Team:Panama/Notebook

From 2010.igem.org

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==Notebook==
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====Notebook====
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===DNA 101: Information store, replication. 26 May===
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* Instructor: Dr. Abby Guerra
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* Date: 26 May 17h00-20h00
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* Venue: UTP
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* Description: A basic refresher course on how DNA stores information in the cell, and how it is involved in cellular replication.
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<gallery>
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Image:Panama-01.JPG|Dr. Abby Guerra
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Image:Panama-04.JPG|Dr. Abby Guerra
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</gallery>
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{{:Team:Panama/calendar2}}
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<center>
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===DNA 102: Protein creation relationship to cellular function. 26 May===
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* Instructor: Dr. Abby Guerra
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* Date: 26 May 17h00-20h00
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* Venue: UTP
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* Description: Introduction to how DNA drives cellular functions by creating proteins
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<gallery>
<gallery>
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Image:Panama-02.JPG|Dr. Abby Guerra
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Image:INDICASAT-11.JPG|
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Image:Panama-03.JPG|Dr. Abby Guerra
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Image:INDICASAT-05.JPG|
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</gallery>
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Image:INDICASAT-02.JPG|
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Image:DSC04818.JPG|
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===DNA 103: DNA modification, plasmids===
 
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* Instructor: Dr. Abby Guerra
 
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* Date: 26 May 17h00-20h00
 
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* Venue: UTP
 
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* Description:Introduction to long tested combinant DNA techniques, the role of plasmids in bacteria, and their use as a vector for DNA modification.
 
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<gallery>
 
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Image:Panama-05.JPG|Dr. Abby Guerra
 
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Image:Panama-06.JPG|Dr. Abby Guerra
 
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Image:Panama-07.JPG|Dr. Abby Guerra
 
