GcatWiki - User contributions [en]

File:Curtiss3.jpg

2010-06-18T20:12:57Z

Clane3:

IGEM 2010 Project

2010-06-18T20:12:42Z

Clane3: /* Biology Sub-Projects */

* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
* [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 

== We need to start capturing what we are doing, and why. ==
Please use this page as a starting place.

We need an overall description of our project at the overview level as well as the subsections and phases of implementation.

== Math Sub-Projects ==

'''Counting Permutations'''

'''Improving Oligo Assembler'''
We adapted the lancelator (http://gcat.davidson.edu/IGEM06/oligo.html), a program created by Lance Harden as a part of the 2006 iGem team, so that it would execute faster and can handle longer sequences. The old program could only handle sequences of 300 bp or shorter. Also, the more oligos the program broke the sequence into, the longer it took to run, and for 8 or more the run time was simply unreasonable. However, for the sequences it could handle it always finds the optimal oligos to use.
Our program allows the user to enter a sequence of any length, and the length does not significantly effect runtime. In addition, we added extra features such as checking for and removing BioBrick restriction sites and adding BioBrick primers. While our program does not always find the optimal oligos, it still does very well which is an acceptable compromise because the runtime is improved so dramatically.

http://gcat.davidson.edu/iGem10/index.html

== Biology Sub-Projects==

'''Codon Optimization''' 

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Segment
|'''Number of Base Pairs'''
|'''Wild Type Sequence'''
|'''Optimized Sequence'''
|'''Deoptimized Sequence'''
|-

| 1 || 141 || Atgaaatctaacaatgcgctcatcgtcatcctcggcaccgtcaccctggatgctgtaggcataggcttggttatgccggtactgccgggcctcttgcgggatatcgtccattccgacagcatcgccagtcactatggcgtg || ATGAAATCTAACAACGCGCTGATCGTTATCCTGGGTACCGTTACCCTGGACGCGGTTGGTATCGGTCTGGTTATGCCGGTTCTGCCGGGTCTGCTGCGTGACATCGTTCACTCTGACTCTATCGCGTCTCACTACGGTGTT || ATGAAGAGTAATAATGCCCTAATAGTCATACTAGGAACAGTCACACTAGATGCCGTCGGAATAGGACTCGTCATGCCCGTCCTACCCGGACTACTAAGGGATATAGTCCATAGTGATAGTATAGCCAGTCATTATGGAGTC
|-

| 2 || 138 || ctatatgcgttgatgcaatttctatgcgcacccgttctcggagcactgtccgaccgctttggccgccgcccagtcctgctcgcttcgctacttggagccactatcgactacgcgatcatggcgaccacacccgtcctg || CTGTACGCGCTGATGCAGTTCCTGTGCGCGCCGGTTCTGGGTGCGCTGTCTGACCGTTTCGGTCGTCGTCCGGTTCTGCTGGCGTCTCTGCTGGGTGCGACCATCGACTACGCGATCATGGCGACCACCCCGGTTCTG || CTATATGCCCTAATGCAATTTCTATGTGCCCCCGTCCTAGGAGCCCTAAGTGATAGGTTTGGAAGGAGGCCCGTCCTACTAGCCAGTCTACTAGGAGCCACAATAGATTATGCCATAATGGCCACAACACCCGTCCTA
|-

| 3 || 177 || tacgccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcaccgatggggaagatcgggctcgccacttcgggctcatgagcgcttgtttcggcgtgggtatggtggcaggccccgtggccgggggactgttgggcgccatctcc || TACGCGGGTCGTATCGTTGCGGGTATCACCGGTGCGACCGGTGCGGTTGCGGGTGCGTACATCGCGGACATCACCGACGGTGAAGACCGTGCGCGTCACTTCGGTCTGATGTCTGCGTGCTTCGGTGTTGGTATGGTTGCGGGTCCGGTTGCGGGTGGTCTGCTGGGTGCGATCTCT || TATGCCGGAAGGATAGTCGCCGGAATAACAGGAGCCACAGGAGCCGTCGCCGGAGCCTATATAGCCGATATAACAGATGGAGAGGATAGGGCCAGGCATTTTGGACTAATGAGTGCCTGTTTTGGAGTCGGAATGGTCGCCGGACCCGTCGCCGGAGGACTACTAGGAGCCATAAGT
|-

| 4 || 81 || ccattccttgcggcggcggtgctcaacggcctcaacctactactgggctgcttcctaatgcaggagtcgcataagggagag || CCGTTCCTGGCGGCGGCGGTTCTGAACGGTCTGAACCTGCTGCTGGGTTGCTTCCTGATGCAGGAATCTCACAAAGGTGAA || CCCTTTCTAGCCGCCGCCGTCCTAAATGGACTAAATCTACTACTAGGATGTTTTCTAATGCAAGAGAGTCATAAGGGAGAG
|-

|}

Note: All above segments have been optimized and deoptimized using the online [http://genomes.urv.es/OPTIMIZER/ Optimizer] program.

To create the optimized and deoptimized segments of the Tet A gene we used the sequence that the Optimizer program gave us and put it into the [http://gcat.davidson.edu/IGEM06/oligo.html Lancelator] a program created by Lance Harden as part of the 2006 iGEM team. After getting the recommended Oligo sequences from the Lancelator, we added necessary "sticky ends" that were compatible with the naturally occurring restriction enzyme sites that we discovered (see Restriction Enzymes below). At this time we have ordered Oligo parts for segments 1 and 2 of the Tet A gene. The Oligos that were ordered can be seen below.

