"
Team:Imperial College London/Extras/Brainstorming/Energy/Others
From 2011.igem.org
(Created page with "{{:Team:Imperial_College_London/Templates/Banner}} <span id="Top"></span> {{:Team:Imperial_College_London/Templates/Menu}} {{:Team:Imperial_College_London/Templates/Brainstorming...") |
|||
| Line 1: | Line 1: | ||
| - | {{:Team:Imperial_College_London/Templates/ | + | {{:Team:Imperial_College_London/Templates/Header}} |
| - | + | ||
| - | + | ||
{{:Team:Imperial_College_London/Templates/BrainstormingTab4}} | {{:Team:Imperial_College_London/Templates/BrainstormingTab4}} | ||
| + | <html> | ||
| + | <body> | ||
| + | <a name="Top"></a> | ||
| + | <h1>Ideas</h1> | ||
| + | <p> | ||
| + | <a href="#Graphite">Synthetic Graphite</a><br /> | ||
| + | <a href="#Sand">Sand Brick Produced by Bacteria</a><br /> | ||
| + | <a href="#Termites">Termites</a><br /> | ||
| + | <a href="#Transform">New Way of Transforming Bacteria</a><br /> | ||
| + | <a href="#Tattoo">Bacterial Tattoo</a><br /> | ||
| + | <a href="#DNA">DNA Hard Drive</a><br /> | ||
| + | </p> | ||
| - | + | <h1><a name="Graphite">Synthetic Graphite</a></h1> | |
| - | + | <p>- Synthetic Graphite normally has a high electrical conductivity than the natural ones.</p> | |
| - | + | <p>- the process involves turning amorphous carbon into crystal under extremely high temperature.</p> | |
| - | + | <p>- no evidence shows that carbon(element) can be either iuput or output of bacterial metabolism.</p> | |
| - | + | <p>- therefore, we can pass this topic (Text by Nina)</p> | |
| + | <p><a href="#Top">Back to top</a></p> | ||
| - | + | <h1><a name="Sand">Sand Brick Produced by Bacteria</a></h1> | |
| + | <p>Sporosarcina pasteurii --> urease</p> | ||
| + | <p>Calcium carbonate bricks can be made by using urease, urea, sand and calcium chloride. The urease cleaves the urea and creates ammonia and carbon dioxide. The ammonia raises the pH and causes the calcium ions to precipitate with the dissolved carbonate ions.</p> | ||
| + | <p>Ammonia is currently a problem since it can run off to cause algal bloom. A method to remove ammonia must be obtained. Solution? Possibly express all the urea cycle enzymes in the chassis (5 total enzymes). Use slovenia's DNA scaffold so that the process does not produce too many possibly problematic intermediaries in the bacteria.</p> | ||
| + | <p>When should ammonia be converted back to urea? When calcium is depleted. Need some sort of Calcium sensor.</p> | ||
| + | <p><a href="http://www.msnbc.msn.com/id/32558231/ns/technology_and_science-science/t/study-bacteria-can-make-salt-water-drinkable/" rel="nofollow">http://www.msnbc.msn.com/id/32558231/ns/technology_and_science-science/t/study-bacteria-can-make-salt-water-drinkable/</a></p> | ||
| + | <p>So that's pretty cool, but perhaps the bacteria that store salt can be used to spread salt in the winter and stop the country grinding to a halt every time it snows? (Text by Frank)</p> | ||
| + | <p><a href="#Top">Back to top</a></p> | ||
| - | + | <h1><a name="Termites">Termites</a></h1> | |
| + | <p>Termites are known for their ability to digest nutritionally poor food sources such as lignocellulose. A recent paper has studied the synergistic properties of cellulases from Reticulitermes flavipes. Three enzymes were studied, two cellulases and a laccase. The cellulases were 1 β-glucosidase and Cell-1 (a GHF9 endoglucanase). The phenol-oxidizing laccase that is involved in lignin degradation is LacA.</p> | ||
| + | <p>Cell-1 and β-glu showed >300-fold and >70-fold increases in glucose production (when degrading pine sawdust and beechwood xylan) when combined. When Lac-6 was added in the pine saw-dust experiment, glucose production rate decreased. The authors say that this is likely due to the process of end-product inhibition on β-glu. However, glucose production increased when all three enzymes were used on beechwood xylan. Lac-6 enhances glucose release from hemicellulose by cellulases? Microcrystalline cellulose results were nearly identical to sawdust.</p> | ||
| + | <p>The idea of this project is to use bacteria to express Lac-6, β-glu and Cell-1 in order to produce monosaccharides from other sources of biomass such as wood. It has recently been discovered that these termite derived cellulases have synergetic properties. Therefore I postulate that future effective biomass conversion will rely on obtaining the most efficient mixtures of enzymes. Lignin (the material hardest to digest) releases pentoses (like xylose and arabinose). Since sawdust degradation by the three enzymes works best when only Cell-1 and β-glu are used whereas all three enzymes gave the largest production rate when degrading beechwood xylan, I propose the construction of a module that will allow the bacteria to produce the most efficient enzyme mixtures depending on the rate of glucose production. This circuit might make it possible to digest complex mixtures of materials most efficiently. The bacteria used should also ideally only use an alternative carbon source to glucose.</p> | ||
