SciBlogs

Monday Micro – Is the new Saudi coronavirus a pandemic in waiting? Siouxsie Wiles May 13

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Between November 2002 and July 2003, a novel respiratory virus appeared in South China, spreading first to Hong Kong and going on to infect people in 37 countries around the world. As the virus spread, thousands were quarantined, schools were shut, and many airports implemented thermal screening programmes to stop potentially infected people from getting on planes. By the end of the pandemic, the Severe Acute Respiratory Syndrome (SARS) coronavirus (SARS-CoV) had resulted in 8,273 cases and 775 deaths, a case fatality rate of 10%.

So it’s not surprising that many are now nervous after the World Health Organisation (WHO) reported that a novel coronavirus (nCoV), closely related to the SARS virus, has emerged in the Middle East. Since early 2012, there have been 34 confirmed cases of infection with nCoV, which causes severe acute pneumonia and renal failure. With 18 deaths so far, the case fatality rate currently sits at over 50%, a frightening statistic. But is this new coronavirus going to go pandemic, like the SARS virus did? With such a small number of cases to date, it is too early to say for sure.

In 2002/2003, the SARS virus spread rapidly, infecting otherwise healthy individuals. It arrived in Hong Kong via a mainland doctor who stayed at a hotel in Kowloon. He infected 16 of the hotel visitors, who themselves traveled on to Canada, Singapore, Taiwan, and Vietnam, taking SARS with them.

In contrast, the majority of nCoV cases have remained within Saudi Arabia and while there have been cases exported to Jordan, Qatar, the United Arab Emirates, the United Kingdom and France, the virus does not seem to have spread much beyond the index cases. There have been a small number of cases of family members becoming infected. This confirms that nCoV can transmit from person to person but suggests that prolonged exposure is needed to become infected, at least for healthy people.

One of the interesting features of this novel coronavirus, is that the majority of infections have occurred within health care facilities. The most recent cluster of cases within Saudi Arabia have occurred within a single facility and all patients had at least one other underlying disease. Furthermore, the Ministry of Social Affairs and Health in France has just informed the WHO of a confirmed case of nCoV in a patient who spent three days sharing a hospital room with France’s first nCoV patient. These cases suggest that underlying diseases may also make people more vulnerable to infection with nCoV.

So far, the evidence is suggesting that nCoV is unlikely to turn into a pandemic. But the thing about viruses is that you never know. What we do know is that nCoV is highly infectious to human airway epithelial cultures in the laboratory, and that the virus can hide itself from the human immune system (1). But somehow this isn’t currently translating into epidemic spread out in the real world. But we shouldn’t be complacent. It is certainly not inconceivable that nCoV could mutate in some way to become more infectious to healthy people, the first step towards a SARS-like scenario. And there is still so much we don’t know about nCoV. Where did it come from? What is nCoV’s natural reservoir? In the case of SARS, the virus was found in samples of wild animals sold as food in the local markets, many of which show no clinical signs of infection. So far, there is limited information on any potential links between nCoV cases and exposure to animals, although nCoV is closely related to coronaviruses from bats (2).

If nothing else, though, the emergence of nCoV is another warning of the threat we face from novel viruses. As many of these viruses cross over to humans from wild animals, these threats are going to increase as humans continue to encroach on the natural habitats of so many creatures. And our interconnected global world means any virus is less than 24 hours from anywhere else on earth. A sobering thought.

References:

1. Kindler E, Jónsdóttir HR, Muth D, Hamming OJ, Hartmann R, Rodriguez R, Geffers R, Fouchier RAM, Drosten C, Müller MA, Dijkman R, Thiel V. 2013. Efficient replication of the novel human betacoronavirus EMC on primary human epithelium highlights its zoonotic potential. mBio 4(1):e00611-12. doi:10.1128/mBio.00611-12.

2. van Boheemen S, et al. 2012. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio 3(6):e00473-12. doi:10.1128/mBio.00473-12.

New Zealand’s National Science Challenges announced Siouxsie Wiles May 01

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NZ’s National Science Challenges announced alongside a massive funding boost

In the beautiful blue Ocean gallery at the Auckland War Memorial Museum, the Prime Minister John Key, the Honourable Minister for Science and Innovation Steven Joyce and the Prime Minister’s Chief Science Advisor Sir Peter Gluckman, today announced the 10 National Science Challenges.

