The Lab, Hacks and Recipes

DNA Extraction

You can extract DNA from organisms including an onion or your own mouth. The extracted DNA can be seen as stringy white clumps in the glass or test tube.

Opskrift

Recipe

1. Chop an onion into small pieces, and cover the pieces with a salt solution made from 100ml water, 2 tsp liquid soap and 3g salt. The soap breaks down the cell membrane of the onion, so that the DNA can come out into the liquid.
2. Cool the mixture down, halting the DNA-degradation process (or use soap with proteases).
3. Filter out any large particles and onion residues.
4. Pour ice-cold alcohol slowly on top of the solution, so that it lies in a layer on top. The DNA will then migrate up into the alcohol.

Back-story

This simple DNA extraction process has become a biohacker workshop classic, and is even used in schools. It underlines the message that no special tools or equipment are needed to start working with DNA. This simple protocol works on many types of organic material - plants, vegetables and even animal tissue. There is DNA everywhere, and the DNA itself is not dangerous.

Technical Details

Laboratory recipes are called protocols. “Open wet ware” is an online wiki where people can share protocols and get inspiration. The wiki can also be used as a collaboration platform for scientists working on the same problem across the globe. Another good source for biotechnology protocols is “current protocols”, administrated by Wiley.

Homemade Magnetic Stirrer

The adjustable magnetic stirrer is a practical device that allows you to mix fluids and dissolved chemicals without touching them.

Recipe

What do you need?

Used 12V computer fan: 0 kr
New 12V computer fan control (motor controller): 35 kr
Plexiglas, wood, magnets and screws from the hackerspace Labitat: 0 kr

Back Story

Stirrers are used for everything from homemade beer or biodiesel to laboratory experiments. There are therefore countless models, built from components such as propellers or computer cooling fans. Numerous videos on youtube show you how to construct your own.

Technical details

This homemade magnetic stirrer is under development. It is based on a 12V DC motor and a controller from a computer fan. The motor controller was bought cheaply over the internet, and the rest of the components were recovered from electronic waste, including magnets taken from an old hard disk drive.

Webcam Microscope

In biology experiments, microscopes are used to identify which organisms are in the sample, and to check how they are doing. With a digital microscope you can also take pictures to document the work and help with analysis.

Recipe

What do you need?

Web camera, second-hand or purchased online: 50-200 kr.
Lim, wood screws from Labitat: 0 kr.

Back story

In research laboratories, pictures of experiments are often made with big, expensive microscopes, at a higher magnification than necessary. It's easy to get hold of an old webcam and convert it into a microscope, which is good enough for many purposes.

Technical details

It can, however, be tricky to get a webcam microscope to work well. The distance between the lens and the object being examined must be fine-tuned to get a good focus, and all the parts must be stabilised so the picture doesn’t shake. How difficult this is depends partly on how well the webcam-microscope is built. Some models are being developed where a holder for the camera and object is 3D printed or laser cut, and screws inserted for adjustment. “The devil is in the detail” – here in the precision engineering.

Sourdough

Sourdough makes bread rise, adds taste, and acts as a preservative. Each sourdough is a small ecosystem – there may be 50 different lactic acid bacteria and 20 wild yeast species existing together in a fine balance.

Recipe

Recipe

1 part organic buttermilk and / or yogurt
1 part rye flour
Mix the ingredients together in a dish and leave at room temperature for 2-3 days. When the mixture starts to bubble and smells sour, like fermented beer, it is ready. The starter dough can be used for many different recipes.

Back-story

Bacteria and yeast are not dangerous, and working with them in the kitchen allows you to make many things you’d otherwise buy. Biologigaragen has published a small booklet where you can read more about yoghurt and sourdough. Take a copy here in the lab or download from biologigaragen.org.

Technical details

A sourdough can be started by simply mixing flour and water, but using yogurt or buttermilk helps. The consistency can vary, producing different kinds of bread. If your sourdough is runny it should be shaken or whipped every day. Sourdough often smells sour and fermented, which is fine, but if it gets mouldy or smells rotten, throw it out!

Genegun

The genegun is an air pressure device used to accelerate small gold particles coated with DNA into cells. The DNA can then be expressed in the new cell, or incorporated into its own genetic material.

Recipe

Recipe

1. Purified DNA fragments are stuck to gold particles and loaded into the genegun.
2. The particles are shot into the target cell, using air pressure.
3. The target cells are examined, and cells that successfully incorporate the new DNA can be grown into new plants.

Back-story

Genegun technology has been used to produce many of the genetically modified plant species currently cultivated in our fields. The two homemade geneguns presented here have been constructed by DIY biologist Rüdiger Trojok, and demonstrate how simple genetic engineering techniques can be. At the moment such instruments cannot be used to exchange genetic material outside of authorized labs, but the biohacker community is involved in worldwide discussion about whether these techniques should be available outside of institutional and industrial laboratories.

Technical Details

The genegun was invented by John C. Sanford, Ed Wolf and Nelson Allen of Cornell University, and Ted Klein of DuPont, 1983-1986. Initially tungsten particles were used, but gold is less reactive and thus less toxic. This method is only suitable for large cells such as those from plants and animals, not for microorganisms. It can also be used as a DNA-vaccine delivery method.

