IPN UNAM 2006

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<center>[[Image:IGEMEXICO.jpg | width=200px | height=100px ]]</center>
<center>[[Image:IGEMEXICO.jpg | width=200px | height=100px ]]</center>
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== '''First bulletin of iGEM MEXICO''' November 1, 2006 (bulletin in Spanish). [[Media:Bulletin-1.pdf]] ==
[[Image:IPN_logo.jpg]]
[[Image:IPN_logo.jpg]]
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[http://www.ipn.mx/ Instituto Politécnico Nacional, México]
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[http://www.ipn.mx/ Instituto Politécnico Nacional-Universidad Nacional Autónoma de México, México]
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== Mexican Staff - iGEM MEXICO==  
== Mexican Staff - iGEM MEXICO==  
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<center>
 
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{|border="0.75" cellpadding="4"  cellspacing="0.5" style="text-align:rigth
 
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!width="60"|
 
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!width="3"|
 
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!width="60"|
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<font size=2> '''STUDENTS'''</font>
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!width="3"|
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|-
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|<font size=2> '''STUDENTS'''</font>
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|<font size =2> '''INSTRUCTORS''' </font>
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|-
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Iván Y. Fernández Rosales (najtaaj#gmail.com), Paulina A. Leon Hernández (pauanana#gmail.com), Tania G. Bermúdez Cisneros (tgbermudez#hotmail.com), Pablo Gerardo Padilla (tyomero#gmail.com), Julio N. Argota Quiróz (julioargota#hotmail.com), Alejandra Sánchez Arzate (alesa#ciencias.unam.mx)
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Rosario E. Gordillo Padilla (extraterrestre710#hotmail.com) and Rafael Peña Miller (rpena#ciencias.unam.mx)
 +
 
 +
 
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<font size =2> '''INSTRUCTORS''' </font>
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Genaro Juárez Martínez (genarojm#correo.unam.mx), Pablo Padilla Longoria (pablo#mym.iimas.unam.mx), Edgar Salgado Majarrez (esalgado#ipn.mx), Juan S. Aranda Barradas (jaranda#acei.upibi.ipn.mx), Rosaura Palma Orozco (rpalma#math.cinvestav.mx), Ma Carmen Oliver Salvador (oliveripn#hotmail.com) and Arturo Becerra Bracho (abb#fciencias.unam.mx), Elias Samra Hassan (elias#uxmcc2.iimas.unam.mx), Fabiola Ramírez Corona (framirez#miranda.ecologia.unam.mx), Paola B. Zarate Segura (Pbzars#yahoo.com), Ulises Vélez Saldaña (ulises.velez#gmail.com), Jaime López Rabadan (rabadanlorj#gmail.com), Carlos Silva Sánchez (sscarlos#gmail.com) and Claudia I. Franco Arteaga (claudia_imelda#yahoo.com)
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|-
 
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| '''María E. González Jiménez''' <br> maruhtfl#hotmail.com
 
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|'''Genaro Juárez Martínez''' (COM) <br> genarojm#correo.unam.mx
 
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|-
 
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| '''Raúl I. López Gómez''' <br> raul.ivan.lopez.gomez#hotmail.com
 
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|'''Pablo Padilla''' (COM) <br> pablo#mym.iimas.unam.mx
 
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|-
 
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| '''Tania G. Bermúdez Cisneros''' <br> tgbermudez#hotmail.com
 
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| '''Edgar Salgado''' (BIO) <br>esalgado#ipn.mx
 
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|-
 
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| '''Paulina A. Leon Hernández''' <br> pauanana#gmail.com
 
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| '''Rosaura Palma Orozco''' (COM) <br>rpalma#math.cinvestav.mx
 
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|-
 
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| '''Pablo Gerardo Padilla''' <br>tyomero#gmail.com
 
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| '''Juan Aranda''' (BIO) <br> jaranda#acei.upibi.ipn.mx
 