The PEAK panel*, chaired by Sir Peter Gluckman, was charged with developing the Challenges using the following criteria:
1) Target high level goals, which if achievable would have a major public benefit to NZ
2) Be seen as being of public importance, hence the public engagement campaign
3) Have scientific research as essential to solving the Challenge
4) The scientific capability and capacity existing in NZ

The panel considered 223 submissions from the science and research sector, 138 from the public via the web, and 616 ideas and comments posted to the Great NZ Science Project website and Facebook page. The main 10 Challenges are listed on the Ministry for Business, Innovation and Employment’s website here, and the document explaining them in a little more detail is here.

The big surprise came with the announcement that the budget for the Challenges had been more than doubled with the allocation of an extra $73.5M, bringing the total budget over the next four years to $133.5M. It will be interesting to see where this money has come from. The second exciting announcement was of a special extra ‘Science and Society leadership Challenge’ brought about by what the panel identified as deficits in science education, science communication, science literacy and the application of evidence in all levels of decision making. This challenge therefore covers a huge array of themes, from promotion of science literacy in schools, to developing science communication as an academic discipline and encouraging members of the public to participate in science as ‘citizen scientists’.

But other than the Science and Society Challenge, is it ‘business as usual’? It does look awfully like it. Just looking at the biomedical related Challenges, I was really shocked to see that infectious diseases don’t get a mention. In fact, in the Challenge 3 Healthier Lives: Research to reduce the burden of major New Zealand health problems, they are specifically excluded as the focus is on non-communicable diseases (NCDs). I do hope the 792 people who ‘voted’ for my illustrative ‘Fighting Diseases‘ Challenge on the Great NZ Science Project didn’t think they were actually voting for me! I asked Sir Peter about this at the Science Media Centre’s media briefing afterwards and he explained that they had considered infectious diseases, but that more people die from NCD’s in NZ, and that in the panel’s opinion, infectious diseases research in NZ didn’t meet the criteria of having sufficient capability and capacity to address a Challenge. This is depressing as NZ is bucking international trends, with our rates of infectious diseases on the increase rather than decreasing, which is what would be expected of a developed country like ours.

At the media briefing I also specifically (and rather cheekily) asked Steven Joyce and Sir Peter how much of the funds would be used to support post-doctoral fellows and PhD students to actually do the science, and how much would be spent on the salaries of Principal Investigators. It is an important question, especially given that the Challenges have multi-disciplinarity and collaboration at their heart. If the Challenges are funded like normal contestable granting bodies like the Marsden and Health Research Council, we could find most of the money going to pay the time contribution of the ‘silverbacks’ and not on salaries for younger researchers. Both the minister and Sir Peter answered that ‘workforce development’ would be a key measure of success so we’ll see how that works out.

*PEAK panel members: Peter Gluckman, Jacqueline Rowarth, Ian Ferguson, William Denny, Elf Eldridge, Peter Hunter, Mary O’Kane, David Penman, Te Ahu Karamu Charles Royal, Richie Poulton and Rachel Wiltshire.

UPDATE: I live-tweeted the announcement so have storified the tweets here.

Monday Micro: living night lights Siouxsie Wiles Apr 29

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One of the latest Kickstarter projects to create a buzz is promising its backers a living nightlight that shines without electricity. Enter the Glowing Plant project, developed by a group of biohackers from BioCurious* in California. Launched just a few days ago, Antony Evans, Omri Amirav-Drory and Kyle Taylor have already exceeded their $65,000 target needed to create a genetically engineered plant that glows in the dark. In fact, they have already passed the $115,000 mark with over a month left to go. Their new goal is $400,000 to create a glowing rose. Check out their short video by clicking the link below:

Glowing plant vid

So how are they going to do it? Back in 2010, Alexander Krichevsky and colleagues published a paper in PLOS One showing that tobacco plants could be engineered to glow in the dark by incorporating the genes (known as the lux operon) which make the marine bacterium Photobacterium leiognathi** glow (1). The light generated by one of the plant lines they created could be detected by eye in a dark room after about 5-10 minutes suggesting they could make quite neat night lights. This was exciting stuff as previous attempts to make glowing plants had revolved around getting the plants to express the luciferase gene from the firefly, which required plants to be sprayed with luciferin, the substrate for the reaction, in order for light to be produced. In contrast, cells that express the whole bacterial lux operon glow without needing any additional cofactors.

