7 weeks in Sudbury

By Joanna Wolstenholme

Sudbury, on first inspection, is a rather bland, spread-out mining town, inhabited by many, many trucks (most of them blue). When I first arrived, to help out on a project run by Andrew Tanentzap, I have to say I was a little underwhelmed. However the more you explore, the more remarkable the town becomes. It is one of the few areas of the world where remediation has really worked, and the next generation will inherit a greener and cleaner city than the one that their parents inherited. This remarkable change, from a barren ‘moonscape’ caused by years of acid rain (Sudbury was once the largest point source of sulphuric oxide fumes in the world, thanks to the extraction of large amounts of nickel from many mines in the area), to an area with burgeoning first generation forest cover, and recovering lakes, is a great success story that the area can be immensely proud of.

A hard day at work...

A hard day’s work…

With its industrial heritage, Sudbury, with its 330 lakes, makes an idea experimental location for a research group dealing in ecosystems and global change. Our test lake, Daisy Lake, is perfectly set up for studying the effects of terrestrial influences on aquatic ecosystems, as along its length the shores and wetlands have been remediated to various degrees. One section has been limed (spread with calcium carbonate, neutralising the otherwise very acidic soils) and so the growth is relatively lush, and the trees, although young, are not stunted. Other areas, closer to the smelter at the far end of the lake, are far more barren; bare, stained rock predominates, with a few stunted trees.

In Daisy, we were studying eight stream deltas, each with very different personalities. At each site Andrew’s post-doc Erik and I collected algae samples (through a variety of fairly low tech contraptions, more of which later), sediment samples, water samples, and used the Floroprobe and BenthoTorch (two very expensive, high tech contraptions) to characterise the algal species found in the littoral zone (water near the edge of the lake) and benthic layer (the area at the top of the sediment) respectively. This all sounds very easy in theory, but in practice (as with any fieldwork, as I came to learn) things were far harder and more complicated… and often involved some rather novel solutions. If nothing else, this placement has certainly given me plenty of opportunities to stretch my problem solving skills!

My first job was to build umpteen algae-collectors, which were incredibly scientific looking plastic tubes with cut up swim floats attached, from which 6 microscope-slides dangled from fluorescent string. These floated on the surface, but we also sank clay pot holders tied to bricks, as another surface for algae to grow on. We left these in the lake (on a beautiful sunny day) at each of the deltas and then returned to collect them 3 weeks later. After those three weeks had passed, We set out early, trying to avoid a storm that was due around lunchtime, only to find that between two boats we only had one working fuel cable. Great. So we towed each other around the lake, with our little motor struggling along at a snail’s pace. Whilst the clay pot holders had proven attractive to algae at most of the sites, trying to scrape the algae off the pot and into a rather narrow-necked falcon tube proved difficult. However, these still looked like our best bet, as the microscope-slide contraptions had only a thin layer of algae on each slide – we may actually have just built elaborate feeding platforms for the algae-eating zooplankton! The rain set in in earnest after we had got through just half the sites, and the wind got up – heavy rain whilst trying to scrape algae off clay plates tends to complicate things somewhat! Eventually though, we made it around all the sites, collected all the contraptions, and the rain stopped. Fieldwork is great fun, but the weather makes such a difference, especially when you are out on a very exposed lake!

Busy collecting algae

Busy collecting algae

On a more high-tech note, we also made use of two fancy algae-counting probes – the Fluoroprobe (which detects the level of various algal species in the water column) and the BenthoTorch (which, as the name suggests, measures benthic algae growing on the top of the sediment). Both were a little baffling to start with; their comprehensive manuals detailing many things, but not necessarily the answers to what we actually needed to know! After several dry runs measuring the amount of algae on Erik’s office floor, we took them out to the lake, and used them at each of the deltas three times between when we deployed the contraptions and when we scooped them up. The unseasonal amount of rain that Sudbury was experiencing, however, complicated things, and meant that in some sites Erik had to swim down to the sediment with the Benthotorch, as we couldn’t reach it from the boat. Holding the boat still enough to steady the Benthotorch whilst it was measuring was also a challenge, especially on windy days – we often resorted to having one person standing on submerged logs holding the boat still, whilst the other measured! Again, something which sounds easy in theory, but when you are out on a lake, at the mercy of the elements, often proves more complicated…

