Wednesday, 12 December 2012

The Signal and the Noise

Ever since I was dragged along to a baseball game in 1996 and watched Steve Finley hit two home runs, Ken Caminiti hit a home run, and then Trevor Hoffman close out a tense ninth inning to enable the San Diego Padres beat the evil Los Angeles Dodgers, I've become an avid baseball (and Padres) fan. I'm also a political junkie, dating back to my undergraduate days when I was treasurer of the student union. I once spent a day sitting in a hotel room in Palo Alto watching the World Series of Poker on ESPN rather than working on the scientific talk I was supposed to give the following day. And in 1992 when I was a PhD student interested in computational predictions of membrane protein structure, I brought my friend Jon in to help analyze the data, he used some black magic called Bayesian statistics, and produced some interesting findings that at the time didn't match with my preconceptions, so I didn't do take it any further; years later another group published experimental data showing that Jon's findings were correct (sorry Jon!).

What do all these things have common?

I've just finished reading Nate Silver's excellent book "The Signal and the Noise. Why so many predictions fail- but some don't". Nate is a Bayesian statistician who has had a very unusual career, amongst his claims to fame, he developed PECOTA, a system for predicting future performance of baseball players, he spent a couple of years making a lucrative living playing online poker, and he now runs a highly successful blog FiveThirtyEight which provides statistical analysis of political polling data. I first started following FiveThirtyEight during the 2008 US presidential campaign and have been a regular reader ever since then. Nate's now become a celebrity with his uncannily accurate predictions of both the 2008 and 2012 US presidential elections.

Since I work in scientific fields that rely on empirical analysis of massively large data sets, and we are also moving towards undertaking iterative modeling of both bacterial communities and the metabolism of individual bacterial cells, I found Nate's book fascinating. And I think the take home message is very important for us- that anyone doing modeling or forecasting should avoid overconfidence, and recognise the degree of uncertainty in one's models or predictions.


Friday, 7 December 2012

Transporter Workshop

My first scientific passion was studying membrane transport- how cells use specific transporter proteins to bring in nutrients and pump out toxins and waste products. I spent my PhD studying how the pathogen Golden Staph (Staphylococcus aureus) has become resistant to antibiotics and antiseptics by employing multidrug efflux pumps that pumps these compounds out of the bacterial cell. Later on as a postdoctoral fellow at the University of California at San Diego I became interested in trying to predict the complete set of transporter proteins in different organisms, to build a complete picture of membrane transport.

Yesterday, I attended a mini-conference or workshop on Membrane Transporters & Channels & Their Role In Human Disease. It was a fun meeting which made me feel all nostalgic for membrane transporters. I gave a talk on recent work of ours on finding an entirely new type of multidrug efflux pump, and Karl Hassan from my group gave a short 3 minute talk on his work on multidrug efflux pumps in the bacterial pathogen Acinetobacter baumannii. One aspect of the meeting that worked really well was a series of short rapidfire 3 minute talks from young researchers. There were also some great talks at the meeting on the structures of various membrane transporter proteins.

This was the first workshop in Australia dedicated to membrane transporters, and I think Richard Callaghan, Megan O'Mara, and Chris McDevitt did a great job organizing the meeting. Hopefully, this can become a regular event. Turning it into a 2 day meeting held once every couple of years I think would be a great outcome.

Not this type of transporter

Friday, 30 November 2012

BMFRC Retreat

Today, most of my group is at the lovely Epping Club for the Biomolecular Frontiers Research Centre (BMFRC) annual retreat. Unlike Napoleon (see image below), summer is the season for retreats here in Australia, we have another retreat for a different centre coming up in a week or two. Our BMFRC retreat is an all day event where each of the research groups involved in the centre have 10 minutes to present their research highlights for the year. In addition, we have guest speakers from academia and industry, and a presentation from our silver medal winning iGEM students. Finally, we wind up with a discussion session on the future directions of our research centre. Should be a fun day.

Image of another famous retreat

Thursday, 29 November 2012

International Visitors

A clear sign that summer in Sydney is almost upon us, we are hosting a number of international visitors to the Paulsen lab at the moment. We have Peter Henderson and Scott Jackson visiting from the University of Leeds for 5-6 weeks, collaborating on biophysical analyses of multidrug transport proteins that our group are working on. These are proteins that sit in the membranes of bacterial cells and pump drugs out of the cell to make the bacteria resistant to antibiotics and antiseptics. Peter is a  world-leading expert in biochemical analysis of membrane transporters, so it's great having him visit. Anne-Brit Kolsto and Aniko Voros from the University of Oslo are also visiting our lab for 1-2 months collaborating on a project to look at multidrug transport proteins in Bacillus cereus, a pathogen that causes food poisoning (and is the reason why you shouldn't eat cooked rice that has sat at room temperature for too long). Anne-Brit is one of the world's leading researchers on this bacterium, and continues our tradition of having Norwegian collaborators visit here in Sydney. We also have Rebecca Watts visiting from the Queensland Institute of Medical Research (ok, so technically, Queensland isn't really another country). Rebecca is working on a project looking at whether strains of Pseudomonas aeruginosa that infect cystic fibrosis patients are functionally different from strains isolated from the environment and other sources.

