http://2008.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=500&target=Philippe+b&year=&month=2008.igem.org - User contributions [en]2024-03-29T04:53:23ZFrom 2008.igem.orgMediaWiki 1.16.5http://2008.igem.org/Team:Paris/ConstructionTeam:Paris/Construction2008-10-30T04:39:34Z<p>Philippe b: /* Synchronization module */</p>
<hr />
<div>{{Paris/Menu}}<br />
'''Have a look at our [[Team:Paris/Notebook|notebook]].'''<br />
<br />
=Model constructions: from the modelling to the characterization=<br />
<br />
Our project BacterioClock is based on an oscillating FIFO synchronized at the population level. To obtain and have preliminary results of this system we divided it in three "little" modules as the modeling team exposed them previously.<br />
==The First is to demonstrate the [[Team:Paris/Analysis#FIFO_behaviour|FIFO]] which constitutes our core system==<br />
<br />
A simple manner is to implement two class II promoter followed by fluorescent reporter genes like GFP in a bacteria strain that is able to produce the flagella. <br />
<br />
By this way, we are able to see in single cell the order of the activation of pFliL then pFlgA then pFlhB and then the inactivation in the same order as a FIFO will do.<br />
<br />
These constructions are equivalent to the experiments realized by Uri Alon in the article "Using quantitative Blueprint to reprogram the Dynamics of the Flagella Gene Network" Kalir S, Alon U. Cell 2004.<br />
<br />
A better way to observe the FIFO is to study the system with an inducible regulator of class II gene in a bacteria strain deleted for this gene. We are extremely grateful for Alon U. that send us the inducible gene ''FlhDC'', and ''FliA'' in pBad18 plasmid.<br />
These plasmids with our own araC/pBad-EnvZ* will allowed us to study the system in mutated strains that we have in our lab (ΔFlhD, ΔFliA, ΔFlgM, ΔEnvZ). By cotransforming in mutated strains the inducible regulators of the class II promoters with one of this promoter associated to a fluorescent protein, we could characterize the influence of the master regulators of the flagella on their promoter. The fluorescence is normalized to the OD<sub>600</sub>.<br />
<br>For example below are some constructions to see and induce the FIFO:<br />
<br><br><br><br />
[[Image:Felipe01.jpg|500px|center|thumb|pFliL alone]]<br><br><br><br />
[[Image:Felipe02.jpg|500px|center|thumb|3 promoters of the FIFO in one Cell]]<br><br><br><br />
[[Image:Felipe03.jpg|500px|center|thumb|FIFO and oscillating constructions in a single cell due to the flhDC repression by EnvZ*. ]]<br><br><br><br />
<br />
<br />
To perform such a cotransformation we take care about the ORI of each low copy plasmid which are often incompatible and we made all our final constructions in the pSB4T5 plasmid that care the only one resistance that was not already used and the pSC101 ORI which is compatible with the ColE1.<br />
<br />
We could see the FIFO in a more convenient manner with the assembly of two class II promoters associated to different fluorophores. Then we could observed two kinds of fluorescents in One Cell along time. <br />
One problem that could occur is the interaction between the different fluorescents proteins due to the cross-over of their emission and excitation spectra and moreover in our final system that count three fluorophores.<br />
<br />
[[Image:Spectre.jpg |600px |thumb| emission and excitation spectra of ECFP, YFP and mRFP]]<br />
<br />
<br>The choice of ECFP, YFP and mRFP is based upon this consideration and upon the order of appearing in the FIFO.<br />
Indeed by putting the mRFP in last position, we improve the visualization of the FIFO like the maturation time of the protein is about of one hour.<br />
<br />
We thank a lot Arnau Montagu, advisor of the iGEM Valencia Team. He advised us, after his team had troubleshooting with fluorescence, to take care about ''spurious FRET''. This phenomenon occurs even with non covered fluorescent spectra when the concentration of two fluorophores is sufficient so they are enough closer to induce some FRET. But it could happen at lower concentration than 40 μM. <br><br />
<br>- "DsRed as a Potential FRET Partner with CFP and GFP" Michael G. Erickson, Daniel L. Moon, and David T. Yue Biophysical Journal 2003. <br />
<br>- "A Comparison of Donor-Acceptor Pairs for Genetically Encoded FRET Sensors: Application to the Epac cAMP<br />
Sensor as an Example" Gerard N. M. van der Krogt, Janneke Ogink, Bas Ponsioen, Kees Jalink PLoS 2008.<br />
<br />
<br><br />
<br />
==[[Team:Paris/Analysis#Oscillations|Oscillating]] module==<br />
Few approaches have been thought in order to create the oscillating module. The pTet/TetR system that allows us to precisely control the inhibition of TetR on the Tet promoter. Another system use the natural inhibition of OmpR and of EnvZ via OmpR. We finally perform this system that we have developed since we know thanks to the modeling team that the oscillations are the only way to see the full development of the FIFO.<br />
<br />
==Synchronization module==<br />
The modeling simulation showed us that to have some oscillations that are difficult to obtain in a simple feedforward loop without the delay introduce by the quorum sensing synchronization, and for us it is more interesting to have the FIFO behavior at the population level. We did not achieved this module but we started the construction of it and have already some intermediate parts that you will find below.<br />
<br />
==The constructions we were able to obtain were characterised by fluorescence microscopy (see examples below):==<br />
[[Image:ParisGfp.jpg|thumb|300px|center|Green fluorescence]]<br />
[[Image:ParisRfp.jpg|thumb|300px|center|Red Fluorescence]]<br />
[[Image:ParisCfp.jpg|thumb|300px|center|Cyan Fluorescence]]<br />
<br />
== Table of the constructions we realized==<br />
{|<br />
|- style="background: #649cd7;"<br />
!colspan=4 style="background: #649cd7" | FIFO<br />
|- style="background: #649cd7; text-align: center;"<br />
|width=30%| Construction<br />
|width=55%| Description<br />
|width=15%| Validation Date<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136039 pFliL(RBS WT)-ECFP tripart (LVA+)]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFliL is ECFP fused with a LVA tag.<br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]]<br>[http://partsregistry.org/Part:BBa_K136037 pFliL(+ RBS WT)-GFP]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFliL is GFP.<br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136012 pFlgA(+ RBS WT) - YFP Tripart (LVA+)]<br />
|align=|Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is EYFP fused with a LVA tag. <br />
|align="center"| [[Team:Paris/August 22|August 22]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136013 pFlgA(+ RBS WT) - YFP Tripart (LVA-)]<br />
|align=|Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is EYFP fused without a LVA tag. <br />
|align="center"| [[Team:Paris/August 22|August 22]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136054 pFlgA(+ RBS WT)-YFP tripart (AAV+)]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is EYFP fused with a AAV tag. <br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]]<br>[http://partsregistry.org/Part:BBa_K136053 pFlgA(+ RBS WT)-GFP]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is GFP. <br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136055 pFlhB(+ RBS WT)-mRFP tripart (+LVA)]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlhB is mRFP with a LVA tag. <br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]]<br>[http://partsregistry.org/Part:BBa_K136065 pFlhB(+ RBS WT)-GFP]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlhB is GFP. <br />
|align="center"| [[Team:Paris/October 26|October 26]]<br />
|-<br />
|colspan=4 style="background: #649cd7" | <center>'''OSCILLATION'''</center><br />
|-<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136064 pFliL(+ RBS WT)-EnvZ*]<br />
|align=| pFliL is regulated by FlhDC and EnvZ regulates pFlhDC thanks to a negative feedback loop, origin of an oscillation behavior.<br />
|align="center"| [[Team:Paris/October 26|October 26]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136069 pFliL(+ RBS WT)-EnvZ*-GFP generator]<br />
|align=| The same construction as before but with a GFP in order to follow the dynamic of expression of pFliL.<br />
|align="center"| [[Team:Paris/October 29|October 29]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136051 pFlhB(+ RBS WT)-EnvZ*]<br />
|align=| pFlhB is regulated by FlhDC and EnvZ regulates pFlhDC thanks to a negative feedback loop, origin of an oscillation behavior.<br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136070 pFlhB(+ RBS WT)-EnvZ*-GFP generator]<br />
|align=| The same construction as before but with a GFP in order to follow the dynamic of expression of pFlhB.<br />
|align="center"| [[Team:Paris/October 29|October 29]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136066 araC/pBad-EnvZ*]<br />
|align=| A construction made for characterizing the repression power of the mutated EnvZ on our system<br />
|align="center"| [[Team:Paris/October 27|October 27]]<br />
|-<br />
|colspan=4 style="background: #649cd7" | <center>'''SYNCHRONISATION'''</center><br />
|-<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136029 pLas - gfp Tripart]<br />
|align=| Construction for characterization of the pLas promoter<br />
|align="center"| [[Team:Paris/August 1|August 1]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136027 pLas - ECFP]<br />
|align=| The same as before but with another fluorophore<br />
|align="center"| [[Team:Paris/August 1|August 1]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br> [http://partsregistry.org/Part:BBa_K136024 strongest promoter-rbs-lasR-dble ter]<br />
|align=| A construction for a strong constitutive expression of the Las Regulator in order to get maximal expression in presence of AHL<br />
|align="center"| [[Team:Paris/August 20|August 20]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136023 Strong promoter-rbs-lasR-dble ter]<br />
|align=| A derived construction of the previous one for smaller constitutive expression of LasR in the Bacteria.<br />
|align="center"| [[Team:Paris/August 20|August 20]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136044 Strongest RBS (1)- LasR activator (+LVA)]<br />
|align=| Intermediary construction. We uses different rbs for Las R in order to get various response dynamic to the presence of AHL<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136048 rbs-lasR + dbl ter]<br />
|align=| Intermediary construction. We uses different rbs for Las R in order to get various response dynamic to the presence of AHL<br />
|align="center"| [[Team:Paris/August 19|August 19]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136052 lasR activator + LVA - Double Terminator]<br />
|align=| Intermediary construction<br />
|align="center"| [[Team:Paris/August 1|August 1]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136057 RBS lasI - GFP tripart]<br />
|align=| Construction that has to be associated with the FIFO. We will know when LasI is expressed and then when AHL is produced.<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br> [http://partsregistry.org/Part:BBa_K136056 RBS-lasI - ECFP]<br />
|align=| The same as the previous one but with another fluorophore.<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|-<br />
|colspan=4 style="background: #649cd7" | <center>'''NEW GENE AND PROMOTER BIOBRICKS'''</center><br />
|-<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136010 pFliA]<br />
|align=| Natural promoter of E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC.<br />
|align="center"| [[Team:Paris/October 04|October 04]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136009 pFliL (+RBS WT)]<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA.<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136006 pFlgA (+RBS WT)]<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA..<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br> pFlgB (+RBS WT)<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA.<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136008 pFlhB (+RBS WT)]<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA.<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136046 EnvZ*]<br />
