Team:Valencia UPV/Results
Goals
At the start of the summer, 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