On Saturday 8th June the Williamson Art Gallery & Museum in Birkenhead was host to a special butterfly-themed family drop-in session. Louise Reynolds and Greg Hurst from the department of evolution, ecology and behaviour were on hand to discuss all things butterfly and also brought with them some butterflies, caterpillars and pupae to show the different parts of a butterfly life cycle. The butterflies were an excellent source of inspiration for the making of many beautiful crafts and drawings. Towards the end of the afternoon everyone was captivated when we were lucky enough to watch as some butterflies emerged from their chrysalides. Thank you to Pam Sullivan for helping with the crafts and for letting us bring our butterflies to visit.
Viruses can be found everywhere and are the most abundant “organisms” on the planet. However, they are often (wrongly) thought of only as evil entities causing human disease, which leaves out important viruses/bacteriophages capable of, for example, helping to fight the current antibiotic crisis that is affecting people all over the globe. This is why the “Battle Station: Infection” event, as part of the “Meet the Scientists” initiative, was the perfect setting to talk about the “good” and the “bad” viruses and how they can help us in the battle against antibiotic resistance.
On Saturday 27th of January, an IIB team comprised of Evelien Adriaenssens, Wai Yee Fong, Siân Owen and Lizeth Lacharme-Lora joined me at the World Museum in the “Let’s get viral” activity, supported by a Wellcome Trust Public Engagement grant. I was aiming to inspire children to take an interest in viruses/bacteriophages and to raise awareness of their importance & lesser-known benefits, which was successfully accomplished with an extraordinary turn up of over 1500 participants!
“Let’s get viral” was designed as a virus/bacteriophage assembly workshop in which children had the opportunity to put together and decorate models of viruses while speaking to experts in the field. The virus model used was chosen depending on the age and skills of the child, but we strongly encouraged parents/guardians to engage in the activity as well. For older children and skilful (highly tolerant to frustration) adults, we had pre-cut paper models designed by Siân Owen (check them out and give it a go!), whereas polystyrene models were decorated by younger children.
The journey started days before the event, with hundreds of paper and polystyrene virus models prepared for assembly thanks to the valuable help of members of IIB’s Lab H (in exchange for treats and drinks –of course!) at the “Phage Cutting Marathon”. These models, together with posters and plush toys of real viruses (www.GiantMicrobes.com), helped us convey fundamental virology concepts in a format understandable to children.
After a very busy day, and with hands covered in glue stick, we all agreed that the experience was a total success and we encourage anyone who would like to run it again!
Getting children out of the classroom to connect with the natural world should be a feature of primary education and is also an excellent way to introduce science. This is why, towards the end of the summer term on July 5th, children from Pinfold Junior School in Scarisbrick near Southport found themselves in their local Millennium Wood for the day.
Along with building dens, hunting for treasure and making mini scarecrows with their teachers, they went on a bug hunt with Dr James Davies, a postdoctoral associate in the Institute of Integrative Biology. Extracting creepy crawlies from the undergrowth and then admiring dragonflies and butterflies as they flew past kept the young hunters, and James, very busy.
In addition, Patrick Hamilton, Lois Ellison and Kelly Roper, undergraduate students from the School of Life Sciences Student Outreach Society, were on hand with activities in the local church hall that was the base for lunch. Kelly said ‘We all really enjoyed the day and it has sparked some new ideas for outreach activities we can develop further. Therefore it was a beneficial experience for us as well.’
‘I would say the main thing I took away from the day was how much fun the children had applying what we had told them about adaptations, to the creation of their own creatures which had a whole range of creative/imaginative features.’
This event is the most recent in the Institute of Integrative Biology’s relationship with Pinfold School that began in 2010 and has included a project that won the annual national Rolls-Royce Eden Award for the best implemented environmental project meeting the needs of a school in 2013.
Meet the Scientists on Tour is an initiative that aims to bring science to the public in places they don’t expect it. Activities centre around magnetic whiteboards where the public can spot caterpillars or match parasite to their hosts. The founders, Klara Wanelik, Rebecca Jones, Gabriel Pedra and Beth Levick have been visiting a number of locations in Liverpool and a folk music festival in Newcastleton where events ran 11am to 3pm. Here’s what they had to say about the events:
St John’s Shopping Centre
The first event was held at St John’s Shopping Centre on the first Bank Holiday Monday (May 1st) and was a success. We engaged with about 40 people although it was so busy we had to work hard to get people to come over to play our activities. It also didn’t help that people thought we were trying to sell them something! We had some great interactions with people though, with comments from participants including: “I really enjoyed the session”, “Caterpillar game – Thank you!” There were also college students asking about studying biology at the University!
