Tuesday, April 28, 2009

Argh, these reviewers...

The guys down at Dr. Jekyll & Mrs. Hyde have recently published a post entitled "Dr Jekyll's Guide for Reviewers".

It's a funny (ok, to me) satire of the practices of some annoying little reviewers...

After reading it, I would like to add two suggestions to the list, if I may.... (please check "Dr Jekyll's Guide for Reviewers" first, or this will make absolutely no sense):

11. Please do not hesitate to demand that the authors cite some of your previous work, despite it being only marginally related to the work being submitted.

12. You are encouraged to ask the authors to reduce their manuscript by 50%. And no.. you don't have to give any directions as to what to edit.

UPDATE (29/4): DrDoyenne has just left the following cartoon at the post:


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Saturday, April 25, 2009

You can follow "Around the journals" through RSS

Last March we highlighted a new feature here at MolBio Research Highlights: "Around the journals" (AtJ). This feature came to solve a problem regarding the number of articles being posted and shared with all of you [New feature in MolBio Research Highlights].
We consider this feature to be very helpful as it allows us to share with you articles we think of as being interesting, despite not being able (mainly because of time constrains) to discuss them all in detail.
When we posted this new feature we mentioned that the only downside to it was that it could not be followed through RSS feed, so you had to visit the site to check the articles being shared. Nevertheless, we recently found out that the articles can indeed be followed through RSS feed! (Here's the link)

I hope this comes as a help to everyone following the blog and those wanting to stay current in molecular biology research by receiving the best articles right into their RSS readers [Again, I recommend Google Reader].


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Friday, April 24, 2009

Happy DNA day! (Ok, tomorrow)

April 25th marks the National DNA Day in America.
"National DNA Day is a unique day when students, teachers and the public can learn more about genetics and genomics! The day commemorates the completion of the Human Genome Project in April 2003, and the discovery of DNA's double helix". Click here to learn more.

So What Are You Doing for National DNA Day?


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Friday, April 17, 2009

BioRad does it again...

As you may remember, a few weeks ago I wrote a post commenting on the fact that some companies have been making videos to promote equipment and new technologies [Commecials in life science research: Roche].
Well, Biorad has done it again...


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Monday, April 6, 2009

What is Epigenetics? An operational definition

ResearchBlogging.orgEpigenetics is a hot topic; its usage in articles included in PubMed has increased by more than tenfold in the last 10 years.

This trend, however, could be explained, to some degree, by its loose usage. Although there is a clear meaning to the concept, it has been used to define things that are not exactly epigenetics per se, but rather something else.

Indeed, on a recent News Feature1 in Nature discussing concepts described as “difficult to define” (concepts on which the community, as a whole, has not found consensus, or which are not perceived the same way by everyone) “epigenetics” was selected as a tough concept and was discussed at length [Language: Disputed definitions]. To illustrate my point, see what Adrian Bird, a professor at the University of Edinburgh has to say about it:

"Epigenetics is a useful word if you don't know what's going on — if you do, you use something else"
There is a generalized misconception (mainly among scientists that are not experts on chromatin) on what epigenetics means.

So what exactly is epigenetics? On a recent meeting (last December) on chromatin-based epigenetics, hosted by the Banbury Conference Center (a beautiful place) and Cold Spring Harbor Laboratory, several aspects of epigenetic control of gene expression and function were discussed and there was an intent to arrive at a consensus definition of epigenetics to be considered by the broader community.

Berger et al.,2 illustrate the concept and provide us with an operational definition of epigenetics. As it is now clear that there are several mechanisms involved in the initiation, maintenance, and heritability of epigenetic states, it’s important to integrate this knowledge into an operational framework.

Let’s start by getting the concept of "epigenetics" out of our way: “An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence.” Nothing more, nothing less.

How this state is initiated, maintained and inherited is what constitutes the operational definition of epigenetics and an exciting topic at present.

The authors propose that there are three categories of signals that lead to the establishment of a stably heritable epigenetic state: 1) “Epigenator,” which includes an environmental cue and the intracellular pathways that can lead to an epigenetic phenotype; 2)“Epigenetic Initiator”, which responds to the Epigenator and mediates the establishment of a local chromatin context at a precise location and 3) “Epigenetic Maintainer”, which sustains the epigenetic chromatin state, in the first and subsequent generations, but is not sufficient to initiate it. (See figure).

Figure 1.

