Hello and welcome to my blog! My name is Caroline and I am a PhD student at the University of Sheffield. My research project focuses on Striga - a genus of parasitic plants that devastates harvests by infecting food crops. I am exploring the defence reactions that can make host plants more resistant against Striga. Due to my ongoing battles with anorexia, I haven't made as much progress as I would have liked but I am determined to finish the course.


This blog charts the ups and downs of life in the lab, plus my dreams to become a science communicator and forays into public engagement and science policy....all while trying to keep my mental and physical health intact. Along the way, I'll also be sharing new plant science stories, and profiles of some of the researchers who inspire me on this journey. So whether you have a fascination for plants, are curious about what science research involves, or just wonder what exactly I do all day, read on - I hope you find it entertaining!


Thursday, 25 December 2014

Merry Christmas!

Whether you read this blog regularly or stumbled on it by accident , I wish you a very Merry Christmas and may God bless you,over the year to come. It certianly has been a busy one for me and who knows what the next will bring?

Monday, 22 December 2014

Can't see the roots for the trees.... and an update on POST


It's been a busy few days as the lab prepares for the great annual "Shutdown".... watering rotas, last orders, cleaning down benches... fortunately my second supervisor has kindly offered to water my plants over the Christmas Period itself so I can snatch a few days in Solihull with my family.


Meanwhile, I have been trying to perfect my rhizotron systems before I start working on valuable mutant lines. My main problem at the moment is that it is essential to see the roots of my little seedlings in order to measure the extent of parasite infection. But Arabidopsis plants have white roots... and I grow them on a delicate white mesh to stop the roots from penetrating into the growth medium (if they stay on the surface, it is easier to infect them with parasites).  Trying to analyse the photos gives me a headache so I have been trying a few alternatives. Attempting to dye the roots had some effect (see below) but this isn't really suitable as it could have an adverse consequence on the parasites, influencing the results. Dying the mesh didn't really work either so my first supervisor made a trip to that great supplier of scientific materials ... John Lewis! But the dark-coloured mesh she found there could be just the thing and I have just sown a new batch of seedlings which will be the guinea pigs to try this on. Watch this space!



White roots on White mesh... tricky


Arabidopsis roots dyed with Toluidine Blue

For those that read the  Post  "POST me a note as fast as you can..." (published on 23rd November), I am afraid that I am no longer in the POSTNote competition as my team literally disintegrated! Pressures of deadlines and experiments (in one case, even a Viva to prepare for) forced my teammates to pull out until I was the last one standing. As the competition is designed as a team effort, the organisers suggested it would be best if I withdrew. But with the amount of things that have been going on just recently, perhaps it is just as well...
The new Black Mesh - from a reputable supplier of scientific equipment!

Thursday, 11 December 2014

What can we learn from Badgers?

It's an issue that crops up in the media again and again.... Badger culling to prevent TB in cattle. Dr Rosie Woodroffe (Zoological Society of London), whose research sits right at the heart of the debate, had been invited by the Science in Policy group to describe her attempts to ensure the government's policy on this issue is based on sound science.
'If anyone at DEFRA knew I was giving a talk on how to influence policy they would be laughing their socks off' she began. During her ten years as a Government Advisor, Dr Woodroffe has campaigned compellingly for culling practices to cease. But this is no horror reaction to the killing of cute, furry animals; as an impartial scientist, her arguments are based on sound evidence that culling simply doesn't work. In fact, it actually seems to make the problem WORSE.

When this 'surprising' result was discovered in 2007, 'the ministers didn't want to hear it and didn't believe it', especially as the researchers themselves were at a loss to explain the result. Since then, it has emerged that removing such highly territorial animals encourages the remaining individuals to disperse, effectively spreading TB across a larger area.  Eventually in July 2008, her reasoning prevailed and the government dropped impending plans for culls.

But it seems that contentious policies, even those based on sure facts, have a lifetime set to parliamentary elections. After only being in power for 'ten minutes', the new coalition government announced plans to reintroduce badger culling in May 2007. It seemed that Dr Woodroffe was back to square one.