Our second event was run on Saturday 6th May at Liverpool Central Station and was very well received. The public passing through the station got stuck in: spotting caterpillars, spreading infection and matching parasites to their animal hosts!
We engaged more people than our last even at St John’s Shopping Centre (approx. 50) and were pleasantly surprised by how positive people were about engaging with our science in such a busy place! The majority of our visitors were young children aged 2-10 years. However, parents seemed equally as interested and we also had a few questions about studying at the University. Comments (from some of our younger participants) included: “I really liked the visit. I hope you come again”, “Really fun and interesting,” and “I liked the games because I learnt things”.
New Mersey Retail Park
Our final event in Liverpool was at the New Mersey Retail Park in Speke on the 29th May. The weather wasn’t great so we were very grateful for our gazebo! Due to the weather we engaged with slightly fewer people (approx. 25) but we had people actively coming over to the gazebo upon recognizing either the University of Liverpool or Meet the Scientists logo. We even had a small girl run into the gazebo exclaiming that she wanted play games in the science tent!
Overall we had a brilliant time across our three locations in Liverpool and are keen to go back and take along some new activities. However, we found that we were mostly engaging with families or the elderly and missed out on the middle age bracket.
Newcastleton Traditional Music Festival
Our most recent location was up in Newcastleton on the Scottish border, close to Kielder Water and Forest Park. We chose this location as Klara is part of a project sampling field voles in Kielder forest and so she was keen to inform the public about what the team was doing. Additionally, we were interested in taking our activities to a music festival as it was a completely new environment for us to do outreach.
We didn’t know what to expect at the festival but it turned out that we were the only stall there and so were able to monopolize the green in the village. On the Saturday (1st July) there were folk music competitions underway but we were able to engage with a large number of local villagers and visitors from further afield. Over both days (4 hours on the Saturday and 1.5 hours on the Sunday) we engaged with a total of 52 members of the public.
We had some great interactions with people, many of whom approached us out of curiosity about why the University of Liverpool was present in Kielder. We were also able to interact with people from a broader age range – particularly with people in their 20’s and 30’s. We had a few local farmers come over who were particularly interested in our ‘Where does the parasite live’ activity. Our competitive game where people spread infections in populations proved very popular again at this event. Furthermore, lots of people were interested in the work with the voles that Klara was describing. Overall, we thoroughly enjoyed carrying out our outreach at the folk music festival which was a very different challenge to the locations in Liverpool. Although, after ceilidh dancing into the morning and being attacked by midges in our tent, we were happy to return to Liverpool for some well-deserved rest!
Finally, we would like to say thank you to everyone who helped make ‘Meet the Scientists on Tour’ possible. We’d like to thank the Wellcome Trust for funding us and Laura Winters for her support. We’d also like to thank Vincent Keenan for assisting at the event at Central Station and Steve Paterson for his additional financial (and moral) support. Most importantly, we’d like to thank everyone at the various locations who made it possible (and so enjoyable!) for us to carry out our outreach.
We’re keen to extend our outreach beyond ecology-based activities and so on the 5th July we ran an activity design workshop with attendees from the Victoria Gallery and Museum, Engineering Department and Institute of Translational Medicine. This was a half-day workshop where people had a go at our activities before settling down to design their own. Attendees then had a chance to present their boards, with much discussion in the group. We look forward to welcoming some more activities soon. Watch this space!
