Freddie’s plantastic experience

I’ve been working from September 2016 – June 2017 year in the lab of one of the top plant research institutes in the world, the John Innes Centre. There are only two interns given a place each year at the institute and although I was not one of them, I was still taken on as an ‘intern’ with a voluntary role which allowed unique flexibility for what I did day to day.

For the last nine months I’ve been helping a 2nd year PhD student, Nicola, with part of her project. Nicola is working on Nitrogen use in forage crops, and a previous student had found that a humic substance called ‘Fulvic acid’ is possibly a biostimulant that could improve the growth of plants without the use of fertiliser.

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A. thaliana root and shoot assay

I normally work 9 – 6 everyday on finding out if there is a replicable phenotype when plants are given this chemical, and finding what the chemical is exactly. There was no pressure on me succeeding but I knew I both wanted to impress the scientists around me, and find an answer for myself.

I started out taking part in the PhD training which covered biological, chemical and general safety. Nicola then started teaching me through actual practice, the various lab techniques I’d need to complete different assays; I took notes on absolutely everything (see picture below) and was lucky that I did, as it wasn’t long before she let me loose to start collecting data on my own. From this point on, I was effectively a full PhD student able to use anything I liked, whenever I liked. I could book any room or equipment, access all facilities and use any chemicals available.

I began by growing plants and supplying them with various amounts of Fulvic acid and Nitrogen to test a few hypotheses, but there was no regular phenotype appearing. I read papers on previous work and adapted my methods to pin down what effect this substance was having, all the while having various meetings and seminars.

I was given a space in the regulated glass houses where I grew other crops too. These I tested for their protein and chlorophyll contents, as well as photosynthetic rates. By the end of the internship I had identified a few phenotypes in a few species but unfortunately have not had enough time to find any genetic markers or a mechanism for the effect.

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The glasshouse with my babies

This was only one part of my project though. The other was finding out what this Fulvic acid was. Everyone at the JIC is top of their field so are always happy to help if you have any questions and are genuinely interested. The lab above mine was filled with hundreds of thousands of pounds’ worth of the latest in mass spectroscopy equipment, and experts who are always available to help, even more so when given a challenge by an eager intern who has no idea what he’s doing. I was in a great position here, where other people with the same problem would have to book months in advance and pay upwards of £90/hr. I could just walk in and have a go whenever the machines were free!

Lionel Hill, a wizard of LC-MS (liquid chromatography gas spectroscopy) was the first port of call. We put in varying concentrations of my Fulvic acids but the results that came out made no sense, there was something very polar in the solution as well as high concentrations of plastic. We tried a few more times with different mobile phases but with no luck, so I decided to try somewhere else. Throughout the placement I ended up being trained on almost every piece of equipment in the room and innumerable more in other labs. The final verdict came after weeks of tweaking, coupled with the wisdom and patience of Paul Brett. We finally managed to isolate the components of Fulvic acid (pictured above), although this only accounts for 70% of the solutions and we don’t know what the other parts were – science is fascinating and infuriating!

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Fulvic acid GC-MS retention spectra

The long journey and finding an answer(ish) at the end was a priceless experience, worth every second. Throughout the time here I wasn’t just a lab volunteer, but like I said, taken on and accepted as a fellow PhD student. I gave seminars, organised events, held a position on the student voice committee, worked on the institute bar, talked to visitors, presented at meetings, attended awards, took part in days out – even teaching others how to use the equipment I had been trained on!

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My filled out notebooks

This year opened my eyes to the possibilities of research, the raw freedom of exploring something new in any way you can. I was given a unique opportunity because I was not limited in what I was permitted to do, nor was I pressured to get results (because I was not actually a PhD student with deadlines to meet, even though some students thought I was). The other students welcomed me with open arms and invited me to all their social events. My housemates were UEA students which gave me access to the university lifestyle as well, where I joined various societies and sports clubs. Words cannot express the years of experience I feel I have gained in 9 short months, this will truly stay with me forever (and of course make my CV look great!)

