Monday, November 25, 2013

Learning to learn. A couple of tips.

Don't you hate those boring bloggers’ explanations of why they have not posted anything recently? I do…. But it is so hard having exams every damn week!!!
… So, to avoid (or reduce) the chances of looking at your paper like this


I'd like to share two study techniques I learned a couple of weeks ago and at the same we give life to this blog again.

Dr. McGuire gave a talk on metacognition and how to teach undergrad students. The talk was, obviously, for teachers. I still don't know what I was doing there. But I did learn a couple of good techniques that I thought worth sharing.

Metacognition is the ability to think about your own thinking and judge your own learning. And by developing these skills you are able to determine at what level of learning you operate. Some classes, for example, it was said ‘high school classes’, operate at the lowest level of the blooms’ taxonomy (understanding, remembering).


Actually, one of the points of this talk was to discuss the effect of the way of learning in high school on the results of some first year college students in science classes. Most of the examples were of students failing terribly or with very poor performances. The idea was to teach college teachers how to teach students to study, using metacognition. This is, teaching them the differences between the levels of the pyramid. I hope you can read some of what each level is in the picture below. Everything was explained in the talk, here isjust a brief description. But there are tons of materials on the web about bloom’s taxonomy.


After reviewing each level, Dr. McGuire explained several techniques to move higher in this taxonomy. And the best was when she actually presented results of people who use them and improved. But not improve like, ‘oh a slightly improvement’. No!!! Some were serious cases of people who got to be the top after having been on the verge of leaving university. It was very impressive.  

I know, definitely our context is different, high school and college education doesn't work same for us. But still, I think it is not difficult to understand these levels and place ourselves, according to how we usually study and learn and then possibly we could also improve, be better learners, despite the differences between the education systems. So, let’s do it then.

The first technique was aimed to improve reading comprehension. Usually we have to read several chapters before one exam or review several papers for a particular assignment. It happens to me very often that I lose track of what I’m reading after two or three paragraphs and realize I was just wandering around. Then I have to read again from the beginning, and the cycle is repeated several times until I finish all the text, but often it is necessary (at least for me) to read more than once. Especially with scientific texts where there is always a new term or a concept to remember. It turns out this is very common, while reading something new you want to learn, it may take time, and one can get easily distracted. So, to deal whit this it was suggested to create a big picture of the text before starting to read. Like when you buy a new book, you usually look at the cover, the back cover, you read the description, and you see the pictures. It is advisable to do same thing for text books and scientific papers, at least when you are learning the topic for the first time. Then, while reading, it is recommended to read by paragraphs. This is, reading ‘one paragraph at a time’, stopping after every paragraph and writing down whatever you understand; it can be a sentence, a couple of words or a paraphrase of the content.

In the end, you will have a nice summary of the text. It seems that one will take longer to read in this way, but this is not true. Because by reading paragraph by paragraph, is no longer necessary to read again. Imagine that you move through the text as if you watch a movie for a few minutes, and then play it back and watch same part again, scene by scene. By the time you finish the movie you will remember everything more clearly. Hope this make sense for you. It did for me.  

I determined to try the technique. Two weeks ago I had to read four chapters on a fairly quite boring topic (for me) and it worked. And the best was that I read the whole thing only once!

The second and last technique was about mathematical thinking. Many people is not very good at math. Usually we learn by doing a lot of examples, a lot of problems. But this is a problem when something that is not similar to the examples comes. For this, it is necessary to actually read the theory behind, whatever the math book explains before going to the examples. I know, this sounds obvious but some students jump immediately to the examples. 

I tried this technique once, and it worked. But much of this was because the teacher in charge of my math class always gave us quite difficult tests, with problems requiring more than plugging numbers into formulas. Knowing how to solve the examples in the book wasn't of much help if you didn't have an idea, at least, of what was the purpose of each equation and how to interpret the results. 

Well, that’s it. A couple of tips. Hope someone out there find this post a bit useful. 

So, even if in your school it is not required to operate at the level of analyzing information and creating solutions/ideas in order to get good grades, it doesn't hurt to try to go higher on your own. Finally, get good grades is not the ultimate purpose, right?


Ok, having said that. I'll read you all on Saturday!



