[DIYbio] mini-symposium on Gene Editing, Art and Ethics in Irvine.... and no biohackers are there?

hoi zäme,

this symposium is happening next friday, february the 5th, at UC Irvince.
hope to see some of the regional biohackers joining...
http://newkirkcenter.uci.edu/2016/01/15/save-the-date-for-limit-biology-2516/

greets,
marc


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Re: [DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

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. :)

On 31 January 2016 06:05:00 GMT+00:00, Yuriy <yuriyology@gmail.com> wrote:
oxidation and desiccation stresses? but it lives in thermal vents, produces hydrogen, so I have a feeling it might have that covered. 

the strain sequenced already has CRISPR

On Saturday, January 30, 2016 at 11:21:08 PM UTC-5, GavinScott wrote:
On Fri, Jan 29, 2016 at 2:38 PM, Dennis Oleksyuk <ma...@dennis-o.com> wrote:
> Now this become curious. How would you test radiation resistance?

Unless thermococcus gammatolerans actually encounters unusually high levels of radiation in its environment (seems unlikely) then as suggested it's probably really just a very good DNA repair mechanism of some sort which it uses to survive some other threat. I think it would be interesting to test its resistance to chemical mutagens and other ways of damaging its DNA which might well give you an effective way of evaluating it without actually using ionizing radiation.

I'd look at papers on DNA repair, because likely many of them will have needed a convenient way of damaging DNA.

I wonder if it would be hard to use CRISPR-derived tools on such a species. It might repair itself as fast as you're trying to cut it with your Cas9 :)

G.



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[DIYbio] Ottawa, Ontario, Canada

Anything happening in Ottawa, Ontario in the ways of DIYbio? I'd love to get in on any action, if it exists.

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Re: [DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

oxidation and desiccation stresses? but it lives in thermal vents, produces hydrogen, so I have a feeling it might have that covered. 

the strain sequenced already has CRISPR

On Saturday, January 30, 2016 at 11:21:08 PM UTC-5, GavinScott wrote:
On Fri, Jan 29, 2016 at 2:38 PM, Dennis Oleksyuk <ma...@dennis-o.com> wrote:
> Now this become curious. How would you test radiation resistance?

Unless thermococcus gammatolerans actually encounters unusually high levels of radiation in its environment (seems unlikely) then as suggested it's probably really just a very good DNA repair mechanism of some sort which it uses to survive some other threat. I think it would be interesting to test its resistance to chemical mutagens and other ways of damaging its DNA which might well give you an effective way of evaluating it without actually using ionizing radiation.

I'd look at papers on DNA repair, because likely many of them will have needed a convenient way of damaging DNA.

I wonder if it would be hard to use CRISPR-derived tools on such a species. It might repair itself as fast as you're trying to cut it with your Cas9 :)

G.


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Re: [DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

On Fri, Jan 29, 2016 at 2:38 PM, Dennis Oleksyuk <mail@dennis-o.com> wrote:
> Now this become curious. How would you test radiation resistance?

Unless thermococcus gammatolerans actually encounters unusually high levels of radiation in its environment (seems unlikely) then as suggested it's probably really just a very good DNA repair mechanism of some sort which it uses to survive some other threat. I think it would be interesting to test its resistance to chemical mutagens and other ways of damaging its DNA which might well give you an effective way of evaluating it without actually using ionizing radiation.

I'd look at papers on DNA repair, because likely many of them will have needed a convenient way of damaging DNA.

I wonder if it would be hard to use CRISPR-derived tools on such a species. It might repair itself as fast as you're trying to cut it with your Cas9 :)

G.


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Re: [DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

"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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[DIYbio] Re: Perth (Australia) Group

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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Re: [DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

It depends on the radioactive isotope used. Some isotopes emit alpha or beta particles, but some emit gamma photons. The most cost effective way to expose cells to ionizing EM radiation would be to leave it outside in the sun. You get a relatively small dose of ionizing UV from sunlight, might not be enough for these experiments, but direct sunlight tends to be fairly damaging to DNA (hence melanoma). Would the damage from gamma rays be the same as UV? They are both ionizing EM radiation, but gamma rays have a lot more energy.

Another, more controllable source of UV would be tanning bed lights.

On Fri, Jan 29, 2016 at 2:38 PM Dennis Oleksyuk <mail@dennis-o.com> wrote:
Now this become curious. How would you test radiation resistance? What would be the most cost efficient way to expose cell culture to ionizing radiation? 

I bet that radioactive isotopes is off the table for majority of places. Can x-ray radiation used? Is it different in its DNA damage properties from radiation from radioactive isotopes? If so, then some old x-ray machine probably good the job. 

Is there any alternative?

