SURF 2018: Resource Usage in TX-TL - Revision history

Wpoole at 22:00, 11 December 2017

2017-12-11T22:00:20Z

← Older revision		Revision as of 22:00, 11 December 2017
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	The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.		The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.

	~~'''Background / Skills '''~~

	Potential SURFs should have taken courses in basic chemistry and biology, including at least one class with a laboratory component. Additionally the ability to simulate ordinary differential equations or models in Python/MATLAB will be necessary. Finally, a large component of this project will be hands-on~~-experiment~~ work to design and construct the reservoir system, so experience building things will be helpful.		'''Background / Skills: '''

			Potential SURFs should have taken courses in basic chemistry and biology, including at least one class with a laboratory component. Additionally the ability to simulate ordinary differential equations or models in Python/MATLAB will be necessary. Finally, a large component of this project will be hands-on work to design and construct the reservoir system, so experience building things will be helpful.


	'''Relevant References:'''		'''Relevant References:'''

Wpoole at 21:58, 11 December 2017

2017-12-11T21:58:41Z

← Older revision		Revision as of 21:58, 11 December 2017
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	The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.		The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.

	~~<!-- Add something here about background skills~~, ~~etc that~~ a ~~student should have~~. -->		'''Background / Skills '''

			Potential SURFs should have taken courses in basic chemistry and biology, including at least one class with a laboratory component. Additionally the ability to simulate ordinary differential equations or models in Python/MATLAB will be necessary. Finally, a large component of this project will be hands-on-experiment work to design and construct the reservoir system, so experience building things will be helpful.

	'''Relevant References:'''		'''Relevant References:'''

Murray: Murray moved page SURF 2018:Resource Usage in TX-TL to SURF 2018: Resource Usage in TX-TL without leaving a redirect

2017-12-09T18:20:24Z

Murray moved page SURF 2018:Resource Usage in TX-TL to SURF 2018: Resource Usage in TX-TL without leaving a redirect

← Older revision		Revision as of 18:20, 9 December 2017
(No difference)

Murray: Murray moved page SURF 2018:Resource Usage in TXTL to SURF 2018:Resource Usage in TX-TL

2017-12-09T18:18:27Z

Murray moved page SURF 2018:Resource Usage in TXTL to SURF 2018:Resource Usage in TX-TL

← Older revision		Revision as of 18:18, 9 December 2017
(No difference)

Murray at 18:18, 9 December 2017

2017-12-09T18:18:11Z

← Older revision		Revision as of 18:18, 9 December 2017
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			'''[[SURF 2018\|2018 SURF]]: project description'''
			* Mentor: Richard M. Murray
			* Co-mentor: William Poole


	The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.		The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.

			<!-- Add something here about background skills, etc that a student should have. -->

	'''Relevant References:'''		'''Relevant References:'''

Wpoole at 20:13, 8 December 2017

2017-12-08T20:13:58Z

← Older revision		Revision as of 20:13, 8 December 2017
Line 1:		Line 1:
	The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.		The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.

	Relevant References:		'''Relevant References:'''

	The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology: https://www.ncbi.nlm.nih.gov/pubmed/26818434		The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology: https://www.ncbi.nlm.nih.gov/pubmed/26818434

Wpoole at 20:12, 8 December 2017

2017-12-08T20:12:59Z

← Older revision		Revision as of 20:12, 8 December 2017
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	Relevant References:		Relevant References:
	The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology: https://www.ncbi.nlm.nih.gov/pubmed/26818434		The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology: https://www.ncbi.nlm.nih.gov/pubmed/26818434
	Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System: http://pubs.acs.org/doi/abs/10.1021/sb400131a
			Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System:
			http://pubs.acs.org/doi/abs/10.1021/sb400131a

	Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”: http://pubs.acs.org/doi/10.1021/sb400203p		Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”: http://pubs.acs.org/doi/10.1021/sb400203p

	Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system: https://www.ncbi.nlm.nih.gov/pubmed/8620031		Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system: https://www.ncbi.nlm.nih.gov/pubmed/8620031

Wpoole at 20:12, 8 December 2017

2017-12-08T20:12:39Z

← Older revision		Revision as of 20:12, 8 December 2017
Line 2:		Line 2:

	Relevant References:		Relevant References:
	~~<a href="https://www.ncbi.nlm.nih.gov/pubmed/26818434">~~The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology~~.</a>~~		The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology: https://www.ncbi.nlm.nih.gov/pubmed/26818434
	~~<a href="http~~://~~pubs~~.~~acs~~.~~org~~/~~doi~~/~~abs/10.1021/sb400131a">~~Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System~~.</a>~~		Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System: http://pubs.acs.org/doi/abs/10.1021/sb400131a
	~~<a href="~~http://pubs.acs.org/doi/10.1021/~~sb400203p">~~Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”~~.</a>~~		Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”: http://pubs.acs.org/doi/10.1021/sb400203p
	~~<a href="https~~://~~www~~.~~ncbi~~.~~nlm~~.~~nih.gov~~/~~pubmed/8620031">~~Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system..</a>		Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system: https://www.ncbi.nlm.nih.gov/pubmed/8620031

Wpoole: SURF 2018: Resource Usage in TXTL

2017-12-08T20:07:29Z

SURF 2018: Resource Usage in TXTL

New page

The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.

Relevant References:
<a href="https://www.ncbi.nlm.nih.gov/pubmed/26818434">The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology.</a>
<a href="http://pubs.acs.org/doi/abs/10.1021/sb400131a">Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System.</a>
<a href="http://pubs.acs.org/doi/10.1021/sb400203p">Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”.</a>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/8620031">Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system..</a>