Team:Bologna

From 2008.igem.org

(Difference between revisions)
 
(57 intermediate revisions not shown)
Line 31: Line 31:
|titolo=[[Team:Bologna/Project|PROJECT]]
|titolo=[[Team:Bologna/Project|PROJECT]]
|contenuto=[[Image:Nome_Progetto2.png|550px|left|Nome Progetto]]
|contenuto=[[Image:Nome_Progetto2.png|550px|left|Nome Progetto]]
-
Our project aims to design a bacterial reprogrammable memory with genetically engineered E.coli colonies in solid medium working as an array of binary memory cells. To engineer bacteria we designed a genetic flip-flop (SR Latch) composed of a binary memory and an UV sensitive trigger. We chose UV to have a fine spatial selectivity in programming the cells and IPTG to reset all the memory cells. We designed the circuit by model-based analysis. Core elements of the genetic memory are two mutually regulated promoters. Each promoter has as an operator site flanking a constitutive promoter. Thus, promoter transcriptional strength and repressor binding affinity can be independently fixed. Operators for LacI, TetR, Lambda and LexA repressors were cloned as BioBricks to allow the rational design of regulated promoters that is still lacking in the Registry. A simple procedure was established to characterize the regulated promoter. We expect these parts to be a benefit in many Synthetic Biology applications. [[Team:Bologna/Project|Click here for more information...]]
+
 
-
<br><br>
+
Our project aims to design a bacterial reprogrammable binary memory (EPROM) with genetically engineered E.coli. To engineer bacteria we designed a genetic Flip-Flop formed by an epigenetic memory sensitive to IPTG -for the memory reset- and an UV-sensitive trigger to set the memory ON. We designed the Flip-Flop circuit by model-based analysis and computer simulation. The core elements are two mutually regulated promoters. Each of them is composed of a constitutive promoter and an independent operator sequence. Thus, transcriptional strength and repressor binding affinity can be independently fixed. Since operator sites are still lacking in the Registry as standard parts, we cloned operator sequences for LacI, TetR, Lambda and LexA repressors and established an experimental procedure to characterize them. These parts allow the rational design of regulated promoters and we expect them to be a benefit in many Synthetic Biology applications.
 +
[[Team:Bologna/Project|Click here for more information...]]
 +
<br><br><br>
}}
}}
Line 40: Line 42:
|titolo=[[Team:Bologna/Team|TEAM]]
|titolo=[[Team:Bologna/Team|TEAM]]
|contenuto=[[Image:TeamBo2.JPG|250px|right]]
|contenuto=[[Image:TeamBo2.JPG|250px|right]]
-
The rationale underpinning the foundation of the Ecoli.PROM team consisted in the synergistically collaboration of various young students with different curricula. These students, pushed by their common desire for new experiences, decided to participate in this exciting competition to discover a new research field and to expand their interest for synthetic biology. Responding to the call of Professor Silvio Cavalcanti, they constituted the Bologna iGEM team, finally composed of students from Biotechnology, Electronics Engineering and Biomedical Engineering faculties.
+
The leading idea behind the UniBO Team was to put in touch students of the same University with different backgrounds to favor competence and skill sharing. Students from different Faculties (Biotechnology, Pharmacy and Engineering) answered to the iGEM call and formed the TEAM. They were moved by a common desire for new experiences and they decided to participate in this exciting competition to go deep in Synthetic Biology. The Team worked hard during the summer to become fully operative, overcoming differences both in training and personality.
-
<br>
+
<br><br>
[[Team:Bologna/Team|Go to the page!]]
[[Team:Bologna/Team|Go to the page!]]
-
<br>
 
}}
}}
Line 49: Line 50:
{{Bologna/finestra100
{{Bologna/finestra100
|titolo=[[Team:Bologna/Modeling|MODELING]]
|titolo=[[Team:Bologna/Modeling|MODELING]]
-
|contenuto=[[Image:Circuito2.jpg|280px|right]]
+
|contenuto=[[Image:Circuito2.jpg|278px|right]]
-
The aim of this work area is to determine the characteristics of the promoters that form the circuit. In this section are also collected a brief description of our model, all the equations that describe analytically our circuit, the most meaningful graphics and the results of simulations. [[Team:Bologna/Modeling|Enjoy yourself!]]
+
Mathematical model analysis and computer simulations were used to design the Flip-Flop circuit. We resorted to this engineer’s approach  to obtain a  rational design of regulated promoters, that are the core element of the circuit. By the model we found the analytic relationships to quote the regulated promoter in terms of transcriptional strength and sensitivity to the repressor. By model-based computer simulation we established such a relevant circuit properties as the bistability and the dynamical response to inputs. A simple procedure to characterize the operator sequence was theoretically derived. [[Team:Bologna/Modeling|Enjoy yourself!]]
<br>
<br>
}}
}}
Line 58: Line 59:
|titolo=[[Team:Bologna/Software|SOFTWARE]]
|titolo=[[Team:Bologna/Software|SOFTWARE]]
|contenuto=[[Image:cuscino.JPG|260px|right]]
|contenuto=[[Image:cuscino.JPG|260px|right]]
-
Into this section you can find the very useful softwares we developed for this competition. The first of them realizes a fluorescence image analysis using two parameters: the bacteria dimensions and the standard deviation and mean fluorescence ratio. The second makes possible to find the registered parts you are searching for in a quick and easy way, to identify their sequence and display parts with similar behaviour. You can also download them from this [[Team:Bologna/Software|page]].
+
Into this section you can find two software tools developed in our lab for this competition and that we would like to share with other Teams. One tool is a bacteria fluorescence image analyzer that segments the bacteria, counts their number, computes the size and the fluorescence intensity for each segmented bacterium. The second tool searches data in the Registry automatically to find parts by entry a part name or a string with short part description or a nucleotide sequence. You can download them from this [[Team:Bologna/Software|page]].
<br>
<br>
}}
}}
Line 67: Line 68:
|contenuto=[[Image:Collage2.JPG|440px|left]]
|contenuto=[[Image:Collage2.JPG|440px|left]]
<br><br><br><br><br><br><br>  
<br><br><br><br><br><br><br>  
-
To obtain regulated promoters we synthesized four libraries of operator sequences, respectively for LacI, TetR, cI and LexA repressor proteins. Here
+
To obtain regulated promoters we synthesized four libraries of operator sequences, respectively for LacI, TetR, CI and LexA repressor proteins. In each library, there are three sequences each with a different repressor binding affinity. The choice of the operator should give a relative fine-tuning of promoter sensitivity to the repressor. In this part, it is explained how we designed the operator libraries and isolated single operators to clone them in the standard format. Moreover, we built and tested: a LacI regulated promoter to tune promoter activation and a lexA based promoter to study the SOS activation (UV and hydrogen peroxide). [[Team:Bologna/Wetlab|So wet!]]
-
[[Team:Bologna/Notebook|So wet!]]
+
}}
}}
</div>
</div>
-
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
= Aknowledgements =
= Aknowledgements =
-
Our Team is funded by:
 