Fieldwork in the Muskokas

Fieldwork in the Muskokas

As well as working on Daisy with Erik, I also helped Andrew collect additional data for a project looking at the interplay between terrestrial and lake ecosystems. This meant going out to 6 other lakes around Sudbury, and six down in the Muskokas, to collect water samples, use the fluroprobe, and deploy and collect the microscope slide contraptions. Key to the project was collecting clean leaf and algal samples, to go off for stable isotope analysis, to allow Andrew to calculate the influence of the terrestrial systems surrounding the lakes were having on the lake ecosystems. In order to grow clean algal samples without the influence of terrestrial DOM, we collected water from each of the lakes, then filtered it into jars and re-inoculated each jar with a small amount of unfiltered lake water, from which wehoped the algae would regrow. Again, simple in theory, but in practice involved hours and hours of standing by a vacuum pump, watching water drip, drip, drip through a filter. One night, on a field trip down to the Muskokas, we actually ended up filtering outside a Best Western hotel, so as not to set the fire alarms off! Safe to say we got many odd looks. However, the field trip down to the Muskokas was one of the best perks of the summer. We went down in September, almost at the peak of the colours changing, and had two lovely dry but crisp days. Driving down dirt tracks through beautiful forest, to find beautiful lakes to paddle out into was great fun, and a real adventure! It definitely offset the tedium of filtering.

At the end of my seven weeks here I am very sad to be leaving. It was a great experience, with plenty of messing about on boats, and exploring new places. I have learnt a lot about the complications of fieldwork, how to solve problems on the fly with limited supplies, and just what really goes on behind those dry-sounding ‘Materials and Methods’.

Global health calls on an old foe to help fight Ebola

by Charlie Whittaker

Since March this year, at least 5,800 people across the countries of Guinea, Liberia, Nigeria, Senegal and Sierra Leone have contracted Ebola. Of those infected, more than 2,800 have died. As well as being the largest outbreak on record, this particular incident is worrying because of its potential scale- in August, the WHO hoped to have it contained within 9 months (and with 20,000 infected) but recent research by American epidemiologists suggests that the process of containment could take up to 18 months, with 100,000s of people infected before the outbreak is brought under control.

Ebola is the common name for Ebola Haemorrhagic Fever, caused by the similarly named ebolavirus. Spread through direct contact with bodily fluids such as blood or vomit, symptoms tend to manifest after a 1-2 week incubation period. Fever, muscle pain, vomiting and declining organ function are all symptoms, usually followed by significant internal and external bleeding.

The disease has a startlingly high mortality rate; this varies from outbreak to outbreak, but is usually put at somewhere between 50 and 90%. Pressingly, there is currently no available specific treatment for the disease, with care usually limited to oral rehydration therapy and intravenous fluids. This lack of effective treatment coupled with the naturally high mortality rate means any outbreak has the potential to claim many lives, and is therefore a serious concern for both the countries involved and the wider international community.

Recent efforts by the American government have seen an experimental vaccine fast tracked and delivered to 2 infected aid workers without the usual rounds of clinical trials. ZMapp contains neutralising humanised antibodies that recognise and bind specifically to ebolavirus particles, rendering them harmless.

Given the potential scale and immediacy required of doses of vaccine, a problem is presented in terms of the means of production. Many thousands of doses are required, often at very short notice. In order to circumvent this potential issue, researchers have been investigating the potential for the use of plants as “bioreactors” to grow and produce these antibodies.

The principle behind this approach involves the inoculation and subsequent infection of a particular strain of tobacco, Nicotiana benthamiana (a close relative of the cigarette supplying cousin Nicotiana tabaccum) with a virus from the group of plant viruses called the Geminiviridae. These have single stranded circular DNA genomes, and although responsible for significant crop losses worldwide, here they have been co-opted for human benefit.

Nicotiana benthamiana  Image Credit: Charles Andres

Nicotiana benthamiana
Image Credit: Charles Andres

Their genomes are exceedingly pliable, and extra sections of DNA can be inserted in without compromising infectivity. In this case, DNA sections encoding the humanised antibodies making up the ZMapp treatment were inserted, and the subsequent genome produced then transfected into the plant. Once inside the plant, the existing viral features of the genome ensure replication and propagation of the entire vector, including the antibody, leading to production of high levels of antibody. These antibodies can then be purified and extracted from the plant, and refined in order to provide doses of the vaccine.

