BLT Stages

Abstract 2020-2021: AUTOMATIZATION OF DIFFERENT METHODS WITH THE OPENTRONS OT-2, QUANTIFICATION OF BACTERIAL COLOR PELLETS AND INTEGRATION OF A PLASMID PRIMER ENZYME STRAIN DATABASE

This Abstract describes several projects. The first one is the automatization of different methods with the Opentrons OT-2, the next one is the quantification of bacterial color pellets and the last one is the integration of a plasmid primer enzyme strain database.

The Opentrons OT-2 is an open-source pipetting robot, recently introduced into the lab. To increase the usage of this device several scripts have been written that can be used by the laboratory technicians to automate several steps in routine methods. Two kinds of scripts have been made for routine method. The first method is to distribute a certain amount of liquid to a whole tube rack/well plate or selected tubes/wells. The second kind is a script that will make a dilution series where every parameter can be changed depending on the situation. Additionally, a script was written specifically for automating the loop assembly method. These scripts will prompt usage of the OT-2 for routine methods in the lab.

In a collaboration with UPCH (Lima, Peru), the Open BioLab Brussels has altered E.coli cell to behave as a whole cell biosensor that renders blue when detecting Mercury. In order to quantify the bacterial color pellets the need for a device that can calculate the RGB values of the pellets emerged. Liljeruhm et al., 20181 describe such a tool in the supplemental figures, but with limited info. Hence, we engineered and built our version.

Under a custom 3D printed Eppendorf holder, a Raspberry Pi High Quality Camera with 3MP 6mm lens was mounted. and connected to a Raspberry Pi model 4b on which our script runs. The script written for this project will take a full picture of the bacterial pellet and subsequently takes a 10x10 pixel close-up picture of a preselected part of the full picture. Next all the RGB values of every pixel are stored in a dedicated list, where the list is sorted to get the median and the standard deviation. All this information is then stored in a csv file. Whilst running the script in the beginning the user will have to name the folder where everything will be stored and name the csv file. During the script, every sample is named by the user before processing. All pictures and the output file are then saved into one folder and this folder is uploaded to OneDrive by using a bash script. So with this custom made construction and script, a bacterial color pellet can be photographed, all RGB values stored and all information that is needed for quantification is delivered to the laboratory technician in a csv file on the OneDrive. 

The last project is the integration of a plasmid primer enzyme strain database. The Open BioLab Brussels has a database in excel but desires a database that can integrate barcodes to be used with a labscanner that will be purchased in the future. So, when the barcode is scanned of a tube, all information is given to the user. Here the project consists of two parts. First all excel tables of the laboratory are converted to tables of a database, but there is no connection between them. Next is the implementation of barcodes into this database. Second part is that a barcode generator is made that can label every sample in all tables and that can interact with the database. Because of lack of time this project is not finished, only all tables are placed into a database and a barcode generator is made that works in excel, here the number it needs to generate the barcode can be random or the date of registration.