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!

Wednesday, 16 September 2015

Time for a HOLIDAY!!!!

I won't be posting over the next week as - fisnlly - I am going on a PROPER holiday ( the Prague conference certainly didn't fall into the category of 'relaxation'...). With no internet or phone, there isn't the remotest chance of doing any work....unless I print off a few scientific papers? Somehow I think I will be too busy reading up on the unique history of La Serenissima and just gazing at that magical marriage of light, water and bobbing Gondolas.....see you soon!

Tobacco Uodate: tobacco are still going strong, one is even starting to flower again! ( perhaps I should rename them 'Resurrection Plants'...) The Striga shoots are beginning to dry out so hopefully I can start harvesting the seed soon. 

Monday, 14 September 2015

Gatsby Annual Network Meeting Day Two - From ancient history to cutting edge science

Nine 'o clock on Friday and we were back in the auditorium for day two of the meeting. Judging by the empty seats, some of the delegates were still recovering from a tour if Oxford's pubs last night...

We started with a topic which, unfortunately, preoccupies many researchers - the money. Or, more accurately, where can we go to get funding? Bizarrely, only 4% of the UK public spend on scientific research goes to Plant Sciences - a proportion which hasn't changed since the 1970s. This despite  the question of how we will feed everyone in a world undergoing climate change, environmental degradation, water scarcity - and so on and so on! 

Of course, the competition is fierce - every scienctist believes their project is fabulous, game-changing and ultimately worthy of a pot of money! So what is the solution for UK-based plant scientists? Cast your net wider and look for international opportunities, particularly those from philanthropic organisations. Perhaps the best known of these is the Bill and Melinda Gates foundation which - with an endowment of $44 billion - also happens to be the wealthiest. "Plant science used to be the poor relation in international development" said Gatsby Mentor Nick Talbot, but that is starting to change. Now plant science is being promoted alongside high profile campaigns, such as providing mosquito nets to combat malaria. Even the biomedical giants, such as the Wellcome Trust, are beginning to take note. "After all, it doesn't matter how much you vaccinate people - if they don't have enough to eat, they will never be well" as Ottoline Leyser, another of the Gatsby Mentors, put it. Such organisations are particularly keen to support programmes that facilitate the exchange of scientists - and hence knowledge - between different countries. This includes both UK institutes inviting foreign scientists to their labs, and UK scientists spending time in overseas labs. Given the size of the problems mankind faces, it makes sense to disseminate ideas on as global a scale as possible. 
Another beautiful morning at Queens

But even when the money IS there, UK scientists - particularly early career researchers - can be afraid to go for it. "There is a tendency for early career researchers or newly established lecturers to be nervous and only apply for small grants" said Nick. "But really, you should be going for a large grant as soon as your CV makes you competitive". To make this less daunting, there are a number of grants specifically aimed at researchers just starting to climb the academic ladder. These include the European Research Council (ERC) 's Starting Grants, open to those who have 2-7 years of research experience after their PhD, besides the BBSRC* Future Leaders Programme and Marie Curie Fellowships. But even these are highly fought for, hence the Gatsby Mentors had some tips. "It is much better to have a consistent record of good solid research than one or two 'blockbuster' publications" said Liam Dolan. "And try to have a really exciting research plan that could potentially change the field". But Ottoline warned against overdoing the hyperbole. "One research proposal I read was going to shift four paradigms - I just got fed up! You don't need to keep spelling it out - it should be obvious that the research will make a difference". Having some preliminary data can also make an application stand out,although this isn't always necessary. I wonder if I ever be in a position to go for a pot of money myself, and put my own ideas on the table?