Glowing tobacco plants

Glowing tobacco plants

Interestingly, Krichevsky declares in his PLOS One paper that he is founder of BioGlow Inc, a company which aims to develop commercially available glowing ornamental plants. BioGlow Inc is listed as a tenant of the Bio-Research & Development Growth (BRDG) Park at the Danforth Plant Science Centre in Missouri, but otherwise doesn’t have much of a web presence.

But back to the Glowing Plant project. Antony and his team say they are planning on building on the work of Krichevsky and colleagues, making a synthetic version of the bioluminescence genes so that they will be better expressed by the plant cells. Fingers crossed!

Reference:
1. Krichevsky A, Meyers B, Vainstein A, Maliga P, Citovsky V (2010) Autoluminescent Plants. PLoS ONE 5(11): e15461. doi:10.1371/journal.pone.0015461

*The BioCurious ethos is that innovations in biology should be accessible, affordable, and open to everyone. They have built up a complete working laboratory and training centre for citizen scientists and hobbyists to get together to do science.

**I’ve blogged about P. leiognathi before. They use their light to trick zooplankton into eating them. In a nutshell, the zooplankton ingest the glowing bacteria but are unable to digest them. The glowing bacteria mean the hapless zooplankton are then more visible to their own predators, nocturnal fish, who devour them. P. leiognathi are unfazed by all this, ending up in the fish’s digestive system which is where they wanted to be in the first place. Genius.

Why stereotyping scientists matters Siouxsie Wiles Apr 27

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I’m always interested to find out what people think I do for a living. No one has ever said scientist. It’s usually something in the arts or fashion*. You know, creative industries. I’m guessing it’s because of my hair. What is interesting about this though is that somehow people don’t think of science as being creative. Such misperceptions are largely due to the way scientists are portrayed in the media. It’s really interesting looking at stock photos to see how different professions are portrayed; some of the best of scientists have been collected together by various bloggers. Male scientists are usually older with crazy hair, while women scientists are scantily clad or have completely forgotten to wear any clothes. White coats abound, as do glass vials of coloured liquids. But how representative are these images of scientists? Not very, I’d say. But should we care? Yes!

This 'scientist' remembered her gloves and safety glasses but forgot her clothes!

This ‘scientist’ remembered her gloves and safety glasses but forgot her clothes!

A few days ago I gave a talk to primary school teachers about why stereotyping scientists matters. It was partly inspired by data looking at pictures of scientists drawn by school children before and after a visit to the Fermi National Accelerator Laboratory, near Chicago, which specialises in high-energy particle physics. Lots of the before images are of crazy haired old men in white coats, with many children describing careers in science as unobtainable. But after the visit, the scientists start to look just like normal people, and the children even start to suggest they could see themselves as scientists one day.

After my talk, the lovely Dr Sally Birdsall sent me a paper published in 1999 that looked at children’s portrayals of scientists [1]. The authors collected 562 drawings done by 281 children aged 5-13 living in different socioeconomic areas of London. I’ve plotted some of the data showing the percentage of drawings that represented male and female scientists, as well as those where scientists are portrayed wearing a lab coat or doing chemistry-type experiments. As you can see, more males are portrayed than females, a trend which increases as the children get older, at least until the age of 10. What is really interesting is that the numbers of drawings of scientists in white coats/doing chemistry increases with age, presumably as children are exposed to media portrayals of stereotypes.