|align=| EnvZ is a membrane protein involved into the osmotic response and is interacting with OmpR that will bind the promoter of FlhDC ad will repress it. EnvZ* is a mutated form of the coding sequence, giving a phenotype where pFlhDC is completely repressed. EnvZ has been extracted by PVR for the correct mutant strain.<br />
|align="center"| [[Team:Paris/September 04|September 04]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_coding.png]]<br>FliA<br />
|align=| FliA is a sigma factor involved into the regulation of very various genes, the promoter used in the FIFO were selected to be higly responding to FliA. In order to have the FliA gene possibly used as biobrick, we mutated 2 sites (EcoRI and PstI) inside the FliA sequence by assemby PCR. <br />
|align="center"| [[Team:Paris/September 04|September 04]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" |[[Image:Icon_coding.png]]<br>FlhDC<br />
|align=| FlhDC is the main regulator of the flagella genetic system in E. coli. FlhDC regulates all the promoter of the FIFO.<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Construction}}</div>Philippe bhttp://2008.igem.org/Team:Paris/ConstructionTeam:Paris/Construction2008-10-30T04:38:19Z<p>Philippe b: /* The First is to demonstrate the FIFO which constitutes our core system */</p>
<hr />
<div>{{Paris/Menu}}<br />
'''Have a look at our [[Team:Paris/Notebook|notebook]].'''<br />
<br />
=Model constructions: from the modelling to the characterization=<br />
<br />
Our project BacterioClock is based on an oscillating FIFO synchronized at the population level. To obtain and have preliminary results of this system we divided it in three "little" modules as the modeling team exposed them previously.<br />
==The First is to demonstrate the [[Team:Paris/Analysis#FIFO_behaviour|FIFO]] which constitutes our core system==<br />
<br />
A simple manner is to implement two class II promoter followed by fluorescent reporter genes like GFP in a bacteria strain that is able to produce the flagella. <br />
<br />
By this way, we are able to see in single cell the order of the activation of pFliL then pFlgA then pFlhB and then the inactivation in the same order as a FIFO will do.<br />
<br />
These constructions are equivalent to the experiments realized by Uri Alon in the article "Using quantitative Blueprint to reprogram the Dynamics of the Flagella Gene Network" Kalir S, Alon U. Cell 2004.<br />
<br />
A better way to observe the FIFO is to study the system with an inducible regulator of class II gene in a bacteria strain deleted for this gene. We are extremely grateful for Alon U. that send us the inducible gene ''FlhDC'', and ''FliA'' in pBad18 plasmid.<br />
These plasmids with our own araC/pBad-EnvZ* will allowed us to study the system in mutated strains that we have in our lab (ΔFlhD, ΔFliA, ΔFlgM, ΔEnvZ). By cotransforming in mutated strains the inducible regulators of the class II promoters with one of this promoter associated to a fluorescent protein, we could characterize the influence of the master regulators of the flagella on their promoter. The fluorescence is normalized to the OD<sub>600</sub>.<br />
<br>For example below are some constructions to see and induce the FIFO:<br />
<br><br><br><br />
[[Image:Felipe01.jpg|500px|center|thumb|pFliL alone]]<br><br><br><br />
[[Image:Felipe02.jpg|500px|center|thumb|3 promoters of the FIFO in one Cell]]<br><br><br><br />
[[Image:Felipe03.jpg|500px|center|thumb|FIFO and oscillating constructions in a single cell due to the flhDC repression by EnvZ*. ]]<br><br><br><br />
<br />
<br />
To perform such a cotransformation we take care about the ORI of each low copy plasmid which are often incompatible and we made all our final constructions in the pSB4T5 plasmid that care the only one resistance that was not already used and the pSC101 ORI which is compatible with the ColE1.<br />
<br />
We could see the FIFO in a more convenient manner with the assembly of two class II promoters associated to different fluorophores. Then we could observed two kinds of fluorescents in One Cell along time. <br />
One problem that could occur is the interaction between the different fluorescents proteins due to the cross-over of their emission and excitation spectra and moreover in our final system that count three fluorophores.<br />
<br />
[[Image:Spectre.jpg |600px |thumb| emission and excitation spectra of ECFP, YFP and mRFP]]<br />
<br />
<br>The choice of ECFP, YFP and mRFP is based upon this consideration and upon the order of appearing in the FIFO.<br />
Indeed by putting the mRFP in last position, we improve the visualization of the FIFO like the maturation time of the protein is about of one hour.<br />
<br />
We thank a lot Arnau Montagu, advisor of the iGEM Valencia Team. He advised us, after his team had troubleshooting with fluorescence, to take care about ''spurious FRET''. This phenomenon occurs even with non covered fluorescent spectra when the concentration of two fluorophores is sufficient so they are enough closer to induce some FRET. But it could happen at lower concentration than 40 μM. <br><br />
<br>- "DsRed as a Potential FRET Partner with CFP and GFP" Michael G. Erickson, Daniel L. Moon, and David T. Yue Biophysical Journal 2003. <br />
<br>- "A Comparison of Donor-Acceptor Pairs for Genetically Encoded FRET Sensors: Application to the Epac cAMP<br />
Sensor as an Example" Gerard N. M. van der Krogt, Janneke Ogink, Bas Ponsioen, Kees Jalink PLoS 2008.<br />
<br />
<br><br />
<br />
==[[Team:Paris/Analysis#Oscillations|Oscillating]] module==<br />
Few approaches have been thought in order to create the oscillating module. The pTet/TetR system that allows us to precisely control the inhibition of TetR on the Tet promoter. Another system use the natural inhibition of OmpR and of EnvZ via OmpR. We finally perform this system that we have developed since we know thanks to the modeling team that the oscillations are the only way to see the full development of the FIFO.<br />
<br />
==Synchronization module==<br />
The modeling simulation showed us that to have some oscillations that are difficult to obtain in a simple feedforward loop without the delay introduce by the quorum sensing synchronization, and for us it is more interesting to have the FIFO behavior at the population level. We did not achieved the this module but we started the construction of it and have already some intermediate parts that you will find below. <br />
==The constructions we were able to obtain were characterised by fluorescence microscopy (see examples below):==<br />
[[Image:ParisGfp.jpg|thumb|300px|center|Green fluorescence]]<br />
[[Image:ParisRfp.jpg|thumb|300px|center|Red Fluorescence]]<br />
[[Image:ParisCfp.jpg|thumb|300px|center|Cyan Fluorescence]]<br />
<br />
== Table of the constructions we realized==<br />
{|<br />
|- style="background: #649cd7;"<br />
!colspan=4 style="background: #649cd7" | FIFO<br />
|- style="background: #649cd7; text-align: center;"<br />
|width=30%| Construction<br />
|width=55%| Description<br />
|width=15%| Validation Date<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136039 pFliL(RBS WT)-ECFP tripart (LVA+)]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFliL is ECFP fused with a LVA tag.<br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]]<br>[http://partsregistry.org/Part:BBa_K136037 pFliL(+ RBS WT)-GFP]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFliL is GFP.<br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136012 pFlgA(+ RBS WT) - YFP Tripart (LVA+)]<br />
|align=|Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is EYFP fused with a LVA tag. <br />
|align="center"| [[Team:Paris/August 22|August 22]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136013 pFlgA(+ RBS WT) - YFP Tripart (LVA-)]<br />
|align=|Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is EYFP fused without a LVA tag. <br />
|align="center"| [[Team:Paris/August 22|August 22]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136054 pFlgA(+ RBS WT)-YFP tripart (AAV+)]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is EYFP fused with a AAV tag. <br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]]<br>[http://partsregistry.org/Part:BBa_K136053 pFlgA(+ RBS WT)-GFP]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlgA is GFP. <br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136055 pFlhB(+ RBS WT)-mRFP tripart (+LVA)]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlhB is mRFP with a LVA tag. <br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_reporter.png]]<br>[http://partsregistry.org/Part:BBa_K136065 pFlhB(+ RBS WT)-GFP]<br />
|align=| Natural Promoter of E. coli regulated by FlhDC and FliA. The natural rbs of the downstream gene is conserved for a more natural expression of the following gene. The fluorescent marker associated with pFlhB is GFP. <br />
|align="center"| [[Team:Paris/October 26|October 26]]<br />
|-<br />
|colspan=4 style="background: #649cd7" | <center>'''OSCILLATION'''</center><br />
|-<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136064 pFliL(+ RBS WT)-EnvZ*]<br />
|align=| pFliL is regulated by FlhDC and EnvZ regulates pFlhDC thanks to a negative feedback loop, origin of an oscillation behavior.<br />
|align="center"| [[Team:Paris/October 26|October 26]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136069 pFliL(+ RBS WT)-EnvZ*-GFP generator]<br />
|align=| The same construction as before but with a GFP in order to follow the dynamic of expression of pFliL.<br />
|align="center"| [[Team:Paris/October 29|October 29]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136051 pFlhB(+ RBS WT)-EnvZ*]<br />
|align=| pFlhB is regulated by FlhDC and EnvZ regulates pFlhDC thanks to a negative feedback loop, origin of an oscillation behavior.<br />
|align="center"| [[Team:Paris/October 24|October 24]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136070 pFlhB(+ RBS WT)-EnvZ*-GFP generator]<br />
|align=| The same construction as before but with a GFP in order to follow the dynamic of expression of pFlhB.<br />
|align="center"| [[Team:Paris/October 29|October 29]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136066 araC/pBad-EnvZ*]<br />
|align=| A construction made for characterizing the repression power of the mutated EnvZ on our system<br />
|align="center"| [[Team:Paris/October 27|October 27]]<br />
|-<br />
|colspan=4 style="background: #649cd7" | <center>'''SYNCHRONISATION'''</center><br />
|-<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136029 pLas - gfp Tripart]<br />
|align=| Construction for characterization of the pLas promoter<br />
|align="center"| [[Team:Paris/August 1|August 1]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136027 pLas - ECFP]<br />
|align=| The same as before but with another fluorophore<br />
|align="center"| [[Team:Paris/August 1|August 1]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br> [http://partsregistry.org/Part:BBa_K136024 strongest promoter-rbs-lasR-dble ter]<br />
|align=| A construction for a strong constitutive expression of the Las Regulator in order to get maximal expression in presence of AHL<br />
|align="center"| [[Team:Paris/August 20|August 20]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_regulatory.png]][[Image:Icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136023 Strong promoter-rbs-lasR-dble ter]<br />
|align=| A derived construction of the previous one for smaller constitutive expression of LasR in the Bacteria.<br />
|align="center"| [[Team:Paris/August 20|August 20]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136044 Strongest RBS (1)- LasR activator (+LVA)]<br />
|align=| Intermediary construction. We uses different rbs for Las R in order to get various response dynamic to the presence of AHL<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136048 rbs-lasR + dbl ter]<br />
|align=| Intermediary construction. We uses different rbs for Las R in order to get various response dynamic to the presence of AHL<br />
|align="center"| [[Team:Paris/August 19|August 19]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_coding.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136052 lasR activator + LVA - Double Terminator]<br />
|align=| Intermediary construction<br />
|align="center"| [[Team:Paris/August 1|August 1]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br>[http://partsregistry.org/Part:BBa_K136057 RBS lasI - GFP tripart]<br />