'''Segment 1 Oligos'''

'''Optimized'''

top 1 5' AATTCGCGGCCGCTTCTAGATGAAATCTAACAACGCGCTGATCGTTATCCTGGGTACCG 3’

top 2 5' TTACCCTGGACGCGGTTGGTATCGGTCTGGTTATGCCGGTTCTGCCGGGTCTGCTGCGTGAC 3’

top 3 5' ATCGTTCACTCTGACTCTATCGCGTCTCACTACGGTGTTCTG 3’

bottom 2 5' CATAACCAGACCGATACCAACCGCGTCCAGGGTAACGGTAC
CCAGGATAACGATCAGCGCGTTGTTAGATTTCATCTAGAAGCGGCCGCG 3’

bottom 1 5' CTAGCAGAACACCGTAGTGAGACGCGATAGAGTCAGAGTGAACGATGTCACGCAGCAGACCCGGCAGAACCGG 3’

'''Deoptimized'''

top 1 5' AATTCGCGGCCGCTTCTAGATGAAGAGTAATAATGCCCTAATAGTCATACTAGGAACAG 3’

top 2 5' TCACACTAGATGCCGTCGGAATAGGACTCGTCATGCCCGTCCTACCCGGACTACTAAGGGA 3’

top 3 5' TATAGTCCATAGTGATAGTATAGCCAGTCATTATGGAGTCCTG 3’

bottom 2 5' GAGTCCTATTCCGACGGCATCTAGTGTGACTGTTCCTAGTATG
ACTATTAGGGCATTATTACTCTTCATCTAGAAGCGGCCGCG 3’

bottom 1 5' CTAGCAGGACTCCATAATGACTGGCTATACTATCACTATGGACTATATCCCTTAGTAGTCCGGGTAGGACGGGCATGAC 3’

'''Segment 2 Oligos'''

'''Optimized'''

top 1 5' CTAGCCTGTACGCGCTGATGCAGTTCCTGTGCGCGCCGGTTCTGGGTGCGCTGTCTGAC 3’

top 2 5' CGTTTCGGTCGTCGTCCGGTTCTGCTGGCGTCTCTGCTGGGTGCGACCATCGACTAC 3’

top 3 5' GCGATCATGGCGACCACCCCGGTTCTGTG 3’

bottom 1 5' GCGCACAGGAACTGCATCAGCGCGTACAGG 3’

bottom 2 5' CCAGCAGAACCGGACGACGACCGAAACGGTCAGACAGCGCACCCAGAACCGGC 3’

bottom 3 5' GATCCACAGAACCGGGGTGGTCGCCATGATCGCGTAGTCGATGGTCGCACCCAGCAGAGACG 3’

'''Deoptimized'''

top 1 5' CTAGCGCTATATGCCCTAATGCAATTTCTATGTGCCCCCGTCCTAGGAGCCCTAAGTG 3'

top 2 5' ATAGGTTTGGAAGGAGGCCCGTCCTACTAGCCAGTCTACTAGGAGCCACAATAGAT 3'

top 3 5' TATGCCATAATGGCCACAACACCCGTCCTATG 3'

bottom 1 5' GGCACATAGAAATTGCATTAGGGCATATAGCG 3' 

bottom 2 5' TAGGACGGGCCTCCTTCCAAACCTATCACTTAGGGCTCCTAGGACGGG 3' 

bottom 3 5' GATCCATAGGACGGGTGTTGTGGCCATTATGGCATAATCTATTGTGGCTCCTAGTAGACTGGCTAG 3'

[[Image:wiki3.jpg]]

'''Restriction Enzymes'''

To insert the annealed Oligo segments that were created we had to digest the Tet A gene using naturally occurring enzyme restriction sites that did not exist in the rest of the gene or in the plasmid (pSBIA2).

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Segment
|'''First Restriction Enzyme'''
|'''Second Restriction Enzyme'''
|-

| 1 || EcoRI || NheI
|-

| 2 || NheI || BamHI
|-

| 3 || BamHI || SphI
|-

| 4 || SphI || SalI
|-

|}

'''Parts Used (to be used)'''
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Part
|'''Registry Link'''
|'''Construct Including Part'''
|-

| Tet A (tetracycline resistance gene) J31007 || [http://partsregistry.org/Part:BBa_J31007 Tet A (forward)] || promoter-RBS-RFP-RBS-TetA on pSBIA2
|-

| pLac-RBS-RFP I715039 || [http://partsregistry.org/Part:BBa_I715039 pLac-RBS-RFP ]|| Possibly: pLac-RBS-RFP-RBS-TetA on pSBIA2
|-

| pLac-RBS-RFP-RBS-TetA-TT on pSBIAK3 S04435 || [http://partsregistry.org/Part:BBa_S04435 pLac-RBS-RFP-RBS-TetA-TT]|| Possibly: pLac-RBS-RFP-RBS-TetA-TT on pSBIA2
|-

| Part Name and Registry Number || [http://partsregistry.org/Main_Page Registry Link]|| Construct
|-

| Part Name and Registry Number || [http://partsregistry.org/Main_Page Registry Link]|| Construct
|-
|}

'''Promoters'''

This chart shows flourescene levels of different promoter constructs with varying levels of IPTG added (error bars with standard error can be seen on the graph). Note: This experiment is still in progress. More data will be posted when available.

