Team:UNAM-Genomics Mexico/Collaboration

From 2010.igem.org

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(New page: <div id="header">{{Template:Team:UNAM-Genomics_Mexico/Templates/Header}}</div> ==Collaborations== Our collaborations are documented in our [http://openwetware.org/wiki/IGEM:UNAM-Genomics...)
 
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<div id="header">{{Template:Team:UNAM-Genomics_Mexico/Templates/Header}}</div>
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{{Team:UNAM-Genomics_Mexico/Templates/Main2
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|Spanish=
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__NOTOC__
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<html><a href="https://2010.igem.org/Team:UNAM-Genomics_Mexico/es/Collaboration"><img src="https://static.igem.org/mediawiki/2010/c/cc/UNAM-Genomics_Mexico_Flag_of_Mexico.svg.png" title="Español" height="20px"/></a></html>
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==Collaborations==
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|English=
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__NOTOC__
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<html><a href="https://2010.igem.org/Team:UNAM-Genomics_Mexico/Collaboration"><img src="https://static.igem.org/mediawiki/2010/2/28/UNAM-Genomics_Mexico_Flag_of_the_United_Kingdom.svg.png" title="English" height="20px" /></a></html>
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Our collaborations are documented in our [http://openwetware.org/wiki/IGEM:UNAM-Genomics_Mexico/2009/Notebook/Collaborations collaborations log].
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|French=
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__NOTOC__
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<html><a href="https://2010.igem.org/Team:UNAM-Genomics_Mexico/fr/Collaboration"><img src="https://static.igem.org/mediawiki/2010/b/b3/UNAM-Genomics_Mexico_Flag_of_France.svg.png" title="Français" height="20px" /></a></html>
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<div align="right"> {{Template:Team:UNAM-Genomics Mexico/Templates/Footer}}</div>
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|Red_Content=
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__NOTOC__
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==Synthetic Biology==
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This is defined as attempting to manipulate living objects as if they were man-made machines, specifically in terms of genetic engineering. See more [[Team:UNAM-Genomics_Mexico/About/Synthetic_Biology|here]].
 +
 
 +
|Green_Content=
 +
__NOTOC__
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==iGEM==
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iGEM is the International Genetically Engineered Machines Competition, held each year at MIT and organized with support of the Parts Registry. See more [[Team:UNAM-Genomics_Mexico/About/iGEM|here]].
 +
 
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|Blue_Content=
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__NOTOC__
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==Genomics==
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We are students on the Genomic Sciences program at the Center for Genomic Sciences of the National Autonomous University of Mexico, campus Morelos. See more [[Team:UNAM-Genomics_Mexico/About/CCG|here]].
 +
 
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|Markup_Content=
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__NOTOC__
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__TOC__
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|Main_Content=
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__NOTOC__
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==Locally-hosted documentation==
 +
 
 +
Since having all the information hosted localy, we present here an overview of our collaborations with other iGEM teams, all of them were very useful and enriched our iGEM experience. We appreciate their valuable help.
 +
 
 +
===Edinburgh===
 +
 
 +
The Illuminati connection proved to be an effective bridge. Parts, ideas, references and experiences were exchanged. We started the communication in July and since then we were sharing our projects progress by E-mail. In order to improve the success of our projects we interchanged different parts, as is described below.
 +
 
 +
====Shipments:Sharing Parts====
 +
 
 +
'''From Edinburgh to Mexico'''
 +
 
 +
'''May 2010'''
 +
 
 +
The Edinburgh’s advisor, Dr. Chris, kindly sent us LuxAB and LuxCDE PCR products and a plasmid containing the YFP protein:Lumazine.
 +
 
 +
'''October 2010'''
 +
 
 +
Dr.Chris sent us a second shipment consisting of the following parts:
 +
 
 +
Plasmids with luxAB genes, lumP gene encoding lumazine protein, luxAB and lumP ligated, luxCDE encoding substrate synthesis system for bacterial luciferase (XbaI site removed by mutation), BBa_K098101 (phycobilin synthesis genes with terminator),BBa_K098010 (phycobilin synthesis genes but with terminator removed), BBa_K191004 (RFP reporter plasmid for LOV-Tap blue light sensor), cph8 red light sensor derived from BBa_M30109.
 +
 
 +
'''From Mexico to Edinburgh'''
 +
 
 +
'''September 2010'''
 +
 
 +
We share with Edinburh team principally our synthesised parts, we sent them PCR amplified products containing green light photosensor CcaS and CcaR response regulator, blue light photosensor LovTAP and YFP protein from the Mr. Gene plasmids. As well we sent them a plasmid with our blue light reduced inducible promoter, a PCR amplified product containing light emitting luciferase genes LuxAB from Vibrio Fischeri and LovTAP ligated to four constitutive promoters: J23102,J23105, J23114 and J23117.
 +
 
