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