And its clearly a lovely time to visit Sydney, and admire how our beaches are currently red during the day and glowing blue at night thanks to a dinoflagellate bloom.

red tide in the morning, swimmers warning (photo courtesy of the Sydney Morning Herald)

Thursday, 22 November 2012

Too dangerous for me to play

As a recovering MMO (massive multiplayer online) gaming addict, I've been tempted by a number of recent(ish) offerings such as Guild Wars 2, The Secret World, Stars Wars Knights of the Old Republic, etc, which I have so far resisted. I was intrigued on the weekend by a new MMO game developed by Google called Ingress, in which one wanders around the real world with your android phone, checking out whether real world objects have secret mysterious energy fields.

I already have too many problems walking into things in the real world while reading stuff on my iPad, so probably this game won't be for me. Once Google combines it with glasses that overlay a virtual reality on the real world, well then it will be much more difficult to resist. Read Vernor Vinge's "Rainbow's End" for a vision of that sort of future.

Hopefully I won't be sued by Google for using this advertising image

Thursday, 25 October 2012

Live by the Grant, Die by the Grant

October and November are always very anxious months for Australian scientists. Traditionally, the results from the major grant rounds from both the Australian Research Council (ARC) and the National Health and Medical Research Council (NHMRC) are announced around this time of the year. It's also an awkward time of the year, if you don't get funding, it's easy to look through the lists of funded projects and become bitter about why was so-and-so funded rather than you when their project is much more boring. Even if you do get funded, you feel bad for your colleagues who didn't get funded (best to avoid making eye contact with them).

The NHMRC grant results came out last Friday, with mixed results for us. We received funding for a collaborative project led by Jon Iredell at Westmead Hospital, to investigate which antibiotics are more likely to disrupt the "society" of beneficial microbes living in a patient's stomach. But we just missed out being funded for our work on looking for novel drug resistance genes in the opportunistic pathogen A. baumannii (on the 0-7 scoring scale used by NHMRC we were about 0.05-0.10 below the funding line).

One thing that became clear to me while sitting on an NHMRC panel this year, is simply the large number of excellent proposals that it's just not possible to fund due to the limited resources of the funding agencies. If we look at the funding statistics from the last ten years or so of NHMRC grants (figure below), usually about three quarters of the grants received are rated as worthy of funding, but only about a quarter of the proposals are actually funded (this year 22%). So, it's always a tough battle for funding.

NHMRC grant stats (taken from the NHMRC web site), lolcat photos are my addition

Tuesday, 23 October 2012

Batten down the hatches sailor!

Martin Ostrowski, one of the ARC post-doctoral fellows in our group is trading his white lab coat for a hat, safety boots and a lot of sunscreen. He is taking part in a research voyage that will study the lifestyles of marine microbes in the Arafura Sea and along the Great Barrier Reef on the Research Vessel Southern Surveyor. The voyage will consist of 8 days transit from Darwin to Cairns and includes scientists from Macquarie Uni, UTS and UNSW. The science team will collect seawater samples to study microbial communities and gain a better understanding of their contribution to important processes, such as photosynthesis and nitrogen fixation in our surrounding seas.

Hopefully the weather will be clement and the swell will not turn our brave sailors into green tomatoes. Keep looking for some updates along the way (as long as the camera does not fall overboard on a particularly large wave!).

"The RV Southern Surveyor is a national facility available to marine scientists to explore and study Australia's oceans. It is owned and managed by CSIRO, and its operations are funded by the Australian Government to enable oceanographic, geo-science, fisheries and ecosystem research." []

The RV Southern Surveyor ready to leave at Darwin's docks

Wednesday, 10 October 2012

Congratulations and Bon Voyage Dr Kent

Congratulations to Kent Lim, who has now officially completed his PhD! This makes Kent the first PhD student to complete in my group here at Macquarie. Yay!

Kent was extremely hard working and has made significant contributions to our understanding of Pseudomonas bacteria that live on plant roots and protect plants from pathogenic organisms. He has first author publications in PLoS One and Environmental Microbiology, co-authorship on a large paper in PLoS Genetics, another first author manuscript currently under review at Applied and Environmental Microbiology, and two more manuscripts currently in preparation.

