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 14 January 2015

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!

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