Smithdown road festival weekend – Being a superhero scientist for a day, engaging with Alder Hey scientists from the Experimental Arthritis Treatment Centre for Children (EATC4Children)

Saturday 4^th May – Sunday 5^th May 2019

It is 8 am on a weekend when the alarm clock goes off and for a moment one might wonder “”why on Earth did I volunteer to help in a public engagement event on my day off?”. Shortly past 10 am we start to set up and any negative thought is simply out the window.

Greeted by amazing Dr Angela Midgely and her family, they are already setting up the small gazebo that will be our base for the next 6 hours. One minute in and we are already having fun. Our objective is to engage with all the wonderful pool of possible future scientists and introduce them to the wonderful Superhero Team in your Body project. Through 4 different activities suited for a wide range of ages our young participants will use games and craft to learn how cells in your immune system are superheroes that keep you safe.

It is 11 am and the community garden is already full with parents and kids ready to start engaging with the event. Together with the scientists from the Alder Hey team, we are ready to start the fun. The kids get to decorate superhero masks, create little microbes, learn about the immune cells of the body through games and even do a couple of experiments to separate cells and detect proteins (with a tailored lab coat of course!).

Superhero Scientist team and some of the participants

At around 17h, on our way home, though tired, we could not possibly be happier. We have spent our day with so many youngsters, full of energy, creativity and inspired to learn that it has really recharged my mood. We engaged with at least 100 children and they all left our stand proudly wearing a badge with the motto “Science rocks” or “Science is Awesome”, a superhero mask and a small lab-book for their future experiments.

What can we say? There are plenty of worthwhile Public Engagement opportunities around us, sometimes it takes a bit of a push to get involved but we can tell you, it is really rewarding and worth your time.

Guest post by Eva Caamano-Gutierrez (IIB) and Rachel Floyd (SoLS)

Meet The Scientists: Engaging the next generation of researchers

‘Meet The Scientists’ celebrates the inter-disciplinary and collaborative approach that the IIB takes in conducting their research activities. The annual event showcases a selection of projects being undertaken across departments, and transforms complex subjects into interactive and engaging tasks for children. More than 1000 children and their parents from across Liverpool attended the event at World Museum on Saturday 27th April.

“As a vet, and PhD student examining Histoplasmosis at the human-animal interface, my interests in infectious disease and global health, influenced the subject of my stand. Different disease scenarios based on IIB research activities were presented to my audience. Children then decided which team of scientists, clinicians and community members were needed to stop the spread of disease (in the more engaging form of a puzzle). This activity highlighted the importance of inter-disciplinary teamwork to obtain a complete picture of infectious disease transmission dynamics, and the impacts of disease on affected communities worldwide. Children were particularly engaged when understanding their role in the global health picture, as students and as the future generation of scientists.

This was a fantastic opportunity for public engagement with an energetic and enthusiastic audience! Thank you to the organisers of this event and for the scientists who gave me permission to showcase their research.”

Tessa Cornell (Functional and Comparative Genomics)

“Despite being incredibly messy, making hundreds of pine cone bird feeders with the families was a lot of fun! At ‘Making a Home for Nature’, families could create bird feeders, bee houses and do some colouring. They could also take home various handouts, for other wildlife-friendly activities or to tick off which birds come to their feeders. I really enjoyed talking to lots of different people, ranging from young children to grandparents. I hope many have continued to enjoy the activity through watching the wildlife attracted to their gardens and the things they made.”

Emma Cartledge (Mammalian Behaviour & Evolution Group)

“It was so much fun to interact with children with all that enthusiasm and curiosity about learning and getting involved in what we did! They have all got very creative while making their viruses by putting a smiley face and a couple of googly eyes to make them less harmful than they are. At the end of the day, they brought their creation of a happy virus home with a little more awareness on what viruses are and what they may cause into.”

