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!

Thursday, 22 June 2017

Is there a kit for that? Getting busy in the lab...

If following a protocol is like cooking to a recipe, then RNA Extraction must be up there among making a croque-en-bouche or a deconstructed soufflé. So why am I attempting such a thing? Well, so far my experiments suggest that a particular plant hormone may determine how resistant plants are against the parasitic weed Striga gesnerioides. Up to now, I have investigated this by testing whether mutant Arabidopsis plants that cannot make or sense this hormone are affected in their susceptibility to Striga. But this doesn’t tell me much about what is going on at the molecular level. Hence the RNA extraction…

RNA acts as an intermediary molecule between DNA and proteins. The DNA sequences of genes encode the amino acids that make up all the proteins in our body, from structural proteins like hair to enzymes that catalyse reactions. But DNA cannot leave the nucleus so it is first transcribed into RNA, which shuttles out of the nucleus to the cytoplasm where it is ‘read’ by ribosomes that assemble the amino acids together. The more active a gene is, the higher the rate it is transcribed and the more RNA molecules are produced. So one way to see what is going on is to capture all the RNA molecules in the cell at any given time – a ‘snapshot’ of gene activity in the host.

But it’s a tricky business for various reasons. First, RNA degrades very easily so the samples must be kept in liquid nitrogen or on ice at all times. Then there is the issue of cross contamination – from gloves, pipette tips, surfaces etc- which requires super vigilance to keep things sterile. And then there is the protocol itself: hundreds of steps, each with very precise centrifugation times and specific amounts of reagents. It’s certainly not for the faint hearted!
Just some of the things needed for RNA extraction: liquid nitrogen, ice box, fume cupboard and of course the QIAGEN RNeasy Mini Kit!

Not surprisingly, some entrepreneur spotted the gap in the market for an RNA extraction ‘kit’ (the same brains behind the PCR machine perhaps?). This jazzy coloured box, that looks like a Christmas present, is filled with all the equipment and reagents needed, all clearly labelled and even with special pink and purple tubes! But it still took me several hours to work my way through it, not helped by a stomach ache that nearly made me pass out a few times!

Did it work? To find out, I ran a sample of the precious RNA solution in an agarose gel. This uses an electric current to force the RNA molecules to move through a viscous medium, causing them to separate out depending on their size (with smaller molecules travelling faster). The gel contains ethidium bromide, which binds to the RNA and fluoresces inn UV light, allowing the RNA bands to be seen under UV light. After so many hours of work, here’s what I had to show for it:

My glorious gel photo - the 2 wells at the extreme left and right contain a reference solution called a Hyperladder, made up of fragments of known sizes. The four wells in the middle were loaded with my samples of RNA solutions.

Hooray! Because there are some bands present, I had some success at least! But unfortunately, the concentration isn’t high enough to take these samples to the next stage and work out which genes were the most active. So there is a bit of tinkering to do yet. But we all have to start somewhere…

On the side, I have also been experimenting with something new for me: hydroponics! My stock of Striga seeds hasn’t been germinating very well: the best I have managed is around 40%. This is probably because I have been using an artificial chemical called GR24 to trigger the seeds, but this is really suited for the related species Striga hermonthica, not S.gesnerioides. So I am going to try collecting the root exudates from cowpea, which is a natural host for S. gesnerioides, to see if this works any better. My little cowpea seedlings look quite content growing in their tubes at the moment, but what happens when they get bigger remains to be seen…
Look, no soil! Growing Cowpea the hydroponic way...
Meanwhile, the countdown for the Society for ExperimentalBiology’s 2017 Summer Conference in Gothenburg has begun in earnest! I have been invited to attend as a science writer and am already trying to arrange interviews for my big feature articles on Palaeogenomic DNA, Carnivorous Plants and incredible Animal Athletes. With a bit of luck, I may even be able to see a bit of the Swedish West Coast as well although the schedule is pretty jam packed! Stay tuned for more updates on that.
Here's wishing you a good end to the week - can't believe we have already had the longest day. Where is the time going???!

Monday, 29 May 2017

I'll never look at a tomato the same way again...!

It takes a lot of work to make something appear effortless”. This weekend, I certainly learnt the truth of this saying and now have an even deeper respect for event managers. The reason? After weeks of planning and countless meetings, the tomato extravaganza had arrived!

