Thursday, 26 July 2012

Fun with Liquid Nitrogen

In case you ever wondered what happens when you freeze roses in liquid nitrogen, then you should watch this video. Many thanks to Adam Wilkins, the lab tech for my CBMS336 unit, who filmed and edited it.

G2G Outlook day 2

Liveblogging of the Genes to Geoscience Outlook retreat, day 2. We had two discussion sessions yesterday, the first of these, everyone brought along a recent "hot" paper, and these were discussed. The paper I suggested for discussion was this Cell paper which describes the first "complete" computational model of a living organism- the bacterium Mycoplasma genitalium.

In our second discussion group yesterday, I chaired a discussion of whether gene richness would follow similiar patterns as species richness, with increasing diversity in tropical vs temperate locations, and how would we design experiments to test this hypothesis.

11.00 am- We've had a series of paleobiology talks this morning, I particularly enjoyed the talk by Charles Marshall from UC Berkeley, which looked at what big events have shaped the modern biota of Australia (and other places) and was a really nice synthesis of geology, paleontology, molecular phylogeny, and genomics.

12.00- Very nice talk from Jenny Graves from Latrobe University giving a tour of her work on genomes, chromosome mapping, and sex determination genes from everything from mammals, marsupials, monotremes, birds, lizards. Cool stuff!

Wednesday, 25 July 2012

Genes to Geoscience

So this is my first attempt at live blogging. The next two days I'm at the Genes to Geoscience Outlook Retreat. Genes to Geoscience is a virtual Macquarie University Research Centre that includes groups with research interests as diverse as genomics, functional ecology, earth system science and palaeontology. One of the objectives of this centre is to get researchers with such eclectic interests talking to each other and hopefully doing cool science together. I've always thought that the most interesting science is done in the overlap between different scientific disciplines.

Outlook is an annual retreat which has an interesting structure, in the morning sessions we have a series of invited talks from local and international speakers, and in the afternoon we have a series of breakout discussion sessions, which serve as sort of thinktanks for new research directions/ideas. I gave a talk at Outlook a couple of years ago, and have chaired breakout discussion sessions the last couple of years.

9.30 The first talk today was by Mick Follows from MIT, who gave a very interesting talk about trying to model marine ecosystems across the entire globe, he has built a "Sim Earth" which attempts to model the distribution of marine phytoplankton through the oceans and looks at impacts of nitrogen, phosphorus and iron on the success of particular phytoplankton lineages. In particular, it shows the importance of iron concentration on the distribution of nitrogen-fixing bacteria across the globe.

11.30 Emma Johnston from UNSW gave a talk on ecotoxicology, not a topic I really know much about, though interestingly some of the work we do on the effects of toxic compounds on microbial gene expression could conceivably fall into this research area.

12.00 Martin Ostrowski from my group gave an interesting talk on his work on using genomics and flow cytometry to look at the distribution and diversity of photosynthetic marine cyanobacteria through the world's oceans

12.40 yay, lunch! followed by breakout discussion groups, probably won't be any blogging during this time. 

This image of chlorophyll abundance in the ocean shows the global distribution of phytoplankton (taken from and seemed relevant to the theme of Outlook.

Thursday, 12 July 2012

Biocontrol bacteria

While I put together the rest of my reflections on five years series, here's something else in the meantime. After a marathon effort, we've finally published our manuscript on the genomes of biocontrol Pseudomonas bacteria in PLoS Genetics. Biological control is the use of biological organisms to control pathogens, parasites or other pests. In this case, we are looking to use Pseudomonas bacteria that live naturally on plant roots, leaves or blossoms to protect plants from plant disease. An example of a bacterial biocontrol agent is Pseudomonas fluorescens A506 which is sold commercially as BlightBan A506 and is used for the suppression or control of the disease fireblight in pear and apple orchards.

This is an area of research I got into through collaboration with Joyce Loper's group in Corvallis, Oregon. Together with Joyce and an army of other collaborators we published the first genome of a biocontrol bacteria, Pseudomonas fluorescens Pf-5 in Nature Biotechnology back in 2005. We decided to follow up this original genome paper by looking at a broader range of biocontrol Pseudomonas bacteria that were specific for different plant hosts and provided protection against different plant pathogens.

