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.

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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.

Winter is coming – time to leaf

Seeing all the beautiful colours of the trees against the backdrop of a swirling autumnal sky, made me want to recap on why some plants lose their leaves in such a kaleidoscopic fashion.

Leaves act as mini factories for plant food production. When light hits the leaf surface, it becomes part of an essential chemical reaction. When carbon dioxide and water are combined with energy from light, the result is glucose (sugar) and oxygen. Chloroplasts within leaf cells are responsible for this reaction. The plant uses up the glucose, but the oxygen is released into the atmosphere.

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Simple photosynthesis equation.

In temperate regions, as the days become shorter and colder, the levels of light are not sufficient enough for plants to photosynthesise. One way many plant species have of adapting to this environmental change is to slow down or halt photosynthesis during winter months. One by one, leaves start to shut down their chloroplast factories; no more sugar is being made. Plants are able to live off sugars they have already stored away.

Chlorophyll is a green pigment which resides in the chloroplasts, and is necessary in helping to create glucose from carbon dioxide and light. Other pigments, such as carotenoids and anthocyanins, are also present in leaves, but they are usually masked by chlorophyll. However, when the chloroplasts begin to shut down, chlorophyll is no longer being produced in order to save the plant’s precious energy. The oranges and yellows result from higher levels of carotenoids, whereas anthocyanins are responsible for the red hues.

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Autumn leaves showing different pigments – anthocyanins (reds) and carotenoids (yellow/orange). [Picture credit Olivia Cousins]

Cell layers start to build up between the leaf and stem, slowing down the transport of sugars, water and nutrients in and out of the leaf. Once the final cell layer, called the abscission layer, is formed, the leaf drops off. It results in a clean break, and entry to the leaf stem is sealed shut, preventing excessive sap loss. Formation of the abscission layer can also act as infection prevention. Leaf cells are filled with water and can be susceptible to freezing, particularly thin leaves, e.g. maple leaves. Freezing inevitably kills the leaf , causing the leaf to wither and fall away from the stem, leaving an open wound. This wound becomes an easy pathway for infection and could cost the plant it’s limb, or its life.

However, some trees don’t fully lose their leaves, even when chlorophyll production has stopped. For example, oaks and beeches don’t fully form their abscission layers until much later, so although many of their leaves freeze over and die, they remain on the branches until new leaf growth pushes them off in spring. This phenomenon is known as marcescence.

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Beech leaves showing marcescence.

The lengths plants will go to in order to protect themselves is fascinating, and yet there is still more that remains to be uncovered. If we can understand the processes that drive plants to photosynthesise, then maybe we can use it to improve photosynthesis of crops, increasing growth and yield. It’s one way to save agriculture.

Winter is coming, but new discoveries might just be around the corner.

Genetic modification with a twist!

DNA editing has always been a controversial topic, with many countries around the globe, particularly in Europe, refusing to grow or import crops that have been genetically modified. General concerns range from risk of cross contamination of GM crops with non-GM plant species, to risks to human consumption of GM foods.

Many experiments have been run to test different outcomes and effects of genetically modified crops, to identify advantages and any disadvantages or risks to cultivating GM on a commercial scale. Several countries already grow a considerable amount of GM crops, though most of these crops are for animal feed or for use as biofuel, with the US, Argentina and Brazil as the biggest growers of GM.

Because of the concerns about GM, scientists are now trying to find other ways to manipulate plants in order to improve crop production. And we might have a possible solution.

A team in South Korea, led by Je Wook Woo at the IBS Center for Genome Engineering in South Korea, have recently published a paper, outlining their most recent experiment, where they managed to edit and manipulate plants without inserting foreign DNA into the genetic code. As it stands, conventional genetic modification results from inserting DNA from another species of plant or other organism into the chosen plant for modification.

Here’s some background information. Genome editing has actually been used for quite a number of years, used to enhance many beneficial qualities in crop plants. It creates very precise targeted mutations within the cell and uses artificial enzymes – molecules which create breaks in the DNA sequence. Under natural circumstances, if a break occurs in the DNA sequence within a cell, the cell will automatically try to repair it using one of two repair mechanisms, either non-homologous end joining or homologous recombination.

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A single stranded break, or double stranded breaks can create mutations in DNA.

Non-homologous end joining basically involves joining the broken DNA strands together, and is really susceptible to errors, often mutating and inactivating a gene as a result. However, if the cell has a suitable DNA template available for repairing the broken DNA strands, it will recreate the DNA sequence that was lost or broken via homologous recombination. This process of homologous recombination is actually more accurate, so you get an exact copy of the original DNA sequence, and everything is as good as new.

