Plant-based biomaterials: engineering the future

I’m lucky enough to have been invited to write for The Biochemist Blog – an online sister publication to their popular in print magazine.

This edition they’re discussing biomaterials, so I jumped on board to share the newest insights into plant tissue engineering and repurposing in biology today.

You can find the article here.

I discuss apple pectins as bone in-growth promoters in dental implants, apple derived cellulose as a scaffold for cell colonisation, and re-purposing spinach leaves as a scaffold for heart tissue growth.

I’d love to hear your feedback!

Meet The Scientist

I was featured in Erica’s ‘Meet the Scientist’ series. Check it out for my thoughts on disability, changing the old-boys-network of science into something more accessible, and what I get up to with my spare time.

A scientist called Erica

Hello everyone and welcome to the latest “Meet the scientist”!

In this series I wanted to show you the range of research being undertaken by PhD students across the country- specifically in the area of Plant science, and shine a light on the secret world of the PhD student. The scientists showcased in this series are all amazing scientists and role models, and will be sharing their stories about life as a Scientist- I hope they interest and inspire you!

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HOW TO: deal with failure in a PhD

I’m writing this as I’m sat in the postgrad office of the Plant Science Department at the University of Warwick. This trip, including reagents, time, hotels, food, and travel, has cost well over £1000 for five days. I’m writing this because my experiment, which I’ve been planning for over 4 months, is no longer viable because of an equipment failure. I’m writing this because I need to remind myself not to beat myself up about something outside of my control. I’m also writing this because if I stress eat any more yoghurt, I will become yoghurt.

There’s no two ways about it, PhD’s are no walk in the park, even for the most experienced and innovative researcher. What works one day might completely stop working the next (and for forever), and it can seem completely overwhelming when everything grinds to a halt. Whether it’s writer’s block, literature overload, or equipment failure, there’s nearly always a way to fix it.

I’ve summed up some of my tips for researchers for successfully navigating equipment failure, result crises, and most importantly, the often crippling self-doubt which invariably accompanies research.

Practical solutions to impractical problems

  • The problem: When well-optimised experiments fail.

It is infuriating when a perfectly optimised and easy-to-follow experiment just stops working. It’s very easy to blame it on the direction of the wind, the day of the week, or an undergraduate. It’s definitely a lot less easy to logically trouble-shoot.

The solutions: draw the steps you normally take to prepare your experiment on a blank page in your lab book. The reagent preparation steps, the centrifugation & mixing steps, the volumes you need, and what you do with them. What temperature do reagents need to be stored at? What kits do they come from? This logical flow chart will show you which crucial steps could determine experimental success, and will provide a handy visual how-to for any future students.

Now you know the workflow off by heart, investigate your reagents one-by-one. Are they being stored in the right temperature or darkness? Are they way past their expiry date? Have they mysteriously reappeared after someone else used them? Has the kit changed slightly or call for a new buffer? Logically interrogate every single variable, and more often than not, you’ll find the culprit. If everything seems in order, ask a more senior researcher, or field your question to useful forums like Bitesize Bio or ResearchGate.

Science is about trial-and-error, and there’s almost definitely someone else out there who can help solve your problem. Or, it may be down to…

  • The problem: Equipment keeps breaking.

On an equal par with experimental failure, broken equipment is impossibly annoying. Thermocycler shut down? UV visualiser for gels broken? Spectrophotometer giving you ridiculous readings? Plant growth-room overheated for the 18th time this week? Take a deep breath.

The solutions: Check with other lab members: are you the first person to experience this problem? If not, someone else might have an innovative work-around that doesn’t compromise your results. Is there another version of the equipment somewhere in your department? Contact the people who own it and dialog with them, they might well be able to sort you out. Contact your technician too, they are invaluable in times of need and will be able to arrange a repair. Most importantly, try not to beat yourself up over it, equipment isn’t psychic and doesn’t know when your big deadline or supervisor meeting is.  If you’re in a large department, see if you, or a technician, can make a list of all equipment available for open use with correct training. It’ll save you in a pinch.

