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!

Sunday, 9 April 2017

Pints, PCR and Publicity...

It's been a while since my last post and a lot seems to have happened in that time - the days are much longer and sunnier now and Easter is ridiculously close. And of course - the Pint of Science Festival has officially launched for 2017! As the official Social Media/Publicity manager for the Sheffield event, I was very busy in the run-up to our launch event on Monday 3rd April, making slideshows and videos to show on the night. Our venue, The Sheffield Tap, couldn't have been more suitable. With hundreds of craft beers lining the walls, it was easy to see why Sheffield is known as the 'real ale cpatial' of the UK. The high ceilings, gorgeous furnishings and brewing installation only added to the intimate atmosphere. Tonight it was crammed full of fun science demos - from Mylo the interactive robot; a model of a working kidney; a virtual reality experience and a highly competitive 'make a neurone' competition. Some of the Festival speakers also gave us a taste of what was to come, and we enjoyed fascinating forays into the political implications of terrorism; structural colour in the natural world; using stem cells to cure hearing loss and the failings of the prison system.

Some very impressive neurons...

Trying out virtual reality at The Sheffield Tap
 The launch perfectly captured what Pint of Science is all about - informal discussions on science between the public and researchers, helped by the presence of alcoholic beverages! It already seems to have generated excitement for the main festival in May as tickets across the whole programme are starting to sell.
Meeting Mylo, the interactive robot

I've also been doing some different things in the lab recently. After mucking about with my plants down in the growth chambers for so long, it was quite challenging to do some 'proper molecular work' again - very intricate, precise and sterile in comparison! One focus of my project is to look at a host of Arabidopsis plants with mutations in different defence-related pathways, to see if these alter resistance to the parasitic weed Striga gesnerioides. One of these mutants, pmr4 (defective in callose production) comes from a very old seed stock, so my supervisor was concerned that the mutation could have been lost. To check this, I decided to perform a PCR (Polymerase Chain Reaction) to amplify the region of DNA that should contain the mutation. In basic terms, DNA extracted from the plants is combined with short DNA sections (primers) that base-pair with the mutated sequence, and an enzyme called Taq DNA Polymerase which extends the length of the primers by adding new DNA bases. If the mutation is present, the primers and Taq DNA Polymerase recognise it and produce short sections of DNA (the product). To see if any product has been made, the solution is loaded into an agarose gel with an electric charge applied across it. Because DNA is negatively charged, it moves across the gel to the positive anode. A UV-sensitive dye is added to the solution before the DNA is run, so that the DNA appears as a 'band' on the gel. 

My wonderful gel photo. The bands in the centre correspond to the DNA product from the pmr4 mutation. The 'ladder' at the left side is a reference solution containing DNA products of known sizes. This allows the size of the experimental product to be calculated by comparing it to the nearest band on the ladder. 

PCR is notoriously difficult to get right - I once spent two weeks of a summer research project trying to get it to work on wheat. The temperatures and timings are very precise and there is little margin for error. So I wasn't hopeful at all that I would be successful, but went ahead anyway: extracting the DNA, performing the PCR, running the gel. Much to my astonishment the gel photo was exactly what I wanted with a neat row of bands right across the middle! This means that my plants definitely have the pmr4 mutation and are suitable for my experiments. If you want to know more, see here for a nice summary on PCR and Gel Electrophoresis. 

I hope you have been able to enjoy the beautiful sunshine of late. Sadly I've been in the library working on Pint of Science videos, or underground with my plants for most of it... but at least things are moving in the right direction. Hopefully I will be able to get out soon - the Peak District is calling! Have a good week and thanks for reading.

Saturday, 11 March 2017

Feeling blue...

If seeing is believing...then what does one do if you don't see what you expect to? This week I have certainly lost belief in my skills as a research  scientist...and all because I can't get the roots of my plants to turn blue!