How kids portray scientists

How kids portray scientists

It seems clear to me that being exposed to more realistic portrayals of scientists makes a difference, at least to children. Meeting real scientists is even better. If you are a scientist reading this, consider getting in touch with your local school and volunteering to go in and meet some of the kids. The younger the better! In the absence of having any scientists volunteer, in my talk I pointed to some online resources that teachers could use to show scientists in all their real glory. There is the fantastic ‘This Is What a Scientist Looks Like‘ which has pictures and profiles for over 600 scientists of all colours, shapes and sizes. There is also the ‘100 Women, 100 Visions‘ project, a series of 100 pictures taken by photographer Jackie King in 2009 to celebrate the variety of women scientists and engineers at Imperial College London**. And finally, there was the Great NZ Science Project, the public engagement campaign for the National Science Challenges***, which used 8 scientists to illustrate the diversity of science going on in New Zealand. What I love about this campaign is that it showed that science happens everywhere, not just in labs. And only three of the 8 scientists are wearing lab coats****. The TV advert below got a lot of airplay on NZ TV so I hope that will go someway to busting some of the stereotypes.

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Slides from my talk:


Reference:
1. Changing children’s images of scientists: can teachers make a difference? Brian Matthews and Daniel Davies (1999). School Science Review. 80 (293): 79-85.

*Fashion always cracks me up. I got the award for being the worst dressed two years running in high school. True, the award was coveted by the ‘alternative’ crowd – it meant your efforts to be different had been recognised :)

**See if you can spot a familiar face.

***Which are being announced on Wed 1st May…

****Make no mistake though, the campaign wasn’t perfect. One of it’s main features seemed to have been to perpetuate the myth that all scientists are bad communicators. One stereotype at a time I guess.

Press Complaints Commission upholds homeopaths complaint Siouxsie Wiles Apr 16

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Tauranga homeopath Clive Stuart has had part of his complaint against an article on homeopathy (Homeopathy – Trick or Treatment?) by Stacey Anyan, published in the July 2012 edition of North & South, upheld by the Press Complaints Commission (PCC)*. While the PCC did not agree with his complaint that balance needed to be numerically equivalent (there were quotes from two people critical of homeopathy and one defending) or that his letter to the editor should not have been accompanied by a response from a critic of homeopathy (Dr Shaun Holt), they did uphold his complaint that the article was wrong to say that “homeopathic remedies have failed every randomised, evidence-based scientific study seeking to verify their claims of healing powers”.

The article title is a reference to the excellent book ‘Trick or Treatment? Alternative Medicine on Trial’ by Dr Simon Singh and Prof Edzard Ernst. Prof Ernst is a doctor and former homeopath who was the world’s first professor of complementary medicine, at the University of Exeter. This is what they conclude about homeopathy:

“Hundreds of trials have failed to deliver significant or convincing evidence to support the use of homeopathy for the treatment of any particular ailment. On the contrary, it would be fair to say that there is a mountain of evidence to suggest that homeopathic remedies simply do not work. This should not be such a surprising conclusion when we recall that they typically do not contain a single molecule of any active ingredient.”

But lets not take their word for it. In 2009-2010 the UK House of Commons Science and Technology Committee performed an ‘evidence check‘ on homeopathy, calling defenders and critics alike to present the evidence for and against homeopathy. Their conclusion:

“…the evidence base shows that homeopathy is not efficacious (that is, it does not work beyond the placebo effect) and that explanations for why homeopathy would work are scientifically implausible.”

It would seem from these that the scientific evidence points to homeopathy having no effect beyond placebo, when evaluated using methodologically sound protocols by people without a vested interest in homeopathy. However, the PCC:

“found the article inaccurate in so far as the state of scientific research into homeopathy is not
as conclusive as North & South had suggested.”

If only Stacey Anyan had included the words ‘well-designed’ in her sentence. What a difference a couple of little words would have made. There is certainly an important lesson for journalists in this debacle.

It is interesting to read in the judgement* how the PCC came to their conclusion. They seem to have been swayed by a 7 page letter from a Dr David St George. We’ll get to who he is in a moment. This is what the PCC say:

Dr St George believed the statement in North & South’s article arose from a misunderstanding of the Lancet study, which had compared 110 published placebo-controlled trials of homeopathy with the same number of published placebo-controlled trials of conventional medical drug treatments. He said most of the 110 homeopathy trials in that study were “randomised, evidence-based scientific studies” which demonstrated an effect beyond a placebo effect.

