Team:UC Chile/Game
From 2013.igem.org
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- | <h4>How does Research help to spread Synthetic Biology?</h4 | + | <h4>How does Research help to spread Synthetic Biology?</h4> |
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- | <h4>Spreading Research</h4 | + | <h4>Spreading Research</h4> |
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 _________(web page of ivo). 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.<br> | 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 _________(web page of ivo). 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.<br> | ||
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.<br> | 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.<br> | ||
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<h3>Biology inside RESEARCH</h3><br> | <h3>Biology inside RESEARCH</h3><br> | ||
WARNING: From now on you will be getting spoilers for the game.<br><br> | WARNING: From now on you will be getting spoilers for the game.<br><br> | ||
- | <h4>The termites</h4 | + | <h4>The termites</h4> |
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.<br><br> | 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.<br><br> | ||
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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.<br> | 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.<br> | ||
This is where Synthetic Biology appears.<br><br> | This is where Synthetic Biology appears.<br><br> | ||
- | <h4>Targeted microorganisms</h4 | + | <h4>Targeted microorganisms</h4> |
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<h4>How to kill the bacteria</h4> | <h4>How to kill the bacteria</h4> | ||
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 <a href="#Referencias">(6)</a>.<br><br> | 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 <a href="#Referencias">(6)</a>.<br><br> | ||
- | <h4>Colicins</h4 | + | <h4>Colicins</h4> |
Partregistry.org offers a solution for this problem: In 2008, Team Heidelberg <a href="#Referencias">(7)</a> created two biobricks related with the production of Colicins. These are toxins produced by Escherichia coli that act against related strains or species.<br> | Partregistry.org offers a solution for this problem: In 2008, Team Heidelberg <a href="#Referencias">(7)</a> created two biobricks related with the production of Colicins. These are toxins produced by Escherichia coli that act against related strains or species.<br> | ||
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.<br> | 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.<br> | ||
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Team Heidelberg tells in its webpage:<br> | Team Heidelberg tells in its webpage:<br> | ||
<span class="cursiva">“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.”</span><br> | <span class="cursiva">“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.”</span><br> | ||
- | Next figures shows the biobrick made by Team Heidelberg. | + | Next figures shows the biobrick made by Team Heidelberg. |
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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.<br> | 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.<br> | ||
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- | <h3>System of recollection</h3> | + | <h3>System of recollection</h3><br> |
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.<br><br> | 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.<br><br> | ||
- | <h4>Magnetosome</h4 | + | <h4>Magnetosome</h4> |
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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.<br> | 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.<br> | ||
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.<br><br> | 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.<br><br> | ||
- | <h4>Recovering the bacteria</h4 | + | <h4>Recovering the bacteria</h4> |
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.<br><br> | 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.<br><br> | ||
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Revision as of 10:02, 27 September 2013
The Game
We thought that one of the most important groups to inform about Synthetic Biology was children and teenagers, since they will grow to be the scientists of tomorrow. We thought that a really good way to reach them was through a video-game.
The idea was to create a RPG game where you need to gather knowledge and information of Synthetic Biology in order to win. We made the game in Spanish and English to spread our message even further and the statistics up to this date says that ---people have played our game.
The idea was to create a RPG game where you need to gather knowledge and information of Synthetic Biology in order to win. We made the game in Spanish and English to spread our message even further and the statistics up to this date says that ---people have played our game.
[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.
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.]
What are those guys talking about so mysteriously? Discover it by playing!
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.
Spoiler Alert: continue reading under your own “risk”
∨
∧
What are threatening the world this time are not evil doctors, death lasers, the Everest meltdown or the sun approaching the Earth: is something much more common. Termites. But these are not normal termites: they are mutated insects that have evolved to reach the ability of eating plastic. In a world were plastic objects are everywhere, this capability is quite menacing, so defeating them is the mission that the main character of our game is going to face. She will have to find a way of fighting this bugs using Synthetic Biology and she will have to do it fast, before every plastic tube and plastic petri dishes disappear and stops her investigation from taking place.
By building different kind of genetic constructs in bacteria to be able to defeat the intrinsic prokaryotic organisms that live inside the termites, the player will learn about microbiology, molecular genetics and Synthetic Biology.
By building different kind of genetic constructs in bacteria to be able to defeat the intrinsic prokaryotic organisms that live inside the termites, the player will learn about microbiology, molecular genetics and Synthetic Biology.
How does Research help to spread Synthetic Biology?
Trapped inside a labyrinth! How to get out from it?
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.
Fly around the MIT!
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 _________(web page of ivo). 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 _________
By the time of the wiki freeze, we have reached ____ people with the spanish, that include people from Spain, Mexico, Argentina, Perú, and Chile.
From the English version, we have reached ____ people from countries like ___.
In total, that means that ____ people know about SynBio because of our game!
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 |
A termite, Zootermopsis angusticollis
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
Trichonympha, one of the protozoa that lives inside Zootermopsis angusticollis
Treponema primitia, a spirochete bacteria.
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.
Colicin E1 operon which contains a colicin with pore-forming activity.
Colicin E9 operon which contains a colicin with nuclease activity.
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
Formation of a magnetosome.
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.
References:
- 1. König, H., Varma, A. Intestinal microorganisms of termites and other invertebrates. Springer. United States, 1° Edition, 2006.
- 2. Ohkuma, M. (July 2008). “Symbioses of plagellates and prokaryotes in the gut of lower termites.” Trends in Microbiology. 2008, Vol. 16, N°7. Pp. 345-352. Available in:
www.sciencedirect.com/science/article/pii/S0966842X08001108 - 3. Adams, L., Boopathy, R. (September 2005). “Isolation and characterization of enteric bacteria from the hindgut of Formosan Termite.” Bioresource Technology. 2005, Vol. 96, N°14. Pp. 1592-1598. Available in:
http://www.sciencedirect.com/science/article/pii/S0960852405000313 - 4. University of Hawaii [internet principal page]. United States. Zootermopsis angusticollis. [consult day: may 3, 2013]. Available in:
http://www2.hawaii.edu/~entomol/glossary/definition_zootermopsis_angusticollis.htm - 5. Bignell, E., Roisin, Y. Biology of Termites: a Modern Synthesis. Springer. United States, 1° Edition, 2011.
- 6. Häusler, T. Viruses vs superbugs. Macmillan. United States, 1° Edition, 2008. Pp. 98-100.
- 7. iGEM, Team Heidelberg. [internet principal page]. United States. Colicins - Project description. [consult day: may 6, 2013]. Available in:
- 8. Parts Registry [internet principal page]. United States. Ribosome Binding Sites/Prokaryotic/Constitutive/Anderson. [consult day: may 6, 2013]. Available in:http://parts.igem.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Anderson
- 9. iGEM, Team Washington [internet principal page]. United States. iGEM Toolkits: magnetosomes. [consult day: may 6, 2013]. Available in:
https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit - 10. Murat, D., Quinlan, A. Vali, H., Komeili,A. (February 2010). “Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle.” Proceeding of the National Academy of Sciences of the United States of America, PNAS. 2010, Vol. 107, N°12. Pp. 5593-5598. Available in:
http://www.pnas.org/content/107/12/5593.long