Where’s the lettuce? Food, Brexit, & Climate Change

*Re-printed with permission from TheGIST: Glasgow’s Insight into Science and Technology, originally published on 18th August 2017*

Disabled & STEM: Reality checking

I’d never considered myself to be disabled until the last few years. I grew up as an Irish dancer, cross-country runner, climber of trees & rider of bikes. Slowly but surely, my ankles started turning purple, then they stopped moving properly. Then my knees hurt, all the time. Then a weird cracking in my neck started. By the age of 13, my shoulders started dislocating. My doctors told me I was double jointed and I’d grow out of it. Except, it just kept getting worse.

My first double knee dislocation aftermath: Crutches for the rest of my life!

I was diagnosed with Ehlers-Danlos Syndrome (Hypermobility Type) when I was 21, 11 years after I first went to a doctor about chronic joint pain. It took me 5 years of self advocacy to get them to pay any attention, and it was only once I started my genetics degree they took me seriously. EDS is a cluster of dominantly inherited connective tissue disorders, affecting collagen biosynthesis, stability, and regeneration. Some people’s cardiac tissue is weak, other people’s skin is incredibly loose and stretchy. Mine manifests in partial and full dislocations of my elbows, wrists, shoulders, ribs, knees, ankles, and hips. These partial dislocations happen daily, with minimal pain. Full dislocations are agonising, but I can often relocate myself. Saturday was a different story.

Suited and booted after my lungs shut down due to dysautonomia

I slipped on a wet pub floor and didn’t have my crutch to hand to stop me falling. I dislocated my left leg in a way I’d never managed before. I relocated it, and then collapsed from the pain, dislocating it again. This time I couldn’t move, or speak.

I waited an hour and a half for an ambulance, was taken to A&E, I think it went like this: x-rays, morphine, CT scans, morphine, gas & air, more morphine, was relocated, and sent home. I got back in at 7am.

Bossing it at the gym with my resistance bands, elbow crutch, & holter heart rate monitor in January 2017

72h later, I still can’t walk properly. The pain is so ridiculous I can’t stand up, sit down, or use the loo safely. I’ve “destroyed” my muscles that hold my leg in place, and have no access to physio to fix it, currently.

This is the harsh reality of being disabled. I got into the lab yesterday to do some basic stuff, and I’ll try and go again today. All I can do at this stage is keep persevering. I’ve got plants to water, growth rates to measure, seeds to sow, RNA sequencing data to analyse. It’s not going to do it itself, and I’m not going to let my disability stop me from doing it, either.

Me, very, very, very high on morphine, 1st October 2017

The only way I’ve found to manage my disability in academia is by laughing, having fun, and being stubborn. As time goes on, maybe I’ll hit the disability management jackpot, but for now, I’m gonna spend the day resting in bed, and ask someone else to help do my work with me. Science is unrelenting, and so is disability, but the biggest progress I’ve made in the past year is admitting when I need to put myself, and my health first.

Sometimes, the science can wait.

I am proudly disabled, I am proudly a woman, and I am proudly a scientist.



TheRadicalBotanical on Instagram!

I’ve started up an instagram account for my blog, documenting day-to-day life in the lab, click here to follow!

Or, you can find my profile on the right hand side of this site, under the live Twitter feed.

I’ve been so busy finalising my Masters by Research thesis, I’ve really let my blog post content slip recently (AKA I haven’t posted for a whole month…) But, once this thesis is in next week I’ll be right back at it.

I’ve been playing around with imaging actively dividing DNA in the root apical meristem. The green blobs are nuclei, containing DNA. If the nuclei are fluorescing green, it means the DNA has actively replicated in the past 24h. All of these are green as the apical meristem drives root growth through active cell division, meaning all of these cells are brand new. I’m hoping to use this technique to better characterise how root meristems grow and produce new cells under different conditions, and in different knockout mutants. This way, we can understand how and if different genes regulate cell division and DNA replication.

WT_pilot_EdU&Fm464 13.9.17

The black part is the quiescent centre, a very important part of the meristem which ensures the right tissue types are produced. It divides only very occasionally, meaning no new DNA was produced here during the 24h incubation. The red part surrounding the cells is FM4-64, a plasma membrane stain which shows us the outline of the cells.

Cool right?



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 quora.com)

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!