Actually the Lancet study Dr St George is quoting concluded “Biases are present in placebo-controlled trials of both homoeopathy and conventional medicine. When account was taken for these biases in the analysis, there was weak evidence for a specific effect of homoeopathic remedies, but strong evidence for specific effects of conventional interventions. This finding is compatible with the notion that the clinical effects of homoeopathy are placebo effects.”

Two disturbing things come to light from this case. The first is that the PCC breached its own rules by accepting Dr St George’s letter which was the third submission in this case (two submissions are allowed by both sides) so it will be interesting to see why this was allowed. The second is finding out who Dr David St George is and what he does for a living. Dr St George has a medical degree from the University of Auckland and a degree in epidemiology from McGill University in Montreal, Canada. He worked as a consultant clinical epidemiologist at the Royal Free Hospital in London and then as Director of Research and Clinical Effectiveness at Southampton University Hospital. He was also the first Director of Research at the Foundation for Integrated Health, a controversial charity founded in 1993 by the Prince of Wales to promote alternative and complementary medicine, lobbying for its inclusion in the UK’s National Health Service. The charity closed in 2010 after it’s finance director, accountant George Gray, was convicted of theft and sentenced to three years in prison. It is unclear what research, if any, the Foundation undertook.

Dr St George’s other ‘achievements’ include helping Middlesex University set up an undergraduate degree in traditional Chinese medicine**, being research committee chairman of the (now defunct) Scottish School of Herbal Medicine and a former member of the British Acupuncture Accreditation Board***. But now he is back in New Zealand and working for the NZ Ministry of Health as ‘Chief Advisor – Integrative Care’. I wonder if this swayed the PCC at all into accepting his unorthodox, rather lengthy and over technical submission. This is what it says on the Ministry’s website about Dr St George’s role:

Dr David St George’s role is to provide professional leadership, direction and advice on complementary and alternative medicine (CAM), and on the integration of CAM with conventional health care, particularly in the area of primary care and chronic care conditions.

Oh dear. I think we need to find out exactly what ‘direction and advice’ Dr St George has been giving to the Ministry for Health. Because by his submission to the PCC I’m not entirely confident it will be based on unbiased methodologically sound scientific evidence. Dr Prue Williams, General Manager of Science Investments for the Ministry of Business, Innovation and Employment, announced at the recent NZ Association of Scientists annual meeting in Wellington that there are plans for all ministries to have scientific advisors in place. I suggest whoever is appointed for the Ministry of Health starts by looking into Dr David St George.

*It’s case 2320, the judgement for which isn’t up on the PCC website yet.

[Update: 14:20 on 16/04/2013 - judgement now available online here]

***On the subject of Traditional Chinese Medicine (TCM) Singh and Ernst conclude: “Some elements may be effective for some conditions, while others (e.g. cupping) are unlikely to offer any benefit above placebo. Many aspects of TCM are potentially harmful. Some individual herbs used in TCM (e.g. liquorice, giner, ginko) undoubtedly have pharmacological effects.. On the other hand, some.. are toxic … may also contain non-herbal ingredients (e.g. endangered animals), contaminants (e.g. heavy metals) or adulterants (e.g. steroids).”

***On the subject of acupuncture Singh and Ernst conclude: “..there is no evidence at all to demonstrate the existence of Ch’i or meridians [the basis for acupuncture points]. There are some high-quality trials that support the use of acupuncture for some types of pain and nausea, but there are also high-quality trials that contradict this conclusion. In short, the evidence is neither consistent nor convincing – it is borderline.”

Reference:
Shang A, Huwiler-Müntener K, Nartey L, Jüni P, Dörig S, Sterne JA, Pewsner D, Egger M (2005). Are the clinical effects of homoeopathy placebo effects? Comparative study of placebo-controlled trials of homoeopathy and allopathy. Lancet 366(9487):726-32.

The legacy of the MMR debacle Siouxsie Wiles Apr 15

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Wales in currently in the grip of a measles epidemic, with nearly 700 people diagnosed with the highly contagious virus since the outbreak began in November last year. To put this in perspective, in 2012 there were 2,016 cases of measles in the WHOLE of England and Wales, with 116 of those in Wales.

