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 25 August 2015

Horsing around away from it all....

I've been feeling a bit low recently, dragged down by the endless cycle of work, work, work. By day, it is the rhizotrons and Petri dishes of the lab: by evening, wrestling with half finished articles covering the Prague conference. Even the weekends have settled into a dull monotony, not even broken by my usual volunteering work with the homeless at The Sunday Centre which, sadly, doesn't run during August. It was high time I had a break, a chance to broaden my horizons beyond the rows of plants or the computer screen before my eyes. And what better way to escape than a weekend trip to the seaside with my dear Mum? 

Neither of us had ever been to Robin Hood's Bay before; I had simply picked it out of a 'Visit Yorkshire' brochure, drawn in by phrases such as 'renown beauty spot' and 'beloved by painters and poets'. I could see why - the town was like something out of a fairy tale, a perfect smuggler's village perched improbably on the the vertiginous cliffs. The buildings were jumbled up together along a maze of crooked, winding alleys ( perfect for hide and seek!)  and apparently many of them have interconnecting attics and basements. It is said that, during the height of smuggling, an illegal barrel of tea or silk could pass from one end of the town to the other without seeing daylight! As for the sea, it was just what I needed, boundless marine blue to empty my troubled mind into, stretching away into eternity...and not a schedule in sight!
Beautiful views over Robin Hood's Bay...

We had a wonderful time catching up during long walks along the cliffs, sampling local crab and whelks, seeing families at play on the beach and watching amusedly as car drivers performed incredible feats of steering to negotiate the steep hills. I was stuck by the beauty of the local fossil specimens in the museums but sadly didn't find any myself on the beach. 

But during one of our rambles, we came arose a glade filled with 'living fossils' - a stand of horsetails. These plants are the only species that survives from the once diverse Equisetopida class, whose members dominated the Carboniferous landscape 290 million years ago, and included trees up to 30 m tall. Horsetails are described as 'primitive' as they reproduce using spores ( like ferns) unlike 'modern' land plants which use seeds.  They also have greatly reduced leaves, called 'microphylls', that each have a single, unbranched vein instead of the intricate networks of veins we admire on most leaves today. You can certainly imagine them as being the sort of thing a dinosaur would munch on...and yet these primitive plants are apparently generating renewed interest among scientists. Horsetail extracts are said to act against all manner of illnesses, including diabetes, osteoporosis and bladder problems. There is even evidence that they may stop the proliferation of cancer cells*. For myself, I simply enjoyed appreciating the beauty of their minimalist architecture and the  pleasure of coming across them unexpectedly. It just proves that with plants, you never know what is round the corner!
The glade of horsetails - a blast from the past

It really was a timely break for me and has hopefully left me refreshed enough to last through to the end of the Academic year. It was also quite nice to have a 'digital detox' although it felt surreal to stay in B and B with free WiFi and to not be able to take advantage of it! Suffice to say, I am not looking forward to seeing the state of my inbox on my return...but, the show must go on, so back to work we go!

* For more information about the uses of horsetail extracts, see  http://www.naturalalternativeremedy.com/sixteen-horsetail-benefits/ For the study investigating horsetail extract effects on cancer cells, see the paper "Antioxidative and Antiproliferative Activities of Different Horsetail (Equisetum arvense L.) Extracts" (Journal of Medicinal Food)
Robin Hood's Bay by morning...worth getting up early for that magical light!

Sunday 16 August 2015

Seeing is believing......

One of the objectives for my PhD ( and hopefully a thesis chapter...?) is to completely characterise the  process by which Striga gesnerioides gains entry into the roots of Arabidopsis thaliana. On the outside,  I can first tell if one of the tiny Striga seeds has successfully infected the host root when it begins to swell into a tubercule. In a really good infection, the root can be strung with tiny bobbles, like a chain of knobbly Christmas baubles. But this is a comparatively late stage of the infection process. To understand how the parasite may be suppressing host defences, I need to know at what point it begins to break through the outer root layer, the epidermis, and starts squeezing through the cortical cells towards the central vascular bundle. The key moment is when the parasite connects to the hosts xylem vessels - at which point it can freely withdraw water and nutrients to fuel it's own growth. All of which is very difficult to tell from the outside!

Hence, I have been busy with my scalpel - hacking off sections of infected root to take samples of tissue. I have then been putting these through a long and convoluted protocol to embed these in a material called Technovit - the whole process takes about two weeks and makes the recipe for a wedding cake seem easy by comparison! But this is necessary because Technovit is strong enough to be able to take ultra thin ( 5-10 micro etre ) slices off the sample using the microtome. I have a 'love- hate' relationship with this machine....For my first attempts, I would spend hours and hours on it and yet my sections would look like a jumbled mess under the microscope. Just lately, I have been having more success, learning to bring the blade down in a smooth, rapid motion ( I think of it like a guillotine - if it was my head on the block, how would I like the blade to come down?!). After staining my latest batch of samples, it was exciting to see how they turned out!

