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 17 October 2018

Science collides with awesome music at Festival of the Mind 2018!

Who says that the arts and sciences should be kept separate? It’s an idea that Festival of the Mindcertainly doesn’t subscribe to. This biannual ‘celebration of ideas, culture and collaboration’ teams up University of Sheffield researchers with artists, animators, musicians and more to deliver a programme of intriguing, mesmerising and sometimes downright bizarre events. A highlight this year was The Sound of Science: a high-energy performance show combining 3D effects, live demonstrations and explosions …. Oh and did I mention a live electronic music band?! It was a combination I couldn’t resist, so I bagged a ticket for the evening performance on Friday 28th September.

Could there be a better way to begin than asking ‘What exactly is light?’ - the ultimate driving force behind our existence. Starting from our caveman ancestor’s fires to the LEDs in our mobile phones, the team used a range of demos (and plenty of music!) to explain the properties of this intangible, unphysical substance. Presenters Professor Duncan Cameron and Dr Nate Adams complemented each other perfectly; the more serious 'proper' academic alongside an overexcited boy-who-never-grew-up who simply loved setting things alight. Indeed, the take-home message of the evening could well have been: “If you want to make it interesting, set fire to it!” We were treated to some dazzling displays from plasma balls to the beautiful pink flames of lithium. Perhaps more impressive than the firepower, as Nate explained, is the fact that lithium is thought to be one of only three elements (alongside hydrogen and helium) that were created just minutes after the Big Bang, even before the first stars and galaxies began to form.

An excited crowd gathers in Firth Hall, University of Sheffield (Image Credit: University of Sheffield)
Coming back to earth, we were then introduced to RoboPlant- a giant robotic plant made by a team of students at the University of Sheffield- for a whistlestop tour of photosynthesis. The team explained how we depend on this complex series of reactions in plants for the glucose that powers our food chains. Ultimately, we convert this into energy during respiration: much of the biochemistry of which was investigated by Nobel-Prize winning scientist Hans Krebs right here in Sheffield. 
Moving seamlessly from chemistry to physics, the team then set about calculating the force of gravity using a giant pendulum (that looked suspiciously like a disco ball…) and an iPad. As an abstract concept, gravity can be a tough subject to grapple with, potentially turning many a young mind away from physics. But seeing it in action here through simple, accessible equipment gave a powerful message that the unseen forces governing our universe can be understood by all.

It wasn't all fun and games though: the evening took a serious turn as we moved to the topic of global warming. Even when presented in a rock song, the facts are stark and a clear call to action to develop more sustainable ways of living. It was a good demonstration of how scientific research and innovation will be critical for us to address the urgent, global-scale challenges we face. Nevertheless, the evening ended on a high, as the presenters sought a way to illustrate what sound really looks like. Forget slinky springs - not surprisingly the answer was fire, this time in the form of a Ruben's tube. As a speaker blasted sound waves down a tube of flammable gas, a row of flames on top responded to the pressure wave passing beneath by dancing higher or lower, beautifully describing the shape of the wave – very impressive!

An endless array of mesmerising demonstrations kept the audience captivated
(Image Credit: University of Sheffield)
There are some who believe that science engagement has become too much about creating spectacular explosions and 'Wow!' moments, rather than conveying meaningful information, or explaining what is really going on. In my view, The Sound of Science shows that this approach still has its place. After all, it is also argued that a teacher cannot teach anything to their pupil unless the latter is in a receptive, 'learning' state of mind. I lost count of the number of times the kids sitting behind me gasped with delight 'This is so so cool!' Surely these memories will follow them into the science classroom and make them more ready to engage with atoms, forces and even plant science. Highly fitting then, that this memorable evening took place in Firth Hall, with the portraits of the University of Sheffield’s benefactors looking on. As patrons of learning in the Steel City, they would no doubt approve of the spectacle of wonder and fascination that unfolded that night - surely one that inspired at least some of the audience to consider a career in science. 
Serious scientific messages were set to awesome music
(Image Credit: University of Sheffield)

Tuesday 4 September 2018

Fifteen minutes of fame!!! My debut on BBC Radio Four

It's no secret that I love BBC Radio Four. Or to be more accurate, I ADORE it. Alongside the various things this PhD has given me (including lab skills, time management ability and the resolve to keep plugging away when absolutely nothing is working) is a lifelong love of the self-described “Speech based news, current affairs and factual network”.  I couldn’t count the number of hours spent transplanting, making up rhizotrons and infecting my plants that have been made less painful – and even enlightening – by the comforting presence of this national institution. Even though I stand hunched over my plants, through its programmes I range across the world, filling in all sorts of knowledge gaps the school curriculum never touched and picking up countless quirky facts.  

