REPARES Seminar 1
Delft, January 20-22, 2020
Impact of DNA extraction from environmental samples on DNA quality and molecular analytical outputs
Together with David Calderón Franco and Ben Abbas, we organized on January 20-22, 2020 at Delft University of Technology the 1st REPARES seminar on the “Impact of DNA extraction from environmental samples on DNA quality and molecular analytical outputs”. On this event, we conveyed 10 young professionals from UCT Prague, UC Porto, Wetsus, and the TU Delft to speak about DNA.
In the science and engineering of wastewater treatment systems, we often use DNA-based analyses to characterize microbial communities and their features like antibiotic resistance genes. However, we seldom speak about DNA per se. Molecular procedures and workflows are taken as granted. However, these are subjected to substantial biases that need to get handled with definite quality control. Specific questions of the in-class and in-lab seminar targeted (i) how we can extract it from complex biological samples like activated sludge, (ii) to which extent the extractions workflows do impact on the outputs of the analytical measurements made on DNA templates, and (iii) how molecular workflows can be harmonized for repeatable and reproducible outputs. Participants could learn and exchange from seminar room to wet-lab hands-on.
We had the opportunity to broaden our perspectives by hosting three invited lecturers. Bruno Bicudo Pérez, Ph.D. candidate at the TU Delft Sanitary Engineering Section brought us on the “Electrocoagulation as a technology to remove microbes from municipal effluents, and associated analytical challenges”, a project that he conducts in the Dutch-Indian international framework LOTUSHR to clean up and recover water and resources from the Barapullah drain in New Delhi. Dr. Ron Dirks, CEO of Future Genomics Technologies in Leiden provided insights on “Fast DNA analyses of environmental samples using Oxford Nanopore sequencing technologies”. Asst. Prof. Thomas Abeel from the TU Delft Bioinformatics Lab went forward on the underpinnings of “Genomics of antimicrobial resistance and DNA quality”.
Asst. Prof. David Weissbrodt
Delft University of Technology