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project:biolab [2013/07/19 16:51]
bluebear [The Lab]
project:biolab [2014/05/16 23:21] (current)
chido
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 image=dna.jpg| image=dna.jpg|
 founder=[[user:chido]]| founder=[[user:chido]]|
-interested=[[user:pasky]]\\ [[user:tomsuch]]\\ [[user:jenda]] \\ [[user:kyknos]] \\ [[user:nephirus]] \\ [[user:bluebear]] |+interested=[[user:pasky]]\\ [[user:tomsuch]]\\ [[user:jenda]] \\ [[user:nephirus]] \\ [[user:bluebear]] |
 status=alive and kicking!| status=alive and kicking!|
 }} }}
  
 +===== Goals =====
  
-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 [[project:brmrat:|]] ) and even heredity experiments. +The goals of this project:
-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.+
  
-===== Goals =====+  * **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 [[http://diybio.org/|DIY Bio]] movement
  
-The goal of this project is mainly to enable access to experimental biology for everyone interested in itgive 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 [[http://diybio.org/|DIY Bio]] movement.+Our interests (can change if a new member arrives!): 
 + 
 +  * bacteriaalgae and plant cultivation 
 +  * DNA extraction and sequencing, heredity experiments 
 +  * behavioral studies (see [[project:brmrat:|]]) 
 + 
 +===== Contact us! ===== 
 + 
 +Currently the core team of biolab is: [[user:chido|]], [[user:pinky]], [[user:pborky]], [[user:jenda]] and [[user:bluebear|]]. Various other members of brmlab conduct occasional experiments. Contact anyone of us - or make a visit! 
 + 
 +We also have a mailinglist: [[https://brmlab.cz/mailman/listinfo/biolab|biolab@brmlab.cz]] ([[https://brmlab.cz/pipermail/biolab/|archives]]).
  
 ===== The Lab ===== ===== The Lab =====
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 [[http://panora.ma/news/2011/brm-meetup/biolabt.html|Panoramatic view of the lab]] [[http://panora.ma/news/2011/brm-meetup/biolabt.html|Panoramatic view of the lab]]
  
-The Biolab is a small room at the back of our Hackerspace at Bubenska. At the momentwe 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 [[user:tomsuch]], [[user:blackhead]] and Pavlik we have a wall now - door still to be done). +The Biolab is a small room at the back of our Hackerspace at Bubenska, beside the hackerspace kitchen, separated by plastic wall (thanks to [[user:tomsuch]], [[user:blackhead]] and Pavlik we have a wall now). 
-We have basic equipment in the form of a computer, desks, chairs - but also some lab equipment which needs to be catalogized (TO DO).+ 
 +We have basic equipment in the form of a computer, desks, chairssome lab glassware and equipment (donations are always welcome! :-) )
  
 **How to behave in biolab:** **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.   * 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.   * 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 (i) please always return things to clean state (ii) if you need to store any substance, keep it in a closed container. +  * The computer (hind3) and all equipment is free to use, including chemical glass. Just
-  * In case of any questions, talk to [[user:chido]] or [[user:Jenda]]. Please let them know if you want to start some longer-running experiment in biolab. +    * please always return things to clean state 
-  * We have a store of chemicals with restricted accessIf you are interested, please talk to [[user:chido]], [[user:Jenda]] or [[user:TomSuch]].+    * 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 [[user:chido]] and [[user:bluebear]]. Please let them know if you want to start some longer-running experiment in biolab. 
 +  * The storage of chemicals is locked for safetyPlease talk to [[user:chido]] or [[user:bluebear]] to get access.
  
