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!

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!

A Whirlwind Journey - The Science of Wellness

As a passionate science communicator, I love inspiring people with science – and I particularly relish the challenge of reaching out to those who normally have little contact with science. It has long been my ambition to organise an event specifically aimed at the mental health community. So when I saw the announcement for the British Science Association’s ‘Connecting Communities’ Grant Scheme, my brain went into overdrive. And that’s how ‘The Science of Wellness’ was born!

The idea was that the participants themselves would become the scientists and do their own experiment to try and boost their mood and wellbeing. Our role as British Science Association volunteers would be to present the scientific evidence for different strategies said to improve mental wellbeing and help them design a robust way to test one of them. But first we needed a partner to help us reach our target audience. Here we were lucky to find Sheffield Flourish, a local organisation that supports people with mental health conditions to live as full lives as possible. We wanted to make sure that the participants had an active role in shaping the project so Sheffield Flourish convened a focus group to decide the themes we would focus on. These became Foods to Improve Mood; Spending time with Nature; Exercise for Mental Wellbeing; Mindfulness; Creative Activities and Reading/Sharing Life Stories.

Learning how positive storytelling can improve wellbeing

 To present the scientific evidence in a fun and interactive way (no boring PowerPoint presentations!) we decided to use a ' speed dating' format, where participants spent ten minutes at each station before moving round to the next. During the planning meetings, we were amazed to find out about how much research has already been done – there are even journals on wellbeing and happiness!

Our hard work was rewarded on the night as we had an amazing turnout from the Sheffield Flourish community and also wider members of the public. The speed-dating format seemed to work very well: the audience were so engrossed that I had to shout to be heard over the hubbub. After all the talking, it was time for refreshments. We had carefully chosen these to include a range of super- mood-boosting superfoods including omega-3 rich mackerel pate, magnesium loaded almonds and walnuts, low GI pitta breads and hummus and the runaway favourite, homemade banana bread.

One BSA volunteer getting a bit excited over the refreshment buffet...

Having heard all the evidence, we then gave each participant their very own lab book and experiment planning began. From taking a daily brisk walk to knitting to dancing – a whole range of different activities were chosen. The evening ended on a real high, buoyed up with optimism and plans.  We couldn’t wait to hear how everybody got on!

A month later, we had our chance during our Follow-Up Event. There were some truly inspiring accounts, including the group of women who formed a creative writing club, the lady who practised gratitude with her children and the gentleman who brought along a stunning art work he had made out of drawing pins. Not everyone had managed to complete their experiments, with some feeling that they had been too ambitious. But we were keen to stress that this need only be the be the beginning of their experiments and that wellbeing should be seen more of a continuous journey.

Presenting the evidence that mindfulness works during our 'speed-dating' event

 This was clearly illustrated by our guest speaker Natalie Beevers, mindfulness practitioner and author of the Being Mindful Yorkshire Blog. Her frank and moving testimony demonstrated how making time for things that make us feel positive creates a firmer foundation for when things get tough. When her marriage fell apart, Natalie found herself thrust into a deep depression. As she put it: “My brain was like treacle but it wouldn’t stop talking…I was too exhausted and had no energy even to do the things I loved”. Things only started to improve when she came across mindfulness by chance at a work event: “It was a way of getting my thoughts to slow down my acknowledging them” she said. Other daily habits, such as yoga and walking through the park each day also had an effect. “The combination of small doses really seemed to work” she said. Whilst these could not prevent Natalie from having a relapse a few months later, crucially “they gave me the tools to get back out of the hole again”.

It’s an incentive to us all to continue to experiment in finding more tools to keep us on the road to wellbeing. As Natalie said in closing: “'No matter the catalyst for your down turning mood it should never be swept under the carpet”.

It may be the end of The Science of Wellness but really, the journey has only just begun! As for myself, I have learnt so much from this experience, including event management, applying for grants, event promotion ...even doing my first online grocery shop. And it's only made me hungry to do more.... where will BSA Sheffield go next?

My team of wonderful BSA Sheffield volunteers!

You can find more photos from The Science of Wellness and the Follow Up Event on our Facebook Page. Do Like it to keep up to date about future BSA Sheffield events! You can also follow us on Twitter @BSA_Sheffield

A tale of two cabinets...

One of the amazing things about plants is how flexible their development is compared with animals. You can take two plants of the same species, even with exactly the same genetic code, but put them in different conditions and they can end up looking completely different. Whereas for animals, their development is much less sensitive to the environment and pretty much determined by their DNA sequence. It’s one of the things that makes plants so interesting to study – and also why it is so important to include all the appropriate controls when doing experiments with them!

