[Come and help the MIT and the humanity against this horrible plastic disappearance nightmare that is threatening the world as we know it!
Don’t wait anymore and try it! Click here to start the download.
*Research was done with RPGmaker VX. If you don’t have the program, you will need to download this archive in order to play our game.]

In Research you, a girl that has come to the MIT in order to participate in the iGEM competition, discover that the contest has been cancelled, and no one is giving you a reason for the hasty decision.
So, you make it your goal to find out what is the cause of this, and discover that something much more important than a contest is at stake: the world as we know it.

How does Research help to spread Synthetic Biology?

We wanted to motivate teenagers to get into Biology and in particular into Synthetic Biology. In order to do so, we have first to teach them about this new exciting area. Our problem here was: how to reach teenagers? We could visit schools or organize activities for them, like other iGEM teams have done. But we thought that the quantity of teenagers that is possible to reach by these means is small. This motivates us to search new methods of reaching them. One was the organization of the School diffusion through teachers: the other one was the generation of this game.
Nowadays a computer in a house is a must, and children, in general, spend a lot of time using and playing with them. So, the idea of a game was ideal: teenagers like to play games way more than learning. What if we could tell them about SynBio while they are playing?
A game has the advantage of being available for a wide spectrum of people through the Internet. It can spread easily with a link, it can be posted on the forums of RPG maker games, and people that like our game can help us promote it among their friends. This way, instead of reaching a small amount of teenagers, we could reach more people, even from out of our native country, Chile. With this objective in mind, we created the game both in Spanish as in English: Spanish was necessary for our own and other Latin American countries, and English was in order to be able to be played by anyone in the world who speaks it, independently of their own native language.

Spreading Research

In order to make our game famous, we put the Spanish version in the Internet on our own website www.igemuc.cl. We also create an English version that was uploaded on our iGEM webpage and on disemination english webpage. Since RPG maker is a game that only works on Windows OS, we investigated and were able to create a version compatible with Mac OS in both languages.
After this we start spreading the game: we wrote about it on our facebook and twitter, on RPGmaker forums, on facebook school pages, we spoke with our friends, family etc.
We also offer the diffusion of the game as a collaboration with other iGEM groups: if they advertised the game in at least four different internet groups with at least 50 people on everyone, they could get this medal as a prove of their collaboration.
We gave this medal to Teams TecMonterrey and Valencia_Biocampus. By the time of the wiki freeze, we have reached 440 people with the Spanish version. The English version wasn’t properly outreached due to lack of time: if we reach the jamboree at the MIT, we are going to distribute it all over the world!

In total, that means that 440 people know now about SynBio because of our game, and that only with Spanish native speakers! Who knows how much people are we going to be able to reach with our newly finished English version!.

Biology inside RESEARCH

WARNING: From now on you will be getting spoilers for the game.

The termites

The truth about Termites is that they aren’t able to eat wood, not without help. Inside them, specifically in their guts, live different microorganisms members of the families Bacteria, Archaea and Protozoa. Table I shows some of these microorganisms and the importance that they have to termites.

Microorganisms that live inside Termites and their characteristics
Genus, Species	Brief Descriptions/Functions of Microbes
Treponema	Swim freely in the gut or attached to the protist; acetogenic, carry out acetogenesis
Bacteroides, Bacteroides termitidis	Fermentative, acidogenic; increase N source by recycling uric acid waste
Desulfovibrio	Sulfate-reducing bacteria; transfer hydrogen as H₂ donor
Citrobacter, Citrobacter freundii, Enterobacter, Enterobacter agglomerans	Nitrogen-fixing bacteria
Enterococcus, Lactococcus	Lactic acid bacteria
Methanobrevibacter	Metanogens, associated with protists as symbionts; carry out metanogenesis and produce methane
Trichonympha, Mixotricha, Dinenympha, Euconomympha	Degrade endocytosed cellulose and produce H₂ plus CO₂. Anaerobic, occur on mitochondria in the cells

Information about Species that live inside Termites (1,2,3).

The termites that are attacking the MIT are Zootermopsis angusticollis, a type that live in several states of USA (4).
In Research, Termites have started to destroy plastic because of a random mutation inside one of its symbionts organisms:  The protozoa Trichonympha, one of the organisms in charge of degrading the cellulose that Termites bring inside their guts.
Termites are hard to kill, so in this hypothetical scenery, destroying them with normal insecticides wouldn’t be a definitive solution for this problem. Termites would probably resist the attacks of insecticides, and if we aren’t able to destroy them all, the plastic mutation would spread in a world that is plastic made, with the force of Darwinian evolution boosting it.
This is where Synthetic Biology appears.