Dilem Shakir (Biochemistry)

“What a day! It was raining buckets outside and this seemed to drive a sheer endless stream of visitors to our ‘Skull Detective’ stand at the Liverpool World Museum, which felt a bit like Noah’s ark at times and kept me and volunteer helpers Kelly Ross and Dan busy for hours on end, with hardly time to catch our breath. Our hope was to inspire the current and next generation among the public to understand the needs of, and ultimately help preserve, the local wildlife around us in a friendly and fun environment. So it was encouraging and satisfying to experience the great curiosity and enthusiasm of children and adults alike about some of the wonders of the animal world. Our display of tracks and remains of common mammalian wildlife in Britain was greatly enhanced by exhibits provided by the friendly staff of the World Museum, including an enormous lower jaw of a juvenile sperm whale that attracted great attention. So would we do it again? I think so!”

Michael Berenbrink (Evolution, Ecology and Behaviour)

“It was a great experience participating in this year’s Meet the Scientist event. I enjoyed engaging with children about how bacteria can become superbugs by acquiring antimicrobial resistance genes from the environment. It was really rewarding to see how engaged both the children and their parents were to learn about the rising problem of antimicrobial resistant due to over use of antibiotics.”

Rebecca Bengtsson (Functional and Comparative Genomics)

We had a fantastic day at the museum. As always, it was great to see so many enthusiastic young people and their families enjoying science! The ball pit ‘discovery tank’ was hugely popular with young and old and really helped explain the challenges of drug discovery! It was challenging seeing so many people and explaining the concept properly, but I think everyone enjoyed it! A great team effort on a very busy Saturday!

Hannah Davies, James Torpey, Alana Maerivoet (Biochemistry)

Thanks also to Laura Winters for organising the event and undergraduate and visiting students for their help on the day.

Talking PhDs and poster judging at St Michaels CoE School Science Fair

Guest post by Natalie Koch, PhD student in the Centre for Proteome Research

On Friday 15^th March, Rosie Maher and I attended St Michaels Church of England High School for their yearly science fair. The morning session began with both of us giving presentations explaining our personal journeys towards a PhD to a group of year 9 female students. Rosie presented first and began by explaining what a PhD is as many of the students hadn’t heard of a PhD. Rosie followed by talking about her journey from leaving school to starting her PhD. Rosie also highlighted extracurricular activities and work experience that helped her obtain her PhD position and that this is something the students could start thinking about now for their future.  Rosie went on to talk about her current research as a PhD student and explained how she is helping to develop a diagnostic test for people with reflux aspiration using proteomics and mass spectrometry.

I presented next, describing my own journey from school to becoming a PhD student, including my time spent volunteering abroad. I explained what my PhD entails and how I am using a new technique to extract information from faeces to help with population monitoring of small mammals. I also highlighted what else we do as PhD students away from the lab including publishing papers, presenting posters and talks, attending conferences and developing new skills. I then went on to explain what potential careers paths other than academic research are available after studying a STEM degree, in particular studying biology. The students were then able to ask us questions. I believe they were particularly encouraged to know they did not have to excel in every scientific topic they covered in class to be able to pursue a career in science. They were also reassured that Rosie and I had experienced setbacks on our journeys towards a PhD. We emphasised that we did not know everything about our particular field of research before starting our respective PhDs. We explained that we are still constantly learning, and that this is the main theme of a PhD to learn new skills and techniques! We explained that both of us have followed our passions and that has taken us to where we are now and we would encourage them to do the same.

During the afternoon session, Rosie and I took part in judging poster presentations at the science fair along with the help of a previous winner. Around 20 students from year 8 to year 11 volunteered to present a poster on a scientific topic of their choosing. The posters were displayed around the school hall, as you would see at a scientific conference. The students’ parents also attended and were able to walk around the hall viewing the posters and asking the students questions about their chosen topic. As judges, we were asked to mark each student out of five on their presentation skills, knowledge of their topic and poster creativity. We viewed the posters separately, approaching each student who then presented their poster and answered any questions we had.

After all of the posters had been marked we collectively chose three winning students for 1^st, 2^nd and 3^rd place. The winners were those who showed a high level of passion and knowledge for their respective topics. The winner’s topics included the effect of mobile phones on our brain and eyes, current advancements in biotechnology and how artificial intelligence works.

