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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:
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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 Transcript, Part 3

    Lutetium • 02/21/2019 at 16:47 • 0 comments

    neil k. sheridanFeb-13 1:30 PM
    Hi everyone! I came late.. Did you talk about baterio-algae fuel cells!? I was just researching about these for CO2 sequestration and power generation! This paper was pretty cool (it's on scihub) https://sci-hub.tw/10.1016/j.rser.2017.01.115

    neil k. sheridanFeb-13 1:30 PM
    *bacterio

    anfractuosityFeb-13 1:31 PM
    ooh that sounds interesting re. radiation resistant microbes

    thethoughtemporiumFeb-13 1:32 PM
    Fuel cells are cool. I did some experimenting with them but gave up when a chance to do mammalian genetics came up. Still have all the materials so maybe I'll come back to it.

    thethoughtemporiumFeb-13 1:33 PM
    I've been trying o isolate R. palustris which is one of the best microbes for fuel cells but it's proven challenging. Buggers just wont seem to grow. Trying to just get a pure culture from someone in the meean time

    thethoughtemporiumFeb-13 1:37 PM
    Also they're the most versatile organism ever described. They eat the most toxic garbage we 've made as a species, excrete electrons, and are photosynthetic. Also they fix nitrogen. And are rich in vitamins so feeding them to fish or other wildlife is good for them. And innoculating soil with them makes plants grow better

    neil k. sheridanFeb-13 1:37 PM
    I thought so! Hopefully I will have a go at making one! Phew I just looked up buying R. palustris culture - it is like £360! Even the algae is expensive!

    Andrew SmartFeb-13 1:37 PM
    @Thomas Shaddack I'm curious about FEP and PTFE now, I do see one claim that there is a PTFE printer. I guess the parts should be printed/made within a flow hood. With appropriate filtering of the exhaust. Next time you hear about a mass bird death you should suspect a chemist venting a ton of fluorocarbons to the atmosphere (only source I have is a BBC documentary on Teflon manufacture pollution ).

    thethoughtemporiumFeb-13 1:38 PM
    look up EM-1 probiotic. It's a mixed culture that contains it. people have had success isolating it from that mix which is what Im tryng to do

    Thomas ShaddackFeb-13 1:38 PM
    @Andrew Smart i was thinking about fluoropolymer coating using a plasma reactor, with the gas feed being thermally depolymerized ptfe.

    neil k. sheridanFeb-13 1:38 PM
    ah ok thanks! Will do!

    anfractuosityFeb-13 1:39 PM
    is that the manufacturer of teflon that produces toxic stuff? i didn't know that

    Thomas ShaddackFeb-13 1:39 PM
    @Andrew Smart with vacuum pyrolysis you won't get as annoying products as in air.

    Thomas ShaddackFeb-13 1:39 PM
    @anfractuosity in european union and california pretty much everything is toxic. those places are dangerous to live in.

    anfractuosityFeb-13 1:40 PM
    i'm genuinely confused, as teflon itself is very unreactive i thought

    Thomas ShaddackFeb-13 1:40 PM
    @anfractuosity even soldering alloys cause cancer in california. stay away from there!

    Thomas ShaddackFeb-13 1:40 PM
    @anfractuosity teflon is unreactive at sanely low temperatures. above 270c it starts decomposing.

    thethoughtemporiumFeb-13 1:41 PM
    its the binder that they use to stick teflon to stuff that's toxic. so in cheap products they haven't baked it off sufficently and when you first use the items you're expsoed. SO baking teflon coated items for a while in a well ventilated area can help drive that crap off, but not so hot that it decomposes

    Thomas ShaddackFeb-13 1:42 PM
    @anfractuosity (for here let's consider teflon===ptfe, sometimes you get other fluorocrap with the same trademark.)

    Thomas ShaddackFeb-13 1:42 PM
    @thethoughtemporium what would you suggest for converting lubricant-grade teflon powder to a coating-grade teflon suspension?

    thethoughtemporiumFeb-13 1:43 PM
    no idea. Haven't worked with teflon enough to say

    Thomas ShaddackFeb-13 1:43 PM
    @thethoughtemporium could your ultrasonic homogenizer work for deaggregation of nanoparticles?

    anfractuosityFeb-13 1:44 PM
    "Fluoroantimonic acid thermally decomposes...

