Bioinformatics: the power of computers in biology

First workshop of the week, Anderson High School, Lerwick. L-R: Daniel Barker (Edinburgh), Yu-Hsin Tseng (Edinburgh), Mike Ritchie (St Andrews), Nicola Cook (St Andrews)

Research staff from the School of Biology in collaboration with colleagues from the University of Edinburgh visited every secondary school in the Shetland Isles over the course of a week in early November 2018. Dr. Nicola Cook and Professors Michael Ritchie and Thomas Meagher from the University of St Andrews and Dr. Daniel Barker and colleagues of the University of Edinburgh delivered a series workshops to pupils to demonstrate “the power of computers in biology”.

This series of workshops on Shetland is part of a larger effort being undertaken by the 4273π project (http://4273pi.org), spearheaded by Daniel Barker at the University of Edinburgh. Bioinformatics is touched on only briefly in the Higher Biology curriculum and 4273π aims to take this seemingly abstract concept and make it tangible to school pupils and teachers across Scotland via hands-on practical sessions. Importantly, these workshops illustrate how the emergent field of bioinformatics is now key to many areas of biology to manage the large datasets that scientists are producing. For many of us this means storing and analysing DNA sequences.

Higher Biology and Higher Human biology pupils used bioinformatics to analyse a “mystery DNA sequence”, using publicly available databases to find information regarding its function, and then made inferences about its evolutionary history and the ecology of the animal the sequence originated from. Pupils worked in a familiar web-based environment and then moved onto working at the command line, using Linux on raspberry pi computers (https://www.raspberrypi.org/).

Stevie Bain (Edinburgh) and Nicola Cook on the ferry to from Mainland Shetland to Yell to deliver a workshop at Mid Yell Junior High School.
Anderson High School, Lerwick.
Out and about on the Shetland Mainland! L-R Daniel Barker (Edinburgh), Stevie Bain (Edinburgh), Nicola Cook (St Andrews), Yu-Hsin Tseng (Edinburgh) and Mike Ritchie (St Andrews).

Dolphins learn from each other to walk on water

While it is well known that dolphins are easily trained to perform tricks, a new 30-year study, led by Whale and Dolphin Conservation with the universities of St Andrews (Dr Luke Rendell) and Exeter, reveals dolphins also learn tricks from each other in the wild.

The research, to be published in the Royal Society’s Biology Letters, focused on a scientific analysis of Adelaide’s famous tail walking dolphins. The paper described how tail walking was learned by a single dolphin called Billie, copied by other dolphins in the local community, and then apparently fading out over time.

You can read more on the university news web page or in today’s email edition of In-the-Loop, or listen to Luke’s Wednesday morning BBC4 interview (47.50 minutes in) with Nick Robinson.

Royal Society of Biology in Scotland Outreach Champion 2018

Congratulations to Evelyn Sutiono who won the Royal Society of Biology in Scotland Outreach Champion Award 2018. The Outreach Champion Award competition is open to all final year undergraduates studying a Biological Science subject in Scotland, and who have participated in public engagement.

The standard of competition applications this year was extremely high, however, Evelyn’s involvement with a range of public engagement events across the School, across disciplines, with local schools and with the wider public was truly exceptional. Evelyn, will receive her award at the 2018 Science in the Parliament event at Our Dynamic Earth, Edinburgh, in November.

Strathkinness Cubs measure a minke


Researchers from SMRU (Debbie Russell) and CREEM (Catriona Harris) spent an evening with Strathkinness Cub Scouts helping them work towards their Scientist Badge. 
 
There was lots of fun with whale and seal skulls, whale sounds, identifying individuals with the SMRU photo-ID matching game and seeing how big a minke whale really is. 
 
We also played some games demonstrating noise pollution and learnt how hard it can be for animals to communicate when humans are so noisy!
 

School of Biology Public Engagement and Outreach awards

These awards aim to mark the outstanding contributions of our staff, postgraduate and undergraduate students, whose voluntary dedication to communicating science to the public are not always recognised.

We are pleased to have made four awards in this first round, highlighting the scope of activities undertaken at the School of Biology.

 

Sophie Harrower

Sophie is currently completing her degree in Biology, and plans to become a school teacher. She is passionate about widening access and is heavily involved locally in Fife, mentoring school pupils from low attainment schools. She participates actively in the University of St Andrews First Chances programme as well as the Reach project and Space School.

