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!

Tuesday 30 June 2015

SEB Prague 2015 DAY TWO Talks, talks and far too many talks!

Ouch...I feel as though I have been sitting in a hedgehog all day. Why is it that three of the sessions I want to write articles about happen to be in the same day??! It's meant that I have had to pick and choose my sessions carefully, targeting the talks which have 'story appeal', rather than those describing new methods, etc. It also means I have to be very rude, constantly getting up just after a talk has finished and zooming off to another session! And when talks run behind schedule things get very complicated...

But today started straightforwardly enough with the plenary session to showcase the entrants for the 'Young Scientists Award'. The SEB has a strong commitment to supporting young scientists, which includes choosing six candidates from all of the abstracts submitted by early-career researchers to give an extended talk during the plenary session ( I.e. Taking place before the main sessions start, meaning that all the delegates can attend, giving a large audience!). Unfortunately, the talks were split between two rooms, so I was only able to see the entrants from the 'Animal' Section, and not the 'Plant' talks. I had to wonder though, what was it that set these apart from all the other students presenting work here? During their talk, it was clear that they all had a dedication to push deeper and deeper with their investigations, besides a real flair for communication. I couldn't help but feel, however, that they had also enjoyed a fair bit of luck in getting some significant results - so many PhD students slog it to the end only to be left with inconclusive data and a list of a thousand ways how NOT to do their experimental assay...I can only hope I don't end up being one of them!
The young scientists from the animal section: left to right: Craig Franklin, chair of the session, Dominique Roche, Heather More and Lauren Nadler. The Professors of the future?

First of all, Dominique Roche described how studies into behaviour, metabolism and stress responses frequently overlooked the 'personality' of the individual organisms. However, his own research on the Olive Flouder fish had unearthed two distinctly different personality types : 'shy' fish who respond to a threat by freezing and hiding, and 'bold' fish that dart away in a rapid 'flight or fight' escape response. Even more surprisingly, these differences extended to the metabolic level: bold fish responding to a stress by increasing their oxygen uptake whereas in shy fish, oxygen uptake decreases. Next, Lauren Nadler took to the stage. I had worked with her on a press release at the SEB meeting last year, on her reasearch into how rising carbon dioxide levels may affect the ability of reef fish to recognise one another. It seems she has moved on to greater things since then, investigating how the environment can affect how easily fish can escape,predators. Her evidence suggests that living in turbid, high- flow reef zones, hones the ability of damselfish to outmanoeuvre their predators.  Finally, Heather More posed an intriguing question: if larger mammals have longer neurones, meaning chemical signals have further to travel, does this delay their escape response? Whilst she concluded that this was indeed the case, this delay is partly offset by the fact that larger mammals move relatively more slowly ( I.e. Their feet remain on the ground for a longer period for each stride). The slight time delay remaining, however, could be problematic when running at speed if the mammal can't respond in time when it stumbles, potentially causing it to fall into the jaws of an enemy! It was a captivating series of talks and would have been even without the photos showing the speakers handling lively fish, diving on coral reefs and measuring reactions in elephants !

Getting up close and personal with DNA and enzymes... One of David Smith's fantastic models. To learn more about David's adventures in the classroom, you can visit his blog at https://davethesmith.wordpress.com/

After the plenary, the main programme got underway. Perhaps the most lively session today was the Education session : 'Innovations and Best Practice in Undergraduate Education'. It was a nice change to see teaching being considered as a worthy practice, rather than a lesser career for those who don't make it in research. And the session truly was a showcase in innovation! There was David Smith from Sheffield Hallam University, who 3D prints models of enzymes, proteins and DNA so his students can playfully explore how they physically interact. Meanwhile, Dr John Love, from the University of Exeter, described how he has done away with the traditional, 'follow-a-recipe' style of delivering undergraduate practicals. Instead he gives them a PROBLEM, three tubes each containing an unknown plant hormone at an unknown concentration....the students simply have to devise experiments to work out what they are!
Apparently it costs £50,000... But it can tell you anything you ever wanted to know about the plant in question...

