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Archive 2012

Outbreak of shellfish poisoning in the Bay of Plenty Siouxsie Wiles Dec 19

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In the last week, twenty people have been poisoned by eating shellfish collected from the Bay of Plenty shoreline according to the Bay of Plenty District Health Board. They are calling it the worst outbreak ever seen in the area. Ten people have required hospital treatment and four people remain in hospital. Symptoms ranged from a tingling sensation around the mouth to difficulty walking.

Paralytic shellfish poisoning (PSP) is contracted by eating contaminated shellfish, such as mussels, pipi, tuatua, cockles, oysters, scallops and kina (sea urchin). Shellfish are filter feeders so can accumulate toxins produced by microscopic algae. The toxins responsible for most shellfish poisonings are water-soluble and heat and acid-stable, so aren’t destroyed by ordinary cooking methods. The main toxin responsible for PSP is called saxitoxin, although other related compounds have been reported. Saxitoxin is one of the most potent natural toxins known. It acts on the voltage-gated sodium channels of nerve cells, preventing normal cellular function leading to paralysis.

Saxitoxin structure (from Wikipedia)

PSP can be fatal in extreme cases. Symptoms usually occur within 12 hours of ingestion, and include nausea, vomiting, diarrhea, or abdominal pain; numbness and tingling around the mouth, face or extremities; difficulty swallowing or breathing; dizziness; double vision; and in severe cases, paralysis and respiratory failure.

The advice is not to collect shellfish from Tairua on the east coast of the Coromandel Peninsula, south to Waihi Beach and along the Bay of Plenty coast to Whakatane Heads in the Eastern Bay of Plenty. This includes Tairua Harbour as well as Tauranga Harbour, Maketu and Waihi estuaries, Matakana and Motiti Islands, and all other inshore islands along this coastline.

What I didn’t realise was that many shellfish can store saxitoxin for several weeks after a harmful algal bloom passes. According to wikipedia, butter clams can store the toxin for up to two years. Think I’ll give them a miss!

Saxidomus gigantea – the butter clam. Photo by Dave Cowles, August 2005.

What makes a good communicator? Siouxsie Wiles Dec 19

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Over the last month or so I’ve been to a lot of talks and its started me really thinking about what makes a good communicator. First it was the Maurice Wilkins Centre (MWC) for Molecular Biodiscovery‘s annual symposium (New ways to image the body – from macro to nano) followed by the New Zealand Microbiology Society‘s annual conference in Dunedin.

The MWC symposium was an exhausting day – 22 speakers with most of the slots just 15 minutes long. The speakers were given quite clear instructions – to do an introductory talk on their imaging technique in 12 minutes, leaving 3 minutes for questions. I know this because I was one of them. What was astonishing to me was that almost every speaker went over time. Most spoke for about 20 minutes. One spoke for almost 30! I’m becoming less and less tolerant of this kind of behaviour. In my mind it shows an immense lack of respect for the audience, the other speakers and the organisors. The other thing that struck me was that quite a few speakers pitched their material to a much more advanced audience than they actually had. Was this because they didn’t know who their audience was? And the jargon! Wow. I’m also becoming really aware of how data is visually presented. Busy slides with loads of different graphs are a nightmare. I think the most I’ve encountered was a single slide with 3 bar charts, 2 line graphs, a table and a pie chart. Where am I supposed to be looking?! Another classic mistake is for the speaker to point to a bit of their slide and telling the audience to ignore it as its irrelevant. What?? Then remove it!

So what makes a good communicator? Well, someone who sticks to time and correctly pitches the talk to the audience for a start. I’m pretty sure these are things we are told when we give our first talk, so why do we all forget them? Something we are not really taught to do is ditch the jargon. Or at least explain it properly first. I think this is important if you are going to speaking at an event with a broad audience. Both meetings I went to recently covered a lot of subject areas. No one is an expert in all of them, so not using hideous acronyms without explaining them first is essential if you don’t want people nodding off. I also think relatively simple, clean slides with good headings help.

