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!)

 

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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

Why can’t we just talk about it?

Agri-Tech East’s mission to get farmers and researchers communicating

Getting two groups of diverse people talking is always difficult, even more so when they are both driven by different goals. Farmers and agriculturalists focus on innovative technology in order to achieve good harvests to try to maximise their returns. Plant scientists however want to understand the underlying biology of their research of interest. So these two groups have different driving factors of profits and principles. Working together is therefore immensely challenging. One way to tackle this is to improve the dialogue between the two groups by identifying the common ground.

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International Undergraduate Summer School

From working with top researchers in the field of plant biology to living with other students of such fun, character and like-mindedness, the John Innes Centre International Undergraduate Summer School was an unforgettable experience. Not only did it confirm my desire to study beyond my degree to PhD level, it has opened my eyes to how research teams run and has given me experience of working in a world-leading lab.

The first day began with settling in to halls on the UEA campus, where all JIC summer students were placed together. After finding the rooms and meeting and greeting, the friendly PhD students met me and the others for the first night’s event. An evening of pizza making and lots of drink meant everyone bonded well from the start. The initial days on the programme involved me meeting my research team and supervisor, as well as establishing the project on which I was about to embark over the next eight weeks. I focused on flowering time in Arabidopsis thaliana with Caroline Dean, whose lab was truly great. I learned new techniques and protocols with state-of-the-art equipment that would only be available at a centre such as JIC.

Making pizza

Making pizza in the evening at the International Undergraduate Summer School. Photograph: John Innes Centre.

Over the weeks, my knowledge of my project grew, and enabled me to work more independently. Alongside this I learned what a great environment JIC is, not only in terms of research, but also the running of the centre. There was always someone at hand willing to help, be it for potting my plants or fixing my bike. In my free time, I often visited local areas around Norwich, and made full use of the heated outdoor pool at JIC! Many activities took place throughout the summer, meaning I met people from across the site. I realised how enthusiastic and loyal all the workers there are.

To finalise the programme, all summer school students took part in a retreat to Cromer. This involved presenting work and raising encouraging questions to one another in a relaxed setting, whilst also getting a feel for how a typical conference would be run. Ending with a quick dip in the sea, it was a great way to conclude the programme.

Students on the 2015 International Undergraduate Summer School. Photograph: John Innes Centre.

Students on the 2015 International Undergraduate Summer School. Photograph: John Innes Centre.

All in all, it was a fantastic experience and has been a truly unforgettable summer. I recommend anyone interested in entering the botanical world of research or academia to apply, not only for the science, but also for the great and interesting people you will meet.

Olivia took part in the 2015 International Undergraduate Summer School, a programme that takes place every year. She tweets as @oliviatasker.

Applications for the 2016 International Undergraduate Summer School will open on Monday 19 October 2015 here.

11 things every new PhD student should know

I started my PhD nearly a year ago now, and the time has absolutely flown by. With many people setting out to start a PhD in September and October it made me think about what I have learned this year, and the top tips I would tell anyone about to embark on a PhD in Science:

1 Don’t be afraid to ask questions

Don't be afraid to ask questions during your PhD.

Don’t be afraid to ask questions during your PhD.

No one minds. It’s better to ask how to do something if you don’t understand than waste your time doing it wrong. Everyone in the lab has been in your position before. We don’t bite!

2 Write down EVERYTHING

And I mean everything. At the beginning of your PhD, you’re excited, you’re in a new lab, doing new things, and sometimes you may not write everything down. It happens. But in a few months’ time when you look back at that crucial PCR – the one where everything amplified beautifully – and you realise you forgot to write down the annealing temperature, you will kick yourself.

3 Label EVERYTHING

Only last week I came a cropper when I realised I had mislabelled one of my early glycerol stocks, which meant I had to redo the previous stage of my experiment. Labelling really well may take you a few extra minutes, but it will be well worth it in the future.

4 Plan your day

Plan your daily activities: it can be hard to keep track of what you're doing otherwise.

Plan your daily activities: it can be hard to keep track of what you’re doing otherwise.

When you have several experiments on the go it can be pretty hectic, and hard to keep track of everything. It can useful to make a list at the beginning of the day, or the evening before, of everything you need to do. That way you won’t end up on Friday realising that you can’t do that experiment because you forgot to prepare the overnight cultures.

5 Make time for yourself

Yes, the PhD is really important, and yes, it’s good to get excited about it and take a huge interest in it, but don’t let it take up all your time. It’s important to have a healthy work-life balance. Personally, I find that taking that extra break, and having that evening off, helps me be more productive and make fewer mistakes. A PhD is a long time, and you should make that time as enjoyable as you can – both inside and outside the lab.

6 Take the time to get to know your lab

This one is easy – just chat to everyone! Go to lunch together, have a tea break, make sure you go to the lab meetings. And if the lab doesn’t do these things you could always suggest it. A lab that has great communication is the best sort of lab, and will make your days at work all the better. A friendly and fun working environment makes everything so much nicer.

7 Get involved

Conferences are a great way to meet new people.

Conferences are a great way to meet new people.

Go to seminars, departmental meetings and conferences, both at home and away. They are a great way to find out what others are doing both in your department, and across the institute. It helps you build those connections up – you never know, they could be crucial in the future. And don’t be afraid to mingle! It’s a big thing at first to get out of your comfort zone, step away from your friends, and talk to someone about their work, but it’s well worth it.

8 Try not to eat at your desk

If you are doing a lot of experiments in a day, and are really rushed off your feet, you may decide to just eat your lunch at your desk. But, this can often leave you feeling dissatisfied. Even if it’s only a 15 minute break, having your lunch away from your desk and lab can be really beneficial. It takes you away from the lab and work completely, and you will return feeling refreshed.

9 Just because you had a bad day today doesn’t mean it will be a bad day tomorrow

Everyone has bad days, the day when your RNA extraction just won’t work, or you run your DNA off your gel. It happens. Take a breath and start over.  Don’t let it get you down.

10 If you are having problems with your PhD speak to someone about it

The first few months can be a bit rocky: settling in to a new city, a new lab, making new friends, learning new things. If you are finding something hard in your project, or are feeling unsatisfied, out of your depth, or just stressed out, chat to your supervisor about it. Or if you feel you don’t want to talk directly to your supervisor, try another PhD student or lab member. It is normal to have periods throughout your PhD where you feel a bit down or stressed. When things aren’t working, it can be demoralising, but having someone you can talk it out with can help.

11 Enjoy!

A PhD can at times be frustrating and hard work but it’s extremely enjoyable and one of the most rewarding things you will ever do.

Erica is a PhD student at the John Innes Centre. She tweets as @EricaHawkins16.