IGEM:IMPERIAL/2007/Ideas

Brainstormings

Vincent 06:05, 3 May 2007 (EDT): You can start posting ideas about possible projects for our iGEM summer. Don't try to limit your imagination, everything is possible in the wonderful world of Synthetic Biology.

Johnsy 00:06, 6 May 2007 (EDT): Well, almost anything...good luck with your project... and if you allow me, I'll make a few comments here and there.

Baijiongjun : Looking forward to all the "WoW" ideas :P

Current Ideas

Distill seawater

To remove minerals and salt from water to make it potable. Requirements:

• Ability to remove salts, especially NaCl
• Ability to remove other micro-organisms (algae, bacteria, etc)
• Ability to remove other minerals (metals, etc)
• Must not add waste to the output water
• Must be separable from the output water
• Nutrient delivery must be done without affecting output water

Random Number Generator

Generating a series of random numbers from bacteria

• A series of biobricks results in generation of a random (intensity of?) response
  • Response can be chemical, fluorescent or anything quantifiable...
• Response generated should be totally random, not from a fixed algorithm
• A numbering system has to be developed
• Links can be made with electronic devices (bio-electronic interface)

Rust-preventing bacteria

Bacteria forms a protective biofilm that wraps metal, preventing it from rusting. It can also self-destruct on demand.

• Forms protective biofilm coating around metal, possible ways of doing this include:
  • Biofilm can prevent oxygen and water contact with the metal
  • Cells are triggered to die (or enter scenescence), leaving a film of protective bacterial cell wall
  • Bacteria actively "eat up" metal oxides
• Must be able to attach to metal
  • Adhesive proteins expressed on bacterial membrane
  • Bacterial "glue" is secreted to form extracellular matrix
• Easily removable when required
  • Stimulus removes adhesive properties of bacteria

The Vacuum Cleaner (Sensor, Collector, Reporter)

With this done we thought about projects that fit this description

• Biosensor
  • Initially thought about the possible inputs: Heavy metals, blood analysis, infections, gas and liquids.
  • We then identified a key consideration; that depending on the purpose of biosensor, we will want to detect either a threshold concentration or a gradient concentration.
  • We identified the devices that can be used in the genetic circuit and reasoned that a logic gate would be suitable.
  • Then we considered outputs for a biosensor: Visible, smell and sound.
• Using Biosensor in more complicated system - Biological Vacuum Cleaner
  • Thought about coupling a biosensor with a collector. e.g. coupling a biosensor for infectious bacterium with collection via phagocytosis to eliminate threat.
  • We then explored the idea of having a full signal, e.g. if we have a collection method we want to have a full signal to turn the system off.

The Vacuum cleaner would work in the Following way :

1. Rubbish dectection: The first part of this process would be detecting whether rubbish is present in the surroundings. We plan to do this by exploiting the 2nd messenger system of the cell. When rubbish is in the area it will bind to its receptor and produce an inducer inside the cell. This inducer will cause a sensor to produce a detecable signal, eg. pH / colour, to signify the presence of rubbish.

2. Hoovering This hoovering action will continue until

3. Capacity Limit Dectection We want a way to see when our vacuum cleaner cells are full. We thought that we could employ a biphasic switch / threshold effect such that when the concentration of the inducer , equivalent to the amount of rubbish collected, reached a certain point the cell could signal to us again to let us know it can hold no more.

4. when the cells reach their limit we would try to replace them, eg. changing the bag on the vacuum cleaner. We would do all of this in a container eg. a vat to avoud contaminating the whole population of what we're trying to clean up.

Further Investigations

Dirk 07:00, 17 July 2007 (EDT)
Pros:

• This idea has good potential applications
• It can probably use the Hrp part in its control stage
• It is novel - controlled removal has not been done before (apparently)

Cons:

• The system is not generic (despite appearances). The process of collection, which would be performed by endocytosis, is very specific. Further, the collection and sensing parts would be the same. And since they are the major parts in the system, changing the target substrate would involve major changes to the system (hence not generic).
• The system is very complicated - there are various different parts and at least two control stages.
• There are no parts in the registry that can aid in the sensing/collecting component.
• The target substrate needs to be identified before literature search can be done, because the sensor/collector is very specific.
• A very complex new part will have to be characterised (the sensor/collector)
• The 'cell is full' signalling system appears to be too difficult to conceive.

