April 2022. Author: Ataur Rahman
My PhD project aims to establish a novel basic knowledge of antimicrobial and antibiofilm compounds from rich marine sources in Arctic and sub-Arctic regions. This project applies a dual approach using marine bacteria for bioactive secondary metabolites and synthesized marine natural product mimics. Our aim is to find and evaluate exciting candidate molecules and document their potential for future drug development.
The discovery and characterization of such compounds may have the potential for clinical or industrial use. The work in this project involves a broad spectrum of experimental activities, from multi-omics to animal infection studies, and requires a good understanding of data analysis. I plan to conduct an RNA-seq experiment on bacterial biofilm, with and without novel antibiofilm compounds present, to determine the mechanism(s) of antibiofilm activity by observing the up- and down-regulation of genes. However, I did not have enough knowledge about the RNA-seq and how the RNA-seq data could be analyzed. When I saw that EMBL-EBI is offering a course on RNA-seq and IBA is funding the course, I applied and was lucky to get the funding for this course.
It was a five-day course starting from 21st February to 25th February this year. I was a bit anxious, as I did not have that much programming knowledge. The course was well designed with theoretical and practical sessions and was delivered by expert scientists from different parts of the world. The course participants were also from different countries. Although the course was held online, it was nice to meet new researchers who are also interested in learning about RNA-seq.
Previously, I planned to take service for the RNA-seq data analysis. However, now I am more confident in doing some coding and knowing different programs that I can use to analyze the RNA-seq data from my experiment. The author is grateful to IBA for funding, which helped to learn new techniques and meet knowledgeable scientists and future colleagues in RNA-seq. This course will help me assist with the functional analysis and interpretation of transcriptomic data that I plan to do in my PhD.