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)

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“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)

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“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.

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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.

 

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!

 

Telling tales of multiple Ps – Dr Lydia Cole

Several weeks ago, I had the opportunity* to talk, twice, about a topic related (slightly tenuously) to my research and very close to my heart.  On the evening of Wednesday 19th September I stood on the stage at Leaf, facing the Ignite Liverpool crowd, to present on “The Three Ps”; and on Saturday 22nd September I stood on a soapbox in Sheffield’s busy shopping district, to shout about “Peanut butter, palm oil and peat; getting un-stuck in the mud” to a bunch of slightly bemused passers-by.  They were quite different forums with which to share my knowledge and passion, but I learnt a good deal from preparing for and presenting at each.  Here’s a quick low-down of each event, which might hopefully inspire you to get involved in the future.

Ignite Liverpool is the brainchild of a community organisation that runs quarterly events, providing a platform on which anyone can talk for a whistle-stop five minutes about a subject they are passionate about.  The challenge is to convey a coherent story in five minutes, in synchrony with the visuals on your 20 slides which flash up for five seconds in a continuous reel.  I managed to mumble in time to the slides until the penultimate one, where my dialogue turned to dust!  It was a fun experience though, and useful in considering how to design succinct propaganda.  If you’d like to know more about the tale of The Three Ps, you can watch my performance here.  I would recommend giving Ignite a go if you live in Liverpool, or any of the other cities where it’s held (e.g. Sheffield); it’s a great opportunity to practice your public speaking and communication skills on any topic of your choice, in front of a very supportive, slightly tipsy crowd.  The most hilarious talk at the last event was entitled Any Colour you like, where all of the slides where shades of black!

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Reeling off about peat at Ignite Liverpool!

Soapbox Science proved a less well-polished, more chilled-out and slightly chillier event!  The initiative was started eight years ago by two female Biologists, with the goal of creating a public outreach platform on which female scientists could promote their science, whilst simultaneously increasing the profile of women in the STEM sector.

I chose to talk about the same issues on the soapbox as I did on the stage: a narrative around the prolific commodity, palm oil, which links our consumption behaviour in the UK to the draining and deforestation of peat swamp forests in Southeast Asia.  Orang-utans, the people of the forest, were the protagonists, of course.  As part of my PhD research (a few years ago now!), I explored the long-term ecology and contemporary management of the coastal peat swamp forests of Sarawak, in Malaysian Borneo, and have since been monitoring their declining condition and the ever-expanding state of industrial oil palm plantations across the region.  Though my Soapbox performance was not as succinct as I’d hoped (more prep required next time to catch the attention of a transient audience), I managed to have an interesting discussion with several members of the general public on topics of environmental sustainability and the RSPO.  The conversation with one chap, as engaged as he was disillusioned, only concluded when we decided that capitalism needed to be scrapped.  Unfortunately, I didn’t feel qualified to propose an alternative solution.

Illustrating the link between peatlands, palm oil and peanut butter

I found both experiences hugely valuable, primarily because I gained some idea of the level of knowledge amongst the general public on some everyday consumer issues.  People were less aware than I’d realised.  To place your science into a ‘real world’ context, to understand how it might fit into the lives of your neighbours, and to learn how you can inspire people to care as you do, I would recommend standing up on as many platforms as you can.

*The opportunity was created by me through signing up to two events without realising they were in the same week!  I questioned my life choices many times when preparing for them into the wee hours of the morning …. though as per usual have no regrets, in retrospect.

Learning synthetic biology techniques in Denmark – Johnston Post Doc Fund report

Learning synthetic biology techniques in Denmark – Johnston Post Doc Fund report

Guest post by Dr Hannah McCue, postdoctoral researcher at the Institute of Integrative Biology

With the help of IIB’s Johnston Postdoctoral Development Fund, I was able to visit a world-leading lab in Denmark in order to enhance my knowledge of advanced synthetic biology techniques. Prof Mortensen’s lab is situated at the technical University of Denmark (DTU) located in Lyngby, just outside central Copenhagen. The Johnston Fund kindly covered costs for my travel and AirBnB accommodation close to the DTU, giving me almost two weeks to experience life working at the DTU and learning novel molecular biology techniques.

The key aim of my trip was to learn the ‘tricks of the trade’ of Uracil-Specific Excision Regent (USER) cloning, a technique which multiple scientists at the university have struggled to utilise. In principle, USER cloning should be a straight forward one-pot cloning reaction which holds several advantages over other traditional and more modern cloning methods. Specifically, USER cloning utilises a ligation-free protocol, generates highly specific sticky ends and does not rely on the presence of restriction enzyme recognition sequences. The premise of USER cloning is that by incorporating a single deoxyuracil around 8-12 bases from the 5’ end of each primer, highly specific and long sticky ends can be created on the resulting PCR product with the USER enzyme mix. USER enzyme contains uracil DNA glycosidase (UNG) which excises uracil nucleotides from PCR products and DNA glycosylase-lyase endo VIII which releases the sequence upstream of the uracil nucleotide. The overhangs created are sufficiently long that DNA assembled into a circular plasmid is suitably stable to be transformed into bacteria without prior ligation.