Natalie and Rosie with the poster winner

Overall, it was a very successful day and Rosie and I very much enjoyed encouraging and engaging with the next generation of scientists.                 

Speed Dating Scientists

Convincing school pupils that scientists are actually ordinary people is no small feat, but scientists from the IIB, along with the social enterprise Farm Urban have been doing just that.

Farm Urban, in conjunction with the University of Liverpool and funded by Shaping Futures, have developed a 12 week STEM club called the Future Food Challenge, where pupils form their own social enterprise to try and help fix the world’s food production problems using high-tech growing technologies such as aquaponics and hydroponics. Before starting the program, the pupils were invited to an introductory day at the Department of Engineering on Wednesday 6th February, where they were built their own mini aquaponics system and were given talks and advice by local business leaders about how to set up their own business. Matt Murphy from the Engineering Department, who helped to organise the day, also gave a talk to help the pupils understand the design and engineering problems they might face.

As part of the day, pupils took part in a Scientist Speed Dating session, where groups of 6-10 pupils got to sit down with a real life scientist and ask them questions about their work, and how they’d ended up in their job. The idea was to break down some of the barriers preventing the pupils seeing themselves as capable of being scientists and show them that some of the scientists had similar life experiences to their own.

Laurence Anderson, Hannah Davies, Jens Thomas and James Torpey from the IIB all took part. At first, students and academics were eyeing each other with some trepidation, but by the end of each session, the groups always had to be forcibly moved on as everyone was getting on so well and didn’t want to stop the conversation. The scientists had to contend with a bewildering array of questions, from what their most important experiment was, to what their favourite food or colour was, and although they were sometimes stuck for answers (I’m still not sure what my favourite colour is) the day went incredibly well.

We hope that the day and the program will broaden the horizons of the pupils and show them that they too could be scientists and entrepreneurs, just like the people they met on the Future Food Challenge.

IIB’s Iain Young, who helped to develop the programme and is now at the Institute of Clinical Sciences, was shortlisted for a public engagement award for his part in creating the Future Food Challenge.

 

Inspiring the next generation of NMR scientists during British Science Week

On Friday 15th March 10 chemistry A-Level students from Range High School visited the Institute for the annual Analytics Day held in the NMR Centre for Structural Biology organised by Dr Jill Madine and Dr Marie Phelan. This visit has been an annual event for the past several years which the students look forward to in order to gain enhanced understanding of NMR to help with their A-level courses and also provide an opportunity to chat with PhD students about what is involved in University life and academic research.  The students were given lectures on the basic applications of mass spectrometry and NMR from Stephen Moss (School of Physical Sciences) and Dr Marie Phelan. This was the followed by practical workshops where the students carried out chromatography and learnt to prepare and run NMR samples along with how to interpret the data.  Prior to their visit, as part of a school practical, they have made salicylic acid – a precursor for aspirin. We obtained these samples and collected NMR spectra of their products ready for analysis on the day.  This enabled them to establish how successful their synthesis had been and compare their results across the class, with previous years’ students (and to the teacher!). The pupils response at the end of the day was that they had learnt a lot and they can now ‘do’ NMR. Watch out for future budding NMR Nobel Prize Winners inspired during British Science Week in IIB!

Pupils were assisted on the day by Michelle Tan, Adika Sen (visiting interns in the NMR Centre), Zain Ghanameh (IACD), Jeremy Chazot (IACD) and James Torpey (IIB).

British Science Week at Eureka Science Museum

Guest post by Emma Cartledge, PhD student in the Mammalian Behaviour and Evolution Group at the Institute of Integrative Biology

Earlier in the year, I attended a public engagement training session at Eureka children’s science museum in Halifax. The training was focused on interacting with young children and families. It highlighted the importance of creating an interesting narrative for your work, as well as understanding its relevance to the target audience. Educational memories are lasting when the activity is unusual and fun – if you think of a time when you were little and learning about science, chances are you are thinking of an occasion where you were not simply sitting in class and filling out worksheets!