Besides the talks, I also had an interview to record with Michael Berenbrink, who had co-chaired a satellite meeting on how Genomics has revolutionised the field of Comparative Physiology. He believes that studying the evolutionary lineage of organisms will open up new understandings of how adaptations help them to tolerate environmental challenges. And in any spare minute, I made a point of visiting the trade stands. The SEB have come up with a new idea for this meeting; each delegate is given a 'passport' in which they can collect stamps from the exhibitors. Completed passports can then be entered into a grand prize draw at the end of the week...A perfect excuse to drop by each stand and pick up the freebies.... So far I have a t-shirt, a coaster, a torch Keyring, a stress-squeeze mouse and more notepads and fridge magnets than I will probably ever need. Aside from that, there are some seriously cool looking pieces of kit for sale...I daren't ask for the prices though!
An artisan melon carver shows us his skill during the wine trail

After such excitement, I was a little too tired to try the wine trail in the evening.... Although I did sample some of the 'Czech themed banquet'. I once heard that cooks in French schools sometimes deep fry broccoli in an effort to persuade the children to eat more vegetables. After trying deep fried cauliflower tonight, I can see why!

Time to retire to bed...who knows what scientific and culinary delights tomorrow will bring?

Monday 29 June 2015

SEB Prague 2015 DAY ONE Careering about careers, climate change, publishing and more...

It's finally arrived!!!! Yesterday, I departed the UK ( just as the weather is predicted to improve - typical!) for the sunny climes of the Czech Republic. My destination? The capital city, Prague. The event? The 2015 Annual Meeting of the Society for Experimental Biology (SEB). My task? To spot the gems amongst the research being presented to write up as feature articles for future SEB publications.

With multiple sessions running concurrently and the topics ranging from climate change, epigenetics,food security and new ways to teach science degrees to undergraduates, this was a daunting task! Even if I had been given another whole month to simply prepare for this conference ( rather than trying to juggle it with my own research!) I still don't think I would have felt ready. But my work was to begin even before the conference proper got under way...somehow I had agreed to help Sarah Blackford ( my 'boss' at the SEB who invited me here to act as official science writer) deliver a career session for phD students...which included giving a talk entitled 'Making the most of your PhD'.
Registration pack - Check!

Unfortunately, the conference isn't being held in the romantic old town of Prague ( the part which gets featured on all the tourist brochures) but in a quarter just outside the main city centre, in a giant hotel/shopping-mall complex with a conference centre on the top floor. Whilst having everything you could need all under one roof must make logistics a bit easier, I can't help but worry that I am going to go the whole week without even seeing the famous clock tower and castle. As it is, the first thing I see when I arrive is... a branch of Marks and Spencer's!  I could almost be back in Sheffield...

First job, collect my registration pack and finally get my hands on a hard copy of the programme - it seems a shame to deface its pristine pages with my notes of the sessions I don't want to miss. Then I meet Sarah and we scout out the room for our session, making sure the setup is 'interaction friendly' - circular tables to stimulate discussion - and that our laptops are talking to the projector screen. The minute the delegates arrive through the door, we put them to work on my idea for an 'icebreaker exercise'. Each person is given a grid of squares with different headings such as 'find someone who has a business card' and 'find someone who can speak more than one language'. Their task is to introduce themselves to each other and put a different name in every box! It works even better than I could have hoped and the delegates are soon on their feet and mingling together. It certainly is a good strategy to avoid the usual silence and awkwardness when you suddenly throw a roomful of strangers together. We reconvene and Sarah introduces the morning session, a focus on activities that early career scientists should do alongside their PhD to show that they have skills beyond basic research, giving them an edge when they face the job market. The butterflies begin to churn in my stomach ( feeding perhaps on the sauerkraut I had for breakfast) as the time for my talk looms. Although I am slowly becoming more comfortable (or at least less terrified!) of public speaking as the years go by, I always fear that I will stumble over my words, keep saying 'erm' or splutter to a halt. Perhaps the 'network bingo game' has helped me to feel more familiar with the audience because I manage to face down my trepidation and launch into my slides. Using examples of some of the activities I do at Sheffield, I outline various ideas of things they could get involved in - science-policy groups, volunteering, departmental committees.... I must have talked too fast though: although the talk was meant to last twenty minutes it felt more like five before I was sitting down again! But the talk seemed to be well received with some delegates kindly telling me afterwards that it had given them some things to think about.
Lively discussion during the careers session 