| + | <p><a href="#Top">Back to top</a></p> | ||
| - | + | <h1><a name="Transform">New Way of Transforming Bacteria</a></h1> | |
| + | <p>Create a plasmid containing Dpn1 under the influence of a strong repressor. In the same plasmid insert the methylase enzyme. The gene is inserted into the methylase and stops its transcription.</p> | ||
| + | <p>If the gene of interest has been successfully inserted into the plasmid and the plasmid has been successfully inserted into the bacteria we can use the inducer to kill off any bacteria that has not been transformed (because the Dpn1 cuts any methylated strands of DNA).</p> | ||
| + | <p>Today we continued developing the bile acid sensor as well as the idea of the anti-venom. For the anti-venom idea we talked to Travis Bayer and obtained a method for screening for the right mutants. We also had a visit from LSE BIOS members that taught us about the point points we should worry about in human practices. We were also given the task to make instructions for a lego structure to show us how difficult it is to standardize parts due to the difficulty of communicating more complicated instructions. (Text by Chris)</p> | ||
| + | <p><a href="#Top">Back to top</a></p> | ||
| - | + | <h1><a name="Tattoo">Bacterial Tattoo</a></h1> | |
| - | + | <p>- After being inspired by a student from the Royal College of Arts who presented us with her work on a project to create a living dress, Frank began to research the notion of a melanin tattoo, so that alpha-melanin stimulating hormone is applied to the skin and held in place until the skin darkens in the shape of the template. The alpha-MSH could be produced by bacteria.</p> | |
| - | + | <p>- the alpha-MSH gene is produced as one gene that also contains beta-MSH and gamma-MSH that are made available through post-transcriptional processing, so only the alpha-MSH region is required as it is the best characterised and has been expressed before</p> | |
| - | + | <p>- Once the alpha-MSH is expressed, it can be collected, soaked into silk (for example) that is cut into a pattern and will allow the hormone to diffuse into the skin, producing a (probably temporary) tattoo. From: <a href="http://en.wikipedia.org/wiki/Melanocyte-stimulating_hormone" rel="nofollow">http://en.wikipedia.org/wiki/Melanocyte-stimulating_hormone</a></p> | |
| - | + | <p>- However, it seems that alpha-MSH is a rather powerful aphrodisiac and so a different hormone will have to be chosen, in addition, it seems that the hormone is unlikely to penetrate the skin as there are many different layers as well as proteases secreted by the skin</p> | |
| + | <p>- alpha-MSH, or its analogues are already used as tanning solutions and the analogues are considerably stronger</p> | ||
| + | <p>- so then, bacteria could express the gene for melanotan - which is a cyclic lactyam analogue, and this will be very difficult to express, as a method will have to be found for cyclisation.</p> | ||
| + | <p>- One further problem: "As of 2010 no compound incorporating the melanotan II peptide has ever been approved for use by any governmental drug regulatory bodies outside of clinical trials. Unlicensed and untested powders sold as "melanotan II" are found on the Internet and are reported to be used by thousands of members of the general public. Multiple regulatory bodies have warned consumers the peptides may be unsafe and ineffective in usage with one regulatory agency warning that consumers who purchase any product labeled "melanotan" risk buying a counterfeit drug. Medical researchers and Clinuvel Pharmaceuticals, the company developing the related peptide afamelanotide, has warned consumers that counterfeit products sold using the names "melanotan I and II", "pose a hazard to public health"." From <a href="http://en.wikipedia.org/wiki/Melanotan" rel="nofollow">http://en.wikipedia.org/wiki/Melanotan</a></p> | ||
| + | <p>- alpha-MSH will have to be used, but this time with the novel method for crossing the skin: Transdermal iontophoresis. This is a non-invasive way for hydrophilic proteins to be transported across the skin but I do not know what kind of resolution is possible with this device. Whatever the pattern achieved, be it a nice dot or a blotted smudge, the students from the RCA will surely help to make it look pretty. (Text by Frank)</p> | ||
| + | <p><a href="#Top">Back to top</a></p> | ||
| - | - the | + | <h1><a name="DNA">DNA Hard Drive</a></h1> |
| + | <p>1. use DNA sequence as a medium to store information (DNA base - quaternary bit - original text)</p> | ||
| + | <p>2. put “tag in” information (i.e some specific base pairs as “prototypes”) to classify the information</p> | ||
| + | <p>3. writing functions in programming language with DNA sequences, use DNA as the function variables</p> | ||
| + | <p>- Sci-Fi ideas developed with RCA people:</p> | ||
| + | <p>a. in the future, a bacteria charm/necklace can be made to store and carry the information, such as exam syllabus, genetic disease history, family photos, etc</p> | ||
