Thursday, 18 September 2014

Congrats Deepa!

Deepa Varkey is a PhD student in my group working on how marine cyanobacteria adapt to different temperatures. She has just won a prize for the best poster at the 9th European Workshop on the Molecular Biology of Cyanobacteria in the Netherlands. Great job Deepa!

Deepa and her prize winning poster

Thursday, 11 September 2014

Eureka Awards

Last night, I was at the Eureka Awards Dinner. The Eureka Awards have been described as the Australian Science equivalent of the Oscars. While not quite as glamorous as the Oscars, it was nevertheless a black tie event at the Sydney Town Hall, and we did have some media celebrities present, such as Adam Spencer and Dr Karl Kruszelnicki. It was also the second top hottest topic on Twitter yesterday in Australia.

I was not nominated for an Award, but was there to fly the flag for Macquarie University. I was very excited that MQ's Professor Lesley Hughes won the Eureka Prize in the category of Promoting Understanding of Australian Science Research for her tireless efforts in communicating the science of climate change. Congratulations to Lesley and to all of the award winners of the 2014 Eureka Prizes. The full list of the 2014 Eureka Prize results can be found here.

The dessert was certainly glamorous

Indigo V and Citizen Oceanography

Martin has beaten me to it and already put up a blog post about the Indigo V expedition and our paper in PLoS Biology. I just have a couple of things to add. Martin and Federico were interviewed on ABC radio on Wednesday morning, here is a link for anyone who wants to listen or read the transcript. I like Martin's line- "Every second breath we take the oxygen is being produced by microbes in the ocean.

Also, I wanted to highlight the beautiful photo from the Indigo V expedition, taken by Rachel Lauro, which is the cover image for the current issue of PLoS Biology:

Wednesday, 10 September 2014

Crowdsourcing Microbial Oceanography

For marine microbiologists getting out into the blue ocean is a big deal. Competition for ship time is fierce and we often propose and plan research voyages years in advance. Even with access to dedicated research vessels the ocean is enormous, and vast swaths of the ocean are rarely visited by scientists and therefore poorly sampled.

To attempt to address this problem I set off on a expedition onboard an 18m sailing yacht in April last year to help prove the concept that citizen scientists onboard sailing vessels can fill the gaps in oceanographic data collection. Together with Federico Lauro, Joe Grzymski and Rachelle Lauro we set off from Cape Town into the Indian Ocean on our way to Mauritius.

The first leg of the Indigo V voyage was far from plain sailing. We encountered foul weather, gear failures, lack of sleep, sea sickness and survived the ravages of a fierce gale and cruel waves 1000s of kilometres from land. Fighting to stay on course, stay onboard and remain afloat were our main priorities. However, we also managed to take measurements and preserve samples for microbial oceanography using relatively simple low cost equipment. We survived and proved that CITIZEN SCIENCE IS POSSIBLE.

The lessons we learned form this expedition form the basis of our community page headlining this weeks PLOS Biology.**

Joe Grzymski strapped-in and doing science out in the Southern Indian Ocean.

The timing of this article coincides with the arrival of Australia's new research vessel. These are exciting times for microbiologists in Australia, particularly for biological oceanographers who have been anxiously waiting the RV Investigator which has been delayed for a year. Investigator was built in Singapore and arrived yesterday in her home port of Hobart where she will be fitted out with some impressive scientific kit.

This newspaper article provides some background and interesting numbers. For example, Investigator will be able to accommodate up to 40 scientists and students on voyages from the equator to the Antarctic ice edge for up to 300 days per year. Scientists requested over 800 days of research project time on board for the first year of operation, but the vessel will be funded for only 180 days at the moment.

If you are a student and have an interest in exploring the blue ocean and the organisms that thrive within it then you should get in contact with our research group here at Macquarie University. We have a number of exciting PhD studentships opening early next year for work on metabolic modelling and genomics of marine microorganisms.

**(This is actually the second paper produced from this project, the first was a review of the links between biogeography and traits of marine microbes, that we mostly wrote while prepping the Indigo V for the first leg in Cape Town.)

Ready to set off across the blue Indian Ocean. A picture of our sailing vessel, Indigo V, tied up alongside squid boats in Port Elizabeth, South Africa. 

Wednesday, 27 August 2014

Laureate Fellowship

I received the exciting news last week that I have been awarded a Laureate Research Fellowship from the Australian Research Council. I flew to Adelaide on Friday for the Awards Ceremony, which was held at St Peter's College in Adelaide. This was an impressive venue, looking like it had been teleported through time from the 19th century.  I also learnt that St Peter's has more Nobel Prize winning graduates (3) than any secondary school outside of New York.

I'm now the proud owner of an ARC Laureate Fellow lapel pin, I'm not quite sure when I'm ever going to have cause to actually wear it. My Laureate Fellowship was awarded for my proposal "Building Virtual Cyanobacteria: Moving Beyond the Genomics Era". You can find a description of the project on my my ARC Laureate Fellowship bio page. There's also some further information in the Macquarie Uni press release. Time to go crack open some bottles of champagne!

The cats were very excited and congratulated me on the good news
Receiving congratulations from Christopher Pyne, the Minister for Education (and yes photographic evidence that I actually own a suit)

The successful 2014 ARC Laureate Fellows (we all look very very happy)

Thursday, 14 August 2014

My Kardashian Index is 0

Earlier this year, I blogged about metrics for measuring scientific output such as a H-index, AltMetric, etc. I just came across an entertaining little paper in Genome Biology by Neil Hall about a new metric- The Kardashian Index. Neil was wondering whether there are scientists who are like Kim Kardashian- famous for being famous. Or more specifically, whether there were scientists who are famous for their twitter feeds or blogs, but have not produced much in terms of published research papers of significance. So, he came up with the Kardashian Index- your number of twtitter followers divided by your number of citations from your published scientific papers.

I'm proud to say my Kardashian Index is 0 - since I have no Twitter followers, and 32,000+ citations. Ok, ok, since I am a conscientious objector to twitter, Facebook, etc, and have never tweeted in my life, it's probably not a relevant metric to me.

Fig. 1 from the Kardashian Index paper- identifying scientists who are highly active on social media but don't actually produce much scientific output. 

Monday, 11 August 2014

Minions in Action!

Some of you may recall we received MinION sequencing devices from Oxford Nanopore as beta testers. It's taken a while, but Mike Gillings now has them up and running. Whether they can actually generate useful data is still something we're working out, but in the meantime here are some action photos.

The MinION is the USB device plugged into the laptop

Each dot on the screen represents a protein nanopore through which a DNA molecule is moving and being sequenced. The different colour of the dots indicates how the sequencing is going.

Who doesn't love bar graphs- this one shows the lengths of DNA molecules being sequenced. Some of our read lengths are up to 70,000 bps in size