All bought in Sheffield, but these tomatoes come from all over the world
When I heard that the British Science Association (BSA) wanted to set up a branch in Sheffield, I knew that I shouldn’t really be taking on any more commitments on top of my PhD. But the opportunity to help establish a completely new group from scratch proved impossible to turn down. However, the initial group was so small at first that I wondered if we really could launch it off the ground. Yet despite being so few, our team was so committed that we soon gained momentum as we planned our first event. This was to be an activity stand at the Sheffield Food Festival which explored how the global transport of food can also spread crop diseases that threaten food security. We chose to give the tomato a starring role so that we could include my colleague Estrella’s own research on mould and blight diseases in this crop. Even though the idea seemed simple on paper, there was a small mountain of paperwork and other issues to sort out. The past weeks have been a blur of filling in risk assessments, finding insurance certificates, finding a microscope, buying playdough, collecting poster boards, designing leaflets…just to name a few! There were so many things to keep track of, I was sure something essential would be missed. Would we be able to pull it off?

One of the 'subtle clues' for our tomato quiz
I needn’t have worried. When I arrived at the Winter Gardens on Sunday, everything was ready for us – tables, chairs, power supply and a prime location opposite the Millennium Galleries.  We had a lot to set up but just about managed to get everything ready before the official opening time. We had a beautiful tasting station with tomato varieties from different countries; the chance to view tomato diseases under the microscope; an activity building electric circuits using tomatoes and other fruits as batteries and children’s crafting with playdough, pipe cleaners and lots of googly eyes. And if that wasn’t enough, I had also hidden interesting tomato facts all around the Winter Gardens for our quiz. Of course, we also had a galore of freebies – ‘Plant Doctor’ stickers, pens, badges and fluffy bugs. We were certainly prepared…but would anyone stop and look?

Our poster on what being a 'Plant Doctor' involves
In the end, it went even better than I could have hoped. I was amazed at how positive people were towards our tomatoes, especially when we had to compete with stalls selling luxury chocolate, hog roasts, pizza stalls and artisan fudge! We were constantly having to cut up more tomatoes for sampling (especially the Yorkshire variety – a biased audience perhaps?!) Even better, many people were actually motivated enough to search for all the clues in our tomato quiz so that they could win their very own tomato seedling to take home. But it was also a lesson in how the simplest of things can be the biggest hit. For instance, one of the most popular activities for the children was being able to wear a mini-lab coat and have their photo taken with a microscope. When you work in research, it can be easy to forget how novel these things are. As for the crafting activity…. I realise now that I was a bit naive to think that a kilogram of red play dough would be more than enough! There were certainly some fantastic fruit and vegetable creations. It looked like we were running a crèche, it was so busy! 

Estrella in full-on Plant Doctor mode!
 Four non-stop hours later, when it was time to pack down, we were tired but elated. Practically every tomato had been eaten and nearly all the tomato seedlings been rehomed. We had managed to keep going despite the tropical temperatures and had kept our enthusiasm. And even though I could no longer say ‘tomato’ properly, I hadn’t ended up despising this quirky, scarlet fruit.  We had made it – and are ready for more!

Just some of the children's marvellous creations
So what’s next for the BSA in Sheffield? This week, we will be holding our first AGM to elect a committee and decide on our constitution, so that we will be a proper, formally recognised branch. After that…well we have so many ideas already: cinema nights, art-science collaborations, theatre productions…watch out for us world, here we come!

And if there is a sudden surge of people becoming plant pathologists in a few years…you will know why!

The TEAM! Everybody was awesome
Thanks for reading, I hope you have a good week! Anyone know a good recipe for tomato salad?

See our Facebook Page for more photos of"The Secret Life of Tomatoes".

Saturday, 20 May 2017

Cheers! Having a blast at Pint of Science 2017!

This past week, I have visited more pubs in Sheffield than during the past three years put together– but don’t worry, it’s all for a good cause! After MONTHS of planning, preparation and promotion – PINT OF SCIENCE 2017 finally landed in Sheffield!

As you may know, Pint of Science is an international science festival where the public meet real researchers in pubs for fun evenings filled with discussions, science demonstrations and interactive activities. The festival first came to Sheffield last year and I helped as a general volunteer for one of the ‘Planet Earth’ themed events. I enjoyed it so much, that I enthusiastically took on the role as Head of Social Media and Publicity for this year’s festival. At the time, I didn’t realise quite what a daunting task this would be: this year, the festival was double the size of the 2016 event, with twice as many events over the three days. It was a big gamble; would this dilute our audience too much? Would we be able to fill each venue?

