[DIYbio] Re: Making Money Out of a Home Bio Lab?

Write a Kindle eBook on how to build a home DIY Bio lab :)?


--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/cf5b96d6-7965-4d70-b2df-7f541e65001c%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

[DIYbio] Re: Where to get project ideas for beginners

Hi, my suggestion would be undertaking a few small projects that involve several steps that are critical to DIY Bio. I can speak from my experience as I own a small vinegar manufacturing company and often analyze my acetic acid bacteria to compare fermentation efficiencies, peak acidity, etc.

Start with a fermented food from the grocery store like (raw and unpasteurized) apple cider vinegar, probiotic yogurt with life culture, kefir, or sauerkraut. First step is learning to culture bacteria properly. You can buy media but it is more instructive to learn how to make it so order so petri dishes off Amazon (100 x 15 mm would be good). Openwetware has a  lot of growth media ingredient lists. For example, if you use raw vinegar you can use the media for Acetobacter Xylinum. I actually have a remix of this recipe adding ethanol and acetic acid (from store bought vinegar) and can post it if you would like. All the ingredients can be found online easily and if  you can't find yeast extract, Marmite works fine. If you are doing yogurt etc. a lactic acid bacteria media is preferable.

From here you would learn how to properly autoclave/sterilize the petri dishes, mix the media with agar in hot water and pour it into the petri dishes to solidify. Culture your bacteria, learn about serial dilution to try to get pure colonies on a new culture, and then the real fun starts.

At this point you can just send the petri dish to a lab to do 16S rRNA sequencing (I recommend Genewiz in NJ for this, about $20 a sample). When you get the sequence back, you can align it in NCBI Blast or download MEGA7 and download a bunch of bacterial 16S rRNA sequences to align and match. From here you can learn about basic bioinformatics like DNA distance metrics, alignment, and making phylogenetic trees to explore the approximate relationship of what you cultured.

If you want to do it the harder, but more educational way, you can learn how to extract chromosome DNA (don't confuse this with plasma DNA) from bacteria using centrifugation and boiling water to get raw DNA. Then you can make a homemade PCR (or buy mini PCR for $650) along with DNA bases, buffer, Taq DNA polymerase, and PCR water along with 16S rRNA primer you can buy from Odin to get a bunch of DNA you can send for Sanger sequencing at a lab for cheap.

Just remember 16S rRNA is a very conserved sequence (and has multiple regions) and evolves so slowly that it is better at distinguishing more distantly related bacteria (see the DIY Bio thread on Odin contamination) than distinguishing between species under the same genus.

Sorry this seems long winded and maybe not quite relevant but I am just trying to give you a simple project that teaches you basic culturing, bioinformatics and phylogeny, DNA extraction, PCR, and sequencing basics. From there you can go wherever you want. Have fun!

Reggie Smith
Supreme Vinegar LLC

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/21a8f8d4-25ce-484b-9550-891822aedbe6%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

[DIYbio] Re: Where to get project ideas for beginners

I'm in a similar situation. If you have a community lab nearby, that would be a great start. The-odin.com has some beginner kits with all the supplies and steps laid out for bacterial cultures and transformations that's been a wonderful starting point. 

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/27a60a54-af00-4ecf-b0f1-305c27569264%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

I agree with ukitel. We got the real bacteria from the original source and they're fine (so we are not too stupid to grow bugs without contamination).But there seems to be another problem with the protocol: the two vectors transform with very different efficiency and it is difficult to get them both in at the same time.


On 23 Dec 2017 18:41, "ukitel" <marco.r.cosenza@gmail.com> wrote:
Hello Nathan,

Maybe there is a misunderstanding going on or we didn't make it clear enough in the post.
The samples analyzed were independently collected from the german authorities. We're talking of two different samples. Actually three, because the bavarian LGL claimed to have analyzed two samples.
Wolfgang Nellen also mentioned that to his knowledge other samples were tested.
In all cases there seemed to be a contamination.

Of course one could argue that the "cold chain" got broken in every single case. IMHO, unlikely that it happened independently many times, but for the sake of the argument, let's assume that some kind of improper storage it is what happened:
even so, maybe there should be a note in the user manual about it, maybe kits should be delivered at cold temperature, maybe the bacteria should be kept in an "air-tight" vial, maybe there could be an "expiry date", maybe there could be an internal control helping the user to know if the kit is still usable...
These are all solution that IMHO could help improving the kit. Not necessarily that kit, but any kit that might include bacteria.

This is the type of discussion that I would wish to see. Instead of turning the face the other way, dismissing the claims, or even suggesting some kind of hidden agenda, let's use this incident to learn and make this stuff better. Because in the end, you might still experiment with those kits in US, but don't forget that's us in Germany (and possibly Europe) that don't have those tools available.

