Wednesday, 25 December 2013

Merry Christmas!

Hi all!

Merry Christmas! (or if you are in the US, Happy Holidays!)
Cheers,

Ian

Lots of new games to play amongst these presents!

Wednesday, 18 December 2013

New type of bacterial drug efflux pump



My PhD research back in the 1990s focused on investigating how Golden Staph becomes resistant to antibiotics and antiseptics. That research described some of the first known bacterial multidrug efflux pumps- proteins that sit in the bacterial cell membrane and can pump antimicrobial compounds out of the cell.

Since that time, our situation has worsened so that we now have highly multidrug resistant "Super Bugs" that are resistant to nearly all available treatment options. The World Health Organisation has recently declared that antibiotic resistance is one of the three greatest threats to human health.

It has been estimated that drug resistant Super Bugs add as much as 20 billion US dollars per year to direct healthcare costs in the USA.

We have just published a paper in PNAS where we investigate resistance to chlorhexidine in the hospital pathogen Acinetobacter baumannii. Chlorhexidine is an antiseptic that is very commonly used in soaps, handwashes, and mouthwashes. Using genomic approaches we identified a gene of unknown function that was highly expressed when cells were exposed to chlorhexidine. Further work revealed this gene encodes a new type of drug efflux pump. This is the first new type of bacterial drug efflux pump discovered in over a decade. This work was undertaken in collaboration with Peter Henderson's group at the University of Leeds. We are continuing this collaboration to investigate the structure of this efflux pump and how it binds chlorhexidine, opening up the possibility of designing inhibitors that would interfere with the pump.

We've received some coverage in the media-

- Aged Care Insite Superbug secret revealed

It is clearly a Super Bug, it has a cape! (Note- this is actually a plush Golden Staph)

Tuesday, 3 December 2013

ASPAB Conference

I am generally not known for being a morning person. So it was a bit of a shock to my system, when I had to get up at 4 am in Melbourne last week in order to get the first flight in the morning back to Sydney, and then a taxi straight to the Sydney Institute of Marine Science (SIMS). Fortunately, there were no flight delays, so I was able to make it in time to give a keynote talk at the Annual Conference of the Australasian Society for Phycology and Aquatic Botany (ASPAB). First time I've actually visited SIMS, it's a beautiful location; and it was an interesting meeting to attend.

View from ASPAB at the Sydney Institute of Marine Science

Christmas comes Early at Macquarie

The Paulsen lab group went out today for an early Christmas lunch today. There's a new bowling alley and laser tag skirmish place opening at the Macquarie Shipping Centre, where we had hoped to go for our Christmas outing, but unfortunately its not open yet. So, it was burgers instead for Christmas this year!

Nothing says Christmas like burgers!

Monash Microbiology 50th Anniversary

One reason I am running behind on my blog is that the last couple of weeks have been a frenzy of travel and talks. This included attending the Monash Microbiology Department 50th anniversary function, otherwise known as Monash Bugs R50 for the twitter literate. This event was held at Deakin Edge at Federation Square in Melbourne, a cool venue with funky modern architecture. There were four talks given by former Monash graduates, including myself, and several talks from current Monash faculty about their future directions. This was a formal event so shockingly enough, I was there in a suit (sorry no photographic proof). Several people asked how they got me out of my usual leather jacket, and my answer was that I had it surgically removed.

There was a great turnout with more than 200 attendees including many retired former staff of the department, so it was a great opportunity for catching up with old friends and colleagues, particularly since the event finished with cocktail party. There were also lots of photos projected on the big screen from across the fifty years of the department history, including many with scary hair from the 60s and 70s.

My talk basically told the story of how my scientific career has been shaped from experiences and interests from my time as an Honours and PhD student with Ron Skurray's research group at Monash Microbiology. One of the other speakers was Mark Schembri, who was in the same Honours class as me (see photographic evidence below) and is now a Professor at the University of Queensland.

I thought it was a great event, and an honour to be invited to talk. It was great fun catching up with many people I haven't seen for decades.