One of my favourites has to be Women's Hour (10.00 am weekdays and 4pm on Saturday) as it demonstrates how radio is so appealingly approachable compared to say, television. If you have a story that fits the topic of the day, they really do want to hear from you and you have a chance of having your voice recorded for prosperity. Back in the days when my heart was set on becoming a Professor, I used to dream of being invited on the show as a distinguished expert, perhaps to talk about GM crops or a fascinating new discovery in plant development. Whilst that particular ambition has died, two weeks ago I did realise my dream of getting on BBC Radio Four....and it had absolutely nothing to do with my research!

Until now, a significant part of my life has been mostly invisible to others. Not because I am ashamed of it, but because most people aren’t familiar with the concept. I am asexual. I do not experience sexual desire AT ALL – not to men, not to women, nothing, nope, nada. As a young child, I naively assumed that everyone felt the way I did: sex was a terrible ordeal that you would only force yourself to go through if you really really wanted children. It was only through novels and films that I realised that – for most people – there was actually a pleasure aspect to it.  My time as an undergraduate student was a very isolating experience, with the overriding culture seeming to be “If you've got even just one drop of red blood in you, you'll be lusting after at least someone, so get your free condoms here!”. I felt very miserable, concluding that either a) I was truly weird and would never be accepted by society or b) At some point I needed to change and 'catch up' with everyone else in terms of sexuality....and I wasn't sure I could be comfortable with that.
In my 'broom cupboard' waiting to go live on air!
Fortunately I stumbled across a magazine article that described people who felt exactly like I did. They had a name for themselves even a community. Isolation transformed into elation. I was not alone! Since then, I have only become even more sure about my identity as an asexual, but it was still something that I felt a bit nervous about telling anyone. Would judge me as a prudish and think I was making a moral judgement, squashing down my sexual desires so I could look down on others? Or would they completely miss the point: “You just haven’t met the right one yet! Have you tired Tinder?” or “It’s probably a hormonal imbalance, your GP can give you something” or even “You’ve just been too focused on your work! ' Just to be clear, I do still appreciate beauty and romance – I even have my own opinions on who is good looking! And ‘finding the right one’ is ultimately a different issue to feeling sexual desire towards others. Surely if I had any drive in me, it would be aroused by those Hollywood actors on screen, or the ‘fine specimens’ I encounter at the gym?!
With asexuality being so unknown and misunderstood, it just seemed pragmatic not to mention it. Yet part of me slightly resented never having a box to tick on all those surveys and forms that, for some reason, need to know your sexual orientation. If your viewpoint isn’t recognised by society, it can suggest that it isn’t valid or can’t be possible – putting pressure on you to change to be like everyone else. So when Women’s Hour announced that they were looking for contributions for ‘Listener’s Week’, it sparked an idea and I sent off an email.

'My' episode, available on the BBC Women's Hour online archive

I wasn’t really expecting a reply but just a few days later one of the producers was in touch. Not only were they interested in asexuality – they actually wanted to interview me live on air! The following week was a whirlwind of phone conversations, arranging logistics and mentally rehearsing what I would say. With such a crowded labwork schedule, it wasn’t feasible to go down to the BBC studios in London and meet Jenni Murray in person (a dream for the future perhaps…) so we arranged that I would be interviewed remotely from the studio at BBC Radio Sheffield. On the day itself, my initial excitement began to tip over into nervousness: what if I blundered and said something utterly appalling? Not only would thousands of people hear it, the programme would be available on the internet for prosperity! Fortunately, my confidence was bolstered by good luck messages from the few people who knew what I was going to talk about. I arrived early, hoping to have a proper look round the studios but alas, I was shunted into a room barely larger than a broom cupboard containing just a chair, table and headset. I ended up reading a magazine for half an hour, with the sound engineer at the London studios occasionally checking in to check I was still there! 

