B. coahuilensis in the blogosphere

Bacillus coahuilensis was mentioned in the Ars Technica's Nobel Intent journal... Nice summary by the way: Living on after the ocean has vanished

platypus = ornitorrinco = Ornithorhynchus anatinus genome

You can watch a brief species description in the next NatGeo video (from youtube):



One of the best examples of morphologic mosaicism is also at the genetic level. Check out the outline of this genome here. The most interesting features are: having one of the basal mammals (monotremes) sequenced, now we are able to test several hypothesis about the origin and evolution of mammals; how this genome reflects the morphological mosaicism at the genetic level, how a mammal thatlay eggs and has a duck bill and what genes are required for that, but at the same time nursing & milk feeding of its pups (not breast feeding 'cause they don't have nipples), male with poisoning needles, lots of sex chromosomes (the "normal" is having a couple of them).... and how several of this features are shared between mammals and reptiles at the genes level.

I think that Ornithorhyncus genome would lead to discover lineage specific genes in mammals. Using this genome as an outgroup to all placentarial mammals will also lead to test all the evolutionary hypothesis about the timing of genetic innovations and molecular errors like pseudogenes.

Check out the genome paper here:
Nature 453, 175-183 (8 May 2008) | doi:10.1038/nature06936

sorry it is not open access :(

computer rampage

Finally back to real hard work.... after a long time trying to setup a computer cluster at the institute with the guide and support of Juan Caballero, things are working.

What is a computer cluster?

From Wikipedia, the free encyclopedia:

"A computer cluster is a group of coupled computers that work together closely so that in many respects they can be viewed as though they are a single computer. The components of a cluster are commonly, but not always, connected to each other through fast local area networks. Clusters are usually deployed to improve performance and/or availability over that provided by a single computer, while typically being much more cost-effective than single computers of comparable speed or availability"

The bioinformatics cluster was named beagle, remembering the Darwin's barque and also the track ability of the beagle dogs.


The cluster is running on ubuntu and you can find out the general guide, gently posted @ Juan Caballero's blog, on how to setup the cluster under ubuntu linux here.


Here is a picture of the new baby....

and this are its specs:

Master Node: AMD Athlon 64 X2 4200+, 2 Gb RAM, 1 hard disk IDE 80 Gb (hda), 1 hd SATA 320 Gb (sda), 1 external USB hd 1 Tb (sdb), network card nForce 10/100/1000 (eth1), network card PCI Realtek 10/100 (eth2) and an external 1 TB unit.

Slave Nodes X10: AMD Athlon 64 X2 4200+, 2 Gb RAM, 1 hard disk IDE 80 Gb, network card nForce 10/100/1000 (eth0).

Network Switch: 24 ports 10/100/1000.

Ubuntu rules!, by the way you should try the newest version (www.ubuntu.com)

Funny things in a newspaper

Last week while taking some tapas with Angel @ Madrid, we were having fun looking at the local newspaper, first a Dilbert comic showing how complex are the women when they are not the center of a conversation:










Then a really weird note about how NOW... yes NOW is a crime to kill women in Guatemala... but still is not punished..... Weird weird & primitive world.....

Bacillus coahuilensis is officially a new species and has a sequenced genome

After almost 3 years and something to be working from the ground on the species description by Cerritos et al. and then decide to go further on the biology of this Bacillus and sequence its whole genome finally we are able to proudly announce the release of this two papers.

Species was isolated (by Rene Cerritos) from a wonderful place in the middle of the Chihuahuan desert in Mexico, named Cuatro Cienegas. If you want to know more about the place you can check out German’s of Fred's (in french) post about it, some pics that I’d uploaded here in the blog or others at my Picasa website:

View Album

Get your own

The species description was done accordingly to the most traditional approaches of bacterial systematics, so much biochemistry, much 16S rRNA sequencing, DNA fingerprinting comparing several type strains, etc. Most of this work was conducted by Rene and the people @ the Ecology Institute at the National University of Mexico (UNAM).

Therefore, after in depth analysis of the microbial diversity within the place, and an unusual high rate of marine-like biota, like described by Souza et al. 2006 it were decided to go further by means of genomics and try to find out first the evolutionary history of the place, revealed by comparative genomics, and then some explanations about what genes are needed in a place well known for its oligotrophic (poor nutrient) environment.

Genome sequencing and most of the experiments were conducted at Cinvestav and the National Lab. of Genomics for Biodiversity (Langebio), Mexico.

A great synopsis of the paper was written by Germán and I really want to thank all the authors!! (Gabriela Olmedo, Germán Bonilla, René Cerritos, Gustavo Hernández, Alfredo Cruz, Enrique Ramírez, Catherine Putonti, Beatriz Jiménez, Eva Martínez, Varinia López, Jacqueline L. Arvizu, Francisco Ayala, Francisco Razo, Juan Caballero, Janet Siefert||, Luis Eguiarte, Jean-Philippe Vielle,, Octavio Martínez,, Valeria Souza, Alfredo Herrera-Estrella, and Luis Herrera-Estrella)

and Alex Mira & Mike Travisano for its suggestions and discussion!

It is great to discuss and work with so many clear minded people!

Check out the Genome paper here:

There is also a local database with our annotation of the B. coahuilensis genome:

http://mazorka.ira.cinvestav.mx:8080/genomicos/bacillus/

Greetings from Paris!