Modeling of biological hash function - Revision history

Eckdahl at 16:29, 28 October 2008

2008-10-28T16:29:21Z

Eckdahl at 16:28, 28 October 2008

2008-10-28T16:28:56Z

Eckdahl at 16:28, 28 October 2008

2008-10-28T16:28:26Z

Eckdahl at 16:27, 28 October 2008

2008-10-28T16:27:38Z

Eckdahl at 16:23, 28 October 2008

2008-10-28T16:23:37Z

Eckdahl at 16:20, 28 October 2008

2008-10-28T16:20:14Z

BoCool at 15:55, 28 October 2008

2008-10-28T15:55:03Z

New page

== Davidson XOR Biological Design ==
[http://partsregistry.org/AHL '''List of auto-inducers and their catalog numbers.''']
 
<center>'''Davidson Approach''' 
'''Here is an idea Malcolm and Laurie developed.''' 
'''Everyone please look at this and ask questions and find holes in it now so we don't waste time building something that won't work.''' </center>

<center> [[Image:XOR_AMC1b.jpg]] </center>
The idea is to have two mirrored halves of the system. LasR is regulated by PAI-1 {3-oxododecanoyl-HSL (3OC12HSL)} and LuxR is activated by AI-1 {3-oxohexanoyl-homoserine lactone ([http://partsregistry.org/3OC6HSL 3OC6HSL])}. There is a potential problem in that the Lux half is more likely to get positive feedback than the Las half. This MAY not be a problem because 0/0 is leaky so we put a weak RBS to minimize leaky protein production. Also, if we add AI-2 and AI-1 is produced by leak, then the entire system shuts down. The repressor site is located between -35 and -10 of the promoter. The activator binding site is upstream of -35. This has been documented [http://www.bio.davidson.edu/courses/synthetic/papers/LuxR.pdf by Egland and Greenberg]

[[Oligos_to_Build]]: Sequences we will need to make this XOR gate.

== Missouri Western XOR Biological Design 1==

These two XOR circuits are designed to complement each other. Each recieves a cell-to-cell signal (AI-1 or AI-2) and a chemical signal (IPTG or AHL) and processes it into a cell-to-cell signal. Colonies that output AI-1 would alternate with colonies that produce AI-2. The input message to be hashed could be encoded by the presence or absence of the chemical signals, which would also alternate.

[[Image:XOR DR AI2.PNG]]

'''Above '''- Input of AI-1 or IPTG turns on production of AI-2 by LuxS. Input by both AI-1 and IPTG allows production of the repressors cI and Mnt, which repress both transcription units. LuxR and LacI are constitutively expressed.

[[Image:XOR DR AI1b.PNG]] 
'''Above''' - Input of AI-2 or aTc turns on production of AI-1 by LuxI. Input by both AI-2 and aTc allows production of the repressors cI and Mnt, which repress both transcription units. LsrK, LsrR and TetR are constitutively expressed.

@@ Line 2: / Line 2: @@
 == LuxR XOR Biological Design ==
-[http://partsregistry.org/AHL '''List of auto-inducers and their catalog numbers.''']
 <br>

← Older revision		Revision as of 16:28, 28 October 2008
Line 1:		Line 1:
−	'''Biological Hash Function Designs''' - Our team conceived of ~~four~~ different ways to build genetic circuits that function as biological XOR gates. These could be used to produce a biological hash function.	+	'''Biological Hash Function Designs''' - Our team conceived of five different ways to build genetic circuits that function as biological XOR gates. These could be used to produce a biological hash function.

	== LuxR XOR Biological Design ==		== LuxR XOR Biological Design ==

← Older revision		Revision as of 16:28, 28 October 2008
Line 53:		Line 53:

	'''Input of AI-2 or aTc turns on production of AI-1 by LuxI. Input by both AI-2 and aTc allows production of the repressors cI and Mnt, which repress both transcription units. LsrK, LsrR and TetR are constitutively expressed.'''		'''Input of AI-2 or aTc turns on production of AI-1 by LuxI. Input by both AI-2 and aTc allows production of the repressors cI and Mnt, which repress both transcription units. LsrK, LsrR and TetR are constitutively expressed.'''
−
−	~~== Missouri Western XOR Biological Design 2==~~
−
−	~~'''XOR Based on Tryptophan Anabolism and the TrpR Repressor'''~~
−
−	~~Notes: LacI could be the new LacI X86+I12. Also, the output gene should be LuxI, not LuxS. With LuxS, the second cell has to have the Las system in place of the Lux system (JB/AMC).~~
−
−	The idea here is that there are two different XOR gate clones. One takes input of AI1 and IPTG and outputs AI2. The other takes inputs of AI2 and IPTG and outputs AI2. These two clones could be alternated in a pathway of colonies (TE/AG).
−
−	~~[[Image:XOR AI2.PNG]]~~
−	~~[[Image:XOR AI1.JPG]]<br>~~

