SciBlogs

SciFund Challenge – Target achieved! Siouxsie Wiles May 20

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Glowing bacteria attract over $3000 for science in 15 days!

For those who don’t know, this month I am taking part in the SciFund Challenge, raising money for my research using the RocketHub crowdfunding platform. My project, Evolution in Action, involves studying how infectious microbes evolve to cause disease and I am raising money to sequence the genomes of my evolved bacteria to unravel the genetic basis of their evolution. It costs about $100 per genome, so the more money I raise the more genomes I can sequence.

So it took just over 2 weeks to reach my $3000 target. I’m currently at $3,288 – that’s almost an extra 3 genomes. Whoohoo! And there is still more than a week to go! I’m really looking forward to doing a little analysis of all my contributors when the challenge is over to find out how many I actually know and how many are strangers, and how those strangers found me.

So a huge thanks to all who have contributed and everyone who helped spread the word. I couldn’t have done it without you guys. And for those who still want to contribute, there is still time, and we have no shortage of evolved bacteria whose genomes we would like to sequence so the more money we raise, the better!

Now we are getting on to preparing our rewards, which includes writing our contributors names/logo’s in glowing bacteria. Watch this space!

Ummm, it should say "science rocks" but the bugs in our 'e' didn't grow properly.... YouTube Preview Image

*In addition to those listed here and here, contributors to date are:

Jon Woods
Stippy
Marius Rowell
Richard Cornford
Dr Alan Koslow
K. Gilbert
Ian
Sefton Billington
Simon Clendon
Dan
Barbara Vanhoeke
Gingiber Theginge
Conor Reilly
Rob Heighway

SciFund Challenge Day 13! Siouxsie Wiles May 14

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So with 18 days still left to go, the 75 projects which make up round 2 of the SciFund Challenge have raised over 58,000 US dollars for scientific research using the RocketHub crowd funding platform.

My own project, Evolution in Action, is just 387 dollars away from reaching its target. So I just wanted to say a big thanks to all my contributors* and everyone who has helped to spread the word.

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*In addition to those listed here, contributors to date are:

Alan Brown
Judy Morris
Ged Hayward
Robin Capper
Cassandra Baker Lee
Ian Hovander
Lorna Strachan
Karen Toast Conger
Kalani Hausman
Samantha Sampson
Sam Egli
Victoria Galbraith
Doug & Wendy
Martin Kennedy
Maria Connor
Celia
Simon Young
Don & Louise Galbraith
Graham & Hazel
Robert van Leeuwen
Bob Sellars
Garrett Butt
Alan Reader
Moira Statham
Ana Elisa Garcia
Cate Macinnis-Ng
Aleks Ksiazkiewicz
Mark Martin
Greg Crowther
Stephen Hawley
Heather Galbraith
Dave Guerin

Nature publishes first of the ‘weaponised’ flu papers Siouxsie Wiles May 04

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And it’s Open Access!

Late last year it was revealed that 2 papers submitted to the journals Science and Nature had been sent to the National Science Advisory Board for Biosecurity (NSABB), an American committee charged with providing guidance on the potential of research to be misused to pose a biological threat to public health or national security. The papers were said to describe the ‘weaponisation’ of H5N1 ‘bird flu’; just a small number of mutations were found to confer the ability of the virus to transmit easily between mammals (in this case ferrets), an ability ‘wild’ H5N1 lacks.

First the NSABB said the papers should be censored, then they retracted that decision. Well now the first of the papers is out. It’s by Yoshihiro Kawaoka’s group at the University of Wisconsin-Madison, and colleagues in Japan.

Ed Yong has done a great job summarising the paper over at Not Exactly Rocket Science. But if you want to see what all the fuss is about, you can read it over at Nature because it’s been published Open Access (at least it is at the moment). So from censored to free for all. That’s quite a reversal!

H5N1 is pretty lethal in people, killing around 60% of those known to have been infected with the current Asian strain. However, transmission from birds to humans is pretty inefficient. What caused the media interest was that Ron Fouchier seemed to be implying that the mutant H5N1 his paper described had become easily transmitted between ferrets while retaining its virulence. Scary stuff and very reminiscent of the movie Contagion. It was interesting at the time that Kawaoka kept a very low profile in the media. This is what it says in the abstract of his paper:

“We identified a reassortant H5 HA/H1N1 virus….that was capable of droplet transmission in a ferret model. The transmissible H5 reassortant virus preferentially recognized human-type receptors, replicated efficiently in ferrets, caused lung lesions and weight loss, but was not highly pathogenic and did not cause mortality.”

This does beg the question why Kawaoka wasn’t more vocal about how his findings contrasted with the scenario being painted by Fouchier and the media. But we shouldn’t be complacent. The paper clearly shows how easily H5N1 evolves to transmit between mammals and that wild viruses are accumulating at least some of the mutations that put them on this path.

As Lawrence Fishburne’s character Ellis Cheever says in Contagion:”Someone doesn’t have to weaponize the bird flu.The birds are doing that”.

