IGEM:PennState/Labbook/Nimrah Ahmed - Revision history

Nimrah Ahmed: cleanup

Nimrah Ahmed — Tue, 20 May 2008 19:30:00 GMT

cleanup

←Older revision		Revision as of 19:30, 20 May 2008
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	\|colspan="2"\|		\|colspan="2"\|
	==Description/Abstract==		==Description/Abstract==
-	* Place short description of project or notes regarding this project	+	Currently working on finding a project


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	__NOEDITSECTION__		__NOEDITSECTION__
	__NOTOC__		__NOTOC__
-
-	~~==Meeting 5/15/2008==~~
-	~~===Circuit project ideas:===~~
-	* Genetic Circuit basics: http://www.princeton.edu/~rweiss/bio-programming/weiss-natural-computing-2003.pdf
-	~~====Sequential cell color change====~~
-	*ex. Green->Red->Yellow->repeat.
-	*System: organic layer & bacterial aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate color change.
-	*Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter
-
-	~~=====Components=====~~
-	* Organic compound: hydrophobic, heavy (won't evaporate), is recognized by cell
-	* Recognition compound(s): recognize organic compound and synthesize/activate something that activates promoter
-	* Promoter: probably lac
-	* Color proteins
-
-	~~=====Circuit=====~~
-
-	~~O -> A~~
-
-	~~A+B -> C, GFP~~
-
-	~~A+C -> B, YFP~~
-
-
-	*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.
-	*Intended result: shake once: GFP, shake again: YFP, shake again, GFP, etc.
-
-	~~=====Options:=====~~
-	*Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...
-	*Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''
-
-	~~(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)~~
-
-
-	~~[[User:Nimrah Ahmed\|Nimrah Ahmed]] 12:26, 15 May 2008 (EDT)~~
-
-
-	~~==Work Day Monday 5/19/2008==~~
-	*Introduction to lab & equipment
-	~~===Making Media===~~

Nimrah Ahmed: 5/19

Nimrah Ahmed — Mon, 19 May 2008 14:22:17 GMT

5/19

←Older revision		Revision as of 14:22, 19 May 2008
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		+	{\|{{table}} width="800"
		+	\|-
		+	\|style="background-color: #cdde95;" align="center"\|
		+	<!-- ## START calendar column -->
		+	<LNCalendar></LNCalendar>
		+	<!-- ## END calendar column -->
		+	\|align="center" style="background-color: #e5edc8;" \|
		+	<!-- ## START search column: Place your logo here. Try keep it below 200px in width and 150px in height. ## -->
		+	[[Image:igem-logo-150px.png\|150px]] <sitesearch>title=Search this Project</sitesearch>
		+	<!-- ## END search column ## -->
		+	\|-
		+	\|colspan="2" style="background-color: #F2F2F2;" align="right"\|[[/Entry_Base\|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page\|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
		+	\|-
		+	\|colspan="2"\|
		+	==Description/Abstract==
		+	* Place short description of project or notes regarding this project
		+
		+
		+	==Notes==
		+
		+	* Team meetings: Monday 5:00pm
		+
		+	\|-
		+	\|colspan="2" style="background-color: #F2F2F2;"\|
		+	{{LnNotebookRecentChanges2}}
		+	\|}
		+
		+
		+	__NOEDITSECTION__
		+	__NOTOC__
		+
	==Meeting 5/15/2008==		==Meeting 5/15/2008==
	===Circuit project ideas:===		===Circuit project ideas:===
Line 33:		Line 64:

	[[User:Nimrah Ahmed\|Nimrah Ahmed]] 12:26, 15 May 2008 (EDT)		[[User:Nimrah Ahmed\|Nimrah Ahmed]] 12:26, 15 May 2008 (EDT)
		+
		+
		+	==Work Day Monday 5/19/2008==
		+	*Introduction to lab & equipment
		+	===Making Media===

Nimrah Ahmed at 16:48, 15 May 2008

Nimrah Ahmed — Thu, 15 May 2008 16:48:32 GMT

←Older revision		Revision as of 16:48, 15 May 2008
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	*Intended result: shake once: GFP, shake again: YFP, shake again, GFP, etc.		*Intended result: shake once: GFP, shake again: YFP, shake again, GFP, etc.

-	Options:	+	=====Options:=====
	*Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...		*Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...
	*Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''		*Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''

Nimrah Ahmed at 16:48, 15 May 2008

Nimrah Ahmed — Thu, 15 May 2008 16:48:10 GMT

←Older revision		Revision as of 16:48, 15 May 2008
Line 8:		Line 8:

	=====Components=====		=====Components=====
-	* Organic compound: hydrophobic, heavy (won't evaporate), activates promoter	+	* Organic compound: hydrophobic, heavy (won't evaporate), is recognized by cell
-	* Promoter: lac~~, responds to organic~~	+	* Recognition compound(s): recognize organic compound and synthesize/activate something that activates promoter
		+	* Promoter: probably lac
	* Color proteins		* Color proteins