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!
!width="80"|[[Image:wiki4.jpg]]
|-
|}

'''Tet-trations''' 

'''Making and Testing lox_ Sites'''
<center>
 '''Green''' Part has been cloned and sequence verified; '''Red''' Part is under construction

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Final Construct
!width="30"|Current Status
!Registry Number and Link
!width="30"|Primary Team Member
|-
| '''''lox5171'' Forward in pSB1A2''' || I got colonies on my second attempt. Once I isolate the plasmid, it will be sent off for sequencing. || [http://partsregistry.org/Part:pSB1A2 pSB1A2] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Nitya
|-

| '''''lox5171'' Reverse in pSB1A2''' || This plasmid will also be sent off for sequencing soon. || [http://partsregistry.org/Part:pSB1A2 pSB1A2] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Nitya
|-

| '''loxm2 Forward in pSB1A2''' || I ligated loxm2 F with the plasmid and have prepared the DNA for sequencing to confirm what is there. || [http://partsregistry.org/Part:BBa_K315004] ''loxm2'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Tom
|-

| '''loxm2 Reverse in pSB1A2''' || I ligated loxm2 F with the plasmid and have prepared the DNA for sequencing to confirm what is there. || [http://partsregistry.org/Part:BBa_K315005] ''loxm2'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Tom
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-
|}
 
</center>

'''Testing Cre Activity''' 
<center>

 '''Green''' Part has been cloned and sequence verified; '''Red''' Part is under construction

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Final Construct
!width="30"|Current Status
!Registry Number and Link
!width="30"|Primary Team Member
|-
| '''I718008 (pBAD+RBS+cre) in pSB4K5''' || At this point, I have isolated both the insert and the plasmid, but my two attempts at ligation have not produced any colonies. || [http://partsregistry.org/Part:BBa_I718008 I718008] [http://partsregistry.org/wiki/index.php?title=Part:pSB4K5 pSB4K5] || Nitya
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-
|}
</center>
 

'''pSBIA7 & pSBIA2'''

Data showing the varying levels of expression between pSBIA7 and pSBIA2

[[Image:curtiss3.jpg]]

File:Curtiss1.jpg

2010-06-18T19:37:25Z

Clane3:

IGEM 2010 Project

2010-06-18T19:36:14Z

Clane3: /* Biology Sub-Projects */

* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
* [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 

== We need to start capturing what we are doing, and why. ==
Please use this page as a starting place.

We need an overall description of our project at the overview level as well as the subsections and phases of implementation.

== Math Sub-Projects ==

'''Counting Permutations'''

'''Improving Oligo Assembler'''
We adapted the lancelator (http://gcat.davidson.edu/IGEM06/oligo.html), a program created by Lance Harden as a part of the 2006 iGem team, so that it would execute faster and can handle longer sequences. The old program could only handle sequences of 300 bp or shorter. Also, the more oligos the program broke the sequence into, the longer it took to run, and for 8 or more the run time was simply unreasonable. However, for the sequences it could handle it always finds the optimal oligos to use.
Our program allows the user to enter a sequence of any length, and the length does not significantly effect runtime. In addition, we added extra features such as checking for and removing BioBrick restriction sites and adding BioBrick primers. While our program does not always find the optimal oligos, it still does very well which is an acceptable compromise because the runtime is improved so dramatically.

http://gcat.davidson.edu/iGem10/index.html

== Biology Sub-Projects==

'''Codon Optimization''' 

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Segment
|'''Number of Base Pairs'''
|'''Wild Type Sequence'''
|'''Optimized Sequence'''
|'''Deoptimized Sequence'''
|-

| 1 || 141 || Atgaaatctaacaatgcgctcatcgtcatcctcggcaccgtcaccctggatgctgtaggcataggcttggttatgccggtactgccgggcctcttgcgggatatcgtccattccgacagcatcgccagtcactatggcgtg || ATGAAATCTAACAACGCGCTGATCGTTATCCTGGGTACCGTTACCCTGGACGCGGTTGGTATCGGTCTGGTTATGCCGGTTCTGCCGGGTCTGCTGCGTGACATCGTTCACTCTGACTCTATCGCGTCTCACTACGGTGTT || ATGAAGAGTAATAATGCCCTAATAGTCATACTAGGAACAGTCACACTAGATGCCGTCGGAATAGGACTCGTCATGCCCGTCCTACCCGGACTACTAAGGGATATAGTCCATAGTGATAGTATAGCCAGTCATTATGGAGTC
|-

| 2 || 138 || ctatatgcgttgatgcaatttctatgcgcacccgttctcggagcactgtccgaccgctttggccgccgcccagtcctgctcgcttcgctacttggagccactatcgactacgcgatcatggcgaccacacccgtcctg || CTGTACGCGCTGATGCAGTTCCTGTGCGCGCCGGTTCTGGGTGCGCTGTCTGACCGTTTCGGTCGTCGTCCGGTTCTGCTGGCGTCTCTGCTGGGTGCGACCATCGACTACGCGATCATGGCGACCACCCCGGTTCTG || CTATATGCCCTAATGCAATTTCTATGTGCCCCCGTCCTAGGAGCCCTAAGTGATAGGTTTGGAAGGAGGCCCGTCCTACTAGCCAGTCTACTAGGAGCCACAATAGATTATGCCATAATGGCCACAACACCCGTCCTA
|-

| 3 || 177 || tacgccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcaccgatggggaagatcgggctcgccacttcgggctcatgagcgcttgtttcggcgtgggtatggtggcaggccccgtggccgggggactgttgggcgccatctcc || TACGCGGGTCGTATCGTTGCGGGTATCACCGGTGCGACCGGTGCGGTTGCGGGTGCGTACATCGCGGACATCACCGACGGTGAAGACCGTGCGCGTCACTTCGGTCTGATGTCTGCGTGCTTCGGTGTTGGTATGGTTGCGGGTCCGGTTGCGGGTGGTCTGCTGGGTGCGATCTCT || TATGCCGGAAGGATAGTCGCCGGAATAACAGGAGCCACAGGAGCCGTCGCCGGAGCCTATATAGCCGATATAACAGATGGAGAGGATAGGGCCAGGCATTTTGGACTAATGAGTGCCTGTTTTGGAGTCGGAATGGTCGCCGGACCCGTCGCCGGAGGACTACTAGGAGCCATAAGT
|-