  • The problem: You have results (and have successfully navigated protocol failure and broken equipment), but they are either negative, or entirely meaningless.

The solution: A result is still a result. It’s still a brand new piece of information you didn’t previously have, or wasn’t previously known. The gene you expected to see upregulated under your specific test condition isn’t? Well, you know something you didn’t know before. Science is hypothesis driven, and we need to test our hypotheses to breaking point. Believe it or not, any information is better than none, no matter how frustrating it is. Is there a way this result can be applied to your research, can you explain why it’s happening? If not, then tell your supervisor and try and come up with a new way to find your answer, as infuriating as it may be at the time.

  • The problem: You are doubting your ability as a researcher. Nothing you have tried has worked, and your experiments keep failing. You are struggling to stay motivated and keep your head above water.

The solution: Take a break. It could be a 10 minute break. It could be a 10 day break. Whatever it is, gift yourself some distance, reflection, and wallowing. Constructive wallowing (which I am currently doing by writing this post instead of doing the experiments I should be) can be a relatively productive way to process the issue (my experiment didn’t work, but that’s okay, we can do it again, even if it costs another £1000.) Constructive wallowing only works you’re able to pick yourself back up after your allotted downtime. If you find yourself entirely demotivated, depressed and stressed, then it might be time to take a course of more serious action.

It’s very important to open a dialog with your supervisor or a member of your advisory panel in this instance, they can impart their years of advice, and steer you in the right direction. This is a lot harder if you’re also suffering from Absent Supervisor Syndrome, but you should still reach out with those who’ve completed their PhD.

Coping with feelings of doubt and imposter syndrome are very hard to manage, but everyone in their research career has experienced moments of this, even your esteemed supervisor. Try and talk to other members of your lab over a coffee, ask them about their biggest ‘what if I’m not good enough’ moments. Get their advice, and see how you can adapt your practices with peer reviewed techniques.

If you’ve tried all of the above, and are really not coping with your workload or failed experiments, contact your University’s mental health services. Most universities offer a 6-week intensive course to help you manage stress and anxieties arising directly from your research and workload. If you already have a pre-existing mental health condition, you may be able to use evidence from your GP to get you more long-term, university-oriented support. I’m lucky enough to have a mental health advisor who helps me manage my workload and research activities.

These are all well and good, but if you feel like you’re at your wits end and really need an intervention, you should contact your GP. They may be able to refer you to NHS services to guide you on your way to better coping mechanisms through active, intensive therapy. This may seem like a pretty big leap to make, but it’ll help you excel in your PhD research if it’s really what you need.

To sum, PhDs can often feel like a trial by fire, and problem-solving and trouble shooting is naturally part of the experience. But that doesn’t stop us from responding negativelyto the situations we can find ourselves in. So, what tips do you have for navigating failures in your line of work? Are they common or rare? What would you share with your younger self? I’m going to enjoy my break away from Glasgow, the English sunny skies and the really tasty coffee from the canteen.

 

 

Health, headaches and (six) hundred followers

Yes, yes, I know. This is my first blog post in two months. But, hopefully I’ll be able to make it count. Those of you who follow me on Instagram, @theradicalbotanical will have seen my story asking you if you wanted to see more plant science, or more PhD life posts. Everyone voted 50:50 so I’m going to touch a little on both over two days.

I’ll start with the PhD life part, mostly because it explains my absence. Virtually all of you know I have a list of medical problems as long as my arm, and then my leg. Through blind chance, I inherited a boat-load of messed up genes, and they find new ways to mess me up at every turn.  What I’m not always so forthcoming about, is the way my brain often fails to work too.

