Year: 2024

eDNA Monitoring and Jellyfish

Cheryl L. Ames from the US Naval Research Laboratory presented at London Calling 2019 on “Field-forward sequencing with Oxford Nanopore technology – a strategy to establish the upside-down mangrove jellyfish Cassiopea xamachana as a bioindicator.” They emphasized the biodiversity of the ocean is largely unexplored… and also threatened by climate change and overfishing. Environmental DNA […]
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Cleaning Up Plant DNA

Stella Loke from Deakin University in Australia spoke at London Calling 2019 about “Optimising plant DNA extraction for nanopore sequencing.” We are considering sequencing plant DNA this summer and, therefore, want to learn more about plant DNA challenges. Loke spoke about wanting the nano spec readings from Qubit to match the nano spectrophotometer. Loke confirms […]
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Fungi and Dog Skin

I started watching London Calling 2019 sessions to learn about fungal genomics and assembly. Sara D’Andreano from the Autonomous University of Barcelona in Spain gave a “lightning talk” on “MinION application: performing long-fragment analysis on pure fungal cultures (3.5 kb and 6 kb) and genome analysis of Malassezia pachydermatis.” D’Andreano is a Ph.D. student working […]
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The Applications of the Suitcase Lab

Tonight I watched a London Calling 2023 session by Ahmed Abd El Wahed from Leipzig University in Germany. The title of the session is “Pathogen and species identification using a mobile suitcase laboratory,” which aligns nicely with the course I am teaching: Portable Genome Sequencing (PGS). The recording had videos outside highlighting the suitcase lab. […]
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Sequencing in Extreme Environments Powered by the Sun

Tonight, I watched an Oxford Nanopore Technologies (ONT) video titled “Totally off-grid nanopore sequencing.” In April 2019, Glen Gowers and a group did an expedition to Vatnajokull in Iceland. They wanted to understand the invisible microbial world in extreme environments. The team had three members. The team did completely off-the-grid sequencing without backup energy. They […]
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Reticulatus

Samuel Nicholls from the University of Birmingham in the UK presented at London Calling on “Long-read nanopore metagenomics for reconstruction of bacterial genomes.” They spoke about the impact of microbial communities on human health and the difficulties we encounter trying to culture some microbes. Nicholls and team published a study sequencing the Zymo mock communities. […]
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User-friendly Computational Workflows

Tonight I watched the EPI2ME updates from Matt Parker, Associate Director of Clinical Bioinformatics at Oxford Nanopore Technologies. We will use EPI2ME next week as part of the Portable Genome Sequencing course, focusing on bacterial genome assembly and metagenomics. This Nanopore Community Meeting Houston update started with a high-energy EPI2ME video highlighting updates to compute […]
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Ultra-long Reads for Sea Snake, Lizard, and Dragon Genomes

I have been reading about the Ultra-long Sequencing Kit from Nanopore to try it this summer. Tonight I found the Ultra-long Reads YouTube playlist from ONT. I watched the session by Jillian Hammond from the Garvan Institute of Medical Research in Australia. They presented on the use of Ultra-long Reads for Australian Reptiles. They noted […]
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Primer Pools and Phylogeographic Analyses

Today we started sequencing in the Portable Genome Sequencing course! We used several Flongle flow cells on the MinION run. I watched the session by Kame A. Galan-Huerta from the Autonomous University of Nuevo Leon, Mexico, tonight. They presented at the Nanopore Community Meeting 2022 on “Identification of resistance mutations to direct-acting antiviral agents against […]
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Fungal-Bacterial Interaction Screens and Plant Pathogens

Manuel Anguita Maeso, a Ph.D. student at the Institute for Sustainable Agriculture at the CSIC in Spain, spoke at the Nanopore Community Meeting 2021. The session’s title was “Unravelling the whole genome of olive antagonist xylem-inhabitant bacteria to fight vascular plant pathogens in olive trees.” I had watched this session previously and wanted to learn […]
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