Difference between revisions of "Group:Biohacking"
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* Pressure cooker (goes up to 15PSI and 121°C (this is industry standard, not actually tested) to be used as autoclave. Autoclave tape. | * 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 in priority order (See [[Biohacking/Wetstuff|wet stuff]] for sources and prices) === | + | === Shopping list in priority order (See [[Biohacking/Wetstuff|wet stuff]] for sources and prices not listed here) === |
+ | |||
+ | '''These prices are the first I found. We should look for better ones.''' | ||
* Ladder (only enough left for 1 gel of current ladder + a few more gels for the an older one) | * Ladder (only enough left for 1 gel of current ladder + a few more gels for the an older one) | ||
* Agarose (nearly run out, less than 10 more gels) | * Agarose (nearly run out, less than 10 more gels) | ||
− | * KPN1 (£27 from [http://www.sigmaaldrich.com/catalog/product/sigma/r1258?lang=en®ion=GB sigma]) and ALU1 (£18.90 from [http://www.sigmaaldrich.com/catalog/product/sigma/r6885?lang=en®ion=GB sigma]) for blood typing | + | * KPN1 (£27 for 1000 units from [http://www.sigmaaldrich.com/catalog/product/sigma/r1258?lang=en®ion=GB sigma] - a unit is "the enzyme activity that completely cleaves |
+ | 1 µg λ DNA in 1 hr. at 37 °C in a total volume of 25 µl of | ||
+ | Buffer SL for restriction enzymes.") and ALU1 (£18.90 for 100 units from [http://www.sigmaaldrich.com/catalog/product/sigma/r6885?lang=en®ion=GB sigma] - can also buy 500 units for £33.80) for blood typing. | ||
* 1.5ml and 0.75ml tubes (around 30 tubes left) | * 1.5ml and 0.75ml tubes (around 30 tubes left) | ||
− | * Taq readymix (less than 20 reactions left) | + | * Taq readymix (less than 20 reactions left). £120 for 100 reactions from [http://www.sigmaaldrich.com/catalog/product/sigma/p2893?lang=en®ion=GB sigma]. We can halve reaction volume with no adverse effects giving us 200 reactions. |
* 10X TBE (running low) | * 10X TBE (running low) | ||
* Jim paid 108.99 for company formation + registered office etc. Needs to be reimbursed. | * Jim paid 108.99 for company formation + registered office etc. Needs to be reimbursed. |
Revision as of 19:28, 12 November 2012
Biohacking / DIYBio at LHS
We are the biohacking group at the London Hackspace, a mix of amateur and professional biologists, attracted by the potential of DIYbio 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.
Our current projects / schedule
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 to refine our DNA extraction and PCR process. In August and September we worked with the UCL igem team to develop a 'public biobrick'.
Our big goal for the next year is to begin projects involving 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.
- Public Biobrick (in collaboration with the UCL igem team)
- Sex typing with amelogenin
- Plant species testing
- Genetic modification
- Blood typing
- Algal biodiesel (on hold)
- DNA forensics (on hold)
- Other genetic tests to try
Schedule
- November/December 2012 - Refine DNA extraction process to get it working consistently, and complete blood typing and sex typing experiments. Also do the self cloning protocol from NCBE to learn transformation procedures.
- November 2012 - early 2013 - Get a larger lab space with a licence to do genetic modification, and get the funding to do this.
People
Andy, Joel, Mike, Nicholas, Paddy, Paul, Simon, Taylor, Tom, Tonderai, Will
How to find us
- 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.
- Post on the biohacking mailing list. You can view the mailing list archives through the previous link or through the google groups interface.
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.
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.
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
- Thermal Cycler (PCR Machine) Perkin Elmer 480
- Gel electrophoresis box
- Incubator with shaker
- Two centrifuges - estimated speed 5000 rpm
- Wet stuff: our inventory of primers, buffers, stains...
- Various pipettes (5-50ul), flasks, beakers, PCR tubes, tip/tube holders, scales (one down to 0.1g, the other down to 0.01g)
- 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 in priority order (See wet stuff for sources and prices not listed here)
These prices are the first I found. We should look for better ones.
- Ladder (only enough left for 1 gel of current ladder + a few more gels for the an older one)
- Agarose (nearly run out, less than 10 more gels)
- KPN1 (£27 for 1000 units from sigma - a unit is "the enzyme activity that completely cleaves
1 µg λ DNA in 1 hr. at 37 °C in a total volume of 25 µl of Buffer SL for restriction enzymes.") and ALU1 (£18.90 for 100 units from sigma - can also buy 500 units for £33.80) for blood typing.
- 1.5ml and 0.75ml tubes (around 30 tubes left)
- Taq readymix (less than 20 reactions left). £120 for 100 reactions from sigma. We can halve reaction volume with no adverse effects giving us 200 reactions.
- 10X TBE (running low)
- Jim paid 108.99 for company formation + registered office etc. Needs to be reimbursed.
- Would be good to get some tubes that can hold up to 10ml for spinning down stuff in the big centrifuge.
Wish list
- 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.
- Another centrifuge, if ours breaks down, or a dremelfuge. One option is a Dremelfuge - microcentrifuge to be made on a 3D printer. Can print a new one, or buy pre printed for £50 from shapeways. Another option could be this £100 13,000rpm centrifuge from ncbe. Says it's only for schools but we can try and persuade them. If we want a chilled centrifuge we can put it in the fridge / freezer.
- Another PCR machine. One option is the Open Source, Hackable PCR machine. Another is the Light Bulb PCR less than $50 to build this machine (including the $30 arduino)
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
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/
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
Proposed code of conduct
See here: http://wiki.hackspace.org.uk/wiki/Biohacking/Code_of_Conduct