Reference:
Imai, Watanabe, Hatta, Das, Ozawa, Shinya, Zhong, Hanson, Katsura, Watanabe, Li, Kawakami, Yamada, Kisos, Suzuki, Maher, Neumann & Kawaoka. 2012. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature. doi:10.1038/nature10831

PS If you want to support some evolutionary infection work that doesn’t involve flu and ferrets then check out my SciFund Challenge Project, Evolution in Action, on RocketHub.

Just who are these SciFunders anyway? Siouxsie Wiles May 03

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Just over 48 hours in and the SciFunders have so far raised nearly 30,000 US dollars for their research. Want to know who these SciFunders are? Here they are!

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SciFund Challenge – Day 1! Siouxsie Wiles May 03

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What a start to round 2 of the SciFund Challenge. Over 18,000 dollars raised for science so far!

How about the stats for my project Evolution In Action? The last 24ish hours have seen 15 contributors donating $840 to support my research – that puts me at a third of the way to my target!

A special thanks go to the brilliant Daniel Hurley for being my first supporter.

Other contributors today were:

Susan and Craig Shearer
Ben and Olivia Albert
Jin Koo Niersbach
Steven Galbraith
Elf Eldridge
Alan Huett
Nathan Hayward
Riccardo Guidi
Jimmy Dalton
Tina Arora
Maire Litchfield
Diana & Michael
Episteme
Sarah Johnson

Thanks also to Ed Yong (@edyong209) writer of the excellent Not Exactly Rocket Science for tweeting and everyone who has posted my #SciFund link to Facebook or shared on Google+.

30 more days to go!

Round 2 of the SciFund Challenge is now live! Siouxsie Wiles May 01

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I’ll be spending the next 31 days trying to raise money for my research using the crowd funding model on the RocketHub platform, where contributors exchange small donations (in the 10-100 dollar ballpark) in return for ‘rewards’. As a microbiologist who makes glow-in-the-dark bacteria for a living, my rewards are things like sending donors a picture of their name written in glowing bacteria or naming one of my bacteria after them.

Your name in lights!

Your name in lights!

The challenge came about partly as a result of the lack of funding for basic science (success rates stand at about 20% in the USA, while for New Zealand’s only blue skies research pot, the Marsden Fund, they are about 8%). But perhaps more importantly, the SciFund Challenge is also about getting the public more interested and involved in science.

So why did I get involved? I want to tell the world how amazing bacteria are. They are masters at adapting to their environment, rearranging their genetic material or gaining new genes from their surroundings. This has allowed them to colonise pretty much every conceivable environment. From boiling hot geysers to human beings. While many are harmless or pretty beneficial, plenty have evolved to cause us serious harm. Bacterial adaptation is how we get antibiotic resistance and new diseases emerging.

So what I want to know is, how do bacteria evolve to cause disease? And that’s where my SciFund project comes in. I need your to help unravel how these amazing microbes keep outsmarting us. For more information, check out my project, Evolution in Action. Wish me luck!

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For those unfamiliar with RocketHub:
• RocketHub is a legitimate site, used mainly by artists and musicians to launch their projects.
• RocketHub is not an investment or charity. It is a site that allows the project owner to exchange rewards for contributions.
• RocketHub is based in the USA so all the rewards are listed in US dollars. For those outside of the US, 10 US dollars are roughly equivalent to: 6.20 UK pounds/ 7.60 EUROs/ 10 AUS dollars/ 12 NZ dollars/ 10 Canadian dollars. For an up to date currency conversion check here.
• RocketHub is an ‘all and more’ funding mechanism. If I don’t reach my financial goal I get to keep what I raise. And if I raise more than my goal I get to do even more cool science.
• RocketHub take a 4% cut of whatever I raise if I make my target, and 8% if I don’t. In addition to this, there is a 4% credit card transaction fee.
• All contributions are handled by RocketHub, and the money raised (minus fees) will not be sent directly to me, but to the University of Auckland like a traditional science grant.

Crowdfunding science: The SciFund Challenge Siouxsie Wiles Apr 11

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In late 2011, two ecologists from the US National Center for Ecological Analysis and Synthesis in California embarked on an exciting experiment: to see if the crowdfunding model [1] successfully used by ‘Creatives’ [2] could be applied to funding science. And enthuse the general public about science in the process.

Dr. Jai Ranganathan and Dr. Jarrett Byrnes set up the SciFund Challenge, tasking a group of scientists to use the power of their various networks (including their family, friends and colleagues) to raise money for their research. Almost 50 projects were offered up, covering topics as diverse as parasitic plants, flying foxes, Amazonian crabs, domesticating algae, duck erections, Roman slaves, zombie fish and undersea kelp forests. Using the popular crowdfunding site RocketHub [3] as a platform, the scientists raised over US$76,000.

Perhaps as a mark of the success of the SciFund Challenge, a similar site has recently launched called Petridish [4], which currently has 18 projects on offer. Meanwhile Round 2 of the SciFund Challenge starts on the 1st May. This time more than 140 scientists from all over the world will be taking part. Here are some teasers to get you interested [5]!

1. Rather than relying on one wealthy benefactor for full funding, crowdfunding seeks small contributions from lots of people to get projects off the ground.

