Sunday, February 28, 2010

Powerful earthquake strikes Chile

On Saturday, at 3:34 am, Chile was struck by a powerful earthquake, one of the most devastating representations of nature. An astounding 8.8-magnitud quake (Richter), one of the most intense recorded in history, has hit Central and Southern Chile, bringing chaos and suffering to many Chilean families. Many people are missing, injured or have been rendered homeless, either due to the quake itself or the accompanying Tsunami, and to date, more than 700 casualties have been confirmed. Sadly, but surely, these numbers will rise. Our heart goes to all those families in this terrible situation.

Infrastructural damages are numerous (thousands of buildings are uninhabitable, including several hospitals) and water, electricity, and other basic services are limited. Mobile and land phone services have collapsed.

This has been the most intense quake in Chile in the last 50 years, and the second one in the world, since 1990. “State of catastrophe” has been declared in the hardest-hit regions, which allows for a faster distribution of aid (See image, taken from El Mercurio).

The current government, led by Michelle Bachelet, and the recently elected one (to take office in March 11th) are working together to bring quick solutions to everyone who has been affected by this quake. Military units have been deployed to critical locations to help and protect the population and maintain order, as supermarkets and other stores have been the target of pillage.

Several presidents around the world have offered their help in these difficult times. Their help will indubitably be of importance as the task ahead, the reconstruction of the affected zones, will be a great one. "This will take a great effort from all sectors, public and private” the president said.

On a personal note, I’d like to thank everyone, both in Chile and abroad, that have gone out of their ways to contact me during the last few hours. We are all OK; your concern is deeply appreciated. Also, I was pleasantly surprised to have received direct messages from Twitter friends, which I will reply to promptly.

I may be posting more updates through Twitter soon.

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Tuesday, February 23, 2010

How NOT To Use Powerpoint

A hilarious take on some common Powerpoint presentation mistakes.

[H/T: BoraZ]

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Monday, February 22, 2010

Quotes from the science blogosphere

If your results sound amazing, take a deep breath & think of several tests that could debunk them. Then do those ten tests. If they survive, go to bed & think of another batch of tests.
Keith Robison at his blog Omics! Omics!, heavily criticizing an article published in BMC Genomics. A cool fact: the editors of BMC Genomics invited Keith to formalize his post (and his comment at the article's website) into an article that was recently published!

Another quote, from the comments section of that same post:

(...) one of my great frustrations with peer review is spending a non-trivial amount of time constructively criticizing a manuscript, only to see it resurface in all its flawed glory at some other journal. Gah!

Check more quotes from the science blogosphere here.

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Sunday, February 21, 2010

Picks of the week has a guest host: Lucas Brouwers over at Thoughtomics!

Another week has gone by and some very interesting molbio blog posts have been aggregated to This week, Picks of the Week has a guest host, just like a couple of week ago, when it was hosted over at LabRat [See Guest hosts for PoW during February].

Lucas Brouwers brings us a fascinating new issue over at Thoughtomics. Check it out!

If you ever want to host an issue, just send me an email.

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Wednesday, February 17, 2010

The Almighty Fungi: The Revolutionary Neurospora crassa

On January 11 2010, a new series of blog posts was born over at Benchfly: BenchFly’s Model Organism Week. The idea was to invite fellow science bloggers to discuss and present some of the many model organism used in biology to the rest of the science blogosphere.

In that post, a poll was displayed asking people´s model organism of choice, and offered the following alternatives:

* Mice
* Flies
* Rats
* Worms
* Zebrafish
* Primates
* Other

Immediately, and still in shock, I posted a comment asking the evident: where´s fungi??

This is what I wrote:

No fungi among the alternatives ?! I'm betting a good part of that "Other" percentage corresponds to fungi researchers
A few hours later, I was DMed through Twitter (to be DMed, refers to receiving a Direct Message -private conversation- through Twitter). Alan Marnett, Benchfly´s founder, invited me to write a post on "the fungi" for this series, to which I replied that "the fungi" is too vast for such a post and suggested focusing on particular fungi model organisms. Indeed, on Monday Benchfly featured a post on Saccharomyces cerevisiae, which as you know, we love! [ See An alternative cloning strategy: yeast recombinational cloning and Fourth time is the charm: the quest for the final plasmid].

