Creatures of the Blue Lagoon: Algae, The Atmosphere, and Animals.

Creatures of the black lagoon: Algae, The Atmosphere, & Animals.

It’s widely accepted scientific fact that millions of years ago, ‘life’ heaved itself out of the oceans and on to land, kickstarting this weird and wonderful world and we know (and love?) today. What’s not so clear, is how our prehistoric primordial partners got their act together.

Research published last week in Nature by a research group from the Australian National University, claim they’ve hit the biological jackpot, giving life as we know it an origin story, at last.

The Cryogenian period (approximately 720-635 million years ago) is most famous (amongst very specific circles) for allegedly seeing the largest glaciations across the globe, covering most of the earth’s surface. This is a relative controversial topic amongst geologists, however what really matters, is that during this period, bacteria were thought to be the only living organisms occupying our planet.

A glacier in Iceland

The research team, led by Jochen Brocks, identified trace amounts of fat, the most stable molecular compound over vast time periods. This algal-specific fat is very close to the cholesterol in our own cell walls, and luckily, was well preserved in sedimentary bedrock from the Cryogenian period, found in Australia.

A fresh water algal bloom

What’s so important about algae? Algae are small, photosynthetic microorganisms, occupying both fresh and marine water. They are at the very bottom of the food chain, and therefore be eaten and their energy passed upward to larger organisms. This sudden algal bloom and explosion in marine algal biodiversity at this period, arguably kick started evolution and development of larger and more complex land animals, giving rise to the massive speciatic diversity we see today.

In a quote taken from a BBC interview, Brock claims, “”The signals that we find show that the algal population went up by a factor of a hundred to a thousand and the diversity went right up in one big bang, and never went back again.”

Noah Planavsky, an Assistant Professor at Yale University provides crucial geochemical evidence about phosphate, an inorganic chemical vital for all plant life today. Brock believes that glaciers ground up rocks holding onto phosphate as they moved across the earth, releasing this crucial nutrient into the seas.

A fossilised fern from approximately 500 million years ago

Phosphate and derivatives are crucial to biological life, forming part of the universal energy currency, ATP, which powers every single living cell. It also forms the backbone of our DNA molecules, meaning all this extra phosphate, may well have kicked started the evolution revolution.

Photosynthetic organisms, like these ancient algal species and the complex higher plant life we see today, produce oxygen as a by-product of light-driven energy production. This added increase in atmospheric oxygen levels, driven by this massive algal explosion, may have contributed to increasing oxygen levels, helping higher organisms like us evolve.

You can find the original Nature article by Brocks et al., here.

And the Nature paper by Planavsky describing phosphate deposition, here.


Imagining Imaging

A very quick post today! Here’s an image of an Arabidopsis primary root, showing the plasma membrane of the cells in red (if you aren’t sure who or what Arabidopsis is, check my last post, here). The green signal is GFP, or green-fluorescent protein. GFP was isolated from jellyfish Aquorea victoria, and fluoresces (glows) bright green under the right conditions.

INTACT August Confirmation.lif - INTACT FM4-64.png
Arabidopsis thaliana primary root with stained plasma membranes (red), and green fluorescent protein tagged nuclei, in the central stele.

This image is generated with a confocal microscope, a very powerful piece of equipment for any molecular biologist. It’s a big improvement on a standard microscope, as a special ‘pinhole’ eliminates out of focus light. A laser of a specific wavelength hits the target (our root), and a sensor detects the emitted signal. This is digitised, and shown back to us on our computer screens screens. This technique is called laser scanning confocal microscopy (LSCM).

In this case, one laser (488nm) was used to excite both the FM4-64 stain, and the GFP tag on the nuclei in the central tissue type (stele). This is because FM4-64 and GFP are both excited by similar wavelengths, but emit light at different ones, which is why I set FM4-64 to be red (a longer wavelength on the spectrum). It’s important to note that the GFP is internal to the plant, but the red stain was introduced so I could visualise the root better.

Where GFP and FM4-64 emission wavelengths fit in on the electromagnetic spectrum. Visible light takes up a tiny proportion. (Image adapted from

You’re probably wondering how the GFP gets into the plants in the first place. In brief, it’s a process called transformation, most commonly mediated through a process called floral dipping, where the flowering buds of a plant are dunked in a bacterial solution, where the bacteria contains GFP and all the other bits and pieces you need.  The plants are then grown and chosen for their GFP signal. We call these ‘stable transformants’. If this seems like a lot to take in, don’t worry! I’ll have a quick and easy illustrated floral dipping guide up soon.