On Friday, 22 December 2017 23:39:51 UTC+1, Nathan McCorkle wrote:


On Fri, Dec 22, 2017 at 12:28 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:
On Thursday, December 21, 2017 at 2:20:55 PM UTC-8, Nathan McCorkle wrote:

I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.

Hi Nathan. I have to admit I don't really understand this comment. What behavior are you objecting to here? 

Patrik


There's no conversation going on here... and it seems like shoddy and misleading work.

If hamburgers were illegal to eat in the EU, and I mailed a hamburger to some food-hacker there... and they cut open the gamma-sterilized vacuum-sealed bag I sent it in, but only smelled it... so they wouldn't break the law. Then months later the hamburger-police show up demanding that now-rotten hamburger, take it to their lab and test it, only to declare "we couldn't find any beef DNA, only flesh-eating bacteria, thus there must have never been any beef at all and only flesh eating bacteria". Then these food-hackers decide they want to double-check the hamburger-police's lab work... so they do their own DNA test on the rotten-hamburger, to discover the same horrific results!

Let me tell you... I would have ordered a fresh hamburger for any re-testing of hamburgers pre and post rotting. Of course if there is hamburger flesh, flesh-eating bacteria will gladly show up and start eating away/ Of course these bacteria will release nucleases, and other reactive waste products that will destroy any detectable trace of beef evidence.

I don't know what's going on here... but something is shady.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/307d48d0-7ddc-48e4-adc4-00ddad319825%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAHygQAwwxJN_Uf-o5Ls3M8HeoK7qC8isDqzGFkGdZ11THiMFMw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

Did you get any response from the Germans yet?
Concerning communication: is there anything like a Facebook site where all communities could talk to each other and discuss issues like the kit? I guess the authorities do not have a clue where the DIY communities are!


On 22 Dec 2017 20:00, "Vanessa lorenzo toquero" <vlorenzolana@gmail.com> wrote:
Hi,

I introduce myself. Vanessa Lorenzo from Hackuarium biohackerspace in Renens, Switzerland, co-leading it together with Rachel Aronoff and the board,

Just to inform that we had a kit from the Odin at the lab. We decided to get in contact with the German authorities who suggested that our kit might also be contaminated. We sent them the kit.

We also got better informed on how our community could contribute
better to the DIY Bio movement. A more dynamic dialogue between the authorities and the affected peers of the DIY Bio movement would had been more desirable but we are now navigating between different landscapes with different time scales and communication protocols. We should push for a better more transparent ones, and of course our door is literally transparent and always open on Wednesdays or on appointment (basically cause we are volunteers and have side jobs or even lives!). Having a constructive and responsible attitude towards the issues we face could help shaping the science we dream of.

Best regards

Vanessa

El viernes, 22 de diciembre de 2017, 9:52:09 (UTC+1), Jonathan Ferooz escribió:
Nathan I think you are wrong, in Belgium we are very interested to collaborate with other groups (and I'm sure in other EU countries too). But in contrast with some other groups we are a small group with no funding.
What do you think we can do?
We are pushing, at our level, to show what is the DIYbio and hope that we'll can adapt our laws to facilitate the DIYbio.
In europe just have the right to put GFP in a genome it's a fight with the authorities.
If other groups want to collaborate with us in Belgium, we are open.
We are not making the show on TV, Nature or other, but yes, we are there.

Le jeudi 21 décembre 2017 23:20:55 UTC+1, Nathan McCorkle a écrit :




I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.


--
-Nathan

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to a topic in the Google Groups "DIYbio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/diybio/PXeoidiWPYA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/1fc60b5a-ee58-463d-8076-99c4d4c3e515%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAHygQAyOh%2BoB3xgW8vtA5dJHhkm5OJ6bD2x6hVcyBPvjfP_XYg%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] titanium: "boils water definitely twice faster then any Al cups" -- can it be?


Silicone mold for tubes mounted directly on automotive heater core ($28 *) for heat transfer (**) with fan ( > $10) mounted below to blow through the radiator fins.  Minimum component cost at least $35 for air design.


* 1980-1997 Ford F250 Heater Core - APDI 9010205.  Note that no new mechanical design will get cheaper or more efficient than this. 

** However the lab market has already moved away/rejected air driven pcr so not sure why rehashing that outdated design is considered productive.  No it won't be made better.  Also, no lab tech wants to deal with gunk on outside of tubes regardless of whether it optimizes heat transfer or for some other purpose.


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

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/e6a99159-0a17-4440-b548-3bfc317b008e%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

I like the food analogy but that's also flawed.

