Wet Lab!!

General objectives

Uriel Laura Nando Abraham Paz

The final aim is to get and test the following device.

I. Biobrick Assembly of the Kamikaze system

Many cuts, pastes and clones for biobrick organization into the suicide system!!
In the hands of:
Abraham and Paz

II. Construction of the standardized P4 vector

An incredible and challenging fight against PCR and logical thinking!!In charge:
Nando and Paz

III. Construction of the P4-producing strain

A passionate struggle with natural selection and recombination!!
leading:
Uriel, Laura, and Miguel

IV. System testing and parameter obtention

The integrative side of the bite back
In the hands of: Laura (and Everyone else soon!)

Are you ready 2 rumble??

Personal Objectives

==== Uriel Urquiza ==== Uriel's Lab Journal

- Construction of the phage production control system.

  In order to produce a grate amount of P4 phage particles that has our death system, we want to avoid the natural
  early lysis that occur when WT P4 and P2 interact. This avoidance will be achieved by taking the control of the 
  two major regulators of P2 morphopoietic genes and deleting them form lysogenic P2, this will yield a P2 phage 
  which only has capsid and tail genes.  The control systems that is going to be implemented is constituted by a 
  promoter inducible by IPTG in conjunction with transactivators cox and ogr from phage P2. All this will 
  allow us to grow bacteria in grate quantities and induce lysis when ever we want and as a consequence a grate
  production of modified P2.

- Qualitative characterization of multipromter.

Laura Gomez

- To obtain all the relevant experimental information about T7 and T3.

 Model validation needs some critical parameters like strain(C1a) growth rate and the T3 and T7 burst sizes. The 
 parameters found in the literature correspond to k12 strain however we used a k12 derivative strain, C1a, for this 
 reason it was indispensable to obtain experimentally a C1a growth plot. In the same way, simulations
 showed us that the burst size is a critical parameter to determine the efficiency of our system.

- Generation of data to feedback the infection model.

 The experimental data would be used to feedback the model in order to obtain the most accurate model as possible.

Abraham Avelar

- Ensamble the kamikaze construction

 Clone the colicines with the multipromoter, design and Clone the asRNA and help in the ensamble of all the device.

- Test the construction

 Obtain the time that E3 takes to kill E. coli, this parameter will be provided to the model. The preference 
 for E3 above E9 is due to a modeling suggestion that shows the effectivity of our system when the translation
 machinery is disrupted, test the efficience of plaquing with the asRNA by itself and the efficience of all the
 device.

Fernando Montaño

====Assembly of the P4 vector.====

I must create an eternal bacterial source of P4 sid1. Therefore I must Infect C1a with it.
I need to develop a good protocol for P4 sid1 lysate production.
I must obtain the essential region of P4 sid1 by PCR. This will add the preffix and suffix to the region.

3) I need to ligate the "biobricked" P4 region to a reporter; better off RFP or a hard-resistance antibiotic.
Then, I have to transform to produce P4 (preferably with our stock producing bacterium) and infect wild-type strains to look for reporter-associated colonies.
(Also try in many bacterial strains)
4) When the kamikaze system is ready, I need to ligate the P4sid1 region to it and transform an E.coli C1a strain with it.
5) then we can start testing the system!
6) ultimate goal: standardize P4 as an iGEM vector.

Testing for activity of the control system

Uriel's cox and ogr construction needs to be tested experimentally to assureThe procedure will be:

1) Transform a P2 lysogenic strain with the construction. 2)assess IPTG induced lysis activation

Enrique Paz

- Desingn of our modified version of bacteriophage P4

What we need to do over P4 genome and how to do it in order to construct a bacteriophage compatible with standards
in synthetic biology.

- Construction and test of the gossip device (quorum sensing)

Some -a lot- restrictions, ligations, transformations, tests, etc. To achieve a high quality device for quorum
sensing that we will use for construction of our "alarm" system.

- Test the host range of our modified P4

According to litterature bacteriophage P4 has an unusual host-range. We would like to test it so we can transport
easily synthetic construction to another interesting bacteria species!