This became somewhat of a marathon project. We wrote the original grant to the United States Department of Agriculture to fund this work back in early 2006. The sequencing work started in 2007. This was then followed by literally years of effort in analyzing the genomes and undertaking functional studies to confirm the findings from genome gazing. We wanted to make this a comprehensive or definitive work on the topic. It was a massive relief when we finally managed to get the manuscript submitted early this year. The reviewers of the manuscript appreciated it's monumental nature, with one of them stating "This manuscript stands well above the crowd, representing an heroic level of genome characterization and overall being a model of what such studies should aspire to." I can honestly say I haven't had a reviewer say that before.

Thanks to the whole team of collaborators who worked hard on this project, particularly Joyce Loper, without whose tireless efforts this paper would never have seen the light of day.

Fig 6 from the PLoS Genetics paper showcasing the different capabilities of the sequenced Pseudomonas biocontrol bacteria- not only informative but also highly attractive!

Tuesday, 10 July 2012

Reflections on five years #1

Scary how fast time goes, but I have now been at Macquarie University for five years. It seems like just yesterday I was faced with the decision of whether or not to move from the J Craig Venter Institute in the US back to Macquarie University in Australia. This was not an easy decision, I had been in the US for twelve years, including the last 7 and a half years at The Institute for Genomic Research/J Craig Venter Institute. So, it was a significant upheaval to move back to Australia.

There were significant risks in this move, I wasn't certain whether the style of genomic research I was interested in would be fundable by granting agencies in Australia; I had never held a teaching position in a university, so I really didn't know how the teaching aspect would go and whether I would enjoy it; I wasn't able to convince any of my staff in the US to relocate to Australia with me, so I had to build a new research group from scratch. Here I must give a huge thank you to Sasha Tetu, who was my first employee here at Macquarie and played a critical role in getting the group up and running. Karl Hassan and Liam Elbourne who joined us later, also played important roles in establishing the research group.

So why did I move to MQ? If I was ever go to move back to Australia, the timing seemed right from both a professional and personal standpoint. The advent of next generation sequencing instruments meant that I no longer needed to be in only one of the few genome sequencing institutes in the world in order to undertake genomic research. I was offered a tenured full professorship (the holy grail of academia) which looked very attractive after seven and a half years of stress in attracting 100% grant funding for my position and my group's research at TIGR/JCVI. One of Macquarie's research strengths was in proteomics, with the Australian Proteome Analysis Facility (APAF) located here along with many proteomics researchers (Indeed the term "proteome" was coined by Marc Wilkins, a PhD student at Macquarie in the early 90s) . I had zero expertise in proteomics, but I was interested in using it to complement my genomics/transcriptomics research, so that seemed a good match. Macquarie was also a leader in the study of mobile DNA elements- pieces of DNA that can "jump" from one organism to another. One class of mobile elements known as integrons had been discovered by Hatch Stokes at Macquarie and by Ruth Hall at CSIRO. One of my main research interests is how bacteria exchange mobile pieces of DNA in a process known as lateral gene transfer, and how this ability to exchange genes may allow bacteria to adapt to new environmental conditions. This also seemed to be a good match in terms of research interests.

Curiously, when I first arrived at Macquarie, I seriously considered starting a blog about my experiences in starting afresh here. I had been inspired by my friend Jonathan Eisen's Phylogenomics blog. But at the time, I wasn't sure I would be able to sustain a regular blog while getting established here at MQ, and so decided against it. It was only this year that I revisited that decision and with the promised help of my research group decided to start a Paulsen Lab Blog.

Garry Myers and I shared a bottle of Grange to celebrate my professorial appointment (can't find the actual photos of that event so took this from the web)

Thursday, 5 July 2012


Tomorrow, we are hosting a visit by Jill Banfield from UC Berkeley. She is giving a  talk on "Genome reconstruction for metabolic and phylogenetic analyses of uncultivated bacterial and archaeal phyla" in F7B 322 at noon for anyone who wants to come along. I'm very excited by Jill's visit and looking forward to her talk, she has been a pioneering researcher in metagenomics and geomicrobiology. In addition to many Nature and Science papers, membership of the National Academy of Sciences (USA), and many other claims to fame, Jill currently leads a NASA-funded project to determine if life ever existed on Mars.

Jill sampling acid mine drainage biofilms under Iron Mountain, California (photo from UC Berkeley website)