| + | <p>b. different coding methods and types of bacteria can be chosen by the clients for different levels of security needs ,(some high risky information can be store in Bacillus anthraci for military use)</p> | ||
| + | <p>c. data can also be stored in E.coli in the human digestive system, it can be erased by intaking antibiotics</p> | ||
| + | <p>- practical problem: we need a bacteria platform to carry out the operation of the data (I.e: bio-compiler? bio-CPU?). A compiler consists of sets of programs and logic relations, it is theoretically workable, but obviously too difficult to do as a ten-week project</p> | ||
| + | <p>- since the bio-compiler idea is abandoned, we thought about other ways to store data:</p> | ||
| + | <p>- ROM memory: 8x8 grid to store 64 bits of data, the bacteria interaction can be modified to give to outputs, which indicates the two binary states (0 or 1)</p> | ||
| + | <p>- JK flip-flop or synchronized counter</p> | ||
| + | <p>- 7-segment display: one bacterium -four input channels-each channel with two states (0 or 1)-nine outputs to give nine numbers (0 to 9)- control the corresponding segments to display the number</p> | ||
| + | <p>-bacterial minesweeper. an inhibitor can be considered as a ”mine”. The main problem is that secondary diffusion is very difficult to control. a mass transfer equation must be modeled for each individual square</p> | ||
| + | <p><a href="#Top">Back to top</a></p> | ||
| - | + | </body> | |
| - | + | </html> | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Revision as of 11:09, 8 August 2011
Ideas
Synthetic Graphite
Sand Brick Produced by Bacteria
Termites
New Way of Transforming Bacteria
Bacterial Tattoo
DNA Hard Drive
Synthetic Graphite
- Synthetic Graphite normally has a high electrical conductivity than the natural ones.
- the process involves turning amorphous carbon into crystal under extremely high temperature.
- no evidence shows that carbon(element) can be either iuput or output of bacterial metabolism.
- therefore, we can pass this topic (Text by Nina)
Sand Brick Produced by Bacteria
Sporosarcina pasteurii --> urease
Calcium carbonate bricks can be made by using urease, urea, sand and calcium chloride. The urease cleaves the urea and creates ammonia and carbon dioxide. The ammonia raises the pH and causes the calcium ions to precipitate with the dissolved carbonate ions.
Ammonia is currently a problem since it can run off to cause algal bloom. A method to remove ammonia must be obtained. Solution? Possibly express all the urea cycle enzymes in the chassis (5 total enzymes). Use slovenia's DNA scaffold so that the process does not produce too many possibly problematic intermediaries in the bacteria.
When should ammonia be converted back to urea? When calcium is depleted. Need some sort of Calcium sensor.
So that's pretty cool, but perhaps the bacteria that store salt can be used to spread salt in the winter and stop the country grinding to a halt every time it snows? (Text by Frank)
Termites
Termites are known for their ability to digest nutritionally poor food sources such as lignocellulose. A recent paper has studied the synergistic properties of cellulases from Reticulitermes flavipes. Three enzymes were studied, two cellulases and a laccase. The cellulases were 1 β-glucosidase and Cell-1 (a GHF9 endoglucanase). The phenol-oxidizing laccase that is involved in lignin degradation is LacA.
Cell-1 and β-glu showed >300-fold and >70-fold increases in glucose production (when degrading pine sawdust and beechwood xylan) when combined. When Lac-6 was added in the pine saw-dust experiment, glucose production rate decreased. The authors say that this is likely due to the process of end-product inhibition on β-glu. However, glucose production increased when all three enzymes were used on beechwood xylan. Lac-6 enhances glucose release from hemicellulose by cellulases? Microcrystalline cellulose results were nearly identical to sawdust.
The idea of this project is to use bacteria to express Lac-6, β-glu and Cell-1 in order to produce monosaccharides from other sources of biomass such as wood. It has recently been discovered that these termite derived cellulases have synergetic properties. Therefore I postulate that future effective biomass conversion will rely on obtaining the most efficient mixtures of enzymes. Lignin (the material hardest to digest) releases pentoses (like xylose and arabinose). Since sawdust degradation by the three enzymes works best when only Cell-1 and β-glu are used whereas all three enzymes gave the largest production rate when degrading beechwood xylan, I propose the construction of a module that will allow the bacteria to produce the most efficient enzyme mixtures depending on the rate of glucose production. This circuit might make it possible to digest complex mixtures of materials most efficiently. The bacteria used should also ideally only use an alternative carbon source to glucose.
