Thursday, 28 February 2013

Happy 2nd Birthday JAMS

The second ever JAMS (Joint Academic Microbial Seminars) Annual Dinner was held yesterday at the Australiam Museum in Sydney. JAMS is normally a monthly seminar series at the museum, but once a year we have an annual dinner and invite 4-5 international/interstate guest speakers. We had extremely entertaining talks from all five speakers. The highlights for me were the talks from Phil Hugenholtz (UQ) who gave us a rapid but exciting trip through what we've learnt from the genomes of unculturable bacteria and Victoria Orphan from CalTech who looked at the function of bacterial communities from deep sea methane vents.

After the talks were dinner and drinks in the Dinosaur Room. The food was pretty good, one of the curiosities of my dinner was the unidentifiable vegetable on my plate that turned out to be a purple carrot. Who knew carrots could be purple? Apparently they are chockful of anthocyanins. I should probably eat alot more purple carrots!

Who knew carrots came in this colour
Many thanks again to JAMS organizer Federico Lauro for a great meeting!

Saturday, 23 February 2013

Life in the Dark

In caves deep beaneath the Nullarbor Plain (a desert region in Australia which is actually the world's single largest piece of limestone, more than a thousand miles across) live strange slimy microbial communities known as microbial "slime curtains". A very poetic name, I think. These organisms live in the dark in ancient salty water, with little or no input of fresh water or organic nutrients from the surface.

In tune with the the title of this blog, we were curious about the lifestyle of these bugs- how do they make a living in such a unusual setting? We've just published a paper entitled- "Life in the Dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism" in the ISME Journal which tries to answer this question.

We received samples of the slime curtains from cave divers exploring Weebubbie Cave, and we broke those cells open, collected the DNA from the whole community, and then sequenced that DNA (this is known as metagenomic sequencing). Computational analyses of the millions of genes detected were used to see what we could learn about these bugs. What we found was that the microbial cave slimes consist of about 1000 different microorganisms, but one particular bug made up almost half of the total community. This dominant bug was a Thaumarcheota (yes I know that just rolls off the tongue) and almost certainly gets its energy by oxidizing ammonia found in the cave water. So, we think that ammonia oxidation is what enables this community to flourish within the caves.

Scanning electron micrograph of the microbial cave slimes, the long filaments we think are the Thaumarcheota

Cave divers (photo courtesy of Liz Rogers)

Microbial cave slimes in Weebubbie cave (photo courtesy of Peter Rogers)

Cave diver taking a sample of cave slimes for our lab to investigate (photo courtesy of Steve Trewavas)

Wednesday, 20 February 2013

I don't know what it means, but it is pretty

From the latest toy on LinkedIn, here's a network connection map of my LinkedIn connections. I should start off by saying I don't very actively look for people to connect to on LinkedIn, mostly I just respond to people's requests. In terms of analyzing my professional network connections, as far as I can tell orange= friends; green= Macquarie University colleagues; blue= TIGR/JCVI colleagues; purple= other academic colleagues, mostly bioinformaticians. The remaining colours are other academic colleagues or friends who live overseas.
So what conclusions can one draw from this? Um, aaah, errrr. I guess I am connected to distinct clusters of people, with no real connections between the clusters. Maybe a sign that I have lived in several different places in my life.
Still it's a fun toy to play with for 5 minutes and does make pretty diagrams.

Friday, 15 February 2013

More Grant Writing and Humour

Still struggling through grant writing season here. Martin is about to submit his Future Fellowship application, and I was up until 2.30 last night finishing my sections of a US Department of Agriculture Grant.
This segues into my next scientific humour post. I've long been a fan of PhD comics, which provides a surprisingly accurate and amusing view of scientific life. Recently, one of my PhD students gave me a copy of the PhD movie- I'm not quite sure what message he was trying to give me. Anyway, hopefully our grant writing frenzy will avoid this outcome:

I absolutely remember going through the shock phase before.