 

The PhD Playlist – Aisling


Each week we put the spotlight on a PhD student at JIC and get them to share three songs in a desert island disc-style game: one song that captures their project (expect some very tenuous links), one song that captures their life as a PhD student and a final motivational
song because – let’s face it – we all need it. 

Screen Shot 2017-05-18 at 11.27.13Aisling is a 3rd year Rotation PhD student working in Myriam Charpentier’s lab. Her project looks at the evolution of symbiosis in land plants and involves growing a lot of liverworts and molecular phylogenetics. Originally from Dublin she likes fluffy animals and making cakes

Twitter: @liverwortlife


The Project Song – Closer by Tegan and Sara

My research looks at arbuscular mycorrhizal symbiosis, where fungi in the soil supply plants with mineral nutrients in exchange for fixed carbon (mostly delicious fats). This relationship between plants and fungi is really very close indeed because the fungus has to grow into the cells in the middle of a plant to exchange nutrients. Plants don’t always want to trade away their lovely fixed carbon though – they might be getting enough minerals by themselves – but the fungus always wants to “get a little bit closer” with the plant because it isn’t able to get food any other way.

 This song also reminds me of symbiosis because it’s about the moment just before two people touch. In AM symbiosis, the plant and fungus exchange signals and start changing gene expression before they physically come into contact. It’s a pretty important time for both of them!”

The PhD Life Song – Boy Problems by Carly Rae Jepsen

“Really, this would better describe my PhD life if the title was PCR Problems, not Boy Problems. That said, this is a really upbeat, sassy song  – everyone has boy (PCR) problems at some point but, after you whinge about it to your friend, you realise that your boy (PCR) problems aren’t really so bad. You break up with your boyfriend (order some new PCR primers), stop lurking in your bedroom and move on. Eventually you and your female friends (fellow PhD students, of all genders) are happily dancing together, surrounded by glitter. Or you go for a drink after work on Friday. Anything is possible.”

The Motivational Song – My Shot from the Hamilton soundtrack

“Look, if Alexander Hamilton can rise from a penniless, orphaned immigrant to the first secretary of the treasury of the United States of America, I can probably power through an afternoon of hairy root transformations, right? And hey, Alex might still be a work in progress, he may not have his degree yet but he’s not going to stop working and writing and picking fights with the other founding fathers until he makes it. So I’m going to carry on writing my scientific reports, even though I’m actually a bit tired and frustrated with my referencing software. (Hamilton didn’t even have referencing software.)”


The PhD playlist is the brainchild of Millie, whose obsession with making playlists is almost as great as her obsession with science. Follow her on twitter: @milliestanton and drop her an email if you’re interested in being featured!

The PhD Playlist – Marie

Each week we put the spotlight on a PhD student at JIC and get them to share three songs in a desert island disc-style game: one song that captures their project (expect some very tenuous links), one song that captures their life as a PhD student and a final motivational song because – let’s face it – we all need it. 

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Marie is a fourth i.e. final year PhD student working with Lars Østergaard in Crop Genetics. Her project started by looking at pod length diversity in Brassica napus (which includes oilseed rape) and has since led her down a long meandering path to look at embryo development and the cell cycle. She has grown up in Belgium but sadly only started liking beer after she moved away so is now working on tasting her way through the great Belgian beers!

Twitter: @MaBruser


The Project Song – Highs and Lows by Emeli Sandé

“I tried to find a song related to oilseed rape, embryos and the cell cycle but perhaps unsurprisingly, I couldn’t find any that touched on this topic (please get in touch if you have one up your sleeve!). Instead, I chose Highs and Lows because that definitely describes what I’ve gone through! A PhD seems to be a constant rollercoaster – the project changes and leads you down new roads, experiments fail, results don’t show what you expect… but it also makes you super excited when something does work, when you have a phenotype, when genes are expressed where you hoped… and overall there are definitely more highs than lows!”

The PhD Life Song – Fighter by Christina Aguilera

“It’s an old one but that doesn’t stop me from getting a buzz from it every time I listen to it! This song makes me determined to succeed, to re-run that PCR that hasn’t worked 6 times, to go and sample what feels like a million plants for DNA extraction and to get the perfect image to show what I want it to. And my PhD has definitely made me stronger, wiser and smarter!”