As part of British Science Week 2019, I had the opportunity to return to Eureka and put this training into practice. Volunteering alongside the British Ecological Society to run a selection of activities, we were mostly visited by pre-school aged children and their families. We had a stall where the children could view fossils, including a huge dinosaur footprint. They then thoroughly enjoyed making footprints in playdough with toy dinosaurs! Another area was about insects. This was where children spent a lot of their time and drew their favourite animal.

My attention was focused on a stall about small mammal tracks and signs. Here, the children (and parents!) could match up poo to their perpetrator, identify the animals based on camera trap images and then draw their own pawprint.

I really enjoyed the day and was particularly thrilled with the parents’ interest in my footprint tunnels. I have recently started using these to monitor small mammals, as part of my PhD project on dormouse conservation. Some even decided that they would try it at home with their kids! Overall, it was a fun and informative day for all involved.

Plant Power at the VGM

On Thursday 21 February 2019, during school half term the Walley group were at the Victoria Gallery and Museum (VGM).  We took with us a display of cultivated brassica crops, and their crop wild relatives to demonstrate how over many years the weedy Brassica oleracea crop wild relatives have been domesticated and bred into so many different vegetables through selection.

Visitors had a go at performing crosses between different brassica crops by transferring pollen between flowers using paint brushes and, inspired by how new vegetables can created, such as flower sprouts or ‘Kalettes’ (crossing a sprout with a kale plant), designed their ideal or fantasy brassica plants for us to display.

The methods of modern plant breeding that we are using within the BRESOV project (Breeding for Resilient, Efficient and Sustainable Organic Vegetable production) were discussed and compared to conventional plant breeding.

Visitors had the opportunity to taste many of the different vegetables derived from wild Brassica oleracea, including cauliflower, sprouts, kale, kalettes, red cabbage, pak choi, chinese cabbage and broccoli- they were very popular!

 

Halloween Science at the Institute of Integrative Biology

Post by Dr Jill Madine

On Wednesday 31^st October 2018 IIB and SoLS held the first Institute-wide School Engagement event within the Life Sciences Building. 82 children from Banks Road, Litherland Moss Primary Schools and home-schooled pupils from the local area attended the morning session with 128 Secondary school children from Notre Dame Catholic College, Prescot School, Kings Leadership Academy Hawthornes, Academy of St Nicholas, Archbishop Blanch and St Michaels High attending the afternoon session.

What an amazing day for Year 3 today at
@livuniIIB
From taxidermy to looking at mysteries under the microscopes. We can’t wait to hear about their next event! #HalloweenScience pic.twitter.com/zkP2Mxgt52

— Banks Road Primary (@BanksRoadSch) October 31, 2018

Pupils took part in a range of fun spooky science activities:

• exploring relationships between skulls and other features of animals (e.g. diet and faeces!) with Michael Berenbrink and PhD student Kelly Ross
• finding out about blood flow and gravity, how holding your breath slows your heart and which animals that make your heart race with SoLS Terry Gleave and Rachel Floyd
• making zombie proteins out of magnetic beads with Luning Liu and Fang Huang, assisted by many students
• looking at model organisms under the microscope with the Centre for Cell Imaging (CCI – Violaine See, Dave Mason, Jen Adcott, Daimark Bennett, Anne Herrmann, Marco Marcello and PhD students Kit Sampat, Hammed Badmos, Rebecca Kelly)
• finding out how much protein is in the foods we eat including fishing in cauldrons for the answers from the Centre for Proteome Research (CPR – Kimberley Burrow, Jos Harris, Victoria Harman and PhD students Max Harris, Rosie Maher, Iris Wagner, Natalie Koch)
• pupils could also get up close and find out more about a range of animals kindly provided by staff from World Museum and from within SoLS with Carl Larsen

https://twitter.com/luningliu/status/1057892900674170880

Additional student and staff helpers including Alice Clubbs Coldron, Lauren Tomlinson, members of Jill Madine group (Hannah Davies, James Torpey and Alana Maerivoet), Louise Colley and Laura Winters were invaluable in organising the day and logistic arrangements on the day.