We recently published a paper on genomic surveillance of a diarrhoeal pathogen Shigella sonnei across Latin America which represented the culmination of over five years of collaboration, as well as training and development in the region
In collaboration with the Wellcome Trust Sanger Institute, the Pan American Health Organisation and PulseNet Latin America and Caribbean (PNLAC), we whole genome sequenced over 400 Shigella sonnei collected from nine countries over two decades. Shigella are the most important bacterial cause of moderate-to-severe childhood diarrhoeal disease in low to middle income nations, and countries in Latin America still experience endemic disease and explosive outbreaks. By sharing information on common pathogen subtypes through public health networks, like PNLAC, pathogens can be traced epidemiologically to facilitate early identification and intervention in disease outbreaks. Whole genome sequencing is transforming surveillance of bacterial pathogens, as it provides the highest resolution of pathogens subtypes and can also be used to explore other genetic factors of interest, like antimicrobial resistance. However, its cost precludes routine use in some areas, which are unfortunately some of those regions where the most Shigella disease is seen.
In this study, we sequenced approximately 50 isolates from nine countries in Latin America and use whole genome phylogenetics to reveal those sublineages that were responsible for most of the disease in the region. We identified a novel global lineage of Shigella sonnei, and by correlating the geography of where isolates came from to their evolutionary relationships, we could see international transmission of some sublineages and what the distribution of different sublineages was across the continent. Visit the microreact page to play with the data yourself.
We were also able to identify key determinants of antimicrobial resistance in the pathogens and how they were distributed among the different sublineages, providing key information for managing this important disease in the region.
In addition to constructing this invaluable regional framework for ongoing surveillance, this project helped build capacity for whole genome sequencing surveillance in the region. Over the course of the collaboration, the World Health Organisation sponsored the establishment of whole genome sequencing facility at the reference laboratory for PNLAC, ANLIS in Buenos Aires, Argentina (see photo). In the paper, we show how locally-generated sequencing data from this facility can be integrated into the regional surveillance framework to determine whether outbreaks were due to locally-circulating lineages or resulted from the importation of new sublineages.
In addition to laboratory capacity building, the collaboration involved training an ANLIS researcher (Josefina Campos – see photo – who now runs the genomics facility there) in bioinformatics, and conducting training courses (in conjunction with Wellcome Trust Advanced Courses) for medical, veterinary and public health professionals in the region, including courses in Argentina, Uruguay and Costa Rica (see picture).
There are 29 authors on our paper and every one of them worked hard on, and cared deeply about, the outcome of the study as well as the training programs and capacity building surrounding it. Every paper has a story behind it, and this one, like so many others, is so much more than it appears.
Photo: Top ANLIS in Buenos Aires, Argentina. Bottom (from right to left) ANLIS collaborator Josefina Campos and co-corresponding author Nicholas Thomson (WTSI) outside the Malbran (ANLIS) Institute; Genomics for Epidemiology and Surveillance of Bacterial Pathogens course instructors and participants held in February 2015 in San Jose, Costa Rica; co-corresponding author Kate Baker with bust of Carlos Gregorio Malbran, the ANLIS institute’s namesake.
Over the years I’ve given many presentations at schools and colleges about what the biological sciences are like at University. So far this year I’ve been to Xaverian College (http://www.xaverian.ac.uk/) in Manchester and King Edward VI College (https://www.kedst.ac.uk/) in Stourbridge near Birmingham.
Xaverian College is in central Manchester and has high expectations of its students. Many continue to higher education and each January the College holds an event with speakers from many universities and subjects areas. This begins support for the students to decide on their career paths post A-level. I go along to talk about the biological sciences. I feel that talking about the subject content is better left to perusal of the websites and prospectuses, and that I should rather include my personal insight from my own experience. My focus is always on the ways that university differs from school, and what sorts of careers are open to those with biological science degrees.
King Edward VI College is on a (large) traffic island in the centre of Stourbridge near Birmingham. The college also has great ambitions for its students. My talk there is at a similar careers event in March that starts the path to UCAS applications and university. This time my topic is the biomedical sciences, and I explain about the important choice between accredited degrees that are a direct pathway to roles within the NHS and non-vocational degrees that can leave additional career paths more open. I also talk about the difference between medical and biomedical degrees and careers.
Both colleges have a large and diverse group of students who take these career events very seriously and ask perceptive questions. Every year, it is a pleasure to see their enthusiasm. It is also great to answer questions from their teachers, who act as hosts during the events.
Last week Mal Horsburgh and I welcomed Northwood Primary School to the IIB, where they undertook activities to teach them about the microbes that surround us all every day.