After wowing us with Gravitational Waves, Dr Ed Daw treats us to a musical performance
Nevertheless, I set myself an ambitious aim of selling 95% of tickets and launched myself into writing press releases, crafting videos, arranging radio interviews and tweeting for all I was worth. But the tickets just weren’t selling! I began having nightmares of the speakers turning up to find only a handful of people in the audience…and as publicity manager, I would feel entirely responsible.

A friend calmed me down, telling me that Sheffield had a reputation for waiting until the last minute to book tickets for events. I didn’t believe her…but it turned out she was right! In the final few days, the tickets suddenly began to fly – nearly every time I checked the computer, another event had run out! In the end, 14/18 events were completely sold out, and we shifted 778 tickets (94.3%)! I think I can be happy with that…!

14/18 of our events in Sheffield sold out - result!

During the festival itself, my main duty was to capture as many different scenes as I could to use in promotional material next year. But I did manage to catch a few of the talks. In ‘I Ain’t afraid of no Cosmic Ghosts’ Dr Ed Daw covered my 6-week cosmology online course in about 20 minutes, as he galloped through the discovery of gravitational waves, before promptly launching into an improvised jazz performance. At the ‘Boost Your Brain: Be Busy, Bilingual & Benevolent’, I learnt the science behind why sitting quietly and doing nothing really is good for the soul – and our physical health too. Meanwhile, over at The Sheffield Tap, hosting the ‘Planet Earth’ events, I enjoyed Jennie Crawley’s presentation of her research on the timber-working elephants of Myanmar; a population that has a uniquely close bond with their human caretakers. Then in the 'Our Body' events, Dr Allan Pacey gave a particularly entertaining argument against the widely-held belief that modern life is threatening male fertility. Each venue had a distinct ambience, from the staidly traditional Old Queen’s Head in a medieval timber building; to the Sentinel Brewing Co, where you can see the entire being process – from ‘grain to glass’- while you drink; to the cosy side room at Harrisons 1854, which felt more like being in someone’s living room!

The Sheffield Tap made a great venue for our Planet Earth themed events - guess the skull anyone?

Judging by the amount of discussion, laughter and engagement on the night, besides the audience feedback so far, just about everybody had a good time. I’ve already got my fingers crossed that Pint of Science will be returning in 2018! I’ve learnt so much from helping promote the 2017 event and would relish the chance to put it all into practice again. Probably the most beneficial thing to me was going from a complete novice to being able to put together a video from scratch.

Harrisons 1854: a more intimate venue for our Beautiful Mind events, where audience members could take part in their own brain-related experiments!

In the meantime, I had some other good news this week: I have won a bursary to attend the 2017 annual meeting of the BIG network of science communicators! Three days of mingling with science communication professionals, learning about everything from safe ways to blow things up in classrooms, to running poetry classes on physics. It’s a real chance for me to target those areas I still lack experience in for the science communication job market. In particular, I have my eye on the introduction to making podcasts and the animation workshops. This year, the BIG Event is taking place at the Centre for Life in Newcastle, 19-21 July. So that gives me a bit of time to crack on with my REAL job and get back to my PhD experiments. Time to do some data analysis methinks…

Thanks for reading, have a good weekend!

Friday, 12 May 2017

Food security challenges - from bugs to beating climate change

Here’s my round up of a recent departmental seminar where Professor Tammy Sage introduced us to a little-known but highly important threat to food security and how plant science is being used to overcome it. Plus I investigate one of the rapidly upcoming food ‘sustainability trends’ – eating insects for dinner!

Climate change is a worrying enough prospect as it is, but imagine if you were a species that simply couldn’t reproduce above a certain temperature? This seems to be the situation with many plants, which worryingly include key staples. Rice, wheat and corn are particularly temperature sensitive during the process of meiosis and mitosis resulting in failed production of the male gametes (sex cells). In many species the pollen aborts upon exposure to temperatures 30°C: a phenomenon which is already starting to occur in some of the major rice, corn and wheat growing regions.

