A deadly, mutating wheat fungus is spreading – here's how to track it

Yellow Rust spores can be seen bursting out of a wheat leaf from the inside, tearing their way through the epidermis. Kim Findlay/John Innes Centre, CC BY-NC-SA

One of the major diseases of wheat is caused by the yellow rust fungus, Puccinia striiformis, which threatens all major wheat-producing areas of the world. Ominously, we have discovered that the UK population of this pathogen is shifting dramatically, with the emergence of new strains which can overcome some of our most important wheat varieties.

We have developed a genetic technique that helps us characterise the pathogen, allowing farmers to make informed decisions about which wheat varieties to plant.

Wheat is a critical staple crop, providing 20% of the calories and 25% of the protein consumed globally by humankind. Despite modern agricultural practices, diseases of major food crops can cause pre-harvest yield losses of up to 15%.

In 2013, I joined forces with colleagues at the John Innes Centre and The Sainsbury Laboratory in Norwich with the National Institute of Agricultural Botany in Cambridge to develop a new genomics-driven surveillance method to track the devastating yellow rust fungus and investigate the genetic basis of the new pathogen population.

Our new “field pathogenomics” method is a fast way to analyse fungal diseases from field samples and pinpoint the exact genotype. Current techniques rely on time-consuming phenotypic characterisation – checking the response of different plant varieties to infection by the pathogen – or costly in-lab processes. These methods can only sample a relatively small proportion of the fungal population.

With help from contributors to the UK Cereal Pathogen Virulence Survey, we collected wheat samples infected with the wheat yellow rust pathogen from 17 different counties across the UK. We then used our newly developed “field pathogenomics” method to characterise the genotypes of the samples. As each field sample consists of both the pathogen and its host plant, we were able to analyse both the pathogen and the susceptible host. In the future, this will provide a rapid means for confirming the presence of disease on wheat varieties that may have previously been resistant to disease.

Under siege: wheat is a major global crop, but threatened by fungal pathogens. Takkk, CC BY-SA

Invasive pathogens

We found that the wheat yellow rust pathogen population has undergone a major shift in recent years. Interestingly, the yellow rust population detected in the UK in 2013 was completely different at the genetic level to previous UK populations. This difference seems to represent a number of recent exotic introductions into the UK and could have serious implications for wheat production in the UK.

A subset of the new pathogen population was able to infect the same wheat varieties as a subset of the older UK pathogen population. Because the same varieties are infected, this new pathogen population would have been missed if analysis were based on traditional phenotypic characterisation alone. Spotting this new pathogen population is important, because even if it infects the same wheat varieties it could still have serious implications for disease incidence. The new pathogen population may have other important traits or infect other wheat varieties not included in our test set.

As we move forward, “field pathogenomics” could be applied to the surveillance of many pathogens besides wheat yellow rust pathogens, and could contribute to addressing human, animal and plant health issues. Such detailed knowledge of shifts in pathogen populations is important for both understanding and managing emerging diseases. For wheat yellow rust, our new technology could provide farmers with early indications of changes in the pathogen population, and have a positive impact on decisions regarding which varieties to plant in the field.

Gemalto hack shows how far we are from deciding acceptable 'security norms'

SIM cards contain the key to unlock your phone. Oleksiy Mark/Shutterstock

Is it true spies hack technology companies? Can governments really listen to your phone calls? Should we care? The latest details of NSA and GCHQ intelligence agency activities to come from files leaked by Edward Snowden are of the apparently massive theft of mobile phone SIM card encryption keys from the Dutch firm Gemalto.

This “great SIM heist” targeted Gemalto because it produces billions of mobile phone SIM cards for 450 telecoms providers worldwide, and acquiring copies of encryption keys would make it possible to eavesdrop on cell phone calls with comparative ease. While press reports state these attempts were successful, after a brief internal audit – far too brief, some experts say – Gemalto has stated that nothing was stolen.

Who is right? Whether this is resolved or not, in this particular case the handbags will no doubt fly. But the fact of the matter is that there are bigger issues we should all be considering.

Putting walls around data

In the physical world we do a fairly good job of keeping ourselves secure. I assume, for example, that you locked your front door when you left your house this morning. In the digital world we tend to be a lot more careless. We tend to leave doors wide open. In many cases we don’t even put doors between the outside world and our data. For intelligence agencies this is very fortunate since our emails, social media posts, and browsing habits are usually conveniently just lying around.