In the morning, the students used light microscopes to identify different bacteria that they would come across in their everyday lives. In the afternoon session, the students were taught about viruses, and made their own bacteriophage 3D paper model. The students were extremely enthusiastic, and really enjoyed the chance to use scientific equipment. Over lunch, we encouraged the students to ask questions to the scientists who were demonstrating to them. My favourite questions included “how long does it take to become a scientist?”, “how do you know when you’ve really proved something scientifically?” and “what’s the most embarrassing thing that’s ever happened to you in the lab?”
Although the event was run by Jo Moran, Renze Gao, a Biological sciences honours student, designed and developed all of the activities and resources for the day for his honours project. Renze hugely enjoyed working out how to make what he knew about microbes accessible to 10 year olds, and is considering doing something similar in his future career.
We busk a little differently to most people. Having assembled from various locations around the UK, warming up with hot drinks in a pokey central London Starbucks, we play our favourite game. When you check out the next BES Annual Meeting (you know you want to), be sure to keep your eyes peeled for it. It will change your life.
As a BES Roadie, I’ve received public engagement training, helped develop busking activities and had the opportunity to attend music festivals and science festivals across the country. The end goal being to better my science communication skills and inform people outside the world of science on diverse matters such as ecology, and the research I conduct for my PhD.
These activities are great for engaging people and spreading the word of ecology, however, there are communities that we are still struggling to reach. As stated in the BES ‘Making Ecology for All’ report from 2013, members of BAME (Black, Asian and Minority Ethnic) community are significantly less likely to be in a STEM profession when compared to White counterparts. In 2010/11, BAME individuals made up 16.7% of all biological science students. This is an underrepresentation when compared to both the total for all STEM subjects, 20.1%, and for all subjects, 18.4%. There are no excuses for this gap; in the 21st century I am appalled that recent figures published by the Higher Education Statistics Agency reveal that no British University is employing a Black academic in a senior management role. This must change.
Now back to our London ‘Poo Game’ trip. The Windsor Fellowship has collaborated with the Royal Society to provide a mentoring scheme for Year 13 Black students living or studying in Greater London, who are studying STEM subjects. This is where we, the BES Roadies, come into the picture. We were given a one hour slot during a day long workshop, to communicate ecology to the students. Jessica opened the session with a brief introduction to the BES and the importance of science communication. We then split the cohort into four groups and took one group each to demonstrate our busking activities. Karen got to play ‘Pollinator Top Trumps’, Arron had ‘Who’s Poo?’ Jessica was on the ‘Mushroom Game’ and I demonstrated the use of taxonomic keys using the ‘Festival Animals’ busk that we took to Wychwood festival back in June. The students rotated around the different activities before reconvening in the seminar room where I then gave a short talk on my research.
I am used to communicating my work to academics back in my University department and at the odd conference. Entertaining a room of A-level students however, was a pretty terrifying prospect. When I asked if anyone had heard of the term ‘symbiosis’ some students nodded their head with a vague look of recollection whilst others shook their heads. Using examples such as corals, the bobtail squid, nitrogen-fixing bacteria in plant roots and deep sea tube worms, I got the students on board with the concept. Explaining the use of fruit flies and their symbiont to study host-shifts was a little trickier, I was nervous that this was where I might lose them. To my surprise, I was bombarded with questions. From the development and maintenance of symbioses and coevolution to the nitty gritty techniques I used to achieve my work and collect data, these students were the most inquisitive and enthusiastic audience I have ever had. It was an enormous pleasure to spend time with them. If I haven’t persuaded them that parasites and mutualists are just about the coolest things to study, then at least they will have left the session with a broader understanding of the term ecology. I hope that we will continue to engage with a diverse range of communities in the BES and look forward to reuniting with the Roadies for more science communication.
This is a guest blog written by Caisey Pulford, a PhD student studying at the Institute for Integrative Biology
On Wednesday 25th January I visited Upton Hall School FCJ to speak with and inspire the next generation of female scientists. I was warmly welcomed to the school with a beautiful, informative and delicious lunch held by the head girls team. I was interested to chat with them informally about their career aspirations and informed them of the many opportunities that University has to offer them.
