Synthetic Biology Network Research - Revision history

Macampbell at 20:21, 7 March 2012

2012-03-07T20:21:11Z

Macampbell at 20:20, 7 March 2012

2012-03-07T20:20:53Z

Macampbell at 20:19, 7 March 2012

2012-03-07T20:19:27Z

ToEckdahl at 13:37, 7 March 2012

2012-03-07T13:37:16Z

ToEckdahl at 13:35, 7 March 2012

2012-03-07T13:35:03Z

ToEckdahl at 22:17, 6 March 2012

2012-03-06T22:17:56Z

ToEckdahl at 20:57, 6 March 2012

2012-03-06T20:57:39Z

Ccarr: /* MWSU */

2012-02-17T23:48:14Z

‎MWSU

Ccarr: /* MWSU */

2012-02-17T23:43:28Z

‎MWSU

Macampbell at 13:33, 26 January 2012

2012-01-26T13:33:49Z

← Older revision		Revision as of 20:21, 7 March 2012
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−	~~<a name="MWSU"></a>~~
	==MWSU==		==MWSU==
	2-17-2012		2-17-2012

← Older revision		Revision as of 20:20, 7 March 2012
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−	This page is designed as a community page for students at ~~<a href="~~#MWSU">MWSU~~</a>~~ and Davidson College who are using synthetic biology to learn more about graph theory and network topology.	+	This page is designed as a community page for students at [[#MWSU\| MWSU ]] and Davidson College who are using synthetic biology to learn more about graph theory and network topology.

	==Davidson College==		==Davidson College==

@@ Line 1: / Line 1: @@
-This page is designed as a community page for students at MWSU and Davidson College who are using synthetic biology to learn more about graph theory and network topology.
+This page is designed as a community page for students at <a href="#MWSU">MWSU</a> and Davidson College who are using synthetic biology to learn more about graph theory and network topology.
 ==Davidson College==
@@ Line 138: / Line 138: @@
+<a name="MWSU"></a>
 ==MWSU==
 -17-2012

← Older revision		Revision as of 13:37, 7 March 2012
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	Programming_Bacteria_for_Optimization_of_Genetic_Circuits: [[Media:Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎]]		Programming_Bacteria_for_Optimization_of_Genetic_Circuits: [[Media:Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎]]

−	~~[[Media:Automated_Design_of_Synthetic_RBS's_to_Control_Protein_Expression.pdf‎~~ Automated Design of Synthetic RBS's to Control Protein Expression]]	+	Automated Design of Synthetic RBS's to Control Protein Expression: [[Media:Automated_Design_of_Synthetic_RBS's_to_Control_Protein_Expression.pdf‎]]

← Older revision		Revision as of 13:35, 7 March 2012
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	Programming_Bacteria_for_Optimization_of_Genetic_Circuits: [[Media:Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎]]		Programming_Bacteria_for_Optimization_of_Genetic_Circuits: [[Media:Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎]]
		+
		+	[[Media:Automated_Design_of_Synthetic_RBS's_to_Control_Protein_Expression.pdf‎ Automated Design of Synthetic RBS's to Control Protein Expression]]

← Older revision		Revision as of 22:17, 6 March 2012
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	-Caleb Carr		-Caleb Carr

−	Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎	+	Programming_Bacteria_for_Optimization_of_Genetic_Circuits: [[Media:Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎]]

← Older revision		Revision as of 20:57, 6 March 2012
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	-Caleb Carr		-Caleb Carr
		+
		+	Programming_Bacteria_for_Optimization_of_Genetic_Circuits.pptx‎

← Older revision		Revision as of 23:48, 17 February 2012
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	Long and short, we give them the tools to solve a problem or to build a pathway, and see if they can get it right. At this stage, there are no restrictions on this idea as it is still in its infancy.		Long and short, we give them the tools to solve a problem or to build a pathway, and see if they can get it right. At this stage, there are no restrictions on this idea as it is still in its infancy.
		+
		+	-Caleb Carr

← Older revision		Revision as of 23:43, 17 February 2012
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	==MWSU==		==MWSU==
		+	2-17-2012
		+
		+	'''"Networks and confusion"'''
		+
		+	I have been attempting to work through the current tentative idea for our approach to network projects. I was originally confused by the idea that we would optimize an entire genome via varying RBC's, promoters, degradation tags, etc, and that we could call that a network. To make sense of the general idea of a network that we could design and eventually "train" to function, I went back to the start of what makes a network a network.
		+
		+	A network is a specified pathway that via interaction with a stimulus produces/degrades/builds/reacts. Antibiotic resistance is a reaction to a stimulus, but generally only uses one gene to create resistance. Whereas a metabolic pathway can use a small number to many different "nodes" or parts to the system to produce a single overall reaction in response to the stimulus.
		+
		+	I had an idea, this is a generalized idea, is in no way complete, but should be used as the jumping-off point. It is this: Evolution, via phenotype variation, has created the myriad of reporters and selection tools we use currently in our labs to determine if our bacteria are behaving the way we want them to. In the evolution of the various types of antibiotics we have discovered and utilize to kill bacterium, so too have those bacteria evolved to resist these killers. Looking at the scope of the interaction that a bacterium community would have to undergo in order to build a resistance to an antibiotic, one can see that it isn't likely a quick thing. however, may antibiotics are similar in function, and the resistance we encode many of our projects with are similar in their DNA construct and function as well.
		+
		+	'''Generalized proposal using antibiotic resistance as the stand-in for network function:'''''Italic text''
		+
		+	Using a bacterial strain resistant to a specific antibiotic, we add the "tools" for said bacteria to become resistant to a different but similar antibiotic by chopping up the DNA that would give them resistance and adding them to the genome of the aforementioned bacteria. Basically, we would be smashing and then giving a Rubik's cube to blind bacteria, and ordering them to put it together or we allow the new antibiotic to shoot them. We then politely poke and prod them to get to work by reassembling, chopping, and trying out new ways to use these pieces. Along the way, we use the phenotypic variation (which is inherent in all organisms) of these bacteria to train some of them (hopefully the ones that at least got part of the puzzle correct) to reach the end of a "stepwise" pathway and put the Rubik's cube back together. This pathway, keeping in mind the phenotype variation of these bacteria, doesn't have to be A-B-C-END. They might start with small a, or a triangle that strongly resembles an A, but still something similar enough to deliver the end result: resistance to a new antibiotic. This will almost assuredly be a poly-divergent pathway from start to finish. Much like many people are tall and many are small, but some of the small and the tall have dark hair or light hair, we would use the variation of our bacteria to get them from ~A through to the END. It wouldn't matter how they got to the end, even if they take shortcuts, as long as they get there, all they have to do is tell us how they did it.
		+
		+	Long and short, we give them the tools to solve a problem or to build a pathway, and see if they can get it right. At this stage, there are no restrictions on this idea as it is still in its infancy.

← Older revision		Revision as of 13:33, 26 January 2012
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−	[[WEEK THIRTEEN (April 9 - 13)]] '''INCLUDES EASTER BREAK'''	+	[[WEEK THIRTEEN (April 9 - 13)]] '''INCLUDES EASTER BREAK'''<br>
		+	Genomics Seminar 4:30 pm April. 11 in '''Dana 146''' and '''lunch''' with [http://guolab.uncc.edu/members/jguo4 speaker Dr. Jun-tao Gua] at UNCC Bioinformatics