Year 1 to Year 2: hop, skip and a jump

So before I knew it the time had come for me to dust off my presentation skills and present my research to my seniors and peers. Awesome if you relish in designing powerpoint slides and presenting them, but me? Not so keen on the whole standing in front of 30 odd people…

Nevertheless, I did it, and I can happily say that I can progress with my PhD! Hello next 3 years, we’re going to get very well acquainted.

So although I am not even halfway through my research, this year has taught me a lot and I thought this could be useful for those just starting, or about to progress from probation period to full candidature. First things first…

  • Communicate

The cool thing about my project is that it’s a jointly awarded program between two different universities. So for me actually one of the biggest challenges has been communicating between everyone, across different timezones despite busy schedules. Thankfully, my supervisors have all been good at dealing with answering my random, badly-worded questions at whatever hour, as well as taking the time to skype when the question can’t be answered in an email.

  • Communicate some more. Learn to brief your supervisors about your work – not wait for them to ask you (if they’re really busy they may forget).

When you start collecting results from your experiment, it’s up to you to schedule meetings with supervisors to discuss your results and experiment. Generally in the first few weeks of your candidature, supervisors are a little more ‘hands-on’ in explaining literature, experiments, equipment, but once you’ve started to piece together your experimental design and started executing it, then the roles reverse. It’s not like undergrad where you’re guided every step of the way. This time you have to take some initiative. Sounds a little daunting, but actually it forces you to be creative with your time and your ideas. It’s now your turn to tell them what you’ve been doing. Don’t be afraid to not understand everything you see, they may not understand everything either. By bringing your ideas and theories to the table, you don’t have to try to understand everything before you decide to have that monthly supervisory meeting.

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Excited with my first experiment set-up

  • Don’t panic

Easier said than done, I know. I’ve been there. And I am only in my first year. But everyone goes through ups and downs. It’s about finding strategies that help you manage that stress. Doing a joint PhD means I get the best of what both universities offer me in terms of research facilities, equipment, and knowledgeable academics. However, it can also mean I get the worst of both – and that is admin. Not that the people who work in admin are stupid but if you are ever considering a joint PhD or co-tutelle program, just remember that you may have to send a few of the same emails reminding admin from both institutes where you are currently studying and that no, you will only be examined by one institute at a time. And yes, sometimes you will have to sign documents even though you are pretty sure you signed the exact same form a month before. Just laugh, grab a pen and keep signing those forms. The paperwork will subside.

In addition, because a joint PhD between my 2 universities was new, I found it funny that most people (both admin and supervisors) didn’t have a clue about how this joint PhD was going to play out. The theory behind it is excellent, and I can’t recommend it enough. However, when it comes to reviewing the student’s progress, questions were raised on multiple occasions: ‘But who reviews me?’ ‘Does I have to repeat my review seminar twice?’ ‘How long do I stay at each institute?’ ‘How does funding work?’ … you get the picture. This meant it was both a learning curve for me and for everyone else involved in my exciting new project. in the end, all that really matters is your research. Focus on what brought you to do a PhD in the first place, and the admin can follow on behind you.

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First time analysing my experiment plants

  • Blogging

For me, this is where I can unwind. I get ideas from everyday situations, places I’ve visited, or the news. I currently manage 3 blogs (because one is never enough), but my most updated one is Meristem Journeys. The essence of it is to convey cool interesting facts about science in a way that everyone can understand, from professors in the field to the inquisitive child. So it gives me a chance to learn science communication skills. On the other hand Dare To Adventure and The Literary Road are different, more travel-based or fictional. They provide another outlet for me to be creative. This time I don’t have to stick to a theme, I write where my fancy takes me. It’s my ‘me-time’.

  • And last but not least, go forth and explore!

Whether you’re in a new city or not, take the time to go on excursions – from afternoon trips to extended weekends. Find interesting, quirky things in the city and beyond. Some of my best memories come from exploring Sydney or a roadtrip to Ayers Rock (Uluru). These breaks gave me time to recuperate from intense harvesting weeks, and I felt better about coming back and knuckling down to data analysis. Even if you are in a familiar city, I’m certain there are new things to be found – make it a fun challenge. Or pick up a new hobby; set yourself a goal that’s fun and completely non-work related. Someone once suggested that I take part in ironing competitions…there are some good hobbies out there! Whatever it is, your brain will thank you.

I may be 1 year wiser but there’s plenty more learning to come. And that’s exciting. If you don’t want to work hard, be criticised and are scared of an experiment failing on you every now and then, a PhD is not for you. But if you enjoy discovering things, communicating with a wide range of audiences, like a challenge, and can learn to find cool things in the midst of trying times, welcome to the world of PhDs.