2. Defined by RocketHub as “entrepreneurs, actors, artists, composers, dancers, designers, directors, filmmakers, inventors, musicians, painters, philanthropists, poets, politicians, programmers, singers, songwriters, teachers, writers, and more”.

3. RocketHub works on an ‘keep it all’ system: the Creative gets to keep all the money they raise, even if they don’t hit their target, minus a 4% RocketHub fee and a 4% credit card transaction fee.

4. Petridish, which charges a 5% fee, works on an “all or nothing” system, where projects will only be funded if they reach their financial goal before a set deadline.

5. Conflict of interest declaration… one of those is for my project!

Coming soon: more science crowdfunding Siouxsie Wiles Apr 08

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Round 2 of the SciFund Challenge starts in May

Next month scientists from all over the world will be taking their passion to the masses to raise money for science. And I’m one of them! Here is a little teaser for my project. Watch this space….

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Find out more about the SciFund Challenge here.

Antibiotics and asthma Siouxsie Wiles Mar 19

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Administering antibiotics in infancy leads to enhanced susceptibility to asthma

At least in mice. Brett Finlay and colleagues, at the University of British Columbia, report in the journal EMBO Reports that treating baby mice with the antibiotic vancomycin not only changed the types of bacteria found in the gut, but was also associated with an increased susceptibility to asthma.

The researchers added one of two different antibiotics, streptomycin and vancomycin, into the animals drinking water. One group of mice were exposed to the antibiotic from during pregnancy (so potentially in the womb) while the other group weren’t exposed till they were 7 weeks old (teenagers by mouse standards). After exposure, the researchers used an experimental asthma model in which animals are sensitised to the protein ovalbumin* (OVA) by giving them two injections into the peritoneal cavity (the space around their abdominal organs). They are then exposed to OVA again a few weeks later by getting them to breathe it in. By measuring the number of immune cells in the lungs, the researchers are able to measure the degree of allergic response AKA asthma.

The bottom line? Nothing much happened to mice fed on streptomycin, while baby but not adult mice fed on vancomycin had a reduced diversity of bacteria in their guts, a reduction in a subset of key regulatory immune cells and increased inflammatory cells in their lungs after exposure to OVA. The researchers therefore propose that vancomycin administered early in life selects for a community of microbes that disrupt the balance of proinflammatory and regulatory immune responses and that this can lead to syndromes like asthma.

Yet another reason to avoid antibiotics unless they are really needed!

* The main protein found in egg white.

Glow sushi! Siouxsie Wiles Mar 18

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When I first heard of this (and thanks to the lovely Alan Huett for the heads up), I immediately thought it was due to the common bioluminescent bacteria often found on fish and which can show themselves if said fish is left too long before eating.

It turns out to be sushi made using genetically modified fluorescent zebrafish (GloFish®). Sold in the USA by Yorktown Technologies, GloFish® available are currently available in five colours (Starfire Red®, Electric Green®, Sunburst Orange®, Cosmic Blue™ and Galactic Purple™). They were developed by incorporating genes for fluorescent proteins, originally derived from jellyfish or sea coral, into zebrafsh embryos. While Yorktown advise that, as with other ornamental fish, GloFish® are not intended for human consumption, Cooking with GloFish offers suggestions* on how to prepare such delicacies as “stop and glow nigirizushi” and “kryptonite roll”.

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While GloFish® are some of the first genetically modified animals to become publicly available as a pet, their origins aren’t in the ornamental fish trade but as a scientific tool. Fluorescent zebrafish are commonly used by scientists to study everything from gene expression and vertebrate development, to wound healing, cancer and cardiovascular disease. The Biotechnology Learning Hub has loads of information on the use of zebrafish by Associate Professor Don Love and his team at Auckland University to study the inherited disease Duchenne muscular dystrophy. They comment on how zebrafish mutants are made, how they are looked after in the lab and the ethics of using them as a model organism.

As Saturday the 24th March is World TB Day, I’ll finish off with a little round up of how the zebrafish is being used in research into Mycobacterium tuberculosis, the agent of TB. I’ve blogged about why TB is such a big problem before, but just to remind you, it is estimated that a third of the world’s population are latently infected, it kills 4,500 people every day and we are now facing strains that are resistant to all currently used antibiotics.

Zebrafish are naturally susceptible to M. marinum, a close relative of M. tuberculosis. M. marinum is also an opportunistic pathogen of man, causing the wonderfully named ‘fish-fancier’s finger’ or ‘fish-tank disease’. Unlike M. tuberculosis, M. marinum is a hazard group 2 organism, meaning it doesn’t require a specialised biosafety level 3 lab to work with. Prof Lalita Ramakrishnan and her team at the University of Washington have shown that M. marinum actively recruits and infects macrophages, using them to aid dissemination. This is forcing a complete rethink of the role of macrophages in human TB infection. Meanwhile Dr David Tobin at Duke University Medical Centre are using zebrafish to look for host genes involved in susceptibility to TB.

* Fluorescent proteins are denatured at high temperatures so best not to cook!