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!

Saturday, 29 April 2017

New beginnings...

As the cherry blossom and bluebells come out, there is an edge of summer in the air....so talk in the department turns to fieldwork expeditions, international conferences and maybe even summer holidays... It's an optimistic time, and I'm buoyed up on good spirits after a few developments in my own project.

Firstly, it looks as though I have finally hit upon one of those elusive 'significant' results. One of my Arabidopsis mutants appears to be more resistant to the parasitic weed Striga gesnerioides. I won't say more here, in case this eventually leads to something publishable, but it could indicate which plant defence pathways - if primed into early action - could stop the parasite from stealing into the host root.

It's amazing the difference one single positive result can have - and it certainly illustrates the true rollercoaster nature of a PhD. It had been a long, dark winter in terms of both my mood and forthcoming data. Countless times, I felt in despair and that I was fruitlessly casting around in the dark for something that may not even be there. There were many occasions where I worried that my thesis would be a gallery of 'failed' experiments that would be impossible to defend in a viva. But suddenly things have been turned on their head. My supervisors are excited, and - like a blossoming shoot - a new line of enquiry has surged into life. I already have a list of another five mutants to try next, that could reveal finer details about what is going on at the molecular level in the host-parasite interaction.
Bluebells in Ecclesall Woods
I can't get carried away though - it really is only a start and subsequent experiments could show that the result was just an anomaly. It is still early days in my terms of developing my project's 'story'. Sadly, this means that I won't be going to the World Parasitic Plants Conference in California this year; I don't have enough data to present a seminar or poster and there are limited travel funds for the lab. But I have been invited to attend the Annual Meeting of the Society for Experimental Biology (SEB), held in Gothenburg this year. I particularly enjoy the SEB meetings as it covers the whole breadth of biology, and its membership includes animal, plant and cell researchers. This means I get to write about areas of science outside my own narrow niche; in the past, I have covered everything from  giraffe biomechanics, microscopic tardigrades, ancient yew trees, bumblebee navigation and even fish memories. It's all invaluable experience for a career in science communication. And I can't deny that being put up in a rather swanky hotel makes it even better! As usual, the programme this year is almost as varied as biology itself but the editor of the SEB Bulletin and I agree that the sessions on Carnivorous Plants and Paleo-genomic DNA have great potential for articles. It's certainly something to look forward to.
Striga gesnerioides growing on tobacco
Finally, an experiment started many months ago has just started to bear fruit. My stocks of Striga gesnerioides seed are down to one and a half tiny vials, not enough to complete all the experiments I will need for my thesis. Fortunately, I foresaw this and way back in January I infected some hale and hearty tobacco seedlings with the parasite. Just as I was beginning to worry that they hadn't attached, I finally spotted some tiny shoots emerging from the soil. That was two weeks ago; since then, the Striga shoots have rocketed up and are now producing (rather beautiful) purple flowers. As long as I am vigilant, and don't manage to kill off the host, I should be able to get a reasonable harvest.

I hope you are enjoying the Bank Holiday weekend (another one?!) I managed to have a brief escape today to see the bluebells out in Ecclesall Woods....but it's back to data analysis tomorrow. Thanks again for reading! Stay tuned for my next post : could climate change make our key crops sterile?

Sunday, 9 April 2017

Pints, PCR and Publicity...

It's been a while since my last post and a lot seems to have happened in that time - the days are much longer and sunnier now and Easter is ridiculously close. And of course - the Pint of Science Festival has officially launched for 2017! As the official Social Media/Publicity manager for the Sheffield event, I was very busy in the run-up to our launch event on Monday 3rd April, making slideshows and videos to show on the night. Our venue, The Sheffield Tap, couldn't have been more suitable. With hundreds of craft beers lining the walls, it was easy to see why Sheffield is known as the 'real ale cpatial' of the UK. The high ceilings, gorgeous furnishings and brewing installation only added to the intimate atmosphere. Tonight it was crammed full of fun science demos - from Mylo the interactive robot; a model of a working kidney; a virtual reality experience and a highly competitive 'make a neurone' competition. Some of the Festival speakers also gave us a taste of what was to come, and we enjoyed fascinating forays into the political implications of terrorism; structural colour in the natural world; using stem cells to cure hearing loss and the failings of the prison system.

Some very impressive neurons...

Trying out virtual reality at The Sheffield Tap
 The launch perfectly captured what Pint of Science is all about - informal discussions on science between the public and researchers, helped by the presence of alcoholic beverages! It already seems to have generated excitement for the main festival in May as tickets across the whole programme are starting to sell.
Meeting Mylo, the interactive robot

I've also been doing some different things in the lab recently. After mucking about with my plants down in the growth chambers for so long, it was quite challenging to do some 'proper molecular work' again - very intricate, precise and sterile in comparison! One focus of my project is to look at a host of Arabidopsis plants with mutations in different defence-related pathways, to see if these alter resistance to the parasitic weed Striga gesnerioides. One of these mutants, pmr4 (defective in callose production) comes from a very old seed stock, so my supervisor was concerned that the mutation could have been lost. To check this, I decided to perform a PCR (Polymerase Chain Reaction) to amplify the region of DNA that should contain the mutation. In basic terms, DNA extracted from the plants is combined with short DNA sections (primers) that base-pair with the mutated sequence, and an enzyme called Taq DNA Polymerase which extends the length of the primers by adding new DNA bases. If the mutation is present, the primers and Taq DNA Polymerase recognise it and produce short sections of DNA (the product). To see if any product has been made, the solution is loaded into an agarose gel with an electric charge applied across it. Because DNA is negatively charged, it moves across the gel to the positive anode. A UV-sensitive dye is added to the solution before the DNA is run, so that the DNA appears as a 'band' on the gel. 

My wonderful gel photo. The bands in the centre correspond to the DNA product from the pmr4 mutation. The 'ladder' at the left side is a reference solution containing DNA products of known sizes. This allows the size of the experimental product to be calculated by comparing it to the nearest band on the ladder. 

PCR is notoriously difficult to get right - I once spent two weeks of a summer research project trying to get it to work on wheat. The temperatures and timings are very precise and there is little margin for error. So I wasn't hopeful at all that I would be successful, but went ahead anyway: extracting the DNA, performing the PCR, running the gel. Much to my astonishment the gel photo was exactly what I wanted with a neat row of bands right across the middle! This means that my plants definitely have the pmr4 mutation and are suitable for my experiments. If you want to know more, see here for a nice summary on PCR and Gel Electrophoresis. 

I hope you have been able to enjoy the beautiful sunshine of late. Sadly I've been in the library working on Pint of Science videos, or underground with my plants for most of it... but at least things are moving in the right direction. Hopefully I will be able to get out soon - the Peak District is calling! Have a good week and thanks for reading.