GcatWiki - User contributions [en]

Sequencing at Agencourt

2009-07-20T14:48:28Z

Kilau: /* Quicklane Sequencing Service */

==Quicklane Sequencing Service==

Quicklane sequencing provides 24-hour turnaround so that you can receive sample sequences more quickly, for a higher price than slower sequencing services. Submitting miniprepped DNA samples with primers premixed is an available and recommended option. You can always find the complete [http://www.agencourt.com/documents/services/agencourt-sample-preparation-guidelines.pdf Sample Preparation] and [http://www.agencourt.com/documents/services/agencourt-sample-submission-guidelines.pdf Sample Submission] instructions on the Agencourt website.

'''Sample preparation'''

*Prepare a 96-well plate or 2D barcoded tubes, provided by Agencourt. Label barcoded tubes with a distinct sample name. Label plates with a distinct name for your sequencing project.
*You must submit 600 - 1000 ng of MP template DNA (mixed with primer) in a final volume of 40 ul for each sequencing reaction. It may be easiest to dry down 600 - 1000 ng DNA and resuspend. Try to submit roughly the same concentration for all samples (15 - 25 ng/ul).
*Add 0.2 pmoles of primer for each sample (if you have 100 uM primer, just dilute it 10X and pipet 2 ul into each tube). If you are sequencing with forward and reverse primers, those are 2 different sequencing reactions, and two different tubes with 1 primer each.
*Resuspend dried DNA and primer in nuclease-free water to a final volume of 40 ul.
*Samples in a well plate must be accompanied by a tab-delimited text file, containing the plate name, well number, and sample name.
*Samples in a well plate can be capped with Optical Cap 8X Strips, or with aluminum adhesive, provided by Agencourt.

'''Sample Submission'''

*Click [http://www.agencourt.com/sample/ here] for sample submission. The sequencing account's username is the professor's full name and the password is the name of the organism studied in Biology111.
*Click "Create a New Project". Give your sequencing project a distinct name.
*Under "Individual Sample Sequencing", select "Quicklane"
*Enter Well ID for each sample, and your given label name under "Sample Name"
*The DNA Template size is the size of the entire plasmid with insert (in basepairs). Enter the Sample Type.
*Check "Primer & Template Premixed" for all samples. You DO NOT have to enter any primer name if you are submitting your own primers premixed.
*Select ".ab1" and ".seq" formats for sequence data.
*Pay with an acquired Purchase Order. The Service Quotation Number, if not already entered, is the one given by the college's sales representative (AGEN #####).
*Include Online Sample Submission and text file with well ID sample names with the samples to ship.
*Package the samples and use Standard Overnight FedEx shipment to mail to: Agencourt Bioscience Corp. / 500 Cummings Center, Suite 2450 / Attention Genomic Services / Beverly, MA 01915

==Sequencing Glycerol Cell Stocks==

SinglePass Plasmid sequencing service allows you to submit a bacterial culture that contains your plasmid to be sequenced, and Agencourt will do the miniprepping, purifying and sequencing for you. You can submit your own primers, or request they use one of their own universal primers for no extra charge. Expect sequence results 4 - 5 days after samples have been received.

'''This sample preparation will require 12 hrs for incubating and growing your cultures. Plan your time wisely.''' You can always find the complete [http://www.agencourt.com/documents/services/agencourt-sample-preparation-guidelines.pdf Sample Preparation] and [http://www.agencourt.com/documents/services/agencourt-sample-submission-guidelines.pdf Sample Submission] instructions on the Agencourt website.

'''Sample Preparation'''

*Prepare LB media, 10% glycerol and 50 ug/mL Ampicillin (or other appropriate antibiotic. Other antibiotic concentrations are detailed in the Agencourt Sample Submission guide).
*Aliquot 180 - 190 ul LB-glycerol into wells of a 96-well plate, provided by Agencourt.
*Inoculate cells containing your plasmid to be sequenced into wells. RECORD WELL ID AND SAMPLE NAME.
*Incubate culture plate at 37C for 12 hours, not shaking and loosely covered with cellophane. More than 90% of the filled wells must have grown to be visibly cloudy.
*Prepare primers in separate microfuge tubes. Agencourt uses 20 ul of 3-uM primer in each well. You can send enough undiluted stock primer (100 uM) for the company to dilute for you before aliquoting. Label all primer tubes.
*After 12 hours of cell growth, seal wells with Optical Cap 8X Strips, or with aluminum adhesive, provided by Agencourt. Freeze plate at -80C.

