It's an infection!

My PhD project - investigating the differences between compatible and susceptible interactions between host plants and parasitic weeds- depends in my model system working. If I cannot get Striga gesnerioides, a vicious parasite which devastates cowpea harvests especially across Africa, to infect Arabidopsis thaliana, the 'fruit fly of the plant world' then my plans would be scuppered and it would mean a compete project redesign. So I was very nervous when it came to opening up my first pilot rhizotrons systems, infected way back in December last year. Peeling off the foil covers, I wondered what I would find. A scattering of dead parasite seed? Or flourishing tubercules, connected to he host root system?

Striga gesnerioides tubercules on Arabidopsis thaliana roots

I need not have worried, the infection was a success! Large, dark knobbly tubercules were clearly visible on the Arabidopsis roots, at the sites where the parasite seed had germinated, sprouted radicles and forced their way into the root system. The parasites are now living off the water and sugars which the poor Arabidopsis hosts supply through their vascular system.  Some of the tubercules had even advanced to the stage of sending up flowering shoots, a clear sign of a happy parasite! So it's chicks away and full throttle forward with my research agenda!

A flowering Striga gesnerioides tubercule

Searching for a needle in a haystack ( or a very rare plant!) just got easier...

One advantage of having a horrendously busy supervisor who is involved in all sorts of groups and networks, is that they occasionally invite you to conferences that they have been called upon to organise. So it was that I was able to attend the Annual Meeting of the UK Plant Phenomics Network on Monday 12th - Tuesday 13th January, held at the Halifax Hotel here in Sheffield.

The topic this year was "Advancing Challenges of Phenotyping Biotic and Abiotic Stress: From Lab to Field". With a growing population to feed, there is tremendous pressure on plant scientists to develop crops with greater resistance to drought, pests, salinity, diseases, etc. But how does one identify the individuals that possess these desirable traits? In a field-trial, there can be hundreds of different genotypes to assess, which would require days of manpower (usually PhD students!) to trawl through by hand. Hence the advent of automated phenotyping systems, the most modern of which were showcased at this meeting.

I felt as though I had been given a tantalising insight into the future - where rows of plants zip along conveyor belts to be screened and analysed from every angle, before being shuttled back to their controlled environment chambers. Such technology is already in place at the National Phenotyping Centre in Aberystwyth, where each plant has its own ID, allowing watering and nutrient schemes to be tailored to individuals. Meanwhile, Lionel Dupuy, from the James Hutton Institute, described cutting-edge methods to image plant roots and the surrounding rhizophere. These included a transparent soil medium and measuring the growing forces of roots using thin layers of elastic glass that the emerging root tips press against. (You may ask "Isn't Agar a type of transparent soil?" Not exactly- it isn't made up of particles and doesn't have the same refractive index and anion-exchange capacities).

Thermal imaging is also a popular method to diagnose plants experiencing drought stress. When water is limiting, plants close their stomata (the tiny pores on the underside of leaves that allow gas exchange) to reduce evaporative water loss. This is the prime cooling mechanism for plants, however, so closing the stomata causes the internal temperature to rise. When scanning a field of crops, drought-resistant genotypes can be spotted because they are significantly cooler as they are able to keep their stomata open for longer. In the most sophisticated systems, mounted aerial cameras can sweep over entire fields, taking seconds to perform a job which would take hours by hand.

Another useful technique is analysing chlorophyll fluorescence to assess the level of photosynthetic function. When sunlight falls onto a plant leaf, some of the energy is used in photosynthesis and the rest is dissipated as heat or re-emitted as fluorescent light. If photosynthetic capacity is reduced (e.g. by disease), then a greater proportion of sunlight is re-emitted as fluorescence which can be measured by a fluorimeter. I used this method myself during my final year undergraduate project at Durham University, when I investigated how drought and salinity affect photosynthetic function in Sorghum.