|align=| Construction that has to be associated with the FIFO. We will know when LasI is expressed and then when AHL is produced.<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_rbs.png]][[Image:Icon_coding.png]][[Image:Part_icon_rbs.png]][[Image:Part_icon_reporter.png]][[Image:Part_icon_terminator.png]][[Image:Part_icon_terminator.png]]<br> [http://partsregistry.org/Part:BBa_K136056 RBS-lasI - ECFP]<br />
|align=| The same as the previous one but with another fluorophore.<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|-<br />
|colspan=4 style="background: #649cd7" | <center>'''NEW GENE AND PROMOTER BIOBRICKS'''</center><br />
|-<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136010 pFliA]<br />
|align=| Natural promoter of E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC.<br />
|align="center"| [[Team:Paris/October 04|October 04]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136009 pFliL (+RBS WT)]<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA.<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136006 pFlgA (+RBS WT)]<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA..<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br> pFlgB (+RBS WT)<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA.<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Part_icon_regulatory.png]]<br>[http://partsregistry.org/Part:BBa_K136008 pFlhB (+RBS WT)]<br />
|align=| Natural promoter with the wild type rbs of its associated gene in E. coli, extracted by PCR and then inserted in a biobrick vector. pFiA is regulated by FlhDC and FliA.<br />
|align="center"| [[Team:Paris/October 10|October 10]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_coding.png]]<br>[http://partsregistry.org/Part:BBa_K136046 EnvZ*]<br />
|align=| EnvZ is a membrane protein involved into the osmotic response and is interacting with OmpR that will bind the promoter of FlhDC ad will repress it. EnvZ* is a mutated form of the coding sequence, giving a phenotype where pFlhDC is completely repressed. EnvZ has been extracted by PVR for the correct mutant strain.<br />
|align="center"| [[Team:Paris/September 04|September 04]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" | [[Image:Icon_coding.png]]<br>FliA<br />
|align=| FliA is a sigma factor involved into the regulation of very various genes, the promoter used in the FIFO were selected to be higly responding to FliA. In order to have the FliA gene possibly used as biobrick, we mutated 2 sites (EcoRI and PstI) inside the FliA sequence by assemby PCR. <br />
|align="center"| [[Team:Paris/September 04|September 04]]<br />
|- style="background: #dddddd;" <br />
| style="background: #D4E2EF;" |[[Image:Icon_coding.png]]<br>FlhDC<br />
|align=| FlhDC is the main regulator of the flagella genetic system in E. coli. FlhDC regulates all the promoter of the FIFO.<br />
|align="center"| [[Team:Paris/August 13|August 13]]<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Construction}}</div>Philippe bhttp://2008.igem.org/Team:Paris/October_27Team:Paris/October 272008-10-30T04:14:10Z<p>Philippe b: New page: October 27</p>
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<div>October 27</div>Philippe bhttp://2008.igem.org/Team:Paris/October_29Team:Paris/October 292008-10-30T04:13:58Z<p>Philippe b: New page: October 29</p>
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<div>October 29</div>Philippe bhttp://2008.igem.org/Team:Paris/October_26Team:Paris/October 262008-10-30T04:13:47Z<p>Philippe b: New page: October 26</p>
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<div>October 26</div>Philippe bhttp://2008.igem.org/Team:Paris/October_24Team:Paris/October 242008-10-30T04:13:33Z<p>Philippe b: New page: October 24</p>
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<div>October 24</div>Philippe bhttp://2008.igem.org/Team:Paris/September_04Team:Paris/September 042008-10-30T04:13:21Z<p>Philippe b: New page: September 04</p>
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<div>September 04</div>Philippe bhttp://2008.igem.org/Team:Paris/October_10Team:Paris/October 102008-10-30T04:13:09Z<p>Philippe b: New page: October 10</p>
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<div>October 10</div>Philippe bhttp://2008.igem.org/Team:Paris/October_04Team:Paris/October 042008-10-30T04:12:57Z<p>Philippe b: New page: October 04</p>
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<div>October 04</div>Philippe bhttp://2008.igem.org/Team:Paris/Team/Instructors%2BAdvisorsTeam:Paris/Team/Instructors+Advisors2008-10-30T04:09:30Z<p>Philippe b: </p>
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<div>{{Paris/Menu}}<br />
{{Paris/Header|Instructors & Advisors}}<br />
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[[Image:Ariel-lindner.jpg|left|130 px]] '''Ariel Lindner''', Biology / Chemistry<br />
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Major in Chemistry (Hebrew University, Jerusalem), M.Sc. and Ph.D. from the Weizmann Institute of Science (Rehovot, Israel) working on catalytic antibodies as enzyme models. After a research period at the Scripps Institute (California, USA), I currently work in Paris as associate professor at the Medicine faculty of medicine, Paris Descartes university where where applpying Physical, Chemical and Biological approaches to study variability between clonal individual bacterial cells and their aging. As a co-initiator and teacher of the Interdisciplinary Approaches to Life Sciences master program at the Center for Research and Interdisciplinarity, I try to help students fulfill their talents and thus instruct our students-initiated iGEM team. <br />
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[[Image:Samuel-bottani2.jpg|left|130px]] '''Samuel Bottani''', Physics<br />
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I am a physicist, associate professor at the University Denis Diderot in Paris. I am interested in self-organization, out of equilibrium dynamics, and the logic of cellular computation. My research interests are on structure, dynamics and evolution of regulatory networks. In particular I am interested in the interplay between genome architecture, spatial organization of the cell and dynamical properties of cell functions. Genomic context and architecture possibly determines or optimizes the output of artificial genetic networks. I am very concerned in innovation in university teaching.<br />
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[[Image:Gregory-batt.jpg|left |130 px]] '''Gregory Batt''', Computer Science<br />
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I'm a research scientist at INRIA. <br />
I work on developing mathematical approaches and computational tools for the analysis of genetic regulatory networks, with applications in systems and synthetic biology.<br />
The central question I try to address is how to obtain relevant predictions despite large parameter uncertainties and environmental fluctuations.<br />
My work combines modeling in biology, maths and computer science. <br />
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[[Image:Thomas-landrain.jpg|left|130 px]] '''Thomas Landrain''', Biology<br />
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I was part of the Paris IGEM 2007 Team and i needed more:-) I'm the president of the Systems ans Synthetic Biology Club of Paris (SYNBIOSYS) and I'm now doing my PhD with Alfonso Jaramillo (Genopole-Ecole Polytechnique) on Zinc-Finger Protein engineering and RNA network engineering.<br />
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{| align="left"<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:David-bikard.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''David Bikard'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Franck-delaplace.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''[http://www.ibisc.univ-evry.fr/~delapla Franck Delaplace]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Engineer in Life Sciences<br />
| style="width:240px;height:20px;" align="left" | Bioinformatics<br />
|-<br />
| style="width:240px;" align="left" | Background & Interests: Engineering, Molecular Biology, Synthetic Biology, Member of the 07' Paris iGEM Team<br />
| style="width:240px;" align="left" | Background & Interests: (Franck)<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:JL-giavitto.jpg|130 px| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''[http://www.ibisc.univ-evry.fr/~giavitto Jean-Louis Giavitto]'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Olivier-michel.jpg|130 px| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''[http://www.ibisc.univ-evry.fr/~michel Olivier Michel]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Bioinformatics<br />
| style="width:240px;height:20px;" align="left" | Bioinformatics<br />
|-<br />
| style="width:240px;" align="left" | Background & Interests: (Jean-Louis)<br />
| style="width:240px;" align="left" | Background & Interests: (Olivier)<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Aurelien-rizk.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Aurélien Rizk'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Gilles-vieira.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''[http://www.genoscope.cns.fr/bioinfo/sections/people/gvieira Gilles Vieira]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Bioinformatics<br />
| style="width:240px;height:20px;" align="left" | Bioinformatics<br />
|-<br />
| style="width:240px;" align="left" | Background & Interests: Computer Science, Systems Biology, Synthetic Biology, Member of the 07' Paris iGEM Team<br />
| style="width:240px;" align="left" | '''Background :''' Bioinformatics & biostatistics, Member of the 07' Paris iGEM Team <br> '''Interests :''' System & synthetic biology <br>Metabolic & network modelling.<br />
<br><br />
|-<br />
<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Richard_Emmanuel_Eastes.jpg|left|130 px]] <br />
| style="width:240px;height:20px;" align="left" |'''[http://www.ens.fr/ree/ Richard Emmanuel Eastes]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Communication and Scientific culture<br />
<br />
|}<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Team}}</div>Philippe bhttp://2008.igem.org/Team:Paris/Team/StudentsTeam:Paris/Team/Students2008-10-30T04:06:47Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header| Students}}<br />
<br />
{| align="center"<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Alexandra-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Alexandra Bouaziz'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Philippe-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Philippe Bouaziz'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry and physicochemistry (nanotechnology)<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.biochimie.univ-paris7.fr/master/home.html Master SPGF Paris diderot] Undergrad Student <br>'''Interests:''' reading ,subaquatique sport ,art,participating in oenologie club Paris 5 descartes '''<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.aiv-paris.org/fr/master-aiv/ Master AIV] and master phamacology at paris descarte paris 5 Undergrad Student <br>'''Interests:''' reading, president of the club of molecular gastronomy, architecture and making Fanny crazy''' <br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Guillaume.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Guillaume Bouchard'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Image_125.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Fanny Caffin'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Physics<br />
| style="width:240px;height:20px;" align="left" | Molecular and Cellular Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www2.ac-lyon.fr/etab/lycees/lyc-69/lyjperrin/index.html Lycée Jean-Perrin de Lyon] High School Student<br>Member of [http://www.scienceacademie.org/ Science Academie]<br>'''Interests:''' Astronomy<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://master.univ-cancerologie.net/ Master Cancérologie]<br> '''Interests:''' Biology, but also drawing, photography, reading... and obviously : kick the butt of [https://2008.igem.org/Image:Philippe-Bouziz.jpg Philippe]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:N764862654 816423 9815.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Benoît d'Hayer'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Audrey-Desgrange.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Audrey Desgrange'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Genetics and Pharmacy<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br> [http://www.pharmacie.univ-paris5.fr/ Pharmacy] [http://www.univ-paris5.fr/ Paris Descartes]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Oenology<br />
