The PhD Playlist – Thom B.

Each week we put the spotlight on a PhD student at the Norwich Research Park 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.

Thom is a 3^rd year PhD student in Molecular Microbiology at the John Innes Centre. He is researching the specialised metabolism of bacteria in the hopes of understanding how drug-like compounds are synthesised. He is also interested in the evolution and ecology of these pathways. Originally from Preston, Thom has also worked in London at the Royal Botanic Gardens, Kew and the Government Office for Science. When not in the lab, he is most likely in the pub or round the table playing board games.

Twitter: @BoothThom

The Project Song – Killer Queen by Queen

“Bacteria make all kinds of compounds to utilise as chemical weapons and there is no doubt that Streptomyces is the ‘Killer Queen.’ The diversity of Actinobacterial specialised metabolites is impressive – one might say it’s guaranteed to blow your mind… Is that tenuous enough?!”

The PhD Life Song – Ain’t No Rest for the Wicked by Cage the Elephant

“Let’s face it, PhD students work hard. We’ve all been in the lab at ridiculous-o’clock taking a time course, trying to finish a particularly complex protocol or scrambling to finish a report/presentation before the deadline. I feel this song really sums up that feeling of resignation, while making it seem pretty rock and roll at the same time. Also, the final verse is a nice reminder that even people who look like they’ve got it all together are still struggling with the same pressures as everyone else.”

The Motivational Song – Bad Motherf*cker by Biting Elbows

“There are loads of songs I could have picked for this category. Sometimes you need a song that will show you the bright side of life. Sometimes you need a song that will improve your focus and get you in the zone. Occasionally though, you just need reminding that you’re a bad motherf*cker!”

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 PI Playlist – Dr Steph Bornemann

Welcome to the hotly demanded spin-off of The PhD Playlist – The PI Playlist! The format is similar, with the spotlight being put on a group leader here at the Norwich Research Park to pick three songs: one song for their current research/job, one song for their life as a PhD student and that final much needed motivational song. So turn the volume up and discover the soundtrack to a science career.

I only spoke German until I went to nursery in Yorkshire where I learned English. I went to school in Wales at a time when my older brother exposed me to a huge range of music via the Old Grey Whistle Test and John Peel. As a sixth former and student in London and Warwick, I played in several bands including Gods Lonely Men, the Fat Ballerinas and Clenched Fish, which did not make me rich. While in London, and in Reading when working in industry, I went to an extraordinary number and range of gigs and lost my Welsh accent. As a post-doc, I had no more time for playing in bands, but continued to write and record music. As a project leader, I didn’t have time for that either, but I put my tracks on Soundcloud. None of these tracks have made me rich. These days, I have limited time to even listen to music, let alone go to gigs or play instruments. The silence is nevertheless broken by my daughters.

The PhD Song – Egg by Mr Bungle

“My PhD (1989-1992) had its ups and downs. The ups and downs of this track from 1990 sum it up. I published 6 papers from my PhD with 4 first-author, which might not have happened because I seriously considered quitting after a few months. I had a lot of autonomy throughout, which taught me a lot, but I had to wait three months on one occasion to have a meeting with my supervisor because he was so busy. I had to change my research project half way through but still managed to submit within three years, which was the default length of a PhD in those days. My supervisor wrote “good” in red ink next to a figure in my draft thesis. This was the highlight of the feedback I received in my time there. After my viva, the examiners left the room to inform my supervisor of the outcome without considering to tell me. I had to sit down to avoid fainting, and when my blood pressure recovered I summoned the courage to find them. It turned out be just a few typos that needed correcting. Phew! Shortly after, and on the day I had to return to my new job in another part of the country, my supervisor took his group out to lunch for my leaving do. A lovely thought, except they neglected to tell me which pub they were going to. This was in the days before mobile telephones. Great! I then made the mistake of leaving the 10 or so corrected pages of my thesis outside his locked office door with a note to swap them over in his copy. This was unwise. He wrote a damning letter to me for being so rude and not presenting him with a bound final version of my thesis. Many years later at his retirement celebration when I thought all was forgiven and forgotten, I thanked him for taking me on as a PhD student. He said it wasn’t him that wanted to recruit me, but one of his colleagues in the funding consortium. At least my PhD put the chemistry in my biochemistry.”

The Current Research Song – Love the Life (Live) by Midnite

“The aim of my current project is to ensure that the postgraduate students at JIC have a much better experience than I did. The life one lives and the life one loves change with time. The studio version of this track is not currently available on Spotify, so here is the live version.”

The Motivational Song – The Life Devine by Carlos Santana and John McLaughlin

“There are occasions when music invokes goosebumps. This is the track that does it regardless of the mood I’m in, bringing energy and focus.”

The PhD and The PI 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 T-B.

