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Doing your own research

Jon Hale introduces his DaffDNA project
I’m John Hale. I’m head of biology at Beaulieu Convent School. And I’m also a part time PhD student at the University of Dundee. And it’s this link with Dundee that I’ve been able to share what was a very small school project with a group of schools across Scotland and studying the chloroplast genomes of nine different rare cultivars in what we call DaffDNA.
There’s around about 30,000 different varieties of daffodils. And what we’re doing as our kind of collective of schools this year is looking at just nine of them. We’re looking at the DNA found in every single one of these cells. But we’re focused in on what’s inside these green cells, inside the chloroplasts of the cell. So we take the DNA found within here, the chloroplasts own genome, and we’re trying to sequence it. Now, this makes a very, very small proportion of the entire genome of these cells. And that makes that an achievable outcome for the students. They can go and take away all of the DNA and extract it.
They can sequence it using a minION, which is very, very small, plugs into a laptop. Then we can assemble these chloroplast genomes of each of these nine very rare cultivars.
Initially, it was all about breaking down those topic silos of students typically do. They learn photosynthesis, they learn gene technologies, so I wanted something that would bring these things together– these difficult parts of the course– and really allow them to see the interconnectedness between these subjects. Students went out and they start to see different daffodils. They start to notice that they’re all daffodils. They see the similarities. But we wanted to look at the differences and really, really, really drive down into what makes these things different, what makes them unique. And that correlates with how they performed in the exams. They showed massive improvement in their knowledge of photosynthesis, in their knowledge of gene technologies.
But it was the little bit that I hadn’t foreseen that really impressed me. We had students really change their aspirations. We had students going from dentistry to natural sciences. We had history teacher aspirations changing to studying biochemistry at a top university. It’s these changes that really made me proud of this project.
So through STEM Learning UK– they introduced me to the Biochemical Society, the Royal Society of Chemistry, and the Royal Society as potential funders of the sequencing project. It was the latter, with the Royal Society’s partnership grant scheme, which is a really natural fit. It brings in scientists as well as the schools working together to make some tangible research happen inside schools. This grant gives the schools 3,000 pounds towards our project for equipment, and consumables, and sometimes time.
The bulk of the funds are largely spent with the mini PCR, which comes in with– they use plastic consumables like micropipette tips but also a blue gel electrophoresis tank, a thermocycler, and lots, and lots, and lots of micropipettes. Now, the other main part is the sequencer itself. The Oxford Nanopore MinION only costs about 900 pounds. And that gives the schools the ability to do five different sequencing runs, which is more than enough for their three cultivars. With an extension grant, they can then move towards a financially sustainable option and work with Flongle flow cells, which are much, much smaller and less wasteful in the grand scheme of things as well.
We saw a huge improvement in terms of their knowledge of gene technologies and genetics within the A-level course, these– historically the harder bits of the A-level course. But it’s their aspirations that I’ve really been proud of. They’ve wanted to become scientists. Their identity as scientists has improved as they’re contributing to scientific knowledge rather than just simply consuming it.
Prior to us starting our little DaffDNA project, there were three chloroplast genomes that were published on the database. We’ve now added five more chloroplast genomes that we can build this phylogenetic tree of life. We hope to be able to use this phylogenetic tree to work out the evolutionary history between these nine different cultivars in Scotland that are all very important when it comes to plant heritage.
Without hesitation, yes. It’s a fantastic opportunity for them to really understand that bioinformatics plays a massive part in our understanding of biology. And it will play a massive part in years to come. I think it’s important that students understand that sequencing isn’t just that– something to learn a textbook, but it’s something that they can really take part in.

Perhaps you and your students have already been involved in a research project and want to try your hand at setting up your own.

This can sound daunting, but thanks to easy-to-use lab kits, including those we discussed in week 1, this can be easier than it sounds. In this video, Jon Hale introduces his DaffDNA project that he runs with his students, and how he’s gained funding to support the project.

Would you have a go at a research project at your school?

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