If this sounds super-technical you’d be right – fortunately we had two things going for us. Firstly, these two techniques have been around for decades and are incredibly well documented. However, more importantly, we had assistance from Dr. Trish Linton at MMU who prepared everything for us and provided a super-simple set of instructions to follow which ultimately ensured that, despite no-one at the meetup having done this before, meant that we at least got some kind of result out of the process (more on this later!)

And so, to the challenge. For PCR you need… a PCR machine! We had not one but three – a commercial-grade machine (kindly supplied by Trish), an OpenPCR which we built at thelast DIYbio meetup, and… the BBQPCR! We’re super-proud of this version – built by Alex from HACman from an Arduino, some parts from B&Q and ample quantities of raw invention, we were keen to see how it would hold up in the red-hot crucible of amateur biological experimentation.

We started the PCR part of the challenge the night before when Trish brought the ingredients around to the Madlab and we plugged everything into the machines to run the PCR reaction (excellently described by this Kubrick-style video here, and in rap form here). The whole cycle took just over 4 hours, after which our samples went into the fridge ready for…

Challenge day!

We had a great turnout, despite some gruesome Manchester springtime weather and, after a quick rundown of what we did the night before and the science behind PCR, we got stuck straight into the results analysis. Gel Electrophoresis as a technique has been around since the 1930s and at its simplest involves using a high voltage power source to push DNA through a very fine gel made from refined Agar (aka Agarose, which unlike Agar you can’t buy from Chinatown). Setting up the gels (one per machine in the challenge) and adding all the other ingredients was super simple (again, thanks Trish!) – the hardest part of the process was getting our samples into the gel using a micropipette.

It turns out there is a bit of an art to pipetting – a couple of attendees already knew their way around a micropipette but the majority of us didn’t. After a quick intro video on the dos and don’ts (do get your sample in the right place, don’t break the gel, no air bubbles etc.) we got stuck in. The more experienced pipettors claimed that it took them weeks to get the proper technique. Everyone tried it out and amazingly it seemed to work so we must have been a talented lot.
Gels prepared we hooked them up to the power supply and left them running for half an hour while people had a cup of tea and admired our soil-based microbial fuel cells from a previous meetup. Half an hour later we stained our gels (using non-toxic Fast Blast DNA stain, which it turns out also stains hands and tables equally well) to reveal the results, which were.. inconclusive!

Something obviously worked, because after a few minutes of staining some bands of DNA started to show up in the gels, but they never developed to an extent that we could determine a clear winner in the challenge (or tell if our John Doe was carrying TB or not). On the basis that we can just about see something I declare the PCR challenge a success!

After a night in stain

We decided to leave the gels in stain over night to see if something more will appear for the morning. Not the best idea it turns out…
Regardless of results, it’s been a learning process for all involved and we are very proud of our PCR machine and all the buzz around it. Seems like amateurs are gaining more and more knowledge in different spheres of science and we love to be part of that development. Stay tuned for a PCR rematch, as well as some more DIYbio experiments in the future!

*Post written by Asa Calow

PCR Challenge

In the last year, over 350 people have dissected octopuses, made fuel cells with soil from Northern Quarter car parks, attended the UK’s first DIY Bio summit, gotten to grips with PCR machines and pipetting or roamed the streets of Manchester swabbing bus-stops for bacteria. They’ve seen malarial jewellery at the Microbiology and Art exhibition, quaffed beer and kimchi at the microbial picnic and bred Malaysian Trumpet snails (RIP).

All this was made possible by funding from the Wellcome Trust and the help of MMU. Shortly after the unveiling of the Manchester Microbe Map at Future Everything in May, the project will come to a close.

BUT! We are going to continue as DIY Bio Mcr and we need your feedback in order to raise further funding and make the changes you want to see.

Please can you take five minutes to fill in this survey. Even if you’ve not been to DIY Bio Mcr yet, we’re keen to hear your thoughts.

