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Old 19th June 2012, 2:21 PM   #1
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Default biohacking - DIY biotechnology

http://www.thebulletin.org/web-editi...hn/diy-biology

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the next revolution in biotechnology is also likely to take place in someone's home or start-up laboratory. Unlike formally trained scientists, self-taught biologists may think a bit more outside of the box. Developing the next-generation vaccines and anti-microbials, and autologous replacement organs -- which have the potential to completely transform medicine and public health -- is going to take novel, visionary approaches. Start-up biotechnology efforts and their creative DIY enthusiasts, like Jobs and Wozniak, have the potential to fuel the economy with thousands of new jobs.
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.
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Last edited by [PnP]dredd; 3rd June 2014 at 1:26 PM. Reason: I hate re-reading posts from ages ago. PCR on sex hormones? What was I thinking!
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Old 20th June 2012, 10:10 AM   #2
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Also this:

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Old 20th June 2012, 10:04 PM   #3
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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.

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Old 20th June 2012, 10:12 PM   #4
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Originally Posted by [PnP]dredd View Post
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 hormones, and running a gel.
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....

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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.
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.
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Old 22nd June 2012, 1:15 PM   #5
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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?
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Old 23rd June 2012, 10:11 AM   #6
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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.
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Old 23rd June 2012, 7:47 PM   #7
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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.
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Old 27th June 2012, 8:10 PM   #8
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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).
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Old 28th June 2012, 7:10 PM   #9
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the next revolution in biotechnology is also likely to take place in someone's home or start-up laboratory. Unlike formally trained scientists, self-taught biologists may think a bit more outside of the box. Developing the next-generation vaccines and anti-microbials, and autologous replacement organs -- which have the potential to completely transform medicine and public health -- is going to take novel, visionary approaches. Start-up biotechnology efforts and their creative DIY enthusiasts, like Jobs and Wozniak, have the potential to fuel the economy with thousands of new jobs.
I'm not sure whether to consider this laughable or worrying.

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Some bacteria are naturally competent and just suck up DNA from the environment.
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.
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Old 29th June 2012, 1:31 AM   #10
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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.
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Old 4th July 2012, 10:36 PM   #11
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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 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.
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Old 4th July 2012, 10:38 PM   #12
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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.
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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Old 19th July 2012, 9:36 AM   #13
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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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Old 2nd October 2013, 9:29 AM   #14
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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.
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Old 2nd October 2013, 10:06 AM   #15
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This looks very interesting
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