The advantages of production and accumulation of antibodies from plant-based bioreactors are numerous. Firstly, the particular viruses in question, the Geminiviridae, are able to replicate extensively within the plant, resulting in high yields. In addition, costs of production are lower as the maintenance of growing conditions is relatively inexpensive. Finally, generating the Ebola antibodies in plants minimises the risk of cross contamination with other mammalian viruses.

All in all then, could this be a timely and effective source of the treatment for this deadly disease? ZMapp has been fast-tracked in this instance, but must first still pass a battery of clinical trials to ensure its efficacy and safety, and questions still remain over the accessibility of it as a healthcare option for the poorest worldwide, for whom it is perhaps most urgently needed. Perhaps more solidly impressive is the global attention gained for the use of plants as bioreactors, and for their ability no act as relatively inexpensive and high yielding sources of various pharmaceutical goods. This makes them potentially able to lower the current cost of production to levels that would make these pharmaceutical products more universally affordable.

50 Shades of Autumn

by Leanne Massie

Photo Credit: Bert Kaufmann

Photo Credit: Bert Kaufmann

Ever wonder why some trees turn stunning shades of red and yellow this time of year while others stay a bright green year round? It’s all about three important things plants need to survive: warmth, light and water.

Evergreens, which are mainly conifers, tend to live in regions that get very cold in the winter and have quite short summers as in the Boreal forests that ring the Arctic Circle. They experience shortages of all three necessary ingredients in the Arctic winter, no sun for months means temperatures of as low as 80 degrees Celsius below zero and any available water being locked away, unreachable to plants, in the form of ice.

Deciduous trees, on the other hand, lead a much more comfy life. They still have chilly winters but temperatures tend to hover around or dip slightly below the zero mark. They also get lovely, long, warm summers with plenty of time to grow and barrels of rainwater to spare. This allows them to store up enough energy during the growing season so they can afford to drop their leaves when it gets cold and have enough energy to regrow the following spring.

But why bother dropping their leaves and re-growing them? The answer is in the third element in our list: water. Leaves have very large surface areas so represent a lot of potential area to lose water from. When it’s winter and all the ground water is frozen, losing any water through the leaves can be very damaging to the tree that need to hang to on as much liquid as possible. By dropping their leaves and thus reducing their surface area, deciduous trees are able to avoid a large amount of water loss. Of course they don’t just fall off, the trees recover as much nutrients as possible from their leaves before dropping them; it is this relocation of the green, nutrient rich chlorophyll in particular that is seen since this exposes the vivid reds and yellows of the anthocyanin and carotenoid pigments that are always present in the leaves but usually masked by the much more abundant green chlorophyll.

Going back to evergreens though, they still have the problem of water loss since they don’t drop their leaves in the winter. They have developed another solution to reduce water loss which is a typical characteristic of conifers; they have reduced their leaves to needles. This again reduces their surface area to minimize water loss while not incurring the huge cost of dropping then re-growing their leaves. Dropping them entirely is not feasibly because the low temperatures slows the actions of the microbial community to practically nothing with the result that nutrient cycling is very slow so the soil is poor quality, thus the trees don’t have the resources to regrow their needles every year.

What you might not know is that cold places are not the only place where evergreens are found. Non-conifer evergreens exist around the equator due to a lack of seasonal change. With good growing conditions all year round there is no need to drop their leaves or reduce them to needles so we find broad-leaf evergreen trees in equatorial regions. Another side effect of the lack of seasons is that the trees don’t lay down the characteristic annual rings in their trunks but have a more or less consistent grain throughout.

So there you have it! Trees that change color do so not to delight us and give us material to make leaf piles with, but because it makes evolutionary sense for them to do so. It allows them to conserve nutrients while avoiding the worst of the winter drought caused by plummeting temperatures and wait for the sun to come back. That certainly doesn’t mean we can’t enjoy the brilliant colors this produces as we always do!

Unbe-leaf-able: Why I don’t back this artificial photosynthesis project, yet.

by Toby McMaster

Silk Leaf, an artificial leaf made from chloroplasts and proteins extracted from silk, is the latest in a series of attempts to mimic photosynthesis. Julian Melchiorri, working with a lab at Tufts University, recently unveiled a synthetic leaf, designed to help humans colonise other worlds by providing us with much needed oxygen. Yet not everything is running as smoothly as it first seems.