The slides of Dr. McGuire are available online. I don’t own these two pictures of the blooms’ taxonomy, both are from Dr. McGuire slides. 

Thursday, November 7, 2013

Day of the death

Hi!
I know day of the death were last week, but I don´t know... I wrote something about it and I still want to share with everyone. It's kinda corny and my grammar is not really good, but I tried! So any comment and correction is welcomed!

It was that time of the year again.

Sitting next to her mother, listening to the endless praying of her aunts and grandmother, the little girl is bored. It is no fun at all if the only thing she has to do is to sit in front of a tomb of a person she never met and hear the old stories from her relatives that she already knows, as they always tell the same ones year by year.

It is a hot day and the sun is barely tolerable at midday. The place where her great grandmother was buried is surrounded by old trees that cannot offer enough shadow for everyone.  “Why can’t it be colder?” she asks to herself with frustration, covering her eyes with both hands, “It is supposed to be autumn. And there’re no clouds in the sky. Stupid sun! ”

The pray ends and then one of her aunts kneels down in front of the tomb,  opens the can of soda she was carrying and buries the tip in the soil, just in front of the cross in which the name of great grandma is written. There is no white marble headstone; the tomb is just an elevation in the ground. Simple as it is, the girl still thinks the tomb is kind of pretty today with all the flowers, yellow and purple, covering it. She still wonders how her mother could dislike such cute flowers. Maybe it’s because they are ordinary. After all, mother loves beautiful and exotic things.

The offering is done and now all her family starts to chat. The first topic is, of course, the can of soda standing in front of the cross. According to his aunts, great grandma loved soda the most and in order to get her enjoy again her favorite drink, they bring the can and leave it in her tomb every year. It’s an old story and it always ends with one of her aunts laughing and asking permission to take a sip of soda before leaving the graveyard.

Since everyone is starting to tell jokes and share old memories, the girl realizes she has no longer the obligation of sitting quietly. All her relatives are distracted and she takes the opportunity of walk away. The graveyard is big and she always has the interest of explore it, but still, she doesn’t go too far from where her mother is. After all, she doesn’t want to get lost.

It is difficult to walk around, there are a lot of people and the tombs are too close to each other. She doesn’t want to step over one, mostly because she doesn’t want the people buried down there to get mad at her.
There is now a beautiful tomb in front of her, all white and covered with flowers. It belongs to a man. No… she corrects herself immediately, it is not a man but a boy. The dates engraved in the marble tell her that if that boy was alive, he would be her age. There is something else written above his name and birth and death dates.

“You’ll always live in your hearts”

Though it’s not the first time she comes to the graveyard and explores other tombs, she cannot help feeling sad at reading the epitaph. Death is never fair. Her own parents have said that so many times and she believes so. Despite her sudden sadness, there something that makes her feel relieved. The boy’s tomb is beautifully adorned, meaning her parents have come to visit him. Several years have passed since his death, but his parents still remember him. She believes that that boy, wherever he is now, would be happy to see his tomb covered in flowers.

“That’s what this day is about, isn’t?” She thinks, remembering the explanation of the teacher at school, “Today is not supposed to be a sad day”

Another tomb catches her attention. It’s even bigger that the boy’s but looks old and abandoned. There are no flowers on its vases and there is a big layer of dust covering it. She has seen many tombs like that in the previous years, some of them with their headstones broken. But this one is not broken and, after getting closer to look at the dates, it is not that old, either.

Now, that is really sad. Where are the relatives of this woman? Did they forget about her?

The girl looks around. The contrast between the tombs adorned and those that were forgotten is great. An idea comes to her, and before she evaluates it, she goes to the next tomb which has many flowers on its vases. She whisper apologies for the person that tomb belongs to, and takes three yellow flowers from one vase. She then places those three insignificant flowers over the tomb of the forgotten woman.

The tomb still looks miserable, but the girl feels somewhat satisfied.

Now someone remembers you,” mutters, thinking the woman can hear her and is pleased with her offering.
Now that she has done it once, the girl believes is now her task to look around for more flowers for the abandoned tombs. It’s kind of difficult because the tombs that can donate some of their flowers are still being visited. And surely, people wouldn’t like to see her stealing their flowers to give them to someone else. Still, she manages to put two or three flowers on four more tombs.

