Projects/Synthetic Biology - Revision history

Georgiev: /* Modular Transcriptional Riboregulation */

2015-03-08T20:59:12Z

‎Modular Transcriptional Riboregulation

Zach at 15:53, 5 March 2015

2015-03-05T15:53:08Z

Georgiev: /* Programmable Dynamic Riboregulation */

2015-03-05T14:44:56Z

‎Programmable Dynamic Riboregulation

Zach: /* Modular Transcriptional Riboregulation */

2015-03-05T14:42:24Z

‎Modular Transcriptional Riboregulation

Hynek: /* Programmable Dynamic Riboregulation */

2015-03-05T14:41:38Z

‎Programmable Dynamic Riboregulation

Georgiev: /* Programmable Dynamic Riboregulation */

2015-03-05T14:40:33Z

‎Programmable Dynamic Riboregulation

Georgiev: /* Programmable Dynamic Riboregulation */

2015-03-05T14:40:08Z

‎Programmable Dynamic Riboregulation

Georgiev: /* Division Control */

2015-03-05T14:39:53Z

‎Division Control

Hynek: /* Programmable Dynamic Riboregulation */

2015-03-05T14:39:28Z

‎Programmable Dynamic Riboregulation

Zach: /* Modular Transcriptional Riboregulation */

2015-03-05T14:33:10Z

‎Modular Transcriptional Riboregulation

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 ==Modular Transcriptional Riboregulation==
 [[File:riboswitch.png|thumb|right|alt=-|Theophylline responsive transcriptional riboregulator.]]
-In cooperation with the Universitat Politécnica de Valencia and IBMCP, Spain, we showed that controller inputs based on metabolite measurements can outperform the controller inputs based on enzyme measurements and that transcriptional regulation is advantageous in the regulation of large operons. To address challenges of rational design of transcriptional regulation based on metabolite measurements, we proposed a novel mechanism motivated by easily designable elements from translational regulation. These adaptors use transcriptional-translational coupling in prokaryotes and are potentially scalable to more larger logic circuits.
+In cooperation with the Universitat Politécnica de Valencia and IBMCP, Spain, we showed that controller inputs based on metabolite measurements can outperform the controller inputs based on enzyme measurements and that transcriptional regulation is advantageous in the regulation of large operons. To address challenges of rational design of transcriptional regulation based on metabolite measurements, we proposed a novel mechanism motivated by easily designable elements from translational regulation. These adaptors use transcriptional-translational coupling in prokaryotes and are potentially scalable to larger logic circuits.
 <br>

← Older revision		Revision as of 15:53, 5 March 2015
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		+	__NOTOC__
	==Gene Tuning==		==Gene Tuning==
	[[File:wiki_GeneTuning.png\|thumb\|right\|alt=gfp under control of placI.\|GFP under control of pLacI.]]		[[File:wiki_GeneTuning.png\|thumb\|right\|alt=gfp under control of placI.\|GFP under control of pLacI.]]

@@ Line 10: / Line 10: @@
 ==Programmable Dynamic Riboregulation==
-[[File:riboswitch.png|thumb|right|alt=-|Dynamic programmable riboregulator workflow.]]
+[[File:Ribocounter_2.png|thumb|right|alt=-|Dynamic programmable riboregulator workflow.]]
 Riboregulators represent an important class of genetic regulatory devices whose behaviour is programmable by specification of the underlying nucleic acid sequence.  Both natural and synthetic riboregulators are often modelled as static devices that activate or repress potential RNA binding sites.   Individual riboregulators are thereby functionally similar to linear gains found in electrical systems.  While in silico design tools have been developed to maximize their in vivo performance, design of dynamic behaviour has yet to be considered.  Herein a simple riboregulator design is proposed that appends programmable dynamic behavior to existing riboswitches.  Specifically, the resulting device is shown to produce an all-or-nothing response.  Simple design rules for this device are derived.
 <br>

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 ==Modular Transcriptional Riboregulation==
 [[File:riboswitch.png|thumb|right|alt=-|Theophylline responsive transcriptional riboregulator.]]
 <br>

@@ Line 9: / Line 9: @@
 ==Programmable Dynamic Riboregulation==
-[[File:riboswitch.png|thumb|right|alt=-|Theophylline responsive transcriptional riboregulator.]]
+[[File:riboswitch.png|thumb|right|alt=-|Dynamic programmable riboregulator workflow.]]
 Riboregulators represent an important class of genetic regulatory devices whose behaviour is programmable by specification of the underlying nucleic acid sequence.  Both natural and synthetic riboregulators are often modelled as static devices that activate or repress potential RNA binding sites.   Individual riboregulators are thereby functionally similar to linear gains found in electrical systems.  While in silico design tools have been developed to maximize their in vivo performance, design of dynamic behaviour has yet to be considered.  Herein a simple riboregulator design is proposed that appends programmable dynamic behavior to existing riboswitches.  Specifically, the resulting device is shown to produce an all-or-nothing response.  Simple design rules for this device are derived.
 <br>

← Older revision		Revision as of 14:40, 5 March 2015
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	[[File:riboswitch.png\|thumb\|right\|alt=-\|Theophylline responsive transcriptional riboregulator.]]		[[File:riboswitch.png\|thumb\|right\|alt=-\|Theophylline responsive transcriptional riboregulator.]]
		+	<br>

	==Division Control==		==Division Control==

← Older revision		Revision as of 14:39, 5 March 2015
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	Time lapse of E. coli with an integrated Min D::GFP fusion protein. Observed spatial-temporal oscillations are critical for correct cell division.		Time lapse of E. coli with an integrated Min D::GFP fusion protein. Observed spatial-temporal oscillations are critical for correct cell division.

−	<mediaplayer width='~~550~~' height='300'>http://www.ccy.zcu.cz/movies/Osc_video.mov</mediaplayer>	+	<mediaplayer width='500' height='300'>http://www.ccy.zcu.cz/movies/Osc_video.mov</mediaplayer>

← Older revision		Revision as of 14:39, 5 March 2015
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	Riboregulators represent an important class of genetic regulatory devices whose behaviour is programmable by specification of the underlying nucleic acid sequence. Both natural and synthetic riboregulators are often modelled as static devices that activate or repress potential RNA binding sites. Individual riboregulators are thereby functionally similar to linear gains found in electrical systems. While in silico design tools have been developed to maximize their in vivo performance, design of dynamic behaviour has yet to be considered. Herein a simple riboregulator design is proposed that appends programmable dynamic behavior to existing riboswitches. Specifically, the resulting device is shown to produce an all-or-nothing response. Simple design rules for this device are derived.		Riboregulators represent an important class of genetic regulatory devices whose behaviour is programmable by specification of the underlying nucleic acid sequence. Both natural and synthetic riboregulators are often modelled as static devices that activate or repress potential RNA binding sites. Individual riboregulators are thereby functionally similar to linear gains found in electrical systems. While in silico design tools have been developed to maximize their in vivo performance, design of dynamic behaviour has yet to be considered. Herein a simple riboregulator design is proposed that appends programmable dynamic behavior to existing riboswitches. Specifically, the resulting device is shown to produce an all-or-nothing response. Simple design rules for this device are derived.
		+
		+	[[File:riboswitch.png\|thumb\|right\|alt=-\|Theophylline responsive transcriptional riboregulator.]]

	==Division Control==		==Division Control==