Suddenly the time had come: “The next voice you hear will be Jenni Murrays’”.  Women’s Hour had begun and I was the lead item. I cringed slightly as Jenni started by reading out the original email I had sent, then it was over to me to elaborate on my experiences. Thankfully, my preparation kicked in as I described how isolated I had felt, particularly during my undergraduate years, and my relief at finding out that I wasn’t alone. Between my responses, Jenni also asked the perspective of my fellow guest on air, Sam Rosen, who is researching the online asexual community as part of her PhD at the University of Nottingham. Bizarrely enough, Sam and I used to share a University flat in Sheffield but had no idea we were both asexual at that time. We kept in touch and I managed to persuade her to come on the programme with me to represent the academic perspective. Although we only made up the first 15 minutes of the show, we felt that we managed to cover the main points about what it means to be asexual. But even as I spoke, part of me was wondering how people would react to me now that it was all out in the open.

“Well Caroline, I have to tell you…” Jenni was drawing the topic to a close and my heart tensed – what was coming next?! “You are NO LONGER invisible!” Relief flooded through me: what a lovely way for her to end the discussion!

Since then, I have been touched by the number of people who made time to listen and even get in touch afterwards with messages of support. Best of all, perhaps, was the email read out at the very end of the programme from a grateful mother whose son had just identified himself as asexual. If the show helps others out there to realise who they really are, and that there is nothing strange or abnormal about being asexual, then it will have done a good service. At the very least, I hope it raises awareness that asexuality really does exist. Maybe one day, even the National Census will realise…

You can learn more about asexuality on the AsexualityVisibility and Education Network (AVEN) website. You can also listen to my debut on Women’s Hour on the programme’s website here.

Monday 23 July 2018

Final countdown...

It really IS the final countdown now....as of today, I have 69 days left to get enough results to write up a ‘substantial and original price of scientific work’ - a.k.a. my thesis. It might sound a lot but I know it is going to fly by - especially as it takes just over a month to run a single one of my experiments from start to finish. That's the problem with studying plants - they need time to grow!

I can't afford for anything to go wrong if I am going to finish the ambitious amount of work I've set myself. Unfortunately, science attracts problems like a magnet attracts iron filings....  and really, it is only to be expected when you work on the very edge of knowledge, attempting things no one has ever tried before. This week has been a classic case of on-the-spot problem solving: just as I finished planning my final experiments, I realised I simply wouldn't have room in my growth cabinet to fit all the plants in. Fortunately, I discovered that my old growth cabinet (which I was using before it broke down) had been fixed and was now sitting idle. So I nervously suggested to my supervisor that perhaps I could start using it again, in addition to the current one all my plants are in...? Amazingly, she actually agreed! I daren't ask about how much it would cost the lab budget...

Space sorted, now to order the plants.... only to find that two of the interesting genetic mutants I hoped to test weren't available to order from the National Stock Centre. After some frantic internet searching, I managed to track down two labs in Germany that had used these lines recently and published papers on them. I sent off two begging emails without much hope but within the day they had replied asking for my address so they could send me some of the seed. Hooray for the spirit of scientific collaboration!

It's surely only a matter of time though before the next problem crops up...  but even when I am not  preoccupied with troubleshooting experiments, my head is a constant turmoil of conflicting emotions:
Doubling my production power! Cabinet 515 (left) full of growing plants in rhizotrons (root observation chambers) and cabinet 502 (right) full of plates of germinating Arabidopsis seed

Disappointment. I had hoped to have found something more conclusive by this point. At best, my results are suggestive ‘maybes’ as to what plant defence pathways are important for resistance against the parasitic weed Striga gesnerioides. For the past four years, I have been groping around in the dark but still have no idea where the light switch is. I do appreciate that facing uncertainty is all part of doing a PhD, especially in science. It could even be argued that if your project was something so simple that you could answer all the questions completely, then it isn't ambitious enough. And, at the end of the day, I am trying to decipher something I can't even see or physically take hold of - the intricate biochemical signalling that takes place between a host plant and an invading parasite. It’s a world that is almost too wonderful to imagine, and certainly more complex than the simplified diagrams in plant physiology textbooks. But I am, as my careers mentor told me, very much a 'completer-finisher'. I don’t like to leave a job with so many unknowns and open questions remaining. That's why I find writing so satisfying – once it’s done, it’s done! Perhaps I should just take it as another indicator that my future doesn't lie in research.