'''Sample Submission'''

*Click [http://www.agencourt.com/sample/ here] for sample submission. The sequencing account's username is the professor's full name and the password is the name of the organism studied in Biology111.
*Click "Create a New Project". Give your sequencing project a distinct name.
*Under "High Throughput Sequencing", select "SinglePass Plasmid Sequencing"
*Enter the number of plates you are submitting, your vector name (ex. pSB1A2), the antibiotic marker, and the number of sequencing directions. Forward and reverse sequencing is Two directions. Check "No" for Are the samples purified?
*Enter the label name and the concentration for each of the primers you are sending in tubes.
*Select ".ab1" and ".seq" formats for sequence data.
*Pay with an acquired Purchase Order; select "Blanket P.O." or submit the Purchase Order amount. The Service Quotation Number, if not already entered, is the one given by the college's sales representative (AGEN #####).
*'''Fax the Purchase Order to the attention of Genomic Services at 978-867-2601.'''
*Wrap frozen plate in aluminum foil.
*Place plate in a styrofoam box with dry ice loaded on top and under the plate. Place Online Sample Submission in a plastic bag with the labeled primers.
*Tape box securely. You can tape a FedEx Small Pak envelope to the top and side of the box to hold the shipping label more securely.
*Use Standard Overnight FedEx shipment to mail to: Agencourt Bioscience Corp. / 500 Cummings Center, Suite 2450 / Attention Genomic Services / Beverly, MA 01915

XOR gate design involving Omp system

2009-05-28T14:27:40Z

Kilau: /* Characterizing pOmpC */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were also induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_K091146 K091146] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively. The pOmpC promoter can be induced with high osmolarity (see [http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). LB media has been proven to act as a 'high osmolarity' media [http://www.ncbi.nlm.nih.gov/pubmed/11973328?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum (1)], while 'low osmolarity' has been achieved with TY media [http://www.ncbi.nlm.nih.gov/pubmed/15713883?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum (2)].

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:25:33Z

Kilau: /* Characterizing pOmpC */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were also induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_K091146 K091146] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively. The pOmpC promoter can be induced with high osmolarity (see http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature], and LB media has been proven to act as a 'high osmolarity' media [http://www.ncbi.nlm.nih.gov/pubmed/11973328?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum (1)]. 'Low osmolarity' has been shown to be achieved with TY media [http://www.ncbi.nlm.nih.gov/pubmed/15713883?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum (2)].

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:24:31Z

Kilau:

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were also induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_K091146 K091146] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively. The pOmpC promoter can be induced with high osmolarity (see http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system 'The Omp system in nature'], and LB media has been proven to act as a 'high osmolarity' media [http://www.ncbi.nlm.nih.gov/pubmed/11973328?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 1]. 'Low osmolarity' has been shown to be achieved with TY media [http://www.ncbi.nlm.nih.gov/pubmed/15713883?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 2].

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:14:15Z

Kilau: /* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature] */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were also induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_K091146 K091146] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:13:17Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were also induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_K091146 K091146] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:08:34Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were also induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_S03984 S03984] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:07:57Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([http://partsregistry.org/Part:BBa_K09100 K09100]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were induced by Las sender ([http://partsregistry.org/Part:BBa_K091136 K091136]) cells.
#pLasLux and Las receiver ([http://partsregistry.org/Part:BBa_S03984 S03984] and [http://partsregistry.org/Part:BBa_K091134 K091134] respectively) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T14:00:49Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#The Lux receiver ([]) was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver cells were induced by Las sender ([]) cells.
#pLasLux and Las receiver ([]) could not be induced by 3OC12 (or 3OC6).