She now has taken flowers from the boy’s tomb, that one who would have been her age if he was alive, and she puts over a tomb of a man who died fifty years ago. The headstone is close to break but she still can read the epitaph.

“From his wife and sons who will never forget him”

The voice of her mother calling for her startles her. Her family is leaving the graveyard now.

“What where you doing over there?” her mother asks her as soon as the girl comes to her side.

“Nothing,” the girl answer, taking the hand of her mother as they start to walk to the exit, trying not to step over the tombs.

Her mother doesn’t seem really interested in her daughter affairs, so she no longer asks questions.

Just once, the girl looks back to the place great grandma is. While is true she never met her, as well as the other people she offered flowers, she feels now glad to be able to visit her, and the others, on this day. 

Saturday, November 2, 2013

Prokaryotic Satur... ok ok... just for today

Hello everyone!

This is one of those days I got several things to do... we are so close to the second midterms L and I’m feeling the panic of the PhD application deadlines. I do not think I'll make it for 2014 L 
So I was thinking to skip this Saturday. But I decided that it won't be nice, and I tried to rush and as you can see it is now Sunday 12:22 AM (damn!). Forgive me for that. Anyway, whatever you will read today it is not much. So, feel free to stop reading………………………………………………………
............................................................................................................................................................

If you are still here, well, let me give you a couple of good and interesting resources I use to spend a bit of time when there is no much to do.

In youtube there is a channel called “GenomeTV”, where you can find great lectures. Personally I strongly recommend that one of the next generation sequencing technologies, by Elaine Mardis. But I warn you, lectures are more than one hour long. Now, if you don't have that much time, then you can visit the channels minutephysics  and ASAPscience. Videos are short and highly interesting.  

Also, another nice youtube channel, which is kind of the style of those two, is “Ted-Ed”, it is not the well known TED-talks, which was previously recommended by another post here in this blog. In TED-Ed you will find short animations explaining simple things, one example:


Since I discovered this channel, I decided that at some point I will have to learn how to animate. Maybe next semester I’ll have more time, I'm planning to take only one class. And talking about classes, there are a couple of online free courses. One that recently started for second time is “Useful genetics”. This course is taught by Dr. Redfield. If you haven’t read the post written by Emilio about Dr. Redfield's most famous work, check it out here.

Actually, Dr. Redfield’s blog, RRResearch  is another excellent site; there you can follow Dr. Redfield's experiments with great detail. This blog is part of the recent tendency of “lab notes published in real time”. Same thing has been done by Dr. Siouxsie Wiles, this is her blog. She works with bioluminescent microbes, there is no much openness as in Dr. Redfield page, but still you will find a couple of interesting posts. Another really nice blog is The Tree of Life, by Dr. Jonathan Eisen, from UC Davis. 

But if you are more of the social networks then you can follow them all, Dr. Redfield, Dr. Eisen and Dr. Wiles in twitter, @RosieRefield, @phylogenomics and @SiouxsieW, who along with Dr. David Shiffman (@WhySharksMatter), Dr. Moore (@moorejh) and Dr. West (@westr) are really cool and always posting very interesting news, they are all scientific-tweetstars. You will learn and have a chance to interact with them sometimes in a while if you follow them.

And now, for you, who stayed until the very end. I have something else for you, a present. I've got some books that I can't carry home when I’m back. So, if you are the very first to give an answer (in the comments section below this post) to the next trivia , you will receive one of these books for FREE
.
Reduction of sulfur is what I do, therefore at the bottom of the column I will be. That column Segei did. Don't get confuse, don't get confuse. I'm not purple I'm not green; these two are always above me. And I can tell you why this is, because light I don't need. Who am I?

Ok, now, terms and conditions. First, the answer should be the one I am expecting (it's my post, it's my trivia, therefore these are my rules). Second, you must have to be the FIRST to answer correctly, answers can be either in English or Spanish. Third, I am sending the book by regular post, so the arrival time depends on your location. Fourth, all books are in English, none is new, but they are all in very good condition. Finally, if you win you will  be able to choose between these titles:

-The fault in our stars(by John Green, by the way, his youtube channel is also great)- this book is one of my favorites of this year. 
-The perks of being a wallflower (by Stephen Chbosky, I really enjoyed the writing style)
-The New York regional mormon singles halloween dance (by Elna Baker, I laughed a lot with this one).