In such a situation, how can one influence policy? There is a depressing trend in campaigning where the willingness of a person to talk to you decreases as their ability to influence policy increases. Dr Woodroffe found a clever way to circumvent this however, by enrolling badger fan and former Queen guitarist, Brian May. MPs were then queuing up to attend her sessions! She also got on side The Badger Trust, a campaign group with a powerful voice that isn't afraid to get legal. For instance, when the Welsh Assembly introduced a plan in 2009 where badgers could be killed under the Animal Health Act , the Badger Trust took the case to court and won - the plan was scrapped. Interestingly, TB rates are falling quicker in Wales now than they are in England...

Perhaps most importantly, however, was her 'community- based' strategy as opposed to a 'top down' policy enforcement approach. According to Dr Woodroffe, badgers can divide rural communities to the point of 'civil war', particularly between farmers trying to make a living and those who appreciate seeing badgers scampering across their garden lawns. By talking to farmers and discussing viable alternatives, such as vaccination, Dr Woodroffe was able to make some headway. 'People are people and don't like being told what to do' she said. 'Being told not to do something may not necessarily be enough to stop people...they need to understand and believe the evidence for it'. Could this be a lesson for improving the profile of GM crops? Instead of targeting ministers and MPs, should we be engaging with the very bedrock of the agricultural community - the farmers and agriculturalists who would actually sow the seed into the ground?

Dr Woodroffe's combined approach bore fruit in March 2014 when there was an overwhelming vote - 214 MPs against 1 - to halt badger culling in England. But the issue is certainly not settled, with new plans for culling expected to be announced soon.

From this roller coaster journey, Dr Woodroffe concluded with some wise points of advice:
1. There are lots of routes to influence policy makers - and you can think outside the box! ( in her case, inviting MPs along to badger tagging sessions where they could handle the furry beasts was another good strategy!)
2. Influence can take a LONG time to achieve
3. The media can be helpful....or detrimental. According to Dr Woodroffe, the medias' desire to achieve balanced coverage meant that she was frequently featured in articles and press releases. And yet her message wasn't always faithfully replicated.....'I could give a talk and have the journalist from. The. Guardian and a farmer sat in the front row and the stories they would write would be 100% different' she said.

Although badgers may be a specialist topic, the lessons here are applicable to many Science policy issues. Does anyone know a celebrity that would support a GM Crop campaign?

Friday, 5 December 2014

A Christmas Lecture with a Difference...

 
'Incredible!' 'Amazing!' ''AWEsome!'

Just some of the reactions I heard from the young attendees of the Animal and Plant Science Department's Annual Christmas Lecture. Over a thousand schoolchildren left inspired by the lecture and interactive demos, beating each other with their free posters and still grappling with the puzzle they had each been given to demonstrate the importance of practice.

The APS Christmas Lecture is modelled on the Royal Society Christmas Lectures, with the theme this year being 'Animal Academy': a showcase of the intellectual powers of our fellow creatures. I can't imagine that the Royal Society has nearly as much fun as we did though...or that they make half as much noise! The classes fairly raised the roof when Head of Department, Professor Michael T Silva-Jothy, did a quick roll call to make sure all the schools were present. Then the lights dimmed, the crowd hushed and the show was underway. First, we were introduced to the incredible problem solving abilities of the crow family, demonstrated wonderfully by Vera the Raven. Though only nine months old, she had already learnt how to ring a bell, pick up rubbish and even sort out the recycling in order to earn a food reward. But then -just as the lecture moved onto the powerful sense of smell that dogs have - the police invaded! Apparently, a thief was suscpeted in the audience...enter Black Labrador Rocco who quickly swept the room to find the stolen article.

The excitement builds in The Octagon as the children and teachers take their seats
The culprit removed, we then learnt about the huge differences in the size of brains of different animals, a concept beautifully illustrated with entertainers in covetable animal onesies and giant, paper mâché brains! We were then able to test our memory against chimps using a number- recall exercise. For a brief second, an image with the numbers 1-7 scattered across it flashed onto the screen , to be replaced with the letters A-G in place of the numbers. The question: which letter is in the same place that number 4 was? I was hopeless and even the children struggled to get it right. Apparently, this is because we are trained to read numbers by their order: as soon as the image appears, we literally try to find them in series, first the 1, then the 2 and so on. Amazingly, a chimpanzee can recall the exact location of ALL the numbers, even if the image only appears for a QUARTER of a second! This is because the chimp doesn't attach any meaning to the numbers and instead takes a mental 'photograph' of the image, allowing it to recall every location from memory.
Police Dog Rocco searches the hall for the thief! 
Despite this, human brains are still powerful, as demonstrated by Callum, a young volunteer who joined a group of neuroscientists on stage to be fitted with an EEG device. This recorded the electrical impulses from neurones firing in his brain. Once the machine had been calibrated to recognise Calum's 'normal' brain activity, an image of a floating box was brought up onto the screen. Simply using the power of focused thought, Calum was able to move the box across the screen at will - without touching the keyboard at all. It felt as though we were delving into the realms of the science- fictional and made the audience shriek with delight as the box zoomed around before them.