| 4 || 81 || ccattccttgcggcggcggtgctcaacggcctcaacctactactgggctgcttcctaatgcaggagtcgcataagggagag || CCGTTCCTGGCGGCGGCGGTTCTGAACGGTCTGAACCTGCTGCTGGGTTGCTTCCTGATGCAGGAATCTCACAAAGGTGAA || CCCTTTCTAGCCGCCGCCGTCCTAAATGGACTAAATCTACTACTAGGATGTTTTCTAATGCAAGAGAGTCATAAGGGAGAG
|-

|}

Note: All above segments have been optimized and deoptimized using the online [http://genomes.urv.es/OPTIMIZER/ Optimizer] program.

To create the optimized and deoptimized segments of the Tet A gene we used the sequence that the Optimizer program gave us and put it into the [http://gcat.davidson.edu/IGEM06/oligo.html Lancelator] a program created by Lance Harden as part of the 2006 iGEM team. After getting the recommended Oligo sequences from the Lancelator, we added necessary "sticky ends" that were compatible with the naturally occurring restriction enzyme sites that we discovered (see Restriction Enzymes below). At this time we have ordered Oligo parts for segments 1 and 2 of the Tet A gene. The Oligos that were ordered can be seen below.

'''Segment 1 Oligos'''

'''Optimized'''

top 1 5' AATTCGCGGCCGCTTCTAGATGAAATCTAACAACGCGCTGATCGTTATCCTGGGTACCG 3’

top 2 5' TTACCCTGGACGCGGTTGGTATCGGTCTGGTTATGCCGGTTCTGCCGGGTCTGCTGCGTGAC 3’

top 3 5' ATCGTTCACTCTGACTCTATCGCGTCTCACTACGGTGTTCTG 3’

bottom 2 5' CATAACCAGACCGATACCAACCGCGTCCAGGGTAACGGTAC
CCAGGATAACGATCAGCGCGTTGTTAGATTTCATCTAGAAGCGGCCGCG 3’

bottom 1 5' CTAGCAGAACACCGTAGTGAGACGCGATAGAGTCAGAGTGAACGATGTCACGCAGCAGACCCGGCAGAACCGG 3’

'''Deoptimized'''

top 1 5' AATTCGCGGCCGCTTCTAGATGAAGAGTAATAATGCCCTAATAGTCATACTAGGAACAG 3’

top 2 5' TCACACTAGATGCCGTCGGAATAGGACTCGTCATGCCCGTCCTACCCGGACTACTAAGGGA 3’

top 3 5' TATAGTCCATAGTGATAGTATAGCCAGTCATTATGGAGTCCTG 3’

bottom 2 5' GAGTCCTATTCCGACGGCATCTAGTGTGACTGTTCCTAGTATG
ACTATTAGGGCATTATTACTCTTCATCTAGAAGCGGCCGCG 3’

bottom 1 5' CTAGCAGGACTCCATAATGACTGGCTATACTATCACTATGGACTATATCCCTTAGTAGTCCGGGTAGGACGGGCATGAC 3’

'''Segment 2 Oligos'''

'''Optimized'''

top 1 5' CTAGCCTGTACGCGCTGATGCAGTTCCTGTGCGCGCCGGTTCTGGGTGCGCTGTCTGAC 3’

top 2 5' CGTTTCGGTCGTCGTCCGGTTCTGCTGGCGTCTCTGCTGGGTGCGACCATCGACTAC 3’

top 3 5' GCGATCATGGCGACCACCCCGGTTCTGTG 3’

bottom 1 5' GCGCACAGGAACTGCATCAGCGCGTACAGG 3’

bottom 2 5' CCAGCAGAACCGGACGACGACCGAAACGGTCAGACAGCGCACCCAGAACCGGC 3’

bottom 3 5' GATCCACAGAACCGGGGTGGTCGCCATGATCGCGTAGTCGATGGTCGCACCCAGCAGAGACG 3’

'''Deoptimized'''

top 1 5' CTAGCGCTATATGCCCTAATGCAATTTCTATGTGCCCCCGTCCTAGGAGCCCTAAGTG 3'

top 2 5' ATAGGTTTGGAAGGAGGCCCGTCCTACTAGCCAGTCTACTAGGAGCCACAATAGAT 3'

top 3 5' TATGCCATAATGGCCACAACACCCGTCCTATG 3'

bottom 1 5' GGCACATAGAAATTGCATTAGGGCATATAGCG 3' 

bottom 2 5' TAGGACGGGCCTCCTTCCAAACCTATCACTTAGGGCTCCTAGGACGGG 3' 

bottom 3 5' GATCCATAGGACGGGTGTTGTGGCCATTATGGCATAATCTATTGTGGCTCCTAGTAGACTGGCTAG 3'

[[Image:wiki3.jpg]]

'''Restriction Enzymes'''

To insert the annealed Oligo segments that were created we had to digest the Tet A gene using naturally occurring enzyme restriction sites that did not exist in the rest of the gene or in the plasmid (pSBIA2).

