Team:Panama/Modeling

From 2010.igem.org

Revision as of 20:33, 6 July 2010

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Notebook

DNA 101: Information store, replication. 26 May

• Instructor: Dr. Abby Guerra
• Date: 26 May 17h00-20h00
• Venue: UTP

A basic refresher course on how DNA stores information in the cell, and how it is involved in cellular replication.

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

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

DNA 103: DNA modification, plasmids

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

INDICASAT lecture: Drug discovery in nature

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

INDICASAT lecture: Innovation

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

DNA 104: BioBricks Protocol

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

iGEM workshop follow up: Software tools

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

iGEM workshop follow up: Safety, ethics

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

Wetlab 101: Tools of the lab and their use

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

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 How does one handle E. coli?

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 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.

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. First we have to be sure that our idea is not the same that the idea published in the reference paper. We want to make a biobrick to produce Rh1. 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 to clone the 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. Decided if we are going to use sticky or blond ends. (Depend on the plasmid).

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

Primers design:

1.Check the gene sequence (In GenBank, FASTA format) 2.Check 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 begging 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.