Kent is now heading off to Charlotte, North Carolina, where he will be a postdoctoral fellow in the lab of Martin Klotz at the University of North Carolina, where I think he is going to be working on global biogeochemical cycles and genome-guided metabolic reconstruction. We'll miss Kent here in the Paulsen lab, but wish him the best of luck in his future scientific endeavours!

Kent and Benny the Beaver (mascot of Oregon State University)- picture taken while Kent was visiting the lab of my collaborator, Joyce Loper in Oregon.

Congrats MQ iGEM team!

Great job by the Macquarie iGEM team, they've brought home a silver medal from Hong Kong (yes silver is the new gold), which is the best result for an Australian team! And they are one of 17 teams (out of 51) from the Asia-Pacific region to be invited to attend the iGEM finals at MIT next month! I'm sure the trip to MIT will be a great experience for the students, and they will be fantastic scientific ambassadors for Macquarie. Full iGEM results can be found here.

The Macquarie iGEM team and their poster in Hong Kong (is that a victory sign? a peace sign? a secret iGEM sign? whats up with the fingers?)

Thursday, 4 October 2012

Good luck Macquarie iGEM team!!!!

Good luck to the Macquarie iGEM team, who are on their way to Hong Kong  for the regional jamboree of the International Genetically Engineered Machine (iGEM) competition. iGEM is a worldwide Synthetic Biology competition for teams of undergraduate students, where they try to build biological systems from standard, interchangeable parts and operate them in living cells.

This is the third year, we have sent teams to iGEM as part of our Biomolecular Sciences Capstone unit. In 2010, the MQ team won a bronze medal, an outstanding achievement for a first time competitor (equal best among Australian teams). The following year's team was able to build on their success and won a silver medal (which made them the top Australian team). This year, we're hoping the MQ team can do even better and Go for Gold! Hopefully, they will be better at that than the Australian swimming team in the London Olympics.

The 2012 Macquarie iGEM team have successfully engineeered a light sensitive genetic switch that turns on when exposed to light in the far red spectrum. For the full details see their wiki site. They have also been very successful in raising money to fund team members to go to the iGEM jamboree. They've done an outstanding job and we wish them the best of luck in Hong Kong! 

Strategy for constructing the light sensitive genetic switch (image taken from the iGEM team wiki site)

Friday, 28 September 2012

Gut bacteria and type II diabetes

The human microbiome (the collection of different bacteria that live on us and in us) has been increasingly in the news of late. For instance, while waiting for a plane at Copenhagen airport a few weeks back, I was interested to see the human microbiome had made the cover of the Economist magazine (that gave me something to read on the plane trip to Prague).

The development of next generation DNA sequencing methodologies has started to give us the tools for investigating the 1000's of differen bacterial species that live with us, and what role they may play in human health. There's increasing evidence that the microbial populations in your gut have an influence on human obesity, and the development of autoimmune diseases such as Crohn's disease. Perhaps one of the more exciting developments is the finding that faecal transplants (yes that is exactly what it sounds like) can save people from life-threatening Clostridium difficile infections.

There's a new paper just out in Nature, that has shown an intriguing association between the makeup of the gut microbiome and the occurrence of type II diabetes. I'm not associated with the study, but I was interviewed this week by the popular science magazine Cosmos about this study. You can find the article here. There's no evidence of any causal link between your gut microbial community and the occurrence of type II diabetes, but the microbial populations may provide a useful tool for classifying type II diabetes.

The furry microbiome

Thursday, 27 September 2012

Playing with Citation Statistics

I've always liked playing with the ISI Web of Science and seeing who has cited my papers (other than myself). My friend and colleague Jonathan Reizer used to say "The only person who references me enough is myself, and I'm not even sure about myself".

And in this day of age of everything being assessed by metrics, it's important to calculate your H-index for grant applications, etc. Last time I checked my H-index was 74 (which means I've published 74 papers that have been cited a minimum of 74 times each).

Apparently, there's a new toy for analyzing publication and citation statistics- Microsoft Academic Search, which I've just been checking out. It's cool in a sort of disturbing stalker-ish way that it's found photos of myself and various of my colleagues and correctly associated them with our publications. The embedded image below shows my 30 most frequent co-authors.

Once can also do silly things like calculating your connectedness to other scientists based on co-publication. Apparently there are four degrees of separation between myself and Albert Einstein:

One issue is that it appears to have missed 30+ papers of mine (possibly those published as Ian Paulsen rather than Ian T. Paulsen, I haven't bothered checking), and so all the statistics such as H-index, total citations, etc are not correct. Apparently I could manually edit it to add those publications, but I think that exceeds my level of enthusiasm. It does come up with fun but probably useless factoids, for instance I've apparently collaborated with 1676 co-authors from 1992 to 2011.