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:54:14Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#pLuxLas was induced by direct administration of both 3OC6 and 3OC12. Furthermore, Lux receiver ([]) cells were induced by Las sender ([]) cells
#Las receiver ([]) could not be induced by 3OC12 (or 3OC6)

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:50:42Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate. The problems were:

#pLuxLas was induced by both 3OC6 and 3OC12. Furthermore, Lux receiver ([]) cells were induced by Las sender ([]) cells
#Las receiver ([]) could not be induced by 3OC12 (or 3OC6)

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:33:47Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Projects_with_Updates#Building_XOR_Gate found here]), that made it difficult to construct a functional XOR gate.

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:32:13Z

Kilau: /* Why are we designing a new XOR gate? */

==Why are we designing a new XOR gate?==

We found a couple of characteristics of the components used in the old design (found here), that made it difficult to construct a functional XOR gate.

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:26:40Z

Kilau:

==Why are we designing a new XOR gate?==

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:21:46Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

The above design, which utilizes both the Omp system and the Lux system ([http://gcat.davidson.edu/GcatWiki/index.php/Lux information about the Lux system here]), should show XOR gate properties if the following assumptions are true:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:16:31Z

Kilau: /* References */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

XOR gate design involving Omp system

2009-05-28T13:14:08Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

# When both inputs A (high osmolarity) and B (3OC6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 3OC6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

==References==

XOR gate design involving Omp system

2009-05-28T13:12:15Z

Kilau: /* Testing the pOmpC promoter */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

# When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

Before ligating all the parts together to make the XOR gate depicted above, I will test the promoters by themselves to make sure that they behave according to our expectations and are suitable for making an XOR gate.
===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

==References==

XOR gate design involving Omp system

2009-05-28T13:10:03Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

# When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.
#When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

==References==

XOR gate design involving Omp system

2009-05-28T13:08:42Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

# When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

# When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

==References==

XOR gate design involving Omp system

2009-05-28T13:07:38Z

Kilau: /* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature] */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system that may not have been covered.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

==References==

XOR gate design involving Omp system

2009-05-28T13:05:40Z

Kilau: /* Possible hash function? */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function is depicted [http://gcat.davidson.edu/GcatWiki/index.php/Math_Modeling_Pages#Models here].

==References==

XOR gate design involving Omp system

2009-05-28T13:02:50Z

Kilau: /* Possible hash function? */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

If the XOR gate is successfully developed, I may implement it to make a simple hash function. A simple hash function (a linear model) is shown below:

==References==

XOR gate design involving Omp system

2009-05-28T12:59:01Z

Kilau: /* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature] */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli'' ([http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]). However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-28T12:58:13Z

Kilau: /* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature] */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

Before you look at the XOR gate design below, you may find it helpful to check out how the Omp system works naturally in ''E. coli''. However, note that the explanation provided on the linked page is much simplified and presents only the information required to understand this project. Feel free to contact me if you would like to know more about certain aspects of the Omp system.

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-26T18:50:32Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-26T18:50:20Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]
[[Image:XOR truth table.jpg]]
If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-26T18:50:00Z

Kilau: /* XOR gate design and concept */

XOR gate design involving Omp system

2009-05-26T18:49:45Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]] <br>
[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-26T18:48:35Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]
[[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-26T18:48:20Z

Kilau: /* XOR gate design and concept */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]][[Image:XOR truth table.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

File:XOR truth table.jpg

2009-05-26T18:47:41Z

Kilau:

XOR gate design involving Omp system

2009-05-26T18:33:49Z

Kilau:

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

==References==

XOR gate design involving Omp system

2009-05-26T18:33:08Z

Kilau:

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

==Possible hash function?==

XOR gate design involving Omp system

2009-05-26T18:28:29Z

Kilau: /* Characterizing pOmpC */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence. As a result, we decided to clone a long and a short version of pOmpC then test those with downstream GFP and RBS-GFP respectively.

