Group:Biohacking

We are the biohacking or DIY biology group at the London Hackspace, a mix of amateur and professional biologists, attracted by the potential of molecular and synthetic biology. Anyone is welcome, so get involved! It's fascinating, the field and community is growing all the time, together with the ability of amateurs to do cool stuff. Over the past year we've been developing our equipment, optimising techniques and running some research projects. Here's quite a good short local news video showing our lab and some of what we do in it.

List of biohacker wiki pages.

We also maintain an outward facing website at BioHackspace.org

How to use this wiki

This wiki is intended to be our main place where we share information on our group and our projects. If you want to go to our main, non-wiki, public facing site, go here To see results, procedures and some discussion of our projects go to the individual project pages. For more general techniques and procedures see the protocols section. For information on getting hold of equipment and reagents, see the here. Please feel free to add or improve any information, it is a wiki after all...

Our current projects / schedule

We're currently working on getting competent in various techniques of synthetic biology: DNA extraction, PCR, gel electrophoresis, ligation and transformation. Once we can do this, and have been certified as a class 1 lab, we plan to start synbio experiments. Right now we're working on genetic testing, identifying specific genes using PCR and electrophoresis. We've been working mainly on sex typing with amelogenin and Blood typing. In August and September we worked with the UCL igem team to develop a 'public biobrick'.

• Public Biobrick (in collaboration with the UCL igem team)
• Sex typing with amelogenin
• Plant species testing
• Growing bacteria
• Genetic modification
• Blood typing
• Making our own reagents
• Algal biodiesel (on hold)
• DNA forensics (on hold)
• Other genetic tests to try

Schedule

• First half of 2013 - If hackspace move goes ahead, secure a larger area for biohacking, and get the H&S approval to do GM work there. Then do GM work! To start off - transformer protocol, genomikon kit, then GFP.

People

Andy, Ben, Jim, Joel, Leo, Lui, Mike, Nicholas, Paddy, Paul, Raphael, Simon, Taylor, Tom, Tonderai, Will, Hamilton

How to find us

1. Come to the Hackspace Open Evening - every tuesday from 7:30pm. There should be a few of us around to show you the lab and give you an idea of what we do. If you want to make sure we find each other you can email us to let us know you're coming.
2. Email us here. You can also sign up to our mailing list where we do most of our communication here (if you see a warning ignore it) (Your posts will be moderated unless you're signed up to the list. If you want to be signed up to the list but not receive messages you can change this in the options). You can view the mailing list archives through the previous link or through the google groups interface.

Membership

We're a subgroup of the London Hackspace, and our rent and utility bills are paid as part of the larger space. Most of us are paying members of the hackspace, you can find out how to become a hackspace member here. However it's not essential to become a member just to come along initially and find out what we do.

We also have a special membership for biohacking. Biohacking is more expensive than the typical hackspace activity, and with your membership we can pay for reagents, lab consumables and any equipment we may need for our experiments. The suggested minimum donation is £2 a week, but again, you can come along without joining. If you start to come regularly and use consumables then we'd like you to pay. To find out how to pay biohacking membership, contact us

Our lab

Biohacking lab

Our standard protocols / how to's

• DNA extraction using Chelex 100
• DNA extraction and precipitation with ethanol / isopropanol
• Run PCR
• Make and run an agarose gel, then visualise with UV

Our reagents + equipment

• Wet stuff: our inventory of primers, buffers, stains...
• Thermal Cycler (PCR Machine) Perkin Elmer 480
• Gel electrophoresis box
• Big centrifuge
• Variable V/I electrophoresis power supply.
• Incubator with shaker
• Two centrifuges - speed ~1400 rpm. Max capacity about 15ml.
• One microcentrifuge: 6000 or 14000 rpm. For 1.5ml tubes. Can also take 0.5ml tubes with washers.
• Various flasks and beakers
• Scale down to 0.1g
• 1-10ul pipette + tips. Tips available for £27.60 from NBSbio
• 5-50ul pipette + tips. Tips from NBSBio or from microsupplies
• 100-1000ul pipette
• Pasteur pipettes (50 for £3 from cheaplabstuff)
• 0.5ml PCR tubes. 1000 for £24 from nbsbio
• 1.5ml tubes. 100 for £3 from ebay or 1000 from NBSbio.
• Pressure cooker (goes up to 15PSI and 121°C (this is industry standard, not actually tested) to be used as autoclave. Autoclave tape.

Shopping list (See wet stuff for sources and prices not listed here)

• 1-10ul tips (quite a few left but running low)
• 100-1000ul pipette tips for new pipette. Microsupplies sells 1000 for £8.90 + shipping
• More autoclavable glass beakers, conical flasks tubes and petri dishes.
• blender for ice crushing

Suppliers

• Sigma-Aldrich - Good for custom primers
• Cole-Parmer
• Farnell
• Chang bioscience - pipettes
• 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. Standard shipping cost is £15
• Web scientific - Taq and ladder
• New England Biolabs They sell very cheap taq. We could also look at their restriction enzymes. However atm they won't sell to us as they only sell to universities or registered biolabs. See this post and this post. Once we have all our registrations for LBL sorted we could try again.
• Thermoscientific - Recommended for good value restriction enzymes. Not tried yet.
• VWR - Big supplier of chemicals, glassware and various lab stuff. Sounds very positive about selling to the hackspace.
• Invitrogen We failed their due diligence check. See post here and here. They have cheap TBE.
• IDT - possible source for primers. Haven't tried them yet.
• cheaplabstuff (ebay) - Cheap 1.5ml and 15ml tubes in small quantities. Also pasteur pipettes.
• microsupplies (ebay) - Cheap 5-200ul and 100-1000ul tips by the 1000
• Cambridge Bioscience - Not yet used, may supply GelRed or GelGreen (enquiry by Bene)

Also see general hackspace suppliers page.

