biohacking - DIY biotechnology

Discussion in 'Science' started by [PnP]dredd, Jun 19, 2012.

  1. [PnP]dredd

    [PnP]dredd Member

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    http://www.thebulletin.org/web-edition/columnists/laura-h-kahn/diy-biology

    I've got a friend with a PCR machine bought off ebay, which she uses to sex her chickens, by amplifying DNA using promers which recognise segments of the sex hormoneschromosomes, and running a gel.

    The hardware to do biotech stuff is now moving towards pricing which makes it accessible to an enthusiastic amateur. We're talking a similar cost to buying and maintaining a rally car or similar.

    The knowledge is more difficult to gather, but there's a good set of tools available for those with some university biochemistry, or equivalent.

    It's going to be a wild ride over the next few decades. I have an idea that when I retire I'd like to tinker with genetically modifying orchids.
     
    Last edited: Jun 3, 2014
  2. Widman

    Widman Member

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  3. PCRman

    PCRman Member

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    Only just signed up but I think I going to like it here! Funny how there is a PCR thread the day I join up.


    Some would say this fits the bill to replace all them pretty ABI sanger sequencers.

    [​IMG]
     
  4. PCRman

    PCRman Member

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    I've got a real-time cycler sitting in my shed. Its mainly for parts (power supplies, TEC's, machine screws etc) but is other wise fine (just old) maybe I should clean her up and sell it....

    A company called kyratek are working on a little real-time cycler called a PCRlive. Ive seen the conventional PCR version and its pretty niffty and I've hear the PCRlive will be cheap(ish) like in the 10k to 20k mark.
     
  5. OP
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    [PnP]dredd

    [PnP]dredd Member

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    Apart from a thermal cycler, I wonder what else one would need in order to insert a gene into a bacteria (let's start with a prokaryote).

    Glassware, pipettes, eppendorfs, centrifuge.
    A gel apparatus might be tricky.
    Liquid nitrogen and a -80 freezer (may be able to do without these?)
    Obtain plasmids and e.coli (perhaps one could obtain these for free with the right contacts at a university).
    Have someone sequence an oligo for the gene of interest, codon optimised and with restriction enzyme sites.
    Buy restriction enzymes, DNA polymerase, buffers, agar, stains (I wonder if they sell ethidium bromide to the public? May also need a UV light source).
    I've heard you can make growth media and even make cells competent using stuff bought at the grocery store.

    I've probably missed a couple of things, but that all seems feasible.

    Of course, there needs to be a reason to insert the gene. Need to come up with a cool project. Is there an interesting protein that could be overexpressed in bacteria and easily purified?
     
  6. PCRman

    PCRman Member

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    Some bacteria are naturally competent and just suck up DNA from the environment. This allows you to make an insertion cassette containing your gene of interest, a selection gene (antibiotic resistance) flanked by sequence complementary to where you want to put the cassette by PCR (or you can have the cassette synthesized commercially). All you need to do is grow your bugs, drop in the cassette and apply selection. It does away with all the donor recipient pili stuff quite nicely. Method was published, something like "natural transformation by pcr products"

    For media, yeast extract, milk powder and glucose/Sucrose gets you most of the way there. Of course some horse or sheep blood works too.

    As far a genes to express goes you can express biocompatible plastics using polyhydroxyalkanoate synthesis genes. There is always fun to be had with GFP. If your really keen you could make your own antibiotics! Not sure I'd take them though.
     
  7. antipody

    antipody Member

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    There was a great special edition in Science a few weeks ago on nanopore sequencing. Sounds amazing. They reckon they are likely to go commercial very soon.

    The biotech revolution is going to make the IT revolution look like kindergarten. :Paranoid:
     
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    [PnP]dredd

    [PnP]dredd Member

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    Here's a great short video demonstrating how easy biohacking is, with a little knowledge: http://www.indiebiotech.com/?p=164#more-164

    Ebay suggests that a second hand electroporator can be had for $US300 (plus nearly $200 shipping, so probably best to wait for an Australian auction).
     
  9. lethoso

    lethoso Member

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    I'm not sure whether to consider this laughable or worrying.

    When I was doing honours a few years back I was doing a bunch of cloning (my PCR product wasn't sequencing well), so I made up a big batch of competent cells. Was fairly straightforward. They weren't as good as the ones that come in the all in one cloning kits we also had in the lab, but they were still perfectly adequate, and they cost a whole shitload less.
     
  10. TaO!

    TaO! Member

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    Molecular biol methods are very easy. I had year 10 visitors to the university doing their own transgenic experiments essentailly unaided. But designing a new outcome and implementing a protocol for those experiments requires a depth of knowledge.
     
  11. PCRman

    PCRman Member

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    The bigger version called the gridion :/ will be very interesting. could be a game changer, then again could be ..meh.. like the pacbio was/is.

    At the demo where the minIon debuted they sequenced a 5kb virus. I'll start to get interested when it can sequence pathogenic viruses to up to 100kb mark. I'm about to start sequencing adenovirus genomes and the prep is still fairly involved. Anything that gets from bug to genome faster is a good thing.
     
  12. PCRman

    PCRman Member

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    You got that right. Even next gen sequencers still use old school molecular biology techniques like ligations, end polishing and nick repair just like you find in maniatis.
    What to do with Gb of data presents more of a problem.
     
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    [PnP]dredd

    [PnP]dredd Member

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    Foudn this interesting bit of information today:

    Since 2008, the cost of genome sequencing has decreased at a massive rate.

    As a Nature article says "The information-generating power of genome-analysis technologies is increasing at a rate that surpasses even the doubling of computer performance that is achieved every 18 months by the semiconductor industry".

    http://www.genome.gov/sequencingcosts/
     
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    [PnP]dredd

    [PnP]dredd Member

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    Been reading about CRISPR/Cas9. This is a genome-editing system that is really taking off.

    In a nutshell, it's a tool that allows for editing DNA. Using this system, it's possible to make point mutations, insert DNA or activate/repress genes. It's cheap and fast, and works in bacteria, plants and animals.

    From a more technical perspective, it's better than other systems (TALEN, ZnF nucleases) because CRISPR uses RNA to target a specific DNA sequence, whereas the other systems depend on producing a custom protein for each new DNA target. RNA is of course much easier to design and cheaper and faster to produce.

    For non-proft researchers, Addgene is a plasmid repository that is disseminating the DNA to allow researchers to make their own CRISPR system: http://www.addgene.org/CRISPR/

    I'm unsure of the patent situation for this technology. I imagine that it's messy, as this is moving so fast.
     
  15. Foliage

    Foliage Member

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    This looks very interesting
     
  16. Veefy

    Veefy Member

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    I read that as electroraptor. :thumbup: :lol:
     
  17. Aetherone

    Aetherone Member

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    Seriously old school (not to mention hazardous). There's newer, safer stains which fluoresce with the right frequency blue LED.
     
  18. Dodge M4S

    Dodge M4S Member

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    So does this mean I can make flying spiders?
     
  19. antipody

    antipody Member

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    I've started Harvard's free Genomic Data Analysis course and I reckon I might see it through.

    https://www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401#.U4nbeBZ4XwI

    I'm not really thinking biohacking, but trying to get some bioinformatics done on my son, so trying to get my head across the technology and interpreting what is ridiculously deep and complex data.

    I'm only up to week 2 but this course is really well done so far. The presenter speaks very clearly and is quite easy to follow. :thumbup:

    Seems like a good way to learn some R, which I've been wanting to do so double :thumbup: :thumbup:
     
    Last edited: May 31, 2014

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