Lancashire Science festival

On Thursday 29th of June, Marie Phelan of the Technology Directorate (NMR Metabolomics) and member of the Biochemical Society helped out the Society at the Lancashire Science Festival held in the Halls of University of Central Lancaster, Preston. The event was attended by primary and secondary schools from Cheshire, Merseyside, Greater Manchester and Lancashire with the aim to engage and inspire the next generation in science technology engineering and mathematics (STEM). The Biochemical Society ran several activities in order to inform and debate genome editing including recent advances such as CRISPR-Cas9 technology with pupils as young as 6 engaging in DNA editing methodology and ethics.

Figures: Some of the Biochemical Society volunteers speaking to local pupils at the Lancashire Science festival. Pupils learn about “Scientific Scissors”. Science Festival Exhibitors Main Hall

HLS Summer School

On 27th June 2017 the School of Life Sciences took part in the Health and Life Sciences Summer School, organised by Widening Participation and Outreach.

HLS Summer School1

Each summer the Widening Participation and Outreach team organises faculty-based residential events for local Year 10 students. These three day events give young people the chance to stay overnight in university accommodation, experience student life and work with staff and students from different subject disciplines.

Here in the School of Life Sciences we ran a session for 35 of the visiting year 10 students. Tom price, Tom Butts, Gwen Cowley and myself organised a series of short activities: extracting DNA from fruit, evolution and vertebrate phylogeny and observing fruit fly behaviour to answer the question “do drunk fruit flies have sex more often?”

Our session in the Summer School received a lot of very positive feedback from participants.

“Really enjoyable and opened up new career choices for me in the future”

“Really enjoyed all the activities as they were interesting especially liked the one about brains”

“The fly sex activity was fun because it showed their behaviour”

“Very interesting with very lovely and friendly people”

 Thanks to everyone who ran sessions or helped out on the day, a good afternoon was had by all!

Meet the Scientists On Tour

Meet the Scientists On Tour

by Rebecca Jones

Meet the Scientists on Tour 

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 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!

 

Central Station

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!

 

If you’re interested in designing an activity or want some more information, contact us on twitter at @MTS_OnTour, or by emailing kwanelik@liv.ac.uk.

The Sciku Project – Using Japanese poetry to explore scientific research

This is a guest post by Andrew Holmes, Postdoctoral Research Associate in the Mammalian Behaviour & Evolution group of the Institute of Integrative Biology.

How quickly can you summarise your research or latest paper? A minute? Thirty seconds? A sentence?

How about 17 syllables?

That’s the challenge set by The Sciku Project, a website designed for scientists and mathematicians to share their latest research findings through the medium of sciku – scientific haiku.

It may seem odd condensing years of work or a complex theory into a handful of words but I promise that the benefits of such drastic minimalism are well worth it, both personally and professionally.

But first, some background. Haiku are a form of Japanese poetry. In the west they are 17 syllables long and written in three lines: five, seven and five syllables. The best haiku are evocative, humorous or beautiful and the very best are all three at once. Their brevity makes them quick to read but their contents linger in the mind – thought stimulants in word-pill form.

You might be asking why anyone would want to write scientific haiku but it’s not as strange as it might seem. Throughout the long history of haiku there has been a strong focus on the natural world; animals, plants, the weather and the cosmos all have been regular subjects for haiku masters and traditional haiku always feature a reference to the season. Using science as subject matter then is not too much of a stretch.

sciku

Haiku have a long tradition of using nature as a subject. Thank you to the Mammalian Behaviour & Evolution group for their gift of this book.

Haiku can also help us think about our own work. They frequently describe a small moment or thought that leads to a wider contemplation of its place in the world. I don’t know about you but all too easily I get wrapped up in the day-to-day details of my research. Scientific haiku help me to remember the bigger picture; writing haiku lets me trim the fat and get to the bones of what matters and why.

Furthermore, evidence suggests that writing scientific haiku can actually help us understand and communicate our own work: undergraduate science students asked to compose haiku subsequently explained their subject matter with greater accuracy and articulation. From my personal experience, haiku also provide a different perspective of my work and a better understanding of its impact – a boon in today’s funding climate.

Finally, and perhaps most importantly, writing scientific haiku is fun. As a researcher I plan experiments, run bioassays, crunch numbers and do rather too much washing up of equipment for my liking. And then there’s the writing: dry research papers and slightly desperate grant applications. Haiku let me revel in my work, they let me play with words again and break out of my usual mould. They remind me of my passion for science.

Have a go yourself. If you’ve had a paper published or read an interesting finding, if you have a favourite theory or statistical test, whatever it is that fascinates you, celebrate it with a sciku. In today’s busy world it takes but a moment to enjoy a haiku and only slightly longer to compose one. And I’ll let you into a little secret – whilst it might be hard to construct the perfect haiku, across only 17 syllables it’s difficult to go too wrong with a sciku. It’s a remarkably forgiving medium.