We then had an update from Ginny Page, from Science And Plants for Schools (SAPS), about the new IntoBiology website. This aims to firmly debunk the notion that 'plants are boring' and there is a wealth of inspiring lectures and resources available to all. It's not just for kids - if this blog has made you at all curious to learn more about plant science, do check it out! In particular, have a look at the 'film advert' to see what a media team can come up with when challenged to make plant science careers look exciting! See http://intobiology.org.uk

During the talks from the third year PhD students, Patrick Diaz described his progress using temperature insensitive  mutants in Arabidopsis to determine genes involved in temperature sensing. I was particularly interested in this, as I helped to identify some of the first of his mutants during an undergraduate summer placement at the John Innes Centre four years ago. His results suggest that the components of the temperature sensing pathway are linked to photosynthesis, a reaction that is itself temperature dependent. The rate limiting step of photosynthesis is the conversion of reduced plastoquinone. As the temperature increases, reduced plastoquinone accumulates and this forms a feedback loop with temperature sensing proteins. It seems an ingenious solution to me, to use a process that already varies with temperature to work out how hot it is!

Whilst we broke for coffee and the undergraduate poster display, I caught up with naturalist John Midgley to talk blogging. His blog (Dr M goes wild) is in a completely different league to this one however with over 1,000 hits on some days! I will be writing a separate post on his blog and further outreach work soon so stay tuned. 
The tree in the courtyard of the Fellows Garden

A couple more talks then a final 'treat' - two scientists from the Cambridge Sainsbury Laboratory described the fascinating research they are doing at this state-of-the-art facility. ( I had a tour once and it's true! They even have whole walls you can write ideas on). Amazing how quickly this lab - completed in December 2010 - has filled itself with pioneering research leaders. Dr Siobhan Braybrook, for instance, is investigating how plants, with their rigid cell walls, can perform delicate 3D movements such as the circling motions of young shoot tips ( known as circumnutation). Professor Yrjö Helariutta, meanwhile, is researching how undifferentiated root stem cells become  highly specialised sieve plate elements. These form part of the phloem vascular system which transports nutrients and carbon sugars around the plant. Seive plate elements are unique - unlike the xylem elements that transport water, they are living cells which form continuous channels connected by seive- like plates ( hence the name).  To do this, the nucleus and organelles completely degrade and the walls undergo thickening. To understand how this takes place, Yrjö is using the latest 3D root imaging systems to compile serial sections into exquisite images that document how the cells change over time. I wish I could borrow it to study how Striga gesnerioides infects my Arabidopsis plants. It would make for some pretty pictures for my thesis!

A priceless relic of British history .... The exquisite Alfred Jewel  © Ashmolean Museum, University of Oxford.

And then quite suddenly it was all over for another year. Farewell lunch, pick up bags, disperse to trains, cars and coaches.I just had time to pop into the Ashmolean Museum to seek out the Alfred Jewel. It was amazing how many people walked past it, despite it being one of the most significant finds of Medieval Britain, commissioned during the reign of King Alfred (871-899). The exquisite  jewel-work depicts a figure - said to be Christ or the personification of Sight - surrounded by the words "AELFRED MEC HEHT GEWYCAN" - "Alfred ordered me to be made". It is all the more alluring in that no one is exactly sure what it was used for - part of a crown? A rod for coiling manuscripts around? A pointer to follow the lines of scripture? Either way, it marks the transition from pagan societies to a culture based on Christianity and learning.

And now it really is time to depart...until next year Gatsby and thanks for the memories!

* The UK Biological and Biotechnological Sciences Research Council

Thursday, 10 September 2015

Gatsby Annual Network Meeting, Day One

It's September so it must be....the Gatsby Plants Annual Network meeting! This yearly pilgrimage to Oxford gives the members of this group the chance to share progresses in plant science research, bounce ideas off each other, suggest new collaborations....and to sample the hospitality of one of Oxford University's 38 colleges. This year it was back to Queen's College, also the venue for the 2013 meeting.

Once we had deposited our baggage and grabbed some lunch, it was time for the afternoon's marathon of talks to start. During this time, the PhD students supported by the Network take centre stage, giving 20-30 minute presentations on their projects. Students funded by a Gatsby scholarship don't just receive a generous sum of money - the programme mentors also provide a comprehensive scheme of training and career development. Hence, each year these students are invited to subject their efforts in the lab to the scrutiny of the Network members. As many of these are world leaders in their field, this is nerve racking to say the least! As my PhD is not funded by Gatsby itself, I ( fortunately!) DIDNT have to give a talk, but as a member of the Network I am allowed to come and cheer on my colleagues and pick up a few ideas for myself!

