off and the CDC quickly rushes in wearing biohazard suits.
  • BioMonitoring (Score:2, Insightful)

    It seems the this could the be the start of the canary and the mine idea.

    It would seem most logical that if these biodetectors have enormous costs then the real decision is not whether to use them but where to use them.

    If we had controlled ports on entry, that would be one place but proabaly not very wise given how open the US really is.

    The other idea is first install them in major hospitals or have a roving CDC action team that would have these biodetectors (which they probably all ready have).

    From the article, there main concern seemed to be cost, but in the light of certain events I think big business may see the benefits do out wiegh the costs

    Thanks for reading
  • We already have overloaded emergency response teams all over the country with anthrax fears every time we see a white powder.

    Now, we'll overload them with automatic notifications from desktop detectors that are miscalibrated, malfunctioning, or 0wned.

    Good idea.

  • by fobbman (131816) on Friday October 19, 2001 @06:44PM (#2453362) Homepage
    I've got some leftovers in there that are really borderline.

  • "Mr. President, we cannot allow a Desktop Biodetector gap!"
  • Parameters (Score:4, Funny)

    by Halloween Jack (182035) on Friday October 19, 2001 @06:55PM (#2453387) Homepage
    Considering what some people do at their desks, with the door closed... better not set the biodetection parameters on the desktop units too wide.


    "Sir, the bioalarm just went off in the boss' office! We need to get a hazmat team up there right away!"


    "Relax, rookie. Look at the DNA profile. Those are gametes. Billions of 'em. Nothing a few paper towels can't clean up."


    "But, sir... they don't match the boss' DNA."


    "...well, whaddaya know. Looks like we have a big raise coming, rookie."

  • by Phrogz (43803) <!@phrogz.net> on Friday October 19, 2001 @06:57PM (#2453393) Homepage

    OK, sure, they're cool gadgets, but saying that is like saying "Too bad we don't have gadgets on the desktop to detect incoming meteors."

    What are there now, somthing like under 30 cases of Anthrax so far? Sent to a few high-profile companies? Sure, that's a MASSIVE INCREASE over previous levels, but statistically you're still in pretty good shape. Don't let the media hype get you worked up.

    Too bad we don't have detectors on our faucets just in case the level of mercury rises rapidly...

    • What are there now, somthing like under 30 cases of Anthrax so far? Sent to a few high-profile companies? Sure, that's a MASSIVE INCREASE over previous levels, but statistically you're still in pretty good shape. Don't let the media hype get you worked up.

      Very true. Also one of the (many) reasons why these things won't work. I'll stick with the three simplest.

      Firstly, in order to detect bacterial DNA you have to lyse (break open) the bacteria. This means you have to filter them out of the air, dissolve them in lysing buffer and apply them to your detector, at the bare minimum. Lysis buffer is expensive, and I doubt there technology actually works without doing more than lyse the cells (removing the cellular protein, much of which binds indiscriminately to DNA, would be a good start. Doing that in reasonable time requires a ~12,000 RPM centrifuge, precipitant compounds and a column, at the minimum.)

      Secondly, DNA from other organisms is going to bind to your probe (including these gold bead things) with a certain frequency (this binding is called "base pairing," which is largely driven by hydrogen bonding but is not called a bond.) So, your background noise from that is going to be more than enough to drown out the signal from an anthrax concentration high enough to kill you, especially if you're standing across the room from the detector holding an envelope; the anthrax concentration drops as the square of the distance from the contaminant source unless there's a wind.

      Thirdly, the reason the previous poster mentioned. In order for these things to be useful the false positive rate has to be on the same order of magnitude, or smaller, than the actual positive rate. Even if you use practical techniques instead of this absurdity with DNA, that's never going to happen. More practical techniques depend on markers on the bacterial cell walls (so you don't need to lyse the bacteria); when the CDC people report "preliminary results" indicating anthrax this is what they're talking about - these results are preliminary because there are many other, more common and harmless bacteria that have the same factors in their cell walls, and because the experiment to detect the stuff occasionally goes wrong for no apparent reason.

