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Biolumination: Turning glowing fish poo into art… sort of! Siouxsie Wiles Jan 22

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Last year I collaborated with artist Rebecca Klee for the Art in the Dark festival, held in Auckland, New Zealand, each year. Our piece, called Biolumination, featured several litres of glowing bacteria, some custom-made glass tubes and three aquarium pumps. A big thanks to Benj from Gather and Hunt who shot some footage of our installation and put together this short video in which I explain why the bacteria we used glows in the first place.

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Will new antibiotic Teixobactin save us all? Umm, not quite. Siouxsie Wiles Jan 08

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soil

Researchers in Germany and the USA have just published a paper in the journal Nature describing a new antibiotic they have called Teixobactin (1). This study is good news; the World Health Organization warned last year that cancer chemotherapy and routine surgery will soon become life-threateningly risky because of the worldwide rise in antibiotic-resistant superbugs (2). So will Teixobactin save us all from a post-antibiotic era? Maybe, but not in the way you think it might. Here’s a little FAQ.

1. What is Teixobactin?

Teixobactin is a newly discovered antibiotic produced by a previously uncultured soil bacterium called Eleftheria terrae. Teixobactin acts by stopping some bacteria from making their cell wall (their outer coating, if you like). It was found to be active against a range of nasty bacteria, including Staphylococcus aureus (also known as MRSA), Clostridium difficile (which causes nasty diarrhoea which can be deadly in elderly people), Bacillus anthracis (which causes anthrax) and Mycobacterium tuberculosis (the cause of TB). This is good news as we have a desperate need for new antibiotics against these superbugs. The researchers also showed that Teixobactin did not have any effect on mammalian cells and could protect mice infected with S. aureus and Streptococcus pneumoniae. This is also good news but it will still take 2-5 years more testing before Teixobactin makes it to a doctors surgery or hospital near you.

2. So why isn’t Teixobactin going to save us all?

Because bacteria roughly divide into two groups based on their cell walls; they are either classified as Gram-positive or Gram-negative*. Teixobactin only works against Gram-positive bacteria. Unfortunately, it can’t get around the extra outer membrane of Gram-negative bacteria. This means the antibiotic doesn’t work against some pretty nasty bacteria that we are running out of antibiotics to kill, like E. coli, Pseudomonas aeruginosa and Klebsiella.

3. Finding new antibiotics – the iChip.

How the researchers discovered Teixobactin is in some ways more important than the antibiotic itself. Many microbes remain undiscovered, partly because it has been impossible to culture them in the laboratory. Given that antibiotics are made by microbes, this means that many antibiotics lie undiscovered all around us.

The researchers made a sort of ‘hotel’ for soil bacteria, that allowed them to cultivate previously uncultivated bacteria. This ‘hotel’ is called the iChip and is basically a board with holes on it. Each whole was seeded with a single bacteria from a sample of soil, and then the whole board, covered in a permeable membrane, was dunked in to a beaker of soil so the bacteria could access all the nutrients they needed to grown. Very clever. The discovery of Teixobactin should be just the tip of the antibiotic iceberg.

4. Is Teixobactin really resistant to resistance?

One of the interesting findings of the study was that the researchers couldn’t produce strains of M. tuberculosis or S. aureus that became resistant to Teixobactin. I think it’s a little premature to suggest that bacteria are unlikely to become resistant to Teixobactin based on the published data; the researchers didn’t try particularly hard to make it happen.

As Dr Prof. Ian Malcolm says: “Life finds a way”….

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*depending on whether or not they can be stained using crystal violet, a method known as Gram-staining.

Reference:
1. Ling et al (2015). A new antibiotic kills pathogens without detectable resistance. Nature. doi:10.1038/nature14098
2. World Health Organisation (2014). Antimicrobial resistance: global report on surveillance 2014. ISBN: 978 92 4 156474 8.

Related posts:

Life as we know it could end in ten years if we don’t start taking drastic action

The antibiotic resistant superbugs threatening New Zealand

A gift for someone special – Part III Siouxsie Wiles Jan 04

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I recently blogged about my experience donating eggs. In this post I want to explain why I chose to write about it.