Dremmelfuge

The centrifuge is an indispensable part of every biology lab. It is used to purify DNA, protein, or cells, by spinning a sample at high speed so that the components separate out according to density.

Recipe

What do you need?

- Eppendorf tube holder, 3D printed in Labitat from thingiverse: ca. 2 kr
- Electric hobby grinder or screwdriver: ca. 250 kr
- Metal Bowl: ca. 30 kr
- Elastic bands: ca. 10 kr
Total: ca. 300 kr

Back-story

The original "Dremelfuge" was designed by Irish DIY biologist Cathal Garvey. It is a classic showcase for DIY biology and is used in several labs. In our machine, the holder for the Eppendorf sample tubes was printed on a RepRap open source 3D printer in hackerspace Labitat – the 3D model can be downloaded free from thingiverse.com.

Technical details

To purify DNA the sample must be spun at ~400 times the force of gravity, or 3000 revolutions per minute. A typical laboratory centifuge has a maximum speed of 16-20,000 rev/min – the hobby grinder used in our machine can reach even higher speeds of over 30,000 rev/min. The machine is fastened with rubber bands to dampen vibrations. If the holder is printed or installed badly it can rupture at high speeds, so we have encased it in a metal bowl.

Gel Electrophoresis

An gel electrophoresis box is used to separate out DNA fragments according to their length. When current is passed across the gel, negatively charged DNA moves toward the positive electrode, but the bigger pieces struggle harder to push through the gel. Staining the DNA allows you to see how far the different pieces have travelled, and thus what size they are.

Recipe

What do yoou need?

100% pure distilled water, which can be purchased at gas stations for use in windscreen wipers, or in supermarkets for ironing.
Acid or base buffer to stabilize the pH and dissolved DNA
Gel made from 1-2% agarose (a type of sugar from seaweed)

Back-story

Before you do experiments with DNA, it’s vital to check that the sample contains what you think it does. Gel electrophoresis boxes were therefore one of the first instruments to be build by DIY biologists, but the gel box and power supply here were donated to the hackerspace Labitat.

Technical Details

To stain the DNA, we use crystal violet or methylene blue as they can be seen with the naked eye – other dyes have to be viewed under UV light. Each little blob on the gel is not a single piece of DNA, but thousands of pieces of the same length – this is why the sample must be multiplied in a PCR machine first. The size of a DNA fragment is measured in base pairs (bp), i.e., the number of A, T, C and Gs that lie along one of the two strands of the double helix.

Yoghurt

It's easy to turn milk into yoghurt, which makes it thick and tart, and last longer.

Recipe

Recipe

1) Heat 1 litre of hot milk to 72-85 ° C for ca. 1 min, then cool to <40 °C.
2) Add ca. 100ml yoghurt and leave at 40 °C for 5-20 hours.
3) Eat and enjoy!

Back-story

Bacteria can be dangerous but there are many kinds that help us in everyday life, including in making traditional fermented foods. Yoghurt is a good place to start if you want to experiment with fermentation, and often contains fewer additives and more healthy bacteria than shop-bought versions. Copenhagen’s Biologigaragen has published a small booklet on yoghurt and sourdough, available at biologigaragen.org.

Technical Details

Making yoghurt: First pasteurize the milk by heating it up. A longer heating time kills more foreign bacteria, but also degrades vitamins and proteins. Next, the milk is rapidly cooled, and a small amount of yoghurt is added, to provide the necessary bacteria. The mixture is then fermented at ca. 40 °C for 5-9 hours, or up to 20 hours for a more sour, thick result. Finished yoghurt must be kept in the fridge to stop the fermentation process. It’s normal for yoghurt to smell and taste sour, but if it gets mouldy or smells rotten, throw it out.

Open PCR

A PCR machine is essentially a DNA photocopier. PCR is short for Polymerase Chain Reaction. Polymerase is the enzyme that copies DNA one element at a time. A PCR machine is needed for virtually all DNA experiments, to copy, analyze, manipulate or splice together DNA fragments.

Recipe

Recipe

1. Purify DNA from cells, organisms, or other biological materials.
2. Add polymerase enzyme to catalyze the reaction, the bases G, C, T and A as ‘building blocks’ for the new DNA and DNA primers that are DNA pieces that tell the polymerase where in the DNA to start copying.
3. Run the PCR reaction 20-35 times.
4. Test the outcome by running a gel electrophoresis (also displayed here).

Back-story

As the PCR machine is such an important instrument, many biohacker groups have built their own. PCR machines utilize the basic copying mechanism found inside all cells, but you have to add expensive enzymes and reagents. A long-term goal is to produce these enzymes within the DIY biology lab. The OpenPCR exhibited here was designed by Tito Jankowski and Josh Perfetto, and crowd-funded through kickstarter.com. It can be bought for $600 which is less than second-hand machines on ebay, and all the design drawings and software are open source.

Technical details

The PCR machine was developed in 1983 by Kary Mullis, winning him the Nobel Prize in Chemistry in 1993. It works by heating the DNA to 95-98 °C for ~2 min, causing the two strands that make up the double helix to pull apart. Then, the sample is cooled to 45-72 °C for ~30s, and finally heated to 74 °C for 1-5min, depending on the length of the DNA strand. This is repeated 20-35 times, doubling the amount of DNA each time.