| style="width:240px;" align="left" | '''Background :''' <br>[http://www.ices.fr/ ICES] Sophomore Student<br> '''Interests:''' Dance, Chocolate, Physiology, Genetics<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Ana-Jimenez.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Ana Jimenez'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Cyprien.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Cyprien Maisonnier'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> Biology [http://www.univ-paris-diderot.fr/ Paris Diderot]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Music, languages, good food, good wine :-)<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.ens.fr/ Ecole Normale Supérieure] Undergrad Student ([http://www.biologie.ens.fr/ Molecular Biology and Genetics]) <br> '''Interests:''' Synthetic Biology, Photoshop, rugby, ''Saccharomyces cerevisiae'', ''Oenococcus oeni'' and ''Penicillium roqueforti''<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Photo 158.JPG| 130 px ]]<br />
| style="width:240px;" align="left" | '''Kok-Phen Yan'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology and Biochemistry<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://www.master.bmc.upmc.fr/ Master BMC] (Molecular and Cellular Biology, specialized in Biochemistry) <br> and [http://www.mastbio.ens.fr/ ENS] <br>'''Interests:''' music, languages<br />
|}<br />
<br><br />
<br />
=Dry Lab=<br />
<br />
<br><br />
{| align="center"<br />
|-<br />
<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Felipe-Golib.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Felipe Golib'''<br />
| style="width:30px;" rowspan="3" |<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Louis-hedde.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Louis Hedde'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Mathematician<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br> [http://www.master-aiv.fr/ Master AIV] <br>'''Interests:''' Computer Science and Integrative Biology<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ensmp.fr/Accueil/ Ecole des Mines de Paris] Undergrad Student<br>'''Interests:''' stinky cheese and thistle vine<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Yann-Lecunff.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Yann Le Cunff'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Hugo-Raguet.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Hugo Raguet'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Applied Mathematics<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.supelec.fr/ Supelec Engineering School] <br> [http://www.master-aiv.fr/ Master AIV]<br>'''Interests:''' coming soon...<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ecp.fr Ecole Centrale des Arts & Manufactures de Paris] Undergrad Student <br>'''Interests:''' Bio, A(p)ero, Psycho. <br>And obviously, [https://2008.igem.org/Image:Ana-Jimenez.jpg the pigeon !]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Romain-Rousseau.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''[http://xrousseau.com/ Romain Rousseau]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Engineer in Life Sciences<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br>[http://www.paristech.org/ ParisTech] Undergrad Student ([http://www.agroparistech.fr/ Biology and Engineering]) <br> '''Interests:''' Computers, Genetics<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Team}}</div>Philippe bhttp://2008.igem.org/Team:Paris/Team/StudentsTeam:Paris/Team/Students2008-10-30T04:05:37Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header| Students}}<br />
<br />
{| align="center"<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Alexandra-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Alexandra Bouaziz'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Philippe-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Philippe Bouaziz'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry and physicochemistry (nanotechnology)<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.biochimie.univ-paris7.fr/master/home.html Master SPGF Paris diderot] Undergrad Student <br>'''Interests:''' reading ,subaquatique sport ,art,participating in oenologie club Paris 5 descartes '''<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.aiv-paris.org/fr/master-aiv/ Master AIV] and master phamacology at paris descarte paris 5 Undergrad Student <br>'''Interests:''' reading, molecular gastronomy, architecture and making Fanny crazy''' <br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Guillaume.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Guillaume Bouchard'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Image_125.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Fanny Caffin'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Physics<br />
| style="width:240px;height:20px;" align="left" | Molecular and Cellular Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www2.ac-lyon.fr/etab/lycees/lyc-69/lyjperrin/index.html Lycée Jean-Perrin de Lyon] High School Student<br>Member of [http://www.scienceacademie.org/ Science Academie]<br>'''Interests:''' Astronomy<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://master.univ-cancerologie.net/ Master Cancérologie]<br> '''Interests:''' Biology, but also drawing, photography, reading... and obviously : kick the butt of [https://2008.igem.org/Image:Philippe-Bouziz.jpg Philippe]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:N764862654 816423 9815.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Benoît d'Hayer'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Audrey-Desgrange.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Audrey Desgrange'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Genetics and Pharmacy<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br> [http://www.pharmacie.univ-paris5.fr/ Pharmacy] [http://www.univ-paris5.fr/ Paris Descartes]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Oenology<br />
| style="width:240px;" align="left" | '''Background :''' <br>[http://www.ices.fr/ ICES] Sophomore Student<br> '''Interests:''' Dance, Chocolate, Physiology, Genetics<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Ana-Jimenez.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Ana Jimenez'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Cyprien.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Cyprien Maisonnier'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> Biology [http://www.univ-paris-diderot.fr/ Paris Diderot]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Music, languages, good food, good wine :-)<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.ens.fr/ Ecole Normale Supérieure] Undergrad Student ([http://www.biologie.ens.fr/ Molecular Biology and Genetics]) <br> '''Interests:''' Synthetic Biology, Photoshop, rugby, ''Saccharomyces cerevisiae'', ''Oenococcus oeni'' and ''Penicillium roqueforti''<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Photo 158.JPG| 130 px ]]<br />
| style="width:240px;" align="left" | '''Kok-Phen Yan'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology and Biochemistry<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://www.master.bmc.upmc.fr/ Master BMC] (Molecular and Cellular Biology, specialized in Biochemistry) <br> and [http://www.mastbio.ens.fr/ ENS] <br>'''Interests:''' music, languages<br />
|}<br />
<br><br />
<br />
=Dry Lab=<br />
<br />
<br><br />
{| align="center"<br />
|-<br />
<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Felipe-Golib.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Felipe Golib'''<br />
| style="width:30px;" rowspan="3" |<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Louis-hedde.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Louis Hedde'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Mathematician<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br> [http://www.master-aiv.fr/ Master AIV] <br>'''Interests:''' Computer Science and Integrative Biology<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ensmp.fr/Accueil/ Ecole des Mines de Paris] Undergrad Student<br>'''Interests:''' stinky cheese and thistle vine<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Yann-Lecunff.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Yann Le Cunff'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Hugo-Raguet.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Hugo Raguet'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Applied Mathematics<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.supelec.fr/ Supelec Engineering School] <br> [http://www.master-aiv.fr/ Master AIV]<br>'''Interests:''' coming soon...<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ecp.fr Ecole Centrale des Arts & Manufactures de Paris] Undergrad Student <br>'''Interests:''' Bio, A(p)ero, Psycho. <br>And obviously, [https://2008.igem.org/Image:Ana-Jimenez.jpg the pigeon !]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Romain-Rousseau.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''[http://xrousseau.com/ Romain Rousseau]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Engineer in Life Sciences<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br>[http://www.paristech.org/ ParisTech] Undergrad Student ([http://www.agroparistech.fr/ Biology and Engineering]) <br> '''Interests:''' Computers, Genetics<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Team}}</div>Philippe bhttp://2008.igem.org/Team:Paris/Team/StudentsTeam:Paris/Team/Students2008-10-30T04:05:03Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header| Students}}<br />
<br />
{| align="center"<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Alexandra-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Alexandra Bouaziz'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Philippe-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Philippe Bouaziz'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry and physicochemistry (nanotechnology)<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.biochimie.univ-paris7.fr/master/home.html Master SPGF Paris diderot] Undergrad Student <br>'''Interests:''' reading ,subaquatique sport ,art,participating in oenologie club Paris 5 descartes '''<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.aiv-paris.org/fr/master-aiv/ Master AIV] and master cellulare phamacology paris descarte paris 5 Undergrad Student <br>'''Interests:''' reading, molecular gastronomy, architecture and making Fanny crazy''' <br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Guillaume.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Guillaume Bouchard'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Image_125.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Fanny Caffin'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Physics<br />
| style="width:240px;height:20px;" align="left" | Molecular and Cellular Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www2.ac-lyon.fr/etab/lycees/lyc-69/lyjperrin/index.html Lycée Jean-Perrin de Lyon] High School Student<br>Member of [http://www.scienceacademie.org/ Science Academie]<br>'''Interests:''' Astronomy<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://master.univ-cancerologie.net/ Master Cancérologie]<br> '''Interests:''' Biology, but also drawing, photography, reading... and obviously : kick the butt of [https://2008.igem.org/Image:Philippe-Bouziz.jpg Philippe]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:N764862654 816423 9815.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Benoît d'Hayer'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Audrey-Desgrange.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Audrey Desgrange'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Genetics and Pharmacy<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br> [http://www.pharmacie.univ-paris5.fr/ Pharmacy] [http://www.univ-paris5.fr/ Paris Descartes]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Oenology<br />