Dr Helen Cockerton, who works on strawberries 

At the conference dinner, I was fortunate enough to sit next to Dr Helen Cockerton, a postdoctoral researcher who works on strawberries at East Malling Research. I wasn't aware of this, but apparently strawberries are under threat from the soil borne pathogen Verticillium dahliae, a broad-spectrum pathogen which affects around 300 plant species. The only effective strategy is fumigating the soil medium with chemical nasties which the EU is keen to phase out. The situation is so severe that most strawberries in this country have to be grown in alternative mediums. Dr Cockerton is part of a research effort to identify resistant strawberry cultivars and to develop a rapid method to screen plants to assess disease symptoms. This is compounded by another pathogen, the root-lesion nematode Pratylenchus penetrans, which can increase a host plants susceptibility to V. dahliae. To me, this perfectly illustrates the complex and never-ending struggles that plant scientists face to safeguard our crops for the future.

Chatting to the other post-docs around the table gave me a chance to contemplate how life might be like for me post- PhD. I was alarmed to find that it wasn't unusual for them to work until 7.00 pm and also at weekends. 'You end up doing so many unlogged hours that you lose count' said one. I was also advised that networking and cultivating contacts early is key to securing a job after the thesis has been written. But if the work really is that gruelling, will I still want to remain in Academia?

I was able to network a little myself by introducing myself to Tony Pridmore of Nottingham University, who has experience with the root- measuring software I hope to use in my project. If my images are suitable, he says that he will be willing to help me analyse them. So, it's back to conviron 502 to prepare my latest batch of Arabidopsis and, hopefully, some good quality data!

Graduation!

Last week felt like stepping back in time as I made a return pilgrimage to Durham to collect my undergraduate Degree ( BSc in cell Biology). Technically. I should have graduated last summer, however I had decided to defer the ceremony as it clashed with my media internship with the Society for Experimental Biology. Although it was numbingly cold, we were fortunate with the weather and the  world heritage site was bathed in winter sunshine. Whilst queuing up in our 'pairs', we did a few Mexican waves to try and warm up a little! As we processed from the Castle to the Cathedral, the scene was a curious juxtaposition of technology; above the ancient Norman shrine of St Cuthbert, fashioned with medieval technology, a modern drone whizzed up and down in the sky, capturing the scenes for the souvenir DVD.

It felt a real privilege to celebrate this achievement in such revered surroundings and although the nerves began to steal over me, everything fell into place and I was able to enjoy my moment when I was called forward to shake the Dean's Hand. After the undergraduates, the PHD candidates were presented; Durham follows a curious, but rather wonderful, tradition of reading out the Theses titles for each candidate. It was inspiring to see the (hopefully!) next stage of my career and started to make me wonder what title I will eventually give to my PhD work. Something sharp, intriguing, perhaps witty - especially if it was to be announced in such a grand way to such a large and varied audience...

But that is all in the future - before that , the thesis itself needs to be written and for that I need some data! So it is back to Sheffield and to my plants. But it was lovely to take a pause and reflect on how far I have already come. It was also very nice to meet up with some of the Academics of Durham Biological Sciences Department who had been real mentors to me. It felt a shame to take the gorgeous robes off but I am fortunate in having a fascinating subject to return to work on... And a dream of a second graduation to come!

The Castle on Palace Green

Entering the Great Hall

Robing up!

Exciting New Year...

Happy New Year to you! If you haven't made any resolutions, don't worry - I always say that if it it important enough , you will start that very day and not wait until the next new year!

I am quite excited already because the year for me has started with my first harvest of Arabidopsis seed. This is my model organism for my PhD but unfortunately there is a bit of a shortage of seed I be department ( as it is a model organism for LOTs of researchers here!). So as soon as the academic term started in October, I was first tasked with inducing some seedlings to flower , self fertilise and produce more seed. Thanks to controlled environment chambers, I was able to convince my seedlings that they were in fact on spbritish summertime, not in the depths if the wet winter outside, and just today, I had my first 'harvest'. Let's hope there are many more to come!

Merry Christmas!

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

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

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


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




White roots on White mesh... tricky

Arabidopsis roots dyed with Toluidine Blue

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

The new Black Mesh - from a reputable supplier of scientific equipment!

What can we learn from Badgers?

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

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

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

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

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

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

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

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