Encryption, on the other hand, provides a secure place with a front door behind which data is inaccessible. That is, unless you have the front door key. Encrypted data is meaningless and of little use to an intelligence agency – to make sense of it the keys to decrypt it are needed.

Mobile phones encrypt calls between the phone and the nearest mobile phone mast, preventing anyone who intercepts the call as it travels through the air from making any sense of it. The encryption key used is derived from the phone’s SIM key, which is a personal key that comes pre-installed on your SIM card. Anyone who knows the SIM key – normally only your phone and your mobile operator – can decrypt the call if they listen in.

Gemalto’s business is putting SIM keys into SIM cards; if someone breaks into Gemalto’s systems then it is certainly possible that they could make off with SIM encryption keys. This isn’t great news for the security of whatever mobile phones they later end up in.

Sidestepping the locks

Bad though this sounds, it’s really just the latest of many revelations of this type that have leaked out of the Snowden files. The picture that has emerged is of intelligence agencies clearly frustrated by the increasing use of encryption in our everyday technology. As the encryption is (mostly) too good to break, so the intelligence agencies have been using every technique imaginable to find a way around it.

Broadly speaking, there are really only two ways to get around good encryption. Option one is to try to access data either before it is encrypted or after it is decrypted – Snowden’s files suggest the intelligence agencies have been doing plenty of that. Option two is to try to get hold of the keys needed to decrypt the data. The Great SIM Heist seems to be the latest example of attempts at this second strategy.

What do we want for the future?

In one sense this is not a new development. As encryption has been deployed more widely, its use has created tension between the rights of the individual to privacy and the duties of the state to protect society. Over the last few decades governments have made several attempts to mediate between these, attempts which appeared to have concluded in favour of strong encryption and individual privacy.

Prior to Snowden it was publicly believed that the “crypto wars” had largely been lost by the intelligence agencies; instead, leaked files such as these reveal that the wars have just become bloodier than any of us really imagined.

Many people are outraged by the many Snowden revelations. Others take the view that this is the intelligence agencies' job and they ought to be left to get on with it. There are good arguments supporting both of these viewpoints.

So, should you care? If you do, then there has never been a better time to stand up and make your feelings known. We as a society really ought to form an opinion on what “security norms” we wish to see developing around our increasing use of the internet as a place where we, partially, live our lives. If we don’t, then clearly others, with perhaps very different agendas, will decide them for us.

Blue is the colour: why do we see #TheDress so differently?

Not since Liz Hurley's safety pin number has a dress caused such a stir. Tumblr

There has been passionate debate on the internet over a blue and black dress that to some people – perhaps even the majority – appears white and gold. But what is the reason behind a discrepancy that has caused such division within households and offices?

The story began when Caitlin McNeill posted a picture of a dress that was worn to a wedding, but no one appeared to be able to agree on what colour it was. The picture, and debate, went viral.

The physical colour of light coming from an object is made up of two components: the colour of the object and the colour of the light that shines upon it. The combined colour can vary widely. For example, daylight is much redder in the evening than at midday. Most of the time, however, we need to know the colour of the object, not the colour of the illumination – we don’t want to think that fruit is ripe in the evening just because the sun is going down. Our visual system has therefore developed to discount the colour of the illumination.

Colour vision in particular works in three main stages. We have receptors in the eye for just three colours, roughly, blue, green and red. We then make comparisons between the colours in a further three ways: red versus green, blue versus yellow (the sum of red and green for lights) and bright versus dark.

These comparisons are made over different times and different points in space. So if we stare at a blue screen for a long time, when we then view a white object it may appear yellow. Similarly, an orange spot will appear red when surrounded by green, and green when surrounded by red.

Finally, the colour signals are passed to the visual cortex, where the brain tries to work out the colour of the illumination from all the colours available and then calibrates the colours of the objects according to this illumination colour. This is called colour constancy, and it’s what stops the apparent colours of objects changing during the day.

The two-tone dress that sparked global debate. Joe Giddens/PA Wire

With the blue dress, it’s possible that some people have more blue photo-receptors than other people, or that their colour contrast system is biased for or against blue. But the most likely explanation is that colour constancy is responsible for the differences of opinion. When the dress occupies most of the image, some people take the blue cloth as their reference for the illumination and so see the dress as white cloth in blue light and the black frills as gold or yellow.

Yellow things don’t reflect much blue and so ought to look dark in a blue light. People correcting for a blue light will therefore see the dark frills as yellow. But other people may use the background objects as their white reference and so see the dress as a blue garment in a yellowish-white light. These people will see the frills as dark because dark frills remain dark when compared with a white light.