Nervous. I’m not just leaving the lab at the end of September - I will be saying ‘goodbye’ to Sheffield itself. As I won’t be able to come into the Department any more and won’t have any funding coming in, then it doesn't make economic sense for me to pay for my flat here. So, typical millennial that I am, I will be staying with my parents while writing up my thesis. But this is putting me under a lot of pressure to think of absolutely every possible little thing I need to do before I depart. There will be no more spontaneous conversations with my supervisors in the corridor, no popping in the lab to check the details of any equipment I used, no access to the university's statistics support centre or even the software I use to make my graphs and figures. I feel in a chronic state of anxiety and too many of my dreams are about trying to finish bizarre experiments!

Hope. It feels sad to have missed out on what has been, weather-wise, the best summer of my life so far. But hopefully this will be a watershed point of my life, after which things will be very different. Just possibly, clocking off at five really could be the norm, ‘leisure time’ could be spent on things other than reading journals and writing up methods, and bank holidays could be just that- holidays- not an opportunity to run as many PCR experiments in three days as I possibly can. The whole of last week, the University of Sheffield has been awash with proud families celebrating graduation day... I am determined that next summer it will be my turn!
Sheffield is so lovely when the sun shines! Catching a brief bit of sun in Weston Park during my lunch break

There’s nothing quite like a job in research, but the system is far from perfect. My original dream of being immersed in my own project has become tarnished by the pressure to find significant results that satisfy the remit of scientific journals, rather than my own curiosity. Measuring a scientist’s abilities by publications ignores the fact that so much of it relies on luck. Perhaps it is an inevitable relic of the olden days, when making scientific progress typically involved cultivating prestige and patronage. Evolution can only work on the existing material… if we were to wipe the slate clean and design scientific research from scratch now, I wonder what would it look like?
I'm looking forward to having a job where I can work hard at work worth doing, with confidence that I will at least have something to show for it. And also to having a life beyond work, opened up to friends, family and my wider interests. Who knows, I may finally get that novel written….
Better get back in the lab – the clock is ticking!

Monday 11 June 2018

Opportunity of a lifetime!

Most of my recent posts have had a slightly desperate, worried tone as I frantically try to finish my remaining lab work before my September deadline. So, it is extremely nice to have some very good news to share for once: quite simply, I have been offered the chance of a lifetime! 

People often ask me what I will 'do next' after my PhD. Whilst I can't give a definite answer beyond 'something else', I am fairly certain that I won't stay within academia. I appreciate that many jobs are stressful, but scientific research has a very particular set of pressures (finding significant results; publishing high impact papers; competing for funding and permanent positions) that I really don't want to be subjected to in the long term. What really excites me are science-policy and science-communication careers where I could help turn scientific research into real impacts. Globally we face many urgent challenges that we can only solve through wide-spread societal change, rather than just the personal decisions of well-informed and well-resourced individuals. For this to happen, science needs to come out of the laboratory. My dream job is likely to be working for a research funding body, non-governmental organisation, international charity…. or even parliament itself.

But careers in this area are competitive and it can be difficult to know where to start. Which is why, for several years now, I have had my eye on the Fellowship scheme run by the Parliamentary Office for Science and Technology (POST). These offer PHD students the chance to work in parliament itself for 3 months, producing a briefing paper (POSTnote) for MPs and other policy makers on a topical issue. Against all other internship schemes, it stood out to me for several reasons:

1.       It is directly related to policy work as the POSTnote would be read by policy makers and could influence debate on the subject

2.       It would be in the very heart of policy making itself – including a security pass for the Houses of Parliament!

3.       The networking opportunities would be unprecedented: interacting every day with MPs, Select Committee staff and other parliamentary bodies such as the libraries of the House of Commons and the House of Lords.
POST produces briefing papers (POSTnotes) on topical science issues which are greatly valued by MPs and policy makers without a scientific background. Photo: Science in Policy Group, University of Sheffield

I had thought that I wasn’t eligible as most of the positions are funded through research councils, such as the Biotechnology and Biological Sciences Research Council, BBSRC, and my PhD isn't funded by any of these. But then I was made aware that the Institute of Food Science and Technology, IFST, is also a partner of the POST Fellowship scheme. Given that I work on a parasitic plant that damages food crops, I thought it was worth an application. Amazingly, I was selected for an interview and suddenly had to organise transport to Westminster, where POST are based.