The ability to recreate leaves sounds fantastic, so what’s the hitch? Well for a start it only pays up half of what it should, it duly takes in water and Carbon Dioxide, and uses light energy, but currently only reliably produces oxygen. There is no glucose and no one is really sure where the Carbon Dioxide goes. This doesn’t initially sound too bad for us: after all, assuming these things are inedible, we only need the oxygen. However if these leaves were ever to become part of a fully functional plant, these plants would need some kind of energy source. They would need glucose.


Another obstacle lies in the physical connection of these currently isolated leaves to produce an entire plant. The xylem and phloem inside a plant’s stem, akin to the blood vessels in animals, are complex structures and at best it is naïve to think we can just stick our artificial leaves on and hope they’ll co-operate.

Finally there is currently no data (as far as I can find) on the environmental cost of producing these leaves, which is clearly a key factor in whether they are viable for a trial run on earth, before they can get anywhere near space.

However this project still has a lot of promise. It’s a step in the right direction, and the leaves actually look like leaves, which means their surface area properties are likely to be good. Moreover the fact they look like real plant bits can only help with public acceptance of them, if we ever reach that stage. This might sound like an attempt to simply come up with something nice to say, but it really is important –GM crops, vaccines and nanotechnology are examples of areas which could do a lot more for human kind if not limited by public scepticism.

Scepticism is healthy. It’s why I’m not proclaiming this project as the next big thing in science. There’s a limit though, change is scary, but sometimes it’s necessary. Scepticism without rational basis can hinder progress. Perhaps one day this leaf will help the sceptics see the light when it comes to artificial biology.

The Daily Grind

by Sarah Wiseman

RNA extractions were my main task for the week. This involved a lot of sample grinding and centrifuging, all to collect small amounts of messenger RNA. The different messenger RNAs (or mRNAs for short) present in a cell can tell us which sections of the genome are being transcribed within it. This allows us to compare the activity of particular genes between the leaves and the roots, for example. We can also use the mRNA to search for the activity of a particular gene that we’re interested in. This is done by carrying out reverse transcription (a technique which uses RNA as a template to make DNA); we can make then sequence strands of DNA to see if different plants have copies of the same genes. My extractions were the first stage in this long process.

To stop the fragile mRNA degrading, most of the extraction process had to be done on ice or (more excitingly) liquid nitrogen! Though this does have its draw backs – wheat grains which have been frozen solid are rather difficult to grind to a powder. I spent several mornings grappling with persistently intact samples and trying to thwart their escape attempts (and not always successfully – many a grain evaded my grasp, making a bid for freedom which could only result in their binning).  I even managed to destroy a motor while trying to grind down the stubborn grains!

Monday and Tuesday were spent optimising the extraction protocol, an important yet dull and quite frustrating process. For someone who didn’t understand exactly what was going on it felt a lot like alchemy – making small adjustments here, using slightly different amounts of something else there for no obvious reason. As it is there are quite a few papers in which various scientists describe their methods for RNA extraction, though deciding which of them was most suitable for our extractions was a challenge. After a period of trial and error we settled on the protocol which gave us the best quality of RNA extracted so far.


The main problem with the initial extractions was the huge amounts of starch present in the wheat grains. This meant that the quantity of RNA we extracted was miniscule, even by mircobiologist’s standards! Thankfully changing the buffer solved that problem, as the before and after pictures show.

The next stage in the process is making cDNA, using the RNA just extracted as a template to create a DNA copy which can eventually be sequenced. The process itself involves more calculations and a very long wait – there is an hour’s incubation at 50oC whilst the added enzymes function.

The week ended with another induction, this one a tour of the Department’s Plant Growth Facility. The PGF is a surprisingly noisy building filled with many temperature and light controlled growth chambers, where most of the experimental plants are grown. My Arabidopsis now have their own shelf in one of the chambers and are looking rather small compared to their neighbours (which are at a much later stage of growth). Over the next few weeks I will be visiting them every few days to check on their progress, but more importantly watering them – something that it’s still best not to leave to the machines, even in 2014!

Greening the Red Planet

By Sophie Harrington

It’s a big universe out there, and it takes a long time to get anywhere. Even just heading to Mars would take us over 6 months. A bit further than popping down to the pub then! But if NASA and a whole host of other private groups get their way, it won’t be too long before we’re sending humans out to Mars.