Hat tip to my old school friend Paul Wakelam for making me aware of the existence of Microsoft Academic Search.

Monday, 24 September 2012

Back in action

Apparently lazing round on beaches, admiring historic architecture, and consuming good food and wine is bad for your health, as I've spent most of my first week back in an enfeebled state with a cough and fever. Probably brought on by looking at all of the emails waiting for me when I came back from vacation. Hopefully I can carve out some time to blog over the next week or two of catching up.

One announcement, this week's JAMS meeting at the Australian Museum includes two speakers from my group- Kent Lim and Anahit Penesyan.

Friday, 24 August 2012

Signing off for 2 weeks

I'm doing something outrageous and actually taking two weeks vacation after ISME (the university has actually ordered me to take vacation leave as I have too much unused leave). So, I'm off to Prague and Portugal. Don't expect any blogging from me while I'm away, but maybe someone from my group will post in my absence.

lovely Prague

Day 4 at ISME

Starting to reach the point of exhaustion here on the last day of ISME. This morning I'm sitting in a session on Light and Microbial Life.

The session I co-chaired yesterday certainly had an eclectic range of talks that showcased some of the diversity of microbial lifestyles that exist. In addition to my talk on microbial slime communities living deep in caves beneath the Nullarbor desert, other talks looked at microbial communities living on truffles, in the air above hurricanes, on avian egg shells, on leaves in Brazilian rainforest trees, in the soil of logged forests, and in rotting corpses. I particularly enjoyed the last of these, Jessica Metcalf from Rob Knight's lab at the University of Colorado at Boulder gave a talk on trying to develop microbial forensics (essentially CSI Microbiology). She was seeing if microbial communities associated with rotting corpses changed over time in a consistent manner that might allow forensic scientists to use the microbial communities to date the age of the corpse. I now know much more about rotting corpses than I used, did you know there are five stages of corpse decomposition, with stages 2 and 3 being bloating and rupture, respectively? Makes for wonderful dinner time conversations. I'm sure Jessica was very popular in her lab with lots of boxes of soil with rotting mice.

We ate at this excellent French restaurant the other night, the menus were only in French and Danish which I took as a good sign. Anyway the name of the restaurant seemed appropriate for scientists to eat at.

Thursday, 23 August 2012

Day 3 at ISME

The Wednesday in the middle of ISME meetings is always an off-day for delegates to explore the host city. I actually left the city and took a tour of Fredericksborg and Kronberg Castles, the latter of which is probably most famous for being the location where the play Hamlet is set.

Today I'm back for day 3 of the ISME meeting. This afternoon I'll be chairing a session and giving my talk on Nullarbor cave bacterial slimes. This morning started with a frustrating wait in line for >30 minutes at the Speakers Ready room to get my powerpoint slides uploaded. However, things are now looking up, I'm sitting in a session this morning on Plant-Microbe Interactions. Two collaborators of mine are giving talks in this session- Jos Raaijmakers and Vittorio Venturi, neither of whom I've ever actually met, all our interactions have been via email.

Other highlights of the meeting which I haven't spoken about yet. Steve Giovannoni from Oregon State University won the Tiedje Award, and gave a great talk Tuesday night on his work on marine SAR11 bacteria. these tiny bacteria make up almost 25% of the bacteria in the world's oceans, probably making them the most numerically dominant organisms on the planet. These bacteria were unculturable until Steve's group developed methods for growing them in the lab. There appears to have been strong selective pressure for these organisms to reduce their genome size, leading to reliance on some unusual metabolites for growth. Their genome reduction has proceeded by very different pathways than that seen in intracellular pathogens and symbionts.

On the first day of the meeting I very much enjoyed the talks by Tanja Woyke from JGI and Ramunas Stepanauskas from Bigelow Labs on Single Cell Genomics. We have recently been funded by the Australian Research Council to develop a Single Cell Genomic facility in Sydney, and I learnt alot about the nuts and bolts of Single Cell Genomics from these two talks which should prove useful.

This very grim looking guy is located in the dungeons in Kronberg Castle in Elsinore, he reminds of characters from Skyrim

Tuesday, 21 August 2012

Day 2 at ISME

In addition to hearing about cool science, one of the other important activities at scientific conferences is networking with other researchers. While I've been to a couple of talks this morning, so far the highlight for me today has been catching up with colleagues from the US and elsewhere. Had great chats with Chris Dupont from the J. Craig Venter Institute and with Brian Palenik from Scripps Institute of Oceanography, both of whom I've collaborated with over the years. Coincidentally, we actually have just had a paper come out this week on nickel transport and regulation in the marine cyanobacteria Synechococcus.
Also seems like there are a lot of Australian researchers here, I continually seem to be running into colleagues from UNSW, UTS, UQ, etc.