Interestingly, post-translational modification of histones could be considered as a Maintenance signal. Nevertheless, it’s not always correct to define histone modifications as epigenetic events. As discussed in the Nature article1, scientists often use the term "epigenetic" to refer to histone modifications in the context of dynamics processes such as transcription induction or DNA repair.

This is wrong. Those are not epigenetic events .

Kevin Struhl at Harvard Medical School in Boston makes the same point1:
"Why did histone marks become epigenetic?" People decided that if they call them that it makes them interesting. Others say that it is not about making things sound important, it is more the lack of any other phrase with which to collectively refer to this type of work"
(I would cringe if someone told me “I’m going to use the term X because I’m not exactly sure what else to use, although I know it may not be the most appropriate word for what I’m trying to say”).

As discussed by Berger et al.,
“(…) certain histone modifications very likely play a role as Maintainers of epigenetic signals; however, this does not mean that all post-translational modifications of histones are epigenetic in nature
Finally, Berger et al. discuss some biological examples for each of the proposed categories, for example, non-coding RNAs (such as Xist, see refs.3,4) as Initiatiors (see figure).

This is an interesting article considering the importance of this “precise and stable control of gene expression and genomic regulation through multiple generations”, and I welcome these kinds of articles that come along every few years to remind us what certain concepts actually refer to in order for everyone to be on the same page.

UPDATE. I wanted to post figure 1 from this paper but I was concerned about it, as one journal has already made a huge deal about 'reproducing figures' on a blog. I requested permission but as I got no answer I didn't post it. Today, however, I received an email from Laureen Connell, Assistant Editor at G&D granting me permission so you can now enjoy the figure as part of the post.

1Nature 455, 1023-1028 (2008)
2Berger, S., Kouzarides, T., Shiekhattar, R., & Shilatifard, A. (2009). An operational definition of epigenetics Genes and Development, 23 (7), 781-783 DOI: 10.1101/gad.1787609

3 Payer B, Lee JT (2008) X chromosome dosage compensation: how mammals keep the balance. Annu Rev Genet. 2008;42:733-72.
4 Ng K, Pullirsch D, Leeb M, Wutz A (2007)Xist and the order of silencing. EMBO Rep. 2007 Jan;8(1):34-9.


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Hilarious (PhD Comics)

"What's a 'control'?".... memorable.


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Thursday, April 2, 2009

Science metrics: the h-index

Nick Oswald at BiteSize Bio has recently published a post explaining the basic pros and cons of the H-index (or Hirsch number, named after his creator Jorge E. Hirsch), one of the many metrics developed to asses the apparent scientific impact of a scientist [Does Your h-index Measure Up?]. Although no single number can "give more than a rough approximation to an individual’s multifaceted profile" (as Jorge Hirsch wisely puts it1), the H-index has been gaining adepts worldwide and it's increasingly being used as the metric of choice for many committees (I'm not saying that I agree with using such numbers for giving grants or for tenure evaluation, though).

Briefly, the advantage of the h-index is that it combines productivity and impact in a single number.

Nick's article is very interesting and enlighting in the sense of explaining the advantages, but also pointing out the limitations, of the h-index.

I encourage everyone to read it.

1Hirsch JE(2005)An index to quantify an individual's scientific research output. PNAS 102 (46): 16569–16572.


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Wednesday, April 1, 2009

Turning points

Nature Cell Biology has started a new series of short autobiographical essays by leading scientists entitled "Turning Points". The idea is for scientists to give a short historical perspective of their career, but mainly, to highlight a story they feel was important in shaping their scientific future. A "turning point" in their careers.
As the editors point out, they "hope (these stories) prove inspirational to scientists early in their career".

The first of these series of articles is from Gottfried Schatz, an Austrian biochemist who discovered mitochondrial DNA1. In this well-written piece he tells us a little about how difficult was for him to get into the biochemistry world in post-WWII Austria and how he got involved in the study of mitochondria [Coming in from the cold: how answering a postcard can launch a scientific career].

While I was reading the article I came across with something I wanted to share with you. I've always hated when scientists don't reply to their emails; "time" is by no means an excuse. It takes less than a minute to send a reprint (it's just an attachment for god's sake!), refer to someone else (e.g. the tech who knows where the plasmid you are requesting is), etc.
Anyway, here's what Gottfried has to say about it:
To this day I promptly answer every letter or email I receive, particularly if it is from a young scientist whose name is unfamiliar to me. Scientists of today are so overburdened with paperwork and mesmerized by competition that they often neglect this simple courtesy. A thoughtful letter to a young scientist in a remote corner of the globe may do more for science than a plenary talk at an international meeting.



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