| style="width:240px;" align="left" | '''Background :''' <br>[http://www.ices.fr/ ICES] Sophomore Student<br> '''Interests:''' Dance, Chocolate, Physiology, Genetics<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Ana-Jimenez.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Ana Jimenez'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Cyprien.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Cyprien Maisonnier'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> Biology [http://www.univ-paris-diderot.fr/ Paris Diderot]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Music, languages, good food, good wine :-)<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.ens.fr/ Ecole Normale Supérieure] Undergrad Student ([http://www.biologie.ens.fr/ Molecular Biology and Genetics]) <br> '''Interests:''' Synthetic Biology, Photoshop, rugby, ''Saccharomyces cerevisiae'', ''Oenococcus oeni'' and ''Penicillium roqueforti''<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Photo 158.JPG| 130 px ]]<br />
| style="width:240px;" align="left" | '''Kok-Phen Yan'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology and Biochemistry<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://www.master.bmc.upmc.fr/ Master BMC] (Molecular and Cellular Biology, specialized in Biochemistry) <br> and [http://www.mastbio.ens.fr/ ENS] <br>'''Interests:''' music, languages<br />
|}<br />
<br><br />
<br />
=Dry Lab=<br />
<br />
<br><br />
{| align="center"<br />
|-<br />
<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Felipe-Golib.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Felipe Golib'''<br />
| style="width:30px;" rowspan="3" |<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Louis-hedde.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Louis Hedde'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Mathematician<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br> [http://www.master-aiv.fr/ Master AIV] <br>'''Interests:''' Computer Science and Integrative Biology<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ensmp.fr/Accueil/ Ecole des Mines de Paris] Undergrad Student<br>'''Interests:''' stinky cheese and thistle vine<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Yann-Lecunff.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Yann Le Cunff'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Hugo-Raguet.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Hugo Raguet'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Applied Mathematics<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.supelec.fr/ Supelec Engineering School] <br> [http://www.master-aiv.fr/ Master AIV]<br>'''Interests:''' coming soon...<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ecp.fr Ecole Centrale des Arts & Manufactures de Paris] Undergrad Student <br>'''Interests:''' Bio, A(p)ero, Psycho. <br>And obviously, [https://2008.igem.org/Image:Ana-Jimenez.jpg the pigeon !]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Romain-Rousseau.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''[http://xrousseau.com/ Romain Rousseau]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Engineer in Life Sciences<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br>[http://www.paristech.org/ ParisTech] Undergrad Student ([http://www.agroparistech.fr/ Biology and Engineering]) <br> '''Interests:''' Computers, Genetics<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Team}}</div>Philippe bhttp://2008.igem.org/Team:Paris/Team/StudentsTeam:Paris/Team/Students2008-10-30T04:03:18Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header| Students}}<br />
<br />
{| align="center"<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Alexandra-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Alexandra Bouaziz'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Philippe-Bouaziz.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Philippe Bouaziz'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry<br />
| style="width:240px;height:20px;" align="left" | pharmacochemistry and physicochemistry (nanotechnology)<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.biochimie.univ-paris7.fr/master/home.html Master SPGF Paris diderot] Undergrad Student <br>'''Interests:''' reading ,subaquatique sport ,art,participating in oenologie club Paris 5 descartes '''<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.aiv-paris.org/fr/master-aiv/ Master AIV] Undergrad Student <br>'''Interests:''' reading, molecular gastronomy, architecture and making Fanny crazy''' <br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Guillaume.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Guillaume Bouchard'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Image_125.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Fanny Caffin'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Physics<br />
| style="width:240px;height:20px;" align="left" | Molecular and Cellular Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www2.ac-lyon.fr/etab/lycees/lyc-69/lyjperrin/index.html Lycée Jean-Perrin de Lyon] High School Student<br>Member of [http://www.scienceacademie.org/ Science Academie]<br>'''Interests:''' Astronomy<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://master.univ-cancerologie.net/ Master Cancérologie]<br> '''Interests:''' Biology, but also drawing, photography, reading... and obviously : kick the butt of [https://2008.igem.org/Image:Philippe-Bouziz.jpg Philippe]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:N764862654 816423 9815.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Benoît d'Hayer'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Audrey-Desgrange.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Audrey Desgrange'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Genetics and Pharmacy<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br> [http://www.pharmacie.univ-paris5.fr/ Pharmacy] [http://www.univ-paris5.fr/ Paris Descartes]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Oenology<br />
| style="width:240px;" align="left" | '''Background :''' <br>[http://www.ices.fr/ ICES] Sophomore Student<br> '''Interests:''' Dance, Chocolate, Physiology, Genetics<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Ana-Jimenez.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Ana Jimenez'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Cyprien.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''Cyprien Maisonnier'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
| style="width:240px;height:20px;" align="left" | Biology<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> Biology [http://www.univ-paris-diderot.fr/ Paris Diderot]<br> [http://www.univ-paris-diderot.fr/magisteregenet/ Master Européen de Génétique]<br> '''Interests:''' Music, languages, good food, good wine :-)<br />
| style="width:240px;" align="left" |'''Background:''' <br>[http://www.ens.fr/ Ecole Normale Supérieure] Undergrad Student ([http://www.biologie.ens.fr/ Molecular Biology and Genetics]) <br> '''Interests:''' Synthetic Biology, Photoshop, rugby, ''Saccharomyces cerevisiae'', ''Oenococcus oeni'' and ''Penicillium roqueforti''<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Photo 158.JPG| 130 px ]]<br />
| style="width:240px;" align="left" | '''Kok-Phen Yan'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Biology and Biochemistry<br />
|-<br />
| style="width:240px;" align="left" |'''Background:''' <br> [http://www.master.bmc.upmc.fr/ Master BMC] (Molecular and Cellular Biology, specialized in Biochemistry) <br> and [http://www.mastbio.ens.fr/ ENS] <br>'''Interests:''' music, languages<br />
|}<br />
<br><br />
<br />
=Dry Lab=<br />
<br />
<br><br />
{| align="center"<br />
|-<br />
<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Felipe-Golib.jpg|130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Felipe Golib'''<br />
| style="width:30px;" rowspan="3" |<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Louis-hedde.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Louis Hedde'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Mathematician<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br> [http://www.master-aiv.fr/ Master AIV] <br>'''Interests:''' Computer Science and Integrative Biology<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ensmp.fr/Accueil/ Ecole des Mines de Paris] Undergrad Student<br>'''Interests:''' stinky cheese and thistle vine<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Yann-Lecunff.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Yann Le Cunff'''<br />
| style="width:30px;" rowspan="3" | <br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Hugo-Raguet.jpg| 130 px ]]<br />
| style="width:240px;height:20px;" align="left" | '''Hugo Raguet'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Applied Mathematics<br />
| style="width:240px;height:20px;" align="left" | Engineer<br />
|-<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.supelec.fr/ Supelec Engineering School] <br> [http://www.master-aiv.fr/ Master AIV]<br>'''Interests:''' coming soon...<br />
| style="width:240px;" align="left" |'''Background:'''<br>[http://www.ecp.fr Ecole Centrale des Arts & Manufactures de Paris] Undergrad Student <br>'''Interests:''' Bio, A(p)ero, Psycho. <br>And obviously, [https://2008.igem.org/Image:Ana-Jimenez.jpg the pigeon !]<br />
|-<br />
| style="width:120px;" align="right" rowspan="3"| [[Image:Romain-Rousseau.jpg| 130 px ]]<br />
| style="width:240px;" align="left" | '''[http://xrousseau.com/ Romain Rousseau]'''<br />
|-<br />
| style="width:240px;height:20px;" align="left" | Engineer in Life Sciences<br />
|-<br />
| style="width:240px;" align="left" | '''Background:''' <br>[http://www.paristech.org/ ParisTech] Undergrad Student ([http://www.agroparistech.fr/ Biology and Engineering]) <br> '''Interests:''' Computers, Genetics<br />
|}<br />
<br />
{{Paris/Navig|Team:Paris/Team}}</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:56:47Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
As for the flagella biosynthesis, our FIFO could be useful for many '''bottom-up assembled molecular machines''' that needs to be assembled in a precise order.<br />
Moreover, as we will show on an example, the FIFO could also be useful in many '''biosynthetic pathways''' subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.<br />
<br />
<br />
== Example 1: type III secretion injectisome == <br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum, surmounted by either a needle, a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically. Studies show that a core of eight proteins share significant similarity with components of the flagellum. From this studies, we can expect that the genes expression is ruled by a sequential FIFO order so we can express it with our bacteriO'clock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure could :<br />
* induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* be a new way to liberate substances produced by bacteria (see bioplastic application).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
Two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:55:47Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
As for the flagella biosynthesis, our FIFO could be useful for many '''bottom-up assembled molecular machines''' that needs to be assembled in a precise order.<br />
Moreover, as we will show on an example, the FIFO could also be useful in many '''biosynthetic pathways''' subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.<br />
<br />
<br />
== Example 1: type III secretion injectisome == <br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum, surmounted by either a needle, a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically. Studies show that a core of eight proteins share significant similarity with components of the flagellum. From this studies, we can expect that the genes expression is ruled by a sequential FIFO order so we can express it with our bacteriO'clock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* be a new way to liberate substances produced by bacteria (see bioplastic application).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
Two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:54:40Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
As for the flagella biosynthesis, our FIFO could be useful for many '''bottom-up assembled molecular machines''' that needs to be assembled in a precise order.<br />
Moreover, as we will show on an example, the FIFO could also be useful in many '''biosynthetic pathways''' subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.<br />
<br />
<br />
