Team:Panama/Notebook

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Republic of Panama

Situated on the isthmus connecting North and South America, it is bordered by Costa Rica to the northwest, Colombia to the southeast, the Caribbean Sea to the north and the Pacific Ocean to the south.

iGEM PANAMA

In this picture: Carolina, Yisett, Claudio, Nicole, Lorena, Grimaldo, Natasha, Laura, Ernesto, Dra. Carmenza, Dr. Rao, Ezequiel

iGEM PANAMA

In this picture: Yisett, Silke, Yaraví, Carlos, Dr. Patrick Nee.

iGEM PANAMA

In this picture: Leyda, Zeuz, Laura

iGEM PANAMA

Labs.

Notebook

Idea Project

Development of a genetically engineered E. coli that can produces the rhamnosyltranferase 1, for the production of a biosurfactant.

Steps to follow: 1.Find the gene sequences in pubmed. 2.In which bacteria is found. 3.After we found the gene, we designed two different set of primers. 4.Look for the sequences of the restriction enzymes E, X, P and S, inside the gene sequence. 5.If we found in the gene sequence a recognition sequence for the restriction enzymes. 6. So we should look for a mutagenesis protocol or kit. 7.We choose the Stratagene lightning mutagenesis kit. We also design three different set of primers, because the base pairs that surround the PstI unwanted sequence were different.

Meeting July 21

Meeting June 26

At this moment we have two ideas for develop. We are debating which idea is more feasible. Idea #1: Carlos´s team idea We want to produce Rhamnolipid in bacteria (E.coli) to use it as a biosurfactant. We have to see how we can isolate the rhamnolipid, and be sure that the translation is functional.

Ernesto's Idea

Steps to follow:

1.Amplified the Rhamnosyltransferase 1 complex from Pseudomona auruginosa and clone this fragment. Size aprox 2.2 Kb. 2.Ligation / Transformation 3.Expression with reporter gen. 4.Isolation 5.Is the protein functional? 6.Make sure that the rhamnolipid is produced in prescence of rhamnose and fatty acid.

Notes:

We can see the reaction (enzymatic measure) by spectrometry. See kind of ligation.

But first, before the amplification we need to design our primers.

Primers design:

1.Check the gene sequence (In GenBank, FASTA format) 2.Design the primer sequence. 3.See kind of cloning. 4.M13 tail for cleavage site. 5.Look for cleavage site inside the rhamnosyltransferase 1 gene for our restriction enzymes. We can´t cut our gene in the process.

In summary the steps that we need to follow are:

I.Primer design II.PCR or amplification III.Cloning IV.Expression V.Sequencing

The most important steps are I and II. We need a good primers design and PCR if we want to have successful.

Idea #2 Ernesto team´s idea

Production of Cecropin compound. We want to produce the antibacterial cecropin compound. Naturally is produced by insects and plants.

We want to use Anopheles gambiae, cecropin precursor. The gene is about 550 pb.

The steps to follow are the same in both groups. Both groups have to design the primers, and have all the experimental design for this week.

1.The sequence of the interested gene. 2.Design the primers. (50-100pb more at the beginning and end of the sequence). 3.Check for cloning sites. Which plasmid we are going to use, identify the restriction enzymes. 4.Assemble the blocks. In paper assemble all the system. Promoter + Ribosomal binding site + interest gene + reporter gene + translation end site.

All the design has to be on paper to analyze them and decided which idea is going to be the elected one.

Wetlab 103: Let's make an E. coli that fluoresce (or some simple BioBrick project)

• Instructor: INDICASAT, Dr. Carmenza Spadafora
• Date: (17h00-20h00 11th of June)
• Venue: INDICASAT
• 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.

INDICASAT	INDICASAT	INDICASAT	INDICASAT
INDICASAT	INDICASAT	INDICASAT	INDICASAT
INDICASAT	INDICASAT	INDICASAT	INDICASAT

Wetlab 102: Let's raise a few E. coli

• Instructor: Lorena Coronado and and Dr. Carmenza Spadafora
• Date: (17h00-20h00 11th of June)
• Venue: INDICASAT
• Description: How does one handle E. coli?

Wetlab 101: Tools of the lab and their use

• Instructor: Dr. Patricia Llanes
• Date: (17h00-20h00 9th June)
• Venue: INDICASAT
• Description: How to handle pipettes, clean test tubes, etc.

iGEM workshop follow up: Safety, ethics

• Instructor: Dr. Ricardo Lleonart
• Date: (17h00-20h00 9th of June)
• Venue: INDICASAT
• Description: There is definetly a "safety considerations" requirement and we should address it early.

Dr. Ricardo Lleonart	Dr. Ricardo Lleonart

iGEM workshop follow up: Software tools

• Instructor: Patrick / Sara
• Date: (17h30-20h00 Monday 7th June)
• Venue: INDICASAT
• Description: Software tools available from the workshop.

Dra. Sara Pinzon

DNA 104: BioBricks Protocol

• Instructor: Sara/Patrick
• Date: (17h30-20h00 Monday 7th June)
• Venue: INDICASAT
• Description: Introduction to the BrioBricks protocol

Dr. Patrick Nee

Dr. Patrick Nee

Dr. Patrick Nee

INDICASAT lecture: Innovation

• Instructor: Dr. Jagannatha Rao, Director of INDICASAT
• Date: (17h30-20h00 Friday 4th June)
• Venue: INDICASAT
• Description: Dr. Rao's lecture on how to innovate.

INDICASAT lecture: Drug discovery in nature

• Instructor: Dr. Sergio Martinez
• Date: (17h00-20h00 Thursday 3rd June)
• Venue: INDICASAT
• 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!...

DNA 103: DNA modification, plasmids

• Instructor: Dr. Abby Guerra
• Date: 26 May 17h00-20h00
• Venue: UTP
• Description:Introduction to long tested combinant DNA techniques, the role of plasmids in bacteria, and their use as a vector for DNA modification.

Dr. Abby Guerra

Dr. Abby Guerra

Dr. Abby Guerra

DNA 102: Protein creation relationship to cellular function. 26 May

• Instructor: Dr. Abby Guerra
• Date: 26 May 17h00-20h00
• Venue: UTP
• Description: Introduction to how DNA drives cellular functions by creating proteins

Dr. Abby Guerra

Dr. Abby Guerra

DNA 101: Information store, replication. 26 May

• Instructor: Dr. Abby Guerra
• Date: 26 May 17h00-20h00
• Venue: UTP
• Description: A basic refresher course on how DNA stores information in the cell, and how it is involved in cellular replication.

Dr. Abby Guerra

Dr. Abby Guerra