PCR here, PCR there but which one to use? We’ve been slowly building up our community lab at DIYBIOMCR, and we want to run the first PCR Challenge! We will be amplifying plasmid DNA, from a few copies to several million in the space of a few hours.

We have our humble MadLab version of a PCR  machine built by Alex from HacMan from some parts we had lying around at the Madlab, and the open-source OpenPCR kit which is being assembled at the build-a-lab day on February 29th (link here). Two is not enough to run a race, so we will also have MMU’s commercial PCR to compete against as well.

If you’d like to take part in this experiment, come along to MadLab and spend an evening putting these machines to the test. We will discuss what PCR is and why it’s useful. Because it takes awhile to run the machines, we will amplify the samples before hand, and this day will be spent processing and visualising the results from the previous PCR-ing using gel electrophoresis, again using equipment built ourselves at the build-a-lab day. This will involve pouring the gels, running them and staining the gels.

There’ll be pipetting! There’ll be agar*! There’ll be plasmids! And, as if that’s not enough, there will also be DNA origami to fold, snails to look at and lots of tea, coffee and cakes.

* Okay not Agar (which is available in Chinatown), but the purer form Agarose which gives us the “gel” part of gel electrophoresis.

We were recently interviewed by Jim Ralley about our partnership. Have a listen to Asa Calow from MadLab and Martyn Amos from MMU.

Last week’s DIYBio was a special event, to get stuck into building a couple of PCR machines. In addition to our home-made one, we also got our hands on what we think is the first OpenPCR machine in the UK.

Getting a bit ahead of myself though. What is PCR?

PCR is a relatively simple and inexpensive tool that you can use to focus in on a segment of DNA and copy it billions of times over. So, even with a small DNA sample, such as from spitting in a tube, or tearing off a piece of a leaf of lettuce, PCR allows to you make a bunch of copies of the DNA so you have enough to analyze. PCR is used every day to diagnose diseases, identify bacteria and viruses, match criminals to crime scenes, and in many other ways.

The OpenPCR is a really neat idea: it’s the first example of truly open-source hardware I’ve ever seen. I was confused about how hardware can be ‘open source’, but what this essentially means is that the precise schematics of all the machine components are readily and freely available. So, if you had the time/materials and tools, you could build yourself one. The kit itself is supplied as an awesome box of bits (wood! Arduino! Metal things!) and costs something like $500 (ish). It then hooks up to a nice AIR app and you can do what you like with it.

In addition to the OpenPCR, the clever chaps at Madlab have put together a fantastic home-grown PCR machine, which is made of pipe, polystyrene, a filament lightbulb, and a plastic lunchbox full of electronics. Really. I didn’t note down the cost at the time, but it’s significantly less than five hundred dollars… I assume it’s also significantly more likely to burn your house down, but that’s all part of the fun, right? Science!

The Madlab version was built by the Hacman experts, so it was only fair that we were allowed to get stuck into building the OpenPCR. On paper it says one person can build it in three or four hours: we decided that as a group we could do far better than that, so we tipped the box out and got stuck in:

Anyway, the plan is to see how the OpenPCR stacks up against the Madlab budget version, and then hopefully we can then see how both machines compare to an actual, cost-lots-of-money, proper PCR machine. We’ve not decided as yet what the criteria for ‘best machine’ will actually be, but it should be really interesting to see how it all turns out anyway.

Oh, and the BBC’s science correspondent turned up too, along with a big camera and a microphone:

I managed to stay out of the firing line as much as possible, but a couple of the guys there made the rookie mistake of sounding knowledgeable and ended up being interviewed. I didn’t escape completely though, and ended up explaining the Microbe Map repeatedly down a microphone, probably for the radio. It was pretty nice to see an event like this being covered anyway, I’m not sure entirely how it’s all being used, but as soon as I find anything out I’ll stick it on here.

There are lots more photos on the Madlab flickr feed, next time we should hopefully have some experiments going and maybe even some idea of how our PCR kit stacks up against expensive kit. For science!