So how am I doing? I’ve started setting an alarm to make sure I don’t go over time. And I’m trying to turn all my talks into more of a story with less emphasis on minute details as I’ve decided they really aren’t going to be of interest to the majority of the audience. I’m also trying to make my slides clearer and easier to follow. One thing I would like to do is have a play with the awesome looking presentation tool Prezi, but that will have to wait till I have some spare time. But I think what I most need to work on is speaking more slowly. I’m finding this really hard though as when I’m nervous or excited my mouth just zooms off! Hopefully practice will make perfect.

So, what do you think of my list? Is there anything that I missed?

Monday Micro Siouxsie Wiles Dec 17

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Tornadoes have always been a bit of an abstract thing for me, bringing to mind films like the Wizard of Oz and Twister. So I was surprised when one blasted through Auckland about 10 days ago killing three people who were crushed by falling concrete on a building site.

Then I saw a paper in my favourite journal PLOS One about some people who died when a catastrophic tornado with wind speeds of over 200 miles per hour hit the city of Joplin in Missouri in May 2011. According to Wikipedia, it was the deadliest American tornado in 65 years, killing 160 people.

Five of those people dies from an extremely rare infection called zygomycosis caused by the ‘flesh eating’ fungus, Apophysomyces. Apophysomyces species live in the soil and decaying vegetation and detritus. The authors describe the patients as having “traumatic inoculation of infective spores”. That is, spores introduced into their bodies through lacerations from contaminated objects literally blown into them by the strong winds. Nasty. The paper describes the sequencing of the genomes of the fungi isolated from 13 patients and finds they aren’t clonal which is consistent with multiple distinct fungal populations from soil and other organic matter being aerosolised by the tornado.

The infection does sound horrendous. Apparently the fungal hyphae rapidly grow, sealing off capillaries and shutting off the blood supply, leaving tissue to rot. Dead, damaged or infected tissues have to be surgically removed. According to the press release, the lead author David Engelthaler said one victim who suffered a deep wound to the upper right chest required a new titanium rib cage after the fungus rapidly destroyed skin and bones. Yikes!

Reference:
Etienne KA, Gillece J, Hilsabeck R, Schupp JM, Colman R, et al. (2012) Whole Genome Sequence Typing to Investigate the Apophysomyces Outbreak following a Tornado in Joplin, Missouri, 2011. PLoS ONE 7(11): e49989. doi:10.1371/journal.pone.0049989

Enough is enough Siouxsie Wiles Dec 16

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So this week I had yet another grant rejection letter. It was quite a nice one though. The panel said that I was a researcher they would like to support and had a great track record. But they noted that my project, which got great reviews, was too far away from being applicable to patients. They also not that while tuberculosis is clearly of global importance, it isn’t a problem in Auckland. They are a local charity so while disappointing, I can understand why they have taken the stance they have.

They also mentioned that a minor concern was that I have not published any papers from my time in Auckland yet. I have two currently under review but it was good feedback to receive as I’ve been thinking about what my next Marsden proposal should be on, and been playing around with a potential Smart Idea for the Ministry of Business, Innovation and Employment. This, combined with a sobering tweet I saw by Ethan Perlstein, has made me say enough is enough. I’m going to spend the next few months finishing papers and working in the lab. Hopefully that will help address at least some of the panel’s concerns next year!

I’ll leave you with Ethan’s tweet and a wonderful infographic on TB, just in case you needed reminding what a problem it is (and H/T to Paul Gardner!).

More party pills… Siouxsie Wiles Dec 10

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A leading New Zealand microbiologist says there is no reason why party pills have to be tested on animals.

I was quite surprised to find out that the “leading” microbiologist they are referring to is me! I say surprised because that wasn’t what I actually said.

