Team:Valencia UPV/Description

Valencia UPV iGEM 2015


The huge progress achieved during the last years in biological sciences has created an enormous amount of information. Thus, nowadays the storage and processing of information has become a real challenge. While some storage solutions have been addressed recently, many limitations on the processing of biological information still remain. In particular, an important constraint is that most biological circuits can only display as many outputs as different inputs they receive. As the choice of signalling molecules in the biotechnologist´s palette is small, the ability to decode on demand specific portions of the total information stored in the system is very limited. To meet this important need, our team embarked on the design of a eukaryotic 2N decoder, an essential improvement in our ability to process biological information.

A 2N decoder is a circuit capable to produce 2N different outputs using only N different inputs arranged in different combinations. Our circuit was specially designed for implementation in plant cells, as we propose plant seeds as the best suited chassis to operate our design for practical purposes. Moreover, the circuit is fed by optogenetic control elements, a choice that enables remote operation of the system using light pulses. This is AladDNA, a device capable to store information and decode it very efficiently in order to make it accessible even in the most remote places. Have a look inside our circuit and click here!

The feasibility of AladDNA design was tested by in silico modeling showing a great operative capability. The system has a high resolution power between products with ratios from 100 to 105 a.u. between each one. If you want to see the hide beauty of AladDNA click here!

Figure 1. Schematic design of our biological circuit decoder.

Once the modeling was complete and the circuit was validated, each of the control elements were assayed by transient expression in plant cells of the Nicotiana benthamiana species. The circuit is initiated by two light-controlled switches, one controlled by red/far-red lights and a second one controlled by violet/cyan pulses. Later recombinase-based checkpoints were introduced to as secondary memory switches. The implementation of light-controlled switches was tested using the luciferase assay and the recombinase checkpoints were tested using equivalent fluorescent reporters. Seedlings from different species were also grown and transiently transformed in order to have an idea of the most suitable implementation chassis. The final winner of the competition was spinach! Do you want to know more about what we get? Click here!

AladDNA provides a portable solution for the production of medicines in remote areas. We did a research of biologics that could work as AladDNA outputs. Then we decided to produce: (i) A neutralizing antibody against rotavirus, the first cause of diarrhea in low income countries; (ii) Lactoferrin, a component of human immune system able to reduce the pneumonia, the first cause of deaths in undeveloped countries.; (iii) Interferon, a drug usually use for hepatitis treatment which is still a matter of public health concern; and finally, (iv) a cholera vaccine, a drug needed mostly after natural disasters.

In order to make decoding of the information as user-friendly as possible and to assure that our project can easily reach isolated areas, we also designed a decoding device that allows to grow seeds anywhere anytime. Our Genie Lamp is a small bioreactor able to irradiate seeds with the required inputs of lights in order to produce the desired compound. See more about our magic lamp

Figure 2. Our device, the magic lamp. Inside is the genie that will make your wishes to come true.

We were aware that our circuit was very ambitious, and summer was too short. Mounting all biological parts together in a single circuit was probably unrealistic. But this did not stop us. We decided to create another reality, one were time is not a constraint and plants grow in a matter of seconds: we decided to create a virtual world with a virtual laboratory… in Minecraft. We created SynBioCraft.

In SynBioCraft we can develop our project as well as many other projects in silico. It is not only a tool to recreate a laboratory, you can actually make your DNA assemblies in a termocycler, transform your constructions, pick colonies and much more. SynBioCraft is also an important part of or Policy and Practices effort, a Computer Game that youngsters (and not that much so) around the world can play to learn the basics of Synthetic Biology. So play with us: let´s produce a cholera vaccine before your live is over by the disease. Take your constructions, and prepare yourself for what is going to happen! If you want to know more about our AladDNA mod click here