Team:Warsaw/Stage1/Modeling

From 2010.igem.org

(Difference between revisions)

Revision as of 20:29, 26 October 2010

Example Tabs

Modeling

Modelling

People used to design computational programs that would automaticall locate bacterialribosome binding sittes, various techniques were used[] including neural networks[]. However the software was capable only of finding the sequence and didn't give any information about the strength of RBS. In 2009 Nature issue the revolutionary software has been described[]. RBS calculator allows prediction of RBS strength, moreover it designs RBS of desired strength for specific gene sequence. In 2010 another RBS strength predictor was created[].

Fig 1.

Fig 2.

@@ Line 11: / Line 11: @@
 <h2>Modeling</h2>
-<div class"note"> drafdt do npt read</div>
+<div class"note"> Modelling </div>
-<p>
+<p>People used to design computational programs that would automaticall locate bacterialribosome binding sittes, various techniques were used[] including neural networks[]. However the software was capable only of finding the sequence and didn't give any information about the strength of RBS. In 2009 Nature issue the revolutionary software has been described[]. RBS calculator allows prediction of RBS strength,
-Durig the brainstorm period of our project we came up with many interesting ideas and we tried to find a way to squeeze all those ideas into one E.Coli Cell. It lead us to one generel dilema. How many different genes can we insert into our Coli at one time andd how precisly regulate their dosage. We decides to use different RBS sequences to controol gene exporession.
+ moreover it designs RBS of desired strength for specific gene sequence. In 2010 another RBS strength predictor was created[].
-We knew from the registry that B0033 is weak and for strong expresssion we should use B0034, but also we have learned that those RBSes were measures in one seup  with standard promoter and GFP reporter gene. We faced two ganeral questios:</p>
-<p>1) Are those 5 measured RBSes in the registry enaugh? Does it make sense to to use any other RBSes?</p>
-<p>2) RBSes were measured with GFP reporter. Are these RBS measurements universal. Would RBS behave differently if we pout our favourite gene uinstead of GFP?  </p>
-<p>We went downstairs, ordered lots of coffe, switched on the laptops and asked google scholar for help.
-We came acrooss a nature paper abut stadarisation of synthetic biological parts and devices []. The parts' evolutionary reliability measurement was perticulary interesting for us. Paper suggest that after 74 culture doubling the measured part mutated and wasn't fuctional anymore. System failiure resulted from deletion bethween repeated DNA sequences due to recombination. In that specific system it occured because terminator B0015 was used 2 times.</p><p>
-This scenario would be probably  repeated if we used the same RBS parts. However teh experiment was performed in the recA+ strain - in other words a strain thet recombinates.2009 Warsaw team used B0032 many times to obtain moderate gene expression, because Top10 (recA-) strain was used there were no recobination events.In the light of these evidence we wanted to refine our design and avoid repeated sequences to make our system portable. This is a problem if you want to use RBSes of similar strength, because there is seldom more than one characterised. </p>