I prepared as thoroughly as I could and was fortunate to have guidance from both Dr Sarah Blackford, my careers mentor, and Dr Helen Hicks, a fellow committee member of the University of Sheffield's Science in Policy group who did a POST Fellowship herself several years ago. Nevertheless, I was still very nervous on the day itself when I arrived at POST's headquarters at Tothill Street in London, just a stone’s throw from the Palace of Westminster. Going through a security check didn’t help! The questions mainly focused the briefing paper I had submitted for the application: they seemed intrigued that I had chosen to write about edible insects as a future protein source. I have recently become very interested in the subject as I had been researching it for the last outreach activity I was involved with for the British Science Association (Food for the Future). Other questions asked me to describe my PhD work and experiences in communicating science to non-specialist audiences.

The time seemed to pass very quickly and soon I was on the coach ride home. I tried to put it out of my mind as much as I could. But the very next day, just when I was checking my emails waiting for some reagents to defrost, the news came through. Everyone in the vicinity was a little alarmed when I fell off the chair and started jumping up and down with excitement!

Westminster, London - where I will be working next year! Photo: Wikipedia Commons, Daniel Bron

So yes, a dream come true. It still doesn't feel real to say the words out loud but next year I will be working at Westminster!!!! It feels especially nice because all the activities and societies I have been involved with -the Science in Policy Group; the British Science Association; the Society for Experimental Biology; Pint of Science, etc- played a part in getting me through as I drew on all of these experiences in the interview. I have often felt guilty for spending time on these activities instead of my main PhD work, even if I try to make up for it by working evenings and weekends. It is also amazing to reflect on how far I have come from the schoolgirl who was too shy to speak in front of the class. Many times in the past I have gone for opportunities like these, only to have fallen short: there was always a slightly better candidate, with more experience, confidence, etc. But just for once, it was actually me.

I can't get carried away though as I still have to write my thesis up first.  After my lab work stops at the end of September, I will focus on getting as much written up as possible before starting at POST in February next year. At least it gives me some time to get a new wardrobe! It does seem slightly ironic that I will spend three months writing up the bulk of my thesis, which will only be read by 2-3 people, before going on to work on a policy briefing note which could be read by hundreds of people, including MPs and other policy makers. I will be proud of both of them of course but in terms of impact, it doesn't come close!

Right, better get back to the plants! Thanks for reading – I hope you have a great week ahead. 
Doing what I love best - Science Communication!  Photograph by Daniella Sasaki

Tuesday 24 April 2018

From plants to posters- It's time to get creative!

It’s been a long time since I last had to present a scientific poster and now, like the 120 buses here in Sheffield, two come along at once.

Unfortunately, it is not good timing. With only four and a bit months before my funding runs out and my lab work has to stop, it’s an added pressure on top of an already chaotic schedule. I am desperately trying to gather enough significant data for a credible thesis – which means most weekends are spent in the department as I try to cram in as many experiments as possible. I’m starting to lose track of everything I’ve currently got on the go: last week for instance, I set aside all of Wednesday to extract RNA (the coding molecule that is the intermediate between DNA and proteins) from eighteen leaf samples. Just before I began, I found the RNA already in the freezer: I had extracted it two weeks ago and completely forgotten. For those that are familiar with how long and fiddly RNA extraction is, that is a considerable amount of work to forget about!

I simply haven’t any mental energy left to be creative these days. But needs must! All PhD research students at the University of Sheffield are required to present a poster at the annual ‘Graduate Science Showcase’. This event brings students from across the whole Faculty of Science together to ‘showcase the excellence of the wide ranging research’ being carried out here. I don’t feel my project is worthy to be exhibited in this way, so it feels like a box-ticking exercise for me. But, not wanting to let my supervisors down (and mildly incentivised by cash prizes on offer for the best posters), I know I should put some effort in.
My poster with its fellows at the Graduate Science Showcase
So, in between the usual jobs of transplanting seedlings, infecting plants and molecular lab work, I squeeze in some time to sift through my data and cherry-pick the most interesting results. I wish I could say I was fluent in using Abode Illustrator or even a bespoke poster-designing software but sadly I am not, so Microsoft PowerPoint will have to do. Still, I manage to create my ‘vision’, with the centre dominated by an Arabidopsis plant being attacked by invading Striga parasites. I am just about to send it off to be printed when I reread the guidelines again (yes I realise that I should have done that first!) and realise – horror of horrors – that the poster boards won’t be big enough to accommodate my beautiful A0 Landscape poster. Luckily it doesn’t take too much fiddling to fix it into a portrait orientation. Phew!