So. Good luck. May the odds be ever in your favor. 
See you next week. 

Saturday, October 26, 2013

Prokaryotic Saturday: everything is always more complex of what it seems

Hi!

Although I skipped last week post, this is the  1st month of PS!  J
Smiling cupcake time:

And for today’s post let me talk about this paper of Sorek and Cossart. You have to pay to get it, but I have it, so if you feel like reading, email me...... did I just say that?.

So, Sorek and Cossart discuss some findings that have been reported by studying transcriptomes of bacteria. They also spend a couple of paragraphs describing the main approaches for transcriptome studies, RNA-Seq and tilling arrays.

First of all, let us clarify what transcriptomes are. From all the definitions I've read, the one that I liked the most (although I don’t remember where I read it, sorry) said that a transcriptome is the dynamic part of a genome. After getting the genome of an organism, the whole research thing doesn't stop there, you have to know where are those genes located, and most importantly what are they doing and how do they interact with themselves and the environment. That information you get it from a transcriptome analysis.

So, for years many eukaryotes have been widely studied, and there are several genomes and transcriptomes available for model eukaryotes. And as usual, bacterias and archaeas were overlooked. Mainly because of that old belief that microorganisms, for being small, are simple and insignificant (well, poor things, what can I say, sometimes that is also believed of short people, or kids). But guess what?!! that is not only wrong, it is WRONG!!!

But that was not the only reason; actually it is more difficult to study transcriptomes of bacteria than those of eukaryotes. Again, more development is there for techniques to work with eukaryotes. In bacteria the major problem is the need to enrich mRNA in the sample. Prokaryotes lack the 3'-end polyA tail, and >95% of the RNA is ribosomal RNA and you need mRNA, the other 5%. But now it is possible to enrich mRNA and Sorek explains a bit of this process in this really cool paper.

 As I told you, the two main approaches that have been used to study transcripts in prokaryotes are RNA-seq and tilling arrays. RNA-seq can be done in several of the platforms available (you know SOLiD, Illumina, etc etc). First you extract your RNA and synthesize cDNA by reverse transcriptase (RT). As bacteria don't have the polyA tail, then some priming step has to be there for RT to work, with oligo(dt), random hexamers or artificial poly adenylation. Then, don’t forget the fact that we need mRNA and it is only a 5% of the sample. So, several methods are there for enrichment, and in Sorek and Cossart paper they are briefly explained. Here they are :
  •  rRNA capture with magnetic beads, so at the end you remove the beads and the sample ends up being mRNA
  • degradation of the 5’P RNAs, so mRNAs in bacteria have an analogous to the cap in eukaryotes, a 5’PPP (triphosphate). So the idea is to get rid of all those RNA species, tRNA and rRNA, that does not have a 5’PPP.
  •  Polyadenylation of mRNA. Here an artificial polyA is added.
  •  Capture the undesirable RNAs with Hfq, a very famous protein originally discovered in E. coli that binds to RNA.

I do not know if there are more enrichment methods. Details about each of these I've told you are presented in the paper, and some other references are suggested in case you want to learn more. Authors also give the name of the kits to do all these protocols, you know, if there are two people in the world doing same thing, there should be a kit for that.

So, once you have your mRNA, you get your cDNA libraries, and again, several methods are there for doing this. And the final output of the RNA-seq are millions of reads (from 20 to 200 bp), that you use to align to a reference genome, and the expression of the genes is measured depending of how many reads are aligned to that particular region in the genome.