Funky architecture of the Bella Sky Hotel, the ISME meeting is in the conference centre next door

Monday, 20 August 2012

Day 1 at ISME

Greetings from lovely Copenhagen! I'll be trying to live blog from the 14th International Symposium on Microbial Ecology (ISME14). I arrived in Copenhagen yesterday, and had a bit of an explore by bike. Amongst other tourist attractions, I visited a sand sculpture exhibition, and found the evolution-themed sand sculpture pictured below, you can see double stranded DNA forming from individual bases. 

DNA Sand Sculpture
Anyway back to ISME. One difficulty is there are usually multiple sessions on at the same time I would like to attend. This morning I had to toss a coin between attending sessions on Microbial Community Diversity; Single Cell Microbiology; Microbial Dispersion and Biogeography; or Microbes in a Changing Ocean. So to hedge my bets I'm dodging in and out of different sessions.

Phil Hugenholtz from the University of Queensland gave a very cool talk on using deep metagenomic sequencing to gain insight into the TM7 group of bacteria, an unculturable group of bacteria which are present in many environments and may play a role in chronic human diseases. However because they can't be grown in the lab and they are usually low abundance organisms in the environment, little is known about their function or lifestyle. Phil presented data showing that by sequencing DNA extracted by two methods from one environmental sample, he could exploit the variable population coverage in the two different DNA preps to assemble complete or near-complete TM7 genomes even though they constituted less than 1% of the bacterial population.

Great line from Ramunas Stepanauskas from Bigelow Labs in response to a speculative question-"It's fun to talk when not constrained by facts"

About to run out of battery power so thats probably it from me for today

Monday, 13 August 2012

Jetsetting Scientific Lifestyle

After a week reviewing grants in Canberra, I'm now heading off to somewhat more glamorous locations. I'm flying out tomorrow to attend a meeting with collaborators in Oslo, followed by a visit to Copenhagen to give a talk and chair a session at the International Symposium on Microbial Ecology. I'll try and blog about highlights of these meetings while on the road. Now, I just need to go pack.

Our meeting in Oslo is in this impressive looking building- The Norwegian Academy of Science and Letters

Saturday, 4 August 2012

What could be more exciting than Canberra in August

I'm driving down to Canberra tomorrow, where I'll be all next week. I'll be serving on one of the NHMRC grant panels, and my panel will assess 100 grants to see if they should be funded. I just need to pack my winter gear so I don't freeze to death. Travelling to Canberra always makes me think of Bill Bryson's comments about Canberra in his book “In a Sunburned Country”. Classic lines like “The difference between breaking your arm and living in Canberra is that when you break your arm you know it is going to get better”.

Speaking of Bill Bryson I heard him speak at the Press Club in Washington DC probably about 10 years ago. He had highly entertaining stories about  his experiences on the Appalachian Trail. I also came away with a signed copy of "A Short History of Nearly Everything".

Anyway, probably won't be much blogging in Canberra, given the confidentiality of the meeting and likely heavy workload.

lovely Canberra

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) 

Saturday, 30 June 2012

It's all a blur!

This week has been a blur of marking exam papers and writing grant rebuttals (where we get to point out how the reviewers criticizing our grants don't know what they are talking about). Anyone trying to find me has probably given up in despair as I've been hiding at home. The final marks of my students have to be finalised by Monday, so its a long weekend of exam marking in store for me so I can meet that deadline.

Saturday, 23 June 2012

Good luck CBMS336/852 students!

Good luck to the sixty or so students sitting my CBS336/852 Molecular Biology and Genomics exam today! (and yes sitting an exam on Saturday afternoon sucks, sorry guys).

Advice that I've always followed

Friday, 22 June 2012

EcoCyc vs Sleep

Those of you who know me are probably well aware that I'm not a morning person, and that I'm not known for my early morning starts. I did get up once at 2.30 am in the morning in order to get to Masada in time to climb it and see the sunrise, and I was awake at 5 am in order to watch the sunrise at Angkor Wat. But this morning I've had 2 hours sleep, and woken up at 1.30 am, and I have a 10.5 hour skype call ahead of me. The reason for my sleep deprivation is that our annual EcoCyc Steering Committee Meeting is occurring today in San Francisco. Unfortunately, I wasn't able to attend in person, as I needed to be in Sydney to mark the exams for my CBMS336 Molecular Biology and Genomics unit. So I have the joy of attending via skype.

I have been a collaborator on the EcoCyc project since 1996 when I met Peter Karp at a conference at Lake Arrowhead and we discussed adding transport reactions to the EcoCyc database. EcoCyc is an online database for the bacterium E. coli, where all of the genes, proteins, metabolic pathways, transporters and regulatory pathways are described. The project combines computationally modeling everything we know about E. coli biology with reading all of the scientific literature published on E. coli and summarizing it in EcoCyc (curation). The role of my group  on the project is twofold- 1. we make sure that all membrane proteins and functions are represented in EcoCyc; 2. we participate in computationally testing the metabolic model of E. coli represented in EcoCyc to test its accuracy.

