Team:Groningen/Brainstorm

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Latest revision as of 17:25, 26 October 2010

Brainstorm

We invite you to browse through the clouds of thoughts and have a look at all of our ideas that have not made it. We hope our thoughts will not go waste, but will inspire other teams to come up with many more creative and fun ideas. Some ideas were thoroughly elaborated and considered while others were obviously not feasible.

Health

Chemotaxis and bacterial conjugation Many bacteria use chemotaxis to move toward, or away from, chemoattractants and chemorepellents. If we could invert this system in pathogenic bacteria it would decrease their ability to infect their host. To spread this inversion mechanism through a population of bacteria we could make use of conjugation plasmids. These plasmids facilitate their own transfer form one bacteria to another and can also carry resistance genes spreading antibiotic resistance. We could create a conjugation plasmid that also carries genes that somehow cause this inversion. Also involving chemotaxis and bacterial conjugation, a conjugation plasmid that disrupts chamotaxis by inducing a constant tumble (no linear movement). At the same time this plasmid could carry a gene for a chemoattractant that would attract more bacteria to the immobilized bacteria. The plasmid is then transferred to these bacteria, starting a chain reaction.

Diet bacteria. Bacteria that live in the guts and consume large quantities of unhealthy nutrients like saturated fats, cholesterol or sugars converting them to substances that can’t be taken up by the body. These bacteria would be eaten by adding them to foods like to yoghurt.

Colon Cancer detecting bacteria MscL (Mechanoselective channels of Large conductance) have been modified to be light and pH sensitive (A. Koçer, 2007). I think we can use this mechanism for the detection of cancerous cells, which have a lower pH in their microenvironment when compared to normal cells. The bacteria (for cancer in the GI tract) could then secrete some sort of detectable marker. Lipid bodies could be used for detection in the rest of the body.

Bacteria that stimulate production of vital minerals in plants Maybe it would be possible to make bacteria that would interact with plants in a symbiotic manner, supplying the plant with high amounts of metabolites that are important for the production of vitamins in the plant. In exchange for these metabolites they plant will maintain the energy needs of the bacteria by supplying them with sugars from photosynthesis. This would be similar to the interaction that plants already have with some nitrogen fixating bacteria. These plant would be much more nutritional than normal crops.

Environmental

Bacterial solar cells Making a multistage solar energy converter using the battery bacteria of the havard team of 2008, by using three groups bacteria. The first would perform photosynthesis storing the solar energy in to simple metabolites like sugars. The second bacteria using these sugars to convert them into the specific nutrients the Harvard bacteria need. Last the Harvard bacteria would convert the products of the second metabolites into electricity. Using Photosynthesis to produce energy in the form of electrons or pH gradient of some sort to transport the energy out of the cell to a circuit (http://adsabs.harvard.edu/abs/1980ises.conf....2S , http://www.ks.uiuc.edu/Highlights/?section=2002&highlight=2002-08)

Deacidifying bacteria The acidification in the oceans due to the high levels of co2 in the air have become a threat to lots of marine life especially coral reefs that are largely made of calcium and are threaded to dissolve in the increasingly acidic oceans. Bacteria with pH sensitive channels (MscL) sensing acidity and that are able to produce a base to counterbalance the acidification.

Bacteria that do not produce methane to replace methanogen bacteria in cow's rumen Isolated microbes in the animal's stomach which allows them to eat grass and plants but without producing the flatulence common to European livestock. Even though kangaroos have a similar system for utilising plants to sheep and cattle, they have evolved independently over many millions of years and so the microbes are extremely different. Rather than produce methane, kangaroos produce acetate which aids digestion.

Oil spill response - Bacteria cleaning it up. After oil spills the oil which is not removed mechanically is mostly degraded by bacteria (bioremediation) so far only adding fertilizer seems to help, the addition of living bacteria has mostly not shown any effect. I can think of three ways to use bacteria in order to improve bioremediation, 1: Nitrogen fixing bacteria could be added instead of fertilizer, Nitrogen fixing bacteria already exist, but I don’t know if they can life in oily environments. 2. Bacteria which can metabolize the compounds which so far can not be degraded by bacteria 3. Bacteria which are actually better at degrading oil than existing ones ( I have however no clue how that could be achieved) 1&3 would enhance speed, 2 would improve endpoint which has so far not been attempted (at least not from what I have read) -[http://www.nature.com/nrmicro/journal/v4/n3/abs/nrmicro1348.html Marine micro-organisms make a meal out of oil], [http://publicfiles.dep.state.fl.us/DEAR/Oil_Spill/Technical%20Information/Bioremediation%20and%20Dispersant%20Literature/Field%20Evaluations%20of%20Marine%20Oil%20Spill%20Biorem.pdf Field evaluation of marine oil spill bioremediation](Very long but also very complete review about the topic)