If you’re curious then visit The Sciku Project. Each scientific haiku is accompanied by a brief explanation and links to the original research. Treat yourself to a Random sciku or Explore the back catalogue. If you discover there’s an area that’s not covered then set us right and Contribute your own sciku. You can also follow The Sciku Project on Twitter and Facebook.

The Sciku Project was set up by Andrew Holmes, a Postdoctoral Research Associate in the Mammalian Behaviour & Evolution group of the Institute of Integrative Biology. Visit https://thescikuproject.com for more information.

Sex & Bugs & Rock ‘n Roll 2017

What happened in June 2017? The GE, summer solstice, Lions vs New Zealand…. OK, so various big events occurred in the month of June, but the highlight for me was the creation of a pop-up city with a population of around 175,000 people. I am of course referring to Glastonbury Festival, where people congregate at Worthy Farm in Somerset to watch music, comedy, dance, circus and other arts. I formed part of team of 6 ecologists from around the UK, headed up by Lancaster University’s Emma Sayer, who took ecology to the Glastonbury. Why take ecology to Glastonbury? Aside from the music and vibrant atmosphere, we could engage with hundreds of members of the general public, over the course of just 5 days. This opportunity does not often occur. Based in the Green Futures field, we shared our pitch with campaigners, visionaries, environmentalists and artists with a passion for sustainability.

Glasto_PE

Left to right: Nick Loughlin, Ali Birkett, Emma Sayer, me (Jo Griffin) and Nigel Fisher 

This was the third year the ‘Sex & Bugs & Rock ’n Roll’ tent exhibited at Glastonbury, albeit my first. This year we had a woodland ecology theme. In the tent we had a collection of new and old ecological activities to offer, including the infamous ‘Whose Poo?’ and ‘How gross is your festival kit?’ There were mixed reactions to the latter. When given the opportunity to have a swab taken from an item of their festival kit and have it spread it on an agar plate, some punters shrivelled up their nose in distaste and replied ‘no thank you’! But the vast majority revelled in the opportunity to see the microbes that were present on their wristbands.

We also teamed up with National Trust Scotland, and for every group/individual who participated in ‘Create you Ideal Woodland’, a native tree will be planted. In the tent, you could also learn about the various woodland invertebrate species that we had on display, including earthworms, dung beetles and orange ladybirds. Did you know we have around 60 species of dung beetles in the UK that are dependent on dung? Without them we would have had to wade through ankle-deep cow dung at Worthy Farm, eugh!

While engaging with punters is extreme fun, busking on what was simultaneously the hottest June day since 1976 and the longest day of the year was tough. But fortunately we didn’t have to negotiate the churned mud bath of the previous year. In total we engaged with over 1000 members of the public during the 5 days, and many of these were high level interactions, lasting over 30 minutes in length. What a success! Never before have I been asked so much about, and had so much interest in the research I carry out for my PhD.

None of this would have been possible without Emma, who organised and designed the tent with the aid of collaborators and funding from the British Ecological Society (BES), Bangor University, University of Kent, Wytham Woods (University of Oxford), Lancaster University and Wiley. Not forgetting the rest of the volunteers: Ali Birkett, Nick Loughlin, Hannah Griffiths and Nigel Fisher, who shared their enthusiasm and love of ecology with festival-goers, and provided fantastic company (and dancing) throughout the week. Finally, the biggest thanks goes to the 1000 punters who gave up their time to talk to us.  by Jo Griffin

You can find more information about ‘Sex & Bugs & Rock ‘n Roll’ at: www.festivalbugs.org

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Quantum dots for Immunofluorescence

Guest post by Dave Mason; reblogged from rapha-z-lab

In modern cell biology and light microscopy, immunofluorescence is a workhorse experiment. The same way antibodies can recognise foreign pathogens in an animal, so the specificity of antibodies can be used to label specific targets within the cell. When antibodies are bound to a fluorophore of your choice, and in combination with light microscopy, this makes for a versatile platform for research and diagnostics.

Most small-dye based fluorophores that are used in combination with antibodies suffer from a limitation; hit them with enough light and you irreversibly damage the fluorochrome, rendering the dye ‘invisible’ or photobleached. This property is the basis of several biophysical techniques such as Fluorescence Recovery After Photobleaching (FRAP) but for routine imaging it is largely an unwanted property.

Over 20 years ago, a new class of fluorescent conjugate was introduced in the form of Quantum Dots (QDots); semiconductor nanocrystals that promised increased brightness, a broad excitation and narrow emission band (good when using multi-channel imaging) and most importantly: no photobleaching. They were hailed as a game changer: “When the methods are worked out, they’ll be used instantly” (ref). With the expectation that they would “…soon be a standard biological tool” (ref).