-Here is a small list of things currently available in the lab:+Things currently available in the lab:
  
-  * 2 graduated cylinders  +  * freezer (please keep the temperature setting unchanged) 
-  * homemade shaker (thanks [[user:axtheb:|]]+  * precision scales (0.01 g calibrated) 
-  * various cuvettes, petri dishes and sample plates+  * 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   * sterile needles and syringes in various sizes
-  * strong UV light source +  * assortment of chemicals (H2SO4, isopropyl alcohol, distilled water, fluorescene, MnO2, sulphur,... complete list on demand- **restricted access**
-  * assortment of chemicals (H2SO4, isopropyl alcohol, distilled water, fluorescene, MnO2, sulphur)+
   * scalpels   * scalpels
-  * Ph-meter +  * set of physiological microscopic slices of mouse organs ideal for microscopic examination 
-  * precision scales (1g calibrated)+  * microscope (long-time loan thanks to Svatopluk+ [[project:brmscope|BrmScope]]
   * etc...   * etc...
  
-**We are at the moment short on equipment and welcome anyone willing to donate material to the lab!** +What we'd like to have
- +  * a more precise microscope 
-What we need+  * water distiller
-  * microscope ([[user:tomsuch]] is working on fine-tunable digital microscope) - we have the [[project:brmscope|BrmScope]] now  +
-  * pipette +
-  * various lab dishes (test tubes, petri dishes, hermetically sealable containers) +
-  * agar and other materials+
   * strong light source (for growing plants)   * strong light source (for growing plants)
-  * insulation material (incubator+  * UV source suitable for exciting EtBr 
-  digital thermometer (incubator)+  * 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).
  
-If you can and want to support the lab with material donation (listed or otherwise), contact [[user:chido:|]] or feel free to stop by at the lab!+====== What have we done so far ======
  
-&lt;note important>**The BrmScope** is now situated in the biolab and connected to Hind3the local PC. For instructions on how to use it, see the [[project:brmscope|project site]] (there is a short note on the wall at the lab too :) )</note> +===== Electrophoresis hackathon ===== 
- +{{:project:10076716473_fb5380cf36.jpg?nolink&amp;200 |}} We hosted the [[event:electrophoresis|]] in September 2013where  
- +[[user: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 herehttp://www.flickr.com/photos/85181478@N07/sets/72157636165317593/ 
-**What have we done so far:**+
  
 ===== Extracting DNA ===== ===== Extracting DNA =====
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 [[user:chido]] tried several fruits - strawberries, melons, oranges, bananas, plums, peaches. It was a big success!  [[user: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. 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.
-  
-~~CL~~ 
-{{:project:dnax-1.jpg?290}} 
-{{:project:dnax-3.jpg?290}} 
  
-===== DIY Laser Microscope =====+===== DIY Microscopes =====
  
-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.+{{:project:brmscope.jpg?nolink&300 |}} 
 + 
 +**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:brmscope|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. 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.
 [[https://picasaweb.google.com/petr.baudis/LaserMicroscope#|Pictures from the first iteration]] [[https://picasaweb.google.com/petr.baudis/LaserMicroscope#|Pictures from the first iteration]]
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 ===== Chlorophyll Extraction and Study of Fluorescence ===== ===== Chlorophyll Extraction and Study of Fluorescence =====
  
-{{:project:biolab_chl2.jpg?290}} {{:project:biolab_chl1.jpg?290}} {{:project:biolab_chl3.jpg?290}}+{{:project:biolab_chl3.jpg?290 }}
  
 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. 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.
 [[https://picasaweb.google.com/radka.haneckova/ChlorophyllExtraction#|Pictures from the experiment]] [[https://picasaweb.google.com/radka.haneckova/ChlorophyllExtraction#|Pictures from the experiment]]
  
-==== Centrifuge ====+===== Centrifuge ====
 + 
 +{{:project:brmcentrifuge.jpg?nolink&300 |}}
  
