Latest revision as of 03:52, 22 October 2009

Brainstorming

The brainstorming for our team started at the beginning of June, 2009. All the team members racked their brains and we have come up with many exciting ideas during this process. We mainly focused on developing engineered bacteria that can benefit our society and promote human health. A list of ideas that we came up with during our brainstorming sessions is provided below.

Mosquito-repelling bacteria

Bacteria that can kill mosquitoes or expel mosquitoes away by releasing some 'anti-mosquito' chemicals and thus can be used to reduce malaria. The engineered bacteria can be distributed to malaria-afflicted area and control the population of the malaria-bearing mosquitoes. We need to manipulate the existing metabolic pathway of bacteria to produce organic repellent such as N,N-Diethyl-meta-toluamide, or DEET in abbreviation. Alternatively, we can also introduce metabolic pathways that enable bacteria to generate mosquito attracting chemical as well as mosquitoe killing agents. However, we found out that this is quite a comprehensive project and we only have 3 months! We decided to follow this project after the iGEM.

Bacteria radio

Bacteria conjugated with nanotubes that can sense the electromagnetic waves and thus wirelessly-controllable. It would be awesome if we were able to wirelessly control a bacterium! We can implant these wireless controlled 'robots' into the human body and guide them to do the cleaning work and even release therapeutic agents according to our design. Researchers at [http://www.physics.berkeley.edu/research/zettl/projects/nanoradio/radio.html UC Berkeley] have successfully developed a nanotube radio using carbon nanotube as the antenna. We want to incorporate the nanotube into our bacteria by conjugating it with a surface protein. When electromagnetic wave arrives at the nanotube, it will produce high frequency mechanical vibration on the nanotube and the signal will be transmitted to the linked protein, causing changes in its conformation. A signal-transduction pathway can be constructed to achieve intracellular amplification of the signal and the bacterium will produce further biochemical response. It is an amazing idea; but owing to the time limit and the difficulties , we have to give up and move on to a more do-able idea.

Bacteria arm

Bacteria connected at ends to form a chain so that their movements are synchronized. Single-cell bacteria like E. coli swim on their own. It will be great if we can organize a bunch of bacteria into a chain or a matrix and synchronize their movements to generate large enough forces to power other devices. The function of this bacteria arm is also implicated in our ‘bacteria signaling chain’ mentioned below.

Desalinating bacteria

Bacteria that can neutralize acidic soil or can convert soluble salts into insoluble precipitation by releasing ions. This will be extremely helpful as China is suffering severe loss of arable soil due to salinization. However, we would have to find a huge energy source for the bacteria to savage a large land area.

Bacteria with toggle switch

Oscillating system that can emanate light with alternating wavelengths. As this project involves a lot of modeling, it is naturally appreciated by people from physics major in our team. However, the project does not have as many potential applications on human health as do our other ideas. In fact, some of our instructors pointed out that in order to achieve an apparent oscillation, the experimenting conditions must be fine-tuned, which would consume a lot of time.

Bacteria calculator

Bacteria that contain molecular logic circuits that can count numbers.

Engineered Cell Memory

Cholera toxins can permanently ribosylate the Gs alpha subunit of the heterotrimeric G protein, resulting constitutive cAMP production (Wikipedia). We wanted to engineer a mammalian cell that can express cholera toxin when given external stimuli (the information we want to store). As mentioned above, the expressed cholera can induce constitutive cAMP production, which is a rather common intermediate step that appears in many signal transduction pathways. This will enable us to exploit a variety of signaling mechanism originally in the cell to achieve the function of memory.

Methane-consuming bacteria

Bacteria that can survive in the stomachs of livestock and convert methane, which is a greenhouse gas, to other compounds with a higher boiling point. The largest methane emissions come from the decomposition of wastes in landfills, ruminant digestion and manure management associated with domestic livestock. We would like to engineer strains of bacteria that can convert the greenhouse gases produced in the rumen of livestock to non-gaseous compound. This requires that the bacteria can survive the acidic enteric environment and colonize in the rumen of livestock. However, this project, similar to the idea of mosquito-repelling bacteria, implicates the manipulation of bacteria’s metabolic pathway. It is rather challenging for us to finish it within 3 months.

Bacteria signalling chain

Construct a chain of bacteria that are conjugated with each other at the ends and use light as the signal. The signals will be produced by luciferase and received by bacteriorhodopsin. Light is produced by the oxidation of luciferin. If we confine this light-emanating protein to one end of the bacterium and install a light-sensing bacteriorhodopsin at the closely-apposed end of another bacterium, luminescence can function as a signal between these bacteria. We only have to couple the changes brought by the bacteriorhodopsin to the cell to the oxidation of luciferase.

When we decide our final goals from a long list of ideas, we took into account the following considerations:

The project has to be do-able within 3 months. We have to have some results to present in the Jamboree!
The project has to have far-reaching implications for the future society.
The project must sound interesting and attract viewer's attention.

We finally chose 'Bactomotor' as our final project. This project, as described in our Wiki, can have great implications for our society in terms of energy utilization. Our Bactomotor can generate forces by metabolizing nutrition in its living environment with a high efficiency. The cost of obtaining clean mechanical energy is only a minuscule amount of glucose!