Of course if the chain of custody is interrupted then a company cannot be blamed.
But that's not always the case here (for example for the LGL), please do not forget that we are talking about different samples.

Let's look at the food analogy: what does it happen normally when some people get sick with a product bought at the supermarket? the entire lot gets withdrawn and all the people that have bought it are informed (when possible) and asked to return their product. You take a moment of pause, check everything, point down where the contamination happened. If there's something to fix, fix it and then start over.
IMHO, this would be a wonderful resolution for the this case.

Of course food doesn't have to be sterile, but there are thresholds, which are more or less strict depending on the danger connected to the contaminant. The problem is that the LGL and us did not find e.coli at all there. But let's not focus on this kit alone and think generally about such kits: do we need similar thresholds here? The product has to be devoid of any contaminant or not? Can we design a kit so that even if contamination is present, it is eliminated by some kind of selective media?


On Saturday, 23 December 2017 09:03:32 UTC+1, BraveScience wrote:
As soon as chain of custody of a given material is interrupted (material is open, seal is broken) how can a company be blamed for the state of it?

Here Nathan's analogy fits, that's the common practice in the whole food industry (in EU at least).

The "indignation" of the authority seems out of place and procedures applied non conforming to standard procedures in matter of sampling. Again, if you want to make sure that goods are free of contamination you should check an "untouched" lot before this reaches the customer.

On the other hand hinting to "EU biohackers" is IMHO not the correct way to frame this and a generalization. EU is not USA, there are many different countries here, the fact happened in Germany, that's a whole different story if compared to Denmark, Netherlands, Italy or whatever.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/7a31dbbe-9233-4143-9316-775c2a4dac6a%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

Hello Nathan,

Maybe there is a misunderstanding going on or we didn't make it clear enough in the post.
The samples analyzed were independently collected from the german authorities. We're talking of two different samples. Actually three, because the bavarian LGL claimed to have analyzed two samples.
Wolfgang Nellen also mentioned that to his knowledge other samples were tested.
In all cases there seemed to be a contamination.

Of course one could argue that the "cold chain" got broken in every single case. IMHO, unlikely that it happened independently many times, but for the sake of the argument, let's assume that some kind of improper storage it is what happened:
even so, maybe there should be a note in the user manual about it, maybe kits should be delivered at cold temperature, maybe the bacteria should be kept in an "air-tight" vial, maybe there could be an "expiry date", maybe there could be an internal control helping the user to know if the kit is still usable...
These are all solution that IMHO could help improving the kit. Not necessarily that kit, but any kit that might include bacteria.

This is the type of discussion that I would wish to see. Instead of turning the face the other way, dismissing the claims, or even suggesting some kind of hidden agenda, let's use this incident to learn and make this stuff better. Because in the end, you might still experiment with those kits in US, but don't forget that's us in Germany (and possibly Europe) that don't have those tools available.

On Friday, 22 December 2017 23:39:51 UTC+1, Nathan McCorkle wrote:


On Fri, Dec 22, 2017 at 12:28 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:
On Thursday, December 21, 2017 at 2:20:55 PM UTC-8, Nathan McCorkle wrote:

I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.

Hi Nathan. I have to admit I don't really understand this comment. What behavior are you objecting to here? 

Patrik


There's no conversation going on here... and it seems like shoddy and misleading work.

If hamburgers were illegal to eat in the EU, and I mailed a hamburger to some food-hacker there... and they cut open the gamma-sterilized vacuum-sealed bag I sent it in, but only smelled it... so they wouldn't break the law. Then months later the hamburger-police show up demanding that now-rotten hamburger, take it to their lab and test it, only to declare "we couldn't find any beef DNA, only flesh-eating bacteria, thus there must have never been any beef at all and only flesh eating bacteria". Then these food-hackers decide they want to double-check the hamburger-police's lab work... so they do their own DNA test on the rotten-hamburger, to discover the same horrific results!

Let me tell you... I would have ordered a fresh hamburger for any re-testing of hamburgers pre and post rotting. Of course if there is hamburger flesh, flesh-eating bacteria will gladly show up and start eating away/ Of course these bacteria will release nucleases, and other reactive waste products that will destroy any detectable trace of beef evidence.

I don't know what's going on here... but something is shady.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/307d48d0-7ddc-48e4-adc4-00ddad319825%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

As soon as chain of custody of a given material is interrupted (material is open, seal is broken) how can a company be blamed for the state of it?

Here Nathan's analogy fits, that's the common practice in the whole food industry (in EU at least).

The "indignation" of the authority seems out of place and procedures applied non conforming to standard procedures in matter of sampling. Again, if you want to make sure that goods are free of contamination you should check an "untouched" lot before this reaches the customer.