Nimrah Ahmed at 16:26, 15 May 2008

Nimrah Ahmed — Thu, 15 May 2008 16:26:11 GMT

←Older revision		Revision as of 16:26, 15 May 2008
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	=====Circuit=====		=====Circuit=====
-	~~<code>~~	+
	O -> A		O -> A
		+
	A+B -> C, GFP		A+B -> C, GFP
		+
	A+C -> B, YFP		A+C -> B, YFP
-	~~</code>~~	+

	*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.		*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.
Line 27:		Line 29:

	(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)		(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)
		+
		+
		+	[[User:Nimrah Ahmed\|Nimrah Ahmed]] 12:26, 15 May 2008 (EDT)

Nimrah Ahmed at 16:24, 15 May 2008

Nimrah Ahmed — Thu, 15 May 2008 16:24:49 GMT

←Older revision		Revision as of 16:24, 15 May 2008
Line 13:		Line 13:

	=====Circuit=====		=====Circuit=====
		+	<code>
	O -> A		O -> A
-
	A+B -> C, GFP		A+B -> C, GFP
-
	A+C -> B, YFP		A+C -> B, YFP
		+	</code>

	*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.		*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.

Nimrah Ahmed: /* Circuit */

Nimrah Ahmed — Thu, 15 May 2008 16:24:21 GMT

Circuit

←Older revision		Revision as of 16:24, 15 May 2008
Line 14:		Line 14:
	=====Circuit=====		=====Circuit=====
	O -> A		O -> A
		+
	A+B -> C, GFP		A+B -> C, GFP
		+
	A+C -> B, YFP		A+C -> B, YFP
		+
	*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.		*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.
	*Intended result: shake once: GFP, shake again: YFP, shake again, GFP, etc.		*Intended result: shake once: GFP, shake again: YFP, shake again, GFP, etc.

Nimrah Ahmed at 16:23, 15 May 2008

Nimrah Ahmed — Thu, 15 May 2008 16:23:52 GMT

←Older revision		Revision as of 16:23, 15 May 2008
Line 6:		Line 6:
	*System: organic layer & bacterial aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate color change.		*System: organic layer & bacterial aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate color change.
	*Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter		*Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter
-	*Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''

	=====Components=====		=====Components=====
Line 12:		Line 11:
	* Promoter: lac, responds to organic		* Promoter: lac, responds to organic
	* Color proteins		* Color proteins
		+
		+	=====Circuit=====
		+	O -> A
		+	A+B -> C, GFP
		+	A+C -> B, YFP
		+	*Degradation tags on A, B, C, GFP, YFP, strongest on A, weakest on B and C.
		+	*Intended result: shake once: GFP, shake again: YFP, shake again, GFP, etc.

	Options:		Options:
	*Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...		*Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...
		+	*Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''
		+
	(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)		(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)

Nimrah Ahmed: Expanding the color changer idea

Nimrah Ahmed — Thu, 15 May 2008 16:20:18 GMT

Expanding the color changer idea

←Older revision		Revision as of 16:20, 15 May 2008
Line 2:		Line 2:
	===Circuit project ideas:===		===Circuit project ideas:===
	* Genetic Circuit basics: http://www.princeton.edu/~rweiss/bio-programming/weiss-natural-computing-2003.pdf		* Genetic Circuit basics: http://www.princeton.edu/~rweiss/bio-programming/weiss-natural-computing-2003.pdf
-	*'''Sequential cell color change~~'''~~	+	====Sequential cell color change====
-	**ex. Green->Red->Yellow->repeat.	+	*ex. Green->Red->Yellow->repeat.
-	**System: organic layer & bacterial aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate color change.	+	*System: organic layer & bacterial aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate color change.
-	**Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter	+	*Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter
-	**Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''	+	*Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''
-	**Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...	+
		+	=====Components=====
		+	* Organic compound: hydrophobic, heavy (won't evaporate), activates promoter
		+	* Promoter: lac, responds to organic
		+	* Color proteins
		+
		+	Options:
		+	*Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...
	(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)		(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)

Nimrah Ahmed: /* Circuit project ideas: */

Nimrah Ahmed — Thu, 15 May 2008 15:34:18 GMT

Circuit project ideas:

←Older revision		Revision as of 15:34, 15 May 2008
Line 4:		Line 4:
	*'''Sequential cell color change'''		*'''Sequential cell color change'''
	**ex. Green->Red->Yellow->repeat.		**ex. Green->Red->Yellow->repeat.
-	**~~Possible system~~: organic layer & aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate ~~expression~~.	+	**System: organic layer & bacterial aquatic layer in liquid form. Shake to combine organic layer w/ bacterial aquatic layer -> initiate color change.
		+	**Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter
	**Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''		**Rather than shake, stir by '''thermal convection''' or a '''magnetic stirrer'''
	**Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...		**Bioluminescense : proteins like "M-Cherry" instead of flourescent proteins...
-	**Structure: Messenger protein downstream of color protein, downstream of organic molecule-activated promoter
	(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)		(Peking U did something like this--sequential color change--but UV activated. MIT team idea: bacterial lava lamp?)