My PhD is investigating what defence pathways may be important in determining how resistant a plant is to the parasitic weed, Striga gesnerioides. I'm particularly interested to see if two of the most well known plant defence hormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have a role. To do this, I have been growing a series of transgenic Arabidopsis hosts, that express reporter genes for either SA or JA. The reporter genes code for the enzyme β-glucuronidase (GUS), which converts the substrate 5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) into a coloured blue product. However the promoter region of the transgene (which controls when the gene is turned on) has been engineered so that is is only activated if either JA or SA is present: for my experiments, the LOX-GUS reporter is  activated by JA is present, and the PR1-GUS reporter by SA.

What I'm looking for - bright blue roots!

 So I have been very busy growing whole batches of these reporter Arabidopsis lines, infecting them with Striga,  harvesting the roots at different time points and adding X-Gluc. If the SA / JA pathway is activated by the parasite, then the GUS enzyme should act on X-Gluc, turning the roots bright blue. But each time I take my samples out of the incubator...nothing. Resolutely white roots. Could there be something wrong with my staining protocol? It's unlikely because each time I  include a few transgenic plants that express GUS all the time, whether or not SA/JA is present. These have perfectly blue roots every time! So the away itself isn't the problem.

In that case, could there be something wrong with the reporter genes themselves? To test this, I took some of the spare plants and applied SA or JA in solution to the roots. But even these didn't turn blue! I'm completely stumped...and so are my supervisors. Just possibly, the transgene isn't expressed in the roots at all....all the published studies I can find using LOX-GUS or PR1-GUS used leaf or shoot tissues. Whilst this negative results are hindering my current  progress, it does raise interesting questions. Does the root system have a different set of SA or JA responsive promoters to the shoots and leaves? Or are other plant hormones, such as auxin or cytokinins, more important for defence in the roots?
What I'm getting- resolutely white roots!

It is frustrating after all the time and effort I have spent growing and infecting these plants...at least I could cheer myself up at the department's Discovery Night on Friday. This annual open evening of interactive lectures,  activity stalls and laboratory tours has become a real highlight for the local community. Helping children extract DNA from strawberries and seeing their delight at things even as simple as a pipette helped take my mind off my  work worries and remind me that it's exploring the unknown that makes science always so fascinating...

Sunday, 19 February 2017

Busy, busy, busy....

My New Year's resolution to pace myself a bit more has quickly gone down the pan - largely due to my inability to say 'no' to things. But it's difficult not to when there is always so much going on within the Faculty of Science: every week seems to bring new  'cv-enhancing' public engagement opportunities. And then there is my PhD to fit on top of it all! Needless to say, although the year is still young, I am already feeling run down - having a bad cold and losing my voice didn't help either!

I've spent a lot of time underground this week, transplanting my Arabidopsis seedlings into rhizotrons: as I spend quite a few hours doing this, I made a basic diagram to illustrate the process. The seed is sterilised in the lab and germinated on petri dishes filled with agar to keep them safe from any bacterial or fungal nasties. When the roots are long enough (usually after 2 weeks), they are ready to transplant into my pre-made rhizotrons ('root observation chamber'). Essentially these are square petri dishes filled with a packing medium called vermiculite, with a hole at the bottom for drainage and one at the top for the seedling to poke through. After moistening the vermiculite with my trusty squirty bottle, I add a layer of mesh on top (to stop the seedling's roots growing into the vermiculite). The seedling is then carefully removed from the agar with tweezers and laid on top of the mesh. Finally, I tape the lid shut then wrap the whole thing in foil to keep the roots in darkness. In my growth cabinet, the rhizotrons are stacked vertically so that the roots grow downwards. When it is time to infect my seedlings, I simply peel back the foil, prise off the lid and apply the parasite seeds onto the roots.

It's intricate work that demands concentration....so after transplanting 60 or so seedlings at a time I am typically done in! It doesn't help that the radio reception is so poor down in the annexe, making it quite a lonely task too.