#workhardplayhard

Getting to the root of the situation

Water. Nature’s currency.

With climate change becoming more obvious everyday, drought is something that farmers are becoming more accustomed to. Climate change figures project that water availability will become more erratic in the near future, with high rainfall over a short period of time, followed by no or low rainfall over a longer period of time.

As a result crops need to be able to function better without adequate rainfall. Fortunately, adaptation is something most plants do well. Scientists from José Dinneny’s lab at the Carnegie Institution for Science have hit upon a strategy some grasses utilise during drought stress. Grasses produce crown roots, which are roots originating from basal nodes (nodes at the base of the shoots). Crown roots are the major channel for water uptake, and they develop relatively early  on in the plant’s growth. Plants use crown roots to sense the availability of water in the surrounding soil and subsequently stimulate further crown root growth. Dinneny’s team discovered that it is possible to induce changes in the root architecture, specifically the crown roots, when under drought stress. By subjecting the model grass Setaria viridis to water stress, crown root growth was suppressed. Root growth was analysed using the GLO-Roots luminescence imaging.

Fig 1 Atkinson et al 2014 wheat roots

Diagram representing a wheat root system with crown roots.

To simulate drought conditions, water stress was induced, with no further watering after germination. This resulted in plants accelerating through their growth development stages – early onset of flowering, increased leaf formation and tiller formation (shoots other than the main shoot of the plant). It also caused a dramatic decrease in crown root growth, with plants maintaining a more limited root system under water-deficient conditions. Dinneny’s team concluded that S. viridis did this as an austerity measure – slowing down their water uptake ultimately means less energy is utilised and so more of the water can be conserved in the plant shoots and not lost through transpiration.

plant roots A B

GLO-Roots luminescence imaging – The roots on the left (A) show changes in crown root growth 11 days after germination under well-watered (WW) and water-deficient (WD) conditions, while the roots on the right (B) were not imaged until 17 days after germination. Both sets of roots show suppressed crown root growth after a period of drought.

Interestingly enough, the fate of the roots can be reversed. When water-deficient plants were re-watered from the base of the pot after a period of dry, the plant could resume a more healthy root growth. In comparison, when the plants were re-watered from the top of the pot, the crown roots revive and development was reactivated. This suggests that the crown of the plant has the ability to sense local water availability in order to induce or pause crown root growth.

roots G

These series of images show the reactivation of crown root growth over time after water-deficient plants were re-watered (G).

So what does this all mean for agriculture?

Suppression of crown root growth was also shown to occur under drought conditions in other members of the Poaceae (grass) family. Sorghum, switchgrass and Brachypodium distachyon also showed strong suppression of crown root growth. In wildtype maize there was a near-complete suppression. Using this knowledge, it could change how plant breeders tackle the issue of variable water supply. Crops could be breed to have better responses to water deficiency, by enhancing the response of the crown roots. With further development of crop management strategies and new breeding techniques, improvement of the environmental and economic sustainability of food production can become a firm reality.

With climate change and the unreliability of rainfall, we don’t just need plants, we need clever plants.

#rootsforthewin

Link to journal paper:

Sebastian J., Yee M.-C., Goudinho Viana W., Rellán-Álvarez R., Feldman M., Priest H. D., Trontin C., Lee T., Jiang H., Baxter I., Mockler T. C., Hochholdinger F., Brutnell T. P. and Dinneny J. R. (2016) Grasses suppress shoot-borne roots to conserve water during drought. Proceedings of the National Academy of Sciences 113, 8861-8866.

http://www.pnas.org/content/113/31/8861.full

 

Let them eat meat – it’s as easy as 1, 2, 3

If you think plants weren’t smart then you would be wrong.

Counting numbers is something we do on a regular basis, how much change for a cup of coffee, calculating how much time we have between meetings, counting the number of days until payday.

But imagine if you had to count numbers so that you could eat. Venus flytraps (Dionaea muscipula) do just that. A group in Germany led by Jennifer Böhm and Rainer Hedrich recently published a paper looking at the mechanism behind mealtime for the popular carnivorous plant. What they really wanted to know was how did the venus flytrap know when to kick-start the glands that produced the digestive juices once its prey had been trapped. What was the mechanism responsible for this?

In areas of infertile, nutrient-poor soils, carnivorous plants thrive. The reason? They feed solely on insects and other small animals. The anatomy of a venus flytrap is pretty simple, yet does a very effective job at capturing and digesting flesh. The trap itself is actually a modified leaf, with a hinged middle, which would act like the central vein of a normal leaf. The edges of the modified leaf (trap) end in spikes which interlock with each other when the trap closes.

