Telling tales of multiple Ps – Dr Lydia Cole

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

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

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Reeling off about peat at Ignite Liverpool!

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

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

Illustrating the link between peatlands, palm oil and peanut butter

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

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

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

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

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

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

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

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

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

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

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

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

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

Meet the Scientists

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Feedback from the CCI stand, seeing is believing:

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

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

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

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

Baltic Science Journal

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

 

My experience of the Aurora Leadership Programme

by Klara Wanelik

In March this year I embarked on a leadership training course for women in higher education, called the Aurora Leadership Programme. You might be thinking, why would I go on a course like this? Well, as an early career researcher (ECR) in this sector, I am very concerned by statistics like this:

“The proportion of female students (55%) and graduates (59%) in the EU exceeds that of male students, but women represent only 18% of grade A (professorial) academic staff”1

The aim of Aurora is to take positive action to address this under-representation of women in leadership positions in the higher education sector.

I attended four development days at the Royal Armouries Museum in Leeds (quite appropriate really!) and met hundreds of women from the higher education sector. It has taken me a while to digest all of this but I think I am finally starting to see the light at the end of the tunnel. I include some of my thoughts in this blog post with the hope of inspiring other female ECRs, and more generally inspiring others, to start questioning what it means to be a good a leader. I focus on two aspects of the programme that I found particularly useful. This choice is personal, and I’m sure that other women attending the programme would choose differently. But here goes…

Exploring core values

In one of the sessions, we were given a list of universal human values and asked to circle those that were most important to us: our ‘core values’. At the end of the session, each group pooled their results together on a kind of ‘value map’, where values were grouped under terms like universalism, benevolence and power. What I found particularly striking was that our table had circled lots of values in the former two groups (like equality, honesty and loyalty) but the power section of the map (with words like social recognition, public image and authority) was completely empty. And it wasn’t just our table, a colleague of mine who attended the programme in London, told me the same happened there.

How could this be? How could these women who had come together for the sole purpose of developing their leadership skills (some of them already in senior leadership positions) not feel that they identified with any of these values? There are two possible answers: 1) they didn’t feel comfortable sharing these values, or 2) they genuinely didn’t prioritise them. Given the spirit of openness that Aurora encourages, I assume that the second answer is the most likely. This isn’t a gender-specific phenomenon – we heard that men in leadership positions who completed this activity also highlighted the non-power-related values. This, I think, calls into question what we think a leader should be. Many of us still hang on to a traditional view of a leader being a dominating individual, with full authority, who is driven to do what he/she does for the recognition, wealth and/or the power they receive in return. This is a view we really need to shift. By doing this activity, we were being encouraged to consider the individuality of leadership and the importance of authenticity; staying true to your values, while leading. As one of the facilitators suggested, the best leaders are those that create the next generation of leaders. I think this is perhaps a more useful (and interesting) view of leadership than the traditional one.

Importance of storytelling and leading with “why”

In another session we learnt about the importance of storytelling in leadership. This sounded a bit odd to me at first, I’d never really put the two together but then I got talking to a woman on my table who proceeded to tell me about some charity work she was doing, somewhat connected to her work as a lawyer. The way she created a narrative about the people she was helping and what she was doing to help them captured my attention. I wanted to sign up straight away, even though I would have been of very little help (I’m a biologist not a lawyer!) It was at this moment though, when she was masterfully telling her story, that I realised how powerful storytelling could be in getting people to do what you want them to do.

The tables were turned on another occasion, after I watched a TED talk by Simon Sinek, which was recommended as part of the pre-work for an Aurora session. In his talk, Simon Sinek talks about inspiring action by leading with why we’re doing something, rather than how or what exactly we’re doing: “people don’t buy what we do, they buy why we do it”. Soon after watching this talk I had the opportunity to re-formulate my ‘elevator pitch’ about the research that I do. There is a real diversity of women on the Aurora programme, from professional services to academics, and from all different fields. On this occasion, I happened to be sat next to (another) lawyer, and to be honest, I was pretty sceptical about being able to really (genuinely) get her on board. To my surprise, my pitch did get her genuinely excited about my research and asking multiple questions. I still remember the look on her face! I’ll be trying my best to lead with “why” from now on.

Thank you

I would like to thank IIB for funding my place on the Aurora programme, all the inspirational women I met during my time on Aurora and my colleagues in IIB for supporting me along the way. Special thanks to Zen Lewis, who provided much needed encouragement and support and pushed me to re-apply for Aurora after I was initially unsuccessful in securing a place.