The article, originally for the Sunday Star Times, was a follow up to my earlier blog post on how animal research is regulated here. I talked to the journalist about the ethical framework that underpins animal use in many countries, mainly the principles of replacement, refinement and reduction, explaining what humane endpoints were*. And I talked a little about the kinds of experiments that are usually done before compounds are put into animals. Like the Ames test which uses bacteria to see if a compound can mutate DNA and may therefore be carcinogenic.

The quote they ended up using was:

There are lots of things you can do to see if a compound is dangerous before you get it into an animal

See why I’m surprised?! Anyway, as toxicologist Rosalind Dalefield so kindly informs me, I “fell for their determination to get a uninformed opinion and misrepresent it as an informed one”. That’s me told, so any journalists please note, Rosalind is the lady to talk to**.

*Animals aren’t left to die but are humanely killed when defined criteria are reached.

**Rosalind has not one but TWO Board certifications in toxicology and offers “the benefit of my expertise” in nonclinical drug development, environmental toxicology, general toxicology and veterinary toxicology.

Monday Micro Siouxsie Wiles Dec 10

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Just a brief Monday Micro today as it will soon be Tuesday!

First up, what looks like quite a neat paper just out in the [Elsevier] journal Cell. Alas, its not open access so I’ve just read the abstract and write up on Science Daily. Marcus Stensmyr and colleagues at the Max Plank Institute for Chemical Ecology have found that fruit flies (Drosophila melanogaster) have a dedicated neural circuit to detect rotten food.

Because fruit flies feed primarily on yeast growing on fermenting fruit, they need to be able to distinguish fruit with safe yeast from fruit containing toxic microbes. Turns out they do this by sniffing out geosmin, a chemical produced by harmful bacteria and fungi.

What I like about this paper is the fact that the authors have made real efforts to communicate their science beyond the actual publication. They have made a short video explaining their results which is available to view on their institutions webpage here. It’s a little too full of jargon for my liking but a great effort nonetheless. Marcus also appears to be a dab hand at modelling clay and has made some great graphical representations of the work such as this below:

Copyright Marcus Stensmyr

Reference:

Marcus C. Stensmyr, Hany K.M. Dweck, Abu Farhan, Irene Ibba, Antonia Strutz, Latha Mukunda, Jeanine Linz, Veit Grabe, Kathrin Steck, Sofia Lavista-Llanos, Dieter Wicher, Silke Sachse, Markus Knaden, Paul G. Becher, Yoichi Seki, Bill S. Hansson. A Conserved Dedicated Olfactory Circuit for Detecting Harmful Microbes in Drosophila. Cell, 2012; 151 (6): 1345 DOI: 10.1016/j.cell.2012.09.046

Animal testing back in the news Siouxsie Wiles Dec 03

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The press seems to be full of people frothing at the mouth over suggestions by Associate Health Minister Peter Dunne that the manufacturers of ‘legal highs’ should be required to provide safety information on their products before they are allowed on New Zealand shelves. This comes on the back of the minister announcing a Temporary Class Drug Notice banning a substance called EAM-2201 found in samples of a synthetic cannabis product. EAM-2201 appears to be a synthetic hybrid of two known cannabinoid compounds previously used as active ingredients in synthetic cannabis blends, but which are now banned in many countries.

What has really got people upset is the suggestion that dogs and rats will be force feed ‘legal highs’ until half of them die (the so-called LD50 assay [the lethal dose at which 50% of animals are killed]) in an effort to provide us with some information on their ‘safety’. There is lots of talk of this test being banned in the UK. It’s certainly banned for the use of cosmetic testing in Europe but I’m not sure about all chemicals.

Four things strike me about this story:

1. Are the majority of people aware that there are products for sale which have essentially never been tested on humans or animals?

2. That people who take ‘legal highs’ are probably taking them because they are a legal alternative to illegal drugs. Ironically, we know an awful lot about illegal drugs so they are probably the safer alternative. It is also ironic that it is perfectly legal to buy tobacco and alcohol, two extremely harmful ‘drugs’.

3. That Peter Dunne and almost everyone else who commented on the story* has no idea how animal testing is regulated in New Zealand. This is what I want to comment on a little later.

