”This is what they don’t tell you in the methods” – the pre-Eurobiofilms Workshops

A summary of the workshops from the first day of Eurobiofilms 2017

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Sep 19, 2017
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To describe the schedule of this meeting as packed would be an understatement. Stacks of parallel sessions with great speakers pulling delegates in every possible direction. Today was no different. Despite not officially being part of the Eurobiofilms conference, it is something of a tradition among the organisers to run a variety of workshops before the conference to showcase their signature techniques.

Except they did much more than showcase, today was a full-blown, behind-the-scenes, warts-and-all look at a diverse array of techniques available to the biofilm field. We covered academic publishing, computer programs, FISH, animal models, bioflux microfluidics, chemostats, flow systems… you get the picture, there was a lot going on.

 Some notable highlight for me from the sessions that I attended were Paul Stoodley and Michel Hoogenkamp’s amazing double act on the 14th floor of the Amsterdam’s new dental school, the ACTA building. Paul explained his world-renowned flow setup in detail while Michel was quickly on hand with tools and equipment when it was needed, it was his home lab after all. The detail Paul went into was the inspiration for the title of this article. At one point, he explained how you put all of your weight on the flow chamber before tightening it with screws, then you know it’s not going to crack. He then handed us over to Michel whose passion for what he does bubbled over as he explained and demonstrated some highly elaborate and then some inventively simple biofilm setups.

 Then the conference organiser Bastiaan Krom took us into a small microscope room to explain how to set up a Bioflux experiment which allows you to monitor cells in real time under flow. The setup looked straight forward and only took a few minutes. He emphasised that this was totally automated that you can set up and experimental run in the evening and have results in the morning. But as with everything that’s too good to be true there is a catch. Each experiment gives you around 20 GB of data which is enough to send most desktop computers to an early grave and if you want to do a few experiments, better find somewhere to store the data as well.

We then went down a few flights of stairs to meet Claus Sternberg who taught us how to use his own software, COMSTAT to analyse biofilm data from a confocal microscope. It’s already on the second version which makes it much more user friendly and full featured. I was very impressed despite Claus’ understatement and caution when it comes to interpreting data and analysing results which was, of course, entirely justified. He also gave us a brief masterclass in the commercial software Imaris which has become an industry standard for analysing confocal data. While this was going on, about 2 meters away Kasper Nørskov gave an energetic account fluorescent in situ Hybridisation complete with beautiful microscopy images and disgusting surgery photos.

As if experimental methods weren’t enough we even had a paper writing masterclass with Elsevier Publisher Sheba Agarwal – Jans, and she was thorough. We covered everything from writing, choosing journals, submitting article and being ethical. It’s always nice to see behind the scenes of what is quite a daunting process for many of us. She challenged us to think about how we write and Tweeting her presentation led to mentions from Biofilms and Microbiomes contributors Elisabeth Bik and Mike Cox, (one was a thank you and one was an argument, you’ll have to go on Twitter to find out which was which).

As diverse and fantastic as these workshops were, I missed Claus Moser, Maria Alhede, Peter Østrup Jensen, Mark Shirtliff, Kendra Rumbaugh, Paul Cos and Thomas Bjarnsholt, I told you it was busy! As I understand from the program, they were demonstrating in vivo biofim models. Hopefully I get a chance to see them next time.

Go to the profile of Ben Libberton

Ben Libberton

Communications Officer, MAX IV Laboratory

I'm a Communications Officer at MAX IV Laboratory in Lund, Sweden and the Community Editor for npj Biofilms and Microbiomes. I'm interested in how bacteria cause disease and look to technology to produce novel tools to study and ultimately prevent infection. Part of my current role is to find ways to use synchrotron radiation to study microorganisms.

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