A couple of weeks ago, I posted about my current seed crisis and my ongoing struggle to obtain enough seed of the parasitic weed I study, Striga gesnerioides, to finish my PhD. To do this, I grew some tobacco seedlings as these are very sysceptible to Striga: my hope was that the parasite would infect them well enough to produce an abundance of flowering shoots that would eventually form seed pods. Unfortuantely, the few parasite shoots that did appear withered and died – despite me following my supervisors instructions from when they did it before a few years ago “and it worked perectly”.  At this point, I was at the stage where my seed supplies were so low, I was having to seriously cut down the number of experiments I could do. So for round two, I couldn’t take any more chances.

The growth cabinet I used in the first attempt, Conviron Number 502, is set to mimic a temperate British climate, with short days at 25 degrees. However, Striga gesnerioides is actually native to Sub-Saharan Africa, where it devastates cowpea crops. I reasoned that it was more than likely that they would fare better in a slightly more tropical climate. So this time, half my Striga-infected tobacco ‘babies’ went in Conviron 502 and the other half went to joint the rice plants in our tropical walk-in growth chamber. Up to that point, they had been treated exactly the same.

Unhappy looking tobacco plants in Conviron 502

So what happened? After only a week or two, the two sets of tobacco looked almost like different species. Those in Convrion 502 were small and squat, with dark green leaves, almost dwarfed by their pots. On the other hand, those in the tropical walk in grew vigorously and probably would have kept going if they had been in bigger containers. As for the Striga…..it was no contest. At first lots of parasite shoots appeared on both sets of plants, putting me in hope of a super-abundant harvest. But the ones in 502 were weak and weedy, flopping over the side of the pot or withering away as before. Meanwhile, the Striga shoots in the tropical cabinet stood up as straight as soldiers with a healthy purple flush to their stems. And they just kept on coming….whenever I felt down, I would go and run my hands over the surface of the soil, delighting in the feel of their buds forcing their way upwards.  

Much happier tobacco plants growing in the simulated tropics - they are even flowering!

Over the weeks that followed, I visited almost every day, agonising over whether I was giving them too much or too little water. I was paranoid that I would somehow kill them all off. But the Striga shoots stayed healthy and in time produced quite a wonderful display of tiny purple flowers. Eventually this colourful show came to an end, the petals fell to the ground, and the seed pods began to swell. And finally the moment I had waited so long for - the pods started to mature, turning  jet black, indicating that they were ripe. It was a happy day last week when I delicately cut the first shoots, taking great care not to agitate the seed pods too much, causing them to burst open. After months of trying, my first harvest at last!

Not again! Withered, dead Striga shoots

There is still a long way to go - the seed pods have to dry out for a few weeks in the 30 degree incubator - and this first harvest is unlikely to see me through to the end of my PhD. But I already have the latest generation of tobacco seedlings coming through ...in fact, I have quite a conveyor belt operation now, with new tobacco seedlings constantly moving along the system to make sure I always have new Striga- infected hosts coming along!

That's better! A beautifully infected tobacco plant with lots of flowering Striga shoots

Photograph by James Bradley

Plants can be frustratingly complex at times, but that does make them fascinating to study. The more we find out about their molecular systems, the more layers of control, regulation and interplay we discover. Which simply means there will surely be no end to the legions of PhD students stepping up to these challenges!

Prepare to be amazed - BSA Sheffield at Fun Palaces Weekend 2017!

No dictionary definition of ‘scientist’ mentions lab coats or googles, but many feel that only people who wear a white coat and work in a laboratory can call themselves a ‘proper scientist’. Similarly, many of us would hesitate to call ourselves an 'artist', even if we quite enjoy drawing, printing other creative activities. We simply don’t feel worthy of these titles.

The Fun Palaces movement is on a mission to change this attitude. Every year, during the first weekend of October, hundreds of temporary Fun Palaces pop up all across the UK. They vary in size, structure and theme, but all have the aim of engaging the public in science and artistic activities that celebrate the innate creativity in all of us – as befits their motto: “Everyone a scientist, everyone an artist”. This year, BSA Sheffield were invited to host our very own science themed Fun Palace.

Our 3D sound demos in our Fun Palace at DINA venue

It took us quite a while to decide the theme as there were so many possibilities – Outer Space? Dinosaurs? The Brain? What we really wanted was something that would thrill the imagination and stimulated all the senses....so what better than the five senses themselves? Once we'd settled on this, the suggestions for activities came thick and fast – it was hard to cut them down to a manageable number!

We might have the Fun but we still needed a Palace....fortunately , DINA a not-for-profit social enterprise stepped in. Besides the advantage of having a prime city centre location, we were given full use of the venue, allowing us to take over every nook and cranny (even the basement!).

The magical illusion cabinet!