The Motivational Song – Bare Necessities from the Jungle Book

“Who doesn’t like this song?! This actually became my motivational song when I started my PhD as someone in the lab was in her final year and being stressed and so we began pinging this song to each other on a bad day. It still gets me every time and it’s a song I don’t mind having stuck in my head all day long. So just “forget about your worries and your strife”!”

 


The PhD playlist is the brainchild of Millie, whose obsession with making playlists is almost as great as her obsession with science. Follow her on twitter: @milliestanton and drop her an email if you’re interested in being featured!

The PhD Playlist – Billy A.

Each week we put the spotlight on a PhD student at JIC and get them to share three songs in a desert island disc-style game: one song that captures their project (expect some very tenuous links), one song that captures their life as a PhD student and a final motivational song because – let’s face it – we all need it. 

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Billy is a third year rotation student working in the lab of Xiaoqi Feng. His project focuses on the tapetum and involves epigenetic studies and single cell sequencing. Originally from East London, loves brewing, wine, and gardening.

Twitter: @Billy_Aldridge


The Project Song – I Would Do Anything For Love (but I won’t do that) by Meatloaf

“I work on the tapetum, a tissue that surrounds the male germline. I think of the tapetum as the plant cell type you’d want to be best friends with. Not only does it provide nutrients for the developing germline but it also creates the pollen coat, make sure the germline is wrapped up warm before it ventures out into the big bad world. Once it has completed its job it even dies so the pollen can be released (aww). What a great guy!

My project is specifically looking at how the tapetum can influence the germline epigenome through the movement of sRNAs. It seems the tapetum will literally do anything for love, but will it do that? I guess I’m gonna have to find out.”

The PhD Life Song – Wanderlust by Björk 

“Björk is my favourite artist of all time and her music is a real source of inspiration for me, so I had to pick one of her songs for the #PhDPlaylist. I chose wanderlust for its sense of discovery, of leaving comfort behind and stepping out into the wider world. As PhD students I think that’s something we can all relate to, not just scientifically but also in discovering our place in the world. Are we still care-free students or are we proper adults? I haven’t got an answer for that one yet.

The amazing music video also took over 9 months to create so of course it fits with a PhD.”

The Motivational Song – MacArthur Park by Donna Summer

“Dramatic, loud, and lyrically weird. I don’t know when I became obsessed with this song but I love it so much. I now try to sneak it onto playlists at parties so I can have a little lip sync and shout at anyone who dares turn it off. This definitely channels my 1½ bottles of red “Shut up, this song is all about me” vibes, but that’s something we all need every now and again.”


The PhD playlist is the brainchild of Millie, whose obsession with making playlists is almost as great as her obsession with science. Follow her on twitter: @milliestanton and drop her an email if you’re interested in being featured!

The PhD Playlist – Nicola

In a new weekly article, we put the spotlight on a PhD student at JIC and get them to share three songs in a desert island disc-style game: one song that captures their project (expect some very tenuous links), one song that captures their life as a PhD student and a final motivational song because – let’s face it – we all need it.

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Nicola is a 2nd year PhD student in Tony Miller’s lab working on improving nitrogen use efficiency. Her research focuses mainly on forage crops with her iCASE funding coming from BAGCD. Originally from Newcastle, still adjusting to life down south.

Twitter @NicolaCapstaff


The Project Song – Cap in Hand by The Proclaimers

“Although this song has absolutely nothing to do with running q-PCRs or using nitrate sensors in soil, it’s the song which most reflects my PhD. All the proclaimer’s songs have an earthy, outdoor feel to them and Cap in Hand always makes me want to go outside; as I spend some of my time on farms this seems apt. Moreover the song is about a fight for freedom (yes it was the song for ‘vote Yes’ in the Scottish Referendum), which speaks to me in our scholarly quest for more knowledge to break down those biological inefficiency barriers.”

The PhD Life Song – B.H.S. by Sleaford Mods

“This past year I’ve really struggled getting to grips with my project, basically a classic case of the 2nd year slump. This song was listened to A LOT, for the angst and also the brutal lyrics. “We’re going down like BHS while the able bodied vultures monitor and pick at us” – who doesn’t think that’s how a PhD feels sometimes?!