Restore gulf stream pump once it breaks down We could try to construct a bacterial pump. This is how it looks in my head: bacteria or something the like which float (sinking could also be possible) change the density of the surrounding media by metabolism of oily substances to sugar or something the now denser media would then sink, sucking fresh media as it goes. Maybe this wont safe the gulf stream but in a bioreactor it might work

plastic degrading bacteria(micro plastic degrading bacteria) Several bacteria and fungi are involved in degrading natural and synthetic plastics. First, polymers are broken down to monomers, these monomers are mineralized further (to CO2, H2O and CH4). This review shows a table with all known micro-organisms and the plastics that they can degrade with references. Biological degradation of plastics: A comprehensive review - Aamer Ali Shah, et al., Biotechnology Advances 26 (2008) 246–265. On the other hand, plastic (PHA) producing bacteria can be very interesting for medical applications (fixation and orthopaedic applications) Bacillus subtilis as potential producer for polyhydroxyalkanoates - Mamtesh Singh et al., Microbial Cell Factories 2009, 8:38

Technological

Biofilm insulating bacteria Having bacteria grown in a biofilm on a building producing a some sort of porous vacuoles or gas vesicles which will give air insulation to the building thereby lowering heating and cooling costs.

Timer bacteria A simple protein clock (can be done using positive (auto-receptive) feedback loops). Can be useful for a lot of things. Like self-destruction or the smell of coffee in the morning. (If one would repress the expression of a gene essential for cell growth with a substance that is degraded by the cell itself, you could tell your cells when to start growing. This would prevent me from coming to the lab tonight for example. If a second similar clock existed to start the expression of another gene after the cells grew for some time (or before they start, or switches off after some time or whatever you want), you could set up whole protein expression experiments and the like at once.

Molecular fishing rod Using the Biotin – Avidin connection bacteria could maybe be bound to a surface or the like. The bacteria could express biotin or avidin to the surface (the bricks exist) at a certain metabolic state, on command, as long as they are alive, when you flash them with light… and then be fished out of the solution with a device coated with Biotin or avidin.

Radio wave bacteria Using magnetized components, like Neodynium an earth indigenous magnetic substance, and some sort of rotary mechanism attached (possibly like the bacterial flagellum) it can be possible to rotate a magnet around another magnetized pole. By modulating the frequency(by controlling the rotation speed) this effectively creates an FM signal.

Bacterial camera If bacteria with photosensitive receptors are properly laid out in a grid it can be possible to create a rudimentary camera. If the photoreceptors trigger a signal which sets in motion a cascade to a measurable effect. Measurable effects can be increased expression of a specific gene (slow), the opening of certain membrane channels (through second messenger systems) or the activation of certain proteins.

Biological Computer The area of research in biological computing is increasing and opens waves of new possibilities into the miniaturization of computers. All research in the area shares the same basic idea: DNA is a perfect carrier of data and the expression of genes into proteins provides enormous possibilities for calculation (as life itself demonstrates). Two kinds of research can be discriminated (superficially): The utilization of bacterial colonies which perform calculations by setting in motion signaling processes(Conway's Game of Life being an example of the more general principle of Cellular Automata) and the utilization of signals cells as computers by designing mechanisms to store and retrieve data in the form of proteins or other molecules. While not a 'readymade' project, with sufficient interest in the subject this can be a very exciting summer! (Conway's Game of Life seems like a interesting thing to do, even though we probably won't be able to raise the dead, systems that simulate this behaviour might be possible, does anyone know if there is cells that organize in a strict pattern that can be grown in a dish? (We probably won't toy with tissues even though any honest scientist has to admit that a brain in a jar would be ultimate victory, especialy if it was wondering if it might just be a brain in a jar:) I know that fungi have very definitive structures, maybe this could be tinkered with

Biological Anti freeze Bacteria which produce anti frost agent, induced by low temperatures, the agent could be degraded if temperatures rise again.

Air refreshener Ideal situation: the bacterium would take up CO2 (just so that problem will also become less :P) and release some nice smelling, non-toxic compound (maybe vanilla)

Bacterial (gas) filter (previously gas pump) Have bacteria in some sort of rigid structure (like a platinum / magnesium plate with microscopic pores) and produce some … this is is very bad idea, now that I'm writing it. The original train of thought of thought was as follows: create vesicles susceptible to a certain gas on one side of the bacteria and having the vesicles transported through the other side and releasing them(using a re-uptake mechanism for the vesicles). Effectively creating a selectively permeable gas filter. This is however a bad idea because gas diffuses and it's next to impossible to find a structure that is both selective and non-porous to gasses. On top of that coordinating the movement of the vesicles through the dense packed inner world of a bacterium is a project in itself. Amongst other reasons (size/controlling the expressed location of the entry / exit points).