The host Arabidopsis root is on the left and the parasite tubercule is on the right, before I reach the point of contact. 

These sections were taken 14 days after I applied the Striga seed to the roots. When I take sections, I slice along a length of root latitudinally. So as I go along the root, all I can see at first is the host root until I reach a tubercule. As the tubercule swells up around the point of entry, initially it doesn't seem to be attached to the root. But as I continue taking sections, the tubercule seems to get closer and closer until I reach the point of contact. At this stage, I can begin to see how much the parasite has disrupted the host root and how extensive its connections to the vascular bundle are.

The point of entry - Striga gesnerioides forces its way in...

Even with these sections however, it can be difficult to tell what is going on ( but you should have seen my first attempts!). Consequently, I am now taking sections from some very exciting Arabidopsis mutants expressing an enzyme called GUS. This means that when I treat the root sections with a certain dye, they will turn green. Because only the host Arabidopsis only expresses GUS and not the parasite, only the host tissue will change colour. So it should be easier to work out which cells belong to Striga and which belong to Arabidopsis. That's the theory anyway - I'll let you know how I get on!

A big jumbled mess....an Arabidopsis root infected with Striga gesnerioides

Can you see the difference? The infected root sample on the right was taken from a GUS-expressing Arabidopsis host, whilst the one on the left comes from a control 'wild-type' host.

Monday 10 August 2015

Biotech YES!!! Let the Challenge commence...

My life seems hectic enough with my full-time research, voluntary commitments, blogging and science writing... So is it really a good idea for me to enter the prestigious BiotechYES Challenge as part of a team from the University of Sheffield? But I just cannot resist such a good opportunity! The challenge of this competition is to come up with an idea for a novel biotechnologically based product or service and draw up a business plan to pitch to a panel of industry experts. In the process, teams develop their financial awareness, meet major biotech industry players and receive expert training from business mentors. Having out my name down, it was now up to me to represent my team at the Briefing Session held at the University of Nottingham.

I had hoped that this competition would be a bit of 'fun' with plenty of networking and career-enhancing workshops thrown in. But on entering the lecture theatre at Nottingham University's Business School, I suddenly realised just how serious this was going it be! The room was packed to the very back row with delegates from over a hundred teams, from across the whole UK. I was lucky to only have had to travel from Sheffield! There was a steely edge amongst the chatter and it was clear that these people hadn't come here for a holiday. Fortunately I spotted Emily Seward, who is also in the Gatsby Plants Network, so had a friend to sit next to. It's funny how these plant scientists crop up everywhere!
The delegates arrive at Nottingham University Business School, Jubilee Campus ( Photograph courtesy of Haydn Green Institute for Innovation and Entrepreneurship). 

Simon Mosey, a Professor in Entrepreneurship and Innovation at Nottingham University, welcomed us by explaining that this year was a very special one for BioTechYES. This would be the 20 th year of the competition, which has grown so rapidly from its origins that soon over 5,000 students will have progressed through it. As he described the prestigious 'BiotechYES Alumni Network' I began to feel woefully inadequate of reaching the high standards of the competition. But Simon was keen to dispel some common myths about successful business people. "Entrepreneurs are not special people who can see the future or who have different chromosomes to the rest of us" he said. "Rather, they just have the courage to try the things you may think of but be too scared to do". Instead of simply waking up one day with a brilliant idea, entrepreneurs typically have to experiment with hundreds of different ideas and get used to most of them failing. Furthermore, "entrepreneurs don't do it all themselves". Although one person may be the figurehead of a product or business ( such as Steve Jobs was with Apple ), behind them will be a highly talented and motivated team. Hence, the ability to work with very different people is critical. According to a recent survey of company CEOs, the key piece of advice that they would give those hoping to launch their own start up is to use every opportunity to build your network.

The stage was then handed to Dr Simon Cutler, a Senior Innovation and Skills Programme Manager at the Biotechnology and Biological Sciences Research Council (BBSRC). He explained the value of taking time away from our normal research to enter the competition. Besides the obvious transferable skills we would develop - such as teamwork and communication - we would also acquire some less obvious ones, including the ability to handle conflict and work through sleep deprivation! ( WHAT have I let myself I for?!) We would also have the chance to work with major bioscience businesses and forge valuable contacts for the future. "Hopefully we will all be winners" he said. "You will develop an enterprise mindset and have the opportunity to think about what you want to do for the rest of your life".
The crowded auditorium
( Photograph courtesy of Haydn Green Institute for Innovation and Entrepreneurship). 

