User:Etienne Robillard/Notebook/Agent Ecoli:SolidPhasePeptideSynthesisReagentEvidencesInAgentScoobyDoo - Revision history

Etienne Robillard: /* Hypothesis */

Etienne Robillard — Thu, 13 Dec 2012 01:01:26 GMT

Hypothesis

←Older revision		Revision as of 01:01, 13 December 2012
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	* artificial cos-mid size is 30-45 bp length => reduced genome ?		* artificial cos-mid size is 30-45 bp length => reduced genome ?
	* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]		* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]
-	* [[IPTG]] induction is a chemical reaction which may be neutralized with 1mL NaHC03... (Sodium bicarbonate, 2.99$) [[http://en.wikipedia.org/wiki/Sodium_bicarbonate#Neutralization_of_acids_and_bases 1]] [[http://bioserv.fiu.edu/~biolab/labs/genetics/lac%20operon.htm 2]] [[http://www.openwetware.org/wiki/BE.109:Protein_engineering/Assessing_beta-galactosidase 3]]	+	* [[IPTG]] induction is a chemical reaction which may be neutralized with 1mL NaHC03... (Sodium bicarbonate, 2.99$) [[http://en.wikipedia.org/wiki/Sodium_bicarbonate#Neutralization_of_acids_and_bases 1]] [[http://bioserv.fiu.edu/~biolab/labs/genetics/lac%20operon.htm 2]] [[http://www.openwetware.org/wiki/BE.109:Protein_engineering/Assessing_beta-galactosidase 3]] [[http://www.openwetware.org/wiki/Beta-Galactosidase_Assay_(A_better_Miller) 4]]

	=== Experiment ===		=== Experiment ===

Etienne Robillard: /* Hypothesis */

Etienne Robillard — Thu, 13 Dec 2012 00:52:18 GMT

Hypothesis

←Older revision		Revision as of 00:52, 13 December 2012
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	* artificial cos-mid size is 30-45 bp length => reduced genome ?		* artificial cos-mid size is 30-45 bp length => reduced genome ?
	* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]		* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]
-	* [[IPTG]] induction is a chemical reaction which may be neutralized with 1mL NaHC03... (Sodium bicarbonate, 2.99$) [[http://en.wikipedia.org/wiki/Sodium_bicarbonate#Neutralization_of_acids_and_bases 1]] [[http://bioserv.fiu.edu/~biolab/labs/genetics/lac%20operon.htm 2]]	+	* [[IPTG]] induction is a chemical reaction which may be neutralized with 1mL NaHC03... (Sodium bicarbonate, 2.99$) [[http://en.wikipedia.org/wiki/Sodium_bicarbonate#Neutralization_of_acids_and_bases 1]] [[http://bioserv.fiu.edu/~biolab/labs/genetics/lac%20operon.htm 2]] [[http://www.openwetware.org/wiki/BE.109:Protein_engineering/Assessing_beta-galactosidase 3]]

	=== Experiment ===		=== Experiment ===

Etienne Robillard: /* Hypothesis */

Etienne Robillard — Thu, 13 Dec 2012 00:13:53 GMT

Hypothesis

←Older revision		Revision as of 00:13, 13 December 2012
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	* artificial cos-mid size is 30-45 bp length => reduced genome ?		* artificial cos-mid size is 30-45 bp length => reduced genome ?
	* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]		* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]
		+	* [[IPTG]] induction is a chemical reaction which may be neutralized with 1mL NaHC03... (Sodium bicarbonate, 2.99$) [[http://en.wikipedia.org/wiki/Sodium_bicarbonate#Neutralization_of_acids_and_bases 1]] [[http://bioserv.fiu.edu/~biolab/labs/genetics/lac%20operon.htm 2]]

	=== Experiment ===		=== Experiment ===

Etienne Robillard: /* References */

Etienne Robillard — Mon, 10 Dec 2012 14:36:18 GMT

References

←Older revision		Revision as of 14:36, 10 December 2012
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	* [http://cgsc.biology.yale.edu/Strain.php?ID=11958 E.coli B]: WOOP WOOP		* [http://cgsc.biology.yale.edu/Strain.php?ID=11958 E.coli B]: WOOP WOOP
	* [[IPTG]]		* [[IPTG]]
		+	* [[EDTA]]

Etienne Robillard: /* Hypothesis */

Etienne Robillard — Mon, 10 Dec 2012 14:35:38 GMT

Hypothesis

←Older revision		Revision as of 14:35, 10 December 2012
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	* methylamino buffering agents used as intermediates for orthogonal protection; (probably a side-effect of Magnesium chelation with EDTA?)		* methylamino buffering agents used as intermediates for orthogonal protection; (probably a side-effect of Magnesium chelation with EDTA?)
	* artificial cos-mid size is 30-45 bp length => reduced genome ?		* artificial cos-mid size is 30-45 bp length => reduced genome ?
-	* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of [[EDTA]] (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]	+	* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]

	=== Experiment ===		=== Experiment ===

Etienne Robillard: /* Hypothesis */

Etienne Robillard — Mon, 10 Dec 2012 14:34:06 GMT

Hypothesis

←Older revision		Revision as of 14:34, 10 December 2012
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	* methylamino buffering agents used as intermediates for orthogonal protection; (probably a side-effect of Magnesium chelation with EDTA?)		* methylamino buffering agents used as intermediates for orthogonal protection; (probably a side-effect of Magnesium chelation with EDTA?)
	* artificial cos-mid size is 30-45 bp length => reduced genome ?		* artificial cos-mid size is 30-45 bp length => reduced genome ?
		+	* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of [[EDTA]] (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]