I was very impressed and humbled by how my fellow BSA volunteers took ownership of their activities, giving up hours of their own time to research optical illusions, cut out thaumatropes, source craft materials and decorate the rooms. On the day itself, their hard work was rewarded as we welcomed a steady stream of visitors. Some were Fun Palace veterans who had sought us out specially, others simply wandered in off the street.... but everyone, young and old, found something to captivate them. We had 3D sound demonstrations, ‘guess the contents' boxes, jelly bean tasting and even a fruit orchestra! (I’m still not entirely sure how that actually worked but it did!) Crafting was especially popular for all ages - including making Victorian thaumatropes - a popular 19^th century optical illusion made of a disk with a picture on each side, attached to string on either side. If the strings are twirled quickly enough, the two images seem to blend into one, due to the persistence of images on the retina. Simple but highly effective and fun to make – why not have a go yourself?

Learning how to play 'Mary had a little lamb' with a lemon,

a cucumber and an orange

Perhaps the biggest hit was the 'Illusion Cabinet' – those who dared to enter inside appeared to lose their body, with their head being suspended in the air. Built by an intriguing former Professor in the Biology Department where I work, it had been languishing in a store cupboard and I was determined to get it out. The lovely people in Research Outreach team had also lent us an Infra Red camera so that we could demonstrate the senses that some animals have but we don’t, such as 'snake vision'. It went down very well, although when I found out how much it cost, I nearly didn't dare to take it! Apparently, I have one of the coldest noses in England….

There is a curious phenomenon ( or is it an illusion?) that time simply flies by when you do science outreach and suddenly it was time to close the doors and pack everything up ...It had gone so fast, especially as we had been preparing for months. We’ll simply have to start preparing for the next one!

Who has the hottest cup of coffee? Playing with the Infra-Red Camera

And in the meantime – if you enjoy science or art, then dare to call yourself a scientist or an artist! You don’t need any further qualification than that.

You can find lots more photos of the event on our Facebook page.

Head to the hills....

It strikes me that doing a PhD is a lot like digging a very narrow tunnel further and further into the ground. Maybe someone else started it but now you are the one chiselling away at the rock face, wedged into such a small niche that there is only room for one person to chip away, slowly progressing forwards by eking out flakes of knowledge. It's an intense, often lonely time, compulsively driven towards a single aim. But every now and then, you need to reverse back out of the hole and come out, remember that you are also a creature of the surface world. Otherwise mental and physical fatigue await. I know this too well - my family will testify to how I habitually bury and overwhelm myself with work until I literally burn out to the point of exhaustion and am forced to stop. Then I do it all over again....

Fortunately those who love me take action to stop this self sabotage. My wonderful Mum is particularly good at this; after a stressful summer, this month she whisked me away for a week in Austira, to enjoy the hospitality and mountain scenery of the Tirol region above Innsbruck.

Mountain dreaming...

I have been looking forward to this break for months, daydreaming of long walks in glorious sunshine, overlooking expansive mountain panoramas. Sadly these plans didn't quite work out....on many days, we didn't even see the mountains due to the thick cloud and rain. Lifts and cable cars promptly shut after a heavy snowfall, making the more scenic reigons inaccessible. And then my poor Dad picked up a nasty bug that really laid him low. Yet I have returned feeling refreshed and armed with a number of life lessons to stand me in good stead as I return to my work.

It ended up being a real exercise in flexible thinking and learning to roll with the circumstances. I know I can be very rigid-minded, especially when I decide to do something. But if the cable car is closed because of the snow, then the planned walk simply isn't going to happen! It's a reminder that sometimes there are no right or wrong choices, only different ones that lead to different experiences. For instance, if the weather hadn't been so bad, we wouldn't have ended up at the Alpine Zoo ( don't let the Z word put you off, it was actually very well done) , getting up close to ibex, otters, wolves, bears and a captivatingly beautiful Lynx.


Meet the animals - a brown bear and a baby ibex at Innsbruck Alpine Zoo

I also learned to appreciate the value of taking time for personal wellness - difficult not to when your hotel had a free spa with sauna, steam room and whirlpool ! I do struggle with this at times: in a world where so many have so little or are displaced due to conflict and disaster, it can seem disrespectful and frivolous to enjoy the sensory pleasures of a jacuzzi. Such experiences aren't limited to posh hotels or holidays of course, and can even be found in simple things such as a lunchtime stroll through the park or meeting a friend for a leisurely rendez-vous at a cafe. But when work constantly beckons, these are the things that get squeezed out.

These two things, learning to move fluidly with problems and making time for self restoration, will be critical for my third year of my PhD. During this time, the pressure will really be on me to get enough meaningful data for a thesis worth defending. I know the time will fly by, as indeed this whole year seems to have done. I only hope I am up to the challenge. At least in those frustrating moments, when my experiments run into problems, or the equipment refuses to cooperate, I can breathe deeply and, in mind at least, wander the mountains again. And look forward to the next time I set my feet on the hills.