Bacteria creating (carbon) nanotubes. While microscopic structures in cells are not uncommon (think neuronal axons and other micro tubulea) the mass production of nano tubes is still tedious. However they do play a major part in most of nanotechnology advances. Having bacteria to produce them and then being able to harvest them (without breaking the structures) would be a good idea. Also carbon nanotubes can conduct electricity (outer-layer electron movement?) which might provide chances of more tight integration of silicon-based computers and bacterial systems.

Alcohol content control by apoptosis Right now alcohol content is controlled either by sugar availability, alcohol cytotoxicity, or manual killing of the yeast at a certain alcohol level (the idea could be applied to other fermentation products as well). It would be useful to have a system in which you could decide beforehand to which degree the yeast will grow, this could be done by getting the yeast to recognize a certain ratio between alcohol and a second substance and kill themselves once that ratio is reached. By dosing that second substance it could be determined when the yeast starts killing itself and hence the final alcohol level.

Seismo detecting bacteria(sound detecting bacteria) Mechanical pressure sensitive bacteria. Two ideas: colony sensing bacteria, if most of them die in a certain area the pressure must be great. This can be done by having all bacteria release a simple chemical, if concentration drops beyond a certain threshold trigger a signal. Other idea, completely different scale: use the fact that bacteria can change shape (to some extend). Position a specific receptor on the outer membrane, position a donor at a known distance from the receptor. This creates an auto-receptive system with known concentrations (taking into account diffusion) in the loop. If the distance between the receptor and the donor changes (due to changes in the bacteria shape) the concentration changes which can be used in a cascade towards other signals. Effectively creating a mechanical pressure sensor.

Miscellaneous, Fun

Synthetic communities Synthetically design an microbial consortium of different types of bacteria that have facilitating or symbiotic interactions with one another, creating a communities that sustains itself.

Bacterial lamp There are these bacteria found on fish that have luminescence. During a practical course some people had to acquire a pure culture of this bacterium from fish bought at the market. There was something about that if you put a culture of these bacteria in a large tube and flip it upside down (thus making oxygen bubbles) making the bacteria illuminate. Maybe we could make this into some kind of biological lamplight.

Bacteria changing the taste of yogurt Bacteria that can change the taste of yoghurt (over a period of time) so that you don't know which taste that yoghurt has at the moment. Or that the bacteria change it per period of the the day, so that you have "breakfast" yoghurt in the morning and "dessert" yoghurt in the evening

Smelling (coffee) bacteria responsive to circadian rythm Cells which react to a long period of darkness (night) followed by light (the sensors for light exist so this should be possible) produce either smell of coffee or caffeine (your blanket as a biofilm so you absorbe it) to assure a gentle awakening

Detect bad milk bacteria bad milk turns sour, so all you would need is a bacterium that would show us that the pH of the milk has gone below a certain value. It could show this by changing colour. The bacteria would have to be separated from the milk in order to not spoil it though. A stripe like the coolness indicator on beer cans would warn you if the milk is bad.

Detection of movement A system consisting of two organisms, a) Bacteria and b) a creature able to move over solid surface (Amoeba, nematode, snail…). The bacteria would cover the ground (agar plate) completely and would detect the organism moving over them, either by a chemical which this organism releases or by pressure, depending on size of the moving agent pressure might not work, and start to produce a fluorescent or color signal hence leaving a mark of the organisms way .Using chemotaxis the organisms could be sent through a maze or be steered in order to gain world domination.

The tron version of movement detection In addition to a color or fluorescence marker the bacteria also produce a repellent for the used organism. This will hinder the organism of crossing its own path or the path of another “Player”. Which basically is what Tron does. For all sorry souls who have never played it: http://gamepuma.com/action-games/Tron.html