So what can be done about this ticking time-bomb for food security? Professor Tammy Sage (University of Toronto, California) and her lab group are working on the problem by identifying plant genes that confer high-temperature resilience during pollen development. This would be very difficult to do in rice: although it has the smallest genome of the major cereal crops, it is still around 430 million base pairs and 12 pairs of chromosomes. So, like me, Tammy uses Arabidopsis thaliana, the model organism of the plant science world which has a fully sequenced genome of only 135 million base pairs and 5 chromosome pairs. This makes is much quicker to identify gene sequences related to thermotolerance that can be used to develop markers to search for these in crops.
Pollen grains germinating on the stigma of the model grass, Brachypodium. 
Photo credit: Professor Tammy Sage.

Tammy began by comparing Arabidopsis accessions with high and low seed production when exposed to 33°C. Through this process, a gene was identified (called HTT for High Temperature Tolerance) that was highly expressed in a pollen-specific fashion to a greater degree in the thermotolerant cultivar. But how exactly does it work? Tammy’s research has shown that HTT has a role in preventing dangerous molecules called reactive carbonyl species (RCS) from accumulating in pollen grains. Like reactive oxygen species (ROS), RCS can function as signalling molecules at low temperatures but excessive amounts (which can be caused by high temperatures) can be damaging. RCS have a much longer half-life than ROS and can also cross membranes, allowing them to reach DNA in the nucleus. In humans, RCS contribute to diseases such as Parkinson’s, diabetes, arthritis and Alzheimer’s.

In plants, HTT is expressed during the later stages of pollen development and Arabidopsis mutants with an inactive version of the gene produce nonviable pollen grains. So how exactly does HTT protect against the damage caused by RCS? It is still unclear but Tammy’s research indicates that HTT protects the enzymes involved in plastidic glycolysis from becoming carbonylated. Plastidic glycolysis liberates energy from starch in small organelles in the plant cells. This is needed to fuel the growth of the pollen tube once it lands on the female stigma. As well, HTT prevents carbonylation of signalling proteins that activate the heat transduction pathway. These act like an alarm system for high temperatures and turn on a range of responses that increase thermotolerance, including altering the fluidity of cell membranes and removing damaged proteins.

After all these years of study, it’s now time to turn these insights into action. Tammy is now working on introducing these genes into rice and also Camelina sativa (used to make jet fuel). Curiously, HTT1 is NOT naturally expressed in rice pollen, which may explain why it is so temperature sensitive. Hopefully, introducing HTT could act as a ‘protective sunscreen’ that will allow our crops to keep reproducing in our warming world.
Tasty? Bugs for dinner...

As for me, I recently attended a seminar called “Would you eat bugs?” as part of the Sheffield Festival of Debate, organised by the Grantham Centre for Sustainable Futures. As insect farming requires only a fraction of the land and water resources used for other animals, this could be a real viable option for a more sustainable protein source. But this would require overcoming several hurdles including the Western ‘Yuck! Factor’, the high temperatures (and thus energy costs) that many species require and allengenicity issues. Perhaps the most promising way forward is insect-fortified flours that can be made into pasta or cereal bars. At the event, we were able to sample Yumpa Bars, high-energy and protein bars made using cricket flour, besides mixes containing whole bugs. Whilst I particularly enjoyed the spicy crickets, I’m not convinced that insects will be going mainstream in the UK soon. More likely, they will be a bigger part of the solution in countries which already have the infrastructure, climate and cultural attitudes in place to facilitate their adoption. But for something different, it’s certainly worth a try!

And with that, I had better hop off to my plants…. Thanks for reading!

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.

Saturday, 11 March 2017

Feeling blue...

If seeing is believing...then what does one do if you don't see what you expect to? This week I have certainly lost belief in my skills as a research  scientist...and all because I can't get the roots of my plants to turn blue!

My PhD is investigating what defence pathways may be important in determining how resistant a plant is to the parasitic weed, Striga gesnerioides. I'm particularly interested to see if two of the most well known plant defence hormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have a role. To do this, I have been growing a series of transgenic Arabidopsis hosts, that express reporter genes for either SA or JA. The reporter genes code for the enzyme β-glucuronidase (GUS), which converts the substrate 5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) into a coloured blue product. However the promoter region of the transgene (which controls when the gene is turned on) has been engineered so that is is only activated if either JA or SA is present: for my experiments, the LOX-GUS reporter is  activated by JA is present, and the PR1-GUS reporter by SA.

What I'm looking for - bright blue roots!