 We are enhancing the hard disk based centrifuge to have build instructions and proper control software and solid hardware: We are enhancing the hard disk based centrifuge to have build instructions and proper control software and solid hardware:
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 Arduino sketch: [[project/biolab/centrifuge-sketch]] Arduino sketch: [[project/biolab/centrifuge-sketch]]
- 
 CAD file: [[project/biolab/centrifuge-scad]] CAD file: [[project/biolab/centrifuge-scad]]
- 
 Currently, we are able to attain 6200 RPM (without eppendorfs). Maybe we are not at the limit yet. 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 ===== ===== Operant conditioning chamber for cognitive experiments on rats =====
  
-{{http://farm7.static.flickr.com/6157/6168637877_b6524e3018_o.jpg?300}}+{{http://farm7.static.flickr.com/6157/6168637877_b6524e3018_o.jpg?300 }}
  
 This project has graduated to a separate page! See [[project:ratbox]] for details. This project has graduated to a separate page! See [[project:ratbox]] for details.
  
 ===== Taste Receptor Electrostimulation ===== ===== Taste Receptor Electrostimulation =====
 +
 +{{:project:biotaste.png?nolink&200 |}}
  
 See [[project/biolab/taste]]. See [[project/biolab/taste]].
  
-===== 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** +====== Current Projects ======
-  * [[http://www.mall.cz/autochladnicky/campingaz-powerbox-36-l-classic|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 ([[user:nephirus]])+
  
-**What needs to be done** +===== PCR and electrophoresis =====
-  * Fasten the storage scaffold onto the wall to make it stable +
-  * Light source. [[user: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. ([[user:nephirus]])+
  
 +([[user:bluebear]]
  
 +subproject page: http://brmlab.cz/project/brmpcr
  
-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.  +DNA electrophoresis using the OpenPCR [[http://openpcr.org/]]
-** +
-If you are interested to partake in this project, have ideas for how to proceed, or want to donate material, contact [[user:chido]]! Any help appreciated.**   +
  
-===== Playing with microorganisms =====+Many things can be done just with PCR, electrophoresis and well selected restriction enzymes:
  
-  * investigate possible ways how to grow bacteria colonies and fungi using homebrew equipment and chemicals +  * DNA barcoding identification of various substances 
-    * agar ([[http://zdravavyzivahronov.com/internetovy-obchod/agar-agar|surprisingly cheap]]), maybe mixed with sugar +    * let's check what meat is in which products 
-    * broth (hovězí vývar) +  * identification of specific alleles
-    * 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 :) +
- +
-Interresting reading: +
-  * https://secure.wikimedia.org/wikipedia/en/wiki/Gram_staining +
-  * https://secure.wikimedia.org/wikipedia/en/wiki/Discoveries_of_anti-bacterial_effects_of_penicillium_moulds_before_Fleming  +
-  * https://secure.wikimedia.org/wikipedia/en/wiki/Penicillium +
-  * https://secure.wikimedia.org/wikipedia/en/wiki/Penicillin +
-  * https://secure.wikimedia.org/wikipedia/en/wiki/Alexander_Fleming#Accidental_discovery +
-  * http://botit.botany.wisc.edu/toms_fungi/nov2003.html +
-  * http://202.114.65.51/fzjx/wsw/newindex/wswfzjs/pdf/21-3flemingchainabraham.pdf +
-  * http://jenda.hrach.eu/brm/penicillin.jpg 8-) +
- +
-===== 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! +
- +
-[[http://pastebin.com/zTy2uLjB|Shaddack's proposal]]+
  
-===== openPCR and electrophoresis =====+==== 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:
  
-Acquiring and assembling a device capable of DNA electrophoresis and an open-source PCR [[http://openpcr.org/]] - targeted by [[user:bluebear]] and [[user:kyknos]]+{{:project:biolab:img_6511.jpg?200|}} 
 +{{:project:biolab:img_6512.jpg?200|}}
  
