Friday, June 27, 2014

Felicidades Omar!



Congratulations to Inty Omar for his successfully defense of his thesis work with honors, today June 27th 2014. He did an excellent work at his presentacion and at answering the questions from his examiners. Thank you for your guidance, advices and support throughout your time in the lab!

Our thanks go also to Dr. David Huber, Professor, Department of Biology, West Virginia State University, Institute, WV, USA for his guidance and support as one of the directors of Omar’s thesis. We hope that Omar's work will form the base for more future works and ideas about biodigesters management.

Gracias y muchas felicidades, Omar! :)

Sunday, June 8, 2014

Best wishes Inty Omar & Jesus


Our best wishes to Inty Omar Hernandez De Lira & Jesus Jimenez Ascencio for their trip today to participate and present their work on “Dynamics of bacterial & archaeal communities of a performing and non-performing lagoon type biodigesters at Comarca Lagunera, Mexico” (Oral presentation by Inty Omar) & “Correlation between fluorescence intensity & methane production by a mixed methanogenic cultures at different growth phase & different culture conditions” (Poster presentation by Jesus) at the 2nd International Conference on Biogas Microbiology to be held at Uppsala, Sweden.
We are sure that they will do their best and on return will share their learnings and experiences to our team. I am sure their participation will motivate us to do much more things.
We, Biorem lab gratefully acknowledge Our University, Presidencia-Torreon, COECYT, Presidencia-Gomez Palacio and Government of Durango, Government of Tabasco for making possible this trip of Inty Omar and Jesus. Further, we also acknowledge the help of Karla, Daniela, Leslie, Gaby, Thalia, Denise, Hector & Karla's friend in helping withour activities to raise funds for this trip. 

Monday, May 19, 2014

Felicidades Ale

photo-thanks to WVSU
We at biorem lab are sure that you would have received much accolades from your colleagues & teachers at West Virginia State University, USA for your accomplishment for getting admission in the Doctorate Program at Max Planck Institute forTerrestrial Microbiology, Marburg, Germany. But it brings us more joy to see this news appearing in the web page of WVSU. It is a proud moment for all of us to see this & we share the same to all our friends through our blog. We know its not luck, but only hard work and dedication has taken you to next level in your professional career. We are extremely proud that alumini from biorem lab of our school-Biologicas Torreon, Universidad Autonoma de Coahuila, Mexico are spreading their wings to fly high and hope your achievements will motivate & inspire more students from biorem lab & school to follow your footsteps.
For more info at
http://wvstateu.edu/announcement/2014/05/19/WVSU-Research-Student-to-Pursue-Ph-D-at-Prestigiou.aspx
On a side note, we are also extremely proud that both Ale & Aldo, two students mentioned in the page as a badge of honor for WVSU are badge of honor for our lab & school too since both completed their Bachelors degree with us.
Congrats & best wishes Ale. En hora buena

Wednesday, March 5, 2014

Aldo, Mejores deseos de la Comarca Lagunera


It is heartening that Aldo, one of the alumni from our lab and school has started his Doctorate Program from this week at Department of Plant & Environmental Sciences, University of Copenhagen, Copenhagen, Denmark. Hope you will do an excellent work as have done at Biorem, at lab of Dr. Umesh, WVSU and leave your imprint at Dr. Soren's lab. Aldo, best wishes for a purposeful and enjoyable stay at Denmark.

Sunday, January 12, 2014

The ocean is ¨capital B-capital I-capital G¨

I am a fan of this TED-Ed videos, every time I watch one I have to suppress the urge to post it, but this one in particular made ​​me think a lot. If the ocean is so big, how serious is the acidification?
My vision is pretty limited, but ever since I read about ocean acidification, I can't avoid skepticism.



Saturday, January 4, 2014

Un nuevo comienzo

Después de pasar las fiestas navideñas en compañía de los seres queridos y dejando atrás el año que termina, con cosas buenas y malas, nunca es tarde para un nuevo comienzo.
Nunca es tarde para cambiar la perspectiva de nuestra vida, cambiar nuestra mentalidad y así buscar un mejor desempeño en nuestras actividades, ya sean laborales, escolares, familiares, en cualquier ámbito; y así devolverle al mundo un poco de lo mucho que nos regala. Enfoquemonos en construir un buen futuro haciendo las cosas bien en el presente, pues como dijo alguna vez Jorge Luis Borges: "Modificar el pasado no es modificar un solo hecho, es anular sus consecuencias, que tienden a ser infinitas".
Como lo hace la naturaleza, hay que adaptarse a los cambios que surgen día con día en nuestro entorno, y la única manera de hacerlo es por medio de la evolución, aquella que desde hace miles de años permitió el perfeccionamiento de los seres vivos y que hoy en día nos mantiene en constante transformación.

Por eso iniciemos este año con una actitud positiva y no dejemos para mañana lo que podemos hacer hoy.


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.