@@ Line 1: / Line 1: @@
-{{Team:Groningen/Header}}
+__NOTOC__
-==current brainstorming (12 march 2010)==
+== Brainstorm ==
--Food: loose weight consumes fat and chlorestorial
+We invite you to browse through the clouds of thoughts and have a look at all of our ideas that have not made it. We hope our thoughts will not go waste, but will inspire other teams to come up with many more creative and fun ideas. Some ideas were thoroughly elaborated and considered while others were obviously not feasible.
-We could design probiotic bacteria (Like that useless Actimel crap but useful!! Imagine that!!1!) which are destined to waste a certain amount of calories. They would be eaten added to yoghurt or the like (In contrast to Actimel we could even make it tasty). So lets say for some reason you feel like not becoming a diabetic or a heart attack victim, you just compensate all the extra calories by munching our genetically modified never tested on animals or the like bacteria which we only have a vague idea of what they might do and TARAAA! Technology beats nature… again. The easiest would be to get the bacteria to produce something that can’t be digested in the intestines like fat or even better, a substance that smells good (for obvious reasons) After a while the indigenous bacteria will outcompete our sissy lab bacteria and everything is back to normal –Ramon Sieber
+===Health===
--Biodegradable fabric: good & green
+'''Chemotaxis and bacterial conjugation'''
+Many bacteria use chemotaxis to move toward, or away from, chemoattractants and chemorepellents. If we could invert this system in pathogenic bacteria it would decrease their ability to infect their host. To spread this inversion mechanism through a population of bacteria we could make use of conjugation plasmids. These plasmids facilitate their own transfer form one bacteria to another and can also carry resistance genes spreading antibiotic resistance. We could create a conjugation plasmid that also carries genes that somehow cause this inversion.
+Also involving chemotaxis and bacterial conjugation, a conjugation plasmid that disrupts chamotaxis by inducing a constant tumble (no linear movement). At the same time this plasmid could carry a gene for a chemoattractant that would attract more bacteria to the immobilized bacteria. The plasmid is then transferred to these bacteria, starting a chain reaction.
--Fertilizing Gounds: cactus, nitrogen fixing compatible to all plants
+'''Diet bacteria.'''
+Bacteria that live in the guts and consume large quantities of unhealthy nutrients like saturated fats, cholesterol or sugars converting them to substances that can’t be taken up by the body. These bacteria would be eaten by adding them to foods like to yoghurt.
--Bacteria -> Colon Cancer DETECTION
+''' Colon Cancer detecting bacteria'''
+MscL (Mechanoselective channels of Large conductance) have been modified to be light and pH sensitive (A. Koçer, 2007). I think we can use this mechanism for the detection of cancerous cells, which have a lower pH in their microenvironment when compared to normal cells. The bacteria (for cancer in the GI tract) could then secrete some sort of detectable marker. Lipid bodies could be used for detection in the rest of the body.
--Laundry machine -> encymes producing bacteria for washing machines
+'''Bacteria that stimulate production of vital minerals in plants'''
+Maybe it would be possible to make bacteria that would interact with plants in a symbiotic manner, supplying the plant with high amounts of metabolites that are important for the production of vitamins in the plant. In exchange for these metabolites they plant will maintain the energy needs of the bacteria by  supplying them with  sugars from photosynthesis. This would be similar to the interaction that plants already have with some nitrogen fixating bacteria. These plant would be much more nutritional than normal crops.
--Sponge - ISOLATION
+=== Environmental===
--biological Anti freeze so it can detect temperature change and unfreeze for example the car window.
+'''Bacterial solar cells'''
+Making a multistage solar energy converter using the battery bacteria of the havard team of 2008, by using three groups bacteria. The first would perform photosynthesis storing the solar energy in to simple metabolites like sugars. The second bacteria using these sugars to convert them into the specific nutrients the Harvard bacteria need. Last the Harvard bacteria would convert the products of the second metabolites into electricity.
+Using Photosynthesis to produce energy in the form of electrons or pH gradient of some sort to transport the energy out of the cell to a circuit (http://adsabs.harvard.edu/abs/1980ises.conf....2S , http://www.ks.uiuc.edu/Highlights/?section=2002&highlight=2002-08)
--Bacteria to reduce air pollution
+'''Deacidifying bacteria'''
+The acidification in the oceans due to the high levels of co2 in the air have become a threat to lots of marine life especially coral reefs that are largely made of calcium and are threaded to dissolve in the increasingly acidic oceans. Bacteria with pH sensitive channels (MscL) sensing acidity and that are able to produce a base to counterbalance the acidification.
-Biological Computer. The area of research in biological computing is increasing and opens waves of new possibilities into the miniaturization of computers. All research in the area shares the same basic idea: DNA is a perfect carrier of data and the expression of genes into proteins provides enormous possibilities for calculation (as life itself demonstrates). Two kinds of research can be discriminated (superficially): The utilization of bacterial colonies which perform calculations by setting in motion signaling processes(Conway's Game of Life being an example of the more general principle of Cellular Automata) and the utilization of signals cells as computers by designing mechanisms to store and retrieve data in the form of proteins or other molecules. While not a 'readymade' project, with sufficient interest in the subject this can be a very exciting summer! (Joël)