On the other hand hinting to "EU biohackers" is IMHO not the correct way to frame this and a generalization. EU is not USA, there are many different countries here, the fact happened in Germany, that's a whole different story if compared to Denmark, Netherlands, Italy or whatever.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/0933e627-7565-4ca1-b774-52fd121bcd99%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

Bacteria are not hamburgers. Much better shelf life. If I put E. coli in a tube (under more or less sterile conditions) there are still be some viable bugs in there after a few months, usually even years… this is my personal experience – but I'm looking forward to be contradicted.

Re-testing a fresh sample makes total sense - if we want to see if the problem was fixed in the meantime. Any volunteer with a sequencer?

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/309b43bc-119e-453d-a3be-299739be2a38%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?



On Fri, Dec 22, 2017 at 12:28 AM, Patrik D'haeseleer <patrikd@gmail.com> wrote:
On Thursday, December 21, 2017 at 2:20:55 PM UTC-8, Nathan McCorkle wrote:

I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.

Hi Nathan. I have to admit I don't really understand this comment. What behavior are you objecting to here? 

Patrik


There's no conversation going on here... and it seems like shoddy and misleading work.

If hamburgers were illegal to eat in the EU, and I mailed a hamburger to some food-hacker there... and they cut open the gamma-sterilized vacuum-sealed bag I sent it in, but only smelled it... so they wouldn't break the law. Then months later the hamburger-police show up demanding that now-rotten hamburger, take it to their lab and test it, only to declare "we couldn't find any beef DNA, only flesh-eating bacteria, thus there must have never been any beef at all and only flesh eating bacteria". Then these food-hackers decide they want to double-check the hamburger-police's lab work... so they do their own DNA test on the rotten-hamburger, to discover the same horrific results!

Let me tell you... I would have ordered a fresh hamburger for any re-testing of hamburgers pre and post rotting. Of course if there is hamburger flesh, flesh-eating bacteria will gladly show up and start eating away/ Of course these bacteria will release nucleases, and other reactive waste products that will destroy any detectable trace of beef evidence.

I don't know what's going on here... but something is shady.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2B82U9KJEmY7Dm1J6RiGG%3DHwM1fh_5-%3DeucTMeh6CwQ0TVR9Mw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Freedom Evo Tecan Troubleshooting - HELP!

Can you get old software for them easily?

I have a 75 Freedom Evo and the PC it originally came with.  However, the computer is locked via windows and I tried rainbow tables but wasn't able to crack the password.

It's an older Tecan,but a shame to have a decent robot sitting on a shelf because I can't find software to run it.

On Fri, Dec 22, 2017 at 10:45 AM, flamingnerd <marypaniscus@gmail.com> wrote:
I work with Tecans. (I'm also looking for a good online community to troubleshoot with them but I am having a hard time finding it. Perhaps I should try Stack Overflow?)

My first thought about your problem was perhaps it's something with power settings. Windows sometimes turns of idle devices to conserve power. Hope you managed to fix it.

Mary

On Monday, 5 June 2017 19:30:19 UTC+2, Ana Santos wrote:
Hi diybio community!

I was wondering if anyone out there has experience with the Freedom Evo Tecan Robot. 

We have ours for a few years (>5) and no one has good memories of working with it. And basically, we're just trying to use it to read 96 well plates (between 8 and 12) for 24h.

Everything starts out OK, it runs for about 6h and afterward it just stops working showing messages like "Your run has been stopped" or "Your run was aborted". No red light blinking. No alarm. 

However, if we hit the recover bottom, it re-starts working, as if nothing had happened. If we're really lucky, the run then proceeds until the end, but normally it keeps crashing systematically afterwards.

The only pattern we've been able to detect is that the robot normally stops working when the plate is inside the plate reader.

The technicians from Tecan are now almost part of the lab, because of all the problems we have with the Robot, but they never manage to tell us exactly is the problem. Whatever they do (switch a cable, tweak the software, plug/unplug all machinery) works for a couple of hours but we then go back to the same original problem.

We're just desperate to know if someone else has faced the same problem or if it is a problem with our machine.

I look forward to your feedback.

Best regards and DO GREAT SCIENCE!

Ana

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/fa19e96e-6aa7-494a-9488-616e612120a1%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAGdeWmQ1JNiKAZrtSipVRTDaizzZj%3DXztOA77tJC_%3DRtxwBqVQ%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

[DIYbio] Re: Freedom Evo Tecan Troubleshooting - HELP!