-== what we already have ==+  * now, we need primers 
 +    * there are online companies that will synthetize custom primers for a fee 
 +      * [[http://www.operon.com]] 
 +      * [[http://www.biogen.cz]] 
 +    * which primers? 
 +      * check for horses/rats/cockroaches in food [[http://journals.tubitak.gov.tr/veterinary/issues/vet-07-31-3/vet-31-3-3-0601-30.pdf]] 
 +      * some human diagnostic primers? may be we can find some interesting [[http://www.snpedia.com/index.php/SNPedia|SNPs]] which we can detect with some available restrictase (getting useful info about our genes without sequencing anything) 
 +      * **universal [[http://en.wikipedia.org/wiki/DNA_barcoding|DNA barcoding]] primers** - 5'-GAAAATCATAATGAAGGCATGAGC-3' / 5'-TCCACTAATCACAARGATATTGGTAC-3 [[http://www.biomedcentral.com/1471-2164/9/214]] (advanced, needs DNA sequencing to be useful) 
 +      * primer design guide: [[http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html]]
  
-  * openPCR device assembled, dry run succesful! 
-  * SW: [[https://github.com/cathalgarvey/OpenPyCR]], running, we should kill the binary cat! 
-  * mini gelbox with Pt electrodes 
-  * loading dye (Iva) 
-  * borax for SB buffer 
-  * some ultra pure water 
  
-== what we need == +What we'd like to have: 
- +  * more agarose 
-  * **build a power supply for electrophoresis** +  * better loading dye (Iva?
-  * **electrophoresis buffer** (TAE/TBE) +  * some DNA ladders 
-     * already have EDTA, need Tris and acetic or boric acid +  * an illuminator for EtBr or some safer stain + an illuminator in the needed range (SYBR Safe+Blue LED...) 
-     * or just borax? [[http://letters.cathalgarvey.me/cargo-cults-and-electrophoresis/]] +     * we can use methylene blue (no illuminator needed), but it is not very sensitive --> a test is planned FIXME
-  * **electrophoresis grade agarose** +
-     * already have some crude agar we may try to purify +
-  * a fridge and a **reliable freezer (-20°C)** for DNA/enzyme storage +
-  * **Taq/dNTP PCR mix** (possibly from [[http://www.openbiotech.com]])  +
-  * some dye for DNA staining and an illuminator in the needed range (EtBr+UV, SYBR Safe+Blue LED...) +
-     * we can use methylene blue (no illuminator needed), but it is not very sensitive+
      * EtBr spectrum for reference: [[http://www.invitrogen.com/site/us/en/home/support/Product-Technical-Resources/Product-Spectra.1305dna.html]]      * EtBr spectrum for reference: [[http://www.invitrogen.com/site/us/en/home/support/Product-Technical-Resources/Product-Spectra.1305dna.html]]
-  * some restriction enzymes  +  * some restriction enzymes 
-  * centrifuge for better DNA isolation +  * tips for micropipettes 
-  * **micropipettes** +  * bigger centrifuge for better DNA isolation
-  * DNA ladder +
-  * pure water!+
   * 260/280nm spectrophotometer would be great for measuring DNA quantity and quality   * 260/280nm spectrophotometer would be great for measuring DNA quantity and quality
   * single drop fluorimeter? possible alternative to electrophoresis (in some cases)   * single drop fluorimeter? possible alternative to electrophoresis (in some cases)
-  * **primers!!!** 
  