+'''Bacteria that do not produce methane to replace methanogen bacteria in cow's rumen'''
+Isolated microbes in the animal's stomach which allows them to eat grass and plants but without producing the flatulence common to European livestock. Even though kangaroos have a similar system for utilising plants to sheep and cattle, they have evolved independently over many millions of years and so the microbes are extremely different. Rather than produce methane, kangaroos produce acetate which aids digestion.
-(Conway's Game of Life seems like a interesting thing to do, even though we probably won't be able to raise the dead, systems that simulate this behaviour might be possible, does anyone know if there is cells that organize in a strict patern that can be grown in a dish? (We probably won't toy with tissues even though any honest scientist has to admit that a brain in a jar would be ultimate victory, especialy if it was wondering if it might just be a brain in a jar:) I know that fungi have very definitive structures, maybee this could be thinkered with -Ramon Sieber)
+'''Oil spill response - Bacteria cleaning it up.'''
+After oil spills the oil which is not removed mechanically is mostly degraded by bacteria (bioremediation) so far only adding fertilizer seems to help, the addition of living bacteria has mostly not shown any effect. I can think of three ways to use bacteria in order to improve bioremediation, 1: Nitrogen fixing bacteria could be added instead of fertilizer, Nitrogen fixing bacteria already exist, but I don’t know if they can life in oily environments.
+. Bacteria which can metabolize the compounds which so far can not be degraded by bacteria 3. Bacteria which are actually better at degrading oil than existing ones ( I have however no clue how that could be achieved) 1&3 would enhance speed, 2 would improve endpoint which has so far not been attempted (at least not from what I have read) -[http://www.nature.com/nrmicro/journal/v4/n3/abs/nrmicro1348.html Marine micro-organisms make a meal out of oil], [http://publicfiles.dep.state.fl.us/DEAR/Oil_Spill/Technical%20Information/Bioremediation%20and%20Dispersant%20Literature/Field%20Evaluations%20of%20Marine%20Oil%20Spill%20Biorem.pdf Field evaluation of marine oil spill bioremediation](Very long but also very complete review about the topic)
+'''Restore gulf stream pump once it breaks down'''
+We could try to construct a bacterial pump. This is how it looks in my head: bacteria or something the like which float (sinking could also be possible) change the density of the surrounding media by metabolism of oily substances to sugar or something the now denser media would then sink, sucking fresh media as it goes. Maybe this wont safe the gulf stream but in a bioreactor it might work
--Oil spill responce - Baceria cleaning it up.
+'''plastic degrading bacteria(micro plastic degrading bacteria)'''
+Several bacteria and fungi are involved in degrading natural and synthetic plastics. First, polymers are broken down to monomers, these monomers are mineralized further (to CO2, H2O and CH4). This review shows a table with all known micro-organisms and the plastics that they can degrade with references. Biological degradation of plastics: A comprehensive review - Aamer Ali Shah, et al., Biotechnology Advances 26 (2008) 246–265.
+On the other hand, plastic (PHA) producing bacteria can be very interesting for medical applications (fixation and orthopaedic applications) Bacillus subtilis as potential producer for polyhydroxyalkanoates - Mamtesh Singh et al., Microbial Cell Factories 2009, 8:38
-After oil spills the oil which is not removed mechanically is mostly degraded by bacteria (bioremediation) so far  only adding fertilizer seems to help, the addition of living bacteria has mostly not shown any effect. I can think of three ways to use bacteria in order to improve bioremediation, 1: Nitrogen fixing bacteria could be added instead of fertilizer, Nitrogen fixing bacteria already exist, but I don’t know if they can life in oily environements. 2. Bacteria which can metabolize the compounds which so far can not be degraded by bacteria 3. Bacteria which are actually better at degrading oil than existing ones ( I have however no clue how that could be achived)
+===Technological===
-&3 would enhance speed, 2 would improve endpiont which has so far not been attempted (at least not from what I have read)
-''-Marine microorganisms make a meal out of oil, nature reviews 2006''
-''-Field evaluation of marine oil spill bioremediation, microbial reviews 1996'' (Very long but also very complete review about the topic)
--Ramon Sieber
--Detecting clusters of bacteria
+'''Biofilm insulating bacteria'''
+Having bacteria grown in a biofilm on a building producing a some sort of porous vacuoles or gas vesicles which will give air insulation to the building thereby lowering heating and cooling costs.
--Synthetic biomolecules on synthetic biomolecules
+'''Timer bacteria'''
+A simple protein clock (can be done using positive (auto-receptive) feedback loops). Can be useful for a lot of things. Like self-destruction or the smell of coffee in the morning. (If one would repress the expression of a gene essential for cell growth with a substance that is degraded by the cell itself, you could tell your cells when to start growing. This would prevent me from coming to the lab tonight for example. If a second similar clock existed to start the expression of another gene after the cells grew for some time (or before they start, or switches off after some time or whatever you want), you could set up whole protein expression experiments and the like at once.
-Radiowave bacteria. Using magnetized components, like Neodynium an earth indigenous magnetic substance, and some sort of rotary mechanism attached (possibly like the bacterial flagellum) it can be possible to rotate a magnet around another magnetized pole. By modulating the frequency(by controlling the rotation speed) this effectively creates an FM signal.(Joël)