Just a few more pictures from yesterdays #HalloweenScience, well done to the fab CPR team and IIB for a great day! @livuniIIB @astacus @ClaireEEyers pic.twitter.com/OcUOrAWc1c

— CPR Liverpool (@c4pr_liv) November 1, 2018

Summer school: “Big data Analytics and Machine Learning Meets Omics”

In summer 2018 the faculties of Health and Life Sciences, and Science and Engineering, hosted a ten week summer school for students interested in data science, analytics and machine learning. The five successful students received supervision from leading experts in the field, as well as a stipend.

The projects focussed on the application of data science techniques in the area of biological and biomedical research, called “omics”. These areas include the study of genomes and related technologies that produce large amounts of complex data, suitable for data mining. Researchers at Liverpool are using these techniques for “personalised health” research (e.g. to understand how your genetics relate to your likelihood of getting a disease), for cancer research (e.g. for understanding how certain genes are switched on or off during cancer progression), and to understand how infectious diseases can spread or how we can better detect them.

“Insightful, collaborative, applied”

We asked the students to explain their research project and experience of the summer school:

Di Liu (BSC Computer Science) worked on the project “Topological data analysis for bioinformatics”.

 Can you tell us a little bit about your current research project

The intention of the project is to visualize the gene-gene interactions by analysing correlation coefficient of gene pairs as the pair’s weight score.

To achieve this we are analysing glioma gene scores by MPI and visualizing the analysis’ results on Cytoscape.

 How have you found the project? What has been the highlight?

The project has been excellent! Working with Drs Kurlin and Krishna broadened my vision and enriched my experience of using the knowledge I have learned.

Also, the project group is awesome. Two supervisors and one teammate, they helped me to overcome any obstacles during my internship.

The highlight for me was successfully using the C++ knowledge to fix the problem we met in the project, and learning how to use MPI to complete parallel programming to save a lot computer running time.

Has anything surprised you about the project?

I was expecting a more reserved role and have solo solved the data part of tasks because of the trust shown in me by Drs Kurlin and Krishna.

Have you seen the University in a different light as a researcher, compared to being here as a student?

Yes, the research side of the University is awesome. On the one hand, it practised the knowledge I have learned at University. On the other hand, it gave me a chance to learn more skills that can’t be learned in lectures. I think this will assist me in the future studies.

Has the research project changed your expectations of the future?

This project is relational with my expectation of the future. So, it let me realize my future’s expectation more clearly. Besides, it also let me see more possibilities to connect my subject with other subjects.

If you were to describe the experience in 3 words, what words would you choose?

Enjoyable, teamwork, rewarding.

Weiyi Ren (BSC Mathematics) worked on the project “Building a statistical model to help quantify molecules important for cell signalling and cancer”

Can you tell us a little bit about your current research project?

The project aims to understand how genetics relate to the likelihood of getting a disease, and to understand how infectious diseases can spread or how we can better detect them. My task was to build a statistic model to predict the change of intensity or retention time between the modified or unmodified peptide.

How have you found the project? What has been the highlight?

The team lead by Professor Andy Jones was searching for undergraduate students to help them build a statistic model. We tried several new approaches: random forest and neural network. The results were very successful comparing with the linear regression model.

Has anything surprised you about the project?

The project was very smooth. We met each week to talk about the progress. The supervisors were very passionate to help us with our difficulties. We could get detailed explanations from them on time.

Have you seen the University in a different light as a researcher, compared to being here as a student?

Yes, the research side of the University is excellent. Participating in a research is very different from being a student. It involves much more communication between the supervisor and the students, which would be no doubt a valuable experience for one’s future academic life.

Has the research project changed your expectations of the future?

Yes, this experience provides me with more possibilities for my future career. Data science is definitely a very good choice for me.

If you were to describe the experience in 3 words, what words would you choose?

Enjoyable, productive, full.

 BSC e-Finance student Ash Myall worked on the project “Distributed computing and analytics to annotate the human genome”.

Can you tell us a little bit about your current research project

The intention of the project has been to develop a web-based visualization suite for results of Peptide Search Engines within proteomics analysis, focused specifically on the crowdsourced search engine which operates on a distributed network.

To develop this, we have used R and shiny, which together can quickly produce interactive dynamic visualizations.

