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)

Geomicrobiology

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) 

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.

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

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

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

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