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project:biolab [2013/07/19 16:51]
bluebear [The Lab]
project:biolab [2014/09/29 22:38] (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 =====+  * **Lab for everyone** - enable access to experimental biology for everyone with interest and basic knowledge of biology, unrelated to formal education. We do not need you to have a degree, just curiosity and a willingness to learn is enough. Just stopping by to say hi is welcome as well - we're here to allow everyone to get acquainted with usually inaccessible laboratory procedures, try them out, learn some basics or start a project. 
 +  * **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. 
 +  * **No Fear!** - showing that biology, biochemistry and genetics can be done safely in relatively simple conditions. There'​s a lot that can be done with basic tools and in accordance with the laws - you can't make GMOs at our lab, but you can use molecular genetics to identify meat content in your breakfast, for example.
  
-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!):​ 
 + 
 +  * bacteria, algae and plant cultivation 
 +  * DNA isolation and analysis 
 +  * heredity and development experiments 
 +  * DNA security 
 +  * behavioral studies (see [[project:​brmrat:​|]]) 
 +  * electrophysiology (see [[project/​biolab/​taste]]) 
 + 
 +===== Contact us! ===== 
 + 
 +Currently the core team of biolab ​is: [[user:​chido|]][[user:​pinky]],​ [[user:​pborky]],​ [[user:​jenda]],​ [[user:​pasky]],​ [[user:​mrkva]],​ [[user:​tomsuch]] ​and [[user:​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: ​[[https://brmlab.cz/​mailman/​listinfo/​biolab|biolab@brmlab.cz]] ([[https://​brmlab.cz/​pipermail/​biolab/|archives]]).
  
 ===== The Lab ===== ===== The Lab =====
  
-[[http://​panora.ma/​news/​2011/​brm-meetup/​biolabt.html|Panoramatic view of the lab]]+The Biolab is a large room located downstairs from the main hackerspace premises, right behind the chemistry-focused laboratory, chemlabThe two projects cooperate closely with eachother and share some equipment, but at the same time have their own workspaces and desighnated material storage to assure safety and viability ​of both chemistry-related and biology-related experiments. If you are interested in the chemlab project, or would like to use their equipment or material, contact [[user:​pinky]].
  
-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 kitchenbut 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). +Hackerspace ​members ​have access cardsnon-members ​are premitted entry accompanied ​with members anytime ​the hackerspace is open
-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:** +We started out in a small space behind ​the brmlab kitchen: [[http://panora.ma/​news/​2011/​brm-meetup/​biolabt.html|Panoramatic view of the old lab]] 
-  * 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 (i) please always return things to clean state (ii) if you need to store any substance, keep it in a closed container. +
-  * 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. +
-  * We have a store of chemicals with restricted access. If you are interested, please talk to [[user:​chido]], [[user:​Jenda]] or [[user:​TomSuch]].+
  
-Here is small list of things currently available in the lab:+** We have recently moved to new place! ** 
  
-  * 2 graduated cylinders  +TODO Pictures!
-  * homemade shaker (thanks [[user:​axtheb:​|]]) +
-  * various cuvettes, petri dishes and sample plates +
-  * sterile needles and syringes in various sizes +
-  * strong UV light source +
-  * assortment of chemicals (H2SO4, isopropyl alcohol, distilled water, fluorescene,​ MnO2, sulphur) +
-  * scalpels +
-  * Ph-meter +
-  * precision scales (1g calibrated) +
-  * etc...+
  
-**We are at the moment short on equipment ​and welcome anyone willing to donate material to the lab!**+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 computer workstation ​and basic lab equipment like pipette tips, glassware, chemicals etc. 
  
-What we need: +** Donations of material are always welcome, since we are self-funded. **  
-  * microscope ([[user:tomsuch]] is working on a fine-tunable digital microscope) - we have the [[project:​brmscope|BrmScope]] now  +Contact ​[[user:chido]] if you have something you would like to contribute! We do not accept dangerous chemicals or other potentially harmful ​materials.
-  * pipette +
-  * various lab dishes (test tubes, petri dishes, hermetically sealable containers) +
-  * agar and other materials +
-  * strong light source (for growing plants) +
-  * insulation material (incubator) +
-  * digital thermometer (incubator)+
  
 +===== How to behave in biolab =====
 +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 upstairs to accompany you! 
  
