Sebastian Maerkl, Apr 2013 - Revision history

Murray: /* Seminar */

2014-04-06T20:55:11Z

Seminar

← Older revision		Revision as of 20:55, 6 April 2014
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	7 Apr (Mon), 2-3 pm<br>		7 Apr (Mon), 2-3 pm<br>
	<s>111 Keck</s><font color=blue>213 Annenberg</font>		<s>111 Keck</s> <font color=blue>213 Annenberg</font>

	Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.		Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.

	One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.		One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.

Murray: /* Seminar */

2014-04-06T20:55:02Z

Seminar

← Older revision		Revision as of 20:55, 6 April 2014
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	7 Apr (Mon), 2-3 pm<br>		7 Apr (Mon), 2-3 pm<br>
	<s>111 Keck></s><font color=blue>213 Annenberg</font>		<s>111 Keck</s><font color=blue>213 Annenberg</font>

	Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.		Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.

	One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.		One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.

Murray: /* Seminar */

2014-04-06T20:54:47Z

Seminar

← Older revision		Revision as of 20:54, 6 April 2014
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	7 Apr (Mon), 2-3 pm<br>		7 Apr (Mon), 2-3 pm<br>
	<~~s111~~ Keck></s><font color=blue>213 Annenberg</font>		<s>111 Keck></s><font color=blue>213 Annenberg</font>

	Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.		Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.

	One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.		One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.

Murray: /* Seminar */

2014-04-06T20:54:38Z

Seminar

← Older revision		Revision as of 20:54, 6 April 2014
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	7 Apr (Mon), 2-3 pm<br>		7 Apr (Mon), 2-3 pm<br>
	<s111 Keck></s><font color=blue>213 Annenberg</~~blue~~>		<s111 Keck></s><font color=blue>213 Annenberg</font>

	Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.		Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.

	One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.		One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.

Murray: /* Seminar */

2014-04-06T20:54:29Z

Seminar

← Older revision		Revision as of 20:54, 6 April 2014
Line 28:		Line 28:

	7 Apr (Mon), 2-3 pm<br>		7 Apr (Mon), 2-3 pm<br>
	~~111~~ Keck		<s111 Keck></s><font color=blue>213 Annenberg</blue>

	Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.		Living cells maintain a steady state of biochemical reaction rates by exchanging energy and matter with the environment. These exchanges usually do not occur in in vitro systems, which consequently go to chemical equilibrium. This in turn has severely constrained the complexity of biological networks that can be implemented in vitro. We developed nanoliter-scale microfluidic reactors that exchange reagents at dilution rates matching those of dividing bacteria. In these reactors we achieved transcription and translation at steady state for 30 h and implemented diverse regulatory mechanisms on the transcriptional, translational, and posttranslational levels, including RNA polymerases, transcriptional repression, translational activation, and proteolysis. We constructed and implemented an in vitro genetic oscillator and mapped its phase diagram showing that steady-state conditions were necessary to produce oscillations.

	One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.		One potential application of in vitro synthetic biology is rapid prototyping of genetic circuits. This in turn requires that components and systems can be transferred from in vitro to in vivo, which has not yet been demonstrated for more complex genetic circuits. I will present recent results indicating that it is possible to transfer a functional in vivo genetic circuit (the repressilator) to our in vitro environment as a first step towards closing the loop between in vitro characterization and optimization of genetic circuits and their in vivo implementation.

Murray: /* Schedule */

2014-04-06T20:54:09Z

Schedule

← Older revision		Revision as of 20:54, 6 April 2014
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	* 1:30 pm - Open		* 1:30 pm - Open
	* 2 pm - Seminar, 213 ANB		* 2 pm - Seminar, 213 ANB
			** Michael Elowitz and Rustem Ismagilov will attend
	* 3 pm - Open discussions (after seminar)		* 3 pm - Open discussions (after seminar)
	* 4 pm - Dan Siegal-Gaskins		* 4 pm - Dan Siegal-Gaskins

Murray: /* Schedule */

2014-04-06T20:53:31Z

Schedule

← Older revision		Revision as of 20:53, 6 April 2014
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	Monday		Monday
	* 10 am - meeting with Richard		* 10 am - meeting with Richard, 109 Steele Lab
	* 11 am - open (Zach?)		* 11 am - open (Zach?)
	* 12 pm - lunch with Richard and Zach?		* 12 pm - lunch with Richard and Zach
	* 2 pm - ~~Informal seminar~~		* 1:30 pm - Open
	* 3 pm - Open discussions		* 2 pm - Seminar, 213 ANB
	* 4 pm - Dan ~~(flexible; any time on Monday)~~		* 3 pm - Open discussions (after seminar)
			* 4 pm - Dan Siegal-Gaskins

	Tuesday		Tuesday
	* ~~Individual meetings~~		* 9 am - noon: Biocircuits group meeting, 111 Keck (optional)
	* ALL demo and microfluidics discussion (Enoch/Sean) ~~(time flexible)~~		* 11 am - ALL demo and microfluidics discussion (Enoch/Sean)
	* 2 pm - Yutaka ~~(time flexible; any time in Tuesday afternoon)~~		* 12:30 - Lunch
			* 2 pm - Yutaka Hori
	* 5 pm - Done for the day		* 5 pm - Done for the day

Dsiegalg: /* Schedule */

2014-04-04T21:36:02Z

Schedule

← Older revision		Revision as of 21:36, 4 April 2014
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	* 2 pm - Informal seminar		* 2 pm - Informal seminar
	* 3 pm - Open discussions		* 3 pm - Open discussions
	* 4 pm - ~~Individual meetings~~		* 4 pm - Dan (flexible; any time on Monday)

	Tuesday		Tuesday

Srsanche at 18:29, 4 April 2014

2014-04-04T18:29:48Z

← Older revision		Revision as of 18:29, 4 April 2014
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	Tuesday		Tuesday
	* Individual meetings		* Individual meetings
	* ALL demo (Sean~~/Enoch~~)?		* ALL demo and microfluidics discussion (Enoch/Sean) (time flexible)
	* 2 pm - Yutaka (time flexible; any time in Tuesday afternoon)		* 2 pm - Yutaka (time flexible; any time in Tuesday afternoon)
	* 5 pm - Done for the day		* 5 pm - Done for the day

Yhori: /* Schedule */

2014-04-04T05:50:52Z

Schedule

← Older revision		Revision as of 05:50, 4 April 2014
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	* Individual meetings		* Individual meetings
	* ALL demo (Sean/Enoch)?		* ALL demo (Sean/Enoch)?
			* 2 pm - Yutaka (time flexible; any time in Tuesday afternoon)
	* 5 pm - Done for the day		* 5 pm - Done for the day