As for my 'other' work, outside the PhD....my main focus at the moment is the 24 hour Inspire event taking place on 30/31 March. This is a non-stop 24 hour series of lectures designed to enthral and entertain, whilst raising money for charity. As part of the publicity committee, I'm researching ways we can raise awareness - everything from having a stall in the student's union, parading around in animal costumes and appearing on local radio. The speaker programme for the Pint of Science Festival in May is also about to be announced, after which my work as social media secretary for this will really get underway. My aim is to make a series of short videos for Facebook and Twitter to promote the different talks and events. The trouble is, I haven't had much experience of video editing before so I duly attended some Creative Media Workshops this week hosted by the University's Computing Services Team. These proved a great way to boost my confidence and I managed to put together some pre-shot footage into a short film entitled "How to make a perfect cup of tea". Maybe not Speilberg standard but it's a start! The next step will be to borrow a camera and arrange some interviews with the Pint of Science speakers.
Putting together my video masterpiece

All of which is quite enough to be getting on with...but I haven't even mentioned the Science and Engineering Festival coming up and the demonstrating work I have signed up for. I think I really must put a filter on my email inbox, so that I stop seeing all these opportunities.....ooh, look! A science communication essay competition! How could I not say 'no' to that....?

I hope you have a good week and thanks for reading!

Friday, 3 February 2017

I survived! FameLab 2017!

"I don't care - I know I'm going to look stupid but I can't back out now" I gabbled anxiously to my patient friend as the room steadily filled up around us. "As long as I can make them laugh and they learn something, then I'll be happy!"

At school, I was always the one who wimped out of giving presentations or talking in front of the class.....so what on EARTH was I doing here as an entrant to FameLab 2017??! In this international competition, budding science communicators have the challenge of explaining a scientific topic of their choice in just three minutes...but here's the catch : No PowerPoint, No audio and only the props you can carry on stage. All to be followed by 2 minutes of questioning from the judging panel. I felt completely out of my depth - not helped by the fact that I'd inexplicably chosen to talk about something completely outside my own field of plant science. And also that the event had been a complete sell-out, with all the tickets being snapped up within days by the audience members now entering the room. Amazing that so many members of the public would gladly give up their evening to come to the Crucible Theatre and hear about science.... even though we
using the main stage, I was still so nervous that I begged to go first to get it over and done with!
With the rest of the FameLab competitors for the Yorkshire Heat.

Fortunately the atmosphere was supportive rather than pressured. Our compere for the evening, Simon Watt - TV presenter, writer and president of the Ugly Animal Preservation Society - gave me some wise advice for calming myself down, including to stand at the front of the stage before the show began to get habituated to the audience. It was reassuring to spot a few friendly faces but it was a really mixed crowd - families with children, young couples, retired folk. Eventually my breathing began to ease...

...and in the nick of time, as without further ado Simon launched the proceedings. I took a deep gulp and went for it. Staggering onto the floor, I gave my best impression of being caught in a force-ten gale.

"Goodness me - it must be blowing a HURRICANE out there! Oops - I  shouldn't really say that as hurricanes *actually* only form under very particular conditions..."

Don't ask me why but yes - my chosen topic was the science behind how hurricanes (also known as tropical cyclones and typhoons) form! I came across it on an online course on understanding the weather and it had simply intrigued me. It also gave me the chance to wave my arms around and make wild gesticulations to try and describe how the evaporation of water molecules off the surface of warm oceans provides the 'engine' that drives the storm. As I got underway, my rehearsals paid off and I managed to make it through without stumbling.

The scary judging panel....from left to right: Professor Simon Foster (Director of the Krebs Institute at the University of Sheffield), Nancy Fielder (Editor of the Sheffield Star, Sheffield Telegraph and Doncaster Free Press)  and Professor Elena Rodriguez-Falcon (Faculty Director of Communications and External Relations for Engineering at the University of Sheffield)

"and the winds get faster and faster and stronger and stronger - until eventually they clock 74 miles per hour and IT'S OFFICIAL! You can call it a hurricane...but what NAME you actually give it - Hurricane Boris or Hurricane Gertrude....is a COMPLETELY DIFFERENT story!!!" I finished with a dramatic flourish before running back to my seat so fast, I had to be called back for the questions. Fortunately I was able to give reasonable answers to these (THANK YOU, World Meteorological Organisation for your "FAQ on Cyclones" webpage!) and then it was all over!