 +
===Cambridge===
 +
 
 +
The Cambridge collaboration was mostly one-way. They've really helped us with parts we were unable to obtain. We contacted them in July and during the next months we were following their progress with the Lux operon from Vibrio fischeri and other luciferases. After we failed trying to obtain the LuxAB genes ligated to a constitutive promoter, we again contacted them at the ends of September and they kindly sent us the following parts:
 +
 
 +
'''Shipment'''
 +
 
 +
'''From Cambridge to Mexico'''
 +
 
 +
'''October 2010'''
 +
 +
1.enhanced Photinus pyralis luciferase (EPIC) and P. pyralis LRE with no promoter.
 +
 
 +
2.enhanced Photinus pyralis luciferase (EPIC) and P. pyralis LRE under pBad promoter.
 +
 
 +
3.Luciola cruciata luciferase and L. cruciata LRE with no promoter.
 +
 
 +
4.Luciola cruciata luciferase and L. cruciata LRE under pBad promoter.
 +
 
 +
 
 +
===UNAM-Cinvestav===
 +
 
 +
This collaboration with our "brother" team on the main campus consists of Modelling aiding, we started the collaboration at the ends of August. We had some meetings to discuss about our projects  dealing with the experimental and theoretical aspects of each project in order to establish how we were going to help us.
 +
 
 +
The guys from UNAM-Cinvestav team have a good background in the usage of mathematical tools applied to analyze biological systems, so that they made a model to describe the evolution of the communication process between the three bacterial chassis that we designed. The idea was to look for the parameters that could allow an oscillatory behavior in the light based communication process, analyzing the dynamics of  the feed-back activation loop designed as the circuit of communication.
 +
The idea and model is hosted [[Team:Mexico-UNAM-CINVESTAV/Human_Practices/Collaboration|here]]
 +
There is also some information for the individual model [[Team:UNAM-Genomics_Mexico/Modeling|link]]
 +
Merging our model results with those obtained by them we could analyse the following:
 +
 
 +
*The possibility to engineer coordinated cellular behavior in cell populations: Synchronizing oscillations.
 +
 
 +
*The system response to a predefined range of signal stimuli.
 +
 
 +
*Investigate spatiotemporal patterning of gene expression.
 +
 
 +
Our team was working with the experimental procedures to characterise the promoter activities in terms of RPUs (relative promoter units) as well with the PoPS protocol. We were going to make the characterisation experimental procedures of UNAM-Cinvestav's cool-shock biobrick. But, unfortunately the construction of the cold-shock promoter with GFP was nos finished, so we just provided them some samples of plasmid pSB1C3 digested with EcoRI.
 +
 
 +
 
 +
 
 +
 
 +
==Full documentation==
 +
 
 +
The full documentation on each collaboration is documented in other servers.
 +
 
 +
 
 +
===Edinburgh===
 +
 
 +
Our team has recently established contact with [[Team:Edinburgh|Edinburgh's Illuminati]] team. Given that both projects are strikingly similar, and the good-natured collaboration between both teams, we decided to work together. Thus BRIDGING with people!
 +
 
 +
The following [http://openwetware.org/wiki/IGEM:UNAM-Genomics_Mexico/2009/Notebook/Collaborations Collaborations Log] will attempt to document the progress and facilitate communication between these teams.
 +
 
 +
 
 +
===Cambridge===
 +
 
 +
Likewise, we are also working with the [[Team:Cambridge|Cambridge team]]. Since they are interested in maximizing bioluminescent reactions, we are quite interested in their work ;) That collaboration is documented [http://openwetware.org/wiki/IGEM:UNAM-Genomics_Mexico/2009/Notebook/Collaborations.Cambridge here].
 +
 
 +
 
 +
===UNAM-Cinvestav===
 +
 
 +
Model oriented stuff, here is their acurate aproach:
 +
[[Image:System_dinamics_UNAM_CINVESTAV.pdf | Whole model]]
 +
 
 +
 
 +
}}

Latest revision as of 03:55, 28 October 2010



Locally-hosted documentation

Since having all the information hosted localy, we present here an overview of our collaborations with other iGEM teams, all of them were very useful and enriched our iGEM experience. We appreciate their valuable help.

Edinburgh

The Illuminati connection proved to be an effective bridge. Parts, ideas, references and experiences were exchanged. We started the communication in July and since then we were sharing our projects progress by E-mail. In order to improve the success of our projects we interchanged different parts, as is described below.