+'''Molecular fishing rod'''
+Using the Biotin – Avidin connection bacteria could maybe be bound to a surface or the like. The bacteria could express biotin or avidin to the surface (the bricks exist) at a certain metabolic state, on command, as long as they are alive, when you flash them with light… and then be fished out of the solution with a device coated with Biotin or avidin.
+'''Radio wave bacteria'''
+Using magnetized components, like Neodynium an earth indigenous magnetic substance, and some sort of rotary mechanism attached (possibly like the bacterial flagellum) it can be possible to rotate a magnet around another magnetized pole. By modulating the frequency(by controlling the rotation speed) this effectively creates an FM signal.
--bacteria changing the taste of yogurt
+'''Bacterial camera'''
+If bacteria with photosensitive receptors are properly laid out in a grid it can be possible to create a rudimentary camera. If the photoreceptors trigger a signal which sets in motion a cascade to a measurable effect. Measurable effects can be increased expression of a specific gene (slow), the opening of certain membrane channels (through second messenger systems) or the activation of certain proteins.
--making a bacterial community( to mimic the interaction between bacteia in real world)
+'''Biological Computer'''
+The area of research in biological computing is increasing and opens waves of new possibilities into the miniaturization of computers. All research in the area shares the same basic idea: DNA is a perfect carrier of data and the expression of genes into proteins provides enormous possibilities for calculation (as life itself demonstrates). Two kinds of research can be discriminated (superficially): The utilization of bacterial colonies which perform calculations by setting in motion signaling processes(Conway's Game of Life being an example of the more general principle of Cellular Automata) and the utilization of signals cells as computers by designing mechanisms to store and retrieve data in the form of proteins or other molecules. While not a 'readymade' project, with sufficient interest in the subject this can be a very exciting summer!
-Bacterial camera. If bacteria with photosensitive receptors are properly laid out in a grid it can be possible to create a rudimentary camera. If the photoreceptors trigger a signal which sets in motion a cascade to a measurable effect. Measurable effects can be increased expression of a specific gene (slow), the opening of certain membrane  gates (through second messenger systems) or the activation of certain proteins. (Joël)
+(Conway's Game of Life seems like a interesting thing to do, even though we probably won't be able to raise the dead, systems that simulate this behaviour might be possible, does anyone know if there is cells that organize in a strict pattern that can be grown in a dish? (We probably won't toy with tissues even though any honest scientist has to admit that a brain in a jar would be ultimate victory, especialy if it was wondering if it might just be a brain in a jar:) I know that fungi have very definitive structures, maybe this could be tinkered with
+'''Biological Anti freeze'''
+Bacteria which produce anti frost agent, induced by low temperatures, the agent could be degraded if temperatures rise again.
--UV detected bacteria
+'''Air refreshener'''
+Ideal situation: the bacterium would take up CO2 (just so that problem will also become less :P) and release some nice smelling, non-toxic compound (maybe vanilla)
--bacteria that has a capable of altering one type of aa to another or producing essential amino acid
+'''Bacterial (gas) filter (previously gas pump)'''
+Have bacteria in some sort of rigid structure (like a platinum / magnesium plate with microscopic pores) and produce some … this is is very bad idea, now that I'm writing it. The original train of thought of thought was as follows: create vesicles susceptible to a certain gas on one side of the bacteria and having the vesicles transported through the other side and releasing them(using a re-uptake mechanism for the vesicles). Effectively creating a selectively permeable gas filter. This is however a bad idea because gas diffuses and it's next to impossible to find a structure that is both selective and non-porous to gasses. On top of that coordinating the movement of the vesicles through the dense packed inner world of a bacterium is a project in itself. Amongst other reasons (size/controlling the expressed location of the entry / exit points).
--molecular fishing rod
+'''Bacteria creating (carbon) nanotubes.'''
+While microscopic structures in cells are not uncommon (think neuronal axons and other micro tubulea) the mass production of nano tubes is still tedious. However they do play a major part in most of nanotechnology advances. Having bacteria to produce them and then being able to harvest them (without breaking the structures) would be a good idea. Also carbon nanotubes can conduct electricity (outer-layer electron movement?) which might provide chances of more tight integration of silicon-based computers and bacterial systems.
-Using the Biotin – Avidin connection bacterias could maybee ( I don’t know how strong that connection really is, but it is the strongest at hand) be bound to a surface or the like. The bacteria could express biotin or avidin to the surface (the bricks exist) at a certain metabolic state, on command, as long as they are allive, when you flash them with light or whatever… and then be fished out of the solution with a device coated with Biotin or avidin.
+'''Alcohol content control by apoptosis'''
--Ramon Sieber