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Segment
|'''First Restriction Enzyme'''
|'''Second Restriction Enzyme'''
|-

| 1 || EcoRI || NheI
|-

| 2 || NheI || BamHI
|-

| 3 || BamHI || SphI
|-

| 4 || SphI || SalI
|-

|}

'''Parts Used (to be used)'''
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Part
|'''Registry Link'''
|'''Construct Including Part'''
|-

| Tet A (tetracycline resistance gene) J31007 || [http://partsregistry.org/Part:BBa_J31007 Tet A (forward)] || promoter-RBS-RFP-RBS-TetA on pSBIA2
|-

| pLac-RBS-RFP I715039 || [http://partsregistry.org/Part:BBa_I715039 pLac-RBS-RFP ]|| Possibly: pLac-RBS-RFP-RBS-TetA on pSBIA2
|-

| pLac-RBS-RFP-RBS-TetA-TT on pSBIAK3 S04435 || [http://partsregistry.org/Part:BBa_S04435 pLac-RBS-RFP-RBS-TetA-TT]|| Possibly: pLac-RBS-RFP-RBS-TetA-TT on pSBIA2
|-

| Part Name and Registry Number || [http://partsregistry.org/Main_Page Registry Link]|| Construct
|-

| Part Name and Registry Number || [http://partsregistry.org/Main_Page Registry Link]|| Construct
|-
|}

'''Tet-trations''' 

'''Making and Testing lox_ Sites'''
<center>
 '''Green''' Part has been cloned and sequence verified; '''Red''' Part is under construction

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Final Construct
!width="30"|Current Status
!Registry Number and Link
!width="30"|Primary Team Member
|-
| '''''lox5171'' Forward in pSB1A2''' || I got colonies on my second attempt. Once I isolate the plasmid, it will be sent off for sequencing. || [http://partsregistry.org/Part:pSB1A2 pSB1A2] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Nitya
|-

| '''''lox5171'' Reverse in pSB1A2''' || This plasmid will also be sent off for sequencing soon. || [http://partsregistry.org/Part:pSB1A2 pSB1A2] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Nitya
|-

| '''loxm2 Forward in pSB1A2''' || I ligated loxm2 F with the plasmid and have prepared the DNA for sequencing to confirm what is there. || [http://partsregistry.org/Part:BBa_K315004] ''loxm2'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Tom
|-

| '''loxm2 Reverse in pSB1A2''' || I ligated loxm2 F with the plasmid and have prepared the DNA for sequencing to confirm what is there. || [http://partsregistry.org/Part:BBa_K315005] ''loxm2'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Tom
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-
|}
 
</center>

'''Testing Cre Activity''' 
<center>

 '''Green''' Part has been cloned and sequence verified; '''Red''' Part is under construction

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Final Construct
!width="30"|Current Status
!Registry Number and Link
!width="30"|Primary Team Member
|-
| '''I718008 (pBAD+RBS+cre) in pSB4K5''' || At this point, I have isolated both the insert and the plasmid, but my two attempts at ligation have not produced any colonies. || [http://partsregistry.org/Part:BBa_I718008 I718008] [http://partsregistry.org/wiki/index.php?title=Part:pSB4K5 pSB4K5] || Nitya
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-
|}
</center>
 

'''pSBIA7 & pSBIA2'''

Data showing the varying levels of expression between pSBIA7 and pSBIA2

[[Image:curtiss1.jpg]]

IGEM 2010 Project

2010-06-18T19:35:28Z

Clane3: /* Biology Sub-Projects */

* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
* [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
* [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 

== We need to start capturing what we are doing, and why. ==
Please use this page as a starting place.

We need an overall description of our project at the overview level as well as the subsections and phases of implementation.

== Math Sub-Projects ==

'''Counting Permutations'''

'''Improving Oligo Assembler'''
We adapted the lancelator (http://gcat.davidson.edu/IGEM06/oligo.html), a program created by Lance Harden as a part of the 2006 iGem team, so that it would execute faster and can handle longer sequences. The old program could only handle sequences of 300 bp or shorter. Also, the more oligos the program broke the sequence into, the longer it took to run, and for 8 or more the run time was simply unreasonable. However, for the sequences it could handle it always finds the optimal oligos to use.
Our program allows the user to enter a sequence of any length, and the length does not significantly effect runtime. In addition, we added extra features such as checking for and removing BioBrick restriction sites and adding BioBrick primers. While our program does not always find the optimal oligos, it still does very well which is an acceptable compromise because the runtime is improved so dramatically.

http://gcat.davidson.edu/iGem10/index.html

== Biology Sub-Projects==

'''Codon Optimization''' 

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Segment
|'''Number of Base Pairs'''
|'''Wild Type Sequence'''
|'''Optimized Sequence'''
|'''Deoptimized Sequence'''
|-

| 1 || 141 || Atgaaatctaacaatgcgctcatcgtcatcctcggcaccgtcaccctggatgctgtaggcataggcttggttatgccggtactgccgggcctcttgcgggatatcgtccattccgacagcatcgccagtcactatggcgtg || ATGAAATCTAACAACGCGCTGATCGTTATCCTGGGTACCGTTACCCTGGACGCGGTTGGTATCGGTCTGGTTATGCCGGTTCTGCCGGGTCTGCTGCGTGACATCGTTCACTCTGACTCTATCGCGTCTCACTACGGTGTT || ATGAAGAGTAATAATGCCCTAATAGTCATACTAGGAACAGTCACACTAGATGCCGTCGGAATAGGACTCGTCATGCCCGTCCTACCCGGACTACTAAGGGATATAGTCCATAGTGATAGTATAGCCAGTCATTATGGAGTC
|-

| 2 || 138 || ctatatgcgttgatgcaatttctatgcgcacccgttctcggagcactgtccgaccgctttggccgccgcccagtcctgctcgcttcgctacttggagccactatcgactacgcgatcatggcgaccacacccgtcctg || CTGTACGCGCTGATGCAGTTCCTGTGCGCGCCGGTTCTGGGTGCGCTGTCTGACCGTTTCGGTCGTCGTCCGGTTCTGCTGGCGTCTCTGCTGGGTGCGACCATCGACTACGCGATCATGGCGACCACCCCGGTTCTG || CTATATGCCCTAATGCAATTTCTATGTGCCCCCGTCCTAGGAGCCCTAAGTGATAGGTTTGGAAGGAGGCCCGTCCTACTAGCCAGTCTACTAGGAGCCACAATAGATTATGCCATAATGGCCACAACACCCGTCCTA
|-

