My PhD in pictures


Image by the author’s mother

Last Friday I donned a strange-looking outfit to graduate with my PhD. I had a lovely day with my family, and many of my friends who came back to Norwich to graduate. Despite having a certificate (and photographic evidence), it is still quite hard to believe that my PhD is now well and truly finished.

The last 5 years have been a mix of fun, exciting, busy, challenging and frustrating times. Overall, the good times more than outweigh the bad and I have learnt loads about science and myself along the way, so the experience was definitely worth the hard work.  To mark the occasion, I have put together some photos that represent my PhD journey.

In the lab

In the lab

All images by the author

I studied Medicago truncatula, a member of a plant family that can form friendly relationships with soil bacteria called rhizobia. The rhizobia infect into the root through root hair cells (bottom left; bacteria stained in blue) and provide the plant with nitrogen in return for sugars. For most of my experiments, I grew seedlings on agar (jelly-like substance; top middle). Then I put the seedlings under a microscope (bottom right) to study plant responses to signals produced by rhizobia. Unfortunately,  these experiments had to be done in the dark so at times I felt a bit like a vampire! For some of my other experiments, I grew M. truncatula in soil and then had to dig them up a few weeks later to examine the roots. Most of my plants were grown in controlled environments where temperature, light and humidity were carefully regulated (top right).

Out of the lab

out of the lab

All images by the author, except bottom left (Sense About Science).

Alongside my lab-based research, I had many opportunities to take part in other activities outside the lab. These activities included:

  • Science outreach sessions with schoolchildren and adults including fun demonstrations (e.g. dry ice!) and experiments (top left)
  • Training activities such as the BiotechnologyYes! competition and a Sense about Science Media Workshop (read my blog post about it).
  • International scientific conferences were a great opportunity to get updates on research in my field and network with other scientists. (Read my report on the recent Plant Calcium Signalling Meeting in Münster, Germany). After the conferences I would try to spend a day or two exploring the local area if possible. For example, a conference in Münich, Germany in 2012 was a great excuse to explore the city and take a train journey to Nuremberg (top right).
  • Meetings with other Norwich-based scientists to discuss research and establish new collaborations, including the John Innes Centre Annual Meeting and departmental seminars. My lab and two other research groups also went to Yorkshire on a “lab retreat” for a couple of days to exchange ideas for future experiments (bottom right).

The thesis

All images by the author.

All images by the author.

Towards the end of my PhD I exchanged the lab bench for a desk in the library to write my thesis. When I started my PhD I had dreaded the idea of thesis writing, but when it came to it I actually really enjoyed it. (Read my post on the stages of PhD thesis writing). After initial submission of my thesis the next step was the viva. I celebrated surviving my viva with friends and colleagues and one of my friends even gave me some homemade wine (top right) he had made from grapes grown on my grapevine (I can’t take any credit for the grapevine, it was there when I moved in to my house). After completing minor corrections to my thesis I submitted the final copy (bottom right) and received official notification that I had passed my PhD :-) This all happened around my birthday so my mum made me a “PhD cake”.

All the other moments

The photos here only give snapshots of my PhD journey. There are a whole host of other moments that haven’t been caught on camera but will still be remembered. Silly moments, like when I almost tripped over a bright yellow “caution wet floor” sign, and lab tea breaks when we cut cake into ever smaller pieces so that everyone could have a slice. Fun times socialising in the John Innes Centre bar on Friday evenings and at special events like the Fireworks Night party. Stupid moments, like when I hit my head on a shelf while checking on some plants I had growing, which negatively affected my PhD studies more than anyone could have predicted. And important moments, like the first time I observed calcium signalling in root hair cells from a plant line I had spent over a year developing.

One of the most important things I learnt is that there is a lot more to a PhD than carrying out a few experiments and writing a big book at the end. It is a learning experience where what you learn outside the lab can be just as important as what you learn in it.

Dr. Sarah

Some of my fellow PhD students from the John Innes Centre, The Sainsbury Laboratory and the Institute of Food Research

New Doctors of Philosophy from the John Innes Centre, The Sainsbury Laboratory and the Institute of Food Research. Image by the author’s mother.


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Leishmania parasites: neglected tropical killers

Later this year I will be visiting The Gambia in West Africa to work on a GirlGuiding community project. Before I go I will need to have some vaccinations to protect me from several of the diseases found there. Unsurprisingly, this has rekindled my interest in tropical diseases. This week, I have strayed from my usual subjects to write about the leishmaniases, a group of tropical diseases found across Africa, Asia and the Americas. Included in the World Health Organisation’s (WHO) list of Neglected Tropical Diseases, the leishmaniases are a big burden on public health services in many countries, and were responsible for an estimated 50,000 deaths worldwide in 2010 alone.

Leishmaniases are caused by parasitic single-celled organisms of the genus Leishmania. The parasites are carried between mammal hosts by several species of blood-sucking sandflies. The parasites live within the mouthparts of the sandflies and can be transmitted to mammals when the sandflies bite. The parasites exist in different forms in sandflies and mammalian hosts. In the sandfly, Leishmania cellsbecome promastigotes and move around the insect gut using string-like structures called flagella. Within a mammal host, the parasites “hide” within host immune cells (called macrophages) and lose their flagella to become amastigotes.

Leishmania parasite lifecycle requires sandfly and mammalian hosts. This image is a work of the Centers for Disease Control and Prevention (US Federal Government). The image is in the public domain (via Wikipedia).

The Leishmania parasite lifecycle requires both sandfly and mammalian hosts. This image is a work of the Centers for Disease Control and Prevention (US Federal Government). The image is in the public domain (via Wikimedia Commons).