Potential Applications

We then thought about an application for such a project

This Vacuum Cleaner idea we think could be applied to the global problem of Eutrophication.

Eutrophication is the process by which excess fertiler from farmlands washes into nearby water sources eg. lakes & rivers.

The presence of fertilisers causes amplified growth of plants in said water supply.

This casuses amplified oxygen consumption which then causes death of life in water supply eg. fish.

We hope that the vacuum cleaner can clean up the fertiliser in the water source eg. using phosphorus receptors

When full we think we can flush the full vacuum cleaners and replace them with empty ones

This would all be done in a containment vessel eg. a vat

Techniques

Cell self-destruction

This is something we might be using, but not the project itself.

(In Vitro Protein Synthesis) Not a project idea

• In vitro protein synthesis (ambion)
• In vitro gene expression (promega)
• EasyXpress Protein Synthesis Mini Kit (Qiagen)
• Effects of growth rate on cell extract performance in cell-free protein synthesis
• In Vitro Synthesis of Protein in Microbial Systems

Working with Yeast

Yeast, unlike bacteria, is an eukaryote, and thus is able to synthesis a wider range of proteins, and is also more suitable for integrating into humans.

Working with Lactobacillus Casei Shirota

The fact that this bacteria is ingestible and extremely helpful to our digestive system, is a widely known fact. This can aid in commercialisation and integration into the food market, much better than a model bacteria E.coli. Also, it can be genetically engineered to make vitamins and essential amino acids that would allow many vitamin defciencies in third world countries to be solved.

Exo/endocytotic bacteria

Keeping the idea. Different application needed, possibly similar to the vacuum cleaner proposal
Treat diabetes by releasing insulin at high glucose levels and taking up insulin at low glucose levels

Characteization of a Chassis

1. Rate of replication
2. Plasmid permeability
3. Type of vectors
4. How long it stays adhered to the surface
5. Suitable environmental conditions
6. Compatibiliy issues Chassis VS Biobricks
7. Structure and physical features]
8. Genome information
9. Safety issues
10. Stability and predictability
11. Life span
12. Cell-cell communication

Characterization of Basic Parts of a Biobrick

Promoter/Sensor

Sensitivity Specificity Substrates invoved Spatial patterns (intra/intercells) Saturation range/kinetics Inducible/repressible

Operator

Other regulatory factors (methylation, sigma factors) Length of gene Physical conditions (contraints)

Gene of interest

Codon optimization Length Cleavage sites POPs Accessibility (e.g.RBS) Fusion Protein

Reporter

Light intensity (analogue signal) Response time and fucntion Color Smell Spaial Patterns Protein trafficking/diffusion POPs

1. Engineering V Approach

Initially we set out, using the engineering V approach, to determine what we wanted our project to achieve.
a) Key Goals of project:

• Application driven
• Use recent research and knowledge

b) Considerations for applications:

• Low cost - In terms of energy source and materials
• Portable and can operate in vivo/in vitro
• Safe - Need to contain our product to prevent contamination.
• Inspire confidence in new field - Want to change current concerns and stigmas about synthetic biology.

c) Project Limitations:

• Containment
• Interfacing parts and our system
• Time limits of project

Notes on Brainstorming Techniques

• Brainstorming sessions work best if there is a specific problem or opportunity statement to guide the thinking, that describes what is to be achieved or investigated. However, the statement must not hint at the type of solution, as this may hinder idea generation. It is often suggested that thinkers not look into other solutions to the problem before brainstorming, as this tends to restrict the line of thinking to already existing solutions and results in similar answers.
• Appointing a facilitator also aids in the process. This person should state the objective, keep track of time, and make sure the session rules are obeyed. They must ensure that the session runs smoothly, that participants feel comfortable, that everyone participates, and they will also rekindle the creative process if it slows down. The facilitator position is sensitive, though. It is often prudent to appoint a person from outside the group, without a vested interest, biased point of view, or complicated relation to other members of the group.
• Participants should be encouraged to develop each others ideas further, or to use other ideas to create new ones. However, single ideas should not be discussed for too long.
• Plenty of paper and pens should be available for writing down thoughts. All thinkers should have a writing pad, and if possible, flip-charts should be within easy reach for everyone. All ideas should be written down, without discrimination.
• An enthusiastic, uncritical attitude should be encouraged - it must be ensured that no one criticises or evaluates ideas during the session. Criticism adds an element of risk to proposing new ideas, and this stifles the creativity and flow of the session. In no way should participants be made to feel criticised, uncomfortable, or threatened (i.e. mean looks, derogatory jokes, imposing body language, supervisors hovering behind participants, etc. should all be avoided.)
• The environment and arrangement of participants will also affect the process. Richer environments tend to produce better sessions than bland ones, but distractions should be avoided. Participants should, ideally, sit around a circular table, such that each individual has an equal standing and no one becomes the focus of attention by virtue of their position (that is, avoid having a 'head of table').
• Having random material such as books, magazines, toys, strange objects, etc. may help rekindle the process if it slows down, or offer a source of inspiration. However, participants must not spend too much time with these - ten or twenty seconds should be enough, but more may interfere with focus.

For those who want to read more about brainstorming, the following references were useful. In particular, the Wikipedia article linked below gives a very good overview of the process, and of a few different methods to conduct a session.

References

Brainstorming.co.uk
Mindtools.com
UNC.edu
Wikipedia

Discarded Ideas

Remove methane from air or cow gut

Criteria 1:

Lvl 1 OK - Proj is Application Driven

Criteria 2:

Lvl 1 OK - Proj will generate Research

Criteria 3:

Registry: Problems

P1 Parts not found in the registry

S1 Potential proteins can be extracted from methanotrophic bacteria

Literature : OK

Criteria 4:

Lvl 1 Prob - Proj not Novel

P1 Methane 'Removal' has already been attempted by industry in New Zealand (although it has not been achieved). This project has already been attempted and published in the journal: Chang, 2000.

S1 Attempt 'Removal' in a novel way. So far there is a vaccine that discourages methanogenic archaea (Major, 2000).

BIG PROBLEM : We don't have a solution yet.

Further Investigations:
Dirk 07:07, 17 July 2007 (EDT)

http://rucus.ru.ac.za/~wolfman/Essays/Cow.html

Fertilizer-producing bacteria

This is a system of bacteria that produce nitrogen-containing compounds, or plant growth factors (eg auxin). The system will probably require:

• the necessary metabolic pathways to produce the fertilizer compounds
• the ability to survive in nature, competing with other organisms for nutrients
• not have a negative impact on the ecological system it is introduced into
  • probably a detailed study of the ecology would be required

(This project seems way over our abilities, as the whole ecology and 'survival in the wild' problems are difficult to overcome. They will be more science than engineering project. A proof of concept project could be done instead, but this would be much less interesting.)

Solar-powered bacteria

• Requires photosynthetic bacteria (cyanobacteria)
  • Difficult to transfer proteins into E.coli, many proteins involved
• Output is glucose, application not known

Electrical Biological Interface

This is an electrode-based interface between the biological system and a computer. This might be electrode-plate reactions with an enzyme cascade, or the more exotic embedding of ions on cell membranes. For electrode plate reactions, the following is required:

• a selective enzyme-substrate redox reaction
• a second stage enzyme-mediator redox reaction
• a third stage mediator-electrode redox reaction
• the enzyme-mediator-electrode component must be physically isolated from the rest of the system, with the exception of the substrate, which can reach the enzyme
  • this may be done by a selectively permeable membrane encasing the component
• the substrate of the enzyme must be related to a parameter we want to measure

OR if the embedded ionic proteins are used, then:

• ion-containing proteins must be designed/found
• we must be able to direct the location of the protein in the cell (ie, put it in the membrane, or export it)
• we must prevent interaction with undesired elements (ie, floating ions, static electricity, etc)

• Knowledge : Lack of pre-existing platform on which to implement this task - i.e. overambitious for a period of 9 weeks.
• Scope : As above, too great a task for such period

• However, novel and particularly important in terms of application - biobricks registry)

Remove heavy metals from water

This includes Mercury, Arsenic, Zinc, Lead, Cadmium, Barium, Aluminium. If we want to look at other compounds that also harm the environment, there are other examples like DDT, PCBs, and Dioxins, all of which causes animals, humans, and the environment alot of harm.

