GMU:Synthetic Biology/Bacteria Game: Difference between revisions

Latest revision as of 11:14, 31 October 2010

Bacteria Game is part of the Synthetic Biology project which entered into the 2010 iGem competition.

Bacteria Game

"Is our game playing the rules of evolution?"

Created by Lorenz Adlung, Andreas Beyer, Matthias Breuer, Prof. Ursula Damm and Frank C. Kieschnick

Product Description

Bacteria Game box contents

The Bacteria Game is a simple all-in-one kit to let homegrown bacteria compete against each other. March in lockstep with nature, breed your own creatures and become coach of your very own athletes. Simply use the included breeding kit to raise your own team and challenge your friends.

Included is everything you need to start instantly:

Petri dishes
Bacteria starter set (bacteria culture, agar, toothpicks)
2 Game scenarios
Different Game objects (barriers, forts)

Use the agar to build different landscapes and as a nutrient for your creatures. Inoculate your team on the agar and watch the game begin. Use the included game objects to evolve your team.

Race

Below is an example of a recorded race between two strains of Escherichia coli bacteria using the Bacteria Game kit supplied via the SuperCell online store which allows you to race home-bred bacteria. <videoflash type=vimeo>16214526|640|360</videoflash>

Technical Desciption

Arctic race game scenario

The concept of the game is based on the ability of some harmless wild-type bacteria to swim in soft media. Swimming enables the microbes to consume further nutrients if those in their vicinity are already consumed. All bacteria try to get away from the starting point as fast as possible to access fresh media. This mechanism can be employed for a game set-up. Selection and culturing of best swimmers leads to propagation of ideal swimming characteristics, which is why training may help gain a competitive edge. These bacteria can easily be stored in the fridge along with the supplied materials without any risk. The showdown competition is run by synthetic bacteria. Predators and prey communicate and regulate each other's density. Via molecular signals, the predator cells kill the prey while living prey rescues predators. The diverse and colorful crowd surrounding the spectacle was genetically engineered to carry different pigments, which was appreciated at the iGEM competition in 2009.

Our bacteria in motion

While developing the game we also experimented with a synthetic predator-prey system and other types of bacteria which got recorded.

Thanks go to Dr. Ilka Bischof-Pfeifer who kindly provided the videos. <videoflash type=vimeo>16245346|320|240</videoflash> <videoflash type=vimeo>16248328|320|240</videoflash> <videoflash type=vimeo>16245555|320|240</videoflash> Even more videos can be found on Vimeo.