And in the other method, tiling arrays, after the cDNA synthesis, the library is hybridized to an array and expression is measured using signal intensities. Enrichment is not necessary here. So both methods require a reference genome, and tilling arrays do not need an enrichment step. Several prokaryotic transcriptomes that have already been completed using these methods include: Listeria monocytogens, Bacillus subtilis, Halobacterium salinarum, Burkholderia canocepacia, Listeria monocytogens, E. coli, Salmonella, Sulpholobus solfataricus

And what all people found, in general, is that prokaryotic transcriptomes are decidedly complex. Gene structures had to be remodeled as new genes were discovered and specially important ncRNA (non coding RNAs that are well know to play key roles in regulation of gene expression) were found. In this paper they mentioned one study (Wurtzel et al), in which they found 162 transcription start sites equivocally annotated. Although I don't know exactly why ORFs are usually predicted upstream of their actual places, this clearly shows how useful transcriptomes are.

Also, several riboswitches structures (you can read more about riboswitches in this previous PS) were discovered. It looks like 2% of bacterial genes are under riboswitch-mechanisms control. The detection of riboswitches is done by analyzing contiguous regions of the 5’UTRs at different conditions, when expression of such regions is interrupted at one growth condition and not in the other, you have spotted a riboswitch. Although this is a paper from 2010, an important comment they did is that there should be more focus on the 3'UTRs, especially in the case of archaea, which were already reported to have 3'UTR with regulatory roles. It'd be nice to find out what has been done in this regard in the last three years.

And now, to almost conclude this post, the most exciting (in my very personal point of view) part of the paper: gene plasticity. In this paper I found the reference of an experiment conducted in 2007, in which Mycoplasma pneumoniae was grown in 173 different conditions (woooth?!! ….... well, this shouldn't surprise us, we know someone who likes experiments of 100+ reactors ;)

So in this study, the found that operons (the bacterial genes) act in an homologous way to eukaryote genes, emulating alternative splicing… although, bacteria were here before eukaryotes, should we say that eukaryotes are emulating bacteria?

Probably, yes. In this study of the oh-so-many-conditions they saw that polycistronic regions can be transcribed as monocistronic when conditions varied, so, from one part with many genes, sometimes only one was expressed. So operons are versatile entities. And it looks like archaea act similar. So, who is copying who?

Another important discoveries were the definition of some ncRNAs in critical processes such as quorum sensing (more about this amazing bacterial signaling processes here) and the antisense transcription of some genes. So, isn't this cool? Although they are small, with small chromosomes and everything, prokaryotes overlap their genes, and it looks like "this is the rule, rather than the exception". 

I would like to keep writing, but this post is already too long. Please, check out the paper and if you have any comments, leave them down below these lines .
thanks. 

Wednesday, October 23, 2013

Want to read minds?


What do you think if, while you’re Reading books you get an ability to read minds?
in Science journal, mentioned that reading can help develop the ability to read minds or rather factions that other people express when conversing with them.
“The skills we use to navigate these ambiguous fictional worlds serve us well in real life” David Kidd (the author of this study) said. But it is not a fact.
So, if you are interested you can read here.

To continue reading, at the bottom you will find several comments with differing points of view on what the author is trying to explain. One of them mentions the book "Thinking Fast and Slow" by Daniel Kahneman and I couldn't avoid to look for it, and then I search in Google (and if you do the same, you will find this link).
In the book I found some interesting that I want to share with us.

And reads:

Now look at the following problem:

17 × 24

You knew immediately that this is a multiplication problem, and probably knew that you could solve it, with paper and pencil, if not without. You also had some vague intuitive knowledge of the range of possible results. You would be quick to recognize that both 12,609 and 123 are implausible. Without spending some time on the problem, however, you would not be certain that the answer is not 568. A precise solution did not come to mind, and you felt that you could choose whether or not to engage in the computation. If you have not done so yet, you should attempt the multiplication problem now, completing at least part of it. You experienced slow thinking as you proceeded through a sequence of steps. You first retrieved from memory the cognitive program for multiplication that you learned in school, then you implemented it. Carrying out the computation was a strain. You felt the burden of holding much material in memory, as you needed to keep track of where you were and of where you were going, while holding on to the intermediate result. The process was mental work: deliberate, effortful, and orderly—a prototype of slow thinking. The computation was not only an event in your mind; your body was also involved. Your muscles tensed up, your blood pressure rose, and your heart rate increased. Someone looking closely at your eyes while you tackled this problem would have seen your pupils dilate. Your pupils contracted back to normal size as soon as you ended your work— when you found the answer (which is 408, by the way) or when you gave up.