New Way of Transforming Bacteria
Create a plasmid containing Dpn1 under the influence of a strong repressor. In the same plasmid insert the methylase enzyme. The gene is inserted into the methylase and stops its transcription.
If the gene of interest has been successfully inserted into the plasmid and the plasmid has been successfully inserted into the bacteria we can use the inducer to kill off any bacteria that has not been transformed (because the Dpn1 cuts any methylated strands of DNA).
Today we continued developing the bile acid sensor as well as the idea of the anti-venom. For the anti-venom idea we talked to Travis Bayer and obtained a method for screening for the right mutants. We also had a visit from LSE BIOS members that taught us about the point points we should worry about in human practices. We were also given the task to make instructions for a lego structure to show us how difficult it is to standardize parts due to the difficulty of communicating more complicated instructions. (Text by Chris)
Bacterial Tattoo
- After being inspired by a student from the Royal College of Arts who presented us with her work on a project to create a living dress, Frank began to research the notion of a melanin tattoo, so that alpha-melanin stimulating hormone is applied to the skin and held in place until the skin darkens in the shape of the template. The alpha-MSH could be produced by bacteria.
- the alpha-MSH gene is produced as one gene that also contains beta-MSH and gamma-MSH that are made available through post-transcriptional processing, so only the alpha-MSH region is required as it is the best characterised and has been expressed before
- Once the alpha-MSH is expressed, it can be collected, soaked into silk (for example) that is cut into a pattern and will allow the hormone to diffuse into the skin, producing a (probably temporary) tattoo. From: http://en.wikipedia.org/wiki/Melanocyte-stimulating_hormone
- However, it seems that alpha-MSH is a rather powerful aphrodisiac and so a different hormone will have to be chosen, in addition, it seems that the hormone is unlikely to penetrate the skin as there are many different layers as well as proteases secreted by the skin
- alpha-MSH, or its analogues are already used as tanning solutions and the analogues are considerably stronger
- so then, bacteria could express the gene for melanotan - which is a cyclic lactyam analogue, and this will be very difficult to express, as a method will have to be found for cyclisation.
- One further problem: "As of 2010 no compound incorporating the melanotan II peptide has ever been approved for use by any governmental drug regulatory bodies outside of clinical trials. Unlicensed and untested powders sold as "melanotan II" are found on the Internet and are reported to be used by thousands of members of the general public. Multiple regulatory bodies have warned consumers the peptides may be unsafe and ineffective in usage with one regulatory agency warning that consumers who purchase any product labeled "melanotan" risk buying a counterfeit drug. Medical researchers and Clinuvel Pharmaceuticals, the company developing the related peptide afamelanotide, has warned consumers that counterfeit products sold using the names "melanotan I and II", "pose a hazard to public health"." From http://en.wikipedia.org/wiki/Melanotan
- alpha-MSH will have to be used, but this time with the novel method for crossing the skin: Transdermal iontophoresis. This is a non-invasive way for hydrophilic proteins to be transported across the skin but I do not know what kind of resolution is possible with this device. Whatever the pattern achieved, be it a nice dot or a blotted smudge, the students from the RCA will surely help to make it look pretty. (Text by Frank)
DNA Hard Drive
1. use DNA sequence as a medium to store information (DNA base - quaternary bit - original text)
2. put “tag in” information (i.e some specific base pairs as “prototypes”) to classify the information
3. writing functions in programming language with DNA sequences, use DNA as the function variables
- Sci-Fi ideas developed with RCA people:
a. in the future, a bacteria charm/necklace can be made to store and carry the information, such as exam syllabus, genetic disease history, family photos, etc
b. different coding methods and types of bacteria can be chosen by the clients for different levels of security needs ,(some high risky information can be store in Bacillus anthraci for military use)
c. data can also be stored in E.coli in the human digestive system, it can be erased by intaking antibiotics
- practical problem: we need a bacteria platform to carry out the operation of the data (I.e: bio-compiler? bio-CPU?). A compiler consists of sets of programs and logic relations, it is theoretically workable, but obviously too difficult to do as a ten-week project
- since the bio-compiler idea is abandoned, we thought about other ways to store data:
- ROM memory: 8x8 grid to store 64 bits of data, the bacteria interaction can be modified to give to outputs, which indicates the two binary states (0 or 1)
- JK flip-flop or synchronized counter
- 7-segment display: one bacterium -four input channels-each channel with two states (0 or 1)-nine outputs to give nine numbers (0 to 9)- control the corresponding segments to display the number
-bacterial minesweeper. an inhibitor can be considered as a ”mine”. The main problem is that secondary diffusion is very difficult to control. a mass transfer equation must be modeled for each individual square