 

Evelyn Sutiono

Evelyn is a fourth year undergraduate student in Cell Biology.  As President of the Biology Society, she has led a number of events aimed at engaging both non-science students and the public. She also created a science illustration booklet with fellow student Alex Gilmore to introduce biomolecules to schoolchildren. Evelyn plans to continue working in science communication after she graduates.

 

Frances Entwistle

Frances is completing a PhD in Dr Peter Coote´s lab, looking at using wax moth larvae as an alternative model organism to study mycobacterial infections. She has been involved since its inception with Cell Block Science, a programme that helps promote STEM (Science, Technology, Engineering and Mathematics) in local prisons, and has been active in the Sutton Trust Summer School, Explorathon and the XX Factor. She has also worked with the “Retirement is Opportunity” schemes for adults and retirees.

 

Dr Monica Arso Civil

Monica is a research fellow at SMRU (Sea Mammal Research Unit) whose work focuses on the monitoring of marine mammals, such as bottlenose dolphins and harbour seals, around Scotland to inform conservation efforts.  This requires strong ties and communication with local communities, for which Monica created a blog about the Harbour Seal Decline Project. She is also a regular participant at outreach events such as the Dundee Science Festival, and has spoken on radio programmes like BBC Orkney.

 

 

For more information on some of these projects:

RSE Masterclass

On Saturday 19th May, researchers from the School of Biology ran a Royal Society of Edinburgh Start-up Science Masterclass for 20 school students (S1 and S2) from ten different schools across Fife and central Scotland. 

We spent the morning in the Bell Pettigrew Museum and four different research groups from across the school ran activities.  We also made the most of being surrounded by all the amazing museum exhibits – it was a lovely venue to spend a few hours learning about the biological research going on in St Andrews. 

The students will now go on to spend a Saturday with the School of Physics & Astronomy, the School of Chemistry and Geobus (https://www.geobus.org.uk/)

Double science

On Saturday 10th March Centre for Research into Ecological & Environmental Modelling (CREEM) and the Sea Mammal Research Unit (SMRU) joined forces to enable representation of both groups at the Science Discovery Day in St Andrews and at Dundee Science Centre as part of their “Meet the Expert” programme. Both events coincided with the start of British Science week.

 

Danielle Harris, Popi Gkikopoulou, Marco Casoli and Filippo Franchini based themselves in St Andrews with activities relating to marine mammal acoustics and density estimation from acoustics.

Charles Paxton, Rick Camp, Claudia Faustino, Gui Bortolotto, Janine Illian, Katherine Whyte and Catriona Harris based themselves in Dundee and ran activities showcasing a number of different methods for estimating abundance and used the SMRU photo-identification game to demonstrate mark-recapture methods. In addition Charles gave a talk on the “Science of sea monsters”.

Fife (five) polar explorers and plenty of kids = Cool fun

In early December, a team of polar enthusiasts from the School of Biology in St Andrews (Dr Sonja Heinrich, Dr Rebecca Kinnear and 5 postgraduate students), visited St Columba’s R C Primary School in Cupar. As part of the UK’s “Polar Explorer STEM Programme”, St Columba’s pupils had spent the last couple of months learning all about the Polar Regions.

Full details in the St Andrews Students in the Antarctic Blog here.

A summer of genome editing

The School of Biology hosted Nabihah Akhtar, a 6th year pupil at Glenwood High School in Glenrothes, for 4 weeks this Summer on a Nuffield Foundation Research Placement. These placements are particularly aimed at pupils without a family history of going to university or who attend schools in less well-off areas, and provide over 1,000 pupils each year with the opportunity to work alongside professional scientists, technologists, engineers and mathematicians.

Nabihah’s project in the MacNeill lab in the Biomedical Sciences Research Complex saw her using cutting-edge CRISPR-Cas9 gene editing technology (being used elsewhere to repair damaged genes in human embryos) to delete previously unstudied genes encoding conserved microproteins in fission yeast, giving her first-hand experience of on- and off-target effects encountered during the editing process.

Nabihah presented her results at the Nuffield Research Placement 2017 Celebration Event at the Royal College of Surgeons in Edinburgh at the end of August, where she was presented with a certificate by Rolls-Royce STEM Ambassador Dr Andrew Russell.

Sponsor: The Nuffield Foundation
Photographs: Alan Richardson Photography