In some ways, you know, people that don't exist are much nicer than people that do.

-- Lewis Carroll

Bacillus coahuilensis : the genomical TexMex

After a long publication struggle, two articles from two close friends have finally been published: the description of novel species Bacillus coahuilensis by my former bacteriology teacher and former owner while doing my Social Service and actually the one to blame for my adscription to the lab I work in now, René Cerritos (a.k.a. Dr. Chapultepec) in the IJSEM Journal. The other is the publication of the complete genome sequence of the very same strain in PNAS by my former schoolmate, my former Represenant in the Universitary Council and beermate Luis Alcaraz (a.k.a. The Dude). Both are the product of a weird collaboration between the CINVESTAV and LANGEBIO in Iruapuato, the Texan universities of Rice and Houston and the institutes Biotechnology and Ecology in UNAM, where I'm at.

In short:

Cuatrociénegas Valley is in a 750 m basin above sea level in North Mexico, deep in the Chihuahuan Desert and formerly a coastal region during the Jurassic. It is characterized by the presence of many oligotrophic ponds in the middle of the desert supporting large bacterial communities, appearingly from a marine origin (as shown by Souza and Desnues), that have been studied by my labgroup leaded by Valeria Souza and Luis Eguiarte (the very same place where I'm conducting my Theses). Cerritos isolated many bacilli strains from one of the widest and shallowest pond (Churince's Laguna Grande) and found many moderately halophilic species (that tolerate slightly salty envirnoments). A novel aerobic strain (m44) belonged to a group of aquatic, moderatedly halophilic species (B .marisflavi, B. aquimaris, B. vietnamensis) , and could not grow on most sugar-contaning media (uncommon for the bacilli). The team in CINVESTAV sequenced the genome (leaded by Gaby Olmedo and Luis Herrera-Estrella) and Alcaraz anotated it. He also conducted most of the sequence analises, with some help of Siefert from Rice University, Putonti from the UofH and me, during our stay in Houston a year ago. The genome turned out to be the smallest genome within bacilli with 3.35 Mbp with many mobile elements.

The most important feature of B. coahuilensis is that this is the second mexican microbial genome sequenced to date (the two bacteria genomes sequenced in Mexico are Rhizobium etli by the CCG and this), but whose sequence has been analized in the light of ecology and evolution (remember Dobzhansky's maxima?), that is, the adaptations of a formerly marine lineage to an oligotrophic lentic environment.

That is, the sequence pointed towards an adaptation to growth within low-phosphorus environment: namely the presence of sulfoquinovose synthase (sdq1) that synthesises sulfolipids to replace membrane phospholipids (which constitute around 30% of the total phosphorus), never reported before outside chloroplasts and unicellular cyanobacteria. The CINVESTAV team looked into the membrane and corroborated its sulfolipid composition.

The genome also codes for a sensory bacteriorrhodopsin gene, reminiscent of its marine origin where they are very abundant (see work by Venter and Rusch). The expression analyses proved it to be constitutive and not -light dependent, suggesting it to be an adaptation to shallow-water irradiance exposure.

Analysing the enconded transmembrane importers is a good way to analyse what the organism is uptaking for the environment, that is, it's "feeding-habits". The family of Iron-Siderophore importers is overrerpresented in B. coahuilensis, a feature shared with other aquatic bacilli, suggesting that marine bacilli actively scavenge for iron. It also show a preference for the uptake of single aminoacids and not large polypeptides, with absolute requirement of 8 aa and partial of another 5, a feature shared by the aquatic, small-genome organism Minibacterium massiliensis.

This, taken together with the fact that it has the lowest number of genes involved in nitrogen cycle, together with the experimental evidence of being incapable of utilizing a wide variety of sugars, suggests that this organism is totally dependent of the rest of the community to live on, and has evolved from a primitive bacterial component of that community with specific adaptations for a novel environment.

I'm very proud of the product of this collaboration and expect to continue this way. And also very happy because from the moment of this publication on, The Dude is able to obtain its PhD!!!

My Geek Pride is hurt: BLOSUM matrices

BLOSUM (BLOcks of Amino Acid SUbstitution Matrix) are the canonical substitution matrices used for scoring protein sequence alignments. In essence, it calculates the relative frequencies of all aminoacids in each position within an alignment and assigned a probability to the substitution of a particular residue. BLOSUM matrices built with closely related sequences are more stringent and have high numbers (BLOSUM80) indicating the percentage similarity allowed to include a sequence in the matrix (in the latter case, all proteins share at least 80% sequence identity).

