Prokaryotic Saturday: Movies of the microbial marine world… coming soon on your favorite theater

Hello!
I hope you all are spectacular!
......

.... I am spectacularly tired. It was a good week, actually was a lot less hectic than the previous week (believe me, A LOT!), but still, I feel tired. So for today I’ll keep this short  :)

I have some bad news, nobody called in the middle of the night from Stockholm this week. I think is still too soon. Maybe in a couple of decades I’ll get that call. For now, from my little space on the internet I congratulate the winners of the Nobel Prize 2013, here they are:

• Physics: François Englert and Petter W. Higgs. "For the theoretical discovery of a mechanism that contributes to our understanding of the origin of mass of subatomic particles, and which recently was confirmed through the discovery of the predicted fundamental particle, by the ATLAS and CMS experiments at CERN's Large Hadron Collider".
• Chemistry: Martin Karplus, Michael Levitt and Arieh Warshel. "For the development of multiscale models for complex chemical systems".
• Pysiology (Medicine): James E. Rothman, Randy W. Schekman and Thomas C. Südhof . "For their discoveries of machinery regulating vesicle traffic, a major transport system in our cells"
• Literature: Alice Munro "master of the contemporary short story" (I really liked this, "a master", hehe).
• Peace: Organization for the Prohibition of Chemical Weapons (OPCW). "For its extensive efforts to eliminate chemical weapons".
• Economy: this one will be announced on Monday 14 (they know how to keep the suspense). 

And you can read more about them here, here and here.

So for today’s PS I was planning to talk about that paper I left last week, Sorek et al., 2010. But then it happened that I came across something else. In the last few days I've been reading several reviews of Dr DeLong (this and this other). And most recently this one named “Microbial Earth: the motion picture”. In this paper DeLong is writing about what would be the difficulties in making a documentary about the marine MICROBIAL life. 

How will you make a documentary about marine microbial life at the level of one of those BBC documentaries about nature? It would be very difficult. As DeLong pointed out, there are many interactions that “microbiologically” speaking you won’t be able to capture. At least for now it’s impossible. In this super short and super-easy-to-read paper, four movies about several microbial dramas are announced… can’t wait to watch them. 

If you want to know more about the impressive work of Dr DeLong, here is his web page, and his wikipedia page. And here is a really cool picture of him working:

Nice.
Here is a lecture he gave in 2009, I warn you, it's an hour long.

Please, if you got something to say, leave your comments below this post or in twitter @ale_alvarador.
Although if you don’t, I understand, this is not the best PS, I have to do justice to DeLong in a post, later.

All right, if you want to suggest a topic for the upcoming PSs, something you would like to discuss, feel free.  Would it be a good idea to write some PS in spanish?

See you next week!!

Prokaryotic Saturday: molecular switches and Travis' experiment

You won’t believe how much I love Saturdays. It’s very difficult to be depressed in a Saturday, seriously. Who can be depressed on Saturday? I mean, you can be depressed on Monday, that’s fine, or Wednesday, I understand. But Saturdays are just perfect. See, no matter at what time you sleep or wake up, you won’t be late to anywhere and you can also work whenever you want and it won’t be wrong.  It’s perfect!

And another good thing I have on Saturdays is the Prokaryotic Saturday, yeeey!!! 

For today’s writing I had three papers from where to choose. The options were:

1) Sorek, R., and Cossart, P. 2010. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat. Rev. Genet. 11 (1): 9-16. (this one is behind a paywall right here, but I have it, so if you would like to read it, email me –hope this is not considered an illegal statement-)

2) Joint, I., Doney, S.C. and Karl, D.M. 2011. Will ocean acidification affect marine microbes? ISME J. 5(1): 1-7(Available online here).

3) Smolke, C. 2005. Molecular switches for cellular sensors. Engineering and Science. 68 (4): 28-37. (Available online here).

So I chose the last one. Anyway, if you would like me to write about the other two, just let me know. I will probably write about Sorek and Cossart paper next week, the other of ocean acidification I’m not really sure, maybe later. 

Now, let me tell you why I chose Smolke’s paper. Reason #1, because I liked it so much, reason #2, because I had a test about this paper and although I read it my test wasn't very good AT ALL... :( aaaaaaah!! This was my face when I saw my result:

 So I want to use this Prokaryotic Saturday to redeem myself (gosh, I'm such a nerd).  

The paper is a little old but it is very enjoyable (something you can’t say about many scientific readings) because Smolke writes this particular paper in a very “friendly manner” (maybe that’s why I didn't take it too seriously-damn!). 