How some frogs survive killer fungus may reveal new weapon in fight to save amphibians

A Madagascan bright-eyed frog (Boophis rappiodes), one of more than 400 species on the island. Axel Strauß, CC BY-SA

The loss of amphibian species across the world from chytridiomycosis, an infectious disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has been described as “the most spectacular loss of vertebrate biodiversity due to disease in recorded history”. So it’s of grave concern that the pathogen has been discovered in Madagascar, an incredibly biodiverse region previously thought free of the fungus.

Madagascar has the 12th highest rate of amphibian species richness in the world, with more than 400 species, 99% of which are indigenous to the region. But this biodiversity hotspot is already under severe pressure – a quarter of its species are under threat, according to the latest Global Amphibian Assessment. It’s rightly feared that the arrival of Bd, as reported in the journal Scientific Reports, could bring about mass amphibian decline – and even extinctions – as has been seen elsewhere.

An scanning-electron micrograph image of a Chytrid fungus (Bd) spore. Alex Hyatt/CSIRO, CC BY

Testing of the samples of the Bd fungus found in Madagascar reveals the strain is closely related to BdGPL, the hyper-virulent lineage behind all the known outbreaks of the chytrid fungus pathogen that have decimated amphibian populations. However what’s interesting is that the rate of infection is extremely low and there’s no clinical signs of chytridiomycosis: the frogs have the fungus, but they haven’t developed the disease.

What could this mean?

This discovery presents us with a number of scenarios, which need further investigation.

Perhaps the comprehensive monitoring plan put in place by A Conservation Strategy for the Amphibians of Madagascar (ACSAM) has worked as planned, in that the presence of the Bd pathogen has been detected – for the first time in 2010 – before amphibian declines have occurred.

Perhaps the strain of Bd detected in Madagascar is not a virulent kind that poses a serious threat to amphibians. This was seen with the introduction of the BdCape fungus lineage into Mallorca, where it had little effect on the population of Alytes muletensis toads there.

It’s possible that the Bd detected in Madagascar has been present on the island for a long time, but undetected. It may be an endemic, non-virulent lineage as seen in Brazil and Asia, where certain lineages endemic to the regions appear to have evolved alongside the native amphibians.

Or perhaps there is an endemic, previously undetected chytrid fungus on the island, related or not to Bd, which could be acting as a buffer for local amphibians against the invasion of BdGPL – acting, in effect, as a natural vaccine.

Alternatively, Malagasy amphibians may have developed some intrinsic resistance to Bd, for example through protective bacteria in their skin. This could explain the low infection rates and the ambiguous test results reported in the paper showing that some Bd-positive samples did not conform to any known lineage of the fungus. Although rare, resistance to BdGPL is not unprecedented – this has been seen and documented in Brazil.

The last known surviving Rabb’s Fringe-limbed Treefrog, a species ravaged by the Bd fungus. briangratwicke, CC BY

A potential threat or a potential benefit

The first scenario would be a disaster – and should be a priority. If this turns out to be the case, the survival of Malagasy amphibians could depend on the conservation and scientific groups involved in ACSAM managing to restrict the spread of the disease. Tackling invasive species such as the Asian Toad that might spread the disease and ensuring tourists and researchers stick to strict hygiene protocols would be necessary. Perhaps even more drastic conservation measures, such as capturing animals from particularly vulnerable species for raising in captivity.

On the other hand, the fourth scenario presents an intriguing possibility: if it’s the case that Malagasy amphibians are resisting a fungal invasion, discovering how this works could provide crucial information to help save amphibians elsewhere from the disease.

The research on the amphibian skin microbiome, for example, and its role in the creature’s immune system is producing some exciting results. It’s also apparent that the diversity of the Chytrid fungus species as a whole, and in particular of Bd, has not been appreciated. It’s possible there are many types of chytrid fungus associated with amphibians that we’re not yet aware of which provide some protection against BdGPL.

So without a doubt, this report will sound warning bells loud and clear for conservationists, and Bd’s appearance in Madagascar could still result in a huge loss of amphibians. However, the lack of chytridiomycosis symptoms also suggest there’s something special in Madagascar that could yield a breakthrough in how the disease spreads – something that may not only benefit Malagasy amphibians, but those throughout the world.

Superfast evolution observed in soil bacteria

Two mutations allowed soil bacteria (Pseudomonas fluorescens) to re-evolve flagella: One pumped up levels of a protein than controls nitrogen uptake, and one that switched that protein’s job to flagella production control.