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-= Bacteria Game - How to =
+Bacteria Game is part of the [[GMU:Synthetic_Biology|Synthetic Biology project]] which entered into the [http://2010.igem.org/Team:Weimar-Heidelberg_Arts 2010 iGem competition].
-Prepare the '''agar''' with '''nutrient powder''' and fill it up with water, following the enclosed protocols. '''Boil''' the media in your microwave until the mixture turns clear and the seems to be completely dissolved. Let it cool down to approx. 50°C. Plates for the challenge have to be '''poured''' with 35 ml. The mixture can be supplied with antibiotics and inducers. Feel free to establish your own procedures. It turned out to be most precisely to inoculate by carefully pipetting 3 μl of '''liquid culture''' into the '''solidified''' agar. Nevertheless, swarm plates can also be inoculated by transferring a bacteria colony using a tooth-pick which can found in the game kit. Swarm plates are ordinarily '''incubated''' at room temperature.
+[[Image:Bacteriagame-title.jpg|right|thumb|250px|Bacteria Game]]
-<br/>
+==Bacteria Game==
-''E. coli'' cells with a functional chemotactic system swarm (= “swim”) on soft agar plates.
+<blockquote>'''"Is our game playing the rules of evolution?"'''</blockquote>
-The field of '''chemotaxis''' is perspicuously defined. Studies deal with migration depending on chemicals. To be more precise: cells '''sense''' the presence of diverse substances in their environment and respond to gradients of chemical attractants or repellents by moving. The bacteria spread radially due to the attractant gradients formed by '''metabolizing''' the different nutrients in the agar.
+Created by Lorenz Adlung, Andreas Beyer, [[Matthias Breuer]], [[Ursula Damm|Prof. Ursula Damm]] and Frank C. Kieschnick
-'''Swimming''' of the cells can be described as a '''biased random walk''' in a '''spatial gradient''' of media. The microbe runs in favorable directions towards high concentrations of '''attractant''' (i. e. nutrient) and away from '''repellents''' (i. e. antibiotic). Straight '''runs''' are only interrupted by '''short tumbles''' where the cell reorients randomly for the next run. The probability for tumbling increases with higher repellent concentrations. Likewise the tumbling frequency rises during runs down attractant gradients (see figure below). As a result, the cell almost swims along curly '''trajectories'''.
+<br clear="both"/>
-<br/>
+===Product Description===
-Limitations
+[[Image:Bacteriagame-boxshot-1.jpg|right|thumb|250px|Bacteria Game box contents]]
-* “culturing” / “breeding” meaning selection of best swarmers
+The Bacteria Game is a simple all-in-one kit to let homegrown bacteria compete against each other. March in lockstep with nature, breed your own creatures and become coach of your very own athletes. Simply use the included breeding kit to raise your own team and challenge your friends.
-** evolutionary effect on molecular level (i. e. signal network properties)
-* training effect has to be experimentally determined, since it is still unknown here
+Included is everything you need to start instantly:
-<blockquote>''“I am as free as nature first made man,<br />
+* Petri dishes
-Ere the base laws of servitude began,<br />
+* Bacteria starter set (bacteria culture, agar, toothpicks)
-When wild in woods the noble savage ran.”''<ref>http://en.wikipedia.org/wiki/Noble_savage#Origin_of_term</ref></blockquote>
+* 2 Game scenarios
+* Different Game objects (barriers, forts)
-===The Migration of Destiny (more than a bacteria game)===
+Use the agar to build different landscapes and as a nutrient for your creatures. Inoculate your team on the agar and watch the game begin. Use the included game objects to evolve your team.
-====Concept====
+<br clear="both"/>
-Charles Darwin developed his work "The origin of species" on a long journey.
-The sight of thitherto unknown landscapes and their respective flora and fauna enabled him to develop a general and formal concept of formation and development of the same – the evolutionary follow-up of Nature.
-We have developed a game play that enables us to observe bacteria on their journey through different landscapes. Our landscapes are made from agar and small samples of bacteria can be put into them by means of a pipette.
-There, one can observe in detail how landscapes may influence the behaviour and development of organisms (manifold landscape -> biodiversity?).
-In our game, we are not only creators of the lands and territories, but we are also creators of species that live there.
+===Race===
-In our game, synthetically optimized organisms meet their natural ancestors. Players may observe throughout several generations how this encounter develops.
+Below is an example of a recorded race between two strains of Escherichia coli bacteria using the Bacteria Game kit supplied via the [http://super-cell.org/shopping/product-21/ SuperCell online store] which allows you to race home-bred bacteria.
-The appropriate selection of barriers, bridges and fortifications makes it possible to individually influence the events. On the basis of their respective colours, one can recognize which bacteria live longest and which bacteria strains move fastest. All the time, it is up to the players if they prefer to build pretty landscapes or raise lissom bacteria which compete against each other in special arenas.
+<videoflash type=vimeo>16214526|640|360</videoflash>
+===Technical Desciption===
+[[Image:Bacteriagame-artic-race.jpg|right|thumb|250px|Arctic race game scenario]]
+The concept of the game is based on the ability of some harmless wild-type bacteria to swim in soft media. Swimming enables the microbes to consume further nutrients if those in their vicinity are already consumed. All bacteria try to get away from the starting point as fast as possible to access fresh media. This mechanism can be employed for a game set-up. Selection and culturing of best swimmers leads to propagation of ideal swimming characteristics, which is why training may help gain a competitive edge. These bacteria can easily be stored in the fridge along with the supplied materials without any risk. The showdown competition is run by synthetic bacteria. Predators and prey communicate and regulate each other's density. Via molecular signals, the predator cells kill the prey while living prey rescues predators. The diverse and colorful crowd surrounding the spectacle was genetically engineered to carry different pigments, which was appreciated at the iGEM competition in 2009.
+<br clear="both"/>
+====Our bacteria in motion====
+While developing the game we also experimented with a synthetic predator-prey system and other types of bacteria which got recorded.
-[[File:IGEM_bgame_petri.jpg|700px|petri dishes: procaryotic civilization?]]
+Thanks go to Dr. Ilka Bischof-Pfeifer who kindly provided the videos.
+<videoflash type=vimeo>16245346|320|240</videoflash>
+<videoflash type=vimeo>16248328|320|240</videoflash>
+<videoflash type=vimeo>16245555|320|240</videoflash>
+Even more videos can be found on [http://vimeo.com/user4731954/videos Vimeo].
-====Setting====
+===Links===
-A culture dish is the habitat and arena for the bacteria, consisting of coloured nutritious agar on the one hand, and transparent liquid agar on the other hand. In the liquid agar (the “oceans”), the bacteria move quickly; in the viscous food (the “continents”) they act more statically. Spatially confined from these areas, there are “fortresses” with gates and bridges. By means of a pipette and samples from various bacteria strains, this miniature world may come alive. <br />
+* [http://super-cell.org/shopping/product-21/ SuperCell] online store
-Some of the bacteria are wild (wild type ''E. coli''), others rather not - in fact, they are even very disciplined and (mostly) do what they are programmed to do. <br />
+* [http://2010.igem.org/Team:Weimar-Heidelberg_Arts/Project/Bacteria_Game iGem 2010 competition entry]
-The synthetically cultivated bacteria are initially kept in fortresses (forts), separated from the surrounding landscape. Within these fortresses, these bacteria are - behind safety glass and fences - optimized as a predator-and-prey system - potent and highly efficient agents. Everything unimportant is kept away from them, their world only consists of hunting and eating to survive. The predator starves to death if there is no prey.<br />
+* [http://vimeo.com/user4731954/videos Our Bacteria Videos] on Vimeo
-Around the fortress extend varied landscapes which are inhabited by “indigenous” wild bacteria. Some of those can be discriminated by their pigment colors. <br />
-Normally, the Wild and the Civilized live on separate continents. We – the creators of this world - may now open the gates of the fortress / the borders of the continents. <br />
-What will happen when both meet?<br />
-Will the hunters have advantages compared with their peaceful conspecifics?
-What will happen when prey meets peaceful bacteria. Who will consolidate their future? How colorful will this future be?<br />
-By transferring the bacteria to new culture dishes with new fortresses and territories again and again, the further development of the bacteria may be modified and diversified.
-====Further planning====
-Design of a “game set” with a petri dish, samples from wild type bacteria (non-glowing ''E. coli'' and glowing ''Photobacterium spec.''), tooth picks, small modular bricks to build fortresses in the dish, a construction manual for the fortresses, a small quantity of agar, nutrients to mix with the agar and a set with three dishes for people who want to inoculate their bacteria for training purposes. <br />
-Competition between different wild type strains could be placed everywhere since there is no S1 safety condition required for that. Players could meet each other wherever they want. Swarming could be even more challenging at different temperatures (swarm matches: home and away, evolved bacteria at the edge of a swarm ring will be collected for next match - “never change a winning stream”). One could also think about a kind of championship for synthetic bacteria in a special “arena” (located in an S1 Lab).
-<references />