Clearly an excellent year for Microbiology Honours students- I'm the tallish person roughly in the middle; Mark Schembri is second on the right from me
A Skurray lab group meeting in late 1989 or early 1990. That's me in the middle with way too much hair, a Violent Femmes T-shirt and scarily bright red shoes. Also pictured from left to right- Ron Skurray, Dario DiBerardino and Linda Messerotti,

Cocktail party after the scientific talks
The venue at Deakin Edge, Federation Square

Friday, 29 November 2013

Eitan Bibi Seminar

I'm massively behind on stuff I want to blog about, but hopefully I can catch up in the next few days. Today though, we are hosting a visit from Professor Eitan Bibi from the Weizmann Institute in Israel. Eitan is giving a seminar on his research on multidrug efflux pumps entitled "Tricky relationships between the multidrug transporter MdfA and divalent cationic drugs" in F7B322 at 12.00 pm.

I've long had an interest in multidrug efflux pumps- proteins that sit in the membrane and make bacteria resistant to a broad range of drugs by pumping the compounds out of the cell. A major focus of multidrug efflux research has been trying to understand how a single protein can recognise a variety of structurally distinct compounds, and I'm sure Eitan will have interesting insights in this area.


Theoretical model of the MdfA protein taken from the Weizmann Institute web site


Thursday, 28 November 2013

The 9th International Sponge Conference, 4th-8th November 2013

At the beginning of November, I attended the international sponge conference in Fremantle, Australia. My main research so far, in the UK and Australia, has been concentrated on the ecological and genomic adaptation of marine photosynthetic microbes to their environmental niche. I have only fairly recently started my foray into sponge related science. Sponges (porifera) are very interesting animals which are believed to have been some of the first evolved multicellular eukaryotes. They are practically found on every aquatic bed (freshwater and seawater) and carry out major roles within the marine ecosystem, from structural to chemical. Unfortunately, they are one of the most ignored key players within the bentho-pelagic interactions, with the coral stealing most of the limelight in reef areas and the difficulty of classification presented by sponge species. My main interest lays in the fact that porifera are forming symbiotic relationships with numerous microbes, amongst which are some major photosynthetic microbes. That close bond can even lead to some sponges becoming net primary producers, instead of relying on their heterotrophic particulate food from the water-column for their source of carbon and energy. That sounds pretty groovy to me, and my main interest is now to try and dissect the interaction between the sponge and its cyanobacterial symbiont at the genomic and biochemical level. I would also like to compare those photosynthetic symbionts to the free living related cyanobacteria I have been studying so far.

The sponge conference was an unequalled opportunity to get up to speed with the latest in sponge related science and meet a wide array of researchers, without having to travel the world. I only knew two people in the sponge world at the beginning of the conference, only one was present and quite busy chairing the whole conference! So that means that I had an amazing time of networking. The sponge science community is like a very big family with a nice convivial atmosphere. This contrasts with some other fields of research where there is harsh competition between research groups and character clashes can overshadow meetings.

For a newcomer in all things sponges, the conference was a high intensity crash course. With 6 major research themes, comprising 6 plenary/keynote addresses, 117 oral presentations, 107 posters over 4 days, and various evening events where sponge discussions were helped by a few drinks and nibbles.

I have been impressed by the wide breadth of subjects covered. The much discussed traditional and molecular taxonomy where both sides don't always agree, biotechnology applications (who knew that sponges could be at the basis of nano-circuits and bone implants?) and industry, evolution, ecology, population biology and symbiosis. Enough to be both amazed and completely sponged-out by the close of the formal conference.

We finished the meeting by a sumptuous dinner conference at the Fremantle Yacht club, and the "traditional" sponge songs (as far as I could gather that appears to be a recurrent theme at the close of each sponge conference), which consisted in well known songs with sponge-themed modified lyrics (some of this year's offering comprised Paul Kelly's "from little things big things grow", the Beegees' "staying alive", Men at Work's "down under").

It seems that the next conference will be held in Ireland in about 3 years and I hope I will be able to attend.

The flight back was a bit of an extra adventure with my flight being diverted after a mislanding in Sydney due to horrendous weather, first to Newcastle then to Brisbane, a sleepless night where we have been transfered and given a motel room for the whole of the 2 hours (2-4am) we could stay there before going back to take a flight back to Sydney early in the morning.... I also had to go away straight afterwards for a 3h+ drive from the airport in a (bad!) rented car. Coffee was welcome!


photo from Marie-Claire Demers

Friday, 8 November 2013

Bushfires

The bushfire season has started very well early in the Sydney area this year. We've had a fire today in Lane Cove National Park, a couple of kilometres from Macquarie University, which is now under control according to the NSW Fire Service.
I took some photos of the regular procession of helicopters visiting the Macquarie University lake to pick up water for water-bombing the fire:





Monday, 14 October 2013

Congrats 2013 MQ iGEM team

Congratulations to the 2013 Macquarie iGEM team for winning a Silver medal, as well as Special Awards for Best Poster and Best Mascot at the Asia Region Jamboree in Hong Kong! The  International Genetically Engineered Machine (iGEM) competition 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 year there were 204 University teams competing from all around the world.