Amazing, isn't it?
I don’t know how real is that reading books help to understand people, unless you read this kind of books, but I think it is a good tool to perform our personality and most of all for self-knowledge.

Friday, October 18, 2013

Desayunando




Hola ! les comparto una foto que tomé hace unos domingos afuera de mi casa, me encontraba fotografiando esas flores, y de pronto llegó este invitado a desayunar, fue difícil capturarlo pero al fin se quedó quieto. Espero les guste! y si de paso me ayudan a identificar la especie estaría bien jeje, Saludos!






Thursday, October 17, 2013

Are you on the road ?

Hola a todos!

Por X o Y, hoy debía publicar algo en el blog (no me pregunten por qué jeje), bien, pasé buscando algún tema para compartir con ustedes pero no, no se me ocurría nada, revisé las páginas que usualmente leo en mis ratos libres pero no, no encontraba nada :/ así que decidí solo escribir lo que me viniera a la mente, y husmeando en mis entrañas me puse a pensar, llevo 1 año y 8 meses dentro del lab, nuestro lab, y comencé a procesar varias ideas. Destino ? Casualidad ? Causalidad ? o que había pasado ? jeje (de inmediato visualicé mi situación actual), ahora estoy todas mis tardes dentro de un laboratorio, tratando de encontrarle un porque a las cosas, tratando de superarme día a día, tratando de sacar una buena investigación, trabajo, tesis o como lo quieran llamar, y de pronto me pregunto: Realmente vale la pena ? realmente vale la pena dejar mis ratos libres y ponerme a leer un articulo ? dejar plantados a mis amigos por sacar mi trabajo a tiempo ? valdrá la pena aprender una técnica para que mañana ya esté obsoleta? Valdrá la pena todo lo que estoy haciendo ? ... La respuesta es Si, y creo que muchos de los que leemos este blog coincidirán conmigo, en todo este tiempo que he estado en el lab, siento que he crecido mucho en todo aspecto, desde el académico hasta el personal (importantisimo), he cambiado mi forma de ver la cosas y le he dado una dirección a mi vida (tal vez a veces no lo demuestre jeje), siento que he encontrado el camino que debo seguir para ser lo que quiero ser, y creo que es lo importante, saber qué quieres ser y a donde quieres llegar, tomando en cuenta dónde estas, realmente no se que estaría haciendo en este momento de no haber sido invitado a formar parte de este gran equipo, sinceramente cuando ingresé al lab no sabía lo que me esperaba, pero fué realmente satisfactorio ir descubriendo poco a poco, conocí a muchas personas dignas de admirar, personas que me han inspirado y motivado para seguir por este camino, personas que me han enseñado muchisimas cosas no solo del tipo académico, personas que podría considerar genios, hice grandes amigos también! . Hoy sé a donde quiero llegar, la pregunta es: Estoy haciendo lo que tengo que hacer para lograrlo ? (créanme que no es la primera vez que me hago esta pregunta) la respuesta no la se, tal ves yo diga que si, sin embargo para alguien que ya pasó por donde me encuentro actualmente la respuesta será no, me he dado cuenta que "estar en el lab" no es solo ir y sentarte a tomar café, leer un par de cosas interesantes, medir producción de metano e irte, me he dado cuenta que no es así. Que si me di cuenta tarde? No, solo que tenía otra concepción de las cosas, ahora sé que se trata de estar generando día a día ideas que puedan ayudar a tu trabajo y al de los demás, hablar de temas de interés social, no solo temas científicos, tratar de contribuir con los trabajos de los demás, generar discusión entre los que estemos en el momento, colaborar unos con otros, transmitiendo conocimiento para crecer todos y así hacer crecer al lab y al mismo tiempo generar un cambio, entonces la respuesta es SI ? Aun no lo se. Solo sé que el estar ahí me llena de responsabilidades que debo cumplir, no tendría sentido estar sin hacer nada, quejándome de una y otra cosa sin generar un cambio, si estoy es por algo y para algo que no ? aunque nunca me he quejado de tener mucho trabajo, tal ves lo he mencionado, pero al fin y al cabo estoy haciendo lo que me gusta! y eso me hace sentir bien. 
Somos una generación totalmente nueva y tal ves los old school que me lean ya sabrán las respuestas a muchas de estas preguntas, pero espero y los nuevos tomen lo que les sirva para seguir creciendo, porque, quién tiene las respuestas para todo ? realmente nadie, todos en su momento estuvimos confundidos de lo que realmente queremos, todos tuvimos dudas y miedos pero supongo que es normal, y también es normal que vayan desapareciendo (y aparezcan otras nuevas) conforme continuemos creciendo en los distintos aspectos. Es bueno platicar con alguien que ya pasó por lo mismo, te da otro panorama, piensas las cosas de otra manera, y así debe de ser creo yo, aprender de los demás, es bueno salir y conocer el mundo, darte cuenta que todos estamos conectados sin importar cuan lejos nos encontremos, en fin, pertenecer a este gran equipo es una de las mejores cosas que me han pasado, he aprendido muchisimas cosas, he sufrido, he llorado, conocí al otro isco, he ganado confianza en mi mismo, me he dado cuenta que soy capaz de alcanzar mis metas y eso me hace realmente feliz porque nada se me ha regalado, pero sobre todo, le di un enfoque a mi vida, hoy sé lo que quiero ser y sé como lo voy a lograr. No digo que todo esté trazado, porque he hablado con personas que han cambiado sus planes por una u otra razón, pero al menos tengo la visión puesta en algo y creo que es importante. 
Tal vez piensen que andaba existencial jaja, pero hace unos días una persona  me dijo que sino expresamos nuestra forma de pensar tal vez las otras personas jamás conozcan quienes somos y de qué somos capaces, por eso quise compartir algo de mis pensamientos con ustedes ;) espero sus comentarios, regaños, etc etc ...

