Science

D.radiodurans is so radiotolerant because of mechanisms it evolved to resist dessication-induced double-stranded breaks (and deamination/depurination?). So, let's generalise basic radiotolerance to repair of or avoidance of DSBs and specific classes of SN-mutations.

If this bug lives in the *plume* of a thermal vent, it may have to deal with a lot of cavitation from thermal bubbles, which I'm guessing may lead to sonication-indiced DSBs. But, the same mechanisms wouldn't lead to an abnormally high level of SN-mutations. However, heat *does* increase the odds of such mutations, so it may have convergently evolved the same radio-defences as D.radiodurans despite a totally different environment.

All guesses on my part, of course. :)

"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 already exists. Easier thing would be to request the strain from the people that had it during sequencing. Or request it from a repository.

I haven't yet looked at the paper but, you could look through its expressome as opposed to expression of a non-radio-resistant strain and from there find out what there is vs what there isn't in the strain to find out what can or cannot be used in mammalian cells.

If DARPA is calling for proposals on radiation resistance and early warning indicators, I don't think you would be the go to guy.

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Oh my goodness! Synthetic bio people in Perth!!!?? I had no idea that there were more of us!

Hello to all, I'm Rhiannon or Rhee. I'm a student in the synthetic biology lab at Harry Perkins. Glad to have found you all. Will have to alert my lab mates as to this forum.

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Wow, what a haul! All great stuff IMO.

The mass-spec and liquid handler seem like the most interesting to
non-bio non-chem electronics-interested hackers. The former would be a
treasure-trove for anyone into Analog or tube-based electronics, the
latter is a 3D printer's cousin.

I wonder if the mass-spec has any/all the vacuum pumps...

What kind of rotovap? I've got one that needs some parts, in case the
one you're talking about isn't complete and needs to be disposed of.

On Tue, Jan 26, 2016 at 10:47 PM, Nathan Burnham <nburn42@gmail.com> wrote:
> Hey I'm from the hackerspace Freeside Atlanta.
>
>
> We just got a huge bio lab donation and we don't really know what to with
> it. We have a couple people in the space who are interested but most of our
> members don't know much about biology or chemistry.
>
>
> So most of our members don't see much use for the donation and are thinking
> about getting rid of most of it. They gave me a date to show them that there
> would probably be enough interest and project ideas to justify it taking up
> some prime real estate in our space.
>
>
> I'm not in bio or chemistry, but I'm trying to save the bio lab by finding
> people who would use it for cool things and i'm trying to figure out what
> kinds of cool things we can do with the equipment we got.
>
> The equipment includes:
>
> A big hood with a hepa filter,
> Incubators,
> a liquid handling machine,
> a rotary evaporator,
> tons of glassware for airless chemistry,
> a mass spectrometer for organic stuff,
> microscopes and stains,
> a centrifuge,
> and a bunch of other stuff I'm not even sure what it is.
>
> So my main question is where should I reach out to find the people who would
> like to play with this stuff. And my secondary question, is all of this
> stuff useful for bio / chemistry hacking.
>
>
> Any help is appreciated.
>
>
> Thanks,
>
> Nathan
>
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--
-Nathan

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## Jonathan Cline  ## jcline@ieee.org  ## Mobile: +1-805-617-0223  ########################    

I love the idea of a thin copper or aluminum plate stamped with tight-fitting dimples for the sample containers, and making a box with this as the lid, and running hot and cold water inside the box.

You get the temperature stability of a large water bath, and the rapid heat cycling without having to move the samples. Two large water baths kept at the two temperature extremes, and you just drain them through the box with the samples nestled in their dimples in the lid.

Spraying mineral oil or paraffin onto the sample containers before closing the lids also sounds like it would eliminate the need for heating the lids. So does the idea of simply filling the containers all the way to the top. No condensation if there is no vapor. The oil sounds a bit messy, though. At least paraffin is solid at room temperature. Why aren't the sample containers filled to the top? Even with distilled water?