	=== Experiment ===		=== Experiment ===

Etienne Robillard: /* Measuring the amplitude of the synthetic reagent lysis TE buffer on NMDA receptor */

Etienne Robillard — Mon, 10 Dec 2012 13:47:28 GMT

Measuring the amplitude of the synthetic reagent lysis TE buffer on NMDA receptor

←Older revision		Revision as of 13:47, 10 December 2012
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	* Date: 2012/12/03 10:29 AM EDT		* Date: 2012/12/03 10:29 AM EDT
	* Organism: E. coli (K-12 substr.)		* Organism: E. coli (K-12 substr.)
-	* Strain: ~~Probably D1210, a HB101~~/~~K-12 hybrid strain which overexpress the Lacl repressor~~.	+	* Strain: [http://cgsc2.biology.yale.edu/Strain.php?ID=65553 BW26434]


	=== Hypothesis ===		=== Hypothesis ===

-	Amine protection groups (piperidine based) undergo chiral nucleophilic substitution on Histidine based autophosphorylation.	+	* Amine protection groups (piperidine based) undergo chiral nucleophilic substitution on Histidine based autophosphorylation.
		+	* Cosmid like recombinase system for -35 lacl+ (LacZ) transcription, thus no infection produced; (no lacY)
		+	* orthogonal oligo/peptide protection using methylamino (methyltransferase) agents;
		+	* methylamino buffering agents used as intermediates for orthogonal protection; (probably a side-effect of Magnesium chelation with EDTA?)
		+	* artificial cos-mid size is 30-45 bp length => reduced genome ?

	=== Experiment ===		=== Experiment ===

Etienne Robillard: /* Expected results */

Etienne Robillard — Fri, 07 Dec 2012 13:23:14 GMT

Expected results

←Older revision		Revision as of 13:23, 7 December 2012
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	*** HB101 F– Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Strr) xyl-5 mtl-1 recA13h		*** HB101 F– Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Strr) xyl-5 mtl-1 recA13h
	* (2R)-2-(methylamino)succinic acid - An orthogonal N-methyltransferase/NH2 base labile compound; exogenous NMDA receptor antagonist compound (Ketamine-like); synthetically recombined oligonucleotide protection group (dA-dT) for solid-phase peptide synthesis (SPPS), etc (see also [[PHP]], [[Succinic_acid]], and BW26434.)		* (2R)-2-(methylamino)succinic acid - An orthogonal N-methyltransferase/NH2 base labile compound; exogenous NMDA receptor antagonist compound (Ketamine-like); synthetically recombined oligonucleotide protection group (dA-dT) for solid-phase peptide synthesis (SPPS), etc (see also [[PHP]], [[Succinic_acid]], and BW26434.)
		+	** important: N-methyl-D-asparte receptor is a "sensory" neurotransmitter with analogous functions to the TRPV neurotransmitter but for brain functions including learning and memory.

	==== References ====		==== References ====

Etienne Robillard: /* Expected results */

Etienne Robillard — Fri, 07 Dec 2012 12:56:31 GMT

Expected results

←Older revision		Revision as of 12:56, 7 December 2012
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	** From [http://www.sigmaaldrich.com/life-science/molecular-biology/cloning-and-expression/learning-center/genotypes-of-e-coli.html Sigma], the expected genotype matching the laclq strain is:		** From [http://www.sigmaaldrich.com/life-science/molecular-biology/cloning-and-expression/learning-center/genotypes-of-e-coli.html Sigma], the expected genotype matching the laclq strain is:
	*** HB101 F– Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Strr) xyl-5 mtl-1 recA13h		*** HB101 F– Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Strr) xyl-5 mtl-1 recA13h
		+	* (2R)-2-(methylamino)succinic acid - An orthogonal N-methyltransferase/NH2 base labile compound; exogenous NMDA receptor antagonist compound (Ketamine-like); synthetically recombined oligonucleotide protection group (dA-dT) for solid-phase peptide synthesis (SPPS), etc (see also [[PHP]], [[Succinic_acid]], and BW26434.)

	==== References ====		==== References ====

Etienne Robillard: /* Measuring the amplitude of the synthetic reagent lysis TE buffer on NMDA receptor */

Etienne Robillard — Wed, 05 Dec 2012 00:57:33 GMT

Measuring the amplitude of the synthetic reagent lysis TE buffer on NMDA receptor

←Older revision		Revision as of 00:57, 5 December 2012
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	* Date: 2012/12/03 10:29 AM EDT		* Date: 2012/12/03 10:29 AM EDT
	* Organism: E. coli (K-12 substr.)		* Organism: E. coli (K-12 substr.)
-	* Strain: ~~MG1655(?)~~	+	* Strain: Probably D1210, a HB101/K-12 hybrid strain which overexpress the Lacl repressor.
		+

	=== Hypothesis ===		=== Hypothesis ===
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	* [http://cgsc.biology.yale.edu/Strain.php?ID=9130 AB266]		* [http://cgsc.biology.yale.edu/Strain.php?ID=9130 AB266]
	* [http://cgsc.biology.yale.edu/Strain.php?ID=11958 E.coli B]: WOOP WOOP		* [http://cgsc.biology.yale.edu/Strain.php?ID=11958 E.coli B]: WOOP WOOP
		+	* [[IPTG]]