Measles is preventable with the combined Measles, Mumps and Rubella vaccine, more commonly known as MMR. Rates of MMR uptake in the UK are well below the 95% needed for herd immunity to protect those too young or vulnerable to be vaccinated. In 2011-2012, uptake rates for the 2 doses stood at 86% in England and 82.4% in Wales. Dr Meirion Evans of Public Health Wales has said that there are an estimated 40,000 children across Wales who have not been vaccinated and that the number of cases could easily double. This is a frightening prospect as measles can mean more than just a fever and rash – it can also lead to ear infections, pneumonia, inflammation of the brain and death.

Most people would now agree that the low uptake rates for MMR are a result of a now retracted paper by discredited gastroenterologist Andrew Wakefield (who was struck off by the medical register by the General Medical Council in the UK in 2010) linking the MMR vaccine with autism, the refusal of former UK Prime Minister Tony Blair to disclose whether his son Leo had been vaccinated, and some pretty shocking media coverage. While the health service in Wales has been setting up mass drop in vaccination clinics in an attempt to reduce the pool of potential measles victims, it was therefore a strange and dangerous decision by the Independent newspaper’s Health Editor, Jeremy Laurance to run a press release from Wakefield along with an article which appeared on the front page of the newspaper under the headline:

MMR scare doctor Andrew Wakefield breaks his silence:
Measles outbreak in Wales proves I was right

Wakefield claims that the drop in vaccination was due to the government’s decision not to grant an import licence for single vaccines, which at the time he was suggesting be offered in place of the MMR vaccine. Turns out he had a vested interest in pushing single vaccines, which would have increased the time taken before children were fully protected against measles, mumps and rubella. True, the article written by Laurance is critical of Wakefield, but why provide any fuel for the fire? Perhaps this description of Laurance from the Independent’s webpage says all we need to know:

Jeremy Laurance is Health Editor of The Independent and the i and has covered the specialism for more than 20 years. He thinks the harm medicine does is under-appreciated, the harm it prevents over-rated, and that cycling works better than most drugs. He was named Specialist Journalist of the Year in the 2011 British Press Awards.

Monday Micro – Influ-Venn-Za! Siouxsie Wiles Apr 15

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A new strain of bird flu (H7N9*) has appeared in China. Since the first report two weeks ago, 51 people are known to have been infected of which 11 have died. Transmission seems to be from close contact with poultry and many birds are being culled as a precaution. Cases started in Shanghai and the eastern provinces of Jiangsu and Zhejiang but have now been reported in Beijing.

For those struggling to tell their H7N9 from their H5N1, the lovely peeps who run Information is Beautiful have come up with a handy guide to flu in the form of a beautiful Venn diagram:

Influenza types

Influ-Venn-Za!

*Flu viruses are classified into subtypes based on antibody responses to the two large glycoproteins on the outside of the viral particles, hemagglutinin and neuraminidase.

Astrosquid! Siouxsie Wiles Mar 27

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What is the value of blue-skies research?

This is a question often asked by politicians and the public. Why should public money be spent funding science that seems to have no obvious benefit beyond generating scientific knowledge? The simple answer is that it can be almost impossible to predict what new avenues that scientific knowledge will open up. Take the Hawaiian bobtail squid, for example. What could studying this little nocturnal hunter possibly lead to? Take a guess. No ideas? Let me help you out.

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It lead to the discovery that bacteria are able to communicate with each other, including how they sense when the time is right to turn on genes needed to cause disease. I’m not sure anyone could have seen that coming! Importantly, this research has provided scientists with another potential weapon with which to fight antibiotic resistant superbugs. In a world rapidly running out of antibiotics, we need all the weapons we can get.

This animation was produced with the support of a public engagement grant from the UK Society for Applied Microbiology, to engage the services of graphic artist Luke Harris and his team. Dr Siouxsie Wiles (@SiouxsieW) is a microbiologist and bioluminescence enthusiast who heads up the Bioluminescent Superbugs Group at the University of Auckland in New Zealand. She and her team make nasty bacteria glow in the dark to help understand and combat infectious diseases.