On Fri, Jan 29, 2016 at 3:15 PM Koeng <koeng101@gmail.com> wrote:
"This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized"

Direct injection of proteins will likely do more harm than good, and they don't even know the exact proteins that confer to their resistance. Finding the *exact* genes is the first task

On Thursday, January 28, 2016 at 3:59:23 PM UTC-8, Finn Daffron wrote:
Thank you for your help and the link. I have, based on information provided in the paper and by you, determined a method that does not involve live thermococcus gammatolerans but instead the recombinant proteins that provide DNA repair in thermococcus gammatolerans.

On Thursday, January 28, 2016 at 3:11:22 PM UTC-5, Finn Daffron wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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Urgent Client Need: Manual Tester; Boston MA; Long Term

Please send your resumes at kumar@my3tech.com

 

Hi 

 

This is Vinay from My3tech hope you are doing well.

Please go through below description and reply with your resume, contact details and current location, if you feel comfortable

 

Title: Manual Tester 

Location : Boston MA

Duration : Long Term 

 

Retail Experience is Must

 

 

Required skills 

  • 3-5 years of experience as a QA tester
  • Need Retail background
  • Experience with application lifecycle management (ALM) software specifically with Quality Center
  • Creating/building reports by working with excel and other Microsoft office tools
  • Ability to write their own test cases and test plans

 

Thanks and Regards,

 

Vinay Kumar M 

My3Tech, Inc.

IT Solutions, Staffing & Consulting

401 E. Sioux Ave, Suite # 2

Pierre, SD 57501-3162

Phone : 605-220-5051 | Fax:  (605) 609-2010

kumar@my3tech.com

URL:  www.my3tech.com

 


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Urgent Client Need: Manual Tester; Boston MA; Long Term

Please send your resumes at kumar@my3tech.com

 

Hi 

 

This is Vinay from My3tech hope you are doing well.

Please go through below description and reply with your resume, contact details and current location, if you feel comfortable

 

Title: Manual Tester 

Location : Boston MA

Duration : Long Term 

 

Retail Experience is Must

 

 

Required skills 

  • 3-5 years of experience as a QA tester
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  • Experience with application lifecycle management (ALM) software specifically with Quality Center
  • Creating/building reports by working with excel and other Microsoft office tools
  • Ability to write their own test cases and test plans

 

Thanks and Regards,

 

Vinay Kumar M 

My3Tech, Inc.

IT Solutions, Staffing & Consulting

401 E. Sioux Ave, Suite # 2

Pierre, SD 57501-3162

Phone : 605-220-5051 | Fax:  (605) 609-2010

kumar@my3tech.com

URL:  www.my3tech.com

 

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Re: [DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

Now this become curious. How would you test radiation resistance? What would be the most cost efficient way to expose cell culture to ionizing radiation? 

I bet that radioactive isotopes is off the table for majority of places. Can x-ray radiation used? Is it different in its DNA damage properties from radiation from radioactive isotopes? If so, then some old x-ray machine probably good the job. 

Is there any alternative?

On Fri, Jan 29, 2016 at 3:15 PM Koeng <koeng101@gmail.com> wrote:
"This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized"

Direct injection of proteins will likely do more harm than good, and they don't even know the exact proteins that confer to their resistance. Finding the *exact* genes is the first task

On Thursday, January 28, 2016 at 3:59:23 PM UTC-8, Finn Daffron wrote:
Thank you for your help and the link. I have, based on information provided in the paper and by you, determined a method that does not involve live thermococcus gammatolerans but instead the recombinant proteins that provide DNA repair in thermococcus gammatolerans.

On Thursday, January 28, 2016 at 3:11:22 PM UTC-5, Finn Daffron wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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[DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

"This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized"

Direct injection of proteins will likely do more harm than good, and they don't even know the exact proteins that confer to their resistance. Finding the *exact* genes is the first task

On Thursday, January 28, 2016 at 3:59:23 PM UTC-8, Finn Daffron wrote:
Thank you for your help and the link. I have, based on information provided in the paper and by you, determined a method that does not involve live thermococcus gammatolerans but instead the recombinant proteins that provide DNA repair in thermococcus gammatolerans.

On Thursday, January 28, 2016 at 3:11:22 PM UTC-5, Finn Daffron wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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[DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

Identification of exactly what proteins (with references) confer to this resistance is the first step. 

Since biological systems for the most part are not modular between different domains (lots of exceptions), you will have to verify that these do, indeed, confer to resistance to radiation. What will your controls be for that? How will you prove statistical significance in mice? Are all proteins needed, some, or just 1?

I agree with Dennis, it will probably not work first try around. Perhaps it will with extreme modification, but that is out of the realm of DIYbio.

-Koeng

On Thursday, January 28, 2016 at 3:59:23 PM UTC-8, Finn Daffron wrote:
Thank you for your help and the link. I have, based on information provided in the paper and by you, determined a method that does not involve live thermococcus gammatolerans but instead the recombinant proteins that provide DNA repair in thermococcus gammatolerans.

On Thursday, January 28, 2016 at 3:11:22 PM UTC-5, Finn Daffron wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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Required || Sr. Oracle R12 Financials Techno-Functional || Baltimore, MD

Dear Partner

Hope you are doing great!!

Please add me on yahoo at arpittechwire and do share me your hotlist also at Arpit@tresourceinc.com.

Please go through the requirement and let me know if you have any consultant for the same position.

 

Sr. Oracle R12 Financials Techno-Functional

Baltimore, MD

24+ Months

Phone / Skype

 

  

Job Description:

 

a Sr. Oracle R12 Financials Techno-Functional consultant with expertise around Financial modules. Candidate must have strong functional and technical experience around AP, AR, GL, iExpense, and AGIS. Experience with Global Trade Management is preferred, however not required.  The ideal candidate must have strong technical experience around OAF, PL/SQL, Forms, Reports, etc.

 

 

Thanks & Regards,

 

Arpit Arora | Assistant Team Lead-Recruitment

Technology Resource Group Inc. 
3736 Hillsdale Court Santa Clara, CA 95051

Office:408-709-1760 Ext : 961, Cell: 408-502-5132

Fax: 408-884-2409

Arpit@tresourceinc.com | www.tresourceinc.com

 

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[DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

Thank you for your help and the link. I have, based on information provided in the paper and by you, determined a method that does not involve live thermococcus gammatolerans but instead the recombinant proteins that provide DNA repair in thermococcus gammatolerans.

On Thursday, January 28, 2016 at 3:11:22 PM UTC-5, Finn Daffron wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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[DIYbio] Re: Anyone have a method of synthesizing thermococcus gammatolerans?

Thank you for your help. I appreciate the link.

On Thursday, January 28, 2016 at 3:11:22 PM UTC-5, Finn Daffron wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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Re: [DIYbio] Trying to save Freeside Atlanta's bio lab

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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Re: [DIYbio] Anyone have a method of synthesizing thermococcus gammatolerans?

Thermococcus gammatolerans is probably relying on its extremely efficient chromosome reconstruction mechanism to repair DNA damage caused by radiation. Considering that it is an Archaea with a puny DNA it is almost certain that whatever mechanism it is using will be completely incompatible with mammals cell physiology.

In case you still want to try, I suggest starting from reading this paper.

On Thu, Jan 28, 2016 at 3:11 PM Finn Daffron <finndaffron@gmail.com> wrote:
I am trying to create a batch of thermococcus gammatolerans. This is because I want to use CRISPR to inject thermococcus gammatolerans into rats in order to create radiation resistance with possible implications being people working in nuclear power plants, astronauts, etc. Does anyone have any ideas on how it would be synthesized? Please get back to me.

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Re: [DIYbio] What's wrong with open source PCRs

You don't want to use mineral oil near the lids.  It is frequently noted as a band-aid to the problem that ends up being messy and possibly resulting in contamination.  It's also been mentioned previously in this group as well as a bad idea.

"Why aren't the sample containers filled to the top [such as with anything, ex. distilled water]"..  Umm.. because it's not beneficial from many angles - some Bio Lab 101 might be useful research here.  The purpose of PCR is commonly to amplify product as much as possible within a volume, so metaphorically watering it down is a bit opposite of the purpose.  Plus the experimental risk probabilities add up.  Pure water would add to reagent cost as well [not significantly if there's a steady source available, but still would add].   Ideally there would be a flux capacitor generating a neutron field which holds the target molecule in perfect chemically inert and isolated suspension while under operation by your chosen reagent, so the opposite of this ideal is an unknown chemical mix [liquid or solid] surrounding your target and interfering with it in random unknown ways and then unable to be removed later - you know what I mean?   The tiniest droplet which can later be removed 100% from the tube is best.

I believe John asked about the cooling use case (i.e. to 4C).  Yes it is a very necessary use case.

Where did the biologists go who want to explain these design criteria?  Hopefully they don't leave the fate of discovering the world's final new antibotic in the hands of an electrical engineer like myself, that only works in zombie movies.

## Jonathan Cline  ## jcline@ieee.org  ## Mobile: +1-805-617-0223  ########################    
On 1/28/16 12:00 PM, Simon Quellen Field wrote:
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  ########################             

 

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Re: [DIYbio] What's wrong with open source PCRs

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  ########################             

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