== Example 1: type III secretion injectisome == <br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum, surmounted by either a needle, a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* be a new way to liberate substances produced by bacteria (see bioplastic application).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
Two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:52:22Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
As for the flagella biosynthesis, our FIFO could be useful for many '''bottom-up assembled molecular machines''' that needs to be assembled in a precise order.<br />
Moreover, as we will show on an example, the FIFO could also be useful in many '''biosynthetic pathways''' subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.<br />
<br />
<br />
== Example 1: type III secretion injectisome == <br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:51:34Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
Moreover, as we will show on an example, the FIFO could also be useful in many biosynthetic pathways subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We will develop below two examples: type III secretion injectisome and PHA biosynthesis pathway.<br />
<br />
<br />
== Example 1: type III secretion injectisome == <br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example 2: metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:47:14Z<p>Philippe b: /* Complexes nanomachine Factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
<br />
<br />
== Complexes nanomachine Factory == <br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:46:40Z<p>Philippe b: /* Bibliographie */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes nanomachine Factory == <br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
* The type III secretion injectisome Guy R.Cornelis Nature reviews<br />
<br />
* Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates <br />
Ilana S Aldor and Jay D Keasling<br />
Department of Chemical Engineering, 201 Gilman Hall, University of California, Berkeley, 94720-1462, USA <br />
23 September 2003<br />
<br />
* PHA synthase engineering toward superbiocatalysts for custom-made biopolymers.<br />
Nomura CT, Taguchi S.<br />
Department of Chemistry, State University of New York - College of Environmental Science and Forestry, 121 Jahn Laboratory, Syracuse, NY 13210, USA.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:43:27Z<p>Philippe b: /* Complexes nanomachine Factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes nanomachine Factory == <br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus.<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
"The type III secretion injectisome " Guy R.Cornelis Nature reviews</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:43:15Z<p>Philippe b: /* Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes nanomachine Factory == <br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
<br />
== Bibliographie ==<br />
<br />
"The type III secretion injectisome " Guy R.Cornelis Nature reviews</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:39:59Z<p>Philippe b: /* Complexes nanomachine Factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes nanomachine Factory == <br />
As for the flagella biosynthesis, our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:39:23Z<p>Philippe b: /* Complexes molecular machine Factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes nanomachine Factory == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:38:57Z<p>Philippe b: /* Complexes molecular machine Factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes molecular machine Factory == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:37:48Z<p>Philippe b: /* Nanomachine Factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Complexes molecular machine Factory == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:37:00Z<p>Philippe b: /* More general applications */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== Nanomachine Factory == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:34:43Z<p>Philippe b: /* Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:34:18Z<p>Philippe b: /* More general applications */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
<br />
The injectisome is related to the flagellum genetically, studies show that a core of eight proteins share significant similarity with components of the flagellum from this studies , we can expected that the genes expression is rule by a sequential FIFO order so we can express it with our bacterioclock system .<br />
Moreover, the injectisome will find a lot of applications for example ,bacteria that express this kinds of structure can :<br />
* Induce apoptosis of eucaryote cells so we can developed by our system new kinds of in-vivo compatible anticancer therapy,<br />
* Be a new way to liberate bioplastic without killing our bacteria (new kinds of optimized chemoreactor).<br />
<br />
In conclusion, our bacterioclock can be used in a lot of new applications like for instance, bottom-up molecular machines self-assembly or new kinds of optimized chemoreactor.<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T03:06:29Z<p>Philippe b: /* More general applications */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
For instance ,the type III secretion injectisome.<br />
The Injectisome is a complex nanomachine that allows bacteria to deliver protein effector across eucaryotic cellular membranes.<br />
The injectisom consists of a basal structure, which resembles the basal structure of the flagellum,surmounted by either a needle ,a needle and a filament or a long pilus[ref].<br />
<br />
[[Image:injectisome.JPG]]<br />
<br />
The injectisome is related to the flagellum genetically studies show that a core of eight proteins share significant similarity with components of the flagellum from this study we can expected that the genes expression is rule by a sequential FIFO order like the flagellum biosynthesis .<br />
<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/File:Injectisome.JPGFile:Injectisome.JPG2008-10-30T03:03:38Z<p>Philippe b: uploaded a new version of "Image:Injectisome.JPG"</p>
<hr />
<div></div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T02:59:04Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
As for the PHA biosynthesis a FIFO could be useful to any pathways subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We believe that these 2 classes of applications are frequently encountered.<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.</div>Philippe bhttp://2008.igem.org/File:Injectisome.JPGFile:Injectisome.JPG2008-10-30T02:51:28Z<p>Philippe b: uploaded a new version of "Image:Injectisome.JPG"</p>
<hr />
<div></div>Philippe bhttp://2008.igem.org/File:Injectisome.JPGFile:Injectisome.JPG2008-10-30T02:49:26Z<p>Philippe b: </p>
<hr />
<div></div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T02:09:13Z<p>Philippe b: /* More general applications */</p>
<hr />
<div>{{Paris/Menu}}</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T02:07:56Z<p>Philippe b: /* Applying bacterioclock to metabolic engineering of polyhydroxyalkanoate biosynthesis pathways */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
As for the PHA biosynthesis a FIFO could be useful to any pathways subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We believe that these 2 classes of applications are frequently encountered.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T00:19:58Z<p>Philippe b: /* Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways */</p>
<hr />
<div>{{Paris/Menu}}<br />
== Applying bacterioclock to metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities of 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetylcoA into its final product PHA.<br />
This biosynthesis is subjected to two contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
As for the PHA biosynthesis a FIFO could be useful to any pathways subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We believe that these 2 classes of applications are frequently encountered.</div>Philippe bhttp://2008.igem.org/Team:Paris/ProjectTeam:Paris/Project2008-10-30T00:05:25Z<p>Philippe b: /* Specifications */</p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header|Presentation of the project}}<br />
= Outlines =<br />
[[Image:Specmontre.jpg|right|250 px|thumb|Mechanisms of a watch]]<br />
<br />
Our project aims at constructing a '''sequence of genes activated sequentially in a First In First Out (FIFO) order and periodically and synchronized at population scale'''. To this end we implement a biological FIFO circuit in a negative feedback loop and a cell-cell communication channel. Such a setup is designed to trigger a sequence of several genes successive activations repeated periodically. Thus, it can be considered as a biological clock. <br />
<br />
* '''FIFO behavior''' : Our setup involves three genes which will get activated and deactivated successively following a “FIFO : First In, First Out” order. This sequence is monitored by a logic structure called Feed-Forward Loop (FFL).We base this part of our project on an already existing structure, partly fulfilling the evoked specifications: the system that leads to the production of ''E. coli'' flagella. What is most interesting in a FIFO is the study of the ON and OFF steps. An easier way to observe the FIFO would be to have automatic oscillations.<br />
<br />
* '''Oscillatory behavior''' : It will consist in providing a periodic output for the duration of the experiment. To do so, we will use a genetic cascade, initiated by a specific inducer which last step will inhibit the previously mentioned inducer. The period of the oscillations is even more interesting if it allows the sequential switching on and off of several genes.<br />
<br />
* '''Synchronization''' : Yet, being able to control this sequential activation within a single cell can be seen as a “first step” in biological clock devising. In order to amplify this phenomenon (to observe it in an easier way or even to find future applications), it has to be extended to a whole population of bacteria. Here comes the synchronization issue: we will use methods based on the “quorum sensing” phenomenon.<br />
<br />
= Motivations =<br />
<br />
== FIFO ==<br />
<br />
[[Image:Queue2.jpg|left|thumb|300px|A queue in front of the Post Office traditionally works as a FIFO : the person arrived first will be the first served, and will ''probably'' leave the Post Office first.]]<br />
<br />
<br />
First In First Out (FIFO) systems are present everywhere from flux management or electronics to genetic networks. A queue in front of the post office works as a FIFO. More generally, it is interesting in any process that requires several steps in a defined order. FIFO behavior indeed prevents from needlessly performing the first steps while the last ones are OFF.<br />
<br />
<span style="font-size:10; color:grey;">''If you want to make French fries you need to produce potatoes before you can cut them and you need to cut them before frying them. But it would be a waste to continue producing potatoes if you've already turned off the fryer. You would accumulate unprocessed intermediates !''</span><br />
<br />
<br />
<br />
The same goes for the bacterium flagella. To be efficient they naturally need to produce the proteins of the base first. But when you stop making flagella, the base proteins are also the first thing you need to stop producing. It has been proposed [http://www.ncbi.nlm.nih.gov/pubmed/15186773?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum| (Kalir S., Alon U. 2004)] that the gene network controlling the production of E.coli flagellum behaves as a FIFO. We thus decided to use this regulatory network to implement our FIFO.<br />
<br><br><br />
<br />
== Oscillations ==<br />
[[Image:Oscill.png|right|250px]]<br />
Genetic oscillators based on the interaction of a small set of molecular components have been shown to be involved in the regulation of the cell cycle, the circadian rhythms, or the response of several signaling pathways. Uncovering the functional properties of such oscillators then becomes important for the understanding of these cellular processes and for the characterization of fundamental properties of more complex clocks.<br />
<br />
Creating an oscillating device has always been at the core of synthetic biology. There are many systems that can lead in theory to this complex behavior with different properties : number of cycles, oscillating period and robustness. Our oscillator has an original structure that has not been tested yet, based on a particular gene network called Feed Forward Loop.<br />
