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Science

Biology's McGyver: DIY DNA P.C.R. 55

Posted by michael from the cheaper-is-better dept.
joesao writes "In this short, charming interview, Dr. Eva Harris talks about popularizing biology by doing what she calls "knowledge-based" technology transfer: "...people purify DNA for P.C.R. processing with a fancy substance made of silica particles, which costs about $100 for a few milliliters. [...] So what we've done is buy a 20-pound bag of ceramic dust for $5 at the hobby store. And you wash the stuff in nitric acid and sterilize it, and then you have thousands of tubes of that substance. We're not violating anything because the commercial manufacturers have their way of doing this, and we have ours." Open-source biology, anyone?"
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Biology's McGyver: DIY DNA P.C.R. More

Biology's McGyver: DIY DNA P.C.R.

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  • What I want... (Score:4, Funny)

    by TitaniumFox ( 467977 ) * on Tuesday September 30, 2003 @05:58PM (#7098929) Journal
    Is a DYI thermocycler. Programmable. With a heated top.

    Additionally, you can snag the silica gel needed for PCR purification from Vacutainers used to collect and subsequently separate blood.
    • How do I moderate this as (+1 Huh?)
    • I read about this method recently: it performs PCR of a drop of liquid in a mineral oil-filled capillary by moving the droplet through different static heating elements. Kinda like the old way of moving the tube from heat bath to heat bath, but without the tube. The drop is small, so you don't get a lot of product, but the heat transfer is really great, so it works very quickly. Alternatly, you could probably make a hot-air cycler, like the one that Idaho Technologies (?) sells, much easier and cheaper t

  • talk about a markup! (Score:3, Insightful)

    by bscott ( 460706 ) on Tuesday September 30, 2003 @06:06PM (#7098995)
    Looks like I.T. markups [slashdot.org] are tame by comparison...
  • It really warms my heart to see liberals focus their concern for the poor in a specific and effective way. I feel the same when a conservative does so as well. No one is so callous as to completely not give a rat's ass about their neighbor, but it is more than difficult to find ways to help them than to feign contempt.

    When effective people like Dr. Eva here go out and turn their ideas into reality it benefits everyone. If she were to go into politics the world would have been less one innovative scienti
    • I see where you're coming from, but that IMO is the biggest problem with liberals today. We are too disorganized politically. How many innovative scientists do you think we've -lost- due to the current Bush shenanigans (hint: read up on what the PATRIOT act and its ilk have done to the ability of scientists to be honest with their reports versus having to fudge or simply not research in certain areas to keep their jobs).

      The more the liberal community cedes the political realm, the harder it will be to be l
      • How many innovative scientists do you think we've -lost- due to the current Bush shenanigans (hint: read up on what the PATRIOT act and its ilk have done to the ability of scientists to be honest with their reports versus having to fudge or simply not research in certain areas to keep their jobs).

        Three? Zero? I would be astonished if the number is more than ten. (And that's before you get to "innovative".) Maybe in a handful of sensitive areas there'll be some useful work that doesn't get done. But the ide

        • Wow ... 3 ... then in that case every single scientist who is either being stifled or worried about being stifled must have already been interviewed. And these were only in relation to PATRIOT specifically, not the administration's policies having similar effects in general.

          http://www.suntimes.com/output/zinescene/cst-fi n -e col30.html

          http://www.mafhoum.com/press4/129P1.htm

          http://www.thorsett.org/archives/000013.html

          http://www.research.ucla.edu/ocga/memo_OFAC.htm

          Still believe 10 is a high number?
          • Number of scientists "lost" as described in those articles: zero

            I stand by what I said -- there will be some useful work that doesn't get done but I would be astonished if the number of people who leave research will reach double digits.

  • NYTimes Article (Score:1, Offtopic)

    by Momomoto ( 118483 )
    Remember, folks, if you don't want to register with the New York Times you can always use:

    User: slashdoteffect
    Password: slashdot

  • pffft! (Score:3, Informative)

    by ziggles ( 246540 ) * on Tuesday September 30, 2003 @06:48PM (#7099327) Homepage
    It's MacGyver, not McGyver.. how ignorant can you be! :P
    • It's MacGyver, not McGyver.. how ignorant can you be! :P

      Yeah, really, like some Irish guy is going to be able to figure out how to get out of a maximum security prison using a nail clipper and a watch battery. A Scot, sure, but - OK, well, maybe if the Irish guy was trying to get to a pint of Guinness. ;)

  • Rather hyperbolic (Score:5, Insightful)

    by Otter ( 3800 ) on Tuesday September 30, 2003 @07:01PM (#7099405) Journal
    I'm sure this work is very valuable, but either she or the reporter (or both) make her come across as far, far more revolutionary than she is.