For the initial post where the problem relates to a software timeout, EVOware has a default "timeout" of ~ 6 minutes.
this means that if a command is sent to a device and no confirmation/message is returned within 6 minutes - the software stops the script with an error
it is possible to extend the timeout for specific applications - refer to the help menu and search for "AnswerTimeout" parameter defined in EVOware.inf file
i have had similar problems and defined an AnswerTimeout=3600000 to give the software 1 hour to wait for a command response

hope this helps


On Friday, December 22, 2017 at 2:59:22 PM UTC-5, flamingnerd wrote:
I work with Tecans. (I'm also looking for a good online community to troubleshoot with them but I am having a hard time finding it. Perhaps I should try Stack Overflow?)

My first thought about your problem was perhaps it's something with power settings. Windows sometimes turns of idle devices to conserve power. Hope you managed to fix it.

Mary

On Monday, 5 June 2017 19:30:19 UTC+2, Ana Santos wrote:
Hi diybio community!

I was wondering if anyone out there has experience with the Freedom Evo Tecan Robot. 

We have ours for a few years (>5) and no one has good memories of working with it. And basically, we're just trying to use it to read 96 well plates (between 8 and 12) for 24h.

Everything starts out OK, it runs for about 6h and afterward it just stops working showing messages like "Your run has been stopped" or "Your run was aborted". No red light blinking. No alarm. 

However, if we hit the recover bottom, it re-starts working, as if nothing had happened. If we're really lucky, the run then proceeds until the end, but normally it keeps crashing systematically afterwards.

The only pattern we've been able to detect is that the robot normally stops working when the plate is inside the plate reader.

The technicians from Tecan are now almost part of the lab, because of all the problems we have with the Robot, but they never manage to tell us exactly is the problem. Whatever they do (switch a cable, tweak the software, plug/unplug all machinery) works for a couple of hours but we then go back to the same original problem.

We're just desperate to know if someone else has faced the same problem or if it is a problem with our machine.

I look forward to your feedback.

Best regards and DO GREAT SCIENCE!

Ana

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/e5e01101-95bf-40e8-9c81-994266fc4c8f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

[DIYbio] Re: Freedom Evo Tecan Troubleshooting - HELP!

I work with Tecans. (I'm also looking for a good online community to troubleshoot with them but I am having a hard time finding it. Perhaps I should try Stack Overflow?)

My first thought about your problem was perhaps it's something with power settings. Windows sometimes turns of idle devices to conserve power. Hope you managed to fix it.

Mary

On Monday, 5 June 2017 19:30:19 UTC+2, Ana Santos wrote:
Hi diybio community!

I was wondering if anyone out there has experience with the Freedom Evo Tecan Robot. 

We have ours for a few years (>5) and no one has good memories of working with it. And basically, we're just trying to use it to read 96 well plates (between 8 and 12) for 24h.

Everything starts out OK, it runs for about 6h and afterward it just stops working showing messages like "Your run has been stopped" or "Your run was aborted". No red light blinking. No alarm. 

However, if we hit the recover bottom, it re-starts working, as if nothing had happened. If we're really lucky, the run then proceeds until the end, but normally it keeps crashing systematically afterwards.

The only pattern we've been able to detect is that the robot normally stops working when the plate is inside the plate reader.

The technicians from Tecan are now almost part of the lab, because of all the problems we have with the Robot, but they never manage to tell us exactly is the problem. Whatever they do (switch a cable, tweak the software, plug/unplug all machinery) works for a couple of hours but we then go back to the same original problem.

We're just desperate to know if someone else has faced the same problem or if it is a problem with our machine.

I look forward to your feedback.

Best regards and DO GREAT SCIENCE!

Ana

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/fa19e96e-6aa7-494a-9488-616e612120a1%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

Hi,

I introduce myself. Vanessa Lorenzo from Hackuarium biohackerspace in Renens, Switzerland, co-leading it together with Rachel Aronoff and the board,

Just to inform that we had a kit from the Odin at the lab. We decided to get in contact with the German authorities who suggested that our kit might also be contaminated. We sent them the kit.

We also got better informed on how our community could contribute
better to the DIY Bio movement. A more dynamic dialogue between the authorities and the affected peers of the DIY Bio movement would had been more desirable but we are now navigating between different landscapes with different time scales and communication protocols. We should push for a better more transparent ones, and of course our door is literally transparent and always open on Wednesdays or on appointment (basically cause we are volunteers and have side jobs or even lives!). Having a constructive and responsible attitude towards the issues we face could help shaping the science we dream of.

Best regards

Vanessa

El viernes, 22 de diciembre de 2017, 9:52:09 (UTC+1), Jonathan Ferooz escribió:
Nathan I think you are wrong, in Belgium we are very interested to collaborate with other groups (and I'm sure in other EU countries too). But in contrast with some other groups we are a small group with no funding.
What do you think we can do?
We are pushing, at our level, to show what is the DIYbio and hope that we'll can adapt our laws to facilitate the DIYbio.
In europe just have the right to put GFP in a genome it's a fight with the authorities.
If other groups want to collaborate with us in Belgium, we are open.
We are not making the show on TV, Nature or other, but yes, we are there.

