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Open Source Biology and Biohacking Hack Chat

Hacking carbon, oxygen and nitrogen, not just silicon

Wednesday, February 13, 2019 12:00 pm PST Local time zone:
Hack Chat
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Justin Atkin will be hosting the Hack Chat on Wednesday, February 13, 2019 at noon PST.

Time zones got you down? Here's a handy time converter!

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Justin's name might not ring a bell, but you've probably seen his popular YouTube channel The Thought Emporium, devoted to regular doses of open source science. Justin's interests span a wide range, literally from the heavens above to the microscopic world. His current interest is to genetically modify yeast to produce spider silk, and to perhaps even use the yeast for brewing beer. He and the Thought Emporium team have been busy building out a complete DIY biology lab to support the effort, and have been conducting a variety of test experiments along the way. 

Please join us for this Hack Chat, in which we'll cover:

  • The how's and why's of yeast genetic engineering;
  • What it takes to set up an effective biology lab from scratch;
  • An update on the current status of the spider-silk yeast project; and
  • Where the open-source biology field is, and where it's going.

  • Hack Chat Transcipt

    Lutetium6 days ago 0 comments

    Chuck.untulis11:58 AM
    Is this the place for DIY biology chat?

    anfractuosity11:59 AM
    yup

    Dusan Petrovic11:59 AM
    yes welcome!

    konsgn11:59 AM
    speaking of diy bio, How to?

    Dan Maloney12:00 PM
    @Chuck.untulis indeed it is. We'll get started in just a minute.

    tocatrooper joined  the room.12:00 PM

    Dan Maloney12:01 PM
    Actually, it's noon, so let's get to it. Welcome to the Hack Chat! I'm really excited to have Justin Atkin here today...

    thethoughtemporium12:01 PM
    Hi Everyone!

    Dan Maloney12:02 PM
    He'll be under @thethoughtemporium handle for the chat, please welcome him and start asking questions about DIY biology

    konsgn12:02 PM
    ohhh pst is 3 hours off est no wonder it didn't start a couple hours ago

    Dan Maloney12:02 PM
    Time zones - getcha every time

    Jarrett12:02 PM
    hullo!

    Anthony joined  the room.12:02 PM

    Jan12:02 PM
    hi there!

    Jarrett12:03 PM
    I don't use timezones

    Jarrett12:03 PM
    they're just not that useful, to me

    Dan Maloney12:03 PM
    @thethoughtemporium - Maybe you can kick us off with a little bit about yourself, and how you got interested in DIY bio

    lawrence_vpi12:03 PM
    Hey, I am in Ontario and was wondering where you get your perishables?

    tocatrooper12:03 PM
    Best machines/tools for a start up lab? Cost? Best place?

    thethoughtemporium12:04 PM
    Ok will do! my background is pretty odd. Been experimenting in a home lab since I was in highschool. My current goal is to not only do fun and exciting research in a variety of fields, but to show that science can be done anywhere on any budget

    thethoughtemporium12:05 PM
    I've always been interested in bio because of the immense potential it holds. Bio is essentially the best way of converting one sort of matter into another so you can kind of do anything with it if you're clever and have enough time to mess with it.

    lawrence_vpi12:05 PM
    Hi Justin I to have been working in a home lab for quite awhile.

    thethoughtemporium12:06 PM
    It's everything I love about physics and chemistry, but applied at the smallest and largest scales at once.

    Dan Maloney12:07 PM
    The funny thing about biology is that for every "rule" there are a dozen exceptions. I always found that to drive the chemists and physicists crazy - they couldn't deal with the exceptions

    thethoughtemporium12:08 PM
    @lawrence_vpi I get my perishables from a variety of sources. And it really depends how perishable the item in question is. Most stuff I get on ebay and amazon honestly. It's crazy how much stuff is available. Anything specialty I have to get from the larger supply companies. If you set up a company and have a non residential address, you can order from them without issue.

    Jan12:08 PM
    so, we're talking petry dish biology here?

    Dan Maloney12:10 PM
    Really? Suppliers balk at residential addresses?

    thethoughtemporium12:10 PM
    @Jan Yes and no. Bio is interesting because most of it is moving small volumes of liquid around. But then you take that tiny starter and it can grow to kilometers wide depending on what the thing is. In my case I'm modifying yeast because then I can grow them in massive tanks to produce stuff

    tocatrooper12:10 PM
    Best diy molecular biology communities? Support/resources

    Dan Maloney12:10 PM
    I mean, I can see ordering radioisotopes as a problem, but enzymes and reagents?

    Thomas Shaddack12:11 PM
    why not lactobacilli?

    OnlyOneCannolo12:11 PM
    In your experience, what are the most cost-prohibitive aspects of diy bio that could benefit from more accessible equipment and tooling?

    Jan12:11 PM
    ah, I can relate! baking with a sourdough starter which I feed at least once a week for like ten years...

    Dan Maloney12:11 PM
    @Jan -- Mmmmm - sourdough...

    Sina Booeshaghi joined  the room.12:12 PM

    thethoughtemporium12:12 PM
    @Dan Maloney Yup they're really picky. It's a bunch of paperwork for some companies like thermo or sigma. So most of...

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mendezjr wrote 6 days ago point

lost OFF Cop are goin to be save with it

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mendezjr wrote 6 days ago point

I have a new light Armor Shield ( line x ) shild

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Lutetium wrote 6 days ago point

Sorry everyone for the false alarm. I fell victim to the "12 AM v 12PM" problem when I set up this event, and had the wrong time zone to boot. The event is fixed and you should be mgetting an email a half hour before it really starts.

*Furiously checks MailChimp settings...*

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anfractuosity wrote 02/12/2019 at 15:00 point

I'm curious about trying this protocol - https://openwetware.org/wiki/McClean:_Colony_PCR_(Yeast)


A couple of things I'm wondering, I've never done electrophoresis before:

* What voltage do you use (I've got an old electrophoresis PSU that outputs up to 400V)

* Would this potentially let me compare a couple of different brewers yeasts?

Thanks

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Dan Maloney wrote 02/12/2019 at 16:40 point

It's been a painfully long time since I've been in the lab, so don't quote me on this, but I seem to remember our power supplies for agarose gels being constant current supplies that generally started at around 60-80 V.

As for PCR, you'd be able to use it to study different yeast strains if the primers in the kit are for an area that shows some genetic variation. All PCR does is provide boatloads of DNA between to specific sites that the primers bind to. If the DNA between those two sites is different between two strains, then PCR will give you tons to analyze. 

How you analyze it is another question. Agarose gel electrophoresis will only be able to tell you if the DNA produced by PCR has a significant difference in size between the two strains - like "is the gene there or not?" different - because all it can do is sort DNA by size. If the two strains have the same gene that differs only by a few base pairs or has the same length but some base pair substitutions, then you'd need to sequence the DNA. We used to do that with polyacrylamide gel electrophoresis (PAGE) after running the Sanger reaction and labeling the DNA with S-35 radioisotopes, but that's ancient technology now. I believe you can send off a sample to someone now and have it sequenced for a nominal fee.

All that said, Justin probably has better, more current information than a dinosaur like me. I'll be sure to ask him about this on Wednesday if you don't. Thanks!

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anfractuosity wrote 02/12/2019 at 17:51 point

Thanks a lot for your reply! That's very interesting about what PCR does too.

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Jarrett wrote 02/07/2019 at 19:47 point

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Lutetium wrote 02/11/2019 at 15:56 point

Good one - I'll be sure to add it to the list. Hope you'll come along to ask it yourself, though. Thanks!

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