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A carnivorous beauty. Tiny hairs are present on the inner surface of the trap. Touching these stimulate action potentials which trigger the trap to close and produce digestive juices (Photo credit).

A starving flytrap will release a smell much like a fruity cocktail. This attracts numerous insects and small animals (frogs have even been known to succumb to the venus flytrap). When an unsuspecting fly lands on the trap, its movement triggers tiny hairs present on the inner epidermis of the trap.

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A wasp caught in the hinges (Photo credit).

These hairs then convert the mechanical stimulation to an electrical excitation, otherwise known as an action potential. The trap shuts once two action potentials have been fired within approximately 30 seconds, caging in the insect. As the trapped insect continues to struggle, inevitably more hairs are triggered. As many as 60 action potentials per hour can be fired. Böhm and her group observed that after 3 action potentials were fired, the level of calcium within the cytoplasm (of the plant cells) increased. This then stimulated the expression of the touch hormone jasmonic acid. The jasmonic acid signalling pathway is usually used as a defense mechanism in a non-carnivorous plant when it is wounded. However, in carnivorous plants, the pathway stimulates the production of digestive enzymes by switching on certain transcription factors (proteins that control gene activity). Effectively, the closed trap turns into a green stomach and the insect is mercilessly broken down into its basic molecules, e.g. carbon, nitrogen, phosphorus etc., which are absorbed by glands in the trap. Also, digestion of prey increases production of a specific transporter which allows for greater uptake of sodium, which in turn is important in regulating the nutrient uptake channels found in the glands. The group also noted that the flytrap seemed to regulate the amount of digestive juices secreted into the trap by how many action potentials had been fired. The flytrap could potentially use this as a clue to the size of its prey, so it wouldn’t over-flood its trap therefore conserving as much energy as possible.

More research is going into sequencing the genome of the venus flytrap to understand how these carnivorous traits have developed, and how they can thrive in nutrient-poor environments. Maybe from that we can take what information we know about nutrient uptake in carnivorous plants and transfer that to other plants. Or do we risk creating Frankenstein plants?

Who knows. All I know is that you won’t find out if you don’t try.

#tryscience

Link to journal paper:

Böhm J., Scherzer S., Krol E., Kreuzer I., von Meyer K., Lorey C., Mueller T. D., Shabala L., Monte I., Solano R., Al-Rasheid K. A. S., Rennenberg H., Shabala S., Neher E. and Hedrich R. (2016) The venus flytrap Dionaea muscipula counts prey-induced action potentials to induce sodium uptake. Current Biology 26, 286-295

http://www.sciencedirect.com/science/article/pii/S0960982215015018

 

 

How do I know I’m doing enough work?

You’ve started your PhD, reading papers, writing your literature review, reading papers, designing your first experiment, oh and did I mention reading more papers.

You’ve amassed a pile of journal articles, scientific papers and book chapters either piling high on your desk and the floor around you, or metaphorically piling around you, a.k.a. on your computer. So probably safe to say you’re doing enough reading.

How do you pluck out that all-too golden information and enter that into your all-too empty word document? It all seems so relevant.

Write a sentence. Any sentence.

Doesn’t have to be a good one. It doesn’t even have to make sense. It can be as broad as ‘plants are cool, we need plants’. Obviously you’re never going to submit a paper with that introduction, but it gets the writing juices flowing, it makes you think – why are plants cool, why do we need plants…etc. Whatever your story or argument, set it out in one simple sentence and go from there.

Lives are already complicated enough without the added of flouncy words and highly convoluted sentences.

 

 

Life in the PhD lane

Starting a PhD is one of the most daunting things I have ever done. When I first heard that I had got the offer, I had a mix of emotions, ranging from excitement to worry. I have just started, and I want to look at the ways in which we can manipulate the microbiology of the soil in order to improve plant responses to drought and nutrient stresses. It is something I am really interested in, and it has so much potential in this current agricultural climate.

After my first 4 weeks, there are a couple of things I learnt – an amalgamation of other people’s advice.

  1. Don’t stress about things you don’t even know yet. You won’t know a lot of things, and that’s perfectly fine. As long as your willing to acknowledge that you don’t know everything, and that you want to learn, then you are in a very good position to do well.
  2. Talk to your supervisor. They have a lot of answers to a lot of the questions you have. Plus, how else will they know how you are doing if you don’t communicate. They’re not here to molly-coddle you; they’re there to guide you to progress into a fully fledged scientist.
  3. Take lots of tea breaks. Vital. Especially at the start when all you seem to be doing is reading scientific papers and note taking. Having a chat with other students helps you to remember you’re not the only one doing this. It’s. Perfectly. Normal.

