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Biotech Hardware Hacking Science Build

CPU's Heat Output to Amplify DNA Could Make Drastically Cheaper Tests 27

Posted by timothy
from the only-waste-heat-is-wasted dept.
MTorrice (2611475) writes "Researchers have harnessed that heat from a computer CPU to run the polymerase chain reaction (PCR) to amplify DNA in a blood sample. The team developed software that cycles the temperature of the CPU to drive PCR's three distinct steps.The method allowed them to detect miniscule amounts of DNA from a pathogenic parasite that causes Chagas disease. They hope their technique will lead to low-cost diagnostic tests in developing countries." (Always good to put waste heat to a practical purpose.)
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CPU's Heat Output to Amplify DNA Could Make Drastically Cheaper Tests

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  • by Anonymous Coward

    The big deal is they could do this with the existing machine, and they didn't need to make modifications.

    Waste heat has nothing to do with it.

    • by EvilSS (557649)

      The big deal is they could do this with the existing machine, and they didn't need to make modifications.

      Waste heat has nothing to do with it.

      Thank you. I was trying to figure out what the heck I was missing in the summary that would make this a big deal.

    • by thesupraman (179040) on Wednesday September 03, 2014 @05:03PM (#47820953)

      No, it is a stupid article. Someone has come up with an over-complex solution to a non existent problem.

      The use of the CPU to create temperature is a overly complex and difficult approach, compared to using a simple regulated heater which would be much simpler, more reliable, more repeatable, and cost less.
      Really, they are using a whole computer just to generate the heat, and a separate computer (cellphone) to run the reaction. stupid and overly complex.
      If there is a demand for a usb controlled accurate heat generator it would be trivial to build one with a usb microcontroller, its pwm output, and a heating resistor.
      it would cost less, be more accurate, smaller, waste less power, more reliable, cheaper. I doubt it would be difficult to find a suitable device already from some
      similar application.

      Temperature regulation is absolutely NOT a contributing factor to high cost of such tests.

      Hell, a power supply, some switches, and some resistors would do it if you didnt want automatic control.

      • Mod parent up. I've read only the abstract of the article, but even still, the proposed system as described is a terribly expensive way to do PCR for another reason. Typical PCR reaction runs usually thermocycle around 20-30 times. That is 20 to 30 times you will need to change the temperature of your heat sink from a high denaturing temp to a low annealing temp to facilitate DNA replication. One of the first things I was taught in heat transfer as an electrical engineer is that the overwhelming factor
        • by MattskEE (925706)

          Indeed. Using a CPU as a heater is just silly, it would be like frying an egg on the engine block of your Ferrari: technically possible but there are better and cheaper ways to get the same thing done. It wouldn't be that hard to hack together a decent computer controlled heater and sample holder/heat exchanger from a few hundred to a thousand bucks in parts (depending on how much labor you want to put into it).

          Instead they have this fiddly system where they have to load samples onto the heatsink of a run

      • by pepty (1976012)
        1. You're right, temperature control is pretty tangential to the costs, but you absolutely do need automated control. 2. The cell phone acts as an imager for the results, it doesn't control the reaction.
  • The basics of dna replication are well known. We know they need to cycle heat.

    They should have been using a standard heater, using the CPU's chip seems like a kludge.

    It might work, but it seems unlikely to be the better than a purpose built device. At most it saves a bit of cash and energy, at the expense of accuracy and complex programming.

  • by UnderCoverPenguin (1001627) on Wednesday September 03, 2014 @12:19PM (#47818095)

    This reminds me of a CPU fan that is powered by the heat using a tiny Sterling Engine. Maybe not the kind of "practical use" of the waste heat the editor had in mind, but still an interesting idea.

  • by Rich0 (548339) on Wednesday September 03, 2014 @12:22PM (#47818121) Homepage

    Do you really want to stick a whole PC in a lab, expose it to chemicals, and put its CPU through repeated heat/cool cycles just to save on a thermocycler?

    They mention costs like $19k to obtain one otherwise. I'm sure they sell for that much just as I'm sure you can go spend $2000 on a linux license, but all a thermocycler needs to do is heat samples and cool them. Clearly the CPU isn't going to be a high-performance cycler - you could probably build a little cycler that just uses radiative cooling and some resistive heating for $50. I see peltier heat sinks selling for $40 these days, so I'm sure for $100 you could build a thermocycler on the cheap.

    An ideal thermocycler just needs to heat samples to about 95C for a few seconds, cool them down to about room temperature for a few seconds, and then hold them at something around body temperature for a minute or two, The time spent ramping temperature up/down is basically dead time, and you have to repeat this 20-30 times, so if your cycler can change temperature in seconds instead of minutes you can save a LOT of time per test. Peltier effect tends to be the way things are done, or at least it was back when I was using these in the labs.

    It looks like openpcr.org has a unit for $600. I'm sure it could be improved on, but I imagine that as you get cheaper, you lose precision, and that does matter. I can't imagine that a CPU can maintain a temperature +/- 0.5C without quite a bit of effort.

  • by Anonymous Coward

    A PCR reaction needs 3 temperatures - a denaturing temp (usually 95C), an annealing temp (usually around 55C), and an elongation temp (usually around 75). The reaction is cycled between the temperatures to cause a 2^n increase in copy number in the reaction where n is one cycle through the temperatures.

    A low-tech heating solution could be obtained for less than $50, would not require any special modifications of reaction conditions (the article states that they used DMSO to lower the denaturing temperature)

  • by gerf (532474) <edtgerf@gmail.com> on Wednesday September 03, 2014 @12:25PM (#47818145) Journal
    Obviously they use the spacebar to toggle the heat on and off. https://xkcd.com/1172/ [xkcd.com]

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