| 3 || 177 || tacgccggacgcatcgtggccggcatcaccggcgccacaggtgcggttgctggcgcctatatcgccgacatcaccgatggggaagatcgggctcgccacttcgggctcatgagcgcttgtttcggcgtgggtatggtggcaggccccgtggccgggggactgttgggcgccatctcc || TACGCGGGTCGTATCGTTGCGGGTATCACCGGTGCGACCGGTGCGGTTGCGGGTGCGTACATCGCGGACATCACCGACGGTGAAGACCGTGCGCGTCACTTCGGTCTGATGTCTGCGTGCTTCGGTGTTGGTATGGTTGCGGGTCCGGTTGCGGGTGGTCTGCTGGGTGCGATCTCT || TATGCCGGAAGGATAGTCGCCGGAATAACAGGAGCCACAGGAGCCGTCGCCGGAGCCTATATAGCCGATATAACAGATGGAGAGGATAGGGCCAGGCATTTTGGACTAATGAGTGCCTGTTTTGGAGTCGGAATGGTCGCCGGACCCGTCGCCGGAGGACTACTAGGAGCCATAAGT
|-

| 4 || 81 || ccattccttgcggcggcggtgctcaacggcctcaacctactactgggctgcttcctaatgcaggagtcgcataagggagag || CCGTTCCTGGCGGCGGCGGTTCTGAACGGTCTGAACCTGCTGCTGGGTTGCTTCCTGATGCAGGAATCTCACAAAGGTGAA || CCCTTTCTAGCCGCCGCCGTCCTAAATGGACTAAATCTACTACTAGGATGTTTTCTAATGCAAGAGAGTCATAAGGGAGAG
|-

|}

Note: All above segments have been optimized and deoptimized using the online [http://genomes.urv.es/OPTIMIZER/ Optimizer] program.

To create the optimized and deoptimized segments of the Tet A gene we used the sequence that the Optimizer program gave us and put it into the [http://gcat.davidson.edu/IGEM06/oligo.html Lancelator] a program created by Lance Harden as part of the 2006 iGEM team. After getting the recommended Oligo sequences from the Lancelator, we added necessary "sticky ends" that were compatible with the naturally occurring restriction enzyme sites that we discovered (see Restriction Enzymes below). At this time we have ordered Oligo parts for segments 1 and 2 of the Tet A gene. The Oligos that were ordered can be seen below.

'''Segment 1 Oligos'''

'''Optimized'''

top 1 5' AATTCGCGGCCGCTTCTAGATGAAATCTAACAACGCGCTGATCGTTATCCTGGGTACCG 3’

top 2 5' TTACCCTGGACGCGGTTGGTATCGGTCTGGTTATGCCGGTTCTGCCGGGTCTGCTGCGTGAC 3’

top 3 5' ATCGTTCACTCTGACTCTATCGCGTCTCACTACGGTGTTCTG 3’

bottom 2 5' CATAACCAGACCGATACCAACCGCGTCCAGGGTAACGGTAC
CCAGGATAACGATCAGCGCGTTGTTAGATTTCATCTAGAAGCGGCCGCG 3’

bottom 1 5' CTAGCAGAACACCGTAGTGAGACGCGATAGAGTCAGAGTGAACGATGTCACGCAGCAGACCCGGCAGAACCGG 3’

'''Deoptimized'''

top 1 5' AATTCGCGGCCGCTTCTAGATGAAGAGTAATAATGCCCTAATAGTCATACTAGGAACAG 3’

top 2 5' TCACACTAGATGCCGTCGGAATAGGACTCGTCATGCCCGTCCTACCCGGACTACTAAGGGA 3’

top 3 5' TATAGTCCATAGTGATAGTATAGCCAGTCATTATGGAGTCCTG 3’

bottom 2 5' GAGTCCTATTCCGACGGCATCTAGTGTGACTGTTCCTAGTATG
ACTATTAGGGCATTATTACTCTTCATCTAGAAGCGGCCGCG 3’

bottom 1 5' CTAGCAGGACTCCATAATGACTGGCTATACTATCACTATGGACTATATCCCTTAGTAGTCCGGGTAGGACGGGCATGAC 3’

'''Segment 2 Oligos'''

'''Optimized'''

top 1 5' CTAGCCTGTACGCGCTGATGCAGTTCCTGTGCGCGCCGGTTCTGGGTGCGCTGTCTGAC 3’

top 2 5' CGTTTCGGTCGTCGTCCGGTTCTGCTGGCGTCTCTGCTGGGTGCGACCATCGACTAC 3’

top 3 5' GCGATCATGGCGACCACCCCGGTTCTGTG 3’

bottom 1 5' GCGCACAGGAACTGCATCAGCGCGTACAGG 3’

bottom 2 5' CCAGCAGAACCGGACGACGACCGAAACGGTCAGACAGCGCACCCAGAACCGGC 3’

bottom 3 5' GATCCACAGAACCGGGGTGGTCGCCATGATCGCGTAGTCGATGGTCGCACCCAGCAGAGACG 3’