+Right now alcohol content is controlled either by sugar availability, alcohol cytotoxicity, or manual killing of the yeast at a certain alcohol level (the idea could be applied to other fermentation products as well). It would be useful to have a system in which you could decide beforehand to which degree the yeast will grow, this could be done by getting the yeast to recognize a certain ratio between alcohol and a second substance and kill themselves once that ratio is reached. By dosing that second substance it could be determined when the yeast starts killing itself and hence the final alcohol level.
+'''Seismo detecting bacteria(sound detecting bacteria)'''
+Mechanical pressure sensitive bacteria. Two ideas: colony sensing bacteria, if most of them die in a certain area the pressure must be great. This can be done by having all bacteria release a simple chemical, if concentration drops beyond a certain threshold trigger a signal. Other idea, completely different scale: use the fact that bacteria can change shape (to some extend). Position a specific receptor on the outer membrane, position a donor at a known distance from the receptor. This creates an auto-receptive system with known concentrations (taking into account diffusion) in the loop. If the distance between the receptor and the donor changes (due to changes in the bacteria shape) the concentration changes which can be used in a cascade towards other signals. Effectively creating a mechanical pressure sensor.
--biofilm color
+===Miscellaneous, Fun===
--Detection of movement
+'''Synthetic communities'''
+Synthetically design an microbial consortium of different types of bacteria that have facilitating or symbiotic interactions with one another, creating a communities that sustains itself.
-A system consisting of two organisms, a) Bacteria and b) a creature abel to move over solid surface (Amoeba, nematode, snail…) . The bacteria would cover the ground (agar plate) completely and would detect the organism moving over them, either by a chemical which this organism releases or by pressure, depending on size of the moving agent pressure might not work, and start to produce a fluorescent or colour signal hence leaving a mark of the organisms way (I know snails do that anyway but…)
+'''Bacterial lamp'''
-Using chemotaxis the organisms could be sent through a maze or be steered in order to gain world domination.
+There are these bacteria found on fish that have luminescence. During a practical course some people had to acquire a pure culture of this bacterium from fish bought at the market. There was something about that if you put a culture of these bacteria in a large tube and flip it upside down (thus making oxygen bubbles) making the bacteria illuminate. Maybe we could make this into some kind of biological lamplight.
-- The tron version of movement detection
+'''Bacteria changing the taste of yogurt'''
+Bacteria that can change the taste of yoghurt (over a period of time) so that you don't know which taste that yoghurt has at the moment. Or that the bacteria change it per period of the the day, so that you have "breakfast" yoghurt in the morning and "dessert" yoghurt in the evening
-In addition to a colour or fluorescence marker the bacteria also produce a repellent for the used organism. This will hinder the organism of crossing its own path or the path of another “Player”. Which basically is what Tron does. For all sorry souls who have never played it:
+'''Smelling (coffee) bacteria responsive to circadian rythm'''
-http://gamepuma.com/action-games/Tron.html
+Cells which react to a long period of darkness (night) followed by light (the sensors for light exist so this should be possible) produce either smell of coffee or caffeine (your blanket as a biofilm so you absorbe it) to assure a gentle awakening
--Ramon Sieber
+'''Detect bad milk bacteria'''
+bad milk turns sour, so all you would need is a bacterium that would show us that the pH of the milk has gone below a certain value. It could show this by changing colour. The bacteria would have to be separated from the milk in order to not spoil it though. A stripe like the coolness indicator on beer cans would warn you if the milk is bad.
--restore gulf stream pump once it breakes down
+'''Detection of movement'''
+A system consisting of two organisms, a) Bacteria and b) a creature able to move over solid surface (Amoeba, nematode, snail…). The bacteria would cover the ground (agar plate) completely and would detect the organism moving over them, either by a chemical which this organism releases or by pressure, depending on size of the moving agent pressure might not work, and start to produce a fluorescent or color signal hence leaving a mark of the organisms way .Using chemotaxis the organisms could be sent through a maze or be steered in order to gain world domination.
-We could try to construct a bacterial pump. This is how it looks in my head: bacteria or something the like which float (sinking could also be possible) change the density of the sourounding media by metabolism of oily substances to sugar or somethinng (Someone who knows chemistry is welcome to help) the now denser media would then sink, sucking fresh media as it goes. Maybee this wont safe the gulf stream but in a bioreactor it might work –Ramon Sieber
+'''The tron version of movement detection'''
+In addition to a color or fluorescence marker the bacteria also produce a repellent for the used organism. This will hinder the organism of crossing its own path or the path of another “Player”. Which basically is what Tron does. For all sorry souls who have never played it: http://gamepuma.com/action-games/Tron.html
--anti-rust bacteria
--anti-anxiety bacteria
--anti-acidification bacteria for ocean
--maleria repelling bacteria
--smelling (coffee) of circadian rythm bacteria
-Cells which react to a long period of darkness (night) followed by light (the sensors for light exist so this should be possible) produce either smell of coffe or caffein (your blanket is a biofilm so you absorbe it) to assure a gentle awakening –Ramon Sieber