BLOSUM matrices were developed in 1992 by Henikoff and Henikoff and since then have been extensively used in all analyses involving protein sequences...

and then, here comes he "AAARRGHHHH!!!"

Styczynski et al (2008) were killing their time looking at the evolution of the BLOCKS database and found the unthinkable.... an error in the source code for the algorithm that calculates de BLOSUM matrices!!!! that means... the results obtained with the available BLOSUM matrices differ significantly from the expected algorithm from Henikoff & Henikoff... merde!

Weirdest thing of all.. when corrected and tested back for the use of the matrices in database sequence search, it turned out that the "wrong" matrices performed much better in retrieving protein homologs than the "corrected" matrices.

Fortunately, it seems that though the difference is statistically significative, it is not big. That means, we haven't fucked it up so bad.

Epilogue to the blosum...

1) 16 years of extensive usage doesn't mean it is RIGHT.

2) how come that no one, ever, in 16 years, ever noticed this difference!!! THAT is what happens with dogma... when you take anything from granted

3) messing things up is not always THAT bad...

4) I didn't understand from the article if they proposed that the matrices were corrected even if they performed worse...

5) I would expect to see a huge ocean of erratas everywhere because "when using the revised blosum matrices... our results from the past ten years have completely changed!!"

Bound to...

Diving into my ipod, I rediscovered what I think is one of the best breaking up songs ever. I'm not in that mood now, but I keep recognizing it. So, this post goes dedicated to all those girls that actually are brave enough to say 'I'm through'... I mean, there must be some!


"I've thought about it for a while
and I've thought about that many miles
but I think it's time that I've gone away

The feelings that you had for me
have gone away it's plain to see
and it looks to me
that you're pulling away

I'm gonna pick it up
I'm gonna pick it up today
I'm bound to pack it up
I'm bound to pack it up
and go away

I found it hard to say to you
that this is what I have to do
but there is no way that I'm gonna stay

there are someone many things
you need to know
and I wanna tell you before I go
but it's hard to think of just what to say

I'm gonna pick it up
I'm gonna pick it up today
I'm bound to pack it up
I'm bound to pack it up
and go away

I'm sorry to leave you all alone
you're sitting silent by the phone
but we've always known there would come a day

The bus is warm and softly lit
and a hundred people are ridin' it
I guess I'm just another running away

I'm gonna pick it up
I'm gonna pick it up today
I'm bound to pack it up
I'm bound to pack it up
and go away

Oh yeah, yeah"

The White Stripes, De Stijl...

Lotharingie... la breve

"Uno cree que siempre ha sido así, pero no... no todo lo es todo. Aquello era vastísimo, y aunque no todos se asumían como francos, la dominancia carolingia era indiscutible. Siempre había sucedido así, los grandes imperios se resquebrajaban hasta minúsculos territorios. Así pasó con Cárthago, el Senatus Populusque Romanus de Trajan, el Khanato de Ögedei y el Califato Umyyad... así pasaría después con la dinastía Qing, la Totius Hispaniae de los Habsburgo, el Imperio Napoleónico, el Brazil de Braganza y la Soyuz Sovetskikh... así pasará con la Rossiyskaya transcontinental, la Francia de Ultramar, el paternalismo neocolonialista de la Norteamérica intervencionista y el mayor imperio en tiempo y extensión: el United Kingdom del imperio británico.

El entonces imperio franco de Charlemagne había sido dividido por primera vez burdamente por Louis I (el primero de una veintena de luises hasta ahora) en imperios del Este y del Oeste. Lothair llevaba ya diez años defendiendo ferozmente su derecho legítimo sobre los territorios Francos. La última guerra civil (que entonces respondía a un pleito entre hermanos) culminó esa noche del 843 con el Tratado de Verodunum. Esa noche a la orilla del Meuse Lothair recordaba la figura de su abuelo, aún abatido al fondo del valle por el Juramento de Strazburg. Así nacía la Lotaringia, Lotharii regnum, bajo la tradicion divisionista hereditaria de los carolingios.