Ninjatacoshell/Wikimedia Commons (CC BY-SA 3.0)

You can take the flagella out of the bacteria, but you can’t take the flagella out of the bacteria’s genetic arsenal.

By deleting a gene that controls flagella growth, Tiffany Taylor of the University of Reading in England and colleagues engineered the soil bacteria Pseudomonas fluorescens so they lacked their tiny tails. Bacteria that can move around and find food are more likely to survive, and after a mere 96 hours in a low-food environment, the bacteria were once again growing flagella.

How did the bacteria manage such a swift feat? Two mutations in regulatory genes jump-started flagella production, suggesting that natural selection can rewire genetic networks with a few key mutations, the researchers report February 26 in

UK has little to be proud of as survey reveals sorry state of European cybersecurity

That sinking feeling of inaction ... geralt

The European Commission’s annual Eurobarometer Cyber Security Survey, the third edition of which was recently released, is a substantial survey of more than 27,000 respondents from 28 countries. It contains interesting and, more often than not, disappointing revelations about the state of Europe’s security.

As specialists in the field, we look forward to the report’s release. But as we wrote a year ago, the complete lack of media and expert interest in the study is amazing. Heaven help the survey authors if they have to justify its impact based on media coverage.

Falling on deaf ears

The UK government has adopted a bizarrely triumphalist discourse around cybersecurity, one that is clearly at odds with the experience of the 1,329 survey participants from the UK. In fact, year on year the survey results reflect that the UK is not in a good position, particularly in comparison to some of our more advanced neighbours. This is probably not what Downing Street wants to hear or publicise – particularly in an election year – as it seems that providing some sort of external or independent accountability for the impact of the hundreds of millions of public money spent is not a top priority.

The UK is not alone in its disdain for the survey’s results, which were similarly disregarded by most other Europeans. It’s a sad outcome for the only large, non-commercial, unbiased, and independent survey on this important topic.

Eurobarometer survey results

There are lots of facts in the report, including some that are very apparent to most people: internet use is up, mobile internet use is leading the way, Europe shows a marked digital divide between nations like Sweden and The Netherlands and others like Bulgaria, Romania and Greece. Other findings include how more than half (57%) of Europeans shop online, 23% sell online, and 54% use online banking. That last figure is relatively large, in our view, taking into account the associated risks.

The UK is among the worst EU countries for identity theft. Eurobarometer 2015

The two most common concerns of European citizens are the misuse of personal data and the security of online payments – responders were significantly more worried about both than they were last year. At least, good practices such as installing antivirus software (61%), not opening suspicious-looking emails (49%), and being careful not to give away personal information (38%) seem to be increasingly popular.

UK almost tops the charts for fraud from goods bought online. Eurobarometer 2015

Not only are people more concerned with the risks of cybercrime but 47% believed they were well informed, up from 44% last year. They claimed to avoid disclosing personal information online (89%), believed the risk of cybercrime is increasing (85%), and were concerned their personal information is not kept sufficiently secure by websites (73%) or public authorities (67%). This last point is worth emphasizing: two thirds of the citizens don’t trust the government or any other public authorities to keep their personal data safe – there is a large margin for improvement here.

Citizens are worried about identity theft (68%), malware infection (66%), online banking or bank card fraud (63%), having email or social media accounts hacked (60%), receiving scam phonecalls or emails (57%), or coming across racial or religious hate material (46%) or child pornography (52%) online. Interestingly, 47% are concerned with cyber-extortion and ransomware – a relatively new method that’s been very profitable for cybercriminals of late. In all cases, concern is up on last year.

UK number one in Europe for bank card and online banking fraud Eurobarometer 2015

Quite shocking is the finding that, despite being apparently aware of the many risks they face online, an incredible 74% of respondents thought they were able to protect themselves sufficiently from cybercriminals. We simply haven’t the words to express what overconfidence this demonstrates, and how unrealistic and dangerous it is. Computers and network security are complex matters – most people’s understanding of them, including ours, is at best incomplete and at worst practically absent. How people can believe they can protect themselves after, for example, having already discovered malware on their devices (as reported by 47% of respondents) is beyond us.

What needs to be done

Denmark, the Netherlands and Sweden are the three leading European countries for internet use. That might naturally imply correspondingly higher levels of cybercrime – but the survey findings suggest not. Whatever these nations are doing in terms of education, investment and technology development, we can do much worse than learning from then – or at the very least imitating their good practises.