Scientists can artificially make breaks in the DNA sequence of a plant using an artificial enzyme. Instead of allowing the cell to provide its own repair template, scientists can provide a synthetic repair template. The synthetic repair template could be a new DNA sequence which codes for a new gene, for example giving the plant resistance to a particular disease. One genome editing technique used is the CRISPER-Cas9 system.

This system was first identified in bacteria, as part of their immune system response if under pathogen attack, and scientists thought it would be a good idea to use it for targeting genes for genetic modification. The CRISPR-Cas9 system uses a molecule, called a single guide RNA, to find and latch onto a gene which is the target for genetic modification. An enzyme, called Cas9, comes along and breaks up the targeted gene. The cell then repairs the broken DNA sequence using a synthetic repair template. And voilà you have a new gene incorporated into your plant’s DNA.

What Je Wook Woo and his team did was create pre-assembled ribonucleoproteins, which are effectively protein-RNA complexes. They mixed the Cas9 enzyme with single guide RNA molecules which targeted genes from 3 plant species. Once they had this mixture of molecules, they infected plant cells from tobacco, lettuce and rice with it to create mutations in the target genes.

Nature article Je Wook Woo

Lettuce seedlings with the edited DNA sequence (taken from Je Wook Woo’s paper, see link below).

The results were that the Cas9-ribonucleoprotein complex created mutations in the target genes of the plant cells immediately after infection. The Cas9-ribonucleoprotein complex was quickly degraded by the cell once it had created the mutations so it couldn’t mutate anything else in the cell. The bonus factor of this experiment, was that these gene mutations remained in the DNA even after the plant cells had regenerated themselves. The team was able to grow seeds from the plants with the edited DNA, and the offspring still maintained the genetic mutation.

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Different stages of tobacco plant cell regeneration, showing wild type (WT) and mutant (bi-allelic KO) plants (taken from Je Wook Woo’s paper, see link below).

No need for inserting foreign DNA as a repair template!

The IBS team have made a revolutionary discovery; they have now paved a path to engineer plants that might not be subjected to GMO regulations, since foreign DNA was not actually inserted. Hopefully, in the next few years, we can see some more progress in this area.

Saving agriculture one cell at a time!

Link to journal paper:

Woo, J. W., Kim, J., Kwon, S. I., Corvalan, C., Cho, S. W., Kim, H., Kim, S.-G., Kim, S.-T., Choe, S. & Kim, J.-S. (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnologyhttp://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3389.html

The life of plants with Jagadish Bose

Recently, I’ve been reading a lot more into various scientists prominent in the field of plant science, and one that has captured my attention is Jagadish Chandra Bose (1858-1937). Known for being a polymath, an expert in various branches of science, he was passionate about physics, biophysics, biology and archaeology research. Not to mention plants.

Bose was born in what is now Bangladesh, and received degrees from both the University of Calcutta, and University of Cambridge. In his some of his earliest research, Bose invented a piece of equipment that could generate electromagnetic radiation and subsequently detect and receive 5 millimetre long microwaves. However, at the turn of the 20th Century in 1901, he decided to turn his attention to plants and their movements and electrical signalling.

He designed experiments to test plants’ sensitivity to various stimuli, such as light, heat, wounding, chemicals, and noise. In order to test his hypothesis that plants can ‘feel pain, understand affection’, he designed an instrument that could both observe and record the plants’ responses to these external stimuli. Simply put, the crescograph measures growth of plants. Bose wanted to use it to calculate the growth rate of plants when exposed to heat, light, or chemicals.

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A crescograph at the Bose Institute in Kolkata, India.

In 1901, on the 10th May, Bose took his research and crescograph to the Royal Society in London, to demonstrate his findings. One experiment using the crescograph detailed a plant delicately attached to the ends of wires, the opposite ends being attached to finely tuned clockwork. The plant was subjected to a poisonous solution of bromide, either through its roots or leaves. As the plant absorbed the bromide, this ingenious piece of machinery documented the plant’s response by detecting a series of minute vibrations or movements and recording them onto a smoked glass screen. These measurements were taken at really short time intervals, from less than 1 second to 2 seconds. Within minutes, the vibrations increased violently, and then quickly stopped. There was no further response from the plant; its exposure to the poisonous chemical resulted in its death. Bose actually compared it to a rat dying from poisoning.