Continue reading

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Sabotage of plant cell communication by invading bacteria

Leaf speck on a tomato leaf caused by Pseudomonas syringae infection. Image by Alan Collmer via Wikimedia Commons (CC0).

Leaf speck on a tomato leaf caused by Pseudomonas syringae infection. Image by Alan Collmer via Wikimedia Commons (CC0).

To protect themselves from infection by disease-causing microbes, plants have systems that detect potentially harmful microbes and activate defence responses. Disease-causing microbes can overcome these defences by producing proteins called effectors that can enter host plant cells and disrupt them. Understanding what these effectors do in host plants could be useful for the development of more disease-resistant crop plants. Unfortunately, the roles of many effector proteins are not yet understood.

One of the ways effector proteins can interfere with plant defence responses is to prevent the relay of danger messages from the site of microbe detection at the plasma membrane to other locations in the cell. For the signal relays to function, the various protein components need to be located in the right places in the cell (plasma membrane, cytoplasm, nucleus, vacuole etc.). The cytoskeleton, consisting of filaments of the protein actin, is required for this organisation and moves proteins contained within (or on) small membrane-bound structures called vesicles. Continue reading

Posted in Bacteria, Cell Signalling, Plants | 3 Comments

Making waves at the Plant Calcium Signalling meeting

Last week I went to the Plant Calcium Signalling Meeting in Münster, Germany. I really enjoyed the meeting and it was a great opportunity to get an update on the most recent research in the area.

I have a guest blog on Annals of Botany blog about my personal highlights of the conference click the link to read it.

If you haven’t seen it already, read the article I posted earlier this week about a new drought-tolerant barley variety that has been developed by some of my colleagues at the John Innes Centre in collaboration with researchers at the University of Jordan.

And don’t forget that the Organism of the Month here at Plant Scientist is the poppy. There are still loads in flower in the UK at the moment to take a look if you can. If you want to know more read Kirsty Jackson’s article.


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Why we should all be interested in drought-tolerant barley

Image by Gerste Ähren (licenced under CC BY-SA 3.0)

Image by Gerste Ähren (licenced under CC BY-SA 3.0)

Last week, it was announced that researchers from the John Innes Centre, UK and the University of Jordan have developed a variety of barley that is four times more drought-tolerant than other barley varieties. Why do we need drought-tolerant crops, and what is so significant about this barley?

All plants need water to grow. Consequently, agriculture is highly dependent on water and accounts for 70% of global water consumption. This is a massive amount of water. To put it another way, it takes around 2000-3000 litres of water to produce the food that one person typically eats in a single day! In many regions, not enough rain falls to provide sufficient water to crops and the fields have to be irrigated with water taken from rivers and underground sources. Continue reading

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Guest Post. Poppies: A blessing, a curse and a moment of reflection

Papaver dubium in Norfolk, UK. Photo by the author.

Papaver dubium in Norfolk, UK. Photo by the author.

A week early, the red poppy is the Organism of the Month of July here at Plant Scientist. I didn’t want to delay the publication of this post since there are loads of red poppies in flower in Europe at the moment!

By Kirsty Jackson (@kjjscience)

At this time of year poppies seem to spring out of anywhere and everywhere they can. In the last few weeks I have seen them in gardens, motorway central reservations and even poking out of Norwich’s medieval city wall.

Opium poppy (Papaver somniferum). From Prof. Dr. Otto Wilhelm Thomé Flora von Deutschland, Österreich und der Schweiz 1885

Opium poppy (Papaver somniferum). From Prof. Dr. Otto Wilhelm Thomé Flora von Deutschland, Österreich und der Schweiz 1885 (via Wikiemedia Commons).

Humans have used poppies in food, medicines and beauty treatments for around 6,000 years. The opium poppy (Papaver somniforum) was widely used by the Greeks, Romans and even thought to be used by Neolithic tribes. When looking upon the pretty flower of the opium poppy, you could be forgiven for thinking that it is harmless. In fact, the opium poppy has been both a blessing and curse for humanity.

During the ripening of the opium poppy seed capsule, the head produces a milky sap, which is the source of the drug opium. In the 18th Century, China suffered greatly due to the addictive properties of opium. Britain, in an attempt to gain trade from China, supplied the Chinese with opium (from Bengal), despite resistance from the Chinese government. The effects of opium began to destabilise China and enabled the British to prosper in Opium Wars of the mid-19th Century. It was at this time (~1842) that Hong Kong became a colony of the British Empire and it was not returned to China until 1997. Continue reading

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The GM debate is distracting us from the real issues in agriculture

Image credit: Photograph by Dako99 (CC BY-SA 3.0)

Image credit: Photograph by Dako99 (CC BY-SA 3.0)

The debate over the use of genetically modified (GM) crops has been going on for a long time. Despite the controversy, GM crop production has grown rapidly since 1996, and GM crop varieties are now planted on 3.5% of the World’s total agricultural land (1). In an article published his week in PLOS Biology, Ottoline Leyser argues that this debate is distracting us from addressing the real challenges facing modern agriculture: global food security and environmental sustainability (2).

Leyser starts by discussing how GM is considered by many to be the epitome of all that’s bad in modern agriculture: the dominance of profit-driven multinational corporations, high-intensity monoculture farming and the accompanying use of large quantities of environmentally-damaging chemicals. As a plant scientist and nature-lover, I am also concerned about these farming practises. However, as Leyser points out, they have nothing to do with GM technology. It is a situation that was reached long before GM-crops were first grown commercially and is prevalent all over the world, including in the EU, where GM-crops have never been widely grown. Continue reading

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