So Smolke’s team designs biosensors using RNA molecules. So basically she is trying to engineer sensors based on the RNA property to associate with proteins. Remember that RNA (and DNA) can form tertiary structures and create binding sites. In the case of RNAs, they can actually act as regulatory elements forming structures called switches, or riboswitches. These riboswitches are in bacteria, they are RNA structures that can fold and bind specifically to certain molecules (or ligands), these can be a protein, a mineral, etc. And as you can see in the picture, the binding between the aptamer (the part of the RNA that binds to the target) and the target molecule modify the structure of the entire RNA molecule, “hiding “ either transcription start sites or ribosome binding sites, in both cases controlling (turning on and off) gene expression. 

Other regulatory RNA elements are the antisense RNAs. These are small RNA pieces that are complementary to mRNA, so when they both, mRNA and antisense RNA bind, translation is blocked. 

Smolke in her paper explains how she takes advantage of these RNA tricks in the design of sensors. She is not giving any methodology, just an idea of how the process works. The first step is to combine the target molecule (the molecule you want your sensor to detect) with RNA, and RNA can be synthesized in the lab from DNA, and you can buy nucleic acids from several companies. Which DNA you use to make your RNA and exactly how do you decide which sequences you use it is not explained here. But once you have your RNAs and your target molecule, you incubate both. Then you will see that some RNAs will bind with the target, some will not. Later you take those RNAs that worked, you amplify and you continue again, with the incubation of the target molecule and the now smaller pool of RNAs. It is, as Smolke defines it, a talent search. 

But the sensors also need to be measurable. So you can add a sequence that codes for a fluorescent protein in a way that if the target molecule binds, the RNA will or will not express the protein. So imagine, you place these sequences in a cell, you add your target molecule and you wait and see. If the cell glows (or “produce” the fluorescence), then your sensor either is on or off, depending on how you designed. And according to Smolke, it is also possible to design biosensors that are able to detect concentrations of the target molecule, this is, it is not only an on and off response, but either how much of the target is in the medium. .. wooow!! 

At some point she explains the experiment of one of her students, Travis, and at the end you can’t conclude something else than “Travis is a really smart guy”. And now you will see why. What Travis did is to create a biosensor that detects a chemical called theophylline, which is found in tea and is similar in its structure to caffeine. He used yeast to insert the sensor. And this is the figure of the results of Travis’ experiment:

In the y-axis we have the expression of GFP (green fluorescent protein), so basically what he did was measure how much the yeast cells were glowing depending on the amount of target molecule (theophylline), x-axis. 

So the blue line is the switch response. And in the beginning the binding wasn't changing, but a dramatic change was observed when the target molecule reached something around 1 mM, meaning that the biosensor needed to have a certain concentration of target so this can actually be “detected”. So Travis’ biosensor worked, after the binding with theophyline, GFP production stopped, in other words, the biosensor was off when the target molecule was detected. And the picture is also showing how specific the biosensor is. The orange line is caffeine, an analogue of teophyline, as I told you before, while the green line is the biosensor only with no target and the red line is the biosensor plus an antisense RNA complementary to the binding site of the theophyline, so GFP was never produced here. As you can see, both, green and orange line shows that GFP was constantly produced, therefore, the biosensor wasn't detecting the target, because there was no target! Isn't this super interesting?  

Later Smolke explains a couple of other biosensors her students synthesized, and how they are applied. In the future, she concludes, biosensors can be engineered to detect unhealthy levels of molecules in blood samples, or to detect growth factors that drive cells to go carcinogenic. A very interesting promise. 

For now I’m going to stop here because this is already to long. But if you read the paper and would like to discuss more, not only about this experiment with the theophyline, but also the one Travis run with the caffeine, you can email me or write something in the comments. Also, if you find more recent applications of biosensors, or something cool related with this field of research, please, share it! :)

See you next week! 

The picture of the riboswitches was taken from Kim, J. N.; Breaker, R. R., Purine sensing by riboswitches. Biology of the Cell 2008, 100, (1), 1-11. Although I copied it from here. And obviously the picture of Travis' results was taken from Smolke paper. I mean, just saying. 

Self-Revolution??

2 de Octubre ni se olvida, ni se perdona??
October 2nd, don't forget, don't forgive...

When I see the nationals news I just can say... For real???

Or is just my perception that Mexico is going under...??? Chaos everywhere... community police out of the law, due to the lack of gov in many towns; millions of kids with more than a month without classes; a bunch of "teachers" collapsing the Capitol (sorry capital); delinquency everywhere, and a very silent but unstoppable abatement of the freedom of speech... If you see/read Mexican news you have a perception, which is totally the opposite of see/read the news of Mexico from abroad... The economy, security, etc... honestly I fell if where living in 1984 (the novel).

