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Project Biolab

Project Biolab
dna.jpg
founder: chido
depends on:
interested: pasky
tomsuch
jenda
kyknos
nephirus
bluebear
software license:
hardware license:
status: alive and kicking!

Goals

The goals of this project:

  • No Fear! :-) - showing that biology, biochemistry and genetics can be done safely in relatively simple conditions
  • Bio for everyone - enable access to experimental biology for everyone interested in it, allowing everyone to get acquainted with usually inaccessible laboratory procedures
  • Do it yourself - 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

Our interests (can change if a new member arrives!):

  • bacteria, algae and plant cultivation
  • DNA extraction and sequencing, heredity experiments
  • behavioral studies (see BrmRat)

Contact us!

Currently the core team of biolab is: chido, kyknos and bluebear. Various other members of brmlab conduct occasional experiments. Contact anyone of us - or make a visit!

We also have a mailinglist: biolab@brmlab.cz (archives).

The Lab

Panoramatic view of the lab

The Biolab is a small room at the back of our Hackerspace at Bubenska, beside the hackerspace kitchen, separated by plastic wall (thanks to tomsuch, blackhead and Pavlik we have a wall now).

We have basic equipment in the form of a computer, desks, chairs, some lab glassware and equipment (donations are always welcome! :-) )

How to behave in biolab:

  • Don't be shy to enter - just be careful with the door. :-) Only exception is if the display above door says entry is prohibited, you could ruin some experiment.
  • Keep biolab clean. Don't eat in there and bring drinks only in closed bottles.
  • The computer (hind3) and all equipment is free to use, including chemical glass. Just:
    • please always return things to clean state
    • if you need to store any substance, keep it in a closed and described container (at a minimum, write your name on it).
  • In case of any questions, talk to chido or kyknos and bluebear. Please let them know if you want to start some longer-running experiment in biolab.
  • The storage of chemicals is locked for safety. Please talk to chido, kyknos or bluebear to get access.

Things currently available in the lab:

  • freezer (please keep the temperature setting unchanged)
  • precision scales (0.01 g calibrated)
  • pH-meter - currently not working, needs fixing
  • OpenPCR
  • a small electrophoresis device
  • various cuvettes, graduated cylinders, petri dishes and sample plates, pipettes + pipette tips, sterile equipment…
  • sterile needles and syringes in various sizes
  • assortment of chemicals (H2SO4, isopropyl alcohol, distilled water, fluorescene, MnO2, sulphur,… complete list on demand) - restricted access
  • scalpels
  • set of physiological microscopic slices of mouse organs - ideal for microscopic examination
  • microscope (long-time loan thanks to Svatopluk) + BrmScope
  • etc…

What we'd like to have:

  • a more precise microscope
  • water distiller
  • strong light source (for growing plants)
  • UV source suitable for exciting EtBr
  • always welcome:
    • agarose (PCR-grade is most welcome :-) )
    • more material (pipette tips, lab glass…)

If you can and want to support the lab with material donation (listed or otherwise), contact the core team (or anyone else in brmlab).

Current Projects

PCR and electrophoresis

(bluebear, kyknos)

subproject page: http://brmlab.cz/project/brmpcr

DNA electrophoresis using the OpenPCR http://openpcr.org/

Many things can be done just with PCR, electrophoresis and well selected restriction enzymes:

  • DNA barcoding - identification of various substances
    • let's check what meat is in which products
  • identification of specific alleles

Status

  • openPCR working, dry run successful (SW: https://github.com/cathalgarvey/OpenPyCR, running.)
  • Taq/dNTP PCR mix obtained from http://www.openbiotech.com
  • electrophoresis working, tested at hackathon
  • got chemicals:
    • TAE buffer (and all needed components for both TAE and TBE http://letters.cathalgarvey.me/cargo-cults-and-electrophoresis/)
    • some ultra pure water (need more)
    • PCR grade agarose (quite little, expensive)
    • EtBr, methylen blue (unknown concentration, veterinary grade)
    • DIY loading dye (sucrose and cresol red)
    • some DNA fragments for experimentation
  • freezer (-20°C) for DNA/enzyme storage is ready
  • we have a wonderful power supply (up to 300V) thanks to Tomsuch
  • 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:

What we'd like to have:

  • more agarose
  • better loading dye (Iva?)
  • some DNA ladders
  • an illuminator for EtBr or some safer stain + an illuminator in the needed range (SYBR Safe+Blue LED…)
  • some restriction enzymes
  • tips for micropipettes
  • bigger centrifuge for better DNA isolation
  • 260/280nm spectrophotometer would be great for measuring DNA quantity and quality
  • single drop fluorimeter? possible alternative to electrophoresis (in some cases)

Fun with Bioluminescence

(targeted by bluebear and kyknos)

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:

what is needed

  • establish basic microbiology workflow
  • autoclave - pressure cooker (121 °C)
  • strong light source + timer
  • f/2 Medium for coastal marine algae: https://ncma.bigelow.org/node/83 (but we may try luck with simplified medium, see below)
    • sea salt (aquarium - not kitchen - grade) FIXME
    • NaNO3 FIXME
    • NaH2PO4*H2O FIXME
    • Na2SiO3*9H2O FIXME
    • EDTA
    • FeCl3*6H2O FIXME
    • MnCl2*4H2O
    • ZnSO4*7H2O
    • CoCl2*6H2O
    • CuSO4*5H2O
    • Na2MoO4*2H2O FIXME
    • H2SeO3
    • NiSO4*6H2O
    • Na3VO4 FIXME
    • K2CrO4
    • thiamine HCl (vitamin B1) FIXME are vitamins needed? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539151/
    • biotin (vitamin H/B7) FIXME
    • cyanocobalamin (vitamin B12)
  • medium for marine bacteria:
    • glycerol
    • agar
    • sea salt (aquarium grade) FIXME
    • yeast extract FIXME
    • peptone/tryptone FIXME
    • calcium carbonate FIXME

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?)

Playing with microorganisms

  • investigate possible ways how to grow bacteria colonies and fungi using homebrew equipment and chemicals
    • agar (surprisingly cheap), maybe mixed with sugar
    • broth (hovězí vývar)
    • incubator with controlled temperature (peltier cell), humidity and illumination
  • Is it possible to do gram staining with standard hackerspace technology?
  • grow some grampositive bacteria in petri dishes, add Penicillium chrysogenum (at best) and see what happens :)
  • BioStrike project: gamify open drug discovery of antibiotics over Petri dishes, See BioStrike: Open Antibiotics Discovery

Interresting reading:

Planned Projects

Project Incubator

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

  • Portable fridge - this can cool down to approx. 15 K below ambient temperature. For lower temperatures, we have to either lower the ambient temperature somehow or make a fridge-in-a-fridge box, that will make greater temperature difference.
  • A set of thermometers, that need to be assembled and installed into incubator (nephirus)

What needs to be done

  • Fasten the storage scaffold onto the wall to make it stable
  • Light source. chido has a broken desk lamp which could be used in the beginning, but it might be too small/not the right spectrum. Needs investigating.
  • Set up a temperature control circuit, that will keep inside of the fridge at defined temperature. (nephirus)

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.

Enzyme extraction

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!

Shaddack's proposal

What have we done so far

Electrophoresis hackathon

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

dnax-2.jpg

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.

DIY Microscopes

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

Chlorophyll Extraction and Study of Fluorescence

biolab_chl3.jpg

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

Centrifuge

We are enhancing the hard disk based centrifuge to have build instructions and proper control software and solid hardware:

  • WIP: Hard disk plates replaced with dremelfuge-like reprapped holder
    • We need to put holder sources on thingiverse
  • DONE: Hard disk with electronics ripped off
  • DONE: Noname HobbyKing 20A ESC brushless motor controller soldered on motor pins instead
  • WIP: Arduino controls the ESC
    • The ESC keeps resetting and losing calibration settings
  • WIP: RPM turning speed detection and control
    • CNY70 provided by Nephirus + collector-sense circuit + duct tape and black marker
    • TODO: Resolder on mini-PCB, more robust construction and wiring
    • TODO: Dynamic motor control for “RPM hold” (we need reliable ESC control first)
  • TODO: Port sketch to LaunchPad, swap with Arduino
  • TODO: Control software for PC

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.

Operant conditioning chamber for cognitive experiments on rats

6168637877_b6524e3018_o.jpg

This project has graduated to a separate page! See Conditioning Chamber for Cognitive Experiments for details.

Taste Receptor Electrostimulation

Other Possible Projects

References

 
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