Why am I doing this? I’m checking to see if my GFP signal is there (it is!), my GFP-tagged cells will then be sorted through a FACS machine. FACS stands for Fluorescent Assisted Cell Sorting, and works by separating fluorescent cells (green) from non-fluorescent cells (red, as the stain in the above image was introduced by me). Then, we have two specific populations of cell types. We can do loads of different things we these cells, but these ones will have their genomic information extracted, examined, and compared, helping me understand how different tissue types in root systems work.

Got any more questions? Tweet me @emilyXarmstrong or, leave a comment below. Catch you next time!



Plant Model Species: Who, What & Why?

Plant life: Model plant species: Who, what, and why?

Every sub-section of biology has a model species that every biologist loves (or loathes). A model species is a well characterised and easy to grow organism, often with a fully sequenced genome. This makes it way easier for biologists to understand, investigate, and uncover new information and translate. Once this new finding is discovered in one model species, more often than not, it’s also found in a close evolutionary partner. This then gives us insights into how a particular pathway, mechanism, or response is conserved across species, or even entirely different biological kingdoms. Model organisms are also chosen based on behavioural similarity. You may think human beings are a cut above the rest, but you’d be surprised how similar we are to our ‘distant’ cousins.

Mammalian genetics mostly revolves around two very unassuming heavyweights: the fruit fly and the zebra fish (AKA Drosophila melanogaster and Danio rerio) (and no, the second isn’t a Game of Thrones character). The fruit fly has a tiny genome, which means nearly every biological function is mapped, and characterised. Fruit flies are especially well suited to developmental biology: how an organism grows, from fertilisation through to a fully differentiated and functional fruit fly.

model organisms
A fruit fly (Drosophila melonogaster) and a zebra fish (Danio rerio), common model organisms used in developmental human genetics

What about zebra fish? They first made mainstream news headlines in 2003, when glow in the dark fish were introduced to US markets, based on the work of Singaporean scientist, Dr. Zhiyuan Gong. Initially, these fluorescing fishes were developed as a toxicity sensor for polluted rivers in the fish’s native India. But, the ingenious sensor was capitalised on, and you can now buy GloFish® in aquariums up and down the US.

Danio GloFish, harbouring a gene isolated from a jellyfish

Moving on from fish and flies, it’s time to look at plant science’s big guns: a weed, and a highly regulated addictive substance.

Arabidopsis thaliana (ara-bid-op-sis tha-lee-an-a) is commonly known as Thale cress. It’s a small, radial plant, with leaves growing flat to the ground, shooting flowers near vertically up. It can grow nearly anywhere, in a variety of harsh conditions. It’s also a global plant, so different accessions (the same species identified from a different location) allow plant scientists to unpick what makes these plants tick under a variety of different stressors.

Arabidopsis is dicotyledenous, meaning when it first germinates from a seed, two tiny ‘leaflets’ (not the kind the takeaway puts through the door) are produced. From there, two ‘true leaves’ are formed, and the plant continues to grow. Underground, a taproot system forms: think of a carrot. There’s a main root, with a series of lateral roots, which forage for nutrients and water in the soil, to ensure a healthy, happy plant. Arabidopsis plants grow fast, are hardy, and can be made to harbour specific genes of interest (yes, this includes glow in the dark proteins!)

So, what about this addictive substance? It’s tobacco! Most labs use either Nicotiana benthamiana or tabacum. Benth is standard tobacco’s smaller, more flimsy cousin, but both are frequently used in plant labs all over the world. So, why use tobacco? It’s no secret, for corporate tobacco companies, it made a lot of sense to get their best selling product sequenced. Before this, loads of information had already been accrued, given its importance socially, historically, and economically.

Model plant species
A: Arabidopsis thaliana (Thale cress) B: Nicotiana tabacum (Tobacco). 

