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

Preliminary Brainstorming 12.07.2007

We had a preliminary brainstorming session today. Here is a list of ideas that came up:

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

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 Unlike using the bacteria as a sensor, this bacteria must be used as a sieve throughout the waters. It is very difficult to harvest them once they have been dispersed all over the place.

Remove methane from air or cow gut

This is to design bacteria that will reside in a cow's gut, trap methane, and polymerise it into longer hydro-carbon chains that will not be emitted into the atmosphere. This required:

• bacteria must be able to survive in cow gut
  • must be able to compete with natural cow gut bacteria for survival
• must be able to trap and polymerise methane
• product must not be toxic to the environment

OR

• must have a competitive advantage over natural cow gut bacteria
• the methane production pathway must be disrupted

Cell self-destruction

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

A bionsensor for CO

Maybe: CO might not be allowed. BUT biosensors are no longer novelty.

Brainstorming Morning 13.07.2007

Ben, Cheuk, Lucas, Maira, Facilitator: Frank

Battery bacteria

More informatiomn required.

Make use of proton pumps e.g. ATPase

Bacterial lamp

Yes..? More information required.

Make use of bioluminescence of Vibrio fischeri or Firefly

Rust-preventing bacteria

More information required.

Bacteria to form biofilm that wraps metal and to self-destruct on demand

Vitamin-producing bacteria

More information required.

Not very original, though...

Bacteria produce vitamins to be harvested.

Fertilizer-producing bacteria

More information required.

Bacteria to produce nitrogen-containing compounds or plant growth factors e.g. auxin

Bacteria that prevent eutrophication

Needs clearer definition. Algae or nitrates ?

Solar-powered bacteria

Needs more thought ...
Make use of photosynthesizing bacteria

Exo/endocytotic bacteria

Keeping the idea. Different application needed
Treat diabetes by releasing insulin at high glucose levels and taking up insulin at low glucose levels

Alex, Dirk, Peixuan, Facilitator: Vincent

(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.

Electrical Biological Interface

More information required. Electrode-based interface between the system and a computer. This might be electrode-plate reactions with an enzyme cascade, or the more exotic embedding of ions on cell membranes.

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!

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

Anthony, James, Jerry, Facilitator: Matthieu

Summary of Today's two brainstorming sessions :

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

2. Potential Projects

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.

3. 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

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

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.