The brainstorming process is a valuable experience for our team. As everyone has to find sufficient evidence to support his own idea, we got a lot to read and we learned a lot!

@@ Line 4: / Line 4: @@
 =Brainstorming=
-The brainstorming for our team started at the beginning of June. All the team members racked their brain and we have come up with a heap of ingenous ideas during this process. We mainly focused on developing engineered bacteria that can help tackle some of the most troublesome problems our society faces and that can promote the human health.
+The brainstorming for our team started at the beginning of June, 2009. All the team members racked their brains and we have come up with many exciting ideas during this process. We mainly focused on developing engineered bacteria that can benefit our society and promote human health. A list of ideas that we came up with during our brainstorming sessions is provided below.
-The list of ideas generated during our brainstorming session go as follows.
 ====Mosquito-repelling bacteria====
-Bacteria that can ward off mosquitoes by releasing some 'anti-mosquito' chemicals and thus can be used to reduce malaria. The engineered bacteria can be distributed to malaria-afflicted area and control the population of the malaria-bearing mosquitoes. We need to manipulate the existing metabolic pathway of E.coli to make the bacteria produce organic repellent such as DEET. Alternatively, we can also introduce metabolic pathways that can generate mosquito repelling chemical into the bacteria. However, we found out that this project is a quite involved one and we only have 3 months! We decided to follow this project after the iGEM.
+Bacteria that can kill mosquitoes or expel mosquitoes away by releasing some 'anti-mosquito' chemicals and thus can be used to reduce malaria. The engineered bacteria can be distributed to malaria-afflicted area and control the population of the malaria-bearing mosquitoes. We need to manipulate the existing metabolic pathway of bacteria to produce organic repellent such as N,N-Diethyl-meta-toluamide, or DEET in abbreviation. Alternatively, we can also introduce metabolic pathways that enable bacteria to generate mosquito attracting chemical as well as mosquitoe killing agents. However, we found out that this is quite a comprehensive project and we only have 3 months! We decided to follow this project after the iGEM.
 ====Bacteria radio====
-Bacteria conjugated with nanotubes that can sense the electromagnetic waves and thus wirelessly-controllable. This idea is proposed by Brooks. Imagine how awesome it is to be able to wirelessly control a bacterium! We can then implant these nano-scale robots into the human body and let them do the cleaning work or release therapeutic agents according to our will. Researchers at Berkeley have successfully developed a nanotube radio using carbon nanotube as the antenna. (http://www.physics.berkeley.edu/research/zettl/projects/nanoradio/radio.html) We firstly want to incorporate a nanotube used by Berkeley researchers into our bacteria by binding it to a surface-expressed protein. When the EM waves arrive at the nanotube, it will induce high frequency mechanical vibration of the nanotube, and the vibration is conducted to the linking protein causing changes in its conformation. We can then construct a signal-transduction pathway that can achieve intracellular amplification of the signal and react correspondingly. It is an amazing idea; but owing to the time limit, we have to give up and move on to the next idea!
+Bacteria conjugated with nanotubes that can sense the electromagnetic waves and thus wirelessly-controllable. It would be awesome if we were able to wirelessly control a bacterium! We can implant these wireless controlled 'robots' into the human body and guide them to do the cleaning work and even release therapeutic agents according to our design.  Researchers at [http://www.physics.berkeley.edu/research/zettl/projects/nanoradio/radio.html UC Berkeley] have successfully developed a nanotube radio using carbon nanotube as the antenna. We want to incorporate the nanotube into our bacteria by conjugating it with a surface protein. When electromagnetic wave arrives at the nanotube, it will produce high frequency mechanical vibration on the nanotube and the signal will be transmitted to the linked protein, causing changes in its conformation. A signal-transduction pathway can be constructed to achieve intracellular amplification of the signal and the bacterium will produce further biochemical response. It is an amazing idea; but owing to the time limit and the difficulties , we have to give up and move on to a more do-able idea.
-====Bacteria chain====
+====Bacteria arm====
-Bacteria connected at ends to form a chain so that their locomotion is synchronized. Single-cell bacteria like E.coli swim on their own. It will be great if we can tie up a bunch of bacteria into a chain and synchronize their locomotion to generate large enough forces to power other devices. Also, the function of this bacteria chain is also implicated in our ‘bacteria signaling chain’ mentioned below.
+Bacteria connected at ends to form a chain so that their movements are synchronized. Single-cell bacteria like ''E. coli'' swim on their own. It will be great if we can organize a bunch of bacteria into a chain or a matrix and synchronize their movements to generate large enough forces to power other devices. The function of this bacteria arm is also implicated in our ‘bacteria signaling chain’ mentioned below.
 ====Desalinating bacteria====
-Bacteria that can neutralize acidic soil by releasing ions.
+Bacteria that can neutralize acidic soil or can convert soluble salts into insoluble precipitation by releasing ions. This will be extremely helpful as China is suffering severe loss of arable soil due to salinization. However, we would have to find a huge energy source for the bacteria to savage a large land area.
 ====Bacteria with toggle switch====