Tax, education and energy reforms have polarized the already divided country... From my perspective I don't trust and I don't want the tax and energy reforms, is there a way in which a citizen like I can do something to avoid them??

45 years ago a group of youngsters gave their lives for what they believe, they express against the government, and the gov react... With the consequences that we know...

Now I have almost 30 years... I'm not a youngster anymore... Before I believed that doing the things right, give the best of my in my job, supporting the less fortunate was enough for make this a better place to live.... Now I think this is not enough ... I see the passivity, the lack of commitment, the prejudiced comments, the double moral of my society and I'm sick of it...

But I know that "feel sick of it" don't make any change... We have to be part of the solution, not of the problem.... Be prepared... Cause I'm tired of just being sick... I'll start to do something first with myself, with my weakness and then I have to do something more to this country that I love the most...

U're welcome to help me, any idea is welcome!!!


Emilio


P.s. Doc maybe there's still those revolutionary youngsters in Mexico, of whom you read of them when you where in India.

Prokaryotic Saturday: tales of a glowing bacteria

Today is Saturday and it is also the first Prokaryotic Saturday of this blog!!! Yeyy!

So, today I want to talk about this little crazy guy called Vibrio fischeri.

I won’t say anything new, so if you already know what this guy does, then you can safely stop reading this post………………………… Now that I have that part of the audience that does not know or it is just too bored and doesn't have anything more interesting to read, let me continue. V. fischeri is a gram negative bacteria, which lives in the mantle of the hawaiian bobtail squid. This bacterium is the proud owner of the “canonical quorum sensing system”. It is called 'canonical' because it is by far the most studied and the best described system, since this one was the very first quorum system ever discovered (around 1980, by Nealson et al.).  

You might be wondering what does “quorum sensing” mean. Well, quorum sensing is when bacteria modify in some way the expression of their genes depending on the amount of other bacteria in the medium (cell density). It is believed that bacteria are able to “talk” using chemical signals, not only with other bacteria of the same species but also with organisms of other kingdoms. It’s like when you go out by yourself, you can have a good time of course, but definitely it is not the same when you go out with your friends. And the more you are, the more fun it is. Same here, the more bacteria there in the medium the more behavioral changes they express.

Although the topic of this Prokaryitic Saturday it is not quorum sensing (I probably talk about it later), you can visit Dr. Bonnie Bassler webpage (or just google her name) and learn more about this amazing and tremendously interesting field.

Now, for some reason I feel this post is already getting boring. So, let’s go back with the V. fischeri. This bacterium lives in the mantle of the hawaiian bobtail squid as I just told you. And when you isolate it in the lab you can create some funny stuff like this petri dish:

Because V. fischeri is a bioluminescent bacteria, it glows in the dark, and you don’t have to do anything. :o 

But how does this happen? Here is when the quorum sensing thing comes into action. This bacterium can glow thanks to the expression of two genes, luxR and luxI. These genes are part of the operon luxICDABE. These two genes, luxR and luxI produce two proteins, proteins LuxR and LuxI (yeah, people were not very creative here). And protein LuxI triggers the synthesis of an autoinducer, the homoserine lactone molecule (HSL). So HSL accumulates in the intra and extra cellular environment, and as the number of cell increases, so does HSL. And when concentration of this autoinducer reaches something around 10 ug/ml, HSL binds protein LuxR, then this complex (LuxR-HSL) binds to the operon luxICDABE and bang!!! Genes express and cells glow like crazy!! woooww!!!

Isn’t this cool?

But now, don’t you wonder why? I mean, a glowing bacteria? Why is this crazy bacteria producing light? Maybe she just like showing off.

Well, actually not. There is a good reason and it is the same reason that explains most of animal's behaviors (other than human): survival.

   

The squid, which is the home of V. fischeri, uses this bioluminescence to hide from predators in a very clever manner. This squid (Euprymna scolopes) hunts at night, and uses the light emitted by V.fischeri to simulate the moon light and hide its shadow. The next video of Dr Siouxsie Wiles (@SiouxieW) explains it better. But the thing is, V.fischeri gets food from the squid, and the squid gets an “invisibility cloak”. Plus other few thing, like this light emission mechanism also help the squid to attract predators and mates. So, it's a win-win. 

Now, you can’t say this is not cool.

So that is it. First Prokaryotic Saturday went well, I think. Although you can find many animations and videos online about the LuxI/LuxR gene regulation process, I have a very cool animation (which I created, hehe) so email me if you want to see it, I will send it to you (for some reason I couldn’t upload it here, sorry). And if you have any questions or suggestions, please, leave them in the comments or at @ale_alvarador. 