Billy is a first-year PhD student in Lars Østergaard’s lab. He is a local boy, from rural Norfolk. His first visit to the JIC was when he was 15 as part of a school visit. Billy remembers hearing of students spending 4 years studying the same small weed and being dumbfounded. Despite trying to escape Norfolk (and England) by moving up to St. Andrews for his undergraduate, Norfolk has drawn him back to its sandy embrace. Needless to say, Billy’s opinion of the small weed that people spend so much time studying has changed. His project is on the radial to bilateral symmetry change during gynoecium development; specifically how the cell cycle is controlled during this process. When not in the lab he spends his time thinking about birds (the flying variety), beer, his wife and football (not in that order).

The Project Song – The Circle of Life by Elton John

“Studying the cell cycle makes this song an obvious choice. The cell cycle underpins development and disruptions can be fatal. Since starting my PhD the complexity of gynoecium development has fascinated me. The lyrics ‘There’s far too much to take in here, more to find than can ever be found’ is poignant, and I like to think that Elton John was thinking of Arabidopsis genetics when writing these lyrics.”

The PhD Life Song – Three Little Birds by Bob Marley & The Wailers

“One of my hobbies is bird-watching, and I wish that three (different species of) little birds would come to my doorstep every morning. I picked this song because everything that can possibly go wrong whilst doing a PhD generally does. At some point, you have to shrug your shoulders and blast this song out whilst in the lab. In my mind’s eye, I see myself walking in slow motion along a chaotic street with the buildings exploding around me and this song playing over the top.”

The Motivational Song – Always Look on the Bright Side of Life by Monty Python

“When you are a bit down in the dumps, a ‘Cheer up, Brian’ is always sufficient to lift your spirits. If you are struggling with anything just remember that it isn’t as difficult as doing the can-can on a crucifix. Doing a PhD can be tough, so blast this out when you are feeling insufficient. Count your blessings, change your perspective and I expect to hear whistling filling the labs of JIC over the next week.”

The PhD Playlist – Joanna

Screen Shot 2017-06-02 at 11.36.05 Joanna is a 1^st year Rotation PhD student from Edmonton, AB in Canada, working in Jonathan Jones’ lab at The Sainsbury Laboratory. Her project involves suppressor screens to look for novel genetic components of downstream immune signaling in plants. When she’s not obsessing over phytopathology she’s playing bluegrass guitar and mandolin, or she’s at the gym.

Twitter: @jofeehan

The Project Song – Shimmy Shimmy Ya by Ol’ Dirty Bastard

“Here I am at the beginning of my PhD, having just a week or two ago decided on a final lab and project after rotating. Yeah, “oh, baby I like [my data] raw”, is on the nose as any data I have is pretty crude, but really, this song is all about getting hyped on myself for the next three years. Thanks, ODB.”

The PhD Life Song – One More Dollar by Gillian Welch

“This song resonates with my current situation; moving far away, from my beautiful home in Alberta, to pursue an adventure (hard labor) with plants (apple picking). And the fear of ending up destitute and having to make money through gambling (in the stock market) seems like a real possibility.”

The Motivational Song – Eye of the Tiger by Survivor

“A classic. Whenever I’m feeling like my PhD needs to be put in its place, I’ll just put this song on and montage myself running PCRs and westerns and lunging down the hallways of TSL. I have definitely not done that yet.”

The PhD Playlist – John

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.

John in a 1^st Year PhD student working in Paul Nicholson’s lab. He’s looking at a number of approaches to control Fusarium Head Blight in wheat. More specifically, he’s working on identifying important plant hormone signalling pathways including hormone manipulation strategies by Fusarium, and combining these with fungicide application. John is half Greek and Spanish but lived in Oxford for most of his life. He loves a good game of squash every now and then.

The Project Song – Invaders Must Die by The Prodigy

“Despite the different nature of this song to my other choices, I felt its title best describes the theme of my project. In order to stop the ever-growing horde of invading pathogens, a combination of control strategies need to be used. With my project, limiting infection and development of Fusarium when wheat is at is most susceptible is one key way to control the invasion.”

The PhD Life Song – Precious Time by The Maccabees

“Unfortunately, time is a constraint to all PhD projects. Time is always on my mind from designing experiments to seeing if its lunch yet. Despite having four years to complete my PhD, I feel like its relatively short and every second of it is precious. It is also amazing that for every deadline, we somehow manage to get things done on time!”

The Motivational Song – Learn to Fly by Foo Fighters

“Who doesn’t like a bit of Foo Fighters in their life! This song can be played at loads of occasions and always manages to improve the mood (especially if you watch the Rockin1000 video!).”

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 2^nd 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.

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.

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!

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!

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

Screen Shot 2017-05-18 at 11.27.13 Aisling is a 3^rd 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.)”

John Innes SVC