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:

Brainstorming Morning 13.07.2007

Ben, Cheuk, Lucas, Maira, Facilitator: Frank

Battery bacteria

Make use of proton pumps e.g. ATPase

Bacterial lamp

Make use of bioluminescence of Vibrio fischeri or Firefly

Rust-preventing bacteria

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

Fertilizer-producing bacteria

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

Water-retaining bacteria

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

pH-controller bacteria

To prevent adverse effects of acid rain on the soil

Air-freshener bacteria

Bacteria to take up unpleasant stench

Solar-powered bacteria

Make use of photosynthesizing bacteria

Fat-absorbing bacteria

Used to cure heart diseases, clear arterial blockage

Mucus-eating bacteria

Prevents asthma attack, clear mucus to prevent narrowing of windpipe

Exo/endocytotic bacteria

Treat diabetes by releasing insulin at high glucose levels and taking up insulin at low glucose levels

Gobbler bacteria

Eat Influenza virus or HIV virus

Alex, Dirk, Peixuan, Facilitator: Vincent

In Vitro Protein Synthesis

• 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

A Bacteria Made Meal

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

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.

Minimal Bacteria Frame

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

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

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

Another more expressive cell component other than gene expression

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

This is the essential crux of synthetic biology.

Fragrant bacteria/biosensor in the mouth

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

Fat Absorbing Bacteria

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

Bacteria that neutralises greenhouse gases (cows)

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

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

Characterizatio 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

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