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.

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]

Learning to Communicate – a Johnston Post-Doctoral Development Fund report

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

 

The Johnston Post-Doctoral Development Fund enabled me to attend a Royal Society residential course in in communication and media skills in June 2017. The course was hosted at the Kavli Royal Society International Centre at Chicheley Hall in Buckinghamshire, a Grade I listed 18th century mansion set in 80 acres of beautiful grounds that has been used in films such as Pride and Prejudice and The Meaning of Life. Hidden amongst the trees near the house lurk two large fiberglass pterodactyls from an earlier Royal Society event, now abandoned and eerily weather-beaten.

Andrew1.pngImage: Chicheley Hall and gardens (left); Pterodactyls amongst the trees (right).

The course was run by Dr Jon Copley, an Associate Professor at the University of Southampton and former reporter and editor at New Scientist, and Geoff Marsh, a freelance multimedia producer and science writer for publications including Nature. It was great to ask them about their own experiences in science communication, in particular Dr Copley was able to provide insight into his experiences working with the BBC on nature documentaries.

In the first half of the course we discussed and practiced how to write short popular science articles, using the ‘inverted triangle’ approach to present what was most important in a concise and engaging starting paragraph and then going into more details as the article continued. This approach is great for communicating to non-specialist audiences as well as in the lay summary sections of grant proposals.

We also covered writing press releases, long-form science writing and using social media. I have recently started my own website (https://thescikuproject.com) using scientific haiku to explore research findings. I have very little experience of using social media and the course has given me the confidence to start using it to promote my own website and research.

Andrew2Image: Andrew Holmes (left); Chicheley Hall Gardens (centre); a resident of Chicheley Hall (right).

The second half of the course covered the media and science, discussing the differences in function, requirement and audience expectations between media types – radio, tv, print and online reporting. By learning how the media works and the requirements of journalists we were able to understand how to interact with the media and retain more guidance of how our work is reported.

We also practiced being interviewed: a ‘soft’ radio interview; a ‘hard’ radio interview with probing questions about the ethical and societal issues associated with our work; and a TV interview via a remote link. Discussing our work in different contexts and having an awareness of the practical requirements of media production has helped me feel more confident about interacting with the media and promoting my work to the public in general.

I felt the course was excellently run and covered some very interesting and useful topics that as scientists we aren’t often trained to consider. By learning how better to present my research to a variety of audiences and through a number of formats I feel much better prepared to use my communication skills to help improve the impact of my research and promote my science to the world outside of academia.

I thank the Johnston Post-Doctoral Development Fund committee for this opportunity and hope they feel that it was justified – I certainly feel that I gained a lot from it.

 

 

Speed (dating) Science Careers

On the 19th January, 40 Year 12 students from Life Sciences UTC visited Life Sciences to take part in a Speed Science event with 5 PhD students from IIB.  This was part of their Build My Future Festival.

Small groups of students spent 5 minutes listening to a PhD student talk about their research before being given 5 minutes to ask questions on things such as the PhD student’s research, what university is like? What being a PhD student is like? Which degree programmes the PhD students had taken? before moving to the next PhD student to start the process again. Using this approach the students were able to speak to and ask lots of questions to a 5 different PhD students in a short space of time

The students were really engaged and asking lots of questions, whilst it gave the PhD students chance to practise their science communication.

Thanks to Tushar Piyush, Matthew Agwae, Hammed Badmos, Gospel Nwikue and Jonathan Temple for volunteering to help out at this event

Christmas lectures

Each year we are welcoming students from various secondary schools to our Christmas lectures. This year was once again a success:

Thanks to Jay Hinton (“It’s amazing you’re not dead yet”), Dada Pisconti (“The secret life of stem cells”) and James Hartwell (“Plants to save the world”) for their inspiring talks and thanks to our young visitors for coming.

Earlier version of Jay’s talk:

How we set about mending damaged knees with stem cells

Anthony Hollander, University of Liverpool

A meniscal tear is one of the most common knee injuries, especially in young, active people. Over a million new cases are diagnosed each year in Europe and the US alone, and it also affects professional sportspeople – footballer Luis Suarez, tennis player Roger Federer and Olympic swimmer Sharon Davies are among the many elite athletes to have suffered a meniscal tear. Unfortunately, there is no effective treatment for this injury, but my team and I believe we are one step closer to providing one. Our “living bandage” uses stem cells and collagen to regrow the damaged meniscal cartilage, which acts as a special kind of shock-absorber.

Knees are rather wonderful things – first class engineering provided through millennia of evolution. Huge forces are channelled through the knees when we stand up, walk or run, amounting to three to five times our body weight in normal daily use. And they must survive these extreme conditions every day while also giving us the flexibility that we enjoy whenever we move. When they work we don’t really notice them. But if we damage them, we suffer incredible pain and lose the freedom to live a normal, active life.

One of the reasons knees work so well is because of the meniscal cartilage, which sits between the bone-ends like stiff cushions. There are two of these menisci in each knee and they are incredibly important for protecting the bones in the joint. If we damage them we are in trouble. However, they can easily tear if we suffer a trauma to the knee and this is a very common type of sporting injury.

Most tears will not heal because there is no blood supply and so no chance for natural healing mechanisms to kick in. The standard way to treat them is an operation to remove the damaged part of the meniscus. This works quite well at first, but, in the long-term, our knees don’t do well with only a part of the meniscus. So, with time, there is wear-and-tear of the bone ends and this often leads to premature osteoarthritis. Once the arthritis sets in, it’s a one-way track to chronic pain and ultimately a joint replacement. Because meniscal tears often happen to young athletic people, this can mean many years of disability from arthritis and great cost to the health service.

MRI of knee with meniscus injury.
Semnic/Shutterstock.com

The long road to finding a cure

My research team began to focus on this problem about 13 years ago. We wanted to deliver living cells with healing properties into the middle of the tear and drive the repair from within. At that time we were studying the biology of a special kind of cell, the mesenchymal stem cell, that is found in small numbers in the bone marrow and which is important for natural healing mechanisms in the body.

But simple injection of the stem cells into the tear was not enough because they didn’t end up in the right place. We had to find a way to hold them close to the two injured surfaces of the tear so that they could migrate into the damaged tissue and release their molecular signals for repair. We eventually found a way to do this by placing them in a membrane made from collagen and inserting the stem cell-collagen combination into the tear. Over a few weeks the stem cells migrated into the surrounding meniscus and then the collagen degrades away, allowing healing across the tear boundary.

We published our findings, filed a patent to protect our discovery and then set about turning the science into medicine, coming up with a product called the Cell Bandage to test in patients. The first five patients have now been treated and although two of them suffered retear, the other three are all doing fine more than three years later. Although repair of the very outer edge of the meniscus is possible without stem cells because it has a blood supply, most of the meniscus is not repairable and all patients would be expected to re-tear within about a year. So the 60% success rate in this first group of patients to be treated with the Cell Bandage is very encouraging indeed and paves the way for much larger trials in the future.

Knees are indeed wonderful things but so too, it seems, are stem cells.

The Conversation

Anthony Hollander, Head of Institute of Integrative Biology, University of Liverpool

This article was originally published on The Conversation. Read the original article.