4. What does everyone mean by ‘safety’ in reference to these ‘legal highs’? Do they mean LD50 (presumably we would want to know the dose likely to kill people rather than rats and dogs)? Or do they want to know if they are addictive? There was mention in the original press release banning EAM-2201 of its use being tied to “elevated heart rate, vomiting, anxiety and psychosis”. So is it anxiety and psychosis we are interested in? These are important questions, as they will determine the kinds of tests that need to be performed.

In New Zealand we have the Animal Welfare Act 1999 which came into force on the 1st January 2000. There is information about the Act on the Ministry for Primary Industry’s website here. Part 6 of the Act relates to the use of animals in research, teaching and teaching. It sets out that:

1. No research, testing or teaching may be carried out on any live animal unless the person or organisation involved holds an approved code of ethical conduct.

2. No project may proceed without the approval of an animal ethics committee (AEC) established under such codes.

3. The AEC comprises 3 members from outside the organisation holding the code of ethical conduct.

4. The AEC is subject to independent review.

5. The AEC will only approve research if there is a proven benefit and if that benefit outweighs the cost to the animals used.

6. The AEC will promote the use of the 3 Rs: replacement of animals with a non-living or non-sentient alternatives, reduction of numbers to the minimum required, and refinement of techniques to minimise harm and suffering.

So let’s get one thing clear. It is highly unlikely any ethics committee would approve LD50 tests for party pills in New Zealand. I should know because I’m a member of one. So should these untested products be on our shelves? And if they are to be tested, what are the criteria? It’s a tricky one. Personally I’d like to see how they do on the spider web test!

From Noever, R., J. Cronise, and R. A. Relwani. 1995. Using spider-web patterns to determine toxicity. NASA Tech Briefs 19(4):82. Published in New Scientist magazine, 29 April 1995.

*With the exception of Virginia Williams, the chair of the National Animals Ethics Advisory Committee (NAEAC) who appears to be the lone voice of reason.

Monday Micro Siouxsie Wiles Dec 03

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Welcome back to Monday Micro. Last week’s Monday was lacking in microbiology factoids as I was at the New Zealand Microbiology Society‘s annual meeting*. This year it was at the University of Otago in Dunedin. Highlights for me were keynotes by Rob Knight (microbiomes and Next Gen Sequencing), Eric Ruben (TB) and Steven Wilhelm (cyanobacterial blooms). Tweets of some of the talks are here.

Highlights for me:

Finding that lots of people flush public toilets with their feet, that cyanobacteria are a bad food source “like ordering pizza and only eating the box”** and that “we are all accidents of history”***.

Moving on, Round 3 of the SciFund Challenge is in full swing so if you fancy supporting some microbiology projects Amy Truitt wants so study butterflies and their sexually transmitted diseases, Will Helenbrook is studying the effects of infectious diseases on Mantled howler monkeys and Andy MacDonald is working on Lyme disease.

* The slides for my talk (Fireflies and superbugs: when science and nature collide) are up on slideshare. I started my talk with my Meet the Lampyridae animation….



** Steven Wilhelm
*** Unknown kilted MC of conference dinner :)

Monday Micro Siouxsie Wiles Nov 19

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“Would you chop your vegetables on your toilet seat? I think pretty much all of us would say No. But maybe we should think again.”

So writes the BBC’s Charlotte Pritchard in her article Is the toilet seat really the dirtiest place in the home?. According to Prof Charles Gerba* of the University of Arizona, it most certainly is not. With the average toilet seat harbouring around 50 bacteria per square inch, much more dangerous is the humble kitchen cloth with a million bacteria per square inch. If you want to see just where all the microbes in your home are likely to be lurking, check out this fabulous infographic on the Hygiene Council’s website. And in case you thought you were safe at work, a recent paper by Gerba and colleagues published in PLOS One (open access, yay!) sampled 90 randomly chosen offices in three different office buildings in New York, San Francisco and Tucson [1]. Their findings?