First we heard from the final year students, who face the daunting task of wrapping up their experiments and settling down to some thesis writing. I was particularly intrigued by Suvi Honkanen's presentation describing the genetic control of rhizoid development in bryophytes ( mosses and liverworts). These species are often described as 'primitive', partly because they lack true roots and instead have weak, thread-like structures called rhizoids. Little is known about how these rhizoids form, so Suvi screened a population on Marchantia polymorpha for mutants with altered rhizoid development. This isn't so time consuming for bryophytes as it is for more 'modern' plants because in these species the dominant life cycle stage is the 'haploid' generation. This only has one set of chromosomes instead of two ( 'diploid' ) and is equivalent to the sperm/ egg cell stage of humans. It also means that, if a gene does have a mutation, it can't be masked by a functional copy on the other chromosome. From this screen, Suvi identified RSL as a critical  regulator of rhizoids: when this gene is mutated, the rhizoids fail to form properly. On the other hand over- expression of RSL causes  additional 'ectopic' rhizoids to develop on the upper surface of the leaf. Curiously, when the equivalent gene is knocked out in Arabidopsis thaliana - belonging to the utterly different race of 'vascular' plants-the roots don't develop. Thus, RSL is an ancient gene with a conserved mechanism that was already present in the last common ancestor of vascular plants and bryophytes. Another illustration of how the same genes and mechanisms crop up again and again in completely different contexts!
Queen's College, venue for this year's meeting 

I also enjoyed hearing Stephanie Johnston from Durham University on  'StayGreen Sorghum'. Although we don't eat much of it here, Sorghum is a dietary staple for over 500 million people, and is also important as a livestock feed and a biofuel. Drought resistance varies considerably across sorghum cultivars but StayGreen lines are the champions  as their leaves remain green even under severe drought. But no one is entirely sure why, hence Stephanie is currently investigating the potential mechanisms behind this. I must admit a vested interest in this as I worked with Stephanie on this for my undergraduate research project when I was at Durham! She started her search by performing a microarray to identify genes differentially regulated in StayGreen sorghum compared to more drought-susceptible lines. But this identified over 2,000 genes - like looking for a needle in a haystack! Fortunately, many of these genes had been characterised so Stephanie was able to identify common themes and functions. These included genes relating to the control of the stomata - tiny pores onthe underside of leaves that allow water and gas exchange. This suggested that StayGreen Sorghum may retain water by having fewer stomata or by keeping the apertures more tightly closed. It appears that both may be the case. Besides having fewer stomata, StayGreen Sorghum expresses high levels of a gene called SDIR1 ( Salt andDrought Induced Ring Finger 1) . If this is over expressed in Arabidopsis, the stomatal apertures decrease and the plants lose water more slowly. But this comes at a price - smaller pore openings restrict the amount of carbon dioxide the plants can take up for photosynthesis. As a result, StayGreen Sorghum have reduced yields under well-watered conditions. Hence, plant breeders face a challenge in improving stress-tolerance in crops without compromising harvests.
There was also an update from Emma Johnston on the 'explosive transgenic grasses' developed by Liz Dylott's lab at the University of York (see my previous post "Explosive Plant Science" http://scienceasadestiny.blogspot.co.uk/2014/04/explosive-plant-science.html). It's now thought that the genes that allow detoxification of explosives like TNT may also confer resistance to multiple herbicides. If so, these could be a new target for herbicide activity - amazingly, there hasn't been a new mode of herbicide action sincere 1980s. I can't help but feel a little jealous of Emily - this work has just been published in the prestigious journal Science. Most researchers dream of getting at least one paper into Science during their whole career and she has done it before finishing her PhD! 
Enjoying the Fellows Garden over coffee
Throwing the floor open to questions can be nerve wracking for the speaker but the feedback and suggestions given by the audience are invaluable. I lost count of the number of times audience members asked " have you ever thought of trying..." Or "why don't you look at...?" The talks also showed how ingenious researchers are when it comes to troubleshooting. Take Jenny Walton, for instance, who worried that growing her Medicago plants in soil was contaminating her trace metal analyses. So she invented her very own hydroponic system using fine mesh and a cat litter tray!   It just goes to show the importance of bringing scientists together for encouragement and inspiration - it's not just about free conference dinners!