So what happened? Check the published literature or walk into any imaging lab today and you’ll find antibodies conjugated to all manner of small dyes from FITC and rhodamine to Cyanine and Alexa dyes. Rarely will you find QDot-conjugated antibodies used despite them being commercially available. Why would people shun a technology that seemingly provides so many advantages?

Based on some strange observations, when trying to use QDot-conjugated antibodies, Jen Francis, investigated this phenomenon more closely, systematically labelling different cellular targets with Quantum dots and traditional small molecule dyes.

Francis_et_alFig3_GM

Figure 3 from doi:10.3762/bjnano.8.125 shows Tubulin simultaneously labelled with small fluorescent dye (A) and QDots (B). Overlay shows Qdot in green and A488 in Magenta. See paper for more details. 

The work published in the Beilstein Journal of Nanotechnology (doi: 10.3762/bjnano.8.125) demonstrates a surprising finding. Some targets in the cell such as tubulin (the ‘gold standard’ for QDot labelling) label just as well with the QDot as with the dye (see above). Others however, including nuclear and some focal adhesion targets would only label with the organic dye.

2190-4286-8-125-graphical-abstract.png

The important question of course is: why the difference in labelling when using Quantum Dots or dyes? This is discussed in more detail in the paper but one explanation the evidence supports is that it is the size of the QDots that hinder their ability to access targets in the nucleus or large protein complexes. This explanation further highlights how little we really know about the 3D structure of protein complexes in the cell and the effect of fixation and permeabilisation upon them. Why for example, can tubulin be labelled with QDots but F-actin cannot, despite them both being abundant filamentous cytosolic structures? At this point we can’t say.

So why is this study important? Publication bias (the preferential publication of ‘positive’ results) has largely hidden the complications of using QDots for immunofluorescence. We and others have spent time and money, trying to optimise and troubleshoot experiments that upon closer study, have no chance of working. We therefore hope that by undertaking and publishing this study, other researchers can be better informed and understand when (or whether) it might be appropriate to use Quantum Dots before embarking on a project.

This paper was published in the Beilstein Journal of Nanotechnology, an Open Access, peer-reviewed journal funded entirely by the Beilstein-Institut.

 

Breaking up is hard to do: New insights into cell signalling revealed

Press release originally issued by the University of Liverpool on June 23, 2017:

A rewrite of biology classroom textbooks could soon be on the cards as scientists at the Universities of Liverpool and Washington reveal important new insights into how cells communicate with each other. The research is published today in the prestigious journal Science.

Cell signalling refers to the mechanisms cells use to communicate with each other. In humans, signalling normally regulates cell growth and repair and therefore contributes to diverse basic processes that control tissue physiology and brain function. However, abnormal cell signalling contributes to many diseases, including diabetes, cancer and neurodegeneration. For this reason, the proteins that control disease signaling are important targets for many types of clinically-approved drugs.

In the new study, the researchers focused on understanding how proteins assemble into higher order signalling complexes, which control aspects of cell communication and cell fate such as the decision to live or die, using the ‘textbook’ cyclic AMP (cAMP) signalling pathway.

In the late 1960s, cAMP was shown to activate an enzyme complex termed Protein Kinase A (PKA), which can exist in both ‘active’ and ‘inactive’ forms depending upon the type of complex assembled.  It had long been thought that cAMP levels were sensed in cells by a release of the active kinase component from the larger PKA complex, rather like ice cubes breaking apart after being added to a drink.

Using contemporary scientific strategies, including electron microscopy, mass spectrometry, chemical genetics and real-time imaging, the researchers found that instead of being broken apart by physiological levels of cAMP, the signalling complexes remain intact, directly delivering the appropriate message into the correct part of the cell interior.

The study was carried out by Dr Dominic Byrne and Dr Matthias Vonderach in the laboratories of Dr Patrick Eyers and Professor Claire Eyers in the Department of Biochemistry at the University’s Institute of Integrative Biology, in collaboration with Dr Donelson Smith and Professor John Scott and colleagues at the University of Washington.

Dr Patrick Eyers explained: “We believe the finding that PKA protein complexes respond to the second messenger cAMP in a different way than we had assumed for nearly half a century, might bring about other changes in how we understand cell communication, especially the type of signaling we study that involves protein modification (phosphorylation) by protein kinases.

“It might also prove important for a better biochemical understanding of how medicines affect PKA signaling complexes, allowing us to develop drugs with fewer side-effects.”

The next challenge for the team will be to try to explain how the larger PKA signalling complex functions in cells, and how it is regulated by various factors.

The research received funding support from the UK Biotechnology and Biological Sciences Research Council, North West Cancer Research and the Howard Hughes Medical Institute.

The paper ‘Local protein kinase A action proceeds through intact holoenzymes’ is published in Science [DOI: 10.1126/science.aaj1669]