SGM Presentation

A quick note about the Slidecast I promised. I have the sound track, but recorded it at too high a quality in Audacity, (which is great, in case you haven't tried it) so I need to squeeze it down in size a bit - suggestions welcomed. In the meantime, you can whet your appetite on the slides themselves.

Secrets of Shipwrecks

My last summer student of the season just finished. For the past eight weeks I've been supervising James Wong and Steve Hooton as they attempted to wrestle with projects entitled "Bacterial Treasure! Secrets of Shipwrecks"...an excellent example of naff titling. They were both looking at different aspects of bacterial diversity in some quite tricky samples - lumps of wood rescued from the wreck of the James Eagen Layne, a Liberty Ship torpedoed on 21st March 1945 on her maiden voyage and currently sat 24 m down in Whitsand Bay. She was carrying US army military cargo, which included tanks parts and pick axes, and a deck cargo of motorboats and timber; it is samples of the timber that we managed to get our hands on.

My dad is an advanced diving instructor and he and some of the other instructors at Fort Bovisand were kind enough to dive down to the JEL and extract some samples of timber. Not as easy a process as it sounds when I demanded as little handling as possible of the samples by the divers to maintain the natural bacterial population of the samples. They added tags to the zip-lok bags that I provided them with and also a method of cleaning the knife used so that, although it wasn't sterile, it wasn't contaminating the samples with grease used to protect the blades of divers' knives - as you can see below:



And this is a piece of wood that was actually sampled (the end was trimmed off one of those loose spars):



And just to prove that there's big stuff down there for those who like their organisms larger: gratuitous dogfish, spider crab and sea-snail shots (all photos taken by my dad!):







Another tricky part of the exercise was actually getting the samples from Plymouth to Liverpool as they needed to be stored in dry ice - with a little help from some friends at the Diving Disease Research Centre and Plymouth Marine Laboratory we were able to purloin some dry ice and get the samples couriered up. Then the fun began!

James was sponsored by the Society for General Microbiology and concentrated on attempting metaproteomics on the samples, looking for cellulases and chitinases. He used protein gels to look at some strains of bacteria that had been isolated from the same area. Steve concentrated on extracting DNA from the wood samples and using DGGE (denaturing gradient gel electrophoresis) to characterise the populations of bacteria in the different samples and was sponsored by the Nuffield Foundation. Both projects were a tall order and both students rose to the challenge. Our major problem was the nature of the samples themselves, the wood wasn't very degraded and there was evidence that it had been treated in some way (a strong smell of bitumen when some of the samples were freeze-dried was a give-away!). There wasn't likely to be much DNA or protein present in the samples, and the presence of co-extracting compounds was likely to foil down-stream analyses. In the end, after many attempts of different methods and James' and Steve's tenacity, it became clear that we weren't going to be able to extract any DNA or protein from the samples. A bit of a shame, but not really the ultimate aim of the projects.

These summer studentships are a great opportunity for undergraduates between their second and final years, to get experience of a working lab and of carrying out a defined piece of research, with all the frustrations that go with that intact. I was lucky enough to do one myself as an undergrad, at the Marine Biological Association with Willie Wilson and it really gives you a taste for research. Plus as the students are new to the subject and the methods and full of enthusiasm, it's good to view things through their eyes when it's easy to become jaded.

We never managed to find any bacterial treasure (or even a scrap of DNA or protein) but hopefully they both enjoyed themselves and they'll certainly get a head-start in their final year research projects. Both my students from last year are now doing PhDs or applying for them and knowing that a summer project may have helped them decide to go ahead with that (or at least not put them off it) is a really satisfying feeling. Hopefully James and Steve enjoyed themselves too!

To coin a phrase.

MetaprotogenomoSIPolomics is where it's at. At least that's what I tried to convince the audience at the Edinburgh SGM meeting with my slightly rushed and results-lite presentation. I failed to record the talk, but will do a soundtrack myself so you can get an 'almost there' feel. Hopefully a Slideshare slidecast is all it's cracked up to be! When I get some time I'll mention some of the more interesting talks too, it was a good meeting, my buttocks have just recovered from sitting through it.

A quick note

Just getting packed for Edinburgh. The talk is at least set in my mind, the slides will change several times - it's not until Thursday and I keep thinking that I'll have all the evenings free. There are too many people to catch up with for that to be true!

Last week (or the one before) I stuck a note on my Facebook profile asking for help and suggestions writing the talk (mainly help avoiding bullet points - ick) and received 13 stunningly rude and innuendo laden replies. It's not me, it's my friends. It did serve as a reminder that there is, somewhat inevitably, a Facebook group for microbial ecologists, Microbial Ecologists United - linky (hope that works). Not as active as it could be, I always have intentions of posting job ads at least, lets see if I manage.

