STATUS:
Contact
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| Day | Events | |||
| 3 Friday | 1900 2k6 | |||
| 7 Tuesday | 1900 meetup | |||
| 14 Tuesday | 1900 meetup | |||
| 16 Thursday | 1900 MCM - Monthly Commodore Meeting / Mesicni Commodore Mecheche | |||
| 18 Saturday | 1200 + LED Neon Signs Workshop. Slots booked out. | |||
| 21 Tuesday | 1900 meetup | |||
| 24 Friday | ||||
| 28 Tuesday | 1900 meetup | |||
| Day | Events | |||
Sponsors
The goals of this project:
Our interests (can change if a new member arrives!):
Currently the core team of biolab is: chido, sachy, Jenda, pasky, mrkva, sumie-dh and bluebear. Various other members of brmlab conduct occasional experiments. Contact anyone of us - we'll be glad to show you around in person aswell.
We also have a mailinglist: biolab@brmlab.cz (archives).
The Biolab is a large room located in the main hackerspace premises, right next to the chemistry-focused laboratory, chemlab. The two projects cooperate closely with eachother and share some equipment, but at the same time have their own workspaces and designated material storage to assure safety and viability of both chemistry-related and biology-related work. If you are interested in the chemlab project, or would like to use their equipment or material, contact sachy.
We started out in a small space behind the brmlab kitchen: Panoramatic view of the old lab
We have recently moved to a new place!
TODO Pictures!
We now have larger premises housing a lab bench, a large microscope (dubbed the macroscope), several smaller optical microscopes, a large freezer, a fridge, a set of micropipettes, an elecrophoresis chamber with power supply, an OpenPCR thermocycler, a shaker, precision scales, a microwave, a biological incubator, a flowbox and basic lab equipment like pipette tips, glassware, chemicals etc.
Donations of material are always welcome, since we are self-funded. Contact sumie-dh or sachy if you have something you would like to contribute! We do not accept dangerous chemicals or other explicitly harmful materials.
First and foremost, don't be shy visit - if the door is open, just walk in and say hi, if it's closed, ask a brmlab member to accompany you!
In order for the biolab to be able to function safely and be available to a large community of people as equally as possible, there are some basic rules:
What we already have:
What we'd like to have:
)If you can and want to support the lab with material donation (listed or otherwise), contact the core team (or anyone else in brmlab).
We hosted the Electrophoresis: Collective Building Hackathon in September 2013, where
chido held an introductory lecture on molecular genetics, how gel electrophoresis works and what it is used for. We made agar gel, experimented with various power supplies and UV sources for visualizing the gel. Great pictures from the event can be found here: http://www.flickr.com/photos/85181478@N07/sets/72157636165317593/
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.
The BrmScope is now situated in the biolab and connected to Hind3, the local PC. For instructions on how to use it, see the project site (there is a short note on the wall at the lab too :) )
Another set-up we experimented with was a laser microscope: 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.
Some members are collecting photos and other evidence of (micro)organisms which can (not) be seen from behind the computer screen. Please see the BioOSM project pages.
We are cultivating flatworms! Flatworms (plostenky in Czech) are famous for their regeneration abilities - cut them in half, get two fully functional animals. Cut their head, and get two full heads on one body. The non-sexual species are actually reproduced by tearing themself in half!
Recently we learned how to pour our macroscopic samples into a transparent epoxide to be able to show them without risking damage. No more fridges full of formaldehyde bottles :)
DNA electrophoresis using the OpenPCR http://openpcr.org/
the first test run with crude agar, self made TAE, DIY loading dye (cresol red+sucrose), 60V (with the power source from hwlab), 1.5h:
second test run with agarose and several restriction digest samples using a strong laser and SYBR gold for visualization - blue light filter from infra-soldering station:
some notes for using SYBR gold:
first test run of the openPCR
Template: pTracer plasmid
Primers: inf pTracer F + R (10uM) designed by chido to amplify the GFP/Bsd gene
PCR mix:
dH2O 33ul mastermix Openbiotech 5x 10 ul primer F 2ul primer R 2ul template 1ng/ul 3ul
total volume 50 ul
Thermocycler settings:
95 °C 60 sec 95 °C 30 sec 60 °C 30 sec 72 °C 60 sec x30 4 °C 20 sec
SYBR gold gel stain:
30 ml TAE, 0.3g agarose gel stained in 10ul SYBR gold diluted in 100ml TAE, 40 min
Results:
We obtained the desired product using Openbiotech master mix that has been stored in -20 °C, but there was no product at all when using a mastermix that has been stored in the fridge. We aliquoted both SYBR gold gel stain and the PCR mastermix so thawing the stock solution is not necessary. OpenPCR works fine! Pictures and analyzed gel coming soon. Next step: devise a protocol for DNA isolation that can be used as a PCR template.
Useful links:
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:
are vitamins needed? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539151/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?)
Interresting reading:
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!