What I have just been through is what some companies are encouraging their female staff to do so they can be ‘career women’ without leaving it too late to have a family. Apparently companies like Facebook and Apple are offering to pay for staff to have their eggs frozen. It’s likely most women will undergo two to three rounds of stimulation to have enough eggs to freeze down for future use. Personally, I’d like to see companies make it easier for people to have families and successful careers, not lull them in to a false sense of security that all will be fine because they have some eggs in the freezer.

Putting aside that going through the process of producing a bumper crop of eggs and having them collected is hardly a walk in the park, or indeed, risk free, I’m not sure many people realise what the chances of having a successful pregnancy are using in vitro fertilisation (IVF). Cil and colleagues published a paper in 2013 with some graphs that make interesting reading. They did a meta analysis of 10 studies with 1805 patients and looked at how the rates of live births changed with the age of the woman and how the eggs were frozen (1). This is the relevant graph to look at, with the % probability of a live birth after implantation of between 1 and 3 embryos, plotted against the woman’s age. The dotted lines are for eggs that were frozen using a method called vitrification (VF), the solid lines are for eggs that were slowly frozen (SF).

ivf live births

As you can see, the probability of a live birth drops with age. At its highest, the probability is less than 35% for young women when 3 embryos are implanted, dropping to 5% when only one embryo is implanted into a 42 year old woman. To put all this in context, of the 11 eggs that were sucked out of me recently, only 6 were good enough to go forward to be fertilised. Of those, 5 were successfully fertilised but a week later only one had developed into an embryo suitable for implantation. I can’t begin to tell you how gutted I was about that. The little embryo has now been frozen down but will soon be implanted into my friend. Based on the data presented by Cil and colleagues, the chances are slim that it will result in a pregnancy which makes me both really sad and very disappointed but I’m going to have all my fingers and toes crossed that it’s the 5%. One of them has to be!

Reference:
1. Cil, AP, Bang, H, and Oktay, K. Age-specific probability of live birth with oocyte cryopreservation: an individual patient data meta-analysis. Fertil Steril. 2013; 100: 492–499

A gift for someone special – part II Siouxsie Wiles Jan 02

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I recently blogged about my experience donating eggs. In this post I want to explain why I decided to become an egg donor. There are three main reasons:

1. Someone very special to me needed a donor.

2. My family is complete and I’ve no more need of my eggs.

I’m not sure if it’s because I’m a biologist or an atheist but I’m not particularly freaked out by the idea of my genetic material being used to make a child who won’t be mine. The law in New Zealand is very clear – if a child is made using my eggs, that child is the child of the woman who gave birth to it, not mine. Yes, it may have my green eyes and my dimples, but I won’t be it’s mother. The law is also very clear that if a child is born, that child will have the right to know who I am when they reach a certain age. In my case, the person I have donated my eggs to is a permanent feature in my life. We have been open with our families about everything so if we are lucky enough that there is a child from my donation, my role will not be a big secret.

3. Society functions because ordinary people do generous things.

I’m not special. Yes, I have given someone a special gift but this is the kind of world I want to live in. I want to be able to have a life-saving blood transfusion if I need one – something only made possible because people give blood. I urge you all to think about what generous things you could do in the coming year. Perhaps you could look into joining a bone marrow register, or let your family know you are happy to be an organ donor. Think about how you would feel if you were the one who needed that generous gift.

A gift for someone special Siouxsie Wiles Dec 31

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Regular readers may have noticed I’ve been a little quiet for the last month. I’ve been feeling ‘under the weather’, to use a common euphemism. In reality I’ve been through a really interesting experience that isn’t often spoken about in public. That must make it the perfect material for a blog, right? Right!

Warning: I will mention the word vagina at least once. Giggle if you must.

Over the last month I’ve put my middle-aged body through quite an ordeal in order to be an egg donor. I’m not talking Easter eggs here, but my ova. The gametes that contain half my genetic material and one of the main ingredients required to make a baby. My journey down this path started almost a year ago, and has involved numerous tests to rule out genetic mutations and sexually transmitted diseases, several counselling sessions to assess mine and my husband’s understanding of the law around egg donation, our rights regarding the eggs and any babies they may produce, and to determine whether I was making the donation of my own free will. We also had to apply for permission from an ethics committee as laid out by the New Zealand Human Assisted Reproductive Technology Act of 2004.