Le jeudi 21 décembre 2017 23:20:55 UTC+1, Nathan McCorkle a écrit :




I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.


--
-Nathan

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/1fc60b5a-ee58-463d-8076-99c4d4c3e515%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

On Thursday, December 21, 2017 at 2:20:55 PM UTC-8, Nathan McCorkle wrote:

I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.

Hi Nathan. I have to admit I don't really understand this comment. What behavior are you objecting to here? 

Patrik

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/7fbc3384-98a4-4e80-957a-fdd3b52fadd6%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?

Nathan I think you are wrong, in Belgium we are very interested to collaborate with other groups (and I'm sure in other EU countries too). But in contrast with some other groups we are a small group with no funding.
What do you think we can do?
We are pushing, at our level, to show what is the DIYbio and hope that we'll can adapt our laws to facilitate the DIYbio.
In europe just have the right to put GFP in a genome it's a fight with the authorities.
If other groups want to collaborate with us in Belgium, we are open.
We are not making the show on TV, Nature or other, but yes, we are there.

Le jeudi 21 décembre 2017 23:20:55 UTC+1, Nathan McCorkle a écrit :




I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.


--
-Nathan

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/a082787c-31bd-402d-ac56-5513bc110644%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] Re: Were the DIY CRISPR kits contaminated?



On Thu, Dec 21, 2017 at 7:13 AM, Ruediger Trojok <ruediger.t@gmail.com> wrote:
Hey everyone,

Alison Abbott from Nature participated in my event crispr.kitchen in Munich at UnternehmerTUM earlier this year.
 Since then, we kept contact. I explained her what was going on with the CRISPR kit from the ODIN
and the trouble it had caused us. I also informed her about our own investigation and results.

This is what she made out of it:


Have nice christmas holidays and a happy new year!

Best,
Rüdiger




I am surprised this has got any more attention, given the lack of response the EU biohackers have provided here on this mailing list. It gives the impression that EU biohackers are not interested in collaboration, and are making noise for some self-serving goals. This behavior only makes me wary of EU biohackers. Very sad.


--
-Nathan

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2B82U9KzxwABkeu4USV56ROLqx30tom3cVYNfOXViXudYLagBw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

[DIYbio] Re: Were the DIY CRISPR kits contaminated?

Hey everyone,

Alison Abbott from Nature participated in my event crispr.kitchen in Munich at UnternehmerTUM earlier this year.
 Since then, we kept contact. I explained her what was going on with the CRISPR kit from the ODIN
and the trouble it had caused us. I also informed her about our own investigation and results.

This is what she made out of it:

https://www.nature.com/articles/d41586-017-08807-z

Have nice christmas holidays and a happy new year!

Best,
Rüdiger

Am Samstag, 16. Dezember 2017 14:20:03 UTC+1 schrieb Wolfgang Nellen:

When you inspect an alleged chicken farm and find that all animals have four legs and say „muh" and none has feathers, you can certainly confirm your findings by a metagenome analysis. But it is pretty obvious that this is not a chicken farm!

 

I appreciate the efforts by some colleagues to do an in depth molecular analysis but the problem appears to be on a much more trivial level.
Contaminated bacterial samples were not an isolated incident. To my knowledge, at least four independently purchased samples were tested (by different, more or less sophisticated methods) and all tests came to the same result: Enterobacter, Klebsiella, no E. coli.

To check for a single contaminated batch was not possible because there are no batch numbers.

I assume (just my speculation!) that THE ODIN's 16S analysis was done on their stock but not on the material that was shipped to the users.

 

There appear to be other problems with the kit – we are working on it at www.Sciencebridge.net  but are still reluctant to publish before we have fool-proof evidence.

 

We have to join efforts to clean up the mess! It is not useful to put pressure on the labs that contribute to the clean-up. We and others do not want to publish preliminary results before all controls are done. But the accumulating evidence is sufficient to ban the kit for the time being.

We are quite happy that the media coverage is (so far) reasonable and not blown out of proportion. We tried to contribute a bit (http://www.hr-fernsehen.de/sendungen-a-z/alles-wissen/sendungen/bio-hacking,bio-hacking-100.html).

 

Just a remark on the side: even though Strep resistance is not an environmental hazard, it is strategically bad to do editing on antibiotic resistance! It needs a lot of additional explanation for "normal" citizens and distracts from the core issue of editing. We need a different trait for editing!



Am Montag, 11. Dezember 2017 17:55:16 UTC+1 schrieb ukitel:

Were the DIY CRISPR kits contaminated?