 So I have been very busy growing whole batches of these reporter Arabidopsis lines, infecting them with Striga,  harvesting the roots at different time points and adding X-Gluc. If the SA / JA pathway is activated by the parasite, then the GUS enzyme should act on X-Gluc, turning the roots bright blue. But each time I take my samples out of the incubator...nothing. Resolutely white roots. Could there be something wrong with my staining protocol? It's unlikely because each time I  include a few transgenic plants that express GUS all the time, whether or not SA/JA is present. These have perfectly blue roots every time! So the away itself isn't the problem.

In that case, could there be something wrong with the reporter genes themselves? To test this, I took some of the spare plants and applied SA or JA in solution to the roots. But even these didn't turn blue! I'm completely stumped...and so are my supervisors. Just possibly, the transgene isn't expressed in the roots at all....all the published studies I can find using LOX-GUS or PR1-GUS used leaf or shoot tissues. Whilst this negative results are hindering my current  progress, it does raise interesting questions. Does the root system have a different set of SA or JA responsive promoters to the shoots and leaves? Or are other plant hormones, such as auxin or cytokinins, more important for defence in the roots?
What I'm getting- resolutely white roots!

It is frustrating after all the time and effort I have spent growing and infecting these plants...at least I could cheer myself up at the department's Discovery Night on Friday. This annual open evening of interactive lectures,  activity stalls and laboratory tours has become a real highlight for the local community. Helping children extract DNA from strawberries and seeing their delight at things even as simple as a pipette helped take my mind off my  work worries and remind me that it's exploring the unknown that makes science always so fascinating...

Sunday, 19 February 2017

Busy, busy, busy....

My New Year's resolution to pace myself a bit more has quickly gone down the pan - largely due to my inability to say 'no' to things. But it's difficult not to when there is always so much going on within the Faculty of Science: every week seems to bring new  'cv-enhancing' public engagement opportunities. And then there is my PhD to fit on top of it all! Needless to say, although the year is still young, I am already feeling run down - having a bad cold and losing my voice didn't help either!

I've spent a lot of time underground this week, transplanting my Arabidopsis seedlings into rhizotrons: as I spend quite a few hours doing this, I made a basic diagram to illustrate the process. The seed is sterilised in the lab and germinated on petri dishes filled with agar to keep them safe from any bacterial or fungal nasties. When the roots are long enough (usually after 2 weeks), they are ready to transplant into my pre-made rhizotrons ('root observation chamber'). Essentially these are square petri dishes filled with a packing medium called vermiculite, with a hole at the bottom for drainage and one at the top for the seedling to poke through. After moistening the vermiculite with my trusty squirty bottle, I add a layer of mesh on top (to stop the seedling's roots growing into the vermiculite). The seedling is then carefully removed from the agar with tweezers and laid on top of the mesh. Finally, I tape the lid shut then wrap the whole thing in foil to keep the roots in darkness. In my growth cabinet, the rhizotrons are stacked vertically so that the roots grow downwards. When it is time to infect my seedlings, I simply peel back the foil, prise off the lid and apply the parasite seeds onto the roots.

It's intricate work that demands concentration....so after transplanting 60 or so seedlings at a time I am typically done in! It doesn't help that the radio reception is so poor down in the annexe, making it quite a lonely task too.

As for my 'other' work, outside the PhD....my main focus at the moment is the 24 hour Inspire event taking place on 30/31 March. This is a non-stop 24 hour series of lectures designed to enthral and entertain, whilst raising money for charity. As part of the publicity committee, I'm researching ways we can raise awareness - everything from having a stall in the student's union, parading around in animal costumes and appearing on local radio. The speaker programme for the Pint of Science Festival in May is also about to be announced, after which my work as social media secretary for this will really get underway. My aim is to make a series of short videos for Facebook and Twitter to promote the different talks and events. The trouble is, I haven't had much experience of video editing before so I duly attended some Creative Media Workshops this week hosted by the University's Computing Services Team. These proved a great way to boost my confidence and I managed to put together some pre-shot footage into a short film entitled "How to make a perfect cup of tea". Maybe not Speilberg standard but it's a start! The next step will be to borrow a camera and arrange some interviews with the Pint of Science speakers.
Putting together my video masterpiece

All of which is quite enough to be getting on with...but I haven't even mentioned the Science and Engineering Festival coming up and the demonstrating work I have signed up for. I think I really must put a filter on my email inbox, so that I stop seeing all these opportunities.....ooh, look! A science communication essay competition! How could I not say 'no' to that....?