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|-
 
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| '''Izchel N. Ríos Gaspar''' <br>nayb_juice#yahoo.com.mx
 
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|'''Carmen Oliver Salvador''' (BIO) <br> oliveripn#hotmail.com
 
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|-
 
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|'''Arturo Rodríguez Martínez''' <br> arturo_rguez_mtz#yahoo.com.mx
 
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|'''David Araujo Díaz''' (COM) <br>daraujo#ipn.mx
 
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|-
 
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|'''Claudia I. Franco Arteaga''' <br>claudia_imelda#yahoo.com
 
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|'''Paola Zarate''' (BIO)<br> Pbzars#yahoo.com
 
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|-
 
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|'''Alejandra Sánchez Arzate''' <br> alesa#ciencias.unam.mx
 
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|'''Claudia Benítez''' (BIO) <br> beni1972uk#yahoo.com.mx
 
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|-
 
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|'''Julio N. Argota Quiróz''' <br>julioargota#hotmail.com
 
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|'''Arturo Becerra Bracho''' (BIO) <br>abb#fciencias.unam.mx
 
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|-
 
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|'''Iván Y. Fernández Rosales''' <br> najtaaj#gmail.com
 
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|'''Elias Samra Hassan''' (COM) <br>elias#uxmcc2.iimas.unam.mx
 
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|-
 
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|'''José C. Rodríguez Chico''' <br> rodriguez_chico#hotmail.com
 
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|'''Carlos Silva Sánchez''' (COM) <br>sscarlos#gmail.com
 
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|-
 
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|'''Rogelio Basurto Flores''' <br>larckov#hotmail.com
 
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|'''Jaime López Rabadan''' (COM) <br>rabadanlorj#gmail.com
 
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|-
 
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|'''Rosario E. Gordillo Padilla''' <br>extraterrestre710#hotmail.com
 
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|-
 
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|'''Juan C. Gómez Sánchez''' <br>thunder2099#hotmail.com
 
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|-
 
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|'''Armando Galicia Naranjo''' <br>armandushko#hotmail.com||
 
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|-
 
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|'''Abraham J. Leal Baena''' <br>fenixaj#hotmail.com ||
 
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|-
 
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|}
 
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</center>
 
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Line 79: Line 29:
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==iGEM - México Project==
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==Line of Investigation==
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----
 +
Our main line of investigation uses unconventional computing as a
 +
means of building novel computing paradigms, such as in biology,
 +
physics and chemistry.
 +
We are attempting to construct discrete dynamical systems capable of
 +
simulating cellular computation. Therefore, our work focuses on
 +
molecular computation. We thus have three models using cellular
 +
automata theory (you can see our original contributions [http://uncomp.uwe.ac.uk/genaro/ click here]).
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EXPERIMENT PROPOSAL: �Engineering a genetic signaling cascade to produce a green flourescence protein expression/repression system in Escherichia coli.  
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Cellular automata (CA) operate over a scales ranging from the
-
 
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molecular level to n-dimensions and are massively parallel. Also,
 +
they are capable of supporting universal computation, self-repair and
 +
self-reproduction.
We wish contribute to the iGEM project development various protein
We wish contribute to the iGEM project development various protein
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implement broader real biological scenarios.
implement broader real biological scenarios.
 +
----
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We study two-dimensional cellular automaton, where every cell
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==iGEM México Project==
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takes states 0 and 1 and updates its state depending on sum of states of
+
----
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its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there
+
-
are exactly two neighbors in state 1, otherwise the cell remains in state
+
-
0. Cell in state 1 remains in state 1 if there are exactly seven neighbors
+
-
in state 1, otherwise the cell switches to state 0. CA governed by such
+
-
cell-state transition rule exhibits reaction-diffusion like pattern dynamics,
+
-
so we call this '''Diffusion Rule'''.
+
 +
'''EXPERIMENT PROPOSAL:''' Engineering a genetic signaling cascade to produce a green flourescence protein expression/repression system in ''Escherichia coli''.
-
[[Image:Diffusionrule.JPG]]
 
