Monday, 17 November 2014

Escaped scientists spotted in Tasmania!

It appears that we forgot to lock the lab and office doors again! A few of our researchers escaped and boarded the brand new Australian Marine National Facility research vessel from the CSIRO, The Investigator.

They are taking part in one of the first scientific sea trials which left from Hobart, Tasmania, last Monday. The transect is going northward criss-crossing the continental shelf. These first sets of voyages are used to check, test and optimise all of the equipment onboard, so they can be used to full capacity when the full research voyages start early next year. A few things are still getting sorted on the ship with the usual teething problems, but it seems that a lot of very good science was still being done, so we should have a good crop of seawater samples and other experiments to analyse. Our escapees also had a fantastic time watching various whales jumping around a little way off the ship. I'm sure Martin and Deepa will tell us more about their adventures when we recapture them this week! So stay tuned...
photo of the Investigator from the ship's blog

Thursday, 6 November 2014

Music Videos from iGEM

A number of iGEM teams made parody music videos. A couple of my favourites are here:
Plasmid'outai from the INSA-Lyon team which has a nice Bollywood fell to it.
The St2ool Project from the Valencia Biocampus team- a parody of YMCA.
There was also a Katy Perry parody I liked, but I haven't been able to find the video yet, I'll update this post when/if I find it.


Congratulations to the Macquarie IGEM team, who are the first Australian team to ever win a gold medal at an iGEM competition! Congrats to all of the other medal and award winners (full results here), especially the Grand Prize winners, Heidelberg in the undergrad category, and UC Davis in the overgrad category.

The 2014 iGEM contestants-the Macquarie team and myself are in the very front, slightly left of the centre

Sunday, 2 November 2014

Greetings from Boston

I'm in Boston along with the Macquarie iGEM team attending the iGEM Giant Jamboree. iGEM is the International Genetically Engineered Machine competition where teams of undergraduate students from around the world showcase their synthetic biology research achievements. This year there are 245 teams with over 2500 participants attending the iGEM Giant Jamboree. In addition to the Macquarie University team, there are two other Australian teams from Melbourne University and Sydney University.

The Macquarie project was Photophyll: the Green Machine, where our students were looking to express the chlorophyll biosynthetic pathway in the bacterium E. coli, with the idea of trying to make a photosynthetic E. coli that could use light energy to make hydrogen gas as a biofuel by linking photosystem II to a hydrogenase enzyme. We also have a great outreach project- So You Think You Can Synthesize- the worlds first online synthetic biology reality contest, which I have blogged about previously.

Our team gave a great presentation today and did a good job handling the questions from the judging panel, who were excited by So You Think You Can Synthesize. I think our team has a chance at a gold medal, we will have to see how we go. This is the fifth year we have had a Macquarie team competing in the competition, so far we have been the top Australian team each year, and we have won 1 bronze and 3 silver medals.

It has been an interesting experience for me attending iGEM for the first time, quite different from going to a normal scientific conference. There is an enormous range in the quality of the research projects from pretty weak to absolutely amazing. So far the highlights for me were the teams from Imperial College London, Paris Bettencourt, and Stanford-Brown-Spelman. Imperial College would be my pick for the top team overall with their project of making bacterial cellulose that could be used for water filtration, and functionalised with specific binding proteins to remove water contaminants. Paris Bettencourt had a broad ranging project investigating different ways to manipulate the bacteria that live on human bodies in order to change human body odour. Stanford-Brown-Spelman had an ambitious project to make a biosynthetic unmanned aerial vehicle manufactured out of a bacterial cellulose acetate with biologically-programmed waterproofing, programmed timed biodegradation and biosensing capabilities. The imagination and creativity of some of the teams has been very impressive.