Dear all,


We would like to give you an update on the situation regarding the possible contamination of the DIY Bacterial Gene Engineering CRIPSR kit distributed by The Odin online shop. We believe it is an issue that should be openly discussed as it can potentially affect the DIY biology community as a whole.


In March 2017, the authorities for health and food safety (LGL) of Bavaria, in Germany, issued a press release revealing their results of an investigation on the DIY Bacterial Gene Engineering CRIPSR kit supplied by The Odin, a company selling biotechnology reagents over the web. The LGL stated that the bacterial strain supplied in the kit was contaminated with potentially pathogenic species, such as Enterobacter species and Klebsiella pneumoniae. Based on these findings, the kit was subsequently banned from being used in Germany.


The press release came shortly after Rüdiger Trojok organized an event entitled "CRISPR kitchen". LGL representatives requested the organizers from the Institute for Technology Assessment of Karlsruhe (KIT) to hand out a vial of the bacteria obtained from an Odin CRISPR kit, there on display. At the time, the LGL did not specify that they had already found a contamination in another sample.


After the press release, some people involved in activities of the DIYbio community of Europe felt that a proactive attitude was needed to address the issue in the most transparent manner and organized a volunteer committee.


It has been difficult to gather information from both the LGL and the Odin. The LGL press release did not contain any detailed information and we had only access to a leaked report containing a summary of their results. We managed to get some additional information about the methodology used from LGL, but we could not access any of the raw data. LGL researchers told us they would not release the data until their investigation is completed, and will only publish their results in a peer-reviewed journal at a later point.


The Odin produced blast mapping of the E.coli 16S sequence to their bacterial stock and showing 99% identity. They also showed that the strain was negative for lactose fermentation. Both these results were in contradiction with the findings described in the LGL report.

It was decided that gathering more information was necessary to evaluate the situation independently and start an open discussion on how we can promote safe and lawful use of these and other kits offered in and to the DIYbio community. The goal was to evaluate whether contamination was indeed a systematic problem or an isolated accident.


We gathered 3 samples independently from LGL and analyzed them. Two of these samples came from the incriminated CRISPR kit and the last one was an Escherichia coli HME63 strain identical to that included in the kits, all of them being sold by The Odin and shipped to European customers. To obtain high-quality DNA sequencing data, we secured a collaboration to sequence the samples at the European Molecular Biology Laboratory (EMBL) Genomics Core Facility in Heidelberg, Germany. We discussed with the authorities in Berlin (LAGESO, the LGL equivalent) how to safely handle the samples and shipped them to EMBL for analysis.


EMBL Genomics Core Facility collaborators were able to revive only one of the three samples, which showed bacterial growth both in liquid culture and on agar plate. From the 16 colonies grown on the agar plate, 10 colonies were chosen for library preparation and DNA sequencing on an Illumina platform (MiSeq). The sequencing reads have been uploaded at ENA database under the following ID PRJEB23486. We encourage everyone to go and analyze the data if interested. The Core Facility is analyzing the data, but we wanted to share with you some preliminary results:


The E.coli MG1655 strain is the closest strain relative to the E.coli HME63 supplied with the kit and whose complete genome is available. Therefore, we first aligned the sequencing reads to the E.coli MG1655 genome, but noticed that only 30% of the reads are mapping, which wouldn't be expected if the colonies contained E.coli HME63.

 

We then proceeded to assemble the unmapped reads in large sequences (>50 kb) and checked to which bacteria species they were matching. The analysis returned various Enterobacter species (aerogenes, cloacae and hormaechei), as well as Escherichia coli and Salmonella enterica. However, given the relative phylogenic proximity of these species, with this approach it was not possible to pin down the exact bacteria in the colonies. Nevertheless, it gave an indication of the possible bacteria identity.

 

Given the recurrence of Enterobacter species in the results, we aligned the reads this time to the genome of Enterobacter hormaechei subsp. Steigerwaltii and we could now see that 83% of the reads were mapping and corresponded to an expected good mapping rate on a specific genome. Notably, the presence of Enterobacter species was also mentioned in the LGL report.

 

Moreover, as The Odin made available to us 16S sequence of the E.coli bacteria stock in their possession, we sought to determine if that sequence could be found in our reads. Unfortunately, the reads encompassing the 16S region showed again a much better match to Enterobacter hormaechei rather than E.coli.

 

This suggests that the bacteria in the colonies are most probably an Enterobacter species and not E.coli HME63. The 30% of reads mapping to E.coli are probably the result of cross mapping reads between E.coli and Enterobacter genomes.