Isco.

Saturday, October 12, 2013

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!!

Saturday, October 5, 2013

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. 

Wednesday, October 2, 2013

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.

Saturday, September 28, 2013

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!

Monday, September 9, 2013

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.

Tuesday, August 27, 2013

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.



Thursday, August 22, 2013

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.

Tuesday, August 13, 2013

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



Friday, June 28, 2013

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.





Wednesday, June 26, 2013

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!

Friday, May 17, 2013

Felicidades Eliab!

Felicidades Eliab for successfully defending your work with honors against a volley of really interesting & tough questions from your board of examiners. You really demonstrated your abilities in maintaining your nerve and relating the aspects you learned all through your graduate program. Of course, the credit goes to Dr. German Calderon & Dr. Erick Sierra too in realizing this work. 

We are hopeful that your work will form the base for more interesting future works to emerge from our lab on attending the problems of biodigesters with a new perspective and at the same time consolidating collaboration of our Biorem with Dr. Erick Sierra of Facultad de Quimicas of UJED at Gomez Palacio, Dr. Ricardo Oropeza of IBT of UNAM at Cuernavaca & Dr. David Huber at WVSU, WV, USA. 

One more Graduate from Biorem. Good work & Well done Eliab 


Sunday, May 5, 2013

Congrats Arge & Salvador


 
Congratulations to Arge & Salvador. Two more Grads from our lab. Both of them successfully defended their thesis with honors on 3rd May, 2013. It was nice to see their presentations & the spirit with which they defended their work to the queries of the examiners and those of the public.

Full credit for the good work of Salvador is due to the guidance and untiring efforts of Dra. Norma Margarita de la Fuente Salcido, Professor of our school as Director of his thesis. Congratulations from our lab to her and to Dr. Jose Eleazar Barboza-Corona, Universidad de Guanajuato, Mexico, Co-Director of Salvador's thesis. Well done Salvador, you are a part of us & our lab.

In the case of Arge, our thanks are due to Dr. David Huber, Professor, Department of Biology, West Virginia State University, Institute, WV, USA for his guidance as one of the Directors and his unconditional support to Arge in her thesis work and to our lab in general. The credit of Arge's work goes to him & with deep sense of gratitude we are happy to extend our warm congratulations to Dr. Huber. Excellent work & Well done Arge.
PS: Sorry for the delay in posting this happy news, which is due to the difficulty in getting a photo of Salvador on his D-day.



