Hello and welcome to my blog! My name is Caroline and I am a PhD student at the University of Sheffield. My research project focuses on Striga - a genus of parasitic plants that devastates harvests by infecting food crops. I am exploring the defence reactions that can make host plants more resistant against Striga. Due to my ongoing battles with anorexia, I haven't made as much progress as I would have liked but I am determined to finish the course.
This blog charts the ups and downs of life in the lab, plus my dreams to become a science communicator and forays into public engagement and science policy....all while trying to keep my mental and physical health intact. Along the way, I'll also be sharing new plant science stories, and profiles of some of the researchers who inspire me on this journey. So whether you have a fascination for plants, are curious about what science research involves, or just wonder what exactly I do all day, read on - I hope you find it entertaining!
Tuesday, 29 April 2014
The key difference is that synthetic biology seeks to re-design or introduce complete biological processes. This is done by introducing artificial systems through a "bottom up" approach using DNA "modules" or "parts", a bit like the building blocks found in Lego kits. This is only possible where there is a sound knowledge of the processes concerned, and where they can be introduced without interrupting the normal functioning of the organism.
Plants are attractive candidates for synthetic biology as their cells are split into defined compartments (chloroplasts, mitochondria, etc.), and have well-understood pathways that determine the flow of metabolites. Hence, new functions can be packaged into organelles, where they cannot disturb other vital processes. This concept is highly exciting and has prompted a wealth of inspired "blue sky thinking" projects. Just imagine - what functions would you introduce into a plant? "Naturally fluorescent" Christmas Trees? (Just think - no more tangled wires or broken bulbs on the fairy lights!). "Odour-removing" houseplants that exude pleasing fragrances? Foodstuffs that combined novel or unusual flavours? Perhaps these are more "cosmetic" than useful, but one idea with great potential is the use of plants as biosensors.
Carbon monoxide poisoning is a constant threat from appliances that burn fuel, particularly as this lethal gas cannot be seen or smelt. The gas is produced when there in insufficient oxygen for the combustion process to be complete. Besides causing death, symptoms of carbon monoxide poisoning include headaches, breathlessness, nausea and dizziness. Hence, gas boards and product manufacturers advise clients to be vigilant in checking their homes and appliances regularly. But what if there was a "natural sensor" - a plant capable of giving out a clear signal when CO levels crept dangerously high?
An attractive idea and not as outlandish as it sounds! Professor June Medford from Colorado State University and her group have introduced a similar idea into the model plant, Arabidopsis thaliana (thale cress). Their aim was to design a sensory system for
Synthetic reporter systems are already well developed in plants and include introducing the gene for Green Fluorescent Protein (GFP) from Jellyfish, producing a green glow under standard conditions. The problem with these systems is that they are difficult to reset, and often require specialist equipment to detect, making them unsuitable for constant monitoring. Medford's group decided to use chlorophyll loss, a natural process which we are familiar with during Autumn, when the leaves die (senesce). Normally this occurs very slowly, over the course of several days; for chlorophyll loss to act as a useful biosensor, however, this would have to happen much faster. Outside of Autumn, the chlorophyll pigment is constantly turned over, with levels maintained by balancing synthesis and degradation. To induce rapid chlorophyll loss, the team introduced two synthetic gene circuits that would respond to an input signal by both inhibiting chlorophyll synthesis and promoting breakdown. In this case, the input signal was the synthetic steroid hormone 4-hydroxytamoxifen (4-OHT). To prevent chlorophyll from being manufactured, this gene circuit contained double stranded interfering RNA (diRNA) constructs specific for two key enzymes for chlorophyll manufacture, protochlorophyllide oxidoreductase (POR) and GENOMES UNCOUPLED 4 (GUN4). Interfering RNA constructs work by binding to the mRNA products of target genes (the coding molecules which allow DNA sequences to be translated into proteins) and causing them to be degraded by the RNA Induced Silencing Complex (RISC). This effectively silences the genes, whilst leaving the nuclear DNA intact. The group also introduced a gene circuit which activated the enzymes which break down chlorophyll. Interestingly, when the circuits were introduced to Arabidopsis separately, there was no detectable change in "greenness", suggesting that the plants could compensate by inhibiting degradation or upregulating synthesis. However when both synthetic circuits were introduced, the plants rapidly lost chlorophyll, becoming white within 48 hours. This is a distinct phenotype from the yellow colour which is revealed when the leaves senesce in Autumn - very useful to avoid confusion between a natural process and an alarm system! In addition, when 4-OHT was removed, the plants regained their green colour, effectively "resetting" the system. This is crucial to allow multiple detection and for the plants to act as "long-term sentinels".
Intriguing science! And what would you do with it? Please leave your comments below!
Reference: "A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity", Antunes et al. 2006. Plant Biotechnology Journal, Volume 4, Issue 6.
Tuesday, 15 April 2014
A final lunch, a last look around the gardens laid out in the glorious sunshine then home... But not quite yet! Before catching my train, I had arranged to meet two friends who had also been on the Amgen Scholars Scheme during the same year that I was. This programme sponsors roughly twenty students each year to do an eight week research placement in Cambridge each year. We stayed together in St Edmunds college but worked on completely different things ( everything from NMR to diabetes to brain scanning) across a wide range of departments. It was lovely to catch up and we had a look at the temporary exhibition in the Fitzwilliam Museum: From Root to Tip: Botanical Art in Britain. My friends were very patient with me as I spent quite a while peering at the delicately worked petals and lustrous colours, as though by looking closely at them I would obtain the skill myself by osmosis. Although not a large collection of drawings, they were carefully chosen to show a range of compositions, from scenes of wildflowers to bunches of mixed ornamentals and single species. It has renewed my enthusiasm for botanical art and I have resolved to try and improve my skills although enrolling on a course at The Royal a botanical Gardens at Kew might be taking it too far...
