“Microbes around us” outreach event with Northwood Primary School, 15.03.17

Written by Jo Moran

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.

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BES Roadies: Who’s poo?

by Jo Griffin

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.

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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.

If you would like to become involved with the BES Roadies, please see upcoming public engagement and training events on the BES website: http://www.britishecologicalsociety.org/learning-and-resources/public-engagement/

IIB PhD student visits Upton Hall School as an inspiring alumnus

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:

http://www.uptonhallschool.co.uk/news/?pid=3&nid=1&storyid=181

A Tale of Two Salmonellas

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 timehinton, 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 global gene 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 313th Salmonella 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.hmi-jh-figure“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.hmi_group-photoJay’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:

What is the Institute of Integrative Biology?

Guest writer Erica Brockmeier introduces a new series of posts featuring our scientists by first giving you an overview of the Institute of Integrative Biology.

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The Three Graces, Liverpool Waterfront

Liverpool is a city famous for its Fab Four, Three Graces, two rival football teams,
and instantly recognisable regional accent. Liverpool is also home to one of the six original ‘red brick’, Victorian-era universities, a university with a history spanning over 200 years. The University of Liverpool is associated with 9 Nobel Prize winners whose academic achievements include a better understanding of malaria and the economics of UK property rights.

However our University is not just an institution focused on its past—it also plays an active part in shaping the future of our city, our community, and the world. Here at the Institute of Integrative Biology (IIB), we’re working for a better understanding of the science of life at all ends of the spectrum. Our scientists study life across all scales, from genes, proteins, cells, animals and even ecosystems. You can think of biology as a ladder, where you start at the lowest rung (genes and proteins) and climb your way to the top (ecosystems). You need each step of the ladder to make it to the top in the same way that we need to study more than one area of biology in order to make progress towards a cleaner and safer world.

Delving into the intricacies of life as we know it isn’t an easy task. That’s why here at IIB, we’ve split up our efforts into four research themes to help us break down these complex systems into parts that we can see and study more clearly:

In the From Genomes to Biological Systems theme, scientists use state-of-the-art technologies to answer questions on how the instructions of life are encoded into the long, complex blueprints known as genomes. Researchers in this theme also work on how we can use knowledge of genes and genomes to address problems related to food security and energy.

Scientists working in the Molecular Basis of Therapeutic Targets theme are investigating how to make more effective drugs by studying how diseases target specific proteins and cells in the body. Members of this group are also working on understanding the differences in people that make some of us more susceptible to diseases (or drugs) than others.

Researchers of the Dynamics and Management of Host-Microbe Interactions study topics ranging from how infection occurs, why some individuals are more affected than others, and how the dynamics of a population can influence how fast a disease spreads.

On the top of biology ladder, our Adaptation to Environmental Change scientists are focused on how groups of animals and plants respond to altered habitats or extreme environmental changes, including global warming. They’re investigating ways to better protect sensitive species and to make sure that the food and materials we need can grow and thrive in a world faced with climate change.

In this blog series, we’ll be talking in-depth about each of our research themes as we highlight the work of four of our IIB scientists. If you’re interested in learning more about IIB and the work we do, be sure to check out our website and stay tuned for our series highlighting the work done here at IIB in the coming weeks!