This is the fourth year Macquarie has entered a team in the competition, and so far we've won three Silver medals and one Bronze medal. We've also been the top Australian team in the competition in each of the four years! Last year's team won a Silver medal for their work on engineeering a light sensitive genetic switch. This year's successful project was "Green is the new Black- expression of chlorophyll within Escherichia coli", where our team of 22 students successfully expressed many of the genes required for chlorophyll biosynthesis in E. coli, with the longer term goal of making a photosynthetic E.coli that could be used in bioenergy production. I'd like to say fantastic job to all of the team and their tireless advisors Dr Louise Brown and Associate Professor Rob Willows.

The Macquarie students also presented their work at the Second Australasian Conference of Undergraduate Research and won a $500 prize for Best Presentation in Plant Science or Molecular Biology.


The green and charismatic Chlorophyll Man, winner of best team mascot
The successful MQ iGEM team in Hong Kong with their award winning poster



Friday, 11 October 2013

BacPath

It's been a struggle recently to find time to blog. Last week I was away at BacPath, an Australian conference on the Molecular Analysis of Bacterial Pathogens. My cunning plan of live blogging from the conference was foiled by the fact there was practically no internet connections available at the meeting. I guess that's one of the downsides of having the meeting located on a sub-tropical island paradise (well Moreton Island anyway).

BacPath is one of my favourite scientific meeting, and in many ways reminds me of a Gordon Research Conference. Several features about BacPath I particularly like-
1. The relatively small size of the conference (150-180 people), which really gives you an pportunity to mix with and meet many of the delegates.
2. The fact that the meeting is always held at a relatively isolated location, so all of the delegates spend their entire time at the meeting, you end breakfast, lunch and dinner together, providing many opportunities to network, discuss science, arrange collaborations, etc.
3. The philosophy that junior scientists (PhDs students and postdocs) should give the vast majority of presentations rather than senior scientists.

In the interests of full disclosure I should say I was a member of the organizing committee for the 2011 BacPath meeting. BacPath is held once every two years, with each state taking a turn to host the meeting. In 2015 it will be Victoria's turn. This year it was in a lovely location, though sadly I think I set foot on the beach for about 10 minutes, although I should point out that I hand fed a dolphin in that 10 minutes.

There was a great set of talks at the meeting. Highlights for me included Cynthia Whitchurch's talk with beautiful videos of how exploding bacteria help bacterial biofilms develop. Also, Mike Jennings, the invited speaker for an Outstanding Contribution by an Australian Researcher, gave a great talk on phase variation of human pathogens. There were many other great talks at the meeting from Dena Lyras, Tim Stinnear and many others. Karl Hassan from my group gave a talk on a new type of drug efflux pump we've discovered.

The main problem with BacPath is at the end of it I'm always exhausted, as the talks start at 8.30 in the morning and the conference runs to 11 pm every night with poster sessions in the evening accompanied with alcoholic inducements for scientific discussion.

Moreton Island- its all made of sand
 


Friday, 27 September 2013

Quoting Donald Rumsfeld

Some of you may remember (perhaps not very fondly) Donald Rumsfeld, former US Secretary of Defense in the administration of George W. Bush. Surprisingly, the title of our latest publication actually quotes Donald Rumsfeld, whose famously said
"There are known knowns; there are things we know that we know.
There are known unknowns; that is to say, there are things that we now know we don't know.
But there are also unknown unknowns – there are things we do not know we don't know."

We've just published a paper in the journal PLoS One entitled Dead End Metabolites- Defining the Known Unknowns of the E. coli Metabolic Network. E. coli is the best model organism for studying bacteria, it is the single bacterium we know the most about after 50-60 years of study, and yet we still don't know what a quarter of it's genes do. In this paper, we use the E. coli metabolic network represented in the EcoCyc database, and try and work out what are the gaps in our knowledge about E. coli metabolism, or as Donald Rumsfeld would put it- what are the known unknowns of E. coli metabolism. Hopefully this list of known unknowns provides researchers targets for future study to enlarge our understanding of E. coli. As for the unknown unknowns, um well I guess we don't know yet.