-
 
-
<br>
 
* ''' [http://www.unibo.it/Portale/default.htm University of Bologna] '''
* ''' [http://www.unibo.it/Portale/default.htm University of Bologna] '''
Line 83: Line 80:
<br>
<br>
-
[[Image:AlmaMaterStudiorum.jpg|center]]
+
[[Image:AlmaMaterStudiorum.jpg|left|100 px]]
-
<br><br>
+
<br><br><br><br><br><br><br>
* ''' [http://serinar.criad.unibo.it Ser.In.Ar. Cesena] '''  
* ''' [http://serinar.criad.unibo.it Ser.In.Ar. Cesena] '''  
Line 91: Line 88:
<br>
<br>
-
[[Image:Ser_In_Ar.jpg|center|800px]]
+
[[Image:Ser_In_Ar.jpg|left|500px]]
-
<br><br>
+
<br><br><br><br><br>
----
----
[https://2008.igem.org/Team:Bologna ''Up'']
[https://2008.igem.org/Team:Bologna ''Up'']

Latest revision as of 02:39, 30 October 2008

Logo1a.gifTestata dx.jpg
HOME PROJECT TEAM SOFTWARE MODELING WET LAB LAB-BOOK SUBMITTED PARTS BIOSAFETY AND PROTOCOLS


Logo Bologna


PROJECT
Nome Progetto

Our project aims to design a bacterial reprogrammable binary memory (EPROM) with genetically engineered E.coli. To engineer bacteria we designed a genetic Flip-Flop formed by an epigenetic memory sensitive to IPTG -for the memory reset- and an UV-sensitive trigger to set the memory ON. We designed the Flip-Flop circuit by model-based analysis and computer simulation. The core elements are two mutually regulated promoters. Each of them is composed of a constitutive promoter and an independent operator sequence. Thus, transcriptional strength and repressor binding affinity can be independently fixed. Since operator sites are still lacking in the Registry as standard parts, we cloned operator sequences for LacI, TetR, Lambda and LexA repressors and established an experimental procedure to characterize them. These parts allow the rational design of regulated promoters and we expect them to be a benefit in many Synthetic Biology applications. Click here for more information...



TEAM
TeamBo2.JPG

The leading idea behind the UniBO Team was to put in touch students of the same University with different backgrounds to favor competence and skill sharing. Students from different Faculties (Biotechnology, Pharmacy and Engineering) answered to the iGEM call and formed the TEAM. They were moved by a common desire for new experiences and they decided to participate in this exciting competition to go deep in Synthetic Biology. The Team worked hard during the summer to become fully operative, overcoming differences both in training and personality.

Go to the page!


MODELING
Circuito2.jpg

Mathematical model analysis and computer simulations were used to design the Flip-Flop circuit. We resorted to this engineer’s approach to obtain a rational design of regulated promoters, that are the core element of the circuit. By the model we found the analytic relationships to quote the regulated promoter in terms of transcriptional strength and sensitivity to the repressor. By model-based computer simulation we established such a relevant circuit properties as the bistability and the dynamical response to inputs. A simple procedure to characterize the operator sequence was theoretically derived. Enjoy yourself!

SOFTWARE
Cuscino.JPG

Into this section you can find two software tools developed in our lab for this competition and that we would like to share with other Teams. One tool is a bacteria fluorescence image analyzer that segments the bacteria, counts their number, computes the size and the fluorescence intensity for each segmented bacterium. The second tool searches data in the Registry automatically to find parts by entry a part name or a string with short part description or a nucleotide sequence. You can download them from this page.


WET LAB
Collage2.JPG








To obtain regulated promoters we synthesized four libraries of operator sequences, respectively for LacI, TetR, CI and LexA repressor proteins. In each library, there are three sequences each with a different repressor binding affinity. The choice of the operator should give a relative fine-tuning of promoter sensitivity to the repressor. In this part, it is explained how we designed the operator libraries and isolated single operators to clone them in the standard format. Moreover, we built and tested: a LacI regulated promoter to tune promoter activation and a lexA based promoter to study the SOS activation (UV and hydrogen peroxide). So wet!











































Aknowledgements

  • [http://www.unibo.it/Portale/default.htm University of Bologna]


AlmaMaterStudiorum.jpg








  • [http://serinar.criad.unibo.it Ser.In.Ar. Cesena]


Ser In Ar.jpg








Up