-== which primers?! ==+===== Fun with Bioluminescence =====
  
-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! +(targeted by [[user:bluebear]]
- +
-Some ideas: +
- +
-  * check for horses/rats/cockroaches in food [[http://journals.tubitak.gov.tr/veterinary/issues/vet-07-31-3/vet-31-3-3-0601-30.pdf]] +
-  * some human diagnostic primers? may be we can find some interesting [[http://www.snpedia.com/index.php/SNPedia|SNPs]] which we can detect with some available restrictase (getting useful info about our genes without sequencing anything) +
-  * **universal [[http://en.wikipedia.org/wiki/DNA_barcoding|DNA barcoding]] primers** - 5'-GAAAATCATAATGAAGGCATGAGC-3' / 5'-TCCACTAATCACAARGATATTGGTAC-3 [[http://www.biomedcentral.com/1471-2164/9/214]] (advanced, needs DNA sequencing to be useful) +
- +
-Primer design guide: [[http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html]] +
-===== Fun with Bioluminescence ===== +
-(targeted by [[user:bluebear]] and [[user: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: 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:
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 Bioluminescent bacteria can be used for water pollution detection: Bioluminescent bacteria can be used for water pollution detection:
-  * [[http://cdn.intechopen.com/pdfs/6921/InTech-Bacterial_bioluminescent_biosensor_characterisation_for_on_line_monitoring_of_heavy_metals_pollutions_in_waste_water_treatment_plant_effluents.pdf]]+  * [[http://cdn.intechopen.com/pdfs/6921/InTech-Bacterial_bioluminescent_biosensor_characterisation_for_on_line_monitoring_of_heavy_metals_pollutions_in_waste_water_treatment_plant_effluents.pdf|bioluminiscent biosensors]]
   * [[http://www.instructables.com/id/Bioluminescent-Bacterial-Lightbulb-Water-Polluti/]]   * [[http://www.instructables.com/id/Bioluminescent-Bacterial-Lightbulb-Water-Polluti/]]
 +
 === what is needed === === what is needed ===
   * establish basic microbiology workflow   * establish basic microbiology workflow
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 +===== Playing with microorganisms =====
 +
 +{{:project:bio_micro.jpeg?nolink&300 |}}
 +  * investigate possible ways how to grow bacteria colonies and fungi using homebrew equipment and chemicals
 +    * agar ([[http://zdravavyzivahronov.com/internetovy-obchod/agar-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 [[project/biolab/BioStrike]]
 +
 +
 +Interresting reading:
 +  * https://secure.wikimedia.org/wikipedia/en/wiki/Gram_staining
 +  * https://secure.wikimedia.org/wikipedia/en/wiki/Discoveries_of_anti-bacterial_effects_of_penicillium_moulds_before_Fleming 
 +  * https://secure.wikimedia.org/wikipedia/en/wiki/Penicillium
 +  * https://secure.wikimedia.org/wikipedia/en/wiki/Penicillin
 +  * https://secure.wikimedia.org/wikipedia/en/wiki/Alexander_Fleming#Accidental_discovery
 +  * http://botit.botany.wisc.edu/toms_fungi/nov2003.html
 +  * http://202.114.65.51/fzjx/wsw/newindex/wswfzjs/pdf/21-3flemingchainabraham.pdf
 +  * http://jenda.hrach.eu/brm/penicillin.jpg 8-)
 +
 +
 +
 +
 +
 +
 +====== 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**
 +  * [[http://www.mall.cz/autochladnicky/campingaz-powerbox-36-l-classic|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 ([[user:nephirus]])
 +
 +**What needs to be done**
 +  * Fasten the storage scaffold onto the wall to make it stable
 +  * Light source. [[user: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. ([[user: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 [[user: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!
 +
 +[[http://pastebin.com/zTy2uLjB|Shaddack's proposal]]
  
  
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   * [[http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822003000200004|magnetotactic bacteria]]   * [[http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822003000200004|magnetotactic bacteria]]
   * ...feel free to suggest your own projects!   * ...feel free to suggest your own projects!
 +
 ===== References ===== ===== References =====
   * Great introductory website to the world of genetics: [[http://learn.genetics.utah.edu/]]   * Great introductory website to the world of genetics: [[http://learn.genetics.utah.edu/]]
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   * Pocket PCR for pennies (work in progress): [[http://lava-amp.com/]]   * Pocket PCR for pennies (work in progress): [[http://lava-amp.com/]]
   * Neuroscience for everyone! [[http://backyardbrains.com/Spikerbox.aspx]]   * Neuroscience for everyone! [[http://backyardbrains.com/Spikerbox.aspx]]
- 
 
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