• The bacteria must have a channel specific for absorption of these water pollutants
• Be able to retain these in either the cell or a specific organelle
• Must be able to harvest the bacteria easily
• Must not have negative effects on the aquatic ecosystem

Criteria 1:

Lvl 1 OK - Project is application driven i.e. to remove harmful heavy metals.

Criteria 2:

Lvl 1 OK - Research would be needed on our particular metal binding method unless we pursue an already partially characterized heavy metal based project.

Criteria 3:

Lvl 1 Problem - Unless we use a previous project as a base then will have problems finding specific heavy metal receptors.

Criteria 4:

Lvl 1 Problem - Project is not novel, the idea of binding heavy metals either for removal or biosensing has been done before. Arsenic and iron are examples of projects based upon metal binding.

Criteria 5:

Lvl 1 Problem - Will need approval for the heavy metals used in the project. Would have to limit our choice of metals we can use e.g. lead and copper.

Criteria 6:

Lvl 1 - Without an easy part for binding of lead we would need to characterize a new part.

A bionsensor for CO

Bacteria must

• Have a channel or receptor for interaction with CO (CO is highly soluble and diffusable and can penetrate the cell membrane easily, and receptors for these would be within the cell, instead of the cell surface membrane.)
• It must be hypersensitive to the presense of CO in the air as CO does not exist in high concentrations in the normal air that we breathe
• Must have a method for reporting on the presence or absense of CO. This is most probably a reporter gene, that either emits light, or changes the color of the bacteria.

Battery bacteria

This is a system that stores energy that is put into it, for later use. This may be by photosynthesis or by aggregating nutrients. Delivery of stored energy can be done through ATP production, or by releasing simple carbohydrates.

For all types, the energy would probably be stored as large polymers inside or outside the cells. So the following is required:

• ability to create long polymers (fats, amin-acids, or carbohydrates)
• ability to break down these polymers into single monomers, for conversion into energy
• ability to store these polymers inside the cell, OR to retrieve them from outside the cell

For photosynthesis, the following would be required:

• a photosynthesis pathway
  • this pathway is known to be very inefficient
  • we might be able to tweak this pathway, but it's probably very difficult
• a good method to deliver the necessary CO2 for photosynthesis
  • CO2 must come in at a rate that can sustain the required photosynthesis rates

For aggregating nutrients already present in the solution, the system would have to be able to:

• find and pick up the necessary nutrients for polymerisation
• a method for efficient delivery of nutrients to target cells is necessary
  • it could be that simply putting nutrients in solution is enough
  • or a directed stream might be used instead

Make use of proton pumps e.g. ATPase

Problems: Can be done using Rhodoferax ferrieducens, but is not synthetic biology - no need for If implemented using E.coli, need to modify the membrane proteins - has been attempted but yielded low efficiency No parts in registry Research has been done on the field - not very novel Open ended research, no concrete solution to problem

Vitamin-producing bacteria

With regards to the requirements below, assume that only one vitamin is in context here. This type of bacteria can solve the major vitamin deficiency problems in third world countries e.g. Vitamin A deficiency. One way of utilising these bacteria is by ingesting them such that they would stay in the gut. E.coli would fail this purpose of ingestion as gaining the acceptance of the public would be hard. Hence, it would be ideal to find another bacteria that humans have already accept as a friendly bacteria. One good example would be the Yakult bacteria Lactobacillus. Though it is not characterized well, we can simply use it as a test system.