Even though I didn't stop shaking until the interval, I greatly enjoyed watching the rest of the talks. From lab-grown meat to 'Why is poo brown?"...it's astonishing just how much information you can convey in 3 minutes and the lightning-speed style meant there was no time to get bored. Perhaps this is how proper academic conferences should be done??!
Our winner, Ashley Carley: "Making those papier mache fried eggs also took quite a long time!"

In the end, first prize went to Ashley Carley, studying for a Masters in Science Communication at the University of Sheffield - although it seems she has mastered this skill already! With ingenious use of balloons and papier-mâché 'eggs', she neatly demonstrated the concept of mitochondrial donation and three-parent embryos. "I was in disbelief when they announced my talk as the winner as I nearly dropped out several times" she said. "I'm really looking forward to seeing all of the other amazing talks and meeting more passionate people at the regional final".

Even though I was a teeny bit disappointed not to get selected for the regional finals in Manchester, the real achievement for me was simply being able to put myself forward without bottling out. In any case, at least I have a whole year now to think about my topic for next time....Monsoons perhaps? Anything's possible in three minutes!

Friday, 20 January 2017

Quick, Quick, Slow...

Where is the time going?! I have only just started to remember that it is 2017, not 2016, and already half of the first month has gone. This week in particular seems to have flown by and I don't seem to have much to show for it, having spent most of it reading about the remarkable exploits of other researchers. I have been compiling a literature review on all the investigations so far into what strategies plants use to protect themselves against root pathogens (such as soil-borne fungi and nematode worms). I intend to use this to draw up a list of interesting mutants in the model plant Arabidopsis to test to see if they are more or less resistant to the parasitic plant Striga gesnerioides.

All this means spending long hours in front of the computer screen that send my eyes funny ....but it needs to be done before I can really get going with my lab work. But I have been doing some small experiments this week, mainly to check that my seed stocks still germinate. Kept properly, most types of plant seed can survive for years, or even decades...but given that mine were apparently stored in a cardboard box on the roof of the department (?!) while I was on leave of absence means it's just as well to check!

And the results so far have been intriguing... despite being kept in the same box, my tubes of Arabidopsis seed had very different outcomes: some had 100% germination, others more like 50% and others none at all. Why this is the case is a complete mystery to me...and one that is beyond the scope of this PhD!
Seed from Tube F (left) : dead as a doornail. But Tube A - 100% vitality. Why...???!

As the days speed by, they bring me ever closer to my first daunting challenge of the year - FameLAB 2017! Contestants have just 3 minutes to explain a scientific topic of their choice, without PowerPoint or audio, and only using the props they can carry on stage. I don't expect to get further than the regional heats, but to me, the experience is the main thing and it's all useful 'Public Engagement' evidence for the CV. My decided topic is a little outside the realm of plant science...so much so that this week I went to a completely different department to check my understanding with an real expert on the subject! I won't say more here....but if you want to see my make an idiot of myself, come along to the Yorkshire heats on Thursday 2nd February, 7.00pm at the Crucible Theatre (follow the link here to book- tickets are free).

Don't forget, I'm active on the TwitterSphere now, and you can share my moments in the lab by following me @sciencedestiny or #backtoworkinthelab

And with that, I wish you a happy, slow and restful weekend!

Thursday, 12 January 2017

The Little Event 2017 - for BIG ideas in Science Communication!

“On my count then – three, two, one – RUBBER CHICKEN!!!!