Friday, 11 April 2014
I couldn’t distract myself for too long however as I had to settle into “scientific presentation mode”. Each PhD student had been asked to prepare an 8 minute powerpoint presentation on their projects, to be followed by 4 minutes for questions. I was hoping that I would score some “novelty” points for working on parasitic plants but worried that I would be confronted with technical enquiries that were out of my depth (4 minutes is a long time to be interrogated!). I barely had time to drop my bag off in my room and grab a cup of tea before we launched into the talks.
I was disappointed with my talk, both with my delivery ( stumbling over the odd word) and how I handled the questions ( I realise that I could improve my knowledge on the more technical details of MALDI-MS). At least I managed to get the words out although I was extremely put off when I realised that we were being filmed! My strategy for giving presentations is to try and learn my words by rote but I do worry that this makes me sound too 'mechanical'. As though I am not even interested in what I am speaking about. ( and nothing could be further from the truth!). Certainly the most engaging speakers this afternoon had a natural style and gave the impression that they could talk about their work at any time, in any setting as they were so familiar and comfortable with it. A level to aspire to, in my case! As mine was the last talk, everyone's thoughts are probably already on dinner, a formal three course meal we enjoyed in the upper hall.
The after dinner speaker was Michael Akam, a developmental biologist whose papers on Hox genes I remember studying for my final year undergraduate exams. Through his own diverting career he was able to give some sage advice to the assembled PhD students. Mainly, to KEEP GOING and accept that there will be weeks at a time when nothing will seem to go right. It is all very well to get the interesting result you were hoping for but to replicate it is quite another thing again! He also encouraged us to make sure we chose an area we had a real attraction to : there is no point investigating an answer to a question that we are not personally interested in answering. Meanwhile, he also emphasised how important it is to capture the imagination if others with your science. He pointed out that palaeontology never ceases to attract funding, despite the fact that studying dinosaurs could have little 'useful' application in the modern age. I think Jurassic Park has a lot to answer for this!
Although the stream of questions showed no sign of abating, at half past none, it was decided to adjourn to the bar. As for me, I headed to my lovely college room to try and get some rest for tomorrow
Wednesday, 9 April 2014
- Developing plants whose cell walls are more easily digestible WITHOUT compromising field performance
- Finding novel enzymes that allow a more effective pre-treatment.
Saturday, 5 April 2014
And just in case you were wondering... the above is all true and NOT an April Fool!
Day two and another early start in the name of plant science.... I had worried that I wouldn't get much sleep I the shared dorm at the youth hostel but with only two other ladies in the room, it was pleasantly quiet!
The first set of sessions centred on the theme 'Environment, diversity and adaptation'. Tina Sarkinen, of the Royal Botanic Garden in Edinburgh gave a fascinating introduction to life in the Andes, where plants have to be incredibly resilient to survive in a land where the climate can vary between that the extremes of North Africa and Greenland. Clearly, Peru is a hotbed of diversity and an estimated 29% of the plants and animals that remain undiscovered will be found here. Meanwhile, I was pleased to pleased to finally meet Sebastian Schornack of the ( brand spanking new) Sainsbury Laboratory in Cambridge, who works on filament out plant pathogens and with whom I once applied to do a PhD with. His presentation focused on the devastating pathogen Phytophthora palmivora: his belongs to a distinct, and little known, class of fungal like organisms called oomycetes. Clearly however, there is a pressing need for greater knowledge of this genus, which is responsible for a wide range if plant diseases, including ash dieback and potato blight. Over coffee, I engaged in a spot of 'networking' to raise the possibility of some collaborative work to compare the response of host plants to parasitic plants ( such as Orobanche ) and the Phytophra oomycete... Watch this space!
The second session, 'Plants as Factories', presented a fascinating mix of pioneering research seeking to encourage the production of desirable compounds and chemicals in plants. This included anthocyanin production in blood oranges. These cancer fighting compounds are specifically found in blood oranges ( as opposed to 'blonde' oranges) however these can only be cultivated in certain regions, such as Sicily, as they require a cold period to develop their distinct colour. Blood oranges have recently garnered interests through studies which suggest their juice could be an aid to weight loss: mice fed on a high fat diet gain less weight when given blood orange juice to drink, compared with standard orange juice. As such, there is great interest in introducing the anthocyanin- producing trait into more easily cultivated orange species. Cathie Martin, of the John Innes Centre, described the progress made so far in identifying genes responsible for anthocyanin production. I was also able to hear a first hand account of the development of omega-3 fatty acid producing oilseed crops ( see the previous post 'Something Fishy...') from Jonathan A. Napier from Rothamsted Research. This was followed by Simon McQueen-Mason's (University of York) account of the various approaches being made to engineer crops more suitable for use as biofuels (see the post 'Fuelling the Future'). After the depressing start yesterday, I was feeling much more inspired and invigorated!
It was even sunny enough to enjoy a buffet lunch out on the waterfront, in the company of the resident ducks and geese. Then the final session, which described some of the various new technologies being introduced into plant science. These included a CT scanning method being developed at the Centre for Plant Integrative Biology ( University of Nottingham) to map root architecture non- invasively. The closing speech was delivered by Jackie Hunter, Chief Executive of the funding body BBSRC (Biological and Biomedical Sciences Research Council) who stressed the organisation's commitment to developing world-leading plant science in the UK. Then a flurry of activity as cases were snatched up, coats collected, feedback forms handed in.... We may enjoy getting together but plant scientists are generally busy people! As the crowd dispersed, I paused to reflect on the hundreds of fascinating avenues of research we represented collectively, and to which we would return with renewed excitement.