When I go to collect it and see it life-size, I am disappointed; I can see straight away that there is far too much text. Even so, I hang it up next to its 203 fellows in the Octagon building. At least I am in the first judging session so don’t have to wait too long for a man with a clipboard to come round. He seems to take a genuine interest in my work (or good at pretending to at least!) but it’s clear my poster won’t be in the running for the departmental prize. I console myself by picking up some freebies from the sponsor’s stands…one day I must actually start using all these pens.
From plants to Alzheimer's disease - a very different poster!
Photograph by Ellen Bradley
Fortunately, the second poster I have to make doesn’t bring so much pressure. For the Sheffield Branch of the British Science Association’s latest event – ‘The Science of Multilingualism’ at Weston Park Museum – I had offered to run an activity showing the evidence that learning foreign languages can help prevent Alzheimer’s disease. It’s a topic that personally interests me due to my grandmother having the disease, and it gives me a chance to explore something completely unrelated to my own line of research.
Once again, I probably put far too much text on it but when the topic is so relevant for today’s society, it is always difficult to know what to leave out. Still, many adults do stop to read them (unlike my poster for the Graduate Science Showcase!) before examining the model brains I had prepared to show the difference in pathology between mono- and bilinguals. I was a bit thrown though when one mum asked me “Does this explain why pregnancy can make you lose your memory?” !!!
One of my carefully-prepared brain models to show how being bilingual affects our susceptibility to Alzheimer's disease. Photograph by Ellen Bradley
Overall the event is a success, if a bit chaotic at times as we have experiments being performed in multiple languages, a buffet of international food samples and kids charging round the museum trying to find hidden words for our quiz sheet. In addition, it’s a welcome break for me from the lab and a chance to be reinspired by how scientific research can benefit the wider public. Doing a PhD can be like burrowing yourself into an increasingly narrow tunnel, so it is easy to get jaded with the whole process at times. Look out for my blog post on the event soon on www.bsasheffield.org! You can also view our gallery of photos from the event on our Facebook page here.
It will probably be some time – maybe never – before I am called on to present a scientific poster again. Maybe I will have a chance to learn how to use the Adobe Illustrator in the meantime….
Thanks for reading, I hope you are having a happy springtime!
Me volunteering at The Science of Multilingualism. Photograph by Ellen Bradley

Wednesday 31 January 2018

White knuckle ride...

I always knew that a PhD would be a rollercoaster but now it's turning into such a white knuckle ride, I'm not sure I would ever have got on in the first place had I only known.

Science is full of ups and downs - that just the nature of it. You can spend months, even years  doggedly following a line of enquiry, only for it to end up fruitless or flawed. Or a whole day carefully setting up an experiment only for the critical machine to 'have an off day'. Working on living things, of course, adds a whole new dimension in which things go wrong. Problems are inevitable...but then you have those moments when a result throws up something completely unexpected, and sends your research off done an exciting, unforeseen new direction. Suddenly all the frustrations don't seem to matter.

Right now I could certainly do with some more ups. As I wrote in my last blog post, time really isn't on my side if I am going to get enough good data for a PhD. So as soon as the new year started, I began carefully setting up a HUGE gene expression assay, to try to work out what happens on the molecular level when my parasite of study, Striga gesnerioides, infects its host. I had over 120 plates of Arabidopsis seed squashed into my cabinet which took hours and hours to prepare but then - disaster! Almost every plate was contaminated with bacteria. The seedlings, now useless,  had to be binned. A whole month of work wasted. I really can't afford setbacks like this - a couple more could tip the balance in terms of whether I have any chance of finishing in time. 

Very poorly looking Arabidopsis seedlings! 

Fortunately, I have identified the probable cause. It seems that the tap for distilled water that I suspended the seed in after sterilising them,  is not as clean as it should be - when I put some water on an agar plate just to see what happened, sure enough bacterial colonies appeared. So from now on, I sterilise my water in the autoclave just to be sure. I have also tightened up any over potential entry points for nasties - using ultra sterile pipettes tips; irradiating my pipettes with UV light, autoclaving the Eppendorf tubes, even taking my watch off (surely a treasure trove of germs!). So far the next lot of (120 plus) plates seem free from contamination, so fingers crossed!