E. coli is the one with the name tag

Tuesday, 10 September 2013

Transport Protein Workshop

I've gotten back from England, with the addition of about 4 kilos of weight from eating too many full English breakfasts. I'm going to need to need to fire up Dance Central 3 on the Xbox to work off the English sausages, bacon, black pudding, etc.

The last day in Leeds was a membrane transport workshop hosted  by Peter Henderson at the the Astbury Centre for Structural Molecular Biology, University of Leeds. Karl and I both gave talks on our groups work on characterizing multidrug efflux pumps, proteins that sit in the cell membrane, and pump out antibiotics and other drugs making the bacteria resistant.

The workshop dinner was held in the Royal Armoury in Leeds. After all of the tourists had gone home, we were able to stroll around the museum at our leisure, and see their collection of historical military and hunting artifacts, including a magnificent suit of Indian elephant armour. We then had dinner in an imitation English drawing room, whose walls were covered with leather bound books, stuffed animal heads, random weapons and other historic artifacts. A very memorable ending to an entertaining day of scientific presentations.

The Only Surviving Suit of Indian Elephant Armour in the World (dating from ~ 1600)
Here I am at dinner caught by a camera in mid-gesticulation. Also in the photo are Anne-Brit Kolsto and Ole Andreas Oksted from the University of Oslo.




Thursday, 29 August 2013

Musings on leg 1 of the IndigoV expedition and the meaning of science

As we near the start of the second leg of the IndigoV Indian Ocean expedition, it is time to reflect on what we have learnt during the first leg of the voyage.

- No matter how well prepared, something will go wrong
- When trying to lay low, try not to appear in newspapers
- Very fresh tuna is chewy but better than 2-minute noodles
- The Indigo V is relatively water-tight even during very big storms (luckily)
- If we say there will be restaurant quality food on board, let's not kid ourselves, the 2-minute noodles will do very well...
- Electrical equipment and seawater do not mix (actually, any equipment and seawater does not mix)
- Clothing drenched in seawater never drys properly
- There are a lot of (very) big ships sailing the Indian Ocean
- Never let a certain Martin Ostrowski at the helm when there are big waves and you want to sleep below deck. (I heard he likes to surf...)
- Whales are amazing and always appear when all the camera's batteries are flat

Jokes apart, the whole experiment of the Indigo V expedition was a unique experience, showing it is possible to run scientific expeditions with less expensive equipment, and in a more cash efficient way. Indeed, the whole expedition is running at the price of a single day from a standard research vessel.
"Accessible" projects such as the IndigoV Indian Ocean expedition are important on scientific grounds, but also vital to engage interest within the scientific community, as well as the general public and media.

This opens the wide and exciting world of crowd funding of science. We might never be as successful as the guys building a space telescope, but the general idea is the same in that research should not be conducted in a small dark laboratory, behind closed doors. Scientist should be engaging with wider community and be approachable even if it takes time out of staring at computers or petri dishes.

The main aim of science is to make people think, feel included and want to participate. I'm not particularly proud of myself when I have blank stares from people when I am trying to explain what I do!

So onward and upward (or north-east-ward to be more precise!) with the IndigoV Indian Ocean expedition. Good luck to the brave sailors.

To be continued....


Tuesday, 13 August 2013

My cats have probably forgotten me

After a week in Canberra, I was home for a day or so, and then had to fly off to England. I've just arrived in Leeds after 36 hours of travel time, where I am about to collapse into a coma. I'm here to visit with my collaborators and to give a talk at a membrane transporter workshop. My talk has one of my sillier titles to date- "Channeling David Attenborough- Studying Bacterial Drug Efflux Pumps in their Native Habitat".



The Met Hotel, my room is somewhere on the 3rd floor

Catching up on posts from last week

My birthday at the NHMRC panel. The chairperson's wife baked me a birthday cake! It came complete with birthday candles thanks to the NHMRC!


Photo thanks to Mark Schembri

Monday, 5 August 2013

If it's August this must be Canberra

It's that time of the year again, where I get to spend a week in Canberra on an NHMRC Grant Review Panel. Here's last year's post. Actually, even though my blog posts complain about it, I actually enjoy serving on the panel, it's interesting to see what other researchers are up to. Although, it's a little unfortunate that every year it seems to coincide with my birthday.

