Education Corner

Suzanne Duce, Ph.D.

Suzanne Duce has a PhD in magnetic resonance imaging (MRI) from the University of Cambridge. She was awarded a Wellcome Trust Re-entry Fellowship in 2007 at the University of Dundee to use MRI to visualize aspects of developmental biology and study disease aetiology and treatments. Since 2014, Suzanne has been the Jalview and Dundee Resource Outreach and Training Officer at the School of Life Sciences. In addition to running hands-on training workshops, she has produced a range of Jalview training videos hosted on YouTube and Vimeo. The Jalview YouTube Online Training channel has had over 90,000 views from more than 140 countries, attracting in excess of 550 subscribers.

Suzanne has participated in a wide range of public engagement activities. She helps organise ‘Open Doors’ days at the University of Dundee, has taken part in the International Society for Neglected Tropical Diseases Festival in London and supports primary and secondary school STEM events. This year she won the School of Life Sciences’ Brian Cox Public Engagement Project of the Year award for her outreach work with Jalview.

Suzanne is interested in exploring the different media available for science communication. In addition to making science-related videos, she has published science-themed children’s books and comics, including the illustrated book ‘Kirsty’s Project: Searching for a New Medicine’. Her Sci*Art and photographs have been exhibited in galleries across Dundee, and also in London. One of these images was featured on the front cover of the Journal of Medicinal Chemistry.

Suzanne can be contacted at s.duce@dundee.ac.uk.

As most of the elements that make up cells are microscopic and cellular processes are complex, cell biology can be difficult for High School pupils to grasp. One solution is to let students view and interact with DNA, RNA and proteins, the fundamental building blocks of cells, for themselves by using visualization software such as Jalview¹.

For example, Jalview’s interactive, multiple window interface allows the sequence and 3D structure of a molecule to be viewed side-by-side. Jalview has a number of analysis tools and it can compare sequences and produce trees, enabling evolutionary relationships to be explored. Furthermore, Jalview’s ability to view the DNA of a specific gene alongside the sequence of the protein that it codes, allows the genetic mutations linked to diseases to be identified, and their position on the protein structure located.

The idea that this highly visual bioinformatics research tool could help schoolteachers introduce 15-18-year olds to the fundamental molecules in biology was the motivation that prompted Suzanne to study the Scottish and English High School biology syllabuses. The challenge was to try and produce a series of easy-to-use, hands-on Jalview-based exercises that secondary school biology pupils could complete by themselves. The aim being that these worksheets would help reinforce the principles being taught in the classroom. Jalview has two key features that make this possible. First, Jalview is relatively easy to use. A complete novice can quickly start using Jalview if some brief instructions are provided. Second, the Jalview team with the help of Prof Bob Hanson at St. Olaf College, Minnesota have recently developed a JavaScript version of Jalview called JalviewJS. JalviewJS can be launched from a web-link and runs in a web browser. It does not require any software to be downloaded. Consequently, all that is needed to run these bioinformatics practicals is a desktop or laptop computer with a web browser and internet access.

After some initial testing, the exercises were collected together in a booklet entitled Visualizing DNA, RNA & Proteins Jalview School Workbook². The workbook contains four practical projects. Project 1 views a fragment of DNA and an RNA sequence alongside their 3D structures. Project 2 allows students to view the different classes of proteins alongside their structures. Project 3 compares the sequence of the human myoglobin protein with myoglobin sequences from other animals. The student can then view the coding DNA sequence, and codons, alongside the myoglobin protein sequence in a split-screen view. In Project 4, students view the exons and introns in the human haemoglobin subunit b (HBB) gene. This is the gene involved in sickle cell anaemia, an inherited red blood cell disorder which affects millions of people throughout the world³. Pupils can identify the genetic mutation linked to this disease by viewing the HBB gene’s coding DNA and protein in Jalview’s split-screen DNA and protein alignment view.