See you next week!

Volviendo a las raíces

El pasado viernes 30 de Agosto, Diego Devora, egresado de nuestra actual Escuela de Ciencias Biológicas como Ingeniero Bioquímico, impartió una interesante platica acerca de su actual estudio relacionado con la motilidad de Trypanosoma cruzi, protozoario hemoflagelado causante de la enfermedad conocida como chagas, este microorganismo se encuentra en insectos de la familia Reduviiae de los que en México existen alrededor de 30 especies distribuidas. Estos transmisores, llevan las formas infectantes (tripomastigotes metacíclicos) de T. cruzi en su materia fecal, la cual es depositada en la piel durante o después de la alimentación.

El estudio se está llevando a cabo en el Cinvestav (unidad Monterrey) el cual es un centro de investigación multidisciplinario que nos brinda la oportunidad de ampliar nuestra capacidad intelectual, desarrollando un proyecto desde diferentes perspectivas.

“No es fácil, pero con dedicación se puede lograr” nos dice Diego. Dentro de la misma plática, uno de mis compañeros comentó:

“¿De los conocimientos que adquiriste durante tu carrera como Ing. Bioquímico, cuales te han ayudado en tus estudios de posgrado?”

A lo que diego contestó:

“Todo lo que veas a lo largo de la carrera algún día te será útil”. Esta frase nos alienta a creer que no hay conocimiento pequeño ni grande, si en algún momento uno decide extender las alas e ir por un camino distinto lo puede hacer, solo se necesita determinación y dedicación.

Ánimo compañeros, que no existen cosas imposibles, hemos visto partir a muchos de nuestros compañeros y de pronto enterarse que continuaran con sus estudios de posgrado, teniendo ofertas aquí y allá.

Lo bueno no es obtener títulos, sino regresar a donde encontraste tu primer impulso y motivar a todos aquellos que están ahí, dejando tu granito de arena para continuar con la cadena.

WVSU Experience

25 Agosto 2013

Después de 9 horas en el aeropuerto de Dallas, por fin tomé el ultimo vuelo hacia Torreón, pero primero hay muchas cosas que contar ...

El pasado 25 de julio de 2013 me encontraba esperando un vuelo rumbo a Charleston WV (con un par de escalas). Fueron 31 días los que estuve fuera de casa pero igual me sentí dentro de un hogar. Ese mismo día aproximadamente a las 7pm arribamos a Charleston WV, y en ese momento se cumplía un sueño que había tenido desde hace bastante tiempo. De inmediato nos llevaron al departamento y nos instalamos, al siguiente día fue el primero en el laboratorio del Doctor David Huber en la West Virginia State University, conocimos al doctor, una persona muy amable y agradable a quien en varias ocasiones había oído mencionar por otros de mis compañeros del lab, hablamos un poco de los proyectos que se están realizando y nos dio la bienvenida. Después fuimos a conocer el que seria nuestro laboratorio por un mes y a trabajar, después de terminar de conocer a los demás chavos que forman parte del lab fuimos a conocer la planta piloto, tomamos muestra para estar trabajando durante ese tiempo, después regresamos al lab. Para comenzar realizamos extracción de ADN, prosiguiendo con varias electroforesis, de igual manera PCRs, aprendimos a usar el famoso nanodrop, también realizamos extracción de RNA, todo con asesoría de los chavos encargados de los laboratorios, ya en los ultimos dias realizamos clonacion, insertando productos de PCR en E.Coli, todo siguiendo los kits adecuados para cada técnica  Para toda técnica o procedimiento, se lee el protocolo antes de comenzar, se realiza y se espera un resultado el cual en varias ocasiones no fue el esperado pero no por eso dejamos de intentar, ya que, cabe mencionar, teníamos todas las facilidades para practicar. Pienso que solo así se puede perfeccionar la realización de una técnica y obtener el resultado esperado.

Cambiando un poco de tema, conocí a muchas personas de diversas partes del mundo, algunos con 10 años viviendo acá, otros con apenas una semana de haber llegado, es muy grato platicar con personas a las que no se les cierra el mundo, es decir, salen de su país buscando una mejor oportunidad de estudios o incluso de vida, eso motiva para que a nosotros tampoco se nos haga algo imposible estudiar en otro país y residir ahí por un largo tiempo sin papás, sin tu cama, casa, familia, etc., pero con la oportunidad de mejorar, con la visión al frente, con la vista bien puesta en la superación personal y académica.