Anyway , as part of our funding from the National Institutes of Health (NIH) we have a Steering Committe which meets annually to advise us, which I am currently attending via skype. Hopefully I stay awake at least long enough to give my presentation to the committee, which is probably around 5-6 am my time.

Overview of the metabolic map of E. coli from EcoCyc

Tuesday, 19 June 2012

Gaming vs Science (Literally)

Well, I finally finished my reviews for the NHMRC grant panel at 1.48 am Sunday night. After that I was a little too stressed to go straight to bed, so I had a look for new iPad games that might be fun, and I came across Plague Inc, which I've downloaded and played a little. There's a certain irony here, part of our research at Macquarie is focussed on understanding how pathogenic bacteria become resistant to antibiotic drugs. In Plague Inc., one plays as a bacterium which is trying to infect and kill all humans on the planet before research scientists can find a cure. In order to achieve that goal it needs to be evolve new abilities such as drug resistance. I don't really have an opinion about the game yet, but the game difficulty screen made me laugh, here are the options:
Casual- Noone washes their hands, research doctors don't work, sick people given hugs
Normal- 2/3 of people wash hands, doctors work 3 days a week, sick people ignored
Brutal- Compulsive hand washing, doctors never go home, sick people locked in prison.

I suspect the real world is closer to the casual difficulty settings than either of the other two.

Images from the iTunes app store cause I'm too lazy to photograph my iPad

Your bacteria can evolve lots of other nasty abilities other than drug resistance just like in real life

Thursday, 14 June 2012

Grant Reviews vs Root Canal

This week is a frenzy of grant reviewing, I'm a member on a National Health and Medical Research (NHMRC) Grant Review Panel this year, which means I need to review 16 grants by the end of this week, and read a total of 100 grants before August. There will be difficult decisions to make, as only 22% or so of grants will be funded, yet i would say well over half the grants are worthy of being funded. The fun of grant reviewing was interrupted mid week by the slightly more painful experience of having a root canal performed on one of my teeth.

Not my actual tooth, but my abscess was sadly bigger than this one

Tuesday, 12 June 2012

Typical Quiet Day in the Paulsen lab

Here's a photo of a typical day in the Paulsen lab. The large number of people wearing lab coats and looking busy? Thats normal. It's just a coincidence that the vice chancellor was coming through the labs for a tour.

Just another day on the cutting edge of scientific research

Wednesday, 6 June 2012

Membrane Transport Protein Humour

One of my research interests for my entire career has been membrane transporter proteins, particularly multidrug efflux pumps that make bacteria resistant by pumping antibiotics out of the cell. After 20 or so years researching membrane transport proteins, I can honestly say this is the first membrane transport protein humour I've seen.
The Best Way to Break Through a Cell Wall

Thursday, 31 May 2012

Dance Dance DNA

Often as part of research grant applications, we include an “outreach component”, where we try to communicate scientific research to the broader public. Savvy readers of this blog may realize that this blog that it is itself an attempt at “outreach”. I was recently sorting through files of old photos, and I came across these from the most fun outreach activity that I’ve participated in. Brian Palenik at Scripps Institute of Oceanography and myself wrote a US National Science Foundation Grant to study the genomes of marine photosynthetic cyanobacteria that live in coastal waters and how they differ from those that live in the open ocean, and this generated some cool data showing that coastal strains may be adapted to higher concentrations of toxic metals like copper (Palenik et al, 2006) and we developed novel approaches to look at the whole communities of cyanobacteria living in coastal environments (Palenik et al., 2009).
But probably the actual reason we got the funding for this research was the exciting outreach component we included in this project- organizing an exhibition of marine genomics for the Birch Aquarium in San Diego. It was certainly an interesting experience for Brian and myself to work together with the aquarium exhibition staff. These photos show pictures from that exhibition “Sea of Genes” that ran at the aquarium for more than two years. My favourite part of the exhibition was the Dance Dance Revolution machine which was set up so that you could dance out the DNA genetic code (GATC) and see the amino acid sequence of the protein encoded by your dance moves. They called this the Codon Hoedown. Sadly, despite years of wasted swing dance classes, I remain completely uncoordinated, and I can honestly say that I suck at Dance Dance Revolution, which you can probably guess from the photos.