One of my conditions is called postural orthostatic tachycardia syndrome (try saying that with a mouthful of peanut butter, I dare you). As described in this post here, it can do ridiculous things to my body. It, combined with a variety of other less-palatable factors, means I’ve spent my life so anxious that receiving a text message gives me physical chest pain. So does people coughing, doors closing, and the start-up sounds of Mac computers. Funnily enough, there’s only so much every-day-every-thing-anxiety you can take before you completely shut down. Which I managed to do in a very big way. I couldn’t get out of bed, and when I could, I couldn’t get to the lab. If I could get into the lab without being sick on my journey (an open apology to those living at number 50) then there was no way I was going to do practical work. So, I didn’t. For a month. I sat, staring at my RNA sequencing data hoping and praying that the answer to my permanent-anxiety-depression-catatonia was somehow hidden away in transcriptional network causality modelling. (Hint: it’s not. Nothing is hidden in the RNA sequencing data apart from data, who knew?).

a lovely gift from one of my thoughtful & brilliant colleagues

My mental health advisor (who is a saint), was genuinely at her wits end, and so was I. I marched to my GP (who is also a saint) and we discussed my options. We tried fluoxetine (Prozac) for a month. I stopped eating and sleeping and stopped doing any work whatsoever. The work I did try and do, I forgot about, everything I tried to do, I couldn’t. I was locking myself in the disabled loo for half the day to cry until I went home for Christmas on the 15th of December. I did manage to give a small symposium presentation without bursting into (visible) tears, but that was only due to diazepam (thanks, b). The day before I left, my GP switched me to a serotonin and noradrenaline reuptake inhibitor, mirtazapine. Side effects: sleeping for 14h per day, uncontrollably intense dreams, uncontrollable appetite increase (I type, after eating my fourth meal of the day). Why am I dealing with these (expensive) side effects? Because for the first time in my life, I am not anxious.   I have been able to make media for my plants, without chest pain. I spoke in front of my lab group without swallowing my tongue and worrying about sounding stupid. I can look people in the eye. I didn’t take my supervisors critical examination of my annual review personally. I thought in a straight-forward, and goal oriented manner. I have designed my experiments for the next 4 months. I’ve achieved more in 4 days than I did in two months. Now I’m not for one moment claiming I’m somehow magically cured of my life-long multiple mental health issues; that would require a complete re-write of my formative years. But I am feeling positive toward my research, I’m not scared of it, it’s suddenly not this impossible-to-navigate byzantine labyrinth of mysteries shrouded in enigma wrapped in confusion. It’s just answering some questions that I know how to answer.

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skwot til u drop (in avo sox)

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I suffer from depersonalisation and periods of dissociation- taking ridiculous selfies is a pretty fun way to combat this.

Over ½ of PhD students will experience mental health problems during their PhD for the first time in their life.

  • Speak to your supervisor straight away. Don’t put it off (unless they’re an asshole).
  • If your supervisor is an asshole, go to your mental health or counselling service. They may offer drop ins, a fixed period of sessions, or, if your GP supports your claim, offer long term support (like I receive).
  • Even if your supervisor is a lovely angel sent from heaven, still go to your university’s mental health service. They can equip you with the toolkit you need to get through your studies
  • Identify your academic triggers: what’s making you feel bad? Your workload? Colleagues? Your office space? Broken equipment? Try and identify where the issues are arising.
  • Come up with practical solutions. Your workload? Reduce it for a month. Colleagues and office space? Ask to switch offices if possible. Or, try doing dry-work from home until you feel rested. Broken equipment or rubbish protocols? Contact your technician or lab manager, alert them to the negative impact it’s having on your work and why it needs fixed Don’t sit on your suffering.
  • Disclose and confide in a trusted friend who works in a similar environment, they may have their own (much better) advice they can tailor to your exact sitatuion.
  • Please don’t suffer in silence! If you are really struggling, go to your GP, call Samaritans, get in contact with your community mental health services.

So now you’ve endured my excuses for not posting anything in two months. I’d also like to celebrate the fact that right now, there are over 630 of you following my Instagram posts! And 30 of you just in the past 10 days. I am truly humbled by the lovely messages and support I receive through insta every day, you’re all stars.

Check out Nicola’s post on Fresh Science here for more mental health truth

and

Check out Rebecca’s fantastic tips on coping with anxiety in a PhD here too.