From his many experiments, Bose began to notice that plants used a form of electrical signalling between their cells in order to respond to external stimuli. He then tried to prove that these electrical pulses or signals were responsible for the minute movements or vibrations that plants made. Bose also used electrical probes attached to different parts of the plant to measure electrical currents moving through the plants as a result of a response to a stimulus, i.e. a wound.This helped to further cement his idea that plants were responsive and attentive to the world around them.

Although his contributions to engineering and physics were applauded and respected, in his plant physiology research, Bose was deemed quite controversial. The famous playwright George Bernard Shaw once visited one of his demonstrations and was said to be horrified at a cabbage ‘convulsing’ in boiling water.

Nowadays more scientists are gaining interest in Jagadish Bose’s work with plants and the crescograph. The crescograph has actually been modified, and research is now conducted around the world, looking into the hows and whys of plant communication and response mechanisms. Why is this important? Our environment is changing. If we can understand how plants both respond to their surroundings and communicate with each other, then maybe we can anticipate future environmental and biological changes.

What more are plants not telling us?

“The science that will transform our future.”

This blog post was written last month for a science communication competition, in which we had to write an article about the science that we thought would transform our future.

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The art of science has changed dramatically over the last 100 years, and it continues to change and evolve as time passes, and as we gather more information about the world. From Isaac Newton’s discovery of gravity, to Gregor Mendel’s realisation of the rules of genetics using humble garden peas, to Charles Darwin’s proposal of the theory of evolution, science encompasses so many different topics, and each of them are all applicable to our lives in one form or another. But have you ever wonder how many scientific discoveries can be attributed to plants? Plants have helped shape the world, and are necessary for survival. The things that are possible with plants are boundless, and here are just a few of their potentials.

As more land is being used up for infrastructure, housing, mining and agriculture, the race is on to find suitable land for raising even more livestock and growing crops to cope with rising population numbers. When all the suitable fertile land is expended, we will have to turn to less fertile land or brownfield sites contaminated with hazardous wastes, such as deserts or abandoned mines, respectively. If it were possible to produce crops on these soils, it would both jeopardise their health and yield. The use of genetically modified (GM) crops, aquaponics, and phytoremediation are three possible solutions to this problem.

Although heavily controversial, GM has the ability to transform global agriculture, by increasing crop yield and tolerance to saline soils, drought conditions, toxic metals or pesticides. A really good example of how genetic modification was successful can be seen with the case of drought-tolerant barley. Scientists from the John Innes Centre, alongside the University of Jordan developed a barley variety that is four times as drought tolerant than its parent stock. Dr Wendy Harwood, at the John Innes, explained that due to poor water availability in many countries, GM can definitely make a positive impact, especially when we consider that approximately 70% of global water is used for agriculture. They were able to identify a gene that regulates opening and closing of stomata, the small pores on leaf surfaces. The gene was subsequently altered so that during times of water scarcity, the stomata would close, thus avoiding water loss through these pores, and therefore being more drought resilient.

Plants also have natural abilities to adapt to environmental changes and develop new tolerance strategies. Phytoremediation, the use of plants to clean up both soils and water of toxic waste metals, has shown to be a promising technology, not to mention environmentally friendly. The most commonly used method is phyotextraction, where plants accumulate heavy metals from soils, which are then extracted and safely treated. These hyperaccumulator plants absorb metals, chemically bind them to organic compounds, and sequester these modified compounds in storage vessels within their cells, thus avoiding metal poisoning and damage. A high biomass and ability to accumulate metals quickly and efficiently are the two most desirable traits in a hyperaccumulator. This can be further enhanced by using genetic modification to generate plants more tolerant to toxic waste substances, and modify their uptake and regulation in the plant.

Deserts or areas of soil infertility could still be used to grow crops without the excessive need for fertilisers with the help of aquaponics. It combines the raising of aquatic animals, such as freshwater fish (aquaponics), with growing plants in water (hydroponics). The plants get their necessary nutrients from the aquaculture effluent which is fed into the hydroponic system. Any organic matter in the water is broken down by nitrification bacteria, which convert ammonia into nitrates for plants to absorb. Once the water has been stripped of its nutrients, it is oxygenated and recycled back into the aquaculture tank. This system has been successful with several vegetable varieties, including lettuce, tomatoes and peppers benefiting from this symbiotic environment.

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Aquaponics growing system

None of these three technologies are perfect, and they lend themselves to further study; but the possibilities are endless. This is an opportunity to use science to counteract climate change and improve lives through increasing food provisions to avoid malnutrition and starvation.

But in the meantime, it’s back to the lab.