After sampling more traditional Czech delights over lunch ( fortunately I am a big fan of smoked mackerel and beetroot), it was time for the afternoon sessions. Whilst Sarah delivered her masterclass on writing cvs, I joined Mary Williams for an insight into the academic world of publishing. Mary produces resources for Teaching Tools in Plant Biology, a wonderful organisation which aims to improve the quality of plant science teaching resources for Unviersity students, and so hopefully convince more of them that plants are just as worthy a career choice as animals! Fist of all, Bennet Young, an assistant editor at the Journal of Experimental Biology, described the process by which papers are considered for publication in scientific journals. It was surprising to learn what a convoluted process it is, even for papers which are ultimately rejected. Mary then led a discussion on the 'black box' of the peer review system, introducing us to some of the new systems that have recently been piloted. I'm not sure I like the idea of 'open review' where ANYONE can leave an anonymous comment against your research...to me it seems likely to lead to the type of aggressive, bickering behaviour seen sometimes on Twitter and Facebook- after all,  scientists are very passionate about their work!
Getting it out of the way...giving my talk during the careers session

We have a short break before the evenings activities - I decide to relocate to a nearby cafe to plan my next few days over a calming ginger tea. I return in time to join the 'Science with Impact' session, with the theme this year of  'Rising CO2 - it's not just about Global Warming'. It was sobering to be reminded how unlikely it is that the human race will curb carbon dioxide emissions enough to keep the temperature from rising above the critical two degree threshold. Which makes it more important than ever that researchers investigate the probable effects on the environment and ecosystems. Jodie Rummer, who studies coral reef systems at James Cook University, Australia, described some of the surprising ways in which ocean acidification (caused by increased levels of dissolved carbon dioxide) can affect reef fish, interfering with their cognitive processes to the extent that they appear to be 'dumb fish'. Following this, Hans-O.Pörtner, of the Alfred-Wegener-Institute, Germany, described the process by which the IPCC ( Intergovernmental Panel on Climate Change) reports are compiled. I had no idea it took as long as five years for each report - it makes the literature reviews I have had to do for my course seem rudimentary! Alison Smith, from the University of Cambridge, then gave a review of the feasibility of using algae to make the biofuels of the future. Whilst algae are attractive in that they can be cultivated with low- technology methods ( even just a plastic bag filled with water!), and they can also produce other high quality products  (such as vitamins) at the same time, scaling the process up is a huge problem. It would take 17 million hectares of cultivated algae to meet the UK's fuel needs... And the UK is only 24 million hectares in size! Finally, Bill Davies offered a story of hope to counter the 'perfect storm' brewing for the future, where food, energy and water will likely be in short supply. Using low- technology methods and working with farmers, an international collaboration of researchers working in Northwest China were able to restore an ancient oasis that had been ravaged to a desert state by unsustainable farming. Now, lakes that had been dry for sixty years are beginning to flow with water again. These methods include 'alternating irrigation', where the plant roots are only watered intermittently and allowed to dry in between. It is not known HOW exactly this works, but it is thought to manipulate the plant's intrinsic hormone signalling systems, making it more sensitive to drought. This causes the plant to close the stomata ( tiny pores on the underside of the leaf that allow gas exchange) and conserve water. 
It felt like a real call to arms - as Alison Grey said 'The future of science is in this room'. If there could ever be a worthy way for scientific research to have an 'impact' , then promoting the world to take action against climate change would be a good place to start.
Visions of a future indeed...but for now, the immediate matter to hand is the pre-meeting networking event. I have interviews to arrange so dodge about between the crowds sampling the gherkins and cheese counter. It's been a busy first day - but what could I expect from the SEB?
See you tomorrow!

Alun Anderson, of the SEB Education and Public Affairs section, chairs the Science with Impact Session

Saturday 20 June 2015

Let's play - Name that Flower!

When I tell people that I am a plant scientist, a frequent response is 'Ah! So you know the names of lots of flowers then?" Unfortunately not. Whilst I am quick to point out that the naming and classification of plants is, strictly speaking, the science of Botany, I do feel that I am letting the side down. It embarrasses me when I see familiar floral faces when out walking but can't put a name to them. But these things simply don't seem to be taught anymore ( at least at Universities ) with the focus more on how plants function and survive, rather than what they are called. The art of naming the natural world is becoming very rare indeed...

