Where ideas come from

Creativity is all important in science. In this previously unpublished note, SciFi author Isaac Asimov analyses some of his reflexions on the act of creating new ideas.

Organizing the second PVC conference

Just to tell you quickly that we started organizing the second conference entirely dedicated to PVC bacteria research.

It will be held from the 2nd to the 4th of June 2015 in Carmona , a very lovely town close to Sevilla, Andalucia, Spain.

The first PVC conference was already successful and we are all looking forward to the second one.

So please start saving the dates. More information soon.

Peptidoglycan in Chlamydia

Related to the discussion about the exceptional status of the PVC cell plan to which we dedicated two recent posts, on the TiM and AvL articles by Devos, and the latest by Fuerst's team, is a new article reporting detection of peptidoglycan in Chlamydia. Liechti et al. describe in Nature a new cell-wall labelling method that finally settles the 50 years old debate concerning the chlamydial anomaly. important question not answered by this manuscript is where is the PG located in Chlamydia? Is it in between the two membranes, where Devos suggests it should be, or is it found outside the outermost membrane, where Fuerst would have it? Although not directly addressed by the authors, it seems pretty clear that the green signal, marking the OM ring is located outside of the red signal, marking the PG (see Fig. 2 or supplementary figure 5). Thus, it seems that PG is located internal to the OM, supporting a more classical G- interpretation of the cell plan, at least in Chlamydia.

Improve your figure

Nice little paper in the '10 simple rules' collection of PLoS Comp. Bio. about drawing better figures.
We could all get something out of this paper. It also contain good references about how to make them colorblind friendly
Like most of the paper in the 10SR series, nice, short and useful.

A call for a genomic catalog of all cultured Bacteria and Archaea

Microbes are the keys to everything. If you read this blog, you will agree. And genomes are the keys to those microbes. However, the current practice of deciding which genome to sequence is very much left to the major interest of each scientist. Now, Kyrpides et al., PLoS Biology 2014 call for a structured approach to the sequencing of micro-organisms. Of course this means money. However, great expectations are placed on such approach.

Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently~11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Very nice article, timely. Let's hope the politics get the message.

Excellence vs diversity. Is it really?

In a post for European scientist, FS Labini is discussing the point of funding excellence vs diversity. But is it really? Do we really have to choose between excellence and diversity? Does this mean to imply that funding more diverse type of science mean abandoning excellence to turn towards more diverse but less good science? That is certainly not what is implied by the post. However, the title might be misleading in this sense. I would argue that to the opposite, there is certainly plenty of excellent science to be funded while exploring diversity, as opposed to all those big consorcium planned, lobbied, organised and composed by what begin to look like a feodal system of science in Europe, and elsewhere. Look at the ESFRI for example.

Introducing the Myojin parakaryote

Eukaryotes are derived from prokaryotes. This is demonstrated by the fact that eukaryotic endosymbionts are derived from prokaryotes. Opponents to this have objected that such a transition must have left intermediary organisms, the lack of which strongly weakened this possibility.
Such an organism has in fact been discovered. Yamaguchi et al., J. Electron Microscopy (2012) report the identification from deep see survey of an organism with features that appear to be intermediary between prokaryotes and eukaryotes. This organism, named "Parakaryon myojinensis" for its intermediary location, is big, >100 times bigger than  your usual prokaryote like E. coli. Its genome is composed of naked DNA fibers, instead of the classical eukaryotic chromosomes, and is surrounded by a single membrane instead of the classical double (single folded) membrane of eukaryotes. It also harbor various endosymbionts but no mitochondria. Thus, this organism appear neither to classify as eukaryote or prokaryote, but more like something in between.
The study is far from definitive. Indeed, there is no molecular identification of domain markers, like ribosomal RNA, or proteome oriented studies, most likely because of the lack of isolation and cultivation of this organism.
However, this is another example of the value of sampling the biodiversity that is out there.
Interesting article and I am looking forward to read more about this thought-provoking organism.