If you are a female ECR like me, I hope this post will encourage you to give the Aurora programme a go and to start thinking of yourself as a leader!

  1. Morley, L (2013) Women and Higher Education: Absences and Aspiration

AEC Outreach at BBC Gardeners’ Question Time

The BBC Gardeners’ question time event at Ness Botanical Gardens on the 16th of September was a great avenue for Researchers from the Department for Evolution, Ecology and Behaviour to showcase how the nature of gardens is underpinned by ecology and evolution.

Gardens are much more than the plants they contain. Georgia Drew, Jo Griffin & Louise Reynolds introduced visitors to the fascinating world of bees, butterflies, fruit flies and the ecosystem of microbial symbionts that these organisms host. Visitors were fascinated and horrified, in equal measure, at the case of male-killing bacteria in a population of tropical butterflies. Many were eager to know the potential applications of such information, including the fascinating role of symbionts in the control of aphid and other plant pest populations. Jo talked to the BBC producers about the use of symbionts in the prevention of insect-borne disease.

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Meanwhile, Franziska Brunner, Stew Plaistow & David Atkinson gave tours around their newly-renovated experimental ponds at Ness, and introduced visitors to their work on climate change impacts on aquatic ecosystems and pond life. Many were very impressed by the experimental ponds, and the logistics and methods needed to carry out this kind of study. The group’s pond-dipping tour gave visitors a chance to reconnect with their “inner child”, and come face-to-face with the incredible biodiversity concealed just beneath the surface of the garden pond. Catching sticklebacks turned out to be a major attraction during these pond-dipping sessions!

pond_dipping

Last but not least, visitors attended guided tours of an ongoing long-term experiment investigating how grassland plants cope with climate change, given by Raj Whitlock, Christoph Hahn, Di Yang, and George Airey. Visitors learned of the vital importance of grasslands for conservation and for providing crucial services to people, and of the threats posed to grasslands by climate change. The tour introduced a large drought manipulation experiment comprising 1,952 model grasslands, which assessed the potential for climate-driven evolution within plant species. After some hands-on botanical training, almost all of the visitors were able to identify all of the plant species in this experiment (although there were none keen enough to taste the delicious salad burnet [Sanguisorba minor] or sweet vernal grass [Anthoxanthum odoratum] on offer).

mesocosm_poster

All of us were impressed by the depth of questions that visitors asked, and by their enthusiasm for the underpinning science. It was a rewarding day, and we are looking forward to our next visit to Ness!

Science fun at the Gardener’s Question Time Anniversary Garden Party

The Mammalian Behaviour and Evolution Group (MBE) from the Institute of Integrative Biology was represented by four members (Paula Stockley, Holly Coombes, Callum Duffield and Stefan Fischer) at the Gardener’s Question Time Anniversary Garden Party in Ness Botanical Garden. The event saw more than 2000 guests visiting the garden and the live broadcasting of the BBC Radio 4 show. The whole day on Saturday 16th September was reserved for this massive event and the garden staff showed an immense effort to deal with all the visitors and exhibitors.

The MBE group secured a table in one of the huge exhibition marquees next to other exhibitors such as the Wirral Wildlife Trust, RSBP, and the Wirral Barn Owl Trust.

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We showed visitors the diversity of small mammals occurring in the UK with small posters, video clips and, as the highlight, two small rodents to observe. We chose two very different species for visitors to observe: a harvest mouse and a bank vole. Harvest mice are the smallest mouse species and are listed as a Biodiversity Action Plan Species because of their scarcity and the required conservation actions to stop their population decline. Bank voles are a very common rodent species occurring throughout Europe. The harvest mouse was definitely the star of our exhibition and every visitor left with a big smile after finding the little mouse inside the well-structured enclosure. It was particularly nice to see how every person visiting our stand, old or young, woman or man, reacted to the little rodents and how everyone was immediately interested in their behaviour and ecology and asked more facts about rodents in general. We had very nice conversations about topics as diverse as the work of the MBE group, conservation and general behaviour of rodents as well as pest control measurements. I think it was an extremely productive and well received exhibition and visitors of the stand left with a smile because they saw cute rodents and learned more about small mammals in the UK. Moreover visitors will remember that the MBE group of the University of Liverpool is engaged in diverse research areas to better understand and ultimately better conserve mammals in the UK and around the world.

Find out more about the Mammalian Behaviour and Evolution Group.