In other news, apparently we have a federal election happening, and there's even some chance Australia might win a cricket test. My schedule in Canberra is too busy to have time to pop over to see Kevin Rudd. Actually, he's probably off campaigning in a marginal electorate somewhere.

The Shine Dome- Home to the Australian Academy of Sciences, and where we have our initial briefing session for our Grant Review Panel

Thursday, 1 August 2013

Be Excellent to Each Other

I'm currently working on an ARC Centre of Excellence bid led by Eddie Holmes at the University of Sydney- The Centre of Excellence in Microbial Diversity, Evolution and Control. Eddie has done a heroic job herding us all together, and putting together an exciting proposal for what would be a globally unique Centre. This Centre aims to characterize the biodiversity of microbial species in Australia, how these microbes evolve, jump species boundaries and cause disease, and how best to control and eradicate them. 
Assuming no nervous breakdowns occur, the Centre proposal will be submitted next week. For those of you who haven't seen a Centre of Excellence proposal before, when printed out it makes a stack of paper about a foot or two high. I feel sorry for the panel that will have to review 22 of these applications.
I've previously been funded by the ARC as part of a SuperScience Fellowship, if our Centre of Excellence is funded that would make us both super and excellent.

And Party on Dudes

Wednesday, 24 July 2013

Seminar at ANU

It's clearly the month to be popping around giving seminars. Tomorrow morning I fly out to Canberra to give a seminar at ANU.

Monday, 15 July 2013

Apologies to Charles Dickens

For anyone who is interested, I'm giving a talk tomorrow at UNSW on "A tale of two bacteria and many omics". Half of the talk will be on our marine cyanobacterial research and the other half on discovery of new drug efflux pumps in the opportunistic pathogen Acinetobacter baumannii.

Tuesday, 2 July 2013

Martin is a shell of his former self

Martin is still recovering from his experiences on the Indigo V expedition.  As can be seen in this photo, he is really a shell of his former self.


Wednesday, 26 June 2013

The Indigo V expedition: a prototype for citizen oceanography. Drs Federico Lauro (UNSW) and Martin Ostrowski (Macquarie U)

Tonight (Weds 26th June. 6pm): Joint Academic Microbiology Seminars. The Australian Museum. Sydney

Tonight Federico and I will present the concept, science and experience of the first leg of the IndigoV expedition.

While there is an abundant excess of water in the Oceans, marine scientists encounter numerous difficulties in obtaining samples for research. This is particularly true for blue waters of the Southern Hemisphere because research voyages are expensive (> $100,000 per day) and there is fierce competition amongst scientists for ship time.

The IndigoV is a privately owned 18m sailing yacht that has been converted into a state-of-the-art, wind propelled, floating laboratory. The IndigoV expedition is a proof-of-concept to show that new, readily available, and relatively cheap technology provides almost anyone with the opportunity to undertake scientifically rigorous oceanographic sampling.

"We plan to raise awareness as to both the importance and the accessibility of ocean sampling, encouraging ships/ yachts of opportunity to get equipped and sample as they go. Every day there are thousands of manned vessels of opportunity that cruise the ocean and we hope one day to turn them into in situ marine microbe monitoring platforms!"

Tonight we'll discuss some of the highs and lows of the first Leg which departed Cape Town, South Africa, and sailed through high seas and foul weather in the Southern Indian Ocean to Mauritius. Despite gale force winds (~50 knots) and huge waves (11m) our 18m yacht successfully navigated to to out destination and proved that we could get science done along the way!

This is also an opportunity to thank the many people that have helped make the first leg a success, including crew, and generous shore supporters that were incredibly helpful:

Steve the electrical engineer;
Ed Rybicki, Dr Maya Pfaff and Prof. Maryna van der Venter and for Liquid Nitrogen;
Linda for an amazing brai at the Port Elizabeth Power Boat club;
Roy Finkelstein for the best fibreglass coolboxes in the Southern Hemisphere;
to name but a few...

Hope to see you at the Australian Museum tonight. If you can't make it check out the progress of the IndigoV expedition at <http://indigov.unsw.edu.au/> or listen to the latest radio interview http://blogs.abc.net.au/nsw/2013/06/sailor-scientists-make-it-home.html?site=southeastnsw&program=south_east_nsw_mornings

Martin

The IndigoV tied up alongside Squid 'chokka' boast waiting for spares in Port Elizabeth, South Africa.