</gallery>
</gallery>
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</center>
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===INDICASAT lecture: Drug discovery in nature===
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* Instructor: Dr. Sergio Martinez
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* Date: (17h00-20h00 Thursday 3rd June)
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* Venue: INDICASAT
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* Description:Would be a brainstorming session as students start thinking about projects. It would be GREAT if we could take a molecule discovered by INDICASAT in coral/frogs/nature and put it in E. coli!...
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===INDICASAT lecture: Innovation===
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* Instructor: Dr. Jagannatha Rao, Director of INDICASAT
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* Date: (17h30-20h00 Friday 4th June)
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* Venue: INDICASAT
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* Description: Dr. Rao's lecture on how to innovate.
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<gallery>
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Image:INDICASAT_LECTURE-02.JPG
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Image:INDICASAT_LECTURE-04.JPG
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Image:INDICASAT_LECTURE-08.JPG
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</gallery>
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===DNA 104: BioBricks Protocol===
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* Instructor: Sara/Patrick
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* Date: (17h30-20h00 Monday 7th June)
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* Venue: INDICASAT
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* Description: Introduction to the BrioBricks protocol
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<gallery>
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Image:INDICASAT_LECTURE-09.JPG|Dr. Patrick Nee
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Image:INDICASAT_LECTURE-10.JPG
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Image:INDICASAT_LECTURE-11.JPG|Dr. Patrick Nee
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Image:INDICASAT_LECTURE-12.JPG|Dr. Patrick Nee
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</gallery>
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===iGEM workshop follow up: Software tools===
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* Instructor: Patrick / Sara
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* Date: (17h30-20h00 Monday 7th June)
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* Venue: INDICASAT
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* Description: Software tools available from the workshop.
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<gallery>
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Image:INDICASAT_LECTURE-13.JPG|Dra. Sara Pinzon
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</gallery>
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===iGEM workshop follow up: Safety, ethics===
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* Instructor: Dr. Ricardo Lleonart
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* Date: (17h00-20h00 9th of June)
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* Venue: INDICASAT
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* Description: There is definetly a "safety considerations" requirement and we should address it early.
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<gallery>
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Image:INDICASAT_LECTURE-02.JPG
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Image:INDICASAT_LECTURE-04.JPG
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Image:INDICASAT_LECTURE-08.JPG
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</gallery>
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===Wetlab 101: Tools of the lab and their use===
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* Instructor: Dr. Patricia Llanes
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* Date: (17h00-20h00 9th June)
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* Venue: INDICASAT
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* Description: How to handle pipettes, clean test tubes, etc.
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===Wetlab 102: Let's raise a few E. coli===
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* Instructor: Lorena Coronado and and Dr. Carmenza Spadafora
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* Date: (17h00-20h00 11th of June)
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* Venue: INDICASAT
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* Description: How does one handle E. coli?
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<gallery>
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Image:INDICASAT-01.JPG|INDICASAT
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Image:INDICASAT-02.JPG|INDICASAT
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Image:INDICASAT-03.JPG|INDICASAT
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Image:INDICASAT-04.JPG|INDICASAT
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Image:INDICASAT-05.JPG|INDICASAT
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Image:INDICASAT-06.JPG|INDICASAT
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Image:INDICASAT-07.JPG|INDICASAT
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Image:INDICASAT-08.JPG|INDICASAT
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Image:INDICASAT-09.JPG|INDICASAT
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Image:INDICASAT-10.JPG|INDICASAT
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Image:INDICASAT-11.JPG|INDICASAT
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Image:INDICASAT-12.JPG|INDICASAT
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</gallery>
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===Wetlab 103: Let's make an E. coli that fluoresce (or some simple BioBrick project)===
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* Instructor: INDICASAT, Dr. Carmenza Spadafora
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* Date:  (17h00-20h00 11th of June)
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* Venue:  INDICASAT
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* Description: We identify a simple project based on past iGEM work and do our first BioBrick protocol project. Nothing innovative, but an opportunity to practice the protocols.
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===Meeting June 26===
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At this moment we have two ideas for develop.  We are debating which idea is more feasible.
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Idea #1:  Carlos´s  team idea
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We want to produce Rhamnolipid in bacteria (e.coli) to use it as a biosurfactant.
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First we have to be sure that our idea is not the same that the idea published in the reference paper.
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We want to make a biobrick to produce Rh1.
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We have to see how we can isolate the rhamnolipid, and be sure that the translation is functional.
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<gallery>
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Image:ErnestoIdea.jpg|Ernesto's Idea
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</gallery>
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Steps to follow:
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1.Amplified the Rhamnosyltransferase  1  complex from Pseudomona Auruginosa to clone the fragment. Size aprox 2.2 Kb.
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2.Ligation / Transformation
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3.Expression with reporter gen.
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4.Isolation
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5.Is the protein functional?
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6.Make sure that the rhamnolipid is produced in prescence of rhamnose and fatty acid.
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Notes:
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We can see the reaction ( enzymatic measure) by spectrometry.
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See kind of ligation.
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Decided if we are going to use sticky or blond ends. (Depend on the plasmid).
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But first, before the amplification we need to design our primers.
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Primers design:
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1.Check the gene sequence (In GenBank, FASTA format)
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2.Check the primer sequence.
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3.See kind of cloning.
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4.M13 tail for cleavage site.
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5.Look for cleavage site inside the rhamnosyltransferase 1 gene for our restriction enzymes.  We can´t cut our gene in the process.
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In summary the steps that we need to follow are:
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I.Primer design
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II.PCR or amplification
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III.Cloning
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IV.Expression
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V.Sequencing
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The most important steps are I and II. We need a good primers design and PCR if we want to have successful.
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Idea #2
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Ernesto team´s idea
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Production of Cecropin compound.  We want to produce the antibacterial cecropin compound. Naturally is produced by insects and plants.
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We want to use Anopheles gambiae cecropin precursor. The gene is about 550 pb.
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The steps to follow are the same in both groups.
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Both groups have to design the primers, and have all the experimental design for this week.
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1.The sequence of the interested gene.
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2.Design the primers. (50-100pb more at the begging and end of the sequence).
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3.Check for cloning sites. Which plasmid we are going to use, identify the restriction enzymes.
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4.Assemble the blocks. In paper assemble all the system. Promoter + Ribosomal binding site + interest gene + reporter gene + translation end site.
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All the design has to be on paper to analyze them and decided which idea is going to be the elected one.
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Latest revision as of 17:57, 14 October 2010