     Read more »

  • Hack Chat Transcript, Part 2

    Lutetium • 02/21/2019 at 16:42 • 0 comments

    thethoughtemporiumFeb-13 12:39 PM
    you can already use lots of plants for that. it just won't be quite so magically effective

    JarrettFeb-13 12:39 PM
    true

    thethoughtemporiumFeb-13 12:40 PM
    Come spring I'm planning on filling the space I work in with plants and air filters

    thethoughtemporiumFeb-13 12:40 PM
    And putting algae growing tubing over the windows

    Dan MaloneyFeb-13 12:40 PM
    Looks like the DIY biodiesel crowd is big into making their own centrifuges to spin down waste frying oil. Found one video where they cast a big continuous flow rotor from aluminum alloy wheels and machined it into shape.

    Thomas ShaddackFeb-13 12:41 PM
    there's a genemodded germ that acts as immunization against tooth decay. modded streptococcus mutans. not on the market due to some paperwork/lawyer wrangling. any chance of getting it done by alternative channels if the sequences can be found in literature?

    thethoughtemporiumFeb-13 12:41 PM
    I have some in my fridge XD

    thethoughtemporiumFeb-13 12:42 PM
    Been tinkering with it in the background

    JarrettFeb-13 12:42 PM
    I'd definitely be interesting in the algae growing tubes

    thethoughtemporiumFeb-13 12:42 PM
    I also have the same plasmid that the crispr baby guy used basically

    Thomas ShaddackFeb-13 12:42 PM
    ...ugh!!!

    Thomas ShaddackFeb-13 12:43 PM
    (droooool)

    thethoughtemporiumFeb-13 12:43 PM
    I mean it's a pretty crappy plasmid as these things go, but it's funny to have

    thethoughtemporiumFeb-13 12:45 PM
    The other fun one I can think of is one we're testing to see if it'll make plants grow faster.

    Thomas ShaddackFeb-13 12:45 PM
    what about making the plants more tolerant to drought or saltwater or other stressors?

    thethoughtemporiumFeb-13 12:46 PM
    Very doable, sometimes it's onyl 1 gene you need to kick, but it depends one the stressor

    sparkrisp joined  the room.Feb-13 12:47 PM

    Thomas ShaddackFeb-13 12:47 PM
    another thought.very simple. modded fish that has melanine gene expressing in bones.

    thethoughtemporiumFeb-13 12:47 PM
    The thing is we have the tech to do all kinds of weird stuff to plants to make them super tough and more nutritous and such, but it freaks people out so we don't do it. It's one of those things where you could make apples that taste like lemons and are rich in vitamin A, but that'd be too weird for people to handle

    Thomas ShaddackFeb-13 12:47 PM
    making the bloody bones more visible.

    Thomas ShaddackFeb-13 12:47 PM
    screw the people!

    Andrew SmartFeb-13 12:48 PM
    @OnlyOneCannolo I suppose one opportunity would be microwave assisted digestion vessels, they're pricey.

    I can see a technique to digest samples in a household microwave (instead of a $$$ lab microwave) using a thicker PFTE vessel: https://www.nature.com/articles/srep37186

    But I suppose there may be other uses for "microwave-assisted liquefaction": https://pubs.acs.org/doi/full/10.1021/acssuschemeng.6b02447

    Dan MaloneyFeb-13 12:48 PM
    @thethoughtemporium - Do you find that access to current literature is hampered by paywalls on journal sites? Any tips for getting around them?

    Thomas ShaddackFeb-13 12:48 PM
    we don't need the people's opinions. we need enough underground labs to just get the things done.

    Thomas ShaddackFeb-13 12:48 PM
    re papers, sci-hub does the trick.

    Andrew SmartFeb-13 12:48 PM
    #OnlyOneCannolo More DIY instrument ideas: http://www.sciencemadness.org/talk/viewthread.php?tid=83552

    There is also the recently released Chemputer (open-source), the syringe pumps and 6-way valves are all DIY 3D printed (PFTE filament for chemical contact parts). Seriously an outstanding marvel, but I expect there would be hardware-hacking utility to bring part costs down (computer controllable rotovap & hotplate). Author estimates total cost is $10k, and idea is to use inexpensive off the shelf parts as much as possible:

    http://science.sciencemag.org/content/suppl/2018/11/28/science.aav2211.DC1...

    Read more »

  • Hack Chat Transcript, Part 1

    Lutetium • 02/13/2019 at 21:08 • 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...

    Read more »

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mendezjr wrote 02/13/2019 at 16:29 • point

lost OFF Cop are goin to be save with it

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mendezjr wrote 02/13/2019 at 16:25 • point

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

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Lutetium wrote 02/13/2019 at 16:09 • 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

  Are you sure? yes | no

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

Thoughts on the GM Pothos that can break down chloroform?

https://www.newscientist.com/article/2188798-house-plants-dont-clean-your-air-that-much-but-this-gm-pothos-might/

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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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