Tuesday, 25 June 2013

Expert marking assistance

This week I am hiding at home and marking exams for my unit Molecular Biology and Genomics. As you can see in the photo I am receiving some expert assistance.

Lyra says this stack of exams passes, the others are not comfortable enough

Tuesday, 18 June 2013

Lost at sea: sailing log part 3

The second week of the expedition was only marginally easier than the first. Following the rough weather of the first week, we have been motor-sailing towards Mauritius with some beautiful sunny skies as the wind has not been fully with us and we had some time to make up. We saw the biggest pod of blue whales I have ever seen (actually the only pod I have ever seen) and it adopted Indigo as a new member of the clan coming alongside at less than 50 meters. A little scary but beautiful. Of course every single camera on board had flat batteries...
We succeeded to do some great sampling, while trying to avoid poking the whales. We only just stopped sampling before entering  the french territorial waters of ‘La Reunion’. We had some tough night waiting for breeze or wishing the breeze would abate! But we made quick progress towards Mauritius and soon have seen our first coconut floating in the water.


The Indian Ocean was not going to let us go without one last challenge. On our last night at sea, we battled through 25 knots of breeze and 5 meters swells and had to slow down to avoid getting airborne. Moreover being back close to civilization has its downfalls: we had to dodge ships all night long...
So, as much as we would have liked to be sipping martinis in Port Louis, we had still a few miles to cover. And then the predicted wind just didn’t show up in time and we were just about out of fuel.

We finally made it to Mauritius on the 12th June, shaken but not stirred. The first leg of the expedition is done and everybody has a full head of memories that will pass on for generations to come... (or at least a few months).


A next load of fresh sailing scientist will descend onto Mauritius in a few weeks time, so keep coming back for further updates or go and see the dedicated blog (IndigoV).


Martin


In full sampling mode

Land!!!


Thursday, 6 June 2013

Sailing log part 2

That has been a hard first week on the boat!
We started out of Port Elizabeth with some decent weather, calm seas and sunshine. There are plenty of cargo ships heading in and out in roughly the same direction as us so we need to keep a constant eye on the radar. Our automated information system tracks when one is near, gives us info about name, size and what it is carrying and warns us if we are going to collide, that's always handy!
We started sampling as soon as we hit the international waters and all went smoothly for a while. That is until the weather front which was supposed to pass quickly over us changed its mind...

We got hit by some very nasty weather and had to heave to for more than 30h. That means stop everything, keep your head low and wait for it to pass, while still keeping an eye for those big ships!
The boat was completely shut with occasional big waves breaking across the deck.

Luckily the weather has now become more clement and the stomachs have settled. It is amazing how the boat has transformed from survival, to science mode. We have taken some great samples and continuing to do so. The run to Mauritius should be straight forward now and the forecast is set to absolutely gorgeous with favourable winds! What more could a bunch of green sailors need!!

Martin


Maybe a bit dramatic, but that's how it felt!


Tuesday, 4 June 2013

Not sailing through the Indian Ocean

Well it's not as romantic as sailing through the Indian Ocean on a yacht, but I am also overseas this week. I flew into California yesterday, and I am currently at SRI International in Silicon Valley to attend the annual Steering Committee meeting for the EcoCyc and PortEco projects. I have been a collaborator on the EcoCyc project since 1996, and later this year we will have to write our NIH grant renewal, so hopefully we can get good feedback from our Steering Committee.

There was some excitement last week when I dug through a cupboard and dusted off my passport, and suddenly realised that my passport had expired in February. After much swearing and panic, the Australian passport office proved to be unbelievably helpful and efficient, and turned round a new passport in less than 24 hours.

Helps to have one of these

Friday, 31 May 2013

Sailing log part 1

Day 1

We finally made it out of Port Elizabeth on the evening of the 29th May following delays of all sorts. We are now well underway on our route to Mauritius. We will start taking water samples when we are out of the 200 nautical miles range. On our first day the weather was gorgeous, 15 kts of wind and we caught our first yellowfin tuna (5 kg) on the line that we trawl ‘just in case’. The tuna then magically transformed into sushi that we all very much enjoyed. You can't get any fresher than this. Life is great!!!

The Indigo V in Port Elizabeth

It has been a very hot first full day of sailing. The winds died and we have been getting knocked by the Agulhas current. We should be into fairer currents and winds tomorrow. Everyone was getting their sea-legs, especially down below where everything is moving around.