P.S. My project blues are behind me (for the time being at least) so if I was allowed another song it would be Black Magic by Little Mix, just to prove I’m not totally depressing all the time and it’s a wicked tune.

P.P.S. I will not acknowledge anyone who disagrees about Little Mix being the pioneers of modern British music.”

The Motivational Song – Cream by Prince

“I LOVE PRINCE and playing any of his songs gets my motivation on to work, or at least dance in my lab chair. If I get control of music in the Rec expect a sexy Prince tune like Cream.”


The PhD playlist is the brainchild of Millie, whose obsession with making playlists is almost as great as her obsession with science. Follow her on twitter: @milliestanton and drop her an email if you’re interested in being featured!

 

Five free personal training courses you should sign up for.

Personal Development training is one of the requirements that we as PhD students need to fulfil before we can fully complete our PhD programme. But beyond that, these training courses also help us to develop and grow as a professional by giving us various transferable skills, which will come in handy when applying for jobs. I would like to share with you five free training courses I found very useful, either provided by John Innes Centre or UEA:

  1. Career Service Mentoring Programme by UEA career central

I joined the programme in August 2015 and initially it was set up as a 6-month, one-to-one mentoring programme, with Career Central finding you a match based on your interests and what you would like to get out of a mentor/mentee relationship. However, after the official period of the programme finished, my mentor and I decided to keep in contact and continue to do so. I have a mentor who is an expert in industry and has been giving me advice on the career path into industry, how to form a valuable network for your career advancement, some insights into the industry settings and also some tips on constructing an action plan to achieve your dream job. I have learnt so much through this process and it only takes an hour meeting each month with the mentor to discuss my plan and progress. I highly recommend this course, especially if you are thinking of going for a career outside academia or simply want to keep your job options open.

  1.  Turbo Charge your Writing by Hugh Kearns, Think Well

This is the training course that got me started assimilating my experimental data (even the negative ones) into thesis format and made me feel more positive about writing. It changed my perspective from “I will write when I’m ready” to “I’m writing now even if I don’t feel like doing it” and also trying not to make the first draft perfect but instead going through multiple drafts and trying to get feedback from supervisor as much as I can. It is a short course which only lasts one morning, so definitely worth signing up!

  1. Scientific Writing Academic Papers Workshop by Sophien Kamoun

This 1-day workshop goes through some examples of the dos and don’ts when writing a scientific paper, with the aim of helping you better understand the structure of scientific papers and identifying writing techniques that are required. I found this very useful when it comes to writing not only manuscripts, but also thesis chapters.

  1. The Biotechnology Young Entrepreneurs Scheme (Biotechnology YES) by John Innes Centre or UEA

Technically it’s not training, but a competition that allows you to go wild with your crazy scientific idea and try to to convince venture capitals to invest in your management team. I learned a lot about commercialisation, intellectual property, marketing and finance through the preparation for this competition. The competition itself only requires 2 days, during which your team get help and advice from the experts on commercialising your idea. My team didn’t win the competition, but I can happily say that it was a worthwhile experience.

  1. Developing Teaching Skills by the Centre for Staff and Educational Development (CSED) and the School of Education and Lifelong Learning (EDU), UEA

This is a Masters equivalent module that explores various aspects of teaching, such as giving effective lectures, demonstrating in the lab, leading seminars and assessment and evaluation of student learning while considering the student needs and their learning styles. It is designed for postgraduate students and postdocs with little or no prior teaching experience (like me) who would like to go into teaching and academia later in their career path. I really enjoyed how this course was delivered through practical and discussion-based approaches rather than a lecture-based seminar, which we get mostly in other training courses. It is quite a time consuming course though (3 hr/module + 1 portfolio assignment on the teaching experience that you participate in) so you might need to ask for your supervisor’s permission for this one, but in my opinion it is a valuable course that you should not miss if you have some spare time.

Sue is a 3rd Year Rotation PhD student in Biological Chemistry department at John Innes Centre.  She is on LinkedIn as linkedin.com/in/sakonwansue