I hope you have a good week and thanks for reading!

Friday, 3 February 2017

I survived! FameLab 2017!

"I don't care - I know I'm going to look stupid but I can't back out now" I gabbled anxiously to my patient friend as the room steadily filled up around us. "As long as I can make them laugh and they learn something, then I'll be happy!"

At school, I was always the one who wimped out of giving presentations or talking in front of the class.....so what on EARTH was I doing here as an entrant to FameLab 2017??! In this international competition, budding science communicators have the challenge of explaining a scientific topic of their choice in just three minutes...but here's the catch : No PowerPoint, No audio and only the props you can carry on stage. All to be followed by 2 minutes of questioning from the judging panel. I felt completely out of my depth - not helped by the fact that I'd inexplicably chosen to talk about something completely outside my own field of plant science. And also that the event had been a complete sell-out, with all the tickets being snapped up within days by the audience members now entering the room. Amazing that so many members of the public would gladly give up their evening to come to the Crucible Theatre and hear about science.... even though we
using the main stage, I was still so nervous that I begged to go first to get it over and done with!
With the rest of the FameLab competitors for the Yorkshire Heat.

Fortunately the atmosphere was supportive rather than pressured. Our compere for the evening, Simon Watt - TV presenter, writer and president of the Ugly Animal Preservation Society - gave me some wise advice for calming myself down, including to stand at the front of the stage before the show began to get habituated to the audience. It was reassuring to spot a few friendly faces but it was a really mixed crowd - families with children, young couples, retired folk. Eventually my breathing began to ease...

...and in the nick of time, as without further ado Simon launched the proceedings. I took a deep gulp and went for it. Staggering onto the floor, I gave my best impression of being caught in a force-ten gale.

"Goodness me - it must be blowing a HURRICANE out there! Oops - I  shouldn't really say that as hurricanes *actually* only form under very particular conditions..."

Don't ask me why but yes - my chosen topic was the science behind how hurricanes (also known as tropical cyclones and typhoons) form! I came across it on an online course on understanding the weather and it had simply intrigued me. It also gave me the chance to wave my arms around and make wild gesticulations to try and describe how the evaporation of water molecules off the surface of warm oceans provides the 'engine' that drives the storm. As I got underway, my rehearsals paid off and I managed to make it through without stumbling.

The scary judging panel....from left to right: Professor Simon Foster (Director of the Krebs Institute at the University of Sheffield), Nancy Fielder (Editor of the Sheffield Star, Sheffield Telegraph and Doncaster Free Press)  and Professor Elena Rodriguez-Falcon (Faculty Director of Communications and External Relations for Engineering at the University of Sheffield)

"and the winds get faster and faster and stronger and stronger - until eventually they clock 74 miles per hour and IT'S OFFICIAL! You can call it a hurricane...but what NAME you actually give it - Hurricane Boris or Hurricane Gertrude....is a COMPLETELY DIFFERENT story!!!" I finished with a dramatic flourish before running back to my seat so fast, I had to be called back for the questions. Fortunately I was able to give reasonable answers to these (THANK YOU, World Meteorological Organisation for your "FAQ on Cyclones" webpage!) and then it was all over!

Even though I didn't stop shaking until the interval, I greatly enjoyed watching the rest of the talks. From lab-grown meat to 'Why is poo brown?"...it's astonishing just how much information you can convey in 3 minutes and the lightning-speed style meant there was no time to get bored. Perhaps this is how proper academic conferences should be done??!
Our winner, Ashley Carley: "Making those papier mache fried eggs also took quite a long time!"

In the end, first prize went to Ashley Carley, studying for a Masters in Science Communication at the University of Sheffield - although it seems she has mastered this skill already! With ingenious use of balloons and papier-mâché 'eggs', she neatly demonstrated the concept of mitochondrial donation and three-parent embryos. "I was in disbelief when they announced my talk as the winner as I nearly dropped out several times" she said. "I'm really looking forward to seeing all of the other amazing talks and meeting more passionate people at the regional final".

Even though I was a teeny bit disappointed not to get selected for the regional finals in Manchester, the real achievement for me was simply being able to put myself forward without bottling out. In any case, at least I have a whole year now to think about my topic for next time....Monsoons perhaps? Anything's possible in three minutes!