From 2007.igem.org

https://static.igem.org/mediawiki/2007/f/f5/800px-Edinburgh_City_15_mod.JPG

This is a list of ideas that we decided not to use for one reason or another

Please note that this is not an exclusive list of every idea, it has been summarised a bit (with things like killer bees that target terrorists removed)

Contents 1 Drug Synthesis 1.1 Alternative synthesis routs 1.2 MRSA 2 Bio-remediation 2.1 Removal of Contaminants 2.1.1 Immobilisation of Heavy metals 2.1.2 Plants 2.1.3 Gathering of Micro-Organisms 2.2 Safety Issues 2.2.1 Danger of mutation and effecting environment in adverse ways 2.2.2 Danger of continuing to live after the job is done 2.2.2.1 Sterility 2.2.2.2 Division Counter 2.2.3 Conjugation 3 Self flavouring yogurt 4 Bacterial Blood 5 Bacterial Insulin Sensor

Drug Synthesis

Alternative synthesis routs

Synthesis of drugs that are hard to produce in nature

• Taxol
  • an anticancer drug, which is extracted from the pacific yew tree or semi-synthesised from European yew needle extracts, at a cost of $6000 per treatment.

• Immunosuppressants
  • cyclosporin
  • rapamycin

MRSA

MRSA is becoming a major health problem within our hospitals, with the number of deaths rising from 148 in 1993 to over 500 in 1999. There are several natural compounds that have been discovered, which lower the resistance of MRSA to antibiotics, enabling its irradiation. Epicatechin gallate and totarol both inhibit the penicillin binding protein, and lower the resistance of MRSA to methicillin. Is it plausible to engineer bacteria, which synthesis and release these two molecules within air conditioning systems and other hard to clean areas?

Bio-remediation

There are many areas of the world with contaminated soils, such as Chile, which has problems with the heavy metals antimony, copper and arsenic. The ability to clean up these sites would be a great benefit however there are many problems to overcome.

Removal of Contaminants

How do we remove or make safe any contaminants found in the ground. The ability to clean up these sites would be a great benefit however there are many problems to overcome.

Immobilisation of Heavy metals

conversion of uranium and other heavy metals to insoluble metal phosphates or reduced states, which can easily be separated out or immobilised in the ground.

• There appears to be several groups researching this area at the moment, and several have published articles on the conversion.

• Whist the immobilisation of heavy metals in the ground is good in terms of keeping them out of the water table, it will not completely solve the problem with uranium or any other radioactive substances.

Plants

Remove uranium and other heavy metal contamination from soils.

There are already several bio-remediation tools available on the market to remove heavy metal contamination, but these do not have an output system to tell you whether they have done their job. One idea was to create plants that bioilluminesce to make the harvesting of plants which have adsorbed an acceptable level of heavy metals easier.

This would involve engineering plants to uptake uranium from the soil, then being harvested and safely disposed - have not yet looked into this idea in much detail as we weren't sure of the feasibility of working with plants.

• Shewanella has a strong affiliation to certain Uranium ions, perhaps use this to bind with the plants mentioned above routs rather than engineering the plant to be attracted to it.

Gathering of Micro-Organisms

Another idea was to create micro-organisms that aggregate together for easy removal, once they have adsorbed an acceptable level of heavy metals.

Safety Issues

We cant just release genetically manipulated organisms into the wild to help clean up the environment for a number of reasons. Possible things to consider:

Danger of mutation and effecting environment in adverse ways

Possibility of looking at Deinococcus radiodurans which have multiple genomes to see if the resistance to radiation can be applied to other organisms and reduce the chance of mutations occurring.

Danger of continuing to live after the job is done

One of the main problems with releasing GM organisms into the environment is their ability to persist and interbreed with non GM organisms of the same species. One idea was to generate E. coli which could only divide for a certain number of generations before dying, removing its self from the ecosystem.

• This system must be fail safe.

• It was pointed out that the DNA would have to be destroyed with the host or other bacteria may pick up the genetically engineered DNA, defeating the purpose of the kill-switch.

Sterility

Sterility is popularly defined as Cell death, but this system would make use of the cell’s continued protein production to perform a set task despite failure to reproduce. Bacterium longevity is the limiting factor and could maybe be tweaked.

Task-processing code – a function of choice. Should be rendered dysfunctional upon cellular death. Thermodynamic instability to innate cell death pathway activity (lysozyme?) or make it rife with restriction sites or similar. Plasmid-uptake recognition (Marker) – use host oligotrophs and keep a genomically absent metabolic pathway element in the vector. This is the least hazardous marker I can come up with. If we use a toxin resistance gene we run the risk of increasing free microbial artillery. Sterility – renders a preferentially conserved mitotic element dysfunctional. Antisense for mitotically crucial protein mRNA or steric intervention at the active site. Alternatively bacteria with point mutations in DNA polymerase with supplied DNA polymerase at the site of synthesis/growth. Uptake might prove tricky, but the idea design is the same.

Division Counter

• This project continued in a modified form

One idea that was thrown up involved counting the cell divisions, then after a set number setting of the kill switch.

There were ideas to keep quantitative mitotic input and render different qualitative outputs with respect to how many septations the cell had undergone.

Depending on what bactieral strain is picked, tasks (and maybe ultimately cell death) can be performed at different rates.

“Generation times for bacterial species growing in nature may be as short as 15 minutes or as long as several days.”

• http://textbookofbacteriology.net c/o K. Todar, University of Wisconsin

A eukaryotic device could be stably incorporated into telomeres and, as telomerase fails to keep up with a rapidly replicating cell, a constitutive peripheral repressor is disintegrated and a highly processive downstream endonuclease gene can ensure DNA disintegration and cell death.

Conjugation

Need to ensure the GM bacteria does not conjugate with natural bacteria and pass on the GM DNA, allowing it to persist in the environment

Self flavouring yogurt

Idea is to create lactobacilli or acidophillus which are capable of flavouring as well as producing yogurt, to cut down on the number of steps required in yogurt production. Could have a multitude of colours and flavours engineered into the bacteria, such as the traditional strawberry, chocolate and banana and the less common mint, jaffa cake and coffee.

• Project continued

Bacterial Blood

With the problems present with blood transfusions and blood shortages, would it be possible to produce bacterial blood? Would it be easiest to produce just type O blood type, which can be used by all recipients, or to create a full range of blood types. Also sterile production of blood would reduce the risk of people contracting blood borne diseases from unhealthy donors.

Bacterial Insulin Sensor

For those afraid of needles Why inject your self with insulin, when you could have a bacterial colony living under your skin that monitors blood sugar levels and releases the correct levels of insulin in response.