My visit to Prof Mortensen’s lab gave me hands on experience of USER cloning alongside established experts in the field of cell factory construction and engineering. Whereas my expertise lies mainly with the use of bacteria for the production of heterologous proteins and secondary metabolite pathways, Prof Mortensen’s lab focuses on yeast and fungi such as Aspergillus. The main focus of the lab is the discovery of valuable products from fungi and the development of optimal cell factories for their production. To this end, they use CRISPR technology both to insert gene pathways into the organism of interest and to regulate the pathway to give optimal output of the desired molecule.

I was lucky enough to work alongside Dr Katherina Vanegas Garcia who developed “SWITCH” and “TAPE” techniques to help speed up strain construction when developing yeast cell factories. Using these techniques strains can be generated that can iteratively switch between a genetic engineering and a pathway control state. For instance a multi-gene pathway can be inserted into an innocuous location in the genome of the desired strain using Cas9 nuclease in genetic engineering mode. Subsequently the cell factory can be switched into the pathway control state using a dCas9 mutant to up or down regulate different genes in the pathway and monitor the effects to optimise final product yield. She also helped developed a Technique to Assess Protospacer Efficiency (TAPE) whereby the efficiency of particular sgRNA protospacer sequences are assessed for their efficiency to target Cas9 to genomic DNA and cause double strand breaks. The principle is that double strand breaks are lethal in yeast and therefore the efficiency of a protospacer sequence should be reflected in the survival rate of transformants in the absence of a repair template. This technique is also applicable in Aspergillus nidulans NID1 strain which is deficient for non-homologous end joining and hence double strand breaks will also be lethal in this strain.

I designed two experiments to test the application of USER cloning for future use in GeneMill. The first was to assemble 5 stretches of DNA encoding an operon of 13 genes and spanning almost 14 kilobases. USER overhangs were designed to assemble these genes into a USER backbone developed by Dr Vanegas Garcia. Unfortunately, a plasmid encoding all 13 genes was not obtained from these experiments, however, staff and students at the DTU have succeeded in cloning large gene constructs in this manner. Presumably there is an issue with the specific DNA sequence used in this construct which has also proved problematic when using other cloning techniques in the past.

The second experiment was to clone three sgRNA protospacer sequences into a USER backbone designed for CRISPR in Aspergillus nidulans. This cloning was successful on the first attempt and subsequently I was able to carry out CRISPR TAPE experiments to assess the efficiency of targeting of the protospacer sequences to my gene of interest in A. nidulans. All three sgRNA constructs were lethal in NID1 strain when compared to the control transformation showing that all three protospacer sequences were highly efficient. In parallel, I also transformed each sgRNA along with a repair oligo to insert single amino acid changes in my gene of interest. Unfortunately, all three transformants were extremely sick with only one colony from one sgRNA proving viable. This could indicate either that the mutations encoded by the rescue oligos were also lethal or repair using the rescue oligo was not achieved. Without viable transformants to PCR from this is difficult to check. Instead I plan to design oligos encoding silent mutations in the hope that I will then obtain viable transformants.

In summary, my visit to the DTU gave me the opportunity to test USER cloning in both challenging and simple applications. I was also able to conduct a series of CRISPR experiments in A. nidulans, an organism with which I had no prior experience. In addition to receiving hands-on training in the lab, I was given the opportunity to speak to members of different research groups and attend a number of research seminars during my stay. Research areas ranged from discovery of novel antibiotics in fungi to pleasant smelling moss that can be used as an alternative to air freshener! Of particular interest was the Diversify project which is a huge collaboration between many different researchers at the DTU and industrial partners Novozymes and Novo Nordisk. This project aims to take hundreds of yeast and fungal strains and adapt them for the aforementioned SWITCH technique by identifying innocuous sites for heterologous pathway integration. These strains can then be rapidly screened for optimal production of desired metabolites. Ambitious, high throughput, multi-partner, synthetic biology challenges such as this have the ability to change the wider approach to industrial biotechnology enabling sufficient production of useful or valuable compounds that would otherwise be ignored due to underperforming host strains.