      Even in a laboratory setting, if you want to detect the DNA from this stuff you have to *culture* it. The idea of a desktop machine, as opposed to a highly trained scientist with a lab full of sophisticated equipment, being able to detect the DNA from the amount of this stuff that is actually floating in the air is patently and absolutely absurd.

      A handheld is even more so, since it wouldn't even be able to dissolve the bacteria it filtered.

      These devices are either a pipe dream, a scam, or both. Either they'll just report A-OK all the time or, even worse, they'll periodically start an unjustified anthrax scare by giving off an alarm.
    • statistically you're still in pretty good shape

      But potentially we're in very bad shape.

      The day after the attack on Pearl Harbor, people on the mainland were as statistically safe as they were the day before. The difference was the country was at war and many more casualties were certain.

      What the anthrax statistics mean is that people have biological agents and are willing to use them. There no reason to think they will stop with anthrax. The threat will continue for many years.

      There's some hope that this attack will be limited because of the crudeness of the delivery mechanism and the fact that anthrax wasn't engineered to resist antibiotics. There even a faint hope that this attack isn't part of the events of 9/11.

      However, no other terrorist organization has ever stopped with one attack. If bioterrorism is part of their arsenal, we can expect the terrorists to use it again the way the IRA continues to plant bombs.

      It's reasonable to expect devices like the one in this article to become as common as smoke detectors.

      • Devices in the wild detecting DNA?

        How long before the gene screener is applied to human DNA? After all, you'd want to detect all those threats from people with "criminal" genes too...

        If something like this were to ever be deployed, how long before people start mailing polymorphic-self-mutatating-stealth-viruses, applying computer virus technology to bio weapons??
        I think the idea that a desktop detector can stop this kinda of terror attack is naive. Why not just vaccinate everyone who could be in a position of risk?? Surely a lot cheaper....

        I can see it now... Damn, I got infected with Anthrax 9b, duh, you forgot to apply those bio-security patches in time....
        • I think the idea that a desktop detector can stop this kinda of terror attack is naive.

          Early detection doesn't stop the attacks, it reduces the consequences by alerting people that the are in danger the way smoke detectors do not stop fires but still save lives.

          Why not just vaccinate everyone who could be in a position of risk??

          It depends on the level of the threat. It's easy to conceive of a bioterrorist threat that is so persistent that mass vaccination will be a feature of normal life the way polio and smallpox vaccination used to be.

          However, insofar as we are dealing with threats, not actual attacks, detection devices in public areas might be cheaper than mass vaccination. They would also raise public confidence that public areas were safe. Because vaccination programs are not 100 per cent effective, you might still need detection devices.

          Finally, it might be faster to deploy detection devices against a new threat than to set up a mass vaccination program.

  • Even though the "DNA profiling" concern is often a standard part of this science, this kind of technology seems like it might underline that concern. A "consumer level analyzer" could give bigots and xenophobes an easy way to test and target a particular group.

    Just a thought...
  • by Soko (17987) on Friday October 19, 2001 @07:05PM (#2453415) Homepage
    So, you think Windows will be able to detect a virus? Riiiiiiggghttt....

    Soko

  • Could these be used to detect an individual person?


    I'm getting a lot of Invalid form key errors: Invalid form key: CuhZiMm1UB !

    U.S. government corruption: What should be the Response to Violence? [hevanet.com]
  • Ridiculous... (Score:3, Insightful)

    by ryanwright (450832) on Friday October 19, 2001 @07:09PM (#2453421)
    What a ridiculous idea. What with people stocking up on gas masks these days, we don't need them clamoring for "desktop biodetectors" that will never prove useful for more than 0.0001% of the population. Way to add to the paranoia, /.
    • no no no... it's all wrong, man...

      0.0001% of the population would be barely enough to include you, me, and poor little timmy, who had a limb ripped off by a rabid subterranean sea-cow. Ok, so it's a decimal (or fourteen) place in the other direction after checking it again, but anyway....

      The math:

      Population of the US is somewhere around 280 million (P = 2.8e8)
      Percentage as a decimal is 1e-6.

      Multiply the two together and you get 280; there have only been ~30 Anthrax scares.