What we couldn’t fit into 3 minutes…

The Hawaiian bobtail squid, Euprymna scolopes, is just 3 cm in length and lives in the shallow moonlit waters off Hawaii. It spends its days sleeping buried in the sand, emerging at night in search of food. It has a very cunning trick to hide its shadow from fish looking for a meal, or from creatures like shrimp that it feeds on. It houses a colony of glowing bacteria (Vibrio fischeri) in a special organ on its underside. These bioluminescent bacteria shine their light down so that to any creatures looking up, the squid just looks like the moon. What is even more clever is that the squid uses its ink sac to match the intensity of moonlight hitting its back, dimming the light from the glowing bacteria as needed. This is important not just for cloudy nights but as the squid moves through different depths of water.

Baby squid are born without V. fischeri or a light organ. Instead they just have a small opening in their mantle (the bulbous bit of their body) that is bathed by sea water. What is incredible is that only V. fischeri can colonise this opening – once they do, the squid cells start to change and the light organ forms. The ability to glow is crucial though – scientists have made versions of V. fischeri which can’t glow and they aren’t able to colonise either.

Adult squid have an ingenious way of ensuring that there is plenty of V. fischeri floating around in the water to colonise baby squid. Each morning, before they settle down in the sand to sleep for the day, they expel 99.9% of the bacteria from their light organ into the sea. This serves another purpose too, ensuring the bacteria left behind in their light organ are constantly growing and have plenty of nutrients. Bacteria that run out of nutrients start to shut down to save energy. Producing light takes quite a bit of energy and the last thing the squid wants is a mantle full of lazy dim bacteria!

When scientists first identified V. fischeri and grew it in the lab they noticed something quite interesting. The bacteria only switch on their light when they have reached a critical population size. This makes perfect sense. There is no point going to all the trouble of making light if it isn’t bright enough to be seen. Each bacterium produces a chemical, called the autoinducer, that diffuses out of the bacterial cell. The more bacteria there are, the more autoinducer is produced. If those bacteria are growing in a confined space like a flask, or the light organ of the squid, the autoinducer will accumulate. Once it reaches a critical concentration, the autoinducer triggers the bacteria to switch on the genes for producing light*. This phenomenon is called quorum sensing.

Scientists then used the bioluminescence reaction to see if other species of bacteria produce autoinducers. Surprise, surprise, it turns out that lots of different bacteria use quorum sensing to signal to each other that they are in the right numbers or environment to do something, which is not worth doing otherwise. From the bacterial form of sex, to swimming, to switching on the genes needed to cause disease in plants, animals and humans. Now we just have to find a way of exploiting this to our advantage!

You can hear me chatting about the squid and quorum sensing on Radio New Zealand’s Nine to Noon programme with Kathryn Ryan here (13’12”):

*For those who really want to know, the autoinducer is the product of the luxI gene. When it reaches a critical concentration, it interacts with the product of the luxR gene, and together this complex binds to a region of DNA upstream of the genes under their control called the lux box which then triggers their transcription.

Monday Micro – World TB Day Siouxsie Wiles Mar 25

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Yesterday, the 24th of March, was World TB Day which aims to build awareness for tuberculosis, a lung disease which kills about 2 million people around the world each year. That’s 3 people a minute. Why the 24th March? This was the day, in 1882, that Dr Robert Koch* announced he had discovered the bacterium that causes TB, Mycobacterium tuberculosis.

TB, or consumption as it was known, had long been thought to be a hereditary disease. In 1869, French physician Jean-Antoine Villemin showed the disease was infectious. He injected rabbits with material taken from people who had died of TB. Not surprisingly, the rabbits became ill. Thirteen years later, Robert Koch, purified the microorganism responsible, for which he won the Nobel Prize in Physiology or Medicine in 1905.

But despite it being over 100 years since M. tuberculosis was discovered, we are a long way from eradicating TB, hence World TB Day. The Global Fund, supported by the Gates Foundation and others, have put together this nice infographic highlighting some facts and figures.

GatesTB20130321FINALJPG

M. tuberculosis is one of the organisms my lab at the University of Auckland are busy working on. If you want to know what we are doing, here’s the little animation I made with graphic artist Luke Harris and his team to show how we are using fireflies to make TB research faster and more humane.