The MQ iGEM team in Boston flanking our team banner there in the background

Friday, 10 October 2014

PhD scholarships available

We have a number of PhD scholarships available as part of my ARC Laureate Fellowship- Here's our advertising blurb:

ARC Laureate Fellowship PhD Scholarships- Marine Cyanobacteria

Photosynthetic marine microorganisms are responsible for the production of half of the oxygen in our atmosphere, equal to the contribution of all land-based vegetation. They underpin the entire marine food web and shape the health and sustainability of all ocean resources.  Despite their critical role we know surprisingly little about this crucial group. The Paulsen research group is using a range of cutting edge methodologies (ecogenomics, transcriptomics, single-cell analyses, mass spectrometry, bioinformatics and modelling) to investigate the lifestyle of these key primary producers.

We are looking for motivated candidates with excellent academic records to join our ARC Laureate Award funded research team. Our group is located in a state-of-the-art research facility which is part of the Biomolecular Frontiers Research Centre within Macquarie University, Sydney, Australia.  Our dynamic research team has a wide range of expertise in microbiology, molecular biology, oceanography, bioinformatics, systems and synthetic biology. We currently have a number of scholarships (both Masters and PhD) that span the following research areas:

      1.     Ecogenomics, evolution and interactions in natural environments:
This research project will involve fieldwork at coastal sites and on Australia’s new research vessel RV Investigator, working in blue water from the tropics to the Antarctic ice-edge. Techniques include single cell genomics and Stable-Isotope-Probing to unravel interactions and trace the flow of cyanobacteria-derived compounds and energy through the ecosystem.

2.      How marine cyanobacterial adapt to environmental change
Many variable factors, biotic (microbial competition, infection, predation) and abiotic (seawater chemistry and physical parameters), influence the distribution and survival of marine cyanobacteria. A range of interdisciplinary projects will use a combination of "omics" tools (e.g. comparative genomics, transcriptomics and proteomics) to study the molecular responses of these microbes to relevant environmental factors.

3.      Building virtual cyanobacteria
Developing computational models at both a single cell and ecosystem level.  This project will create and model metabolic processes, and generate working virtual cell/ecosystem units supported by experimental data. This research will deliver the first model of marine phototrophic organism and address fundamental questions such as ‘what defines the minimal set of genes required for a free living photosynthetic organism?’

4.      Cyanobacterial transporter characterisation
Membrane transporters have a central role in determining the success of an individual in any given environment; essential for nutrient import, waste export and maintenance of osmolarity. This project will have an informatic focus, involving developing tools for handling large datasets, algorithms for transporter characterisation and visualisation. Transporter characterisation is a long-term interest and strength of the Paulsen group and this project will integrate closely with the cyanobacterial modelling work.

5. Synthetic Biology, building a molecular tool kit
Novel gene circuits that respond to signals in a predictable way can be built experimentally by modelling metabolic and regulatory networks in silico. This project will identify and optimise vital molecular pathways within cyanobacteria and develop genetic tools to undertake high-throughput mutant screens, validate models and enable us to optimise cyanobacteria for bioengineering.

These PhD positions carry scholarships of AUD$25,392 per annum, tax exempt.

Application process:
Interested individuals are invited to discuss these projects with Laureate Fellow Professor Paulsen ( Initial expression of interest should contain a CV and short statement of your research interests. There is potential for additional projects which connect to the overall research focus of the group to be considered and developed together with prospective candidates.

Application for the PhD positions will be through the Macquarie University HDR website. Please see the website and links within for further information about eligibility and submission procedures. (

Learn more about Macquarie University's profile, the facilities available and its campus life ( and

Wednesday, 8 October 2014

I have the grey hairs to prove it

Macquarie University has apparently noticed the grey hairs I'm starting to get, they announced last week that I am one of six new Distinguished Professors. On top of that, on the same day, the Macquarie University Research Excellence Awards were presented, and Karl Hassan and I won the Research Excellence Prize in Science and Engineering. They made 90 second videos summaries for each of the research projects nominated for an award. Here's the video for our project on identification of a new type of bacterial drug efflux pump-


Yeast 2.0 on the radio

I was interviewed on 2SER this morning on the topic of yeast 2.0, biofuels and beer.
Transcript and podcast can be found here.
Louise Brown came along for moral support and snapped this action shot of the back of my head: