Biotop Community Lab interacted since the beginning with the Heidelberg community of makers and tinkerers. We merge the maker culture, tools and skills with biology. So we have focused on creating low-cost open-source prototypes of standard laboratory equipment, built with off-shelf hardware or 3D printed and laser-cut parts. These prototypes are designed with educational and citizen science application in mind, diminishing the entry barrier to biology and thus promoting a more scientifically literate society and spark discussion on bioethics and responsible research and innovation concepts.
We also receive donations of unused laboratory equipment that we restore to its original condition, and we aim to further donate it to research institutes in developing countries to promote equal access to science.
We mainly meet and work at the local makerspace. As we do not have access to a registered biology laboratory, only certain activities with biological materials are allowed by law. However, we engage with other local associations and research institutes for collaborations in this regard. In any case, Biotop Community Lab members value safety, responsibility, accountability and transparency in their work and celebrate open science.
Here below you can find some examples of the projects we have developed over time:
The thermocycler is an essential piece of equipment in molecular biology. It is used to control temperature of solutions in numerous molecular biology techniques. Its main application is in DNA amplification by means of Polymerase chain reaction (PCR). The thermocycler works by heating or cooling an aluminum block with several housings for reaction tubes (0.2 mL volume). In the current setting, the temperature is controlled with +-1°C accuracy. Biochemical reactions are performed by enzymes which are active at a specific temperature range. For example, in DNA extraction, a protease is needed to digest tissues and release DNA. Such protease is active at 65°C and becomes inactivated at 95°C. In this context, a thermocycler can be used to incubate the DNA extraction mixture at the optimal temperature (65°C) and then stop the reaction by increasing the temperature (95°C). In the case of a PCR, the thermocycler proceeds through 3 temperature steps in a cycle, to allow specific events in the reaction to occur at each step.
The thermocycler is homebrew and was built by the maker community during the LowCostPCR workshop. The participants also covered partially the costs of the components (now 100% of it), feel free to donate some money to help develop the project and keep it running.
How Does It Work
The case is laser cut and it’s transparent for educational purposes, so all components can be clearly seen in the inside. On the top there is an aluminum block with conical housings for reaction tubes of 0.2 mL, and on the side there is a sensor monitoring the temperature, which an accuracy of +/-1°C. Right below the block, there is a peltier element which is responsible for heating and cooling the block. The heat is dissipated through a heat-sink for microprocessors. On the side of the case it is possible to see a breadboard and an Arduino. The breadboard hosts few electronic component, among which there is a microprocessor to calculate and match the heating/cooling process with the readings of the temperature sensor. The arduino is used to communicate with the user and trasmit the data between the user and the microprocessor, and thus control temperature cycles and schemes. On the bottom there is a computer power supply with the on/off switch. When switched on the fan starts working, but the arduino gets its power from the laptop through the USB port. The thermocycler is controlled thanks to an Arduino. At the moment, it needs to be connected to a laptop, but we’re developing a phone app that would communicate with it via bluetooth.
Different solutes absorb light in a different manner. This can be visualized and measured with a spectrometer, by splitting light into its color spectrum and measuring absorbance at each wavelength. In biology and chemistry it can be used to analyze the contents of solutions.
Essentially our spectrometer is a wooden box with a light source, a refraction grid and a detector.
The light source is interchangeable and can be as simple as natural sunlight or an LED. The light enters the sample held in a cuvette and into the optical system which is composed by a slit, made with two razorblades, and a diffraction grid. The absorbed light is thus opened up into its spectral components and detected by a webcam or even a smartphone.
The instrument resolution power and calibration can be done by using a cold fluorescent light as a reference, because it show very specific peaks in its emission spectra.
Alessandro Volpato showed us how to build it during a workshop.
The transilluminator is a device used to detect DNA bands in an agarose gel, used as a readout in many molecular biology applications. DNA itself is invisible, but can be visualized by fluorescent molecules that can bind to it. One class of these molecules can be excited by blue light and emits green light.
The transilluminator is a tray, made with laser cut acrylic parts, which can accomodate an agarose gel. All around it, a blue LED strip lights up the gel, causing the DNA stain to emit green fluorescence light. Above the gel a transparent orange-tinted acrylic plate blocks out the blue light letting the green DNA fluorescence to show through and can thus be visible by human eye.
Microfluidics deals with the control and manipulation of liquids at micrometer scales. In biotechnology, microfluidics promises to bring a revolution in terms of speed, throughput and automation.
Manufacturing of microfluidics devices normally requires costly and highly specialized techniques. However, recently more and more papers get published about alternative methods of manufacturing. These alternatives rely on CNC machines that have become widely available in makerspaces, such as 3d printers and laser cutters.
We are developing manufacturing methods based on sandwiching of acrylic plates or engraving of plates with channels. The possibility of replicating such methods in a reliable way could open great possibilities for citizen science, education and schools.
The freezer is a common freezer re-purposed for storing materials and reagents. We equipped it with a transmitter to keep track of the freezer’s temperature. Biotop members will be notified in case the freezer gets too warm. You can see the current temperature below.