Esta experiencia me ayudo en muchos aspectos, desde comprender conceptos básicos hasta nuevas e innovadoras tecnologías usadas en la investigación  al igual me di cuenta que vivir alejado de la común atmósfera rutinaria te ayuda a pensar, te pone de frente ante una situación en la que tienes que aprender a madurar y a pensar en tu futuro. Chavos: El idioma, suuuper importante !.

Estar acá me ayudo a esclarecer cosas de mi trabajo en lab, debido a que los chavos estudian la digestión anaerobia fue grato entablar una conversación sobre el tema con "cheve" y Natalia, o perderle el miedo a lo molecular y platicarlo con Arge, escuchar el interesante y siempre divertido punto de vista de Aldo, o tomar de ejemplo el esfuerzo y la dedicación de Ale a su trabajo y por otro lado pensar: ¿Que voy a ser en el futuro? ¿Que voy a hacer después de graduarme? ¿Maestría? ¿Doctorado?, son mil cosas las que piensas al estar en otro ambiente, y digo otro ambiente solo porque estaba a varios kilómetros de distancia, porque el contexto es el mismo: Chavos, estudiantes, o como lo quieran llamar, en un lugar llamado laboratorio, haciendo algo llamado "ciencia".

Todos podemos, el mundo esta ahí, la ciencia ... pues siempre sera ciencia jaja.

A los chavos del lab: Los conozco lo suficiente para saber que si nosotros queremos, nos podemos comer al mundo siempre y cuando nos preparemos bien, tenemos la capacidad y el conocimiento.

Me despido porque ya llegaremos a Torreón  no sin antes agradecerle a la persona que me cambio mi manera de ver las cosas, Doctor Nagamani: Thanks so much.

-Isco.

Lectura para toda ocasión

A lo largo de la vida ocurren sucesos que no tienen importancia en su momento, otros que toman un tiempo extra de tí para buscar la razón de ello y sin embargo no con frecuencia se tiene la suficiente madurez para reconocer que todo tiene un motivo de ser.

¿Que dirias si al morir todas esas dudas quedaran aclaradas?

Si encontraras a ciertos extraños y al conversar con ellos resuelvas un tiempo de vida más largo; cuando en su momento ignoraste el verdadero motivo de ciertos accidentes.

Para darnos una idea de lo que puede suceder al momento de fallecer, Mitch Albom nos relata una historia de un anciano cansado de su trabajo y la rutina creyendo que no hay nada de bueno en eso, pues su esposa murió y a él no tarda en visitarlo la muerte.

Pero para su sorpresa encuentra a cinco personas las cuales le dan sentido a su ya agotada vida.

Una historia excelente que binda una moraleja: No esperes a morir para valorar la vida.

Aguja en un pajar ...

Hola a todos ! :) recientemente me encontré con esto, la imagen corresponde al eXtrem Deep Field (XDF), es una imagen creada a partir de una compilación de 10 años de imágenes tomadas por el telescopio espacial Hubble, y es solo una pequeñísima parte del espacio ! la imagen fue lanzada en septiembre del año pasado (2012) y muestra galaxias de aproximadamente 13.2 billones de años de antigüedad, la otra imagen hace una comparación entre el tamaño del XDF y la luna, lo cual nos muestra que solo es una pequeña parte del universo la que estamos observando ! les dejo el link donde encontré la información por si quieren conocer un poco mas ;) espero les guste, Saludos !

http://www.nasa.gov/mission_pages/hubble/science/xdf.html

Felicidades Edy y Sara!

Felicidades a Edy y Sara, por su defensa de Tesis para obtener su grado de Ing. Bioquímica de forma exitosa. Sabemos del esfuerzo, trabajo y dedicación a lo largo de su estancia en el Laboratorio.

Esperamos que su aprendizaje a lo largo de estos últimos meses las ayude a continuar con su carrera profesional de forma exitosa.

Felicidades! Se les extrañará en el Lab.

Felicidades Lorena!

Felicidades a Lorena, por su exitosa defensa de Tesis para obtener su grado de Ing. Bioquímico, recibiendo mención honorifica por su trabajo realizado en colaboración con el Instituto de Biotecnología de la UNAM, bajo la co-dirección del Dr. Ricardo Oropeza, a quién agradecemos el noble gesto de viajar y participar en el examen profesional de Lorena.

Estamos seguros que tu trabajo será la base para más estudios que se desarrollarán en el Laboratorio y de gran realce para el estudio de sistemas anaerobios en Tiempo Real.

Felicidades y en Hora Buena, Bien Hecho Lorena!