What on earth was I doing jumping up and down and screaming at the top of my lungs with forty other people at the ThinkTank Science Museum in Birmingham?! We were all here because we had one thing in common - we were budding young Science Communicators who wanted to turn our passion into a thrilling career. Each year, BIG (the UK-based network for STEM Communicators) organise a 'Little Event' for those just starting their journeys in Science Communication to help them both develop key skills (e.g. presenting, planning engagement activities, evaluation) and scout out the job market. As for the jumping up and down…David Price was simply warming us up before his masterclass on presenting skills!

"Studies have found that we trust TV presenters more than journalists, even though they basically do the same job' David said. "The difference is that TV presenters bring a bit of themselves into what they present". Clearly Dave is an expert at doing this. Despite having no formal science qualifications, his passion for the subject ultimately led to him setting up Science Made Simple, which delivers interactive science workshops to schools and festivals. A key lesson for today was how to use props strategically to captivate audiences. What could be better, for instance, than a giant whoopee cushion to explain that sounds are caused by vibrations?  When the hilarity following this demonstration had died down, it was our turn to come on stage and take it in turns to present mystery random objects from David’s bottomless bag. There were some very imaginative stories – particularly when we couldn’t work out what the object even were!

Demonstrating that sound is caused by vibrations.....using the world's second largest Whooppee Cushion! (inflated with a hairdryer)
Later on, Bridget Holligan from ScienceOxford shared some sound advice in approaching the job market. For myself, I was reassured to hear that it isn't always necessary to have a specific science communication qualification and that a PhD can even be viewed favourably under some circumstances. "There are a growing number of science communication jobs in universities and an understanding of the research environment is often appreciated" said Bridget. But with competition so fierce, a PhD alone certainly isn’t enough to land a Sci-Comm job. We were all encouraged to get involved with as many activities as possible to bump up our CVs: science festivals, school projects, STEM Ambassador schemes and so on. "Your progression is your responsibility; no one else will do it for you” said Rachel. 

Careers session: speed-dating style

We then had a lively speed dating round so we could pitch our burning questions to Sci-Comm workers from a range of sectors. It struck me that a career in Sci-Comm is rarely a straightforward progression: instead, periods of unemployment, freelancing or a series of temporary contracts seem to be the norm. Learning how to cope with (and bounce back from) redundancy was something many had learnt the hard way. "It is a very fluid field and lots of jobs are lost, but also created' said Dom MacDonald from the Wellcome Trust. “Remember that redundancy is almost never personal. The best thing you can do is to build a network of people around you to look out for you".

Our venue - The ThinkTank Science Museum, Birmingham

Dom then introduced us to his toolkit to make the daunting task of Project Evaluation “as painless as possible”. The most critical thing is to define what success looks like before you begin – “Only then can you be honest about what you have achieved'. For instance, if 300 people turn up to your event, how do you know if that is good or bad unless you already set a target? And take the time to consider which data is most relevant.  “Just because you can measure it, that doesn't make it valuable” Dom said, “Instead, know what you value, then measure it". Unless you know what you want to look for, whole areas of success can be missed. A public engagement event that only attracts a low turnout may be regarded as a failure, but this could still have had good coverage in the local press, inspired those who attended and led to new collaborations. 

Mechanical Things exhibition, ThinkTank Museum

To round off the day, Rachel Mason from BIG took us through a whirlwind tour of project management - a task that is “a bit like learning to repair a puncture if you want to cycle - it's necessary admin." It seems you can never start to plan too far in advance, and that working backwards from the event makes everything a lot easier. When it comes to budgeting, little extras quickly add up so always leave room for contingency. It's incredible how much more a litre of orange juice costs if you are paying someone to pour it into a jug!

Putting our heads together in the Project Management session

The venue, the activities, the fascinating range of people .... the Little Event has certainly cemented my desire to enter the dynamic, exciting and rapidly evolving world of science communication. That said, I'm much more aware of the challenges that this could involve: multiple redundancies, constantly hunting for funding and having to live in London to name a few. But perhaps it's the challenge that makes the job more satisfying and the moments when you know you have inspired someone more worthwhile. And, as BIG and the Little Event have shown me, we are all in this together!