    For instance, people purify DNA for P.C.R. processing with a fancy substance made of silica particles, which costs about $100 for a few milliliters.

    I incubate a piece of tissue with a couple of cents worth of buffer and proteinase, and then dilute the resulting glop in water. Obviously different protocols call for different methods, but routine clinical preps shouldn't call for anything nearly as elaborate as what she describes. Anyone know what this silica thing she's talking about is? Qiagen spin preps?

    This is called manual cycling. Suddenly, you don't need that $10,000 machine. Now, I didn't discover manual cycling or P.C.R., but I've helped popularize it.

    Uh, no kidding you didn't invent manual cycling. That's how everybody did PCR until the cyclers became available.

    Like I said, I can easily see where it's a very valuable activity to generate manuals and reagent sources for cheap techniques, but the interview makes her sound vastly more inventive than she is.

    • Re:Rather hyperbolic (Score:3, Informative)

      by Anonymous Coward
      Almost every company that sells you some sort of PCR purification / gel purification / miniprep kit that has a spin column or a vac manifold column has some "proprietary formulation" in their columns, but it's silica based. Decrease the pH to about 3.5-4 and your DNA sticks via its phosphodiester backbone. Change it back to 7-8, and the DNA elutes into your TE/H2O/whatever. This is exactly what she is talking about. There were 2 papers published around '83-'84 that describe the use of silica gel for DNA
      • Back in the day? Hell, we used to do PCR with Klenow and three water baths! And we purifed our own dNTPs! From ourselves!

        Actually, I was the source of our hemoglobin standard for a while....

        As for the technique, we've used a setup for gel purification from a Science technical QC for years. Freeze 'n Squeeze. Take a .5 mL tube and poke a hole in the bottom with a 18ga needle. Put some sterilized poly fiber in it (pillow stuffing from WalMart stuck in a strong uv source for ~10'. UV crosslinker works great)

    • $10000 thermal cycling machine is nothing more than variable heating/cooling bath. It is about as complicated as a home-breadmaking machine and I am sure that if there was large market for it (if it was sold like home appliance) it would cost maybe $200. One can do just as well manualy, with a beaker of hot and cold water, as described in the article. This is completely common with all lab equipment and lab chemicals - being overpriced over comparable bulk or common products by order of magnitude.

      One busin
      • PCR, sorry.
      • lab equipment and lab chemicals - being overpriced over comparable bulk or common products by order of magnitude.

        What you're paying for in lab-grade materials is purity. Bulk reagents have a lot of crap in them, depending on what you're working with. Bulk organics might have significant traces of solvents or purification substrate and bulk acids/minerals will have traces of heavy metals. When you're doing sensitive, small-scale biological research, these pollutants can really screw things up.

        The proc

    • Re:Rather hyperbolic (Score:2, Insightful)

      by Anonymous Coward
      I'm sure this work is very valuable, but either she or the reporter (or both) make her come across as far, far more revolutionary than she is.

      For instance, people purify DNA for P.C.R. processing with a fancy substance made of silica particles, which costs about $100 for a few milliliters.

      Funny, I read it a different way. I took it as someone who was very politely saying that the 'Propietary' chemical supply stores are robbing medicals blind. If she was an IT worker, I would have expected to hear
    • Many countries cannot afford $10,000 machines for their hospitals; they can afford lots of bags of ceramic dust and labour, though.

  • Business Model (Score:3, Interesting)

    by Zarf ( 5735 ) on Wednesday October 01, 2003 @07:43AM (#7102534) Journal
    Why not set up a business where the lab work gets done in a place where IP isn't enforced and use the cheaper methods and such that you can't in the US to do the lab work. Then you send the data back stateside over the 'net. Viola, you've got a cheaper lab! Does someone run a business like this? Why not? Can you use these primative techniques to get results as good as the fancier techniques?

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