-Oscillating system that can emanate light with alternating wavelengths. As this project involves a lot of modeling, it is naturally appreciated by physics majors in our team. However, the project serves mainly as an experimental demonstration of some beautiful differential equations; it doesn’t have as many implications of human health as do our other ideas. In fact, some of our instructors pointed out that in order to achieve an apparent oscillation, the experimenting conditions must be finely tuned and consumes a lot of time.
+Oscillating system that can emanate light with alternating wavelengths. As this project involves a lot of modeling, it is naturally appreciated by people from physics major in our team. However, the project does not have as many potential applications on human health as do our other ideas. In fact, some of our instructors pointed out that in order to achieve an apparent oscillation, the experimenting conditions must be fine-tuned, which would consume a lot of time.
 ====Bacteria calculator====
-Bacteria that contains molecular logic circuits that can count numbers.
+Bacteria that contain molecular logic circuits that can count numbers.
 ====Engineered Cell Memory====
-Cholera toxin can permanently ribosylate the Gs alpha subunit of the heterotrimeric G protein, resulting constitutive cAMP production (Wikipedia). We originally wanted to engineer a mammalian cell that can express cholera toxin when given external stimuli (the information we want to store). As mentioned above, the expressed cholera can induce constitutive cAMP production, which is a rather common intermediate step that appears in many signal transduction pathways. This enables us to exploit a variety of signaling mechanism originally in the cell to achieve the function of memory.
+Cholera toxins can permanently ribosylate the Gs alpha subunit of the heterotrimeric G protein, resulting constitutive cAMP production (Wikipedia). We wanted to engineer a mammalian cell that can express cholera toxin when given external stimuli (the information we want to store). As mentioned above, the expressed cholera can induce constitutive cAMP production, which is a rather common intermediate step that appears in many signal transduction pathways. This will enable us to exploit a variety of signaling mechanism originally in the cell to achieve the function of memory.
 ====Methane-consuming bacteria====
-Bacteria that can survive in the stomachs of livestock and convert methane, which is a grennhouse gas, to other compounds with a higher boiling point. It is reported by Lerner et al. in 1998  that the largest methane emissions come from the decomposition of wastes in landfills, ruminant digestion and manure management associated with domestic livestock, natural gas and oil systems, and coal mining. We would like to engineer a strain of bacteria that can convert the greenhouse gases produced in the rumen of livestock during digestion to non-gaseous compound. This requires that the bacteria can survive the acidic enteric environment. However, this project, similar to the idea of mosquito-repelling bacteria, implicates the manipulation of bacteria’s metabolic pathway. It is rather challenging for us to finish it within 3 months.
+Bacteria that can survive in the stomachs of livestock and convert methane, which is a greenhouse gas, to other compounds with a higher boiling point. The largest methane emissions come from the decomposition of wastes in landfills, ruminant digestion and manure management associated with domestic livestock. We would like to engineer strains of bacteria that can convert the greenhouse gases produced in the rumen of livestock to non-gaseous compound. This requires that the bacteria can survive the acidic enteric environment and colonize in the rumen of livestock. However, this project, similar to the idea of mosquito-repelling bacteria, implicates the manipulation of bacteria’s metabolic pathway. It is rather challenging for us to finish it within 3 months.
-====Bactomotor====
-Our current project.
 ====Bacteria signalling chain====
-Construct a chain of bacteria that are conjugated with each other at ends and use light as the signal. The signal is produced by luciferase and received by rhodopsin.
+Construct a chain of bacteria that are conjugated with each other at the ends and use light as the signal. The signals will be produced by luciferase and received by bacteriorhodopsin. Light is produced by the oxidation of luciferin. If we confine this light-emanating protein to one end of the bacterium and install a light-sensing bacteriorhodopsin at the closely-apposed end of another bacterium, luminescence can function as a signal between these bacteria. We only have to couple the changes brought by the bacteriorhodopsin to the cell to the oxidation of luciferase.
 ----
 When we decide our final goals from a long list of ideas, we took into account the following considerations:
-# The project has to be do-able within 3 months. We have to have some results to demonstrate on the Jamborree!
+# The project has to be do-able within 3 months. We have to have some results to present in the Jamboree!
 # The project has to have far-reaching implications for the future society.
 # The project must sound interesting and attract viewer's attention.
-We finally chose 'Bactomotor' as our final project. This project,as described in our wiki, can have great implications for our soceity in terms of energy utilization. Our Bactomotor can generage forces by metabolizing nutrition in its living environment with a high efficiency. The cost of obtaining clean mechanical energy is only a minuscule amount of glucose!
+We finally chose 'Bactomotor' as our final project. This project, as described in our Wiki, can have great implications for our society in terms of energy utilization. Our Bactomotor can generate forces by metabolizing nutrition in its living environment with a high efficiency. The cost of obtaining clean mechanical energy is only a minuscule amount of glucose!
 The brainstorming process is a valuable experience for our team. As everyone has to find sufficient evidence to support his own idea, we got a lot to read and we learned a lot!
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Team:HKU-HKBU/Brainstorming

From 2009.igem.org