      Assuming the range of the detectors is about 10m, that's about 314 m^2 area covered; at about 20 square meters per person (pretty stinkin' nice size cubicle, if I must say so - 4mx5m, about), that's 15 people. So 1 out of every 15 people needs to have one *where there has been an attack*.

      Now, say you have 150 people who would be *directly* affected by the anthrax. So multiply that by the ratio of the number of people who would need it, and you get 10 - the number of people who would need to get one for them to be saved.

      Now, since 30 cases have been found, that means about 4500 would have been directly affected; also, 300 anthrax detectors would have been needed.

      And it's time for the fun stuff ;)

      4500 people would have been directly affected. That means 4.5e3 out of 2.8e8 people, or about .16% would be directly affected.

      Those people come in contact with about 150 other people before they figure out what's going on (maybe a day later?). So that means the number of people indirectly affected in a single day would be about 4500*150, or 675000 people in a single day, or 2.4 percent of the population. Say they run into 150 people in the day before they die. You get a nice little series that calculates the death count.

      (and now Brian notices what he just found out, and takes about a half hour to write the rest)

      Now to the not-so-nice part, and I'm hoping my math is seriously completely wrong (though that wouldn't cause enough error to throw it off more than a few days):

      Within something on the order of less than a week, the whole population of the United States would be dead. Everyone.

      Now I know why I've never really heard any of the stats from how long we would last.
      • You forgot that Anthrax isn't communicable (human-to-human) most of the time. I think the white supremacist group that is sending these letters will run out of Anthrax soon, and everything will be fine once again.

        Invalid Form Key: BnriPp5v4i ! What you say!!

  • Cool! can they embed this thing into a Tricorder-like device?

    'Captain, I am reading no signs of Anthrax on the surface'

    tee hee!!

  • Economist Article (Score:3, Informative)

    by cosyne (324176) on Friday October 19, 2001 @07:19PM (#2453440) Homepage
    The economist is running an article about a anthrax detector at http://www.economist.com/science/displayStory.cfm? Story_ID=821937 [economist.com].

    "A better solution would be to screen on the spot. And technology to do this is now available. It uses a test strip, costing $20, that looks like a pregnancy-detection kit."

    May be useful it you (or your employer) regularly do(es) things to piss people off so much that they'd want to kill you....
    • These things really work, by the way.

      Since the antibodies are to compounds exposed on the cell wall, you don't need to lyse the cells (see my previous post).

      Also, antibodies are sufficiently specific in their binding that you'll get negligible false positives.

      However, the detection thresh-hold is very high. These devices are very useful for (say) detecting anthrax in powdered form that was mailed to you. However, if someone put a bunch of anthrax spores in an air vent and let it blow around a building, and you had one of these things stuck up to a wall; well, aside from the fact that the antibodies degrade fairly quickly, it isn't sensitive enough to detect the minimum lethal amount of anthrax blowing around in the air.

      Quick assays exist that are more sensitive, but they generate false positives, and as such are more useful for spreading panic. More sensitive assays exist that also employ antibody technology, but they're time consuming, not portable and they're *very* expensive.
  • It uses some pretty cool technology to identify the target pathogen's DNA

    But what about nonbiologic things? Poisons for example. I didn't read anything about that, how can they be detected?
    • Poisons for example. I didn't read anything about that, how can they be detected?

      Short answer: They can't.

      Long answer: Some can, but you need specific methods to deal with each one. Most highly lethal airborne toxins are organic; in order to detect them, they need to be differentiable from the organic compounds that we human beings (and paper, and cleaning supplies, and so on and so on) put off into the environment all the time. Most airborne toxins can be differentiated, but the method to do so is different for each and every one. Any method that reliably detects a wide range of airborne toxins falls into the "false positive" problem - it's going to be going off continuously as things which are not toxins fool it for some reason or another.

      So, you could build a machine that detects Serin nerve gas (which has, I'm just making this up, a very different UV absorption spectrum from what you usually have in the air; you take a sample periodically and check it's UV absorbance.) Okay, there are a certain number of harmless compounds, or combinations of harmless compounds, that duplicate the UV absorption and fool the assay. If you expand the assay to include mustard gas and cyanide, the number of harmless compounds that give false positives goes up. Anything that detects a wide range of harmful compounds is going to be going off continuously because your cup o ramen sent vaporised Yellow #5 floating through the air.