iGEM Panama

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Notebook

May
MTWTFSS
          [http://2010.igem.org/wiki/index.php?title=Team:Panama/1_May_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=Team:Panama/2_May_2010&action=edit 2]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/3_May_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=Team:Panama/4_May_2010&action=edit 4] [http://2010.igem.org/wiki/index.php?title=Team:Panama/5_May_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=Team:Panama/6_May_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=Team:Panama/7_May_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=Team:Panama/8_May_2010&action=edit 8] [http://2010.igem.org/wiki/index.php?title=Team:Panama/9_May_2010&action=edit 9]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/10_May_2010&action=edit 10] [http://2010.igem.org/wiki/index.php?title=Team:Panama/11_May_2010&action=edit 11] [http://2010.igem.org/wiki/index.php?title=Team:Panama/12_May_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=Team:Panama/13_May_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=Team:Panama/14_May_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=Team:Panama/15_May_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=Team:Panama/16_May_2010&action=edit 16]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/17_May_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=Team:Panama/18_May_2010&action=edit 18] [http://2010.igem.org/wiki/index.php?title=Team:Panama/19_May_2010&action=edit 19] [http://2010.igem.org/wiki/index.php?title=Team:Panama/20_May_2010&action=edit 20] [http://2010.igem.org/wiki/index.php?title=Team:Panama/21_May_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=Team:Panama/22_May_2010&action=edit 22] [http://2010.igem.org/wiki/index.php?title=Team:Panama/23_May_2010&action=edit 23]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/24_May_2010&action=edit 24] [http://2010.igem.org/wiki/index.php?title=Team:Panama/25_May_2010&action=edit 25] [http://2010.igem.org/Team:Panama/26_May_2010 26] [http://2010.igem.org/wiki/index.php?title=Team:Panama/27_May_2010&action=edit 27] [http://2010.igem.org/wiki/index.php?title=Team:Panama/28_May_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=Team:Panama/29_May_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=Team:Panama/30_May_2010&action=edit 30]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/31_May_2010&action=edit 31]
June
MTWTFSS
  [http://2010.igem.org/wiki/index.php?title=Team:Panama/1_June_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=Team:Panama/2_June_2010&action=edit 2] [http://2010.igem.org/Team:Panama/3_June_2010 3] [http://2010.igem.org/Team:Panama/4_June_2010 4] [http://2010.igem.org/wiki/index.php?title=Team:Panama/5_June_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=Team:Panama/6_June_2010&action=edit 6]
[http://2010.igem.org/Team:Panama/7_June_2010 7] [http://2010.igem.org/wiki/index.php?title=Team:Panama/8_June_2010&action=edit 8] [http://2010.igem.org/Team:Panama/9_June_2010 9] [http://2010.igem.org/wiki/index.php?title=Team:Panama/10_June_2010&action=edit 10] [http://2010.igem.org/Team:Panama/11_June_2010 11] [http://2010.igem.org/wiki/index.php?title=Team:Panama/12_June_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=Team:Panama/13_June_2010&action=edit 13]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/14_June_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=Team:Panama/15_June_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=Team:Panama/16_June_2010&action=edit 16] [http://2010.igem.org/wiki/index.php?title=Team:Panama/17_June_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=Team:Panama/18_June_2010&action=edit 18] [http://2010.igem.org/wiki/index.php?title=Team:Panama/19_June_2010&action=edit 19] [http://2010.igem.org/wiki/index.php?title=Team:Panama/20_June_2010&action=edit 20]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/21_June_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=Team:Panama/22_June_2010&action=edit 22] [http://2010.igem.org/wiki/index.php?title=Team:Panama/23_June_2010&action=edit 23] [http://2010.igem.org/wiki/index.php?title=Team:Panama/24_June_2010&action=edit 24] [http://2010.igem.org/wiki/index.php?title=Team:Panama/25_June_2010&action=edit 25] [http://2010.igem.org/Team:Panama/26_June_2010 26] [http://2010.igem.org/wiki/index.php?title=Team:Panama/27_June_2010&action=edit 27]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/28_June_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=Team:Panama/29_June_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=Team:Panama/30_June_2010&action=edit 30]