I have been extremely privileged to have been selected for receipt of the Johnston Fund and as a consequence I have obtained invaluable experience of how another synthetic biology-focused research lab works. I have renewed enthusiasm that synthetic biology can revolutionise biological research and has the potential to have a significant impact on how we think about the future of industrial biotechnology. Not only am I now equipped to teach and supervise students and colleagues about how to utilise USER cloning, the visit to Denmark has given me a wider perspective on how to approach various industrial projects with which I am involved. I therefore believe that the experience has greatly enhanced my professional development and will aid my productivity across all aspects of my work.

Meet the Scientists

On Saturday 17th March IIB led the Meet the Scientists Event at the World Museum. Activities included stands led by the CCI and Madine group from IIB along with other stands from Life Sciences, ITM and IGH.

The CCI had a large team, and all worked together brilliantly on the Seeing is Believing stand! The team included:

Violaine See (CCI staff): Preparation of samples for imaging, and assistance at the event.

Dave Mason (CCI staff): Preparation of samples, imaging of samples, produced posters for the event, and assistance at the event.

Marco Marcello (CCI staff): Organisation of virtual reality tours of microscopy images, with Virtual Arcade

Daimark Bennett (CCI staff): Preparation of samples for imaging, and assistance at the event.

Raphael Levy (CCI staff): Preparation of samples for imaging, and assistance at the event.

Anne Herrmann (Postdoctoral researcher): Imaging of samples, preparation of printed materials for the drawing microscopy station.

Sophie Cowman (PhD student): Filmed and produced a tour of the CCI facility, which was on display during the event.

Rebecca Kelly (PhD student): Preparation of CCI postcards, set up and take down of stand, and assistance at event especially for the match the picture quiz.

Claire Kelly (PhD student): Set up and take down of stand, and assistance at event especially for the virtual reality microscopy tour.

Hammed Badmos (PhD student): Preparation of samples, and assistance at event especially for the microscope demonstrations.

Jen Francis (PhD student): Assistance at event especially for the microscope demonstrations.

Sumaira Ashraf (Postdoctoral researcher): Set up and take down of stand, and assistance at event especially for the microscope demonstrations.

Jen Adcott (CCI Staff): Organisation of the Seeing is Believing stand and co-ordinator of activities, imaging of samples, designed and produced the match the picture quiz and microscopy stickers, and assistance at the event.

Feedback from the CCI stand, seeing is believing:

Violaine See – “It was great, and the activities were all very popular. What I really liked about our exhibit is that it was real science. Well done Jen A for leading this, the result was absolutely awesome. Well done Jen F, Hammed, and Sumaira for guiding the kids with the microscopes with so much patience and enthusiasm. Dave has been an absolute star with the colouring sheets and at explaining what we do with microscopes. Rebecca and Claire have been fantastic with the quiz and virtual reality. An amazing team effort. I feel very fortunate to have you all around, you are amazing.”

Daimark Bennett – “Fantastic effort by everyone and great activities – it was great to see how busy it was even later on. The VR clearly went down a storm and everything from the stickers to the CCI movie looked really professional and well put together. It really is hard to convey the science when it’s so chaotic but I think the exhibit was pitched at the right level. In any case, my daughter, who is not easy to impress, gave the thumbs up 🙂 Well done everyone!”

Jen Adcott – “It’s great to work with such a fantastic team of people! The day was busy, and the CCI stand seeing is believing was hugely popular with many repeat visitors. I am looking forward to meeting more future scientists at the next events.”

The Madine group ran 2 activities ‘How does the heart work?’ and return of the popular ‘A lego treasure hunt for new medicines!’ with the help of PhD students James Torpey and Nathan Cumberbatch, MRes student Kiani Jeacock and undergraduate volunteers.  Visitors enjoyed learning how blood is transported around the body by watching blood cells flow around the giant circulatory system (borrowed from IACD created with a Wellcome Trust Public Engagement award, granted to Dr Valentina Barrera). Children of all ages were keen to take part in the Lego treasure hunt around the museum to find the correct drug that fit the Lego protein molecule, and be rewarded with a Lego Scientist to take home. Thanks to members of the group for their help and enthusiasm when describing the drug development process through the use of Lego.

Baltic Science Journal

This journal is founded by year 12 students from Liverpool Life Sciences UTC with support from Senior Editors from Liverpool and Wigan UTC, University of Sheffield and Dr Hannah Davies, Institute of Integrative Biology, University of Liverpool. Hannah’s involvement began a couple of years ago working with the students to design and run projects incorporating cell culture as a research tool supported by a Biochemical Society Outreach grant (link to previous posts).  This journal provides an excellent way for students to engage with other young scientists around the world and develop their skills in written scientific communication and networking. Through reporting their research findings they will develop important skills that will be invaluable in their future careers. The journal has received a lot of attention and positive feedback. We praise all of the contributors and editors for their hard work and hope that the BSJ will continue to grow in the coming months and years. Please visit the first edition of the journal here.