|2000 Code Night (FPGA cipher cracking)|
|1930 - meetup|
|1900 Code Night (x86 asm)|
|1900 Code Night (cracking a OpenCL)|
This is an old revision of the document!
The aim of the project is to get acquainted with usually inaccessible laboratory procedures - extraction of various organic substances and study them further, growing bacteria on agar plates, DNA extraction and sequencing, explant cultures, various behavioral studies (see BrmRat ) and even heredity experiments. A lot of this may be simple stuff you do not need a well-equipped lab for - once we understand the principles, we can make our way forward.
The goal of this project is mainly to enable access to experimental biology for everyone interested in it, give an opportunity to everyone with interesting ideas for experiments and try to reproduce what normally is done in big labs with as little need for professional equipment as possible - in the spirit of the DIY Bio movement.
The Biolab is a small room at the back of our Hackerspace at Bubenska. At the moment, we have to share the room with the Hackerspace kitchen, but arrangements are being made to divide the room in half with a makeshift wall (IN PROGRESS, thanks to tomsuch, blackhead and Pavlik we have a wall now - door still to be done). We have basic equipment in the form of a computer, desks, chairs - but also some lab equipment which needs to be catalogized (TO DO).
How to behave in biolab:
Here is a small list of things currently available in the lab:
We are at the moment short on equipment and welcome anyone willing to donate material to the lab!
What we need:
If you can and want to support the lab with material donation (listed or otherwise), contact chido or feel free to stop by at the lab!
What have we done so far:
Extracting DNA - originally inspired by Strawberry Mayhem. Fruit juice + jar + salt + isopropyl = DNA!
chido tried several fruits - strawberries, melons, oranges, bananas, plums, peaches. It was a big success! Strawberries seem to be working very well, there were similar results with plums and peaches. Both were relatively easy to mash and mix with the solvent (detergent “Jar” + water + salt) and filtered nicely. Melons and oranges also mash and filter easily but due to their watery nature do not result in a usable amount of DNA material due to their watery nature (less nuclei per amount of fruit flesh?). Banana did not work at all, after getting mashed and mixed with solvent only an insignificant amount of liquid passed through the filter due to the sticky and very dense nature of the fruit.
A makeshift apparatus that uses a 1 mW green laser and a scaffolding holding a suspended syringe in front of it. The drop of water at the tip of the syringe refracts the laser beam and projects a magnified image of the drop content on the wall. Works nicely - we examined the following suspensions: Water filtered through the earth of a pot plant, Blaptica dubia droppings, mucus and blood. Each time we observed a different content. After leaving the first sample (pot plant earth) in a glass for two days, the content seems to have tripled. Pictures from the first iteration
We used a leaf sample from Primula vulgaris as source for the chlorophyll. To break up cell walls, we suspended the leaf in liquid nitrogen and proceeded to ground it to a fine powder once the nitrogen evaporated. After adding isopropyl alcohol, we centrifuged the suspension using a disassembled hard drive as centrifuge, until all the remaining residue collected at the bottom. When exciting the resulting suspension with UV light, the chlorophyll emitted red light. Pictures from the experiment
We are enhancing the hard disk based centrifuge to have build instructions and proper control software and solid hardware:
Arduino sketch: centrifuge-sketch
CAD file: centrifuge-scad
Currently, we are able to attain 6200 RPM (without eppendorfs). Maybe we are not at the limit yet.
This project has graduated to a separate page! See Conditioning Chamber for Cognitive Experiments for details.
In order to enable us to do some basic bio-experimenting like the project below, we need (apart from other things) some form of controlled environment. This would enable us to grow plant samples, breed bacteria cultures etc. with a larger chance of success. The idea is to convert one part of the storage space into a form of incubator. It is going to be largely a trial-and-error process - eg. we start with insulating the space, add a light source, a thermometer, and - if possible - something to regulate humidity and temperature. Some ventilation including dust filtering etc. would be nice too. If this gets hooked to Hind3, the lab PC, it should be possible to write some software to control the environment within the incubator.
What we already have
What needs to be done
For the first “project” using the incubator it would be sensible to try growing molds inside it - maybe try various setups of the device regarding light source, humidity source, temperature regulation etc. If you are interested to partake in this project, have ideas for how to proceed, or want to donate material, contact chido! Any help appreciated.
Enzymes for DNA experiments (thermostable DNA-p, restriction endonucleases…) can be ordered online, but the price is really high (1000 USD). Extracting them ourselves will be a great project that may grant access to advanced gene technology to the masses!
Available primers pretty much define what we can use the PCR machine for. There are online companies that will synthetize custom primers for a fee (for example, http://www.operon.com/ advertises a pair of custom primers for 10 USD not including the tax and shipping). But before ordering, we should design some interesting primers to have fun with!
Primer design guide: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
GFP rats, GloFish and even GFP yeasts (for glowing beer) are forbidden by EU, but we can still play with natural non-GM bioluminescent organisms:
Bioluminescent bacteria can be used for water pollution detection:
Just an (untested) idea for simplified algae medium: sea salt + nitrate + phosphate + soil extract + B-complex (incl B1/7/12) (but we need to find B-complex with minimum added sugar, possibly i.v. solution?)