Much thought has been invested in the design and layout of the workbook. University of Dundee graduates Dmitry Finkelbergs and Charlotte Campbell helped Suzanne explore aspects of usability in education during their Science Communication final year honours projects. One thing was clear, since teachers have little spare time, the guiding design principle for the materials should be to facilitate independent learning. The learning objectives are displayed in coloured boxes at the start of each exercise. The majority of the workbook is taken up with instructions. Since we know that people assimilate information in different ways, the instructions are arranged in two columns. The first column contains text that describes each step, whilst the second contains annotated screenshots that illustrate them. If the student needs extra help, there are a variety of videos available including walk-through videos. Each project also includes questions at different stages to encourage the student to think about the biology that underpins the exercises. There is an appendix at the back of the workbook with extra information to help answer the questions and directs pupils to other sources of information.

All the materials are available from the schools webpage⁴ on the Jalview website. This page includes links to open the workbook, launch JalviewJS and run the exercises. As bioinformatics is often considered to be complicated, the practicals have been made as straightforward as possible. They can also be completed by pupils at home as well in the classroom, thanks to Suzanne’s guiding design principles. Getting started requires three simple steps: (1) Open the schools webpage⁴ on the Jalview website; (2) Click the ‘View the School Workbook’ link to open the booklet² in an adjacent window (or download the PDF depending on the web browser); (3) Follow the instructions in the workbook. The links in Section 2 on the webpage start the exercises; they launch JalviewJS and display the sequences automatically.

Testing has been integral in the design process. In December 2019, Ben Soares, one of Jalview’s developers, accompanied Suzanne on a visit to a nearby school: Forfar Academy, in Angus, where National 5 biology⁵ pupils worked through the exercises. Their feedback allowed the team to improve the design of both the workbook and the website. One of these improvements was to use Jalview’s command-line arguments to simplify the start-up step. For example, in Project 1 and 2, PDB files open in JalviewJS as it launches. More school visits are being organised, but the Covid-19 lock-down has complicated these plans. Going forward, the team will run some of the school visits remotely.

A similar design was used to produce worksheets suitable for primary school children (5-11 years old). These have proved very popular at public science outreach and school events. One worksheet lets pupils view the protein extracted from a fossil of the T-Rex dinosaur⁶. Another compares the sequence of osteocalcin protein extracted from Neanderthal bone fossils⁷ with osteocalcins from other animals including humans. The team often take some of the excellent PDB-101’s Learn educational material⁸, such as the paper models and colouring sheets, to these events.

The Jalview School Workbook uses data from the Protein Data Bank (PDB) to run several of the exercises. It also includes links to the PDB-101’s Molecule of the Month webpages⁹. These articles are informative and visually appealing and thus great resources for an inquisitive mind. In fact, it is the team’s hope, that after a student completes the practical exercises in the Workbook that they would be inspired to branch out and investigate more of the molecules found in nature. The educational resources in PDB-101 make an excellent springboard for further study.

Citations

1. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25 (9): 1189-1191 (2009). doi: 10.1093/bioinformatics/btp033
2. https://www.jalview.org/sites/jalview.org/files/Jalview_Schools_Workbook_9June2020.pdf
3. https://www.cdc.gov/ncbddd/sicklecell/facts.html
4. https://www.jalview.org/school-resources
5. https://www.sqa.org.uk/sqa/47427.html
6. Asara JM, Schweitzer MH, Freimark LM. Phillips M, Cantley LC. Protein Sequences From Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 316 (5822): 280-285 (2007). doi: 10.1126/science.1137614
7. Osteocalcin Protein Sequences of Neanderthals and Modern Primates. Nielsen-Marsh CM, Richards MP, Hauschka PV, Thomas-Oates JE, Trinkaus E, Pettitt PB, Karavanic I, Poinar H, Collins MJ. Osteocalcin Protein Sequences of Neanderthals and Modern Primates. PNAS 102 (12): 4409-4413 (2005). doi: 10.1073/pnas.0500450102
8. http://pdb101.rcsb.org