• Preferably adhere to the gut wall and maintain an approximate constant population
• Does not compete with the existing microflora. If the bacteria medium is lactobacillus, the more the merrier (tentatively speaking)
• Must be able to detect a lack in the vitamin, and synthesize more of it.
• Must have a feedback loop that prevents overproduction of the vitamin (too much of a vitamin can cause diseases too)
• Must have a generic operating gene system whereby any vitamins can be synthesized as long as the genes coding for the sensor and final product (the vitamin)are swapped.

http://www.foodnavigator.com/news/ng.asp?id=68451-campina-nizo-food-research-riboflavin-yoghurt

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TB0-4JG5FH4-3&_user=217827&_coverDate=06%2F30%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000011279&_version=1&_urlVersion=0&_userid=217827&md5=c1e32119c8b9c2218bc31a8f985025aa

http://www.foodnavigator.com/news/ng.asp?n=56365-bacteria-offer-novel

Bacterial lamp

Yes..? More information required.

Make use of bioluminescence of Vibrio fischeri or Firefly

Light Glowing Furniture

Cultivating bacteria

Idea is not new, and has been gaining momentum the past few years.

Bacteria that prevent eutrophication

Needs clearer definition. Algae or nitrates ?

This is a system of bacteria that EITHER kills and removes algae from water, OR removes the nutrients that algae require for growth. In both cases, the system will probably require:

• the ability to survive in nature, competing with other organisms for nutrients
• not have a negative impact on the ecological system it is introduced into
  • probably a detailed study of the ecology would be required
• the bacteria must not create a similar problem to that of algae (ie, remove algae, but cause eutrophication through other means).

(This project seems way over our abilities, as the whole ecology and 'survival in the wild' problems are difficult to overcome. They will be more science than engineering project. A proof of concept project could be done instead, but this would be much less interesting.)

For removal of algae, the system will require:

• the ability to target algae cells
• the ability to break them down OR the ability to bind and separate them from water
  • a fixed structure that selectively binds algae cells can be assembled

For removal of nutrients, the system will require:

• the ability to process nutrients into a form not useable by algae

Fat Absorbing Bacteria

Research industrial applications.

This bacteria can be placed in the gut and absorb the fats that are present in our food. This can be a dieting breakthrough!

Trap CO2 from the atmosphere

Off

Biofilm wrapping for food

Off

Biofilm over tissue for repairs

Off

Biofuels

Off

Bacteria that make coffee fresh

Off

Memory

Off

Artificial bacteria

Off

Degrading plastic

Off

Biochip

Off

Cell programming

Off

Autoimmune disease

Off

Target cancer cells

Off

Water-retaining bacteria

OFF
Bacteria to capture water and store water as crystals in the top soil

pH-controller bacteria

OFF To prevent adverse effects of acid rain on the soil

Air-freshener bacteria

OFF
Bacteria to take up unpleasant stench

Fat-absorbing bacteria

OFF
Used to cure heart diseases, clear arterial blockage

Mucus-eating bacteria

OFF
Prevents asthma attack, clear mucus to prevent narrowing of windpipe

Gobbler bacteria

OFF

Eat Influenza virus or HIV virus

A Driving Sensor

OFF
A device that not only reacts to the ongoings in a system (sensor) but also is able to control the same parameters in the system (controller)

A Bacteria Made Meal

OFF
By adding bacteria to a block of wood, the cellulose in the wood would be digested to an edible form for human consumption.

Minimal Bacteria Frame

OFF
Instead of building an artificial bacteria from scratch, we can minimise the housekeeping genes of a bacterium such that most of the biobrick systems would be able to intergrate easily into it without worrying about excessive crosstalking between protein components.

Farts that smell like Bananas

OFF
A gut bacteria can be engineered to become a biosensor for e.g. a lack of nutrients, and produce a certain small as an indication.

Another measument tool for gene expression other than PoPs

OFF
This will enable more versatility between the biobricks system and generic inputs and outputs.

Another more expressive cell component other than gene expression

OFF
Gene expression can be rather slow and tedious due to the time lag of activation, transription and translation. In the case of a biosensor, if another method can be found that is able to react faster to the inputs applied, it would be an advancement in the field of synthetic biology.

Characterization of different parts of a gene and type of organism used

OFF
This is the essential crux of synthetic biology.

Fragrant bacteria/biosensor in the mouth

OFF
This is similar to the one above " Farts that smell like Bananas ".

Bacteria that neutralises greenhouse gases (cows)

OFF

Once again, a gut bacterium can be altered, or a bacterium can be made to absorb and breakdown CO, CO2, or polymerize methane.