Re: [DIYbio] Re: New

Water is not the most common heat sink for PCR these days, I think...
metal probably is, as in heat sink blocks. You don't need a small air
volume near the heat exchanger, what John is describing is basically a
box you've pointed a hair blow drier into... you get even temperatures
throughout the samples in the box by stirring or swirling the air
(actively or through some vortex/twisting design of the chamber) or
rotating the samples in the air (temperature controlled centrifuge,
then, basically).

You could do this many ways... you could have a carousel (like at an
amusement park) where some rotating arm with a wheel at the end rests
on a circumferential, which would be shaped like a wave with the
height of the track going up and down. When the arm rotates, it
'drives' on the outside track, since the 'arm' has a hinge, when the
track goes up or down, the arm 'drives' up or down to follow. Now
imagine just past this circumference are pools of hot or cold water,
every hill on the track would lift a basket at the end of the arm out
of the water, then when the arm is coming down the next hill on the
track, it would be lowering into the next water bath of a different
temperature.

See this reference to a childhood amusement park I frequented:
http://nicolecoomer.com/jour232/wp-content/gallery/kennywood/kangaroo.jpg

Note that the hinge in this picture is associated with a
pneumatic/hydraulic arm... that isn't to lift up the basket (full of
people here) but rather to slowly lower them down after the car has
been driven up a hill (simulating a gliding sensation).
http://www.themeparkcritic.com/Uploads/2108/Kennywood%20074%20copy.jpg



for capillaries, some have found just constant cooling from below is
fine, then heating with laser pulses.... others have had different hot
and cold zones, then snaked a capillary back and forth between the
zones. Pumping the fluid at a constant rate allows the cycle time to
remain constant (as long as the zig-zag of the capillary is the same
over the entire stretch).


On Thu, Jun 5, 2014 at 6:55 AM, Jebus Jones <raid517@hotmail.com> wrote:
> Bare in mind I am a total novice, but I am interested in how one might
> maintain an even temperature gradient through (say for example) a capillary
> type system?
>
> I thought initially of a 'turntable' (or 'stage') type arrangement (like an
> old turntable from a record player) around which a capillary type tube
> could be wound. This tube could be filled with the PCR target under
> consideration. Three (or perhaps more?) distinct temperature zones could be
> maintained by adding three heating elements and/or heatsinks (perhaps coiled
> around the capillary?) set at different temperatures at different zones
> around the outer edge of the disk. I thought to make the disk 'wobble' about
> it's axis slightly to both facilitate and enhance fluid flow through the
> tube? A small air gap could be left in the tube to allow the fluid to flow
> freely. One could in effect set up a 'production line' type arrangement
> where each segment in this apparatus would be at a different stage in the
> PCR process.
>
> This of course is just a crude thought experiment. There has already been
> some extremely advanced work done in microfluidic and other systems that
> employ a temperature gradient type arrangement to a similar effect.
>
> http://www.abebooks.com/Continuous-flow-temperature-gradient-microfluidics-Spatial-polymerase/10797610401/bd
> (I wish I could read this full article!)
>
> http://www.newscientist.com/article/dn11763.
>
> The problem however (although it's likely significant progress has been made
> in recent years) is how to prevent 'mixing' between the different
> temperature zones?
>
> Nonetheless one of the above articles appears to indicate that mixing
> between different temperature zones might be less problematical than one
> might think? I would certainly like to think more about taking a pop at
> building something along these lines, providing a stable temperature
> gradient cold be maintained.
>
> On Sunday, 1 June 2014 09:16:06 UTC+1, Jebus Jones wrote:
>>
>> OK be gentle with me. I'm brand new. I live in I am a mature student (aged
>> 44) studying for a degree in cellular and molecular biology in Newcastle
>> upon Tyne in the UK. I have been interested in science and technology since
>> I was a very young boy, but for various reasons (family/work) etc. never
>> really got around to applying myself to a formal pursuit of science until
>> quite late in my life.
>>
>> Anyway it seems to me if/when I complete my degree that the opportunities
>> for middle aged newly qualified biologists is likely to be rather limited,
>> particularly if I am interested in any sense in being at the bleeding edge
>> of research. I have long read about the Open Biology movement, and to my
>> eyes in a great many ways this is the bleeding edge. An attempt to bring
>> biology and make it accessible to the masses is a deeply noble aspiration I
>> feel. College professors spend too long isolated in their comfortable
>> crystal towers. However due to having been intensely busy for this last 2
>> years I have not been able to delve into the topic in significant depth.
>>
>> My initial response in finding this forum (and any other resources that
>> users here might care to recommend?) is one of both astonishment and
>> enthusiasm. I feel it is astonishing how far this community and this
>> movement have developed and can't imagine why I have waited so long to
>> explore it.
>>
>> However, I have hit something of a small snag. I enjoyed hugely reading
>> about the DIY projects available on the DIYbio web site. I initially set out
>> and found this list because I had been vaguely contemplating for some time
>> building my own PCR thermal cycler. However lacking sufficient knowledge and
>> experience to do so, I concluded that it was likely someone had probably
>> already beaten me to it - and that they might have plans. Unfortunately
>> while this has proved to be the case, all of the DIY equipment projects I
>> have come across so far seem to require access to a laser cutter and/or a 3D
>> printer.
>>
>> This seems to rather go against the spirit of 'democratizing biology', as
>> very few ordinary people are likely to have access to these resources.
>> Indeed as I live in a small city centre apartment close to my University,
>> these resources are likely to be forever beyond my grasp. We do have a Maker
>> Space in Newcastle and they do have a laser cutter and a number of 3D
>> printers. But the laser cutter is very jealously guarded by those few
>> members who paid for and bought it - and the 3D printers are in general all
>> the property of individual members. The attitude appears to be 'if you want
>> to use a 3D printer, you should probably make one.' There may be some merit
>> in this argument, but really what I want to do is learn about biology, so
>> this seems like a bit of a side issue for now.
>>
>> I am also almost certain I must be the only person in this entire city who
>> is interested in, or even remotely aware of these topics. I would love to be
>> proved wrong however. But my question is, how do I get my hands on the
>> relevant parts for any of these DIYbio projects without needing a laser
>> cutter and a 3D printer?
>>
>> I know some folks here might ask why don't I just use the lab equipment at
>> my university? Unfortunately as an undergraduate I am not presently granted
>> the luxury of just messing around in a lab and doing what I want - and in
>> any case, the point in building stuff from the ground up is to better
>> understand how they work, so I can build on that experience in the future.
>>
>> Anyway sorry for the slightly long intro. As a side note I am also
>> desperate for any spare lab equipment I can get my hands on, as I am
>> archetypal penniless starving student and the prospect of being able to find
>> the money to set up my own small domestic lab seems daunting. So if anyone
>> has anything going spare they can share or give me please feel free to get
>> in touch privately. In any case I hope I can play a very small part in this
>> vast and exciting revolution.
>
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--
-Nathan

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