I have to constantly remind myself that my supervisors would not have chosen me to carry out this project if they didn’t see something in me. If they didn’t think I was capable of using my brain to come up with something exciting and innovative.

If, in the end, my PhD teaches me nothing but perseverance and responsibility, then it will still be worth 4 years of my life.

Start small, dream big. After all, we all have something worth to say and contribute to this world.

What’s that smell?

On the 1st February, I had the privilege of seeing the titan arum lily flowering at the Adelaide Botanic Gardens. I was prepared to get a waft of something similar to rotting flesh, but maybe the flower decided not to shower us with its best quite yet.

Six quirky facts about the titan arum lily:

  •  Amorphophallus titanum, commonly known as ‘the stinky flower’, is endemic to island of Sumatra in Western Indonesia. The Indonesian word for the plant is bunga bangkai which literally translates as ‘flower’ ‘corpse, cadaver, carrion’. A pretty descriptive name. The chemicals released from the spadix have been tested, and the results show that the flower’s smell is a result of the production of chemicals like isovaleric acid (sweaty socks), trimethylamine (rotting fish) and indole (like human feaces). These smells attract insects, flies and carrion beetles, and they act as pollinators.
  • The reason why people flock to see the flowering of the titan arum is the rarity of its flowering. A first-time bloomer won’t flower until between 7-10 years old. After the first flower, some plants might not bloom for another 7-10 years, though others may bloom every 2-3 years. The plant must replenish energy spent from flowering, so every year that it doesn’t flower it sends up a leaf shoot.
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Non-flowering titan arum – the plant sends up a single leaf with a large surface area to maximise photosynthesis. [Photo credit Olivia Cousins, Adelaide Botanic Gardens]

  • Once the flowering has started, it will only last for 24-36 hours. The blooming generally starts overnight, as that is when the pollinating insects are most active.
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Flowering titan arum – the burgundy sheath wrapping the base of the inflorescence (flowering structure) is called the spathe, and it protects the female flowers which sit towards the base of the spadix (spike). The male flowers cover the spadix from the base upwards. [Photo credit Olivia Cousins, Adelaide Botanic Gardens]

  • It holds the record for having the largest unbranched inflorescence (flowering structure), reaching over 3m in some cases!
  • Sir David Attenborough actually coined the name ‘titan arum’ in his documentary The Private Life of Plants.
  • The titan arum is classed as vulnerable due to the increasing rate of deforestation. There are over 170 different species of titan arum, so efforts are continuously being made to try to cultivate titan arums in glasshouses and botanic gardens to ensure conservation of the species.

A celebrity of the plant world, it needs 7 years to get ready for its dramatic red carpet event.

#naturefreaks

Meristem Journeys’ first steps

Woke up this morning to this delightful little summary blog from WordPress. Over the last 8 months that I have been writing my blog, I have had 470 views, and numerous likes and comments. Not bad going for a blog that I thought no one would read!

But in the last month, two people have kindly shared my blog post ‘Genetic modification with a twist’. That possibly was the hardest post I’ve written! It’s not always easy conveying information from a scientific paper littered with complex words that I don’t even understand.

I have loved plants and all things related to their science and discovery since I was very little. Over the years, as I went through school, sixth-form college and then university, many of the people I met would often say, very respectfully, ‘plants don’t really interest me’ or  ‘plants are boring’. And I get that. I understand why the majority of people don’t have the same love and enthusiasm for the green things that cover our planet. Simply because they don’t move around like animals. But I can’t help but notice that part of the reason is to do with the way it is taught in schools. Whenever the topic of photosynthesis or plant anatomy came in Biology class, it was always taught the same way, with no umph of enthusiasm and with no room for creativity or originality. If I didn’t love plant science so much, I would have been bored.

So it was only in my final year of university that I toyed with the idea of a blog. I knew I couldn’t make people love plants. All I wanted to do was to give people a better understanding of them. I wanted to share little snippets of plant-related facts. Some you may already know, some you don’t. But it was also about explaining things in a way everybody can understand, from those with a completely different science background, to those who have never studied science. It was about making people more aware of what goes on around them, and bring back people’s inquisitiveness about life.

Having read my blog’s summary, it makes me happy knowing some of my posts have made their way around the world to various people. I basically wanted to write this to say thank you to my readers that have followed this blog since its beginning, and I hope you have found enjoyment in learning new things.

As the physicist Edward Teller once said, “The science of today is the technology of tomorrow.”

Happy New Year!

Olivia 🙂

The WordPress.com stats helper monkeys prepared a 2015 annual report for this blog.

Here’s an excerpt:

A San Francisco cable car holds 60 people. This blog was viewed about 470 times in 2015. If it were a cable car, it would take about 8 trips to carry that many people.

Click here to see the complete report.