Then I had my second disaster, one which nearly made me made me walk out of the lab for good. One of my most interesting results so far has been with a certain Arabidopsis mutant that fails to produce a particular protein. For some reason it is much more susceptible to Striga, so I propagated the seed to give me enough to do more experiments to investigate it further. This requires care, especially if you have other plants in the same cabinet, to make sure that they don't cross fertilise each other and create hybrid offspring. But I was confident that I had used the special 'aracons ' ( plastic tubes used to keep  flowering Arabidopsis plants separate) correctly.  When I tested the protein expression in these plants however - disaster!!! The plants were still producing the protein! Somehow, the plants must have mixed themselves up and the mutation had been lost. I was devastated and spent a very low evening wondering what in earth I was going to do now for the rest of my PhD. 

Our distilled water tap - was this the source of the bacterial contamination? 

But then I had another look at the data - and it turns out that the protein exists in two different forms and my plants were actually one of these, but not another. When I checked the position of the genetic mutation, this made perfect sense : it should disrupt the disrupted the coding sequence of just one of the protein forms, but not the other. And in fact, given that these different forms have very different functions, it actually makes a really interesting result, which could set the direction of the rest of my experiments.... it certainly interested my supervisors anyway!
Lots of new plates of Arabidopsis seed crammed into my growth cabinet - so far, bacteria free!

So a typical week in science, traversing the whole range from despair and misery, to a minor breakthrough. Last week I also had the pleasure of interviewing an old friend for a careers feature I am working on for a magazine. Having completed a PhD investigating drought resistance in Sorghum, she decided to follow her passion for science communication and now works as a medical writer. One of the things that struck me the most was how refreshing she found it to to have a role where your hard work would always be rewarded with a physical output, rather than being derailed by things outside your control. I couldn't agree more!

Friday 12 January 2018

2018 - A challenging year ahead...

"Your project has ended up being rather....challenging". 
So said my second supervisor during our progress meeting this week. We were surrounded by graphs, tables and scribbled on pieces of paper. I had come with high hopes that we work out a meticulous strategy for the rest of my PhD. Instead, I was despairing that I would ever be able to make sense of the data I already had, let alone make a plan for going forward.

The clock is rapidly counting down the remainder of my PhD. I have 9 months of funding left, then it will be time to leave the lab and somehow work everything I have done into an acceptable thesis. This ought to be a compelling body of work where my experiments elegantly prove or disprove the chosen hypotheses. But it currently feels like I am trying to assemble a jigsaw puzzle without the picture, and not even being certain that all the pieces are in the box. 
Striga gesnerioides - a very effective parasite...

Mr project is a tricky system to get your head around. Basically, I am trying to work out why the parasitic weed Striga gesnerioides is so capable of infecting the model  plant, Arabidopsis thaliana, when other parasites, including the close relative, Striga hermonthica, are  barred entry. Is the parasite producing effector molecules that actively suppress the host immune system? Does the host lack a receptor for recognising the foreign organism? Does the parasite produce plant hormones that mimic those of the host, and thus hijack defence signalling pathways?

I still have no idea and the experiments I have done so far - including testing genetic mutant Arabidopsis plants and analysing changes in gene expression - haven't really shed any light on the problem. I'm beginning to panic. I can't see how this will ever impress a viva examiner. Do I really have enough time to turn it around? I'm not afraid of hard work - long, unsocial hours are par for the course in a PhD. What I worry about is getting enough data in the remaining time - and that will require careful experimental planning and no mistakes. Talk about pressure!
Filling my growth cabinet with plants...

I know what they say: Most PhD students get 90% of their data in their final year. I'd say it to anyone else in the same situation, but can't convince myself that it will apply to me. Especially when I am so good at sabotaging myself by a) not prioritising rest when I need to b) getting distracted and taking on too many other commitments and c) not giving myself adequate nutrition - a relic from the 'bad old days' of anorexia. 

In short, this year will need a really focused strategy. I have cut down on my extra writing projects and try to delete all of those emails starting with 'We are looking for volunteers...' without reading them. And in my growth cabinet are 120+ plates of germinated Arabidopsis seed on agar, for my next big assay. If it works, it could give me a shed load of data to occupy myself with for at least a month or two. If not....well let's not think that far.

So from me to you, here's hoping for a highly successful and productive 2018!