July
MTWTFSS
      [http://2010.igem.org/wiki/index.php?title=Team:Panama/1_July_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=Team:Panama/2_July_2010&action=edit 2] [http://2010.igem.org/wiki/index.php?title=Team:Panama/3_July_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=Team:Panama/4_July_2010&action=edit 4]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/5_July_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=Team:Panama/6_July_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=Team:Panama/7_July_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=Team:Panama/8_July_2010&action=edit 8] [http://2010.igem.org/wiki/index.php?title=Team:Panama/9_July_2010&action=edit 9] [http://2010.igem.org/wiki/index.php?title=Team:Panama/10_July_2010&action=edit 10] [http://2010.igem.org/wiki/index.php?title=Team:Panama/11_July_2010&action=edit 11]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/12_July_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=Team:Panama/13_July_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=Team:Panama/14_July_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=Team:Panama/15_July_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=Team:Panama/16_July_2010&action=edit 16] [http://2010.igem.org/wiki/index.php?title=Team:Panama/17_July_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=Team:Panama/18_July_2010&action=edit 18]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/19_July_2010&action=edit 19] [http://2010.igem.org/Team:Panama/20_July_2010 20] [http://2010.igem.org/Team:Panama/21_July_2010 21] [http://2010.igem.org/Team:Panama/22_July_2010 22] [http://2010.igem.org/Team:Panama/23_July_2010 23] [http://2010.igem.org/Team:Panama/24_July_2010 24] [http://2010.igem.org/wiki/index.php?title=Team:Panama/25_July_2010&action=edit 25]
[http://2010.igem.org/Team:Panama/26_July_2010 26] [http://2010.igem.org/Team:Panama/27_July_2010 27] [http://2010.igem.org/Team:Panama/28_July_2010 28] [http://2010.igem.org/Team:Panama/29_July_2010 29] [http://2010.igem.org/Team:Panama/30_July_2010 30] [http://2010.igem.org/wiki/index.php?title=Team:Panama/31_July_2010&action=edit 31]
August
MTWTFSS
            [http://2010.igem.org/wiki/index.php?title=Team:Panama/1_August_2010&action=edit 1]
[http://2010.igem.org/Team:Panama/2_August_2010 2] [http://2010.igem.org/wiki/index.php?title=Team:Panama/3_August_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=Team:Panama/4_August_2010&action=edit 4] [http://2010.igem.org/Team:Panama/5_August_2010 5] [http://2010.igem.org/wiki/index.php?title=Team:Panama/6_August_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=Team:Panama/7_August_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=Team:Panama/8_August_2010&action=edit 8]
[http://2010.igem.org/Team:Panama/9_August_2010 9] [http://2010.igem.org/Team:Panama/10_August_2010 10] [http://2010.igem.org/Team:Panama/11_August_2010 11] [http://2010.igem.org/Team:Panama/12_August_2010 12] [http://2010.igem.org/Team:Panama/13_August_2010 13] [http://2010.igem.org/wiki/index.php?title=Team:Panama/14_August_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=Team:Panama/15_August_2010&action=edit 15]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/16_August_2010&action=edit 16] [http://2010.igem.org/wiki/index.php?title=Team:Panama/17_August_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=Team:Panama/18_August_2010&action=edit 18] [http://2010.igem.org/Team:Panama/19_August_2010 19] [http://2010.igem.org/Team:Panama/20_August_2010 20] [http://2010.igem.org/wiki/index.php?title=Team:Panama/21_August_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=Team:Panama/22_August_2010&action=edit 22]
[http://2010.igem.org/Team:Panama/23_August_2010 23] [http://2010.igem.org/Team:Panama/24_August_2010 24] [http://2010.igem.org/wiki/index.php?title=Team:Panama/25_August_2010&action=edit 25] [http://2010.igem.org/wiki/index.php?title=Team:Panama/26_August_2010&action=edit 26] [http://2010.igem.org/wiki/index.php?title=Team:Panama/27_August_2010&action=edit 27] [http://2010.igem.org/wiki/index.php?title=Team:Panama/28_August_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=Team:Panama/29_August_2010&action=edit 29]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/30_August_2010&action=edit 30] [http://2010.igem.org/wiki/index.php?title=Team:Panama/31_August_2010&action=edit 31]