      So, if you allready have reason to believe that there is Serin in the air, you can detect it. If you want something that sits on a table and detects the most likely/common poison gases, you can do that, with only occasional false positives. However, someone smart enough to make Serin is probably smart enough to get a copy of your list of common nerve gasses and make something else.

      Finally, some never gases are lethal in such tiny quantities that there really is no way of "abiotically" detecting them without allready knowing that they're there (biotic detection = people keeling over dead.) Fortunately, they're difficult and hazardous to make.
  • by oliverk (82803) on Friday October 19, 2001 @07:29PM (#2453460)
    Can you see the reports to management?

    EMPLOYEE: JONES, PAUL
    Biohazards: Clean
    Infectious Diseases: Clean
    Genetic anomolies: Clean
    Pharmacopia: Found -
    ** ASPIRIN - Trace Amounts

    ==================

    Report submitted to Human Resources for individual factors improvements...

    These reports, while "sold" as providing the ability to detect hazardous materials could in fact be used in a manner similar to the Gattica theory: testing for genetic predispositions or even medications (say, the AIDS cocktail) to determine whether you should get that promotion or not. Really, from the business end--you've got rounds of layoffs, shouldn't you have the best information when selecting who goes and who stays?

    :|
  • What? Why do we need desktop biodetectors? I thought Anthrax was just being distributed in the mail! Not the e-mail! Nooooo! I haven't been handling my keyboard with biomedical gloves!
  • I really can't see these things ever being useful in a normal office context.

    Sure, a handheld tricorder-like device would be really good for military situations, labs or post offices (sit one over the line), even-more-so if it could be extended to other pathogens.

    However, it seems like another non-product who's market rides on peoples current paranoia. Unfortunately in this case, the terror will hopefully be over way before this is even a prototype!
  • Like detecting human DNA.

    Perhaps not with current technology, though this is of course the first step... Let us hope that people can collectively take notice of Gattaca-esque warnings.

    They won't of course, though hopefully I'll not be around to see it.
  • ...detect the presence of pathogens like anthrax and smallpox.

    Anthrax and smallpox are diseases, not pathogens. The pathogens causing those diseases are Bacillus anthracis and Variola major/minor.
  • Cork said that when targets such as anthrax, smallpox or tuberculosis are in the sample, electrical resistance across the gap typically drops by a factor of about 1 million, thus providing a definitive sign of their presence.
    I'm sorry but I don't believe it. It's very unlikely that the cells are so different and no other cells (i.e. benign microorganisms) have this property. Can anybody comment on this?
    • The detector is not detecting the organism, it is detecting its DNA. The basic idea is as follows: suppose you have a nasal swab that you suspect has anthrax in it. You extract DNA from the swab, and chemically tag the DNA with gold. In your detector, you have a piece of cloned anthrax DNA that consists of sequence unique to Bacillus anthracis, also chemically tagged with gold. The cloned DNA in the detector can be thought of as half of a capacitor; without the other half, current cannot flow and thus you have strong resistance. If there is anthrax DNA in the swab sample, it hybridizes to the detector DNA via Watson-Crick base-pairing. Because this hybridization is DNA sequence-dependent, only DNAs with identical sequences will hybridize to each other (this is an oversimplification but suffices for this discussion). When the gold-tagged sample DNA binds to the detector DNA, this completes a circuit and resistance drops dramatically. On the other hand, if no anthrax DNA is present in your nasal swab sample, then nothing hybridizes to the detector, and no current flows through the circuit. Even if there is DNA from other bacterial and/or viral species, there won't be anthrax-specific sequences and therefore those DNAs will not hybridize to the detector.
  • by myc (105406) on Friday October 19, 2001 @10:06PM (#2453622)
    The term "desktop" as used in the eetimes article probably does not mean what your typical computer geek thinks it means, as evidenced by the many posts so far. It's not a consumer device that sits on top of an home/office desk of the overly paranoid. Rather, it probably means that the device is sufficiently bulky as to make it not portable, and therefore must sit on a workbench in a lab. While such a device is useful for testing labs, its utility is somewhat less because it can't be used in the field.

