Continuing with London Calling 2022 recordings, tonight I watched Marissa Le Lec from the University of Otago in New Zealand and Lara Urban from Helmholtz Munich, Germany speak about “Portable real-time sequencing to safeguard critically endangered wildlife.” They spoke about mammalian predators including domestic cats affecting bird diversity. Le Lec spoke about the kākāpō, a flightless parrot endemic to New Zealand. Their population is 197! The species breeds every 2-4 years. Intensive conservation management has been implemented. The chicks are carefully weighted and checked often. The team has used artificial insemination to increase representation. The team wanted to “develop and deploy a rapid test for parentage and sex.” They decided to do this with portable Nanopore sequencing equipment. The protocol had to be accessible to people not familiar with molecular biology. Le Lec first asked how much data? They downsampled a data set and determined about 1 Gbase is enough. They packed everything into a portable lab setup and then collected blood samples (~ 5 ul) for DNA extractions. The team used the QIAGEN spin-column based purification and the Bento Lab setup. The Oxford Nanopore Technologies Rapid library prep kits were used to determine sex and parent results for chicks. Le Lec noted that artificial insemination worked! Urban spoke about the research as a Humboldt Research Fellow in New Zealand. Their interest was in epidemiology and learning about an Aspergillus fumigatus affecting the kākāpō. They used Copan eSwabs and extracted fungal DNA. They used a handheld pestler and glass beads for lysis. Urban swabbed chicks in the field and used the NVIDIA Jetson AGX for live basecalling and adaptive sampling in the field! They even tried adaptive sampling to deplete host reads and focus on Aspergillus. Urban is interested in eDNA and is setting up a research group. I did not know about the Bento lab and NVIDIA Jetson AGX! This was a fascinating talk! They took a helicopter to an island, monitored nests, and used portable lab equipment. It is also interesting that chicks have a baseline load of Aspergillus.