Needles, needles and more needles

After passing all the tests and with ethics permission granted, on Tuesday the 2nd December I took a dose of antibiotics and started giving myself a hormone injection into my abdomen every evening. I really hate injections but the needle was very fine and didn’t really hurt. That all changed 5 days later when I had to start giving myself a second injection each day, this one in the morning. This injection really stung and left me with a new little bruise each day. Normally every month a woman’s body matures one egg which is released from the ovary in anticipation of being fertilised. The hormones I was taking were to make as many eggs as possible develop at once. I felt sore and very tired.

Three days after starting the morning injections I was back at the fertility clinic for blood tests and a scan to see how many eggs were developing and the size of the follicles they were developing in. Once enough follicles had reached a certain size, I stopped having the two daily injections, took my ‘trigger’ injection which makes the eggs do their final maturation step and then 36 hours later went into the clinic for the egg collection. Under a mild sedation, the eggs were sucked out of me using a fine needle inserted through my vagina. The antibiotics I took at the beginning were to prevent me getting an infection from this procedure. I went home and slept for the rest of the day. For the next couple of days I was sore and uncomfortable so took some pain killers and spent most of the time sleeping.

A slight complication…

At this point I should have started feeling better, but I was one of the unlucky few who go on to develop a rare complication called Ovarian Hyperstimulation Syndrome. Fortunately mine was just a mild case; I had a painful swollen abdomen, shortness of breathe, nausea and aching arms. Severe cases can require hospitalisation to drain fluid from the lungs and abdomen. About a week later the swelling had gone down, the nausea abated and my arms were back to normal. Alas, I’d missed all the work pre-Christmas parties but was back to full strength for the family festivities. Phew!

In a future post, I’ll explain why I became an egg donor and give some of the stats around success rates for in vitro fertilisation. In the meantime, to see what happens during ovarian stimulation watch this neat little animation:

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Edit 04/01/15: On reflection, I’d just like to state for the record that even though it was touch, I would do it all again! Here’s my post on why and my post on why we should talk about it.

The science of Rudolf’s glowing nose! Siouxsie Wiles Dec 24

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Rudolf by Latharion

Rudolf by Latharion

This festive season AUT University Prof’s Steve Pointing and Allan Blackman released a marvelous little video explaining the science behind some of the unanswered mysteries of Christmas. How does Santa get to all those houses unseen in one night? And how does he get down the chimney? I’ve been sent the video so many times as they also cover the science that could explain Rudolf’s red nose. Bioluminescence of course!

Except…. they get it a little bit wrong. So I talked to the fantastic Rebecca Watson from Skepchick and explained the real science behind Rudolf’s red nose. Enjoy!

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PS Slight correction… while we are being pedantic, in the video I say that GFP is excited by UV light. This is true for wild-type GFP but there are also lots of variants now so it’s probably the case that the GFP-expressing animals are made with a modified GFP that is excited by blue light rather than UV.

PPS If you like Rebecca’s video, you can support her to make more on Patreon, and if you can think of other science stories you would like explaining like this then let us know!

Tales from the Ivory Tower: when ‘Publish or Perish’ becomes ‘Publish & Perish’ Siouxsie Wiles Nov 30

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A few days ago the UK media ran a story about the death of Prof Stefan Grimm, a professor of toxicology at Imperial College London. Prof Grimm was found dead in September, and anonymous colleagues are quoted as saying he had felt under increasing pressure by Imperial after a series of unsuccessful grants, and had been placed under performance review.

In academia we live by the mantra ‘Publish or Perish’. Publications are the currency on which jobs are won and lost, and we all know that if we fail to publish we will be unemployable*. The institution I work at has actually set metrics for the numbers of publications required for promotion. Hence the ‘perish’, although I’m not sure the person who coined that phrase meant for it to be taken literally. According to his profiles on Research Gate and Google Scholar, Prof Grimm had published a respectable 53 publications, 11 of them in the last 2 years, and had an h-index of 24. He had also published in a number of high impact journals which is very important to those who believe (mistakenly in my opinion) that the impact factor is a reliable measure of academic quality. My point is that Prof Grimm was publishing.