Dr Nessa Carey, from PraxisUnico ( a research innovation network )  rose to introduce us to the role of Technology Transfer Officers and how they help researchers to increase the impact of their work. She began by encouraging us to 'play with' our career choices until we find the role we feel especially called to. "Your career is the one area that you can experiment with and you will always gain" she said. Her own story is a singular example of this. Having originally applied to study veterinary medicine she quickly realised that "I was hopeless at it - I can't think in 3D and I'm allergic to hay, fur and feathers". After a stint as a forensic scientist for the Metropolitan Police, she decided to do a scientific degree then found herself back at the veterinary faculty to do a PhD! Eventually she came to work for the pharmaceutical giant, Pfizer, having been drawn to a role where she could make a difference beyond the laboratory. "I now work at the interface between the Academic and Industrial worlds, working out how to make research have an impact" she said. 

And yet Nessa insists that she has never had any formal training for what she does now. "I've never been a Technical Transfer Officer but I've done all the bits needed to become one" she said. "The great news is that you can pick up all the skills for a job without doing the job itself - all while being a really average scientist!" This was wonderful for me to hear since I have long realised that I am not a member of the tier of 'brilliant scientists' on course to become the Professors of the future. Indeed, Nessa assured us that "there are very few great scientists - although there are lots who think they are" , yet it was still possible for us to dream of a career with variety, travel and impactful work. Including that of being a technical transfer officer ( TTO). Nessa explained that, rather than being the "battle axes or walls" that block exciting research from getting out into the world, TTOs are more like navigation aids to help academics through the maze of patents, legal requirements, etc surrounding their work. For science to be delivered properly to society, it needs to have someone with a firm grounding in the 'real world'. She told a humorous story about an Academic who rang her on a Thursday with a 'brilliant idea'. When she asked when he was thinking of disclosing it, he answered "Oh, on Monday". Cue a mad dash to Cambridge to find an attorney at the last minute so the patent could be filed before the office closed at 5 pm on Friday! Academics may be brilliant at what they do, but they haven't always got their finger on the pulse of the practicalities of industrialising research...
Delegates mingle over the lunch break
( Photograph courtesy of Haydn Green Institute for Innovation and Entrepreneurship). 

We were then introduced to the 2014 winners of BiotechYES. They had certainly had a glamorous time since last year's competition - £2,500 prize money, a whirlwind of gala dinners and a trip to Houston, USA to take part in the RISE Business Plan competition. But they had also clearly out in a lot of time and effort into their Biotech entry. Their science was convincing, their PowerPoint slides highly professional and even for this relatively informal occasion, their delivery was slick and polished. They had even thought to bring wine as a 'thank you' to the Biotech organisers! We were all keen to hear their advice to us, the next batch of entrants. Firstly - be comfortable with generating bad ideas. It had taken a giant pool of brainstorming to find their winning idea! Secondly - do as much advance preparation as possible as time at the workshops is extremely limited and highly pressured. Third - the science behind the product is not as important as the market potential - you need a convincing story to draw your investors in. In their case, their winning product was a naturally decaffinated coffee bean. So they began their pitch by inviting the judging panel to sample some of their delicious new blend before launching into their spiel: "It looks like coffee....it smells like coffee...and as you can see, it tastes like coffee....but there's one thing missing!" Hence, the art of 'storytelling' can be added to that list of transferable skills!

By this time we were ready for lunch. I had been so inspired by Nessa's talk that I acted on the advice to network, network, network and caught up with her for a chat and to exchange business cards. Meanwhile, the delegates took advantage of the sunshine to relax outside, reviving themselves on the fountain of cupcakes...
Delegates during the lunch break
( Photograph courtesy of Haydn Green Institute for Innovation and Entrepreneurship). 

In the afternoon session, Dr David Park from Newzpark Ltd gave us his perspective as someone who had 'been there and done it' when it came to starting his own business. "If I had my time again, I would tell myself to focus more and not try to take over the world!" He said. Indeed his first business, in the area of "Integrated Data Systems and Processing" had a rather haphazard start, involving writing a hurried business plan on a train to an interview and asking his wife at the last minute "How would you like to live in New Zealand?" Subsequently, he set up the Geospatial Research Station, a consultancy company based in Christchurch. Life could certainly be hectic at times, dodging volcanoes and emperor penguins besides overcoming the usual financial hurdles of establishing a business. "It will be stressful at times and you will be sick to the stomach" he said "but starting a business should be fun and you have to take a moment to enjoy the good times". Although the GRS didn't survive the recession, David was adamant  "I'd absolutely do it again". He encouraged all of us to have the courage to follow our entrepreneurial dreams : "Don't be afraid to give it a go - you won't be left with a pile of broken experiences" he said.

