Group:Biohacking

Biohacking / DIYBio at LHS

We are the biohacking group at the London Hackspace, mostly beginners to biology attracted the potential of DIYbio and synthetic biology, with a couple of professional biologists as well, so get involved! Over the past year we've been developing our research equipment, optimising techniques and running some research projects of our own.

Our current projects

We're currently working on genetic testing, identifying specific genes using PCR and electrophoresis. We've been working mainly on sex typing with amelogenin, and have just started working on plant species testing.

Our big goal for the next year is to begin genetic modification. For this we'll need to become certified as a class 1 lab, we are currently collecting information on how to do this.

Projects

• Sex typing with amelogenin
• Plant species testing
• Genetic modification
• Blood typing

People

Andy, Mike, Nicholas, Paddy, Paul, Simon, Tom, Tonderai, Will

How to find us

1. Come to a meeting: we meet at 7pm every Wednesday in the London Hackspace: Unit 24, Cremer Business Centre, 37 Cremer Street, London E2 8HD. Email Nicholas if you can't find the place.
2. Post on the biohacking mailing list

Older / on-hold projects

• DNA forensics
• Algal biodiesel

Other genetic tests to try

[List_of_Mendelian_traits_in_humans]

[MC1R]

[Rhd]

[Mendelian_Inheritance_in_Man]

What was in those brownies, anyway?

Expenses

Kitty: -£27.19 (as of July 25) (Yes, negative)

Spent on:

• Pressure cooker: £28.95 (May 02)
• Cabinet: £65.94 (July 25)

Membership

We encourage you to become a member of the biohacking group. Biohacking is more expensive than the typical hackspace activity, and with your membership we can pay for chemicals, primers, and any random equipment we may need. Our members.

To become a member, set up a standing order to the London Hackspace with the reference "biohacking". You need to become a hackspace member before you can see the direct debit details. Look here for more information. If you want to become a Biohacking member without joining the space (you really should join the hackspace! It's great), get in contact with Nicholas.

The suggested donation is £2 a week.

Shopping list

As of June 27, 2012, we need:

• Ladder, ideally 50-2000 bp (or two ladders spanning different distances) (Our current ladder works but isn't great)
• Agarose (nearly run out)
• Taq master mix (to replace that probably ruined by the freezer being turned off)
• Positive control (Our current positive control is suspect)

Standard chemicals and reagents we use

• List of possible DNA stains

DNA extraction:

• Chelex 100
• 70% isopropanol (rubbing alcohol) - widely and cheaply available

PCR:

• Taq ReadyMix. Click on bulletin for useful info about procedure for using it.
• Purified water (non-sterile).

Electrophoresis:

• 1KB DNA ladder. Current ladder is aliquoted with loading dye from a 50 ug sample of concentration 0.2 ug / ul
• Ethidium bromide stock solution - 2 ul ethidium bromide solution to 40 ml water

Lab Notebook Entries

• 13-04-2011 First attempt at electrophoresis of DNA on agarose gel
• 11-05-2011 Gene detection trial run: Cheek swab -> PCR -> Electrophoresis

Videos

Bugs and Sara ran an Introduction to Biohacking workshop, giving a crash course in molecular biology and a great overview of what biohackers around the world are getting up to. The talks were recorded and are now on YouTube: [Intro to mol. biol], [Groups around the world].

Resources

Education

• Nature.com comic about Synthetic Biology - Nice introduction to playing with genetic engineering/cloning, though aimed at kids

• Bugs' Crash Course in Molecular Biology - Recorded at the hackspace
• Sara's Introduction the the Biohacking Community - Recorded at the hackspace

• Good introduction to gel electrophoresis - Explaining one of the core techniques for working with DNA
• Good introduction to the Polymerase Chain Reaction (PCR) - Explaining one of the core techniques for working with DNA
• Nature.com article on Biohacking - Free access. Nice explanation of what's needed in a lab and how different groups are managing it.

• Bioinformatics Resources
• Cathal Garvey's beginner's guide to biotech

Community

• Interesting DIYBio community blog - Interesting blog taking articles from a few different groups
• Bio Curious - A well-established bihacking group in California
• Brain-Computer interface at Paris hackspace
• Nature.com article about biohacking community - Not the same one as above. Interesting, but behind a paywall :(.
  • you can access it here: http://www.synbioproject.org/process/assets/files/6452/_draft/nbt-2009-12d_-_biotech_nin_the_basement.pdf -- kanzure 70.114.205.110 19:40, 2 January 2011 (UTC)

Our equipment - some info on testing it in links

• Thermal Cycler (PCR Machine); Perkin Elmer 480
• Open Source, Hackable PCR machine - We'll probably buy one of these when they become available
• Light Bulb PCR " less than $50 to build this machine (including the $30 arduino)"
• Open Source Electrophoresis tanks - They sell kits, but we can probably just use their published plans to laser-cut our own. Also [1]
• Two centrifuges - estimated 5000 rpm
• Dremelfuge - microcentrifuge to be made on a 3D printer. We have one, but using it is a bit ... character building. Need to print a new one.
• Wet stuff Wet stuff: our inventory of primers, buffers, stains...

PCR primer design

• http://www.cybertory.org/exercises/primerDesign/index.html
• http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
• http://www.premierbiosoft.com/primerdesign/index.htm
• http://molbiol-tools.ca/PCR.htm
• http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome
• http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
• http://bibiserv.techfak.uni-bielefeld.de/genefisher2/

Suppliers

Cf. Suppliers.

• Sigma-Aldrich - Good for custom primers
• Cole-Parmer
• Farnell
• NBSBio - Good for ladders and cheap agarose (only low concentration) [NB: Be sure to navigate to http://www.nbsbio.co.uk NOT http://nbsbio.co.uk, or their payment system doesn't work. Weird.]
• New England Biolabs Good for TAQ
• VWR] - Big supplier of chemicals, glassware and various lab stuff. Sounds very positive about selling to the hackspace. Bugs is in the process of setting up an account with them.
• Invitrogen Don't seem to want to sell to us

Contact

If you want to chat about biohacking, post to the Biohacking Mailing List or contact one of us directly :).

Pledges

Assorted biohacking pledges can be found here. Current Pledges:

• Gene detection experiment kit

Proposed code of conduct

See here: http://wiki.hackspace.org.uk/wiki/Biohacking/Code_of_Conduct

FAQ

• official do-it-yourself biology FAQ

News

• DIYbio-in-the-news is listed on the FAQ..

Electrophoresis box

• 7 / Apr / 2011: Photos from the outer box construction are here: http://lardcave.net/biohacking/
• 13 April 2001: Photos of the first Electrophoresis experiment

We've made one. Measurements for the outer box, in mm:

   Width: 102.45 to 102.9 (not a perfect glue job)
   Height to top (container): 31.8
   Height to top holes (for electrodes): 22.16
   Depth: about 171
   Thickness (of the perspex): about 3.2

Measurements for the inner box (which we ended up using, roughly):

   Width: 100
   Height to top: 20
   Depth: 100

So that is two panels measuring 100 x 20 (for the sides), and one panel measuring 100 x 100 (for the bottom).