Wish list

• Autoclave strips. These supposedly tell you if the autoclaving has been done at the required conditions, unlike autoclave tape which only tells you if the temperature has been reached.
• If extractions keep failing, lets look at some extraction kits. This one recommended by Tom is ∼£100 for 100 reactions or ∼£250 for 500 extractions.
• A more consistent and effective way of crushing/homogenising small amounts of tissue for DNA extraction. Blenders are good but not for small quantities. Pestles are ok, but not great. One idea is to make a small pestle by melting a pipette tip then using a PCR tube as a mortar. Some labs use liquid nitrogen or a sonicator.
• Spectrophotometer for measuring DNA concentration. Simon and Tom are on this.
• Good microscope enabling us to see cells (Possible mag: 100x, 400x, 1000x).
• Better imaging system

Costs (assuming prices on wet stuff)

Per Chelex DNA extraction:

• Chelex: £0.33 (0.15g)
• Pasteur pipettes: £0.06 (1 disposable)
• Tubes: £0.04 (1 for chelex incubation, 1 to save supernatant)
• Tips: £0.06 (1 for mixing chelex, 1 removing supernatant)

Total per sample: £0.49

Per PCR reaction Assume 25ul total volume. 12.5ul Taq Readymix, 5ul primers

• Taq Readymix: £0.72 (12.5ul)
• Primers: Not calculated but likely to be small
• Tubes: £0.02 (1 tube for PCR)
• Tips: £0.15 (Assuming 1 tip for template, 1 for PF, 1 for PR, 1 for dH20, 1 for Taq)
• Paraffin: Negligible

Total per sample: £0.89 + primers

Per restriction digest for blood typing: This estimate may be wrong. Need to calculate quantities definitively

• KPN1 and ALU1: £2.08

Total per sample: £2.08 + another gel

Per sample on a gel: For each sample:

• Tubes: £0.02 (1 to mix loading buffer with PCR product)
• Tips: £0.03 (1 to add product to loading buffer and then load into well)
• Loading buffer: Negligible

Total per sample: £0.05

Per gel: Assume a 1% 50ml agarose gel with 100ml buffer and 2.2ul EtBr

• Agarose: £0.23
• TBE: £0.13
• Ladder: £0.30
• Tips: £0.03 (1 to add loading buffer to all tubes)
• dH20: Negligible
• EtBr: Negligible

Total per gel: £0.69

So for a chelex extraction, PCR and gel it costs at least £1.43 per sample. A gel costs £0.69, so a typical session involving 4 extractions + PCRs, followed by a gel costs at least £6.14.

Ideas for cost+efficiency savings

• Cheaper Taq would make the biggest contribution. Investigate NEB (won't sell to us at the moment), web scientific and nbs.
• Smaller gels and gel box could halve amount of TBE and agarose used.
• Reduce concentration of agarose and TBE in gel and buffer. E.g. we could use 0.5% TBE not 1%.
• Use TAE instead of TBE (TAE is 1/2 to 1/3 the price of TBE). However it is claimed TBE is better for small DNA lengths like ours
• Buy powdered TBE. NBSBio - £33.60 for 1 litre of 10x (50p per gel+buffer), and £76.80 for 5L (23p per gel+buffer). Dry premix powders are even better value than this. £18 for 1L (27p per gel+buffer), and £28 for 4L (13p per gel+buffer).
• Make our own TBE. Recipe here. Advantage that we could also make TE.
• Invitrogen do http://products.invitrogen.com/ivgn/product/15581044# cheaper TBE] but won't sell to us atm
• Cheaper sources for tubes and tips e.g. ebay
• Heated lid making paraffin unnecessary. Save on paraffin + extra tubes for mixing loading buffer with PCR product as loading buffer could be added directly to it if there are no further plans for it. Mostly efficiency saving rather than cost.
• Same result could be achieved by using a taq readymix with loading buffer included (e.g. sold by webscientific)
• Larger quantities of agarose. Our agarose from NBSBio works out at £0.23 per gel for 100g, but if we bought 500g it would be £0.18 per gel. Not a massive saving though.

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. Slides
• Sara's Introduction the the Biohacking Community - Recorded at the hackspace

A primer for synthetic biology

• 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
• Slides from Bioinformatics workshop August 2012
• Cathal Garvey's beginner's guide to biotech
• Flowchart diagram of DNA extraction protocol

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)

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/

Proposed code of conduct

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

FAQ about DIYBio

• official do-it-yourself biology FAQ