 

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On Thu, Jan 28, 2016 at 8:56 AM, Jonathan Cline <jcline@ieee.org> wrote:

On 1/27/16 6:50 AM, Bryan Jones wrote:

My understanding is that PCR machines typically use solid metal blocks because they make it much easier to heat all the samples evenly and keep a steady temperature. The high heat capacity of the metal minimizes spacial and temporal fluctuations.

Yes, but wasn't that in the dark ages before today's machining could cheaply craft a perfectly shaped *hollow* form which could circulate a more thermally-conductive liquid into a much, much larger capacity mass i.e. external temperature bath?    For example:  newer very highly thermally conductive ceramic epoxies, cast as a PCR tube-shaped mold yet hollow to allow rapid fluid pumping to/from hot & cold baths would be very temp stable and physically light with faster ramp rates; note: temperature sensors embedded during the setting process to algorithmically control this.

Even temperatures across all samples is critically important.  Any thermocycler design must absolutely guarantee this within some very small % tolerance and the design must be verified to work within this tolerance.

On the rant about the use of outdated technology in designs, an analogy, tankless water heaters for home use (showers and kitchen faucets) have been available for some time, yet are still niche products despite their technology superiority, mainly because builders are either not aware of the benefits or are stick-in-the-muds.  So lab device technology is not so different from the same builders of a kitchen toaster in that way either.

## Jonathan Cline  ## jcline@ieee.org  ## Mobile: +1-805-617-0223  ########################      

On Tue, Jan 26, 2016 at 9:09 PM Jonathan Cline <jcline@ieee.org> wrote:

Excellent point about a single-well thermocycler.  Rarely do you want to run 1 tube at a time however.  Need several tubes at a minimum, for experimental controls, redundancy, etc.  OpenPCR is considered personal-pizza-size with only 16.  Apple's USB-C laptop charger is rated at 29W ( 2A @ 14.5V ), for the Macbook which has no other power supply input, only USB-C -- so the supply isn't in either the 60W or 100W class.  Plastic tubes are unfortunately not very thermally conductive.  The liquid volumes are under 100 uL (typical synbio anyway).  I didn't check your math, I do agree that static temperature baths are the cheapest solution - either move the tubes to the bath or move the bath medium to the tubes.  Most of the energy goes into heating/cooling the metal mass holding the tubes, which oddly enough are machined out of large solid metal blocks -- there may be a benefit to this that I can't see, otherwise I consider it a baffling choice (no pun intended).  Some thermocyclers physically halve the heater block mass (I suppose you could call this, decoupling) when ramping temperature down.  Note the use cases may include incubation temperature for long periods of time (37 C typical, or up to 65C in some cases, for up to several hours total), this would result in steady state power draw, not peak power -- this is important regarding the assumption that a battery could be used instead (not sure I'd want to use a battery unless it was remote field use).  Another static temperature use case is 4C for many hours, for example.

The Lava-amp micro thermocycler was under 1W (I think).  Even had it worked out, I'm not sure it would have gained acceptance because it used a different form factor - didn't use "old fashioned" tubes.  Although there could be real experimental differences in results if changing equipment, obviously the ideal thermocycler would increase the surface area of the liquids for maximizing energy transfer -- i.e. not use plastic tubes.  That's one part of the approach the Lava-amp design took.

About this assumption:

>Now suppose I have two water baths, one at 60 degrees, and another at 90 degrees.
>I use a small motor to move the 96 tubes from one bath to the other.
>I can have a small fan that blows over the tubes when they go from the hot bath to the cold bath to speed the cooling, so that when the tubes hit the 60 degree bath they are already at 60 degrees.

Historically there are thermocyclers designs which use fans and electronically controlled vents to direct heated (or room temperature) air for assisted ramping.

Here's an example typical use case (synbio purification-ligation) to contrast to your example.

100 cycles	12 °C	60 s
	22 °C	60 s
	12 °C	60 s
	22 °C	60 s
	12 °C	60 s
	22 °C	60 s
	12 °C	60 s
	22 °C	60 s
Hold	16 °C	infinite

## Jonathan Cline  ## jcline@ieee.org  ## Mobile: +1-805-617-0223  ########################