...so when the Animal and Plant Science Department hosted a 'Plant Identification Day', I was quick to jump aboard! Working in the teaching laboratories, our host - wildflower enthusiast Emma Jardine - started by giving us a basic introduction to the main flowering plant families. It was daunting at first to hear that there are over 2,500 plant species native to the UK, grouped within 140 families. However, it turns out that 80% of UK species can be grouped into just 20 key families. Emma kindly made things easier still by focusing the session on just ten of these. She had been busy that morning, scouring the local hedgerows and had brought along representatives of these ten families...  But she wasn't going to tell us which was which!

Armed with copies of Francis Rose's 'The Wild Flower Key: How to Identify Wild Flowers, Trees and Shrubs in Britain and Ireland', we paired up and got to work. Although wildflower keys can be excruciatingly complex, being able to group the plant into a family straightaway saves a great deal of work. Fortunately, there are some simple rules that make this easier. Are the flowers bilaterally symmetric? ( that is, if you cut it in half from top to bottom, the two halves form a mirror image). Then it probably belongs to Lamiaceae or Fabaceae. Do the fruiting bodies have a long beak-like extension, similar to the bill of a crane? Then you may have a member of Geraniaceae. But identifying the family is only the beginning. The fun really starts when delving into the complicated keys to pinpoint the exact species. The details can be very exacting - are the leaves 'smooth', 'hairy' or 'more or less hairless'? Is the flower pedicel less than 5 mm? What colour are the stamens? Where did I put that eye lens??!

Got there in the end! We finally managed to key out Geranium columbinum, otherwise known as Long-Stalked Crane's Bill.

I was soon enjoying myself, especially as the key drew my attention to many exquisite features which I had never considered before - each one serving to distinguish each unique species. Sadly, my afternoon experimental plans prevented me from joining the others on an excursion to a local nature reserve, but I could already feel the tangible benefits from the session as I walked home that evening. Instead of merely thinking 'What a pretty flower!', I found my thoughts running more along the lines of 'Palmate leaves and a terminal inflorescence with an actionomorohic shape...surely a member of Ranunculaceae?

Friday 12 June 2015

Downy Mildew ROUND TWO

Another week gone....time really does speed up as you get older but at least it is finally staring to get a bit warmer here in Sheffield. Although I'm not quite ready to break out into the short sleeves and shorts like all the undergraduates, who celebrated end of exams today. I remember THAT feeling!

This morning marked the critical stage of my second attempt to investigate whether infection by the root parasitic weed Striga gesnerioides makes the host plant more susceptible to above ground pests, in this case Downy Mildew ( Peranospora parasitica). You may remember how my first experiment was turned upside down when my growth cabinet broke, sending the temperature skyrocketing and putting my plants into a 'stress response'. My supervisors advised me to finish that assay anyway, as good practice, and to score the leaves. The data didn't suggest that there was a below- above ground interaction but we decided it was worth checking once more. Last week, I infected half of my host plants with Striga and today was the day to challenge my plants with the downy mildew pathogen. Next week, I will score the leaves to see if there is any difference in the susceptibility of Striga infected and non-infected Arabidopsis plants. I am not looking forward to that bit - many hours of staring down a microscope, struggling to discern the microscopic pathogen. And there will be a lot of leaves : 8 leaves per plant, forty plants in total... No, I am going to STOP that calculation before I become depressed....

We use some very sophisticated equipment for infecting...

But how DO you challenge a plant with downy mildew? This part is beautifully simple but involves a bit of advance planning. First, you make sure that there will be a culture of downy mildew available on the day in question, growing on a susceptible host ( an Arabidopsis genetic mutant that has reduced salicyclic acid regulated defences). Then, you harvest leaves from said host into a falcon tube, shake well with distilled water, then drain through a fine cloth into a new tube to remove the leaves. This gives a cloudy solution containing ( hopefully!) oodles of downy mildew spores. This has to be quantified under the microscope by counting the number of spores in a single droplet using a counting chamber. If necessary, the solution can then be diluted to the correct concentration. Now the fun part: fill a perfume spray bottle with the solution and dowse your plants with 'eau de Peranospora'. I can get carried away sometimes, imagining that I am a perfume trader...
Infecting my plants with downy mildew. Red labelled ones have the Striga parasite