Research funding is another thing that my institution has set metrics for and I’m sure Imperial is no different. It seems like we are moving into the era of ‘Get Funded or Perish’.Many people outside of academia don’t know that we don’t just get handed a pot of money to carry out our research. Instead we spend a huge amount of time applying for funding. Purses are tight and competition is tough (and many reviewers and panels are unconsciously biased but that’s another story….). All around the world success rates have plummeted and many excellent applications go unfunded.

This year I have written 12 applications to support three different research projects in my lab. I have had the outcomes for 6 of them and they have all been rejected. I was lucky though. Last year I applied for nine grants, one of which was an Explorer grant from the Health Research Council of New Zealand. It’s an interesting new funding stream that awards relatively small amounts of money** at random to three or four of the applications that are deemed to meet the criteria for funding. My application was one of the lucky ones to be randomly selected for funding. The grant started in October and so one of the three projects I have been trying to fund can now progress. But the other two are stuck in limbo. Is there pressure on me to get those projects funded? I’ll let you know after I have my annual performance review early next year.

*Both this and the ‘Publish or Perish’ mentality leads to some interesting gaming of the system by some academics, slicing pieces of work into as many papers as can be squeezed out of it (we refer to this is as the ‘minimum publishable unit’…).

**Just $150,000 over 2 years (‘proper’ grants with full overheads are more like $300,000 PER year).

Skeptical Thoughts – acupuncture, Dr Oz & ‘aboriginal’ medicine Siouxsie Wiles Nov 26

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I now have a regular radio slot, called Skeptical Thoughts, with Graeme Hill on his RadioLive Weekend Variety Wireless show. Here are links to a few of my recent editions:

Here, I do my bit for Acupuncture Awareness Week (revealing my own sordid history with acupuncture), talked about Dr Oz’s bad week on Twitter and was disgusted by a story from Canada about a woman’s right to refuse to allow her child’s leukemia to be treated with chemotherapy in preference for ‘aboriginal’ medicine. Did you know high dose vitamin C was ‘aboriginal’? Me neither.

Here I talk about drinking bleach and a rather fantastic way of spotting ghosts.

Feedback welcomed, as are suggestions for future slots.

Monday Micro: Ebola update and NZ preparedness Siouxsie Wiles Nov 24

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With Ebola now moving into Mali, I thought it was time for a quick update and some links. According to the CDC and WHO, as of the 16th November 2014 there have been an estimated 15145 cases, including 5420 deaths. Since the end of October there have been 6 cases in neighbouring Mali; all cases have died. American Dr Craig Spencer who had recently returned from working with Doctors Without Borders in Guinea came down with Ebola but survived and has been discharged from hospital.

What is NZ doing to prepare for an Ebola case?

Good question! The Goodfellow Unit at the University of Auckland recently ran an event for GPs and TV3′s Third Degree programme filmed an exercise with St John’s Ambulance transferring a suspected Ebola ‘patient’ to hospital. You can watch their piece here. [Disclaimer: they interviewed me too...].

Need a quick Ebola recap?

Check out the slides from a recent talk I gave in Christchurch. Most of the slides are in the form of infographics, so are pretty easy to understand without me to explain them. Or listen to Prof John Crump from the University of Otago explain to Graeme Hill how Ebola compares to other diseases in Africa on RadioLive here.



Naturopathy vs Science Siouxsie Wiles Nov 03

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Today Wellington’s Dominion Post newspaper ran a piece of (in my opinion..) misleading propaganda they passed of as a cartoon which can be summed up as naturopathy vs science.

I assume it is in response to the bad press that homeopathy received last week after Green Party MP Steffan Browning signed a petition calling for the World Health Organisation to start using homeopathy to treat people in west Africa with Ebola. I had the pleasure of explaining what homeopathy is on breakfast TV.

Inspired by the fantastic @WieldARedPen on twitter, I fixed the cartoon. Enjoy!

Dom Post Naturopathy cartoon - Nov14a

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