Trying to dance GATC in a specific order is harder than it looks
Yes, back in those days I was not only unco, but I also had a goatee
A genome circle archway

go right ahead and dive into the Sea of Genes

Brian doing his impersonation of Indiana Jones

Sunday, 27 May 2012

Cats of the Paulsen lab

Apparently, one of the requirements for joining the Paulsen group is to be a cat parent. Here are the current cats in the Paulsen Research Group.

Lyra and Chihiro
Dots and Rainy

Chocolate Rex

Billy and Doris

Sunday, 20 May 2012

What do Professors spend most of their time doing?

Yay I've managed to set up a poll.
My vote is for writing grants. I’m not sure people outside of academia realise just how much time is spent writing grants. Between 2010 and 2011, I’ve been involved in writing the following grants-
2 Australian Research Council (ARC) Discovery Grants (both funded)
9 National Health and Medical Research Council (NHMRC) Grants (1 funded)
3 National Institutes of Health (USA) Grants (2 funded)
2 US Department of Agriculture Grants (1 funded)
1 ARC Centre of Excellence Grant (0 funded)
3 ARC LIEF equipment Grants (2 funded)

 And it's not like these are short in length. For example, the ARC LIEF grant I wrote last year on Single Cell Genomics was 121 pages in length.

So what conclusions can we make from this catalogue of grant frenzy:
- I spend way too much time writing grants
- the ARC clearly love me, whereas I appear not to be very popular with the NHMRC.
- I’m averaging 10 grant applications a year, I seem to be on track for the same number this year (4 NHMRC and 2 ARC LIEF grants submitted this year)
- apparently we're not excellent, but we have had an ARC SuperScience proposal funded, so we must be super

Of course, since my staff seem to like getting paid, we don't really have much choice but a continuous frenzy of grant writing, unless I become independently wealthy or we find a rich benefector.
 I'm sure there will be subsequent blog posts on the grant system, but my colleague Nick Coleman probably summed up many scientists feelings about the grant system in this article in the Sydney Morning Herald

Thursday, 10 May 2012

100-fold increase in North Pacific plastic waste

When caught at the checkout without my own shopping bags last week I was utterly shocked at the amount of plastic bags that were used to pack my groceries. Some plastic bags were even packed with one single item?!  While most of our plastic waste ends up in landfill, a significant amount of it gets washed out to sea where it is slowly degraded by sunlight and the action of waves.

A recent study published by Scripps researchers document a 100-fold increase in plastic waste in the middle of the North Pacific. Out here, where few people go, the ocean circulation patterns accumulate floating debris into massive garbage patches. The Scripps researchers found that the plastic particles, some of which are about the size of a fingernail, provided rafts for a marine invertebrate (Halobates) to lay its eggs.

When thinking about this problem the issue that comes to mind is plastic toxicity. This article is interesting because it discusses the wider ecosystem effects of all of those plastic objects making their way into our oceans: by creating additional solid surfaces and numerous new habitats for microbes and larger organisms this waste has the potential to change the the ecosystem structure in the open ocean. It makes me wonder whether we will soon be describing new species that have adapted to living in the shade of floating plastic particles?

Tuesday, 1 May 2012

Introducing the Team: The Biolog Omnilog

First stop on tours around the Paulsen lab is usually our Biolog Omnilog instrument (a note from our sponsors- this instrument was purchased by grant support from the Australian Research Council). This is the only Omnilog machine in Australia, a fact that is mentioned in almost every grant we write. The Biolog instrument gives us the capability of screening bacteria for 2000 functions simultaneously; e.g., testing their ability to grow on different carbon compounds, their resistance to various drugs and toxic compounds, or their ability to withstand various stresses. These tests are performed in a 96-well plate format where each well contains the specific compound we are testing.

2000 cellular functions may sound like a lot, and it certainly beats making up 2000 separate agar plates to test each function. However, it is only testing a tiny fraction of the functional diversity that exists out there in the microbial world. Recently, we have been making our own “custom” Biolog plates by taking blank plates, adding in the Biolog proprietary buffers and dye, but then adding in the specific compounds we would like to test. For instance, we are interested in bacteria that grow on plant roots and provide beneficial effects for the plant, and we would like to know why particular bacteria prefer specific plant species. So we have been making our own Biolog plates that include specific compounds that the plant species secrete to find out what these bacteria like to eat.

We’re also happy to collaborate with other research groups; if you have a unique and interesting problem that might benefit from customized Biolog analyses, feel free to contact us.

it even matches the colour scheme of our lab!

Friday, 27 April 2012

Scientists essentials

Research laboratories function differently than other places of work. There are no set office hours, although you are obviously expected to turn up at some point! But that means that some (crazy) person like me turns up rather early at work to benefit from the first warm rays of the sun. Some people might argue than 7am isn't that early but I shall remind the readers that our research group is in a University and undergraduate students are not renowned for getting up bright and early...

