Team:Newcastle/Stochasticity
From 2009.igem.org
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[[Team:Newcastle/ Bistability in B.Subtilis|Natural stochastic switches:Bistability in ''Bacillus subtilis'']] | [[Team:Newcastle/ Bistability in B.Subtilis|Natural stochastic switches:Bistability in ''Bacillus subtilis'']] | ||
+ | We intend to design a synthetic stochastic switch by using an invertible segment of our DNA that codes a promoter. Depending on the direction of the promoter, coding sequiences will be expressed which reflect the decision to be a metal container or not. | ||
+ | |||
+ | We looked at the following possibilities: | ||
+ | |||
===Hin/Hix system=== | ===Hin/Hix system=== | ||
In 2006, Davidson team tried to solve the burnt pancake problem by using DNA rearrangement using Hin/Hix system from ''Salmonella typhimurium''. (http://parts2.mit.edu/wiki/index.php/Davidson_2006.) Basically they tried to use the bacteria as a biomemory! They also have a paper published which is attached. | In 2006, Davidson team tried to solve the burnt pancake problem by using DNA rearrangement using Hin/Hix system from ''Salmonella typhimurium''. (http://parts2.mit.edu/wiki/index.php/Davidson_2006.) Basically they tried to use the bacteria as a biomemory! They also have a paper published which is attached. | ||
+ | The Hin system will be the main DNA rearrangement system within our stochastic switch, | ||
+ | Unlike the ''fim'' system the ''hin'' system allows the DNA segment to be flipped back and forth, We can therefore | ||
Their animation explains the process quite well. | Their animation explains the process quite well. | ||
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===fimE switch=== | ===fimE switch=== | ||
+ | The FimE switch is a similar switch to the Hix system, however it acts as a latch, meaning once flipped, the segmant will not flip back. | ||
# [http://genomics.lbl.gov/Stuff/TimHam-BandB-online%20version.pdf fimE switch for DNA re-arrangement] | # [http://genomics.lbl.gov/Stuff/TimHam-BandB-online%20version.pdf fimE switch for DNA re-arrangement] | ||
A Tightly Regulated Inducible Expression System Utilising the fim Inversion Recombination Switch.(''E. Coli'') Timothy S. Ham, Sung Kuk Lee, Jay D. Keasling,Adam P. Arkin,Received 21 December 2005; accepted 2 March 2006 Published online 13 March 2006 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/bit.20916 | A Tightly Regulated Inducible Expression System Utilising the fim Inversion Recombination Switch.(''E. Coli'') Timothy S. Ham, Sung Kuk Lee, Jay D. Keasling,Adam P. Arkin,Received 21 December 2005; accepted 2 March 2006 Published online 13 March 2006 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/bit.20916 |
Revision as of 08:46, 24 July 2009
Contents |
Stochasticity
One of the most unique aspects of our project is our synthetic stochastic switch which regulates the decision to be a metal container spore, or a spore that can go on to germinate as part of the normal life cycle.
Natural stochastic switches:Bistability in Bacillus subtilis
We intend to design a synthetic stochastic switch by using an invertible segment of our DNA that codes a promoter. Depending on the direction of the promoter, coding sequiences will be expressed which reflect the decision to be a metal container or not.
We looked at the following possibilities:
Hin/Hix system
In 2006, Davidson team tried to solve the burnt pancake problem by using DNA rearrangement using Hin/Hix system from Salmonella typhimurium. (http://parts2.mit.edu/wiki/index.php/Davidson_2006.) Basically they tried to use the bacteria as a biomemory! They also have a paper published which is attached. The Hin system will be the main DNA rearrangement system within our stochastic switch, Unlike the fim system the hin system allows the DNA segment to be flipped back and forth, We can therefore
Their animation explains the process quite well. (http://www.bio.davidson.edu/people/kahaynes/FAMU_talk/Living_computer.swf)
The parts they submitted to the parts registry have "W" flag which means they are working. http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Davidson
fimE switch
The FimE switch is a similar switch to the Hix system, however it acts as a latch, meaning once flipped, the segmant will not flip back.
- [http://genomics.lbl.gov/Stuff/TimHam-BandB-online%20version.pdf fimE switch for DNA re-arrangement]
A Tightly Regulated Inducible Expression System Utilising the fim Inversion Recombination Switch.(E. Coli) Timothy S. Ham, Sung Kuk Lee, Jay D. Keasling,Adam P. Arkin,Received 21 December 2005; accepted 2 March 2006 Published online 13 March 2006 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/bit.20916
We could use it switch off or on the production of a protein of our choice, such as the genes involved in germination.
The search for fimE equivalent in Bacillus subtilis
Gene list from BLAST search output in Subtilist web-server (7 matches)
Organism |No. | Gene |Bp | Putative Function | Score | E-value
B.subtilist|BS000101011332|RipX: 295 site specific integrase... 82 | 2.00E-17
B.subtilist|BS000101010965|CodV: 303 sitespecific integrase... 73 | 1.00E-14
B.subtilist|BS000101012099|YdcL: 367 unknown; similar to int... 30 | 0.13
B.subtilist|BS000101011909|AraM: 393 L arabinose operon 27 | 0.64
B.subtilist|BS000101013550|YoeC: 94 unknown; similar to unkn... 25 | 3.2
B.subtilist|BS000101013687|YorC: 125 unknown 24 | 7.1
B.subtilist|BS000101011532|IlvD: 557 dihydroxyacid dehydratase 24 | 7.1
B.subtilist|BS000101010010|YybT: 658 unknown similar to unk... 23 | 9.2
- [http://jb.asm.org/cgi/reprint/183/14/4190?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=subtilis&searchid=1&FIRSTINDEX=880&resourcetype=HWFIG Control of the Arabinose Regulon in Bacillus subtilis by AraR In Vivo: Crucial Roles of Operators, Cooperativity, and DNA Looping]
- [http://ukpmc.ac.uk/articlerender.cgi?artid=310841 Binding of the Bacillus subtilis spoIVCA product to the recombination sites of the element interrupting the sigma K-encoding gene] =>...DNA rearrangement that depends on the spoIVCA gene product...
Spo0A phosphorylation
Spo0A phoshorylation controls sporulation and is also a bitsable switch. A subset of the population will be on spo0A ON state [2,3]. We can trigger sporulation therefore by expressing more KinA on one side of the switch.
- http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1449569
- http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2430929&blobtype=pdf
- http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.micro.62.081307.163002
Stochastic Modelling Tools
Matlab
Matlab can be used for stochastic modelling. Glasgow team used Matlab implementing Gillespie algorithm to incorporate noise among cells. They also used deterministic modelling using ODEs and compared their results. When the number of cells increase two approaches become similar since the noise is cancelled out.
Stocks 2
Stocks 2 is another stochastic simulation tool which also uses Gillespie’s direct method and supports SBML.
News
Events
- 20 – 21 June 2009 - Europe workshop (London)
- 23 – 24 June 2009 - UK iGEM meetup (Edinburgh)
- 23 October Practice Presentation (Newcastle)
- 23 October T-shirts are ready
- 27 October Practice Presentation (Sunderland)
- 27 October Poster is ready
- 30 October – 2 November 2009 - Jamboree (Boston)
Social Net
- Newcastle iGEM Twitter
- [http://www.facebook.com/home.php#/group.php?gid=131709337641 Newcastle on Facebook]
- [http://www.youtube.com/user/newcastle2009igem Newcastle Youtube Channel]