As ever the UK results are discouraging. Britain misses the leading group by a large margin, and despite well-publicised government campaigns and huge investment in cybersecurity, we show very little overall improvement. Britain leads the way in misplaced confidence: 89% feel we can protect ourselves against cybercrime, which is a bad omen. It experienced the largest yearly increase on accidentally finding materials promoting racial hatred or religious extremism. And the UK also tops European tables of bank card and online bank fraud with 17% of citizens affected. The average is 8%, and in Germany for example the rate is 2%. The UK performs poorly in other areas too, casting a cloud not only on the UK but on crime rates for the whole of Europe.

More positively, the UK seems to be good at changing passwords and feeling well-informed about cybercrime, is among the leading countries where citizens are concerned over the use of their personal data, and also enjoyed the largest fall in scam emails and phone calls. Despite the large increase from last year, it’s also still extremely rare for UK users to encounter child pornography or racial or religious extremism materials online.

One problem is that the government’s information campaigns are focused largely on companies rather than individuals – some may argue that in this respect it’s no exception to Tory policy in other areas. Thus the Eurobarometer survey is probably not doing justice to the current UK government’s considerable, but possibly misguided, efforts.

People, not companies, should be prioritised; legislation and incentives should be aimed at protecting citizens and helping them to protect themselves. The main response to mistrust of government use of their data, in particular, should be to give them back more control. There have been some positive moves from Labour and the Liberal Democrats in that direction – but for now they are merely pre-election promises.

At the very least, could future governments please copy whatever it is they’re doing right in Sweden, Denmark, the Netherlands and some of our other more competent neighbours?

Molecular 'GPS' helps stem cells navigate inside the body

Saving lives, one ear at a time. Mirko Sobotta//Shutterstock

Recent research has identified a novel molecule that could help localise stem cells within the body. Cell therapy holds significant promise for treating a wide range of diseases and tissue defects including arthritis, cardiovascular disease, multiple sclerosis and Crohn’s disease. But in current therapies, most cell types do not reach diseased or damaged tissues efficiently.

Controlling cells once they have been introduced into the body is a key challenge to overcome. There are all kinds of tools and techniques that can be used to manipulate cells outside of the body in a petri dish and get them to do almost anything we want. But once cells have been transplanted, it is difficult to control them. We have now been able to identify small molecules that can be used to treat cells before injection into the body, programming them to target blood vessels in diseased or damaged tissue once inside the body.

This molecular targeting is especially important in the case of adult mesenchymal stem cells (MSCs), which are known to secrete several therapeutic factors and are being explored in more than 450 clinical trials. A major challenge has been getting MSCs to target – and stay at – sites of damage within the body, where they can secrete high levels of therapeutic factors to suppress inflammation and promote recovery.

Our team of bio-engineers from Brigham and Women’s Hospital and imaging experts at the Massachusetts General Hospital (led by Charles Lin), with collaborators at the pharmaceutical company Sanofi, has identified small molecules that can be used to program stem cells to home in on sites of damage, disease and inflammation. We tested more than 9,000 compounds for their ability to send stem cells in the right direction. We used a multi-step approach – including a sophisticated micro-scale set up and a novel imaging technique – to select and test the most promising compounds.

8,888…8,999…9,000!! science photo/Shutterstock

A molecular navigation system

We had previously found that it is possible to use bioengineering techniques to chemically attach molecules to the surface of a cell, to act as a GPS, guiding the cell to the site of inflammation.

Screening thousands of compounds, looking for ones that activated key molecules on the surface of the MSCs, we found six promising molecules, including one known as Ro-31-8425, the most potent of the group. We treated cells with each of these promising molecules and then flowed the cells into microscale glass channels, to simulate the flow of cells in the bloodstream. The glass channels were coated with a protein which is also found on the surface of blood vessels at inflamed tissue within the body. Cells pre-treated with Ro-31-8425 stuck to the coated channels – a sign that they might be able to home in on sites of inflammation.

The next step was to test our cells in an animal. We injected cells that had been pre-treated with Ro-31-8425 into the blood stream of a mouse with one inflamed ear. We then examined both ears using unique real-time microscopy, a technique that allows researchers to capture images of tissue in live animals. We observed that the cells treated with the compound not only homed in on the inflamed ear, but also reduced inflammation.

These findings, along with the multi-step screening platform we developed, have the potential to improve delivery of injected stem cells to sites of disease, where they can release their therapeutic cargo at high levels. This will greatly boost the clinical impact of cell-based therapies in treating life-threatening diseases.