September
MTWTFSS
    [http://2010.igem.org/wiki/index.php?title=Team:Panama/1_September_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=Team:Panama/2_September_2010&action=edit 2] [http://2010.igem.org/wiki/index.php?title=Team:Panama/3_September_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=Team:Panama/4_September_2010&action=edit 4] [http://2010.igem.org/Team:Panama/5_September_2010 5]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/6_September_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=Team:Panama/7_September_2010&action=edit 7] [http://2010.igem.org/Team:Panama/8_September_2010 8] [http://2010.igem.org/Team:Panama/9_September_2010 9] [http://2010.igem.org/Team:Panama/10_September_2010 10] [http://2010.igem.org/wiki/index.php?title=Team:Panama/11_September_2010&action=edit 11] [http://2010.igem.org/wiki/index.php?title=Team:Panama/12_September_2010&action=edit 12]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/13_September_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=Team:Panama/14_September_2010&action=edit 14] [http://2010.igem.org/Team:Panama/15_September_2010 15] [http://2010.igem.org/Team:Panama/16_September_2010 16] [http://2010.igem.org/wiki/index.php?title=Team:Panama/17_September_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=Team:Panama/18_September_2010&action=edit 18] [http://2010.igem.org/wiki/index.php?title=Team:Panama/19_September_2010&action=edit 19]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/20_September_2010&action=edit 20] [http://2010.igem.org/wiki/index.php?title=Team:Panama/21_September_2010&action=edit 21] [http://2010.igem.org/Team:Panama/22_September_2010 22] [http://2010.igem.org/Team:Panama/23_September_2010 23] [http://2010.igem.org/Team:Panama/24_September_2010 24] [http://2010.igem.org/wiki/index.php?title=Team:Panama/25_September_2010&action=edit 25] [http://2010.igem.org/wiki/index.php?title=Team:Panama/26_September_2010&action=edit 26]
[http://2010.igem.org/wiki/index.php?title=Team:Panama/27_September_2010&action=edit 27] [http://2010.igem.org/Team:Panama/28_September_2010 28] [http://2010.igem.org/wiki/index.php?title=Team:Panama/29_September_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=Team:Panama/30_September_2010&action=edit 30]
October
MTWTFSS
        [http://2010.igem.org/wiki/index.php?title=Team:Panama/1_October_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=Team:Panama/2_October_2010&action=edit 2] [http://2010.igem.org/wiki/index.php?title=Team:Panama/3_October_2010&action=edit 3]
[http://2010.igem.org/Team:Panama/4_October_2010 4] [http://2010.igem.org/wiki/index.php?title=Team:Panama/5_October_2010&action=edit 5] [http://2010.igem.org/Team:Panama/6_October_2010 6] [http://2010.igem.org/Team:Panama/7_October_2010 7] [http://2010.igem.org/Team:Panama/8_October_2010 8] [http://2010.igem.org/wiki/index.php?title=Team:Panama/9_October_2010&action=edit 9] [http://2010.igem.org/wiki/index.php?title=Team:Panama/10_October_2010&action=edit 10]
[http://2010.igem.org/Team:Panama/11_October_2010 11] [http://2010.igem.org/Team:Panama/12_October_2010 12] [http://2010.igem.org/Team:Panama/13_October_2010 13] [http://2010.igem.org/Team:Panama/14_October_2010 14] [http://2010.igem.org/Team:Panama/15_October_2010 15] [http://2010.igem.org/Team:Panama/16_October_2010 16] [http://2010.igem.org/wiki/index.php?title=Team:Panama/17_October_2010&action=edit 17]
[http://2010.igem.org/Team:Panama/18_October_2010 18] [http://2010.igem.org/Team:Panama/19_October_2010 19] [http://2010.igem.org/Team:Panama/20_October_2010 20] [http://2010.igem.org/Team:Panama/21_October_2010 21] [http://2010.igem.org/wiki/index.php?title=Team:Panama/22_October_2010&action=edit 22] [http://2010.igem.org/Team:Panama/23_October_2010 23] [http://2010.igem.org/Team:Panama/24_October_2010 24]
[http://2010.igem.org/Team:Panama/25_October_2010 25] [http://2010.igem.org/Team:Panama/26_October_2010 26] [http://2010.igem.org/Team:Panama/27_October_2010 27] [http://2010.igem.org/wiki/index.php?title=Team:Panama/28_October_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=Team:Panama/29_October_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=Team:Panama/30_October_2010&action=edit 30] [http://2010.igem.org/wiki/index.php?title=Team:Panama/31_October_2010&action=edit 31]