La Lotharingie sería recordada como el reino entre el Rhin y el Rhône, aunque más adecuado sería medirla entre la costa frisa del Mar del Norte a Roma. Así, con esa división entre el imperio Franco del Este y del Oeste, la Lotharingie iniciaría una larga disputa entre francos y alemanes que parece terminar apenas en la segunda mitad del siglo XX. Además resultaba ser el primer reino que no recibía su nombre del idioma que hablaban sus pobladores (Francs, Alemanii) puesto que comprendía un amalgama cultural y linguístico.

La duración del magno reino lotaringio fue ridículamente corto. Una del 855 presenciamos cómo el gran Lothair ha abdicado a la corona lotaringia para recluírse en la abadía de Prüm. Poco antes de tomar los votos, repartió el reino entre sus tres hijos. La Lotharingie queda reducida de la Frisia a la Suiza, bajo el reinado de Lothair II. Ésta divisón tampoco duraría mucho. Lothair moriría ese mismo año, Lothair II moriría en 869 sin herederos legítimos, lo que conduciría a la repartición territorial entre los hermanos de Lothair I y la consecuente desaparición del reino de Lotharingie con el Tratado de Meerssen... aunque en realidad el territorio norte se encontraba ya bajo el control vikingo danés."

La región es interesante...

más que nada, la aparición y desaparción de Las Cosas Importantísimas me recuerda también la historia de Plasmogenia... y no sin cierto temor me parece que la genómica le da un aire...

insisto, no todo lo es todo

La tektonik

One of the weirdest things I saw in France... a "new" dance style á lá techno-pop that reminds me a LOT of the early 90's... the rediscovery of Michael Jackson's Moonwalker maybe? if fashion has already made a complete turn and rap/dance/moonwalker is cool again... maybe we have a tiny hope of seeing a grunge retro-moment soon?


I find it good for gymnastics... and I think it's cool to see such self-assurance in teens!

Del lado de allà...

Paris nos recibio frio y obscuro. El periferico parisino resulta menos feo pero igual de tedioso para perderse. Aunque se recorre en menos tiempo.

El frio pues total. Bueno, no tanto pero para mi termostato mexica si es demasiado. Frio todo el tiempo, solo se diferencia entre "mucho", "menos" e "intolerable". Y yo sin kleenex no puedo vivir, o al menos no sin manchar de verde clarito mi bufanda. Lo cual tampoco conviene porque despues de un rato la humedad en la bufanda se pone fria tambien. En la calle no hay nadie pero las tiendas (como la fnac por ejemplo) estan atascadas. No es como para irse de compras ni tomarse el cafe-cliché frances, porque se te pueden ir 11 euros en una sentada de cuatro chocolates calientes. !Pero lo valen en el frio!

Nota cultural sobre mi propia ignorancia: existe una diferencia entre le givre y la neige, aunque el resultado es el mismo (casi): todo se ve blanco. El primero dîcese del hielo que se encuentra TODAS las manianas sobre toda superficie congelable, el segundo es la nieve que se forma exclusivamente cuando llueve a 0°C... que por cierto no he visto aun. Todos los autos se congelan en la noche y yo soy el unico en toda Nancy que se maravilla de ello y que disfruta sin bufar (gesto predominantemente frances para expresar disgusto ligero pero incomodo) quitar con la palita de quitar hielo (porque aqui hay una cosa especial para todo) (y que Marie no tiene y por eso usa su tarjeta de credito) (bueno, quien sabe si es la suya). Asimismo, soy el unico que se detiene a tomar fotos de las fuentes congeladas (metaarte cronologico involuntario), las flores muertas por la helada, las bancas bajo el hielo y las ventanas fractalicas (y unas cacas congeladas que no me dejaron fotografiar y que de hecho lalo me habia comentado) y que se detiene a descifrar el origen etnico de cada no-blanco que se cruza en la calle.

Para fumar, hace falta ser un adicto erizo nicotinico pero no friolento, porque sacar los dedos de los guantes es toda una hazania y no se puede fumar mas que en los cafes, los bares y las tabaquerias (y solo hasta el 1° de enero). Como dijo Serguei en NY: "either you drink or either you smoke, because you can't smoke indoors but you can't drink outdoors". De todos modos, pague mis 4.60 € para comprar mis Gauloises brunes-sans-filtre à la Cortâzar.

Finalmente, el tren ES la onda (mas que la Taq! aunque igual de caro), asi que unas mentadas de madre a Ernesto Zedillo por vender los Trenes Mexicanos. Nos quito el romanticismo de viajar en bola, viendo paisajes bonitos y con la oportunidad de ligar chicas guapas. Yo, encontre mi francesa.