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*Koch is best known to microbiologists for what we now refer to as Koch’s Postulates, four criteria he stated needed to be proven to establish a causal relationship between an microorganism and a particular disease. These are:

1. That the microorganism is found in all cases of the disease examined, while absent in healthy organisms
2. That the microorganism be isolated from a diseased host and grown in a pure culture
3. That the microorganism should be capable of producing the original infection when introduced into a healthy host, even after several generations in culture
4. That the microorganism is retrievable from an inoculated/experimental host and cultured again.

As with everything though, it turns out that there are exceptions to every rule, and we now know many microorganisms that fail one or more of Koch’s Postulates but are still clearly the cause of a particular disease. For example, many nasty microorganisms can be carried asymptomatically by healthy people (including Vibrio cholerae, the agent responsible for cholera), while there are a number of microorganisms which we are unable to culture in the laboratory (including Mycobacterium leprae, the agent responsible for leprosy, which can only be grown in the footpad of a mouse, or a nine-banded armadillo).

Monday Micro – roller derby micro! Siouxsie Wiles Mar 18

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There were a smorgasbord of micro stories to choose from this week, but how could I pass up a story which combines microbes, open access and gorgeous women on roller skates?!

James Meadow and colleagues, from the Institute of Ecology and Evolution at the University of Oregon, have just published a paper looking at the effect of contact sports on the microbial communities living on the skin of the participants. This is where the roller skates come into the story, as the contact sport James and his colleagues studied was roller derby*.

This great picture by Emily Thomas AKA Mummy'sLittleMonster sums up roller derby perfectly!

This great picture by Emily Thomas AKA Mummy’sLittleMonster sums up roller derby perfectly!

James’ paper is one of the first to be published in new online open access journal PeerJ which launched recently. More on this new journal below, but one feature I do want to point out is that authors can elect to make the review history of the article public, which James and his colleagues did. It makes for fascinating reading!

But back to the paper. James and colleagues hypothesised that close contact between people would create shifts in the microbial communities living on the skin. And that’s pretty much what they found. Here is a nice plot showing the microbial composition of the skin of each team member before and after playing. Each symbol represents a player, each colour represents a different team (they looked at three teams: the Emerald City Roller Girls, the DC Roller Girls and the Silicon Valley Roller Girls) and the coloured ellipses show the standard deviations around the community variances from each team. Before they started, the skin microbiomes of members of each team clustered nicely together – presumably because they train together and therefore often come into contact with each other. After playing you can see that the skin microbiomes have changed and become much more similar between the teams – they’ve shared their microbes!

Variation in skin microbial community composition is significantly explained by team identity.

Variation in skin microbial community composition is significantly explained by team identity.

The authors concluded that:

“contact sports provide an ideal setting in which to evaluate dispersal of microorganisms between people.”

Certainly looks that way!

Reference:
Meadow et al. (2013) Significant changes in the skin microbiome mediated by the sport of roller derby. PeerJ 1:e53 http://dx.doi.org/10.7717/peerj.53

Conflict of interest statement: I am a PeerJ academic editor but did not handle or review this manuscript.

* For details see the official Women’s Flat Track Derby Association (WFTDA) rules. Two competing teams, each composed of up to 4 ‘blockers’ and 1 ‘jammer’, simultaneously circle the track while the jammers, who start behind the pack, try to score points by lapping players of the opposing side. The catch is that the blockers can use their bodies (arms from shoulder to elbow, torso, hips, booty** and legs from mid to mid to upper thigh) to try to stop the jammers from lapping the pack. There is some great footage of some teams in action on You Tube:

YouTube Preview Image

**Official WFTDA nomenclature..

***PeerJ was founded by Peter Binfield (formerly at PLOS ONE) and Jason Hoyt (formerly at Mendeley) and is backed by O’Reilly Media. PeerJ aims to be a biological and biomedical version of PLOS ONE, with papers judged solely on their scientific and methodological soundness, rather than potential ‘impact’,. Like PLOS ONE, PeerJ papers are freely available to read and published under a Creative Commons licence which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Like PLOS ONE the costs are covered by the researcher but in the form of membership fees per author, rather than article processing charges. a one off payment of $99 allows an author to publish one paper per year for life, while $299 allows an author unlimited publications per year.

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