Tobacco can be used as a model for crop species, as it’s more closely related to barley, wheat, and rice. N. benth is also used for virology studies; helping plant scientists understand the diseases that kill off our food supplies every year. Unlike Arabidopsis, tobacco has a fibrous network of roots.  It’s also useful for ‘transient’ studies, a gene or fluorescent tag can be introduced to quickly check that your experiment is going smoothly, before you ‘stably’ transform Arabidopsis. The downside to tobacco is it’s huge, in size and genome. This makes it much harder to ‘genetically’ navigate and characterise. To stably transform tobacco, it’s not nearly as easy as its weedy counterpart, it needs to be morphed back into a stem-cell-like blob (called a callous), before turning back into a fully functional tobacco plant. Cool, right?

This is just the tip of the botanical iceberg, as we all know. Check back soon for more insights into the weird world of plant science.

Interested in knowing more? Tweet me @emilyxarmstrong, or comment on this post.



So why study plants in the first place?

So why study plants in the first place? Climate change, crops, and crises.

It’s no secret that our fragile planet is changing at a rapid rate (unless you’re Donald Trump). Our population is booming, our cities are growing, and our fresh water supply is shrinking. All whilst our temperature and weather extremes become, well, increasingly extreme. Biologists, chemists, physicists, geologists, scientists, are rapidly trying to invent ingenious solutions to the problems that climate change is presenting.

As a plant scientist, my work focuses on improving plant species to cope with the challenges our climate will bring. These include, drought, flooding, heat, salinity, insect pests, temperature extremes and heavy metal contamination.

Rice, growing here in China, is especially susceptible to flooding risks

Plants are responsible for everything we see around us. Plants as we know them first evolved from microscopic photosynthetic algae around 450 million years ago. They began to produce oxygen, a by-product of photosynthesis, where plants use light to produce energy. This oxygen built up in the atmosphere, providing the perfect starting point for other life to flourish. Even now, plants are responsible for virtually every breath we take. They are also the building blocks of our diet: we can either eat the plants, or eat animals reared on them.  In fact, the whole of humanity is based around hunter-gatherers settling down to begin agriculture and farming.

Wheat growing in the UK

A plant scientist’s work stems from trying to stabilise food security and food sovereignty. Security focuses on four pillars: access to nutritious food (is the food supply chain robust?), availability of suitable food (do people have access to available food?), utilisation of food (is it safe to eat?), and finally food stability (is there enough food to last the winter?). These four fundamental questions guide a plant scientist’s journey into improving what we eat, and how we access it.

Encroaching desert in Africa

Food sovereignty asserts that those who “produce food, distribute, and consume food, should control the mechanisms of production and distribution, rather than market leaders”. This provides a conundrum to the plant scientist: a lot of our work is funded by so-called ‘market-leaders’, but we want to help people directly affected by climate change.

There are loads of ways for us to improve plant resilience; we can help the plant make more of a specific gene, which might improve how a plant copes with heat. We can help the plant make less of a different gene, which might improve how a plant copes with extra salt in water. We can even change entire networks of genes to improve a response to a stress. The possibilities are practically endless. But, as plant scientists, we also need to make sure that our work is ethically sound.

So there we have it, plants are the building block of our entire world and food supply. Without them, we would be nothing. Climate change destabilises our food supply, meaning we need to come up with creative solutions to help our plants, food, or otherwise, thrive.


Since I’ve started my PhD, I’ve found it difficult to tear myself away from the lab, the office, the mentality of ‘constantly-thinking’. I’m pretty sure nearly every other PhD student feels the same way, but it’s pretty hard  to work out how to stop. This weekend I decided to really challenge my body (& mind) by completely detaching myself (even just for half a day) by travelling to Finnich Glen, a beautiful gorge just north of Glasgow.

A quick ten minute walk from the road through woodland led us to the entrance, a steep 20 meter drop with some old stone steps, and lots of ropes.

We were greeted by stunning greens and reds, beautiful fern species, and perfectly clear water. There were a few other people there too, but not enough to disturb us.

Scrambling to the pulpit itself was a challenge for me, as I’ve only just gained enough confidence & muscle tone to really push myself. Shedding the shoes and heading in barefoot (up to my knees) across slippy rocks under water, it was well worth the struggle.

Even though it was a small escape, it’s left me feeling recharged, with a fresh perspective on my research. What seemed to be massive problems on the Friday had shrunk to small, manageable ones by Monday, and all it took was a slight change in perspective. I’d urge all PhD students to get out, escape, and immerse yourself in something different and new, even if it’s just for a day.