Sunday, March 10, 2013

23XandMe: Direct-to-consumer (DTC) genetic testing




I knew about 23XandMe a few days ago, since then I have been looking for information, wondering if it is a good investment. And I have not researched enough and possibly I do not understand half of what I've read, but I would like to share what I've seen.

This company (23XandMe), based in California, has already six years selling personalized genome tests. And last year this companyreceived extra money , which allowed a large cost reduction, from 300 to ~100 dls per test. But what exactly 23xandMe does?

Well, if you agree terms and conditions (exactly, those we never read), register and pay 99 dls, you will receive a box the very next day, like the one in the picture above, with a test-tube in which you have to spit 2.5 ml. Then you have to return your sample to the company (everything is included in the 99 dls). These people will perform a chip test of your DNA (Illumina OmniExpress Plus Genotyping BeadChip), analyzing your genome for 960 000 SNPs (it is estimated that in the human population there are about 10 million SNPs). Later (like two or three weeks later) in the webpage you will be able to see if these SNPs you have make you a person with high risk for diabetes or cancer. Also, the webpage will display your overall probable global origin and your Neanderthal percentage, maternal and parental lineages. There are around 200 traits you will know, but some require additional payments (most of them, actually). If you’d like to know more about the details of this kit, how it looks like, please visit this link .

At first it seemed to me something interesting, I thought it would be an opportunity to learn more about the other 50% of my genetic background, because in my case I do not know anything about that 50%, only the last name, but that has never been of much help. And in fact, I found somepeople that are adopt and bought the kit just for that very reason, to learn more.

But then I read that 23XandMe only analyze a few markersthat account for cancer. Besides, the comparison to determine if you are on average more prone to one illness or another is based on the database of the same company, which include something close to 200,000 people from a few countries (yes yes, we are in total over 7 billion, and counting).

In the webpage this product is announced under the slogan "knowledge is power" ... but I wonder, what power? power to whom?? If my results will be displayed as the sample below, what do exactly does that my DNA may be related to someone like Thomas Jefferson (whoooot?? Yeap, check the picture), what will be different if I know that the composition of my ancestry is mostly from Africa, or America ...





At least, for me at this moment, this is not much. And it is true, we do not need to sequence our genome to know that we have to eat healthy, do more exercise and sleep well in order to reduce illness risk (@moorejh, 2013).  I think, to some extent we have not understood how we work, how we interact with the environment, how our own genes interact, and that’s why predict is very risky, isn't it?
Or maybe it is not, because the technology 23XandMe is using is very (very) accurate. Although as I told you before, measuring and predicting the risk for breast cancer based on two markers that are known account for only 5% of the total incidence, does not give a sense of confidence.

But this does not stop here. The goal of 23XandMe is to increment its database from 200 000 to one million people, obviously, as long as these people allow their data to be used for research. Because that is something else, when you complete your registration you will be asked to accept your data to be used for research (although the webpage says the founders do not seek to publish any paper), apparently in the future the genetic material of a million humans could be used by other research centers to develop serious breakthroughs.

And recently, I saw that if right now, you find any variant that was not tested by 23XandMe, there is an algorithm (the imputationalgorithm), which enables you to calculate the possibility of such variant is in your genome, through a comparison with other databases, such as 1000 Genomes and HapMap. Isn't it amazing?

Now 23XandMe it is not the only DTC company, but as far as I know 23XandMe is the cheapest one, some others like deCODEme charge around 1000 dls (although for some reason deCODEme is not selling directly to consumer), I’d like to know if they test the same markers as 23XandMe.

For now I do not know what to conclude, on the one hand I find fascinating all this and I really want to see what will happen with these technologies, what’s next with the DTC companies. But on the other, I’m not convinced to be part of the million of genomes, first because I'm not rich and I can’t afford to spend 100 dls just out of curiosity, second because I know what I need to improve if I don’t want to get sick, and third, because knowing my paternal lineage will not change anything. Let’s see what happens this year with 23XandMe, let’s see if they manage to get one million genomes.

If you want to know more about 23XandMe, you can check the Wikipediaarticle, although it is not really good, it has useful references.