User:Wolfgang Pernice - Revision history

Wolfgang Pernice: /* Contact Info */

2012-03-12T23:25:46Z

Contact Info

←Older revision		Revision as of 23:25, 12 March 2012
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	*Wolfgang Pernice		*Wolfgang Pernice
-	*~~Imperial College London~~	+	*Columbia University Medical Center
-	*~~18 Courtfield Gardens~~	+	*New York City, US
-	*SW5 0PD	+	*wp2181@columbia.edu
-	*London, UK	+
-	*~~wolfgang.pernice08~~@~~imperial.ac~~.uk	+

	I work in the [[IGEM:IMPERIAL/2010]] at Imperial College London. I learned about [[OpenWetWare]] from my uni, and I've joined because of my participation in the Imperial College iGEM 2010 Team.		I work in the [[IGEM:IMPERIAL/2010]] at Imperial College London. I learned about [[OpenWetWare]] from my uni, and I've joined because of my participation in the Imperial College iGEM 2010 Team.

Wolfgang Pernice: /* Education */

2012-03-12T23:24:31Z

Education

←Older revision		Revision as of 23:24, 12 March 2012
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	==Education==		==Education==
	<!--Include info about your educational background-->		<!--Include info about your educational background-->
-	* ~~2nd, BS,~~ Imperial College London, ~~life sciences~~	+	* 2011 BSc Hon. Imperial College London
		+	* 2012-2015 PhD, Pathology and Molecular Medicine, Columbia University Medical Center

	==iGEM ideas==		==iGEM ideas==

Wolfgang Pernice: /* iGEM ideas */

2012-03-12T23:22:42Z

iGEM ideas

←Older revision		Revision as of 23:22, 12 March 2012
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	# Robust cell-cell communication pathways. Could be illustrated by e.g. stable and efficient communication between cells or directional cell migration in an environment with increased chemical noise.		# Robust cell-cell communication pathways. Could be illustrated by e.g. stable and efficient communication between cells or directional cell migration in an environment with increased chemical noise.
	# Switches, oscillators or logic gates with increased robustness to noises. A great example of how the processivity and functionality of such operators can be illustrated is shown by [http://www.cell.com/retrieve/pii/S0092867409005091 Tabor et al. 2009]: several genetic circuits were linked to an optical sensoring module in e.coli which caused the aggregation of bacterial colonies along light exposed areas. Thus the bacterial lawn reprinted a given projected pattern.		# Switches, oscillators or logic gates with increased robustness to noises. A great example of how the processivity and functionality of such operators can be illustrated is shown by [http://www.cell.com/retrieve/pii/S0092867409005091 Tabor et al. 2009]: several genetic circuits were linked to an optical sensoring module in e.coli which caused the aggregation of bacterial colonies along light exposed areas. Thus the bacterial lawn reprinted a given projected pattern.
-	# Stabilizing genetic information to ensure safety of recombinant organisms.	+	# Stabilizing genetic information to ensure safety of recombinant organisms.

	==Fv-fragment guided input module==		==Fv-fragment guided input module==

Wolfgang Pernice at 14:53, 14 July 2010

2010-07-14T14:53:26Z

←Older revision		Revision as of 14:53, 14 July 2010
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	==Schistosoma sensoring via Cercarial proteases==		==Schistosoma sensoring via Cercarial proteases==
-		+	[[Image:Igem Parasite protease sheme.bmp\|thumb\|right\|400px\|x300px\| Figure 3]]
	The cercarial stage of the schistosoma life-cycle represents the infective form for humans. Living in open or closed water systems, upon detection of skin-lipids the excretion of various proteases from primary secretory glands is triggered by thermal and chemical signals associated with skin lipids. Two major classes of proteases have been identified: a chemotrypsin like protease with specifity for large hydrophobic side chains and a trypsin like with preference for positively charged side chains ([http://www.jbc.org/content/275/49/38667.long (Salter et al 2000)]. A highly potent option is cercarial elastase (reference).		The cercarial stage of the schistosoma life-cycle represents the infective form for humans. Living in open or closed water systems, upon detection of skin-lipids the excretion of various proteases from primary secretory glands is triggered by thermal and chemical signals associated with skin lipids. Two major classes of proteases have been identified: a chemotrypsin like protease with specifity for large hydrophobic side chains and a trypsin like with preference for positively charged side chains ([http://www.jbc.org/content/275/49/38667.long (Salter et al 2000)]. A highly potent option is cercarial elastase (reference).