-Timer bacteria. A simple protein clock (can be done using positive (auto-receptive) feedback loops). Can be useful for a lot of things. Like self-destruction or the smell of coffee in the morning.(Joël)
-(If one would repress the expression of a gen essential for cell growth with a substance that is degraded by the cell itself, you could tell your cells when to start growing. This would prevent me from coming to the lab tonight for example. If a second similiar clock existed to start the expression of another gene after the cells grew for some time (or before they start, or switches off after some time or wathever you want), you could could set up whole protein expression experiments and the like at once. I would have killed for such an organism during my bachelorthesis - Ramnb Sieber)
--spore eating bacteria
--detect bad milk bacteria
--biofilm insulating bacteria (bacteria  cover the building)
--two component gene made by bacteria stolling factor
--vitamine rich food , nice tasting food
-==IGEM Meeting(15.03.2010)==
--anti-hangover bacteria
--quit smoking bacteria
--plactic degrading bacteria(microplastic degrading bacteria)
--caffeine producing bacteria
-Bacterial (gas) filter (previously gas pump). Have bacteria in some sort of rigid structure (like a platinum / magnesium plate with microscopic pores) and produce some … this is is very bad idea, now that I'm writing it. The original train of thought of thought was as follows: create vesicles susceptible to a certain gas on one side of the bacteria and having the vesicles transported through the other side and releasing them(using a re-uptake mechanism for the vesicles). Effectively creating a selectively permeable gas filter. This is however a bad idea because gas diffuses and it's next to impossible to find a structure that is both selective and non-porous to gasses. On top of that coordinating the movement of the vesicles through the dense packed inner world of a bacterium is a project in itself. Amongst other reasons (size/controlling the expressed location of the entry / exit points). (Joël)
--bacteria against the skin disease
--bioglue
--melanin production stimulating baceria
-Bacteria creating (carbon) nanotubes. While microscopic structures in cells are not uncommon (think neuronal axons and other micro tubulea) the mass production of nano tubes is still tedious. However they do play a major part in most of nanotechnology advances. Having bacteria to produce them and then being able to harvest them (without breaking the structures) would be a good idea. Also carbon nanotubes can conduct electricity (outer-layer electron movement?) which might provide chances of more tight integration of silicon-based computers and bacterial systems. (Joël)
--flying and ozone producing bacteria
--Alcohol content controll by apoptosis
-Right now alcohol content is controlled either by sugar availability, cytotoxicity, or manual killing of  the yeast at a certain alcohol level (the idea could be applied to other fermentation products as well). It would be usefull to have a system in which you could decide beforehand to which degree the yeast will grow, this could be done by getting the yeast to recognize a certain ratio between alcohol and a second substance and kill themselves once that ratio is reached. By dosing that second substance it could be determined when the yeast starts killing itself and hence the final alcohol level. - Ramon Sieber
--seismo detecting bacteria(sound detecting bacteria)
-Mechanical pressure sensitive bacteria. Two ideas: colony sensing bacteria, if most of them die in a certain area the pressure must be great. This can be done by having all bacteria release a simple chemical, if concentration drops beyond a certain threshold trigger a signal (production of GFP/RFP maybe). Other idea, completely different scale: use the fact that bacteria can change shape (to some extend). Position a specific receptor on the outer membrane, position a donor at a known distance from the receptor. This creates an auto-receptive system with known concentrations (taking into account diffusion) in the loop. If the distance between the receptor and the donor changes (due to changes in the bacteria shape) the concentration changes which can be used in a cascade towards other signals. Effectively creating a mechanical pressure sensor. (Joël)
--glitter bacteria
--sparkling  bacteria
--caffeine biobrick
--cake degrading bacteria
-- Anti-body binding bacteria: for numerous functions, targeted that is
-@Home ideas (Maarten):
--Make bacteria produce a certain compound (like a pigment) which you'll want to apply to a surface of some sort. Let them first produce it cytosolic and then let them secrete it by a light sensitive channel.
-These channels are the MscL (Mechanoselective channels of Large conductance) and have been modified to be light and pH sensitive in stead (A. Koçer, 2007). I think we can use this mechanism for several for our ideas, e.g. biofilm paint and the detection of cancerous cells, which have a lower pH when compared to normal cells. The bacteria (for cancer in the GI tract) could then secrete some sort of detectable marker. Lipid bodies could be used for detection in the rest of the body.
--Bacteria that import vitamins or minerals and inject them into plant cells to make them more nutritional.
-(Djoke):
--We also talked about bacteria which could function as solar cells or produce electricity because that sounded cool and is probably useful for something. They just found a deep sea consortium which does something like this. (Remember the paper I send: Nature, Vol 463, 25 February 2010). Martijn also mailed us al lot of info on this and the 2008 Harvard team made an bacterial battery.
--I also found a paper on magnetic bacteria (Nature nanotechnology, online 14 march 2010) which seemed really cool to me. As I got it, they overexpressed ironoxide in the cells and could then fish these cells out with a magnet. Cool selection tool right?
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