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Attack of the Giant Archaea

Archaea are under-rated. For one, most people don’t really know they exist – and if they do archaea are thought of as a type of bacteria. This goes not only for the general public also for some of my non-microbiology colleagues. (I had to correct quite a few “archaeobacteria” utterances.) The discovery that Archaea are a […]

Lake Arrowhead Microbial Genomics Conference

Quick post: at the Lake Arrowhead Microbial Genomics Conference. I’m a bad microblogger, but thankfully Jonathan Eisen and Ruchira Datta are doing a great job of covering this conference live. There is a friendfeed room. The Twitter hashtag is #LAMG10.  The science, people, food and location are all great. My student, David Ream, is presenting […]

When is it a good idea to cheat?

I have written before about bacterial cooperation, and how cheating works, up to a point, in an environment of bacterial cooperation. That post talked about bacterial quorum sensing, the collective signaling mechanism by which bacteria construct supra-cellular structures called biofilms. Biofilms are tough multicellular enclosures that allow bacteria to survive and thrive in hostile environments, […]

I can’t hear you, the bacteria are too noisy

Much too noisy. When looking at a population of genetically identical bacteria, the number of proteins they produce varies. The picture below shows the levels of one type of protein that was fused to a green fluorescent protein (so we can see it): clearly there is a variation in how much of the protein each […]

Computational Bridge to Experiments

A bit of background information: this is a meeting I am really happy to be part of, and even more so honored to be a co-organizer. One of my main scientific interests is the prediction of the function of genes and proteins of unknown function. Some background information: we have sequenced more than 1000 genomes […]

A non-post about Craig Venter’s new bug

In case you have been vacationing in a parallel universe in the past two days, you should have heard about the new synthetic bacterium created at the J Craig Venter Institute. In a nutshell, the scientific team synthesized an artificial chromosome of the bacterium Mycoplasma mycoides and transferred it to another bacterium, Mycoplasma capricolum. The […]

Comparative Functional Genomics: Penguin vs. Bacterium

No, not the flesh-blood-and-feathers penguin, but rather Tux, the beloved mascot of the Linux operating system. Compared with Escherichia coli, the model organism of choice for microbiologists. We refer to DNA as “the book of life”; some geeks refer to it as the “operating system of life”. Just like in a computer’s operating system, DNA […]

Combrex: Computational Bridge to Experiments

Combrex is an exciting new project at Boston University to bridge computational and experimental techniques to functionally annotate proteins. They are hiring, see below: JOB POST We are seeking to hire a creative computational scientist for a transformative project: COMBREX: A Computational Bridge to Experiments. The work will involve building a novel resource that combines […]

A sh*tload of data

There are more microbial cells in our body than our own. Those microbes are not just passive hitchhikers or conversely, malicious agents of disease. They affect our well-being and health in a much broader spectrum than simply “bad” or “passive”. Among other things our gut microbes play an important role in digestion, have been linked […]

Filling in the evolutionary blanks, genome by genome

After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone. GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of […]

Photosynthesis, phages and structures: there’s treasure everywhere!

Here’s a really cool work, published this September in Nature.. Why did I choose this work?  Well, it’s a major discovery, and it’s all done using bioinformatics, and fairly simple bioinformatics at that. The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and […]

Blog Action Day: the Methane Pulse

Blog Action Day focuses this year on climate change, which, like everything else on this planet, is also a microbial matter. Howzat? Methane (CH4) is a greenhouse gas which has heat retention capability 23 times of that of CO2.  Soil methanogens are the chief global producers of methane. There are an estimated 7.5x 109 tons […]

Freeloading pays off, but only up to a point.

Quorum sensing Social behavior is not exactly the first term that comes to mind with relation to microbes. After all, we assume a certain amount of intelligence and an ability to implement a behavioral pattern in response to peer actions. Humans, yes. Apes, yes. Birds of a feather flock together… so birds, yes. Ants and […]

PLoS Currents: Influenza. Because knowledge should travel faster than epidemics

(Full disclosure before I start: I am an academic editor in PLoS ONE. I have no financial stake in PLoS, and as far as I know, they have none in me. They’d better not, if they know what’s good for them). PLoS have come up with yet another cool mechanism for scientific communication: PLoS Currents. […]

Absolut standards: report from the M3-2009 meeting, part 2: signature genes and big science

Some more presentations from the metagenomics, metadata, and metaanalysis (M3) meeting, Stockholm June 27, 2009 Pathway Signature Genes Lucas A. Brouwers, Martijn A. Huynen and Bas E. Dutilh CMBI / NCMLS, Radboud University Nijmegen Medical Centre, The Netherlands If we take a sample of soil, how can we know whether it is adequate for growing […]