Re: [DIYbio] Abridged summary of diybio@googlegroups.com - 6 updates in 4 topics

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Robb Greathouse

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Feb 8, 2016, 1:09:23 AM2/8/16
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Does anyone know where to get a cheap PCR or plans?

On Sun, Feb 7, 2016 at 10:18 PM, <diy...@googlegroups.com> wrote:
Nathan McCorkle <nmz...@gmail.com>: Feb 07 02:58PM -0800


> "I am trying to create a batch of thermococcus gammatolerans." Some things
> are probably lost in translation and I didn't see anyone try to correct
> you. You don't create anything, if it ...more
Yuriy <yuriy...@gmail.com>: Feb 07 06:22PM -0800

Huh, I thought I successfully deleted that communique. Oh well.
 
Context and perception had you dig up a deleted comment. Given the effort you put into correcting my perception (even though I ...more
masoud hasany <masoud...@gmail.com>: Feb 07 12:50AM -0800

Dears
 
Could someone please help me to download video from jove.com?
the IDM only downloads the 20 second of that and then I have only sound
with no motion picture.
 
Thanks
...more
masoud hasany <masoud...@gmail.com>: Feb 07 12:45AM -0800

I want to download from jove.com, but I can't. plz someone help me. It's
only downloaded partially (20 seconds of that). after that we have only
sounds.
 
On Tuesday, September 24, 2013 at ...more
Kalem Tysick <artpholo...@gmail.com>: Feb 06 11:34PM -0800

I checked their website and it appeared that one would have to be a
university student or a postgraduate of university in order to apply to do
work at the lab. Also, they were only doing work on ...more
Kalem Tysick <artpholo...@gmail.com>: Feb 06 11:38PM -0800

Though I could have missed something on their site. I'll be sure to check
again.
 
On Sunday, 7 February 2016 02:34:56 UTC-5, Kalem Tysick wrote:
...more
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Bryan Jones

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Feb 8, 2016, 9:59:42 AM2/8/16
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Depends on how cheap you want. There are numerous plans for light bulb pcr machines available (like here: http://russelldurrett.com/lightbulbpcr.html it here: https://tequals0.wordpress.com/2014/04/05/lightbulb-pcr-build-documentation/ ). This is the cheapest option at under $100 fit the total BOM.  That said, I've yet to see any of these actually work well enough to do a reaction (in still working on getting mine too work well enough)
The cheapest place to buy a new (and functional) Pcr is open Pcr from Chai ( https://www.chaibio.com/openpcr ). This comes in at $650, with assembly required.
The other budget option is find a used machine.  EBay is always a good option.  If you are near a research university, see if they have a place where they sell used equipment. Used,  you should expect to pay 500-1000 usd (if you are lucky, less).


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Dakota Hamill

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Feb 8, 2016, 10:03:16 AM2/8/16
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You can get nice PCR machines off eBay for 50 or 100 dollars.  I've had one for 3 or 4 years I got for 50 bucks and its awesome.  Strangley enough, it uses a halogen lamp and a vortex of air.  Cycles about 45 minutes to an hour faster than a Peltier on 32 repeats.  Only downside is it needs mineral oil but a small price to pay

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John Griessen

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Feb 8, 2016, 10:55:03 AM2/8/16
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On 02/08/2016 09:03 AM, Dakota Hamill wrote:
> it uses a halogen lamp and a vortex of air. Cycles about 45 minutes to an hour faster than a Peltier on 32 repeats. Only
> downside is it needs mineral oil but a small price to pay

I'd like to know the model number and whatever you know about why it needs oil even though it has a vortex of air.

Does that imply that the "heated lid" function in PCR machines is to keep the top of a vial "hotter than" the thermocycling
temperatures?

John Griessen

Sebastian S Cocioba

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Feb 8, 2016, 11:21:50 AM2/8/16
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Yeah the mineral oil is layered on top of reaction mix to keep the liquid below it from evaporating in the absence of a heated Lid. 

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC

John Griessen

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Feb 8, 2016, 11:53:10 AM2/8/16
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On 02/08/2016 10:21 AM, Sebastian S Cocioba wrote:
> Yeah the mineral oil is layered on top of reaction mix to keep the liquid below it from evaporating in the absence of a heated Lid.

So, the lid stays hotter at all times, so no vapor can condense on it? The vials will have caps, so it is close to a sealed
system where some easy thermodynamics rules can be applied. Evaporation will only be local movement and condensing again as
pressure increases a little, and diffusion moves vapor to a cold surface. Is the vapor pressure ever enough to pop caps off?

Sebastian S Cocioba

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Feb 8, 2016, 11:58:16 AM2/8/16
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Yes the caps can and will pop around the 95c region if no lid secures them in place. The higher end tubes tend to hold for longer. Another reason why some heated lids clamp down hard or have a screw-based latching system. If the whole tube is heated uniformly then it should not matter but if there is a thermal gradient the condensate which wont fall back down due to capillary action on the lid and walls will not be exposed to the thermal cycling thus waste the reaction. 


Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC

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Dakota Hamill

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Feb 8, 2016, 12:12:04 PM2/8/16
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The old machine I have (which isn't even serviced by the company anymore) has a really bright and hot halogen lamp in the middle of an open chamber shaped like a flying-saucer.  There are cradles you put either capillary glass tubes in, or a cradle that holds normal strip PCR tubes, and suspends them in the air.  When the machine ramps up, really fast hot air circulates around the chamber and evenly heats the tubes, then when it needs to cool a flap at the back opens up and lets hot air out, and opens and shuts rapidly to keep the temperature steady.  It definitely ramps and cools faster than a normal PCR machine.  

There is a paper here which are the tubes one can get but which I've never tried. 


That machine has had tube caps pop open and the reaction effectively ruined, but if the caps are on tight, they normally don't pop off.  It's basically a highly-engineered professional "lightbulb PCR" machine.


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Dakota Hamill

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Feb 8, 2016, 12:42:35 PM2/8/16
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lol I found an old video I posted from 4 years ago of the machine after we got it, and of it in action.


Not to cringe worthy, it's funny seeing how you were in the past.

Mac Cowell

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Feb 11, 2016, 3:36:10 PM2/11/16
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Look in this thread for ninjapcr and personalpcrv1 if you haven't seen it yet https://groups.google.com/forum/m/?utm_source=digest&utm_medium=email#!topic/diybio/euT3tm4fA_g

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