In lay terms….producing visual representations of large scale data sets, to identify trends in the behaviour of proteins in samples (e.g. the human body).

How have you found the project? What has been the highlight?

The project has been incredibly insightful, which subsequently lead me to pursue postgraduate research in the field. My favourite part has been consolidating my understanding and confidence in using R.

Has anything surprised you about the project?

Yes, before I had little idea how essential data visualisations can be to understanding underlying trends, and how useful making interactive plots is; questions can be answered instantly about the data by a user.

Have you seen the University in a different light as a researcher, compared to being at here as a student?

Yes, I’ve found the independence to give greater flexibility in finding solutions to unseen problems.

Has the research project changed your expectations of the future?

Absolutely, I’m about to start an MRes in Advanced Biological Sciences with the bio informatics pathway following my interest in biological data analysis on the project.

If you were to describe the experience in 3 words, what words would you choose?

Insightful, collaborative, applied.

Is there anything else you would like add?

This has been a great opportunity, I’d recommend it to anyone who’s got an interest in biological sciences and comes from a computational background like myself. Not only has it provided an excellent application from my undergraduate skills, but it’s also set me in a great position for beginning a career or for going into a PhD.

Antoine Rohmer (BSC Computer Science) worked on the project “Exploiting Graph Databases for bioinformatics” which included an internship at IBM.

Can you tell us a little bit about your current research project

The purpose of the project was to gain an understanding of the technologies underlying graph databases and parallel computing to create a large-scale visualization of gene-gene interactions from data provided by the University.

The technologies used in the project include Neo4j and the Cypher querying language on the graph database side. C++ and Python were used in tandem with supercomputers provided by IBM for data processing. Cytoscape was used for visualization. The open source pathway database reactome was used as the foundation of the database created for the project.

 How have you found the project? What has been the highlight?

The project was a great foray into the professional world. Working alongside experts in the field and absorbing their insight was a fantastic learning experience.

The highlight of the project for me was the moment the graph database and parallel computing sides of the project combined to form a coherent whole that until then seemed intangible.

 Has anything surprised you about the project?

Perhaps the biggest surprise was how largely independent I was in pursuing the project. Although a plan and structure existed, most of the meeting setups, deadlines, and choices in technologies were up to me. This in particular was a refreshing excursion from the otherwise rigid structure found in my studies.

 Have you seen the University in a different light as a researcher, compared to being here as a student?

Although at times the project felt like a continuation of my studies due to the large amount of research that had to be conducted, the knowledge that the end product will be used as a stepping stone to other research is a much greater motivator than grades.

 Has the research project changed your expectations of the future?

The project truly validated my interests in data analysis and got rid of any doubts previously had about which postgraduate program to pursue. More importantly it made me even more eager to enter the professional world.

If you were to describe the experience in 3 words, what words would you choose?

Insightful, refreshing, validating

Student’s Biochemical Society summer placement in IIB

Christopher Steel exploring the role of proteoglycans and glycosaminoglycans in aortic aneurysm and dissection funded by Biochemical Society supervised by Hannah Davies and Jill Madine

Aortic aneurysm is a bulge in a section of the aorta. This causes weakening of the aortic wall and increased risk of the blood vessel bursting. A number of biochemical factors can complicate the local environment of an aorta which then has a direct consequence on the mechanical function of the vessel. One factor reported to affect the integrity of the vessel wall is the concentration and distribution of proteoglycans (PGs) and glysaminglycans (GAGs), particularly ‘pooling of PGs’ which may compromise the aorta wall and lead to delamination, aortic aneurysm, and dissection.

In his project Chris investigated the levels of PGs and GAGs in human tissue obtained during aortic surgery at Liverpool Heart and Chest Hospital using a range of gel-based techniques and dot-blots and employed immuno-staining to investigate the distribution of GAGs within the medial layer of the aorta wall. Data is being correlated with existing data on biomechanical properties and biochemical composition of collagen and elastin, along with clinical characteristics for the same patients to assess whether PG and GAG distribution could be contributing to altered aortic wall integrity in disease. PGs and GAGs could provide a future therapeutic biomarker to predict risk of aortic disease and rupture.