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| lovely Prague |
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.
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.
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.
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| 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.
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.
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| 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.
Also seems like there are a lot of Australian researchers here, I continually seem to be running into colleagues from UNSW, UTS, UQ, etc.
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| 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.
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| DNA Sand Sculpture |
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.
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| 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.
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.
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| lovely Canberra |
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