I then spent an hour presenting a talk to the year 12 students about current topical scientific research being conducted at the University and the impact of scientific research on a global scale. I spent time discussing the invasive Non-Typhoidal Salmonella epidemic in Africa and explained how genome sequencing has revolutionised scientific research. They were fascinated to learn more about “real life research” and about the many different options a career in science could offer them! An informal question time followed were the girls asked many questions about the courses at Liverpool and were keen to find out more about research at the Institute. I was delighted to hear that some students had already taken their first step on the research career ladder by focussing their Extended Project Qualifications (EPQs) on epidemics, viruses and bacteria. I have a feeling we will be seeing quite a few of them leading their own research soon!!!
I would like to extend a huge thank you to the staff and girls at Upton for welcoming me to the school so warmly, for listening so intently and for asking lots of questions! As the Upton Hall School Motto goes “Age quad agis” Whatever you do, do it well! (also have fun, learn lots and make a difference!)
I look forward to returning to Upton over the next few months to speak to the year 10 science students.
You can read more about Caisey’s visit and see the pictures on the Upton Hall School website:
Thoughts of Salmonella are more likely to get your stomach churning than stimulate your interest. But Salmonella is more than a bacterium that causes a bad stomach ache: certain types of the bacteria can cause serious damage. Professor Jay Hinton, a professor in IIB’s Dynamics and Management of Host Microbe Interactions theme, is finding out how different types of Salmonella cause such a wide range of symptom severity. His group uses gene expression to find out what factors differ between Salmonella subtypes in order to identify new treatments for the nastier types of Salmonella.
Jay has been working on microbial diseases for the past 30 years. In that time, he’s kept a sharp focus on studying Salmonella ever since he finished his PhD. “Salmonella bacteria are great to work with since you can do just about any experiment you want with them. There are also a lot of scientific resources available, including 50 years of research on their genetics and biochemistry. Anytime you work with Salmonella, you’re really standing on the shoulders of giants.” Jay commented.
For over 20 years, Jay has researched the type of Salmonella which is found all over the world, the one you’d likely run into if you happen to eat a bit of undercooked chicken (we’ll refer to it here as ‘Global Salmonella’). He first focused on the role of globalgene expression in the ability of Salmonella to make people ill. Jay’s work demonstrates that the more potent types Salmonella express higher levels of certain genes in order to make more of the proteins required to infect their host.
Global Salmonella is a rather innocent subtype. It’s tough enough to survive on dry surfaces and is responsible for severe gastroenteritis in healthy individuals—but there are other far more potent strains. One strain now in focus at Jay’s lab belongs to the ST313 sequence type—the numbering system simply means that it’s the 313thSalmonella type to be discovered. ST313 was first discovered in 2002 in sub-Saharan Africa. Global Salmonella is usually responsible for stomach upsets while ST313 causes a much nastier infection. ST313 kills 20% of the people it infects and the disease is also resistant to 9 antibiotics. ST313 also causes an especially dangerous disease if the patient is immunocompromised by malaria, HIV, or malnutrition. When these patients are infected with ST313, the Salmonella can spread to the liver and spleen and cause severe fever and diarrhoea.“To find ways to cure the disease, we must understand how the infection works. There have been very few new antibiotics made against Salmonella in recent years, so our group is using tools to learn why some Salmonella strains are much more dangerous than others.” said Jay. His group’s approach is to look for differences in virulence factors by comparing Salmonella strains at both the genomic and the gene expression levels. “Looking at the genome alone isn’t enough. The gene content of an organism does suggest potential phenotypes, but if a gene’s not expressed then it can’t cause a change in virulence. The approach we use is to consider both what genes are available and what genes are actually being expressed.” Jay commented.
When looking at the genome itself, researchers focus on natural genetic differences known as single nucleotide polymorphisms (SNPs). A SNP occurs when a single letter in a gene’s code is different between two individuals. Even in organisms of the same species, there are many SNPs that exist between individuals. Because of all this diversity, it’s not always easy to interpret the biological role of particular SNPs. For example, when comparing Global Salmonella and the ST313, there are 1000 different SNPs and over 300 genes which distinguish the two types. “It’s difficult to get information that helps us understand the actual biological differences when just looking at SNPs and genes. So we are using gene expression patterns to map functional information onto these two genomes.” says Jay.
