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From 2011.igem.org

Nina Jiayue Zhu   

- 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 (=_______,=)

- anti-venom:-

- traditional way of anti-venom production

  1. injecting venom or detoxified venom into a horse (tiny amount, multiple times) 
  2. after the antigen growing period, contract the horse blood plasma 
  3. use stomach digestive enzyme to breakdown the anti-venom protein into smaller globin molecules 
  4. use (NH4)2SO4 to salt out the globin (purification)

- oxides like K2MnO4 can neutralise venom by denaturing the polypeptide chains

- complex ligase like AuCl2 can denature venom by binding with them, when preventing venom entering the tissues

- 2007 <science> : immune system has a stronger response to venom

 when the mast cells are stimulated, they release histamine  
 histamine can subside the venom  

- histamine producing bacteria:

 found in tuna    
 18 types of bacteria such as Clostridium perfringens,etc 
 anaerobic bacteria 

- to conclude

 1. decide the working mechanism (toxicology) of a specific type of venom 
    attack neurons? brain cells? cardiovascular system? respiratory system? 
 2. does it react with histamine? 
 3. bacterial production of histamine 

Frank Machin

- First, I began to look into the possible production of the alkaloid isorhy, as was brought to my attention by Nina and Si
- It is rumoured to be a potential treatment for Parkinson's and it would make a good project if this were to be produced by bacteria
- On further research it turns out that the evidence for this drug as a treatment is weak and there is no information available about the gene or genes that encode it, so the idea was dropped

- 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, I 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.

- 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".

- 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.

Christopher Schoene

We had a briefing today chaired by James. Key action points of the day were to organize our CID's, organize who was in charge of each team aspect and discuss the problems that we thought could be solved by Synthetic Biology. Once these problems had been discussed, we each chose one project that another team member came up with to research. We also were introduced to Professor Freemont and Professor Kitney who gave us an insightful talk about what awaits us. A trip to the Royal Society of Science exhibition ended up turning into a lunch in China town (the exhibition actually starts tomorrow) and we talked to Nicola Morgan who is interested in investigating the use of bacteria in making patterns on clothing.

Vampiric bacteria:

The aspect of a Vampiric bacteria that is designed to get rid of blood clots produced by trauma induced clotting or during complex medical procedures is intriguing. Expression of Hirudin is possible in systems such as E. coli. In 2007 Berkeley produced a chassis for a E. coli that could be introduced into the blood stream after inactivation. However, it is difficult to have the non-viable cell lysis occur in the correct location and therefore an anticoagulant could just as well be injected into the patient. For this to work, we would require an expression system that is able to express Hirudin (produced usually by leech salivary glands and has been successfully expressed in E. coli), express anti-angiotensin (it is possible to express Fab fragments in E. coli) and targeting the fibrin (can be done by expressing Tissue plasminogen activator). The idea would be to have the chassis recognize a blood clot or an area of damage and prevent clotting and/or clear clots. A method for having the system recognize when to secrete hirudin would be by having the bacteria sense trauma related chemokines and have the chassis secrete the protein only when it senses above a certain threshold of these chemokines or we could try to express protease-activated receptors (GPCR) that are cleaved by activated thrombin (the target of hirudin). Direct application would only benefit over the use of leeches in that the chassis is more aseptic then a leech bite.

The biggest issue remains the fact that for this to work we would have to inject the patient with living E. coli that can evade the human immune system. A new method of boosting biosynthesis has been obtained through the use of RNA scaffolds: http://www.sciencemag.org/content/early/2011/06/22/science.1206938

Yuanwei Li  

Fuel from food waste

Microbes in food waste like heterotrophs, cyanobacteria, microalgae and purple bacteria produce biohydrogen. Hydrogen has more potential energy than petrol. Hence, food waste can be turned into valuable energy. Fermentative bacteria use carbohydrates like sugar to produce hydrogen and acids. Purple bacteria, use light to produce energy (photosynthesis) and make hydrogen to help them break down molecules such as acids. http://www.sciencedaily.com/releases/2008/07/080716204805.htm

Hydrogen is produced by feeding waste products from a chocolate factory to Escherichia coli bacteria. E Coli ferment the sugars in the chocolate waste, which generated organic acids so toxic to the bacteria that they began converting formic acid to hydrogen. http://environment.about.com/od/renewableenergy/a/chocolatefuel.htm

Cellulose waste can be converted to energy by using enzyme cellulase. The gene that codes for cellulase has been isolated and grown in large quantities by E. coli. A number of photosynthetic bacteria, nonphotosynthetic bacteria, cyanobacteria, and green, red, and brown algae produced the enzyme hydrogenase, which is necessary to make hydrogen.

http://www.accessexcellence.org/RC/AB/BA/Future_Fuel.php

Feather-Eating Bacteria Bacillus licheniformis Strain PWD-1 breaks down feather into a feather-lysate compound. Feather-lysate provides a low-cost, highly digestible protein source for livestock feed. Bacillus has also been shown to secrete a keratinase enzyme that hydrolyzes proteins such as collagen, elastin, and keratin. Potential application in breakdown of livestock carcasses. The gene encoding the enzyme keratinase of Bacillus licheniformis is kerA. http://www.accessexcellence.org/RC/AB/BA/The_Smell_of_Wealth.php

http://aem.asm.org/cgi/content/abstract/61/4/1469