Wolfgang Pernice at 14:17, 14 July 2010

2010-07-14T14:17:51Z

←Older revision		Revision as of 14:17, 14 July 2010
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	==Schistosoma sensoring via Cercarial proteases==		==Schistosoma sensoring via Cercarial proteases==

-	The cercarial stage of the schistosoma life-cycle represents the infective form for humans. Living in open or closed water systems, upon detection of skin-lipids the excretion of various proteases from primary secretory glands is triggered by thermal and chemical signals associated with skin lipids. Two major classes of proteases have been identified: a chemotrypsin like protease with specifity for large hydrophobic side chains and a trypsin like with preference for positively charged side chains (Salter et al 2000). A highly potent option is cercarial elastase (reference).	+	The cercarial stage of the schistosoma life-cycle represents the infective form for humans. Living in open or closed water systems, upon detection of skin-lipids the excretion of various proteases from primary secretory glands is triggered by thermal and chemical signals associated with skin lipids. Two major classes of proteases have been identified: a chemotrypsin like protease with specifity for large hydrophobic side chains and a trypsin like with preference for positively charged side chains ([http://www.jbc.org/content/275/49/38667.long (Salter et al 2000)]. A highly potent option is cercarial elastase (reference).

	These proteases could be used to cleave membrane associated Fret-pairs, or release other response mediators from a membrane-scaffhold. This would e.g. produce a color response in the sample.		These proteases could be used to cleave membrane associated Fret-pairs, or release other response mediators from a membrane-scaffhold. This would e.g. produce a color response in the sample.

Wolfgang Pernice at 14:16, 14 July 2010

2010-07-14T14:16:26Z

←Older revision		Revision as of 14:16, 14 July 2010
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	* Production of '''false positives''' has to be prevented. A requirement for clustering and crosslinking of several receptors for signal generation could solve this problem.		* Production of '''false positives''' has to be prevented. A requirement for clustering and crosslinking of several receptors for signal generation could solve this problem.

		+	==Schistosoma sensoring via Cercarial proteases==
		+
		+	The cercarial stage of the schistosoma life-cycle represents the infective form for humans. Living in open or closed water systems, upon detection of skin-lipids the excretion of various proteases from primary secretory glands is triggered by thermal and chemical signals associated with skin lipids. Two major classes of proteases have been identified: a chemotrypsin like protease with specifity for large hydrophobic side chains and a trypsin like with preference for positively charged side chains (Salter et al 2000). A highly potent option is cercarial elastase (reference).
		+
		+	These proteases could be used to cleave membrane associated Fret-pairs, or release other response mediators from a membrane-scaffhold. This would e.g. produce a color response in the sample.
		+
		+
		+	Three key problems exist here:
		+
		+	* Artificial triggering of protease secretion of potential circaria in the sample. This can be achieved by using linoleic acid residues which can mimic skin lipids.
		+	* Targeting of the response carrier protein to the extracellular membrane.
		+	* Releasing a sufficiently strong signal to be detected by simple means. As e.g. spores can be stored easily and used in desired quantities, an additional way exists in which we can increase total concentration of e.g. color-response molecules to be released, in addition to high-level expression mechanisms.

Wolfgang Pernice at 21:02, 13 July 2010

2010-07-13T21:02:06Z

←Older revision		Revision as of 21:02, 13 July 2010
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	To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. [http://2008.igem.org/Team:Illinois/Antibody_RTK_Fusion Illinois 2008]). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.		To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. [http://2008.igem.org/Team:Illinois/Antibody_RTK_Fusion Illinois 2008]). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.
		+	[[Image:AB_signalling_image.bmp\|thumb\|right\|400px\|x300px\| Figure 2]]

-	#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast). ~~[[Image:AB_signalling_image.bmp]]~~	+	#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast).
	#. The detector protein is secreted into the extracellular environment.		#. The detector protein is secreted into the extracellular environment.
	#. Due to the high specificity of the Fv-fragment to its substrate, the detector protein binds to a given pathogen.		#. Due to the high specificity of the Fv-fragment to its substrate, the detector protein binds to a given pathogen.

Wolfgang Pernice at 21:00, 13 July 2010

2010-07-13T21:00:19Z

←Older revision		Revision as of 21:00, 13 July 2010
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	To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. [http://2008.igem.org/Team:Illinois/Antibody_RTK_Fusion Illinois 2008]). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.		To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. [http://2008.igem.org/Team:Illinois/Antibody_RTK_Fusion Illinois 2008]). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.