I should have a post on hormones (the plant kind, not the human kind) up over this weekend, keep your eyes peeled!

-E xo

Disabled&STEM: lab life adjustments

I’ve been getting a lot more attention on Instagram recently, especially with a video of me using a multichannel pipette for some gene expression analysis. The qPCR assay is incredibly sensitive to basically everything, including the DNA destroying enzymes present all over our fingers, hands, and bodies. A few people have asked me why I am not wearing gloves in the video, given it is such a sensitive assay.

The reality of being a disabled scientist is that I cannot always follow conventional lab practice in some instances. I can’t always wear a lab coat, or gloves, or perform shared lab duties, or wash my glassware on time, or use reusable tubes, or lift and change my biohazard waste bin, or be expected to be in for 10 hours a day all week. One of the hardest parts of me adapting to research life was becoming comfortable with my limitations.

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an example of the disposable plastic falcon tube I use to grow my bacterial cultures in, instead of reuseable glass ones.

What’s up with the gloves thing?

In addition to my genetic connective tissue disorder, Ehlers Danlos Syndrome (hypermobility type), which I’ve given a brief overview of here, I also have a form of dysautonomia, called Postural Orthostatic Tachycardia syndrome (POTs). The two are very commonly experienced together.

The autonomic nervous system controls all the stuff in your body you don’t ever need to think about; breathing, heart rate, digestion, heat regulation, blood pressure, dilation & constriction of blood vessels. Mine, for whatever reason, is failing (dys = not working, autonomia = autonomic nervous system)

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Pretty in pink: can you tell what my favourite colour for lab equipment is?

POTS is characterised by an inability to regulate heart rate when you go from sitting/lying down to standing, but has plenty of other symptoms too. When I stand up, my heart rate spikes to 150bpm and my blood pressure drops. This makes me pass out/nearly pass out/appear drunk/slur my speech/forget what I was saying/any combination of the above. This also happens with increases in heat. My body can’t regulate temperature properly, so it gets confused, and makes me pass out instead of actually cooling me down. I am on a very specific (& expensive) beta blocker called nebivolol. It’s specific for my heart tissue, not my lungs, as I’m also severely asthmatic and don’t need my lungs to be anymore slowed down than they already are.

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Unfortunately for me, human bodies are really efficient at losing heat through our feet, heads, and hands. When I wear gloves in a warm environment (like our nice climate controlled lab), I invariably end up feeling incredibly dizzy, sick, and confused. This is because my body forgets how to cool myself back down once it falsely perceives itself as overheating. (This also means as soon as it’s 10°C or below outside, I have to wear the thickest gloves, too).

What about really dangerous protocols? Or RNA sensitive work where your hands might destroy your samples?

There are multitudes of reasons I am studying plants; the relatively low biohazard rate is one of them. I don’t need to work with cell culture, nasty viruses, horrible bacteria, biohazardous materials, or generally other Very Cool but ultimately Very Nasty material that requires a lot of personal protective equipment. Of course I wear gloves for dangerous work, I don’t have a death wish! This does mean I change my gloves every 5 minutes, rest, breathe, and air out my hands to encourage my body to regulate. I’d definitely be a terrible surgeon.

So? Why am I not wearing gloves?

Because I really don’t feel like fainting/damaging equipment/having to fill out safety forms/annoying the building manager/ getting occupational health involved/ making everyone else worry.

But what about your sensitive assays? How does your disability impact those?

Luckily for me, I have a very supportive lab environment. If I really have to do a qPCR or other sensitive DNA/RNA work, I decontaminate my workspace with DNA or RNA away (both commercially available from Thermo-Fischer). I then drench my hands/arms/exposed body parts in 100% ethanol, which gets rid of most nasty things which might perturb the experiment’s function. It’s not ideal, but it’s certainly better than potentially causing myself/lab mates/machines serious harm.

What unconventional lab practice do you follow? Do you do things in your own particular way compared to what you were shown?