[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T18:27:13Z

Kilau: /* Characterizing pOmpC */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===

Two sets of primers were used to clone pOmpC because there are 80 bases between the end of pOmpC and the start codon of OmpC that we do not know the function of. The region could contain an intrinsic RBS, even though this was not evident from simply comparing the sequence of those 80 bases to the consensus RBS sequence.
[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T18:16:48Z

Kilau: /* Is there any backwards activity? */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===
[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T18:16:35Z

Kilau: /* Is there any backwards activity? */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design and concept ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

===Characterizing pOmpC===
[[Image:Characterizing strength of pOmpC.jpg]]

===Is there any backwards activity?===

Backwards activity in either pLux or pOmpC would be detrimental to the design of the XOR gate because an output would still be produced if both inputs are provided.

The first test will be done with Tet resistance placed upstream of both the pOmpC and pLux promoters because Tet resistance has been found to be a sensitive way to measure backwards activity in promoters. If Tet resistance is expressed from the backward activity of pOmpC, then RFP will be used, as this is a less sensitive test for backwards activity.
[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T18:12:30Z

Kilau: /* Testing the pOmpC promoter */

XOR gate design involving Omp system

2009-05-26T18:11:30Z

Kilau: /* XOR gate design */

XOR gate design involving Omp system

2009-05-26T16:03:04Z

Kilau: /* XOR gate design */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design ==

[[Image:XOR gate construct.jpg]]

If all the components work as expected, the above construct will exhibit XOR gate properties. This design relies on a couple of assumptions:

1. When both inputs A (high osmolarity) and B (30C6), the activities of the two promoters should negate each other and no output should be produced.

2. When only one input is present (either high osmolarity or 30C6), the activity of the induced promoter should be able to reach the GFP gene despite the physical separation (the uninduced promoter) between the two components.

== Testing the pOmpC promoter ==

[[Image:Characterizing strength of pOmpC.jpg]]

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T15:49:22Z

Kilau: /* Steps to building the XOR gate */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design ==

[[Image:XOR gate construct.jpg]]

== Testing the pOmpC promoter ==

[[Image:Characterizing strength of pOmpC.jpg]]

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T15:48:34Z

Kilau: /* Steps to building the XOR gate */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design ==

[[Image:XOR gate construct.jpg]]

== Steps to building the XOR gate ==

'''Testing pOmpC'''

[[Image:Characterizing strength of pOmpC.jpg]]

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwards activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T15:48:17Z

Kilau: /* Steps to building the XOr gate */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design ==

[[Image:XOR gate construct.jpg]]

== Steps to building the XOR gate ==

'''Testing pOmpC'''

[[Image:Characterizing strength of pOmpC.jpg]]

[[Image:backwards activity pOmpC.jpg]]

[[Image:backwrads activity pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T15:47:21Z

Kilau:

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

== XOR gate design ==

[[Image:XOR gate construct.jpg]]

== Steps to building the XOr gate ==

'''Testing pOmpC'''

[[Image:Characterizing strength of pOmpC.jpg]]

[[Image:backwards activity of pOmpC.jpg]]

[[Image:backwrads activity of pLux.jpg]]

XOR gate design involving Omp system

2009-05-26T15:42:53Z

Kilau: /* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008 The Omp system in nature] */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008#Omp_cell_signaling_system The Omp system in nature]==

XOR gate design involving Omp system

2009-05-26T15:42:07Z

Kilau: /* The Omp system in nature */

==[http://gcat.davidson.edu/GcatWiki/index.php/Davidson/Missouri_Western_iGEM2008 The Omp system in nature]==

File:Backwards activity pLux.jpg

2009-05-26T15:38:27Z

Kilau: backwards activity of pLux tested with RFPrev and Tetrev

backwards activity of pLux tested with RFPrev and Tetrev

File:Backwards activity pOmpC.jpg

2009-05-26T15:37:41Z

Kilau: backwards activity with pOmpC tested with RFPrev and Tetrev

backwards activity with pOmpC tested with RFPrev and Tetrev

File:Characterizing strength of pOmpC.jpg

2009-05-26T15:37:04Z

Kilau: characterizing pOmpC with GFP

characterizing pOmpC with GFP