- Surfaces in men’s offices were consistently more contaminated than those from women’s offices
- Chairs and phones were the most contaminated of the surfaces tested
- Offices in San Francisco tended to be less contaminated than those in New York or Tucson

Another recent paper (again PLOS One and hence open access, yay!) explored the microbes present in another environment of significance to us [2]. As the authors put it:

“The belly button is one of the habitats closest to us, and yet it remains relatively unexplored.”

Until now! Robert Dunn has been getting people to send him swabs of their belly buttons in his ‘Belly Button Biodiversity’ citizen science project. The upshot? The richness of bacterial life in human belly buttons compares to that of the biodiversity found in rainforests! One participant, who admitted having not showered or bathed for several years, was home to several ‘extremophile’ bacteria not previously reported to live on human skin.

And finally, in more serious news, doctors are celebrating the development of a vaccine against one of the commonest causes of meningitis, meningococcal group B disease, known as MenB. The European Medicines Agency have apparently just given the vaccine, Bexsero, a ‘positive opinion’ and now have 60-90 days to decide whether to grant a licence.

References:
1. Hewitt KM, Gerba CP, Maxwell SL, Kelley ST (2012) Office Space Bacterial Abundance and Diversity in Three Metropolitan Areas. PLoS ONE 7(5): e37849. doi:10.1371/journal.pone.0037849
2. Hulcr J, Latimer AM, Henley JB, Rountree NR, Fierer N, et al. (2012) A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable. PLoS ONE 7(11): e47712. doi:10.1371/journal.pone.0047712

*As an amusing aside, Prof Gerba lists his appearance in numerous** Who’s Who publications. This is presumably to impress, but these publications have apparently been referred to by Tucker Carlson as the “The Hall of Lame”. His argument: the selection process is neither rigorous nor meaningful, people can self nominate and thousands of people not particularly notable are included. The publisher seems to make money by selling tat (sorry, ‘personalised keepsakes’) to those who want to celebrate the ‘achievement’ of being listed. Carlson claims the publisher also makes money selling details of those included to direct mail marketers.

**Who’s Who in Technology Today, 1984, 1986, 1989; International Who’s Who in American Education, 1992-1993, 1995, 1996-1997;Who’s Who in the West, 1987-present; Who’s Who in Emerging Leaders in America, 1989-1990, 1991-1992; Who’s Who in the World, 1989-1995-present; American Men & Women of Science, 1992-1993, 1996-1997-present; Who’s Who in Science and Engineering, 1992-1993, 1996-1997; Who’s Who in America, 1994 – present; Who’s Who in Medicine and Healthcare, 1997-1998-present.

Credit where it’s due? Siouxsie Wiles Nov 18

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H/T to @MyBioTechniques for pointing me to a Chronicle article by Chris Woolston ‘When a mentor becomes a thief‘, which recounts a number of cases of junior scientists finding themselves left out of authorship when papers about their work are published. The peer reviewed publication is the currency of science and as a result all sorts of shenanigans go on. When I looked at the article again, I see it’s almost 10 years old. So has anything changed?

I’m not sure it has. This is in spite of many journals now including a section where each author’s contribution is listed. In my time in science I’ve been left off a couple of paper’s that I contributed data to, had a leading group not cite my work so they could get their paper into a higher impact journal by claiming novelty, and a number of times been shafted with my position on the list of authors not reflecting my contribution. I’ve also had a number of authors foisted on me for ‘political’ reasons.

My favourite line in Chris’ article is:

“Before a single beaker gets rinsed, the question of authorship has to be laid on the table”

This must be one of the most important pieces of advice for a scientist to follow. I have to admit that I almost never do this. Maybe this is why I’ve been shafted so many times. When I start out on a piece of research, I’m not thinking about the papers but the science being addressed. It seems both presumptive and rude to be talking about papers at that early stage!

So how do others do it? I’d be really interested to hear what you think!

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