He also had some useful advice for the BiotechYES competition. When pitching for cash, it is vital to understand the drivers and oriorities of your shareholders. Again, he emphasised the importance of crafting a compelling story to attract investment. "Become the best storyteller ever" he said. "When pitching, practice and refine the start and the end the most - if they are perfect, the rest will fit." Meanwhile, don't underestimate how long things take and how much they cost: "Multiple all estimates of time and cost by pi" he advised. And finally, "Take some time to step back from the technical work and give yourself space to ask 'Why am I doing this?'" David advised. It can be all too easy to loose a sense of perspective when you have a business to run!

Now it was time for us to do some work during the 'Ideas Generation Challenge'. We were introduced to IngenuityOnline, an online portal where different users can sign up to 'challenges' to suggest solutions to a particular problem. First, we had to vote on a topical issue to work on that afternoon, with ageing and increasing longevity coming out on top. Then we had to define the problem, breaking it down into things we associated with it. The ideas here covered the scope from 'going wrinkly' to 'reduced mobility' and 'the cost of care'. As everyone's ideas were pooled together, a complex picture began to form of the social, economic and physical aspects of the 'ageing problem'. Now we had to throw up solutions and were encouraged to be as whacky and adventurous as we liked, although perhaps some people took this a bit too far, using the opportunity to express their dislike of certain political parties ... The online tools allowed us to play about with the ideas suggested by others, merging things together and calling up visual representations. So, for example, could we somehow think of a solution that involved both 'brain training games' and 'fortified green tea extract'? 
Simon Cutler of the BBSRC explains how BiotechYES has evolved over 20 years
( Photograph courtesy of Haydn Green Institute for Innovation and Entrepreneurship). 

It was a fascinating experience of brainstorming in real time but also incredibly complicated to master - in future, I may stick to pen and paper! But it was time to head to the shuttle coaches back to Nottingham Station. Armed with hundreds of new ideas, a Biotech goody bag and a new sense of resolve, I had a team meeting to organise back at Sheffield! The challenge has been set - now we have to get ready for it!

Special thanks for the BiotechYES organisers, especially Tracey-Hassal Jones for organising the event.

Sunday 2 August 2015

And there was evening and there was morning...

I thought life had been busy before the Prague conference.... Now I have discovered another level! During the main part of the day, it is a rush to fit in all my experimental work (which has picked up again alarmingly quickly): booking slots to use the microtome for making sections of harvested root tissues, preparing stock solutions, scoring plants for infection,preconditioning parasite seed, etc. Then, as evening comes on, I head to the library to carry on wading through my notes, interviews and email correspondences from the conference. Slowly, the articles I have been commissioned to write are taking shape but it is a convoluted progress due to the number of different researchers whose work I am featuring! So probably not the best time to take on yet more work by offering to write a few peices for the "Student Guide to Sheffield Univeristy 2015"... When will I learn to say "No"?

Staying so late at work makes me really appreciate my new location close to the Department. I have really settled into my new flat now, and can't now imagine going back to Univeristy Halls - I have finally made the break! My parsley plants have happily colonised the windowsill and I have even started to use them to accompany my fish dinners. I can begin to understand the fuss behind organic food - the taste was so superior to the supermarket varieties - could it be due to the lack of pesticides and chemical inputs?

It has also been a busy week as I have, as they say so often at The Works, been "clearing everything out to make way for fabulous new stock"! I have set up an ambitious experimental plan to test four new mutant Arabidopsis lines, each defective in a certain defence signalling pathway, to see if this makes them more ( or less?) susceptible to infection by the root parasite Striga gesnerioides. But I have found that it is much more fun to plan a slew of experiments than to clear up everything afterwards.... However, I only have so much space in my cabinets so I have had to devote some time to bagging up my poor finished plants and chucking them out. I'm not the most popular person in the annexe when I take over all the sink space to wash hundreds of rhizotrons at a time! 

At least when I am on my way to work, trying to clear my head through the fug of morning tiredness, this wonderful array of wildflowers gives me a lift. It is only a narrow strip in an otherwise ecologically barren desert of lawn but it fairly thrums with bees and butterflies. Judging by the number of posts of Facebook, it has been giving plenty of other people a boost of pleasure as well! I wish I knew who the inspired landscaper was so I could thank them. One of the things I really like about Sheffield is that these little nuggets of greenery are often left to the benefit of wildlife, rather than cleared up to make everything neat and tidy. And it really does make a difference, both to people and animals. I even heard owls on my way home last night...

I hope you are having a more relaxing weekend than me! Right, better get back to these articles....