When comparing gene expression between Global Salmonella and the African ST313 types, Jay’s group came across a protein which was much more highly expressed in ST313. Because this protein helps bacteria to survive in human serum, Jay believes that an increase in the amount of this protein allows ST313 to grow and live in the bloodstream. Jay’s group then wanted to understand the mechanism of the increased expression of this key protein, and focused on the nucleotide sequence differences between the two types of Salmonella. They were able to find a key SNP difference in the regulatory region of the gene that actually controls the level of expression.
This work is the culmination of a 4 year project by Jay and his group which was recently been completed, and his group is now getting ready to submit a manuscript for publication. The paper will include experimental work done by several post-docs and PhD students and will include data from infection models that show the role of this protein in causing disease. Jay hopes that the approach of using both genomics and gene expression will be applied by other researchers to identify and validate how other types of bacteria cause disease. “You need to study more strains to gain a broader understanding of how the extremely dangerous Salmonella infections happen.” said Jay.
Jay greatly enjoys sharing his work outside of his scientific community. He finds it easy to connect to others since most people he meets will have some form of a ‘Salmonella’ story. He also thinks that scientists as a whole need to be more proactive at communicating research. “Scientists don’t do enough to talk about the good we are doing. I’m lucky because my field is one that’s easy for people to understand, since everyone agrees that this research on Salmonella is worthwhile. As scientists, it is good to be outward facing with our research. The way we interact with people influences the way they see our work.” said Jay. Jay always strives to be collaborative and open to new ideas, whether it’s working with clinicians in Malawi or sharing techniques with colleagues. “The key for scientists is not to compete with one another but to work together.” Jay emphasized.
Jay started his career by earning his bachelor’s degree in microbiology. “I love microbiology because your experiments will yield results quite quickly—I’m not patient enough for really long experiments!” said Jay. He completed his PhD in plant pathogenesis by identifying virulence genes of Erwinia, the bacterium that causes potato rot. Jay then became more interested in gene regulation and identified Salmonella as the best available model system to study microbe-host interactions. This combination of a great model system and its impact on human health gives Jay his “get out of bed in the morning” factor.
Jay’s day-to-day job involves research, grant writing, and mentoring a group of 6 post-docs, 3 PhD students, and 1 MSc student. He also lectures first-year biology students on topics including “Infections in the 21st century.” When asked about a normal day at work, Jay motioned to his desk piled with papers and books and replied casually “A bit messy!” While Jay did make it a summer goal to clean his desk (which, by the autumn, was halfway finished), he admitted that it was hard to find the time within his endless to-do list. “There’s always more papers to read, another grant to write, or just rushing around from office to office between meetings.” said Jay. Jay also strives to leave time to step back from his to-do list and make time to reflect on ideas, concepts, and to gain new perspectives.
Jay’s group will be kept busy in the coming months with a new research project just funded by the Global Challenges Research Fund. This “10,000 Salmonella Genome Project” involves sequencing Salmonella isolates from thousands of patients in Africa and South America. “By discovering the types of Salmonella that are causing disease across the developing world, we hope our research will lead to new interventions that will improve the lives of people affected by these diseases.” said Jay about the impact of this newly-funded research.Jay’s group is itself a reflection of the global nature of his work, with researchers from Chile, Spain, Wales, Switzerland, Malawi, Colombia, and the UK. Jay’s research and his group truly embody what it means to be an ‘outward facing’ scientist, including the stuffed microbes that greet you with a friendly smile as you enter his office.
Want to see the Salmonella group in action? Check out their video:
, he’s kept a sharp focus on studying Salmonella ever since he finished his PhD. “Salmonella bacteria are great to work with since you can do just about any experiment you want with them. There are also a lot of scientific resources available, including 50 years of research on their genetics and biochemistry. Anytime you work with Salmonella, you’re really standing on the shoulders of giants.” Jay commented.
“To find ways to cure the disease, we must understand how the infection works. There have been very few new antibiotics made against Salmonella in recent years, so our group is using tools to learn why some Salmonella strains are much more dangerous than others.” said Jay. His group’s approach is to look for differences in virulence factors by comparing Salmonella strains at both the genomic and the gene expression levels. “Looking at the genome alone isn’t enough. The gene content of an organism does suggest potential phenotypes, but if a gene’s not expressed then it can’t cause a change in virulence. The approach we use is to consider both what genes are available and what genes are actually being expressed.” Jay commented.
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