London Calling 2021 online: what's new this week?
Tue 6th April 2021
There are just six weeks to go until London Calling 2021 online (19th-21st May), and from now until the big event, we’ll be sharing a weekly preview of what’s to come from the latest additions to our speaker line-up. For more details on the talks announced so far, covering everything from clinical research to environmental metagenomics, take a look at the agenda here. The conference is totally free to attend – simply register here to get set up.
For this week’s round-up, here are five speakers who are using nanopore sequencing in their work to advance the frontiers of scientific research.
How is nanopore sequencing unveiling the impact of HPV integration in cervical cancer?
Understanding the consequences of human papillomavirus (HPV) integration on the human genome is crucial to the development of novel therapies to treat cervical cancer – the number one cause of cancer-related mortality for sub-Saharan African women. In her plenary talk, Vanessa Porter will share how nanopore sequencing has enabled her team at the University of British Columbia, Canada, to resolve these previously intractable viral and host genomic consequences – including DNA methylation, haplotypes, and complex structural variants.
What do whale snot, drones, and nanopore sequencing have in common?
To better understand events linked to ecosystem changes, Eric Bortz and a team of research students at University of Alaska Anchorage, USA, used a combination of MinIONs and drones - affectionately known as ‘snotbots’ - to collect and sample respiratory vapour from humpback whales, identifying various bacteria and eukaryotes in the process. Rapid nanopore sequencing of a wide variety of environmental samples - including stranded marine mammals, seabird survey samples, and sediment (in addition to whale snot) - allowed for metagenomic analysis of low-quantity sparse samples obtained in the wild, providing data valuable in the identification of hallmarks of environmental change.
Tackling antimicrobial resistance with a MinION
Antimicrobial treatment is an essential method of disease control. However, the effectiveness of antimicrobials has decreased in recent years due to the emergence of antimicrobial-resistant strains representing a significant clinical challenge. Understanding the drivers of antimicrobial resistance (AMR) is therefore critical to overcoming this burden to public health. Genetic processes such as copy number variation have been implicated in the evolution of resistant microbes, but are difficult to investigate. Using a MinION, Elizabeth Skippington (Genentech, USA) sequenced bacteria resistant to a novel antibiotic and successfully identified the resistance mechanisms at play, including copy number variation.
Microbes & MinIONs, continued: predicting the impact of environmental changes
Stromatolite fossils provide a record of one of the first forms of life on planet Earth. Establishing how these ancient microbial communities responded to extreme environmental changes in the past will likely help us predict the impact of extreme weather events in the future. In the Environmental Metagenomics breakout session, Nicole Wagner (Georgetown University, USA) will demonstrate how metagenomic and metatranscriptomic analyses of Antarctic samples sequenced on a MinION reveal the community structures, metabolic activity, and survival mechanisms of these fascinating ecosystems.
A top tip for growing plants from a MinION user?
Guar gum, extracted from the legume (you guessed it) guar, has a range of industrial applications, from its use in the food industry as a stabiliser to being a central agent in petrochemical development. The nitrogen-fixing bacteria in this legume’s roots also make it critical in the process of field rotation between harvests. Sensitivity to long light cycles, however, have thwarted efforts to cultivate the crop in the Northern hemisphere, where long days are typical of the growing period. Identifying the genes important in generating hybrid plants using short-read sequencing have so far been unsuccessful. Using a MinION, Elizaveta Grigoreva (Saint Petersburg State Forestry University, Russian Federation) employed a hybrid approach to sequence and assemble the guar genome. By enabling genome-guided guar transcriptome assembly, nanopore sequencing has unlocked the first step towards finding hybrid strains capable of thriving in the northern hemisphere.