 +
<center>[[Image:Upibifig1.JPG]]</center>
 +
<center>'''Figure 1.''' Green flourescense protein.</center>
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----
 
 +
'''IN THIS PART OF THE PROJECT:''' We intend to emulate some genetic networks already identified in ''Arabidopsis'' responsible for the formation of hair in root and leaves. These networks lead to simple genetic circuits of the repression/expression type. We would like to show that these systems support '''Turing patterns'''.
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==Line of Investigation==
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<center>[[Image:Unam1.JPG]]</center>
-
----
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<center>'''Figure 2.''' Turing patterns.</center>
-
Our main line of investigation uses unconventional computing as a
 
-
means of building novel computing paradigms, such as in biology,
 
-
physics and chemistry.
 
-
We are attempting to construct discrete dynamical systems capable of
+
'''MODELLING PROPOSAL:''' Developing models to describe inside-the-cell metabolic events
-
simulating cellular computation. Therefore, our work focuses on
+
through a cellular automata approach.  
-
molecular computation. We thus have three models using cellular
+
-
automata theory (you can see our original contributions [http://uncomp.uwe.ac.uk/genaro/ click here]).
+
-
Cellular automata (CA) operate over a scales ranging from the
+
 
-
molecular level to n-dimensions and are massively parallel. Also,
+
We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state
-
they are capable of supporting universal computation, self-repair and
+
0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this '''Diffusion Rule'''.
-
self-reproduction.
+
 
 +
 
 +
<center>[[Image:Diffusionrule.JPG]]</center>
 +
<center>'''Figure 3.''' Diffusion rule.</center>
 +
 
 +
 
 +
Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off
 +
ligth with alive o dead cells that shows a luminescence, examples include fluorescence,
 +
bioluminescence and phosphorescence.
 +
 
 +
Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by
 +
the evolution of this initial pattern.
 +
 
 +
 
 +
 
 +
<center>[[Image:Lumi.JPG]]</center>
 +
<center>'''Figure 4.''' Luminescence by diffusion rule.</center>
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== '''Collaborators''' ==
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==Collaborators==
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Paula Figueroa Arredondo (BIO), Absalom Zamorano (BIO), Jovita Martínez (BIO), Juan C. Seck Tuoh Mora (COM), Sergio V. Chapa Vergara (COM), Francisco Hernández Quiroz (COM), Carlos A. Espinosa Soto (BIO), Mark Olson (BIO),  Rafael Baquero (PHY), José U. Cruz Cedillo (COM), Rafael Peña Miller (COM), Rocío Reséndiz Muñoz (COM) and Ulises Vélez Saldaña (COM)
+
Paula Figueroa Arredondo (BIO), Absalom Zamorano (BIO), Claudia Benítez (BIO), Jovita Martínez (BIO), Juan C. Seck Tuoh Mora (COM), Sergio V. Chapa Vergara (COM), Francisco Hernández Quiroz (COM), Carlos A. Espinosa Soto (BIO), Mark Olson (BIO), José U. Cruz Cedillo (COM), Rocío Reséndiz Muñoz (COM), Georgina V. Juárez Martínez (BIO), Giovanna Salamanca Pinzón (BIO), Melina López Meyer (BIO) and Oscar Olmedo (COM).