Targeted microorganisms

The objective of the game is to eliminate the termites that have the mutated Protozoa, in order to save the world from the disappearance of plastic. As the termites are hard to kill, the target is the mutated protozoa, Trichonympha. But a protozoa itself is hard to kill, too. Should we try to attack the protozoa with toxic compounds? If it isn’t effective with termites, there is no reason to believe that is a good and effective strategy for Protozoa. Should we genetically modify them, in order to stop the mutation? But protozoa are eukaryotic, and because of that are hard and slow to modify. The answer Research gives to this problem is: treat this issue just as the old one. If the strategy was killing the protozoa in order to kill the termite, then kill the symbiont bacteria that lives in the surface of Trichonympha in order to kill the protozoa, and with this, kill the termite. It is also necessary to consider that the strategy used should be controlled enough in order to stop it when it is needed. The idea is to kill the termites that possess the mutated Protozoa; not the entire termite community, which could cause horrible imbalances in the ecosystem.
Treponema primitia, a spirochete, is an ectosymbiont of Trichonympha; “symbiont” because both organisms benefit the other with their mutual existence, in a way that if one of them are missing, the other will die, and “ecto”, because one of them lives in the surface of the other, in this case, the spirochete. This bacteria is in charge of giving the protozoa the characteristic appearance that grants the motility of Trichonympha. Without them, the protozoa loses its shape and cannot survive (5).

Synthetic Biology: how to get rid of the bacteria

How to kill the bacteria

When the target is defined, the next problem is: how to kill the spirochetes? The idea of phages appears easily. They are great at killing specific bacteria, and with a cocktail of diverse phages they can be very effective fighting against bacteria. The problem that this option has is how the phages would reach the gut of the termite. They would probably need a vector, and this complicates and slows the procedure. Also, phages can be very delicate, the reason why they failed as a medicine when D’Herelle discovered them in the 1900’s and tried to distribute them around the world, so they are not a good option to deal with T. primitia (6).

Colicins

Partregistry.org offers a solution for this problem:  In 2008, Team Heidelberg (7) created two biobricks related with the production of Colicins. These are toxins produced by Escherichia coli that act against related strains or species.
The biobricks contains: one of the two kinds of toxic colicins, the pore-forming or the nuclease, and two other types needed for the effectiveness of the colicins, the immunity protein, that protects the host from the nuclease effect of the colicins by a protein-protein interaction; and the lysis protein, that lysis the host in order to release the colicins.
In its natural state, the colicins genes are contained inside the plasmids pCOL and controlled by the promoter PSOS that responds to a variety of agents such as UV-light, physical agents and stress.
Team Heidelberg tells in its webpage:
“The immunity gene is under the regulation of two promoters, the PSOS of the colicin operon, and its own constitutive promoter that allows a constitutive production of the immunity protein. This ensures that there is no free colicin inside the cytoplasm, which would kill the host cell. The separated constitutive promoter is located within the structural gene of nuclease colicins. There is no immunity gene in operons encoding pore-forming (ionophoric) colicins: It is located on the opposite DNA strand of the intergenetic space between the colicin and the lysis structural gene and is transcribed from its own promoter under constitutive regulation. The last gene of the colicin operon encodes for the lysis protein, which is controlled by the same promoter as the colicin production. Due to the terminator localized downstream of the colicin gene, the lysis protein is expressed in lower amounts than the colicins. After reaching a certain threshold of lysis protein the host cell is lysed which leads to the release of colicins into the medium.”
Next figures shows the biobrick made by Team Heidelberg.

In Research, you need to gather the pieces of DNA that will form the recombinant plasmid, and all this while you are learning about synthetic biology.
The final structure of the plasmid is:
An inducible promoter  (Para) is needed in order to liberate the colicins inside the termite and no before. Tnos is the terminator. T7 is a strong constitutive promoter that is needed to express the immunity protein, in order to protect the host from the toxin while is producing it. The RBS used, the Ribosome Binding Site, belongs to the Anderson RBS family of partregistry (8). This is a constitutive RBS family that is suitable for prokaryotes, specially for E. coli. It could be chosen, for example, BBa_J61100.
To maximize the effectiveness of the process, a High copy plasmid is used.To get a fast response, you have to work with Escherichia coli: the model bacteria. It also is the bacteria that work best with the chosen biobricks.

System of recollection

After the decision of how to kill the spirochetes is taken, then another problem comes to attention. It is against every biosafety rule in the world to set free a recombinant bacteria into the environment. So, all the modified E. coli needs to go back to the pretri dishes they came from. In order to do this, partregistry.org has yet again the answer.

Magnetosome

There are different ways of attracting bacteria, like chemotaxis and quorum sensing. However, the fastest of them is magnetosomes (9). Magnetosomes are prokaryotic organelle-like invaginations of the cell membrane that contains a specific set of proteins that are able to direct the synthesis of a nanometer-sized magnetite crystal. The genetic information needed for this is contained in a well conserved region known as the magnetosome island, and is present in magnetotactic bacteria (10)
In Research, the biobrick that contains the proteins needed to generate a magnetosome [link al biobrick] is given inside the plasmid pGA1C3, ready to use, by the father of Synthetic Biology, Tom Knight. This is our way of honouring him.
pGA1C3 is a high copy plasmid with high Gibson Assembly efficiency, which has Chloramphenicol resistance. The promoter used is T7, constitutive in order to facilitate the recovering of the bacteria. The terminator is Tnos again, and the ribosome binding site is maintained too.

Recovering the bacteria

A giant magnet from the physics department is used to recover the modified bacteria that contains the magnetosome, which is attracted by electromagnetic force. The termites that contains the bacteria are attracted by the magnet too.