Difference between revisions of "Team:Valencia UPV/Results"

Goals

At the start of the Printeria project, the different members of the Valencia_UPV team set themselves objectives in their respective areas to promote the automation of the cloning process and thus bring synthetic biology closer to the people.

Wet Lab

• Create a standardized Golden Gate basic Parts Collection to supply Printeria with the DNA toolkit to assemble composite parts.

• Provide Printeria with the best way to transform competent bacteria with the highest transformation efficiency rate.

• Avoid the plate colony screening step in order to eliminate the necessity of the researcher visual check, so easing Printeria automation.

Hardware

• Integrate multiple lab equipment around an automated friendly form.

• Design an easy way of handling a big variety of input liquids providing a straightforward integration with Printeria.

• Design an easy to use way of handling a big variety of input liquids with easy integration of the machine.

• Keep the footprint of the machine as small as possible.

• Allow for maximum flexibility on the use of the machine.

Software

• Develop a software that allows the user to control the device.

• Allow the user to design a transcriptional unit with the software.

• Allow the user to design multi-genetic constructions with the software.

• Get non-professional users to print basic genetic circuit.

• Fill out a “recipe” repository with at least 20 recipes.

• Make a user friendly interface to interact with the software.

• Control the device’s inventory through the software.

• Simulate the bacterial growth and the protein expression.

Modeling

• Design simple mathematical models based which allows us to simulate the different Printeria genetic circuits.

• Optimize model parameters to match simulation results to experimental data obtained from Printeria.

• Characterize the parts of our Part Collection from the optimization results and provide the user with all the information about the Printeria kit.

• Develop a Simulation Tool that allows the user to visualize a prediction of the results of their experiment before running it in Printeria.

Results

Once the project was finished, the conclusions reached after our experiments were the following:

Wet Lab

• We have built a complete Part Collection of standardized Golden Braid 3.0 basic parts. It is a fully functional DNA collection with extensive characterization of its parts, so providing the user with useful data to work with.

• We found that the most suitable way to transform bacteria for Printeria is to electroporate electrocompetent cells previously stored at -20ºC and subsequent maintained at 4ºC during the assembly step.

• We proved that the assembly of composite parts using the destination vector in its linearized form significantly reduces the number of bacteria carrying the non-recombinant plasmid (false-positives colonies). However, in order to obtain a pure culture, it will always be necessary to go through the screening plate step.

Hardware

• Laboratory equipment has been designed around digital microfluidic technology. Giving the machine a great degree of control over the processes that occur inside. This equipment includes a thermal cycler and an electroporator.

• The entry system of Printeria allows for quick placement of all the necessary consumables. In addition, it can be further customized for any kind of liquid.

• Thanks to the use of Digital Microfluidics Printeria can produce all the reactions in a small space.

• All parts of the machine have been designed with individual use in mind.

• Sensors have been included to monitor bacterial growth.

• A functional, economical and easy-to-use solution has been achieved.

Software

• We developed Printeria Controller, a web application capable to control all the functions of our device.

• Through the application it is possible to select all the DNA parts needed to design a transcriptional unit.

• We didn’t implement the multi-genetic circuit constructions because the team considered this construction will be part of the future of printeria.

• A non-experienced user can print a genetic circuit already created and stored in our recipe repository.

• We created a database with 27 recipes assembled with our basic parts using the Golden Gate technology.

• The clean and explicative interface of our software allows both experienced and non-experienced users to navigate through all the options.

• In the Inventory tab of the software it is possible to know which cartridges have been drained and register when they are filled.

• With the modeling team we developed a simulation tool that allow us to predict the results.

Modeling

Considerations for replicating the project

Future plans