Latest revision as of 16:39, 20 June 2007

height=100px


Contents

First bulletin of iGEM MEXICO November 1, 2006 (bulletin in Spanish). Media:Bulletin-1.pdf

IPN logo.jpg

Instituto Politécnico Nacional-Universidad Nacional Autónoma de México, México


Mexican Staff - iGEM MEXICO



STUDENTS

Iván Y. Fernández Rosales (najtaaj#gmail.com), Paulina A. Leon Hernández (pauanana#gmail.com), Tania G. Bermúdez Cisneros (tgbermudez#hotmail.com), Pablo Gerardo Padilla (tyomero#gmail.com), Julio N. Argota Quiróz (julioargota#hotmail.com), Alejandra Sánchez Arzate (alesa#ciencias.unam.mx) Rosario E. Gordillo Padilla (extraterrestre710#hotmail.com) and Rafael Peña Miller (rpena#ciencias.unam.mx)


INSTRUCTORS

Genaro Juárez Martínez (genarojm#correo.unam.mx), Pablo Padilla Longoria (pablo#mym.iimas.unam.mx), Edgar Salgado Majarrez (esalgado#ipn.mx), Juan S. Aranda Barradas (jaranda#acei.upibi.ipn.mx), Rosaura Palma Orozco (rpalma#math.cinvestav.mx), Ma Carmen Oliver Salvador (oliveripn#hotmail.com) and Arturo Becerra Bracho (abb#fciencias.unam.mx), Elias Samra Hassan (elias#uxmcc2.iimas.unam.mx), Fabiola Ramírez Corona (framirez#miranda.ecologia.unam.mx), Paola B. Zarate Segura (Pbzars#yahoo.com), Ulises Vélez Saldaña (ulises.velez#gmail.com), Jaime López Rabadan (rabadanlorj#gmail.com), Carlos Silva Sánchez (sscarlos#gmail.com) and Claudia I. Franco Arteaga (claudia_imelda#yahoo.com)



BIO: Biology, COM: Computation, PHY: Physics


Line of Investigation


Our main line of investigation uses unconventional computing as a means of building novel computing paradigms, such as in biology, physics and chemistry.

We are attempting to construct discrete dynamical systems capable of simulating cellular computation. Therefore, our work focuses on molecular computation. We thus have three models using cellular automata theory (you can see our original contributions click here).

Cellular automata (CA) operate over a scales ranging from the molecular level to n-dimensions and are massively parallel. Also, they are capable of supporting universal computation, self-repair and self-reproduction.

We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.

We aim to develop CA software for a specific bio-simulation and gradually implement broader real biological scenarios.


iGEM México Project


EXPERIMENT PROPOSAL: Engineering a genetic signaling cascade to produce a green flourescence protein expression/repression system in Escherichia coli.


Upibifig1.JPG
Figure 1. Green flourescense protein.


IN THIS PART OF THE PROJECT: We intend to emulate some genetic networks already identified in Arabidopsis responsible for the formation of hair in root and leaves. These networks lead to simple genetic circuits of the repression/expression type. We would like to show that these systems support Turing patterns.


Unam1.JPG
Figure 2. Turing patterns.


MODELLING PROPOSAL: Developing models to describe inside-the-cell metabolic events through a cellular automata approach.


We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.


Diffusionrule.JPG
Figure 3. Diffusion rule.


Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.

Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.


Lumi.JPG
Figure 4. Luminescence by diffusion rule.

Collaborators


Paula Figueroa Arredondo (BIO), Absalom Zamorano (BIO), Claudia Benítez (BIO), Jovita Martínez (BIO), Juan C. Seck Tuoh Mora (COM), Sergio V. Chapa Vergara (COM), Francisco Hernández Quiroz (COM), Carlos A. Espinosa Soto (BIO), Mark Olson (BIO), José U. Cruz Cedillo (COM), Rocío Reséndiz Muñoz (COM), Georgina V. Juárez Martínez (BIO), Giovanna Salamanca Pinzón (BIO), Melina López Meyer (BIO) and Oscar Olmedo (COM).



Institutions


IPN logo.jpg Instituto Politécnico Nacional (National Polytechnic Institute)

Unam.gif Universidad Nacional Autónoma de México (National Autonomous University of Mexico)

Hidaldo.jpg Universidad Autónoma del Estado de Hidalgo (National Autonomous University of Hidalgo State)

CINVESTAV1.JPG Centro de Investigación y de Estudios Avanzados (Centre of Advanced Studies and Researche)

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