Could there be any better way to celebrate the extra day in February than by Building an OpenPCR?

What is PCR?

The polymerase chain reaction (PCR) is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
This bit of lab kit is used for amongst other things :

• DNA cloning
• Gene analysis
• Diagnosing hereditary disease
• Identifying genetic fingerprints  (CSI anyone?)

What is OpenPCR?

The OpenPCR is a low-cost, open source Personal PCR machine used in labs around the world.
This little laser cut machine will allow us to do DNA Sequencing and DNA Barcoding.

We’ve had a stab at creating our own version with bits of parts from an old computer and an Arduino (Thanks Alex!).

Now we’ll attempt the flatpack version, and see how they compare.

We’ll also listen to BBC File on 4 programme about Bio Security first broadcast 7th Feb, where their roving reporters visited MadLab to interview our group. Heated discussions to follow and continue on at Common!

Hope to see you there.

The evening of the 25th January is a DIYbio fuel cell special, where we’ll be building and comparing an array of microbe-powered batteries with the help of MMU’s Dr. Trish Linton who also ran the fuel cell session at the DIYbio Summit back in October.

Here’s what happened the first time we ran this workshop during the DIYBIO Summit during the Manchester Science Festival 2011.


Along the way we’ll be trying to answer some crucial microbe-y questions:

• How do microbial fuel cells actually work?
• Which part of the Northern Quarter has the hardest working soil bacteria?
• Who would win in a tug of war? Brewers’ yeast or the instant stuff out of a packet?
• Will microbes fuel the future? When will my car have a composter rather than a fuel tank?

So come on over at 7pm on the 25th Jan – no need to being anything other than some microbe-y enthusiasm. All bugs courtesy of the Northern Quarter.

The first time dissectors found out about basic anatomy (did you know octopi have 3 hearts?), identifies gender (most were female), looked out how tenticles regenerate, tested out the power of the sucker and made some drawings from the inksack.

We plan to run this event again in the new year (2012) so watch this space for more info. You can follow what’s going on through the google group, or @diybiomcr on twitter.

Join us to talk about our recent DIYBio adventure, the first UK DIYBio Summit.

Everyone is welcome, to find out about what we’ve been up to, or join in on the activities.

If you want to get involved in any of these projects, take part in discussions or recommend a new topic, join the mailing list and come to next month’s meeting! (http://groups.google.com/group/diybiomcr)

The First UK DIYBio Summit

29th-30th October, Madlab

Citizen scientists are invited to the first ever UK summit on “DIY biology”: this growing movement takes biology out of the ivory tower and into the hands of everyone! We’ll bring together a diverse group of leading scientists and curious amateurs to share expertise and experiences.

The event includes presentations by international speakers, demonstrations from the Manchester DIYBio group, and hands-on workshop sessions where participants can get involved in do-it-yourself bioscience.

No experience is needed, as full training will be given in a safe and friendly environment. Attendees can sign up for future events, and become part of the DIYbio revolution!

On Saturday, the formal section of the event will take place including plenaries and workshops.  Sunday will be held using an ‘unconference’ format where attendees can contribute to the proceedings and host discussions.

Saturday 29th October: Agenda

10:00-10:30  - Welcome and introductions

10:30-11:30  - Keynote Plenary: Sung Won Lim, Genspace; Cathal Garvey

11:30-11:45 –  Coffee break

11:45-12:30 – Updates from DIYBio groups

12:30-13.30 – Lunch break (food not provided)

13:30-16:30 – Parallel breakout hands-on sessions

16:30-17:30 – Closing keynote:  Marc Dusseiller, Hackteria

17:30-18:00 – Closing session

18:00- Social event

Sunday 30th October: Unconference

10:00-12:00   –     Session one

13:00-15:00    -    Session two

Information on how to submit sessions will be circulated to registered attendees.

This event is part of the Manchester Science Festival