Thanks to a burst of late-summer sunshine, we were able to congregate in the Fellow's Garden during the refreshment break and admire the flowers. Afterwards, we heard from the second year Gatsby PhD students including Alice Baille, who shares the same office as me at Sheffield. She is investigating whether it is possible to increase photosynthetic efficiency by manipulating the size of air spaces in the spongy mesophyll layer of the leaf. Carbon dioxide uptake can account for up to 50% of the limitations on photosynthetic capacity, hence engineering larger air spaces could boost productivity. One strategy may be to modify the production of pectin, a component of the cell walls which helps to 'glue' cells together. Hence, Alice is currently imaging leaves from plants with mutations in pectinmethylesterase enzymes using fluorescent antibodies to see if this affects wall formation. Will this result in bigger spaces? And - crucially - will this boost photosynthesis? No doubt we will hear more at next year's meeting!

We then jumped from leaf spaces to outer space withour before-dinner speaker, Professor Chris Lintott. Chris is Professor of Astrophysics and Citizen Science in the Department of Physics at Oxford University - although better known as presenter of 'The Sky at Night'. Despite the complete change in topic, his talk was riveting and had us in fits of laughter at times. So much so, that I'm going to make it the subject of a separate blog post- look out for it soon!

After all that science, it's time for tea! Day two coming soon!

Thursday, 3 September 2015

And my supervisor told me to get rid of them...

"Get rid of them" my supervisor told me "They're no use of you now, if there were any parasite seed that germinated they must have died by now".

'They' in question were my tobacco plants, Take Two. I had. lovingly raised from seed and, about two months ago, I had carefully transplanted them into pots of soil infested with dormant seeds of the root parasitic weed  Striga gesnerioides, the subject of my PhD project. As every plant scientist knows, the first thing you do when you start working on a new species/ mutant/ culitivar is BULK THE SEED, BULK THE SEED , BULK THE SEED! Especially if you only have one vial of it left that is fast running out...

So the idea was that, as a super susceptible host, the tobacco would act as a 'Striga-seed factory', and I would get hundreds of flowering Striga shoots emerging which would flower and hopefully give me enough seed for the rest of my PhD. So I waited and waited...

...and waited...

And nothing. It got to the stage where my supervisor decided enough was enough, we needed to move on to a different strategy. The tobacco were now taking up space and needed to be cleared out. This was at the end of June and I said I would get on to it, but , with one thing or another, I didn't quite get round to it before leaving for the Annual Meeting of the Society for Experimental Biology ( where I was attending as official science writer) in Prague. So, I put it on the 'To-Do' list for when I got back.

But when I did return....there seemed to be something poking out of the soil  surrounding one of the tobacco plants. A purplish-little dome with a bumpy surface  ...could it be?

I hardly dared to hope but nevertheless I decided to delay taking the tobacco to the tip. And the little something continued to emerge, and turned out to be a tightly closed bud supported by a delicate stem....unmistakably Striga gesnerioides. I was elated but , as the weeks went by, it seemed that this was not 'the first of many' but a fluke. No new shoots emerged and the only one that had eventually went on to flower, set seed and die. 

But then one Monday, as I checked on the plants after the weekend.... What was this??! Not one, but two, three, four....several shoots coming up now - at least one on each tobacco plant. They were finally coming!!! It actually worked!

I now think that I was watering the soil too much, causing the parasite seed to enter 'wet dormancy' (Striga gesnerioides doesn't like getting too wet). Whilst I was away, of course, they had plenty of time to dry out and wake up again!

I have a new favourite hobby now: counting my little darlings with today's  count being 36 parasite shoots in total, with 19 on a single host. My supervisor remains unimpressed though : "You need WAY more than that to get enough seed - I've seen sixty to eighty on a single plant!" Maybe so, but I'm inclined to keep hold of my tobacco for the meantime...after all, who knows what else may turn up?!

The 'Host with the Most' - Striga gesnerioides on tobacco