@@ Line 1: / Line 1: @@
 == LuxR XOR Biological Design ==
 [http://partsregistry.org/AHL '''List of auto-inducers and their catalog numbers.''']
 <br>
-<center>'''Davidson Approach'''<br>
+<br>
 <center> [[Image:XOR_AMC1b.jpg]]<br></center>
 The idea is to have two mirrored halves of the system. LasR is regulated by PAI-1 {3-oxododecanoyl-HSL (3OC12HSL)} and LuxR is activated by AI-1 {3-oxohexanoyl-homoserine lactone ([http://partsregistry.org/3OC6HSL 3OC6HSL])}. There is a potential problem in that the Lux half is more likely to get positive feedback than the Las half. This MAY not be a problem because 0/0 is leaky so we put a weak RBS to minimize leaky protein production. Also, if we add AI-2 and AI-1 is produced by leak, then the entire system shuts down. The repressor site is located between -35 and -10 of the promoter. The activator binding site is upstream of -35. This has been documented [http://www.bio.davidson.edu/courses/synthetic/papers/LuxR.pdf by Egland and Greenberg]
-== Las/Lux XOR Biological Design ==
+== Lsr/Lux XOR Biological Design ==
 These two XOR circuits are designed to complement each other. Each recieves a cell-to-cell signal (AI-1 or AI-2) and a chemical signal (IPTG or AHL) and processes it into a cell-to-cell signal.  Colonies that output AI-1 would alternate with colonies that produce AI-2.  The input message to be hashed could be encoded by the presence or absence of the chemical signals, which would also alternate.
@@ Line 35: / Line 34: @@
-== Lsr/Lux XOR Biological Design ==
+== Las/Lux XOR Biological Design ==

@@ Line 1: / Line 1: @@
-== Davidson XOR Biological Design ==
+== LuxR XOR Biological Design ==
 [http://partsregistry.org/AHL '''List of auto-inducers and their catalog numbers.''']
 <br>
@@ Line 12: / Line 12: @@
-== Missouri Western XOR Biological Design 1==
+== Las/Lux XOR Biological Design ==
 These two XOR circuits are designed to complement each other. Each recieves a cell-to-cell signal (AI-1 or AI-2) and a chemical signal (IPTG or AHL) and processes it into a cell-to-cell signal.  Colonies that output AI-1 would alternate with colonies that produce AI-2.  The input message to be hashed could be encoded by the presence or absence of the chemical signals, which would also alternate.
@@ Line 33: / Line 33: @@
 [[Image:XOR DR AI1b.PNG]]<br>
 '''Above''' - Input of AI-2 or aTc turns on production of AI-1 by LuxI.  Input by both AI-2 and aTc allows production of the repressors cI and Mnt, which repress both transcription units.  LsrK, LsrR and TetR are constitutively expressed.

← Older revision		Revision as of 16:20, 28 October 2008
Line 16:		Line 16:
	These two XOR circuits are designed to complement each other. Each recieves a cell-to-cell signal (AI-1 or AI-2) and a chemical signal (IPTG or AHL) and processes it into a cell-to-cell signal. Colonies that output AI-1 would alternate with colonies that produce AI-2. The input message to be hashed could be encoded by the presence or absence of the chemical signals, which would also alternate.		These two XOR circuits are designed to complement each other. Each recieves a cell-to-cell signal (AI-1 or AI-2) and a chemical signal (IPTG or AHL) and processes it into a cell-to-cell signal. Colonies that output AI-1 would alternate with colonies that produce AI-2. The input message to be hashed could be encoded by the presence or absence of the chemical signals, which would also alternate.

		+	'''Design Variables'''

		+	1. strength on RBS for each of the coding sequences (eg. RBS for enzymes could be weak)
		+
		+	2. order of coding sequences (eg. enzymes could be second for lower expression level)
		+
		+	3. identity of repressors (eg. mutant LacI repressors)
		+
		+	4. presence/absence of degradation tag on proteins

	[[Image:XOR DR AI2.PNG]]		[[Image:XOR DR AI2.PNG]]