Shipments:Sharing Parts

From Edinburgh to Mexico

May 2010

The Edinburgh’s advisor, Dr. Chris, kindly sent us LuxAB and LuxCDE PCR products and a plasmid containing the YFP protein:Lumazine.

October 2010

Dr.Chris sent us a second shipment consisting of the following parts:

Plasmids with luxAB genes, lumP gene encoding lumazine protein, luxAB and lumP ligated, luxCDE encoding substrate synthesis system for bacterial luciferase (XbaI site removed by mutation), BBa_K098101 (phycobilin synthesis genes with terminator),BBa_K098010 (phycobilin synthesis genes but with terminator removed), BBa_K191004 (RFP reporter plasmid for LOV-Tap blue light sensor), cph8 red light sensor derived from BBa_M30109.

From Mexico to Edinburgh

September 2010

We share with Edinburh team principally our synthesised parts, we sent them PCR amplified products containing green light photosensor CcaS and CcaR response regulator, blue light photosensor LovTAP and YFP protein from the Mr. Gene plasmids. As well we sent them a plasmid with our blue light reduced inducible promoter, a PCR amplified product containing light emitting luciferase genes LuxAB from Vibrio Fischeri and LovTAP ligated to four constitutive promoters: J23102,J23105, J23114 and J23117.

Cambridge

The Cambridge collaboration was mostly one-way. They've really helped us with parts we were unable to obtain. We contacted them in July and during the next months we were following their progress with the Lux operon from Vibrio fischeri and other luciferases. After we failed trying to obtain the LuxAB genes ligated to a constitutive promoter, we again contacted them at the ends of September and they kindly sent us the following parts:

Shipment

From Cambridge to Mexico

October 2010

1.enhanced Photinus pyralis luciferase (EPIC) and P. pyralis LRE with no promoter.

2.enhanced Photinus pyralis luciferase (EPIC) and P. pyralis LRE under pBad promoter.

3.Luciola cruciata luciferase and L. cruciata LRE with no promoter.

4.Luciola cruciata luciferase and L. cruciata LRE under pBad promoter.


UNAM-Cinvestav

This collaboration with our "brother" team on the main campus consists of Modelling aiding, we started the collaboration at the ends of August. We had some meetings to discuss about our projects dealing with the experimental and theoretical aspects of each project in order to establish how we were going to help us.

The guys from UNAM-Cinvestav team have a good background in the usage of mathematical tools applied to analyze biological systems, so that they made a model to describe the evolution of the communication process between the three bacterial chassis that we designed. The idea was to look for the parameters that could allow an oscillatory behavior in the light based communication process, analyzing the dynamics of the feed-back activation loop designed as the circuit of communication. The idea and model is hosted here There is also some information for the individual model link Merging our model results with those obtained by them we could analyse the following:

  • The possibility to engineer coordinated cellular behavior in cell populations: Synchronizing oscillations.
  • The system response to a predefined range of signal stimuli.
  • Investigate spatiotemporal patterning of gene expression.

Our team was working with the experimental procedures to characterise the promoter activities in terms of RPUs (relative promoter units) as well with the PoPS protocol. We were going to make the characterisation experimental procedures of UNAM-Cinvestav's cool-shock biobrick. But, unfortunately the construction of the cold-shock promoter with GFP was nos finished, so we just provided them some samples of plasmid pSB1C3 digested with EcoRI.



Full documentation

The full documentation on each collaboration is documented in other servers.


Edinburgh

Our team has recently established contact with Edinburgh's Illuminati team. Given that both projects are strikingly similar, and the good-natured collaboration between both teams, we decided to work together. Thus BRIDGING with people!

The following [http://openwetware.org/wiki/IGEM:UNAM-Genomics_Mexico/2009/Notebook/Collaborations Collaborations Log] will attempt to document the progress and facilitate communication between these teams.


Cambridge

Likewise, we are also working with the Cambridge team. Since they are interested in maximizing bioluminescent reactions, we are quite interested in their work ;) That collaboration is documented [http://openwetware.org/wiki/IGEM:UNAM-Genomics_Mexico/2009/Notebook/Collaborations.Cambridge here].


UNAM-Cinvestav

Model oriented stuff, here is their acurate aproach:

File:System dinamics UNAM CINVESTAV.pdf

iGEM

iGEM is the International Genetically Engineered Machines Competition, held each year at MIT and organized with support of the Parts Registry. See more here.

Synthetic Biology

This is defined as attempting to manipulate living objects as if they were man-made machines, specifically in terms of genetic engineering. See more here.

Genomics

We are students on the Genomic Sciences program at the Center for Genomic Sciences of the National Autonomous University of Mexico, campus Morelos. See more here.

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