May update during the week if I find a nice wifi hotspot - otherwise, wish me luck!

All talk...

The Society for General Microbiology is a UK charity that offers funding for microbiologists and also holds a biannual meeting. As it's a general microbiology society and not specific to microbial ecology my interest in meetings tends to vary from year to year. Next week in Edinburgh is the 161^st meeting and it looks like an interesting one. I'm not saying that simply because I'm presenting. Honest.

I'm in the Hot-Topic session called “Post-genomic analysis of microbial function in the environment” which is joint with the Natural Environment Research Council (NERC) who sponsor my current project. I was a little bit surprised to get a talk, when I submit an abstract for a poster I always tick the 'would you like to be considered for an oral presentation?' box as posters are more easily ignored, and this will probably be the largest audience I've spoken to (at least since assembly at school, we had a big year). As I'm an offered paper rather than an invited speaker I get a slightly shorter slot of 15 minutes. Three to five minutes of that will be reserved for questions leaving me to prepare a 10-12 minute talk. It's an odd length of time, I really can't introduce the subject and cover all the aspects that I would ordinarily include in a longer talk. I think I'm going to give a broad taster of what I'm doing, focussing on approaches that we've decided to take and why rather than presenting detailed results on any one of them. It is easy to slip onto the habit of chucking together formulaic presentations and the shorter time has really made me think about this one.

Hopefully you'll be able to judge for yourself if you can't make it to the meeting (or nod off during my bit – I'm in a fidgety session, just before lunch on the final day of the meeting) as I'll upload the slides to Slideshare and link here. I've also got hold of a lapel microphone and will be recording my talk on my MP3 player. I should be able to sync the two together; voila! a fascinating talk on the metagenomics and metaproteomics of marine polysaccharide-degrading bacteria without the added distraction of my handsome physog. Hopefully it'll also allow me to find out what's wrong with my talks, they always seem to pass in a blur and and people are (mostly) polite afterwards – good for the ego, not so good for improving your technique.

On the topic of talks I should also plug my boss' talk, Prof. Alan McCarthy will be enlightening a rapt (and probably chuckling) audience with the ecology of shiga-toxigenic phage (the ones that make Escherichia coli 0157 as nasty as they are). He's not written it yet - allowing me to be a little smug - as he's being overwhelmed with everyone else's posters to check over; but he is always amusing. No pressure Alan.

In Our Time

I've sporadically kept a blog before about an Alternative reality game (Perplex City - now on sabbatical) and found that I really wanted to post about so many more things than purely that. One of the main distractions was microbial ecology and this blog is my attempt to give free rein to that distraction.

Though in this first post I still can't quite escape. Through the blog of one of the creators of Perplex City, Adrian Hon I came across a series of programmes on Radio 4 called In Our Time, hosted by Melvyn Bragg (gratuitous photo of famous bouffant do left).

I don't listen to the radio very much, it's something I associate with being driven to swimming lessons as a child (not that I didn't like swimming) and The Archers omnibus on a Sunday when my mum was doing the ironing (idyllic huh? And who'd have thought that Debbie Aldridge was much better as a comedian?), but these sounded great; panel discussions on all manner of subjects including hell, negative numbers, Jung and the Higgs Boson (I have a prejudiced view of the Higgs Boson that for the moment I will refrain from letting forth).

Being quite cautious when it comes to sampling new things I scrolled down the substantial list of programmes in the archive, all still available to listen to, to find one that I might know something about already (goodbye chaos theory and Wittgenstein) and found Microbiology. I fully expected to get annoyed at inaccuracies, or at the ecological aspects of microbiology being ignored in favour of the grisly, crowd-pleasing medical aspects, but was unable to. It was a lovely potted history of the subject which managed to cover the history of its development, its impact and future potential in only forty minutes, less than your average undergraduate lecture. Culturabilty, phylogenetics and similar were all mentioned

Though some of the anecdotes anyone with a GCSE in science will have come across - Edward Jenner injecting poor James Phipps with pus and coming up with vaccination for example - other parts of the programme were more novel. I'm sure I've always been taught about microbiology's origins via the history of microscopy and that the two were inextricably linked, but one of the panellists, Andrew Mendelsohn pointed to the real beginnings of the subject being in studies of function of microorgansisms - physiology rather than microscopic observation. It's nice to make these little connections that I've failed to fully appreciate and happily function has also been the subject of my own work. Definitely worth a listen.

And in case you get hooked on In Our Time (sorry), Adrian also has a discussion site about the programme, After Our Time.