    That said, this is really cool technology. It's potentially much faster than the standard tests today, either polymerase chain reaction (PCR) or spore cultures (which is the *only* way to 100% reliably test for anthrax but is also the most time consuming protocol). Aside from testing for microbial agents, it sounds like the technology may have applications in high-throughput gene analysis.

    • As I continuously repeat, often hopping up and down and foaming at the mouth, to people who do not (I do) work with DNA:

      DNA IS NOT THE MOST EFFICIENT WAY TO DETECT ANYTHING. IT IS INSIDE THE CELLS! THE CELL WALLS ARE STUDDED WITH ANTIGENS (things to make antibodies) AND THEY ARE ON THE OUTSIDE. THE CHOICE IS CLEAR.

      I'll wait until I see hard numbers on the technology with the beads; if it really is more sensitive than the photodetection on present day DNA microarrays, than that's very promising. However, I'd like to see an independent group assay the technique's sensitivity before making any judgements on it's utility - I strongly suspect that it will turn out to be actually less sensitive, based on the (scientifically irresponsible) comments made by the crackpots and or sleaze at the company that produces it.
      • FYI I do work with DNA, I am a postdoc at Harvard Med School. The fact of the matter is, antibodies are a bitch to work with. Unless you make a hybridoma you can't mass produce antibodies, and even if you do have a good antibody the best you can do is an ELISA assay. There is no way that ELISA is more sensitive than PCR. This bead technology is likely to be more sensitive than PCR, faster than PCR, or both. It's also not that hard to extract DNA, usually a simple organic extraction gives you a good enough sample to work with.
        • You can buy antibody coated strips (for detecting anthrax) for $20, as mentioned in a previous post. Simple organic extraction gives you good enough samples to work with, but that's simple = an undergrad can do it not simple = a box sitting on a desk can do it internally and automatically; recall that we're talking about desktop detectors, here.

          I want to make a distinction between efficient and sensitive. Yes, nothing is more sensitive than PCR. However, PCR does not always work; the unexplained failure rate is actually rather high and the technique can be exquisitely sensitive to contamination by similar sequences.

          I cannot concieve that the gold bead technology is more sensitive than PCR. It's absolutely going to be faster.
          • Let me clarify one other point about the gold bead technology:

            The limitations on our ability to detect RNA binding to a microarray (or DNA, but PCR is more sensitive) is NOT the minimum amount of RNA that we can detect from it's fluorescent tag. The problem is non-specific annealing to the target sequence; this is also a major problem in PCR. Every spot on the array "lights up" with a certain background intensity and if the RNA you're looking for is present in lower concentration than that, it is below the detection thresh-hold. So, even if those gold beads have a lower absolute detection thresh-hold, which I doubt but it's certainly possible, it doesn't matter because it's the background noise, which they do not promise to reduce, that actually limits your ability to detect signal.
          • yup yup, the strips are good for initial screening, but they are also give lots of false positives, and have shelf lives. They are similar to pregnancy test kits. Basically, they are crude ELISA assays.

            I also agree with you on the distinction between efficiency and sensitivity. Not having seen any data though, I hesitate to draw conclusions on the sensitivity of the bead assay.

  • by amacek (162469)

    The current issue of IEEE Spectrum has a one of its big articles on Biological Warfare Detectors. The article is available at http://www.spectrum.ieee.org/WEBONLY/publicfeature /oct01/bio.html [ieee.org].

    A little ironic that they put together this article before September 11th.

  • It's often said around here that "he who trades a little security for a little freedom will lose both and deserve neither".

    And from casual observations we can say that security definately is a race where the final destination is never reached.

    The same thing applies to these devices, IMHO. Just another gadget to keep care of (the batteries running, the possible filters changes or chemical refills done, etc.) And most technical systems can easily be tricked - with a new strain of Anthrax, with some harmless agent that frequently causes false alarms, rendering the box worthless.

    If this baby really cuts cheese, somebody with a strong determination will find other ways to strike.

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