Job done, my plants are now residing in 'quarantine' - Cabinet 511, especially reserved for downy mildew experiments to avoid cross contamination. With so many growth cabinets in the annexe ( Ok, the 'Sir David Read Controlled Enviornment Facility' to be absolutely precise), there must be a fascinating array of work quietly being carried out, covering everything from soil dynamics, plant defences against disease, boosting the efficiency of photosynthesis .... None of which would want my downy mildew near them! 

I am slowly making progress on getting more sleep and have been making fewer mistakes this week - I did check the microtome properly this time! But right now, my eyes are dropping and my bed beckons. Hopefully, whilst I sleep, those downy mildew spores will start to awaken and make themselves at home on their new hosts...

Saturday 6 June 2015

Getting a slice of the action...

Everybody says that a PhD is tiring but I think I have let things slide a bit too far...my GP, supervisor, friends and family have all made indications that I have been looking a bit run down this week. I can only agree when my head is constantly throbbing with tiredness and I can barely think straight at times. At the moment, I just cannot switch off as I seem to be juggling a few too many things all at once. My research plans, the upcoming conference for the Society for Experimental Biology in Prague which I am attending as a science writer, my voluntary commitments at The Sunday Centre...it all has to come from somewhere and at the moment it has been coming out of my sleep. The phrase 'work- life balance' (bandied around so often at careers events) doesn't mean much when you have to keep going into the lab at the weekend to wake up your sleeping parasite seeds in time for an infection on Monday! 

Seriously though, I know I need more rest as I keep making stupid mistakes. I managed to plan my next experiment so that the time to infect my plants was when i was actually out of the country ( fortunately I managed to rescue the plates of seed I had prepared by breaking the dormancy cycle earlier, moving the infection date to the day before my flight), I dropped my access card and didn't even realise until i received an email telling me it had been handed in, I left my watch behind one day...and then there was the incident with the microtome...

Slicing off a new section from one of my samples - delicate work as the sections are only 10 microns thick ( a micron being a millionth of a metre).

One of my ongoing experiments is to piece together an exact timeframe of the process by which Striga gesnerioides infects an Arabidiosis host. Although this is well known for Striga hermonthica, much less work has been done on gesnerioides so I have been harvesting tissue samples from infected host plants every few days, all carefully labelled so that I can trace them to the date they were collected. I am slowly working my way through them, embedding them in Technovit resin before slicing them into thin sections with the microtome so that they can be viewed under the microscope. Being an expensive bit of kit, one of my lab colleagues, Peijin, gave me a training session, showing me how to load the sample and lower it down onto the blade to slice off a delicate semicircle of embedded tissue. It was quite thrilling to prepare my first slides and have a look under the microscope!

Drying off my first sections prepared on slides

 This week, I tried to go it alone for the first time. Sample loaded, settings adjusted, all ready... but when I lowered the sample down - disaster! Instead of a wafer thin slice, a whole chunk of my sample came off, leaving me with fragments of Technovit and no sample. What was the matter? Did the angle of the blade need adjusting? I moved the blade holder back and forth, fiddled with the section thickness settings and adjusted the sample positioning but to no avail. My sample was becoming increasingly wrecked as flakes were sawn off apparently at random. I decided to give up and returned to the lab. Seeing me looking so glum, Peijin offered to come and have a look at the microtome. At first she was perplexed as I was until she took the blade holder out for a closer inspection. 
'oh...' She said 'there isn't actually a blade in here...'
In my dopey state, I hadn't realised that the blade had been taken out of the holder by the previous microtome user. So I was essentially just bashing my sample against the blunt edge of the holder, which would explain why I couldn't cut a decent section! I was so tired, all I could do was laugh with relief .... And when the blade was actually inserted, I did manage to get some decent sections. I'm hoping to start staining these next week to show the structures of the host root and invading parasite more clearly. 

Meanwhile the parsley plants are doing well. So another job for sometime will be a trip to the Moor Market to get some salmon!

Happy parsley plants In the kitchen!