'''Deoptimized'''

top 1 5' CTAGCGCTATATGCCCTAATGCAATTTCTATGTGCCCCCGTCCTAGGAGCCCTAAGTG 3'

top 2 5' ATAGGTTTGGAAGGAGGCCCGTCCTACTAGCCAGTCTACTAGGAGCCACAATAGAT 3'

top 3 5' TATGCCATAATGGCCACAACACCCGTCCTATG 3'

bottom 1 5' GGCACATAGAAATTGCATTAGGGCATATAGCG 3' 

bottom 2 5' TAGGACGGGCCTCCTTCCAAACCTATCACTTAGGGCTCCTAGGACGGG 3' 

bottom 3 5' GATCCATAGGACGGGTGTTGTGGCCATTATGGCATAATCTATTGTGGCTCCTAGTAGACTGGCTAG 3'

[[Image:wiki3.jpg]]

'''Restriction Enzymes'''

To insert the annealed Oligo segments that were created we had to digest the Tet A gene using naturally occurring enzyme restriction sites that did not exist in the rest of the gene or in the plasmid (pSBIA2).

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Segment
|'''First Restriction Enzyme'''
|'''Second Restriction Enzyme'''
|-

| 1 || EcoRI || NheI
|-

| 2 || NheI || BamHI
|-

| 3 || BamHI || SphI
|-

| 4 || SphI || SalI
|-

|}

'''Parts Used (to be used)'''
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Part
|'''Registry Link'''
|'''Construct Including Part'''
|-

| Tet A (tetracycline resistance gene) J31007 || [http://partsregistry.org/Part:BBa_J31007 Tet A (forward)] || promoter-RBS-RFP-RBS-TetA on pSBIA2
|-

| pLac-RBS-RFP I715039 || [http://partsregistry.org/Part:BBa_I715039 pLac-RBS-RFP ]|| Possibly: pLac-RBS-RFP-RBS-TetA on pSBIA2
|-

| pLac-RBS-RFP-RBS-TetA-TT on pSBIAK3 S04435 || [http://partsregistry.org/Part:BBa_S04435 pLac-RBS-RFP-RBS-TetA-TT]|| Possibly: pLac-RBS-RFP-RBS-TetA-TT on pSBIA2
|-

| Part Name and Registry Number || [http://partsregistry.org/Main_Page Registry Link]|| Construct
|-

| Part Name and Registry Number || [http://partsregistry.org/Main_Page Registry Link]|| Construct
|-
|}

'''Tet-trations''' 

'''Making and Testing lox_ Sites'''
<center>
 '''Green''' Part has been cloned and sequence verified; '''Red''' Part is under construction

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Final Construct
!width="30"|Current Status
!Registry Number and Link
!width="30"|Primary Team Member
|-
| '''''lox5171'' Forward in pSB1A2''' || I got colonies on my second attempt. Once I isolate the plasmid, it will be sent off for sequencing. || [http://partsregistry.org/Part:pSB1A2 pSB1A2] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Nitya
|-

| '''''lox5171'' Reverse in pSB1A2''' || This plasmid will also be sent off for sequencing soon. || [http://partsregistry.org/Part:pSB1A2 pSB1A2] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Nitya
|-

| '''loxm2 Forward in pSB1A2''' || I ligated loxm2 F with the plasmid and have prepared the DNA for sequencing to confirm what is there. || [http://partsregistry.org/Part:BBa_K315004] ''loxm2'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Tom
|-

| '''loxm2 Reverse in pSB1A2''' || I ligated loxm2 F with the plasmid and have prepared the DNA for sequencing to confirm what is there. || [http://partsregistry.org/Part:BBa_K315005] ''loxm2'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || Tom
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-
|}
 
</center>

'''Testing Cre Activity''' 
<center>

 '''Green''' Part has been cloned and sequence verified; '''Red''' Part is under construction

{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
!Final Construct
!width="30"|Current Status
!Registry Number and Link
!width="30"|Primary Team Member
|-
| '''I718008 (pBAD+RBS+cre) in pSB4K5''' || At this point, I have isolated both the insert and the plasmid, but my two attempts at ligation have not produced any colonies. || [http://partsregistry.org/Part:BBa_I718008 I718008] [http://partsregistry.org/wiki/index.php?title=Part:pSB4K5 pSB4K5] || Nitya
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-

| '''Insert Info Here''' || what is built so far? || [http://partsregistry.org/Part:BBa_K199000 change to correct link] describe intermediate || your name here
|-
|}
</center>
 

'''pSBIA7 & pSBIA2'''

Data showing the varying levels of expression between pSBIA7 and pSBIA2

[[Image:wiki1.jpg]]

"Biological Noise"

2010-04-15T17:47:05Z

Clane3:

http://web.ebscohost.com/ehost/pdfviewer/pdfviewer?vid=3&hid=5&sid=edb1f143-a99d-4bef-85f5-953eb41e0858%40sessionmgr11

Bio-Math Connections January - May 2010

2010-04-15T17:43:36Z

Clane3:

Write in which project you will present, your name, and which campus you represent. For example:

* MOWestern/Davidson 2009 project:: Malcolm Campbell:: Davidson
* Cambridge 2009 project:: Michael Rydberg, Nitya Rao, Erin Feeney:: Davidson
* U.C. Berkeley 2009 project:: Anvi Raina, Steph Meador, Linda Kleist:: Davidson
* S.J.T.U. Shanghai 2009 project:: Yihharn Hwang, Stephen Streb, Shashank Suresh:: Davidson
* Stanford 2009 project:: Kris Hendershot, Garrett Smith, Tom Shuman:: Davidson
* NCTU Formosa/WetLab 2009 project:: Clif Davis:: Missouri Western
* Paris 2009 project:: Michel Conn:: Missouri Western
* UCSF 2009 project:: Stacey Holle:: Missouri Western
* [http://2009.igem.org/Team:EPF-Lausanne Lausanne Switzerland]:: Erin Feeney:: Davidson

[[Web pages about randomness]]

[[Papers about randomness]]

[[Biological Examples of random processes]]

[[Previous iGEM projects]]

[[analog computing]]

[[chaos]]

[["random number" generators]]

[["Biological Noise"]]

 
 

== Summer 2010 Brain Storming ==
MWSU will populate the odd numbered ideas and DC will populate the even numbered ideas. Only work on your idea number page and not the entire page to facilitate multiple people working at a given time.