Day 2

We made very good progress last night and we are now sailing at 10 knots of speed in the right direction (always useful!). The seas are quite big and we have nothing else to report other than the usual little dramas on board (spilled coffees, leaking hatches, somebody seasick). Actually all of us have been feeling sick but from late this afternoon, things calmed down. Sea sickness tablets are good! We are now definitely getting better and fully functional.


We were travelling pretty fast but the waves were coming from all sides, and over the deck. I had a watch at 4am but most of the foul weather had subsided to rough weather by then. I enjoyed clear skies and a very bright milky way with the southern cross in the middle.

No fish today. Still fixing many small problems, but we are travelling faster than the motor with the sails.

Martin

Seal snoozing in comfort
Lazy seal

Thursday, 23 May 2013

Getting used to life on board

The Indigo V crew is getting used to life on board the ship and late night watches. We have been sailing along the African coast in the sunshine.
The weather has been reasonably good so far but the wind is blowing head on from the travelling direction, which means we have been motoring for most of the way so far.
After a short refuel and fixes in Port Elizabeth, we will sail out of territorial waters and start the main bulk of the scientific sampling all the way through to Mauritius.


Martin

Tuesday, 21 May 2013

Au revoir Fran!

Over the past 3 months, the Paulsen lab has hosted Dr Fran Pitt, a visiting scientist from the University of Warwick, UK working with Prof Dave Scanlan. Fran is a long time colleague of Martin Ostrowski and Sophie Mazard from their time in the UK. She has been working for quite a few years on all things cyanobacterial, from detailing sensing and regulatory mechanisms of phosphate stress in freshwater Synechocystis sp. to environmental transcriptomics of marine cyanobacteria.
She recently took part in the Atlantic Meridional Transect in October 2012 (AMT) a research expedition sampling waters from Southampton, UK down to Punta Arenas in Chile. And liked it so much she has also obtained a couple of berths to participate in the coming AMT this October. We will certainly talk again about the AMT cruises in future blog posts.
Fran took some time out of her busy schedule in the UK to take advantage of our newly updated Flow Cytometry facility (MQ FC), and continue the development of her work on some fresh water samples she collected during the monthly Port Hacking run (Post).

Fran has gone back home to the UK last week, but we hope she will come back soon to say hi.

Best wishes from all of us on her future adventures!

On the monthly Port Hacking sampling run
With the creator of the Influx cell sorter Ger van den Engh
Sorting cells on a flow cytometer can be fun!

Sunday, 19 May 2013

Finally on the way

Following a few hiccups that delayed the start of the expedition, the Indigo V and its crew left Cape Town bright and early on May, 17th. Sailing shifts and work shifts have been organised (Martin got the lucky pick of the first 3-6am shift!!), the equipment is safely tied down and most importantly the food supplies are plentiful!
Let's hope there will not be too many teething issues with the instruments when the boat is actually out of the calm waters of the harbour, but all the initial tests sails conducted have already sorted a few problems so it should be plain sailing until Mauritius.


Who wants to organise the food?

Best not to have vertigo

Friday, 17 May 2013

Voyage Preparations – Cape Town


Cape Town is a pretty amazing place to start a research voyage. The food is fantastic so I have been filling up my quota of vitamins and minerals, from amazing full breakfasts with Boerewors sausages and fluffy scrambled eggs to thin crust pizza and sourdough smoked salmon sandwiches.

Apart from pre-fuelling the body, we have been hard at work to prepare the yacht, from the sails, engines, supplies and sheets to the batteries and electrical systems that will support our science equipment while we are under sail power.

We have one more day of intense preparations but we are now happy with the safety systems and backups. Just have to do the laundry, fill the fuel tanks and clear customs before sailing tomorrow.

Martin


The Marina in Cape Town
A lazy seal soaking up the sun

Thursday, 16 May 2013

Calling all Evolutionary Genomics Scientists

For any of you who may be interested, Macquarie University Department of Biology is advertising for an Evolutionary Genomics faculty position: http://jobs.mq.edu.au/cw/en/job/492822/lecturersenior-lecturer-in-biological-sciences-evolutionary-genomics
To translate for non-Australians, a lvl B/C faculty position is approximately the equivalent of an Assistant Professor in US terms.