However even the most hardened early riser need something to focus the mind and we are lucky to have some good coffee spots right in the centre of the campus and some pretty enjoyable views to ease ourselves into a productive working day.

Early (or late for some) morning coffee!

Monday, 23 April 2012

So what do you do for a living?

When people ask me what I do for a living and I say "marine microbiologist", the usual assumption is that I play with whales all day long. I'd quite like that myself, however, I work on the things at the other end of the size scale, photosynthetic microbes, that can only be observed under the microscope. Inevitably that sounds less exciting to many people but in reality it is probably one of the most exciting research fields to be in this decade!... So, I have to find ways of explaining how great and important my work is. I could go in the details that cyanobacteria produce more than 50% of the oxygen in our atmosphere, that is to say that every second breath we take is sponsored by my little friends, but I found a way more important reason than that.

A few years back Nestle banned the blue Smarties (another popular and older version of m&m’s) due to health concerns from the artificial colorant needed for its confection. Even though Australia might have gone against other countries and kept the production going (True blue Aussie Smarties won't die off), I was in the UK at the time and this was dramatic!! There were even campaigns launched and facebook pages setup to “save the blue Smarties!”

And then cyanobacteria came to the rescue! The blue Smarties was back, this time coloured with a natural pigment (phycocyanin) extracted from these little bugs. Although a lot of the media referred to Spirulina as seaweed, I won't take much offence to the fact they are not, and keep spreading the word that: cyanobacteria saved the blue Smarties!!! 

A few of my colourful marine cyanobacteria and a (soon to be empty) pack of choccies containing "safe" blue Smarties.

Tuesday, 17 April 2012

Sci-fi science (Part 2): the MinION

After my last post on Sci-fi science, I remembered another cinematic dream of mine.
Being heavily involved in genomics, that is to say doing a lot of sequencing of the genetic material of microbes and teasing out meaningful information out of a large mass of data, I have always been quite wishful of the movie "Gattaca". When Uma Thurman gives a single hair to the sequencing booth and less than a minute later she is informed of the suitability of her love interest. Not that I would like to know how good a match I make with the bugs I grow, but that would save us a lot of time waiting for data to come back and sitting in front of the computer. This year a UK company might have brought sci-fi that little bit closer to reality with their USB sequencer.
The UK company Oxford Nanopore Technologies are planning to release their tweaked USB memory stick that can sequence more than 150 million bases in their 6h life-time (about 20 of those would do a human genome!) and can be purchased for less than US$900! The days of manual sequencing of a couple of 100 bases on large gels are definitely over...

The "old style" room full of machine vs. the  new USB sequencer!

Friday, 13 April 2012

Crowdfunding Science

Crowdfunding is a method of raising money for a project by obtaining small amounts of money from many people to reach a desired monetary goal. Crowdfunding was a central topic of conversation when I had friends over for dinner last Saturday to eat seafood paella (mmmmm, paella). This was due to the fact that one of my favourite webcomics, Order of the Stick, had just raised over US$1.2 million through Kickstarter. And Wasteland 2, a post apocalyptic role playing computer game had just raised over US$2.3 million to turn it into an actual game (Thanks in part to my friend Fraser who contributed to the second of these projects).
Just a day or two later, thanks to the blog of scifi author David Brin, I came across Petridish (great name incidentally), a site for crowdfunding science. Science has long been dependent on rich benefactors, whether individuals or governments, for funding. This goes all the way back to the Middle Ages where one needed a rich patron, preferably the king. Crowdfunding provides an intriguing alternative funding mechanism for scientific research projects. Though clearly scientific researchers can’t yet compete with webcomics or computer games for glamour, since the projects on Petridish are mostly trying to raise $10,000 rather than millions of dollars.
If crowdfunding does become a significant mechanism of scientific funding, this would raise concerns in my mind that we would be prioritizing funding based on gimmicks or pretty pictures rather than on any actual scientific excellence. Of course, whether the current grants system in Western countries really rewards scientific excellence is a topic for future blogging.

Not the paella I cooked, as I drank too much wine and forgot to take a photo of my paella

Sci-fi science on screen

Quite a few years back, while flicking through TV channels, I ended up watching my first (and last) 10 minutes of CSI. My slightly nerdy attention got caught when I saw them in full forensic mode, looking at a sample under a microscope. What was amazing about this microscope was that the characters were able to use it to decipher the entire amino acid sequence of the protein, in real time, contained in their sample. If I had continued watching I would have seen the inevitable arrest of the evil criminal on the basis of his/her protein sequence.

After seeing this amazing bit of kit on CSI I have tried to convince several bosses over the years to buy me one of these molecular microscopes, but they've always laughed at me, though I have not asked Ian yet... 
Working on a particularly puzzling protein sequence...