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 

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.

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.

SPACE.COM

Recommending a good website for those who are interested in astronomy or skywatching, or those who just like to see this kind of animations of the universe, just to realize how little we are.

Aaron Swartz:Open Access

I really feel sad that we have a second post on loss of another precious life at a very short interval. I trust that knowledge of any individual is an accumulation of experiences, learning's, discoveries of many others of own and that of earlier and next generations. One can enrich this world by sharing it. Hope the life of Aaron Swartz inspires us to carry forward his vision. To know more on Aaron Swartz, please visit the following link (thanks to Prof. Jonathan Eisen, UC Davis)

The Tree of Life: RIP: Aaron Swartz (collection of news stories, articles, etc)

Respectful Adios

(photo credit to the web page of Dr. Carl Woese, The school of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign)
I feel as if I have lost a long known friend, but really Dr. Carl Woese is a teacher (like Dronocharya to Ekalavya in Mahabharata) not only to me, but to many microbiologists around the world. I do not know him personally, but that does not diminish my anguish at this moment. He was a pioneer who saw more than what others were seeing into the microbial world. Though i am aware that none and nothing can prevent the functioning of kalachakra, i wish that his inquisitive mind motivate us to continue the exploration into the unseen and unknown microbial world.

¿Progreso?

Iba caminando algo cansado por el tercer piso de mi escuela cuando, justo antes de dar vuelta para tomar el elevador, volteo a ver el pizarrón que frecuentemente es abusado por quien sea que tenga manos y un gis al alcance. En esta ocasión estaba una pregunta interesante que me gustaría compartir con vosotros (diría mi tatara-tatara-tatara-abuelo):

-¿Qué significa progreso?¿Cómo sabemos?

Tomenlo como pregunta de ciencia y/o filosofía, pues en repetidas ocasiones la frontera no es clara entre ciencia y filosofía, además de que afortunadamente respuestas de un ámbito sirven para responder las del otro campo.

Congrats Melisa & Emilio

 

Emilio Nafarrate & Melisa Hermosillo, first batch of graduate students of our lab successfully defended their thesis today. One more milestone for our lab. I am confident that many more are to come. But the work of a graduate student is not finished until he/ she get the work published in a journal. I am hopeful that both Emilio and Melisa will do it and set example for others to follow.Our hearty congratulations to both. Our best wishes to both of them for a challenging and successful career.

Branching Out for Training & Collaboration

Salvador and Sara, who left today early morning (8th October) to the lab of Dr. Umesh Reddy and Dr. Padma at Department of Biology, West Virginia State University, USA to attend a training on Fluorescent In-Situ Hybridization technique (FISH). Thanks to Dr. Umesh and Dr. Padma for giving this opportunity to Salvador and Sara. 

Raul and Edith reached today the lab of Dr. Teodoro Espinosa Solares y Dra. Guadalupe Hernandez Eugenio, Departamento de Ingeniería Agroindustrial, Universidad Autonoma Chapingo for initiating collaborative work between both of our labs. Thanks to Dr. Teodoro and Dra. Guadalupe for this opportunity to Raul and Edith. 

Hope our colleagues make use of this opportunity to update their skills and knowledge and our best wishes are with them for a happy and successful experience.

¿En qué momento?

Contento porque estoy en una computadora con acentos (espero los use bien) empezaré a exponer mis ideas.

No logro concebir la idea de un exceso de gente estudiando, yo lo supondría una meta a lograr, me parece imposible coincidir con quienes afirman que no es bueno hacer un doctorado, aunque a la vez que escribo esto y cada que discuto esto con alguien pienso que quizás tengan algo de razón. Es decir, un estudiante se las ve negras en cuanto a sueldos, estudiar duro, visas, idiomas ajenos, no tiene trabajo estable (desgraciadamente quien sabe si encontrará alguno que le remunere cómodamente para mantener a su familia y dar educación a sus hijos), no hay horarios de trabajo en lab, es duro ver pasar el tiempo y ver que en 2-5 años habrá que empezar de nuevo a buscar otra escuela, nuevo laboratorio, tal vez nuevo país, en fin. Pero al final... ¿me ira bien?¿Iré por el camino correcto?

Otro aspecto de mi desconcierto es sobre la desigualdad sobre algunas regiones del mundo. ¿Cómo es posible que algunos países tengan problemas por tener demasiados PhDs y al mismo tiempo hay otros países que viven con un PhD por cada 10,000 habitantes? ¿No sería tiempo de que los países desarrollados exportaran gente capaz? ¿Será que el problema de exceso de PhDs no nos concierne a los mexicanos?

Por favor lean esto. Alguien expliqueme por Dios