For the grand finale, the children were instructed to open their mystery envelopes and retrieve their metal puzzles. A seemingly simple task - to separate the two interlocked pieces - but fiendishly difficult to accomplish! But on being shown the correct method, the children found that practice really could make perfect. And with that, the hall was once again invaded - this time by a marching samba band and a troop of circus performers keen to demonstrate just what humans are capable of learning with a bit of practice. I think the break dancing schools will be inundated with new recruits after the show we were treated to!

As the clapping died down, I had to zoom from my seat to get to my demonstration stall in time. A dozen or so different stands, all on the theme of 'Animal Intelligence', had been arranged outside the theatre to provide hands on activities for the kids. I was working with Duncan, Lucy and Camilla on the topic of songbirds, and in particular, how they learn their complex repertoires of songs. My fellow demonstrators had been inspired to construct a birdcage to surround our stall. Once inside, 'Alex the Friendly Parrot' would then play some recorded examples of birds that were taught to sing complex, human tunes and even mimic sounds as absurd as chainsaws and camera shutters. Whilst they were waiting to go inside, Camilla and I kept them entertained with a quiz on songbird facts - did you know that starlings can learn the songs of up to 22 different birds?!
Our stall ... featuring Alex the Parrot and the birdsong quiz

As the kids came thick and fast, it was a good lesson in adapting science to suit the audience. With their hyper energy levels, hundreds of distractions and teachers trying to keep order, our messages had to be succinct and memorable to make an impact. It was a far cry from the staid conference hall, where the audience is expected to sit still and keep quiet, no matter how dry the lecture! But the cage and parrot proved a hit, although I'm not sure if some of the children thought Alex was a REAL parrot...for most though, the glasses were a giveaway!

The children may only have been there for just under three hours but a phenomenal amount of planning went into this event, involving dozens of volunteer students across the department. It was a showpiece for the power of science to inspire young minds and something that all universities should aspire to. For students, my advice is to throw yourself into it and get involved! ( you don't necessarily have to wear a parrot costume!) As for me, I am already looking forward to next year and wonder what the theme could be next...fantastic fish? Brilliant bacteria? Marvellous mushrooms? Who knows?! But I do know...I want to be there!
Meeting Vera... a very clever Raven!

Saturday, 29 November 2014

Curious and curiouser...


One of my little Arabidopsis seedlings appears to be a mutant! Out of the hundreds of seeds I have sown so far, one has germinated into a spindly specimen with curiously lobed leaves. This is a little unexpected, as my seed are all a 'wild type' genome. When a lab wants to identify new genes involved with a certain process ( e.g. Shoot development, drought resistance, defence against pathogens), the seed are treated with chemical agents or radiation that induces changes in the DNA. If the change is severe enough, the gene may become inactive. The seed is then germinated and the seedlings screend to identify any aberrant phenotypes. If a gene required for pathogen resistance is mutated, for instance, the resulting seedling may show greater susceptibility to nasty fungi or bacteria.  The mutant can then be used to identify and clone the gene in question.

But I shouldn't have any mutants! My seed didn't undergo any hideous treatment, so this must be one of those 'random mutagenesis' events which my undergraduate lecturers assured us do happen sometimes, and which from the basis of Darwin's theory if natural selection. It is part of what makes working in living organisms so interesting; there is always a degree of 'randomness' thrown into the mix. This can get a little frustrating, however, when it comes to performing statistical analyses and your data is skewed by one or two ridiculous outliers which clearly aren't 'normal'!

As this little plant is clearly an oddity, I can't use it for my experiments but I did enquire in a lab working in shoot development in the department if they might be interested. They seemed curious, but I was warned that the seedling probably wouldn't survive if may even 'grow out of' the phenotype. Indeed, since this photo was taken, my little mutant has indeed got progressively worse. The hypocotyl ( the stem of a seedling ) grew so long and spindly that it fell over and it has only weakened since then. But at least it served as a reminder that you can never take anything for granted in biology - who knows what will turn up?