So today, my post on a fascinating fungus (the model organism of choice in my lab) is up over at Benchfly. Here's the opening paragraph:

“This brief paper, revolutionary in both its methods and its findings, changed the genetic landscape for all time”.

This is how Norman Horowitz started a historical account celebrating the 50th anniversary of the landmark paper by Beadle and Tatum, published in 1941(Horowitz 1991). This work with the filamentous ascomycete fungus Neurospora (Beadle and Tatum 1941), started off a series of important breakthroughs that brought the fields of biochemistry and genetics together and initiated a revolution: the explosive development of biochemical genetics and molecular biology. Undeniably, the one-to-one relationship between genes and enzymes (the “one gene, one enzyme” hypothesis), a concept derived from this and follow-up work, had a tremendous impact on biology.
(continue reading)

So go visit Benchfly and read all about the contributions this fascinating fungus, Neurospora crassa, has made to the advancement of modern molecular biology. It will be a great and informative read on this classic model organism.

Some of the references discussed in the main article:

Perkins DD (1992). Neurospora: the organism behind the molecular revolution. Genetics, 130 (4), 687-701 PMID: 1582553

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Tuesday, February 16, 2010

The hottest molbio topics: the next few years

We are living exciting times in molecular biology. Due to great technical innovations and community efforts, the field is advancing rapidly and new areas of research, some of which were unimaginable just a couple of years ago, are emerging and attracting new generations of molecular biologists and notably, scientists from other fields as well.

Here's a little poll. What do you think will the be hottest molbio topic in the next few years? The one more like to greatly impact the field?

(Think of molbio as a very vast field)

[Image credit:BlueRidgeKitties]

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Monday, February 8, 2010

Guest hosts for PoW during February

Frequent readers of this blog, will be acquainted with our weekly series "Picks of the Week"(PoW), in which we select stand-out molbio-related blog posts aggregated to ResearchBlogging the week before.

After this long year, I've decided to take some time off during February, and due to the success this series has had, I wanted to keep things rolling while I'm away (I may not actually be "away" per se, but I want to take some time off to do some other stuff). So, what better way to keep PoW going than inviting fellow bloggers to host PoW during February?

I invited a few of the ones that are generally part of PoW (and are among my twitter friends ;-) and many were eager to participate!

So, I'm pleased to present this week's "Picks of the Week", hosted by none other than LabRat, a fellow science blogger who has been selected for PoW many times now.

This week's title?

Check it out now!!

(If you want to guest host PoW anytime during the year, just send me an email!)

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Monday, February 1, 2010

GWAS under attack?, historical evolutionary constraints, and a lot more, in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

This week's Picks encompass posts from both last week and the week before, as last week no Picks were posted. Also, this will be the last "Picks of the Week" till March (written by me), as I'm sort of going on vacation (at the very least, I'm going to take some time off from the lab).

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) Drug-induced side effects resulting from secondary targets are an important limitation in drug development. Indeed, “one third of potential therapeutic compounds fail in clinical trials or are later removed from the market due to unacceptable side effects often caused by off-target binding”.
Sometimes, however, a compound binding multiple targets or sites (“polypharmacology”) can be an advantage: a single drug could be used for the treatment of two or three different diseases. Also,

The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeutic potency and against which resistance is less likely to develop
Thus, having a way to predict and identify secondary targets of known molecules, is something useful. Iddo Friedberg at Byte Size Biology discusses a recent paper published in PLoS Computational Biology reporting:

a multidimensional strategy for the identification of secondary targets of known small-molecule inhibitors in the absence of global structural and sequence homology with the primary target protein.
Using this approach, the authors predicted a few secondary targets for a compound that inhibits a protein responsible for RNA processing in Trypanosoma brucei and validated some of them.