 

We would like to mention a few words of caution. First, the methodology we used to obtain these results (whole genome sequencing) is different from the one employed by LGL (metabolic and phenotypic analyses). Second, the sample we analyzed was also different from theirs and a single occurrence could again be anecdotic. Third, we cannot guarantee that the samples were stored appropriately at all times before we collected them and ran the sequencing analysis. However, the fact still remains: both our results and the LGL investigation seem to confirm a contamination of the E. coli strain provided with the kit, possibly with the same bacterial species.


Even though the European Centre for Disease Prevention and Control (ECDC) has pointed out that the risk of infection using such contaminated kit is low, we believe it is not acceptable to have laypeople, often not skilled in laboratory techniques, as it may happen in DIYbio, unknowingly handling potentially harmful biological materials. We believe it is our responsibility to act responsibly, something that was explicitly stated in the DIYbio code of conduct and thus learn from this incident and inform the whole community about it. A failure to handle biomaterials appropriately is detrimental to the goals of the community to democratize the knowledge and technology of life sciences.


Authorities in the EU have to follow generally stricter rules than other parts of the world, including the US. Genetic engineering is particularly heavily regulated and only very few and specific educational experiments can be done outside of authorized laboratories. However, we want to stress here that our findings are not discussing the meaningfulness of European GMO laws. The problem we are concerned with is the shipping of living biological samples, which could contain unwanted bacteria or even potentially pathogenic ones due to insufficient quality assurance procedures. This problem not only unnecessarily endangers the customers, it also calls into question the ability of the DIYbio kit manufacturers.


We believe the value of educational kits needs to be stressed out and we want to support their safe distribution and use. We would like to start a discussion involving DIYbio practitioners, as well as the kit producers, academics, the authorities and the public, to collaboratively develop guidelines, or if necessary develop appropriate and efficient methods and procedures to guarantee the safety of the kits and their users.


We believe this should be a community effort in the spirit of the values of the DIYbio code of conduct and so this is also a call to all of you to get involved. If you have any questions regarding the analysis, please engage in the open discussion here on the google DIYbio mailing list.


Finally we would like to acknowledge the help provided by the EMBL Genomics Core Facility team, Vladimir Benes, Jonathan Landry and Anja Telzerow. Without their work and supportive attitude towards the community this work would have not been possible.


 

Best Regards,

 

Rüdiger Trojok

Marco R Cosenza

Julian Chollet

Luc Henry

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/660155dd-8caf-43ac-afdb-5a297654c541%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS

Re: [DIYbio] titanium: "boils water definitely twice faster then any Al cups" -- can it be?

On 12/19/2017 07:28 PM, Nathan McCorkle wrote:
> Exploring the limits of ultrafast polymerase chain reaction using liquid for thermal heat exchange: A proof of principle
> Appl. Phys. Lett. 97, 264101 (2011); https://doi.org/10.1063/1.3530452

And here's the juicy details of heat transfer:


"Our thermal cycler, Fig. 1, used a liquid interface sand-
wiched between two high-powered Peltier devices,
(Marlow XLT2393, Dallas, TX), that worked in tandem to cycle the
temperature rapidly. They rejected waste heat to a pair of
fan-cooled heat sinks. These high efficiency heat sinks were
sized to allow for increased cooling rates due to their ability
to bias the heat exchange toward lower temperatures, opti-
mizing power usage at less than 400 W. A phenolic gasket
held 2.3 ml of thermal transfer medium, (gallium eutectic),
between the two face surfaces of the Peltiers, making direct
thermal contact between them and the sample capillary tube.
The liquid allowed for excellent thermal contact to the glass
capillary tube. The small volume needed to make thermal
contact required less than 200 J to raise the medium's tem-
perature from 60 to 95 °C. In a typical thermal cycler, the
thermal resistance between the junction of the solid metal
block and the sample tube is a dominant factor in reducing
the ability to transfer heat in and out of the sample, resulting
in slow thermal cycling."

See how they key on, "required less than 200 J"?

Losing the air gap between solid blocks with thermal mass
is a speed up.

My plan to do air PCR with movable doors will allow quick
change from heating to cooling without need to switch the direction
or even on/off state of a Peltier cooler, so any thermal mass
built into the cooler that slows switching between heating and cooling
will have no slowing effect using air and movable doors.

The airpcr air will be the only medium of transfer of heat between hot nichrome
heater element wires and sample tubes. It will be moving fast to
give complete stirring for even temperature, and quick heat transfer.

Still busy with electroporation, but stay tuned.

--
John Griessen
industromatic.com Austin TX building lab gear for biologists

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/ebddd777-8980-19e9-b619-831b27e0cb80%40industromatic.com.
For more options, visit https://groups.google.com/d/optout.

  • Digg
  • Del.icio.us
  • StumbleUpon
  • Reddit
  • RSS