Friday, 28 November 2014

At the Offices of the JXB - Where it all Happens!

The ultimate aim of any research PhD is to break into the world of scientific publishing, presided over by those great journals of esteem. Whilst we may be familiar with the hours of lab work, note taking, analysing data and writing drafts that go into making a paper, the process where these get accepted into the scientific community are less obvious. So I was glad to accept an invitation to view the headquarters of The Journal of Experimental Botany (JXB), at Bailrigg House on the Univeristy of Lancaster campus.
Just some of the illustrious journals published by the JXB over the years


Although Bailrigg House is styled as an Edwardian country house, the interior offices were airy, mixer and remarkably paperless. Nowadays, the entire process whereby papers arrive, are checked, sent for review and edited, occurs wholly online but this wasn't always the case: I was told about the early days of the journal where everything had to photocopied and sent in triplicate. The must have kept the filing cabinet industry in business!

When a manuscript arrives through the online system BenchPress, it is first checked for any obvious formatting errors before being sent on to the editorial staff. If the paper is totally outside the remit of the Journal, it is classed as 'Rapid Reject';  this occurs for about forty per cent of papers. Otherwise, the paper is passed to two reviewers, chosen for having specific knowledge about the topic. Reviewers are typically post doctoral researchers or principal investigators who voluntarily give their time to assess the work of their colleagues. Getting reviewer comments returned is apparently the most difficult part of the process as researchers can be very busy people with lectures , conferences and their own papers to write. The JXB asks reviewers to return their comments within 12 days but this doesn't always happen!
The VERY FIRST Journal of Experimental Botany!


The editor makes a decision on the manuscript based on the reviewers' comments. The JXB has five categories: Acceptance, Minor Revision, Major Revision, Reject, Resubmit or simply Reject. Out of around 1800 manuscripts submitted last year, approximately 350 were accepted for publication. It is very rare though for a paper to be accepted immediately without any corrections required, about 1%. But I was heartened to hear that when a paper requires major revisions, the majority of these still make it into the journal. It is the 'Reject' category that must be avoided at all costs!

Chatting to the office team, it was easy to see the glamorous aspects of the job: travelling to conferences, having access to the latest cutting-edge research, interacting with scientists from around the globe. But it isn't without its downsides; never ending deadlines, new manuscripts constantly coming in and having to deal with researchers that take criticism harshly...
Given that so few PhD students make it up the Academic Ladder however, I shall certainly be keeping my options open for a career in scientific journalism.

Thank you, JXB, for a fascinating tour!

Sunday, 23 November 2014

POST me a note as fast as you can...

Have I bitten off more than I can chew? For some reason, I thought it would be a good idea to enter the Science in Policy Group's POST note challenge. But I am just beginning to realise the scale of the challenge I have taken on...

POST notes are produced by the Parliamentary Office of Science and Technology to provide MPs with enough up to date and relevant information for them to have a comprehensive grasp of key topics that could influence current policy ( for instance, aging populations, agricultural land uses, cybercrime...). These have to be balanced, impartial documents that are strictly factual, rather than advocating a particular policy. Furthermore, no matter how broad the topic, all the information must be contained within 4 A4 pages. Given how I struggle with word limits, this point is particularly daunting!

For the competition, we were given a list of topics to choose from and then sorted into groups. I was teamed up with a chemist, medical biologist and psychologist to produce a POST note on....ageing populations and increasing longevity. Talk about a broad subject! The competition is designed to push us out of our comfort zone and to have us consider areas outside our normal research. But with a topic that impacts on so many aspects of our lives ( health, finance, personal well being...), it is difficult to know where to start!


Fortunately, the competiton launched with a half day workshop on POST writing. Professor Lorraine Maltby started us off with some advice on 'Writing for a non-specialist audience'. She described how people from different scientific disciplines tend to approach a problem in different ways. Engineers are goal oriented and driven to find a solution; social scientists apparently don't see that there IS necessarily a problem or a solution - it's the journey that's more important, and natural scientists float somewhere in the middle. 'We are trained to communicate in the norms of our disciplines' Professor Maltby said 'which is fine if we talk to ourselves, but problematic if we talk to each other'. And this is just within academia - when non-specialists and policy makers are added to the mix, the fun really starts!