-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!+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: 
 + 
 +  * **Keep the place clean.** ​If your work is done, put the place back in order for the next person to make a mess of :) This means wash the glass-ware properly, keep containers closed and the bench clean. 
 +  * **No foods and drinks on the workbenches,​ inside the freezer, fridge or microvawe.** There'​s a chill-out corner sharing space with the biolab room, food and drink can be consumed there. 
 +  * **Do not leave unlabeled ​and open containers in the lab.** If you want to store something or have a longer-running experiment on the bench, it's no problem to leave it there - just make sure to label it with your name, what it is, and the date you put it there. For safety reasons, **unlabeled stuff will be disposed of.** 
 +  * You can use all the equipment present. However, some of the machines require at least a small initial introduction on how to use them without you or the machine in question sustaining any damage. We're assuming the microwave is safe in your hands :but: talk to [[user:​pinky]] if you want to use the **macroscope** and to [[user:​chido]] if you'd like to play with the **electrophoresis chamber and open PCR.** 
 +  * **Discuss your projects with the community.** Basicallyanything goes that's safe and legal when it comes to projects you would like to introduce to the lab. But in order to keep the lab a safe and fun place to everyone involved, **please talk to [[user:​chido]] about your biolab project and to [[user:pinky]] about your chemlab project first.** 
 +  * **Some storage places are locked.** Because the hackerspace is open to the public, and some of the reagents are potential health hazards ​or expensive, we keep the storage locked and an inventory registry. If you would like to access to both, members can help you out.  
 +  * **Be nice to eachother.** No, really, this is important :) 
 +  * **If you want to store private equipment or material in the lab, put it in a separate box labeled with your name.** 
 + 
 +===== Equipment ===== 
 + 
 +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...)
  
-<note important>​**The BrmScope** is now situated in the biolab ​and connected ​to Hind3, ​the local PC. For instructions on how to use itsee the [[project:​brmscope|project site]] ​(there is a short note on the wall at the lab too :)</​note>​+If you can and want to support ​the lab with material donation (listed or otherwise)contact ​the core team (or anyone else in brmlab).
  
 +====== What have we done so far ======
  
-**What have we done so far:**+===== Electrophoresis hackathon ===== 
 +{{:project:​10076716473_fb5380cf36.jpg?​nolink&​200 |}} We hosted the [[event:​electrophoresis|]] in September 2013, where  
 +[[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 here: http://​www.flickr.com/​photos/​85181478@N07/​sets/​72157636165317593/ ​
  
 ===== 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]]
Line 83: Line 102:
 ===== 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]]
 +DNA electrophoresis using the OpenPCR [[http://​openpcr.org/​]]
  
 +=== 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 [[http://​letters.cathalgarvey.me/​cargo-cults-and-electrophoresis/​]])
 +    * ddH2O
 +    * PCR grade agarose (quite little, expensive)
 +    * EtBr
 +    * 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:
  
-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.  +{{:project:​biolab:​img_6511.jpg?200|}} 
-** +{{:project:biolab:​img_6512.jpg?200|}}
-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 =====+  * 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]]
  
-  * 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 :) 
  
-Interresting reading: +What we'd like to have: 
-  * https://​secure.wikimedia.org/​wikipedia/​en/​wiki/​Gram_staining +  * more agarose 
-  * https://​secure.wikimedia.org/​wikipedia/​en/​wiki/​Discoveries_of_anti-bacterial_effects_of_penicillium_moulds_before_Fleming  +  * better ​loading dye (Iva?
-  * https://​secure.wikimedia.org/​wikipedia/​en/​wiki/​Penicillium +  * some DNA ladders 
-  * https://​secure.wikimedia.org/​wikipedia/​en/​wiki/​Penicillin +  * an illuminator ​for EtBr or some safer stain + an illuminator in the needed range (SYBR Safe+Blue LED...) 
-  * https://​secure.wikimedia.org/​wikipedia/​en/​wiki/​Alexander_Fleming#​Accidental_discovery +     * we can use methylene blue (no illuminator needed), but it is not very sensitive ​--> a test is planned FIXME
-  * 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 ===== +
- +
-Acquiring and assembling a device capable of DNA electrophoresis and an open-source PCR [[http://​openpcr.org/​]] - targeted by [[user:​bluebear]] and [[user:​kyknos]] +
- +
-== what we already ​have == +
- +
-  * 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 == +
- +
-  * **build a power supply ​for electrophoresis** +
-  * **electrophoresis buffer** (TAE/TBE) +
-     * already have EDTA, need Tris and acetic ​or boric acid +
-     * or just borax? [[http://​letters.cathalgarvey.me/​cargo-cults-and-electrophoresis/​]] +
-  * **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! +[[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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