Monday, May 30, 2011

Report from the BAGECO Conference

Since yesterday, I am hanging out on the Ionnian island of Corfu in Greece, to take part in the BActerial Genetics and ECOlogy conference (BAGECO; not to be confused by Bagheera). I'm very impressed by the quality of the talks and research presented so far. Compared to the last microbiology conference I went to (ISME 2009 in Australia), lots of people are taking advantage of "next-generation" sequencing technologiey and other relatively new, cost-efficient molecular techniques, like custom microarrays (Geochips) and proteomics. The buzzword (or "buzzphrazse") is clearly "integrated -omics approach", which usually means to combine metagenomics, metatranscriptomics, metaproteomics and metabolomics (i.e. sequencing of genomic DNA, reverse-transcribed RNA, MS-based proteomic analysis and screening for metabolic products.) I don't know if I like the term "integrated -omics" since it is not very descriptive; "Integrated analysis" or something would be better, but that is another topic, perhaps for Johnatan Eisen to discuss on his very entertaining "Worst omics word award" section of his blog. Anyway, the combination is really useful and can provide a more holistic picture of microbial communities. Some examples of really interesting talks:

- Maria Westerholm, from the Swedish University of Agricultural Sciences: "Molecular Approaches to detect and quantify syntrophic acetate-oxisizing bacteria in biogas digesters". Very clever study to improve the efficency of metanotrophic biogas reactors.

- Giovanni Pilloni from the Helmholtz Center for Environmental Health in Germany: "Degrader community response to hydraulic disturbance in a tar-oil contaminated aquifier". Cleverly, TFRLP fingerprinting with replication was used to confirm the predictions made using pyrosequencing.

- Pedro Soares-Castro, from the University of Minho, Portugal: "Towards the metabolomic engineering of myrcene pathway of Pseudomonas sp. M1 using an integrated -omic approach". Genome sequencing, transcriptomics and metabolomics combined in a clever way.

- Gavin Lear, from the Lincoln University in New Zealand: "Bacteria as sentinels of freshwater ecological health: An exploration of the relationships between antropogenic impacts and bacterial biodiversity in freshwater streams".

Monday, May 23, 2011

Weather report

This has, seriously, got to be the shittiest May ever recorded in known history. At least weather-wise.

Wednesday, May 4, 2011


These "sunflowers" (that really are a kind of thistles) hung to the door or wall of a house are a very common sign in the Basque Country and protect against evil spirits.

According to legend, many thousands of years ago when men began to populate the Earth, it was very dark as neither the sun nor the moon existed. In this constant darkness, people were scared of the many sorcerers and witches who came from the bowels of the Earth in the shapes of bulls made of fire, huge dragons, flying horses, lamia (a kind of mermaids with birds legs) etc.

Desperate, the people decided to ask for help from Mother Earth (Amalur):

- Amalur, we beg you to protect us from the dangers that surround us!

But Mother Earth was very busy and ignored the humans at first. However, they were so persistent that eventually she responded:

- My sons, you ask me to help you and that I will. I will create a luminous being that will be called the Moon.

And Mother Earth created the moon.

At first, the men were terrified and stayed in their caves not daring go outside, but slowly they got used to it. But like the people, the sorcerers and witches who were also afraid at first to see the bright object in the sky, got used to it also and soon started to harass the humans again.

Once again, the humans came to Mother Earth asking for help:

- Amalur, we are very grateful that you have given us the moon but we still need something more powerful because the sorcerers never cease to haunt us.

- Okay, I will create an brighter thing, that will be called the Sun. The Sun will be the day and the Moon the night.

And Amalur created the sun. It was so big, bright and hot that the people had to get used to it little by little, but their joy was great because thanks to heat and sunlight, colourful plants and fruit trees soon grew up around them and the hills turned green. More importantly, the sorcerers and witches could not get used to the daylight. However, they still harassed the people in the night, so once again the humans had no choice but to ask Mother Earth for help:

- Amalur, we are very grateful that you have given us the Sun and the Moon, but we need something more, to protect us during the night.

Amalur answered:

- I will help you again. I will create a flower for you, so beautiful, that seeing her, the creatures of the night will think that it is the sun itself.

And Mother Earth created the Eguzkilore, which to this day defend our homes from evil spirits, witches, Lamia, sorcerers of disease, storms and lightning.

Thanks, Agurtxu and Itsas for sharing this beautiful legend!

Friday, April 8, 2011

From Ethiopia to Oslo with coffee, water samples and a sun burn

-->Photos on Flickr

I am sitting in an overcrowded Gardermoen and waiting for my flight to take me and my six kilos Ethiopian coffee back to Bergen, after some 15 days of roaming around. The second half of that was not very exotic but spent teaching in a metagenomics course in the University of Oslo. Good for inspiration and work though. Also had good cod at Lofotstua. I can recommend it.

Anyway, the first half was more exciting. I've been down in the ancient kingdom of Ethiopia (3,000 years old, they reckon) to take some samples from alkaline soda lakes in the Rift Valley. This is pretty interesting for a number of reasons. First of all, they are really alkalic and yet with a very high microbial biodiversity, as opposed to many other "extreme environments". Also, they don't taste so nice. I accidentally had some from one of them and now I feel sorry for the poor flamingos who live off their cyanobacteria.

Also, it's interesting because it is the first time I ever do any kind of field work, being in bioinformatics and usually not allowed into the secret world of real biologists that cannot be viewed through a computer screen. It was fun, but it's tough work filtering litres of salty brown lake water with a handpump in 30 degrees heat, surrounded by locals and kids and sometimes thousands of ants. They were really nice and helpful but sometimes in the way when they were sitting more or less on top of our equipment offering to help out or just curiously watching what kind of crazy stuff we were doing. And what we were doing would have looked crazy to most people, even those with television and a grasp about modern science. Probably also to other biologists. Anyway, enjoy the photos.

Tuesday, February 22, 2011

Toilet paper poetry

I unsuspectingly bought toilet paper from Lambi and found it covered in hundreds of metres of love poems, written in Swedish, Norwegian and Danish. Amazing concept! But I can't help but feel strange to wipe my ass with somebody's creative and romantic work just because I paid for it. Does that say something about the core of the problem with copyright or am I just obsessed?.. :)

Sunday, January 16, 2011

Cross-cooking Part II

I have written earlier about the fantastic dish haggis pakora from Glasgow and inspired by this Indian-Scottish cross-cooking I did experiments at home. I am less brave, though, so I have only been trying South-European - Scandinavian combinations.

First up (depicted here) is the famous Iberian morcilla along with potato omelette (tortilla). Morcilla is an Iberian blood-sausage quite similar, but typically superior to, its Swedish cousin the blodpudding. Morcilla contains rice or vegetables whereas blodpudding contains flour and the best ones come from Burgos or Etxarri Aranatz. This one was was from Burgos.

Normally you serve morcilla with beans but sometimes like here with tortilla and tomato sauce. My hypothesis was that it would be even better with lingonsylt (lingonberry jam or "tyttebærsyltetøy" as they say here in Norway; the lingonsylt test area is located in the slightly out-of-focus back of the green plate). I think it was damn good but it was even better with tomato sauce, so this was a negative result. Unable to publish it in a peer-reviewed journal I thus put it here on my blog.