GcatWiki - User contributions [en]

IGEM 2010 Project

2010-06-15T15:49:10Z

Nirao: /* 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''' 

'''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
|-

| '''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>

'''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>

IGEM 2010 Project

2010-06-15T15:25:03Z

Nirao: /* 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''' 

'''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] ''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] ''lox5171'' does not exist in the registry. We ordered oligos and constructed the site in the lab. || 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
|-
|}
 
</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] [http://partsregistry.org/wiki/index.php?title=Part: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>

Bio-Math Connections January - May 2010

2010-04-23T20:56:28Z

Nirao: /* Idea #9 */

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.

http://2009.igem.org/Team:Harvard/Split
The Harvard iGEM team created bacteria-yeast communication system in which the bacteria produced light at a wavelength of 660 nm. The yeast used a phytochrome to absorb the light.

http://2009.igem.org/Team:Chiba/Project#Project_Design
This team modified the LuxR protein so that they take differing lengths of time to active transcription.

== Idea #10 ==

The LasR protein generator follows a similar mechanism as the LuxR, yet uses a different language. It could be used to generate biological noise, and in turn, we could test out mechanism for eliminating noise as described in Idea #8.

== Idea #11 ==
[[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0009182#pone-0009182-g004
Bioessay]]

== Idea #12 ==
[[http://2009.igem.org/Team:TUDelft/Conjugation_Overview]]

[[http://2009.igem.org/Team:Paris]]
long rang communication system between cells

Papers about randomness

2010-04-09T21:01:31Z

Nirao:

[http://gcat.davidson.edu/GcatWiki/index.php/Literature_Read_and_Summaries Olivia's collection of papers with annotations]

Noise and Stochasticity
[http://www.lcg.unam.mx/frontiers/files/frontiers/Losick-Desplan-text-figures-12-5.pdf]
This (possibly unpublished) paper discusses some biological examples of stochasiticity. Though we don't have links, we also found examples of Notch being used to regulate butterfly scales and pigment receptors in drosphila eyes.