"

From 2014.igem.org

Revision as of 23:58, 2 May 2014 (view source) Waqar (Talk | contribs) (→Initial Brainstorm Ideas) ← Older edit		Revision as of 20:38, 13 May 2014 (view source) XIsACross (Talk | contribs) (→Initial Brainstorm Ideas) Newer edit →
Line 57:		Line 57:
	http://www.ncbi.nlm.nih.gov/pubmed/22430017		http://www.ncbi.nlm.nih.gov/pubmed/22430017
		+
		+
		+
		+
		+	--------------------------------------------------------------------------------------------------------------------
		+
		+	13/05/2014 Meeting:
		+
		+
		+	Ideas:
		+
		+	Biological cellular automata
		+
		+	END7 diseases - find out one to tackle?
		+
		+	Photovoltaic algae
		+
		+	Bacteria with built in dormancy to produce protein spores
		+
		+	Degrading petroleum/oil in spills
		+
		+	Does dirty water contain some fuel that might produce light?
		+
		+	Biosensors
		+
		+	Detecting vitamin deficiencies and addressing them
		+
		+	Radioactive bacteria
		+
		+	Magnetic bacteria
		+
		+	Organic art (fractals/chaos)

---

Revision as of 20:38, 13 May 2014

Initial Brainstorm Ideas

• A biosensor for a world wide disease

• Detecting PAMPs in bacterial by a novel cleavage mechanism in simulated serum samples

* Detecting pneumolysin for strep. pneumo by using specific antigens/receptors

IDEA #1

PAMPS are referred to as pathogen associated molecular patterns, they're basically parts of bacteria that are recognized by our immune system as foreign. I've followed up and researched a bit more about this idea and propose that we could possibly:

Introduce a number of genes into a particular cell line, since each of our cells have specific proteins called caspases that are cleaved upon detecting a bacterial product (e.g Flagellin from bacteria); these caspases normally cause a number of processes that leads to cell death but ONLY upon sensing bacterial products, they become active. However, if we could somehow get caspases to recognize a particular protein (e.g green florescent protein - GFP) into our introduced samples and cleave it so that GFP becomes active, then we've developed a cool biological sensor that can detect particular bacterial products. Of course, similarly we'd have to make sure that we prevent cell death from occurring (this could be through the introduction of inhibitors of effector caspases e.g Caspase 3 that are the actual executors of cell death.)

Below I've attached a review on caspases https://yuan.med.harvard.edu/sites/yuan.med.harvard.edu/files/documents/onc2008297a.pdf

An insightful page on GFP (note there's also other different colours e.g YFP, RFP that could also be introduced as well - so that if we introduce other different bacterial products, e.g instead of flagellin something else like LPS than it would florescence a different color)

http://www.conncoll.edu/ccacad/zimmer/GFP-ww/shimomura.html

I've also attached a paper that demonstrates the feasibility of this approach (at least in recognition and cleavage of a fluorescent protein) in this paper they basically were able to engineer a GFP that can be cleaved by caspases and becomes active.

http://www.ncbi.nlm.nih.gov/pubmed/21558267 - probably just read the abstract, bottom lines.

I'm happy too explain to anyone about caspases and how this system works - perhaps when we come to initial ideas and anyone is interested, I can draw a diagram and then just explain it further - Waqar.

1. 2 Placeholder

• Diagnostic tool for cancers
• material generating/ breaking down

* Ammonia generating bacteria

* Bacteria that break down certain polymers

* Hydrogen generation

* Bacteria that create biofuel

- lots of teams have tried this

* Bacteria that excrete sugars converted from CO₂

* An organism for cleaning potassium carbonate from fuel cells

* alkaline fuel cells?

* Toxic waste mediation

• Algae-based photovoltaic cells
• Sanitation use

* Marker for pollution status

• Nano wires

• Optogenetics

- already done a bit by Washington university's 2012 team

Idea #1

I proposed that we used optogenetics to control movement/behavior of vertebrate models such as Xenopus, however I think this approach would be particularly difficult and the consensus on this is that its a hard system to implement in practice. In particular, i feel that it doesn't have any far reaching impacts in terms of trying to then move forward (in respect to synthetic biology and contribution of parts etc) and has already extensively been tried and tested on say, mice. I think the start-up kits are around £2000 also. If anyone wants to expand on this and find out more, feel free to add anything below what I've written. - Waq.

In addition, after researching what the washington team did - i noted that their main problem was in the control of expression levels, which would be expected in such a system due to the fine level of control in respect to light that is required.

Reviews on this system, Karl Deisseroth is the pioneer of this system for behavioral manipulation by using light.

http://www.ncbi.nlm.nih.gov/pubmed/22430017

---

13/05/2014 Meeting:

Ideas:

Biological cellular automata

END7 diseases - find out one to tackle?

Photovoltaic algae

Bacteria with built in dormancy to produce protein spores

Degrading petroleum/oil in spills

Does dirty water contain some fuel that might produce light?

Biosensors

Detecting vitamin deficiencies and addressing them

Radioactive bacteria

Magnetic bacteria

Organic art (fractals/chaos)