<br />
Engineering and tuning such complex cellular behaviors is a real challenge for synthetic biology.<br />
<br />
== Synchronization ==<br />
[[Image:synchro.jpg|left|250px]]<br />
<br />
In order to make visualization easier and to permit the development of future applications, our system must reach a higher scale. As a consequence, the synchronization of the oscillation at a population level is a key issue in our system. The classical way to do so, is to introduce a ''checkpoint'' at the end of each cycle, as in the eukariotic cell cycle.<br />
<br />
Several teams around the world worked on the synchronization of oscillations. The phenomenon of ''quorum-sensing'', is a natural way to synchronize the expression of gene network in bacteria. We will embezzle a natural ''quorum sensing'' system to do so.<br />
<br />
<br />
<br />
<br />
[[Team:Paris|Previous Step : Home]]<br />
<br />
[[Team:Paris/Network_Design1|Next Step : Network Design Part 1 : the FIFO behavior]]</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-30T00:00:41Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
== Example of an application: Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials.<br />
One illustrative example is polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
The biosynthesis of this polymer is currently subject to intensive work.<br />
It consists in expressing in appropriate quantities 3 enzymes PhaA ,PhaB and PhaC that sequentialy process AcetoacetylcoA into its final product PHA.<br />
This biosynthesis os subjected to 2 contraints : <br />
* Intermediate products of this pathway are used in alternatives competing metabolic pathways,<br />
* Only the final product is of interest,so that all intermediates products need to be transformed into PHA.<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
two strategies are commonly used in bioengineering of methabolics pathways :<br />
* Sequential expression of enzymes involved in the pathways,<br />
* Or constitutive expressions of all enzymes.<br />
Because of the above mentioned limitations, none of these approches are adapted here .<br />
Using the sequential expression, intermediate products would accumulate and thus be consummed by competing pathways.<br />
Using the constitutive expression a mixture of final and intermediate product would necessarily be obtained.<br />
<br />
Our FIFO could be useful here. <br />
Indeed a FIFO expression pattern is intermediate between a purely sequential and a purely constitutive expression.<br />
At some point all enzymes are presents ( no accumulation of intermediate products ) and during the last step only the last enzyme (PhC) is presents ( all intermediate products are consummed).<br />
Moreover, the fact that our system oscillate could provide to the cell a metabolic recovering phase.<br />
<br />
== More general applications == <br />
As for the flagella biosynthesis our FIFO could be useful for many bottom-up assembled molecular machines that needs to be assembled in a precise order.<br />
As for the PHA biosynthesis a FIFO could be useful to any pathways subject to competitive alternative pathways and for wich intermediate products must be avoided.<br />
We believe that these 2 classes of applications are frequently encountered.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T23:16:16Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
we hope that if we applied our system to pathways that have differentes cross linked intermediaries like the biosynthesis of PHA (figure 1), by the FIFO we will optimized the expression of the differentes genes in order to avoid waste producte that will increase impurities.<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope that our system will increase the purity and the rate of PHA obtain because we don't activate the 3 genes simultaneously, instead of that we activate by a FIFO order system the 3 genes so we will avoid lost of acetoacetylcoA or others important intermediary product in others metabolic pathways.<br />
<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
In conclusion,our bacterioclock can be use to obtain many polymers or proteins fibers that their production pass by a lot of methabolic cross linked intermediary, in those situations the FIFO order may optimized the purity and the rate of the final products.<br />
<br />
== Bibliography ==</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T23:16:00Z<p>Philippe b: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
we hope that if we applied our system to pathways that have differentes cross linked intermediaries like the biosynthesis of PHA (figure 1), by the FIFO we will optimized the expression of the differentes genes in order to avoid waste producte that will increase impurities.<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope that our system will increase the purity and the rate of PHA obtain because we don't activate the 3 genes simultaneously, instead of that we activate by a FIFO order system the 3 genes so we will avoid lost of acetoacetylcoA or others important intermediary product in others metabolic pathways.<br />
<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
In conclusion,our bacterioclock can be use to obtain many polymers or proteins fibers that their production pass by a lot of methabolic cross linked intermediary, in those situations the FIFO order may optimized the purity and the rate of the final products.<br />
<br />
== Bibliography ==</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T23:15:39Z<p>Philippe b: /* Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<font color=red>''Un petit texte pour expliquer la motivation de cette page'' ne serait-ce que tout simplement:<br />
On this page we report some possible uses of the FIFO device in synthetic applications.<br />
<br />
General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.</font><br />
<br />
<br />
<br />
<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
we hope that if we applied our system to pathways that have differentes cross linked intermediaries like the biosynthesis of PHA (figure 1), by the FIFO we will optimized the expression of the differentes genes in order to avoid waste producte that will increase impurities.<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope that our system will increase the purity and the rate of PHA obtain because we don't activate the 3 genes simultaneously, instead of that we activate by a FIFO order system the 3 genes so we will avoid lost of acetoacetylcoA or others important intermediary product in others metabolic pathways.<br />
<br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
In conclusion,our bacterioclock can be use to obtain many polymers or proteins fibers that their production pass by a lot of methabolic cross linked intermediary, in those situations the FIFO order may optimized the purity and the rate of the final products.<br />
<br />
== Bibliography ==</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T22:04:38Z<p>Philippe b: /* Bibliography */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<font color=red>''Un petit texte pour expliquer la motivation de cette page'' ne serait-ce que tout simplement:<br />
On this page we report some possible uses of the FIFO device in synthetic applications.<br />
<br />
General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.</font><br />
<br />
<br />
<br />
<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.<br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T22:02:02Z<p>Philippe b: /* B.Artificial virus factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<font color=red>''Un petit texte pour expliquer la motivation de cette page'' ne serait-ce que tout simplement:<br />
On this page we report some possible uses of the FIFO device in synthetic applications.<br />
<br />
General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.</font><br />
<br />
<br />
<br />
<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.<br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T22:00:04Z<p>Philippe b: /* Biosynthetic Bottum-up approach */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<font color=red>''Un petit texte pour expliquer la motivation de cette page'' ne serait-ce que tout simplement:<br />
On this page we report some possible uses of the FIFO device in synthetic applications.<br />
<br />
General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.</font><br />
<br />
<br />
<br />
== B.Artificial virus factory ==<br />
<br />
<br />
We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV:<br />
<font color=red> No, you can not produce... You can say (possibly)...<br />
The FIFO device provides also a circuit useful to coordinate the self-assembly of molecular structure. A possible canevas for the production of synthetic virus?</font><br />
<br />
<font color=red> Indeed a virus such as HIV, displays ans organised sequential activation of genes that could be controled by a FIFO circuit. ''ARE YOU SURE OF THIS''</font><br />
<br />
[[Image:HIV.jpg|center]]<br />
<br />
Fig2: genetic organization of HIV virus <br />
<br />
<br />
HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2), those genes are be cleaved by protease P10 and then the subunits of the virus will self-assembled into mature virus. <font color=red>A re-enginered virus could be based on a FIFO setup where gag p10 is first expressed and Env the last (without Pol to avoid pathogenicity). In this case <br />
<br />
* when genes 1 and 2 are expressed, the protease P10 cleaves gag that self-assembles.<br />
<br />
* when 123 is expressed, Env is cleaved and self assembles with the products of gag and P10 that have already been produced.<br />
<br />
* finaly, when 23 is activated alone, this increases the quantity of subunits delivered from the clivage of Env. ''I DO NOT UNDERSTANT''<br />
<br />
''In this setup I maybe understand the sequential order of activation, but I do not see why there should be the same order of inactivation. Justify please''<br />
<br />
<br />
</font><br />
In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.<br />
<br />
If you ask us why?<br />
<br />
For 3 main reasons :<br />
<br />
* First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.<br />
<br />
* Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.<br />
<br />
* Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.<br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-29T21:59:53Z<p>Philippe b: /* A.DNA nanocar factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
<font color=red>''Un petit texte pour expliquer la motivation de cette page'' ne serait-ce que tout simplement:<br />
On this page we report some possible uses of the FIFO device in synthetic applications.<br />
<br />
General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.</font><br />
<br />
== Biosynthetic Bottum-up approach ==<br />
<br />
<font color=red> ''C'est un grand titre de section, où le titre d'une section normale qui manque?'' </font><br />
<br />
<br />
<br />
== B.Artificial virus factory ==<br />
<br />
<br />
We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV:<br />
<font color=red> No, you can not produce... You can say (possibly)...<br />
The FIFO device provides also a circuit useful to coordinate the self-assembly of molecular structure. A possible canevas for the production of synthetic virus?</font><br />
<br />
<font color=red> Indeed a virus such as HIV, displays ans organised sequential activation of genes that could be controled by a FIFO circuit. ''ARE YOU SURE OF THIS''</font><br />
<br />
[[Image:HIV.jpg|center]]<br />
<br />
Fig2: genetic organization of HIV virus <br />
<br />
<br />
HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2), those genes are be cleaved by protease P10 and then the subunits of the virus will self-assembled into mature virus. <font color=red>A re-enginered virus could be based on a FIFO setup where gag p10 is first expressed and Env the last (without Pol to avoid pathogenicity). In this case <br />
<br />
* when genes 1 and 2 are expressed, the protease P10 cleaves gag that self-assembles.<br />
<br />
* when 123 is expressed, Env is cleaved and self assembles with the products of gag and P10 that have already been produced.<br />
<br />