The architectural highlight of Macquarie Uni- the new library

Wednesday, 15 May 2013

All aboard

Our resident sailor Dr Martin Ostrowski has escaped the laboratory once again to take part in an exciting adventure on the high seas. Dr Federico Lauro, an ARC DECRA fellow at UNSW and accomplished sailor, transformed the delivery of a yacht from Cape Town to Singapore into an amazing oceanographic research sampling expedition that will explore marine microbes and their involvement in some of the major global processes throughout some of the most under-sampled waters of the globe.
The Indigo V, a Nautor Swan 61, or for the relatively non-nautical people like me: an 18m sail boat, will accommodate several consecutive 7-strong crews of scientists from around the world during each of the four legs of the transect: Cape Town - Mauritius - Maldives - Phuket - Singapore.

The voyage has already attracted quite a bit of press coverage in some of the major Australian newspapers (Sydney Morning Herald) and radio (ABC). The work and adventures of the sailing scientists will also be recorded in a documentary being filmed on board the ship along the way!

A Live blog and some more details on the research voyage can be found at the following link.

Come back on this blog too for some updates from the escapee.

Indigo V



Monday, 6 May 2013

The New Science

Well, I'm running about 3 weeks behind on my blogging, things have continued to be a little crazy and hectic here. But, the combination of science and gaming has provided the motivational energy to post again. We had dinner last night with my friends Fraser and Lencia. After an excellent dessert of berry and rhubarb cobbler (mmmm, thanks Fraser!), we tried out a new boardgame called "The New Science". My friend Fraser had supported the funding of the game through kickstarter. For a game that had been funded through crowd funding, I was very impressed with the high production values of the game, better looking than many other games I've played. My one criticism was that my dementia-addled brain kept confusing the little square block pieces with the ever so slightly larger square block pieces that were used for a completely different purpose.

Anyway, in the New Science, you play as one of the great scientific thinkers of the 17th century. And science in the 17the century clearly was just as competitive and cutthroat as it is today. You have to beat your fellow scientists to publishing your significant discoveries. Each turn you get 3 actions, where you can either research a scientific theory, experiment to prove your theory is correct, publish your theory to gain prestige (whoever has the most prestige wins the game), gain influence (by schmoozing government, religious, scientific or industry figures), take a random event, or rest. Deciding when the publish was crucial, you don't want to get scooped, but on the other hand, do you want to let your scientific competitors get a free ride on your research? So, pretty much just like real life. Resting at the right time to build up your energy for important scientific work was also crucial. Overall, we all thought it was a very fun game. The irony of relaxing from the stress of science by playing a game simulating the stress of science provided additional entertainment.

I played as Gottfried Leibnitz, my girlfriend played as Isaac Newton, resulting in an animated discussion about who really invented calculus!

Friday, 5 April 2013

It feels like its been 500 years

I've survived (barely) this season of grant writing. Our four National Health and Medical Research Council (NHMRC) grants were submitted a couple of weeks ago. Although I was ready for a vacation by that point, we also participated with an American team on an NIH Center for Translational Medicine application, which was submitted a few days ago. Now, all we have to do is wait six months and keep fingers, toes, eyes, etc crossed.

In the meantime, an interesting paper came out in the journal Nature, and got some press coverage at least in Australia, for instance this article in the Sydney Morning Herald, on the topic of scientific grant writing.To quote the SMH article:

"Australian scientists spent more than 500 years' worth of time preparing research funding applications for the country's largest grant scheme in 2012, according to a survey by Queensland researchers.
And as only one-fifth of proposals to the federal government's National Health and Medical Research Council were successful, scientists wasted the equivalent of four centuries diverted from their research."

At the moment it certainly feels like I've spent 500 years writing grant applications, and certainly I've done little else for the last three months. It does raise interesting questions- is this the best use of scientist's time and effort? Is it even the best way of distributing resources for research? One of my favourite stories on this topic is how in the 1990s Craig Venter and colleagues submitted a grant to sequence the first ever bacterial genome (Haemophilus influenzae) to the NIH. It scored the lowest possible score in the grant scoring scheme and received reviews saying that the grant was ridiculous and that the proposed work was impossible. They then went ahead and got private funding for this work, succeeded, published the genome in Science, and started the genomics revolution. An example of how truly innovative research is highly unlikely to be funded under current grant schemes, which tend to support incremental scientific advances.

Anyway, I'm going to stop here for the moment, but hope to revisit this topic in a subsequent blog post.



We're trying to avoid this situation