-	#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast).	+	#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast). [[Image:AB_signalling_image.bmp]]
	#. The detector protein is secreted into the extracellular environment.		#. The detector protein is secreted into the extracellular environment.
	#. Due to the high specificity of the Fv-fragment to its substrate, the detector protein binds to a given pathogen.		#. Due to the high specificity of the Fv-fragment to its substrate, the detector protein binds to a given pathogen.

Wolfgang Pernice at 20:57, 13 July 2010

2010-07-13T20:57:26Z

←Older revision		Revision as of 20:57, 13 July 2010
Line 32:		Line 32:
	==Fv-fragment guided input module==		==Fv-fragment guided input module==

-	To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. Illinois 2008). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.	+	To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. [http://2008.igem.org/Team:Illinois/Antibody_RTK_Fusion Illinois 2008]). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.

	#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast).		#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast).
Line 41:		Line 41:
	The system has several features which render it interesting:		The system has several features which render it interesting:

-	* An extremely broad array of potential targets that can be detected, exploiting the power of molecular recognition via Antibody fragments.	+	* An extremely '''broad array of potential targets''' that can be detected, exploiting the power of molecular recognition via Antibody fragments.
-	* A highly modular character. Exchangebility of specificity and potential to link the system to virtually any given response system	+	* A '''highly modular character'''. Exchangebility of specificity and potential to link the system to virtually any given response system
-	* Very close to real world applications (parasites, toxins etc).	+	* Very close to '''real world applications''' (parasites, toxins etc).
-	*	+

	Two central issues come along with this system:		Two central issues come along with this system:

-	* A suitable secretion system has to be found to allow efficient trafficing of the detector protein into the extracellular space.	+	* A suitable secretion system has to be found to allow '''efficient trafficing''' of the detector protein into the '''extracellular space'''.
-	* Production of false positives has to be prevented. A requirement for clustering and crosslinking of several receptors for signal generation could solve this problem.	+	* Production of '''false positives''' has to be prevented. A requirement for clustering and crosslinking of several receptors for signal generation could solve this problem.

Wolfgang Pernice: added Fv fragment system

2010-07-13T20:52:14Z

added Fv fragment system

←Older revision		Revision as of 20:52, 13 July 2010
Line 32:		Line 32:
	==Fv-fragment guided input module==		==Fv-fragment guided input module==

-	To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. Illinois 2008). To circumvent	+	To design detection-input mechanism with modular character, as opposed to the use of possibly existing two-component signalling cascades with specificity to e.g. parasite larval stages, we could exploit the specificity of antibodies to their substrate. Several teams in iGEM have used Ab's, attempting to alter the specificity of cell-surface receptors towards a desired target (e.g. Illinois 2008). To circumvent problems with direct manipulation of the receptor molecule, while incorporating the wide spectrum of potential targets, that could be recognized in an anitbody based approach, the Fv fragment of a given antibody is fused to the ligand of a suitable native two-component system. Figure 2 illustrates the principle of the Fv-fragment guided detection system.
		+
		+	#. Expression of the Fv-ligand-fusion protein (detector protein). Since the production of Fv fragments in prokaryotes has not been successful so far, a eukaryotic system is preferred (e.g. Yeast).
		+	#. The detector protein is secreted into the extracellular environment.
		+	#. Due to the high specificity of the Fv-fragment to its substrate, the detector protein binds to a given pathogen.
		+	#. Spatial co-localization of detector proteins on the pathogens surface is mirrored by clustering of receptors for the ligand-fragment, in the detector cell. This leads to the induction of a downstream signalling cascade to trigger a response module.
		+
		+	The system has several features which render it interesting:
		+
		+	* An extremely broad array of potential targets that can be detected, exploiting the power of molecular recognition via Antibody fragments.
		+	* A highly modular character. Exchangebility of specificity and potential to link the system to virtually any given response system
		+	* Very close to real world applications (parasites, toxins etc).
		+	*
		+
		+	Two central issues come along with this system:
		+
		+	* A suitable secretion system has to be found to allow efficient trafficing of the detector protein into the extracellular space.
		+	* Production of false positives has to be prevented. A requirement for clustering and crosslinking of several receptors for signal generation could solve this problem.
		+