The tobacco factory is open for business...

Science is always a numbers game.

The more experiments you do, the more data you get; the more data you have, the more likely you are to find something interesting; the more novel discoveries, the more papers you can write…and so on until that elusive permanent research position comes within reach. ‘Workaholism’ is a virus which spreads easily in labs and I fully admit to being susceptible. I would love to do never-ending series of experiments after experiments, cramming as many plants as possible into my growth cabinet and spending my weekends gleaning through hoards of accumulated data. It’s probably just as well for my mental health and wider interests that I can’t do this. The reason? I simply don’t have enough seed. My stocks of Striga gesnerioides, the parasitic plant that I study, are down to the last vial.

Those of you who have been following this blog for a while may recall that I had the same problem a few years back. In the end, I managed to solve it by getting hold of some tobacco, a very susceptible host for S. gesnerioides (the model host I use for my experiments, Arabidopsis, is so small that the attached Striga never progress to the flowering stage). So I am appalled to find myself in the same position again – but it’s not as though I haven’t been trying. One of the first things I did when I came off leave of absence was to sow some more tobacco and start the process again. When the first shoots came up, I relaxed – complacent with the thought that soon I would have an abundance of seed capsules to harvest. But it never happened. Weeks passed and nothing else appeared….I told myself not to panic, that Striga gesnerioides is notoriously slow to get going and reminded myself that it had taken a while last time. Eventually, after weeks turned to months, I did start to panic. Scrabbling through the soil, I found that the Striga had died underground – withered and black. My supervisor thinks I watered them too much: “They are very sensitive to getting wet!”

 Tobacco plants growing in rhizotrons (left): Tobacco root system infected with Striga gesnerioides 2 weeks ago (right).

So gone are the days when I could do any experiment I fancied. According to the weight of the remaining seed, I am down to my last 14 assays. I can’t afford to waste any more: after all – no seed, no experiments, no PhD. Therefore, I have taken to having a constant stock of tobacco growing in rhizotrons (root observation chambers). Each time I have done an infection as part of my normal experiments, I took the seed that remained at the end, opened up a tobacco rhizotron and applied them directly to the roots with a paintbrush. Infecting them in this way means that I can leave them for a week or two to make sure the Striga are firmly attached before transplanting them carefully into pots (all of different sizes, in case this makes a difference!).

This time, I certainly won’t be so heavy handed with the watering can. And there will be a lot more tobacco plants (going back to the numbers game). I have also given them all names, although it’s not as if I needed more motivation to take good care of them! So meet the team: Serenity, Dimitri, Artemis, Brent, Sentinel, Robert, Halo, Magic, Aristotle, Nighthawk, Angel and Destiny (no there is no explanation, other than that they were the first words I thought of when repotting them, apart from Robert who was named in honour of our summer research assistant). So far, they seem happy enough although I try not to let on how much I am counting on them. Last week, the first Striga shoots started to come up on Artemis, who appears very heavily infected indeed. But I’m not getting my hopes up yet – it could still all go horribly wrong, and so far, none of the others show any signs of the parasite.

Destiny, Robert, Artemis, Sentinel and Nighthawk.

Close up of Striga shoots on Artemis

On a more cheerful note, I have had one recent success. Until now, I have been having terrible trouble getting the S. gesnerioides seed that I do have to germinate properly: the maximum I ever reached was 30% germination. This was probably because I was using an artificial chemical called GR24, which is actually a germination stimulant for the related species Striga hermonthica. So I decided to take a step back to nature…. unlike S. hermonthica, which infects cereal crops such as maize, the original host for S. gesnerioides is cowpea. In their native soil, the parasite seeds germinate in response to chemicals naturally released by the cowpea roots (a handy trick to ensure they only germinate when a suitable host is present!). Although the exact chemical/s Striga responds to are unknown, this needn’t stop me from trying the same thing! Consequently, I have been growing cowpea hydroponically and taking samples from the liquid every few days. I was amazed at how well the cowpea took to it, given that the only support they had was a tube in a rack with the end sawn off. Even better, since using the cowpea extract, the germination rates have shot up to over 50%. It’s a good lesson in putting a problem back into the context it came from.

My super-hyrdroponic cowpea plants!

But it was over all too quickly – cowpea generation one have finally expired: after growing an exuberant display of twirling tendrils and straggly pods, they yellowed, shrivelled and died. But within those pods, they gave me all I needed to carry on and I planted the seeds for generation two last week.

Growing, harvesting and growing again: at the end of the day, it’s basically what continuing plant science, whatever the species you study, comes down to.

Thanks for reading! And if you have any suggestions for the next tobacco names, do get in touch…