* finaly, when 23 is activated alone, this increases the quantity of subunits delivered from the clivage of Env. ''I DO NOT UNDERSTANT''<br />
<br />
''In this setup I maybe understand the sequential order of activation, but I do not see why there should be the same order of inactivation. Justify please''<br />
<br />
<br />
</font><br />
In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.<br />
<br />
If you ask us why?<br />
<br />
For 3 main reasons :<br />
<br />
* First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.<br />
<br />
* Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.<br />
<br />
* Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.<br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-28T15:25:40Z<p>Philippe b: /* Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
== Biosynthetic Bottum-up approach ==<br />
<br />
==A.DNA nanocar factory ==<br />
<br />
<br />
<br />
The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest in nanoscience.<br />
Research in the last decade has shown that species made of components like DNA or proteins are attractive candidates.<br />
Our aims is to build by a bottom-up approched DNA nanocars . <br />
<br />
<span style="color:blue">You have to explain what you mean by "produce energy in vitro". What energy does it use? to convert into what other energy? or to use in what way? Also, why in vitro? Do you plan to use our system in cell-free extracts or in living cells?</span><br />
<br />
Our system is more efficient than a classic system because the FIFO order is very important: the first part will bind by complementarity with part 2 this new part will make the binding site for part 3. <br />
<br />
[[Image:car2.jpg|center]]<br />
<br />
Fig.1:biosynthesis by sequential expression of 3 DNA origamis<br />
<br />
If we add after purifications of our car a complementary miRNA to the loop, the competition of the miRNA will open the DNA strands by broking the hydrogen backbound this processe will delivered energy , the instability of the miRNA may make this processe reversible.<br />
<br />
In conclusion, these kinds of DNA structures can be suitable, reversible and metastable DNA fuels.<br />
<span style="color:blue"> How will they move? I doubt that turning their wheels will be of any help...</span><br />
<br />
== B.Artificial virus factory ==<br />
<br />
<br />
We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV:<br />
<br />
<br />
<br />
[[Image:HIV.jpg|center]]<br />
<br />
Fig2: genetic organization of HIV virus <br />
<br />
HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2)those genes will be cleaved by protease P10 and than the subunits of the virus will self-assembled into mature virus.<br />
In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.<br />
<br />
If you ask us why?<br />
<br />
For 3 main reasons :<br />
<br />
* First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.<br />
<br />
* Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.<br />
<br />
* Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.<br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-28T15:23:51Z<p>Philippe b: /* A.DNA nanocar factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
== Biosynthetic Bottum-up approach ==<br />
<br />
==A.DNA nanocar factory ==<br />
<br />
<br />
<br />
The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest in nanoscience.<br />
Research in the last decade has shown that species made of components like DNA or proteins are attractive candidates.<br />
Our aims is to build by a bottom-up approched DNA nanocars . <br />
<br />
<span style="color:blue">You have to explain what you mean by "produce energy in vitro". What energy does it use? to convert into what other energy? or to use in what way? Also, why in vitro? Do you plan to use our system in cell-free extracts or in living cells?</span><br />
<br />
Our system is more efficient than a classic system because the FIFO order is very important: the first part will bind by complementarity with part 2 this new part will make the binding site for part 3. <br />
<br />
[[Image:car2.jpg|center]]<br />
<br />
Fig.1:biosynthesis by sequential expression of 3 DNA origamis<br />
<br />
If we add after purifications of our car a complementary miRNA to the loop, the competition of the miRNA will open the DNA strands by broking the hydrogen backbound this processe will delivered energy , the instability of the miRNA may make this processe reversible.<br />
<br />
In conclusion, these kinds of DNA structures can be suitable, reversible and metastable DNA fuels.<br />
<span style="color:blue"> How will they move? I doubt that turning their wheels will be of any help...</span><br />
<br />
== B.Artificial virus factory ==<br />
<br />
<br />
We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV:<br />
<br />
<br />
<br />
[[Image:HIV.jpg|center]]<br />
<br />
Fig2: genetic organization of HIV virus <br />
<br />
HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2)those genes will be cleaved by protease P10 and than the subunits of the virus will self-assembled into mature virus.<br />
In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.<br />
<br />
If you ask us why?<br />
<br />
For 3 main reasons :<br />
<br />
* First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.<br />
<br />
* Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.<br />
<br />
* Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential turnover of the enzymatic expression in order to increase the rate of the PHA biosynthesis.<br />
<span style="color:blue">I'm not sure turnover has this meaning</span><br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-28T15:22:52Z<p>Philippe b: /* A.DNA nanocar factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
== Biosynthetic Bottum-up approach ==<br />
<br />
==A.DNA nanocar factory ==<br />
<br />
<br />
<br />
The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest in nanoscience.<br />
Research in the last decade has shown that species made of components like DNA or proteins are attractive candidates.<br />
Our aims is to build by a bottom-up approched DNA nanocars . <br />
<br />
<span style="color:blue">You have to explain what you mean by "produce energy in vitro". What energy does it use? to convert into what other energy? or to use in what way? Also, why in vitro? Do you plan to use our system in cell-free extracts or in living cells?</span><br />
<br />
Our system is more efficient than a classic system because the FIFO order is very important: the first part will bind by complementarity with part 2 this new part will make the binding site for part 3. <br />
<br />
[[Image:car2.jpg|center]]<br />
<br />
Fig.1:biosynthesis by sequential expression of 3 DNA origamis<br />
<br />
If we add after purifications of our car a complementary miRNA to the loop, the competition of the miRNA will open the DNA strands by broking the hydrogen backbound this processe will delivered energy , the instability of the miRNA may make this processe reversible.<br />
<br />
<br />
In conclusion, these kinds of DNA structures can be suitable, reversible and metastable DNA fuels and a new kind of cargo delivery machine.<br />
<span style="color:blue"> How will they move? I doubt that turning their wheels will be of any help...</span><br />
<br />
== B.Artificial virus factory ==<br />
<br />
<br />
We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV:<br />
<br />
<br />
<br />
[[Image:HIV.jpg|center]]<br />
<br />
Fig2: genetic organization of HIV virus <br />
<br />
HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2)those genes will be cleaved by protease P10 and than the subunits of the virus will self-assembled into mature virus.<br />
In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.<br />
<br />
If you ask us why?<br />
<br />
For 3 main reasons :<br />
<br />
* First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.<br />
<br />
* Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.<br />
<br />
* Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential turnover of the enzymatic expression in order to increase the rate of the PHA biosynthesis.<br />
<span style="color:blue">I'm not sure turnover has this meaning</span><br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe bhttp://2008.igem.org/Team:Paris/PerspectivesTeam:Paris/Perspectives2008-10-28T15:21:32Z<p>Philippe b: /* A.DNA nanocar factory */</p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
== Biosynthetic Bottum-up approach ==<br />
<br />
==A.DNA nanocar factory ==<br />
<br />
<br />
<br />
The field of artificial molecular machines and motors is growing at an astonishing rate and is attracting a great deal of interest in nanoscience.<br />
Research in the last decade has shown that species made of components like DNA or proteins are attractive candidates.<br />
Our aims is to build by a bottom-up approched DNA nanocars . <br />
<br />
<span style="color:blue">You have to explain what you mean by "produce energy in vitro". What energy does it use? to convert into what other energy? or to use in what way? Also, why in vitro? Do you plan to use our system in cell-free extracts or in living cells?</span><br />
<br />
Our system is more efficient than a classic system because the FIFO order is very important: the first part will bind by complementarity with part 2 this new part will make the binding site for part 3. <br />
<br />
[[Image:car2.jpg|center]]<br />
<br />
Fig.1:biosynthesis by sequential expression of 3 DNA origamis<br />
<br />
If we add after purifications of our car a complementary miRNA to the loop, the competition of the miRNA will open the DNA strands by broking the hydrogen backbound this processe will delivered energy , the instability of the miRNA may make this processe reversible.<br />
<br />
<br />
<br />
In conclusion, these kinds of DNA structures can be suitable, reversible and metastable DNA fuels and a new kind of cargo delivery machine.<br />
<span style="color:blue"> How will they move? I doubt that turning their wheels will be of any help...</span><br />
<br />
== B.Artificial virus factory ==<br />
<br />
<br />
We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV:<br />
<br />
<br />
<br />
[[Image:HIV.jpg|center]]<br />
<br />
Fig2: genetic organization of HIV virus <br />
<br />
HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2)those genes will be cleaved by protease P10 and than the subunits of the virus will self-assembled into mature virus.<br />
In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.<br />
<br />
If you ask us why?<br />
<br />
For 3 main reasons :<br />
<br />
* First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.<br />
<br />
* Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.<br />
<br />
* Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.<br />
<br />
== Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways ==<br />
Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions.<br />
Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.<br />
<br />
Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).<br />
<br />
This strategy is more efficient than a constitutive activation for 3 main reasons:<br />
*First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.<br />
<br />
*Secondly, we hope by the order of the FIFO to make a synchronized and sequential turnover of the enzymatic expression in order to increase the rate of the PHA biosynthesis.<br />
<span style="color:blue">I'm not sure turnover has this meaning</span><br />
<br />
*Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system. <br />
<span style="color: blue"> Again, you cannot just state this boldly without constructing an argument. </span><br />
<br />
<span style="color: blue"> You never explain why your system is better than simply expressing all the genes continuously at a lower level </span><br />
<br />
<span style="color: blue"> More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.</span><br />
<br />
[[Image:PHA.jpg|center]]<br />
<br />
== Bibliography ==<br />
* Folding DNA to create nanoscale shapes and patterns<br />
Paul W. K. Rothemund <br />
* Design of DNA origami<br />
Paul W. K. Rothemund <br />
* An autonomous polymerization motor powered by DNA hybridization.<br />
Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.<br />
* Catalyzed Relaxation of a Metastable DNA Fuel.<br />
Georg Seelig, Bernard Yurke, Erik Winfree.</div>Philippe b