2) The early atmosphere, the one who witnessed the origin of life, differs greatly from the one present today, the former probably being characterized by very little oxygen and an abundance of carbon dioxide.
The rise of atmospheric oxygen, as stated by Sessions et al., “was an epic event for both the biosphere and geosphere, and paved the way for the evolution of animal life” [Current Biology, 19:R567-R574].

LabRat describes the atmospheric scenery where this marvellous phenomenon took place, billions of years ago, and speculates on the time it took multicellularity to arise from the “blob phase”.

3) After some hard and arduous work, Psi Wavefunction at Skeptic Wonder, a blogger who usually surprises us with fantastic stories from the bizarre and ever-surprising world of protists, now unveils her very own tree of Eukaryotes based on an impressive body of work. You should definitely check it out!

From the post, here’s one of the blogger’s reasons for composing this tree…

Remember how I often refer to the Keeling et al 2005 tree when pointing out where some obscure organism lies on the 'map'? Well, that tree is 5 years out of date now. In fields like molecular biology and genomics, a lot can change in five years; compounded with how the protistan phylogeny was still in murky, squishy swamp of a mess only about 10-15 years ago, the current tree is far from static.

4) A recent study using two vertebrate species (zebrafish and mouse), suggests that genes expressed early during development have a more dramatic effect when knocked out or mutated, and also are more likely to revert to single copy after whole genome duplication, than genes expressed late.

It then appears that constraints are high in early stages of vertebrate development, and that the timing of expression during development, constrains a gene’s "evolvability”

Lucas Brouwers at Thoughtomics comments on a recent paper addressing the following question: are these developmental and genomic constraints associated to the age of origin of the corresponding genes?

5) There has been a lot of fuzz regarding a new paper published in PLoS Biology recently that, according to “various articles around the internet”, supposedly undermines GWAS studies. But does it really?

The only real solid claim in the paper is that, if you do not include rare SNPs in your genome-wide association study, and rare SNPs of large effect are contributing to disease, then you will sometimes pick up more common SNPs as associated, because they are in Linkage Disequilibrium with the rare SNPs.
The paper makes no attempt to say whether this IS happening, just says that it CAN happen, and that we should be AWARE of it.
Luke Jostins at Genetic Interference takes a critical stand against this paper and makes some interesting points, particularly in the comments section.

I have a lot of issues with this paper, but I will be brief and stick to my main objection; the authors attempt to demonstrate that common associations can be caused by sets of rare variants, and in doing so inadvertantly show they most of them are not.[my emphasis]

That's it for this week. Stay tuned for more MolBio Research Highlights!

ResearchBlogging.orgSome of the articles discussed in this week's selected posts:

Durrant, J., Amaro, R., Xie, L., Urbaniak, M., Ferguson, M., Haapalainen, A., Chen, Z., Di Guilmi, A., Wunder, F., Bourne, P., & McCammon, J. (2010). A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology PLoS Computational Biology, 6 (1) DOI: 10.1371/journal.pcbi.1000648

Falkowski PG (2006). Evolution. Tracing oxygen's imprint on earth's metabolic evolution. Science (New York, N.Y.), 311 (5768), 1724-5 PMID: 16556831

KEELING, P., BURGER, G., DURNFORD, D., LANG, B., LEE, R., PEARLMAN, R., ROGER, A., & GRAY, M. (2005). The tree of eukaryotes Trends in Ecology & Evolution, 20 (12), 670-676 DOI: 10.1016/j.tree.2005.09.005

Milinkovitch, M., Helaers, R., & Tzika, A. (2009). Historical Constraints on Vertebrate Genome Evolution Genome Biology and Evolution, 2010, 13-18 DOI: 10.1093/gbe/evp052

Dickson, S., Wang, K., Krantz, I., Hakonarson, H., & Goldstein, D. (2010). Rare Variants Create Synthetic Genome-Wide Associations PLoS Biology, 8 (1) DOI: 10.1371/journal.pbio.1000294

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