== Idea #1 ==

Solving the Knapsack Problem - The problem is to figure out how many (integer) of each of several kinds of items to put into a knapsack when each item weighs a certain amount (real number) and the knapsack can only hold a certain amount of weight. Take three different genes (different kinds of items) with different degrees of toxicity (different weights). How can they be combined to get the closest to 100% toxicity, ie. death?

== Idea #2 ==

-testing for pollutants
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF4-4RC6R98-2&_user=2665120&_coverDate=02%2F04%2F2008&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1269769960&_rerunOrigin=google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=ae9a90f529694c35367e1b25b9e67818]
-cleaning up oil spills
[http://www.wired.com/science/discoveries/news/2004/12/66017]
[http://www.treehugger.com/files/2005/05/oileating_bacte_1.php]
-clean pollutants from air (carbon-capture technology, air scrubbers)
[http://www.gizmag.com/ionic-liquid-co2-emissions-control/11105/]
-bio-batteries
[http://www.sciencedaily.com/releases/2009/09/090907013811.htm]
[http://www.sciencedaily.com/releases/2008/03/080303190535.htm]

== Idea #3 ==
Let's Make a Deal! Our idea is to make E. coli play game shows based on decision making and probability. Playing the game means that E. coli makes a decision that produces a selective response. That response determines the ranking (score) of the E. coli and generates an output from the score. Some of the games we thought of include Deal or No Deal, Let's Make a Deal, Card Sharks, Blackjack, or other casino/mathematical based games.

Another game application for this would be to use E. coli to play Conway's Game of Life. It would be interesting if we could get them to function as oscillator's by having them flouresce in certain patterns. [http://www.math.com/students/wonders/life/life.html/link Wonder's of Math - Conway's Game of Life]

== Idea #4 ==
Our idea is to engineer heat producing E.coli and use them in wetsuits for rescue divers and hypothermia victims. We need to find an inhibitor for the calcium to prevent them from closing. This would produce a non-stop cycle that would produce heat. This is present in some humans with malignant hypothermia and blue fin tuna. We could study the tuna to find a possible protein or enzyme that enables this cycle. Another alternative is to de-flaggelate E. coli and have continious chemotaxis. This would produce heat as ATP would be constantly consumed.
Keeping the e. coli alive:
The challange would be to find a way to keep these E. coli alive. A possibility is haivng pockets of agar that could provide nutrients to E. coli.

== Idea #5 ==
Pascals triangle pattern solving bacteria idea. This idea is not fully developed but we are interested in the idea of bacteria "solving" whether they are divisible by prime factors. i.e divisible by 1= all bacteria, divisible by 2=red, divisible by 3=green, divisible by 5=blue. The colors would allow to us to see when the bacteria solved a particular problem.

== Idea #6 ==
Bio-sensors can be used to detect toxins in the air, water and on surfaces. Our idea is to use E. coli to monitor toxin levels in the air. The possible applications of this include counter-bioterrorism, pollution monitoring, and general detection of the chemical content of the air we breathe. This could also provide insight into the relationship between pollution and global warming.

We would need to pick either a specific toxin or multiple toxins that would trigger a reaction by our E. coli. Detectors could be hand-held objects with functional ends coated with E. coli that respond (perhaps by glowing a certain color) to detect the undesirable toxins. Different toxins could produce different color responses.

Other sensors could be smoke-detector-like rather than hand held, but work in the same way.

I realize that there are already tons of sensors for different chemicals that don't use E. coli. However, using E. coli would allow us to produce one sensor that reacts to a host of different toxins, producing different responses for each toxin.

== Idea #7 ==
Here are some ideas that Stacy and I came up with while brainstorming:

1. An Excel spreadsheet that is driven by E. coli

2. Dancing/synchronized swimming E. coli

3. An E. coli night light or Christmas lights

4. Talking E. coli

5. E. coli musical

6. E. coli jewelry, similar to the neon bracelets

7. Controlling or sensing the weather with E. coli, one possibility would be humidity or an indicator that it is time to water the plants

8. An E. coli cleaner that initially has color so that you could see what had been cleaned

== Idea #8 ==
This idea is based on some work by [http://gcat.davidson.edu/GcatWiki/index.php/Biological_Noise_and_Possible_Uses Olivia Ho-Shing (iGEM2009)]. She has been exploring the possibility of using biological noise to our advantage rather than fighting it.

Olivia is taking an independent study on biological noise and she has collected her resources on a wiki page.

One of her ideas was to produce a device that utilizes a positive feedback to amplify biological noise and kill cells that contain a device that is noisy. For example, imagine some one designs and builds cells that produce the smell of bananas when they reach stationary phase. However, each cell produces a different level of the necessary enzyme and what you want is a uniform population of cells all producing an output at about the same non-zero level.

The Olivilator would be a modular device that could be added to any existing device that utilizes the Lux quorum sensing mechanism. If a particular cells stays inside a band pass filter range of acceptable outputs, the cells live. If they under produce or over produce, then they are killed by the Olivilator.

== Idea #9 ==
Build a bacterial random number generator. Maybe based on noise, as discussed above.

== Idea #10 ==

<hr>