Mizuna growing on the ISS (credit NASA)

Mizuna growing on the ISS (credit NASA)

The logistics of the operation are still being worked out. Some argue it’s better to send astronauts on a one-way mission, setting up a bare-bones colony that will grow over time as more and more colonists make the voyage to the Red Planet. It would be handy not to carry all the fuel needed to launch a rocket off of Mars, but sending humans on a one-way trip might be a bit too much for NASA. Private groups, like Mars One, might seem more likely to support such a remarkable attempt, but it’s unclear where their funding will come from.

Whether or not we send humans to stay on Mars to begin with, it can’t be denied that colonising another planet would certainly capture the imagination. But what would that really entail? It’s well and good to talk about sending humans to Mars, but how on earth are we going to survive?

Enter plants, which will probably be our most prized possession on Mars, and in outer space for that matter. Even Apollo astronauts grew tired of their space-certified food, and they were only in space for a matter of days. While the food has definitely improved, the sheer delight of ISS crewmembers when they were able to have a few mouthfuls of fresh Mizuna, grown on the spacecraft, suggests it still leaves much to be desired.

Artist's conception of a greenhouse on Mars (credit NASA)

Artist’s conception of a greenhouse on Mars (credit NASA)

NASA recognises that to send astronauts on long-term missions, some form of fresh food will likely be necessary. Besides the culinary and psychological benefits of fresh veg, hardly any of the food packages currently in use on the ISS would survive the length of a trip to Mars. Sending astronauts up with lettuce, tomatoes, rocket, and even courgette could provide badly needed nutrition while livening up the interior of the spacecraft. Who said interior design wasn’t important in space?

Once on Mars, one of the first structures built by the colonists would have to be a greenhouse, where vegetables can continue to be cultivated. In the long term, we would be able to grow more intensive crops such as maize and wheat, which while requiring refining to be edible would help bulk up a diet, and reduce the dependence of the colonists on food supplies from the home planet.

Some researchers have even found that plants can grow perfectly well on Mars-simulant soil, in some cases even better than on Earth soil! Perhaps colonists may start gardening outside, beginning a process of terraforming that could change the face of Mars itself.

It might not be called the Red Planet for long!

Born to Pipette?

By Sarah Wiseman

‘So, what are you going to do after you graduate?’ A cruel question often posed by relatives, and sometimes even friends. It is particularly terrifying question for the soon-to-be finalist. Although a question potentially deflected by further study— ‘maybe a Masters or a PhD?’ is always going to be a better sounding answer than admitting that you don’t have a clue.

The Arabidopsis has just germinated, and is growing in one of the growth rooms beneath the Department.

The Arabidopsis has just germinated, and is growing in one of the growth rooms beneath the Department.

Though that does raise a second, slyer question ‘Am I cut out for it?’ Undertaking your own research is a completely different kettle of fish to attending lectures and a couple of practicals a week as an undergrad. With all that in mind I arranged (in an unusually proactive move) to spend roughly seven weeks working in Dr David Hanke’s lab, within the Plant Sciences Department at Cambridge. This blog within a blog will be a record of my time there, and proof that I didn’t just disappear in the Summer of 2014…

The Game is Afoot 

During this first week I have learnt many useful things; the location of the Growth Room (in the basement); how to sow hundreds of Arabidopsis seed (sterilise them in bleach then pipette evenly onto plates of agar); where the liquid nitrogen is kept (under lock and key behind the building) and more importantly, what I will be working towards over the next six weeks.

Harvesting and correctly labelling each variety – if you discover something amazing in a particular wheat sample it’s so good to anyone if you can’t remember which variety it belongs to!

Harvesting and correctly labelling each variety – if you discover something amazing in a particular wheat sample it’s so good to anyone if you can’t remember which variety it belongs to!

All of the experiments that I’m carrying out will be investigating the role of cytokinin binding protein (CKP) in dormancy. Cytokinins are a group of plant hormones involved in cell division/growth and CKP prevents their action – halting germination or growth for a given period of time. The CKP levels in different crops play a role in the security and reliability of our food supply. Low levels of CKP reduce the length of time which potatoes can be stored without sprouting. Whilst in wheat, low levels correlate with greater pre-harvest sprouting (when the grains of wheat germinate whilst still attached to the parent plant, reducing crop yield and making useless bread). My experiments will help provide evidence required to begin conventional breeding programmes in both wheat and potatoes, in order to produce crops with a higher level of CKP.

Grand unifying purpose aside, I did very little towards those ends, mainly collecting and preparing plant material – planting the Arabidopsis, ready for harvest in four weeks or so and picking ears of wheat. It was rather a lazy week, but you have to start somewhere!