As scientists, we take a lot of knowledge for granted when communicating with each other. But given that only 13 % of the current lot of MPs has a science-related degree, a very different language has to be used. Professor Maltby urged us to 'know your audience' and 'write to be understood, not to impress'. This seems the very reverse of writing scientific papers- we presume the audience knows a fair bit about the subject already and we try our hardest to 'wow' them with our research! One also has to consider the time constraints of MPs - if they ask for evidence, it's no good directing them to a primary research paper - they wouldn't have time to read it and probably wouldn't understand it anyway. Apparently the key criterion if success for a POST note is 'The Breakfast Challenge'. If David Cameron reads your note whilst eating his morning wheatabix, will he be totally up to speed on the topic by the time he finishes? Conciseness is key, every word must count although we are fortunately allowed to use diagrams and images ( a JPEG tells 1,042 words)...but only if they are ABSOLUTELY NECESSARY. Professor Maltby's final point was to 'revise, revise, revise'; show your note to anybody and everybody and be prepared to spend more time correcting it than actually writing it!

Further practical advice was given by Dr Helen Hicks in the next talk 'Writing a POSTnote – the process and the fellowship experience'. This was especially useful as Dr Hicks is an old hand at publishing POST notes, having authored POST note 418 (Balancing Nature and Agriculture) whilst completing a POST Fellowship scheme (12 week placements that allow early career scientists to get a flavour of Westminster and write a real POST note). She advised us to focus our notes on the IMPACTs that the topic had on people- apparently this 'makes the eyes of an MP light up'. We had to remember that what is important to scientists ( publishing potential, funding, etc) does not necessarily hold true for MPs, who are thinking about what legislation would be acceptable to the public and whether they have a chance of keeping their seat in the next election. Our mission was to consider as many angles as possible to produce a balanced document that summarised the full weight of evidence. But a scientific balance does NOT equal the BBC's view. A good example is climate change: although there is considerable evidence for anthropogenic global warming, on televised/ radio debates, the BBC will always give almost equal air time to a climate change denier, giving the audience the mistaken impression that there is still much uncertainty about whether this phenomenon is actually happening.

Given that we would be working in teams drawn across the whole faculty of science, Dr Nick Worsfold (from The University of Bedfordshire ) then provided some theory in 'Working in multidisciplinary groups'. Terms such as 'interdisciplinary',' multidisciplinary' and 'transdisciplinary' are bandied around a lot these days, especially in attempts to make grant proposals more attractive. But they don't all mean the same thing! 'Multidisciplinary' approaches have at least two different inputs, but these are purely additive and nothing new is gained. Dr Worsfold gave the example of having two scoops of ice cream, one chocolate and the other mint ( although perhaps you have your own preferences?). 'Interdisciplinary' approaches again have multiple inputs but these are combined in a way that adds something on top of these. In the ice cream analogy, this would involve combining different flavours with  additional ingredients to make a knicker bicker glory. As for 'transdisciplinary' methods, these are more focused on a process that can make a completely new product. Hence, eggs, flour, sugar, milk become...a cake!

Which is all very well and philosophical but why do we NEED multidisciplinarity? Quite simply, to solve real world problems. Dr Worsford argued that disciplines are not so very different if they approach problems in a similar way but working together allows new perspectives to be be brought together on complex issues. This is vital for comprehensive services, such as healthcare, which require the whole package to be considered, rather than individual strands, in order for any solution to be successful.
But working together requires a 'common language'. What a mathematician would describe with an equation, a biologist would prefer to see in a graph. As for politicians, very often the message is conveyed by words alone! Hence, the role of POST notes in translating primary research into terms that can be digested by the masses. Even when scientists can communicate successfully with public representatives, however, the result is not always what we, as researchers, would prefer. 'It is perfectly legitimate for elected policy members, representing their constituencies, to look at all the scientific evidence and ignore it' Dr Worsford argued. 'This is part of democracy. I would be really worried if the House of Commons was full of scientists - good science is only one part of the debate'.

That may be so, but weighing up the scientific evidence is quite enough for me to be getting on with in the meantime! After a quick brainstorming session in our teams, juggling diaries to squeeze in the next meeting and rapidly exchanging email addresses, we then departed back to our very real worlds of individual research. From the lofty palaces of Westminster, back to my growth cabinet to top up my Arabidopsis seedlings with enough water for the weekend. It's been a busy week!